niryuu/sni-each-converted huggingface dataset:
Background: Penicillium marneffei is the most important thermal dimorphic fungus causing systemic mycosis in China and Southeast Asia. While miRNAs are increasingly recognized for their roles in post-transcriptional regulation of gene expression in animals and plants, miRNAs in fungi were less well studied and their potential roles in fungal dimorphism were largely unknown. Based on P. marneffei genome sequence, we hypothesize that miRNA-like RNAs (milRNAs) may be expressed in the dimorphic fungus. Methodology/Principal Findings: We attempted to identify milRNAs in P. marneffei in both mycelial and yeast phase using high-throughput sequencing technology. Small RNAs were more abundantly expressed in mycelial than yeast phase. Sequence analysis revealed 24 potential milRNA candidates, including 17 candidates in mycelial and seven in yeast phase. Two genes, dcl-1 and dcl-2, encoding putative Dicer-like proteins and the gene, qde-2, encoding Argonaute-like protein, were identified in P. marneffei. Phylogenetic analysis showed that dcl-2 of P. marneffei was more closely related to the homologues in other thermal dimorphic pathogenic fungi than to Penicillium chrysogenum and Aspergillus spp., suggesting the co-evolution of dcl-2 among the thermal dimorphic fungi. Moreover, dcl-2 demonstrated higher mRNA expression levels in mycelial than yeast phase by 7 folds (P,0.001). Northern blot analysis confirmed the expression of two milRNAs, PM-milR-M1 and PM-milR-M2, only in mycelial phase. Using dcl-1 KO , dcl-2 KO , dcl DKO and qde-2 KO deletion mutants, we showed that the biogenesis of both milRNAs were dependent on dcl-2 but not dcl-1 or qde-2. The mRNA expression levels of three predicted targets of PM-milR-M1 were upregulated in knockdown strain PM-milR-M1 KD , supporting regulatory function of milRNAs. Conclusions/Significance: Our findings provided the first evidence for differential expression of milRNAs in different growth phases of thermal dimorphic fungi and shed light on the evolution of fungal proteins involved in milRNA biogenesis and possible role of post-transcriptional control in governing thermal dimorphism.
Output: Identification of MicroRNA-Like RNAs in Mycelial and Yeast Phases of the Thermal Dimorphic Fungus Penicillium marneffei
Acute graft-versus-host disease (aGVHD) is an important complication of allogeneic stem cell transplantation (alloSCT). High dose glucocorticosteroids, are currently recommended as first-line treatment for grade II-IV aGVHD resulting in overall complete responses (CR) in 40%-50% of patients. No standard second-line regimen has been established. Different options have been reported, including anti-TNFα antibodies. We retrospectively reviewed the outcome of 15 patients with steroid-refractory (SR) aGVHD treated with etanercept at our institution. Patients were transplanted for a hematological malignancy and received either a myeloablative or a non-myeloablative conditioning regimen. Prophylaxis of GVHD consisted of cyclosporin A and mycophenolic acid. Acute GVHD was diagnosed at a median of 61 days post-transplantation. All patients had grade III aGVHD of the gut. Second-line treatment with etanercept was started at a median of 13 days after initiation of first-line therapy. Overall response rate was 53%, with CR in 3 patients and PR in 5 patients. Median overall survival after initiation of treatment with etanercept was 66 days (range 5-267) for the entire group. Median overall survival was 99 days (range 47-267 days) for responders and 17 days (range 5-66 days) for non-responders (p<0.01). Nevertheless, all patients died. Causes of death were progressive GVHD in 7 patients (47%), infection in 6 patients (40%), cardiac death in 1 patient (6.7%) and relapse in 1 patient (6,7%). Second-line treatment with etanercept does induce responses in SR-aGVHD of the gut but appears to be associated with poor long-term survival even in responding patients.
Output: Etanercept for steroid-refractory acute graft- versus-host disease: A single center experience
Asthma is a chronic disease that has a significant impact on quality of life and is particularly important in children and adolescents, in part due to the higher incidence of allergies in children. The incidence of asthma has increased dramatically during this time period, with the highest increases in the urban areas of developed countries. It seems that the incidence in developing countries may follow this trend as well. While our knowledge of the pathophysiology of asthma and the available of newer, safer medication have both improved, the mortality of the disease has undergone an overall increase in the past 30 years. Asthma treatment goals in children include decreasing mortality and improving quality of life. Specific treatment goals include but are not limited to decreasing inflammation, improving lung function, decreasing clinical symptoms, reducing hospital stays and emergency department visits, reducing work or school absences, and reducing the need for rescue medications. Non-pharmacological management strategies include allergen avoidance, environmental evaluation for allergens and irritants, patient education, allergy testing, regular monitoring of lung function, and the use of asthma management plans, asthma control tests, peak flow meters, and asthma diaries. Achieving asthma treatment goals reduces direct and indirect costs of asthma and is economically cost-effective. Treatment in children presents unique challenges in diagnosis and management. Challenges in diagnosis include consideration of other diseases such as viral respiratory illnesses or vocal cord dysfunction. Challenges in management include evaluation of the child's ability to use inhalers and peak flow meters and the management of exercise-induced asthma.
