niryuu/sni-each-converted huggingface dataset:
There is a need for simple and inexpensive diagnostic and screening tests for the detection of Cryptosporidium parvum infection in calves. A sucrose wet mount test and a lateral immunochromatography test were evaluated for epidemiological sensitivity and specificity, cost per test, simplicity, test time and ease of batching. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the Cryptosporidium oocyst wall protein (COWP) gene locus, with gel electrophoresis, was used as a gold standard. Cohen's kappa statistic of agreement (k) between the Ontario Veterinary College (OVC) sucrose wet mount test and COWP PCR-RFLP was 0.82, and the sensitivity and specificity of the OVC sucrose wet mount test were 88.6% and 93.8%, respectively. The sensitivity and specificity of the lateral immunochromatography test were 78.3% and 93.3%, respectively, and agreement between this test and PCR-RFLP was good (k = 0.73). There was substantial agreement between the OVC sucrose wet mount test and the lateral immunochromatography test (k = 0.84). Both tests were inexpensive and easy to use; however, the lateral immunochromatography test was faster and simpler to perform than the sucrose wet mount test, and was generally more user-friendly. These tests provide practitioners and researchers with cheap, quick and accurate methods of detecting C. parvum infection in young calves. #
Output: Multiattribute evaluation of two simple tests for the detection of Cryptosporidium parvum in calf faeces
Development of highly effective, broad-spectrum antiviral agents is the major objective shared by the fields of virology and pharmaceutics. Antiviral drug development has focused on targeting viral entry and replication, as well as modulating cellular defense system. High throughput screening of molecules, genetic engineering of peptides, and functional screening of agents have identified promising candidates for development of optimal broad-spectrum antiviral agents to intervene in viral infection and control viral epidemics. This review discusses current knowledge, prospective applications, opportunities, and challenges in the development of broad-spectrum antiviral agents.
Output: Broad-spectrum antiviral agents
The enteric disease of swine recognized in the early 1970s in Europe was initially described as "epidemic viral diarrhea" and is now termed "porcine epidemic diarrhea (PED)". The coronavirus referred to as PED virus (PEDV) was determined to be the etiologic agent of this disease in the late 1970s. Since then the disease has been reported in Europe and Asia, but the most severe outbreaks have occurred predominantly in Asian swine-producing countries. Most recently, PED first emerged in early 2013 in the United States that caused high morbidity and mortality associated with PED, remarkably affecting US pig production, and spread further to Canada and Mexico. Soon thereafter, large-scale PED epidemics recurred through the pork industry in South Korea, Japan, and Taiwan. These recent outbreaks and global re-emergence of PED require urgent attention and deeper understanding of PEDV biology and pathogenic mechanisms. This paper highlights the current knowledge of molecular epidemiology, diagnosis, and pathogenesis of PEDV, as well as prevention and control measures against PEDV infection. More information about the virus and the disease is still necessary for the development of effective vaccines and control strategies. It is hoped that this review will stimulate further basic and applied studies and encourage collaboration among producers, researchers, and swine veterinarians to provide answers that improve our understanding of PEDV and PED in an effort to eliminate this economically significant viral disease, which emerged or re-emerged worldwide.
Output: Porcine epidemic diarrhea virus: An emerging and re-emerging epizootic swine virus
Spongiform neurodegeneration is characterized by the appearance of vacuoles throughout the central nervous system. It has many potential causes, but the underlying cellular mechanisms are not well understood. Mice lacking the E3 ubiquitin ligase Mahogunin Ring Finger-1 (MGRN1) develop agedependent spongiform encephalopathy. We identified an interaction between a "PSAP" motif in MGRN1 and the ubiquitin E2 variant (UEV) domain of TSG101, a component of the endosomal sorting complex required for transport I (ESCRT-I), and demonstrate that MGRN1 multimonoubiquitinates TSG101. We examined the in vivo consequences of loss of MGRN1 on TSG101 expression and function in the mouse brain. The pattern of TSG101 ubiquitination differed in the brains of wild-type mice and Mgrn1 null mutant mice: at 1 month of age, null mutant mice had less ubiquitinated TSG101, while in adults, mutant mice had more ubiquitinated, insoluble TSG101 than wild-type mice. There was an associated increase in epidermal growth factor receptor (EGFR) levels in mutant brains. These results suggest that loss of MGRN1 promotes ubiquitination of TSG101 by other E3s and may prevent its disassociation from endosomal membranes or cause it to form insoluble aggregates. Our data implicate loss of normal TSG101 function in endo-lysosomal trafficking in the pathogenesis of spongiform neurodegeneration in Mgrn1 null mutant mice.
