niryuu/sni-each-converted huggingface dataset:
Since 2007, many cases of fever, thrombocytopenia and leukopenia syndrome (FTLS) have emerged in Henan Province, China. Patient reports of tick bites suggested that infection could contribute to FTLS. Many tick-transmitted microbial pathogens were tested for by PCR/RT-PCR and/or indirect immunofluorescence assay (IFA). However, only 8% (24/285) of samples collected from 2007 to 2010 tested positive for human granulocytic anaplasmosis (HGA), suggesting that other pathogens could be involved. Here, we used an unbiased metagenomic approach to screen and survey for microbes possibly associated with FTLS. BLASTx analysis of deduced protein sequences revealed that a novel bunyavirus (36% identity to Tehran virus, accession: HQ412604) was present only in sera from FTLS patients. A phylogenetic analysis further showed that, although closely related to Uukuniemi virus of the Phlebovirus genus, this virus was distinct. The candidate virus was examined for association with FTLS among samples collected from Henan province during 2007-2010. RT-PCR, viral cultures, and a seroepidemiologic survey were undertaken. RT-PCR results showed that 223 of 285 (78.24%) acute-phase serum samples contained viral RNA. Of 95 patients for whom paired acute and convalescent sera were available, 73 had serologic evidence of infection, with 52 seroconversions and 21 exhibiting a 4-fold increase in antibody titer to the virus. The new virus was isolated from patient acute-phase serum samples and named Henan Fever Virus (HNF virus). Whole-genome sequencing confirmed that the virus was a novel bunyavirus with genetic similarity to known bunyaviruses, and was most closely related to the Uukuniemi virus (34%, 24%, and 29% of maximum identity, respectively, for segment L, M, S at maximum query coverage). After the release of the GenBank sequences of SFTSV, we found that they were nearly identical (.99% identity). These results show that the novel bunyavirus (HNF virus) is strongly correlated with FTLS.
Output: ): e1002369. Minister of Health of China
Middle East Respiratory Syndrome (MERS) is a zoonotic viral disease that can be transmitted from dromedaries to human beings. More than 1500 cases of MERS have been reported in human beings to date. Although MERS has been associated with 30% case fatality in human beings, MERS coronavirus (MERS-CoV) infection in dromedaries is usually asymptomatic. In rare cases, dromedaries may develop mild respiratory signs. No MERS-CoV or antibodies against the virus have been detected in camelids other than dromedaries. MERS-CoV is mainly acquired in dromedaries when they are less than 1 year of age, and the proportion of seropositivity increases with age to a seroprevalence of 100% in adult dromedaries. Laboratory diagnosis of MERS-CoV infection in dromedaries can be achieved through virus isolation using Vero cells, RNA detection by real-time quantitative reverse transcriptase-PCR and antigen detection using respiratory specimens or serum. Rapid nucleocapsid antigen detection using a lateral flow platform allows efficient screening of dromedaries carrying MERS-CoV. In addition to MERS-CoV, which is a lineage C virus in the Betacoronavirus (betaCoV) genus, a lineage B betaCoV and a virus in the Alphacoronavirus (alphaCoV) genus have been detected in dromedaries. Dromedary CoV UAE-HKU23 is closely related to human CoV OC43, whereas the alphaCoV has not been detected in human beings to date.
Output: Middle East respiratory syndrome (MERS) coronavirus and dromedaries
In order to determine the minimum RNase A concentration to degrade siRNA completely, siRNA (300 ng) was incubated with different amounts of RNase A in TE 1X pH 8 buffer (0.02, 0.07, 0.162, 0.348, 0.7, and 3.3 g RNase A per 1 g siRNA) for 45 min at 37C, in presence or absence of RiboLock ® RNase Inhibitor (RI, 1L = 40U). The concentration of 0.35 g RNase A per 1 g siRNA has been reported in literature to be enough to degrade a large fraction of siRNA in polyplexes, 1, 2 and based on that, the amount of RNase A was varied in this experiment. Next, samples were frozen at -20C overnight, and loaded in the slots of casted agarose gel (1.5 % w/v in TAE 1X pH 8.2 buffer) stained with ethidium bromide (0.5 g  mL -1 ). The electrophoresis was performed at 60V (E0160-VWR Mini Gel Electrophoresis) for 40 min, and the siRNA-dye migration was visualized under UV irradiation (FOTO/Analyst ® Investigator/Eclipse with UV Transilluminator Fotodyne Inc.) and the images were recorded using the FOTO/Analyst ® PC Image software (v.5). The result is shown in Figure S1 , and clearly indicates that free siRNA (not protected by RNase inhibitor) was completely degraded by RNAse A starting at concentration 0.162 g RNase A per 1 g siRNA, since no siRNA band was observed in lane 6 compared to lane 7 and lane 1.