Output: Asthma in Children and Adolescents: A Comprehensive Approach to Diagnosis and Management
Corona Virus Disease 2019 has spread rapidly to more than 70 countries and regions overseas and over 80000 cases have been infected, resulting in more than three thousand deaths. Rapid diagnosis of patients remains a bottleneck in containing the progress of the epidemic. We used automated chemiluminescent immunoassay to detect serum IgM and IgG antibodies to 2019-nCoV of 736 subjects. COVID-19 patients were becoming reactive(positive) for specific antibodies from 7-12 days after the onset of morbidity. Specific IgM and IgG increased with the progression of the disease. The areas under the ROC curves of IgM and IgG were 0.988 and 1.000, respectively. Specific antibody detection has good sensitivity and specificity. Detection of specific antibodies in patients with fever can be a good distinction between COVID-19 and other diseases, so as to be a complement to nucleic acid diagnosis to early diagnosis of suspected cases. All rights reserved. No reuse allowed without permission. the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
Output: Serological detection of 2019-nCoV respond to the epidemic: A useful complement to nucleic acid testing
We summarize findings of SARS-CoV infections in several animal models each of which support viral replication in lungs accompanied by histopathological changes and/or clinical signs of illness to varying degrees. New findings are reported on SARS-CoV replication and associated pathology in two additional strains (C57BL/6 and 129S6) of aged mice. We also provide new comparative data on viral replication and associated pathology following infection of golden Syrian hamsters with various SARS-CoV strains and report the levels of neutralizing antibody titers following these infections and the cross-protective efficacy of infection with these strains in protecting against heterologous challenge. Finally, we summarize findings of a variety of vaccine approaches and discuss the available in vitro and in vivo data addressing the potential for disease enhancement following re-infection in animals previously vaccinated against or infected with SARS-CoV.
Output: Animal Models and Vaccines for SARS-CoV Infection
An urgent demand of assessing passengers' exposure risks in airliner cabins was raised as commercial airliners are one of the major media that carrying and transmitting infectious disease worldwide. In this study, simulations were conducted using a Boeing 737 cabin model to study the transport characteristics of airborne droplets and the associated infection risks of passengers. The numerical results of the airflow field were firstly compared against the experimental data in the literature to validate the reliability of the simulations. Airborne droplets were assumed to be released by passengers through coughing and their transport characteristics were modelled using the Lagrangian approach. Numerical results found that the particle travel distance was very sensitive to the release locations, and the impact was more significant along the longitudinal and horizontal directions. Particles released by passengers sitting next to the windows could travel much further than the others. A quantifiable approach was then applied to assess the individual infection risks of passengers. The key particle transport information such as the particle residence time yielded from the Lagrangian tracking process was extracted and integrated into the Wells-Riley equation to estimate the risks of infection. Compared to the Eulerian-based approach, the Lagrangian-based approach presented in this study is more robust as it addresses both the particle concentration and particle residence time in the breathing zone of every individual passenger.
Output: Evaluation of airborne disease infection risks in an airliner cabin using the Lagrangian-based Wells-Riley approach
Marking the end of the five-year programme initiated by the Chinese Government to lift more than 70 million people out of poverty, the year 2020 is a milestone. Poverty alleviation has moved strongly forward in China and the major health indicators are now better than the average of all middle-and high-income countries. However, the dual burden of infectious and chronic diseases remains a challenge with respect to achieving the health target in the United Nations 2030 Agenda for sustainable development goals (SDGs). In 2015, about 44% of the poor population in China were impoverished by illness but already in 2018, multi-sectoral actions delivered by the Health-related Poverty Alleviation programme had reduced the number almost by half. In the past three years 15 million poor people (98% of the poor population) with infectious and chronic diseases had been treated and taken care of thanks to financial support through multiple health insurance schemes and other governmental subsidies. This article discusses the lessons learnt with regard to health-related poverty alleviation in China with special reference to those still remaining impoverished by illness. Consolidation of the achievements reached and provision of basic needs to those still disadvantaged and in poor health will require a major improvement of accessibility to, and affordability of, health services. The next step towards enhanced productivity and better living conditions will involve upgrading of the capacity of health professionals in the poor regions, promotion of coherent efforts in health-related poverty alleviation and rural revitalization measures. As an additional measure, data monitoring and research on health poverty alleviation should be strengthened as they are essential to generate the evidence and knowledge needed to support the move in the direction envisioned by the SDGs, and the new Healthy China 2030 programme.
Output: The year 2020, a milestone in breaking the vicious cycle of poverty and illness in China
The spike (S) protein is a major structural glycoprotein of coronavirus (CoV), the causal agent of severe acute respiratory syndrome (SARS). The S protein is a potent target for SARS-specific cell-mediated immune responses. However, the mechanism CoV pathogenesis in SARS and the role of special CTLs in virus clearance are still largely uncharacterized. Here, we describe a study that leads to the identification of a novel HLA-A*0201-restricted epitope from conserved regions of S protein. First, different SARS-CoV sequences were analyzed to predict eight candidate peptides from conserved regions of the S protein based upon HLA-A*0201 binding and proteosomal cleavage. Four of eight candidate peptides were tested by HLA-A*0201 binding assays. Among the four candidate peptides, Sp8 (S 958-966 , VLNDILSRL) induced specific CTLs both ex vivo in PBLs of healthy HLA-A2 + donors and in HLA-A2.1/K b transgenic mice immunized with a plasmid encoding full-length S protein. The immunized mice released IFN-γ and lysed target cells upon stimulation with Sp8 peptide-pulsed autologous dendritic cells in comparison to other candidates. These results suggest that Sp8 is a naturally processed epitope. We propose that Sp8 epitope should help in the characterization of mechanisms of virus control and immunopathology in SARS-CoV infection.
