niryuu/sni-each-converted huggingface dataset:
Paragraph: Avian infectious bronchitis virus (IBV) is a member of the group III coronaviruses, which differ from the other groups of coronaviruses in that they do not encode the essential pathogenic factor nonstructural protein 1 (nsp1) and instead start with nsp2. IBV nsp2 is one of the first replicase proteins to be translated and processed in the viral life cycle; however, it has an entirely unknown function. In order to better understand the structural details and functional mechanism of IBV nsp2, the recombinant protein was cloned, overexpressed in Escherichia coli, purified and crystallized. The crystals diffracted to 2.8 Å resolution and belonged to space group P2 1 , with unit-cell parameters a = 57.0, b = 192.3, c = 105.7 Å , = 90.8 . Two molecules were found in the asymmetric unit; the Matthews coefficient was 3.9 Å 3 Da À1 , corresponding to a solvent content of 68.2%. 
 Title: Structural Biology and Crystallization Communications Purification, crystallization and preliminary X-ray analysis of nonstructural protein 2 (nsp2) from avian infectious bronchitis virus
Output: False
Paragraph: Cardio-vascular diseases are the leading cause of morbidity and mortality. Ischemia is a state of oxygen deprivation in tissues, whereas reperfusion is restoration of blood flow in ischemic tissues. Myocardial damage of tissue during reperfusion after ischemic insult is known as myocardial ischemia-reperfusion (I/R) injury. It induces damage to cardiac muscle via increasing expression of oxygen, sodium and calcium ions which are responsible in the activation of proteases and cell death. Heart renin angiotensin system (RAS) plays an important role in the myocardial ischemia and reperfusion injury. Angiotensin (1-7) is responsible for vasodilation and angiotensin II for vasoconstriction. Here-in we reviewed how myocardial I/R injury sets in by up-regulation of angiotensin II that leads to increased infarct size, which can be reduced by the use of ACE inhibitors, ACE2 activators and angiotensin II antagonist. ß 
 Title: Role of cardiac renin angiotensin system in ischemia reperfusion injury and preconditioning of heart
Output: True
Paragraph: Severe viral infections, including hemorrhagic fever and encephalitis, occur throughout the world, but are most prevalent in developing areas that are most vulnerable to infectious diseases. Some of these can also infect related species as illustrated by the threatened extinction of gorillas by Ebola infection in west and central Africa. There are no safe and effective treatments available for these serious infections. In addition to the logistical difficulties inherent in developing a drug for infections that are sporadic and occur mainly in the third world, there is the overwhelming barrier of no hope for return on investment to encourage the pharmaceutical industry to address these unmet medical needs. Therefore, the National Institute of Allergy and infectious Disease (NIAID) has developed and supported a variety of programs and resources to provide assistance and lower the barrier for those who undertake these difficult challenges. The primary programs relevant to the development of therapies for severe viral infections are described and three case studies illustrate how they have been used. In addition, contact information for accessing these resources is supplied. Published by Elsevier B.V. 
 Title: NIAID resources for developing new therapies for severe viral infections
Output: True
Paragraph: Background: An outbreak of leishmaniosis was studied in cats and dogs housed together with no separation in an animal shelter in Israel. The study included recording of clinical signs, serology for Leishmania infection by ELISA, PCR of blood for Leishmania DNA by ITS1 HRM and kDNA PCR, parasite quantification, and trapping of sand flies around the shelter. Results: Thirty-seven % (22/60) of the dogs and 75% (50/67) of the cats were seropositive to L. infantum with a significantly higher seropositivity rate in the cat population (χ 2 = 42.160, P < 0.0001). Twenty-five percent (15/60) of the dogs were positive for Leishmania by blood PCR, 12% by the Leishmania ITS1 HRM PCR and 22% by kDNA PCR. Of the cats, 16% (11/67) were positive by kDNA PCR and none by ITS1 HRM PCR. All the PCR-positive animals were infected by L. infantum verified by DNA sequencing and there was no significant difference between the PCR-positivity in the dog and cat populations. Altogether, 43% (26/60) of the dogs and 79% (53/67) of the cats were positive by serology or PCR for L. infantum. The average Leishmania parasite load in the blood of PCR-positive dogs (42,967 parasites/ml) was significantly higher than in PCR-positive cats (1259 parasites/ml) (t (12) = 2.33, P = 0.037). Dogs that were positive by the Leishmania ITS1 HRM PCR and kDNA PCR had significantly higher parasite loads than dogs positive only by the kDNA PCR (t (11) = − 3.186580, P < 0.009). No significant effect was found for FIV seropositivity on Leishmania infection in the cats (χ 2 = 0.506, P = 0.777). A higher percentage of Leishmania-positive dogs showed clinical signs compatible with leishmaniosis compared to Leishmania-positive cats (100 vs 52.8%, χ 2 =15.242, P < 0.0001). Phlebotomus perfiliewi, a proven vector of L. infantum, comprised 92% of trapped sand flies. Comparisons of populations of cats and dogs exposed to sand flies and L. infantum under the same conditions indicated that although a high rate of exposure was detected in cats as manifested by a significantly greater degree of seropositivity, dogs had significantly higher blood parasite loads, and were likely to be more infectious to sand flies than cats. 
