niryuu/sni-each-converted huggingface dataset:
Paragraph: To evaluate the role of human bocavirus (hBoV) as a causative agent of respiratory disease, the importance of the viral load in respiratory disease type and severity and the pathogenicity of the different hBoV species, we studied all hBoV-positive nasopharyngeal samples collected from children who attended an emergency room for a respiratory tract infection during three winters (). Human bocavirus was detected using the respiratory virus panel fast assay and real-time PCR. Of the 1,823 nasopharyngeal samples, 104 (5.7%) were positive for hBoV; a similar prevalence was observed in all three periods studied. Among hBoV-infected children, 53.8% were between 1-2 years old, and hBoV was detected alone in 57/104 (54.8%) cases. All of the detected hBoV strains belonged to genotype 1. The median hBoV load was significantly higher in samples containing strains with both the N546H and T590S mutations compared to other samples (p<0.05). Children with a single hBoV-1 infection more frequently had upper respiratory tract infections (URTIs) than those who were co-infected (37.0% vs 17.8%, respectively, p = 0.04). The duration of hospitalization was longer among children with high viral loads than that observed among children with low viral loads (8.0 ±2.2 days vs 5.0 ±1.5 days, respectively, p = 0.03), and the use of aerosol therapy was more frequent among children with high viral loads than among those with low viral loads (77.1% vs 55.7%, respectively, p = 0.04). This study shows that hBoV is a relatively uncommon but stable infectious agent in children and that hBoV1 seems to be the only strain detected in Italy in respiratory samples. From a clinical point of view, hBoV1 seems to have in the majority of healthy children relatively low clinical relevance. Moreover, the viral load influences only the duration of hospitalization and the use of aerosol therapy without any association with the site of the respiratory disease. 
 Title: Bocavirus Infection in Otherwise Healthy Children with Respiratory Disease
Output: False
Paragraph: Cryptosporidiosis of calves is caused by the enteroprotozoan Cryptosporidium spp. The disease results in intense diarrhea of calves associated with substantial economic losses in dairy farming worldwide. The aim of this study was to determine calf, herd, and within-herd Cryptosporidium prevalence and identify Cryptosporidium species and subtypes in calves with diarrhea in intensive dairy herds in central Argentina. A total of 1073 fecal samples were collected from 54 randomly selected dairy herds. Cryptosporidium-oocysts were isolated and concentrated from fecal samples using formol-ether and detected by light microscopy with the modified Ziehl-Neelsen technique. Overall prevalence of oocyst-excreting calves was found to be 25.5% (274/ 1073) (95% C.I. 22.9; 28.1%). Of the herds studied, 89% (48/54) included at least one infected calf, whereas within-herd prevalence ranged from the absence of infection to 57% (20/35). A highly significant association was found between the presence of diarrhea and C. parvum infection (χ 2 = 55.89, p < 0.001). For species determination, genomic DNA isolated from oocystpositive fecal samples was subjected to PCR-RFLP of the 18S rRNA gene resulting exclusively in Cryptosporidium parvum identification. C. parvum isolates of calves displaying diarrhea and high rate of excretion of oocysts were subtyped by PCR amplification and direct sequencing of the 60 kDa glycoprotein (GP60) gene. Altogether five GP60 subtypes, designated IIaA18G1R1, IIaA20G1R1, IIaA21G1R1, IIaA22G1R1, and IIaA24G1R1 were identified. Interestingly, IIaA18G1R1 and IIaA20G1R1 were predominant in calves with diarrhea and high infection intensity. Notably, IIaA24G1R1 represents a novel, previously unrecognized C. parvum subtype. The subtype IIaA18G1R1, frequently found in this study, is strongly implicated in zoonotic transmission. These results suggest that calves might be an important source for human cryptosporidiosis in Argentina. 
 Title: Prevalence of Cryptosporidium parvum in dairy calves and GP60 subtyping of diarrheic calves in central Argentina
Output: False
Paragraph: The mRPE65 protein is one form of the RPE65 protein and plays a very important role in the visual cycle. However, its 3D structure and detailed mechanism of function are still unclear because of difficulties with isolation and crystallization. This computational study reports a model for the mRPE65 protein structure derived from a model for sRPE65. The natural substrate for RPE65 has been shown to be a retinyl ester and, by utilizing the Autodock and the Ligplot programs, the interactions between the ester and the protein as well as the effects of several mutations on these interactions are studied. Finally, the position of the binding site is proposed based on an iterative process and the effects of the mutations on the binding site are also discussed. r 
 Title: Computational studies for the structure and function of mRPE65
Output: False
Paragraph: We provide the first genetic sequence data for a Dipylidium species from a wild carnivore plus an analysis of the effects of ecological, demographic, physiological and behavioural factors on Dipylidium sp. infection prevalence in a social carnivore, the spotted hyaena (Crocuta crocuta), in the Serengeti National Park, Tanzania. Our sequence data from a mitochondrial gene fragment (1176 base pair long) had a similarity of between 99% and 89% to Dipylidium caninum. We determined infection prevalence in 146 faecal samples from 124 known animals in three social groups (termed clans) using molecular screening and Dipylidium proglottid presence. Our analysis revealed significantly higher infection prevalence in juveniles (55%) than adults (15.8%), indicating that predominantly juveniles maintained infection in clans. The likelihood of infection in juveniles significantly: (1) increased as the number of adults and older juveniles (>6 months) at communal dens increased, implying a positive relationship between this factor and the size of the intermediate host (probably a flea species) population at communal dens; (2) decreased as the number of younger juveniles (<6 months) increased, suggesting that the chance of susceptible juveniles ingesting infected fleas during self-grooming declined as the number of infected fleas per younger juvenile declined; and (3) decreased during periods of low prey abundance in clan territories when an increased reliance on long-distances foraging excursions reduces the number of clan members visiting communal dens, possibly resulting in a decline in flea populations at dens. Long-distance foraging also increases the intervals (in days) between nursing visits by lactating females to their offspring. Lengthy intervals between milk intake by infected juveniles may reduce adult Dipylidium fecundity and hence decrease infection prevalence in the den flea population. Our study provides useful insights into Dipylidium epidemiology in a social carnivore population subject to large fluctuations in prey abundance. 
