niryuu/sni-each-converted huggingface dataset:
Paragraph: Infiltration and runoff from manured agricultural fields can result in livestock pathogens reaching groundwater and surface waters. Here, we measured the effectiveness of glass wool filters to simultaneously concentrate enteric viruses and bacteria of bovine origin from water. The recovery efficiencies were determined for bovine viral diarrhea virus types 1 and 2, bovine rotavirus group A, bovine coronavirus, poliovirus Sabin III, toxigenic Escherichia coli ,and Campylobacter jejuni seeded into water with three different turbidity levels (0.5, 215, and 447 NTU). Twenty liters of dechlorinated tap water (pH 7) were seeded with the test organisms, and then passed through a glass wool filter using a peristaltic pump (flow rate = 1 liter min -1 ). Retained organisms were eluted from the filters by passing beef extract-glycine buffer (pH 9.5) in the direction opposite of sample flow. Recovered organisms were enumerated by qPCR except for C. jejuni, which was quantified by culture. Mean recovery efficiencies ranged from 55 to 33 % for the bacteria and 58 to 16 % for the viruses. Using bootstrapping techniques combined with Analysis of Variance, recovery efficiencies were found to differ among the pathogen types tested at the two lowest turbidity levels; however, for a given pathogen type turbidity did not affect recovery except for C. jejuni. Glass wool filtration is a cost-effective method for concentrating several waterborne pathogens of bovine origin simultaneously, although recovery may be low for some specific taxa such as bovine viral diarrhea virus 1. 
 Title: Simultaneous Concentration of Bovine Viruses and Agricultural Zoonotic Bacteria from Water Using Sodocalcic Glass Wool Filters
Output: False
Paragraph: The emergence of SARS-CoV and MERS-CoV, triggered the discovery of a high diversity of coronaviruses in bats. Studies from Europe have shown that coronaviruses circulate in bats in France but this reflects only a fraction of the whole diversity. In the current study the diversity of coronaviruses circulating in western Europe was extensively explored. Ten alphacoronaviruses in eleven bat species belonging to the Miniopteridae, Vespertilionidae and Rhinolophidae families and, a SARS-CoV-related Betacoronavirus in Rhinolophus ferrumequinum were identified. The diversity and prevalence of bat coronaviruses presently reported from western Europe is much higher than previously described and includes a SARS-CoV sister group. This diversity demonstrates the dynamic evolution and circulation of coronaviruses in this species. That said, the identified coronaviruses were consistently associated with a particular bat species or genus, and these relationships were maintained no matter the geographic location. The observed phylogenetic grouping of coronaviruses from the same species in Europe and Asia, emphasizes the role of host/pathogen coevolution in this group. 
 Title: SARS-CoV related Betacoronavirus and diverse Alphacoronavirus members found in western old-world ☆
Output: False
Paragraph: The interferon-inducible transmembrane (IFITM) proteins 1, 2 and 3 inhibit the host cell entry of several enveloped viruses, potentially by promoting the accumulation of cholesterol in endosomal compartments. IFITM3 is essential for control of influenza virus infection in mice and humans. In contrast, the role of IFITM proteins in coronavirus infection is less well defined. Employing a retroviral vector system for analysis of coronavirus entry, we investigated the susceptibility of human-adapted and emerging coronaviruses to inhibition by IFITM proteins. We found that entry of the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV) is sensitive to inhibition by IFITM proteins. In 293T cells, IFITM-mediated inhibition of cellular entry of the emerging MERS-and SARS-CoV was less efficient than blockade of entry of the globally circulating human coronaviruses 229E and NL63. Similar differences were not observed in A549 cells, suggesting that cellular context and/or IFITM expression levels can impact inhibition efficiency. The differential IFITM-sensitivity of coronaviruses observed in 293T cells afforded the opportunity to investigate whether efficiency of entry inhibition by IFITMs and endosomal cholesterol accumulation correlate. No such correlation was observed. Furthermore, entry mediated by the influenza virus hemagglutinin was robustly inhibited by IFITM3 but was insensitive to accumulation of endosomal cholesterol, indicating that modulation of cholesterol synthesis/transport did not account for the antiviral activity of IFITM3. Collectively, these results show that the emerging MERS-CoV is a target of the antiviral activity of IFITM Viruses 2014, 6 3684 proteins and demonstrate that mechanisms other than accumulation of endosomal cholesterol can contribute to viral entry inhibition by IFITMs. 