Output: Poly(amidoamine) Dendrimer Nanocarriers and their Aerosol Formulations for siRNA Delivery to the Lung Epithelium
Aim To identify the risk factors in children under five years of age for severe acute lower respiratory infections (ALRI), which are the leading cause of child mortality. We performed a systematic review of published literature available in the public domain. We conducted a quality assessment of all eligible studies according to GRADE criteria and performed a meta-analysis to report the odds ratios for all risk factors identified in these studies. We identified 36 studies that investigated 19 risk factors for severe ALRI. Of these, 7 risk factors were significantly associated with severe ALRI in a consistent manner across studies, with the following meta-analysis estimates of odds ratios (with 95% confidence intervals): low birth weight 3.18 (1.02-9.90), lack of exclusive breastfeeding 2.34 (1.42-3.88), crowding -more than 7 persons per household 1.96 (1.53-2.52), exposure to indoor air pollution 1.57 (1.06-2.31), incomplete immunization 1.83 (1.32-2.52), undernutrition -weight-for-age less than 2 standard deviations 4.47 (2.10-9.49), and HIV infection 4.15 (2.57-9.74). This study highlights the role of the above seven risk factors in the development of severe pneumonia in under-five children. In addition, it emphasizes the need for further studies investigating other potential risk factors. Since these risk factors are potentially preventable, health policies targeted at reducing their prevalence provide a basis for decreasing the burden of childhood pneumonia.
Output: Risk factors for severe acute lower respiratory infections in children -a systematic review and meta-analysis
The concept of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was first reported in 1985. Since then, MALDI MS technologies have been evolving, and successfully used in genome, proteome, metabolome, and clinical diagnostic research. These technologies are highthroughput and sensitive. Emerging evidence has shown that they are not only useful in qualitative and quantitative analyses of proteins, but also of other types of biomolecules, such as DNA, glycans, and metabolites. Recently, parallel fragmentation monitoring (PFM), which is a method comparable to selected reaction monitoring, has been reported. This highlights the potentials of MALDI-TOF/ TOF tandem MS in quantification of metabolites. Here we critically review the applications of the major MALDI MS technologies, including MALDI-TOF MS, MALDI-TOF/TOF MS, SALDI-TOF MS, MALDI-QqQ MS, and SELDI-TOF MS, to the discovery and quantification of disease biomarkers in biological specimens, especially those in plasma/serum specimens. Using SELDI-TOF MS as an example, the presence of systemic bias in biomarker discovery studies employing MALDI-TOF MS and its possible solutions are also discussed in this chapter. The concepts of MALDI, SALDI, SELDI, and PFM are complementary to each other. Theoretically, all these technologies can be combined, leading to the next generation of the MALDI MS technologies. Real applications of MALDI MS technologies in clinical diagnostics should be forthcoming.
Output: Advances in MALDI Mass Spectrometry in Clinical Diagnostic Applications
The coronavirus spike glycoprotein is a class I membrane fusion protein with two characteristic heptad repeat regions (HR1 and HR2) in its ectodomain. Here, we report the X-ray structure of a previously characterized HR1/HR2 complex of the severe acute respiratory syndrome coronavirus spike protein. As expected, the HR1 and HR2 segments are organized in antiparallel orientations within a rod-like molecule. The HR1 helices form an exceptionally long (120 2) internal coiled coil stabilized by hydrophobic and polar interactions. A striking arrangement of conserved asparagine and glutamine residues of HR1 propagates from two central chloride ions, providing hydrogen-bonding bzippersQ that strongly constrain the path of the HR2 main chain, forcing it to adopt an extended conformation at either end of a short HR2 a-helix. D
Output: Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein B
In 2002 the US-based Association for Veterinary Epidemiology and Preventive Medicine (AVEPM) co-organized a symposium in St. Louis, Missouri, to honour the lifetime achievements of Calvin W. Schwabe, who had served as professor of epidemiology in both the medical and veterinary schools of the University of California, Davis until his retirement in 1991. 1 At the symposium, Schwabe gave a keynote address summarizing his ideas about how veterinary medicine should relate to other disciplines-particularly human medicine-and the wider world. Arguing against the compartmentalization of medicine by species, into human and veterinary strands, he used the opportunity to restate his longstanding arguments for a philosophy of One Medicine (OM), which sees veterinary medicine as a close collaborative partner with human medicine, working together towards the broader endeavours of healthcare and furthering knowledge in the life sciences. 2 He claimed that this positioning reflected and recognized the contributions that veterinary medicine made to a range of other fields, including comparative zoology, parasitology, epidemiology, human public health, agriculture CHAPTER 6
Output: Humans, Other Animals and 'One Health' in the Early Twenty-First Century
Companies' internationalization appears to be fundamental in the current globalized and competitive environment and seems important not only for organizational success, but also for societal development and sustainability. On one hand, global business increases the demand for managers for international assignment. On the other hand, emergent fears, such as terrorism, seem to be developing around the world, enhancing the risk of expatriates' potential health problems. The purpose of this paper is to examine the relationships between the emergent concept of fear of expatriation with further workplace fears (economic crisis and dangerous working conditions) and with mental health problems. The study uses a quantitative design. Self-reported data were collected from 265 Italian expatriate workers assigned to both Italian and worldwide projects. Structural equation model analyses showed that fear of expatriation mediates the relationship of mental health with fear of economic crisis and with perceived dangerous working conditions. As expected, in addition to fear, worries of expatriation are also related to further fears. Although, the study is based on self-reports and the cross-sectional study design limits the possibility of making causal inferences, the new constructs introduced add to previous research.