 Title: Factors influencing Dipylidium sp. infection in a free-ranging social carnivore, the spotted hyaena (Crocuta crocuta)
Output: True
Paragraph: This study compares the frequency and severity of influenza A/H1N1pdm09 (A/H1), influenza A/H3N2 (A/H3) and other respiratory virus infections in hospitalised patients. Data from 17 332 adult hospitalised patients admitted to Sir Charles Gairdner Hospital, Perth, Western Australia, with a respiratory illness between 2012 and 2015 were linked with data containing reverse transcription polymerase chain reaction results for respiratory viruses including A/H1, A/H3, influenza B, human metapneumovirus, respiratory syncytial virus and parainfluenza. Of these, 1753 (10.1%) had test results. Multivariable regression analyses were conducted to compare the viruses for clinical outcomes including ICU admission, ventilation, pneumonia, length of stay and death. Patients with A/H1 were more likely to experience severe outcomes such as ICU admission (OR 2.5, 95% CI 1.2-5.5, P = 0.016), pneumonia (OR 3.0, 95% CI 1.6-5.7, P < 0.001) and lower risk of discharge from hospital (indicating longer lengths of hospitalisation; HR 0.64 95% CI 0.47-0.88, P = 0.005), than patients with A/H3. Patients with a non-influenza respiratory virus were less likely to experience severe clinical outcomes than patients with A/H1, however, had similar likelihood when compared to patients with A/H3. Patients hospitalised with A/H1 had higher odds of severe outcomes than patients with A/H3 or other respiratory viruses. Knowledge of circulating influenza strains is important for healthcare preparedness. 
 Title: Epidemiology and Infection Post-pandemic influenza A/H1N1pdm09 is associated with more severe outcomes than A/H3N2 and other respiratory viruses in adult hospitalisations
Output: True
Paragraph: Background: Insect-borne diseases could induce severe symptoms in human and clinical signs in animals, such as febrility, erythra, arthralgia and hemorrhagic fever, and cause significant economic losses and pose public health threat all over the world. The significant advantages of Luminex xMAP technology are high-throughput, high parallel and automation. This study aimed to establish a liquid bead array based on Luminex xMAP technology that was able to simultaneously detect multiple insect-borne pathogens. Methods: Specific probes and primers to detect the nucleic acid of 10 insect-borne pathogens were designed. Probes were coupled with fluorescent carboxylated microspheres. The parameters of the system were optimized, including ratio of forward/reverse primers (1:2), hybridization temperature (50°C) and duration (30 min) and quantity of PCR product (2 μl). The sensitivity and specificity of the system were also evaluated. Moreover mixed nucleic acid of 10 insect-borne pathogens, including Bluetongue virus, Epizootic hemorrhagic disease virus of deer, Coxiella burnetii, African swine fever virus, West Nile fever virus, Borrelia burgdorferi, vesicular stomatitis virus, Rift Valley fever virus, Ebola virus and Schmalenberg's disease virus, and 3000 clinical samples were tested for practicability. Results: The optimized detection system showed high sensitivity, specificity and reproducibility. Each probe showed specific fluorescence signal intensity without any cross-hybridization for the other insect-borne pathogens tested, which included dengue virus, tick-borne encephalitis virus, Japanese encephalitis virus, Xinjiang hemorrhagic fever virus, spotted fever group rickettsiae, ehrlichiae and chikungunya virus. The limit of detection was 10 copies of target gene. Insect-borne pathogens were successfully detected among the 3000 clinical samples, and the results were consistent with those obtained using gold-standard assays or commercial nucleic acid detection kits. Conclusions: This optimized liquid array detection system was high-throughput and highly specific and sensitive in screening of the insect-borne pathogens. It was promising in detection of these pathogens for molecular epidemiological studies. 