Output: BMC Immunology Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV
This unit describes the preparation and transplantation of human neural precursor cells (hNPCs) and mouse neural precursor cells (mNPCs) into the thoracic region of the mouse spinal cord. The techniques in this unit also describe how to prepare the mouse for surgery by performing a laminectomy to expose the spinal cord for transplantation. Here we show NPCs genetically labeled with eGFP transplanted into the spinal cord of a mouse following viralmediated demyelination can efficiently be detected via eGFP expression. Transplantation of these cells into the spinal cord is an efficacious way to determine their effects in neurological disorders such as multiple sclerosis, Alzheimer's disease, and spinal cord injury.
Output: Intraspinal transplantation of mouse and human neural precursor cells
In immune-mediated diseases, Treg and proinflammatory Th17 cells have been suggested to play either suppressor (beneficial) or effector (detrimental) roles, respectively. Tissue damage in viral infections can be caused by direct viral replication or immunopathology. Viral replication can be enhanced by anti-inflammatory responses and suppressed by proinflammatory responses. However, Tregs could suppress proinflammatory responses, reducing immunopathology, while Th17 cell-induced inflammation may enhance immunopathology. Here, the roles of Treg and Th17 cells depend on whether tissue damage is caused by direct virus replication or immunopathology, which differ depending on the virus, disease stage and host immune background. Although the precise mechanisms of tissue damage in multiple sclerosis and myocarditis are unclear, both viral replication and immune effector cells have been proposed to cause pathogenesis. Personalized medicine that alters the balance between Treg and Th17 cells may ameliorate viral pathology during infections.
Output: Regulatory T cells and Th17 cells in viral infections: implications for multiple sclerosis and myocarditis
Middle East respiratory syndrome coronavirus (MERS-CoV) infects host cells through binding the receptor binding domain (RBD) on its spike glycoprotein to human receptor dipeptidyl peptidase 4 (hDPP4). Here, we report identification of critical residues on hDPP4 for RBD binding and virus entry through analysis of a panel of hDPP4 mutants. Based on the RBD-hDPP4 crystal structure we reported, the mutated residues were located at the interface between RBD and hDPP4, which potentially changed the polarity, hydrophobic or hydrophilic properties of hDPP4, thereby interfering or disrupting their interaction with RBD. Using surface plasmon resonance (SPR) binding analysis and pseudovirus infection assay, we showed that several residues in hDPP4-RBD binding interface were important on hDPP4-RBD binding and viral entry. These results provide atomic insights into the features of interactions between hDPP4 and MERS-CoV RBD, and also provide potential explanation for cellular and species tropism of MERS-CoV infection.
Output: Identification of residues on human receptor DPP4 critical for MERS-CoV binding and entry
Old mice will have a subset of lesions as part of the progressive decline in organ function that defines aging. External and palpable lesions will be noted by the research, husbandry, or veterinary staff during testing, cage changing, or physical exams. While these readily observable lesions may cause alarm, not all cause undue distress or are life-threatening. In aging research, mice are maintained until near end of life that, depending on strain and genetic manipulation, can be upwards of 33 months. Aging research has unique welfare issues related to age-related decline, debilitation, fragility, and associated pain of chronic diseases. An effective aging research program includes the collaboration and education of the research, husbandry, and veterinary staff, and of the members of the institution animal care and use committee. This collaborative effort is critical to humanely maintaining older mice and preventing excessive censorship due to non-lethal diseases. Part of the educational process is becoming familiar with how old mice appear clinically, at necropsy and histopathologically. This baseline knowledge is important in making the determination of humane end points, defining health span, contributing causes of death and effects of interventions. The goal of this paper is to introduce investigators to age-associated diseases and lesion patterns in mice from clinical presentation to pathologic assessment. To do so, we present and illustrate the common clinical appearances, necropsy and histopathological lesions seen in subsets of the aging colonies maintained at the University of Washington.
Output: Practical pathology of aging mice
Live cell imaging enables the study of dynamic processes of living cells in real time by use of suitable reporter proteins and the staining of specific cellular structures and/or organelles. With the availability of advanced optical devices and improved cell culture protocols it has become a rapidly growing research methodology. The success of this technique relies mainly on the selection of suitable reporter proteins, construction of recombinant plasmids possessing cell type specific promoters as well as reliable methods of gene transfer. This review aims to provide an overview of the recent developments in the field of marker proteins (bioluminescence and fluorescent) and methodologies (fluorescent resonance energy transfer, fluorescent recovery after photobleaching and proximity ligation assay) employed as to achieve an improved imaging of biological processes in hepatoma cells. Moreover, different expression systems of marker proteins and the modes of gene transfer are discussed with emphasis on the study of lipid droplet formation in hepatocytes as an example.