Output: Abnormal regulation of TSG101 in mice with spongiform neurodegeneration
Background: Streptococcus pneumoniae is an important cause of microbial disease in humans. The introduction of multivalent vaccines has coincided with a dramatic decrease in the number of pneumococcal-related deaths. In spite of this, at a global level, pneumococcal infection remains an important cause of death among children under 5 years of age and in adults 65 years of age or older. In order to properly manage patients and control the spread of infection, a rapid and highly sensitive diagnostic method is needed for routine implementation, especially in resource-limited regions where pneumococcal disease is most prevalent. Methods: Using the gene encoding leader peptidase A as a molecular diagnostics target, a real-time RPA assay was designed and optimised for the detection of S. pneumoniae in whole blood. The performance of the assay was compared to real-time PCR in terms of its analytical limit of detection and specificity. The inhibitory effect of human genomic DNA on amplification was investigated. The potential clinical utility of the assay was investigated using a small number of clinical samples. Results: The RPA assay has a limit of detection equivalent to PCR (4.0 and 5.1 genome equivalents per reaction, respectively) and was capable of detecting the equivalent of <1 colony forming unit of S. pneumoniae when spiked into human whole blood. The RPA assay was 100 % inclusive (38/38 laboratory reference strains and 19/19 invasive clinical isolates) and 100 % exclusive; differentiating strains of S. pneumoniae species from other viridans group streptococci, including S. pseudopneumoniae. When applied to the analysis of a small number (n = 11) of clinical samples (blood culture positive for S. pneumoniae), the RPA assay was demonstrated to be both rapid and sensitive. Conclusions: The RPA assay developed in this work is shown to be as sensitive and as specific as PCR. In terms of reaction kinetics, the RPA assay is shown to exceed those of the PCR, with the RPA running to completion in 20 minutes and capable generating a positive signal in as little as 6 minutes. This work represents a potentially suitable assay for application in point-of-care settings.
Output: Development of a rapid recombinase polymerase amplification assay for the detection of Streptococcus pneumoniae in whole blood
This article reviews the pulmonary route of administration, aerosol delivery devices, characterization of pulmonary drug delivery systems, and discusses the rationale for inhaled delivery of siRNA. Diseases with known protein malfunctions may be mitigated through the use of siRNA therapeutics. The inhalation route of administration provides local delivery of siRNA therapeutics for the treatment of various pulmonary diseases, however barriers to pulmonary delivery and intracellular delivery of siRNA exists. siRNA loaded nanocarriers can be used to overcome the barriers associated with the pulmonary route, such as anatomical barriers, mucociliary clearance, and alveolar macrophage clearance. Apart from naked siRNA aerosol delivery, previously studied siRNA carrier systems comprise of lipidic, polymeric, peptide, or inorganic origin. Such siRNA delivery systems formulated as aerosols can be successfully delivered via an inhaler or nebulizer to the pulmonary region. Preclinical animal investigations of inhaled siRNA therapeutics rely on intratracheal and intranasal siRNA and siRNA nanocarrier delivery. Aerosolized siRNA delivery systems may be characterized using in vitro techniques, such as dissolution test, inertial cascade impaction, delivered dose uniformity assay, laser diffraction, and laser Doppler velocimetry. The ex vivo techniques used to characterize pulmonary administered formulations include the isolated perfused lung model. In vivo techniques like gamma scintigraphy, 3D SPECT, PET, MRI, fluorescence imaging and pharmacokinetic/pharmacodynamics analysis may be used for evaluation of aerosolized siRNA delivery systems. The use of inhalable siRNA delivery systems encounters barriers to their delivery, however overcoming the barriers while formulating a safe and effective delivery system will offer unique advances to the field of inhaled medicine.
Output: Aerosol Delivery of siRNA to the Lungs. Part 1: Rationale for Gene Delivery Systems †
Molecular mimicry, defined as similar structures shared by molecules from dissimilar genes or proteins, is a general strategy used by pathogens to infect host cells. Severe acute respiratory syndrome (SARS) is a new human respiratory infectious disease caused by SARS coronavirus (SARS-CoV). The spike (S) protein of SARS-CoV plays an important role in the virus entry into a cell. In this study, eleven synthetic peptides from the S protein were selected based on its sequence homology with human proteins. Two of the peptides D07 (residues 927-937) and D08 (residues 942-951) were recognized by the sera of SARS patients. Murine hyperimmune sera against these peptides bound to proteins of human lung epithelial cells A549. Another peptide D10 (residues 490-502) stimulated A549 to proliferate and secrete IL-8. The present results suggest that the selected S protein regions, which share sequence homology with human proteins, may play important roles in SARS-CoV infection.
Output: Peptide Mimicrying Between SARS Coronavirus Spike Protein and Human Proteins Reacts with SARS Patient Serum
Background. Interspecies interactions of the nasopharyngeal microbiota are likely to be involved in the pathogenesis of acute otitis media (AOM). Capturing the breadth of microbial interactions requires a detailed description of the microbiota during health and AOM. Methods. The nasopharyngeal microbiota of 163 infants with (n 5 153) or without (n 5 10) AOM was characterized using nasopharyngeal swabs and multiplexed pyrosequencing of 16S rRNA. Nasopharyngeal swab specimens were collected during 4 winter seasons from 2004 through 2010 for infants with AOM and during 2010 for controls. Results. Fifty-eight bacterial families were identified, of which Moraxellaceae, Streptococcaceae, and Pasteurellaceae were the most frequent. Commensal families were less prevalent in infants with AOM than in controls. In infants with AOM, prior exposure to antimicrobials and administration of the heptavalent conjugated pneumococcal polysaccharide vaccine (PCV7) were also associated with reduced prevalence of distinct commensal families (Streptococcaceae and Corynebacteriaceae). In addition, antimicrobial exposure increased the prevalence of Enterobacteriaceae and the abundance of Pasteurellaceae. Other factors, such as age, sex, day care, and a history of recurrent AOM, did not influence the microbiota. Conclusions. Infants' nasopharyngeal microbiota undergoes significant changes during AOM and after exposure to antimicrobials and PCV7, which is mainly attributable to reduced prevalence of commensal bacterial families.
