niryuu/sni-each-converted huggingface dataset:
Background: Although the mini-clinical evaluation (mini-CEX) exercise has been adapted to a broad range of clinical situations, limited studies of the mini-CEX for postgraduate residency training in emergency medicine (EM) have been documented. Aim: The purpose of this study is to analyze the results of implementing the mini-CEX into the one-month postgraduate residency training in EM. Materials and methods: This study is a retrospective review of mini-CEXs completed by ED faculty members from August 2009 to December 2010. All PGY-1 residents enrolled in this study rotated through the one-month EM training. Each PGY-1 resident received one week of trauma training and three weeks of non-trauma training. The clinical competencies of each PGY-1 resident were evaluated with mini-CEXs, rated by a trauma surgeon and three emergency physicians (EPs). We analyzed the validity of weekly mini-CEX and the impact of seniority and specialty training of ED faculties on observation time, feedback time and rating scores. Results: Fifty-seven ED faculty members (42 EPs and 15 trauma surgeons) evaluated 183 PGY-1 residents during the 17 months of EM training. ED faculties with different specialty training provided similar assessment processes. Most competencies were rated significantly higher by trauma surgeons than by EPs. On the computerized mini-CEX rating, no data was missed and junior EPs rated all competencies significantly higher. The evaluators and PGY-1 residents were generally satisfied with the computerized format. As compared to the first assessment, only some competencies of PGY-1 residents were rated significantly higher in subsequent evaluations. Conclusion: The seniority and specialty training of ED faculty affected the mini-CEX ratings. The computer-based mini-CEX facilitated complete data gathering but showed differences for ED faculty with different levels of seniority. Further studies of the reliability and validity of the mini-CEX for PGY-1 EM training are needed.
Output: Implementation of the mini-clinical evaluation exercise in postgraduate Year 1 residency training in emergency medicine: Clinical experience at Chang Gung Memorial Hospital ScienceDirect
Genome signatures are data vectors derived from the compositional statistics of DNA. The self-organizing map (SOM) is a neural network method for the conceptualisation of relationships within complex data, such as genome signatures. The various parameters of the SOM training phase are investigated for their effect on the accuracy of the resulting output map. It is concluded that larger SOMs, as well as taking longer to train, are less sensitive in phylogenetic classifi cation of unknown DNA sequences. However, where a classifi cation can be made, a larger SOM is more accurate. Increasing the number of iterations in the training phase of the SOM only slightly increases accuracy, without improving sensitivity. The optimal length of the DNA sequence k-mer from which the genome signature should be derived is 4 or 5, but shorter values are almost as effective. In general, these results indicate that small, rapidly trained SOMs are generally as good as larger, longer trained ones for the analysis of genome signatures. These results may also be more generally applicable to the use of SOMs for other complex data sets, such as microarray data.
Output: Correspondence: Genome Signatures, Self-Organizing Maps and Higher Order Phylogenies: A Parametric Analysis
Background: While immunization coverage rates for childhood routine vaccines in Hong Kong are almost 100%, the uptake rates of optional vaccines remain suboptimal. Understanding parental decision-making for children's vaccination is important, particularly among minority groups who are most vulnerable and underserved. This study explored how a subsample of new immigrant mothers from mainland China, a rapidly-growing subpopulation in Hong Kong, made decisions on various childhood and adolescent vaccines for their offspring, and identified key influences affecting their decision making. Methods: Semi-structured in-depth interviews were conducted with 23 Chinese new immigrant mothers recruited by purposive sampling. All interviews were audio-taped, transcribed and analyzed using a Grounded Theory approach. Results: Participants' conversation revealed five underlying themes which influenced parents' vaccination decision-making: (1) Institutional factors, (2) Insufficient vaccination knowledge and advice, (3) Affective impacts on motivation, (4) Vaccination barriers, and (5) Social influences. The role of social norms appeared overwhelmingly salient influencing parents' vaccination decision making. Institutional factors shaped parent's perceptions of vaccination necessity. Fear of vaccine-targeted diseases was a key motivating factor for parents adopting vaccination. Insufficient knowledge about vaccines and targeted diseases, lack of advice from health professionals and, if provided, suspicions regarding the motivations for such advice were common issues. Vaccination cost was a major barrier for many new immigrant parents. Conclusions: Social norms play a key role influencing parental vaccination decision-making. Insight gained from this study will help inform healthcare providers in vaccination communication and policymakers in future vaccination programme.
Output: Chinese immigrant parents' vaccination decision making for children: a qualitative analysis
SARS-CoV-2 emerged in China at the end of 2019 and has rapidly become a pandemic with over 400,000 recorded COVID-19 cases and greater than 19,000 recorded deaths by March 24 th , 2020 (www.WHO.org) (1). There are no FDA approved antivirals or vaccines for any coronavirus, including SARS-CoV-2 (2). Current treatments for COVID-19 are limited to supportive therapies and off-label use of FDA approved drugs (3). Rapid development and human testing of potential antivirals is greatly needed. A potentially quicker way to test compounds with antiviral activity is through drug re-purposing (2, 4). Numerous drugs are already approved for use in humans and subsequently there is a good understanding of their safety profiles and potential side effects, making them easier to test in COVID-19 patients. Here, we present data on 20 FDA approved drugs tested for antiviral activity against SARS-CoV-2 that we have previously found to inhibit SARS-CoV and MERS-CoV (4). We find that 17 of these . CC-BY-NC-ND 4.0 : bioRxiv preprint also inhibit SARS-CoV-2 at a range of IC50 values at non-cytotoxic concentrations. From these we specifically followed up with hydroxychloroquine sulfate and chloroquine phosphate.