Output: Recent advances in live cell imaging of hepatoma cells
Aptamers are specific nucleic acid sequences that can bind to a wide range of non-nucleic acid targets with high affinity and specificity. These molecules are identified and selected through an in vitro process called SELEX (systematic evolution of ligands by exponential enrichment). Proteins are the most common targets in aptamer selection. In diagnostic and detection assays, aptamers represent an alternative to antibodies as recognition agents. Cellular detection is a promising area in aptamer research. One of its principal advantages is the ability to target and specifically differentiate microbial strains without having previous knowledge of the membrane molecules or structural changes present in that particular microorganism. The present review focuses on aptamers, SELEX procedures, and aptamer-based biosensors (aptasensors) for the detection of pathogenic microorganisms and viruses. Special emphasis is placed on nanoparticlebased platforms.
Output: Aptasensors for detection of microbial and viral pathogens
A small molecule library containing 480 known bioactive compounds was screened for antiviral activity against poliovirus (PV) using a cellular fluorescence resonance energy transfer (FRET) assay for viral protease activity. The infected reporter cells treated with the viral replicationsuppressing compounds were examined via fluorescence microscope 7.5 h postinfection. Twelve molecules showed moderate to potent antiviral activity at concentrations less than 32 M during the primary screening. Three compounds, anisomycin, linoleic acid, and lycorine, were chosen for validation. A dose-dependent cytotoxicity assay and a secondary screening using conventional plaque assay were conducted to confirm the results. The developed method can be used for rapid screening for molecules with antiviral activity.
Output: Rapid identification of inhibitors that interfere with poliovirus replication using a cell-based assay
COVID-19 is spreading all across the globe. Up until March 23, 2020, the confirmed cases in 173 12 countries and regions of the globe had surpassed 346,000, and more than 14,700 deaths had resulted. The 13 confirmed cases outside of China had also reached over 81,000, with over 3,200 deaths. In this study, a 14 Convolutional Neural Network (CNN) was proposed to analyze and predict the number of confirmed cases. 15 Several cities with the most confirmed cases in China were the focus of this study, and a COVID-19 16 forecasting model, based on the CNN deep neural network method, was proposed. To compare the overall 17 efficacies of different algorithms, the indicators of mean absolute error and root mean square error were 18 applied in the experiment of this study. The experiment results indicated that compared with other deep 19 learning methods, the CNN model proposed in this study has the greatest prediction efficacy. The feasibility 20 and practicality of the model in predicting the cumulative number of COVID-19 confirmed cases were also 21 verified in this study. 22
Output: Multiple-Input Deep Convolutional Neural Network Model for COVID-19 Forecasting in China 2
A novel virulent bacteriophage, vB_BbrM_PHB04, infecting Bordetella bronchiseptica was isolated from wastewater collected at a swine farm in China. Phage vB_BbrM_PHB04 exhibited growth over a wide range of temperature and pH conditions and showed different efficiency of plating values and lytic spectra within the same strains at 25 °C and 37 °C. Highthroughput sequencing revealed that vB_BbrM_PHB04 has a linear double-stranded DNA genome with 124 putative open reading frames. Overall, the genome of vB_BbrM_PHB04 showed very low similarity (the highest nucleotide identity 82%, 1% coverage) to other phage sequences in the GenBank database. Phylogenetic analysis indicated that vB_BbrM_PHB04 is a new member of the family Myoviridae. In addition, polymerase chain reaction-based detection of phage genes in phageresistant B. bronchiseptica variants revealed no evidence of lysogenic activity of phage vB_BbrM_PHB04. Handling Editor: Tim Skern.
Output: Characterisation of a newly detected bacteriophage infecting Bordetella bronchiseptica in swine
Human genetics influence a range of pathological and clinical phenotypes in respiratory infections; however, the contributions of disease modifiers remain underappreciated. We exploited the Collaborative Cross (CC) mouse genetic-reference population to map genetic modifiers that affect the severity of Pseudomonas aeruginosa lung infection. Screening for P. aeruginosa respiratory infection in a cohort of 39 CC lines exhibits distinct disease phenotypes ranging from complete resistance to lethal disease. Based on major changes in the survival times, a quantitative-trait locus (QTL) was mapped on murine chromosome 3 to the genomic interval of Mb 110.4 to 120.5. Within this locus, composed of 31 protein-coding genes, two candidate genes, namely, dihydropyrimidine dehydrogenase (Dpyd) and sphingosine-1-phosphate receptor 1 (S1pr1), were identified according to the level of genome-wide significance and disease gene prioritization. Functional validation of the S1pr1 gene by pharmacological targeting in C57BL/ 6NCrl mice confirmed its relevance in P. aeruginosa pathophysiology. However, in a cohort of Canadian patients with cystic fibrosis (CF) disease, regional genetic-association analysis of the syntenic human locus on chromosome 1 (Mb 97.0 to 105.0) identified two single-nucleotide polymorphisms (rs10875080 and rs11582736) annotated to the Dpyd gene that were significantly associated with age at first P. aeruginosa infection. Thus, there is evidence that both genes might be implicated in this disease. Our results demonstrate that the discovery of murine modifier loci may generate information that is relevant to human disease progression. IMPORTANCE Respiratory infection caused by P. aeruginosa is one of the most critical health burdens worldwide. People affected by P. aeruginosa infection include patients with a weakened immune system, such as those with cystic fibrosis (CF) genetic disease or non-CF bronchiectasis. Disease outcomes range from fatal pneumonia to chronic lifethreatening infection and inflammation leading to the progressive deterioration of pulmonary function. The development of these respiratory infections is mediated by multiple causes. However, the genetic factors underlying infection susceptibility are poorly known and difficult to predict. Our study employed novel approaches and improved mouse disease models to identify genetic modifiers that affect the severity of P. aeruginosa lung infection. We identified candidate genes to enhance our understanding of P. aeruginosa infection in humans and provide a proof of concept that could be exploited for other human pathologies mediated by bacterial infection.
