niryuu/sni-each-converted huggingface dataset:
Paragraph: Acute febrile illness is a common cause of hospital admission, and its associated infectious causes contribute to substantial morbidity and death among children worldwide, especially in low-and middle-income countries. Declining transmission of malaria in many regions, combined with the increasing use of rapid diagnostic tests for malaria, has led to the increasing recognition of leptospirosis, rickettsioses, respiratory viruses, and arboviruses as etiologic agents of fevers. However, clinical discrimination between these etiologies can be difficult. Overtreatment with antimalarial drugs is common, even in the setting of a negative test result, as is overtreatment with empiric antibacterial drugs. Viral etiologies remain underrecognized and poorly investigated. Moresensitive diagnostics have led to additional dilemmas in discriminating whether a positive test result reflects a causative pathogen. Here, we review and summarize the current epidemiology and focus particularly on children and the challenges for future research. 
 Title: Challenges in the Etiology and Diagnosis of Acute Febrile Illness in Children in Low-and Middle- Income Countries
Output: True
Paragraph: A growing body of evidence suggests the non-protein coding human genome is of vital importance for human cell function. Besides small RNAs, the diverse class of long non-coding RNAs (lncRNAs) recently came into focus. however, their relevance for infection, a major evolutionary driving force, remains elusive. Using two commercially available microarray systems, namely Ncode™ and sureprint™ G3, we identified differential expression of 42 ncRNAs during influenza A virus (IAV) infection in human lung epithelial cells. This included several classes of lncRNAs, including large intergenic ncRNAs (lincRNAs). As analyzed by qRT-PcR, expression of one lincRNA, which we termed virus inducible lincRNA (VIN), is induced by several IAV strains (h1N1, h3N2, h7N7) as well as vesicular stomatitis virus. however, we did not observe an induction of VIN by influenza B virus, treatment with RNA mimics, or IFNβ. Thus, VIN expression seems to be a specific response to certain viral infections. RNA fractionation and RNA-FIsh experiments revealed that VIN is localized to the host cell nucleus. Most importantly, we show that abolition of VIN by RNA interference restricts IAV replication and viral protein synthesis, highlighting the relevance of this lincRNA for productive IAV infection. Our observations suggest that viral pathogens interfere with the non-coding portion of the human genome, thereby guaranteeing their successful propagation, and that the expression of VIN correlates with their virulence. consequently, our study provides a novel approach for understanding virus pathogenesis in greater detail, which will enable future design of new antiviral strategies targeting the host's non-protein coding genome. 
 Title: Evidence for a crucial role of a host non-coding RNA in influenza A virus replication
Output: True
Paragraph: doi: bioRxiv preprint molecular biology. Our high-resolution data have enabled a precise study of transcription and translation in both pathogenic and attenuated forms of IBV, and expand our understanding of gammacoronaviral gene expression. We demonstrate that gene expression shows considerable intraspecies variation, with single nucleotide polymorphisms associated with altered production of sgmRNA transcripts, and our RiboSeq data sets enabled us to uncover novel ribosomally occupied ORFs in both strains. We also identify numerous cellular genes and gene networks that are differentially expressed during virus infection, giving insights into the host cell reponse to IBV infection. 3 47 48 49 50 51 52 53 54 55 56 author/funder. All rights reserved. No reuse allowed without permission. 
 Title: Comparative analysis of gene expression in virulent and attenuated strains of infectious bronchitis virus at sub-codon resolution
Output: False
Paragraph: binds to angiotensin-converting enzyme 2 which serves as a cellular receptor. Epidemiological analysis of a hospital outbreak in Hong Kong revealed that blood group O was associated with a low risk of infection. In this study, we used a cellular model of adhesion to investigate whether natural antibodies of the ABO system could block the S protein and angiotensin-converting enzyme 2 interaction. To this aim, a C-terminally EGFP-tagged S protein was expressed in chinese hamster ovary cells cotransfected with an α1,2fucosyltransferase and an A-transferase in order to coexpress the S glycoprotein ectodomain and the A antigen at the cell surface. We observed that the S protein/angiotensinconverting enzyme 2-dependent adhesion of these cells to an angiotensin-converting enzyme 2 expressing cell line was specifically inhibited by either a monoclonal or human natural anti-A antibodies, indicating that these antibodies may block the interaction between the virus and its receptor, thereby providing protection. In order to more fully appreciate the potential effect of the ABO polymorphism on the epidemiology of SARS, we built a mathematical model of the virus transmission dynamics that takes into account the protective effect of ABO natural antibodies. The model indicated that the ABO polymorphism could contribute to substantially reduce the virus transmission, affecting both the number of infected individuals and the kinetics of the epidemic. 1085 P Guillon et al. 