 Title: Establishment and optimization of a liquid bead array for the simultaneous detection of ten insect-borne pathogens
Output: False
Paragraph: A modtfied live virus vaccine against feline infectious peritonitis (FIP) was evaluated in a double blind, placebo-controlled field trial in two high-risk populations. The vaccine was found to be safe and eficacious in one population of cats that had low antibody titre against feline coronavirus (FCo V) at the time of vaccination. Although clinically healthy at the time of vaccination, retrospectively some vaccinees that later came down with FIP were found to be RT-PCR positive for FCoV in plasma and showed changes in blood parameters consistent with early stage of FIP. It is concluded that vaccination can protect cats with no or low FCoV antibody titres and that in some cats vaccine failure was probably due to pre-existing infection. 0 1997 Elsevier Science Ltd. 
 Title: Placebo-controlled evaluation of a modified life virus vaccine against feline infectious peritonitis: safety and efficacy under field conditions
Output: False
Paragraph: There is a continuing threat that the highly pathogenic avian influenza virus will cause future influenza pandemics. In this study, we screened a library of compounds that are biologically active and structurally diverse for inhibitory activity against influenza neuraminidase (NA). We found that aurintricarboxylic acid (ATA) is a potent inhibitor of NA activity of both group-1 and group-2 influenza viruses with IC 50 s (effective concentration to inhibit NA activity by 50%) values at low micromolar concentrations. ATA was equally potent in inhibiting the NA activity derived from wild-type NA and its H274Y mutant which renders NA resistance to inhibition by oseltamivir. Although ATA is structurally distinct from sialic acid, molecular modeling experiments suggested that ATA binds to NA at the enzyme's substrate binding site. These results indicate that ATA may be a good starting material for the design of a novel class of NA inhibitors for the treatment influenza viruses. 
 Title: Aurintricarboxylic acid inhibits influenza virus neuraminidase
Output: False
Paragraph: Eosinophilic enteritis (EOE) is a type of inflammatory bowel disease and is characterized clinically by chronic obstinate diarrhea. Three Japanese Black (JB) fattening cattle (2 males and 1 female) on different cattle farms presented with chronic episodic diarrhea without fever or dehydration. Soft reddish spherical carneous tissues (1−3 cm) were occasionally excreted within the diarrheic feces. Administration of antibiotics, antidiarrheal drugs and vermicides had no therapeutic effect, but dexamethasone improved the fecal characteristics. The symptoms persisted until the animals were slaughtered at 27-30 months of age. Histopathological examination of the intestines revealed marked eosinophilic infiltration in the lamina propria and submucosa. From these findings, we diagnosed these cattle as the first cases of EOE in Jb cattle. KEY WORDS: eosinophilic enteritis, inflammatory bowel disease, Japanese Black cattle 
 Title: Three cases of idiopathic eosinophilic enteritis with chronic obstinate diarrhea in Japanese Black fattening cattle
Output: True
Paragraph: Immunoinformatics has recently emerged as a critical field for accelerating immunology research. Although still an evolving process, computational models now play instrumental roles, not only in directing the selection of key experiments, but also in the formulation of new testable hypotheses through detailed analysis of complex immunologic data that could not be achieved using traditional approaches alone. Immunomics, which combines traditional immunology with computer science, mathematics, chemistry, biochemistry, genomics and proteomics for the large-scale analysis of immune system function, offers new opportunities for future bench-to-bedside research. In this article, we review the latest trends and future directions of the field. The human immune system is highly combinatorial in nature. A large repertoire of immunoglobulins (IG) (10 12 ) and T cell receptors (TR) (10 12 ) is generated by mechanisms such as the combinatorial diversity of the variable (V), diversity (D) and joining (J) genes, the N-diversity, and for IG, the somatic hypermutations Reviews INFORMATICS 
 Title: Immunoinformatics: Current trends and future directions
Output: True
Paragraph: Influenza viruses cause respiratory infections every epidemic season regardless of the patient's age. The aim of this study was to determine the activity of respiratory viruses in the epidemic season 2016/2017 in Poland, with particular emphasis on influenza viruses among people aged over 14. There were 2982 clinical samples taken from patients from four age groups: 15-25, 26-44, 45-64, and 65 years tested under the Sentinel and non-Sentinel surveillance programs. The presence of influenza viruses was confirmed in more than 40% of cases, the predominant type was influenza A virus unsubtyped, followed by subtype A/H3N2/. The results for the four age groups indicate that the highest number of confirmed respiratory viruses was recorded in individuals 65 years of age, slightly less, in the decreasing order, in the age groups 45-64 years, 15-25 years, and 26-44 years. Influenza type B infections were observed only in sporadic cases. Given the epidemiological data, epidemic season 2016/ 2017 was characterized by similar dynamics compared to the previous season in Poland and also in most of the European countries. More than 4 million cases and suspected cases of influenza and influenza-like viruses have been reported in Poland, more than 16,000 hospitalizations, and 25 deaths, of which 20 cases occurred among people 65 years of age in the epidemic season 2016/2017. 