 Title: IFITM Proteins Inhibit Entry Driven by the MERS-Coronavirus Spike Protein: Evidence for Cholesterol-Independent Mechanisms
Output: True
Paragraph: Background. Epidemiological surveillance of HIV infection in Japan involves two technical problems for directly applying a classical backcalculation method, i.e., (i) all AIDS cases are not counted over time and (ii) people diagnosed with HIV have received antiretroviral therapy, extending the incubation period. The present study aimed to address these issues and estimate the HIV incidence and the proportion of diagnosed HIV infections, using a simple statistical model. Methods. From among Japanese nationals, yearly incidence data of HIV diagnoses and patients with AIDS who had not previously been diagnosed as HIV positive, from 1985 to 2017, were analyzed. Using the McKendrick partial differential equation, general convolution-like equations were derived, allowing estimation of the HIV incidence and the time-dependent rate of diagnosis. A likelihood-based approach was used to obtain parameter estimates. Results. Assuming that the median incubation period was 10.0 years, the cumulative number of HIV infections was estimated to be 29,613 (95% confidence interval (CI): 29,059, 30,167) by the end of 2017, and the proportion of diagnosed HIV infections was estimated at 80.3% (95% CI [78.7%-82.0%]). Allowing the median incubation period to range from 7.5 to 12.3 years, the estimate of the proportion diagnosed can vary from 77% to 84%. Discussion. The proportion of diagnosed HIV infections appears to have not yet reached 90% among Japanese nationals. Compared with the peak incidence from 2005-2008, new HIV infections have clearly been in a declining trend; however, there are still more than 1,000 new HIV infections per year in Japan. To increase the diagnosed proportion of HIV infections, it is critical to identify people who have difficulty accessing consultation, testing, and care, and to explore heterogeneous patterns of infection. . Brookmeyer R, Gail MH. 1986. Minimum size of the acquired immunodeficiency syndrome (AIDS) epidemic in the United States. Lancet 2:1320-1322. Brookmeyer R, Gail MH. 1994. AIDS epidemiology: a quantitative approach. New York: Oxford University Press. Brookmeyer R, Goedert JJ. 1989. Censoring in an epidemic with an application to haemophilia-associated AIDS. Biometrics 45:325-335 
 Title: Estimating the incidence and diagnosed proportion of HIV infections in Japan: a statistical modeling study
Output: True
Paragraph: Background: Canine parvovirus 2 (CPV 2) is a major infectious cause of mortality in puppies. The characteristic symptom of CPV 2 disease is intestinal hemorrhage with severe bloody diarrhea. Soon after CPV was first recognized in the late 1970s, the original virus, CPV 2, was replaced in the canine population by strains carrying minor antigenic variants (termed 2a, 2b, and 2c) of the VP2 gene that could be distinguished using monoclonal antibodies and molecular analyses. Here, we provide an updated molecular characterization of the CPV 2 circulating in Taiwan. Methods: In this study, 28 isolates of CPV 2 from 144 dogs with suspected CPV infection were obtained from northern, central, and southern Taiwan from 2008 to 2012 and screened by PCR. The 28 isolates were sequenced, and a phylogenetic analysis of the VP2 gene was performed. Results: Of the 28 Taiwanese CPV 2 isolates, 15 were identified as new CPV 2a, and 13 were identified as new CPV 2b. Compared to the reference CPV 2a, all 15 of the CPV 2a sequences collected in this study contain an Ile324 mutation caused by a TAT to ATT mutation at nucleotides 970-972 of the VP2 gene. Conclusion: Our VP2 sequence data revealed that both types are currently prevalent CPV 2 field strains circulating in Taiwan, and a unique Ile324 VP2 mutation was found in our Taiwanese CPV 2a isolates and recent Asian isolates. CPV 2c was not observed in this study. 
 Title: Genetic characterization of type 2a canine parvoviruses from Taiwan reveals the emergence of an Ile324 mutation in VP2
Output: False
Paragraph: Background: Device-associated infection (DAI) plays an important part in nosocomial infection. Active surveillance and infection control are needed to disclose the specific situation in each hospital and to cope with this problem effectively. We examined the rates of DAI by antimicrobial-resistant pathogens, and 30-day and in-hospital mortality in the intensive care unit (ICU). Methods: Prospective surveillance was conducted in a mixed medical and surgical ICU at a major teaching hospital from 2000 through 2008. Trend analysis was performed and logistic regression was used to assess prognostic factors of mortality. Results: The overall rate of DAIs was 3.03 episodes per 1000 device-days. The most common DAI type was catheter-associated urinary tract infection (3.76 per 1000 urinary catheter-days). There was a decrease in DAI rates in 2005 and rates of ventilator-associated pneumonia (VAP, 3.18 per 1000 ventilator-days) have remained low since then (p < 0.001). The crude rates of 30-day (33.6%) and in-hospital (52.3%) mortality, as well as infection by antibiotic-resistant VAP pathogens also decreased. The most common antimicrobial-resistant pathogens were methicillin-resistant Staphylococcus aureus (94.9%) and imipenem-resistant Acinetobacter baumannii (p < 0.001), which also increased at the most rapid rate. The rate of antimicrobial resistance among Enterobacteriaceae also increased significantly (p < 0.05). After controlling for potentially confounding factors, the DAI was an independent prognostic factor for both 30-day mortality (OR 2.51, 95% confidence interval [CI] 1.99-3.17, p = 0.001) and in-hospital mortality (OR 3.61, 95% CI 2.10-3.25, p < 0.001). Conclusions: The decrease in the rate of DAI and infection by resistant bacteria on the impact of severe acute respiratory syndrome can be attributed to active infection control and improved adherence after 2003. 