 Title: Inhibition of the interaction between the SARS-CoV Spike protein and its cellular receptor by anti-histo-blood group antibodies
Output: True
Paragraph: Viroporins are small, α-helical, hydrophobic virus encoded proteins, engineered to form homo-oligomeric hydrophilic pores in the host membrane. Viroporins participate in multiple steps of the viral life cycle, from entry to budding. As any other membrane protein, viroporins have to find the way to bury their hydrophobic regions into the lipid bilayer. Once within the membrane, the hydrophobic helices of viroporins interact with each other to form higher ordered structures required to correctly perform their porating activities. This two-step process resembles the two-stage model proposed for membrane protein folding by Engelman and Poppot. In this review we use the membrane protein folding model as a leading thread to analyze the mechanism and forces behind the membrane insertion and folding of viroporins. We start by describing the transmembrane segment architecture of viroporins, including the number and sequence characteristics of their membrane-spanning domains. Next, we connect the differences found among viroporin families to their viral genome organization, and finalize focusing on the pathways used by viroporins in their way to the membrane and on the transmembrane helix-helix interactions required to achieve proper folding and assembly. 
 Title: Viroporins, Examples of the Two-Stage Membrane Protein Folding Model
Output: True
Paragraph: Cell-based therapies with embryonic or adult stem cells, including induced pluripotent stem cells, have emerged as potential novel approaches for several devastating and otherwise incurable lung diseases including emphysema, pulmonary fibrosis, pulmonary hypertension, and the acute respiratory distress syndrome. Although initial studies suggested engraftment of exogenously administered stem cells in lung, this is now generally felt to be a rare occurrence of uncertain physiologic significance. However, more recent studies have demonstrated paracrine effects of administered cells, including stimulation of angiogenesis and modulation of local inflammatory and immune responses in mouse lung disease models. Based on these studies and on safety and initial efficacy data from trials of adult stem cells in other diseases, groundbreaking clinical trials of cell-based therapy have been initiated for pulmonary hypertension and for chronic obstructive pulmonary disease. In parallel, the identity and role of endogenous lung progenitor cells in development and in repair from injury and potential contribution as lung cancer stem cells continue to be elucidated. Most recently, novel bioengineering approaches have been applied to develop functional lung tissue ex vivo. Advances in each of these areas will be described in this review with particular reference to animal models. 
 Title: Stem Cells and Cell Therapy Approaches in Lung Biology and Diseases NIH Public Access
Output: False
Paragraph: The nonstructural protein 10 (nsp10) of porcine reproductive and respiratory syndrome virus (PRRSV) encodes for helicase which plays a vital role in viral replication. In the present study, a truncated form of nsp10, termed nsp10a, was found in PRRSV-infected cells and the production of nsp10a was strain-specific. Mass spectrometric analysis and deletion mutagenesis indicated that nsp10a may be short of about 70 amino acids in the N terminus of nsp10. Further studies by rescuing recombinant viruses showed that the Glu-69 in nsp10 was the key amino acid for nsp10a production. Finally, we demonstrated that nsp10a exerted little influence on the growth kinetics of PRRSV in vitro. 
 Title: ScienceDirect protein 10 of porcine reproductive and respiratory syndrome virus in infected cells
Output: True
Paragraph: Scorpions are well known for their dangerous stings that can result in severe consequences for human beings, including death. Neurotoxins present in their venoms are responsible for their toxicity. Due to their medical relevance, toxins have been the driving force in the scorpion natural compounds research field. On the other hand, for thousands of years, scorpions and their venoms have been applied in traditional medicine, mainly in Asia and Africa. With the remarkable growth in the number of characterized scorpion venom components, several drug candidates have been found with the potential to tackle many of the emerging global medical threats. Scorpions have become a valuable source of biologically active molecules, from novel antibiotics to potential anticancer therapeutics. Other venom components have drawn attention as useful scaffolds for the development of drugs. This review summarizes the most promising candidates for drug development that have been isolated from scorpion venoms. 
 Title: Scorpion venom components as potential candidates for drug development
Output: False
Paragraph: Since emerging in 2012, Middle East Respiratory Syndrome Coronavirus (MERS-CoV) has been a global public health threat with a high fatality rate and worldwide distribution. There are no approved vaccines or therapies for MERS until now. Passive immunotherapy with neutralizing monoclonal antibodies (mAbs) is an effective prophylactic and therapeutic reagent against emerging viruses. In this article, we review current advances in neutralizing mAbs against MERS-CoV. The receptor-binding domain (RBD) in the spike protein of MERS-CoV is a major target, and mouse, camel, or human-derived neutralizing mAbs targeting RBD have been developed. A major problem with neutralizing mAb therapy is mutant escape under selective pressure, which can be solved by combination of neutralizing mAbs targeting different epitopes. Neutralizing mAbs are currently under preclinical evaluation, and they are promising candidate therapeutic agents against MERS-CoV infection. 