Output: Expatriates' Multiple Fears, from Terrorism to Working Conditions: Development of a Model
The newly emerged Duck Tembusu virus (DTMUV) is responsible for considerable economic loss in waterfowlraising areas in China since 2010. Meanwhile, the virulent Newcastle disease virus (NDV) has also caused sporadic outbreaks in waterfowl. The individual vaccines against both diseases are available, however, there is no bivalent or combined vaccine for either disease. Here, we constructed a recombinant NDV-vectored vaccine candidate that expresses the pre-membrane (prM) and envelope (E) genes from DTMUV, designated as aGM/ prM + E. The foreign prM and E proteins were stably expressed in aGM/prM + E and exhibited similar pathogenicity but higher growth kinetics than those of the parental virus. The aGM/prM + E carries a fusion cleavage site in accordance with avirulent viruses that have been frequently isolated from waterfowl, and induced remarkably (p < 0.001) higher NDV-specific hemagglutination inhibition (HI) titers than commercially available live NDV vaccines (LaSota strain). The aGM/prM + E also elicited significantly higher (p < 0.05) virus neutralization (VN) titers than commercially available DTMUV inactivated vaccines (HB strain). The aGM/ prM + E not only provided complete protection against NDV challenge but also reduced the gross lesions on ovarian folliculi and provided 80% protection against DTMUV in ducks. We note that the aGM/prM + E vaccine can prevent challenged ducks from shedding of NDV and DTMUV. Our results suggest that the candidate vaccine aGM/prM + E would help decrease NDV and DTMUV transmissions in waterfowl raising areas in China.
Output: Recombinant Newcastle disease virus (NDV) expressing Duck Tembusu virus (DTMUV) pre-membrane and envelope proteins protects ducks against DTMUV and NDV challenge
The sequential determination of crystal structures of the SARS coronavirus spike receptor-binding domain (RBD) in complex with its cellular receptor or neutralizing antibody opened a door for the design and development of antiviral competitive inhibitors. Based on those complex structures, we conduct computational characterization and design of RBD-mediated receptor recognition and antibody neutralization. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics protocols. And the calculations predict a number of single substitutions on RBD, receptor or antibody that could remarkably elevate the binding affinities of those complexes. It is reasonable to anticipate our structure-based computation-derived hypotheses could be informative to the future biochemical and immunological tests.
Output: Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization
This is a prospective observational study of a cohort of inpatients exposed to a severe acute respiratory syndrome (SARS) outbreak. Strict infection control policies were instituted. The 70 patients exposed to the SARS outbreak were isolated from the rest of the hospital. They were triaged, quarantined and cohorted in three open plan wards. Selective isolation was carried out immediately when symptoms and signs suspicious of SARS manifested clinically. The patients' ages ranged from 21 to 90 years and 56% had surgery before the quarantine. Sixteen patients with unexplained fever during the period of quarantine were isolated, seven of whom were eventually diagnosed with probable SARS. The crude incidence of SARS in our cohort was 10%. The SARS case fatality was 14%. No secondary transmission of the SARS virus within the cohort was observed. Strict infection control, together with appropriate triaging, cohorting and selective isolation, is an effective and practical model of intervention in cohorts exposed to a SARS outbreak. Such a management strategy eases the logistic constraints imposed by demands for large numbers of isolation facilities in the face of a massive outbreak.
Output: Management of inpatients exposed to an outbreak of severe acute respiratory syndrome (SARS)
Purpose-Hospital-acquired infections with highly resistant organisms are an important problem among critically ill patients. Control of these organisms has largely focused within individual hospitals. We examine the extent to which transfers of critically ill patients could be a vector for wide spread of highly resistant organisms, and compare the efficiency of different approaches to targeting infection control resources. analyzed the network of interhospital transfers of intensive care unit patients in 2005 U.S. Medicare data and 2004-2006 Pennsylvania all-payer data. We simulated spread of highly resistant hospital-acquired infections by randomly choosing a single hospital to develop a highly resistant organism and following spread of infection or colonization throughout the network under varying strategies of infection control and varying levels of infectivity. Results-Critical care transfers could spread a highly resistant organism between any two U.S. hospitals in a median of three years. Hospitals varied substantially in their importance to limiting potential spread. Targeting resources to a small subset of hospitals based on their position in the transfer network was 16 times more efficient than distributing infection control resources uniformly. Within any set of targeted hospitals, the best strategy for infection control heavily concentrated resources at a few particularly important hospitals, regardless of level of infectivity. Conclusions-Critical care transfers provide a plausible vector for wide-spread dissemination of highly resistant hospital-acquired microorganisms. Infection control efforts can be made more efficient by selectively targeting hospitals most important for transmission.