Output: FDA approved drugs with broad anti-coronaviral activity inhibit SARS-CoV-2 in vitro
Background: Neonatal calf diarrhea is generally caused by infectious agents and is a very common disease in bovine practice, leading to substantial economic losses. Tannins are known for their astringent and antiinflammatory properties in the gastro-enteric tract. The aim of this study was to evaluate the effect of the oral administration of chestnut tannins (Castanea sativa Mill.) in order to reduce the duration of calf neonatal diarrhea. Twenty-four Italian Friesian calves affected by neonatal diarrhea were included. The duration of the diarrheic episode (DDE) was recorded and the animals were divided into a control group (C), which received Effydral® in 2 l of warm water, and a tannin-treated group (T), which received Effydral® in 2 l of warm water plus 10 g of extract of chestnut tannins powder. A Mann-Whitney test was performed to verify differences for the DDE values between the two groups. Results: The DDE was significantly higher in group C than in group T (p = 0.02), resulting in 10.1 ± 3.2 and 6.6 ± 3. 8 days, respectively. Conclusions: Phytotherapic treatments for various diseases have become more common both in human and in veterinary medicine, in order to reduce the presence of antibiotic molecules in the food chain and in the environment. Administration of tannins in calves with diarrhea seemed to shorten the DDE in T by almost 4 days compared to C, suggesting an effective astringent action of chestnut tannins in the calf, as already reported in humans. The use of chestnut tannins in calves could represent an effective, low-impact treatment for neonatal diarrhea.
Output: Oral administration of chestnut tannins to reduce the duration of neonatal calf diarrhea
Background: Anterior gradient homolog 2 (AGR2) is a functional protein with critical roles in a diverse range of biological systems, including vertebrate tissue development, inflammatory tissue injury responses, and cancer progression. Clinical studies have shown that the AGR2 protein is overexpressed in a wide range of human cancers, including carcinomas of the esophagus, pancreas, breast, prostate, and lung, making the protein as a potential cancer biomarker. However, the general biochemical functions of AGR2 in human cells remain undefined, and the signaling mechanisms that drive AGR2 to inhibit p53 are still not clearly illustrated. Therefore, it is of great interest to develop molecular probes specifically recognizing AGR2 for its detection and for the elucidation of AGR2-associated molecular mechanism. Methodology/Principal Findings: Through a bead-based and flow cytometry monitored SELEX technology, we have identified a group of DNA aptamers that can specifically bind to AGR2 with K d values in the nanomolar range after 14 rounds of selections. Aptamer C14B was chosen to further study, due to its high binding affinity and specificity. The optimized and shortened C14B1 has special G-rich characteristics, and the G-rich region of this binding motif was further characterized to reveal an intramolecular parallel G-quadruplex by CD spectroscopy and UV spectroscopy. Our experiments confirmed that the stability of the G-quadruplex structure was strongly dependent on the nature of the monovalent ions and the formation of G-quadruplex structure was also important for the binding capacity of C14B1 to the target. Furthermore, we have designed a kind of allosteric molecule beacon (aMB) probe for selective and sensitive detection of AGR2. Conclusion/Significance: In this work, we have developed new aptamer probes for specific recognition of the AGR2. Structural study have identified that the binding motif of aptamer is an intramolecular parallel G-quadruplex structure and its structure and binding affinity are strongly dependent on the nature of the monovalent ion. Furthermore, with our design of AGR2-aMB, AGR2 could be sensitively and selectively detected. This aptamer probe has great potential to serve as a useful tool for early diagnosis and prognosis of cancer and for fundamental research to elucidate the biochemical functions of AGR2.
Output: Identification, Characterization and Application of a G- Quadruplex Structured DNA Aptamer against Cancer Biomarker Protein Anterior Gradient Homolog 2
Background: During respiratory viral infections host injury occurs due in part to inappropriate host responses. In this study we sought to uncover the host transcriptional responses underlying differences between high-and lowpathogenic infections. Results: From a compendium of 12 studies that included responses to influenza A subtype H5N1, reconstructed 1918 influenza A virus, and SARS coronavirus, we used meta-analysis to derive multiple gene expression signatures. We compared these signatures by their capacity to segregate biological conditions by pathogenicity and predict pathogenicity in a test data set. The highest-performing signature was expressed as a continuum in low-, medium-, and high-pathogenicity samples, suggesting a direct, analog relationship between expression and pathogenicity. This signature comprised 57 genes including a subnetwork of chemokines, implicating dysregulated cell recruitment in injury. Conclusions: Highly pathogenic viruses elicit expression of many of the same key genes as lower pathogenic viruses but to a higher degree. This increased degree of expression may result in the uncontrolled co-localization of inflammatory cell types and lead to irreversible host damage.