Output: Nasopharyngeal Microbiota in Infants With Acute Otitis Media
Infection with mouse hepatitis virus strain 3 (MHV-3) results in lethal fulminant hepatic necrosis in fully susceptible BALB/c mice compared to the minimal disease observed in resistant strain A/J mice. Macrophages play a central role in the pathogenesis of MHV-3-induced hepatitis. In the present study we have shown that MHV-3 infection of macrophages induces these cells to undergo apoptosis. Three methods to detect apoptosis were applied: flow cytometry analysis of nuclear DNA content, fluorescence microscopic visualization of apoptotic cells labeled by the TUNEL assay, and gel electrophoresis to detect DNA laddering. Apoptosis in A/J and BALB/c macrophages was first detected at 8 h postinfection (p.i.) and reached a maximum by 12 h p.i. The degree of MHV-3-induced apoptosis was much greater in A/J-derived macrophages than in BALB/c-derived cells. Apoptosis was inversely correlated with the development of typical MHV cytopathology, namely syncytia formation. Infected macrophages from A/J mice did not form synctia in contrast to the extensive synctia formation observed in BALB/c-derived macrophages. In MHV-3-infected BALB/c macrophage cultures, apoptotic cells were not incorporated into syncytia. Apoptosis was also inversely correlated with the expression of MHV-3-induced fgl2 prothrombinase in macrophages. These results add the murine coronavirus MHV-3 to the list of RNA-containing viruses capable of inducing apoptosis.
Output: Coronavirus MHV-3-Induced Apoptosis in Macrophages
Assembly of virus capsids and surface proteins must be regulated to ensure that the resulting complex is an infectious virion. Here we examine assembly of virus capsids, focusing on hepatitis B virus and bacteriophage MS2, and formation of glycoproteins in the alphaviruses. These systems are structurally and biochemically well-characterized and are simplest-case paradigms of self-assembly. Published data suggest that capsid and glycoprotein assembly is subject to allosteric regulation, that is, regulation at the level of conformational change. The hypothesis that allostery is a common theme in viruses suggests that deregulation of capsid and glycoprotein assembly by small molecule effectors will be an attractive antiviral strategy, as has been demonstrated with hepatitis B virus.
Output: Virus assembly, allostery, and antivirals
As the number of cases of COVID-19 continues to grow exponentially, local health services are likely to be overwhelmed with patients requiring intensive care. We develop and implement an algorithm to provide optimal re-routing strategies to transfer patients requiring Intensive Care Units (ICU) between hospitals within NHS trusts, constrained by feasibility of transfer. We coarse-grain the NHS system at the level of NHS trusts and, subsequently cover the whole set of geopositioned trusts to extract a 4-regular geometric graph which indicates, for a given trust, its four nearest neighbors. Estimates of weekly ICU demand can be extrapolated from an age structured epidemiological model by considering contagion-to-ICU likelihood estimates, and through random search optimisation we identify the best load sharing strategy. The cost function to minimise is based on the total number of ICU units above capacity and we implement and test two optimisation strategies. Our framework is flexible allowing for additional criteria, different cost functions, and this methodology is general enough that it can easily be extended to optimise other resources beyond ICU units or ventilators. Assuming a uniform ICU demand across trusts, we show that using our method it is possible to enable access to ICU treatment to up to 1000 cases nationally in a single step of the algorithm -leading to potentially saving a large percentage of these lives that would otherwise not have access to ICU if no load sharing was implemented.
Output: A flexible load sharing system and implementation to anticipate and organise transfers based on ICU demand in the context of COVID-19 pandemic
A population of Persian cats experienced an epidemic of feline infectious peritonitis (FIP) over 2 years. Twelve cases of FIP occurred in litters born during this period. Cats contracting FIP were all genetically related through the sire. Feline coronavirus (FCoV) genomic RNA was detected consistently in this study in biologic samples from adult cats, kittens suffering from FIP, and their siblings. Analysis of viral 7a/7b open reading frame (ORFs) were analyzed and revealed two distinct virus variants circulating in the population, one with an intact 7a ORF and one with two major deletions in the 7a ORF. The 7b ORFs were intact and similar among all virus isolates, although point mutations resulting in amino acid changes were present. The sire was determined to be infected with both variants, and was persistently virus-infected. We speculate the deletion variant arose from the non-deletion variant during viral replication in this population, possibly in the sire. #
Output: Deletions in the 7a ORF of feline coronavirus associated with an epidemic of feline infectious peritonitis
The post-translational modification ubiquitin can be attached to the e-amino group of lysine residues or to a protein's N-terminus as a mono ubiquitin moiety. Via its seven intrinsic lysine residues and its N-terminus, it can also form ubiquitin chains on substrates in many possible ways. To study ubiquitin signals, many synthetic and semi-synthetic routes have been developed for generation of ubiquitin-derived tools and conjugates. The strength of these methods lies in their ability to introduce chemo-selective ligation handles at sites that currently cannot be enzymatically modified. Here, we review the different synthetic and semi-synthetic methods available for ubiquitin conjugate synthesis and their contribution to how they have helped investigating conformational diversity of diubiquitin signals. Next, we discuss how these methods help understanding the ubiquitin conjugation-deconjugation system by recent advances in ubiquitin ligase probes and diubiquitinbased DUB probes. Lastly, we discuss how these methods help studying post-translational modification of ubiquitin itself. Addresses
Output: Synthetic and semi-synthetic strategies to study ubiquitin signaling
The effects from rising temperatures, a symptom of climate change, have become a significant concern. This study finds that one additional day with a maximum temperature of 30-32°C (86-89.6°F), relative to a day with a temperature of 28-30°C (82.4-86°F), decreases the birth rate 9 months later by 0.24%, or 92 babies per month in South Korea. This result is robust to various specifications and samples. This study also found that the impact of the temperature bin did not vary according to the mother's characteristics, including education and age. That is, high temperature has no differential effect on mothers of different backgrounds. Finally, we found no significant temperature effect on birth outcomes, but we cannot rule out that children born 9 months after summer heat are a selected (healthy) group.
