SkillCompiler/data/format-preference/natural-instructions/tasks/task352_coda-19_classification.json

{
    "Contributors": [
        "Ishan Purohit"
    ],
    "Source": [
        "coda_19"
    ],
    "URL": [
        "https://github.com/windx0303/CODA-19/tree/master/data"
    ],
    "Categories": [
        "Section Classification"
    ],
    "Reasoning": [],
    "Definition": [
        "In this task, you are given a paragraph (from a research paper) and your task is to classify each sentence of the paragraph (assume n sentence) into the following categories: Background, Purpose, Method, Finding/Contribution, or Other. Return the output in this format: 1 - category of sentence 1, 2 - category of sentence 2, ..., n - category of sentence n; where each number indicates the order of the sentence. The categories can be identified using the following questions: \n Background: - Why is this problem important? - What relevant works have been done before? - What did the previous works miss? - What are the high-level research questions? - How might this help other researchers?\n Purpose: - What specific things do the researchers want to do? - What specific knowledge do the researchers want to know? - What specific hypothesis do the researchers want to test?\n Method: - How did the researchers do it or find it out? - What are the procedures and steps of this research?\n Finding/Contribution: - What did the researchers find out? Did the proposed methods work? - Did things behave as the researchers expected?\nOther: put every text fragment that does not fit into any of the categories above here. Put a sentence here if its not in English, is not part of the article, contains numbers and dates, is a caption of a figure or a table, is a formatting error, or you are not sure about it."
    ],
    "Input_language": [
        "English"
    ],
    "Output_language": [
        "English"
    ],
    "Instruction_language": [
        "English"
    ],
    "Domains": [
        "Biology"
    ],
    "Positive Examples": [
        {
            "input": "In many infectious diseases caused by either viruses or bacteria, pathogen glycoproteins play important roles during the infection cycle, ranging from entry to successful intracellular replication and host immune evasion. Dengue is no exception. Dengue virus glycoproteins, envelope protein (E) and non-structural protein 1 (NS1) are two popular sub-unit vaccine candidates. E protein on the virion surface is the major target of neutralizing antibodies. NS1 which is secreted during DENV infection has been shown to induce a variety of host responses through its binding to several host factors. However, despite their critical role in disease and protection, the glycosylated variants of these two proteins and their biological importance have remained understudied. In this review, we seek to provide a comprehensive summary of the current knowledge on protein glycosylation in DENV, and its role in virus biogenesis, host cell receptor interaction and disease pathogenesis.",
            "output": "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose",
            "explanation": "The paragraph contains 13 sentences. The first 10 sentences provide background information about how some infectious diseases are caused by bacteria and viruses. The last 3 sentences talk about the purpose of the study."
        },
        {
            "input": "Dengue (DEN) is an emerging arthropod-borne infectious disease which is caused by DENV. According to the World Health Organization (WHO) (2017), DEN cases have continually increased in recent decades. An estimation of DEN infections worldwide has indicated up to 50-100 million cases per year (WHO, 2017). The virus is transmitted primarily by female Aedes aegypti mosquitoes in tropical and subtropical regions. The spread of DEN in non-tropical areas has been associated to the transmission by the secondary vector, A. albopictus mosquito which is able to withstand winter temperature (Gould et al., 2010) . Four serotypes of DENV (DENV1-4) have been identified to date and co-circulation of these serotypes has been reported in Asia, Africa, and America (Guzman et al., 2010) .",
            "output": "1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding",
            "explanation": "The paragraph contains 9 sentences. The first 3 sentences, gives background information about how infectious Dengue (DEN). The last 6 sentences provide additional information for the research regarding how the disease has been identified of its new serotype."
        },
        {
            "input": "Kawasaki disease (KD) is an acute systemic vasculitis with unknown etiology. The diagnosis of KD depends on clinical manifestations. The prevalence of coronary artery abnormality (CAA) is 11.0% and results in cardiac sequelae, such as myocardial infarction or coronary aneurysm, which are the most serious complications in KD. Methods. We divided KD children into different age groups: ≤6 months old, 7 months to 1 year old, and year old, respectively. Different parameters were compared in each group. Results. Infants ≤6 months old are less likely to fulfill KD major diagnostic criteria within 10 days, are prone to develop incomplete KD with the lowest cholesterol level, and have the greatest chance to have CAA and the laboratory features associated with CAA, such as the longest time needed to confirm CA diagnosis, lower hemoglobin level, lower albumin level, and higher platelet count. Infants <1 year old develop higher percentage of leukocytosis and sterile pyuria. But this group has fewer patients with neck lymphadenopathy.",
            "output": "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding",
            "explanation": "The paragraph contains 19 sentences. The paragraph begins by providing background information relevant to the problem about the Kawasaki disease, followed by the methods where it divided children into the age group that the authors used to study the problem, and at last, it discusses their implications that how infants are prone to develop incomplete KD with the lowest cholesterol level, how some group has fewer patients with neck lymphadenopathy."
        }
    ],
    "Negative Examples": [
        {
            "input": "Upon recognition of the host, bacterial pathogens activate a genetic virulence program to establish their replicative niche. In this study, we selected for mutants in the model intracellular pathogen Listeria monocytogenes that did not up-regulate virulence factors during infection. The screen identified genes involved in sensing the host cell and suggests a model in which expression of virulence factors is spatially and temporally compartmentalized via regulation of transcription and translation.",
            "output": "1 - background, 2 - finding, 3 - finding, 4 - finding",
            "explanation": "Here, the first sentence does not represent the background information. However, it is finding because it provides additional information to research. So, the correct label for the first sentence should be 'finding'."
        },
        {
            "input": "The global \"One Health\" approach, which requires interdisciplinary collaborations and communications in all aspects of health care for humans, animals, and the environment, will support public health in general.",
            "output": "1 - finding, 2 - finding",
            "explanation": "Input paragraph has five sentences, however, output is generated for only 2 sentences."
        },
        {
            "input": "Listeria monocytogenes is an environmental saprophyte and facultative intracellular bacterial pathogen with a well-defined life-cycle that involves escape from a phagosome, rapid cytosolic growth, and ActA-dependent cell-to-cell spread, all of which are dependent on the master transcriptional regulator PrfA. The environmental cues that lead to temporal and spatial control of L.",
            "output": "purpose",
            "explanation": "Here, output generates only one label and also without the order of the sentence, however, there are two sentences in the input paragraph. So, it should provide a label for each label."
        }
    ],
    "Instances": [
        {
            "id": "task352-74d59c7ae9ae4df487884e94eda2675f",
            "input": "Background: From October 2010 through February 2016, Arizona conducted surveillance for severe acute respiratory infections (SARI) among adults hospitalized in the Arizona-Mexico border region. There are few accurate mortality estimates in SARI patients, particularly in adults ≥ 65 years old. The purpose of this study was to generate mortality estimates among SARI patients that include deaths occurring shortly after hospital discharge and identify risk factors for mortality. Methods: Patients admitted to two sentinel hospitals between 2010 and 2014 who met the SARI case definition were enrolled. Demographic data were used to link SARI patients to Arizona death certificates. Mortality within 30 days after the date of admission was calculated and risk factors were identified using logistic regression models. Results: Among 258 SARI patients, 47% were females, 51% were white, non-Hispanic and 39% were Hispanic. The median age was 63 years (range, 19 to 97 years) and 80% had one or more pre-existing health condition; 9% died in hospital. Mortality increased to 12% (30/258, 30% increase) when electronic vital records and a 30-day posthospitalization time frame were used. Being age ≥ 65 years (OR = 4.0; 95% CI: 1.6-9.9) and having an intensive care unit admission (OR = 7.4; 95% CI: 3.0-17.9) were independently associated with mortality. Conclusion: The use of electronic vital records increased SARI-associated mortality estimates by 30%. These findings may help guide prevention and treatment measures, particularly in high-risk persons in this highly fluid border population.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding"
            ]
        },
        {
            "id": "task352-f2a9937e2d4b4e1e9c76a55f79913f21",
            "input": "Wedzicha JA: Respiratory syncytial virus, airway inflammation, and FEV1 decline in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2006, 173:871-876. This paper demonstrated that persistent respiratory syncytial virus infection could contribute to the progression of COPD severity. Models of infection and exacerbations in COPD Papi et al. 263 www.sciencedirect.com",
            "output": [
                "1 - background, 2 - background, 3 - other, 4 - finding, 5 - other"
            ]
        },
        {
            "id": "task352-bc77682faa1f47ed82d34be6d3278a29",
            "input": "0166-0934/$ -see front matter Published by Elsevier B.V.",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-1fa0cef787e74e77827fdface6ffa248",
            "input": "A 1520 bp region of Cochlosoma anatis mtDNA 16S gene was subjected to DNA sequencing and a 466 bp portion was compared with other protozoan 16S sequences to develop PCR primers specific for C. anatis. This PCR diagnostic method allowed identification of C. anatis from house flies, Musca domestica L., turkey gut, and fecal samples within 6 h after fieldcollected samples reached the laboratory. House flies detected carrying C. anatis using the diagnostic 374 bp amplicons represented the first record of this protozoan in house flies. #",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding, 6 - other"
            ]
        },
        {
            "id": "task352-78b7aeb7d0c4443b89a3fb6e896feb4c",
            "input": "The objectives of this study were to evaluate the effects of free-access acidified milk replacer feeding on the pre-and postweaning health of dairy and veal calves. Individually housed calves were systematically assigned at birth to 1 of 2 feeding programs: free-access feeding (ad libitum) of acidified milk replacer (ACD, n = 249) or traditional restricted feeding (3 L fed twice daily) of milk replacer (RES, n = 249). Calves were fed milk replacer containing 24% crude protein and 18% fat. Acidified milk replacer was prepared to a target pH between 4.0 and 4.5 using formic acid. Calves were weaned off milk replacer at approximately 6 wk of age. Weaning occurred over 5 d, and during this weaning period, ACD calves had access to milk replacer for 12 h/d and RES calves were offered only one feeding of milk replacer (3 L) daily. Calves were monitored daily for signs of disease. Fecal consistency scores were assigned each week from birth until weaning. A subset of calves was systematically selected for fecal sampling at 3 time points between 7 and 27 d of age. Fecal samples were analyzed for enterotoxigenic Escherichia coli F5, Cryptosporidium parvum, rotavirus, and coronavirus. Hip width, hip height, body length, heart girth, and body weight were measured at birth and weaning. Postweaning body weight measurements were collected from the heifers at approximately 8 mo of age. Postweaning body weight and carcass grading information was collected from the veal calves at slaughter once a live weight between 300 and 350 kg had been achieved. The odds of ACD calves being treated for a preweaning disease event tended to be lower than that of the RES calves (1.2 vs. 5.2%, respectively). Preweaning mortality, postweaning disease treatment, and postweaning mortality did not differ between feeding treatments. The ACD feeding treatment supported greater preweaning average daily gain (0.59 vs. 0.43 kg/d) and structural growth than RES feeding. Postweaning average daily gain and carcass characteristics were similar for ACD and RES calves. These results indicate that free-access acidified milk replacer feeding tended to support improved health, and greater body weight gain and structural growth during the preweaning period; these effects did not persist in the postweaning period. The growth advantage observed before weaning in the ACD calves likely disappeared due to the weaning methods used.",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - method, 14 - method, 15 - method, 16 - method, 17 - method, 18 - method, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding, 25 - finding, 26 - finding"
            ]
        },
        {
            "id": "task352-87d55ad9d9d3446bb096ebf704e13211",
            "input": "The aim in this study was to assess the effectiveness of a quaternary ammonium chloride (QAC) surfactant in reducing surface staphylococcal contamination in a routinely operating medical ward occupied by patients who had tested positive for methicillin-resistant Staphylococcus aureus (MRSA). The QAC being tested is an antibacterial film that is sprayed onto a surface and can remain active for up to 8 h. A field experimental study was designed with the QAC plus daily hypochlorite cleaning as the experimental group and hypochlorite cleaning alone as the control group. The method of swabbing on moistened surfaces was used for sampling. It was found that 83% and 77% of the bedside surfaces of MRSA-positive and MRSA-negative patients respectively were contaminated with staphylococci at 08:00 hours, and that the staphylococcal concentrations increased by 80% at 1200 h over a 4-hour period with routine ward and clinical activities. Irrespective of the MRSA status of the patients, high-touch surfaces around the bed-units within the studied medical ward were heavily contaminated (ranged 1 to 276 cfu/cm 2 amongst the sites with OPEN ACCESS Int. J. Environ. Res. Public Health 2015, 12 3027 positive culture) with staphylococcal bacteria including MRSA, despite the implementation of daily hypochlorite wiping. However, the contamination rate dropped significantly from 78% to 11% after the application of the QAC polymer. In the experimental group, the mean staphylococcal concentration of bedside surfaces was significantly (p < 0.0001) reduced from 4.4 ± 8.7 cfu/cm 2 at 08:00 hours to 0.07 ± 0.26 cfu/cm 2 at 12:00 hours by the QAC polymer. The results of this study support the view that, in addition to hypochlorite wiping, the tested QAC surfactant is a potential environmental decontamination strategy for preventing the transmission of clinically important pathogens in medical wards.",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - other, 10 - other, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding"
            ]
        },
        {
            "id": "task352-7e285ceaf74344f9b2b569431cf4d56c",
            "input": "The spike protein of Porcine epidemic diarrhea virus is the main surface glycoprotein involved in virus attachment and entry and therefore is the target of neutralizing antibodies. Here, the immunogenicity of a novel antigenic domain found on the carboxy-terminal of the spike protein characterized by the peptide motif GPRLQPY, was evaluated. A synthetic peptide whose linear sequence is identical to the 24 a.a. carboxy-terminal portion of the spike protein (S-CT24) elicited a strong antibody response in BALB/c mice that had specific reactivity against the S-CT24 and PEDV. These antibodies were shown to have a specific affinity to the GPRLQPY motif, as demonstrated by non-reactivity with a peptide that lacks this motif. In addition, antiS-CT24 antibodies exhibited neutralizing activities against KPEDV-9 in focus reduction neutralization tests suggesting that the GPRLQPY motif induces neutralizing antibodies against PEDV.",
            "output": [
                "1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding"
            ]
        },
        {
            "id": "task352-26328414dcd34986824782caabc5a188",
            "input": "Host responses during lethal henipavirus infection in ferrets PLOS Neglected Tropical Diseases",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-d5aed2938ca94cd596c9be16ff355a15",
            "input": "The severe acute respiratory syndrome (SARS) has been one of the most epidemic diseases threatening human health all over the world. Based on clinical studies, SARS-CoV (the SARS-associated coronavirus), a novel coronavirus, is reported as the pathogen responsible for the disease. To date, no e¡ective and speci¢c therapeutic method can be used to treat patients su¡ering from SARS-CoV infection. RNA interference (RNAi) is a process by which the introduced small interfering RNA (siRNA) could cause the degradation of mRNA with identical sequence speci¢city. The RNAi methodology has been used as a tool to silence genes in cultured cells and in animals. Recently, this technique was employed in anti-virus infections in human immunode¢ciency virus and hepatitis C/B virus. In this study, RNAi technology has been applied to explore the possibility for prevention of SARS-CoV infection. We constructed speci¢c siRNAs targeting the S gene in SARS-CoV. We demonstrated that the siRNAs could e¡ectively and speci¢cally inhibit gene expression of Spike protein in SARS-CoV-infected cells. Our study provided evidence that RNAi could be a tool for inhibition of SARS-CoV. ß 2004 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - finding, 11 - finding, 12 - other"
            ]
        },
        {
            "id": "task352-0ba72d314c004818a0ebbeb940c07142",
            "input": "The full genome sequence of a Middle East respiratory syndrome coronavirus (MERS-CoV) was identified from cultured and isolated in Vero cells. The viral genome sequence has high similarity to 53 human MERS-CoVs, ranging from 99.5% to 99.8% at the nucleotide level.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-3a9865caa3b1419aa238d9ca1a5abc92",
            "input": "PLOS Neglected Tropical Diseases, caused by the filarial parasitic nematode Onchocerca volvulus, remains a significant source of morbidity throughout sub-Saharan Africa and is a primary cause of infectious blindness. Research on this disease has been hindered by an absence of suitable small animal hosts. Here we describe the development of humanized mouse models that are susceptible to O. volvulus infection supporting both growth and maturation of the parasite. These novel mouse models have enabled the identification of a number of new O. volvulus biomarkers with potential to play a role in the development of specific and sensitive diagnostic tests for presence of viable parasites. Development of Onchocerca volvulus in NSG mice PLOS Neglected Tropical Diseases",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-f1131cd7708e4d3c877f5d787d78b1dc",
            "input": "Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-96e9e30a177549f4b1a46086115ceaa0",
            "input": "The current re-emergence of human monkeypox (HMPX) is a global concern for endemic and non-endemic countries, but healthcare workers in some regions, like Asia, have less experience with identifying and treating HMPX cases. This study aimed to assess the confidence and its predictors in HMPX case management among general practitioners (GPs), the frontline doctors in Indonesia, and to explore their perspectives on HMPX. Between May and July 2019, GPs in Indonesia completed an online-based survey. The questionnaire collected information on GPs' confidence, perspective, sociodemographic, workplace and professional characteristics, exposure to HMPX information and knowledge on HMPX. A logistic regression analysis was employed to explore the explanatory variables influencing the confidence and the perspective. We included 395 GPs in our analysis (77.4% out of 510 responses received) of which 10.1% and 34.9% were classified having good confidence using an 80% and 70% cut-off for confidence score, respectively. In the adjusted analysis, receiving information about HMPX during medical training was the only variable significantly associated with good confidence (adjusted odds ratio 2.74, 95% confidence interval 1.57 to 4.78 and p < 0.001). Approximately 73.6% and 77.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - purpose, 6 - purpose, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding"
            ]
        },
        {
            "id": "task352-e2144f43424940578a4615a93e7622d6",
            "input": "Rhinovirus was the most prevalent virus and the only virus with a significantly different infection rate in CRS patients and controls in both samples (odds ratio, 3.2 in lavage and 3.4 in scraping samples). This study detected a higher prevalence of respiratory viruses in CRS patients than controls, suggesting that there may be significant associations between inflammation of CRS and respiratory viruses, particularly rhinovirus. Further studies should investigate the exact role of highly prevalent respiratory viruses in CRS patients during symptomatic aggravation and ongoing mucosal inflammation.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-c66d5313befe45c9afee6c5856ad8fb0",
            "input": "A 31 year old male with a history of diabetes mellitus type 1 and recent skin infection of the neck (for which he underwent incision and drainage and levofloxacin treatment) presented to the emergency department with a three day history of fever, cough productive of bloody sputum, and shortness of breath. He had recently returned from a trip to Asia. He was tachycardic but normotensive and had an oxygen saturation of 93 % on 3 L nasal cannula. WBC count was 21.8 K/UL with 90 % neutrophils, BUN and creatinine were 8 mg/dL and 1.0 mg/dL, respectively, and glucose >350 mg/dL. Suspicion of cavitary pneumonia on chest radiograph was confirmed by computed tomography (Fig. 20.1 ).",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - finding"
            ]
        },
        {
            "id": "task352-9d113097fef44ca9b2b7c61ae010ca2f",
            "input": "Objective: In cases of community acquired pneumonia (CAP), it has been known that blood cultures have low yields and rarely affect clinical outcomes. Despite many studies predicting the likelihood of bacteremia in CAP patients, those results have been rarely implemented in clinical practice, and use of blood culture in CAP is still increasing. This study evaluated impact of implementing a previously derived and validated bacteremia prediction rule. Methods: In this registry-based before and after study, we used piecewise regression analysis to compare the blood culture rate before and after implementation of the prediction rule. We also compared 30-day mortality, emergency department (ED) length of stay, time-interval to initial antibiotics after ED arrival, and any changes to the antibiotics regimen as results of the blood cultures. In subgroup analysis, we compared two groups (with or without the use of the prediction rule) after implementation period, using propensity score matching. Results: Following the implementation, the blood culture rate declined from 85.5% to 78.1% (P = 0.003) without significant changes in 30-day mortality and antibiotics regimen. The interval to initial antibiotics (231 min vs. 221 min, P = 0.362) and length of stay (1019 min vs. 954 min, P = 0.354) were not significantly changed. In subgroup analysis, the group that use the prediction rule showed 25 min faster antibiotics initiation (P = 0.002) and 48 min shorter length of stay (P = 0.007) than the group that did not use the rule. Conclusion: Implementation of the bacteremia prediction rule in CAP patients reduced the blood culture rate without affecting the 30-day mortality and antibiotics regimen.",
            "output": [
                "1 - purpose, 2 - purpose, 3 - purpose, 4 - purpose, 5 - purpose, 6 - purpose, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - method, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding"
            ]
        },
        {
            "id": "task352-68a9c2cba3164d64925cc23cfda12596",
            "input": "Objective: Tumor-treating fields are currently used to successfully treat various cancers; however, the specific pathways associated with its efficacy remain unknown in the immune responses. Here, we evaluated tumor-treating fields-mediated initiation of the macrophage-specific immune response. Materials and Methods: We subjected RAW 264.7 mouse macrophages to clinically relevant levels of tumor-treating fields (0.9 V/cm, 150 kHz) and evaluated alterations in cytokine expression and release, as well as cell viability. Additionally, we investigated the status of immunomodulatory pathways to determine their roles in tumor-treating fields-mediated immune activation. Results and Discussion: Our results indicated that tumor-treating fields treatment at 0.9 V/cm decreased cell viability and increased cytokine messenger RNA/protein levels, as well as levels of nitric oxide and reactive oxygen species, relative to controls. The levels of tumor necrosis factor a, interleukin 1b, and interleukin 6 were markedly increased in tumor-treating fields-treated RAW 264.7 cells cocultured with 4T1 murine mammary carcinoma cells compared with those in 4T1 or RAW 264.7 cells with or without tumor-treating fields treatment. Moreover, the viability of 4T1 cells treated with the conditioned medium of tumor-treating fields-stimulated RAW 264.7 cells decreased, indicating that macrophage activation by tumor-treating fields effectively killed the tumor cells. Moreover, tumor-treating fields treatment activated the nuclear factor kB and mitogen-activated protein kinase pathways involved in immunomodulatory signaling. Conclusion: These results provide critical insights into the mechanisms through which tumor-treating fields affect macrophagespecific immune responses and the efficacy of this method for cancer treatment.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-f1e5a84973c743328dcf9dd7785abf71",
            "input": "She was treated successfully with a corticosteroid and anti-mycobacterial therapy. Our observations suggest that pulmonary M. abscessus infection should be added to the list of infectious conditions associated with OP.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-36017d189ab0446baed11f1cbc6a943f",
            "input": "Multiple sclerosis (MS) is the prototypic inflammatory disease of the central nervous system (CNS) characterized by multifocal areas of demyelination, axonal damage, activation of glial cells, and immune cell infiltration. Despite intensive years of research, the etiology of this neurological disorder remains elusive. Nevertheless, the abundance of immune cells such as T lymphocytes and their products in CNS lesions of MS patients supports the notion that MS is an immune-mediated disorder. An important body of evidence gathered from MS animal models such as experimental autoimmune encephalomyelitis (EAE), points to the central contribution of CD4 T lymphocytes in disease pathogenesis. Both Th1 (producing interferon-γ) and Th17 (producing interleukin 17) CD4 T lymphocytes targeting CNS self-antigens have been implicated in MS and EAE pathobiology. Moreover, several publications suggest that CD8 T lymphocytes also participate in the development of MS lesions. The migration of activated T lymphocytes from the periphery into the CNS has been identified as a crucial step in the formation of MS lesions. Several factors promote such T cell extravasation including: molecules (e.g., cell adhesion molecules) implicated in the T cell-blood brain barrier interaction, and chemokines produced by neural cells. Finally, once in the CNS, T lymphocytes need to be reactivated by local antigen presenting cells prior to enter the parenchyma where they can initiate damage. Further investigations will be necessary to elucidate the impact of environmental factors (e.g., gut microbiota) and CNS intrinsic properties (e.g., microglial activation) on this inflammatory neurological disease.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - background, 12 - background, 13 - background, 14 - background, 15 - finding"
            ]
        },
        {
            "id": "task352-233da89bbeec48c2abe569031a6e0cc4",
            "input": "HealthMap is a useful free and open resource employing text-processing algorithms to identify important disease outbreak information through a user-friendly interface. Ⅲ J Am Med Inform Assoc. 2008;15:150 -157.",
            "output": [
                "1 - background, 2 - other"
            ]
        },
        {
            "id": "task352-c57ca0dda469402db2ac356935c2827d",
            "input": "0 1992 Academic PVE.S. Inc.",
            "output": [
                "1 - other, 2 - other"
            ]
        },
        {
            "id": "task352-b731ec9be70d4be49dd3a91aebf11e45",
            "input": "Results: We found that while the early events in HCV infection (i.e. entry plus replication initiation) are cumulatively equivalent or only marginally reduced in PLC and Hep3B cells, later steps of the viral life cycle such as steady-state replication, de novo virus production and/or spread are impaired to different degrees in PLC and Hep3B cultures compared to Huh7 cell cultures. Interestingly, we also observed that interferon stimulated gene (i.e. ISG56) expression was significantly and differentially up-regulated in PLC and Hep3B cells following viral infection. Conclusions: We conclude that the restrictions observed later during HCV infection in these cell lines could in part be attributed to HCV-induced innate signaling. Nevertheless, the identification of two new cell lines capable of supporting authentic HCVcc infection, even at reduced levels, expands the current repertoire of cell lines amendable for the study of HCV in vitro and should aid in further elucidating HCV biology and the cellular determinants that modulate HCV infection.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-a434475602dd4402a9f71294302a8c68",
            "input": ": Viral diseases are one of the leading causes of morbidity and mortality in the world. Virus-specific vaccines and antiviral drugs are the most powerful tools to combat viral diseases. However, broad-spectrum antiviral agents (BSAAs, i.e. compounds targeting viruses belonging to two or more viral families) could provide additional protection of general population from emerging and reemerging viral diseases reinforcing the arsenal of available antiviral options. Here, we reviewed discovery and development of BSAAs and summarized the information on 119 safe-in-man agents in freely accessible database. Future and ongoing pre-clinical and clinical studies will increase the number of BSAAs, expand spectrum of their indications, and identify drug combinations for treatment of emerging and re-emerging viral infections as well as co-infections.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - method, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-b517c5d0c57848639837a8b045918821",
            "input": "Background: During the early phases of the 2009 pandemic, subjects with influenza-like illness only had laboratory testing specific for the new A(H1N1)pdm09 virus. Findings: Between 25 th May and 7 th June 2009, during the pandemic CONTAIN phase, A(H1N1)pdm09 virus was detected using nucleic acid tests in only 56 of 1466 (3.8%) samples meeting the clinical case definition required for A(H1N1)pdm09 testing. Two hundred and fifty-five randomly selected A(H1N1)pdm09 virus-negative samples were tested for other respiratory viruses using a real-time multiplex PCR assay. Of the 255 samples tested, 113 (44.3%) had other respiratory viruses detected: rhinoviruses 63.7%, seasonal influenza A 17.6%, respiratory syncytial virus 7.9%, human metapneumovirus 5.3%, parainfluenzaviruses 4.4%, influenza B virus 4.4%, and enteroviruses 0.8%. Viral co-infections were present in 4.3% of samples. Conclusions: In the very early stages of a new pandemic, limiting testing to only the novel virus will miss other clinically important co-circulating respiratory pathogens.",
            "output": [
                "1 - background, 2 - background, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding"
            ]
        },
        {
            "id": "task352-2b98433df5a0416487b6119b31791212",
            "input": "We evaluated if interventions aimed at air travellers can delay establishment of a SARS-CoV-2 outbreak in a previously unaffected country. Methods: For countries with no sustained SARS-CoV-2 transmission and with no shared border with affected regions we simulated arriving infected air travellers. We assessed the effectiveness of syndromic screening at departure and/or arrival & traveller sensitisation to the COVID-2019-like symptoms with the aim to trigger rapid self-isolation and reporting on symptom onset to enable contact tracing. We assumed that syndromic screening would reduce the number of infected arrivals and that traveller sensitisation reduce the average number of secondary cases. We report the minimal expected delay achievable in 50% (75% & 97.5%) of simulations. In the simulations we account for uncertainty in the number of secondary cases in the absence of air traveller targeted interventions and the arrival times of infected cases and also present sensitivity analyses on arrival rates of infected travellers and the effectiveness of traveller sensitisation. Results: Under baseline assumptions exit and entry screening combined with traveller sensitisation can delay a local SARS-CoV-2 outbreak by at least 83 (75% of simulations: at least 36, 97.5% 8) days while there is no more than 1 infected traveller per week. The benefit of entry screening is small if exit screening is effective: the combination of only exit screening and traveller sensitisation can delay an outbreak by at least 76 (75%: 33, 97.5%: 7) days. With increasing rates of infected travellers, less effective sensitisation or without screening these delays shrink rapidly to a week or less. Conclusion: Syndromic screening and traveller sensitisation in combination could delay outbreaks in yet unaffected countries and support local containment efforts, but only if infected traveller numbers are very low.",