Output: A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections
Human infection with a novel coronavirus named Middle East respiratory syndrome coronavirus (MERS-CoV) was first identified in Saudi Arabia and the Middle East in September, 2012. The aim of this study was to establish the most pathognomonic radiological sign(s) to diagnose MERS CoV. Patients and methods: This is a retrospective descriptive study. All patients were subjected to serial X-ray. High resolution non-contrast CT chest was also obtained for 10 patients. The scans were reviewed for findings including consolidation, ground-glass opacities, nodules, reticular opacities and hilar and mediastinal adenopathy. Results: A total of 12 patients were included in our study with prevalence of males (2:1) with ages ranging between 18 and 76 years having an average age of 36 ± 2 years. The outcome of these patients was as follows: 6 were treated with average hospital stay ranging between 21 and 35 days, one case died after 14 days, and 5 cases were transferred to Central Governmental hospital according the local authority rules. Conclusions: MERS CoV virus may have a specific pattern in chest X-ray and CT developing a single or multiple opacities progressing into a widespread multifocal bilateral patches of ground glass opacities or confluent consolidation resembling organizing pneumonia.
Output: MERS-CoV: Middle East respiratory syndrome corona virus: Can radiology be of help? Initial single center experience
INTRODUCTION HB assay and construction of plasmids: HeLa cells were transfected with appropriate plasmids, pretreated with different concentrations of HB (Sigma), and labeled with [ 35 S] methionine/cysteine (Amersham). Cells were incubated in the presence or absence of HB, harvested and lysed. Total proteins were immunoprecipitated with appropriate antibodies, and analyzed by SDS 15% polyacrylamide gel electrophoresis. Plasmids pFlagE and pFlagN was constructed by cloning an EcoRV-and EcoRIdigested PCR fragments into EcoRV-and EcoRI-digested pFlag vector. The Flag-tag was fused to the N-terminal end of the E protein. Mutations were introduced into the E gene by two rounds of PCR and confirmed by automated sequencing. The mutant constructs included in this study are summarized in Fig. 1.  RESULTS Alteration of Membrane Permeability by the Expression of E Protein
Output: VIROPORIN ACTIVITY OF SARS-CoV E PROTEIN
Plants are able to perform post-translational maturations of therapeutic proteins required for their functional biological activity and suitable in vivo pharmacokinetics. Plants can be a low-cost, large-scale production platform of recombinant biopharmaceutical proteins such as vaccines and antibodies. Plants, however, lack mechanisms of processing authentic human N-glycosylation, which imposes a major limitation in their use as an expression system for therapeutic glycoproducts. Efforts have been made to circumvent plant-specific Nglycosylation, as well as to supplement the plant's endogenous system with human glycosyltransferases for nonimmunogenic and humanized N-glycan production. Herein we review studies on the potential of plants to serve as production systems for therapeutic and prophylactic biopharmaceuticals. We have especially focused on recombinant vaccines and antibodies and new expression strategies to overcome the existing problems associated with their production in plants.
Output: Expression of Recombinant Vaccines and Antibodies in Plants
Mutation of mevalonate kinase (MVK) is thought to account for most cases of hyperimmunoglobulinemia D syndrome (HIDS) with recurrent fever. However, its mechanism and the relationship between elevated serum immunoglobulin D (IgD) and the clinical features of HIDS are unclear. In this study, we generated by fusion PCR a vector to express high levels of chimeric secretory IgD (csIgD) specifically in the liver. We then generated seven founder lines of transgenic mice by co-microinjection, and verified them using genomic PCR and Southern blotting. We detected the expression of csIgD by reverse transcription PCR, quantitative PCR, western blotting, and enzyme-linked immunosorbent assays. We demonstrated that csIgD could be specifically and stably expressed in the liver. We used flow cytometry to show that overexpression of csIgD in the bone marrow and spleen cells had no effect on B cell development. Morphologic and anatomical observation of the transgenic mice revealed skin damage, hepatosplenomegaly, and nephromegaly in some transgenic mice; in these mice, pathological sections showed high levels of cell necrosis and protein-like sediments in the liver, spleen, and kidney. We demonstrated that the genomic insertion sites of the transgenes did not disrupt the MVK gene on mouse chromosome 5. This transgenic mouse will be useful to explore the pathogenesis of HIDS. sIgD, liver-specific expression vector, HIDS, MVK Wang P, Wei Z G, Yan B W, et al. Establishment of a transgenic mouse model with liver-specific expression of secretory immunoglobulin D. Sci
Output: SCIENCE CHINA Establishment of a transgenic mouse model with liver-specific expression of secretory immunoglobulin D
Classifying the mechanisms of antibiotic failure has led to the development of new treatment strategies for killing bacteria. Among the currently described mechanismswhich include resistance, persistence and tolerancewe propose defiance as a subclass of antibiotic failure specific to prodrugs. Using locked antimicrobial peptides (AMP) that are activated by bacterial 5 proteases as a prototypic prodrug, we observe that although treatment eliminates bacteria across the vast majority of environmental conditions (e.g., temperature, concentration of growth nutrients), bacteria spontaneously switch from susceptibility to defiance under conditions that alter the competing rates between bacterial proliferation and prodrug activation. To identify the determinants of this switch-like behavior, we model bacteria-prodrug dynamics as a multi-rate 10 feedback system and identify a dimensionless quantity we call the Bacterial Advantage Heuristic (BAH) that perfectly classifies bacteria as either defiant or susceptible across a broad range of treatment conditions. By recognizing that the bacterial switch from susceptibility to defiance behaves analogously to electronic transistors, we construct prodrug logic gates (e.g., AND, OR, NOT, etc.) to allow assembly of an integrated 3-bit multi-prodrug circuit that kills defiant bacteria 15 under all possible combinations of BAH values (i.e., 000, 001, …, 111) that represent a broad range of possible treatment conditions. Our study identifies a form of bacterial resistance specific to prodrugs that is described by a predictive dimensionless constant to reveal logic-based treatment strategies using multi-prodrug biological circuits.