 Title: viruses Neutralizing Monoclonal Antibodies as Promising Therapeutics against Middle East Respiratory Syndrome Coronavirus Infection
Output: True
Paragraph: Background Public health measures to prevent, detect, and respond to events are essential to control public health risks, including infectious disease outbreaks, as highlighted in the International Health Regulations (IHR). In light of the outbreak of 2019 novel coronavirus disease (COVID-19), we aimed to review existing health security capacities against public health risks and events. We used 18 indicators from the IHR State Party Annual Reporting (SPAR) tool and associated data from national SPAR reports to develop five indices: (1) prevent, (2) detect, (3) respond, (4) enabling function, and (5) operational readiness. We used SPAR 2018 data for all of the indicators and categorised countries into five levels across the indices, in which level 1 indicated the lowest level of national capacity and level 5 the highest. We also analysed data at the regional level (using the six geographical WHO regions). Findings Of 182 countries, 52 (28%) had prevent capacities at levels 1 or 2, and 60 (33%) had response capacities at levels 1 or 2. 81 (45%) countries had prevent capacities and 78 (43%) had response capacities at levels 4 or 5, indicating that these countries were operationally ready. Interpretation Countries vary widely in terms of their capacity to prevent, detect, and respond to outbreaks. Half of all countries analysed have strong operational readiness capacities in place, which suggests that an effective response to potential health emergencies could be enabled, including to COVID-19. Findings from local risk assessments are needed to fully understand national readiness capacities in relation to COVID-19. Capacity building and collaboration between countries are needed to strengthen global readiness for outbreak control. 
 Title: Health security capacities in the context of COVID-19 outbreak: an analysis of International Health Regulations annual report data from 182 countries
Output: True
Paragraph: Background: The HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has thus far not been systematically manipulated. The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, thus resulting in replication-impaired virus mutants. We present the first attempt to increase and decrease the A-count in a relatively small polymerase (pol) gene segment of HIV-1 RNA. To minimize the mutational impact, a new mutational approach was developed that is inspired by natural sequence variation as present in HIV-1 isolates. This phylogeny-instructed mutagenesis allowed us to create replication-competent HIV-1 mutants with a significantly increased or decreased local A-count. The local A-count of the wild-type (wt) virus (40.2%) was further increased to 46.9% or reduced to 31.7 and 26.3%. These HIV-1 variants replicate efficiently in vitro, despite the fact that the pol changes cause a quite profound move in HIV-SIV sequence space. Extrapolating these results to the complete 9 kb RNA genome, we may cautiously suggest that the A-rich signature does not have to be maintained. This survey also provided clues that silent codon changes, in particular from G-to-A, determine the subtype-specific sequence signatures. 
 Title: HIV-1 tolerates changes in A-count in a small segment of the pol gene
Output: False
Paragraph: As a city famous for tourism, the public healthcare system of Macau SAR has been under great pressure during the outbreak of the Coronavirus Disease 2019 . In this study, we report clinical and microbiological features of ten COVID-19 patients enrolled in the Centro Hospitalar Conde de São Januário (CHCSJ) between January 21 to February 16, 2020. Clinical samples from all patients including nasopharyngeal swab (NPS)/sputum, urine, and feces were collected for serial virus RNA testing by standard qRT-PCR assay. In total, seven were imported cases and three were local cases. The median duration from Macau arrival to admission in imported cases was 3 days. Four patients required oxygen therapy but none of them needed machinal ventilation. No fatal cases were noted. The most common symptoms were fever (80%) and diarrhea (80%). In the "Severe" group, there was significantly more elderly patients (p=0.045), higher lactate dehydrogenase levels (p=0.002), and elevated C-Reactive protein levels compared to the "Mild to Moderate" group (p<0.001). There were positive SARS-CoV-2 RNA signals in all patients' NPS and stool specimens but negative in all urine specimens. Based on our data on SARS-CoV-2 RNA shedding in stool and the possibility of a lag in viral detection in NPS specimens, the assessment of both fecal and respiratory specimen is recommended to enhance diagnostic sensitivity, and also to aid discharge decision before the role of viral RNA shedding in stool is clarified. 
 Title: Evaluation of SARS-CoV-2 RNA shedding in clinical specimens and clinical characteristics of 10 patients with COVID-19 in Macau
Output: False
Paragraph: Isopeptide bond-tethered triple-stranded coiled coils of HIV-1 gp41 N-terminal heptad repeat (NHR) peptides have been designed with de novo auxiliaries to guide site-directed trimerized cross-linking. The presence of isopeptide bridges in the rationally designed trimerization motifs provides extraordinary stability to withstand thermal and chemical denaturation. As a result, these ultra-stable and well-folded trimeric coiled coils direct and yield proteolysis-resistant and remarkably potent N-peptide chimeric trimers with HIV-1 fusion inhibitory activities in the low nanomolar range, much more effective than the corresponding unstructured N-peptide monomers and reaching the potency of clinically used T20 peptide (enfuvirtide). Thus, these isopeptide bond-crosslinked de novo coiled coils may also be used as attractive scaffolds for isolating NHR-trimers in other class I enveloped viruses for therapeutic intervention. Furthermore, this isopeptide bridge-tethering strategy could be extendable to the construction of ultra-stable proteins interfering with certain biological processes. 