            "output": [
                "1 - background, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-0ce5673fad1a4c64b55265895831878f",
            "input": "Conclusions and Clinical Importance: Results suggested that nasopharyngeal carriage of M. bovis was detrimental to health and growth of dairy calves in small herds with a high incidence of BRD.",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-2ff748b6efd74d20adfef43a63ac0732",
            "input": "The porcine respiratory and reproductive syndrome virus (PRRSV) nucleocapsid (N) protein is a multiphosphorylated protein.It has been proved that the phosphorylation of N protein could regulate the growth ability of PRRSV in Marc-145 cells. However, further investigation is needed to determine whether phosphorylation of the N protein could affect PRRSV virulence in piglets. In this study, we confirmed that the mutations could impair PRRSV replication ability in porcine primary macrophages (PAMs) as they did in Marc-145 cells. The animal experiments suggested that the pathogenicity of the mutated virus (A105-120) was significantly reduced compared with parent strain (XH-GD). Our results suggested that the phosphorylation of the N protein contributes to virus replication and virulence. This study is the first to identify a specific modification involved in PRRSV pathogenicity. Mutation of PTMs sites is also a novel way to attenuate PRRSV virulence. The mutations could be a marker in a vaccine. In conclusion, our study will improve our understanding of the molecular mechanisms of PRRSV pathogenicity.",
            "output": [
                "1 - background, 2 - background, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-14c5708704254a67aecf69137a281dfa",
            "input": "The results of this study support previous findings that points towards genus Enterococcus and species E. coli to be involved in the pathogenesis of NNPD. Moreover, the results indicate that NNPD is associated with a disturbed bacterial composition and larger variation between the diarrhoeic piglets.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-7d3495a2e88a4f059630390459fb8bb8",
            "input": "Citation Avirutnan P, et al. 2011. Complement-mediated neutralization of dengue virus requires mannose-binding lectin. mBio 2(6):e00276-11.",
            "output": [
                "1 - other, 2 - finding, 3 - other"
            ]
        },
        {
            "id": "task352-fba6a41fbd474617a36b812d9c27b3f1",
            "input": "In this study, infrared thermography (IRT) was assessed as a means of detecting foot-and-mouth disease virus (FMDV)-infected cattle before and after the development of clinical signs. Preliminary IRT imaging demonstrated that foot temperatures increased in FMDVinfected animals. The maximum foot temperatures of healthy (n = 53), directly inoculated (DI) (n = 12), contact (CT) (n = 6), and vaccine trial (VT) (n = 21) cattle were measured over the course of FMD infection. A cut-off value was established at 34.4°C (sensitivity = 61.1%, specificity = 87.7%) with the aim of detecting FMDV-infected animals both before and after clinical signs were observed. Seven of 12 (58%) DI and 3/6 (50%) CT animals showed maximum foot temperatures exceeding the 34.4°C cut-off before the development of foot vesicles. In contrast, only 5/21 (24%) VT animals displayed pre-clinical foot temperatures above this cut-off possibly indicating partial vaccine protection of this group. These results show IRT as a promising screening technology to quickly identify potentially infected animals for confirmatory diagnostic testing during FMD outbreaks. Further evaluation of this technology is needed to determine the value of IRT in detecting animals with mild clinical signs or sub-clinical infections. Published by Elsevier Ltd.",
            "output": [
                "1 - purpose, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - other"
            ]
        },
        {
            "id": "task352-19e6689296284db5b2e0c0d66f97ff2d",
            "input": "In the present work, a single-step purification of recombinant nucleocapsid protein (NP) of the Newcastle disease virus (NDV) directly from unclarified feedstock using an expanded bed adsorption chromatography (EBAC) was developed. Streamline 25 column (ID = 25 mm) was used as a contactor and Streamline chelating adsorbent immobilized with Ni 2+ ion was used as affinity adsorbent. The dynamic binding capacity of Ni 2+ -loaded Streamline chelating adsorbent for the NP protein in unclarified feedstock was found to be 2.94 mg ml À1 adsorbent at a superficial velocity of 200 cm h À1 . The direct purification of NP protein from unclarified feedstock using expanded bed adsorption has resulted in a 31% adsorption and 9.6% recovery of NP protein. The purity of the NP protein recovered was about 70% and the volume of processing fluid was reduced by a factor of 10. The results of the present study show that the IMA-EBAC developed could be used to combine the clarification, concentration and initial purification steps into a single-step operation.",
            "output": [
                "1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-3708d83dbc3945899d7e39774941b515",
            "input": "The prevalence of antibodies to bovine coronavirus (BCV) and bovine respiratory syncytial virus (BRSV) infections was studied in 20 conventional and 20 organic dairy herds. The organic farms had produced 'certified' milk for at least 2 years. On two occasions, with a 1-year interval, 699 serum samples from 624 peri-parturient cows were tested by ELISA for antibodies to BCV and BRSV. Accompanying data relating to the sampled animals were collected in order to identify potential factors associated with increased antibody prevalence. The antibody prevalence was high at both sampling times with approximately 85% and 80% of animals positive for antibodies to BCV and to BRSV, respectively. Conventional herds had a significantly higher mean antibody prevalence to BCV and BRSV than the organically managed herds (P < 0.01). Animal age was significantly associated with increased antibody prevalence (P < 0.001). The findings of this study suggest that organic farm management may be effective in reducing the seroprevalence of these viruses relative to conventional farming methods.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-7de5bf227f1b495eabd63dd3be8ff9fd",
            "input": "From December 2019, an outbreak of unusual pneumonia was reported in Wuhan with many cases linked to Huanan Seafood Market that sells seafood as well as live exotic animals. We investigated two patients who developed acute respiratory syndromes after independent contact history with this market. The two patients shared common clinical features including fever, cough, and multiple ground-glass opacities in the bilateral lung field with patchy infiltration. Here, we highlight the use of a low-input metagenomic next-generation sequencing (mNGS) approach on RNA extracted from bronchoalveolar lavage fluid (BALF). It rapidly identified a novel coronavirus (named 2019-nCoV according to World Health Organization announcement) which was the sole pathogens in the sample with very high abundance level (1.5% and 0.62% of total RNA sequenced). The entire viral genome is 29,881 nt in length (GenBank MN988668 and MN988669, Sequence Read Archive database Bioproject accession PRJNA601736) and is classified into β-coronavirus genus. Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/ 4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21. Evolutionary analysis based on ORF1a/1b, S, and N genes also suggests 2019-nCoV is more likely a novel CoV independently introduced from animals to humans.",
            "output": [
                "1 - background, 2 - purpose, 3 - background, 4 - background, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding"
            ]
        },
        {
            "id": "task352-bc15ce186c58403582392a4ed83cb38c",
            "input": "Profiles of antibodies to the nucleocapsid protein of the severe acute respiratory syndrome (SARS)-associated coronavirus in 445 probable SARS patients and 3,749 healthy people or non-SARS patients were analyzed by antigen-capturing enzyme-linked immunosorbent assay. Antinucleocapsid antibodies were elucidated in 17.5% of the probable SARS patients 1 to 7 days after the onset of symptoms and in 80% of the patients 8 to 14 days after the onset. About 90% of the probable SARS patients were positive 15 or more days after illness. Antibody titers increased up to 70 days, and high antibody titers were maintained at least for another 3 months. Of the healthy people and non-SARS patients, only seven (0.187%) were weakly positive. FIG. 1. Development of anti-N protein antibody titers over time in 445 patients who probably had SARS. 228 NOTES CLIN. DIAGN. LAB. IMMUNOL.",
            "output": [
                "1 - background, 2 - background, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - other, 9 - finding, 10 - other, 11 - other, 12 - other, 13 - other"
            ]
        },
        {
            "id": "task352-e05fd9c27c104bcc86a0b2707a0c0c72",
            "input": "Trial registration: ClinicalTrials.gov NCT02644135 (retrospectively registered).",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-a33d9f54b0a84f23ae78bc2e82be4756",
            "input": "To reduce computation time, scalar transport for airborne virus spread was simulated based on a database for the CFD computed airflow in the investigated area using representative wind conditions. The simulation results, and the weather data were then used to make a database for a web-based forecasting system that could be accessible to users. ScienceDirect jo urnal homepage: www .e lsev ie r.com/ locate/issn/153 75110 b i o s y s t e m s e n g i n e e r i n g 1 2 9 ( 2 0 1 5 ) 1 6 9 e1 8 4",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - other"
            ]
        },
        {
            "id": "task352-e21eeeaa76734deb9441f2d6a94670d1",
            "input": "Conclusions. Streptococcus pneumoniae, RSV, and rhinovirus may be the major microorganisms associated with pneumonia infections in children <5 years of age from developing and emerging countries. Increasing S. pneumoniae vaccination coverage may substantially reduce the burden of pneumonia among children in developing countries.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-29e944e5f5e745d4a69d43219e182d37",
            "input": "Detection and characterisation of the canine parvovirus (CPV-2) strains that are currently circulating are essential for the understanding of viral evolution and the development of measures to control its spread. In the present study, stool samples from 144 dogs were analysed by polymerase chain reaction (PCR) for CPV-2, and 29.2% (42/144) of them were positive. From the 42 positive strains, 71.4% (30) of the dogs had signs of haemorrhagic gastroenteritis. The sequencing of the 583 bp fragment of the VP2 gene from the positive strains identified 78.6% (33/42) of them as type 2c, 19% (8/42) as type 2b and 2.4% (1/42) as type 2a. A phylogenetic analysis of the variants circulating in the canine population of Brazil showed that they are very similar to those found in other countries and type 2c has become the predominant type circulating in Brazil.",
            "output": [
                "1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-81b1dd0a5237490a9071a320768a2f8f",
            "input": "The number in square brackets following a selected paper, e.g. [7], refers to its number in the annotated references of the corresponding review.",
            "output": [
                "1 - method, 2 - method"
            ]
        },
        {
            "id": "task352-11deba2f4772465986665f3dd7e5e8cc",
            "input": "Even after one hundred years, the Golgi apparatus remains a major challenge in the field of Cell Biology. This is particularly true in terms of transport and of protein sorting. For example, the question how cargo proteins are transported through this organelle is still a matter of debate. Emphasis has been put on the role of anterograde and retrograde transport vesicles. These have been proposed to carry cargo from cisterna to cisterna and to recycle components needed for further rounds of transport. Alternatively, anterograde movement of cargo takes place in cisternal membranes rather than transport vesicles. These membranes assemble and mature in a cis to trans direction. In this case, retrograde transport vesicles need to recycle all components of the Golgi apparatus and this demands a highly dynamic and efficient sorting machinery. Here we will discuss possible mechanisms for protein sorting in the context of cisternal maturation and propose that a common mechanism is sufficient to explain both transport of cargo and sorting of resident proteins. ß 1998 Elsevier Science B.V. All rights reserved.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - purpose, 11 - other"
            ]
        },
        {
            "id": "task352-560cbc8d1bb24a5f9978e063cdaea250",
            "input": "Porcine aminopeptidase N (pAPN) is a cellular membrane protein and a functional receptor for porcine coronaviruses. Here, we describe the heterologous expression of pAPN without signal peptide in BL21(DE3)pLysS host cells. The Escherichia coli (E. coli) harboring the recombinant construct was efficiently induced to express the pAPN protein at a high level. The most optimal expression profile for pAPN expression was investigated. By inoculating a rabbit with the purified pAPN, a high tittered specific antibody was achieved. Biologically, the antibody reacted with either pAPN-expressing E. coli or native pAPN on the surface of swine testis cells. The pAPN and its specific antibody blocked transmissible gastroenteritis coronavirus infection in vitro. Furthermore, the localization of pAPN on the small intestine of swine was analyzed by immunohistochemistry.",
            "output": [
                "1 - background, 2 - purpose, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-00d9cf2eae4c4b7797d7180905215af6",
            "input": "We have investigated the role of two polymorphic sites (R190W and N192K) on the binding and activation of the formyl peptide receptor (FPR) by viral and formyl peptides. WEDWVGWI, a peptide with antiviral activity derived from the membrane proximal region of feline immunodeficiency virus, binds with high affinity to FPR. The three tryptophans in the peptide are all essential for FPR binding, just as they were essential for antiviral activity (Giannecchini, S. et al., J. Virol. 77 (2003) 3724). Formyl-NleWEDWVGWI behaved as a weak partial agonist with FPR W190/N192 but a stronger partial agonist with FPR R190/K192 and FPR R190/N192. Formyl-NleNleWEDWVGWI behaved as a full agonist toward all three FPRs but exhibited a much higher EC 50 with W190/N192 FPR (300±45 nM) than for R190/K192 FPR (40±3 nM) or R190/N192 (60 ±8 nM). Formyl-MYKWPWYVWL preferentially activated R190/K192 and R190/N192 FPRs by >5 fold compared to W190/N192 FPR. Formyl-MFEDAVAWF, a peptide derived from a protein in Mycobacterium avium subsp. paratuberculosis and formyl-MFTFEPFPTN, a peptide derived from the N-terminus of chemotaxis inhibitory protein of Staphylococcus aureus with an added N-terminal methionine exhibited the greatest selectivity for R190/K192 and R190/N192 FPRs with ~10 fold lower EC 50S than that observed with FPR W190/N192. Thus, individuals with the W190 polymorphism may display a reduced ability to detect certain formyl peptides.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-a4d98ea134434b89997ece99d0cbc078",
            "input": "A multiplex quantitative real-time polymerase chain reaction (mqPCR) assay was developed and validated for the detection and differentiation of porcine circovirus type 3 (PCV3) and type 2 (PCV2) strains. The assay coverage was 97.9% (184/188) for PCV3 and 99.1% (1889/1907) for PCV2 sequences that were available from the current GenBank database. The PCR amplification efficiencies were 98-99% for plasmids, and 92-96% for diagnostic samples, with correlation coefficients all greater than 0.99. The limit of detection (LOD) determined as plasmid copies per reaction was 17 for PCV3 and 14 for PCV2. The assay specifically detected the targeted viruses without cross reacting to each other or to other common porcine viruses. Among 336 swine clinical samples collected in 2018, 101 (30.1%) were PCV3 positive, 56 (16.7%) were PCV2 positive and 18 (5.4%) were co-positives. Sixty selected PCV3 positives were confirmed by Sanger sequencing, and 53 of the 56 PCV2 positive samples were tested positive by another validated PCR assay.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-aed7d7850e9b494dba8010ed7ad528c9",
            "input": "Results: During OV, the number of patients simultaneously treated at the NIMCU increased from 18 to 22, resulting in a reduced bed-to-bed space. Nurse: patient ratio was 4:22 during OV compared to 3:18 during PRAE-OV. Cumulative incidence of MDRGN was 4.7% in OV and 2.4% POST-OV compared to 4.8% to PRAE-OV, respectively, without any significant variations. During OV and POST-OV, septic episodes due to MDRGN were not observed. In one case, potential nosocomial transmission of Enterobacter cloacae resistant to Piperacillin and 3rd/4th generation cephalosporins was observed. Conclusions: Prevention of nosocomial spread of MDRGN in an overcrowded NIMCU is based on staff's diligent training and adequate staffing. Concise microbiological surveillance should be guaranteed to escort through overcrowding periods. In our setting, impact of bed-to-bed distance on MDRGN transmission seemed to be less strong.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding"
            ]
        },
        {
            "id": "task352-6f3790eb015245c88fa9c16de9fab747",
            "input": "Pet owners frequently administer antimicrobials to their pets and therefore have an important role to play in promoting antimicrobial stewardship in veterinary medicine. However, best methods of educating pet owners about antimicrobial stewardship have yet to be defined. While visual materials such as brochures and posters are often used in health promotion campaigns, their effectiveness in veterinary medicine is unknown. The objective of this study was to determine whether pet owners noticed and retained the message of a poster with an antimicrobial stewardship message placed in veterinary clinic exam rooms. A total of 111 pet owners from five veterinary clinics (three general practices, two low-cost clinics) in the greater Philadelphia area participated in the study. Participants completed a survey asking whether they noticed the poster and if they could paraphrase its message. In a follow-up survey, an antibiotic knowledge score was calculated from answers to questions assessing their knowledge of the poster message. Baseline knowledge was assessed by asking participants to define antibiotic resistance. At the end of the study, veterinarians at participating clinics were interviewed about their experiences with the poster. Only 51 (46.4%) participants noticed the poster, and only 11 (9.9%) could partially or completely reproduce its message. No demographic or clinic-level factors were significantly associated with noticing the poster or recalling its message. Antibiotic knowledge scores were highly correlated (ρ = 0.87, p < 0.001) with baseline knowledge and not affected by viewing the poster (p = 0.955). Veterinarians expressed skepticism that the poster was effective in conveying a message of judicious antibiotic use to clients and noted no difference in the frequency with which they discussed antibiotic resistance or felt pressured to prescribe antibiotics by their clients. Posters alone will likely have limited impact in conveying a message of judicious antibiotic use to pet owners. However, they might be useful as part of an active, multi-modal education strategy, especially if complemented by veterinarian actions.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding"
            ]
        },
        {
            "id": "task352-48a361ce029f4ed098b400d7bfd26acf",
            "input": "Post-translational modifications (PTMs), including phosphorylation, ubiquitylation and acetylation, of signal transduction proteins involved in the pathways engaged downstream of virus sensing are crucial to reach a fine-tuned regulation of the innate immune response 27 . In light of the very well documented importance of phosphorylation PTMs in the regulation of the antiviral response, the protein phosphatases negatively regulating the signaling events have started to be identified. The exact role of the Ser/Thr protein phosphatase 1 (PP1) in the antiviral response remains elusive as PP1α and PP1γ were found to dephosphorylate MDA-5 and RIG-I leading to their activation 28 , while they were also described to be responsible for the dephosphorylation of key C-terminal phosphoresidues of IRF3 leading to its inhibition 29 . Most . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . doi: bioRxiv preprint 15 Clement, J. F. et al. Phosphorylation of IRF-3 on Ser 339 generates a hyperactive form of IRF-3 through regulation of dimerization and CBP association.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - finding, 7 - background, 8 - other, 9 - background, 10 - other, 11 - other, 12 - other"
            ]
        },
        {
            "id": "task352-868b4f2853594edbae679e5587e8e82c",
            "input": "Porphyromonas gulae is a major periodontal pathogen in dogs, which can be transmitted to their owners. A major virulence factor of P. gulae consists of a 41-kDa filamentous appendage (FimA) on the cell surface, which is classified into three genotypes: A, B, and C. Thus far, inhibition of periodontal disease in dogs remains difficult. The present study assessed the inhibitory effects of a combination of clindamycin and interferon alpha (IFN-α) formulation against P. gulae and periodontal disease. Growth of P. gulae was significantly inhibited by clindamycin; this inhibition had a greater effect on type C P. gulae than on type A and B isolates. In contrast, the IFN-α formulation inhibited the expression of IL-1β and COX-2 elicited by type A and B isolates, but not that elicited by type C isolates. Furthermore, periodontal recovery was promoted by the administration of both clindamycin and ifn-α formulation to dogs undergoing periodontal treatment; moreover, this combined treatment reduced the number of fimA genotypes in oral specimens from treated dogs. these results suggest that a combination of clindamycin and ifn-α formulation inhibit P. gulae virulence and thus may be effective for the prevention of periodontal disease induced by P. gulae.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - purpose, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding"
            ]
        },
        {
            "id": "task352-508d20f7401841a1bf5f9ad5b20a8182",
            "input": "Background: Respiratory protection effi ciency of facemasks is critically important in the battle against communicable respiratory infections such as infl uenza and severe acute respiratory syndrome (SARS). We studied the spatial distributions of simulated virus-laden respiratory droplets when human subjects wore facemasks and were exposed to regulatory viral droplets by conducting in vivo experiments in facemask use. Methods: Transmission pathway of aerosols of Fluorescein-KCl solution through facemasks and protective effi ciency of facemasks were examined by using normal surgical facemasks and two facemasks with exhaust valves (Facemask A) and exhaust holes (Facemask B) covered with the same surgical fi lters situated at the back of the facemasks. Fluorescein-KCl solution was sprayed onto the faces of participants wearing the facemasks and performing intermittent exercises on a treadmill in a climatic chamber. Results: Experimental results showed that when droplets spread onto a person face-to-face over short distances, 92.3% to 99.5% of droplets were blocked by the front surface of the facemask, whereas only 0.5% to 7.7% of droplets reached the back of the facemask. Both facemasks A and B had near or over 99% protection effi ciency, compared with that of 95.5% to 97% of surgical facemasks. Using the same fi lters as normal surgical masks, facemasks A and B provided more effective respiratory protection against communicable respiratory infections such as infl uenza and SARS by the location of the breathing pathway to the back of the facemasks. Conclusions: Separating the breathing pathway from the virus-contaminated area in facemasks can provide more effective protection against communicable respiratory infections such as infl uenza and SARS.",
            "output": [
                "1 - background, 2 - purpose, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-4ca97d0f709349c4b4542ba552753635",
            "input": "Direct-acting antivirals are effective tools to control viral infections. SARS-CoV-2 is a coronavirus associated with the epidemiological outbreak in late 2019. Previous reports showed that HIV-1 protease inhibitors could block SARS-CoV main protease. Based on that and using an in silico approach, we evaluated SARS-CoV-2 main protease as a target for HIV-1 protease inhibitors to reveal the structural features related to their antiviral effect. Our results showed that several HIV inhibitors such as lopinavir, ritonavir, and saquinavir produce strong interaction with the active site of SARS-CoV-2 main protease. Furthermore, broad library protease inhibitors obtained from PubChem and ZINC (www.zinc.docking.org) were evaluated. Our analysis revealed 20 compounds that could be clustered into three groups based on their chemical features. Then, these structures could serve as leading compounds to develop a series of derivatives optimizing their activity against SARS-CoV-2 and other coronaviruses. Altogether, the results presented in this work contribute to gain a deep understanding of the molecular pharmacology of SARS-CoV-2 treatment and validate the use of protease inhibitors against SARS-CoV-2.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding"
            ]
        },
        {
            "id": "task352-f47c6114420b41b3b40fcad6fe77f71e",
            "input": "www.ajpmonline.org",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-717a753d5af442578259863f17dbbdce",
            "input": "Over the past few decades, global metapopulation epidemic simulations built with worldwide air-transportation data have been the main tool for studying how epidemics spread from the origin to other parts of the world (e.g., for pandemic influenza, SARS, and Ebola). However, it remains unclear how disease epidemiology and the air-transportation network structure determine epidemic arrivals for different populations around the globe. Here, we fill this knowledge gap by developing and validating an analytical framework that requires only basic analytics from stochastic processes. We apply this framework retrospectively to the 2009 influenza pandemic and 2014 Ebola epidemic to show that key epidemic parameters could be robustly estimated in real-time from public data on local and global spread at very low computational cost. Our framework not only elucidates the dynamics underlying global spread of epidemics but also advances our capability in nowcasting and forecasting epidemics.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - method, 6 - finding"
            ]
        },
        {
            "id": "task352-0b166799b5054c99a01079aa6235450f",
            "input": "This paper assesses the impact of the September 11 terrorist attacks and its after-effects on U.S. airline demand. Using monthly time-series data from 1986 to 2003, we find that September 11 resulted in both a negative transitory shock of over 30% and an ongoing negative demand shock amounting to roughly 7.4% of pre-September 11 demand. This ongoing demand shock has yet to dissipate (as of November 2003) and cannot be explained by economic, seasonal, or other factors.",
            "output": [
                "1 - purpose, 2 - method, 3 - finding, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-7a82a64fd32c4230932f639d66aea2d2",
            "input": "No highlights are required as this is not a research article",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-85ffe5ad22124ae096f358c1931aa9c3",
            "input": "Conclusions: Normal cough produced a turbulent jet about 0.7 m towards the end of the bed from the recumbent subject. N95 mask was more effective than surgical mask in preventing expelled air leakage during coughing but there was still significant sideway leakage.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-f39806cfb4814594891b72d960b6397b",
            "input": "Streptococcus mutans is a bacterial cause of dental caries that is resistant to bacitracin. The aim of this study was to elucidate the mbrABCD-related bacitracin resistance mechanism of S. mutans. Transcriptome data demonstrated that the expression levels of 33 genes were induced more than twofold by bacitracin. Fourteen genes were selected from the upregulated genes, and defective mutants of these genes were constructed for measurement of their sensitivity to bacitracin. Among the mutants, only the mbrA-or mbrB-deficient mutants exhibited 100-to 121-fold greater sensitivity to bacitracin when compared with the wild-type strain. Moreover, knockout of the mbrC and mbrD genes abolished the bacitracin-induced mbrAB upregulation. These results suggest that both mbrC and mbrD are required for mbrAB upregulation that confers the bacitracinresistant phenotype on S. mutans.",
            "output": [
                "1 - background, 2 - purpose, 3 - finding, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-03a9faa623f14f8c9de9a7091fbc2154",
            "input": "www.nature.com/reviews/molcellbio",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-2584c3a3c4a7474b87c7f936dc35cf13",
            "input": "Abbreviations: B16M -B16 melanoma; ELISA -enzyme-linked immunosorbent assay; IL-18 -interleukin-18; i.p.intraperitoneal; LPS -lipopolysaccharide; MHV -Mouse Hepatitis Virus; TNF-a -tumor necrosis factor a",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-9d706af7e5a840bf9dd5c936ba746176",
            "input": "We found that the sensitivities of 3 rapid influenza antigen tests for pandemic influenza A/H1N1 virus were low to moderate: BD Directigen EZ Flu A+B test (Becton Dickinson), 46.7%; BinaxNOW Influenza A&B (Inverness Medical), 38.3%; and QuickVue Influenza A+B Test (Quidel), 53.3%. A patient with influenza-like illness who has a negative rapid antigen test result should undergo further testing using reverse-transcription polymerase chain reaction.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-b0b6020df5cf43b98b0e2594344ede29",
            "input": "Background: Despite current knowledge of mutations in 45 genes that can cause nonsyndromic sensorineural hearing loss (SNHL), no unified clinical test has been developed that can comprehensively detect mutations in multiple genes. We therefore designed Affymetrix resequencing microarrays capable of resequencing 13 genes mutated in SNHL (GJB2, GJB6, CDH23, KCNE1, KCNQ1, MYO7A, OTOF, PDS, MYO6, SLC26A5, TMIE, TMPRSS3, USH1C). We present results from hearing loss arrays developed in two different research facilities and highlight some of the approaches we adopted to enhance the applicability of resequencing arrays in a clinical setting. Results: We leveraged sequence and intensity pattern features responsible for diminished coverage and accuracy and developed a novel algorithm, sPROFILER, which resolved >80% of no-calls from GSEQ and allowed 99.6% (range: 99.2-99.8%) of sequence to be called, while maintaining overall accuracy at >99.8% based upon dideoxy sequencing comparison. Conclusions: Together, these findings provide insight into critical issues for disease-centered resequencing protocols suitable for clinical application and support the use of array-based resequencing technology as a valuable molecular diagnostic tool for pediatric SNHL and other genetic diseases with substantial genetic heterogeneity.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-d488ee5bdd434b46991347633b26ada8",
            "input": "Pandemic growth rates from sequences E. de Silva et al. 1807 ",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-019e389c06344fa28076a6f36dea19cf",
            "input": "This study aimed to determine the aetiology of community-acquired pneumonia (CAP) by adding polymerase chain reaction (PCR) to conventional methods and to describe the clinical and laboratory features between patients with bacterial pneumonia (BP) and viral pneumonia (VP). Adults with CAP admitted from November 2009 to October 2010 were included. Demographics, comorbidities, severity and clinical features were recorded. Conventional microbiological methods included blood and sputum cultures, acute and convalescent serologic samples, and antigen urinary detection. New methods included multiplex PCR for Mycoplasma pneumoniae, Legionella pneumophila, Chlamydophila pneumoniae, Bordetella pertussis and 15 respiratory viruses. A total of 169 patients were included. Using conventional methods, we identified a pathogen in 51 % of cases. With PCR, up to 70 % of cases had an aetiological diagnosis. Fortyfive patients had BP (34 %), 22 had VP (17 %) and 25 (19 %) had co-infection (BP and VP). Pneumococci and respiratory syncytial virus (RSV) were the most frequently identified pathogens. Procalcitonin (PCT) and C-reactive protein (CRP) median values were significantly higher in BP than in VP patients. Shaking chills, higher CURB score and shock were significantly more frequent in BP. A viral infection was identified in more than one-third of patients with CAP. Clinical and laboratory features could help to differentiate between VP and BP and to guide empirical therapy. A. Sangil : E. Calbo : S. Benet : M. E. Viladot : V. Pascual :",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding"
            ]
        },
        {
            "id": "task352-24d4b7673dec4eaca4c476f61a05af1b",