Output: Prodrug defiance reveals logic-based strategies for treating bacterial resistance
Background: Calf disease may result in great economic losses. To implement prevention strategies it is important to gain information on management and to point out risk factors. The objective of this internet based survey was to describe calf management practices on registered dairy breeding farms in Austria and to estimate differences in calf disease incidences depending on farm structure and management practices. Results: A total of 1287 questionnaires were finally analysed (response rate 12.2 %). Herd characteristics and regional distribution of farms indicated that this survey gives a good overview on calf management practices on registered dairy farms in Austria. The median number of cows per farm was 20 (interquartile range 13-30). Significant differences regarding farm characteristics and calf management between small and large farms (≤20 vs >20 cows) were present. Only 2.8 % of farmers tested first colostrum quality by use of a hydrometer. Storing frozen colostrum was more prevalent on large farms (80.8 vs 64.2 %). On 85.1 % of the farms, whole milk, including waste milk, was fed to the calves. Milk replacer and waste milk were more often used on large farms. In accordance with similar studies from other countries, calf diarrhoea was indicated as the most prevalent disease. Multivariable logistic regression analysis revealed that herd size was associated with calf diarrhoea and calf respiratory tract disease, with higher risk of disease on large farms. Furthermore, feeding waste milk to the calves was associated with increasing calf diarrhoea incidence on farm. In the final model with calf respiratory tract disease as outcome, respondents from organic farms reported less often a respiratory tract disease incidence of over 10 % compared with conventional farms [odds ratio (OR) 0.40, 95 % confidence interval (CI) 0.21-0.75] and farmers that housed calves individually or in groups after birth significantly reported more often to have an incidence of respiratory tract disease >10 % compared with farms where all calves were housed individually (OR 2.28, 95 % CI 1.16-4.48). The results obtained in this study provide an overview on calf management on dairy breeding farms in Austria and may help to further point out areas to be improved on farm. Abbreviations OR: odds ratio; 95 % CI: 95 % confidence interval; p.n.: post natum. Additional file 1. The original online questionnaire in German, distributed to the farmers.
Output: Results of an online questionnaire to survey calf management practices on dairy cattle breeding farms in Austria and to estimate differences in disease incidences depending on farm structure and management practices Open Access
Dicer-substrate siRNAs equipped with CpG oligodeoxyribonucleotides overcome the major hurdle in cell-specific siRNA delivery. The CpG-siRNA molecules are actively internalized by TLR9 + cells, without the need for transfection reagents, leading to RNA interference both in vitro and in vivo. Here, we elucidate the molecular mechanisms of CpG-siRNA processing in target cells. We show that shortly after uptake into early endosomes (EE), CpG and siRNA parts of the conjugate are uncoupled in the presence of Dicer endonuclease. Diced siRNA molecules are translocated from endosomes to endoplasmic reticulum, where they can interact with the RNA interference machinery. We previously observed that even though TLR9 is not involved in CpG-siRNA uptake, it is indispensable for induction of gene silencing. To explain the role of TLR9 in intracellular processing of CpG-siRNA, we used primary macrophages derived from wild-type and Tlr9-deficient mice. Macrophages lacking TLR9 showed extended endosomal colocalization of CpG and siRNA parts of the conjugate. However, Tlr9 ablation did not interfere with the interaction of CpG-siRNA with Dicer as shown by in situ proximity ligation assay. Using CpG-siRNA labeled with pH-sensitive dye, we finally identified that lack of TLR9 in macrophages resulted in significant retention of the siRNA in endosomes. Thus, TLR9 facilitates the critical step following CpG-siRNA uncoupling, which is cytoplasmic release of the diced siRNA. These findings suggest that the class of immunostimulatory siRNAs may benefit from activation of
Output: Intracellular processing of immunostimulatory CpG-siRNA: Toll- like receptor 9 facilitates siRNA dicing and endosomal escape NIH Public Access
Health care workers are exposed to potentially infectious airborne particles while providing routine care to coughing patients. However, much is not understood about the behavior of these aerosols and the risks they pose. We used a coughing patient simulator and a breathing worker simulator to investigate the exposure of health care workers to cough aerosol droplets, and to examine the efficacy of face shields in reducing this exposure. Our results showed that 0.9% of the initial burst of aerosol from a cough can be inhaled by a worker 46 cm (18 inches) from the patient. During testing of an influenza-laden cough aerosol with a volume median diameter (VMD) of 8.5 μm, wearing a face shield reduced the inhalational exposure of the worker by 96% in the period immediately after a cough. The face shield also reduced the surface contamination of a respirator by 97%. When a smaller cough aerosol was used (VMD = 3.4 μm), the face shield was less effective, blocking only 68% of the cough and 76% of the surface contamination. In the period from 1 to 30 minutes after a cough, during which the aerosol had dispersed throughout the room and larger particles had settled, the face shield reduced aerosol inhalation by only 23%. Increasing the distance between the patient and worker to 183 cm (72 inches) reduced the exposure to influenza that occurred immediately after a cough by 92%. Our results show that health care workers can inhale infectious airborne particles while treating a coughing patient. Face shields can substantially reduce the short-term exposure of health care workers to large infectious aerosol particles, but smaller particles can remain airborne longer and flow around the face shield more easily to be inhaled. Thus, face shields provide a useful adjunct to respiratory protection for workers caring for patients with respiratory infections. However, they cannot be used as a substitute for respiratory protection when it is needed.