Output: Collaborative Cross Mice Yield Genetic Modifiers for Pseudomonas aeruginosa Infection in Human Lung Disease
Macrophages have important protective functions during infection with herpes simplex virus type 1 (HSV-1). However, molecular mechanisms that restrict viral propagation and protect from severe disease are unclear. Here we show that macrophages take up HSV-1 via endocytosis and transport the virions into multivesicular bodies (MVBs). In MVBs, acid ceramidase (aCDase) converts ceramide into sphingosine and increases the formation of sphingosine-rich intraluminal vesicles (ILVs). Once HSV-1 particles reach MVBs, sphingosine-rich ILVs bind to HSV-1 particles, which restricts fusion with the limiting endosomal membrane and prevents cellular infection. Lack of aCDase in macrophage cultures or in Asah1 −/− mice results in replication of HSV-1 and Asah1 −/− mice die soon after systemic or intravaginal inoculation. The treatment of macrophages with sphingosine enhancing compounds blocks HSV-1 propagation, suggesting a therapeutic potential of this pathway. In conclusion, aCDase loads ILVs with sphingosine, which prevents HSV-1 capsids from penetrating into the cytosol.
Output: 18 Cluster of Excellence RESIST (EXC 2155
Most paramyxoviruses enter the cell by direct fusion of the viral envelope with the plasma membrane. Our previous studies have shown the colocalization of Newcastle Disease Virus (NDV) with the early endosome marker EEA1 and the inhibition of NDV fusion by the caveolin-phosphorylating drug phorbol 12-myristate 13-acetate (PMA) prompted us to propose that NDV enters the cells via endocytosis. Here we show that the virus-cell fusion and cell-cell fusion promoted by NDV-F are increased by about 30% after brief exposure to low pH in HeLa and ELL-0 cells but not in NDV receptor-deficient cell lines such as GM95 or Lec1. After a brief low-pH exposure, the percentage of NDV fusion at 29°C was similar to that at 37°C without acid-pH stimulation, meaning that acid pH would decrease the energetic barrier to enhance fusion. Furthermore, preincubation of cells with the protein kinase C inhibitor bisindolylmaleimide led to the inhibition of about 30% of NDV infectivity, suggesting that a population of virus enters cells through receptor-mediated endocytosis. Moreover, the involvement of the GTPase dynamin in NDV entry is shown as its specific inhibitor, dynasore, also impaired NDV fusion and infectivity. Optimal infection of the host cells was significantly affected by drugs that inhibit endosomal acidification such as concanamycin A, monensin and chloroquine. These results support our hypothesis that entry of NDV into ELL-0 and HeLa cells occurs through the plasma membrane as well as by dynamin-low pH-and receptor-dependent endocytosis.
Output: Entry of Newcastle Disease Virus into the host cell: Role of acidic pH and endocytosis
Knowledge of the host factors required for norovirus replication has been hindered by the challenges associated with culturing human noroviruses. We have combined proteomic analysis of the viral translation and replication complexes with a CRISPR screen, to identify host factors required for norovirus infection. The core stress granule component G3BP1 was identified as a host factor essential for efficient human and murine norovirus infection, demonstrating a conserved function across the Norovirus genus. Furthermore, we show that G3BP1 functions in the novel paradigm of viral VPg-dependent translation initiation, contributing to the assembly of translation complexes on the VPg-linked viral positive sense RNA genome by facilitating ribosome recruitment. Our data uncovers a novel function for G3BP1 in the life cycle of positive sense RNA viruses and identifies the first host factor with pan-norovirus pro-viral activity.
Output: Noroviruses subvert the core stress granule component G3BP1 to promote viral VPg-dependent translation
Background: In 2009, an outbreak of respiratory illness caused by influenza A H1N1 virus occurred worldwide. Some patients required Intensive Care Unit (ICU) admission. The use of non-invasive ventilation (NIV) in these patients is controversial, as the aerosol dispersion may contaminate the environment and health-care co-workers. Methods: Describe the respiratory profile, the mortality rate, and the benefit of using NIV in patients with confirmed diagnosis of influenza AH1N1 who were admitted in the ICU during the year 2009. Results: A total of 1, 401 cases of influenza A H1N1 were confirmed in our hospital by real-time RT-PCR in 2009, and 20 patients were admitted to the ICU. The patients' ages ranged from 18 to 74 years (median of 42). Acute Respiratory Failure (ARF) was present in 70% of patients. The median Acute Physiology and Chronic Health Evaluation II score was 7 (range 7 to 25). Of the 14 patients who developed ARF, 85.7% needed NIV and 14% needed invasive MV at admission. Our success rate (41.6%) with NIV was higher than that described by others. The hospital mortality rate was 2.1%. When influenza A H1N1 arrived in Brazil, the disease was already on endemic alert in other countries. The population was already aware of the symptoms and the health-care system of the treatment. This allowed patients to be properly and promptly treated for influenza A H1N1, while health-care workers took protective measures to avoid contamination. Conclusion: In our study we found a high success and low mortality rates with non-invasive ventilation in patients with influenza A H1N1.