 Title: Leishmania infection in cats and dogs housed together in an animal shelter reveals a higher parasite load in infected dogs despite a greater seroprevalence among cats
Output: True
Paragraph: Collagen is one of the most abundant and important proteins in the human body. Human collagen type III (hCOL3A1) belongs to the fibril-forming collagens and is widely distributed in extensible connective tissue like skin, internal organs, or the vascular system. It plays key roles in wound healing, collagen fibrillogenesis, and normal cardiovascular development in human. The charged residues are considered to be an important characteristic of hCOL3A1, especially for collagen binding and recognition. Here we found that a triple helix fragment of hCOL3A1, Gly489-Gly510, contained multiple charged residues, as well as representative Glu-Lys-Gly and Glu-Arg-Gly charged triplets. We solved the crystal structure of this new fragment to a high-resolution of 1.50 Å and identified some important conformations of this new triple-helix region, including strong hydrogen bonds in interchain and interhelical interactions in addition to obvious flexible bending for the triple helix. We also found that the synthetic collagen peptides around this region exhibited potent activities through integrin-mediated peptide-membrane interaction. We then developed a method to produce a recombinant protein consisting of 16 tandem repeats of the triple-helix fragment of hCOL3A1 with strong activity without cytotoxicity. These results provide a strong base for further functional studies of human collagen type III and the method developed in this study can be applied to produce hCOL3A1-derived proteins or other tandem-repeat proteins with membrane adhesion activity. 
 Title: Characterization by high-resolution crystal structure analysis of a triple-helix region of human collagen type III with potent cell adhesion activity
Output: False
Paragraph: . MOG 35-55 -specific T cell responses in J␣18 Ϫ/Ϫ mice treated with CEACAM1-Fc fusion protein or with AgB10. J␣18 Ϫ/Ϫ mice were treated with CEACAM1-Fc fusion protein (A) or AgB10 (B) twice per week from the day of immunization with MOG 35-55. Eleven days after the immunization, draining lymph node cells were incubated with MOG 35-55. Supernatants were collected from the culture and measured for the concentration of IFN-␥ and IL-17 by ELISA. Data represent the mean Ϯ SEM of samples from one of two independent experiments (n ϭ 3 mice). 
 Title: Carcinoembryonic Antigen-Related Cell Adhesion Molecule 1 Modulates Experimental Autoimmune Encephalomyelitis via an iNKT Cell-Dependent Mechanism
Output: True
Paragraph: Administration of recombinant feline interferon-v (rFeIFN) has been proposed for the prophylaxis of canine and feline parvovirosis. In the present study, the influence of the administration of rFeIFN on blood markers of inflammation (a-globulins, a 1acid glycoprotein) and immune system activation (g-globulins, IgG, IgM, specific anti-feline parvovirus IgG or IgM) was evaluated in a cattery developing an outbreak of feline panleukopenia due to feline parvovirus (FPV) infection few days after initial administration of rFeIFN. Kittens (n = 23) were injected with rFeIFN (1 MU/kg subcutaneoulsy, once a day for 3 days) and their blood parameters were compared with those of 17 untreated cats. Cats that survived the outbreak were vaccinated and re-sampled 1 month after the last rFeIFN administration. Time of emergence of clinical signs and survival rate were not significantly different between the two groups. Controls and treated cats surviving the infection had high levels of g-globulins, total-and anti-FPV specific IgGs, likely due to passive transfer of maternal immunity. Compared to controls, treated kittens had lower levels of a 1 -globulins and higher mean values of g-globulins and immunoglobulins. Data from samples collected after vaccination revealed a higher level of gglobulins, total-and anti-FPV specific IgGs in treated kittens, compared with controls, suggesting that rFeIFN stimulates antibody production. Based on this results, rFeIFN should be administered to the queen, to increase passive maternal immunity, or to kittens before introduction in a potentially contaminated environment. # * P < 0.05 vs. CI. y P < 0.05 vs. CII and vs. TI. 
 Title: Evaluation of inflammation and immunity in cats with spontaneous parvovirus infection: Consequences of recombinant feline interferon-v administration
Output: True
Paragraph: Multipartitism counts amongst the weirdest lifestyles found in the virosphere. Multipartite viruses have genomes segmented in pieces enclosed in different capsids that are independently transmitted. Since all segments have to meet in the host for complementation and completion of the viral cycle, multipartite viruses are bound to fight the loss of genomic information. While this is an obvious disadvantage of this strategy, no consensus on its actual advantages has been reached. In this review we present an exhaustive summary of all multipartite viruses described to date. Based on evidence, we discuss possible mechanistic and evolutionary origins of different groups, as well as their mutual relationships. We argue that the ubiquitous interactions of viruses with other unrelated viruses and with subviral elements might be regarded as a plausible first step towards multipartitism. In agreement with the view of the Virosphere as a deeply entangled network of gene sharing, we contend that the power of multipartitism relies on its dynamical and opportunistic nature, because it enables immediate adaptive responses to environmental changes. As such, perhaps the reasons for its success should be shought in multipartitism itself as an adaptive mechanism, to which its evolutionarily short-lived products (that is, the extant ensemble of multipartite viral species) are subordinated. We close by discussing how our understanding of multipartitism would improve by using concepts and tools from systems biology. 
 Title: Multipartite viruses: adaptive trick or evolutionary treat?