            "input": "MERS-coronavirus infection is currently responsible for considerable morbidity and mortality in Saudi Arabia. Understanding its burden, as an emerging infectious disease, is vital for devising appropriate control strategies. In this study, the burden of MERS-CoV was estimated over 31 months period from June 6, 2012 to January 5, 2015. The total number of patients was 835; 528 (63.2%) patients were male, 771 (92.3%) patients were ≥25 years of age, and 210 (25.1%) patients were healthcare workers. A total of 751 (89.9%) patients required hospitalization. The median duration between onset of illness and hospitalization was 2 days (interquartile range, 0-5). The median length of hospital stay was 14 days (IQR, 6-27). The overall case fatality rate was 43.1%. Basic reproductive number was 0.9. Being Saudi, non-healthcare workers, and age ≥65 years were significantly associated with higher mortality. In conclusion, MERS-CoV infection caused a substantial health burden in Saudi Arabia.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding"
            ]
        },
        {
            "id": "task352-5ac5b8b8f472412a975daf026f17def9",
            "input": "The optimal template for homology modeling of the E protein of SARS-CoV-2 was the E protein of SARS(PDB ID: 5x29.1), with the sequence identity of 91.38% and author/funder. All rights reserved. No reuse allowed without permission.",
            "output": [
                "1 - finding, 2 - finding, 3 - other, 4 - other"
            ]
        },
        {
            "id": "task352-3b17a4b8fd8c4b7b9a0e6b40df8104da",
            "input": "In particular, 63% (12 of 19) of fecal samples from Miniopterus pusillus were positive for the virus. These findings suggest that this virus might be commonly circulating in M. pusillus in Hong Kong.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-b6b8291261c94cbd807f2fbb6b3d0d50",
            "input": "Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 12503 |",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-aab7f9e107ba42a6ba1dde7003a98c23",
            "input": "Public Health jo urnal homepage: www .e lse vi er.co m/ pu he p u b l i c h e a l t h 1 5 0 ( 2 0 1 7 ) 1 4 9 e1 5 1.",
            "output": [
                "1 - other, 2 - other"
            ]
        },
        {
            "id": "task352-64ecc6bc758745dfa2e1882218233cf8",
            "input": "Hepatocytes are key effector cells in anti-Coxsackievirus immunity PLOS Pathogens.",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-652249d302cf462bbc3e692df4f2b62a",
            "input": "Mannheimia haemolytica is the most important bacterial agent associated with the bovine respiratory disease complex (BRDC), which causes worldwide economic losses to the cattle industry. M. haemolytica cells initially colonize the tonsillar crypts in the upper respiratory tract of cattle, from where they can subsequently descend into the lungs to cause disease. Many bacteria exist as biofilms inside their hosts. We hypothesize that M. haemolytica colonization of cattle during its commensal state may include biofilm formation. To begin to assess this possibility, we developed an in vitro system to study biofilm formation directly on bovine respiratory epithelial cells. Using fixed primary bovine bronchial epithelial cells, we observed M. haemolytica biofilm formation after a 48 h incubation period at 37 C. Addition of mucin, the main component of mucus present in the upper respiratory tract, decreased M. haemolytica biofilm formation on bovine epithelial cells. We investigated the effects of prior viral infection of the epithelial cells on subsequent biofilm formation by M. haemolytica and found negligible effects. Utilization of this model system will provide new insights into the potential role of biofilm formation by M. haemolytica in the pathogenesis of BRDC.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-e0cc737c49ff49b180d8c1727b835102",
            "input": "License, which permits unrestricted use, provided the original author and source are credited.",
            "output": [
                "1 - other, 2 - other"
            ]
        },
        {
            "id": "task352-3bcebadff0114bef8f82b7deb2660e2b",
            "input": "Citation Chan JM, Rabadan R. 2013. Quantifying pathogen surveillance using temporal genomic data. mBio 4(1):e00524-12.",
            "output": [
                "1 - other, 2 - other, 3 - other"
            ]
        },
        {
            "id": "task352-c6573959de4f4dedb11d6a4402f0eb16",
            "input": "WIDER IMPLICATIONS: This is the first comprehensive review of rodent models of both infectious and autoimmune disease of testis/ epididymis, and their clinical implications, i.e. their importance in understanding male infertility related to infectious and non-infectious/ autoimmune disease of the reproductive organs.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-e6170e9eabad43f3bff1160eedd15b1d",
            "input": "The objective of this study was to develop a symptom scoring system for use in clinical studies that differentiates children with cold symptoms who have an identifiable viral etiology for their upper respiratory tract infection (URI) from those in whom no virus is detected. Nasal swabs for PCR testing for identification of respiratory viruses were obtained on children aged 2-11 y at baseline and when parents thought their child was developing a cold. Parentalrecorded severity of specific symptoms in children with and without a documented viral URI were compared. Nasal swabs were obtained on 108 children whose parents reported their child was developing a cold. A viral etiology was identified in 62 of 108 (57.4%) samples. Symptom measures that best differentiated children with a viral etiology from those without were significant runny nose and significant cough on days 1-4 of the illness. A URI symptom score was developed based on these symptoms, with a sensitivity of 81.4%, specificity of 61.9%, and accuracy of 73.3%. Parental impression is only a moderately accurate predictor of viral URI in children. Our URI symptom score provided a more accurate method for identifying children with viral URIs for clinical studies. (Pediatr Res 68: 252-257, 2010)",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - other"
            ]
        },
        {
            "id": "task352-41e570c625f0455297fe3f59aac65341",
            "input": "within the receptor binding domain (RBD) of the MERS-CoV S protein. We used a complex consisting of the epitope peptide of the MERS-CoV S protein and CpG-DNA encapsulated in liposome complex to immunize mice, and produced the monoclonal antibodies 506-2G10G5 and 492-1G10E4E2. The western blotting data showed that both monoclonal antibodies detected the S protein and immunoprecipitated the native form of the S protein. Indirect immunofluorescence and confocal analysis suggested strong reactivity of the antibodies towards the S protein of MERS-CoV virus infected Vero cells. Furthermore, the 506-2G10G5 monoclonal antibody significantly reduced plaque formation in MERS-CoV infected Vero cells compared to normal mouse IgG and 492-1G10E4E2. Thus, we successfully produced a monoclonal antibody directed against the RBD domain of the S protein which could be used in the development of diagnostics and therapeutic applications in the future. [BMB Reports 2019; 52(6): 397-402] BMB Rep. 2019; 52(6): 397-402 www.bmbreports.org",
            "output": [
                "1 - background, 2 - method, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - other"
            ]
        },
        {
            "id": "task352-c3741a38e83348ecba8441c9e015013c",
            "input": "Mis-secreted glycoproteins (LGI1, reelin) are emerging causes of epilepsy. LMAN2L belongs to a glycoprotein secretion chaperone family. One recessive LMAN2L missense mutation predicted to impair the chaperone's interaction with glycoproteins was reported in a family with intellectual disability (ID) and remitting epilepsy. We describe four members of a family with autosomal dominant inheritance of a similar phenotype. We show that they segregate a NM_001142292.1:c.1073delT mutation that eliminates LMAN2L's endoplasmic reticulum retention signal and mislocalizes the protein from that compartment to the plasma membrane. LMAN2L mislocalization, like impaired glycoprotein interaction, disturbs brain development, including generation of developmentally restricted epilepsy.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-b9b4d34b3ceb4280b4f779e24de61618",
            "input": "Citation Peng X, et al. 2011. Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection. mBio 2(6):e00198-11.",
            "output": [
                "1 - finding, 2 - finding, 3 - other"
            ]
        },
        {
            "id": "task352-4c4500aaf8624507bdca6f61f965bf44",
            "input": "Musk of musk deer has been one of the most precious traditional medicinal materials for treatment of stroke, but trading is prohibited. Musk of muskrat, Ondatra zibethicus, is an accessible substitute for musk of musk deer. However, neuroprotective effects of the musk of muskrat on stroke model are so far unclear. Aim of the study is to determine neuroprotective effects of the musk of muskrat on focal cerebral ischemia. The protective effects against focal cerebral ischemia were evaluated using a model of middle cerebral artery occlusion (90-minute occlusion followed by 24-hour reperfusion). Musk of muskrat was collected from scent bag of muskrat and orally administered at doses of 100 and 300 mg/kg twice at times of 0 and 90 min after occlusion. The effects on sensorimotor dysfunction were investigated by using balance beam test and rotarod test after brain ischemia. The expression of cyclooxygenase-2 (COX-2) was investigated by immunohistochemistry. Oral administration of musk at 300 mg/kg significantly reduced (p<0.001) the infarct volume by 32.4% compared with a vehicle-treated group. Oral administration of musk at 300 mg/kg also ameliorated ischemia-induced spontaneous and vestibule sensorimotor dysfunction in balance beam test and rotarod test compared with control group and COX-2 upregulation. Musk of muskrat may have neuroprotective effects against transient focal cerebral ischemia with recovery of sensorimotor dysfunction. Regarding the immunohistochemistry, the effects of muskrat may be due to anti-inflammatory properties through inhibition of COX-2 expressions.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - finding, 12 - finding, 13 - finding"
            ]
        },
        {
            "id": "task352-45a2baa74d074f02a2a5f8e93841ddc8",
            "input": "The copyright holder for this preprint (which was not peer-reviewed) is . 1101 updating the predictions with the use of fresh data and using more complicated mathematical models.",
            "output": [
                "1 - other, 2 - other, 3 - other"
            ]
        },
        {
            "id": "task352-7837802d171b4fe896d1431949f07201",
            "input": "Research program was established by the U.S. National Institute of Allergy and Infectious Diseases to investigate host-pathogen interactions at a systems level. This program generated 47 transcriptomic and proteomic datasets from 30 studies that investigate in vivo and in vitro host responses to viral infections. Human pathogens in the Orthomyxoviridae and Coronaviridae families, especially pandemic H1N1 and avian H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus (SARS-CoV), were investigated. Study validation was demonstrated via experimental quality control measures and meta-analysis of independent experiments performed under similar conditions. Primary assay results are archived at the GEO and PeptideAtlas public repositories, while processed statistical results together with standardized metadata are publically available at the Influenza Research Database (www.fludb.org) and the Virus Pathogen Resource (www.viprbrc.org). By comparing data from mutant versus wild-type virus and host strains, RNA versus protein differential expression, and infection with genetically similar strains, these data can be used to further investigate genetic and physiological determinants of host responses to viral infection.",
            "output": [
                "1 - background, 2 - method, 3 - method, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding"
            ]
        },
        {
            "id": "task352-2e1494d515f443f2af73dc164238182a",
            "input": "Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 12226 |",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-42dad6b692c54450b1b29e512029df61",
            "input": "A total of 123 community paediatricians and 23 microbiology laboratories studied the clinical and bacteriological efficacy of treatment of group A streptococcal pharyngitis in Italy. Of 1065 patients, from whom Streptococcus pyogenes was isolated, 723 returned to follow up and of these 138 (19%) still had a positive throat culture. The erythromycin resistance (ER) rate was 23.7% with resistance phenotype distribution of: 31.7% constitutive (CR), 26.6% inducible (IR) and 41.7% efflux pump (M) resistance phenotype. All strains were susceptible to the b-lactam agents tested. CR strains were highly resistant to all 14, 15 and 16 membered macrolides with the exception of rokitamycin which showed activity against 37.8% of isolates. All phenotype M and some IR isolates were susceptible to clindamycin, rokitamycin, josamycin and spiramycin; clarithromycin was active against a small percentage of strains belonging to the IR and M phenotype. Bacterial eradication was found in 85.5, 78.7 and 75.8% of the penicillin, macrolide and cephalosporin treated groups. Genotyping of strains showed that 8.7% of the 19% of cases classified as 'failed bacterial eradication' were due to recolonization with a different isolate, observed exclusively among b-lactams treated patients. Clinical cure was achieved in a high percentage of cases, irrespective of the antibiotic prescribed, with the best clinical efficacy being found following therapy with amoxycillin and clarithromycin (90.9%).",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding"
            ]
        },
        {
            "id": "task352-22840182790e4fb68564223d5a98688f",
            "input": "Fig. 6. Input mzML/mzXML les were processed with OpenMS 34 and low-quality MS/MS spectra .",
            "output": [
                "1 - method, 2 - other"
            ]
        },
        {
            "id": "task352-ea3f05183e264988ae652c4b2d0be166",
            "input": "News exposure and collective attention during epidemics PLOS Computational Biology.",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-f2e6411fd016480dbae8b113a372a51e",
            "input": "In an effort to rapidly discover lead compounds targeting M pro , two compounds (11a and 11b) were designed and synthesized, both of which exhibited excellent inhibitory activity with an IC 50 value of 0.05 μ M and 0.04 μ M respectively. Significantly, both compounds exhibited potent anti-SARS-CoV-2 infection activity in a cell-based assay with an EC 50 value of 0.42 μ M and 0.33 μ M, respectively. The X-ray crystal structures of SARS-CoV-2 M pro in complex with 11a and 11b were determined at 1.5 Å resolution, respectively. The crystal structures showed that 11a and 11b are covalent inhibitors, the aldehyde groups of which are bound covalently to Cys145 of M pro . Both compounds showed good PK properties in vivo, and 11a also exhibited low toxicity which is promising drug leads with clinical potential that merits further studies.",
            "output": [
                "1 - purpose, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-3a1c91b05f9b41c9b42afc636b42b2cc",
            "input": "Objectives of this study were to determine prevalence of infection in feral cats in Northern Florida with a select group of infectious organisms and to determine risk factors for infection. Blood samples or sera from 553 cats were tested with a panel of antibody, antigen or PCR assays. Male cats were at higher risk for FIV, Mycoplasma haemofelis, and M. haemominutum. Infection with either FeLV or FIV was associated with increased risk for coinfection with the other retrovirus, M. haemofelis, or M. haemominutum. Bartonella henselae had the highest prevalence and was the only organism that did not have any associated risk for coinfection with other organisms. Feral cats in this study had similar or lower prevalence rates of infections than those published for pet cats in the United States. Thus, feral cats assessed in this study appear to be of no greater risk to human beings or other cats than pet cats.",
            "output": [
                "1 - purpose, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-aa0bd6f46de644a98b3d14c1e2900ab7",
            "input": "Bordetella bronchiseptica isolate KM22 has been used in experimental infections of swine as a model of clinical B. bronchiseptica infection and to study host-to-host transmission. The draft genome sequence of KM22 was reported in 2014. Here, we report the complete genome sequence of KM22.",
            "output": [
                "1 - background, 2 - background, 3 - purpose"
            ]
        },
        {
            "id": "task352-a427d0dc16a444358c8b6872aaa7f859",
            "input": "Define the space of probability distributions on the action space (0 ≤ a i ≤ 1) [0, 1] as ([0, 1]). A mixed strategy profile σ (·) is a function that maps the state s ∈ {0, 1} n to the space of probability distributions on the actions space, i.e., σ i : {0, 1} n → ([0, 1]). The definition of a mixed MMPE strategy profile σ * := {σ * i : {0, 1} n → [0, 1]} is a distribution on the action space that satisfies the following, for all t = 1, 2, . . . , and i ∈ N ,",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method"
            ]
        },
        {
            "id": "task352-269377e26f404a3282f4527dcaf006e8",
            "input": "Design, synthesis and biological evaluation of a series of 5-chloropyridine ester-derived severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors is described. Position of the carboxylate functionality is critical to potency. Inhibitor 10 with a 5-chloropyridinyl ester at position 4 of the indole ring is the most potent inhibitor with a SARS 3Clpro IC 50 value of 30 nM and antiviral EC 50 value of 6.9 μM. Molecular Docking studies have provided possible binding modes of these inhibitors.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - finding"
            ]
        },
        {
            "id": "task352-30cb3a52caec4eed9808deb697415cee",
            "input": "The AsiaFluCap Simulator is freely available software (www.cdprg.org) which can be used by policy makers, policy advisors, donors and other stakeholders involved in preparedness for providing evidence based and illustrative information on health care resource capacities during future pandemics. The tool can inform both preparedness plans and simulation exercises and can help increase the general understanding of dynamics in resource capacities during a pandemic. The combination of a mathematical model with multiple resources and the linkage to GIS for creating maps makes the tool unique compared to other available software.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-e42caf6dff8f4806af7c6655ba56637a",
            "input": "publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. Comment 544 www.thelancet.com/infection Vol 14 July 2014 5 Lowe R, Barcellos C, Coelho C, et al. Dengue outlook for the World Cup in Brazil: an early warning model framework driven by real-time seasonal climate forecasts. Lancet Infect Dis 2014; published online May 17.",
            "output": [
                "1 - background, 2 - other, 3 - other, 4 - other, 5 - background, 6 - other, 7 - other"
            ]
        },
        {
            "id": "task352-a826853ac30a45b5932517c09289a84d",
            "input": "Citation Perlman S, Zhao J. 2013. Human coronavirus EMC is not the same as severe acute respiratory syndrome coronavirus. mBio 4(1):e00002-13.",
            "output": [
                "1 - other, 2 - finding, 3 - other"
            ]
        },
        {
            "id": "task352-ea10ad18c0404696931bb96f2cb2d07a",
            "input": "Glycyrrhiza glabra L. has become an endangered medicinal plant due to the unabated extraction of glycyrrhizin. Glycyrrhizin is a triterpenoid saponin that is a root centric secondary metabolite having numerous pharmacological properties, such as anti-inflammatory, immunomodulatory, antiallergic, antiulcer, and is found to be effective even against HIV. Harvesting of the roots for high value glycyrrhizin destroys the whole plant causing existential threat to the plant itself and consequent damage to biodiversity. The present study establishes that hairy root cultures of G. glabra, using an optimized elicitor, can dramatically enhance focused production of glycyrrhizin at a much faster pace year-round without causing destruction of the plant. Hairy root cultures of G. glabra were developed using the Agrobacterium rhizogenes A4 strain. The glycyrrhizin content was enhanced using different biotic and abiotic elicitors, for example, PEG (polyethylene glycol), CdCl 2 , cellulase, and mannan at different concentrations and durations. PEG at 1% concentration enhanced the yield of glycyrrhizin up to 5.4fold after 24 h of exposure, whereas 200 µg mL −1 cellulase enhanced glycyrrhizin yield to 8.6-fold after 7 days of treatment. Mannan at 10 mg L −1 concentration enhanced the production of glycyrrhizin up to 7.8-fold after 10 days of stress. Among different antioxidant enzymes, SOD activity was significantly enhanced under drought, cellulase and mannan stress. This identification of elicitors can result in abundant supply of valuable glycyrrhizin to meet broad spectrum demand through commercial production without endangering G. glabra L.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - purpose, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding"
            ]
        },
        {
            "id": "task352-62bf4eaaecf04ea59aff9d7c68b1030c",
            "input": "Background: Emerging viral diseases, most of which are caused by the transmission of viruses from animals to humans, pose a threat to public health. Discovering pathogenic viruses through surveillance is the key to preparedness for this potential threat. Next generation sequencing (NGS) helps us to identify viruses without the design of a specific PCR primer. The major task in NGS data analysis is taxonomic identification for vast numbers of sequences. However, taxonomic identification via a BLAST search against all the known sequences is a computational bottleneck. Description: Here we propose an enhanced lowest-common-ancestor based method (ELM) to effectively identify viruses from massive sequence data. To reduce the computational cost, ELM uses a customized database composed only of viral sequences for the BLAST search. At the same time, ELM adopts a novel criterion to suppress the rise in false positive assignments caused by the small database. As a result, identification by ELM is more than 1,000 times faster than the conventional methods without loss of accuracy. Conclusions: We anticipate that ELM will contribute to direct diagnosis of viral infections. The web server and the customized viral database are freely available.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-6b6edbf6b3df4b61adae00b62f55c033",
            "input": "Respiratory viruses are frequently detected in association with chronic tonsillar hypertrophy in the absence of symptoms of acute respiratory infection (ARI). The present analysis was done in follow-up to a previous clinical study done by this same group. Nasopharyngeal washes (NPWs) were obtained from 83 of 120 individuals at variable times post adenotonsillectomy, in the absence of ARI symptoms. A look back at virus detection results in NPWs from the same 83 individuals at the time of tonsillectomy revealed that 73.5% (61/83) were positive for one or more viruses. The overall frequency of respiratory virus detection in posttonsillectomy NPWs was 58.8%. Rhinovirus (RV) was the agent most frequently detected, in 38 of 83 subjects (45.8%), followed by enterovirus in 7 (8.4%), human metapneumovirus in 6 (7.2%), human respiratory syncytial virus in 3 (3.6%) and human coronavirus in 1 (1.2%). Remarkably, there was no detection of adenovirus (HAdV) or human bocavirus (HBoV) in asymptomatic individuals in follow-up of adenotonsillectomy. In keeping with persistence of respiratory DNA viruses in human tonsils, tonsillectomy significantly reduces asymptomatic shedding of HAdV and HBoV in NPWs.",
            "output": [
                "1 - background, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-15de8fbbb4484e4ba3fa5a853e2dfd10",
            "input": "Conclusions Infection immunity to a recent human H3N2 virus confers minimal cross-protection against a European swine H3N2 virus. We discuss our findings with regard to the recent zoonotic infections of humans in the United States with a swine-origin H3N2 variant virus. Please cite this paper as: Qiu et al. (2013) Prior infection of pigs with a recent human H3N2 influenza virus confers minimal cross-protection against a European swine H3N2 virus.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-a84cdcd3e3064ab4b221e2650667111d",
            "input": "Results: High prices of medicinal plants are widely considered to reflect resource scarcity. Real-time market prices for three of the four very different TCM species we studied all showed major price fluctuations. The exception was P. polyphylla, whose wild populations are widely known to be increasingly scarce, where there was a steady increase in price, with few fluctuations in the upward price trend. The three other species showed significant price fluctuations. These were driven by multiple factors. Ecological and biogeographic factors that influence abundance or scarcity of supply certainly played a role. But other factors were also influential. These included both national and global economic factors (the influence of the Global Financial Crisis (GFC)), national policy changes that in turn influenced businessmen giving expensive gifts (that included O. sinensis)), climate change (influencing fruiting success of S. sphenanthera), price speculation by traders and lack of information (e.g: reduction in G. gecko prices due to traders incorrectly believing that domestication would increase supplies). Conclusions: Price fluctuations in the four TCM species we examined are influenced by many factors and not just resource scarcity. And the situation is more complex than the trajectory based on Homma's (1992) model, where he predicted that higher prices would result in a shift to cultivation, thus replacing wild harvest. In case of both O. sinensis and P. polyphylla, Homma (1992 Homma ( , 1996 was right in terms of scarcity and high prices stimulating a major investment in cultivation (P. polyphylla) and artificial production (O. sinensis). But in both cases, intensive production through cultivation or artificial propagation do not yet occur on a large enough scale to reduce harvest of wild stocks. Substitution and adulteration occur with all four species. Improving information to doi.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - other"
            ]
        },
        {
            "id": "task352-897d570848f24e299b891cc64bb27572",
            "input": "The heptad repeats (HR1 and HR2) of the spike protein of SARS-CoV are highly conserved regions forming a critical 6-helix bundle during the fusion step of virus entry and are attractive targets of entry inhibitors. In this study, we report that a minimal HR2 peptide, P6 of 23-mer, can block the fusion of SARS-CoV with an IC 50 of 1.04 ± 0.22 M. This finding supports the structural prediction of the deep groove of HR1 trimer as a target for fusion inhibitors, and suggests P6 as a potential lead peptide for future drug development. Moreover, combination of an HR-1 peptide, N46, and its mutated version, N46eg, shows synergistic inhibition with an IC 50 of 1.39 ± 0.05 M and combination index of 0.75 ± 0.15, suggesting a common strategy to achieve promising inhibition by HR1 peptide for other class I envelope viruses.",
            "output": [
                "1 - background, 2 - purpose, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-7e6265f5ec614d70b6bd204427665cea",
            "input": "After 3-day acclimation, pigs in the challenged group were inoculated with a prototype US PEDV isolate US/Iowa/18984/ 2013 (GenBank accession #KF804028) (Hoang et al., 2013), 10 3 plaque-forming units/pig, via oro-gastric gavage as previously described (Madson et al., 2014). Pigs in the control group received virus-free cell culture media. Some of these pigs were inoculated again with the same strain in the identical manner at day 56 post-inoculation (PI).",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-343a26d2ff2540b3a4f24fb08af7d591",
            "input": "Viral channel forming proteins (VCPs) have been discovered in the late 70s and are found in many viruses to date. Usually they are small and have to assemble to form channels which depolarize the lipid membrane of the host cells. Structural information is just about to emerge for just some of them. Thus, computational methods play a pivotal role in generating plausible structures which can be used in the drug development process. In this review the accumulation of structural data is introduced from a historical perspective. Computational performances and their predictive power are reported guided by biological questions such as the assembly, mechanism of function and drug-protein interaction of VCPs. An outlook of how coarse grained simulations can contribute to yet unexplored issues of these proteins is given. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-1fb8c02c66684c8ab69e56d877e32b82",
            "input": "Trial registration: UKCRN ID number 19086, registered May 2015; as well as registration at www.trialregister.nl under the acronym 'BreathDx' with trial ID number NTR 6114 (retrospectively registered on 28 October 2016).",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-2b148cb37cb44898b8c0bf09a0d7892d",
            "input": "The dynamics of H5N1 influenza virus pathogenesis are multifaceted and can be seen as an emergent property that cannot be comprehended without looking at the system as a whole. In past years, most of the high-throughput studies on H5N1-host interactions have focused on the host transcriptomic response, at the cellular or the lung tissue level. These studies pointed out that the dynamics and magnitude of the innate immune response and immune cell infiltration is critical to H5N1 pathogenesis. However, viral-host interactions are multidimensional and advances in technologies are creating new possibilities to systematically measure additional levels of 'omic data (e.g. proteomic, metabolomic, and RNA profiling) at each temporal and spatial scale (from the single cell to the organism) of the host response. Natural host genetic variation represents another dimension of the host response that determines pathogenesis. Systems biology models of H5N1 disease aim at understanding and predicting pathogenesis through integration of these different dimensions by using intensive computational modeling. In this review, we describe the importance of 'omic studies for providing a more comprehensive view of infection and mathematical models that are being developed to integrate these data. This review provides a roadmap for what needs to be done in the future and what computational strategies should be used to build a global model of H5N1 pathogenesis. It is time for systems biology of H5N1 pathogenesis to take center stage as the field moves towards a more comprehensive view of virushost interactions.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - finding, 10 - finding"
            ]
        },
        {
            "id": "task352-79e1bb219b7b477aad1ec546ec94b77f",
            "input": "Porcine epidemic diarrhea virus (PEDV) is a coronavirus which causes severe diarrhea and fatal dehydration in piglets. In general, probiotic supplements could enhance recovery and protect piglets against enteric pathogens. Seven local lactic acid bacteria (LAB), (Ent. faecium 79N and 40N, Lact. plantarum 22F, 25F and 31F, Ped. acidilactici 72N and Ped. pentosaceus 77F) from pig feces were well-characterized as high potential probiotics. Cell-free supernatants (CFS) and live LAB were evaluated for antiviral activities by coincubation on Vero cells and challenged with a pandemic strain of PEDV isolated from pigs in Thailand. Cell survival and viral inhibition were determined by cytopathic effect (CPE) reduction assay and confirmed by immunofluorescence. At 1:16, CFS dilution (pH 6.3-6.8) showed no cytotoxicity in Vero cells and was therefore used as the dilution for antiviral assays. The diluted CFS of all Lact. plantarum showed the antiviral effect against PEDV; however, the same antiviral effect could not be observed in Ent. faecium and Pediococcus strains. In competitive experiment, only live Lact. plantarum 25F and Ped. pentosaceus 77F showed CPE reduction in the viral infected cells to <50% observed field area. This study concluded that the CFS of all tested lactobacilli, and live Lact. plantarum (22F and 25F) and Pediococcus strains 72N and 77F could reduce infectivity of the pandemic strain of PEDV from pigs in Thailand on the target Vero cells.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - method, 9 - method, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding"
            ]
        },
        {
            "id": "task352-4a9b4775d2234885a8d713a115cc660d",
            "input": "The present work was conducted to investigate the antioxidant activity and neuroprotective effects of Tripterygium regelii extract (TRE) on H 2 O 2 -induced apoptosis in human dopaminergic cells, SH-SY5Y. TRE possessed considerable amounts of phenolics (282.73 mg tannic acid equivalents/g of extract) and flavonoids (101.43 mg naringin equivalents/g of extract). IC 50 values for reducing power and DPPH radical scavenging activity were 52.51 and 47.83 lg, respectively. The H 2 O 2 scavenging capacity of TRE was found to be 57.68 lM 9 lg -1 min -1 . By examining the effects of TRE on SH-SY5Y cells injured by H 2 O 2 , we found that after incubation of cells with TRE prior to H 2 O 2 exposure, the H 2 O 2 induced cytotoxicity was significantly reversed and the apoptotic features such as change in cellular morphology, nuclear condensation and DNA fragmentation was inhibited. Moreover, TRE was very effective attenuating the disruption of mitochondrial membrane potential and apoptotic cell death induced by H 2 O 2 . TRE extract effectively suppressed the up-regulation of Bax, Caspase-3 and -9, and down-regulation of Bcl-2. Moreover, TRE pretreatment evidently increased the tyrosine hydroxylase (TH) and brain-derived neurotrophic factor (BDNF) in SH-SY5Y cells. These findings demonstrate that TRE protects SH-SY5Y cells against H 2 O 2 -induced injury and antioxidant properties may account for its neuroprotective actions and suggest that TRE might potentially serve as an agent for prevention of neurodegenerative disease associated with oxidative stress.",