Output: Assistant Professor of Internal Medicine, Pulmonary & Critical Care Medicine, 3A23 300 NIB, SPC 5419, 300 North Ingalls
The formyl peptide receptors (FPRs) are G protein-coupled receptors that transduce chemotactic signals in phagocytes and mediate host-defense as well as inflammatory responses including cell adhesion, directed migration, granule release and superoxide production. In recent years, the cellular distribution and biological functions of FPRs have expanded to include additional roles in homeostasis of organ functions and modulation of inflammation. In a prototype, FPRs recognize peptides containing N-formylated methionine such as those produced in bacteria and mitochondria, thereby serving as pattern recognition receptors. The repertoire of FPR ligands, however, has expanded rapidly to include not only N-formyl peptides from microbes but also non-formyl peptides of microbial and host origins, synthetic small molecules and an eicosanoid. How these chemically diverse ligands are recognized by the three human FPRs (FPR1, FPR2 and FPR3) and their murine equivalents is largely unclear. In the absence of crystal structures for the FPRs, site-directed mutagenesis, computer-aided ligand docking and structural simulation have led to the identification of amino acids within FPR1 and FPR2 that interact with several formyl peptides. This review article summarizes the progress made in the understanding of FPR ligand diversity as well as ligand recognition mechanisms used by these receptors.
Output: molecules The Formyl Peptide Receptors: Diversity of Ligands and Mechanism for Recognition
Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease. The potential recurrence of the disease from animal reservoirs highlights the significance of development of safe and efficient vaccines to prevent a future SARS epidemic. In this study, we expressed the recombinant receptor-binding domain (rRBD) in mammalian (293T) cells, insect (Sf9) cells, and E. coli, respectively, and compared their immunogenicity and protection against SARS-CoV infection in an established mouse model. Our results show that all rRBD proteins expressed in the above systems maintained intact conformation, being able to induce highly potent neutralizing antibody responses and complete protective immunity against SARS-CoV challenge in mice, albeit the rRBD expressed in 293T cells elicited stronger humoral immune responses with significantly higher neutralizing activity (P < 0.05) than those expressed in Sf9 and E. coli cells. These results suggest that all three rRBDs are effective in eliciting immune responses and protection against SARS-CoV and any of the above expression systems can be used for production of rRBD-based SARS subunit vaccines. Preference will be given to rRBD expressed in mammalian cells for future evaluation of the vaccine efficacy in a non-human primate model of SARS because of its ability to refold into a native conformation more readily and to induce higher level of neutralizing antibody responses than those expressed in E. coli and insect cells.
Output: Recombinant receptor-binding domain of SARS-CoV spike protein expressed in mammalian, insect and E. coli cells elicits potent neutralizing antibody and protective immunity NIH Public Access
Background: Nucleoli are composed of possibly several thousand different proteins and represent the most conspicuous compartments in the nucleus; they play a crucial role in the proper execution of many cellular processes. As such, nucleoli carry out ribosome biogenesis and sequester or associate with key molecules that regulate cell cycle progression, tumorigenesis, apoptosis and the stress response. Nucleoli are dynamic compartments that are characterized by a constant flux of macromolecules. Given the complex and dynamic composition of the nucleolar proteome, it is challenging to link modifications in nucleolar composition to downstream effects. Results: In this contribution, we present quantitative immunofluorescence methods that rely on computer-based image analysis. We demonstrate the effectiveness of these techniques by monitoring the dynamic association of proteins and RNA with nucleoli under different physiological conditions. Thus, the protocols described by us were employed to study stress-dependent changes in the nucleolar concentration of endogenous and GFP-tagged proteins. Furthermore, our methods were applied to measure de novo RNA synthesis that is associated with nucleoli. We show that the techniques described here can be easily combined with automated high throughput screening (HTS) platforms, making it possible to obtain large data sets and analyze many of the biological processes that are located in nucleoli. Conclusions: Our protocols set the stage to analyze in a quantitative fashion the kinetics of shuttling nucleolar proteins, both at the single cell level as well as for a large number of cells. Moreover, the procedures described here are compatible with high throughput image acquisition and analysis using HTS automated platforms, thereby providing the basis to quantify nucleolar components and activities for numerous samples and experimental conditions. Together with the growing amount of information obtained for the nucleolar proteome, improvements in quantitative microscopy as they are described here can be expected to produce new insights into the complex biological functions that are orchestrated by the nucleolus.
Output: Computer-based fluorescence quantification: a novel approach to study nucleolar biology
We previously described isolation of a potentially new mammalian reovirus, designated BYD1, which can cause clinical symptoms similar to that of severe acute respiratory syndrome (SARS) in guinea pigs and macaques, from throat swabs of one SARS patient of Beijing, in 2003. For this study, we determined the genome sequences of BYD1 and the S1 gene sequences of other five mammalian reovirus isolates (BLD, JP, and BYL were isolated from different SARS patients during the outbreak, 302I and 302II were isolated from fecal specimens of two children of Beijing in 1982) to allow molecular comparison with other previously reported mammalian reoviruses (MRVs). Comparative analyses of the BYD1 genome with those of three prototype mammalian reovirus strains demonstrated that BYD1 is a novel reassortant virus, with its S1 gene segment coming from a previously unidentified serotype 2 isolate and other nine segments coming from ancestors of homologous T1L and T3D segments, which supports the hypothesis that mammalian reovirus gene segments reassort in nature. Further analyses of the S1 segments of the six isolates showed that all the isolates are novel serotype 2 MRVs based on their S1 gene sequences, which are markedly different from those of all previously reported, and the S1 genes of the four new isolates share more than 99% identity with each other, proving that they diverged from a common ancestor most recently, and the S1 genes of the four new isolates share about 65% identity with those of the two strains isolated in 1982.