 Title: Surveillance on secular trends of incidence and mortality for device-associated infection in the intensive care unit setting at a tertiary medical center in Taiwan, 2000-2008: A retrospective observational study
Output: True
Paragraph: respiratory symptoms in adults in general practice. Family Practice 2004; 21: 317-323. Background. Community studies have shown that ~30% of patients with acute respiratory tract symptoms have no identifiable infective aetiology. This may not be applicable in general practice. Objective. The purpose of this study was to determine the infective aetiology in patients who presented to primary care doctors with acute respiratory symptoms. Methods. A prospective study was carried out in all nine primary care clinics belonging to the National Healthcare Group Polyclinics (NHGPs) in Singapore. The subjects comprised 594 consecutive patients (318 males, 276 females) aged у21 years who presented with complaints of any one of cough, nasal or throat symptoms of Ͻ7 days duration. Data collection was through interview using structured questionnaire, physical examination, throat swabs for bacterial culture and nasal swabs for virus identification by immunofluorescence (IF) and polymerase chain reaction (PCR). Additional PCR was performed on a subsample of 100 patients. Patients were followed-up until resolution of symptoms. Results. The aetiological diagnosis by infective agent is as follows: 150 patients (25.2%) had virus infections, of which 90.7% (136/150) were by rhinovirus. Fourteen patients (2.4%) had bacterial infections, of which 10 were due to group G streptococcus. Group A streptococcus was not detected. Nineteen patients with new pathogens were identified by further PCR. These included parainfluenza 4, human coronavirus OC43, adenovirus, enterovirus and Chlamydia pneumoniae. No pathogen could be identified in 49% of patients. There were no differences in clinical presentation and socio-demographic variables between patients who had viral infections and those in whom no pathogen could be identified. In about half of patients who presented at NHGPs, no pathogens could be identified even after PCR. A non-infective aetiology could be considered in these patients. 
 Title: Acute respiratory symptoms in adults in general practice
Output: False
Paragraph: To generate the most diverse phylogenetic dataset for the flaviviruses to date, we determined the genomic sequences and phylogenetic relationships of 14 flaviviruses, of which 10 are primarily associated with Culex spp. mosquitoes. We analyze these data, in conjunction with a comprehensive collection of flavivirus genomes, to characterize flavivirus evolutionary and biogeographic history in unprecedented detail and breadth. Based on the presumed introduction of yellow fever virus into the Americas via the transatlantic slave trade, we extrapolated a timescale for a relevant subset of flaviviruses whose evolutionary history, shows that different Culex-spp. associated flaviviruses have been introduced from the Old World to the New World on at least five separate occasions, with 2 different sets of factors likely to have contributed to the dispersal of the different viruses. We also discuss the significance of programmed ribosomal frameshifting in a central region of the polyprotein open reading frame in some mosquito-associated flaviviruses. 
 Title: New Insights into Flavivirus Evolution, Taxonomy and Biogeographic History, Extended by Analysis of Canonical and Alternative Coding Sequences
Output: True
Paragraph: The discovery of a novel coronavirus (CoV) as the causative agent of severe acute respiratory syndrome (SARS) has highlighted the need for a better understanding of CoV replication. The replication of SARS-CoV is highly dependent on host cell factors. However, relatively little is known about the cellular proteome changes that occur during SARS-CoV replication. Recently, we developed a cell line expressing a SARS-CoV subgenomic replicon and used it to screen inhibitors of SARS-CoV replication. To identify host proteins important for SARS-CoV RNA replication, the protein profiles of the SARS-CoV replicon cells and parental BHK21 cells were compared using a quantitative proteomic strategy termed "stable-isotope labeling by amino acids in cell culture-mass spectrometry" (SILAC-MS). Our results revealed that, among the 1,081 host proteins quantified in both forward and reverse SILAC measurements, 74 had significantly altered levels of expression. Of these, significantly upregulated BCL2-associated athanogene 3 (BAG3) was selected for further functional studies. BAG3 is involved in a wide variety of cellular processes, including cell survival, cellular stress response, proliferation, migration, and apoptosis. Our results show that inhibition of BAG3 expression by RNA interference led to significant suppression of SARS-CoV replication, suggesting the possibility that upregulation of BAG3 may be part of the machinery that SARS-CoV relies on for replication. By correlating the proteomic data with these functional studies, the findings of this study provide important information for understanding SARS-CoV replication. 
 Title: Quantitative Proteomics Analysis Reveals BAG3 as a Potential Target To Suppress Severe Acute Respiratory Syndrome Coronavirus Replication ᰔ
Output: True
Paragraph: Background: One of the most commonly applied protectotype vaccination protocol against infectious bronchitis (IB) in broiler chickens in the EU is simultaneous or alternate use of Ma5 and 4/91 vaccine strains. After IB vaccination and infection, systemic and upper respiratory tract (URT), humoral and cell-mediated immunity (CMI), are stimulated. The level of this stimulation correlates with the level of protection against IB. Results: We've investigated the development of URT and systemic, cell-mediated and humoral immunity in commercial broiler chickens vaccinated with Ma5 and/or 4/91 strains at hatch day. We've demonstrated that the group vaccinated with Ma5 and 4/91 strain simultaneously developed the most desirable immunity which reflects the level of CD8 + T cells stimulation in spleen and Harderian gland, as well as the level of IgA and IgY in URT washings and serum and their cross-reactivity with 7 IBV strains. Conclusions: Although we did not demonstrate directly why Ma5 + 4/91 protocol is so efficient it seems that it combines the benefits of monovalent vaccination with either Ma5 or 4/91 and while Ma5 seems to stimulate CMI more efficiently, the 4/91 strain generates a wider spectrum of immune system cross-reactivity and higher URT IgA production. 