 Title: De novo design of isopeptide bond-tethered triple- stranded coiled coils with exceptional resistance to unfolding and proteolysis: implication for developing antiviral therapeutics †
Output: False
Paragraph: Background Acute lower respiratory infection (ALRI) remains a major cause of childhood hospitalization and mortality in young children and the causal attribution of respiratory viruses in the aetiology of ALRI is unclear. We aimed to quantify the absolute effects of these viral exposures. 
 Title: VIEWPOINTS PAPERS journal of health global Aetiological role of common respiratory viruses in acute lower respiratory infections in children under five years: A systematic review and meta-analysis
Output: False
Paragraph: Infection prevention remains a major challenge in emergency care. Acutely ill and injured patients seeking evaluation and treatment in the emergency department (ED) not only have the potential to spread communicable infectious diseases to healthcare personnel and other patients, but are vulnerable to acquiring new infections associated with the care they receive. This article will evaluate these risks and review the existing literature for infection prevention practices in the ED, ranging from hand hygiene, standard and transmission-based precautions, healthcare personnel vaccination, and environmental controls to strategies for preventing healthcare-associated infections. We will conclude by examining what can be done to optimize infection prevention in the ED and identify gaps in knowledge where further research is needed. Successful implementation of evidence-based practices coupled with innovation of novel approaches and technologies tailored specifically to the complex and dynamic environment of the ED are the keys to raising the standard for infection prevention and patient safety in emergency care. 
 Title: Infection Prevention in the Emergency Department
Output: False
Paragraph: Middle East respiratory syndrome (MERS) is an emerging respiratory disease caused by the MERS coronavirus (MERS-CoV). MERS has been endemic to Saudi Arabia since 2012. The reservoir of MERS-CoV is the dromedary camel, suggesting that MERS is primarily a zoonotic disease. MERS-CoV is common in dromedaries throughout the Middle East, North Africa, and East Africa as evidenced by neutralizing antibodies against MERS-CoV; however, human cases have remained limited to the Middle East. To better understand the cause of this difference, the virological properties of African camel MERS-CoV were analyzed based on the spike (S) protein in Ethiopia. Nasal swabs were collected from 258 young dromedaries (≤ 2 years old) in the Afar region of Ethiopia, of which 39 were positive for MERS-CoV, as confirmed by genetic tests. All positive tests were exclusive to the Amibara woreda region. Using next-generation sequencing, two full-length genomes of Amibara isolates were successfully decoded; both isolates belonged to the C2 clade based on phylogenetic analysis of full-length and S protein sequences. Recombinant EMC isolates of MERS-CoV, in which the S protein is replaced with those of Amibara isolates, were then generated to test the roles of these proteins in viral properties. Amibara S recombinants replicated more slowly in cultured cells than in EMC S recombinants. In neutralizing assays, Amibara S recombinants were neutralized by lower concentrations of sera from both Ethiopian dromedaries and EMC isolate (wild-type)immunized mouse sera, relative to the EMC S recombinants, indicating that viruses coated in the Amibara S protein were easier to neutralize than the EMC S protein. Neutralization experiments performed using S1/S2 chimeric recombinants of the EMC and Amibara S proteins showed that the neutralization profile was dependent on the S1 region of the S protein. These results suggest that the slower viral replication and the ease of neutralization seen in the Ethiopian MERS-CoV are due to strain-specific differences in the S protein and may account for the absence of human MERS-CoV cases in Ethiopia. 
 Title: Middle East Respiratory Syndrome Coronavirus in Dromedaries in Ethiopia Is Antigenically Different From the Middle East Isolate EMC
Output: True
Paragraph: Objective. To implement a learner-led, discussion-based course aimed at exposing second-year pharmacy learners to the study of emerging infectious diseases from a global health perspective and to assess the role and importance of pharmacists in the management of disease outbreaks. Design. Learners examined literature pertinent to an emerging infectious disease in a 3-credit, discussionbased course and participated in peer discussion led by a designated learner. Instructional materials included journal articles, audio-visual presentations, documentaries, book chapters, movies, newspaper/ magazine articles, and other materials. Learning outcomes were measured based on the ability of learners to perform critical thinking and analysis, communicate with their peers, and participate in class discussions. Assessment. The course was offered to 2 consecutive cohorts consisting of 14 and 16 learners, respectively. Overall, every learner in the first cohort achieved a final grade of A for the course. In the second cohort, the overall grade distribution consisted of grades of A, B, and C for the course. Learner evaluations indicated that the active-learning, discussion-based environment significantly enhanced interest in the topic and overall performance in the course. Conclusion. The elective course on emerging infectious diseases provided in-depth exposure to disease topics normally not encountered in the pharmacy curriculum. Learners found the material and format valuable, and the course enhanced their appreciation of infectious diseases, research methodology, critical thinking and analysis, and their roles as pharmacists. 
 Title: TEACHERS' TOPICS A Learner-led, Discussion-based Elective on Emerging Infectious Disease
Output: False
Paragraph: Nature is the most abundant source for novel drug discovery. Lycorine is a natural alkaloid with immense therapeutic potential. Lycorine is active in a very low concentration and with high specificity against a number of cancers both in vivo and in vitro and against various drug-resistant cancer cells. This review summarized the therapeutic effect and the anticancer mechanisms of lycorine. At the same time, we have discussed the pharmacology and comparative structure-activity relationship for the anticancer activity of this compound. The researches outlined in this paper serve as a foundation to explain lycorine as an important lead compound for new generation anticancer drug design and provide the principle for the development of biological strategies to utilize lycorine in the treatment of cancers. 