 Title: Respiratory Infections with Particular Emphasis on Influenza Virus Activity in Persons Over 14 Years of Age in the Epidemic in Poland
Output: False
Paragraph: Understanding the interactions between host and pathogen is important for the development and assessment of medical countermeasures to infectious agents, including potential biodefence pathogens such as Bacillus anthracis, Ebola virus, and Francisella tularensis. This review focuses on technological advances which allow this interaction to be studied in much greater detail. Namely, the use of "omic" technologies (next generation sequencing, DNA, and protein microarrays) for dissecting the underlying host response to infection at the molecular level; optical imaging techniques (flow cytometry and fluorescence microscopy) for assessing cellular responses to infection; and biophotonic imaging for visualising the infectious disease process. All of these technologies hold great promise for important breakthroughs in the rational development of vaccines and therapeutics for biodefence agents. 
 Title: The Impact of ''Omic'' and Imaging Technologies on Assessing the Host Immune Response to Biodefence Agents
Output: True
Paragraph: Cut-off Cut-off Supplementary Figure 1 | Setting cut-off to identify links and hidden source. (a) Coarse-grained distribution of element values ln(1 − λ i )a ij times −1 in the reconstructed vector X of all nodes in a Newman-Watts small-world network (NW), where bin accumulation is implemented for the original distribution. The peak centered at zero corresponds to null connections and the other corresponds to actual links. A cut-off value can be set within the gap between the two peaks. (b) The values of ln(1 − λ i )a ij times -1 in the reconstructed vector X for Erdös-Rényi random networks (ER), Watts-Strogatz small-world networks (WS), NW and Barabási-Albert scale-free networks (BA), where green and yellow points correspond to existent links and null connections, respectively. All the networks share the same cut-off value of about 0.13. (c) Coarse-grained distribution of the structural variance σ in the NW network, where bin accumulation is exercised on the original distribution. The largest peak centered close zero corresponds to nodes of indirect neighbors of the hidden source and the large positive values of σ are associated with the immediate neighbors of the hidden source. A cut-off can be set within the largest gap. (d) The variance σ * i of element values in the reconstructed vector x of all nodes in the presence of a hidden source for ER, WS, NW and BA networks, where green and yellow points correspond to immediate neighbors and indirect neighbors of the hidden source, respectively. All the networks share the same cut-off values of about σ * i = 0.9. The network size in a,b is 200 and in c,d is 50, Θ = 0.25, ∆ = 0.45, λ i and δ i are uniformly distributed in the ranges (0.2, 0.4) and (0.4, 0.6), respectively. SIS dynamics are used for the illustration. Panels a and c correspond to Fig. 2a with nt = 0.4 and Fig. 5 in the main text, respectively. 
 Title: Supplementary Figures
Output: False
Paragraph: Porcine epidemic diarrhea virus (PEDV) is an important pathogen that has a significant economic impact on the swine industry by imposing a high rate of mortality in suckling piglets. However, limited information on the productivity values of gilts and sows infected with PEDV is available. Here, we evaluate the productivity index in gilts and sows during the 1year period before (19 
 Title: Impact of Mated Female Nonproductive Days in Breeding Herd after Porcine Epidemic Diarrhea Virus Outbreak
Output: False
Paragraph: Background: Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium harbors useful information on the shape of the molecule that in turn can give insights into the interplay of its functional domains. Result: Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between a fixed pair of nucleotides can be computed in polynomial time by means of dynamic programming. While a naïve implementation would yield recursions with a very high time complexity of O(n 6 D 5 ) for sequence length n and D distinct distance values, it is possible to reduce this to O(n 4 ) for practical applications in which predominantly small distances are of of interest. Further reductions, however, seem to be difficult. Therefore, we introduced sampling approaches that are much easier to implement. They are also theoretically favorable for several real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules. Conclusions: The graph-distance distribution can be computed using a dynamic programming approach. Although a crude approximation of reality, our initial results indicate that the graph-distance can be related to the smFRET data. The additional file and the software of our paper are available from http://www.rna.uni-jena.de/RNAgraphdist.html. The distance distribution within an RNA molecule is of interest in various contexts. Most directly, the question arises whether panhandle-like structures (in which 3' and 5' ends of long RNA molecules are placed in close proximity) are the rule or an exception. Panhandles have been reported in particular for many RNA virus genomes. Several studies [1-4] agree based on different models that the two ends of single-stranded RNA molecules are typically not far apart. On a more technical level, the problem 
 Title: Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures
Output: True