Output: Ambient temperature, birth rate, and birth outcomes: evidence from South Korea
Because information on biological agents in the workplace is lacking, biological hazard analyses at the workplace to securely recognize the harmful factors with biological basis are desperately needed. This review concentrates on literatures published after 2010 that attempted to detect biological hazards to humans, especially workers, and the efforts to protect them against these factors. It is important to improve the current understanding of the health hazards caused by biological factors at the workplace. In addition, this review briefly describes these factors and provides some examples of their adverse health effects. It also reviews risk assessments, protection with personal protective equipment, prevention with training of workers, regulations, as well as vaccinations.
Output: Biologically Hazardous Agents at Work and Efforts to Protect Workers' Health: A Review of Recent Reports
Recently, pattern of viral attachment (PVA) in human respiratory tract was determined for highly pathogenic avian influenza virus of subtype H5N1. However, PVA of human influenza viruses and other avian influenza viruses in either humans or experimental animals is unknown. Therefore, we compared PVA of two human influenza viruses (H1N1 and H3N2) and two low pathogenic avian influenza viruses (H5N9 and H6N1) with that of H5N1 virus in respiratory tract tissues of humans, mice, ferrets, cynomolgus macaques, cats, and pigs by virus histochemistry. We found that human influenza viruses attached more strongly to human trachea and bronchi than H5N1 virus and attached to different cell types than H5N1 virus. These differences correspond to primary diagnoses of tracheobronchitis for human influenza viruses and diffuse alveolar damage for H5N1 virus. The PVA of low pathogenic avian influenza viruses in human respiratory tract resembled that of H5N1 virus, demonstrating that other properties determine its pathogenicity for humans. The PVA in human respiratory tract most closely mirrored that in ferrets and pigs for human influenza viruses and that in ferrets, pigs, and cats for avian influenza viruses.
Output: Human and Avian Influenza Viruses Target Different Cells in the Lower Respiratory Tract of Humans and Other Mammals
Kawasaki disease was first reported in Japan in 1967 by Dr. Tomisaku Kawasaki. It has since been recognized worldwide, and in at the United States and Japan is the most important cause of acquired heart disease in children, surpassing other more recognized conditions such as rheumatic fever, endocarditis and myocarditis. It is primarily a disease of children less than 5 years of age but has been reported in older children and adults. Risk factors for the illness include Asian ancestry, male gender and certain familial predispositions. Observations such as similarity to certain exanthematous infectious diseases, temporal-geographic clustering of cases and seasonality in incidence favors an infectious etiology. Pathology and pathogenesis of the disease indicate that it is a medium-sized artery vasculitis that results from a dramatic immune activation that in most cases reversed by immune modulating agents such as intravenous immunoglobulin. Unfortunately, the etiology of the illness remains obscure, although recent studies favor a possible viral etiology.
Output: Pediatric Infectious Diseases Revisited 273 Epidemiology and etiology of Kawasaki disease
The objective of this research was to investigate the prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) infection primarily in dromedary camel farms and the relationship of those infections with infections in humans in the Emirate of Abu Dhabi. Nasal swabs from 1113 dromedary camels (39 farms) and 34 sheep (1 farm) and sputum samples from 2 MERS-CoVinfected camel farm owners and 1 MERS-CoV-infected sheep farm owner were collected. Samples from camels and humans underwent real-time reverse-transcription quantitative PCR screening to detect MERS-CoV. In addition, sequencing and phylogenetic analysis of partially characterized MERS-CoV genome fragments obtained from camels were performed. Among the 40 farms, 6 camel farms were positive for MERS-CoV; the virus was not detected in the single sheep farm. The maximum duration of viral shedding from infected camels was 2 weeks after the first positive test result as detected in nasal swabs and in rectal swabs obtained from infected calves. Three partial camel sequences characterized in this study (open reading frames 1a and 1ab, Spike1, Spike2, and ORF4b) together with the corresponding regions of previously reported MERS-CoV sequence obtained from one farm owner were clustering together within the larger MERS-CoV sequences cluster containing human and camel isolates reported for the Arabian Peninsula. Data provided further evidence of the zoonotic potential of MERS-CoV infection and strongly suggested that camels may have a role in the transmission of the virus to humans.