Output: High success and low mortality rates with non- invasive ventilation in influenza A H1N1 patients in a tertiary hospital
Vesicle-membrane-protein-associated protein A (VAPA) and oxysterol-binding protein (OSBP) regulate intracellular cholesterol homeostasis, which is required for many virus infections. During entry, viruses or virus-containing vesicles can fuse with endosomal membranes to mediate the cytosolic release of virions, and alterations in endosomal cholesterol can inhibit this invasion step. We show that the antiviral effector protein interferon-inducible transmembrane protein 3 (IFITM3) interacts with VAPA and prevents its association with OSBP, thereby disrupting intracellular cholesterol homeostasis and inhibiting viral entry. By altering VAPA-OSBP function, IFITM3 induces a marked accumulation of cholesterol in multivesicular bodies and late endosomes, which inhibits the fusion of intraluminal virion-containing vesicles with endosomal membranes and thereby blocks virus release into the cytosol. Consequently, ectopic expression or depletion of the VAPA gene profoundly affects IFITM3mediated inhibition of viral entry. Thus, IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry, further underscoring the importance of cholesterol in virus infection.
Output: The Antiviral Effector IFITM3 Disrupts Intracellular Cholesterol Homeostasis to Block Viral Entry
Our previous in vitro comparative study on a feline coronavirus (FCoV) pair, differing only in the intactness of their ORF3abc regions, showed that the truncated ORF3abc plays an important role in the efficient macrophage/monocyte tropism of type II feline infectious peritonitis virus (FIPV). In the present study, we describe a challenge experiment with the same recombinant FCoVs in order to gain data on the in vivo characteristics on these viruses. While parent virus FIPV DF-2 developed feline infectious peritonitis in all the infected cats, its recombinant virus PBFIPV-DF-2, differing only in seven nucleotides, proved to be surprisingly low virulent, although caused an acute febrile episode similarly to the original FIPV DF-2. PBFIPV-DF-2 infection induced significantly lower virus neutralization titers than its parent virus, and lacked the second phase of viremia and development of fatal course of the disease. The recombinant PBFIPV-DF-2-R3i with completed ORF3abc gained biological properties that differentiate between the feline enteric coronavirus (FECV) and FIPV biotypes such as intensive replication in the gut, absence of viremia and weak or no serological response. Using reverse genetic approaches our study is the first experimental proof that ORF3abc is indeed responsible for the restriction of FECV replication to the intestine in vivo. Citation: Bálint Á , Farsang A, Zádori Z, Belák S (2014) Comparative In Vivo Analysis of Recombinant Type II Feline Coronaviruses with Truncated and Completed ORF3 Region. PLoS ONE 9(2): e88758.
Output: Comparative In Vivo Analysis of Recombinant Type II Feline Coronaviruses with Truncated and Completed ORF3 Region
Phosphatidylinositol 4-kinases (PI4Ks) and small guanosine triphosphatases (GTPases) are essential for processes that require expansion and remodeling of phosphatidylinositol 4-phosphate (PI4P)-containing membranes, including cytokinesis, intracellular development of malarial pathogens, and replication of a wide range of RNA viruses. However, the structural basis for coordination of PI4K, GTPases and their effectors is unknown. Here, we describe structures of PI4KB (PI4KIIIβ) bound to the small GTPase Rab11a without and with the Rab11 effector protein FIP3. The Rab11-PI4KIIIβ interface is unique compared with known structures of Rab complexes, and does not involve switch regions used by GTPase effectors. Our data provide a mechanism for how PI4KIIIβ coordinates Rab11 and its effectors on PI4P-enriched membranes, and also provide strategies for the design of specific inhibitors that could potentially target plasmodial PI4KIIIβ to combat malaria.
Output: Structures of PI4KIIIβ complexes show simultaneous recruitment of Rab11 and its effectors Europe PMC Funders Group
Serious viral infections are a common cause of morbidity and mortality after allogeneic stem cell transplantation. They occur in the majority of allograft recipients and are fatal in 17-20%. These severe infections may be prolonged or recurrent and add substantially to the cost, both human and financial, of the procedure. Many features of allogeneic stem cell transplantation contribute to this high rate of viral disease. The cytotoxic and immunosuppressive drugs administered pre-transplant to eliminate the host hematopoietic/immune system and any associated malignancy, the delay in recapitulating immune ontogeny post-transplant, the immunosuppressive drugs given to prevent graft versus host disease (GvHD), and the effects of GvHD itself, all serve to make stem cell transplant recipients vulnerable to disease from endogenous (latent) and exogenous (community) viruses, and to be incapable of controlling them as quickly and effectively as most normal individuals.