Output: Efficacy of Face Shields Against Cough Aerosol Droplets from a Cough Simulator
Background: Chemokines and chemokine receptors cooperate to promote immune cell recruitment to the central nervous system (CNS). In this study, we investigated the roles of CXCR2 and CXCL1 in leukocyte recruitment to the CNS using a murine model of neuroinflammation. Methods: Wild-type (WT), CXCL1 −/− , and CXCR2 −/− mice each received an intracerebroventricular (i.c.v.) injection of lipopolysaccharide (LPS). Esterase staining and intravital microscopy were performed to examine neutrophil recruitment to the brain. To assess endothelial activation in these mice, the expression of adhesion molecules was measured via quantitative real-time polymerase chain reaction (PCR) and Western blotting. To identify the cellular source of functional CXCR2, chimeric mice were generated by transferring bone marrow cells between the WT and CXCR2 −/− mice. Results: Expression levels of the chemokines CXCL1, CXCL2, and CXCL5 were significantly increased in the brain following the i.c.v. injection of LPS. CXCR2 or CXCL1 deficiency blocked neutrophil infiltration and leukocyte recruitment in the cerebral microvessels. In the CXCR2 −/− and CXCL1 −/− mice, the cerebral endothelial expression of adhesion molecules such as P-selectin and VCAM-1 was dramatically reduced. Furthermore, the bone marrow transfer experiments demonstrated that CXCR2 expression on CNS-residing cells is essential for cerebral endothelial activation and leukocyte recruitment. Compared with microglia, cultured astrocytes secreted a much higher level of CXCL1 in vitro. Astrocyte culture conditioned medium significantly increased the expression of VCAM-1 and ICAM-1 in cerebral endothelial cells in a CXCR2-dependent manner. Additionally, CXCR2 messenger RNA (mRNA) expression in cerebral endothelial cells but not in microglia or astrocytes was increased following tumor necrosis factor-α (TNF-α) stimulation. The intravenous injection of the CXCR2 antagonist SB225002 significantly inhibited endothelial activation and leukocyte recruitment to cerebral microvessels. Conclusions: CXCL1 secreted by astrocytes and endothelial CXCR2 play essential roles in cerebral endothelial activation and subsequent leukocyte recruitment during neuroinflammation.
Output: CXCR2 is essential for cerebral endothelial activation and leukocyte recruitment during neuroinflammation
Bovine respiratory disease (BRD) often occurs when active respiratory virus infections (BHV-1, etc.) impair resistance to Mannheimia haemolytica infection in the lower respiratory tract. The interactions that occur when the respiratory epithelium encounters these viral and bacterial pathogens are poorly understood. We used Agilent bovine gene microarray chips containing 44,000 transcripts to elucidate bovine bronchial epithelial cell (BBEC) responses following in vitro exposure to BHV-1 alone, M. haemolytica alone, or both BHV-1 and M. haemolytica. Microarray analysis revealed differential regulation (>2-fold) of 978 transcripts by BHV-1 alone, 2040 transcripts by M. haemolytica alone, and 2189 genes by BHV-1 and M. haemolytica in combination. M. haemolytica treatment produced significantly greater inductions (>10-fold) of several inflammation associated genes, such as CXCL2, IL-6, IL-1␣, e-selectin, and IL-8, than to BHV-1 alone. Functional analysis of the microarray data revealed a significant upregulation of genes involved in important biological processes such as inflammation (TNF-␣, IL-8, Tlr-2, IL-1, CXCL2, CSF2), vascular functions (VEGF, EDN2) and leukocyte migration (ICAM1, IL-16) during a co-infection with BHV-1 and M. haemolytica compared to either pathogen alone. This study provides evidence to support that lung epithelial cells are a source of mediators that may promote inflammatory changes observed during bovine respiratory disease.
Output: Gene expression profiling of bovine bronchial epithelial cells exposed in vitro to bovine herpesvirus 1 and Mannheimia haemolytica
As viruses do not possess genes encoding for proteins required for translation, energy metabolism or membrane biosynthesis, they are classified as obligatory intracellular parasites that depend on a host cell to replicate. This genome limitation forces them to gain control over cellular processes to ensure their successful propagation. A diverse spectrum of virally encoded proteins tackling a broad spectrum of cellular pathways during most steps of the viral life cycle ranging from the host cell entry to viral protein translation has evolved. Since the host cell PI3K/Akt signaling pathway plays a critical regulatory role in many cellular processes including RNA processing, translation, autophagy and apoptosis, many viruses, in widely varying ways, target it. This review focuses on a number of remarkable examples of viral strategies, which exploit the PI3K/Akt signaling pathway for effective viral replication.