 Title: Lycorine: A prospective natural lead for anticancer drug discovery
Output: True
Paragraph: Background: The Iberian lynx (Lynx pardinus) is considered the most endangered felid species in the world. In order to save this species, the Spanish authorities implemented a captive breeding program recruiting lynxes from the wild. In this context, a retrospective survey on prevalence of selected feline pathogens in free-ranging lynxes was initiated. 
 Title: Feline Leukemia Virus and Other Pathogens as Important Threats to the Survival of the Critically Endangered Iberian Lynx (Lynx pardinus)
Output: False
Paragraph: The chicken MHC has been associated with disease resistance, though the mechanisms are not understood. The functions of macrophages, critical to both innate and acquired immunity, were compared between the more infectious bronchitis virus-resistant B2 and the more infectious bronchitis virus-susceptible B19 lines. In vivo peripheral blood concentrations of monocytes were similar in B2 or B19 homozygous haplotypes. Peripheral blood-derived macrophages were stimulated with poly I:C, simulating an RNA virus, or IFNγ, a cytokine at the interface of innate and adaptive immunity. Not only did B2-derived peripheral monocytes differentiate into macrophages more readily than the B19 monocytes, but as determined by NO production, macrophages from B2 and B2 on B19 genetic background chicks were also significantly more responsive to either stimulant. In conclusion, the correlation with resistance to illness following viral infection may be directly linked to a more vigorous innate immune response. 
 Title: Dramatic differences in the response of macrophages from B2 and B19 MHC-defined haplotypes to interferon gamma and polyinosinic:polycytidylic acid stimulation
Output: False
Paragraph: a b s t r a c t 5-Arylcarbamoyl-2-methylisoxazolidin-3-yl-3-phosphonates have been synthesised from N-methyl-Cdiethoxyphosphorylnitrone and N-arylacrylamides in good yields. cis-and trans-isoxazolidine phosphonates obtained herein were evaluated for activity against a broad range of DNA and RNA viruses. None of the compounds were endowed with antiviral activity at subtoxic concentrations. Isoxazolidines having phenyl substituted with halogen (Ar = 2-F-C 6 H 4 ; 3-Br-C 6 H 4 ; and 4-Br-C 6 H 4 ) have been found to inhibit proliferation of L1210, CEM as well as HeLa cells with IC 50 in the 100-170 lM range. 
 Title: Design, synthesis, antiviral and cytostatic evaluation of novel isoxazolidine nucleotide analogues with a carbamoyl linker
Output: False
Paragraph: The burden of stroke is comparatively greater in Asian countries than in the Western world. While there has been a documented recent decline in the incidence of stroke in several Western nations due to better risk factor management, much less is known about the nature and trajectory of stroke in Asia over the last decade. The objective of this study was to explore risk factors, medication use, incidence, and one-year recurrence of stroke in Taiwan. Methods We conducted a nationwide cohort study by reviewing all hospitalized patients ( ≥ 18 years) with a primary diagnosis of ischemic stroke between 2001 and 2011 from Taiwan National Health Insurance Research Database. Results A total of 291,381 first-ever ischemic stroke patients were enrolled between 2000 and 2011. The average age was about 70 years and approximately 58.6% of them were men. While prevalence of diabetes mellitus and hyperlipidemia, as well as use of statins, antiplatelet agents, and oral anticoagulant agents for atrial fibrillation significantly increased; incidence (142.3 vs. 129.5 per 100,000 in 2000 and 2011, respectively) and one-year recurrence (9.6% vs. 7.8% in 2000 and 2011, respectively) of stroke declined during this period of time. Conclusions Over the last decade in Taiwan, rates of primary ischemic stroke and one-year recurrent stroke decreased by 9% and 18% respectively. 
 Title: Trends in Incident and Recurrent Rates of First-Ever Ischemic Stroke in Taiwan between 2000 and 2011
Output: False
Paragraph: DNA resequencing arrays enable rapid acquisition of high-quality sequence data. This technology represents a promising platform for rapid highresolution genotyping of microorganisms. Traditional array-based resequencing methods have relied on the use of specific PCR-amplified fragments from the query samples as hybridization targets. While this specificity in the target DNA population reduces the potential for artifacts caused by cross-hybridization, the subsampling of the query genome limits the sequence coverage that can be obtained and therefore reduces the technique's resolution as a genotyping method. We have developed and validated an Affymetrix Inc. GeneChip array-based, whole-genome resequencing platform for Francisella tularensis, the causative agent of tularemia. A set of bioinformatic filters that targeted systematic base-calling errors caused by cross-hybridization between the wholegenome sample and the array probes and by deletions in the sample DNA relative to the chip reference sequence were developed. Our approach eliminated 91% of the false-positive singlenucleotide polymorphism calls identified in the SCHU S4 query sample, at the cost of 10.7% of the true positives, yielding a total base-calling accuracy of 99.992%. 