Paragraph: Waste ashes from three types of hospital waste (HW) incinerators, built in SARS (Severe Acute Respiratory Syndrome) period and currently running in China, were collected and polycyclic aromatic hydrocarbons (PAH) properties in the ashes were investigated. The mean ∑PAH levels in the waste ashes varied widely from 4.16 mg kg − 1 to 198.92 mg kg − 1 , and the mean amounts of carcinogenic PAHs ranged from 0.74 to 96.77 mg kg − 1 , exceeding the limits regulated by several countries. Among the three types of incinerators, two medium-scale incinerators generated relatively high levels of PAHs (mean ∑PAH 22.50 and 198.92 mg kg − 1 ) compared to small-scale and large-scale incinerators (mean ∑PAH 4.16 and 16.43 mg kg − 1 ). Bottom ashes were dominated by low molecular weight PAHs (LM-PAH; containing two-to three-ringed PAHs) and medium molecular weight PAHs (MM-PAH; containing four-ringed PAHs), while fly ashes were abundant in MM-PAH and high molecular weight PAHs (HM-PAH, containing five-to six-ringed PAHs). Statistical analysis indicated that there was a positive relationship (R 2 = 0.88) between organic matter and total PAHs thus it has the potential to be used as an indicator for PAHs in HW ashes. Moreover, it was found that PAHs in the ashes correlated highly with some metallic elements either positively (e.g. Fe, Ti, Mg) or negatively (Ca), indicating that these elements might promote or prevent PAH formation during HW combustion. Although bottom ash resulted from HW incinerators has not been classified as hazardous material, the results of this study indicated that this type of waste ash contained high levels of PAHs thus need special treatment before landfill. Hospital waste ash Carcinogenic substance Molecular weight distribution Heavy metal ⁎ Corresponding author. Tel.: +86 10 6284 9515; fax: +86 10 6289515. a v a i l a b l e a t w w w. s c i e n c e d i r e c t . c o m w w w. e l s e v i e r. c o m / l o c a t e / s c i t o t e n v 
 Title: Levels of polycyclic aromatic hydrocarbons in different types of hospital waste incinerator ashes
Output: True
Paragraph: Murine hepatitis viruses provide excellent animal models for the study of virus-induced diseases of the central nervous system and gastrointestinal tract. Several studies have indirectly provided evidence that the spike glycoprotein (S) of these coronaviruses bears determinants for pathogenesis and the induction of protective immunity. In order to directly evaluate the immunogenicity of this protein, it was purified by affinity chromatography with an in vitro neutralizing and in vivo protective monoclonal antibody which immunoprecipitated the 180-kDa spike glycoprotein of the neurotropic A59 strain of murine hepatitis virus (MHV-A59). Mice immunized twice with approximately 1 ag of purified S in Freund's adjuvant developed high titers of neutralizing and fusion inhibiting antibodies, even though the protein was at least partially denaturated after elution from the affinity column. Moreover, these mice were protected from lethal encephalitis when challenged intracerebrally with 10 LDso of MHV-A59. This study provides a direct demonstration of the importance of the coronavirus spike giycoprotein in the induction of a protective immune response. o 1SSoAcademic press. Inc. 
 Title: Protection from Lethal Coronavirus Infection by Affinity-Purified Spike Glycoprotein of Murine Hepatitis Virus, Strain A59
Output: False
Paragraph: Shigella spp. are pathogenic bacteria that cause bacillary dysentery in humans by invading the colonic and rectal mucosa where they induce dramatic inflammation. Here, we have analyzed the role of the soluble PRR Pentraxin 3 (PTX3), a key component of the humoral arm of innate immunity. Mice that had been intranasally infected with S. flexneri were rescued from death by treatment with recombinant PTX3. In vitro PTX3 exerts the antibacterial activity against Shigella, impairing epithelial cell invasion and contributing to the bactericidal activity of serum. PTX3 is produced upon LPS-TLR4 stimulation in accordance with the lipid A structure of Shigella. In the plasma of infected patients, the level of PTX3 amount only correlates strongly with symptom severity. These results signal PTX3 as a novel player in Shigella pathogenesis and its potential role in fighting shigellosis. Finally, we suggest that the plasma level of PTX3 in shigellosis patients could act as a biomarker for infection severity. Soluble pattern recognition molecules, PRMs, are components of the humoral arm of innate immunity. The long pentraxin 3, PTX3, is a prototypic soluble PRM that is produced in response to primary inflammatory signals. Shigella spp. are human enteropathogens which invade colonic and rectal mucosa where they cause deleterious inflammation. We show that PTX3 acts as an ante-antibody and contributes to the clearance of extracellular Shigella. As a countermeasure, Shigella uses invasiveness and low-inflammatory LPS to control PTX3 release in infected cells. This study highlights that the PLOS Pathogens | https://doi. 
 Title: Role of a fluid-phase PRR in fighting an intracellular pathogen: PTX3 in Shigella infection
Output: True
Paragraph: Exotic small mammal medicine is a relatively new specialty area within veterinary medicine. Ferrets, rabbits, and rodents have long been used as animal models in human medical research investigations, resulting in a body of basic anatomic and physiologic information that can be used by veterinarians treating these species. Unfortunately, there is a paucity of veterinary articles that describe clinical presentation, diagnosis, and treatment options of gastrointestinal (GI) disease as it affects exotic small mammals. Although there is little reference material relating to exotic small mammal GI disease, patients are commonly presented to veterinary hospitals with digestive tract disorders. This article provides the latest information available for GI disease in ferrets (Helicobacter mustelae gastritis, inflammatory bowel disease [IBD], GI lymphoma, systemic coronavirus, coccidiosis, and liver disease), rabbits (GI motility disorders, liver lobe torsion, astrovirus, and coccidiosis), guinea pigs (gastric dilatation volvulus [GDV]), rats (Taenia taeniaeformis), and hamsters (Clostridium difficile). Both noninfectious diseases and emerging infectious diseases are reviewed as well as the most up-to-date diagnostics and treatment options. 