 Title: Immunological aspects of the efficiency of protectotype vaccination strategy against chicken infectious bronchitis
Output: True
Paragraph: Background: Infections are often associated to comorbidity that increases the risk of medical conditions which can lead to further morbidity and mortality. SARS is a threat which is similar to MERS virus, but the comorbidity is the key aspect to underline their different impacts. One UK doctor says "I'd rather have HIV than diabetes" as life expectancy among diabetes patients is lower than that of HIV. However, HIV has a comorbidity impact on the diabetes. Results: We present a quantitative framework to compare and explore comorbidity between diseases. By using neighbourhood based benchmark and topological methods, we have built comorbidity relationships network based on the OMIM and our identified significant genes. Then based on the gene expression, PPI and signalling pathways data, we investigate the comorbidity association of these 2 infective pathologies with other 7 diseases (heart failure, kidney disorder, breast cancer, neurodegenerative disorders, bone diseases, Type 1 and Type 2 diabetes). Phenotypic association is measured by calculating both the Relative Risk as the quantified measures of comorbidity tendency of two disease pairs and the φ-correlation to measure the robustness of the comorbidity associations. The differential gene expression profiling strongly suggests that the response of SARS affected patients seems to be mainly an innate inflammatory response and statistically dysregulates a large number of genes, pathways and PPIs subnetworks in different pathologies such as chronic heart failure (21 genes), breast cancer (16 genes) and bone diseases (11 genes). HIV-1 induces comorbidities relationship with many other diseases, particularly strong correlation with the neurological, cancer, metabolic and immunological diseases. Similar comorbidities risk is observed from the clinical information. Moreover, SARS and HIV infections dysregulate 4 genes (ANXA3, GNS, HIST1H1C, RASA3) and 3 genes (HBA1, TFRC, GHITM) respectively that affect the ageing process. It is notable that HIV and SARS similarly dysregulated 11 genes and 3 pathways. Only 4 significantly dysregulated genes are common between SARS-CoV and MERS-CoV, including NFKBIA that is a key regulator of immune responsiveness implicated in susceptibility to infectious and inflammatory diseases. Our method presents a ripe opportunity to use data-driven approaches for advancing our current knowledge on disease mechanism and predicting disease comorbidities in a quantitative way. 
 Title: Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies
Output: False
Paragraph: There is little information on the role of nitric oxide ( • NO) in innate immunity to respiratory coronavirus (CoV) infections. We examined • NO levels by Greiss assay in bronchoalveolar lavage (BAL) of pigs infected with either porcine respiratory coronavirus (PRCV) or porcine reproductive and respiratory syndrome virus (PRRSV), a member of Nidovirales, like CoV. The antiviral effects of • NO on these two viruses were tested in an in vitro system using a • NO donor, S-nitroso-N-acetylpenicillamine (SNAP). We detected a large increase in • NO levels in BAL fluids of PRCV-infected pigs, but not in PRRSV-infected pigs. Pulmonary epithelial cell necrosis induced by PRCV coincided with increased • NO. Moreover, • NO levels in cell culture medium of PRRSV-infected alveolar macrophages (AMs) did not differ from that of mockinfected AMs. Antiviral assays showed that • NO significantly inhibited PRCV replication in swine testicular (ST) cells, whereas PRRSV was not susceptible to • NO based on the conditions tested. Our study suggests that unlike PRRSV which induces apoptosis in AMs, respiratory CoVs such as PRCV that infect pulmonary epithelial cells and cause cytolysis, induce • NO production in the respiratory tract. Thus, • NO may play a role in innate immunity to respiratory CoV infections by inhibiting viral replication. 
 Title: Nitric oxide is elicited and inhibits viral replication in pigs infected with porcine respiratory coronavirus but not porcine reproductive and respiratory syndrome virus
Output: True
Paragraph: Up to November 2014, Middle East respiratory syndrome coronavirus (MERS-CoV) has infected 935 individuals and killed 371, all originating in or with links to the Middle East. The mechanisms of transmission of the disease are not fully understood, but MERS-CoV seems to sustain itself in the human population through repeated re-introduction from a camel reservoir and is able to cause nosocomial outbreaks. The risk of a global spread of MERS-CoV is low. Epidemiological, serological and phylogenetic research, combined with one health surveillance, dynamic case definitions, active case finding, rigorous infection control, culturally sensitive risk communication and a continuous re-evaluation of new evidence will enable to better understand the disease, limit its spread and quantify its risk in order to better prepare for a hypothetical spread. 
 Title: What needs to be done to control the spread of Middle East respiratory syndrome coronavirus?
Output: True
Paragraph: Multiple sclerosis (MS) is an autoimmune disease of the central nervous system, and CD4 + T cells form the core immunopathogenic cascade leading to chronic inflammation. Traditionally, Th1 cells (interferon-γ-producing CD4 + T cells) driven by interleukin 12 (IL12) were considered to be the encephalitogenic T cells in MS and experimental autoimmune encephalomyelitis (EAE), an animal model of MS. Currently, Th17 cells (Il17-producing CD4 + T cells) are considered to play a fundamental role in the immunopathogenesis of EAE. This paper highlights the growing evidence that Th17 cells play the core role in the complex adaptive immunity of EAE/MS and discusses the roles of the associated immune cells and cytokines. These constitute the modern immunological basis for the development of novel clinical and preclinical immunomodulatory therapies for MS discussed in this paper. 