            "output": [
                "1 - purpose, 2 - finding, 3 - finding, 4 - finding, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding"
            ]
        },
        {
            "id": "task352-ec48dc4d134a443ea339bc83cf8d7666",
            "input": "The findings indicate that the frequency of PCV2 infections in aborted porcine foetuses from the State of São Paulo is rather low (10.7%) and that co-infection with other pathogens is common and may be involved in PCV2 associated reproductive failure. No repeatable, characteristic amino acid motifs for regions of the PCV2 capsid protein seemed to be associated with abortion in sows.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-28770b5b96e344ce80d11a8e897dead9",
            "input": "Flies were transferred to plates of Escherichia coli or Pseudomonas aeruginosa and allowed to walk on the bacteria for a total of 5 min. After the flies were contaminated, they were either immediately collected to quantify bacteria or were placed onto sterile plates to clean for 5 or 10 min. After cleaning, flies were placed into tubes with 1 ml of sterile 0.85% saline and were gently shaken for 1 min to remove bacteria. A serial dilution was made and 50-ml spot titers were plated. Cleaning behavior was also monitored and scored for a period of 5 min. Results demonstrate a bacterial reduction for both bacteria on all three fly species. Sarcophaga bullata and D. virilis both showed a significant reduction of both bacteria within 10 min, whereas M. domestica only showed a significant reduction in P. aeruginosa. Cleaning behavior increased significantly in flies that were exposed to bacteria compared to flies that were not exposed to bacteria. This study is important, as it demonstrates that fly cleaning could affect mechanical transmission of disease, and additional studies should look at flies' abilities to remove other types of microorganisms.",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-43fe39d8187b47daa843195f7a399166",
            "input": "Mycoplasma haemofelis\" and \"Candidatus Mycoplasma turicensis\" are feline hemoplasmas that induce hemolytic anemia. Protection from homologous re-challenge was recently demonstrated in cats recovered from primary infection. Here, we determined if cats recovered from \"Cand. M. turicensis\" infection were protected against infections with the more pathogenic M. haemofelis. Ten specified pathogen-free cats were exposed to M. haemofelis. Five of the ten cats had recovered from \"Cand. M. turicensis\" bacteremia (group A), and five cats were naïve controls (group B). No cross-protection was observed. By contrast, the \"Cand. M. turicensis\"-recovered cats displayed faster M. haemofelis infection onset (earlier PCR-positive and anemic) than the controls. No \"Cand. M. turicensis\" was detected in any cat. M. haemofelis shedding was observed in saliva, feces and urine. In both groups, evidence of a Th1 response was observed (high IFN-γ, low IL-4), but IL-10 levels were also high. In group A, total, CD4+ and CD8+ T cells increased within days after M. haemofelis exposure. At times of maximal bacteremia, macrocytic hypochromic anemia, neutropenia, monocytosis and a decrease in leukocyte, eosinophil, and lymphocyte counts and subsets thereof (B-and T-cells, CD4+, CD8+ and CD4+CD25+ cells) were particularly significant in group A. Moreover, an increase in protein concentrations, hypoalbuminemia and a polyclonal hypergammaglobulinemia were observed. Five of ten M. haemofelis-infected cats subsequently cleared bacteremia without antibiotic treatment. In conclusion, the study suggests that a previous hemoplasma infection, even when the cat has ostensibly recovered, may influence subsequent infections, lead to an enhancement phenomenon and other differences in infection kinetics.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - background, 5 - method, 6 - method, 7 - method, 8 - method, 9 - background, 10 - finding, 11 - finding, 12 - background, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding, 25 - finding, 26 - finding, 27 - finding, 28 - finding"
            ]
        },
        {
            "id": "task352-124dffd3adee46f8913881468cc562f7",
            "input": "-TUB, EF, and ATPase for temperature treatments. Stable reference gene combinations may reduce bias in normalization. This work provides for the first time a comprehensive list of appropriate reference genes and facilitates future studies on gene function of M. separata.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-3efa410096254477b8b05bde1e861a93",
            "input": "A novel series of (3-diethoxyphosphoryl)isoxazolidines substituted at C5 with various quinazolinones have been synthesized by the 1,3-dipolar cycloaddition of N-methyl-C-(diethoxyphosphoryl)nitrone with N3-substitued 2-vinyl-3H-quinazolin-4-ones. All isoxazolidines were assessed for antiviral activity against a broad range of DNA and RNA viruses. Isoxazolidines trans-11f/cis-11f (90:10), trans-11h and trans-11i/cis-11i (97:3) showed weak activity (EC 50 = 6.84, 15.29 and 9.44 µM) toward VZV (TK + strain) which was only one order of magnitude lower than that of acyclovir used as a reference drug. Phosphonates trans-11b/cis-11b (90:10), trans-11c, trans-11e/cis-11e (90:10) and trans-11g appeared slightly active toward cytomegalovirus (EC 50 = 27-45 µM). Compounds containing benzyl substituents at N3 in the quinazolinone skeleton exhibited slight antiproliferative activity towards the tested immortalized cells with IC 50 in the 21-102 µM range.",
            "output": [
                "1 - method, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-d32d945925ff4a0da4788fb053409148",
            "input": "co (J.A. Hincapié-García). Research in Social and Administrative Pharmacy xxx (xxxx) xxx-xxx 1551-7411/",
            "output": [
                "1 - other, 2 - other"
            ]
        },
        {
            "id": "task352-499845cd4fe04e6aaeef1c0b30ecd497",
            "input": "In vivo MRA showed that the SNR-reducing effect of DM-was greater than that of D-USPIO (P , 0.05). With in vitro MRI scans, SNR was significantly lower in rabbits treated with dose 2 of DM-USPIO compared with D-USPIO treatment (P , 0.05), and it tended to be lower at dose 3 (P , 0.1). In conclusion, we suggest that DM-USPIO is superior to D-USPIO for the study of atherosclerotic lesions in rabbits.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-7e96f65e25ba4f11ab40bfa57a2b958f",
            "input": "June 19, 2017) from four Manatee County sites (Fig. 1a) . To avoid cross contamination of 33 mosquito viromes, each year eggs from each site were hatched independently in distilled 34 water, reared to adulthood, speciated and then frozen. Female abdomens were pooled (N= 35 20/pool) separately for the four collection sites for a total of eight individual pools. Total RNA 36 was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen), and rRNA depleted with the 37 NEBNext rRNA Depletion Kit (New England BioLabs). The NEBNext Ultra II Directional RNA 38 Library Prep Kit (New England BioLabs) was used to prepare shotgun metagenomics libraries. 39 Reverse-transcribed RNA libraries were sequenced using a HiSeq 3000 (Illumina) instrument 40 in 2x101 run mode. The data were deposited into the NCBI Sequence Read Archive and 41 Biosample archive under BioProject PRJNA547758. 42 43 Initial assembly and metavirome analysis 44 BBduk was used to trim adaptor 45 sequences and remove contaminants. Ae. aegypti sequences were removed using BBsplit 46 author/funder. All rights reserved. No reuse allowed without permission. : bioRxiv preprint 9 assembly with Spades in meta mode [8] and classification using Diamond [9] for a complete 71 DENV4 genome. Read-mapping with Bowtie [10] revealed incorrect bases near the 3' end, 72 which were manually corrected. The genome was annotated using the Genome Annotation 73 Transfer Utility [16] from the Virus Pathogen Database and Analysis Resource (ViPR) [17]. 74 75 Phylogenetic and Molecular Clock analyses 76 Two hundred thirty-four DENV4 genome sequences from GenBank (Table S1) were aligned 77 using MAFFT version 7.407 [18] with the L-INS-I method [19]. IQ-TREE software [20] was 78 used to evaluate phylogenetic signal in the genomes by likelihood mapping [21] and to infer 79 maximum likelihood (ML) phylogeny based on the best-fit model according to the Bayesian 80 Information Criterion (BIC) [20, 22]. Statistical robustness for internal branching order was 81 assessed by Ultrafast Bootstrap (BB) Approximation (2,000 replicates), and strong statistical 82 support was defined as BB>90% [23]. 83 84 To estimate when DENV4 entered Florida, we used 145 strains including all isolates from the 85 Americas, related Asian and African isolates, and randomly reduced oversampled Brazilian 86 isolates. The strains in this dataset were not recombinant, as assessed by scanning the 87 alignments for possible recombination points using the RDP, GENECONV, MaxChi, 88 CHIMAERA, and 3Seq algorithms implemented in the RDP4 software [24]. Correlation between root-to-tip genetic 90 divergence and date of sampling was conducted [25] to assess clock signal before Bayesian 91 phylodynamic analysis. Time-scaled trees were reconstructed using the Bayesian 92 phylodynamic inference framework in BEAST v.1.8.4 [26,27]. Markov Chain Monte Carlo 93 (MCMC) samplers were run until 200/250 million generations to ensure Markov chain mixing, 94 author/funder. All rights reserved. No reuse allowed without permission.",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - other, 13 - method, 14 - other, 15 - other, 16 - method, 17 - finding, 18 - finding, 19 - method, 20 - method, 21 - method, 22 - method, 23 - finding, 24 - method, 25 - method, 26 - method, 27 - method, 28 - finding, 29 - finding, 30 - finding, 31 - finding, 32 - finding, 33 - finding, 34 - finding, 35 - other, 36 - other"
            ]
        },
        {
            "id": "task352-15300f21976141268321a2a3d5fe459c",
            "input": "The results indicate that 36.1% of the respondents expressed willingness to be vaccinated. Those with the greatest trust in the government were the most likely to be vaccinated (43.4%), and those least confident were the least willing (15.8%). From the ones reporting being confident in the local health system, 38.4% were willing to be vaccinated, and from those not confident, only 23.5% were willing to be vaccinated. Conclusion: The decision to get vaccinated in the midst of a contagious outbreak involves many considerations. Trust in the government's technical and organization skill to deal with the infectious outbreak along with trust in medical organizations predict the adoption of recommended protection measures. The results indicate that public compliance with vaccination plans in health crisis requires the development of social and institutional trust.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding"
            ]
        },
        {
            "id": "task352-9e050f98c81640cfa6d015e14b1b2f2c",
            "input": "A high proportion of dogs suffer from respiratory disease when they are placed in kennels for vacation or re-homing. The role of Mycoplasma cynos as an initiating agent in canine infectious respiratory disease was investigated by examining the serological response of dogs to this organism at the time of entry into a large re-homing kennel. Forty-two paired serum samples from dogs (21-day interval) were examined for antibody to M. cynos using Western blotting. The development of antibody in the serum was related to clinical disease recorded over the same period. Sixty seven per cent of the dogs showed a two-fold or greater rise in antibody to M. cynos during the first 3 weeks in the kennel. Reactivity with a 45 kDa antigen was dominant. Of those showing a positive serological reaction, 80% had recorded clinical respiratory disease while 20% remained healthy. The findings of this study show that an antibody response to M. cynos is common in dogs entering the re-homing kennel and is positively related to the development of clinical respiratory disease. #",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - other"
            ]
        },
        {
            "id": "task352-f14424e5bb4e469cac4e05223b7e858d",
            "input": "Background: Infection by multidrug-resistant (MDR) pathogens leads to poor patient outcomes in intensive care units (ICUs). Contact precautions are necessary to reduce the transmission of MDR pathogens. However, the importance of the surrounding environment is not well known. We studied the effects of ICU relocation on MDR respiratory pathogen detection rates and patient outcomes. Methods: Patients admitted to the ICU before and after the relocation were retrospectively analyzed. Baseline patient characteristics, types of respiratory pathogens detected, antibiotics used, and patient outcomes were measured. Results: A total of 463 adult patients admitted to the ICU, 4 months before and after the relocation, were included. Of them, 234 were admitted to the ICU before the relocation and 229 afterward. Baseline characteristics, including age, sex, and underlying comorbidities, did not differ between the two groups. After the relocation, the incidence rate of MDR respiratory pathogen detection decreased from 90.0 to 68.8 cases per 1,000 patient-days, but that difference was statistically insignificant. The use of colistin was significantly reduced from 53.5 days (95% confidence interval [CI], 20.3 to 86.7 days) to 18.7 days (95% CI, 5.6 to 31.7 days). Furthermore, the duration of hospital stay was significantly reduced from a median of 29 days (interquartile range [IQR], 14 to 50 days) to 21 days (IQR, 11 to 39 days). Conclusions: Incidence rates of MDR respiratory pathogen detection were not significantly different before and after ICU relocation. However, ICU relocation could be helpful in reducing the use of antibiotics against MDR pathogens and improving patient outcomes.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding"
            ]
        },
        {
            "id": "task352-a3f30735b9ea489b916d4ea068891e4f",
            "input": "C. Xu et al.",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-21bfcb420251423187ae37c78ed4434b",
            "input": "Cite this article: Rojek AM, Horby PW. 2017 Offering patients more: how the West Africa Ebola outbreak can shape innovation in therapeutic research for emerging and epidemic infections. Phil. Trans. R. Soc. B 372: 20160294.",
            "output": [
                "1 - other, 2 - purpose, 3 - other, 4 - other, 5 - other, 6 - other, 7 - other"
            ]
        },
        {
            "id": "task352-7795c989b6d04d409ba2d05230a9839a",
            "input": "Public Health jo urnal homepage: www .e lse vi er.co m/ pu he p u b l i c h e a l t h 1 5 0 ( 2 0 1 7 ) 8 7 e9 2.",
            "output": [
                "1 - other, 2 - other"
            ]
        },
        {
            "id": "task352-0a4a81316a9e455aa8192c38da6b376e",
            "input": "Abbreviations: b 2 M, b 2 microglobulin; ALP, alkaline phosphatase; d.p.i.",
            "output": [
                "1 - other, 2 - other"
            ]
        },
        {
            "id": "task352-c1f329455c9241e2ac14e53825744fcc",
            "input": "Conclusion: S. pneumoniae-induced IL-8 expression by human epithelial BEAS-2B cells depended on activation of JNK and recruitment of phosphorylated c-Jun to the il8 promoter.",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-525964e49c9e4d2bac21e9ac7be1999a",
            "input": "In this section, we present results for the 30 countries used for model specification and tuning and compare with the overall results in order to access the extent to which tuning and model specification may have affected results for these countries. We experimented with different model specifications and combinations of features on a subset of data consisting of 30 countries, prior to applying our models to the entire collection of countries. Table 2 -2 presents the model performance metrics for both the entire collection of 72 countries and for the subset of 30 countries used for model specification and tuning. Model performance was slightly diminished on the entire collection of countries compared with the 30 countries used for model specification and tuning. In part, the poorer performance can be explained by the fact that the average number of articles per week in the entire collection of countries was lower than in the 30 countries used for model specification -0.14 articles per week versus 3.50 articles per week. We have shown that in general our models perform best on country-disease pairs that receive substantial news coverage.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-3c67df70dc584bb18143bab29654e4ca",
            "input": "Journal of Infection (2012) 64, 96e103 sampled elderly (>65 years, 3.2%) than in middle aged adults (25e65 years; 2.0%) and teenagers (14e25 years; 0.9%). During the study period, hMPV infections showed a biennial rhythm of seasonality, peaking from",
            "output": [
                "1 - background, 2 - background, 3 - finding"
            ]
        },
        {
            "id": "task352-50b4b4073a834f29bfb43597e0492846",
            "input": "a b s t r a c t HCMV infection represents a life-threatening condition for immunocompromised patients and newborn infants and novel anti-HCMV agents are clearly needed. In this regard, a series of 1-[x-(phenoxy)alkyl]uracil derivatives were synthesized and examined for antiviral properties. Compounds 17, 20, 24 and 28 were found to exhibit highly specific and promising inhibitory activity against HCMV replication in HEL cell cultures with EC 50 values within 5.5-12 lM range. Further studies should be undertaken to elucidate the mechanism of action of these compounds and the structure-activity relationship for the linker region.",
            "output": [
                "1 - background, 2 - method, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-7c2f902c2bcc423e90cbd34f2503a5e2",
            "input": "Although the provincial supplementary immunization activities (SIAs) conducted in 2009 and 2010 were able to reduce the transmissions from 2009 to 2011, larger values of R for children aged 0-6 years were observed after 2012, indicating that the benefits of the SIAs were short-lived. In addition, the transmissions from adults aged between 26 and 45 years PLOS ONE.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-ecca7a214b5c4aedbf95a8fe00e72198",
            "input": "Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, \"conronavirus\", \"case\", \"transmission\" and \"detection\" were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - method, 14 - method, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding"
            ]
        },
        {
            "id": "task352-e8091adc42cb46b3b1104148fa9ec10f",
            "input": "Background: Respiratory viral infections can cause significant morbidity and mortality in immunocompromised patients. Conventional tests routinely available at most institutions are limited by the number of detectable pathogens, by a poor sensitivity and/or a long turnaround time. Objectives: To compare the performance of routine conventional testing with direct fluorescent antibody assays and viral culture to a customized TaqMan® array card (TAC) real-time PCR method, targeting 24 viruses, 8 bacteria and 2 fungi simultaneously. Study design: We collected 143 respiratory samples from 120 symptomatic immunocompromised patients. Samples for which conventional and TAC results were discordant underwent further verification testing. Results: The TAC assay identified viral pathogens in more samples than did conventional testing (77/143 versus 27/143; McNemar P < 0.0001), even when TAC results for viruses that could not be detected by conventional testing were excluded from analysis (59/143 versus 26/143; P < 0.0001). In addition, the TAC assay identified 18 samples with non-viral pathogens. Verification testing confirmed positive TAC results for 50 out of 55 samples for which conventional testing was negative. Two out of three samples with a positive conventional test but negative TAC result were confirmed positive. A viral and a total pathogen co-infection rate of 5.6% and 11.8% were found, respectively. Conclusions: The customized TAC assay resulted in a significantly increased identification of respiratory viruses. This study provides a practical real-life assessment of the performance of the TAC assay in a population for whom rapid and accurate diagnosis of viral and atypical pathogens is crucial for appropriate clinical management.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - purpose, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding"
            ]
        },
        {
            "id": "task352-1711811a9d9e437dabc3754c33a158fa",
            "input": "One sentence summary: A systematic review and meta-analysis of randomised clinical trials investigating antimicrobial prophylaxis or metaphylaxis against naturally occurring bovine respiratory disease. Editor: Edmundo Calva ABSTRACT A distinct difference between veterinary and human medicine is the routine use of antimicrobial mass medications (prophylaxis, metaphylaxis) to healthy individuals. The need for antimicrobial mass medications is based on beliefs that group/s of animals will contract a bacterial disease (i.e. morbidity) and/or die (i.e. mortality). Bovine respiratory disease (BRD) represents the major indication for cattle antimicrobials worldwide. The objectives were to perform a systematic review and meta-analysis of randomised controlled clinical trials (RCTs) for naturally occurring BRD investigating antimicrobial prophylaxis/metaphylaxis to prevent morbidity/mortality. In total, 58 publications met the inclusion criteria summarizing 169 individual RCTs, spanning 50 years . Antimicrobial prophylaxis and metaphylaxis demonstrated moderate, yet highly variable relative risk reductions in BRD morbidity. These were dependent on the antimicrobial classes used, dependent on metaphylaxis definition, BRD attack rates and duration of the RCTs. Best relative risk reductions were from broad-spectrum critically important antimicrobials, or combinations. BRD prophylaxis/metaphylaxis represents major antimicrobial consumption for highly variable short-term gains in absolute risk reduction of morbidity/mortality. Despite widespread use of prevention products, the need for antimicrobial mass medications should be re-evaluated since the underlying problem is more likely the segmented infrastructure of the feedlot and veal calf industries compared to the disease itself.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-7d6fdbcecfcf4a16a63c9047806ecdb3",
            "input": "The method specifically detected S. pyogenes within 8 min from clinical specimens and can be potentially use within a point-of-care setting.",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-f7277cf58ea04667a80b11fa09f0c72b",
            "input": "Prism 7 software is used for statistical analysis. Student's t test was performed for twogroup analysis. Pearson's correlation coefficients were calculated. P values less than 0.05 were considered to be statistically significant.",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - method"
            ]
        },
        {
            "id": "task352-3b3403ce1e9b4f74aab311fb3f5f2956",
            "input": "Viruses are replication competent genomes which are relatively gene-poor. Even the largest viruses (i.e. Herpesviruses) encode only slightly .200 open reading frames (ORFs). However, because viruses replicate obligatorily inside cells, and considering that evolution may be driven by a principle of economy of scale, it is reasonable to surmise that many viruses have evolved the ability to co-opt cell-encoded proteins to provide needed surrogate functions. An in silico survey of viral sequence databases reveals that most positive-strand and double-stranded RNA viruses have ORFs for RNA helicases. On the other hand, the genomes of retroviruses are devoid of virally-encoded helicase. Here, we review in brief the notion that the human immunodeficiency virus (HIV-1) has adopted the ability to use one or more cellular RNA helicases for its replicative life cycle.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose"
            ]
        },
        {
            "id": "task352-fbcc71e8c0b14f8e91eab899b3e07bab",
            "input": "Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log 10 genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log 10 GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. However, no fecal shedding, seroconversion, histological lesions, and clinical disease were detected in PEDV-inoculated calves. Our data indicate that calves are susceptible to infection by the newly emerged PDCoV, but not by the swine coronavirus, PEDV.",
            "output": [
                "1 - method, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-002fd2ac053d463780f3a10a1835158b",
            "input": "Conclusion: The analysis indicates that the pig faecal virome shows a high variability and that its general composition is mainly dependent on the age of the pigs. Changes caused by feeding with the probiotic bacterium E. faecium could not be demonstrated using the applied metagenomics method.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-23d0ebe26856498d9d3c441cdd1a3ebd",
            "input": "Conclusion-ABS complicates 8% of URI in young children. Girls have more frequent ABS episodes than boys. Presence of rhinovirus and M. catarrhalis during URI are positively correlated with the risk for ABS complication.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-c7ac465a1c474adab5f5a06e64e5dbbc",
            "input": "A total of 446 serum samples from 88 herds in Korea were examined for antibody to porcine respiratory coronavirus (PRCV) using blocking enzyme-linked immunosorbent assay (ELISA). All serum samples were collected from 24-to 26-week-old finishing pigs between December 1998 and June 1999. By ELISA, 237 out of 446 sera tested (53.1%) and 54 out of 88 sampled herds (61.3%) were positive against PRCV. Of 446 sera from 88 herd tested, 185 (41.5%) serum samples from 22 (25%) herds were seronegative against PRCV and transmissible gastroenteritis virus infection. Our data suggested that seropositive herds for PRCV are distributed diffusely throughout South Korea. #",
            "output": [
                "1 - background, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - other"
            ]
        },
        {
            "id": "task352-9687e3c61959481db10f60ddef4839dd",
            "input": "The role of respiratory viruses in the pathogenesis of Kawasaki disease (KD) remains controversial. In this study we showed that 8.8 % of KD patients had documented respiratory viral infections. Patients with concomitant viral infections had a higher frequency of coronary artery dilatations and were significantly more often diagnosed with incomplete KD. The presence of a concomitant viral infection should not exclude the diagnosis of KD.",
            "output": [
                "1 - background, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-0e1a69264ecb4d7dacace6a1e1894282",
            "input": "Objectives: Many patients with influenza have more than one viral agent with co-infection frequencies reported as high as 20%. The impact of respiratory virus copathogens on influenza disease is unclear. We sought to determine if respiratory virus co-infection with pandemic H1N1 altered clinical disease. Methods: Respiratory samples from 229 and 267 patients identified with and without H1N1 influenza respectively were screened for the presence of 13 seasonal respiratory viruses by multiplex RT-PCR. Disease severity between coinfected and monoinfected H1N1 patients were quantified using a standardized clinical severity scale. Influenza viral load was calculated by quantitative RT-PCR. Results: Thirty (13.1%) influenza samples screened positive for the presence of 31 viral copathogens. The most prominent copathogens included rhinovirus (61.3%), and coronaviruses (16.1%). Median clinical severity of both monoinfected and coinfected groups were 1. Patients coinfected with rhinovirus tended to have lower clinical severity (median 0), whereas non-rhinovirus co-infections had substantially higher clinical severity (median 2). No difference in H1N1 viral load was observed between coinfected and monoinfected groups. Conclusions: Respiratory viruses co-infect patients with influenza disease. Patients coinfected with rhinovirus had less severe disease while non-rhinovirus co-infections were associated with substantially higher severity without changes in influenza viral titer.",
            "output": [
                "1 - purpose, 2 - purpose, 3 - purpose, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding"
            ]
        },
        {
            "id": "task352-555d2f41c8cc432bb81a82d90678ff87",
            "input": "Pseudotyped lentiviral vectors expressing green fluorescence protein (GFP) were delivered intratracheally (i.t.) to C57BL/6 and",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-2909a0d74e6e4b7d9bc900d0b56a4d9a",
            "input": "The present study was performed to elucidate the clinical outcome, and etiology of acute otitis media (AOM) in children based on virologic and bacteriologic tests. The study group consisted of 120 children aged 6 to 144 months with AOM. Middle ear fluid (MEF) was tested for viral pathogens by reverse transcriptase polymerase chain reaction (RT-PCR) and for bacteria by gram-staining and culture. Clinical response was assessed on day 2 to 4, 11 to 13, 26 to 28. Respiratory viruses were isolated in 39 patients (32.5%). Respiratory syncytial virus (RSV) (46.5%) was the most common virus identified in MEF samples, followed by human rhinovirus (HRV) (25.6%), human coronavirus (HCV) (11.6%), influenza (IV) type A (9.3%), adenovirus type sub type A (AV) (4%), and parainfluenza (PIV) type -3 (2%) by RT-PCR. In total 69 bacterial species were isolated from 65 (54.8%) of 120 patients. Streptococcus pneumoniae (S. pneumoniae) was the most frequently isolated bacteria. Viral RNA was detected in 31 (56.3%) of 55 bacteria-negative specimens and in 8 (12.3%) of 65 bacteria-positive MEF samples. No significant differences were found between children representing viral infection alone, combined viral and bacterial infection, bacterial infection alone, and neither viral nor bacterial infection, regarding clinical cure, relapse and reinfection rates. A significantly higher rate of secretory otitis media (SOM) was observed in alone or combined RSV infection with S. pneumonia or Haemophilus influenzae (H. influenzae) than in other viruses infection. Conclusion. This study provides information about etiologic agents and diagnosis of AOM in Turkish children. The findings highlight the importance of common respiratory viruses and bacterial pathogens, particularly RSV, HRV, S. pneumoniae and H. influenzae, in predisposing to and causing AOM in children.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding, 25 - finding, 26 - finding"
            ]
        },
        {
            "id": "task352-d97469c647f94c029b25c64f321c0219",
            "input": "Cut-off Cut-off Supplementary Figure 1 | Setting cut-off to identify links and hidden source. (a) Coarse-grained distribution of element values ln(1 − λ i )a ij times −1 in the reconstructed vector X of all nodes in a Newman-Watts small-world network (NW), where bin accumulation is implemented for the original distribution. The peak centered at zero corresponds to null connections and the other corresponds to actual links. A cut-off value can be set within the gap between the two peaks. (b) The values of ln(1 − λ i )a ij times -1 in the reconstructed vector X for Erdös-Rényi random networks (ER), Watts-Strogatz small-world networks (WS), NW and Barabási-Albert scale-free networks (BA), where green and yellow points correspond to existent links and null connections, respectively. All the networks share the same cut-off value of about 0.13. (c) Coarse-grained distribution of the structural variance σ in the NW network, where bin accumulation is exercised on the original distribution. The largest peak centered close zero corresponds to nodes of indirect neighbors of the hidden source and the large positive values of σ are associated with the immediate neighbors of the hidden source. A cut-off can be set within the largest gap. (d) The variance σ * i of element values in the reconstructed vector x of all nodes in the presence of a hidden source for ER, WS, NW and BA networks, where green and yellow points correspond to immediate neighbors and indirect neighbors of the hidden source, respectively. All the networks share the same cut-off values of about σ * i = 0.9. The network size in a,b is 200 and in c,d is 50, Θ = 0.25, ∆ = 0.45, λ i and δ i are uniformly distributed in the ranges (0.2, 0.4) and (0.4, 0.6), respectively. SIS dynamics are used for the illustration. Panels a and c correspond to Fig. 2a with nt = 0.4 and Fig. 5 in the main text, respectively.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - background, 12 - background, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding"
            ]
        },
        {
            "id": "task352-85b2f2862b7547c3bd641091f4953077",
            "input": "The results of this study showed that simultaneous colonization of the intestinal mucosa by adherent non-ETEC E. coli and Enterococcus spp. can be involved in the pathogenesis of neonatal porcine diarrhea. These bacteria should be considered in diagnosis of diarrhea in piglets, when detection of common, well-known enteric agents is unsuccessful.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-c98ae53cd95d4664a75fc1ca6d583f62",
            "input": "Genetic sequences highly related to Bovine coronavirus (BCoV) were detected in fecal samples from Peruvian 1-3 week old alpaca crias located on six farms in Puno department, some of which shared pastures with cattle. A total of 60 samples were screened for coronavirus using a nested PCR amplification of a fragment of the RNA-dependent RNA polymerase (RdRp) gene. Sequences from 11 positive samples were highly similar to the Kakegawa, Quebec and Mebus BCoV strains (99.5-100.0%) and 99.2% identical to an alpaca Coronavirus (CoV) previously detected in the USA. The detection of genetic sequences related to BCoV from Peruvian alpaca crias suggests possible role of this virus on enteric disorders etiology in the High Andes.",
            "output": [
                "1 - finding, 2 - finding, 3 - method, 4 - finding, 5 - finding, 6 - finding"
            ]
        },
        {