Output: False
Paragraph: Objectives. Assess how people perceive the risks of coronavirus infection, whether people take preventive measures, and which (pre-outbreak) factors contribute to the perceived risks and measures taken, such as (pre-outbreak) respiratory problems, heart problems, diabetes, anxiety and depression symptoms, loneliness, age, gender, marital status and education level. Methods. Data were collected in the longitudinal LISS panel, based on a random sample of the Dutch population. The coronavirus survey started on March 2, and the data collection ended on March 17 2020. Data were linked with surveys on health and social integration conducted at the end of 2019 (N study sample =3,540). Results. About 15% perceived the risk of infection as high, and 11% the risk becoming ill when infected. Multivariate logistic regression analyses showed the following. Older age-groups perceived the risk for coronavirus infection as lower (all adjusted Odd Ratio's [aOR] ≤ .058). In total, 43.8% had taken preventive measures, especially females (aOR=1.47, 95% CI=1.27-1.69). Those with lower education levels less often used preventive measures (aOR=0.56, 95% CI=0.46-0.69). Those with preoutbreak respiratory problems (aOR=2.89, 95% CI=2.24-3.73), heart problems (aOR=2.17, 95% CI=1.49-3.16) and diabetes (aOR=3.10, 95% CI=2.02-4.74) perceived the risk becoming ill when infected as higher than others. However, respondents with pre-outbreak respiratory problems and diabetes did not more often take preventive measures. Vulnerable patients more often recognize that they are at risk becoming ill when infected by the coronavirus, but many do not take preventive measures. Interventions to stimulate the use of preventive measures should pay additional attention to physically vulnerable patients, men and those with lower education levels. 
 Title: Pre-outbreak determinants of perceived risks of corona infection and preventive measures taken. A prospective population-based study Perceived risks and preventive measures corona outbreak
Output: True
Paragraph: Foxp3 + regulatory T (Treg) cells limit inflammatory responses and maintain immune homeostasis. Although comprised of several phenotypically and functionally distinct subsets, the differentiation of specialized Treg cell populations within the periphery is poorly characterized. We demonstrate that the development of T-bet + Treg cells that potently inhibit T helper 1 (Th1) cell responses was dependent on the transcription factor STAT1 and occurred directly in response to interferon-g produced by effector T cells. Additionally, delayed induction of the IL-12Rb2 receptor component after STAT1 activation helped ensure that Treg cells do not readily complete STAT4-dependent Th1 cell development and lose their ability to suppress effector T cell proliferation. Thus, we define a pathway of abortive Th1 cell development that results in the specialization of peripheral Treg cells and demonstrate that impaired expression of a single cytokine receptor helps maintain Treg cell-suppressive function in the context of inflammatory Th1 cell responses. Immunity 
 Title: Article T-bet + Treg Cells Undergo Abortive Th1 Cell Differentiation due to Impaired Expression of IL-12 Receptor b2
Output: True
Paragraph: The acute phase of respiratory distress caused by porcine reproductive and respiratory syndrome virus (PRRSV) is likely a consequence of the release of inflammatory cytokines in the lung. IL-8, the main chemokine and activator of neutrophils, might be related to the lung injury upon PRRSV infection. In this study, we showed that PRRSV induced IL-8 expression in vivo and in vitro. Subsequently, we demonstrated that JNK and NF-κB pathways were activated upon PRRSV infection and required for the enhancement of IL-8 expression. We further verified that PRRSV-activated TAK-1 was essential for the activation of JNK and NF-κB pathways and IL-8 expression. Moreover, we revealed an AP-1 binding motif in the cloned porcine IL-8 (pIL-8) promoter, and deletion of this motif abolished the pIL-8 promoter activity. Finally, we found that the JNK-activated AP-1 subunit c-Jun was critical for the up-regulation of IL-8 expression by PRRSV. These data suggest that PRRSVinduced IL-8 production is likely through the TAK-1/JNK/AP-1 pathways. http://dx. 
 Title: Porcine reproductive and respiratory syndrome virus (PRRSV) up-regulates IL-8 expression through TAK-1/JNK/AP-1 pathways
Output: True
Paragraph: Farm animals are sources of meat, milk and eggs for the humans, and animal health ensures the quality and security of these agricultural and sideline products. The animal raising conditions in livestock stations and poultry houses play vital roles in both animal health and production. One of the major factors affecting raising conditions, relative humidity, has not received much attention even though it is important for animal husbandry. In this review, we summarize the impacts of relative humidity on animal health and welfare to draw attention for its importance in the improvement of animal raising conditions in the future. 