 Title: Current Status of the Immunomodulation and Immunomediated Therapeutic Strategies for Multiple Sclerosis
Output: True
Paragraph: It has been more than three decades since the first monoclonal antibody was approved by the United States Food and Drug Administration (US FDA) in 1986, and during this time, antibody engineering has dramatically evolved. Current antibody drugs have increasingly fewer adverse effects due to their high specificity. As a result, therapeutic antibodies have become the predominant class of new drugs developed in recent years. Over the past five years, antibodies have become the best-selling drugs in the pharmaceutical market, and in 2018, eight of the top ten bestselling drugs worldwide were biologics. The global therapeutic monoclonal antibody market was valued at approximately US$115.2 billion in 2018 and is expected to generate revenue of $150 billion by the end of 2019 and $300 billion by 2025. Thus, the market for therapeutic antibody drugs has experienced explosive growth as new drugs have been approved for treating various human diseases, including many cancers, autoimmune, metabolic and infectious diseases. As of December 2019, 79 therapeutic mAbs have been approved by the US FDA, but there is still significant growth potential. This review summarizes the latest market trends and outlines the preeminent antibody engineering technologies used in the development of therapeutic antibody drugs, such as humanization of monoclonal antibodies, phage display, the human antibody mouse, single B cell antibody technology, and affinity maturation. Finally, future applications and perspectives are also discussed. 
 Title: Development of therapeutic antibodies for the treatment of diseases
Output: True
Paragraph: is the etiologic agent of the febrile respiratory illness, commonly referred to as 'flu'. The lysosomal protease cathepsin B (CTSB) has shown to be involved in the lifecycle of various viruses. Here, we examined the role of CTSB in the IAV lifecycle. Methods-CTSB-deficient (CTSB −/− ) macrophages and the human lung epithelial cell line A549 cells treated with CA-074Me were infected with the A/Puerto Rico/8/34 strain of IAV (IAV-PR8). Viral entry and propagation were measured through quantitative real-time RT-PCR; production and localization of hemagglutinin (HA) protein in the infected host cells were analysed by Western blots, flow cytometry and confocal microscopy; production of progeny viruses were measured by a hemagglutination assay. Results-CTSB −/− macrophages and CA-074Me-treated A549 cells had no defects in incorporating IAV-PR8 virions and permitting viral RNA synthesis. However, these cells produced significantly lower amounts of HA protein and progeny virions than wild-type or untreated cells. Conclusion-These data indicate that CTSB is involved in the expression of IAV-PR8 HA protein and subsequent optimal production of IAV-PR8 progeny virions. Targeting CTSB can be a novel therapeutic strategy for treating IAV infection. 
 Title: Cathepsin B plays a key role in optimal production of the influenza A virus
Output: False
Paragraph: Traditionally, most of the proposed probabilistic models of decision under uncertainty rely on numerical measures and representations. Alternative proposals call for qualitative (non-numerical) treatment of uncertainty, based on preference relations and belief orders. The automation of both numerical and non-numerical frameworks surely represents a preliminary step in the development of inference engines of intelligent agents, expert systems, and decision-support tools. In this paper we exploit Answer Set Programming to formalize and reason about uncertainty expressed as belief orders. The availability of ASP-solvers supports the design of automated tools to handle such formalizations. Our proposal reveals particularly suitable whenever the domain of discernment is partial. We first illustrate how to automatically "classify ^^, according to the most well-known uncertainty frameworks, any given qualitative uncertainty assessment. Then, we show how to compute an enlargement of the assessment, to any other new inference target. 
 Title: Management of uncertainty orderings through ASP
Output: True
Paragraph: Sensor placement Markov matrix Set cover problem Indoor air quality Transmission of infectious diseases Chemical and biological warfare a b s t r a c t Air quality has been an important issue in public health for many years. Sensing the level and distributions of impurities help in the control of building systems and mitigate long term health risks. Rapid detection of infectious diseases in large public areas like airports and train stations may help limit exposure and aid in reducing the spread of the disease. Complete coverage by sensors to account for any release scenario of chemical or biological warfare agents may provide the opportunity to develop isolation and evacuation plans that mitigate the impact of the attack. All these scenarios involve strategic placement of sensors to promptly detect and rapidly respond. This paper presents a data driven sensor placement algorithm based on a dynamical systems approach. The approach utilizes the finite dimensional Perron-Frobenius (PF) concept. The PF operator (or the Markov matrix) is used to construct an observability gramian that naturally incorporates sensor accuracy, location constraints, and sensing constraints. The algorithm determines the response times, sensor coverage maps, and the number of sensors needed. The utility of the procedure is illustrated using four examples: a literature example of the flow field inside an aircraft cabin and three air flow fields in different geometries. The effect of the constraints on the response times for different sensor placement scenarios is investigated. Knowledge of the response time and coverage of the multiple sensors aides in the design of mechanical systems and response mechanisms. The methodology provides a simple process for place sensors in a building, analyze the sensor coverage maps and response time necessary during extreme events, as well as evaluate indoor air quality. The theory established in this paper also allows for future work in topics related to construction of classical estimator problems for the sensors, real-time contaminant transport, and development of agent dispersion, contaminant isolation/removal, and evacuation strategies. 