Output: Make Yourself at Home: Viral Hijacking of the PI3K/Akt Signaling Pathway
We have isolated a novel lectin, named HRL40 from the green alga Halimeda renschii. In hemagglutination-inhibition test and oligosaccharide-binding experiment with 29 pyridylaminated oligosaccharides, HRL40 exhibited a strict binding specificity for high-mannose N-glycans having an exposed (α1-3) mannose residue in the D2 arm of branched mannosides, and did not have an affinity for monosaccharides and other oligosaccharides examined, including complex N-glycans, an N-glycan core pentasaccharide, and oligosaccharides from glycolipids. The carbohydrate binding profile of HRL40 resembled those of Type I high-mannose specific antiviral algal lectins, or the Oscillatoria agardhii agglutinin (OAA) family, which were previously isolated from red algae and a blue-green alga (cyanobacterium). HRL40 potently inhibited the infection of influenza virus (A/H3N2/Udorn/72) into NCI-H292 cells with half-maximal effective dose (ED 50 ) of 2.45 nM through high-affinity binding to a viral envelope hemagglutinin (K D , 3.69 × 10 −11 M). HRL40 consisted of two isolectins (HRL40-1 and HRL40-2), which could be separated by reverse-phase HPLC. Both isolectins had the same molecular weight of 46,564 Da and were a disulfide -linked tetrameric protein of a 11,641 Da polypeptide containing at least 13 half-cystines. Thus, HRL40, which is the first Type I high-mannose specific antiviral lectin from the green alga, had the same carbohydrate binding specificity as the OAA family, but a molecular structure distinct from the family.
Output: A Novel High-Mannose Specific Lectin from the Green Alga Halimeda renschii Exhibits a Potent Anti-Influenza Virus Activity through High-Affinity Binding to the Viral Hemagglutinin
One Health approaches have tended to focus on closer collaboration among veterinarians and medical professionals, but remain unclear about how ecological approaches could be applied or how they might benefit public health and disease control. In this chapter, we review ecological concepts, and discuss their relevance to health, with an emphasis on emerging infectious diseases (EIDs). Despite the fact that most EIDs originate in wildlife, few studies account for the population, community, or ecosystem ecology of the host, reservoir, or vector. The dimensions of ecological approaches to public health that we propose in this chapter are, in essence, networks of population dynamics, community structure, and ecosystem matrices incorporating concepts of complexity, resilience, and biogeochemical processes.
Output: The Human Environment Interface: Applying Ecosystem Concepts to Health
Nucleopolyhedrovirus (NPV) is divided into Group I and Group II based on the phylogenetic analysis. It has been reported that Group I NPVs such as Autographa californica multiple NPV (AcMNPV) can transduce mammalian cells, while Group II NPVs such as Helicoverpa armigera single NPV (HaSNPV) cannot. Here we report that AcMNPV was capable of stimulating antiviral activity in human hepatoma cells (SMMC-7721) manifested by inhibition of Vesicular Stomatitis virus (VSV) replication. In contrast, the HaSNPV and the Spodoptera exigua multiple NPV (SeMNPV) of group ІІ had no inhibitory effect on VSV. Recombinant AcMNPV was shown to induce interferons alpha/beta even in the absence of transgene expression in human SMMC-7721 cells, while it mediated transgene expression in BHK and L929 mammalian cells without an ensuing antiviral activity.
Output: Group I but not Group II NPV induces antiviral effects in mammalian cells
Respiratory syncytial virus (RSV) infection is the leading cause of hospitalisation for respiratory diseases among children under 5 years old. The aim of this study was to analyse RSV seasonality in the five distinct regions of Brazil using time series analysis (wavelet and Fourier series) of the following indicators: monthly positivity of the immunofluorescence reaction for RSV identified by virologic surveillance system, and rate of hospitalisations per bronchiolitis and pneumonia due to RSV in children under 5 years old (codes CID-10 J12.1, J20.5, J21.0 and J21.9). A total of 12,501 samples with 11.6% positivity for RSV (95% confidence interval 11 -12.2), varying between 7.1 and 21.4% in the five Brazilian regions, was analysed. A strong trend for annual cycles with a stable stationary pattern in the five regions was identified through wavelet analysis of the indicators. The timing of RSV activity by Fourier analysis was similar between the two indicators analysed and showed regional differences. This study reinforces the importance of adjusting the immunisation period for high risk population with the monoclonal antibody palivizumab taking into account regional differences in seasonality of RSV.