 Title: ScienceDirect Effects of relative humidity on animal health and welfare
Output: True
Paragraph: Objectives: No international consensus has been reached on the empirical use of antibiotics with atypical coverage in nursing homeeacquired pneumonia (NHAP). Aspiration is an important cause of NHAP, but it may not require antimicrobial treatment. This study aimed to investigate the prevalence and clinical characteristics of AP infections and review the need for empirical antibiotics with atypical coverage in NHAP. Design: A prospective cohort study. Setting: Four nursing homes with a total number of 772 residents. Participants: Patients were aged ! 65 years, hospitalized for NHAP, which was defined as the presence of respiratory symptoms and abnormal chest radiographs, from April 2006 to March 2007. Measurements: Demographics, clinical parameters, and investigation results were recorded. Microbial investigations comprised sputum routine and mycobacterial cultures, blood and urine cultures, serology, and nasopharyngeal aspirate viral culture and polymerase chain reaction tests. Suspected aspiration pneumonitis was arbitrarily defined as NHAP without pathogens identified. Results: After excluding lone bacteriuria, 108 episodes of NHAP in 94 patients were included. Twelve APs were detected in 11 patients. There was no clinical feature to distinguish between infections caused by APs and other pathogens. The commonest APs were Mycoplasma pneumoniae (6) and Chlamydophila pneumoniae (3). No Legionella pneumophila was detected by urinary antigen test. None of the patients with AP infection received antibiotics indicated for AP infections. However, AP infections did not result in mortality. No pathogen was isolated in 31.5% of cases. Patients without pathogens isolated were less likely to have purulent sputum and crepitations on chest auscultation, compared with those with pneumonia caused by identified pathogens. Conclusions: Atypical pathogens (APs) were not associated with mortality even in cases where the prescribed antibiotics did not cover APs. NHAP may not necessarily be treated with empirical antibiotics covering APs. 
 Title: Role of Atypical Pathogens in Nursing HomeeAcquired Pneumonia
Output: False
Paragraph: Objective To fabricate an active and stable enzyme through covalent immobilization, a Ubl-specific protease (Ulp1) was used to cleave small ubiquitin-like modifier (SUMO) fusion proteins. Results We immobilized Ulp1 on N-hydroxysuccinimide (NHS)-activated Sepharose with a coupling efficiency of 1.7 mg/ml. The immobilized Ulp1 maintains 95% substrate-cleavage ability and significantly enhances pH and thermal stability, especially can withstand pH of 10.5. Besides resistance against some small molecules, the immobilized Ulp1 can tolerate 15% (v/v) DMSO and 20% (v/v) ethanol. It can be reused for more than 15 batch reactions with 90% activity retention. This provides a fast purification system to quickly obtain cleaved recombinant proteins with 95% purity from cell lysates with the application of immobilized Ulp1. Conclusions Ulp1 used in immobilization form is a potentially useful tool for cleavage of SUMO-tagged proteins and may reduce time and cost of protein purification. 
 Title: Immobilization of Ulp1 protease on NHS-activated Sepharose: a useful tool for cleavage of the SUMO tag of recombinant proteins
Output: True
Paragraph: The influences of indoor environment quality on occupant health have long been one of the main focuses in built environment and public health research. However, evidence to this effect has been inconsistent. Furthermore, previous urban studies have indicated the interaction between urban morphology and indoor environment. This study thus goes beyond indoor environment to investigate: i) the effects of neighborhood environment on occupant health; and ii) the mediating roles of indoor environment on the neighborhood environment and occupant health relationships. To achieve this aim, buildings located in different neighborhood environment in Hong Kong are selected. Data are collected by post-occupancy evaluation (occupant health), indoor environment assessment (thermal comfort, indoor air quality, ventilation, visual comfort, and acoustic comfort) and neighborhood environment assessment (neighborhood building density, building height, cleanliness and greenspace) through questionnaire survey. Through correlation analysis, regression modelling and Sobel test, it is found that: i) occupant health is significantly affected by neighborhood building height, building density and cleanliness; ii) the relationships between neighborhood environment and occupant health are significantly mediated by indoor environment, in terms of visual and acoustic comfort; and iii) neighborhood greenspace affects occupant health indirectly through influencing indoor air quality. To cross validate the results of the survey study, which is conducted using subjective data, objective measurements and analyses are further conducted. The objective study, echoing the survey study results, indicates that buildings with lower neighborhood building density and height, and cleaner neighborhood environment have better visual (higher illuminance level) and acoustic (lower noise level) performances. 
 Title: Effects of neighborhood building density, height, greenspace, and cleanliness on indoor environment and health of building occupants
Output: False
Paragraph: The laboratory diagnosis of dengue has largely relied on serological assays, although many different RT-PCR protocols have been reported. Owing to its limited use, the value of RT-PCR in the clinical laboratory has not been fully evaluated. During the outbreak of severe acute respiratory syndrome (SARS) in Singapore in 2003, RT-PCR to detect dengue viral RNA was used as a rapid diagnostic tool to differentiate dengue from SARS among patients who presented to a hospital designated to manage and quarantine SARS cases. A total of 343 results for RT-PCR and 439 results for serology were analysed and compared with the final discharge diagnosis. Our experience indicates that RT-PCR for dengue can be set up rapidly in a clinical laboratory, with very sensitive and specific results for the diagnosis of dengue, particularly in the first 5 days from onset of symptoms. 
 Title: The performance of RT-PCR compared with a rapid serological assay for acute dengue fever in a diagnostic laboratory
Output: False
Paragraph: Innate immune cells are endowed with many nucleic acid receptors, but the role of sequence in the detection of foreign organisms remains unclear. Can sequence patterns influence recognition? And how can we infer those patterns from sequence data? Here, we detail recent computational and experimental evidence associated with sequence-specific sensing. We review the mechanisms underlying the detection and discrimination of foreign sequences from self. We also describe quantitative approaches used to infer the stimulatory capacity of a given pathogen nucleic acid species, and the influence of sequence-specific sensing on host-pathogen coevolution, including endogenous sequences of foreign origin. Finally, we speculate how further studies of sequencespecific sensing will be useful to improve vaccine design, gene therapy and cancer treatment. 