 Title: A methodology for optimal placement of sensors in enclosed environments: A dynamical systems approach
Output: False
Paragraph: In this review, we report that the receptor of mouse hepatitis virus (MHV), carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1), is an important determinant of mouse susceptibility to MHV infection. This finding was revealed by using mouse strains with two different allelic forms of the MHV receptor, Ceacam1a and Ceacam1b. Although previous studies indicated that susceptibility is determined by a single gene, Ceacam1, our recent work in gene-replaced mice with chimeric Ceacam1 pointed toward the involvement of other host factors (genes) in the susceptibility. Studies on mouse susceptibility to MHV, as well as the factors involved in their susceptibility, are overviewed. 
 Title: MINI REVIEW ARTICLE Mouse hepatitis virus receptor as a determinant of the mouse susceptibility to MHV infection
Output: False
Paragraph: As viruses do not possess genes encoding for proteins required for translation, energy metabolism or membrane biosynthesis, they are classified as obligatory intracellular parasites that depend on a host cell to replicate. This genome limitation forces them to gain control over cellular processes to ensure their successful propagation. A diverse spectrum of virally encoded proteins tackling a broad spectrum of cellular pathways during most steps of the viral life cycle ranging from the host cell entry to viral protein translation has evolved. Since the host cell PI3K/Akt signaling pathway plays a critical regulatory role in many cellular processes including RNA processing, translation, autophagy and apoptosis, many viruses, in widely varying ways, target it. This review focuses on a number of remarkable examples of viral strategies, which exploit the PI3K/Akt signaling pathway for effective viral replication. 
 Title: Make Yourself at Home: Viral Hijacking of the PI3K/Akt Signaling Pathway
Output: False
Paragraph: Identification and typing of human enterovirus (HEVs) are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. Here we report a novel method for identification and typing of HEVs based on information derived from their whole genomes. Specifically, we calculate the k-mer based barcode image for each genome, HEV or other human viruses, for a fixed k, 1,k,7, where a genome barcode is defined in terms of the kmer frequency distribution across the whole genome for all combinations of k-mers. A phylogenetic tree is constructed using a barcode-based distance and a neighbor-joining method among a set of 443 representative non-HEV human viruses and 395 HEV sequences. The tree shows a clear separation of the HEV viruses from all the non-HEV viruses with 100% accuracy and a separation of the HEVs into four distinct clads with 93.4% consistency with a multiple sequence alignmentbased phylogeny. Our detailed analyses of the HEVs having different typing results by the two methods indicate that our results are in better agreement with known information about the HEVs. 
 Title: Identification and Typing of Human Enterovirus: A Genomic Barcode Approach
Output: True
Paragraph: Antiviral roles of natural killer (NK) cell subsets were examined in C57BL/6 mice infected with murine cytomegalovirus (MCMV) and other viruses, including lymphocytic choriomeningitis virus (LCMV), vaccinia virus (VV), and mouse hepatitis virus (MHV). Each virus vigorously induced an NK cell infiltrate into the peritoneal cavity and liver, causing some redistributions of NK cell subsets defined by monoclonal antibody (mAb) directed against Ly49A, C/I, D, and G2. Striking results were seen with a mAb (1F8) reactive with the positively signaling molecule Ly49H, present in MCMV-resistant C57BL/6 mice. mAb 1F8 also stains Ly49 C and I, but exclusion of those reactivities with mAb 5E6, which recognizes Ly49 C and I, indicated that Ly49H ϩ cells infiltrated the peritoneal cavity and liver and were particularly effective at synthesizing interferon ␥ . Depletion of 1F8 ϩ but not 5E6 ϩ cells in vivo by mAb injections enhanced MCMV titers by 20-1,000-fold in the spleen and approximately fivefold in the liver. Titers of LCMV or VV were not enhanced. These anti-MCMV effects were attributed to prototypical NK1.1 ϩ CD3 Ϫ NK cells and not to NK1.1 ϩ CD3 ϩ "NK/T" cells. This is the first evidence that control of a virus infection in vivo is mediated by a distinct NK cell subset. 
 Title: Murine Cytomegalovirus Is Regulated by a Discrete Subset of Natural Killer Cells Reactive with Monoclonal Antibody to Ly49H
Output: True
Paragraph: a b s t r a c t EGFR-mutant lung adenocarcinomas contain a subpopulation of cells that have undergone epithelial-tomesenchymal transition and can grow independently of EGFR. To kill these cancer cells, we need a novel therapeutic approach other than EGFR inhibitors. If a molecule is specifically expressed on the cell surface of such EGFR-independent EGFR-mutant cancer cells, it can be a therapeutic target. We found that a mesenchymal EGFR-independent subline derived from HCC827 cells, an EGFR-mutant lung adenocarcinoma cell line, expressed angiotensin-converting enzyme 2 (ACE2) to a greater extent than its parental cells. ACE2 was also expressed at least partially in most of the primary EGFR-mutant lung adenocarcinomas examined, and the ACE2 expression level in the cancer cells was much higher than that in normal lung epithelial cells. In addition, we developed an anti-ACE2 mouse monoclonal antibody (mAb), termed H8R64, that was internalized by ACE2-expressing cells. If an antibody-drug conjugate consisting of a humanized mAb based on H8R64 and a potent anticancer drug were produced, it could be effective for the treatment of EGFR-mutant lung adenocarcinomas. 