Output: Epidemiological investigation of Middle East respiratory syndrome coronavirus in dromedary camel farms linked with human infection in Abu Dhabi Emirate, United Arab Emirates
Cough etiquette and respiratory hygiene are forms of source control encouraged to prevent the spread of respiratory infection. The use of surgical masks as a means of source control has not been quantified in terms of reducing exposure to others. We designed an in vitro model using various facepieces to assess their contribution to exposure reduction when worn at the infectious source (Source) relative to facepieces worn for primary (Receiver) protection, and the factors that contribute to each. In a chamber with various airflows, radiolabeled aerosols were exhaled via a ventilated soft-face manikin head using tidal breathing and cough (Source). Another manikin, containing a filter, quantified recipient exposure (Receiver). The natural fit surgical mask, fitted (SecureFit) surgical mask and an N95-class filtering facepiece respirator (commonly known as an "N95 respirator") with and without a Vaselineseal were tested. With cough, source control (mask or respirator on Source) was statistically superior to mask or unsealed respirator protection on the Receiver (Receiver protection) in all environments. To equal source control during coughing, the N95 respirator must be Vaseline-sealed. During tidal breathing, source control was comparable or superior to mask or respirator protection on the Receiver. Source control via surgical masks may be an important adjunct defense against the spread of respiratory infections. The fit of the mask or respirator, in combination with the airflow patterns in a given setting, are significant contributors to source control efficacy. Future clinical trials should include a surgical mask source control arm to assess the contribution of source control in overall protection against airborne infection.
Output: Respiratory source control using a surgical mask: An in vitro study
Cilia are hair-like organelles projecting from a eukaryotic cell, used either for locomotion or as sensors. Cilia commonly occur in patches. To take this into consideration, we represent cilia in multiple patches, instead of the conventional 'dense mat' representation. We focus on the combined action and interplay of these patches. The effects of varying the frequency, spacing and phase lag of the beating of one cilia bunch with respect to the beating of adjacent patches are studied. We model the Airway Surface Liquid (ASL) as a three-layer structure. The possibility of an optimum frequency of beating is noted and the change of mucous flow under different spacing and phase differences are observed.
Output: Effect of bunching of cilia and their interplay on muco-ciliary transport
Germ-free piglets were orally infected with virulent rotavirus to collect jejunal mucosal scrapings at 12 and 18 hours post infection (two piglets per time point). IFNgamma mRNA expression was stimulated in the mucosa of all four infected piglets, indicating that they all responded to the rotavirus infection. RNA pools prepared from two infected piglets were used to compare whole mucosal gene expression at 12 and 18 hpi to expression in uninfected germ-free piglets (n = 3) using a porcine intestinal cDNA microarray. Microarray analysis identified 13 down-regulated and 17 up-regulated genes. Northern blot analysis of a selected group of genes confirmed the data of the microarray. Genes were functionally clustered in interferon-regulated genes, proliferation/differentiation genes, apoptosis genes, cytoskeleton genes, signal transduction genes, and enterocyte digestive, absorptive, and transport genes. Downregulation of the transport gene cluster reflected in part the loss of rotavirus-infected enterocytes from the villous tips. Data mining suggested that several genes were regulated in lower-or mid-villus immature enterocytes and goblet cells, probably to support repair of the damaged epithelial cell layer at the villous tips. Furthermore, up-regulation was observed for IFN-c induced guanylate binding protein 2, a protein that effectively inhibited VSV and EMCV replication in vitro (Arch Virol 150:1213-1220. This protein may play a role in the small intestine's innate defense against enteric viruses like rotavirus.
Output: Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus
We describe a pilot study that attempted to infect human volunteers with Cyclospora cayetanensis. Seven healthy volunteers ingested an inoculum of Cyclospora oocysts (approximately 200-49,000 oocysts). The volunteers did not experience symptoms of gastroenteritis, and no oocysts were detected in any stool samples during the 16 weeks volunteers were monitored. C yclospora cayetanensis is a protozoan parasite that may cause gastroenteritis with prolonged, intermittent diarrhea in humans. Characterization and magnitudes of risk factors associated with food and water consumption are unclear because the dose-response relationship and other host-parasite factors for infection with Cyclospora are unknown. To characterize infectivity, we performed a study in which inocula of Cyclospora oocysts were administered to human volunteers. Stool samples containing high concentrations of Cyclospora oocysts and serum specimens were collected from persons with cyclosporiasis in Haiti and the United States. Informed consent was obtained from persons providing the specimens. The Centers for Disease Control and Prevention (CDC) institutional review board (IRB) reviewed specimen collection, informed consent, and patient counseling procedures. Stool specimens were homogenized with water and sieved through cheesecloth. Since Cyclospora oocysts must form sporocysts outside the human host before becoming infectious, the filtrate was resuspended in potassium dichromate (2.5%) and shaken for about 3 weeks at room temperature to induce sporulation. After sporulation (67%-94% of oocysts sporulated), samples were stored at room temperature until further processing (2-3 months). Suspensions with the DISPATCHES 726 Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 10, No. 4,
Output: Human Challenge Pilot Study with Cyclospora cayetanensis
The spike (S) protein of severe acute respiratory syndrome (SARS) coronavirus (CoV), a type I transmembrane envelope glycoprotein, consists of S1 and S2 domains responsible for virus binding and fusion, respectively. The S1 contains a receptor-binding domain (RBD) that can specifically bind to angiotensin-converting enzyme 2 (ACE2), the receptor on target cells. Here we show that a recombinant fusion protein (designated RBD-Fc) containing 193-amino acid RBD (residues 318-510) and a human IgG1 Fc fragment can induce highly potent antibody responses in the immunized rabbits. The antibodies recognized RBD on S1 domain and completely inhibited SARS-CoV infection at a serum dilution of 1:10,240. Rabbit antisera effectively blocked binding of S1, which contains RBD, to ACE2. This suggests that RBD can induce highly potent neutralizing antibody responses and has potential to be developed as an effective and safe subunit vaccine for prevention of SARS.