Output: Comparative sequence analyses of a new mammalian reovirus genome and the mammalian reovirus S1 genes from six new serotype 2 human isolates
Angiotensin-converting enzyme-2 (ACE2) is the first human homologue of ACE to be described. ACE2 is a type I integral membrane protein which functions as a carboxypeptidase, cleaving a single hydrophobic/basic residue from the C-terminus of its substrates. ACE2 efficiently hydrolyses the potent vasoconstrictor angiotensin II to angiotensin (1-7). It is a consequence of this action that ACE2 participates in the renin-angiotensin system. However, ACE2 also hydrolyses dynorphin A (1-13), apelin-13 and des-Arg 9 bradykinin. The role of ACE2 in these peptide systems has yet to be revealed. A physiological role for ACE2 has been implicated in hypertension, cardiac function, heart function and diabetes, and as a receptor of the severe acute respiratory syndrome coronavirus. This paper reviews the biochemistry of ACE2 and discusses key findings such as the elucidation of crystal structures for ACE2 and testicular ACE and the development of ACE2 inhibitors that have now provided a basis for future research on this enzyme.
Output: Angiotensin-converting enzyme-2: a molecular and cellular perspective
and occasionally lead to death. Furthermore, every few decades, respiratory virus pandemics emerge, putting the entire world population at risk. thus, there is an urgent need to quickly and precisely identify the infecting agent in a clinical setting. However, in many patients with influenza-like symptoms (ILS) the identity of the underlying pathogen remains unknown. In addition, it takes time and effort to individually identify the virus responsible for the ILS. Here, we present a new next-generation sequencing (NGS)based method that enables rapid and robust identification of pathogens in a pool of clinical samples without the need for specific primers. The method is aimed at rapidly uncovering a potentially common pathogen affecting many samples with an unidentified source of disease.
Output: A method to identify respiratory virus infections in clinical samples using next-generation sequencing
Nonstructural protein 3 of the severe acute respiratory syndrome (SARS) coronavirus includes a "SARS-unique domain" (SUD) consisting of three globular domains separated by short linker peptide segments. This work reports NMR structure determinations of the C-terminal domain (SUD-C) and a two-domain construct (SUD-MC) containing the middle domain (SUD-M) and the C-terminal domain, and NMR data on the conformational states of the N-terminal domain (SUD-N) and the SUD-NM two-domain construct. Both SUD-N and SUD-NM are monomeric and globular in solution; in SUD-NM, there is high mobility in the two-residue interdomain linking sequence, with no preferred relative orientation of the two domains. SUD-CadoptsafrataxinlikefoldandhasstructuralsimilaritytoDNA-binding domains of DNA-modifying enzymes. The structures of both SUD-M (previously determined) and SUD-C (from the present study) are maintained in SUD-MC, where the two domains are flexibly linked. Gelshift experiments showed that both SUD-C and SUD-MC bind to singlestranded RNA and recognize purine bases more strongly than pyrimidine bases, whereby SUD-MC binds to a more restricted set of purine-containing RNA sequences than SUD-M. NMR chemical shift perturbation experiments with observations of 15 N-labeled proteins further resulted in delineation of RNA binding sites (i.e., in SUD-M, a positively charged surface area with a pronounced cavity, and in SUD-C, several residues of an anti-parallel β-sheet). Overall, the present data provide evidence for molecular mechanisms involving the concerted actions of SUD-M and SUD-C, which result in specific RNA binding that might be unique to the SUD and, thus, to the SARS coronavirus.
Output: SARS Coronavirus Unique Domain: Three-Domain Molecular Architecture in Solution and RNA Binding
Keywords critical care; acute respiratory distress syndrome; refractory hypoxemia; rescue therapy; editorial Since the first description of Acute Respiratory Distress Syndrome (ARDS) in 1967 (1), the scientific community has strived to elucidate effective treatments for this clinical entity. Despite the extensive work that has emerged over decades, we continue to lack effective treatments for this syndrome. It continues to be associated with significant mortality, most recently estimated as high as 44% (2). To date, the most widely accepted effective intervention with a significant impact on mortality is low tidal volume ventilation (3). A category of therapies receiving recent attention is a group termed "rescue therapies", named such for their role in treating hypoxemia that is refractory to standard management strategies for ARDS. These include high-frequency oscillatory ventilation (HFOV), inhaled epoprostenol and nitric oxide, prone position ventilation, and extracorporeal membrane oxygenation (ECMO). Traditionally, these are interventions reserved for patients whose hypoxemia progresses despite recognition and treatment of ARDS. Intensivists generally agree these different therapies rapidly improve oxygenation, but no clear consensus exists on whether or not they improve mortality (4-7).