 Title: A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip Õ whole-genome resequencing platform
Output: False
Paragraph: Although there are a large number of thesauri for the biomedical domain many of them lack coverage in terms and their variant forms. Automatic thesaurus construction based on patterns was first suggested by Hearst [1], but it is still not clear how to automatically construct such patterns for different semantic relations and domains. In particular it is not certain which patterns are useful for capturing synonymy. The assumption of extant resources such as parsers is also a limiting factor for many languages, so it is desirable to find patterns that do not use syntactical analysis. Finally to give a more consistent and applicable result it is desirable to use these patterns to form synonym sets in a sound way. We present a method that automatically generates regular expression patterns by expanding seed patterns in a heuristic search and then develops a feature vector based on the occurrence of term pairs in each developed pattern. This allows for a binary classifications of term pairs as synonymous or non-synonymous. We then model this result as a probability graph to find synonym sets, which is equivalent to the well-studied problem of finding an optimal set cover. We achieved 73.2% precision and 29.7% recall by our method, out-performing hand-made resources such as MeSH and Wikipedia. We conclude that automatic methods can play a practical role in developing new thesauri or expanding on existing ones, and this can be done with only a small amount of training data and no need for resources such as parsers. We also concluded that the accuracy can be improved by grouping into synonym sets. 
 Title: Synonym set extraction from the biomedical literature by lexical pattern discovery
Output: True
Paragraph: Air cleaning techniques have been applied worldwide with the goal of improving indoor air quality. The effectiveness of applying these techniques varies widely, and pollutant removal efficiency is usually determined in controlled laboratory environments which may not be realized in practice. Some air cleaners are largely ineffective, and some produce harmful by-products. To summarize what is known regarding the effectiveness of fan-driven air cleaning technologies, a state-of-the-art review of the scientific literature was undertaken by a multidisciplinary panel of experts from Europe, North America, and Asia with expertise in air cleaning, aerosol science, medicine, chemistry and ventilation. The effects on health were not examined. Over 26,000 articles were identified in major literature databases; 400 were selected as being relevant based on their titles and abstracts by the first two authors, who further reduced the number of articles to 160 based on the full texts. These articles were reviewed by the panel using predefined inclusion criteria during their first meeting. Additions were also made by the panel. Of these, 133 articles were finally selected for detailed review. Each article was assessed independently by two members of the panel and then judged by the entire panel during a consensus meeting. During this process 59 articles were deemed conclusive and their results were used for final reporting at their second meeting. The conclusions are that: (1) None of the reviewed technologies was able to effectively remove all indoor pollutants and many were found to generate undesirable by-products during operation. (2) Particle filtration and sorption of gaseous pollutants were among the most effective air cleaning technologies, but there is insufficient information regarding long-term performance and proper maintenance. (3) The existing data make it difficult to extract information such as Clean Air Delivery Rate (CADR), which represents a common benchmark for comparing the performance of different air cleaning technologies. (4) To compare and select suitable indoor air cleaning devices, a labeling system accounting for characteristics such as CADR, energy consumption, volume, harmful by-products, and life span is Atmospheric Environment 45 (2011) 4329e4343 necessary. For that purpose, a standard test room and condition should be built and studied. (5) Although there is evidence that some air cleaning technologies improve indoor air quality, further research is needed before any of them can be confidently recommended for use in indoor environments. 
 Title: Can commonly-used fan-driven air cleaning technologies improve indoor air quality? A literature review
Output: False
Paragraph: Background: To control the spread of Corona Virus Disease , 30 screening large numbers of suspected cases for appropriate quarantine and 31 treatment is a priority. Pathogenic laboratory testing is the diagnostic gold standard 32 but it is time consuming with significant false negative results. Fast and accurate 33 diagnostic methods are urgently needed to combat the disease. Based on 34 COVID-19 radiographical changes in CT images, we aimed to develop a deep 35 learning method that could extract COVID-19's graphical features in order to provide 36 a clinical diagnosis ahead of the pathogenic test, thus saving critical time for 37 disease control. 38 Methods and Findings: We collected 1,065CT images of pathogen-confirmed 39 COVID-19 cases (325 images) along with those previously diagnosed with typical 40 viral pneumonia (740 images). We modified the Inception transfer-learning model 41 to establish the algorithm, followed by internal and external validation. The internal 42 validation achieved a total accuracy of 89.5% with specificity of 0.88 and sensitivity 43 of 0.87. The external testing dataset showed a total accuracy of 79.3% with 44 specificity of 0.83 and sensitivity of 0.67. In addition, in 54 COVID-19 images that 45 first two nucleic acid test results were negative, 46 were predicted as COVID-19 46 positive by the algorithm, with the accuracy of 85.2%. 47 Conclusion: These results demonstrate the proof-of-principle for using 48 artificial intelligence to extract radiological features for timely and accurate 49 COVID-19 diagnosis. 50 
 Title: Breast Cancer Prevention and Therapy, Ministry of Education
Output: True
Paragraph: More than 60% of human infectious diseases are caused by pathogens shared with wild or domestic animals. Zoonotic disease organisms include those that are endemic in human populations or enzootic in animal populations with frequent cross-species transmission to people. Some of these diseases have only emerged recently. Together, these organisms are responsible for a substantial burden of disease, with endemic and enzootic zoonoses causing about a billion cases of illness in people and millions of deaths every year. Emerging zoonoses are a growing threat to global health and have caused hundreds of billions of US dollars of economic damage in the past 20 years. We aimed to review how zoonotic diseases result from natural pathogen ecology, and how other circumstances, such as animal production, extraction of natural resources, and antimicrobial application change the dynamics of disease exposure to human beings. In view of present anthropogenic trends, a more eff ective approach to zoonotic disease prevention and control will require a broad view of medicine that emphasises evidence-based decision making and integrates ecological and evolutionary principles of animal, human, and environmental factors. This broad view is essential for the successful development of policies and practices that reduce probability of future zoonotic emergence, targeted surveillance and strategic prevention, and engagement of partners outside the medical community to help improve health outcomes and reduce disease threats. 