Output: Receptor-binding domain of SARS-CoV spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine
Hepatitis C virus (HCV) causes chronic hepatitis, which often results in the development of liver cirrhosis and hepatocellular carcinoma (HCC) worldwide. In this study, we demonstrated that the non-structural protein NS3 of HCV enhances cyclooxygenase-2 (COX-2) gene promoter activity, COX-2 mRNA expression, COX-2 protein production, and prostaglandin E2 (PGE2) release in HepG2 cells in a concentration-dependent fashion. We also showed that transcription factor NF-κB is required for the activation of COX-2 regulated by NS3. In addition, multiple signaling pathways are involved cooperatively in the expression of COX-2 activated by the viral protein in a calcium-independent manner, which requires signaling components including JNK, ERK, and PKD2. A thorough investigation of mechanism involved in the activation of COX-2 regulated by HCV would provide insights into our understanding the processes of liver inflammatory response and hepatocellular carcinoma development caused by the viral infection and also into the development of novel therapeutics against HCV infection.
Output: NS3 protein of hepatitis C virus regulates cyclooxygenase-2 expression through multiple signaling pathways
Type 1 interferons (IFN-I) exert pleiotropic biological effects during viral infections, all which contribute to balancing virus control and immune pathology. Despite extensive antiviral functions that subdue virus replication, recent studies demonstrate pathogenic and pro-viral roles for IFN-I signaling during acute and persistent virus infection. IFN-I signaling can promote morbidity and mortality through induction of aberrant inflammatory responses during acute viral infection. In contrast, IFN-I signaling during persistent viral infection supports immune suppression, lymphoid tissue disorganization and CD4 T cell dysfunction. Systematic characterization of the cellular populations and intricacies of IFN-I signaling that promote pathology or immune suppression during acute and persistent viral infections, respectively, should inform the development of treatments and modalities to control viral associated pathologies.
Output: Type I interferons in viral control and immune regulation
Structured RNA elements may control virus replication, transcription and translation, and their distinct features are being exploited by novel antiviral strategies. Viral RNA elements continue to be discovered using combinations of experimental and computational analyses. However, the wealth of sequence data, notably from deep viral RNA sequencing, viromes, and metagenomes, necessitates computational approaches being used as an essential discovery tool. In this review, we describe practical approaches being used to discover functional RNA elements in viral genomes. In addition to success stories in new and emerging viruses, these approaches have revealed some surprising new features of well-studied viruses e.g., human immunodeficiency virus, hepatitis C virus, influenza, and dengue viruses. Some notable discoveries were facilitated by new comparative analyses of diverse viral genome alignments. Importantly, comparative approaches for finding RNA elements embedded in coding and non-coding regions differ. With the exponential growth of computer power we have progressed from stem-loop prediction on single sequences to cutting edge 3D prediction, and from command line to user friendly web interfaces. Despite these advances, many powerful, user friendly prediction tools and resources are underutilized by the virology community.
Output: Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs
Upon recognition of viral components by pattern recognition receptors, such as the toll-like receptors (TLRs) and retinoic acid-inducible gene I (RIG-I)-like helicases, cells are activated to produce type I interferon (IFN) and proinflammatory cytokines. These pathways are tightly regulated by the host to prevent an inappropriate cellular response, but viruses can modulate these pathways to proliferate and spread. In this study, we revealed a novel mechanism in which hepatitis C virus (HCV) evades the immune surveillance system to proliferate by activating microRNA-21 (miR-21). We demonstrated that HCV infection upregulates miR-21, which in turn suppresses HCV-triggered type I IFN production, thus promoting HCV replication. Furthermore, we demonstrated that miR-21 targets two important factors in the TLR signaling pathway, myeloid differentiation factor 88 (MyD88) and interleukin-1 receptor-associated kinase 1 (IRAK1), which are involved in HCV-induced type I IFN production. HCV-mediated activation of miR-21 expression requires viral proteins and several signaling components. Moreover, we identified a transcription factor, activating protein-1 (AP-1), which is partly responsible for miR-21 induction in response to HCV infection through PKCe/JNK/c-Jun and PKCa/ERK/c-Fos cascades. Taken together, our results indicate that miR-21 is upregulated during HCV infection and negatively regulates IFN-a signaling through MyD88 and IRAK1 and may be a potential therapeutic target for antiviral intervention.