Output: Antiviral T-cell therapy
In 2003, Taiwan's nurses were terrified by severe acute respiratory syndrome (SARS), and four of them sacrificed their life in the course of their work with SARS patients. This study attempted to identify the stage-specific difficulties encountered by Taiwan's surviving frontline nurses during the anti-SARS process. A two-step within-method qualitative triangulation research design was used to obtain the in-depth and confidential thoughts of 200 participants during the precaring, tangible caring, and postcaring stages. Six major types of stage-specific difficulties with and threats to the quality of care of SARS patients were identified according to each specific stage of the caring process. Four themes were further explored; these are discussed to provide a background context in obtaining better understanding of the multifaceted needs of nurses during this crisis. Consequently, a conceptual framework was developed to depict this complex phenomenon.
Output: Dying and caring on the edge: Taiwan's surviving nurses' reflections on taking care of patients with severe acute respiratory syndrome
In this study, we investigated lentiviral vector development and transduction efficiencies in well-differentiated primary cultures of pig airway epithelia (PAE) and wild-type pigs in vivo. We noted gene transfer efficiencies similar to that observed for human airway epithelia (HAE). Interestingly, feline immunodeficiency virus (FIV)-based vectors transduced immortalized pig cells as well as pig primary cells more efficiently than HIV-1-based vectors. PAE express TRIM5α, a well-characterized species-specific lentiviral restriction factor. We contrasted the restrictive properties of porcine TRIM5α against FIV-and HIV-based vectors using gain and loss of function approaches. We observed no effect on HIV-1 or FIV conferred transgene expression in response to porcine TRIM5α overexpression or knockdown. To evaluate the ability of GP64-FIV to transduce porcine airways in vivo, we delivered vector expressing mCherry to the tracheal lobe of the lung and the ethmoid sinus of 4-week-old pigs. One week later, epithelial cells expressing mCherry were readily detected. Our findings indicate that pseudotyped FIV vectors confer similar tropisms in porcine epithelia as observed in human HAE and provide further support for the selection of GP64 as an appropriate envelope pseudotype for future preclinical gene therapy studies in the porcine model of cystic fibrosis (CF).
Output: Citation: Molecular Therapy-Nucleic Acids (2012) 1, e56; Molecular Therapy-Nucleic Acids (2012) 1, e56
We have established a mouse model which shows the symptoms of coronary arteritis after consecutive injections of CAWS, which is released from Candida albicans. In this study, we examined neutrophil activation in the initial period after CAWS injection intraperitoneally. During 10 min to 16 h after the injection, blood profiles and neutrophil functions were determined. At the same time, levels of inflammatory cytokines and chemokines in plasma were measured. Furthermore, level of ICAM-1 as a marker of lesion in arterial endothelial cells was measured. Counts of the peripheral leukocytes increased immediately after CAWS injection, especially involving neutrophil. In vitro sensitivity of neutrophils to stimuli was enhanced. Moreover, proinflammatory cytokines (IL-1β, IL-12 and IL-6) increased in plasma initially followed by an increase in IL-10, G-CSF, MIP-2 and soluble ICAM-1. Locally, ICAM-1 message in arterial walls was significantly increased 16 h after CAWS injection. A decrease in C3 levels was observed in plasma, suggesting complement activation and consumption. In summary, neutrophil activation occurred after CAWS injection, followed by complement activation, and production of proinflammatory cytokines chemokines and G-CSF which may be involved in development of coronary arteritis.
Output: Neutrophil activation and arteritis induced by C. albicans water-soluble mannoprotein-β-glucan complex (CAWS)
Exchange of the extremities of the NS segment of type A and C influenza viruses in reverse genetics systems was used to assess their putative role in type specificity. Restoration of each specific proximal panhandle was mandatory to allow the rescue of viruses with heterotypic extremities. Moreover, the transcription level of the modified segment seemed to be directly affected by the distal panhandle strength. Citation: Crescenzo-Chaigne B, Barbezange C, van der Werf S (2013) The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression. PLoS ONE 8(11): e81550.
Output: The Panhandle Formed by Influenza A and C Virus NS Non-Coding Regions Determines NS Segment Expression
The evolution of influenza viruses is remarkably dynamic. Influenza viruses evolve rapidly in sequence and undergo frequent reassortment of different gene segments. Homologous recombination, although commonly seen as an important component of dynamic genome evolution in many other organisms, is believed to be rare in influenza. In this study, 256 gene segments from 32 influenza A genomes were examined for homologous recombination, three recombinant H1N1 strains were detected and they most likely resulted from one recombination event between two closely rated parental sequences. These findings suggest that homologous recombination in influenza viruses tends to take place between strains sharing high sequence similarity. The three recombinant strains were isolated at different time periods and they form a clade, indicating that recombinant strains could circulate. In addition, the simulation results showed that many recombinant sequences might not be detectable by currently existing recombinant detection programs when the parental sequences are of high sequence similarity. Finally, possible ways were discussed to improve the accuracy of the detection for recombinant sequences in influenza.