Output: Respiratory syncytial virus seasonality in Brazil: implications for the immunisation policy for at-risk populations
A panel of 28 monoclonal antibodies (MAb) against the structural proteins of murine hepatitis virus-4, strain JHM (MHV-4) was used in three antigen binding assays to determine the extent of antigenic homology among six strains of murine coronaviruses. The antigenic determinants studied were highly conserved on the El glycoproteins and nucleocapsid (N) proteins of all strains tested. In contrast, antigenic polymorphism was observed among the E2 glycoproteins. Of three previously described antigenic determinants against which neutralizing antibodies are directed, only one, termed A(E2), was conserved on all strains. Antigenic site.B(E2) was found only on the strongly neurotropic MHV4 and site C(E2) was present on the virulent MHV4 and MHV-3 (hepatotropic) strains, but absent on the weakly pathogenic MHV-A59, MHV-1 and MHV-S strains. Four non-neutralizing antibodies against at least one topographically distinct antigenic determinant, which we previously designated D(E2), gave binding patterns consistent with two distinct sites. One of these was present on all MHV strains tested and the other was present on all strains except MHV-S. These non-neutralizing antigenic sites were redesignated E(E2) and D(E2) respectively. coronavirus, antigen, glycoprotein, monoclonal antibody, epitope, polymorphism
Output: Antigenic variation among murine coronaviruses: Evidence for polymorphism on the peplomer glycoprotein, E2
Immunological checkpoints, such as the inhibitory CD200 receptor (CD200R), play a dual role in balancing the immune system during microbial infection. On the one hand these inhibitory signals prevent excessive immune mediated pathology but on the other hand they may impair clearance of the pathogen. We studied the influence of the inhibitory CD200-CD200R axis on clearance and pathology in two different virus infection models. We find that lack of CD200R signaling strongly enhances type I interferon (IFN) production and viral clearance and improves the outcome of mouse hepatitis corona virus (MHV) infection, particularly in female mice. MHV clearance is known to be dependent on Toll like receptor 7 (TLR7)-mediated type I IFN production and sex differences in TLR7 responses previously have been reported for humans. We therefore hypothesize that CD200R ligation suppresses TLR7 responses and that release of this inhibition enlarges sex differences in TLR7 signaling. This hypothesis is supported by our findings that in vivo administration of synthetic TLR7 ligand leads to enhanced type I IFN production, particularly in female Cd200 2/2 mice and that CD200R ligation inhibits TLR7 signaling in vitro. In influenza A virus infection we show that viral clearance is determined by sex but not by CD200R signaling. However, absence of CD200R in influenza A virus infection results in enhanced lung neutrophil influx and pathology in females. Thus, CD200-CD200R and sex are host factors that together determine the outcome of viral infection. Our data predict a sex bias in both beneficial and pathological immune responses to virus infection upon therapeutic targeting of CD200-CD200R.
Output: CD200 Receptor Controls Sex-Specific TLR7 Responses to Viral Infection
The study evaluated the effect of New Neonatal Porcine Diarrhoea Syndrome (NNPDS) on average daily gain (ADG) and mortality and described the clinical manifestations in four herds suffering from the syndrome. NNPDS is a diarrhoeic syndrome affecting piglets within the first week of life, which is not caused by enterotoxigenic Escherichia coli (ETEC), Clostridium perfringens (C. perfringens) type A/C, Clostridium difficile (C. difficile), rotavirus A, coronavirus, Cystoisospora suis, Strongyloides ransomi, Giardia spp or Cryptosporidium spp. Results: Piglets were estimated to have a negative ADG of 9 and 14 g when diarrhoeic for 1 day and >1 day respectively. However, if only diarrhoeic on the day of birth, no negative effect on ADG was seen. Piglets originating from severely affected litters were estimated to have a reduced ADG of 38 g. The study did not show an overall effect of diarrhoea on mortality, but herd of origin, sow parity, birth weight, and gender were significantly associated with mortality. In one of the herds, approximately 25% of the diarrhoeic piglets vs. 6% of the non-diarrhoeic piglets died, and 74% of necropsied piglets were diagnosed with enteritis. These findings indicate that the high mortality seen in this herd was due to diarrhoea. Conclusions: NNPDS negatively affected ADG in piglets, and even piglets that were diarrhoeic for one day only experienced a reduction in ADG. However, the study showed that diarrhoea restricted to the day of birth did not affect ADG and suggested this phenomenon to be unrelated to the syndrome. Since the diarrhoeal status of the litter had important effects on ADG, future research on NNPDS probably ought to focus on piglets from severely affected litters. The study showed important dissimilarities in the course of diarrhoea between the herds, and one herd was considerably more affected than the others. Within this herd, NNPDS seemed to be associated with a higher mortality, whereas in general the study did not show lethal effects of NNPDS.
Output: The effect of New Neonatal Porcine Diarrhoea Syndrome (NNPDS) on average daily gain and mortality in 4 Danish pig herds
The aim of the present survey was to evaluate the prevalence of Canine rotavirus (CRV) infection in companion dogs in Ahvaz district, Iran. The studied dogs were selected between referred cases to Shahid Chamran University of Ahvaz. Fecal samples were collected from 98 diarrheic dogs between December 2011 and August 2013. The dogs were classified according to age, sex, breed, clinical signs, and season. They were divided into three age groups (<3 months, 3-6 months, and >6 months), five different breeds, and another two groups on the basis of clinical symptoms (hemorrhagic and non-hemorrhagic diarrhea) using Chi-square analysis, Fischer's exact test, and Z test. The prevalence of rotavirus infection was 16.33 % (16 out of 98) (95 % CI for proportion 9.1-23.6 %) by means of immunochromatography assay (ICA) (Catalog No. RG18-03). The infection had significantly more prevalence in dogs less than 3 months (48.15 %; 13 out of 27) compared with dogs between 3 and 6 months (6.06 %; 2 out of 33) and above 6 months (2.63 %; 1 out of 38) (p<0.05). Prevalence was higher in males (17.54 %; 10 out of 57) than females (14.63 %; 6 out of 41), in winter season (21.74 %; 5 out of 23), and breed of German shepherd (19.05 %; 4 of 21), but the difference was not significant between the prevalence of infection relative to gender, season, and breed (p>0.05). Nevertheless, infection was significantly higher in none-hemorrhagic diarrheic dogs (23.08 %; 15 of 65) (p<0.05). The obtained results provide useful information on the epidemiology of Canine rotavirus in this area.