Output: HCV-Induced miR-21 Contributes to Evasion of Host Immune System by Targeting MyD88 and IRAK1
Antigenically related feline coronaviruses cause two distinct disease manifestations in infected cats. The diseases are feline infectious peritonitis (FIP), in which the virus is widely disseminated, and feline enteric coronavirus (FECV), a mild disease in which the virus is usually limited to the villi. These two viruses were found to differ in their growth in cell culture. FIPV grows to higher titer, forms larger plaques and switches offhost cell protein synthesis more effectively than FECV. Cross neutralization studies showed antigenic differences between the strains. There also appeared to be a difference in the nucleoprotein molecular weight of the viruses causing these two different disease syndromes.
Output: Archives of Virology Antigenic and biological diversity of feline coronaviruses: feline infectious peritonitis and feline enteritis virus*
Aim: To investigate the prevalence of urinary tract infections in hospitalized patients with type 2 diabetes mellitus and identify corresponding risk factors. Methods: We conducted a cross-sectional study on 7.347 patients with type 2 diabetes mellitus as the principal diagnosis, using hospitalization discharge summary data from January 1 to December 31, 2015. Disease stages were classified as stages 1, 2, and 3. Results: Of 7.347 patients, 16.2% had urinary tract infections. The urinary tract infection prevalence was 24.4% in 428 patients in stage 1 and 4.8% in 2.840 patients in stage 2; it was higher among patients who underwent medical procedures than among those who underwent surgery (24.4% vs 4.8%). In multivariate regression analysis, age (OR = 1.031; 95% CI = 1.02-1.04), length of hospitalization (OR = 1.018; 95% CI = 1.013-1.024), sex (woman) (OR = 2.248; 95% CI = 1.778-2.842), comorbidity of stage 3 cerebrovascular disease (OR = 1.737; 95% CI = 1.111-2.714), and comorbidity of stage 1 colorectal cancer (OR = 2.417; 95% CI = 1.152-5.074) were found to be the risk factors of urinary tract infection in the ten hospitals considered. Conclusions: Our findings suggest that urinary tract infection prevalence was higher in women without evidence of organ injury and those receiving medical treatment. Comorbidities (cerebrovascular disease and colorectal cancer) were identified as risk factors.
Output: Potentially preventable urinary tract infection in patients with type 2 diabetes -A hospital-based study
Introduction Since acute respiratory tract infections inflict a high burden of disease in children worldwide, a multiplex reverse transcription polymerase chain reaction combined with a microwell hybridization assay (m-RT-PCR-ELISA) to detect 19 different respiratory pathogens was developed and validated. Methods A total of 430 respiratory specimens were retrospectively tested in parallel by both the advanced 19-valent m-RT-PCR-ELISA as well as by culture or individual RT-PCR assays used in clinical routine. The mean (median) sensitivity of the m-RT-PCR-ELISA in the retrospective test was 93.3% (95.1%; range 83.3-100 %), and the mean (median) specificity was 99.8 and 100 % (range 98.6-100 %), respectively. The mean positive predictive value was 99.3 % (range 93.4-100 %) and the mean negative predictive value was 95.3 % (range 98.4-100 %). Feasibility and clinical value of the 19-valent method was prospectively shown on 16,231 incoming clinical specimens from patients between 0 and 16 years of age with acute respiratory tract infections admitted to pediatric hospitals or private practices from October 2003 to June 2010 in three regions in Germany (Kiel, Mainz, Freiburg; Freiburg to June 2007 only). At least one microorganism was detected in 10,765 of 16,231 (66.3 %) clinical specimens: 5,044 RV, 1,999 RSV, 1,286 AV, 944 EV, 737 seasonal IVA, 173 pandemic IVA H1N1 -2009, 899 MPV, 518 CV, 383 PIV3, 268 PIV1, 259 Mpn, 205 IVB, 164 PIV2, 144 PIV4, 103 Bp, 29 Cpn and 29 Bpp, while reovirus and Lpn were not present in these specimens from a pediatric population. More than one organism could be detected in 13.4 % of the specimens. Conclusions The m-RT-PCR-ELISA evaluated here improves the spectrum for diagnosing respiratory infections and is a feasible instrument for individual diagnostic and epidemiological studies. Keywords m-RT-PCR-ELISA Á Respiratory tract infections Á Validation Á Sensitivity Á Diagnosis Á Enterovirus (EV) Á Influenza virus type A (IVA) Á Influenza virus type B (IVB) Á Respiratory syncytial virus (RSV) Á Parainfluenza virus type 1 (PIV1) Á Parainfluenza virus type 2 (PIV2) Á Parainfluenza virus type 3 (PIV3) Á Parainfluenza virus type 4 (PIV4) Á Adenovirus (AV) Á Rhinovirus (RV) Á Human metapneumovirus (MPV) Á Coronavirus (CV) Á Reovirus (ReoV) Á Mycoplasma pneumoniae (Mpn) Á
Output: Validation of a multiplex reverse transcriptase PCR ELISA for the detection of 19 respiratory tract pathogens
The coronavirus nucleocapsid (N) protein packages viral genomic RNA into a ribonucleoprotein complex. Interactions between N proteins and RNA are thus crucial for the assembly of infectious virus particles. The 45 kDa recombinant nucleocapsid N protein of coronavirus infectious bronchitis virus (IBV) is highly sensitive to proteolysis. We obtained a stable fragment of 14.7 kDa spanning its N-terminal residues 29-160 (IBV-N29-160). Like the N-terminal RNA binding domain (SARS-N45-181) of the severe acute respiratory syndrome virus (SARS-CoV) N protein, the crystal structure of the IBV-N29-160 fragment at 1.85 Å resolution reveals a protein core composed of a five-stranded antiparallel b sheet with a positively charged b hairpin extension and a hydrophobic platform that are probably involved in RNA binding. Crosslinking studies demonstrate the formation of dimers, tetramers, and higher multimers of IBV-N. A model for coronavirus shell formation is proposed in which dimerization of the C-terminal domain of IBV-N leads to oligomerization of the IBV-nucleocapsid protein and viral RNA condensation.