Output: The Ongoing Challenge of Evaluating Rescue Therapies in ARDS NIH Public Access
Bats of different species play a major role in the emergence and transmission of highly pathogenic viruses including Ebola virus, SARS-like coronavirus and the henipaviruses. These viruses require proteolytic activation of surface envelope glycoproteins needed for entry, and cellular cathepsins have been shown to be involved in proteolysis of glycoproteins from these distinct virus families. Very little is currently known about the available proteases in bats. To determine whether the utilization of cathepsins by bat-borne viruses is related to the nature of proteases in their natural hosts, we examined proteolytic processing of several viral fusion proteins in cells derived from two fruit bat species, Pteropus alecto and Rousettus aegyptiacus. Our work shows that fruit bat cells have homologs of cathepsin and furin proteases capable of cleaving and activating both the cathepsin-dependent Hendra virus F and the furin-dependent parainfluenza virus 5 F proteins. Sequence analysis comparing Pteropus alecto furin and cathepsin L to proteases from other mammalian species showed a high degree of conservation; however significant amino acid variation occurs at the C-terminus of Pteropus alecto furin. Further analysis of furin-like proteases from fruit bats revealed that these proteases are catalytically active and resemble other mammalian furins in their response to a potent furin inhibitor. However, kinetic analysis suggests that differences may exist in the cellular localization of furin between different species. Collectively, these results indicate that the unusual role of cathepsin proteases in the life cycle of batborne viruses is not due to the lack of active furin-like proteases in these natural reservoir species; however, differences may exist between furin proteases present in fruit bats compared to furins in other mammalian species, and these differences may impact protease usage for viral glycoprotein processing.
Output: Analysis of Cathepsin and Furin Proteolytic Enzymes Involved in Viral Fusion Protein Activation in Cells of the Bat Reservoir Host
Seven monoclonal antibodies (MAbs) with neutralizing activity against feline infectious peritonitis virus (FIPV) strain 79-1149 (type II) were prepared. When the polypeptide specificity recognized by these monoclonal antibodies (MAbs) was investigated by Western immunoblotting, all of the MAbs reacted with peplomer glycoprotein (S) of the virus. By competitive binding assay these MAbs were found to recognize at least 3 different epitopes. The reactivity of these MAbs with 6 viruses classified as FIPV type I (UCD-1, UCD-2, UCD-3, UCD-4, NW-1, and Black), feline enteric coronavirus (FECV) type II strain 79-1683, canine coronavirus (CCV) strain 1-71, and transmissible gastroenteritis virus (TGEV) strains TO-163 and SH was examined by neutralization tests. All MAbs neutralized FECV strain 79-1683, CCV strain 1-71, and TGEV strains TO-163 and SH, while they did not neutralize the 6 FIPV type I viruses. Moreover, the MAb against TGEV strain TO-163, which has strong neutralizing activity against 7 TGEV viruses, neutralized CCV strain 1-71, FECV strain 79-1683, and FIPV strain 79-1146, but did not neutralize the 6 FIPV type I viruses. These results demonstrated that there are at least 3 epitopes involved in the neutralization of FIPV type II strain 79-1146, and that these epitopes are not present in FIPV type I viruses but are present in FECV strain 79'-1683 which does not induce feline infectious peritonitis, TGEV strains TO-163 and SH, and CCV strain 1-71. These results suggest the presence of 2 serotypes of FIPV which can be clearly distinguished by the neutralization test using MAbs.
Output: Characterization of monoclonal antibodies against feline infectious peritonitis virus type II and antigenic relationship between feline, porcine, and canine coronaviruses
Toroviruses are gastroenteritis causing agents that infect different animal species and humans. To date, very little is known about how toroviruses cause disease. Here, we describe for the first time that the prototype member of this genus, the equine torovirus Berne virus (BEV), induces apoptosis in infected cells at late times postinfection. Observation of BEV infected cells by electron microscopy revealed that by 24 hours postinfection some cells exhibited morphological characteristics of apoptotic cells. Based on this finding, we analyzed several apoptotic markers, and observed protein synthesis inhibition, rRNA and DNA degradation, nuclear fragmentation, caspase-mediated cleavage of PARP and eIF4GI, and PKR and eIF2a phosphorylation, all these processes taking place after peak virus production. We also determined that both cell death receptor and mitochondrial pathways are involved in the apoptosis process induced by BEV. BEV-induced apoptosis at late times postinfection, once viral progeny are produced, could facilitate viral dissemination in vivo and contribute to viral pathogenesis.
Output: Equine Torovirus (BEV) Induces Caspase-Mediated Apoptosis in Infected Cells
The 5' ends of trypanosome mRNAs consist of an identical sequence of 35 nucleotides. This "mini-exon" sequence is derived from the 5'end of a 137 nucleotide RNA (medRNA). The remainder of each mRNA is derived from a protein-coding exon that is not linked to the mini-exon. We propose that medRNA is spliced in trans to de-novo-initiated transcripts of protein-coding genes. This frans splicing model predicts that the downstream portion of medRNA will be part of a branched structure and then be released as a free product (minRNA). We demonstrate that significant levels of minRNA exist in trypanosome RNA. Furthermore, minRNA can be released from high molecular weight RNA by a HeLa cell SlOO "debranching'lextract. Wa conclude that frans splicing is the physiological process by which mature mRNA molecules are synthesized in trypanosomes.