Output: Antigenic detection of Canine rotavirus group A in diarrheic dogs in Ahvaz district, Southwestern Iran
Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (Electronic Supplement) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology, and important host-virus interactions. Supplementary information: is available at rna.uni-jena.de/supplements/bats, the Open Science Framework (doi.org/10.17605/OSF.IO/4CMDN), and GitHub (github.com/rnajena/bats_ncrna).
Output: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
The induction of immunological memory, which is mediated by memory T and B cells, is central to adaptive protective immunity to pathogens induced by previous infection and is the cornerstone of effective vaccine design. Recent studies in mice have suggested that memory T cells that accumulate in tissues, termed tissue-resident memory T (TRM) cells, play a crucial role in maintaining long-term protective immunity to mucosal pathogens. CD4 and CD8 TRM cells can be induced following infection at mucosal sites or the skin, where they are maintained and poised to respond rapidly to reinfection with the same pathogen. TRM cells can also be generated by vaccination, but their induction is influenced by a number of factors, including the type of vaccine, the adjuvant, and the route of immunization. Live attenuated vaccines appear to be more effective than killed or subunit vaccines at inducing TRM cells and mucosal immunization, especially by intranasal route, is more effective than parenteral delivery. However, evidence is emerging that formulation of killed or subunit vaccines with novel adjuvants, especially those that generate Th1 and Th17 responses, can promote the induction of TRM cells. While TRM cells are also present at high number in mucosal tissues in humans, one of the challenge will be to develop methodologies for routine quantification of these cells in humans. Nevertheless, the identification of approaches for optimum induction of TRM cells in mice should assist in the design of more effective vaccines that sustain protective immunity against a range of human pathogens.
Output: a section of the journal Frontiers in Immunology CD4 T RM Cells Following infection and immunization: implications for More effective vaccine Design
Several excellent reviews have been published of the current mechanistic understanding of how viral infections increase susceptibility to secondary bacterial pneumonias. 46-49 Thus, this article provides only a brief overview, with a primary focus on virally mediated effects on pulmonary host defense and subsequent impairment of bacterial clearance (Table 2) . However, the authors acknowledge that microbiologic and epidemiologic factors can contribute to the pathogenesis of viral-bacterial coinfections.
Output: Postviral Complications: Bacterial Pneumonia
RNA interference (RNAi) is a powerful method for specific gene silencing which may also lead to promising novel therapeutic strategies. It is mediated through small interfering RNAs (siRNAs) which sequence-specifically trigger the cleavage and subsequent degradation of their target mRNA. One critical factor is the ability to deliver intact siRNAs into target cells/organs in vivo. This review highlights the mechanism of RNAi and the guidelines for the design of optimal siRNAs. It gives an overview of studies based on the systemic or local application of naked siRNAs or the use of various nonviral siRNA delivery systems. One promising avenue is the the complexation of siRNAs with the polyethylenimine (PEI), which efficiently stabilizes siRNAs and, upon systemic administration, leads to the delivery of the intact siRNAs into different organs. The antitumorigenic effects of PEI/siRNA-mediated in vivo gene-targeting of tumor-relevant proteins like in mouse tumor xenograft models are described. RNAi is an evolutionarily conserved, sequence-specific, posttranscriptional gene silencing phenomenon. It is triggered by 2 Journal of Biomedicine and Biotechnology DNA DNA dsRNA dsRNA processing Dicer ATP siRNA ADP + P i Interferon response Nonspecific gene silencing RISC assembly RISC activation Binding of RISC to target mRNA mRNA degradation Cleavage Target mRNA Expression RISC ATP ADP + P i RISC £ Figure 1 : Mechanism of RNA interference (RNAi) in mammalian systems. Long double-stranded RNA molecules (dsRNA), which are expressed from DNA vectors (left red arrow) or directly enter the cell (center red arrow), are processed by the Dicer complex resulting in the formation of small inhibitory RNAs (siRNAs). Alternatively, to induce RNAi these small 21-23 bp duplexes are directly delivered into the cell (right red arrow). The siRNAs are incorporated into a nuclease-containing multiprotein complex called RISC, which becomes activated upon the ATP-dependent unwinding of the siRNA duplex by an RNA helicase. The now single-stranded siRNA guides the RISC complex to its complementary target mRNA which is then cleaved by the endonucleolytical activity of RISC. While the RISC complex is recovered for further cycles, the cleaved mRNA molecule is rapidly degraded due to its unprotected RNA ends.
Output: Review Article Delivery Systems for the Direct Application of siRNAs to Induce RNA Interference (RNAi) In Vivo