 Title: Zoonoses 1 Ecology of zoonoses: natural and unnatural histories
Output: False
Paragraph: Respiratory Pathogen 13 Detection Kit (13× kit) is able to simultaneously detect 11 respiratory viruses, Mycoplasma pneumoniae (MP) and Chlamydia in a single reaction. Using 572 Nasopharyngeal aspirates collected from hospitalized children, the clinical performance of 13× kit for detecting 11 respiratory viruses was evaluated in comparison with a routinely used 2-tube multiplex reverse transcription PCR assay (2-tube assay) at provincial Centers for Disease Control and Prevention in China. The clinical performance of 13× kit for detecting MP and Chlamydia was evaluated by commercial real-time quantitative PCR (qPCR) kits or sequencing. For tested viruses, the assay concordance was 95.98% and the kappa coefficient was 0.89. All the MP and Chlamydia positive samples detected by 13× kit were confirmed as true positives. The utilization of the 13× kit in clinical settings will be helpful for doctors to assess clinical outcome according to virus type or multiple infections, and to limit the use of antibiotics. 
 Title: Clinical evaluation of a new single-tube multiplex reverse transcription PCR assay for simultaneous detection of 11 respiratory viruses, Mycoplasma pneumoniae and Chlamydia in hospitalized children with acute respiratory infections
Output: False
Paragraph: Background: Mathematical and statistical models are used to project the future time course of infectious disease epidemics and the expected future burden on health care systems and economies. Influenza is a particularly important disease in this context because it causes annual epidemics and occasional pandemics. In order to forecast health care utilization during epidemics-and the effects of hospitalizations and deaths on the contact network and, in turn, on transmission dynamics-modellers must make assumptions about the lengths of time between infection, visiting a physician, being admitted to hospital, leaving hospital, and death. More reliable forecasts could be be made if the distributions of times between these types of events ("delay distributions") were known. Methods: We estimated delay distributions in the province of Ontario, Canada, between 2006 and 2010. To do so, we used encrypted health insurance numbers to link 1.34 billion health care billing records to 4.27 million hospital inpatient stays. Because the four year period we studied included three typical influenza seasons and the 2009 influenza pandemic, we were able to compare the delay distributions in non-pandemic and pandemic settings. We also estimated conditional probabilities such as the probability of hospitalization within the year if diagnosed with influenza. Results: In non-pandemic [pandemic] years, delay distribution medians (inter-quartile ranges) were: Service to Admission 6.3 days (0.1-17.6 days) [2.4 days (-0.3-13.6 days)], Admission to Discharge 3 days (1.4-5.9 days) [2.6 days (1.2-5.1 days)], Admission to Death 5.3 days (2.1-11 days) [6 days (2.6-13.1 days)]. (Service date is defined as the date, within the year, of the first health care billing that included a diagnostic code for influenza-like-illness.) Among individuals diagnosed with either pneumonia or influenza in a given year, 19% [16%] were hospitalized within the year and 3% [2%] died in hospital. Among all individuals who were hospitalized, 10% [12%] were diagnosed with pneumonia or influenza during the year and 5% [5%] died in hospital. Conclusion: Our empirical delay distributions and conditional probabilities should help facilitate more accurate forecasts in the future, including improved predictions of hospital bed demands during influenza outbreaks, and the expected effects of hospitalizations on epidemic dynamics. 
 Title: Patterns of seasonal and pandemic influenza-associated health care and mortality in Ontario, Canada
Output: False
Paragraph: One of the daunting challenges facing modern medicine lies in the understanding and treatment of tumor heterogeneity. Most tumors show intra-tumor heterogeneity at both genomic and proteomic levels, with marked impacts on the responses of therapeutic targets. Therapeutic target-related gene expression pathways are affected by hypoxia and cellular stress. However, the finding that targets such as eukaryotic initiation factor (eIF) 4E (and its phosphorylated form, p-eIF4E) are generally homogenously expressed throughout tumors, regardless of the presence of hypoxia or other cellular stress conditions, opens the exciting possibility that malignancies could be treated with therapies that combine targeting of eIF4E phosphorylation with immune checkpoint inhibitors or chemotherapy. 