            "id": "task352-5a086b97c46349c294157c625f40b35c",
            "input": "Hepatitis B virus Á HepG2.2.15 cell line Á Lentiviral vector Á RNAi Á Doxycycline Abbreviations CP Core promoter DOX Doxycycline DR1 Direct repeat 1 EN2 Enhancer II region HAV Hepatitis A virus HBV Hepatitis B virus HBcAg Hepatitis core antigen HBsAg Hepatitis B surface antigen HBeAg Hepatitis B e antigen HCC Hepatocellular carcinoma HCV Hepatitis C virus HIV Human immunodeficiency virus HSV Herpes simplex virus KRAB Krüppel associated box Electronic supplementary material The online version of this article (",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-90a092202a9640ae89613f6b8c1c7402",
            "input": "Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RePoRts | (2018) 8:3490 |",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-3e1282e9edf64baab31d6962fd033962",
            "input": "An antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) method was developed for the efficient detection of the UL24 antigen of the duck enteritis virus (DEV) using polyclonal antibodies. Ducks and rabbits were immunized, respectively, with expressed UL24 recombinant protein. The IgG antibodies against UL24 from ducks and rabbits were purified and used as the capture antibodies. The specificity of the optimized AC-ELISA was evaluated by use of DEV, duck hepatitis virus (DHV), duck hepatitis B virus (DHBV), gosling plague virus (GPV), Riemerella anatipestifer (R.A.), Escherichia coli (E. coli), Pasteurella multocida (P.M.) and Salmonella Enteritidis (S.E.). Only DEV specimens yielded a specific and strong signal. The limit of the sensitivity of this method for the detection of DEV was 46 ng/100 l. Compared with PCR and virus isolation, the rate of agreement for the detection of experimentally infected sera was 100%. A comparative test used on clinical specimens between the neutralization test and the AC-ELISA showed that the proportions of true positives and true negatives by the AC-ELISA were 0.90 and 0.67 respectively. These results indicated that the AC-ELISA approach is rapid, sensitive, and reliable for specific detection of DEV antigen.",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding"
            ]
        },
        {
            "id": "task352-a43509b70070492b81a7c178ed13a25f",
            "input": "Geo-social interaction patterns Geo-social scale Location-based social network Agent-based epidemic models Social network analysis Infectious disease transmission and control High performance computing A B S T R A C T Cities play an important role in fostering and amplifying the transmission of airborne diseases (e.g., influenza) because of dense human contacts. Before an outbreak of airborne diseases within a city, how to determine an appropriate containment area for effective vaccination strategies is unknown. This research treats airborne disease spreads as geo-social interaction patterns, because viruses transmit among different groups of people over geographical locations through human interactions and population movement. Previous research argued that an appropriate scale identified through human geo-social interaction patterns can provide great potential for effective vaccination. However, little work has been done to examine the effectiveness of such vaccination at large scales (e.g., city) that are characterized by spatially heterogeneous population distribution and movement. This article therefore aims to understand the impact of geo-social interaction patterns on effective vaccination in the urbanized area of Portland, Oregon. To achieve this goal, we simulate influenza transmission on a large-scale location-based social network to 1) identify human geo-social interaction patterns for designing effective vaccination strategies, and 2) and evaluate the efficacy of different vaccination strategies according to the identified geo-social patterns. The simulation results illustrate the effectiveness of vaccination strategies based on geosocial interaction patterns in containing the epidemic outbreak at the source. This research can provide evidence to inform public health approaches to determine effective scales in the design of disease control strategies.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - method, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-9c791a1b844243b98a92e8ba06b8942f",
            "input": "Standard precautions should be applied to prevent health care-associated infections during every nursing activity. However, adherence to standard precautions was reported to be inadequate. Therefore, this study aimed to identify the rates of standard precaution adherence and the association between perception of patient safety management and standard precaution adherence. In this cross-sectional descriptive study, a convenience sample of nurses was recruited from a university-affiliated teaching hospital in Seoul, Korea. Data were collected using a structured self-report questionnaire. Among the 332 questionnaires returned (response rate: 94.9%), a total of 329 nurses were analyzed. In the present study, the overall standard precaution adherence rate was approximately 53.5%. The multiple linear regression results revealed that participants' perceptions of patient safety management were only significantly associated with standard precaution adherence after adjusting other covariates (β = 0.412, p < 0.001). Nurse supervisors should focus more on raising awareness about nurses' perception of patient safety management based on the specific work environment, such as the total number of nurses working together and the nurse-to-patient ratio. Nurse educators should develop integrated curricula to help graduate nurses transition smoothly into professional practice and enhance adherence to standard precautions in diverse health care settings.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding"
            ]
        },
        {
            "id": "task352-ee7f1d31ae4448fbb32b258f29097714",
            "input": "A capsid protein of porcine circovirus 2 (PCV 2) serves as a diagnostic antigen for the detection of PCV 2-associated disease known as a postweaning multisystemic wasting syndrome (PMWS). In this report, a bacterial expression system was developed for the expression and purification of the full-length PCV 2 capsid (Cap) protein from a codon-optimized cap gene. Replacement of rare arginine codons located at the 5 end of the cap reading frame with codons optimal for E. coli was found to overcome the poor expression of the viral protein in the prokaryotic system. The Cap protein was purified to greater than 95% homogeneity by using a single cation-exchange chromatography at a yield of 10 mg per litre of bacterial culture. Despite the failure of the E. coli-expressed Cap protein to self-assemble into virus-like particles (VLPs), the immunization of mice with recombinant Cap yielded antibodies with the same specificity as those raised against native PCV 2 virions. In addition, the antigenic properties of the purified Cap protein were employed in a subunit-based indirect ELISA to monitor the levels of PCV 2 specific antibodies in piglets originating from a herd which was experiencing PCV 2 infection. These results pave the way for a straightforward large-scale production of the recombinant PCV 2 capsid protein and its use as a diagnostic antigen or a PCV 2 subunit vaccine.",
            "output": [
                "1 - background, 2 - method, 3 - finding, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-6faaa4b172c045cf8571b03d2cf56b76",
            "input": "Purpose Influenza A viruses, human coronaviruses (hCoV) and human bocavirus (hBoV) are emerging respiratory viruses. This study investigated the association between influenza A viruses co-infection with hBoV and hCoV and severity and the sensitivity of a real-time polymerase chain reaction (RT-PCR) assay for identification of 15 coronaviruses. Methodology Published sequences for the 15 human coronaviruses were used to design a consensus PCR targeting the replicase open reading frame 1b. A previously published PCR targeting the NS1 Gene of all known human bocavirus strains was also utilized. A series of 217 samples from patients aged 37.7 (SD ± 30.4)] with seasonal influenza A viruses (SeasFluA) identified between 06/2011 and 06/2012 in NW England were tested for hCoV and hBoV using RT-PCR. Association between coinfection and disease outcome was assessed using logistic regression. Results The limit of detection of hCoV RT-PCR assay was 2 copies/µl of human coronavirus RNA template, a sensitivity comparable to a previously published SYBR green assay for human coronaviruses. A total of 12 hCoV and 17 hBoV were identified in the 217 influenza A positive samples. A higher proportion (61.5 %; 8/13) of SeasFluA/hBoV co-infections were identified in patients",
            "output": [
                "1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding"
            ]
        },
        {
            "id": "task352-56917207a9164add9761b18c3a26507e",
            "input": "Background: On December 8 th , 2015, World Health Organization published a priority list of eight pathogens expected to cause severe outbreaks in the near future. To better understand global research trends and characteristics of publications on these emerging pathogens, we carried out this bibliometric study hoping to contribute to global awareness and preparedness toward this topic. Method: Scopus database was searched for the following pathogens/infectious diseases: Ebola, Marburg, Lassa, Rift valley, Crimean-Congo, Nipah, Middle Eastern Respiratory Syndrome (MERS), and Severe Respiratory Acute Syndrome (SARS). Retrieved articles were analyzed to obtain standard bibliometric indicators. Results: A total of 8619 journal articles were retrieved. Authors from 154 different countries contributed to publishing these articles. Two peaks of publications, an early one for SARS and a late one for Ebola, were observed. Retrieved articles received a total of 221,606 citations with a mean ± standard deviation of 25.7 ± 65.4 citations per article and an h-index of 173. International collaboration was as high as 86.9%. The Centers for Disease Control and Prevention had the highest share (344; 5.0%) followed by the University of Hong Kong with 305 (4.5%). The top leading journal was Journal of Virology with 572 (6.6%) articles while Feldmann, Heinz R. was the most productive researcher with 197 (2.3%) articles. China ranked first on SARS, Turkey ranked first on Crimean-Congo fever, while the United States of America ranked first on the remaining six diseases. Of retrieved articles, 472 (5.5%) were on vaccinerelated research with Ebola vaccine being most studied. Conclusion: Number of publications on studied pathogens showed sudden dramatic rise in the past two decades representing severe global outbreaks. Contribution of a large number of different countries and the relatively high h-index are indicative of how international collaboration can create common health agenda among distant different countries.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - purpose, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding"
            ]
        },
        {
            "id": "task352-3c9636cf94f74fa5bee055121b3557ec",
            "input": "A defective-interfering (DI) RNA of mouse hepatitis virus (MHV) was developed as a vector for expressing MHV hemagglutinin/esterase (HE) protein. The virus containing an expressed HE protein (A59-DE-HE) was generated by infecting cells with MHV-A59, which does not express HE, and transfecting the in vitro-transcribed DI RNA containing the HE gene. A similar virus (A59-DE-CAT) expressing the chloramphenicol acetyltransferase (CAT) was used as a control. These viruses were inoculated intracerebrally into mice, and the role of the HE protein in viral pathogenesis was evaluated. Results showed that all mice infected with parental A59 or A59-DE-CAT succumbed to infection by 9 days postinfection (p.i.), demonstrating that inclusion of the DI did not by itself alter pathogenesis. In contrast, 60% of mice infected with A59-DE-HE survived infection. HE-or CAT-specific subgenomic mRNAs were detected in the brains at days 1 and 2 p.i. but not later, indicating that the genes in the DI vector were expressed only in the early stage of viral infection. No significant difference in virus titer or viral antigen expression in brains was observed between A59-DE-HEand A59-DE-CAT-infected mice, suggesting that virus replication in brain was not affected by the expression of HE. However, at day 3 p.i. there was a slight increase in the extent of inflammatory cell infiltration in the brains of the A59-DE-HE-infected mice. Surprisingly, virus titers in the livers of A59-DE-HE-infected mice were 3 log 10 lower than that of the A59-DE-CAT-infected mice at day 6 p.i. Also, substantially less necrosis and viral antigen were detected in the livers of the A59-DE-HE-infected mice. This may account for the reduced mortality of these mice. The possible contribution of the host immune system to this difference in pathogenesis was analyzed by comparing the expression of four cytokines. Results showed that both tumor necrosis factor-␣ and interleukin-6 mRNAs increased in the brains of the A59-DE-HE-infected mice at day 2 p.i., whereas interferon-␥ and interleukin-1␣ mRNAs were similar between A59-DE-HE-and A59-DE-CAT-infected mice. These data suggest that the transient expression of HE protein enhances an early innate immune response, possibly contributing to the eventual clearance of virus from the liver. This study indicates the feasibility of the DI expression system for studying roles of viral proteins during MHV infection.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding"
            ]
        },
        {
            "id": "task352-9df6a693bc5d486d9db81777c01a8b48",
            "input": "Porcine epidemic diarrhea (PED) is an emerging disease of pigs in several countries. In the present study, individual sow productivity of Berkshire sows exposed to PED virus at different stages of production was compared. On a commercial farrow-to-finish farm in Kagoshima Prefecture, Japan, the clinical presence of PED was observed in the farrowing barn on January 6, 2014, and all gilts and sows were immunized on January 9, except those in the farrowing barn. The sows were categorized into six groups based on the period in which they were exposed to PED virus: between days 0-30 (G1), 31-60 (G2), 61-90 (G3), or after 91 days of pregnancy (G4), during lactation (L), and after weaning (W). The control group was not exposed to PED during the period of PED outbreak. The study was based on 574 production records. The sows of the G4 and L groups had the fewest piglets weaned (4.8 ± 0.4, and 4.0 ± 0.3 pigs, respectively; P < 0.05) and the greatest pre-weaning mortality (33.1 ± 4.8%, and 39.7 ± 4.1%, respectively; P < 0.05). The number of piglets weaned and pre-weaning mortality, however, did not differ among the G1, G2, G3, and uninfected groups. The G4 and W groups had slightly lesser farrowing rates than the uninfected group (P < 0.05), however, similar subsequent piglet litter performance as the uninfected group. In conclusion, the effect of PED on individual sow productivity differed with the production stage in which sows were exposed to PED virus.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - method, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding"
            ]
        },
        {
            "id": "task352-56e9ce88320340e3a6e8ffdec625de7b",
            "input": "We analyzed hospital records to provide a populationbased estimate of zygomycosis incidence and trends over a 10-year period at a national level in France. Data showed an increasing incidence from 0.7/million in 1997 to 1.2/million in 2006 (p<0.001). We compared our data with those from the French Mycosis Study Group, a recently established voluntary network of French mycologists coordinated by the National Reference Center for Mycoses and Antifungals. We documented that incidence of zygomycosis increased, particularly in patients with hematologic malignancies or bone marrow transplants. The role of previous exposure to antifungal drugs lacking activity against zygomycetes could explain this increase but does not appear exclusive. Incidence also increased in the population of patients with diabetes mellitus. We conclude that observed trends reflect a genuine increase of zygomycosis cases in at-risk populations.",
            "output": [
                "1 - method, 2 - finding, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-8dad70a0bebd456fa8a5ff32baec49db",
            "input": "Results: A total of five RCTs were identified. All of the RCTs were of high risk of bias with flawed study design and poor methodological quality. All RCTs included children aged between 6 months to 14 years. Results of individual trials showed that Shuanghuanglian oral liquid (RR 4.00; 95% CI: 2.26 to 7.08), and Xiaoer Resuqing oral liquid (RR 1.43; 95% CI: 1.15 to 1.77) had higher cure rates compared with antivirus drugs. Most of the trials did not report adverse events, and the safety of CPMs was still uncertain. Conclusions: Some CPMs showed a potential positive effect for the common cold on cure rate. However, due to the poor methodology quality and the defects in the clinical design of the included RCTs, such as the lack of placebo controlled trials, the inappropriate comparison intervention and outcome measurement, the confirmative conclusions on the beneficial effect of CPMs for the common cold could not be drawn.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-71419b661c114e40863629fbcc38b1e6",
            "input": "A codon-optimized gene encoding the Kozak sequence, 6xHis-tag, HCVcp (1-122) and KDEL peptide in tandem (from N-to C-terminal) was designed and inserted into potato virus-X (PVX) and classic pBI121 binary vectors in separate cloning reactions. The resulted recombinant plasmids were transferred into Agrobacterium tumefaciens and vacuum infiltrated into tobacco leaves. The effect of gene silencing suppressor P19 protein derived from tomato bushy stunt virus on the expression yield of HCVcp by each construct was also evaluated by co-infiltration in separate groups. The expressed HCVcp was evaluated by dot and western blotting and ELISA assays. Results: The codon-optimized gene had an increased adaptation index value (from 0.65 to 0.85) and reduced GC content (from 62.62 to 51.05) in tobacco and removed the possible deleterious effect of \"GGTAAG\" splice site in native HCVcp. Blotting assays via specific antibodies confirmed the expression of the 15 kDa HCVcp. The expression level of HCVcp was enhanced by 4-5 times in P19 co-agroinfiltrated plants with better outcomes for PVX, compared to pBI121 vector (0.022% versus 0.019% of the total soluble protein). The plant-derived HCVcp (pHCVcp) could properly identify the HCVcp antibody in HCV-infected human sera compared to Escherichia coli-derived HCVcp (eHCVcp), indicating its potential for diagnostic/immunization applications. Conclusions: By employment of gene optimization strategies, use of viral-based vectors and suppression of plant-derived gene silencing effect, efficient transient expression of HCVcp in tobacco with proper antigenic properties could be possible.",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-f3fb2dabc5d34f7ab6ab9eac1ecf54e9",
            "input": "As expected, cats from endemic areas produce IFN-γ after ex vivo blood stimulation with LSA and therefore are able to activate a cell-mediated adaptive immune response against the parasite that is variably associated with antibody or blood PCR positivity. The association of this assay to serological and molecular tests provides a better estimate of cat exposure to L. infantum.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-d41db15f6e2a4f1cb8c60ca3ddc18d72",
            "input": "Background. Kawasaki disease (KD) is characterized by systemic vasculitis of unknown etiology. Our previous studies showed expression of CD40 ligand on CD4+ T cells correlated to the coronary artery lesion (CAL) and disease progress in KD. Other studies from Japan suggested the role of CD40L in the pathogenesis of CAL, and this might help explain the excessive number of males affected with KD but cannot be reproduced by Taiwanese population. This study was conducted to investigate the CD40 polymorphism in KD and CAL formation. Methods. A total of 950 subjects (381 KD patients and 569 controls) were investigated to identify 2 tagging single-nucleotide polymorphisms (tSNPs) of CD40 (rs4810485 and rs1535045) by using the TaqMan allelic discrimination assay. Results. A significant association was noted with regards to CD40 tSNPs (rs1535045) between controls and KD patients (P = 0.0405, dominant model). In KD patients, polymorphisms of CD40 (rs4810485) showed significant association with CAL formation (P = 0.0436, recessive model). Haplotype analysis did not yield more significant results between polymorphisms of CD40 and susceptibility/disease activity of KD. Conclusions. This study showed for the first time that polymorphisms of CD40 are associated with susceptibility to KD and CAL formation, in the Taiwanese population.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-49749eaf7b184e4dab04d9efd9107d80",
            "input": "Rationale: After lung transplantation, insults to the allograft generally result in one of four histopathologic patterns of injury: (1) acute rejection, (2) lymphocytic bronchiolitis, (3) organizing pneumonia, and (4) diffuse alveolar damage (DAD). We hypothesized that DAD, the most severe form of acute lung injury, would lead to the highest risk of chronic lung allograft dysfunction (CLAD) and that a type I immune response would mediate this process. Objectives: Determine whether DAD is associated with CLAD and explore the potential role of CXCR3/ligand biology. Methods: Transbronchial biopsies from all lung transplant recipients were reviewed. The association between the four injury patterns and subsequent outcomes were evaluated using proportional hazards models with time-dependent covariates. Bronchoalveolar lavage (BAL) concentrations of the CXCR3 ligands (CXCL9/MIG, CXCL10/ IP10, and CXCL11/ITAC) were compared between allograft injury patterns and \"healthy\" biopsies using linear mixed-effects models. The effect of these chemokine alterations on CLAD risk was assessed using Cox models with serial BAL measurements as time-dependent covariates. Measurements and Main Results: There were 1,585 biopsies from 441 recipients with 62 episodes of DAD. An episode of DAD was associated with increased risk of CLAD (hazard ratio, 3.0; 95% confidence interval, 1.9-4.7) and death (hazard ratio, 2.3; 95% confidence interval, 1.7-3.0). There were marked elevations in BAL CXCR3 ligand concentrations during DAD. Furthermore, prolonged elevation of these chemokines in serial BAL fluid measurements predicted the development of CLAD. Conclusions: DAD is associated with marked increases in the risk of CLAD and death after lung transplantation. This association may be mediated in part by an aberrant type I immune response involving CXCR3/ligands.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding"
            ]
        },
        {
            "id": "task352-f0b2c5a766c64162a2b86760e0a07754",
            "input": "Understanding how disease affects commercial production is imperative for pig producers to quantify its full impact on pig performance, carcass quality, and net returns. The objective of this experiment was to assess the productivity and economic importance of naturally occurring health challenges (HC) under commercial conditions. Three 1,000 pig grow-finish facilities received 936 pigs each. The experimental period started approximately 34 d post placement at an average start BW of 13.1 ± 0.2 kg.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - method, 5 - method"
            ]
        },
        {
            "id": "task352-60e65cbd2d0d426e8354de925c880fe7",
            "input": "This study provides a fundamental evaluation of simultaneous detection and differential identification of genetically diverse RNA viruses with a minimal number of prototype sequences. The results demonstrated that the newly designed RPM-Flu v.30/31 can provide comprehensive and specific analysis of HRV and HEV samples which implicates that this design strategy will be applicable for other genetically diverse viruses.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-6f8bd056c1104cad9e862a0b8d6fc560",
            "input": "Citation Yuan S. 2015. Statins may decrease the fatality rate of Middle East respiratory syndrome infection. mBio 6(4):e01120-15.",
            "output": [
                "1 - other, 2 - finding, 3 - other"
            ]
        },
        {
            "id": "task352-f71423754ef14e388ed549dc72cca089",
            "input": "Cereal commodities are frequently contaminated with mycotoxins produced by the secondary metabolism of fungal infection. Among these contaminants, deoxynivalenol (DON), also known as vomitoxin, is the most prevalent type B trichothecene mycotoxin worldwide. Pigs are very sensitive to the toxic effects of DON and are frequently exposed to naturally contaminated feed. Recently, DON naturally contaminated feed has been shown to decrease porcine reproductive and respiratory syndrome virus (PRRSV) specific antibody responses following experimental infection. The objective of this study was to determine the impact of DON naturally contaminated feed on the immune response generated following vaccination with PRRSV live attenuated vaccine. Eighteen pigs were randomly divided into three experimental groups of 6 animals based on DON content of the diets (0, 2.5 and 3.5 mg DON/kg). They were fed these rations one week prior to the vaccination and for all the duration of the immune response evaluation. All pigs were vaccinated intra-muscularly with one dose of Ingelvac ® PRRSV modified live vaccine (MLV). Blood samples were collected at day −1, 6, 13, 20, 27 and 35 post vaccination (pv) and tested for PRRSV RNA by RT-qPCR and for virus specific antibodies by ELISA. Results showed that ingestion of DON-contaminated diets significantly decreased PRRSV viremia. All pigs fed control diet were viremic while only 1 (17%) and 3 (50%) out of 6 pigs were viremic in the groups receiving 3.5 and 2.5 mg of DON/kg, respectively. Subsequently, all pigs fed control diet developed PRRSV specific antibodies while only viremic pigs that were fed contaminated diets have developed PRRSV specific antibodies. These results suggest that feeding pigs with DON-contaminated diet could inhibit vaccination efficiency of PRRSV MLV by severely impairing viral replication.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding, 16 - finding"
            ]
        },
        {
            "id": "task352-ab887315d6b04a93ac00be8833f6562b",
            "input": "Fresh demyelinating lesions could be demonstrated in paralyzed animals. Viral antigen was demonstrated and infectious JHM virus could be recovered from one animal which developed clinical signs at 3 months a.i. In one animal with clinical onset of 8 months a.i., completely remyelinated areas as well as recent demyelinating lesions were observed, suggesting a recurrence of the disease process. Remyelinated areas were also found in 40 ~ of clinically silent animals. The morphology of the late onset of the demyelination was similar to that occurring in SDE. Remyelination consisted of both CNS and PNS-type. This animal model offers the possibility to investigate the virus-host relationship which is responsible for the induction of a demyelinating process after a long incubation period.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-298a243fae684729aa6e5326d81ab2ec",
            "input": "PRRSV PEDV Antiviral inhibitor Broad-spectrum 3C-like serine/3C-like protease A B S T R A C T Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) are highly virulent and contagious porcine pathogens that cause tremendous economic losses to the swine industry worldwide. Currently, there is no effective treatment for PRRSV and PEDV, and commercial vaccines do not induce sterilizing immunity. In this study, we screened a library of 1000 compounds and identified two specific inhibitors, designated compounds 2 and 3, which target the PRRSV 3C-like serine protease (3CLSP). First, we evaluated the inhibitory effects of compounds 2 and 3 on PRRSV 3CLSP activity. Next, we determined the anti-PRRSV capacity of compounds 2 and 3 in MARC-145 cells and obtained EC 50 and CC 50 values of 57 μM (CC 50 = 479.9 μM) and 56.8 μM (CC 50 = 482.8 μM), respectively. Importantly, compounds 2 and 3 also targeted the PEDV 3C-like protease (3CL protease) and inhibited PEDV replication, showing EC 50 and CC 50 values of 100 μM (CC 50 = 533.8 μM) and 57.9 μM (CC 50 = 522.3 μM), respectively. Finally, our results indicated that the active sites (His39 in 3CLSP and His41 in 3CL protease) were conservative, and contacted compounds 2 and 3 via hydrogen bonds and hydrophobic forces in the putative substrate-binding models. In summary, compounds 2 and 3 exhibit broad-spectrum antiviral activity and may facilitate the development of antiviral drugs against PRRSV and PEDV.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding"
            ]
        },
        {
            "id": "task352-e0ab2150b41b4aed9019052ea9d984c3",
            "input": "The diagnostic performance of porcine epidemic diarrhea virus (PEDV) IgG and IgA ELISAs was evaluated using paired serum and meat juice samples collected from PEDV-negative (n = 50) and PEDV-inoculated pigs (n = 87). Serum samples were tested by PEDV (IgG, IgA) ELISAs using a procedure performed routinely at the Iowa State University-Veterinary Diagnostic Laboratory (ISU-VDL). Serum samples were tested using PEDV serum IgG and IgA ELISA procedures as routinely performed at the Iowa State University-Veterinary Diagnostic Laboratory (ISU-VDL). Serum samples were diluted 1:50 and conjugate concentrations were 1/20,000 for IgG and 1/3000 for IgA. Meat juice samples were tested using the serum PEDV IgG and IgA ELISAs, with modifications, i.e., meat juice samples were diluted 1:25 and conjugate concentrations were 1/40,000 for IgG and 1/10,000 for IgA. Receiver operator characteristic (ROC) curve analyses were used to estimate diagnostic sensitivities and specificities over a range of sample-to-positive (S/P) cutoffs. Consistent with previous reports, this study showed that the PEDV IgG and IgA meat juice ELISAs provided excellent diagnostic performance and suggest that meat juice recovered from samples collected at slaughter could be used in routine PEDV surveillance.",
            "output": [
                "1 - background, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding"
            ]
        },
        {
            "id": "task352-80797d91550745dca2d8777f77757fe6",
            "input": "The experiment results show that IILLS achieves the AUC values of 0.8675 and 0.9061 with the 10-fold cross validation and leave-one-out cross validation (LOOCV), respectively, which illustrates that IILLS is superior to the competing methods. In addition, the case studies also further indicate that the IILLS method is effective for the virus-receptor interaction prediction.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-ebc53a638ac7431989b5ae7f7c6cc675",
            "input": "Method: This is a cohort study designed to investigate psychiatric complications among SARS survivors treated in the United Christian Hospital 30 months after the SARS outbreak. Psychiatric morbidities were assessed by the Structured Clinical Interview for DSM-IV, the Impact of Events Scale-Revised and the Hospital Anxiety and Depression Scale. Functional outcomes were assessed by the Medical Outcomes Study 36-Item Short-Form Health Survey. Results: Ninety subjects were recruited, yielding a response rate of 96.8%. Post-SARS cumulative incidence of DSM-IV psychiatric disorders was 58.9%. Current prevalence for any psychiatric disorder at 30 months post-SARS was 33.3%. One-fourth of the patients had post-traumatic stress disorder (PTSD), and 15.6% had depressive disorders. Conclusion: The outbreak of SARS can be regarded as a mental health catastrophe. PTSD was the most prevalent long-term psychiatric condition, followed by depressive disorders. Our results highlight the need to enhance preparedness and competence of health care professionals in detecting and managing the psychological sequelae of future comparable infectious disease outbreaks.",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding"
            ]
        },
        {
            "id": "task352-e17890289dac402393e1768ccc5260a6",
            "input": "Citation Stenglein MD, et al. 2012. Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease. mBio 3(4):e00180-12.",
            "output": [
                "1 - finding, 2 - finding, 3 - other"
            ]
        },
        {
            "id": "task352-0b09f615835b40f68b5665e3b3077e80",
            "input": "Objectives: 1) To compare the 2-year completed suicide and reattempt rates in a preintervention group of Hong Kong Chinese suicide attempters (aged 65 years and older) who received standard care and a postintervention group enrolled in a regional elderly suicide prevention program (ESPP) that adopts a two-tiered multifaceted care management model and 2) to examine the trend of suicide rates in older adults aged 65 years and older in the pre-and postintervention periods. Design: The first part is an observational cohort study with baseline, follow-up, and outcome data being identified from a clinical electronic registry. The second part examines changes in suicide rates from official mortality statistics. Setting: A government-funded suicide intervention program serving catchment population (852,796 people aged 65 years and older) in Hong Kong, China. Participants: Suicide attempters (aged 65 years and older) presenting to old-age psychiatric service in the pre-and postintervention phases. Measurements: 1) Two-year rates of completed suicide and suicide reattempt and 2) changes in population suicide rates in the pre-and postintervention periods. Results: The 2-year completed suicide rate was 7.58% in the preintervention group (N = 66) and 1.99% in the ESPP group (N = 351) χ 2 = 6.192; p value: 0.028; df = 1). Reattempt rates were not different. At a population level, suicide rate dropped significantly only in women aged 85 years and older, relative to the preintervention period. Conclusions: The ESPP was associated with a reduced rate of completed suicide in old-age suicide attempters and might have contributed to a fall of suicide rate in women aged 85 years and older. (Am J Geriatr Psychiatry 2011; 19:1-12) ",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - other"
            ]
        },
        {
            "id": "task352-b0cabdc5694f4ebf8751e74cf1209ba9",