 Title: Angiotensin-converting enzyme 2 is a potential therapeutic target for EGFR-mutant lung adenocarcinoma
Output: True
Paragraph: Background: Infrared thermography (IRT) is used to screen febrile passengers at international airports, but it suffers from low sensitivity. This study explored the application of a combined visible and thermal image processing approach that uses a CMOS camera equipped with IRT to remotely sense multiple vital signs and screen patients with suspected infectious diseases. Methods: An IRT system that produced visible and thermal images was used for image acquisition. The subjects' respiration rates were measured by monitoring temperature changes around the nasal areas on thermal images; facial skin temperatures were measured simultaneously. Facial blood circulation causes tiny color changes in visible facial images that enable the determination of the heart rate. A logistic regression discriminant function predicted the likelihood of infection within 10 s, based on the measured vital signs. Sixteen patients with an influenza-like illness and 22 control subjects participated in a clinical test at a clinic in Fukushima, Japan. Results: The vital-sign-based IRT screening system had a sensitivity of 87.5% and a negative predictive value of 91.7%; these values are higher than those of conventional fever-based screening approaches. Conclusions: Multiple vital-sign-based screening efficiently detected patients with suspected infectious diseases. It offers a promising alternative to conventional fever-based screening. 
 Title: Remote sensing of multiple vital signs using a CMOS camera-equipped infrared thermography system and its clinical application in rapidly screening patients with suspected infectious diseases
Output: True
Paragraph: Despite its discovery more than three decades ago and well-established role in protein sorting and trafficking in the early secretory pathway, the intermediate compartment (IC) has remained enigmatic. The prevailing view is that the IC evolved as a specialized organelle to mediate long-distance endoplasmic reticulum (ER)-Golgi communication in metazoan cells, but is lacking in other eukaryotes, such as plants and fungi. However, this distinction is difficult to reconcile with the high conservation of the core machineries that regulate early secretory trafficking from yeast to man. Also, it has remained unclear whether the pleiomorphic IC components-vacuoles, tubules and vesicles-represent transient transport carriers or building blocks of a permanent pre-Golgi organelle. Interestingly, recent studies have revealed that the IC maintains its compositional, structural and spatial properties throughout the cell cycle, supporting a model that combines the dynamic and stable aspects of the organelle. Moreover, the IC has been assigned novel functions, such as cell signaling, Golgi-independent trafficking and autophagy. The emerging permanent nature of the IC and its connections with the centrosome and the endocytic recycling system encourage reconsideration of its relationship with the Golgi ribbon, role in Golgi biogenesis and ubiquitous presence in eukaryotic cells. 
 Title: Intermediate compartment (IC): from pre-Golgi vacuoles to a semi- autonomous membrane system
Output: False
Paragraph: Acute respiratory infection is a frequently transmitted illness of concern to doctors and patients. Considering its airborne transmission, early diagnosis of such disease is particularly important. This study explored respiratory viral infections with influenza virus, parainfluenza virus, respiratory syncytial virus, human metapneumovirus, human bocavirus, coronavirus, and other early diagnostic substances as confirmed by literature resources. This study also used the corresponding monoclonal antibodies that were produced with the use of hybridoma technology, which were fixed on the chip after purification, for further serum detection. Using this method, a new technique to simultaneously detect 6 kinds of febrile respiratory viruses in a protein chip was developed. The accuracy rate of this method can be >99.65%. This product is inexpensive and capable of high-precision and high-throughput screening, which are prominent advantages. 
 Title: Prospective Evaluation of Rapid Antigen Tests for Diagnosis of Respiratory Viral Pathogens
Output: True
Paragraph: The yeast two-hybrid system (Y2H) is a powerful method to identify binary protein-protein interactions in vivo. Here we describe Y2H screening strategies that use defined libraries of open reading frames (ORFs) and cDNA libraries. The array-based Y2H system is well suited for interactome studies of small genomes with an existing ORFeome clones preferentially in a recombination based cloning system. For large genomes, pooled library screening followed by Y2H pairwise retests may be more efficient in terms of time and resources, but multiple sampling is necessary to ensure comprehensive screening. While the Y2H false positives can be efficiently reduced by using built-in controls, retesting, and evaluation of background activation; implementing the multiple variants of the Y2H vector systems is essential to reduce the false negatives and ensure comprehensive coverage of an interactome. 