Output: vidence for Trans Splicing in Trypanosomes
The present study describes the development of SYBR Green based real-time polymerase chain reaction (real-time PCR) for detection and quantitation of canine parvovirus type 2 (CPV 2) in faecal samples of dogs. In this assay, the primers were designed and custom-synthesized based on nucleotide sequence of VP2 gene of CPV 2. A standard curve was plotted using 10-fold serial dilution of standard plasmid DNA and Ct value. The standard curve was found to be linear over a 10 −7 dilution. The real-time PCR results were expressed as the number of DNA copies of CPV 2 per mg of faecal samples and showed range of 1.0 × 10 3 to 7.0 × 10 9 copies of viral DNA per mg of stool samples. The analytical sensitivity of the SYBR Green based real-time PCR was shown to be equivalent to 10 copies. Faecal samples (47) from dogs suspected of CPV 2 infection were analyzed by real-time PCR, haemagglutination (HA) assay and by a conventional PCR and 24, 20 and 22 samples were found positive for CPV 2, respectively. Comparison between the results of three different assays revealed that real-time PCR is more sensitive than HA and conventional PCR and allow the detection of low titers of CPV 2 in infected dogs.
Output: Development of a SYBR Green based real-time PCR assay for detection and quantitation of canine parvovirus in faecal samples
A multi-patch SEIQR epidemic model is formulated to investigate the longterm impact of entry-exit screening measures on the spread and control of infectious diseases. A threshold dynamics determined by the basic reproduction number 0 is established: The disease can be eradicated if 0 < 1, while the disease persists if 0 > 1. As an application, six different screening strategies are explored to examine the impacts of screening on the control of the 2009 influenza A (H1N1) pandemic. We find that it is crucial to screen travelers from and to high-risk patches, and it is not necessary to implement screening in all connected patches, and both the dispersal rates and the successful detection rate of screening play an important role on determining an effective and practical screening strategy.
Output: An Epidemic Patchy Model with Entry-Exit Screening
Background: Despite current knowledge of mutations in 45 genes that can cause nonsyndromic sensorineural hearing loss (SNHL), no unified clinical test has been developed that can comprehensively detect mutations in multiple genes. We therefore designed Affymetrix resequencing microarrays capable of resequencing 13 genes mutated in SNHL (GJB2, GJB6, CDH23, KCNE1, KCNQ1, MYO7A, OTOF, PDS, MYO6, SLC26A5, TMIE, TMPRSS3, USH1C). We present results from hearing loss arrays developed in two different research facilities and highlight some of the approaches we adopted to enhance the applicability of resequencing arrays in a clinical setting. Results: We leveraged sequence and intensity pattern features responsible for diminished coverage and accuracy and developed a novel algorithm, sPROFILER, which resolved >80% of no-calls from GSEQ and allowed 99.6% (range: 99.2-99.8%) of sequence to be called, while maintaining overall accuracy at >99.8% based upon dideoxy sequencing comparison. Conclusions: Together, these findings provide insight into critical issues for disease-centered resequencing protocols suitable for clinical application and support the use of array-based resequencing technology as a valuable molecular diagnostic tool for pediatric SNHL and other genetic diseases with substantial genetic heterogeneity.
Output: High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays
Herbal plants, plant preparations and phytoconstituents have proved useful in attenuating infectious conditions and were the only remedies available, till the advent of antibiotics (many being of plant origin themselves). Among infectious diseases, viral diseases in particular, remain the leading cause of death in humans globally. A variety of phytoconstituents derived from medicinal herbs have been extensively studied for antiviral activity. Based on this rationale, an online search was performed, which helped to identify a large number of plant species harboring antiviral molecules. These herbal sources have been reported individually or in combinations across a large number of citations studied. Activities against rabies virus, Human immunodeficiency virus, Chandipura virus, Japanese Encephalitis Virus, Enterovirus, Influenza A/H1N1 and other influenza viruses were discovered during the literature search. This review includes all such plant species exhibiting antiviral properties. The review also encompasses composition and methodologies of preparing various antiviral formulations around the globe. An elaborate section on the formulations filed for patent registration, along with non-patented formulations, has also been included in this article. To conclude, herbal sources provide researchers enormous scope to explore and bring out viable alternatives against viral diseases, considering non-availability of suitable drug candidates and increasing resistance to existing drug molecules for many emerging and re-emerging viral diseases.
Output: Herbal plants and plant preparations as remedial approach for viral diseases
A new virus isolated from the lungs of rats is prevalent in colony reared and wild rats and induces a fatal pneumonitis in newborn rats. The virus, designated as rat coronavirus (RCV), exhibits properties representative of the coronavirus group: characteristic surface structure, particles somewhat variable in size averaging approximately 90 m~z, apparent R2ffA content, essential lipid, heat sensitivity, and a close serologic relationship with the mouse hepatitis virus complex. I~CV grows well in primary rat kidney cell cultures, exhibits a pathognomonic type CPE, and produces a complement fixing antigen which is sensitive for detection of antibody and useful in sero-epidemiologie studies.