            "input": "A polysaccharide microarray platform was prepared by immobilizing Burkholderia pseudomallei and Burkholderia mallei polysaccharides. This polysaccharide array was tested with success for detecting B. pseudomallei and B. mallei serum (human and animal) antibodies. The advantages of this microarray technology over the current serodiagnosis of the above bacterial infections were discussed. D",
            "output": [
                "1 - background, 2 - background, 3 - finding, 4 - other"
            ]
        },
        {
            "id": "task352-43d45110df564d0fb957d1e07ce3cad7",
            "input": "The estimated costs and TAT were 8.2€ and 2 h for DFA, 31.8€ and 1.5 h for Simplexa™ and 55€ and 3 h for TAC testing. Conclusions: Performing the Simplexa™ test 24 h a day/7 days a week instead of DFA would considerably improve the overall sensitivity and time-to-result, albeit at a higher cost generated in the laboratory. Performing the TAC would increase the diagnostic yield and detection of co-infections significantly.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-d05a6401cacf407cb4be33ee5f8f9692",
            "input": "The term is derived from the Greek word for \"alternative\"-para and for \"mucus\"-myxo. 2. Syncytium A syncytium (pl., syncytia) refers to a multinucleated cell that can result from multiple cell fusions of uninuclear cells. The term is derived from the Greek word for \"together\"-syn and for \"box (cell)\"-kytos.",
            "output": [
                "1 - background, 2 - other, 3 - background, 4 - background"
            ]
        },
        {
            "id": "task352-431041b0612b4b82b78906c314275d88",
            "input": "FilmArray Respiratory Panel (RP) (Idaho Technology, Inc., Salt Lake City, UT, USA) performance was retrospectively evaluated in respiratory samples collected from neonates in 2 reference neonatology units. Using the FilmArray RP assay, 121/152 (79.6%) samples were positive for at least 1 respiratory virus, while 31/ 152 (20.4%) were negative. FilmArray RP results were concordant in 68/72 (94.4%) respiratory samples tested with laboratory-developed real-time PCR assays, while in 4/72 (5.6%) samples, the FilmArray RP assay detected an additional virus (2 human rhinovirus/enterovirus and 2 bocavirus). In addition, FilmArray RP results for 70 of 80 (87.5%) respiratory samples tested were concordant with the Seegene Seeplex RV15® detection assay (Seegene, Inc., Seoul, South Korea), while 10/80 (12.5%) were discordant. The advantages of the FilmArray RP are the rapid detection of respiratory viruses (1 hour), the wide number of pathogens detectable in a single assay, and the reduced hands-on time.",
            "output": [
                "1 - method, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-2e1f187842a54733ac3b6b50c268d7c5",
            "input": "The role of rhinovirus asymptomatic infections in the transmission among close contacts subjects is unknown. We tested health care workers, a pair of one child and a family member and immunocompromised patients (n =191). HRV were detected on 22.9% symptomatic and 3.6% asymptomatic cases suggesting lower transmission among contacts. Rhinovirus infections are among the most frequent causes of the common colds (18). It is the most common etiology of viral respiratory infections among diverse populations, including adults, children and more recent studies have linked HRVs to more severe lower respiratory illnesses in otherwise healthy young children (11-12), immunocompromised (4,6), and elderly patients. (5,13, 23). In Brazil, there are few HRV studies, Arruda et.al. (1991), realized the first Brazilian study detecting a 45.5% rate on symptomatic children in Fortaleza -CE. Another study realized in Salvador -BA also showed a high prevalence (48.5%) (Souza ,2003). The only study",
            "output": [
                "1 - background, 2 - method, 3 - method, 4 - finding, 5 - background, 6 - background, 7 - background, 8 - background, 9 - other, 10 - background, 11 - finding, 12 - finding, 13 - other"
            ]
        },
        {
            "id": "task352-84081c52c13245da802a6b07ba467de6",
            "input": "TCR Vβ CDR3 repertoire diversity in human peripheral blood; spectratype; immune reconstitution; hematopoietic stem cell transplantation Corresponding author: Sarfraz A. Memon, M.D., Experimental Transplantation and Immunology Branch,",
            "output": [
                "1 - other, 2 - other"
            ]
        },
        {
            "id": "task352-d1a5cabf613d424f89485a2b87f94e5e",
            "input": "Here we aim to investigate the importance of spillover transmission for explaining the number and the size of outbreaks. We propose a simple stochastic Susceptible-Infected-Recovered model with a recurrent infection of an incidental host from a reservoir (e.g. humans by a zoonotic species), considering two",
            "output": [
                "1 - purpose, 2 - method"
            ]
        },
        {
            "id": "task352-31adfefaa59c450abd88b7c835d51ee9",
            "input": "Conclusions: Preliminary results show that there is significant air motion associated with a cough (on the order of 0.5 m/s) as far away as 1 m from the mouth of the healthy person who coughs. The results from this pilot study provide the framework for a more extensive participant recruitment campaign that will encompass a statisticallysignificant cohort.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-10de05f5c47c49e29675aef0d64ad16b",
            "input": "Bovine respiratory disease (BRD) often occurs when active respiratory virus infections (BHV-1, etc.) impair resistance to Mannheimia haemolytica infection in the lower respiratory tract. The interactions that occur when the respiratory epithelium encounters these viral and bacterial pathogens are poorly understood. We used Agilent bovine gene microarray chips containing 44,000 transcripts to elucidate bovine bronchial epithelial cell (BBEC) responses following in vitro exposure to BHV-1 alone, M. haemolytica alone, or both BHV-1 and M. haemolytica. Microarray analysis revealed differential regulation (>2-fold) of 978 transcripts by BHV-1 alone, 2040 transcripts by M. haemolytica alone, and 2189 genes by BHV-1 and M. haemolytica in combination. M. haemolytica treatment produced significantly greater inductions (>10-fold) of several inflammation associated genes, such as CXCL2, IL-6, IL-1␣, e-selectin, and IL-8, than to BHV-1 alone. Functional analysis of the microarray data revealed a significant upregulation of genes involved in important biological processes such as inflammation (TNF-␣, IL-8, Tlr-2, IL-1, CXCL2, CSF2), vascular functions (VEGF, EDN2) and leukocyte migration (ICAM1, IL-16) during a co-infection with BHV-1 and M. haemolytica compared to either pathogen alone. This study provides evidence to support that lung epithelial cells are a source of mediators that may promote inflammatory changes observed during bovine respiratory disease.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding"
            ]
        },
        {
            "id": "task352-db51fa52aebc4c1b9696a411a744c3c6",
            "input": "Published: xx xx xxxx OPEN www.nature.com/scientificreports/",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-8a88d30a652a469b9496a03884e3a715",
            "input": "A Chinese isolate of avian infectious bronchitis virus (IBV) designated HH06 was isolated from the kidney tissues of a chicken flock experiencing an outbreak of nephritis. In vivo pathogenicity of the IBV isolate HH06 was determined by inoculating specific pathogen-free (SPF) chickens. The clinical signs and related gross lesions of HH06 infected chickens were similar with those of the field-infected chickens. SPF embryonated eggs were inoculated with virus suspension for serial passage and their genomic RNA was extracted. RT-PCR technique was utilized to amplify the M gene sequence encoding membrane protein of IBV. Recombinant plasmid named T-vector-M was constructed via inserting the M gene into the TA cloning vector, pMD 18-T. The sequenced M gene and its deduced amino acid (aa) sequences were compared with the published sequences of reference strains. The M gene is of 687 bp in length encoding the M protein of 228 amino acids with a predicted molecular weight of 25.4 kDa. The sequences of the M gene and M protein share 83.9-97.9% and 83.6-96.5% homologous identities, respectively, compared with 29 IBV reference strains derived from different regions or countries, which revealed that there are still significant variations between strains. Furthermore, a phylogenetic tree based on these M DNA sequences was generated, and the tree topology suggests that some Chinese IBV strains may have a common ancestor; however, HH06 is a new local IBV isolate that is responsible for the field outbreak of nephritis.",
            "output": [
                "1 - method, 2 - method, 3 - finding, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-732e8c35c43e4e43bc5eb7c1168fd5f4",
            "input": "Maternally-derived antibody to enterotropic mouse hepatitis virus (MHV) strain Y was transferred to pups by both intrauterine (IgG) and lactogenic (IgA and IgG) routes. Antibody present in the gastric whey of pups suckling immune dams dropped to undetectable levels by weaning age (21 days post partum). MHV-specific IgG was found in the serum of passively immune pups up to 10 weeks of age. Immune dams transferred equal levels of antibody to 3 consecutive litters of pups, without evidence of decline. Immunoblots showed that IgA and IgG in whey and serum were directed against nucleoprotein N and glycoprotein S. MHV-specific IgM was not detected in any sample.",
            "output": [
                "1 - background, 2 - finding, 3 - finding, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-a594fb0613b44f239eb2c2edf02e91f0",
            "input": "Statistics. Statistical analyses were conducted using SPSS software (version 20 SPSS, Inc., Chicago, IL). For normally distributed variables, Student's t-test and one-way ANOVA were used for comparisons, and the data are presented as the mean ± SE. The Mann-Whitney U and Kruskal-Wallis tests were used for comparisons of variables that were not normally distributed. Correlations were assessed with Pearson's correlation coefficient for parametric distributions. Statistical significance was set at P < 0.05.",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-249800a13df74114bb3313714782c081",
            "input": "Patients of all ages were recruited to the study. The patients with agreed diagnosis (diagnosed patients; n=794) included more pediatric (≤18 years) than adult (>18 years) patients (445 patients [56%] vs 349 [44%]). The age distribution was relatively uniform for patients aged 20-80 years and peaked at <4 years of age for pediatric patients (Fig.  S2) . The observed age distribution for pediatric patients is consistent with that expected and represents the background distribution in the inpatient setting [4] (e.g., the emergency department [ED], pediatrics departments, and internal departments). Patients of both genders were recruited to the study. The patient population was balanced in respect to gender distribution (47% females, 53% males).",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - other, 5 - finding, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-930d9f8397f048e0a273d3d26f6da96b",
            "input": "T h e ne w e ngl a nd jou r na l o f m e dicine n engl j med 382;13 nejm.org March 26, 2020 WHO -HEO -RDBlueprint%28nCoV%29 -2020 .1 -eng .pdf).",
            "output": [
                "1 - other, 2 - other, 3 - other"
            ]
        },
        {
            "id": "task352-2e8e6311266740b9a3e5b01b2dbc2387",
            "input": "Homogenates obtained by a Dounce homogeniser of oligodendrocyte and whole brain from 2-day-old rats were suspended in Published by Elsevier Science Publishers B. V.",
            "output": [
                "1 - method"
            ]
        },
        {
            "id": "task352-3038f8374d794bd3b9a1d3fb319026b6",
            "input": "Acute respiratory distress syndrome (28.36%), acute cardiac injury (7.89%) and acute kidney 35 injury (7.60%) were the most common complications recorded. 36 37 Conclusions: Clinical and epidemiological characteristics of COVID-19 patients were mostly 38 heterogeneous and non-specific. This is the most comprehensive report of the characteristics of 39",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-e9b1df23536a4c97baeca59e19e5748c",
            "input": "Repurposing antimalarials as dengue antivirals Chloroquine Primaquine Stable replicon cell lines for dengue and West Nile viruses Inhibition of dengue virus replication and infectivity Amodiaquine therapeutic index a b s t r a c t Dengue virus serotypes 1-4 (DENV1-4) are transmitted by mosquitoes which cause most frequent arboviral infections in the world resulting in $390 million cases with $25,000 deaths annually. There is no vaccine or antiviral drug currently available for human use. Compounds containing quinoline scaffold were shown to inhibit flavivirus NS2B-NS3 protease (NS2B-NS3pro) with good potencies. In this study, we screened quinoline derivatives, which are known antimalarial drugs for inhibition of DENV2 and West Nile virus (WNV) replication using the corresponding replicon expressing cell-based assays. Amodiaquine (AQ), one of the 4-aminoquinoline drugs, inhibited DENV2 infectivity measured by plaque assays, with EC 50 and EC 90 values of 1.08 ± 0.09 lM and 2.69 ± 0.47 lM, respectively, and DENV2 RNA replication measured by Renilla luciferase reporter assay, with EC 50 value of 7.41 ± 1.09 lM in the replicon expressing cells. Cytotoxic concentration (CC 50 ) in BHK-21 cells was 52.09 ± 4.25 lM. The replication inhibition was confirmed by plaque assay of the extracellular virions as well as by qRT-PCR of the intracellular and extracellular viral RNA levels. AQ was stable for at least 96 h and had minor inhibitory effect on entry, translation, and post-replication stages in the viral life cycle. DENV protease, 5 0 -methyltransferase, and RNA-dependent RNA polymerase do not seem to be targets of AQ. Both p-hydroxyanilino and diethylaminomethyl moieties are important for AQ to inhibit DENV2 replication and infectivity. Our results support AQ as a promising candidate for anti-flaviviral therapy.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding"
            ]
        },
        {
            "id": "task352-d9665fcab5fb4163bda24c53790b3194",
            "input": "A prospective cohort study was undertaken to determine calf-level factors that affected calf health status between birth and 6 months of age. A convenience sample of approximately 3300 female Holstein calves born in 1991 on two large Florida dairy farms was used for the study. Data collected on each calf at birth included farm of origin, weight, height at the pelvis, birth date, and serum total protein (a measure of colostral immunoglobulin absorption). Birth season was dichotomized into summer and winter using meteorological data collected by University of Florida Agricultural Research Stations. Health data including date of initial treatment and number of treatments were collected for the diseases diarrhea, omphalitis, septicemia and pneumonia. All calves were followed for 6 months. Cumulative incidences of mortality and occurrence of diarrhea, omphalitis, septicemia and pneumonia were 0.12, 0.35, 0.11, 0.24 and 0.21, respectively. Serum total protein (TP) was a significant risk factor for mortality. The association of TP and mortality was quadratic and showed a dramatic decrease in mortality as TP increased from 4.0 to 5.0 g/dl, a small improvement from 5.0 to 6.0 g/d1 and virtually no improvement in mortality rates as TP increased over 6.0 g/dl. The hazard mortality ratio was constant from birth to six months, indicating that the increased risk of mortality associated with low levels of TP was evident through six months of age. No interactions between TP, farm, season, or birth weight were found in these analyses. Serum total protein concentration was a significant risk factor for the 32 G. A. Donovan et al. /Preventive Veterinary Medicine 34 (1998) 31-46 occurrences, age of onset and severity of septicemia and pneumonia. The association between TP and septicemia was linear and an interaction with birth season was found. The association between TP and pneumonia was quadratic, and in contrast to the TP-and-septicemia relationship, the morbidity hazard ratio for pneumonia was not constant over the time measured; that is, colostral immunity protected the calf from developing pneumonia early in life, but this effect disappeared as the calf got older. Total protein was not a significant risk factor for diarrhea or omphalitis. 0 1998 Elsevier Science B.V.",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding, 22 - finding, 23 - finding, 24 - finding, 25 - finding, 26 - finding, 27 - finding, 28 - finding, 29 - other"
            ]
        },
        {
            "id": "task352-4259fa9857d4431cb2f3474ac08ac768",
            "input": "Equivalently, for each detected case there are at least 1.8 (95% CI 0.5-3.4) undetected cases. If the model is correct, this is an upper bound on the detection frequency because (1) Singapore's detection is probably not 100% efficient. Singapore had as of 12 February 2020 eight",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-6f931c6d34e443cab9b1389cc131fbbc",
            "input": "Infectious bronchitis virus (IBV), the first coronavirus described, has been a continuing problem in poultry for more than 70 years. IBV, causing a highly contagious respiratory disease in chickens, resembles the recently described severe acute respiratory syndrome virus in pathogenesis and genome organization. While previous studies demonstrated that effector and memory CD8 C T lymphocytes are critical in controlling acute IBV infection and disease in chickens, here chicken anti-IBV antibody (IgG) secreting cells (ASC) in both peripheral blood mononuclear cells (PBMC) and spleens collected following IBV Gray infection were evaluated using an ELISPOT assay. The ASC in peripheral blood and spleens can be detected from 3 to 7 days post-infection (p.i.), which is 3-7 days earlier than anti-IBV IgG detected in the serum. The ASC frequency reached a maximum at 7-10 days p.i., and decreased more than 90% in the spleen and 70% in PBMC by 14 days p.i. The ASC levels in the PBMC then decreased gradually to 0.5 ASC/10 6 over the next 8 weeks. The higher concentration of about 20 ASC/10 6 cells in spleens may, at least partially, account for the presence of antibody in the serum although bone marrow ASC were not determined. In vitro stimulation of PBMC and splenocytes with IBV antigen demonstrated that memory B cells can be activated to secrete antibody by 3 weeks p.i. ELISPOT detection of primary B cells could be useful in the early detection of infection following infection with respiratory coronaviruses. q",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - other"
            ]
        },
        {
            "id": "task352-fdb61ff9ee15434296e0740ee11079a2",
            "input": "Quantification of physiologic defensin concentrations in vivo is complex, as defensins are present at high local concentrations within specific cell types or upon release from cells into confined anatomical niches (e.g., crypts of the small intestine) but can become diluted in extracellular fluids. For the myeloid -defensins, Daher et al. estimated ~3 mM (10 mg/ml) HNPs in neutrophils, with even higher local concentrations in the azurophilic granules in which they are stored 1 . For the enteric -defensins, Ayabe et al. estimated concentrations of ≥3.5 mM (15-100 mg/ml) in the crypt lumen, the site of Paneth cell degranulation 31 . These concentrations are likely similar in the human small intestine, where HD5 expression exceeds that of HD6 by 6-fold 32 . In healthy patients, epithelial lining fluid of the lung contains 31-79 nM HNP1-3, nasal fluid contains ~2.7 M HNP1-3, saliva contains 0.3-3 M HNP1-3, and vaginal secretions contain ~1.5 M HNPs and 0.3-14 M HD5 23; 33; 34; 35; 36; 37; 38 . For the -defensins, 5-10 nM HBD2 has been measured in nasal fluid 37; 39 . However, in certain disease states defensin levels can be highly elevated. For example, 57 M to 2.4 mM concentrations of HNP1 have been found in epithelial lining fluid of cystic fibrosis patients 36 . Overall, the concentrations of defensins present in vivo are generally within the range that is needed for direct antiviral activity by -defensins and generally below the concentrations required for direct antiviral activity by -defensins. Wilson et al. ",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - other"
            ]
        },
        {
            "id": "task352-172ce83d90574025a77aed52640d65ff",
            "input": "Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 1212 |",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-30de849baba043b5b70c8238c7f86e7f",
            "input": "www.thelancet.com/respiratory Vol",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-9e1e75c0c25f49d8929f71f4c769daa4",
            "input": "Acute otitis media (AOM) is an inflammatory response to microbes in the middle ear, sometimes associated with rupture of the tympanic membrane. Human leukocytes produce different patterns of inflammatory mediators in vitro when stimulated with Gram-positive and Gram-negative bacteria, respectively. Here, we investigated the cytokine and prostaglandin E 2 (PGE 2 ) responses in middle ear fluids (MEFs) from children with spontaneously perforated AOM, and related the mediator levels to the presence of pathogens detected by culture (live) or PCR (live or dead). Furthermore, the in vivo cytokine pattern was compared with that induced in leukocytes stimulated by dead bacteria in vitro. MEFs with culturable pathogenic bacteria contained more interleukin (IL)-1b (median: 110 lg/L vs. <7.5 lg/L), tumour necrosis factor (TNF) (6.3 lg/L vs. <2.5 lg/L), IL-8 (410 lg/L vs. 38 lg/L) and IL-10 (0.48 lg/L vs. <0.30 lg/L) than culture-negative fluids, irrespective of PCR findings. IL-6 and PGE 2 were equally abundant (69-110 lg/L) in effusions with live, dead or undetectable bacteria. Cytokine levels were unrelated to bacterial species and to the presence or absence of virus. Similar levels of TNF and IL-6 as found in the MEFs were obtained by in vitro stimulation of leukocytes, whereas 11 times more IL-1b and 3.5 times more IL-8 were produced in vivo, and 22 times more IL-10 was produced in vitro. Vigorous production of proinflammatory cytokines accompanies AOM with membrane rupture, regardless of the causative agent, but the production seems to cease rapidly once the bacteria are killed and fragmented. IL-6 and PGE 2 , however, remain after bacterial disintegration, and may play a role in the resolution phase.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - purpose, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding"
            ]
        },
        {
            "id": "task352-2509ed9b22714828ad568befc3a40f0c",
            "input": "We thank Héctor R. Morbidoni for critical reading of this manuscript and Paola Gallo for English revisions.",
            "output": [
                "1 - background"
            ]
        },
        {
            "id": "task352-ebbd8ecf0ca4416b8d3c39e59eedaec9",
            "input": "Attaching and effacing Escherichia coli are involved in diarrhea in 2 to 8-week old calves. The virulence factors of these bacteria include: (i) the secretion of proteins (i.e. EspB) involved in microvilli effacement, (ii) the production of the intimin, a 94 kDa outer membrane protein encoded by the eaeA gene and involved in the intimate attachment of bacteria to epithelial cell and (iii) the production of verotoxins: VT1 and/or VT2. We investigated the presence and the pathotype of these strains in several calf populations by colony hybridization or by genetic amplification. Using the colony hybridization method we showed first that only 5% of calves who died from diarrhea presented EaeA E. coli strains and secondly that 19% of healthy calves showed an asymptomatic carriage. However, using colony hybridization and genetic amplification, we identified EaeA strains in 91% of calves living in farms with recurrent diarrhea problems. In 66% of the calves, there was a correlation between the presence of AEEC and diarrhea. At the pathotype level, most of the EaeA isolates were negative for VT probes. In VT bacteria, the majority were VT1. The number of VT positive bacteria was significantly higher in calves who died from diarrhea than in healthy or sick calves. This underlined the aggravating role of verotoxins in the disease. Moreover, only 25% of the bovine AEEC were positive with the EaeB probe. Surprisingly, the proportion of EaeB strains was significantly higher in healthy calves than in other populations. # 1998 Elsevier Science B.V. All rights reserved.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - purpose, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding"
            ]
        },
        {
            "id": "task352-f7a2ccc231424fe38c43daa5f0eb6b56",
            "input": "hemorrhagic fever in humans. The geographic range of human CCHF cases largely reflects the presence of ticks. However, highly similar CCHFV lineages occur in geographically distant regions. Tick-infested migratory birds have been suggested, but not confirmed, to contribute to the dispersal. Bats have recently been shown to carry nairoviruses distinct from CCHFV. In order to assess the presence of CCHFV in a wide range of bat species over a wide geographic range, we analyzed 1,135 sera from 16 different bat species collected in Congo, Gabon, Ghana, Germany, and Panama. Using a CCHFV glycoproteinbased indirect immunofluorescence test (IIFT), we identified reactive antibodies in 10.0% (114/1,135) of tested bats, pertaining to 12/16 tested species. Depending on the species, 3.6%-42.9% of cave-dwelling bats and 0.6%-7.1% of foliage-living bats were seropositive (two-tailed t-test, p = 0.0447 cave versus foliage). 11/30 IIFT-reactive sera from 10 different African bat species had neutralizing activity in a viruslike particle assay. Neutralization of full CCHFV was confirmed in 5 of 7 sera. Widespread infection of cave-dwelling bats may indicate a role for bats in the life cycle and geographic dispersal of CCHFV.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - purpose, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding, 16 - finding"
            ]
        },
        {
            "id": "task352-957add0866eb492eae84ab24054f05b7",
            "input": "Several studies have demonstrated that administration of EBOV GP-specific antibodies protects nonhuman primates from lethal EBOV infection and may constitute a leading treatment option for EVD in humans [12] [13] [14] [15] [16] . During the West African EVD outbreak, EBOV GP-specific monoclonal antibody (MAb) cocktails (e.g., ZMapp) 12 , were used to treat several patients 17-20 . However, most of characterized therapeutic MAbs to date are EBOV GP-specific and cross-neutralizing activity against any other ebolavirus species (e.g., SUDV and",
            "output": [
                "1 - background, 2 - background, 3 - finding, 4 - background, 5 - background"
            ]
        },
        {
            "id": "task352-207cc35986ab4571b7c0d536f54231fb",
            "input": "Outbreaks of zoonotic diseases in humans and livestock are not uncommon, and an important component in containment of such emerging viral diseases is rapid and reliable diagnostics. Such methods are often PCR-based and hence require the availability of sequence data from the pathogen. Rattus norvegicus (R. norvegicus) is a known reservoir for important zoonotic pathogens. Transmission may be direct via contact with the animal, for example, through exposure to its faecal matter, or indirectly mediated by arthropod vectors. Here we investigated the viral content in rat faecal matter (n = 29) collected from two continents by analyzing 2.2 billion next-generation sequencing reads derived from both DNA and RNA. Among other virus families, we found sequences from members of the Picornaviridae to be abundant in the microbiome of all the samples. Here we describe the diversity of the picornavirus-like contigs including near-full-length genomes closely related to the Boone cardiovirus and Theiler's encephalomyelitis virus. From this study, we conclude that picornaviruses within R. norvegicus are more diverse than previously recognized. The virome of R. norvegicus should be investigated further to assess the full potential for zoonotic virus transmission.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - purpose, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-3937c17b0d554a8ea831257739a4965f",
            "input": "The average accuracy based on leave-one-out (LOO) cross validation of a Bayesian classifier generated from 143 amyloidogenic sequences is 60.84%. This is consistent with the average accuracy of 61.15% for a holdout test set comprised of 103 AM and 28 non-amyloidogenic sequences. The LOO cross validation accuracy increases to 81.08% when the training set is augmented by the holdout test set. In comparison, the average classification accuracy for the holdout test set obtained using a decision tree is 78.64%. Non-amyloidogenic sequences are predicted with average LOO cross validation accuracies between 74.05% and 77.24% using the Bayesian classifier, depending on the training set size. The accuracy for the holdout test set was 89%. For the decision tree, the nonamyloidogenic prediction accuracy is 75.00%. Conclusions: This exploratory study indicates that both classification methods may be promising in providing straightforward predictions on the amyloidogenicity of a sequence. Nevertheless, the number of available sequences that satisfy the premises of this study are limited, and are consequently smaller than the ideal training set size. Increasing the size of the training set clearly increases the accuracy, and the expansion of the training set to include not only more derivatives, but more alignments, would make the method more sound. The accuracy of the classifiers may also be improved when additional factors, such as structural and physico-chemical data, are considered. The development of this type of classifier has significant applications in evaluating engineered antibodies, and may be adapted for evaluating engineered proteins in general.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding"
            ]
        },
        {
            "id": "task352-b044ecd30a0a476a9412e4767d399c73",
            "input": "Background: Data for predicting which patients with pandemic influenza A (H1N1) infection are likely to run a complicated course are sparse. We retrospectively studied whether the admission serum C-reactive protein (CRP) levels can serve as a predictor of illness severity. Methods: Included were all consecutive adult patients who presented to the emergency department (ED) between May-December, 2009 with a flu-like illness, a confirmed diagnosis of pandemic influenza A (H1N1) infection and a serum CRP level measured within 24 hours of presentation. Patients with a proven additional concurrent acute illness (e.g., bacteremia) were excluded. We used the ROC curve analysis, Kaplan-Meier curves and the Cox proportional hazard model to evaluate the predictive ability of CRP as a prognostic factor. Results: Seventeen (9%) of the 191 enrolled patients were admitted to the intensive care unit (ICU), of whom eight (4%) required mechanical ventilation and three (2%) died. The median admission serum CRP levels were significantly higher among patients who required subsequent ICU care and mechanical ventilation than among patients who did not (123 mg/L and 112 mg/L vs. 40 mg/L, p < .001 and 43 mg/L, p = .017, respectively). A Cox proportional hazard model identified admission serum CRP levels and auscultatory findings over the lungs as independent prognostic factors for ICU admission. Admission serum CRP levels were the only independent prognostic factor for mechanical ventilation. Thirty days after presenting to the ED, none of the patients with admission serum CRP level <28 mg/L (lower tertile) required either ICU admission or mechanical ventilation. At the same time point, 19% of the patients with admission serum CRP level ≥70 mg/L (upper tertile) needed to be admitted to the ICU and 8% of the same upper tertile group required mechanical ventilation. The differences in the rates between the lower vs. upper tertile groups were significant (Log-Rank p < .001 for ICU and p < .024 for mechanical ventilation). Conclusions: In our study group, serum CRP levels obtained in the early ED admission stage from patients presenting with pandemic H1N1 influenza A infection were found to serve as a useful gauge for predicting disease course and assisting in patient management.",
            "output": [
                "1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding"
            ]
        },
        {
            "id": "task352-58ddec551bc14ebeb9bb9a4b63862685",
            "input": "Discussion: While several pathogens from the highest priority group already have a high profile in national and international health policy documents, high scores for other pathogens (e.g., Helicobacter pylori, Respiratory syncytial virus or Hantavirus) indicate a possible under-recognised importance within the current German public health framework. A process to strengthen respective surveillance systems and research has been started. The prioritization methodology has worked well; its modular structure makes it potentially useful for other settings.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-a800888034994789b37701446e558d03",
            "input": "The video component of this article can be found at jove 15, 23 . The qRT-PCR-based assay described here can detect attachment events using as few as 20 plaque forming units (PFUs) of virus, which translates into an MOI of 0.0004 for a 48-well plate. Therefore, the strong sensitivity of the assay overcomes the requirement for high MOI as well as any virus labeling or concentration steps. Further, the assay can be i) adapted to measure virion endocytosis Journal of Visualized Experiments",
            "output": [
                "1 - other, 2 - finding, 3 - finding, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-9a5fc3198dde459bbf5a0aa703e77cda",