 Title: TOPICS IN MEDICINE AND SURGERY GASTROINTESTINAL DISEASE IN EXOTIC SMALL MAMMALS
Output: True
Paragraph: Background: Middle East respiratory syndrome coronavirus (MERS-CoV) consists of a positive-sense, single-stranded RNA genome and four structural proteins: the spike, envelope, membrane, and nucleocapsid protein. The assembly of the viral genome into virus particles involves viral structural proteins and is believed to be mediated through recognition of specific sequences and RNA structures of the viral genome. Methods and Results: A culture system for the production of MERS coronavirus-like particles (MERS VLPs) was determined and established by electron microscopy and the detection of coexpressed viral structural proteins. Using the VLP system, a 258-nucleotide RNA fragment, which spans nucleotides 19,712 to 19,969 of the MERS-CoV genome (designated PS258(19712-19969) ME ), was identified to function as a packaging signal. Assembly of the RNA packaging signal into MERS VLPs is dependent on the viral nucleocapsid protein. In addition, a 45-nucleotide stable stem-loop substructure of the PS258(19712-19969) ME interacted with both the N-terminal domain and the Cterminal domain of the viral nucleocapsid protein. Furthermore, a functional SARS-CoV RNA packaging signal failed to assemble into the MERS VLPs, which indicated virus-specific assembly of the RNA genome. Conclusions: A MERS-oV RNA packaging signal was identified by the detection of GFP expression following an incubation of MERS VLPs carrying the heterologous mRNA GFP-PS258(19712-19969) ME with virus permissive Huh7 cells. The MERS VLP system could help us in understanding virus infection and morphogenesis. 
 Title: Nucleocapsid protein-dependent assembly of the RNA packaging signal of Middle East respiratory syndrome coronavirus
Output: False
Paragraph: A unique subline of BALB/c mice, designated BALB/cV, exhibits an intermediate mammary tumor incidence (47%) and harbors a distinct milk-transmitted mouse mammary tumor virus (MMTV). The BALB/cV subline was used to study the molecular basis of potential virus-host interactions involving cell surface-expressed MMTV proteins. Cell surface iodination identified virus-specific proteins expressed on BALB/cV primary mammary tumor cells grown in culture. In contrast to (C3H)MMTV-producing cell lines which expressed MMTV gp52, BALB/cV tumor cells lacked gp52 and expressed instead a 68K, env-related protein. The 68K"" protein was also detected on the surface of metabolically labeled BALB/cV tumor cells by an external immunoprecipitation technique. The expression of 68Kp"" was restricted to mammary tissues of BALB/cV mice that also expressed other MMTV proteins. Biochemical analysis established that 68K"" was not modified by N-linked glycosylation. '%I-labeled 68K"" was rapidly released into the media of tumor cell cultures and was recovered both in the form of a soluble protein and in a 100,OOOg pellet. The biologic function of this cell surface-expressed viral protein remains unknown. 
 Title: Identification and Characterization of a Mouse Mammary Tumor Virus Protein Uniquely Expressed on the Surface of BALB/cV Mammary Tumor Cells
Output: True
Paragraph: Objectives: To measure the spatial contagion of severe acute respiratory syndrome (SARS) in Beijing and to test the different epidemic factors of the spread of SARS in different periods. Methods: A join-count spatial statistic study was conducted and the given hypothetical processes of the spread of SARS in Beijing were tested using various definitions of 'joins'. Results: The spatial statistics showed that of the six diffusion processes, the highest negative autocorrelation occurred in the doctor-number model (M-5) and the lowest negative autocorrelation was found in the population-amount model (M-3). The results also showed that in the whole 29-day research period, about hour or more days experienced a significant degree of contagion. Conclusions: Spatial analysis is helpful in understanding the spatial diffusion process of an epidemic. The geographical relationships were important during the early phase of the SARS epidemic in Beijing. The statistic based on the number of doctors was significant and more informative than that of the number of hospitals. It reveals that doctors were important in the spread of SARS in Beijing, and hospitals were not as important as doctors in the contagion period. People are the key to the spread of SARS, but the population density was more significant than the population size, although they were both important throughout the whole period. 