 Title: Sequence-specific Sensing of Nucleic Acids
Output: False
Paragraph: Graphical Abstract Highlights d Temporal proteomic analysis quantifies host and viral dynamics during vaccinia infection d Host protein families are proteasomally degraded over the course of vaccinia infection d Vaccinia protein C6 targets HDAC5 for proteasomal degradation d HDAC5 is a host antiviral factor that restricts different families of DNA viruses SUMMARY Vaccinia virus (VACV) has numerous immune evasion strategies, including multiple mechanisms of inhibition of interferon regulatory factor 3 (IRF-3), nuclear factor kB (NF-kB), and type I interferon (IFN) signaling. Here, we use highly multiplexed proteomics to quantify $9,000 cellular proteins and $80% of viral proteins at seven time points throughout VACV infection. A total of 265 cellular proteins are downregulated >2-fold by VACV, including putative natural killer cell ligands and IFN-stimulated genes. Two-thirds of these viral targets, including class II histone deacetylase 5 (HDAC5), are degraded proteolytically during infection. In follow-up analysis, we demonstrate that HDAC5 restricts replication of both VACV and herpes simplex virus type 1. By generating a proteinbased temporal classification of VACV gene expression, we identify protein C6, a multifunctional IFN antagonist, as being necessary and sufficient for proteasomal degradation of HDAC5. Our approach thus identifies both a host antiviral factor and a viral mechanism of innate immune evasion. 
 Title: Quantitative Temporal Proteomic Analysis of Vaccinia Virus Infection Reveals Regulation of Histone Deacetylases by an Interferon Antagonist
Output: False
Paragraph: Viral diseases such as influenza, which are easily transferable from person to person or even country to country, pose one of the biggest threats to health today. Viruses such as avian influenza viruses (N1H5 and H9N1) have been reported to spread in the present decade and, very recently, the novel coronavirus that has caused many life-threatening illnesses and deaths all around the world has received much attention. To prevent these highly contagious viral infections, we have proposed the combination of IMODä and Arbidol to increase their immunomodulatory effects as a novel medicine to prevent and cure influenza and some other infectious diseases such as hepatitis B and C. On the one hand, IMODä within the last few years has been proven to safely and effectively increase the life expectancy for human immunodeficiency virus (HIV)-infected individuals by increasing CD4 lymphocytes. On the other hand, Arbidol, an antiviral agent has been used safely and effectively in the past two decades to prevent and cure all types of influenza and flu. Therefore, the combination of both in a single dosage to further increase CD4 lymphocytes and interferon gamma (IFN-c) could be a better choice for treatment of viral infections. This proposal tries to provide enough support and background for approval of a randomized clinical trial by a relevant team of investigators. ª 2014 Published 
 Title: Combination of IMODä and Arbidol to increase their immunomodulatory effects as a novel medicine to prevent and cure influenza and some other infectious diseases Journal of Medical Hypotheses and Ideas
Output: True
Paragraph: Transmissible gastroenteritis virus (TGEV) is a coronavirus that causes villus atrophy, followed by crypt hyperplasia, reduces the activities of intestinal digestive enzymes, and disrupts the absorption of intestinal nutrients. In vivo, TGEV primarily targets and infects intestinal epithelial cells, which play an important role in glucose absorption via the apical and basolateral transporters Na + -dependent glucose transporter 1 (SGLT1) and facilitative glucose transporter 2 (GLUT2), respectively. In this study, we therefore sought to evaluate the effects of TGEV infection on glucose uptake and SGLT1 and GLUT2 expression. Our data demonstrate that infection with TGEV resulted in increased glucose uptake and augmented expression of EGFR, SGLT1 and GLUT2. Moreover, inhibition studies showed that EGFR modulated glucose uptake in control and TGEV infected cells. Finally, high glucose absorption was subsequently found to promote TGEV replication. Competing Interests: The authors have declared that no competing interests exist. EGFR and SGLT1 protein was dynamic. (A) Cells were treated with PBS, DMSO (100 nM), or AG1478 (100 nM) at 37˚C for 48 h. The culture medium from each group was then assayed. (B) Western blot analysis of the expression levels of p-EGFR, EGFR, SGLT1, GLUT2, and β-tubulin. Experiments were performed separately three times. (C) The intensities of protein bands were quantified using Quantity One and SPSS software. (D) Cells were transfected with shEGFR, shEGFR control, pLVX-EGFR, or pLVX-EGFR control. After 48 h of incubation, culture medium from each group and from mock-infected cells was assayed. (E) The expression levels of p-EGFR, EGFR, SGLT1, GLUT2, and β-tubulin proteins were evaluated by western blot analysis. Experiments were performed separately three times. (F) The intensities of protein bands were quantified using Quantity One and SPSS software. (G) IPEC-J2 cells were treated with phlorizin (500 μM) at 37˚C for 48 h, and culture medium from each group was assayed. (H) The expression levels of SGLT1, EGFR, and β-tubulin were evaluated by western blot analysis. (I) The intensities of protein bands were quantified using Quantity One and SPSS software. (J) IPEC-J2 cells were treated with three SGLT1-specific siRNA molecules for 48 h, and culture medium from each group was assayed. (K) Western blot analysis of the expression levels of SGLT1, EGFR, and β-tubulin. (L) The intensities of protein bands were quantified using Quantity One and SPSS software. Each experiment was performed separately three times. 