Output: The Nucleocapsid Protein of Coronavirus Infectious Bronchitis Virus: Crystal Structure of Its N-Terminal Domain and Multimerization Properties
Viruses may be regarded as dynamic nucleoprotein assemblies capable of assisted multiplication within cells, and of propagation between cells and organisms. Infectious virus particles (virions) assembled in a host cell are dynamic, generally metastable particles: They are robust enough to protect the viral genome outside the cell, but are also poised to undergo structural changes and execute mechanochemical actions required for infection of other cells. This chapter provides an introduction to the structural and physical biology of viruses by including: (i) an elementary overview on virions and the structural basis of virus function; (ii) a concise summary on basic techniques used in structural or physical virology; (iii) brief structure-based general descriptions of the different stages in the virus cycle, especially those in which virions and/or their components are involved. These contents may facilitate a better understanding of the specialized subjects treated in the rest of the book. This chapter is also intended as a "road map" to help interconnect and integrate in a single picture the different topics described in depth in the 21 monographic chapters in this book.
Output: Introduction: The Structural Basis of Virus Function
Enteropathogenic Escherichia coli (EPEC) is a common cause of diarrhea in children from developing countries. Intimate adhesion of the bacteria to intestinal cells occurs via binding of the adhesin intimin to the TIR receptor exposed on cell surfaces. Here, Lactobacillus casei expressing a fragment of ␤-intimin (L. casei-Int cv ) was tested as mucosal vaccines in mice against intestinal colonization with the murine pathogen Citrobacter rodentium. Oral or sublingual immunization of C57BL/6 mice with L. casei-Int cv induced anti-Int cv IgA in feces but no IgG in sera. Conversely, anti-Int cv IgG was induced in the sera of mice after sublingual immunization with purified Int cv . All vaccines were able to decrease C. rodentium recovery from feces. However, this reduction was more evident and sustained over time in mice immunized with L. casei-Int cv by the sublingual route. These mice also displayed an increase in interleukin 6 (IL-6) and gamma interferon (IFN-␥) secretion by spleen cells 10 days after infection. Additionally, oral or sublingual immunization of C3H/HePas mice, which are highly susceptible to C. rodentium infection, with L. casei-Int cv induced anti-Int cv antibodies and significantly increased survival after challenge. Immunohistological analysis of colon sections revealed that C. rodentium was located in deep fractions of the tissue from C3H/HePas mice immunized with L. casei whereas superficial staining was observed in colon sections from mice immunized with L. casei-Int cv. The results indicate that vaccines composed of L. casei expressing intimin may represent a promising approach and that the C3H/HePas infection model with C. rodentium can be used to evaluate potential vaccines against EPEC.
Output: Immunization of Mice with Lactobacillus casei Expressing a Beta-Intimin Fragment Reduces Intestinal Colonization by Citrobacter rodentium ᰔ †
Purpose-Mathematical and simulation models are increasingly used to plan for and evaluate health sector responses to disasters, yet no clear consensus exists regarding best practices for the design, conduct, and reporting of such models. We examined a large selection of published health sector disaster response models to generate a set of best practice guidelines for such models. Methods-We reviewed a spectrum of published disaster response models addressing public health or healthcare delivery, focusing in particular on the type of disaster and response decisions considered, decision makers targeted, choice of outcomes evaluated, modeling methodology, and reporting format. We developed initial recommendations for best practices for creating and reporting such models and refined these guidelines after soliciting feedback from response modeling experts and from members of the Society for Medical Decision Making. Results-We propose six recommendations for model construction and reporting, inspired by the most exemplary models: Health sector disaster response models should address real-world problems; be designed for maximum usability by response planners; strike the appropriate balance between simplicity and complexity; include appropriate outcomes, which extend beyond those considered in traditional cost-effectiveness analyses; and be designed to evaluate the many uncertainties inherent in disaster response. Finally, good model reporting is particularly critical for disaster response models. Conclusions-Quantitative models are critical tools for planning effective health sector responses to disasters. The recommendations we propose can increase the applicability and interpretability of future models, thereby improving strategic, tactical, and operational aspects of preparedness planning and response. Modeling Methodology Disaster Evaluated † Decision Makers Considered * Geographic Setting Decisions Modeled § Outcomes ¶ (Reference) Purpose of Model/Study Modeling Methodology Disaster Evaluated † Decision Makers Considered * Geographic Setting Decisions Modeled § Outcomes ¶ (Reference) Purpose of Model/Study Modeling Methodology Disaster Evaluated † Decision Makers Considered * Geographic Setting
Output: Risk Analysis