 Title: Understanding the spatial diffusion process of severe acute respiratory syndrome in Beijing
Output: True
Paragraph: Global terrorism is a rapidly growing threat to world security, and increases the risk of bioterrorism. In this Review, we discuss the potential threat of bioterrorism, agents that could be exploited, and recent developments in technologies and policy for detecting and controlling epidemics that have been initiated intentionally. The local and international response to infectious disease epidemics, such as the severe acute respiratory syndrome and west African Ebola virus epidemic, revealed serious shortcomings which bioterrorists might exploit when intentionally initiating an epidemic. Development of new vaccines and antimicrobial therapies remains a priority, including the need to expedite clinical trials using new methodologies. Better means to protect health-care workers operating in dangerous environments are also needed, particularly in areas with poor infrastructure. New and improved approaches should be developed for surveillance, early detection, response, effective isolation of patients, control of the movement of potentially infected people, and risk communication. Access to dangerous pathogens should be appropriately regulated, without reducing progress in the development of countermeasures. We conclude that preparedness for intentional outbreaks has the important added value of strengthening preparedness for natural epidemics, and vice versa. This is the second in a Series of three papers about terrorism and health in collaboration with The Lancet Psychiatry 
 Title: Series Terrorism and health 2 Confronting the threat of bioterrorism: realities, challenges, and defensive strategies
Output: True
Paragraph: The human coronaviruses (CoV) include HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1, some of which have been known for decades. The severe acute respiratory syndrome (SARS) CoV briefly emerged into the human population but was controlled. In 2012, another novel severely human pathogenic CoV-the Middle East Respiratory Syndrome (MERS)-CoV-was identified in the Kingdom of Saudi Arabia; 80% of over 2000 human cases have been recorded over five years. Targeted research remains key to developing control strategies for MERS-CoV, a cause of mild illness in its camel reservoir. A new therapeutic toolbox being developed in response to MERS is also teaching us more about how CoVs cause disease. Travel-related cases continue to challenge the world's surveillance and response capabilities, and more data are needed to understand unexplained primary transmission. Signs of genetic change have been recorded, but it remains unclear whether there is any impact on clinical disease. How camels came to carry the virus remains academic to the control of MERS. To date, human-to-human transmission has been inefficient, but virus surveillance, characterisation, and reporting are key to responding to any future change. MERS-CoV is not currently a pandemic threat; it is spread mainly with the aid of human habit and error. 
 Title: An Opportunistic Pathogen Afforded Ample Opportunities: Middle East Respiratory Syndrome Coronavirus
Output: False
Paragraph: Sato, K., Inaba, Y., Kurogi, H., Takahashi, E., Satoda, K., Omori, T. and Matumoto, M.t 1977. Hemagglutination by calf diarrhea coronavirus. Vet. Microbiol., 2: 83--87. The virus was grown in BEK-1 cells, a stable cell line from bovine embryo kidney, and tested for hemagglutinafion (HA) with erythrocytes of a variety of species at 4°C, room temperature and 37°C. HA was observed at all temperatures with chicken, mouse, rat, and hamste~ erythrocytes but not with erythrocytes of human (O), cattle, horses, ~heep, guinea pigs, geese, duck~, pigeons and l-day-old chicks. Chickens showed a~ individual variation in agglutinability of their erythrocytes, requiring selection of birds to obtain erythrocytes for HA. HA reaction was inhibited by specific antiserum. Some factors involved in HA and HA inhibition (HI) were investigated and standard HA and HI tests were worked out. 
 Title: Short Communication HEMAGGLUTINATION BY CALF DIARRHEA CORONAVIRUS
Output: False
Paragraph: Antibody-based therapeutics is attracting more attention in the post-genome era, in contrast to a diminution in the initial high expectation for rapid development of gene-based therapeutic modalities. In support to the antibody-based therapeutics, the advent of recent technologies has made human antibody screening and production progressively more economic. Among those technologies, phage-display antibody library has been successfully applied in the antibody-based drug development both as fully human antibody sources and tools for antibody engineering. Building up a high-quality antibody library with a large library size and high diversity has been crucial for successful isolation of antibodies. Here we describe an efficient strategy for the construction of a large naïve phage-display human Fab library with one-step cloning. Optimization of each key step is extensively discussed and simplified protocols for library panning and Fab production are also described. Phage display; Fab; antibody library; IgM; one-step cloning Building a high-quality phage-displayed antibody library requires a source of large number of well-diversified antibody genes. A variety of immunoglobulin gene sources including blood lymphocytes, bone marrow, and spleen have been used for library construction. From these sources IgM-derived antibody genes have been successfully used for library construction and selection of high-affinity antibodies (4-7), even though IgM-specific antibodies are typically of relatively low affinity in vivo compared to antibodies from the 
 Title: Construction of a Large Naïve Human Phage-Displayed Fab Library Through One-Step Cloning
Output: True
Paragraph: The spike (S) protein of porcine transmissible gastroenteritis virus (TGEV) is located within the viral envelope and is the only structural protein that possesses epitopes capable of inducing virus-neutralizing antibodies. Among the four N-terminal antigenic sites A, B, C, and D, site A and to a lesser extent site D (S-AD) induce key neutralizing antibodies. Recently, we expressed S-AD (rS-AD) in recombinant form. In the current study, we used the rS-AD as an immobilized target to identify peptides from a phage-display library with application for diagnosis. Among the 9 phages selected that specifically bound to rS-AD, the phage bearing the peptide TLNMHLFPFHTG bound with the highest affinity and was subsequently used to develop a phage-based ELISA for TGEV. When compared with conventional antibody-based ELISA, phagemediated ELISA was more sensitive; however, it did not perform better than semi-quantitative RT-PCR, though phage-mediated ELISA was quicker and easier to set up. 