 Title: Transmissible Gastroenteritis Virus Infection Enhances SGLT1 and GLUT2 Expression to Increase Glucose Uptake
Output: False
Paragraph: We employed the staggered extension process (StEP) to shuffle the S1 genes from four infectious bronchitis virus (IBV) strains representing four unique serotypes. Upon creating a shuffled S1 gene library, we randomly selected 25 clones and analyzed them by DNA sequencing. In total, eleven clones contained novel S1 gene recombinants. Based on sequence data, each recombinant was unique and contained a fulllength open reading frame. The average number of crossovers per recombinant was 5 and the average number of point mutations was 1.3, leading mostly to non-synonymous amino acid changes. No recombinant contained sequences from all four parental genes and no recombinant contained any sequence from the distantly related Delaware 072 strain. Our data suggests that recombination between distantly related IBV strains within the S1 gene probably does not readily occur. This finding is extremely important in light of the common industry vaccination practice of mixing different live-attenuated IBV strains. 
 Title: Using DNA Shuffling to Create Novel Infectious Bronchitis Virus S1 Genes: Implications for S1 Gene Recombination
Output: True
Paragraph: Identification of regulatory elements is essential for understanding the mechanism behind regulating gene expression. These regulatory elements-located in or near gene-bind to proteins called transcription factors to initiate the transcription process. Their occurrences are influenced by the GC-content or nucleotide composition. For generating synthetic coding sequences with pre-specified amino acid sequence and desired GC-content, there exist two stochastic methods, multinomial and maximum entropy. Both methods rely on the probability of choosing the codon synonymous for usage in regard to a specific amino acid. In spite the latter exhibited unbiased manner, the produced sequences are not exactly obeying the GC-content constraint. In this paper, we present an algorithmic solution to produce coding sequences that follow exactly a primary amino acid sequence and a desired GC-content. The proposed tool, namely CodSeqGen, depends on random selection for smaller subsets to be traversed using the backtracking approach. 
 Title: CodSeqGen: A tool for generating synonymous coding sequences with desired GC-contents
Output: True
Paragraph: Numerous living organisms possess biophotonic nanostructures that provide coloration and other diverse functions for survival. While such structures have been actively studied and replicated in the laboratory, it remains unclear whether they can be used for biomedical applications. Here we show a transparent photonic nanostructure inspired by the longtail glasswing (Chorinea faunus) butterfly and demonstrate its use in intraocular pressure (IOP) sensors in vivo. We exploit the phase separation between two immiscible polymers (poly(methyl methacrylate) and polystyrene) to form nanostructured features on top of a Si 3 N 4 substrate. The membrane thus formed shows good angle-independent white light transmission, strong hydrophilicity and anti-biofouling properties that prevent adhesion of proteins, bacteria, and eukaryotic cells. We then developed a microscale implantable IOP sensor using our photonic membrane as an optomechanical sensing element. Finally, we performed in vivo testing on New Zealand white rabbits and show that our Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#termsReprints and permission information is available online at www.nature.com/reprints. 
 Title: Multifunctional biophotonic nanostructures inspired by longtail glasswing butterfly for medical devices HHS Public Access Author manuscript
Output: True
Paragraph: With the recent advances in molecular biology and the ability to amplify viral genomes in a non-sequence-dependent manner, several previously unidentified human respiratory viruses have been discovered. There are accumulating data that some of these new pathogens are responsible for a substantial proportion of respiratory tract diseases, particularly in children. This review will focus on several of these newly identified pathogens for which there are clinical data implicating a role of these viruses in respiratory tract disease specifically, human metapneumovirus, human coronaviruses NL63 and HKU1, and the human bocavirus. Antivirals and effective vaccines for these new agents may decrease the burden of respiratory tract diseases. 
 Title: Newly discovered respiratory viruses: significance and implications This review comes from a themed issue on Anti-infectives Edited
Output: False
Paragraph: A major hallmark of the autoimmune demyelinating disease multiple sclerosis (MS) is immune cell infiltration into the brain and spinal cord resulting in myelin destruction, which not only slows conduction of nerve impulses, but causes axonal injury resulting in motor and cognitive decline. Current treatments for MS focus on attenuating immune cell infiltration into the central nervous system (CNS). These treatments decrease the number of relapses, improving quality of life, but do not completely eliminate relapses so long-term disability is not improved. Therefore, therapeutic agents that protect the CNS are warranted. In both animal models as well as human patients with MS, T cell entry into the CNS is generally considered the initiating inflammatory event. In order to assess if a drug protects the CNS, any potential effects on immune cell infiltration or proliferation in the periphery must be ruled out. This protocol describes how to determine whether CNS protection observed after drug intervention is a consequence of attenuating CNS-infiltrating immune cells or blocking death of CNS cells during inflammatory insults. The ability to examine MS treatments that are protective to the CNS during inflammatory insults is highly critical for the advancement of therapeutic strategies since current treatments reduce, but do not completely eliminate, relapses (i.e., immune cell infiltration), leaving the CNS vulnerable to degeneration. 