            "input": "The global spread of Coronavirus Disease 2019 (COVID-19) is overwhelming many health-care systems. As a result, epidemiological models are being used to inform policy on how to effectively deal with this pandemic. We note that the majority of existing models do not take into account differences in the amount of interactions between individuals (i.e. the underlying human interaction network). Using network science we demonstrate how this network of interactions can be used to predict the spread of the virus and to inform policy on the most successful mitigation and suppression strategies. Although applicable to disease modelling in general, our results emphasize how network science can improve the predictive power of current COVID-19 epidemiological models. We provide commented source code for all our analyses so that they can easily be integrated into current and future epidemiological models.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - method, 5 - background, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-0bf8dabf72e34a79a67566d118036b76",
            "input": "A variety of N 0 -[4-[(substituted imino)methyl]benzylidene]-substituted benzohydrazides have been synthesized and evaluated for antimicrobial and anticancer potential. Results from testing of antimicrobial activity indicated the most potent antimicrobial agents had pMIC am = 1.51. The synthesized compounds were bacteriostatic and fungistatic in action. Results from evaluation of antiviral activity indicated that none of the synthesized hydrazide derivatives inhibited viral replication at subtoxic concentrations. Results from anti-HIV screening against HIV-2 strain ROD indicated that one compound was more potent (IC 50 C 1 lg/cm 3 ) than the standard drug nevirapine (IC 50 C 4 lg/cm 3 ) and another was equipotent (IC 50 C 4 lg/cm 3 ). The most effective anticancer agent against both HCT116 and MCF7 cancer cell lines had IC 50 = 19 and 18 lg/cm 3 , respectively. QSAR analysis indicated the importance of Wiener index (W) and energy of the lowest unoccupied molecular orbital (LUMO) in describing the antimicrobial activity of the synthesized compounds.",
            "output": [
                "1 - background, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-b48ccccd53664f2c877c9f1858663f77",
            "input": "Conclusion: Italy is experiencing one of the highest CFR from the COVID-19 pandemic in the world. Time delay adjusted CFR in all the regions in Italy except the Island region were higher than that estimated for Wuhan, China. The CFR in Northwest Italy is 2.5-fold higher than that in Wuhan. Our finding reflects the need of urgent medical support in the Northwest region and the appropriate planning and supplies procurement in other regions of Italy with . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding"
            ]
        },
        {
            "id": "task352-69280d6a423a44438f015c26f841f2de",
            "input": "Control of VSV protein synthesis PLOS Pathogens.",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-2bd2afb8f77b45dfb56cb8cd989bc520",
            "input": "Immunization with different EV types allowed to produce a variety of monoclonal antibodies (MAbs) that are either type-specific (i.e., responsible of virus neutralization) or directed to conserved regions of capsid proteins 15-18 . Reactivity of the latter antibodies may be limited to sets of different EV types or may be directed to a wider range of EV types. Though molecular methods are held to be more informative than classical serologic methods for virus identification 19 , \"pan-EV antibodies\" capable of reacting with all or with the majority of EV types remain desirable reagents for detecting these agents both in the diagnosis of infectious diseases 20-23 and in immunohistochemistry 24 .",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-c243885f6baa499fba2cf061a12f077b",
            "input": "Cooperative interactions play a central role in the regulation of protein functions. Here we show that in multi-site systems like ion channels the application of the Hill formalism could require a combination of different experiments, even involving site-directed mutagenesis, to identify the different sources of cooperativity and to discriminate between genuine and apparent cooperativity. We discuss the implications for the channel function in the bacterial porins PorA (N. meningitidis) and OmpF (E. coli ) and the viroporin SARS-CoV E.",
            "output": [
                "1 - background, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-68a4eb5d7f6c45d9b0be35a891df0a07",
            "input": "Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 1213 |",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-8f88989e227a44e5b3977db1317f3aea",
            "input": "Methods:The non-randomized, controlled trial was conducted on 447 SARS patients treated synchronously with western conventional treatment (WM group, n = 171) alone and ICWM (ICWM group, n = 276). The changes of the cases with normal level ()95 % ) or abnormal level (~95 % ) SaOz were observed dynamically. Results: In the 3rd-14th day of the therapeutic course, the percentage of patients with normal SaC2 in the ICWM group was higher than that in the WM group (OR = 0. 5178, P--0. 0038), and this tendency was more evident in patients of the severe type (OR = 0.18, P = 0. 0001 ). However, the statistical significance of difference was only shown in patients for whom the ICWM treatment started in the early period after the onset (47 days after it, OR = 0. 3803, P = 0. 006), but not shown in those who received ICWM treatment later in the mid-late period of SARS (P~0.05).",
            "output": [
                "1 - method, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding"
            ]
        },
        {
            "id": "task352-9f6b03d2814043f0b8d58c6ced3e23ea",
            "input": "Background: Surveillance of winter respiratory viral illness has been carried out for nearly 30 years using a clinical diagnosis by general practitioners as part of the Scottish Sentinel General Practice (SSGP) network. Contemparaneous laboratory diagnosis has not been available previously. Objectives: To assess the proportion of influenza-like illness (ILI) attributable to influenza, respiratory syncytial virus (RSV) and picornavirus infection during the winter season. To compare the influenza PCR data with serology of paired blood samples. Study design: Combined nose and throat swabs, from patients with ILI attending 15 general practices across Scotland, were submitted to the laboratory in virus PCR sample solution (VPSS). The extracted nucleic acid was tested using a multiplex reverse-transcription polymerase chain reaction (RT-PCR) assay. Serological analysis was performed on paired serum samples using complement fixation assays. The rate of influenza virus positivity was compared with reports of ILI obtained from the SSGP network. Results: Of 240 samples received at the laboratory, 132 (55%) were PCR positive for influenza A virus. There were nine (3.8%) picornavirus and three (1.2%) RSV PCR positives, two (0.8%) were dual influenza A/picornavirus infections. Ninety four (39.2%) were negative for all viruses tested. Results on paired sera from 89 patients showed a rising titre to influenza A in 48 of the 57 PCR positive samples (84.2%). One PCR negative patient displayed a significant rising titre to influenza A. Virological data paralleled the SSGP data but was available at least a week earlier. Conclusions: Influenza A infection was detected in the majority of patients with ILI; picornavirus infection was also shown to be an important cause of illness. PCR is a rapid and sensitive method for respiratory virus surveillance. Serology is slow, insensitive and difficult to interpret at low titres.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - purpose, 5 - purpose, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding, 20 - finding, 21 - finding"
            ]
        },
        {
            "id": "task352-71decfe81aba4a2d98b989d70f526a72",
            "input": "This study investigates and compares the virucidal performances of photocatalytic (PC) and photoelectrocatalytic (PEC) treatments in the presence and absence of halides, such as Br À and Cl À , under comparable experimental conditions. The results confirm that the PC virucidal efficiency can be enhanced in the presence of low halide concentrations (e.g., X = Br À or Cl À ) and further enhanced by applying potential bias onto the photoanode in a PEC system. The PEC treatment in the presence of 1.0 mM Br (PEC-Br) shows the highest virucidal efficiency, enabling complete inactivation of a $1000 TCID50 replication-deficient recombinant adenovirus (RDRADS) population within 31.7 s. The superior virucidal performances of PEC-X treatments can be attributed to the increased production of active oxygen species and additional viricides resulting from the PEC halide oxidation, as well as prolonged lifetime of photoholes (h + ) for direct inactivation. The findings of this work confirm that new forms of active species generated in situ via a PC or PEC process are effective for viruses.",
            "output": [
                "1 - purpose, 2 - purpose, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-63047b02427e4c17b47cbb9ed1719ad6",
            "input": "publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31, 1234-1244 15 Richter, G. et al. (1997 Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - other, 5 - other, 6 - purpose"
            ]
        },
        {
            "id": "task352-a1ce447325de436595d816955191ef1e",
            "input": "Virus replicate inside prokaryotic and eukaryotic cells. Outside cells, they exist as independent particles (i.e. virions) generally composed of a protein shell (sometimes covered with a lipid bilayer) that contains their genetic material made of RNA or DNA. Virus genome replication and transcription are catalyzed by virally encoded polymerases. Although all these enzymes show some homology and share structural features and their catalytic mechanism, they also have important differences that reflect diverse virus replication strategies.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-76a7bac51448462ab2003d6f2c18f0e2",
            "input": "The complexities of the dynamic processes and their control associated with biological and ecological systems offer many challenges for the control engineer. Over the past decades the application of dynamic modelling and control has aided understanding of their complexities. At the same time using such complex systems as test-beds for new control methods has highlighted their limitations (e.g. in relation to system identification) and has thus acted as a catalyst for methodological advance. This paper continues the theme of exploring opportunities and achievements in applying modelling and control in the bio-and ecological domains. #",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - other"
            ]
        },
        {
            "id": "task352-76e5193b5f7e4c808d0de7aff4b91a19",
            "input": "To evaluate the effects of storage conditions on total protein (TP) and globulin fractions in fresh frozen bovine plasma units prepared and stored for transfusion, TP and globulin fractions were evaluated in fresh plasma and at 1 month and 6 and 12 months after blood collection in plasma stored at −20 ∘ C. Significant differences in concentrations were found in the median concentration of total protein ( = 0.0336), between 0 months and 1 month ( = 0.0108), 0 and 6 months ( = 0.0023), and 0 and 12 months ( = 0.0027), in mean concentration (g/dL) of albumin ( = 0.0394), between 0 months and 1 month ( = 0.0131), 0 and 6 months ( = 0.0035), and 0 and 12 months ( = 0.0038), and beta-2 fraction ( = 0.0401), between 0 and 6 months ( = 0.0401) and 0 and 12 months ( = 0.0230). This study suggests that total gamma globulin concentration in bovine frozen plasma is stable for 12 months at −20 ∘ C. Total protein, ALB, and beta-2 fraction have significantly different concentrations (g/dL) when compared to prestorage. This study has shown IgG protein fraction stability in bovine fresh frozen plasma collected for transfusion; therefore, bovine fresh frozen plasma seems to be suitable for the treatment of hypogammaglobulinemia (failure of passive transfer) in calves when stored for 12 months at −20 ∘ C.",
            "output": [
                "1 - purpose, 2 - method, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding"
            ]
        },
        {
            "id": "task352-e3d1041cd7d04fa6a9deb1911e1bcb81",
            "input": "Control of norovirus outbreaks relies on enhanced hygiene measures, such as handwashing, surface cleaning, using disposable paper towels, and using separate toilets for sick and well persons. However, little is known about their effectiveness in limiting further spread of norovirus infections. We analyzed norovirus outbreaks in 7 camps at an international scouting jamboree in the Netherlands during 2004. Implementation of hygiene measures coincided with an 84.8% (95% predictive interval 81.2%-86.6%) reduction in reproduction number. This reduction was unexpectedly large but still below the reduction needed to contain a norovirus outbreak. Even more stringent control measures are required to break the chain of transmission of norovirus.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - method, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-e1f6f448585a4e70b266b30c2912bdec",
            "input": "On the basis of the results presented we assume that the glycosylation of HSV glyeoprotein gC may lead to, at least, two populations of the gtyeoprotein gC, one with terminal N-acetylgalactosamine residues of oligosaccharides 0-glycosidically tinked to the polypeptide and the other without affinity-for HPA. However, both populations of gC contain similar proportions of oligosaccharides of the high 0304-8608/83/0076/0025/$ 02.80 S. OLOFSSO~ et al. : mannose or complex types with N-glycosidic carbohydrate-peptide linkages as indicated by their affinity for Con A.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-55941030ba0047d48b5425b98d111675",
            "input": "('filoviruses') that cause severe hemorrhagic fever with human case fatality rates of up to 90%. Filovirus infection requires fusion of the host cell and virus membranes, a process that is mediated by the envelope glycoprotein (GP). GP contains two subunits, the surface subunit (GP1), which is responsible for cell attachment, and the transmembrane subunit (GP2), which catalyzes membrane fusion. The GP2 ectodomain contains two heptad repeat regions, N-terminal and C-terminal (NHR and CHR, respectively) that adopt a six-helix bundle during the fusion process. The refolding of this six-helix bundle provides the thermodynamic driving force to overcome barriers associated with membrane fusion. Here we report the crystal structure of the MARV GP2 core domain in its post-fusion (six-helix bundle) conformation at 1.9 Å resolution. The MARV GP2 core domain backbone conformation is virtually identical to that of EBOV GP2 (reported previously), and consists of a central NHR core trimeric coiled-coil packed against peripheral CHR α-helices and an intervening loop/helix-turn-helix segment. We previously reported that the stability of the MARV GP2 post-fusion structure is highly pH-dependent, with increasing stability at lower pH [Harrison, J.S.; Koellhoffer, J. K.; Chandran, K.; and Lai, J. R. Biochemistry, 2012Biochemistry, , 51, 2515Biochemistry, -2525. We hypothesized that this pH-dependent stability provides a mechanism for conformational control such that the post-fusion six helix bundle is promoted in the environments of appropriately matured endosomes. In this report, a structural rationale for this pH-dependent stability is described, and involves a high-density array of core and surface acidic side chains at the midsection of the structure, termed the 'anion stripe.' In addition, many surface-exposed salt bridges likely contribute to stabilizing the post-fusion structure at low pH. These results provide structural insights into the mechanism of MARV GP2-mediated membrane fusion.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding"
            ]
        },
        {
            "id": "task352-5dc762d992b4442d9237930a6755581c",
            "input": "Inhibition of extracellular matrix (ECM) degradation may represent a mechanism for cardiac protection against ischemia. Extracellular matrix metalloproteinase inducer (EMMPRIN) is highly expressed in response to acute myocardial infarction (AMI), and induces activation of several matrix metalloproteinases (MMPs), including gelatinases MMP-2 and MMP-9. We targeted EMMPRIN with paramagnetic/fluorescent micellar nanoparticles conjugated with the EMMPRIN binding peptide AP-9 (NAP9), or an AP-9 scrambled peptide as a negative control (NAPSC). We found that NAP9 binds to endogenous EMMPRIN in cultured HL1 myocytes and in mouse hearts subjected to ischemia/reperfusion (IR). Injection of NAP9 at the time of or one day after IR, was enough to reduce progression of myocardial cell death when compared to Control and NAPSC injected mice (infarct size in NAP9 injected mice: 32%±6.59 vs Control: 46%±9.04 or NAPSC injected mice: 48%±7.64). In the same way, cardiac parameters were recovered to almost healthy levels (LVEF NAP9 63% ± 7.24 vs Control 42% ± 4.74 or NAPSC 39% ± 6.44), whereas ECM degradation was also reduced as shown by inhibition of MMP-2 and MMP-9 activation. Cardiac magnetic resonance (CMR) scans have shown a signal enhancement in the left ventricle of NAP9 injected mice with respect to non-injected, and to mice injected with NAPSC. A positive correlation between CMR enhancement and Evans-Blue/TTC staining of infarct size was calculated (R:0.65). Taken together, these results point to EMMPRIN targeted nanoparticles as a new approach to the mitigation of ischemic/reperfusion injury.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding"
            ]
        },
        {
            "id": "task352-592d15da9a3640b89ed92b8e67875883",
            "input": "Citation: Bédubourg G, Le Strat Y (2017) Evaluation and comparison of statistical methods for early temporal detection of outbreaks: A simulation-based study. PLoS ONE 12(7): e0181227.",
            "output": [
                "1 - other, 2 - other, 3 - other"
            ]
        },
        {
            "id": "task352-8fbbb04fc62441639577234393a66749",
            "input": "Incidence was the highest each spring. The odds ratio of the case fatality among pneumococcal/lobar pneumonia patients complicated with empyema to those without was 118 (95% confidence interval 28-492). In conclusion, the populationbased incidences of pneumococcal/lobar pneumonia and empyema among children under five in Taiwan were 44.9 and 10.5 episodes per 100,000 children-year, respectively, and 4-to 5-year-old children had the highest incidences of both pneumococcal/lobar pneumonia and empyema. This population might benefit from a universal pneumococcal vaccination program which might cover about 70% of invasive pneumococcal diseases in Taiwanese children under 5 years old.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-776251a910e4466aa8aab2b970d4e300",
            "input": "The B lymphocytes of the common marmoset Callithrix jacchus can be immortalised by infection with Epstein-Barr virus (EBV) in vitro (Desgranges et al., 1976) . C. jacchus is susceptible to infection with the blood stages of several species of malaria parasite including the line designated MVF1 (Mitchell et al., 1988) from which it recovers and shows immunity to reinfection. By exploiting these two phenomena, EBV-transformed, marmoset lymphoblastoid cell lines secreting antibodies to malaria parasite antigens have been generated and cloned. We believe this to be the first time that monoclonal antibodies (MAbs) have been raised from common marmosets. Since numerous and diverse human pathogens can infect this small primate in the laboratory, these methods may prove generally applicable for the generation of MAbs whose specificities derive from immune responses to infection.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - background, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-09726461b92b4d4db9c1de9cd7fbf17d",
            "input": "Correspondence to: Prof. M. Ackermann, Institut •r Virologic, Vet.-med. Fakult~it, Universit~it Ziirich, Winterthurerstr. 266a, CH-8057 Ziirich, Switzerland. ~Present address:",
            "output": [
                "1 - other, 2 - other, 3 - other, 4 - other, 5 - other"
            ]
        },
        {
            "id": "task352-1e187985315340bd944eda571a6f2b14",
            "input": "Abbreviations: BN, Brown Norway; EHS, enterohepatic Helicobacter species; qPCR, quantitative PCR; RFLP, restriction fragment length polymorphism; w.p.i., weeks post-infection.",
            "output": [
                "1 - other, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-a3454caf2aac4d62a99b68409c8cf889",
            "input": "Coronavirus-like particles were identified by electronmicroscopy in the feces of homosexual men. The particles banded at a density of 1.21 g/ml after cesium chloride density gradient centrifugation. To determine whether the presence of this virus might be related to clinical symptoms, several patient groups were studied prospectively. In 8 of 16 (50%) homosexual males with acquired immunodeficiency syndrome (AIDS) or unexplained lymphadenopathy syndrome (LAS), coronavirus particles were found. In contrast, such particles were found in none of 18 heterosexual controls and in only 3 of 20 homosexual males without AIDS or LAS. Thus, coronavirus excretion correlated significantly (2c~<0.01) with the clinical diagnosis of AIDS or with syndromes belonging to the AIDS-related complex. In addition, such particles identified in the serum of one patient with LAS and diarrhea suggest invasion and systemic spread of the agent and underline that this virus behaves differently from\" common cold\" human coronaviruses.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-b583a7a10539440096285ad71f2f8568",
            "input": "Human bocavirus (HBoV) was recently discovered in children with respiratory distress and/or diarrhea. To our knowledge, no previous study has reported the existence of bocavirus in Saudi Arabia. Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Real-time polymerase chain reaction was used as a sensitive method to detect the HBoV. Direct gene sequencing was used to determine the genotype of the detected virus isolates. HBoV was detected in 22.5% of the examined patients. The NP1 partial gene sequence from all patients showed that the circulated strains were related to HBoV-1 genotype. Most of HBoV infected patients showed evidence of mixed coinfection with other viral pathogens. The current study clearly demonstrated that genetically conserved HBoV1 circulates in Saudi Arabia. Interestingly, most of the HBoV1 infected cases were associated with high rates of co-infections with other viruses.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding"
            ]
        },
        {
            "id": "task352-4bd524c0608e4b8591c466e1cf9655de",
            "input": "j o u r n a l h o m e p a g e : h t t p : / / w w w . j o u r n a l s. e l s e v i e r . c o m / j o u r n a l -o f -h o sp i t a l i t ya n d -t o u r i s m -m a n a g e m e n t.",
            "output": [
                "1 - other, 2 - other, 3 - other"
            ]
        },
        {
            "id": "task352-ae3aa6f4bb9440359da2c335d5c10101",
            "input": "The hydroalcoholic extract of Punica granatum (pomegranate) leaves was previously demonstrated to be anti-inflammatory in a rat model of lipopolysaccharide-(LPS-) induced acute peritonitis. Here, we investigated the anti-inflammatory effects of the ethyl acetate fraction obtained from the pomegranate leaf hydroalcoholic extract (EAFPg) on the LPS-induced acute lung injury (ALI) mouse model. Male Swiss mice received either EAFPg at different doses or dexamethasone (per os) prior to LPS intranasal instillation. Vehicle-treated mice were used as controls. Animals were culled at 4 h after LPS challenge, and the bronchoalveolar lavage fluid (BALF) and lung samples were collected for analysis. EAFPg and kaempferol effects on NO and cytokine production by LPS-stimulated RAW 264.7 macrophages were also investigated. Pretreatment with EAFPg (100-300 mg/kg) markedly reduced cell accumulation (specially neutrophils) and collagen deposition in the lungs of ALI mice. The same animals presented with reduced lung and BALF TNF-α and IL-1β expression in comparison with vehicle controls (p < 0 05). Additionally, incubation with either EAFPg or kaempferol (100 μg/ml) reduced NO production and cytokine gene expression in cultured LPS-treated RAW 264.7 macrophages. Overall, these results demonstrate that the prophylactic treatment with EAFPg attenuates acute lung inflammation. We suggest this fraction may be useful in treating ALI.",
            "output": [
                "1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-105286fbb4c0420ea9c3565da2fe2b3b",
            "input": "The results of the present survey indicated that infection of peafowls with T. gondii is widespread in Yunnan Province, which has significant public health concerns and implications for prevention and control of toxoplamosis in this province. To our knowledge, this is the first seroprevalence report of T. gondii infection in China's southwestern Yunnan Province.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding"
            ]
        },
        {
            "id": "task352-0dc32c9153444b92a4c619b588e9db2c",
            "input": "Escherichia coli O157:H7, an important food-borne pathogen, has become a major public health concern worldwide. The aim of this study was to investigate the molecular epidemiologic feature of E. coli O157:H7 strains in China. 105 E. coli O157:H7 isolates were collected from various hosts and places over 9 years. A multilocus sequence typing scheme (MLST) was applied for bacteria genotyping and polymerase chain reaction (PCR) was used for virulence factor identification. Seven new MLST sequence types (STs), namely ST836, ST837, ST838, ST839, ST840, ST841, and ST842 were identified, which grouped into two lineages. Phylogenetic analysis suggested that the most two frequent STs in China, ST837 and ST836, may be the derivatives of E. coli O157:H7 Sakai or E. coli O157:H7 EDL933. Geographical diversity and host variety of E. coli O157:H7 were observed in China. In addition, the different distribution of tccp was detected. The data presented herein provide new insights into the molecular epidemiologic feature of E. coli O157:H7, and aid in the investigation of the transmission regularity and evolutionary mechanism of E. coli O157:H7.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding"
            ]
        },
        {
            "id": "task352-4c3c55702ea941c4b4207500646dc8be",
            "input": "www.tandfonline.com",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-4165076fb6bd464a9f70709b4c0baf21",
            "input": "Specific sets of cold-repressed and cold-induced proteins in D. pulex can be related to changes in the cellular demand for amino acids or to the compensatory control of physiological processes. The increase of proteolytic enzyme concentration and the decrease of vitellogenin, actin and total protein concentration between 10°C and 20°C acclimated animals reflect the increased amino-acids demand and the reduced protein reserves in the animal's body. Conversely, the increase of actin concentration in cold-acclimated animals may contribute to a compensatory mechanism which ensures the relative constancy of muscular performance. The sheer number of peptidase genes (serine-peptidase-like: > 200, astacin-like: 36, carboxypeptidase-like: 30) in the D. pulex genome suggests large-scaled gene family expansions that might reflect specific adaptations to the lifestyle of a planktonic filter feeder in a highly variable aquatic environment.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-4479b39a2e424ad0ae36d81218804538",
            "input": "The substantial winter influenza peak in temperate climates has lead to the hypothesis that cold and/or dry air is a causal factor in influenza variability. We examined the relationship between cold and/or dry air and daily influenza and pneumonia mortality in the cold season in the New York metropolitan area from 1975-2002. We conducted a retrospective study relating daily pneumonia and influenza mortality for New York City and surroundings from 1975-2002 to daily air temperature, dew point temperature (a measure of atmospheric humidity), and daily air mass type. We identified high mortality days and periods and employed temporal smoothers and lags to account for the latency period and the time between infection and death. Unpaired t-tests were used to compare high mortality events to non-events and nonparametric bootstrapped regression analysis was used to examine the characteristics of longer mortality episodes. We found a statistically significant (p = 0.003) association between periods of low dew point temperature and above normal pneumonia and influenza mortality 17 days later. The duration (r = 20.61) and severity (r = 20.56) of high mortality episodes was inversely correlated with morning dew point temperature prior to and during the episodes. Weeks in which moist polar air masses were common (air masses characterized by low dew point temperatures) were likewise followed by above normal mortality 17 days later (p = 0.019). This research supports the contention that cold, dry air may be related to influenza mortality and suggests that warning systems could provide enough lead time to be effective in mitigating the effects.",
            "output": [
                "1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-cd61a74741ec4b139ccfbfccae5aa1bd",
            "input": "Published: xx xx xxxx opeN www.nature.com/scientificreports/",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-3c7de6dcc00a4d4b9fce38cd25b43cb3",
            "input": "Cytokines and the Brain 289 Edited by C. Phelps and E. Korneva",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-c09837c5257041bca6055bdf347d3d00",
            "input": "BJORKSTRAND, E. AND K. UVN,~S-MOBERG. Central oxytocin increases food intake and daily weight gain in rats. PHYSIOL BEHAV 59(4/5) 947-952, 1996.--The present study was performed to investigate the effects of",
            "output": [
                "1 - other, 2 - background, 3 - other, 4 - purpose"
            ]
        },
        {
            "id": "task352-f8de4cb2f98e45108a84085c7d339f9e",
            "input": "where R 0 is the biggest eigenvalue of matrix F V −1 i.e. R 0 = ρ(F V −1 ). The expression of R 0 is as follows:",
            "output": [
                "1 - method, 2 - finding"
            ]
        },
        {
            "id": "task352-13a15b0db0524d18b685e06d2c766456",
            "input": "Genetically encoded fluorescent proteins are extensively utilized for labeling and imaging proteins, organelles, cell tissues, and whole organisms. In this study, we explored the feasibility of mRFP1 and its variants for measuring intracellular temperature. A linear relationship was observed between the temperature and fluorescence intensity of mRFP1 and its variants. Temperature sensitivities of E. coli expressing mRFP1, mRFP-P63A and mRFP-P63A[(4R)-FP] were -1.27%, -1.26% and -0.77%/°C, respectively. Finally, we demonstrated the potentiality of mRFP1 and its variants as an in vivo temperature sensor.",
            "output": [
                "1 - background, 2 - background, 3 - purpose, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding"
            ]
        },
        {
            "id": "task352-8fb6f091ead54fe68f0a8825fa67c7ea",
            "input": "Human coronavirus HKU1 (HCoV-HKU1) belongs to coronavirus group II and encodes 16 nonstructural proteins (nsps) which mediate genome replication and transcription. Among these nsps, nsp9 has been shown to possess singlestranded DNA/RNA-binding properties. The gene that encodes HCoV-HKU1 nsp9 was cloned and expressed in Escherichia coli and the protein was subjected to crystallization trials. The crystals diffracted to 2.7 Å resolution and belonged to space group P2 1 2 1 2, with unit-cell parameters a = 83.5, b = 88.4, c = 31.2 Å , = = = 90 and two molecules per asymmetric unit.",
            "output": [
                "1 - background, 2 - background, 3 - method, 4 - finding, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-903d675b6422446087c78847fdfd419d",
            "input": "Please cite this paper as: Janjua et al. (2012) Transmission dynamics and risk factors for pandemic H1N1-related illness: outbreak investigation in a rural community of British Columbia, Canada. Influenza and Other Respiratory Viruses 6(3), e54-e62.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-5ccc95dc2dcb4284a8015e7d7f971f35",
            "input": "Routine detection of porcine epidemic diarrhea virus (PEDV) is currently limited to RT-PCR but this test cannot distinguish between viable and inactivated virus. We evaluated the capability of disinfectants to both inactivate PEDV and sufficiently damage viral RNA beyond RT-PCR detection. Five classes of disinfectants (phenol, quaternary ammonium compound, sodium hypochlorite, oxidizing agent, and quaternary ammonium/glutaraldehyde combination) were evaluated in vitro at varying concentrations, both in the presence and absence of swine feces, and at three different temperatures. No infectious PEDV was recovered after treatment with evaluated disinfectants. Additionally, all tested disinfectants except for 0.17% sodium hypochlorite dramatically reduced qRT-PCR values. However, no disinfectants eliminated RT-PCR detection of PEDV across all replicates; although, 0.52%, 1.03% and 2.06% solutions of sodium hypochlorite and 0.5% oxidizing agent did intermittently produce RT-PCR negatives. To simulate field conditions in a second aim, PEDV was applied to pitted aluminum coupons, which were then treated with either 2.06% sodium hypochlorite or 0.5% oxidizing agent. Post-treatment surface swabs of the coupons tested RT-PCR positive but were not infectious to cultured cells or naïve pigs. Ultimately, viable PEDV was not detected following application of each of the tested disinfectants, however in most cases RT-PCR detection of viral RNA remained. RT-PCR detection of PEDV is likely even after disinfection with many commercially available disinfectants.",
            "output": [
                "1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding, 16 - finding"
            ]
        },
        {
            "id": "task352-8d90aeb9a3fc44d185552107c8ae1956",
            "input": "RAP80, a nuclear protein with two functional ubiquitin interaction motifs (UIMs) at its N-terminus, plays a critical role in the regulation of estrogen receptor alpha and DNA damage response signaling. A yeast two-hybrid screen identified the SUMO-conjugating enzyme UBC9 as a protein interacting with RAP80. The interaction of RAP80 with UBC9 was confirmed by co-immunoprecipitation and GST pull-down analyses. The region between a.a. 122-204 was critical for the interaction of RAP80 with UBC9. In addition, we demonstrate that RAP80 is a target for SUMO-1 modification in intact cells. Expression of UBC9 enhanced RAP80 mono-sumoylation and also induced multisumoylation of RAP80. In addition to SUMO-1, RAP80 was efficiently conjugated to SUMO-3 but was only a weak substrate for SUMO-2 conjugation. These findings suggest that sumoylation plays a role in the regulation of RAP80 functions.",