 Title: Phage display for identifying peptides that bind the spike protein of transmissible gastroenteritis virus and possess diagnostic potential
Output: True
Paragraph: The emergence of the highly pathogenic SARS coronavirus (SARS-CoV) has reignited interest in coronavirus biology and pathogenesis. An emerging theme in coronavirus pathogenesis is that the interaction between specific viral genes and the host immune system, specifically the innate immune system, functions as a key determinant in regulating virulence and disease outcomes. Using SARS-CoV as a model, we will review the current knowledge of the interplay between coronavirus infection and the host innate immune system in vivo, and then discuss the mechanisms by which specific gene products antagonize the host innate immune response in cell culture models. Our data suggests that the SARS-CoV uses specific strategies to evade and antagonize the sensing and signaling arms of the interferon pathway. We summarize by identifying future points of consideration that will contribute greatly to our understanding of the molecular mechanisms governing coronavirus pathogenesis and virulence, and the development of severe disease in humans and animals. 
 Title: SARS CORONAVIRUS AND INNATE IMMUNITY
Output: True
Paragraph: Newcastle disease (ND) is regarded throughout the world as one of the most important diseases of poultry, not only due to the serious disease and high flock mortality that may result from some ND virus (NDV) infections, but also through the economic impact that may ensue due to trading restrictions and embargoes placed on areas and countries where outbreaks have occurred. All ages of pheasants are purported to be highly susceptible to infection with NDV, but clinical signs and mortality levels in infected birds vary considerably. This article reviews the available literature relating to infections in pheasants, describing the clinical presentation of the disease and the epidemiological role these hosts may have in the spread of ND. 
 Title: Newcastle disease in pheasants (Phasianus colchicus): A review
Output: False
Paragraph: Cholesterol present in the plasma membrane of target cells has been shown to be important for the infection by SARS-CoV. We show that cholesterol depletion by treatment with methyl-β-cyclodextrin (mβCD) affects infection by SARS-CoV to the same extent as infection by vesicular stomatitis virus-based pseudotypes containing the surface glycoprotein S of SARS-CoV (VSV-ΔG-S). Therefore, the role of cholesterol for SARS-CoV infection can be assigned to the S protein and is unaffected by other coronavirus proteins. There have been contradictory reports whether or not angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV, is present in detergent-resistant membrane domains. We found that ACE2 of both Vero E6 and Caco-2 cells co-purifies with marker proteins of detergent-resistant membranes supporting the notion that cholesterol-rich microdomains provide a platform facilitating the efficient interaction of the S protein with the cellular receptor ACE2. To understand the involvement of cholesterol in the initial steps of the viral life cycle, we applied a cell-based binding assay with cells expressing the S protein and cells containing angiotensin-converting enzyme 2 (ACE2). Alternatively, we used a soluble S protein as interaction partner. Depletion of cholesterol from the ACE2-expressing cells reduced the binding of S-expressing cells by 50% whereas the binding of soluble S protein was not affected. This result suggests that optimal infection requires a multivalent interaction between viral attachment protein and cellular receptors. 
 Title: Importance of cholesterol-rich membrane microdomains in the interaction of the S protein of SARS-coronavirus with the cellular receptor angiotensin-converting enzyme 2
Output: False
Paragraph: The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV Ple ), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA W ST = 0.92; nDNA F ST = 0.18), and reduced gene flow, which, along with large differences in seroprevalence of six distinct FIV Ple subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa (,324,000-169,000 years ago), which expanded during the Late Pleistocene (,100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition (,14,000-7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV Ple variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently. This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. 
 Title: The Evolutionary Dynamics of the Lion Panthera leo Revealed by Host and Viral Population Genomics
Output: True
Paragraph: CD8 + cytotoxic T cell (CTL) responses are necessary for the lysis of virally infected cells and control of infection. CTLs are activated when their TCRs bind a major histocompatibility complex (MHC)-I/peptide complex on the surface of antigen presenting cells such as macrophages (MΦ). It is now apparent that MΦ display remarkable plasticity in response to environmental signals to polarize into classically activated M(LPS + IFN-γ) or alternatively activated M(IL-4). However, little is known about how MΦ activation status influences their antigen presentation function to CD8 + T cell in models of virus infection. Consequently, we tested how polarization of spleen-derived (Sp)-MΦ impacts direct presentation of viral antigens to influence effector and proliferative CD8 + T-cell responses. We show that M(IL-4) Sp-MΦ retain MHC-I surface expression and the ability to stimulate IFN-γ production by CTL following peptide stimulation and lymphocytic choriomeningitis virus infection to levels similar to M0 and M(LPS + IFN-γ) MΦ. However, memory CD8 + T cells cultured in the presence of M(IL-4) MΦ underwent significantly reduced proliferation and produced similar IFN-γ levels as coculturing with M0 or M(LPS + IFN-γ) cells. Thus, these results show a novel ability of polarized MΦ to regulate CD8 + T-cell proliferation and effector functions during virus infection. 
 Title: M(il-4) Tissue Macrophages support efficient interferon-gamma Production in antigen-specific cD8 + T cells with reduced Proliferative capacity
Output: True