Output: Evidence of intra-segmental homologous recombination in influenza A virus
Viruses are fast evolving pathogens that continuously adapt to the highly variable environments they live and reproduce in. Strategies devoted to inhibit virus replication and to control their spread among hosts need to cope with these extremely heterogeneous populations and with their potential to avoid medical interventions. Computational techniques such as phylogenetic methods have broadened our picture of viral evolution both in time and space, and mathematical modeling has contributed substantially to our progress in unraveling the dynamics of virus replication, fitness, and virulence. Integration of multiple computational and mathematical approaches with experimental data can help to predict the behavior of viral pathogens and to anticipate their escape dynamics. This piece of information plays a critical role in some aspects of vaccine development, such as viral strain selection for vaccinations or rational attenuation of viruses. Here we review several aspects of viral evolution that can be addressed quantitatively, and we discuss computational methods that have the potential to improve vaccine design.
Output: Models of RNA virus evolution and their roles in vaccine design
Determining reference values for hematological and biochemical parameters of Asian house shrew (Suncus murinus) is important for wildlife research to protect human health in surrounding communities. This study aimed to establish the reference values for selected hematology and serum clinical chemistry analyses that may contribute to research on shrew in future. Blood samples (n=51) were collected from shrews between July and December 2015, Bangladesh, to estimate the levels of hemoglobin (Hb), packed cell volume (PCV), total leukocyte count (TLC), total erythrocyte count (TEC), lymphocyte, monocyte, neutrophil, eosinophil, basophil, calcium, phosphorus (P), sodium (Na), chloride (Cl), urea, glucose, total protein (TP), creatinine, and alanine transaminase (ALT). Although the values did not differ significantly among sexes, age was found to be a significant factor. Hb, PCV, TEC, glucose, and P were higher in males; eosinophil, Na, Cl, TP, and ALT were higher among females. Adults had significantly greater urea and glucose (p<0.05) while juveniles had insignificantly higher values for TLC, PCV, neutrophil, P, and TP. This study provides the first reference values for this species in Bangladesh and can be used to guide wildlife research studies.
Output: Hematological and biochemical reference values of Asian house shrews (Suncus murinus) in Bangladesh
Background: To ascertain the understanding of 2009 pandemic (H1N1) influenza and relevant infection control measures in an emergency department population and to assess the effectiveness of education campaigns in informing the public about the pandemic. Methods: Questionnaires were administered to patients, visitors, non-clinical staff and volunteers. Data were collected on knowledge, preventative measures, information sources, attitudes to government and media reporting, perceived seriousness, behaviour change and intended compliance with future measures. Results were used to construct an overall knowledge score. Results: There were 252 participants. Traditional forms of mass media (138 [55%]) remained the principal information source. Approximately 70% (176) accurately described mode of transmission and recommended precautions and 68% (175) reported behaviour change because of the pandemic. Gaps in knowledge included failure to identify certain high risk groups. Recall of government campaigns was significantly associated with a higher knowledge score. 60% (151) thought that authorities and media had exaggerated the threat; only 40% (101) would comply with recommended measures in a future pandemic. The knowledge regarding pandemic influenza was high in this population and positively affected by official campaigns. Pandemic planning should address knowledge gaps and the impression that authorities had exaggerated the public-health threat.
Output: A cross-sectional study of pandemic influenza health literacy and the effect of a public health campaign
Background: Myricetin and 1,3,4-thiadiazole derivatives were reported to exhibit favorable antiviral and antibacterial activities. Aiming to discover novel myricetin analogues with potent activities, a series of novel myricetin derivatives containing 1,3,4-thiadiazole moiety were synthesized, and their antibacterial and antiviral activities were evaluated. Bioassay results indicated that some target compounds exhibited potential antibacterial and antiviral activities. Among them, compounds 2, 3a, 3b, 3d, 3f, 3i, 3m and 3p exhibited excellent antibacterial activities against Xanthomonas oryzae pv. Oryzae (Xoo), with EC 50 values of 42.7, 38.6, 20.8, 12.9, 22.7, 27.3, 18.3 and 29.4 μg/mL, respectively, which were better than that of thiadiazole-copper (94.9 μg/mL). Compounds 3b, 3d, 3e, 3f, 3i and 3o showed good antibacterial activities against Ralstonia solanacearum (Rs), with EC 50 values of 37.9, 72.6, 43.6, 59.6, 60.6 and 39.6 μg/mL, respectively, which were superior to that of thiadiazole-copper (131.7 μg/mL). In addition, compounds 3d, 3f, 3i and 3m showed better curative activities against tobacco mosaic virus (TMV), with EC 50 values of 152.8, 99.7, 127.1, and 167.3 μg/mL, respectively, which were better than that of ningnanmycin (211.1 μg/mL). A series of myricetin derivatives containing 1,3,4-thiadiazole scaffold were synthesized, and their antibacterial activities against Xoo and Rs and their antiviral activity against TMV were evaluated. Bioassays indicated that some target compounds exhibited potential antibacterial and antiviral activities. These results indicated this kind of myricetin analogues could be further studied as potential alternative templates in the search for novel antibacterial and antiviral agents.
Output: Synthesis and biological activity of myricetin derivatives containing 1,3,4-thiadiazole scaffold