            "output": [
                "1 - background, 2 - background, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-ca81522f843f4ad98c62752766e0f472",
            "input": "Citation Imperiale MJ, Casadevall A. 2015. The importance of virology at a time of great need and great jeopardy. mBio 6(2):e00236-15.",
            "output": [
                "1 - background, 2 - background, 3 - other"
            ]
        },
        {
            "id": "task352-8ea5edbaa5ed402f945cac82bae6b01f",
            "input": "code availability are available at doi Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-a78a701804f14686b995f0a340cbfd4c",
            "input": "Human bocavirus was detected in 57 (18.3%) of 312 children with acute respiratory infection (ARI) who required hospitalization in Jordan. It was also detected in 30 (21.7%) of 138 children with severe ARI, in 27 (15.5%) of 174 with mild or moderate disease, and in 41 (72%) of 57 with other pathogens.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-532855373b0f4eed8f9cdea58c961db4",
            "input": "An event-based model of superspreading A. James et al. 747",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-373129133f3b4a1cab8aacb922565582",
            "input": "Medicine shortages have been spreading in European countries. In many cases, the unavailability of medicinal products has a substantial impact on the capability of National Healthcare Systems in ensuring the continuity of care. Shortages originate from multifactorial causes. In particular, they can be due to supply-related factors (e.g., manufacturing issues, regulatory issues, logistics, distribution) and demand-related ones (e.g., fluctuating drug demand, parallel market, tendering, price and reimbursement policies). However, some extraordinary geopolitical events (e.g., Brexit) may also affect medicines' availability. The capability of European Regulatory Authorities and other stakeholders, which are involved in the pharmaceutical distribution chain and the healthcare assistance services, to define suitable problem-solving strategies has been limited for years by the fragmentation of the European regulatory framework, starting from the lack of a univocal definition of a medicine shortage. Only in 2019, the EMA and HMA joint task force released the first harmonized \"shortage\" definition in the European Economic Area (EEA) and guidance on public communication. This manuscript aims to review the current European regulatory framework on medicine shortages. To support the activities of regulators, manufacturers and other healthcare professionals, an algorithm was also proposed to be used as a harmonized procedure to determine the shortage/unavailability impact on public health and to rationalize the problem-solving strategies adopted in all different settings.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - purpose, 12 - purpose, 13 - purpose, 14 - method"
            ]
        },
        {
            "id": "task352-66f5f21da0424a6796ca43cf8b4c21a3",
            "input": "Attenuated Salmonella typhimurium (S. typhimurium) was selected as a transgenic vehicle for the development of live mucosal vaccines against transmissible gastroenteritis virus (TGEV) based on the M gene. An approximate 1.0 kb DNA fragment, encoding for glycoprotein M, was amplified by RT-PCR and cloned into eukaryotic expression vector pVAX1. The recombinant plasmid pVAX-M was transformed by electroporation into attenuated S. typhimurium SL7207, and the expression and translation of the pVAX-M delivered by recombinant S. typhimurium SL7207 (pVAX-M) was detected both in vitro and in vivo. BALB/c mice were inoculated orally with SL7207 (pVAX-M) at different dosages to evaluate safety of the vaccines. The bacterium was safe to mice at a dosage of 2 9 10 9 CFU, almost eliminated from the spleen and liver at week 4 post-immunization and eventually cleared at week 6. Mice immunized with 1 9 10 9 CFU of SL7207 (pVAX-M) elicited specific anti-TGEV local mucosal and humoral responses including levels of IgA, IgG, IL-4, and IFN-c as measured by indirect ELISA assay. Moreover, the control groups (pVAX group, PBS group) maintained at a normal level during week 4-8 post-immunization. The results indicated that attenuated S. typhimurium could be used as a delivery vector for oral immunization of TGEV M gene vaccine.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-0be7d089e52e45138578b92342b866ab",
            "input": "Saudi communities still lack awareness of available protective measures to prevent the transmission of the virus. It is necessary to explore the current information-seeking strategies and preferences for communication tools among the Saudi population to promote dissemination of accurate information. Guided by McGuire's Input-Output Persuasion Model and focusing on input variables (receiver characteristics, sources, message, channel and destination), we explored the current information-seeking strategies and preferences for different communication tools among residents of Riyadh (n ¼ 658). Preferred and sought-after information sources on MERS. Most participants in the sample were female (61.7%), and the majority (98.2%) had internet access at home. The internet was the most commonly used source of information (39.5%) and the most endorsed channel for a MERS awareness campaign. Physicians were the preferred source of information (45.6%), followed by other health care providers (31.3%). In univariate multinomial logistic regression models, males and individuals aged 27 years were more likely to seek information from the internet than from physicians. Residents of southern and western Riyadh preferred physicians as a credible source of information over the Ministry of Health. The results of this survey provide valuable information on how to reach this population and for understanding how to launch an effective MERS risk communication campaign in a Saudi population.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-9a46c23a06304aaf80900768d227e320",
            "input": "A series of etacrynic acid derivatives was synthesized and screened for their in vitro activity against Plasmodium falciparum, as well as their activity against recombinantly expressed falcipain-2 and -3. The two most active compounds of the series displayed IC 50 values of 9.0 and 18.8 μM against Plasmodia.",
            "output": [
                "1 - method, 2 - method, 3 - finding"
            ]
        },
        {
            "id": "task352-0839b41a97ed4c61abb38766c6b8b1d6",
            "input": "Virus endosomal trafficking pathways define resistance to IFITM3 PLOS Pathogens.",
            "output": [
                "1 - finding"
            ]
        },
        {
            "id": "task352-01db5413c1e049d89ccb62345c643a1e",
            "input": "Immunopathol., 3: 529-533.",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-861bd899a0e8493faba3ee5f423efcde",
            "input": "Epidemiological models of the spread of pathogens in livestock populations primarily focus on direct contact between farms based on animal movement data, and in some cases, local spatial spread based on proximity between premises. The roles of other types of indirect contact among farms is rarely accounted for. In addition, data on animal movements is seldom available in the United States. However, the spread of porcine epidemic diarrhea virus (PEDv) in U.S. swine represents one of the best documented emergences of a highly infectious pathogen in the U.S. livestock industry, providing an opportunity to parameterize models of pathogen spread via direct and indirect transmission mechanisms in swine. Using observed data on pig movements during the initial phase of the PEDv epidemic, we developed a network-based and spatially explicit epidemiological model that simulates the spread of PEDv via both indirect and direct movement-related contact in order to answer unresolved questions concerning factors facilitating between-farm transmission. By modifying the likelihood of each transmission mechanism and fitting this model to observed epidemiological dynamics, our results suggest that between-farm transmission was primarily driven by direct mechanisms related to animal movement and indirect mechanisms related to local spatial spread based on geographic proximity. However, other forms of indirect transmission among farms, including contact via contaminated vehicles and feed, were responsible for high consequence transmission events resulting in the introduction of the virus into new geographic areas. This research is among the first reports of farm-level animal movements in the U.S. swine industry and, to our knowledge, represents the first epidemiological model of commercial U.S. swine using actual data on farm-level animal movement.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - method, 8 - method, 9 - method, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding"
            ]
        },
        {
            "id": "task352-1ee949a1e96842408d6d57cb64491a95",
            "input": "ACE2 is a monocarboxypeptidase which generates Angiotensin (1-7) from Angiotensin II (1-8). Attempts to target the kidney Renin Angiotensin System using native ACE2 to treat kidney disease are hampered by its large molecular size, 100 kDa, which precludes its glomerular filtration and subsequent tubular uptake. Here, we show that both urine and kidney lysates are capable of digesting native ACE2 into shorter proteins of~60-75 kDa and then demonstrate that they are enzymatically very active. We then truncated the native ACE2 by design from the C-terminus to generate two short recombinant (r)ACE2 variants (1-605 and 1-619AA). These two truncates have a molecular size of~70 kDa, as expected from the amino acid sequence and as shown by Western blot. ACE2 enzyme activity, measured using a specific substrate, was higher than that of the native rACE2 (1-740 AA). When infused to mice with genetic ACE2 deficiency, a single i.v. injection of 1-619 resulted in detectable ACE2 activity in urine, whereas infusion of the native ACE2 did not. Moreover, ACE2 activity was recovered in harvested kidneys from ACE2-deficient mice infused with 1-619, but not in controls (23.1 ± 4.3 RFU/µg creatinine/h and 1.96 ± 0.73 RFU/µg protein/hr, respectively). In addition, the kidneys of ACE2-null mice infused with 1-619 studied ex vivo formed more Ang (1-7) from exogenous Ang II than those infused with vehicle (AUC 8555 ± 1933 vs. 3439 ± 753 ng/mL, respectively, p < 0.05) further demonstrating the functional effect of increasing kidney ACE2 activity after the infusion of our short ACE2 1-619 variant. We conclude that our novel short recombinant ACE2 variants undergo glomerular filtration, which is associated with kidney uptake of enzymatically active proteins that can enhance the formation of Ang (1-7) from Ang II. These small ACE2 variants may offer a potentially useful approach to target kidney RAS overactivity to combat kidney injury.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - finding, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding"
            ]
        },
        {
            "id": "task352-ecafabf5ead149d683cdaf235bb9c951",
            "input": "Recebido para publicação/received for publication: 09.11.03 Aceite para publicação/accepted for",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-65545b2c72c0443b81656784a053ab75",
            "input": "To optimize the preparation process of chitosan microspheres and study its loading capacity, chitosan microsphere was prepared by crosslinking with glutaraldehyde, and bovine serum albumin (BSA) was absorbed onto chitosan microsphere. Scanning electron microscope (SEM), Fourier transform infrared spectroscopy (FITR), TA instruments and zeta potentiometer analyzer were used to characterize the parameters with respect to size, thermal characters, morphology, and zeta potential of the microspheres. The loading capability and in vitro release tests were carried out. The results showed that chitosan microsphere with particle size less than 10 μm and positively charged (+25.97±0.56 mV) can be obtained under the aldehyde group to amino group ratio at 1:1. A loading capacity of BSA at 28.63±0.15 g/100 g with corresponding loading effi ciency at 72.01±1.44% was obtained for chitosan microsphere. In vitro test revealed a burst release followed by sustained-release profi le.",
            "output": [
                "1 - method, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - finding, 10 - finding, 11 - finding"
            ]
        },
        {
            "id": "task352-be5e59914ff34b90b614280f37f60e8d",
            "input": "We successfully produced second-generation cloned cats by somatic cell nuclear transfer (SCNT) using skin cells from a cloned cat. Skin cells from an odd-eyed, all-white male cat (G0 donor cat) were used to generate a cloned cat (G1 cloned cat). At 6 months of age, skin cells from the G1 cloned cat were used for SCNT to produce second-generation cloned cats. We compared the in vitro and in vivo development of SCNT embryos that were derived from the G0 donor and G1 cloned donor cat's skin fibroblasts. The nuclei from the G0 donor and G1 cloned donor cat's skin fibroblasts fused with enucleated oocytes with equal rates of fusion (60.7% vs. 58.8%, respectively) and cleavage (66.3% vs. 63.4%). The 2-4-cell SCNT embryos were then transferred into recipients. One of the five recipients of G0 donor derived NT embryos (20%) delivered one live male cloned kitten, whereas 4 of 15 recipients of the G1 cloned donor cat derived NT embryos (26%) delivered a total of seven male second-generation cloned kittens (four live kittens from one surrogate, plus two stillborn kittens, and one live kitten that died 2 d after birth from three other surrogate mothers). The four second-generation cloned kittens from the same surrogate all had a white coat color; three of the four second-generation cloned kittens had two blue eyes, and one of the second-generation cloned kittens had an odd-eye color. Despite low cloning efficiency, cloned cats can be used as donor cats to produce second-generation cloned cats. #",
            "output": [
                "1 - finding, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - method, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - other"
            ]
        },
        {
            "id": "task352-706b0ab083a74f17a02ac0b43f1c64bd",
            "input": "Human respiratory syncytial virus (HRSV) is the main cause of severe respiratory illness in young children and elderly people. We investigated the genetic characteristics of the circulating HRSV subgroup A (HRSV-A) to determine the distribution of genotype ON1, which has a 72-nucleotide duplication in attachment G gene. We obtained 456 HRSV-A positive samples between October 2008 and February 2013, which were subjected to sequence analysis. The first ON1 genotype was discovered in August 2011 and 273 samples were identified as ON1 up to February 2013. The prevalence of the ON1 genotype increased rapidly from 17.4% in 2011-2012 to 94.6% in 2012-2013. The mean evolutionary rate of G protein was calculated as 3.275 Â 10 À3 nucleotide substitution/site/year and several positively selected sites for amino acid substitutions were located in the predicted epitope region. This basic and important information may facilitate a better understanding of HRSV epidemiology and evolution.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-309e1e5e43754b3ba839694ca8efaf2a",
            "input": "Conclusions: Two E. coli W mutants were engineered that could effectively produce the bio-active flavonol glycosides hyperoside and quercitrin starting from the cheap substrates sucrose and quercetin. This novel fermentationbased glycosylation strategy will allow the economically viable production of various glycosides.",
            "output": [
                "1 - finding, 2 - finding"
            ]
        },
        {
            "id": "task352-5d4fd4c14d7542bdb9bddde81e898e3c",
            "input": "Decoding disease mechanisms for addressing unmet clinical need demands the rapid assimilation of the exponentially growing biomedical knowledge. These are either inherently unstructured and non-conducive to current computing paradigms or siloed into structured databases requiring specialized bioinformatics. Despite the recent renaissance in unsupervised neural networks for deciphering unstructured natural languages and the availability of numerous bioinformatics resources, a holistic platform for real-time synthesis of the scientific literature and seamless triangulation with deep omic insights and real-world evidence has not been advanced. Here, we introduce the nferX platform that makes the highly unstructured biomedical knowledge computable and supports the seamless visual triangulation with statistical inference from diverse structured databases. The nferX platform will accelerate and amplify the research potential of subject-matter experts as well as non-experts across the life science ecosystem.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - finding, 6 - finding"
            ]
        },
        {
            "id": "task352-c031ce1a184c430da5d4f415bcb3ed67",
            "input": "This report of a randomized, double-masked, placebo-controlled clinical study demonstrates the effectiveness of zinc acetate lozenges on common cold symptoms in allergy-tested subjects. Subjects in the zinc and placebo groups were evenly matched with respect to sex, race/ethuicity, allergy test status, and age. Overall symptom duration waz significantly less in the zinc group than in the placebo group (mean, 3.8 days vs 6.1 days). The mean severity rating for all symptoms was lower in the zinc group than in the placebo group; this difference, however, was not statistically significant. Allergypositive subjects who used zinc had a statistically significant shorter duration of nasal symptoms than allergy-negative subjects (3.5 days vs 7.6 days). In conclusion, we propose that zinc acetate lozenges may significantly shorten the duration of common cold symptoms and relieve symptoms associated with allergies.",
            "output": [
                "1 - purpose, 2 - purpose, 3 - method, 4 - method, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-584f8de6541d414b941fffa36bbdc234",
            "input": "Marine organisms are potentially prolific sources of highly bioactive secondary metabolites that might represent useful leads in the development of new pharmaceutical agents. Algae can be classified into two main groups; first one is the microalgae, which includes blue green algae, dinoflagellates, bacillariophyta (diatoms). . . etc., and second one is macroalgae (seaweeds) which includes green, brown and red algae. The microalgae phyla have been recognized to provide chemical and pharmacological novelty and diversity. Moreover, microalgae are considered as the actual producers of some highly bioactive compounds found in marine resources. Red algae are considered as the most important source of many biologically active metabolites in comparison to other algal classes. Seaweeds are used for great number of application by man. The principal use of seaweeds as a source of human food and as a source of gums (phycocollides). Phycocolloides like agar agar, alginic acid and carrageenan are primarily constituents of brown and red algal cell walls and are widely used in industry.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - background, 7 - background, 8 - background, 9 - background, 10 - background, 11 - finding"
            ]
        },
        {
            "id": "task352-dcbcb7093396496896b71ebfb11aa629",
            "input": "Results: Plasmids differed in core-expression capacity: mouse fibroblasts transfected with pCMVcore, pCMVcoreIRES and pCMVcoreKozak expressed 0.22 ± 0.18, 0.83 ± 0.5, and 13 ± 5 ng core per cell, respectively. Single immunization with highly expressing pCMVcoreKozak induced specific IFN- and IL-2, and weak antibody response. Single immunization with plasmids directing low levels of core expression induced similar levels of cytokines, strong T-cell proliferation",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding"
            ]
        },
        {
            "id": "task352-1305f35a5d4c44cd98923f638e4d75f8",
            "input": "Letter pubs.acs.org/acsmedchemlett",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-55a212a6a192487bbdbb23372b2c38e4",
            "input": "A pilot epidemiological inquiry was undertaken in France in a group of 205 nucleus and multiplier pig farms. The aim was to find out a method for a quantitative evaluation of the health level in farms selling young breeders. An exhaustive protocol was prepared for data collection. The sources of information were clinical inspections on the farms, meat inspection data at slaughter and laboratory investigations. Data processing issued in the selection of a profile made of 14 prevailing health indicators. These were then associated so as to set up a health index with an overall score. In a second phase, the relevance of the method with respect to disease transmission was assessed. The principle was a contact challenge within totally controlled facilities between SPF pigs hysterectomy-derived and gilts taken from farms with different health scores as previously checked. The contact lasted for 28 days. Eleven farms were chosen and in every one of them 7 gilts were sampled and 10 SPF pigs were assigned to each of these farms. All the pigs were submitted to a detailed observation. At the end of it the pigs were euthanized at the laboratory and checked to find out any lesions and infectious agents. A wide range of symptoms appeared among the SPF pigs. Mortality rate was 14.6%. Pneumonia affected 23.7% of them. A relationship was found between the germ transfer and the severity of the troubles. The degree of illness in SPF pigs was clearly related to the score obtained previously in the corresponding farms. Consequently, the method was considered as valid with respect to health evaluation.",
            "output": [
                "1 - background, 2 - purpose, 3 - method, 4 - method, 5 - method, 6 - method, 7 - method, 8 - method, 9 - method, 10 - method, 11 - method, 12 - method, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding, 18 - finding, 19 - finding"
            ]
        },
        {
            "id": "task352-85f83f22502a45bc9eb8f098e20bc467",
            "input": "European populations of free-living wildcats have been shown to be exposed to cat viruses. Luxembourg has a high degree of habitat fragmentation, and hybridisation rates between domestic cats and wildcats are high. We therefore assessed the seroprevalence of six viruses in 34 serum samples collected between 2001 and 2016 from wildcats in Luxembourg. The values for feline leukemia virus (FeLV; 52.9%) and feline coronavirus (FCoV; 47.1%) were amongst the highest reported for wildcats. We found evidence for the cumulative likelihood of exposure to FCoV affecting its seroprevalence. Routine monitoring of viral agents in this strictly protected species should be considered.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - finding, 6 - finding, 7 - finding"
            ]
        },
        {
            "id": "task352-8d43804e6fe544ebb41088d312efcfd7",
            "input": "Development of an effective vaccine for severe acute respiratory syndrome (SARS) remains to be a priority to prevent possible re-emergence of SARS coronavirus (SARS-CoV). We previously demonstrated that the receptor-binding domain (RBD) of SARS-CoV S protein is a major target of neutralizing antibodies. This suggests that the RBD may serve as an ideal vaccine candidate. Recombinant adeno-associated virus (rAAV) has been proven to be an effective system for gene delivery and vaccine development. In this study, a novel vaccine against SARS-CoV was developed based on the rAAV delivery system. The gene encoding RBD was cloned into a pAAV-IRES-hrGFP plasmid. The immunogenicity induced by the resulting recombinant RBD-rAAV was evaluated in BALB/c mice. The results demonstrated that (1) a single dose of RBD-rAAV vaccination could induce sufficient neutralizing antibody against SARS-CoV infection; (2) two more repeated doses of the vaccination boosted the neutralizing antibody to about 5 times of the level achieved by a single dose of the immunization and (3) the level of the antibody continued to increase for the entire duration of the experiment of 5.5 months. These results suggested that RBD-rAAV is a promising SARS candidate vaccine.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - method, 6 - method, 7 - method, 8 - finding, 9 - finding"
            ]
        },
        {
            "id": "task352-63525ba530e440aabd6a1c61bf549340",
            "input": "Conclusion: VIRsiRNApred is the first algorithm for predicting inhibition efficacy of viral siRNAs which is developed using experimentally verified viral siRNAs. We hope this algorithm would be useful in predicting highly potent viral siRNA to aid siRNA based antiviral therapeutics development. The web server is freely available at crdd.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding"
            ]
        },
        {
            "id": "task352-7a51d65abde044d5a4b3c25d8e263ffc",
            "input": "Background: Longtime follow-up studies on patients with pharyngotonsillitis are rare. We aimed to describe the patterns of new visits for a sore throat, complications and tonsillectomy during 2 years in a cohort of patients with pharyngotonsillitis and non-infected controls. Methods: A retrospective chart review was performed on a cohort of patients with acute sore throat (n = 207), and non-infected controls (n = 108). New visits, complications and tonsillectomy within 2 years was recorded and analyzed in relation to microbiological findings at inclusion. Results: Patients with Group A streptococci (GAS) (12/66) reconsulted more often within 30 days than patients with no GAS (9/141) (p = 0.009) and patients with F. necrophorum (2/29). After 2 years, we observed no significant differences in reconsultations with regard to aetiology at inclusion. A single complication was recorded and 5 patients were planned for tonsillectomy. Conclusions: Group A streptococci were the sole aetiological agent associated with recurrent sore throat while F. necrophorum did not distinguish itself as a major cause of either recurrent infection or complications in this cohort. More studies, preferably with the focus on adolescents, are needed before F. necrophorum can be considered an important cause of pharyngotonsillitis.",
            "output": [
                "1 - background, 2 - purpose, 3 - purpose, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-f7241411c9a34ce4bf64d3b22c5051ed",
            "input": "M. Heiliö • M. Jabłońska-Sabuka ( )",
            "output": [
                "1 - other"
            ]
        },
        {
            "id": "task352-37c4ebdc14aa43a38d19d273bc976580",
            "input": "The present study aimed to investigate the frequency of pathogenic Leptospira spp. in Brazilian bats and to determine possible risk factors associated to it. Ninety two bats of 12 species were evaluated. Whole genomic DNA from kidneys was extracted and real-time PCR specific to pathogenic Leptospira spp. was applied. Association between the frequency of specimens positive for Leptospira spp. and sex, age, bat species or family, season of collection, geographic localization and feeding habits was evaluated. The results showed that 39.13% of analyzed bats were found positive for Leptospira spp. Nine bat species had at least one positive result. There was no association among the evaluated variables and frequency of pathogenic Leptospira spp. Although the limitations due to lack of Leptospira spp. isolation, leptospiral carriage was demonstrated in bats of different species from southern Brazil, which reinforces the need for surveillance of infectious agents in wild animals.",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding"
            ]
        },
        {
            "id": "task352-66984b93168545ee8031935962a2c2af",
            "input": "Although vaccines and antibiotics could kill or inhibit microbes, many infectious diseases remain difficult to treat because of acquired resistance and adverse side effects. Nano-carriers-based technology has made significant progress for a long time and is introducing a new paradigm in drug delivery. However, it still has some challenges like lack of specificity toward targeting the infectious site. Nanocarriers utilized targeting ligands on their surface called 'active target' provide the promising way to solve the problems like accelerating drug delivery to infectious areas and preventing toxicity or sideeffects. In this mini review, we demonstrate the recent studies using the active targeted strategy to kill or inhibit microbes. The four common nano-carriers (e.g. liposomes, nanoparticles, dendrimers and carbon nanotubes) delivering encapsulated drugs are introduced.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - background, 5 - background, 6 - purpose, 7 - finding"
            ]
        },
        {
            "id": "task352-983872b65b924362828665da273c1b53",
            "input": "Background: Hand hygiene is crucial for safe healthcare. Although the use of alcohol hand rubs is encouraged in clinics, there are few studies that focus on the proper use of alcohol hand rubs among nursing students. Objectives: The aim of this study is to evaluate the effectiveness of alcohol-based hand rub application and proper hand washing techniques which influence nursing students' hand hygiene compliance to make recommendations for future practice of hand hygiene training. Design: This cross-sectional study was carried out from May 3/June 3 2016 with the participation of 257 nursing students. Their hand hygiene techniques were analyzed using a UV lamp and an alcohol-based mix marked with fluorescence. Results: Of the participants, 77.0% were first-year students and 55.3% were males. The percentage of skin surface covered by alcohol-based hand rub was 82.0% on both hands. The lowest percentages of skin area covered by fluorescent-labelled hand rub were identified in the metacarpal area near the wrist and thumbs. While there was a difference between points for using proper hand-rub technique on the dorsal and palmar surfaces of the hands (p < 0.01), no difference was determined between the right and left hands (p > 0.05). It was found that the largest fluorescent remains were on fingers after hand-washing, and there was a difference in terms of hand-washing points between right-left hands and dorsal-palmar surfaces (p < 0.01). Conclusions: There is a need to improve nursing students' compliance with hand hygiene. It is suggested that the use of hand-rub among students should be popularized, and new techniques that prevent the frequently omitted areas of the hands should be integrated into the curriculum.",
            "output": [
                "1 - background, 2 - background, 3 - background, 4 - purpose, 5 - method, 6 - method, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding, 15 - finding, 16 - finding, 17 - finding"
            ]
        },
        {
            "id": "task352-588b46ca161349699aaa33928a3f845b",
            "input": "To assess the risk of infectious bacterial aerosols leaking to the environment, the filtration efficiency of a biosafety level 3 (BSL-3) laboratory high-efficiency particulate (HEPA) filter was investigated using the aerosolized bacteria Serratia marcescens. The aerosol size was measured using an Andersen sampler. Eight first stage HEPA filters (numbered 1-8) were distributed in contaminated labs and exhausts from each of the first stage HEPA filters were aggregated and filtered through one second stage HEPA filter before being released to the environment. In total, 8 first-stage and 1 second-stage HEPA filters from the BSL-3 air purification system were analyzed. No S. marcescens was detected in first stage filters 1, 2, 4, 5, 7 and 8 and the second stage HEPA filter. The filtration efficiencies against aerosolized S. marcescens were >99.9999%. First stage filter numbers 3 and 6 had filtration efficiencies of 99.9825% and 99.9906%, respectively. When filter number 3 was replaced by a new filter and the bracket for filter number 6 was sealed, no aerosolized S. marcescens was detected in the filtered air. Our work suggests that the BSL-3 laboratory HEPA filter air purification system is effective against bacterial aerosols, with little to no bacterial leakage into the environment.",
            "output": [
                "1 - purpose, 2 - method, 3 - method, 4 - method, 5 - method, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding, 11 - finding, 12 - finding, 13 - finding, 14 - finding"
            ]
        },
        {
            "id": "task352-c3adf5b1fdb442de89962f500c195da3",
            "input": "This is the eighth article in our series on the history of pediatric specialties. Dr. Shulman describes the history of infectious diseases over the centuries. Many of these major killers of children were conquered by research that led to understanding the causes of these diseases and eventually to establishing means of prevention and treatment. Dr. Shulman also describes the organizations and publications that have furthered the development of treatment, research and education in this specialty. The future of this field includes the challenges of understanding and treating infectious diseases in immunocompromised children and in developing countries where infectious disease is still a major killer.",
            "output": [
                "1 - background, 2 - purpose, 3 - background, 4 - purpose, 5 - purpose, 6 - finding"
            ]
        },
        {
            "id": "task352-aa70203216044589b5e71f0522ea03a2",
            "input": "The limit of blanks (LoBs) of the RT-dPCR assays were ~1.6, ~1.6 and ~0.8 copies/reaction for ORF 1ab, N and E genes, respectively. The limit of detection (LoD) was 2 copies/reaction. For the 103 fever suspected patients, the sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For close contacts, the suspect rate was greatly decreased from 21% down to 1%. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 90%, 100% and 93 %, respectively. In addition, quantification of the viral load for convalescents by RT-dPCR showed that a longer observation period was needed in the hospital for elderly patients.",
            "output": [
                "1 - finding, 2 - finding, 3 - finding, 4 - finding, 5 - finding, 6 - finding, 7 - finding, 8 - finding, 9 - finding, 10 - finding"
            ]
        }
    ],
    "Instance License": [
        "Unknown"
    ]
}