 Title: Beyond molecular tumor heterogeneity: protein synthesis takes control
Output: False
Paragraph: Porcine epidemic diarrhea virus (PEDV) is the major causative agent of fatal diarrhea in piglets. To study the pathogenic features of PEDV using a mouse model, PEDV with virulence in mice is required. In pursuit of this, we adapted a tissue-culture-passed PEDV MK strain to suckling mouse brains. PEDV obtained after ten passages through the brains (MK-p10) had increased virulence for mice, and its fusion activity in cultured cells exceeded that of the original strain. However, the replication kinetics of MK and MK-p10 did not differ from each other in the brain and in cultured cells. The spike (S) protein of MK-p10 had four amino acid substitutions relative to the original strain. One of these (an H-to-R substitution at residue 1,381) was first detected in PEDV isolated after eight passages, and both this virus (MK-p8) and MK-p10 showed enhanced syncytium formation relative to the original MK strain and viruses isolated after two, four, and six passages, suggesting the possibility that the H-to-R mutation was responsible for this activity. This mutation could be also involved in the increased virulence of PEDV observed for MK-p10. 
 Title: Enhanced cell fusion activity in porcine epidemic diarrhea virus adapted to suckling mice
Output: False
Paragraph: Background: Newcastle Disease virus (NDV) causes severe and economically significant disease in almost all birds. However, factors that affect NDV replication in host cells are poorly understood. NDV generates long double-stranded RNA (dsRNA) molecules during transcription of single-stranded genomic RNA. Protein kinase R (PKR) is activated by dsRNA. The aim of this study was to elucidate the role of PKR in NDV infection. Results: NDV infection led to the activation of dsRNA-dependent PKR and phosphorylation of its substrate, translation initiation factor eIF2α, in a dose-dependent manner by either the lentogenic strain LaSota or a velogenic strain Herts/33. PKR activation coincided with the accumulation of dsRNA induced by NDV infection. PKR knockdown remarkably decreased eIF2α phosphorylation as well as IFN-β mRNA levels, leading to the augmentation of extracellular virus titer. Furthermore, siRNA knockdown or phosphorylation of eIF2α or okadaic acid treatment significantly impaired NDV replication, indicating the critical role of the PKR/eIF2α signaling cascade in NDV infection. Conclusion: PKR is activated by dsRNA generated by NDV infection and inhibits NDV replication by eIF2α phosphorylation. This study provides insight into NDV-host interactions for the development of candidate antiviral strategies. 
 Title: Activation of the PKR/eIF2α signaling cascade inhibits replication of Newcastle disease virus
Output: False
Paragraph: Vaxign is the first web-based vaccine design system that predicts vaccine targets based on genome sequences using the strategy of reverse vaccinology. Predicted features in the Vaxign pipeline include protein subcellular location, transmembrane helices, adhesin probability, conservation to human and/or mouse proteins, sequence exclusion from genome(s) of nonpathogenic strain(s), and epitope binding to MHC class I and class II. The precomputed Vaxign database contains prediction of vaccine targets for > 70 genomes. Vaxign also performs dynamic vaccine target prediction based on input sequences. To demonstrate the utility of this program, the vaccine candidates against uropathogenic Escherichia coli (UPEC) were predicted using Vaxign and compared with various experimental studies. Our results indicate that Vaxign is an accurate and efficient vaccine design program. 
 Title: Methodology Report Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development
Output: True
Paragraph: Severe acute respiratory syndrome (SARS), caused by the novel coronavirus SARS-CoV, produced a scare Abstract when it appeared in 2003 in China and later quickly spread to other countries around the world. Although it has since disappeared, its threat to human health remains. Therefore, studies on the prevention and treatment of SARS are important for dealing with epidemics of this and other infectious diseases. The most promising newly developed technology for intervention in SARS may be RNA interference, an endogenous cellular process for the inhibition of gene expression mediated by sequence-specific double-stranded RNAs. Numerous studies have reported the therapeutic potential of RNA interference for the treatment of various human diseases ranging from cancers to infectious diseases such as HIV and hepatitis. To date, most studies on inhibition of SARS-CoV replication using small interfering RNAs (siRNAs) have been conducted in cell lines in vitro. One study using siRNAs to inhibit SARS-CoV infection in Rhesus macaques demonstrated that siRNAs were effective both prophylactically and therapeutically with no adverse effects in the animals. Challenges remaining for the application of siRNA in vivo for SARS prevention and treatment include the specificity of the siRNAs and the efficiency of delivery. However, with improvements in siRNA design and delivery methods, RNA interference has the potential to become another major weapon for combating dangerous infections due to viruses such as SARS-CoV. 
 Title: Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome Progress to Date
Output: False