 Title: Determining Immune System Suppression versus CNS Protection for Pharmacological Interventions in Autoimmune Demyelination
Output: True
Paragraph: BACKGROUND: Single-nucleotide polymorphisms (SNPs) that impact on the differential expression of interleukin 28B (IL28B) are implicated in the progression of viral-induced diseases. In this prospective longitudinal cohort study, we evaluated the association between IL28B SNPs rs12979860 and rs8099917 and the clinical outcome of bronchiolitis in pediatric patients. METHODS: A total of 682 infants suffering from bronchiolitis, categorized based on the final clinical outcome as mild or severe, were genotyped for IL28B SNPs rs12979860 and rs8099917. RESULTS: When infants were categorized exclusively based on the final clinical outcome, no association was established between IL28B SNPs and the severity of bronchiolitis. However, when stratified by sex, the homozygotes for the minor alleles of rs12979860 (T) and rs8099917 (G) were associated with a mild disease in girls but not in boys. CONCLUSION: SNPs rs12979860 and rs8099917 correlate with the severity of bronchiolitis and display a sex bias, where GG rs8099917 and TT rs12979860 genotypes are associated with a mild disease in girls but not in boys. These findings suggest that innate immunity and female sex links with the outcome of the diseases induced by respiratory viruses, such as RSV. 
 Title: Correlation between female sex, IL28B genotype, and the clinical severity of bronchiolitis in pediatric patients
Output: False
Paragraph: Phage display is the most widely used method for selecting binding molecules from recombinant antibody libraries. However, validation of the phage antibodies often requires early production of the cognate full-length immunoglobulin G (IgG). The conversion of phage library outputs to a full immunoglobulin via standard subcloning is time-consuming and limits the number of clones that can be evaluated. We have developed a novel system to convert scFvs from a phage display vector directly into IgGs without any in vitro subcloning steps. This new vector system, named pMINERVA, makes clever use of site-specific bacteriophage integrases that are expressed in E. coli and intron splicing that occurs within mammalian cells. Using this system, a phage display vector contains both bacterial and mammalian regulatory regions that support antibody expression in E. coli and mammalian cells. A single-chain variable fragment (scFv) antibody is expressed on the surface of bacteriophage M13 as a genetic fusion to the gpIII coat protein. The scFv is converted to an IgG that can be expressed in mammalian cells by transducing a second E. coli strain. In that strain, the phiC31 recombinase fuses the heavy chain constant domain from an acceptor plasmid to the heavy chain variable domain and introduces controlling elements upstream of the light chain variable domain. Splicing in mammalian cells removes a synthetic intron containing the M13 gpIII gene to produce the fusion of the light chain variable domain to the constant domain. We show that phage displaying a scFv and recombinant IgGs generated using this system are expressed at wild-type levels and retain normal function. Use of the pMINERVA completely eliminates the labor-intensive subcloning and DNA sequence confirmation steps currently needed to convert a scFv into a functional IgG Ab. The TG1 E. coli strain (F′ (traD36 proAB+ lacIq lacZΔM15) supE thi-1 Δ(lac-proAB) Δ(mcrB-hsdSM)5, (rK-mK-) was purchased from Lucigen (Middleton, WI). The template Batonick et al. 
 Title: pMINERVA: A Donor-Acceptor System for the in vivo Recombineering of scFv into IgG Molecules
Output: True
Paragraph: Background: Quantitative survey of research articles, as an application of bibliometrics, is an effective tool for grasping overall trends in various medical research fields. This type of survey has been also applied to infectious disease research; however, previous studies were insufficient as they underestimated articles published in non-English or regional journals. 
 Title: New journal selection for quantitative survey of infectious disease research: application for Asian trend analysis
Output: False
Paragraph: DNA aptamers specifically recognizing microbial cells and viruses have a range of analytical and therapeutic applications. This article describes recent advances in the development of aptamers targeting specific pathogens (e.g., live bacteria, whole viral particles, and virally-infected mammalian cells). Specific aptamers against pathogens have been used as affinity reagents to develop sandwich assays, to label and to image cells, to bind with cells for flow-cytometry analysis, and to act as probes for development of whole-cell biosensors. Future applications of aptamers to pathogens will benefit from recent advances in improved selection and new aptamers containing modified nucleotides, particularly slow off-rate modified aptamers (SOMAmers). 
 Title: Selection and analytical applications of aptamers binding microbial pathogens
Output: True
Paragraph: In non-polarized cell culture models, influenza virus has been shown to enter host cells via multiple endocytic pathways, including classical clathrin-mediated endocytic routes (CME), clathrin-and caveolae-independent routes and macropinocytosis. However, little is known about the entry route of influenza virus in differentiated epithelia, in vivo site of infection for influenza virus. Here, we show that in polarized Madin-Darby canine kidney type II (MDCK II) cells, influenza virus has a specific utilization of the clathrin-mediated endocytic pathway and requires Eps15 for host cell entry. 