 Title: Mapping the Protein-Protein Interactome Networks Using Yeast Two-Hybrid Screens
Output: True
Paragraph: High performance liquid chromatography and high performance liquid chromatography/electrospray ionization-mass spectrometry were used to study the effect of N-terminal acetylation and the inhibition activity of acetylated enkephalins on the aminopeptidase M (EC 3.4.11.2)-catalyzed hydrolysis of methionine (Met-enk) and leucine enkephalins (Leu-enk). Acetylation imparts a significant enhancement in the proteolytic stability of these two peptides. After 30 min of the reaction, Ͻ10% of both acetylated enkephalins was hydrolyzed. In an 8-h incubation period, only a maximum of 54% acetylated (Ac)-Met-enk and 38% Ac-Leu-enk was hydrolyzed. V max and K m [infi] for the degradation of Ac-Met-enk were 1.4 nmol/min/50 ng and 2.2 mM, respectively. The corresponding values for the reaction of Ac-Leu-enk were 0.5 nmol/min/50 ng and 0.9 mM. Also, the aminopeptidase M activity on Met-enk can be inhibited in the presence of Ac-Met-enk, which acts as a mixed-type inhibitor with the inhibition constant (K i ) of 1 ϫ 10 Ϫ3 M. 
 Title: The effect of N-terminal acetylation and the inhibition activity of acetylated enkephalins on the aminopeptidase M-catalyzed hydrolysis of enkephalins૾
Output: True
Paragraph: Intracerebral inoculation of Theiler's murine encephalomyelitis virus (TMEV) into susceptible mouse strains produces a chronic demyelinating disease in which mononuclear cell-rich infiltrates in the central nervous system (CNS) are prominent. Current evidence strongly supports an immune-mediated basis for myelin breakdown, with an effector role proposed for TMEV-specific, major histocompatibility complex (MHC) class II-restricted delayed-type hypersensitivity (DTH) responses in which lymphokine-activated macrophages mediate bystander demyelination. The present study examined the possibility that concomitant or later-appearing neuroantigen-specific autoimmune T cell responses, such as those demonstrated in chronic-relapsing experimental allergic encephalomyelitis (R-EAE), may contribute to the demyelinating process following TMEV infection. T cell responses against intact, purified major myelin proteins (myelin 10 basic protein (MBP) and proteohpid protein (PLP)), and against altered myelin constituents were readily demonstrable in SJL//J mice with R-EAE, but were not detectable in SJL//J mice with TMEV-induced demyehnating disease. TMEV-infected mice also did not display T cell responses against the peptide fragments of MBP(91-104) and PLP(139-151) recently shown to be encephalitogenic in SJL/J mice. In addition, induction of neuroantigen-specific tolerance to a heterogeneous mixture of CNS antigens, via the i.v. injection of syngeneic SJL//J splenocytes covalently coupled with mouse spinal cord homogenate, resulted in significant suppression of clinical and histologic signs of R-EAE and the accompanying MBPand PLP-specific DTH responses. In contrast, neuroantigen-specific tolerance failed to alter the development of clinical and histologic signs of TMEV-induced demyelinating disease or the accompanying virus-specific DTH and humoral immune responses. These findings demonstrate that TMEV-induced demyelinating disease can occur in the apparent absence of neuroantigen-specific autoimmune responses. The relationship of the present results to the immunopathology of multiple sclerosis is discussed. 
 Title: Class II-restricted T cell responses in Theiler's murine encephalomyelitis virus (TMEV)-induced demyelinating disease III. Failure of neuroantigen-specific immune tolerance to affect the clinical course of demyelination
Output: False
Paragraph: We propose rational designing of antiviral short-interfering RNA (siRNA) targeting highly divergent HIV-1. In this study, conserved regions within HIV-1 genomes were identified through an exhaustive computational analysis, and the functionality of siRNAs targeting the highest possible conserved regions was validated. We present several promising antiviral siRNA candidates that effectively inhibited multiple subtypes of HIV-1 by targeting the best conserved regions in pandemic HIV-1 group M strains. 
 Title: Optimal design and validation of antiviral siRNA for targeting HIV-1
Output: False
Paragraph: To investigate whether the presence of infections in C57BL/6 mice influences the metastatic ability of B16 melanoma (B16M) cells, we compared the susceptibility to metastasis development of pathogen-free mice with that of mice from a colony endemically infected with several mouse pathogens. We found that, compared to seronegative controls, mice that were seropositive at least to Mouse Hepatitis Virus (MHV) and Mycoplasma pulmonis: (i) exhibited a higher interindividual variability in all the parameters quantifying metastatic progression; (ii) had elevated serum levels of proinflammatory cytokines both before and at the end of the experiment; (iii) were more susceptible to hepatic metastasis. Interestingly, final levels of tumor necrosis factor (TNF)-a and interleukin (IL)-18 correlated with the extent of hepatic colonization by the melanoma cells. To confirm the metastasis-enhancing effect of MHV and M. pulmonis we measured the ability of B16M cells to metastasize in pathogen-free animals housed for increasing time-intervals in the vicinity of MHV + animals. Notably, susceptibility to metastasis was lower in animals seronegative to MHV than in MHV + mice, whereas the latter were less susceptible to metastasis than MHV + M. pulmonis + mice. Seropositive animals had increased levels of TNF-a and IL-18 suggesting that MHV and M. pulmonis enhance the metastatic ability of melanoma cells by inducing the release of proinflammatory cytokines. While our results highlight the importance of using pathogen-free animals in metastasis studies, they emphasize the need for a comprehensive health monitoring of the mice used in such studies, particularly in case of using facilities lacking appropriate containment measures. 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 
 Title: Effect of asymptomatic natural infections due to common mouse pathogens on the metastatic progression of B16 murine melanoma in C57BL/6 mice
Output: True