 Title: Influenza entry pathways in polarized MDCK cells
Output: True
Paragraph: CDC, the Infectious Disease Society of America, and the American Society of Blood and Marrow Transplantation have cosponsored these guidelines for preventing opportunistic infections (OIs) among hematopoietic stem cell transplant (HSCT) recipients. The guidelines were drafted with the assistance of a working group of experts in infectious diseases, transplantation, and public health. For the purposes of this report, HSCT is defined as any transplantation of blood-or marrow-derived hematopoietic stem cells, regardless of transplant type (i.e., allogeneic or autologous) or cell source (i.e., bone marrow, peripheral blood, or placental or umbilical cord blood). Such OIs as bacterial, viral, fungal, protozoal, and helminth infections occur with increased frequency or severity among HSCT recipients. These evidence-based guidelines contain information regarding preventing OIs, hospital infection control, strategies for safe living after transplantation, vaccinations, and hematopoietic stem cell safety. The disease-specific sections address preventing exposure and disease for pediatric and adult and autologous and allogeneic HSCT recipients. The goal of these guidelines is twofold: to summarize current data and provide evidence-based recommendations regarding preventing OIs among HSCT patients. The guidelines were developed for use by HSCT recipients, their household and close contacts, transplant and infectious diseases physicians, HSCT center personnel, and public health professionals. For all recommendations, prevention strategies are rated by the strength of the recommendation and the quality of the evidence supporting the recommendation. Adhering to these guidelines should reduce the number and severity of OIs among HSCT recipients. 
 Title: Guidelines for Preventing Opportunistic Infections Among Hematopoietic Stem Cell Transplant Recipients Recommendations of CDC, the Infectious Disease Society of America, and the American Society of Blood and Marrow Transplantation
Output: True
Paragraph: Many plants contain polyhydroxyalkaloids which are potent inhibitors of glucosidases, enzymes involved in oligosaccharide trimming. These are important in determining the final configuration of specific glycoproteins. Human cytomegalovirus (CMV) encodes a number of glycoproteins, some of which ultimately reside in the outer envelope of the mature virion and are important for virus infectivity. Treatment with three polyhydroxyalkaloids, castanospermine (CAST), deoxynojirimycin (DNJ) and 2R,5R-dihydroxymethyl-3R,4R-dihydroxypyrrolidine (DMDP) blocked the growth of infectious virus, as determined by yield reduction and plaque reduction assays. However, in the presence of CAST, CMV infected cells continued to shed virions into the extracellular medium, as determined by electron microscopy. Envelope glycoproteins of virions produced after treatment with CAST (2.5 mM) were immunoprecipitated with a monoclonal antibody (F5) specific for the gcI family of glycoproteins. Analysis by PAGE-SDS showed an absence of gcI complex 2 (gp52 disulphide-linked to gp130) with a proportional increase in gcI complex 1 (gp52 disulphide-linked to gp95). The results indicated that gpl30 alone, or linked to gp52, was important for CMV infectivity. As well as being potential targets for antiviral agents against CMV, inhibitors of glycoprotein trimming reactions may define components of the virion surface important for infectivity. 
 Title: Loss of cytomegalovirus infectivity after treatment with castanospermine or related plant alkaloids correlates with aberrant glycoprotein synthesis
Output: True
Paragraph: Direct interspecies transmissions of group A rotaviruses (RVA) have been reported under natural conditions. However, the pathogenicity of RVA has never been directly compared in homologous and heterologous hosts. The bovine RVA/Cow-tc/KOR/K5/2004/G5P[7] strain, which was shown to possess a typical porcine-like genotype constellation similar to that of the G5P[7] prototype RVA/Pig-tc/USA/OSU/1977/G5P9[7] strain, was examined for its pathogenicity and compared with the porcine G5P[7] RVA/Pig-tc/KOR/K71/2006/G5P[7] strain possessing the same genotype constellation. The bovine K5 strain induced diarrhea and histopathological changes in the small intestine of piglets and calves, whereas the porcine K71 strain caused diarrhea and histopathological changes in the small intestine of piglets, but not in calves. Furthermore, the bovine K5 strain showed extra-intestinal tropisms in both piglets and calves, whereas the porcine K71 strain had extra-intestinal tropisms in piglets, but not in calves. Therefore, we performed comparative genomic analysis of the K71 and K5 RVA strains to determine whether specific mutations could be associated with these distinct clinical and pathological phenotypes. Full-length sequencing analyses for the 11 genomic segments for K71 and K5 revealed that these strains were genetically nearly identical to each other. Two nucleotide mutations were found in the 5′ untranslated region (UTR) of NSP5 and the 3′ UTR of NSP3, and eight amino acid mutations in VP1-VP4 and NSP2. Some of these mutations may be critical molecular determinants for RVA virulence and/or pathogenicity. 
 Title: Different virulence of porcine and porcine-like bovine rotavirus strains with genetically nearly identical genomes in piglets and calves
Output: False
Paragraph: Although coronavirus tropism is most often ascribed to receptor availability, increasing evidence suggests that for the neurotropic strains of the murine coronavirus mouse hepatitis virus (MHV), spike-receptor interactions cannot fully explain neurovirulence. The canonical MHV receptor CEACAM1a and its spike-binding site have been extensively characterized. However, CEACAM1a is poorly expressed in neurons, and the extremely neurotropic MHV strain JHM.SD infects ceacam1a S/S mice and spreads among ceacam1a S/S neurons. Two proposed alternative MHV receptors, CEACAM2 and PSG16, also fail to account for neuronal spread of JHM.SD in the absence of CEACAM1a. It has been reported that JHM.SD has an unusually labile spike protein, enabling it to perform receptor-independent spread (RIS), but it is not clear if the ability to perform RIS is fully responsible for the extremely neurovirulent phenotype. We propose that the extreme neurovirulence of JHM.SD is multifactorial and might include as yet unidentified neuron-specific spread mechanisms. 
 Title: Pathogenesis of neurotropic murine coronavirus is multifactorial
Output: True