Output: Rat Coronavirus (RCV): A Prevalent, Naturally Occurring Pneumotropie Virus of Rats 1
Background: The 2010 cholera outbreak in northern Nigeria affected over 40,000 people, with a case fatality rate (CFR) of ≥3.75%. We assessed the emergency response of health care workers (HCWs) involved in case management. Method: This was a cross-sectional study with data collected through a selfadministered questionnaire. Data entry and analysis were performed using Epi info software. Results: A total of 56 HCWs were interviewed. The mean age was 31 years (SD ± 8.16 years). The majority of the HCWs (80%; n = 45) were aged 18-39 years. Most were community health extension workers (60%), and 3.6% (n = 2) were medical doctors. Many of the HCWs had less than 2 years of work experience (42%). Additionally, 82% of the respondents had <1 week of cholera emergency response training, and 50% of the HCWs managed >20 suspected cases of cholera per day. Although 78% of HCWs reported the practice of universal safety precautions, 32% (n = 18) knew HCWs who developed symptoms of cholera during the epidemic, most of which was believed to be hospital acquired (78%). We also found that 77% (n = 43) of HCWs had no access to the required emergency response supplies. Conclusion: Inadequate training, a lack of qualified HCWs and a limited supply of emergency response kits were reported. Therefore, the government and stakeholders should address the gaps noted to adequately control and prevent future epidemics.
Output: An assessment of the emergency response among health workers involved in the 2010 cholera outbreak in northern Nigeria Cholera outbreak emergency response in Nigeria
Steroid-induced osteonecrosis of the femoral head (SONFH) is a disabling, aseptic and ischemic disease that develops following steroid therapy. The pathogenesis of SONFH is unclear, so the early diagnosis and treatment for this disease is yet to be established. The purpose of the present study was to identify potential biomarkers for SONFH. The differential expression of serum proteins from patients with SONFH and healthy volunteers was analyzed by the proteomics method. The protein samples were labeled and subjected to isoelectric focusing and two-dimensional gel electrophoresis. The resultant protein spots were matched and quantified by an imaging analysis system. The differentially-expressed protein spots were subjected to in-gel trypsin digestion followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Significantly lower levels of complement component 3 (C3), C4, inter-α-trypsin inhibitor heavy chain H4 and α-2-macroglobulin were found in the serum of patients with SONFH. These proteins are reported to be actively involved in intravascular coagulation, apoptosis and reactive oxygen species imbalance, indicating that multiple pathological reactions occur in SONFH and these proteins may serve as potential biomarkers for the diagnosis of SONFH.
Output: Comparative serum proteome expression of the steroid-induced femoral head osteonecrosis in adults
Therapeutic targeting of host cell factors required for virus replication rather than of pathogen components opens new perspectives to counteract virus infections. Anticipated advantages of this approach include a heightened barrier against the development of viral resistance and a broadened pathogen target spectrum. Myxoviruses are predominantly associated with acute disease and thus are particularly attractive for this approach since treatment time can be kept limited. To identify inhibitor candidates, we have analyzed hit compounds that emerged from a large-scale high-throughput screen for their ability to block replication of members of both the orthomyxovirus and paramyxovirus families. This has returned a compound class with broad anti-viral activity including potent inhibition of different influenza virus and paramyxovirus strains. After hit-to-lead chemistry, inhibitory concentrations are in the nanomolar range in the context of immortalized cell lines and human PBMCs. The compound shows high metabolic stability when exposed to human S-9 hepatocyte subcellular fractions. Antiviral activity is host-cell species specific and most pronounced in cells of higher mammalian origin, supporting a host-cell target. While the compound induces a temporary cell cycle arrest, host mRNA and protein biosynthesis are largely unaffected and treated cells maintain full metabolic activity. Viral replication is blocked at a post-entry step and resembles the inhibition profile of a known inhibitor of viral RNA-dependent RNA-polymerase (RdRp) activity. Direct assessment of RdRp activity in the presence of the reagent reveals strong inhibition both in the context of viral infection and in reporter-based minireplicon assays. In toto, we have identified a compound class with broad viral target range that blocks host factors required for viral RdRp activity. Viral adaptation attempts did not induce resistance after prolonged exposure, in contrast to rapid adaptation to a pathogen-directed inhibitor of RdRp activity.
Output: Potent Host-Directed Small-Molecule Inhibitors of Myxovirus RNA-Dependent RNA-Polymerases
Paneth cells are secretory epithelial cells of the innate immune system of the intestine of several mammals, including alpacas. Little is known about the latter; thus, in the present study we described the morphology and histochemical characteristics of Paneth cells in healthy fetuses, and young and adult alpacas. For this purpose, samples of duodenum, jejunum and ileum were taken from 6 fetuses at different days of pregnancy (between days 221-330), 66 offsprings (between 0 and 45-days-old) and 5 adult alpacas (>2-years-old). Samples were fixed in 10% buffered formalin and processed for histological and morphometrical analysis using HE and Masson Trichomicís technique. Immunohistochemistry was used to identify Paneth cells using anti-lysozyme antibody. In addition, the lectinhistochemichal bindingpattern of Paneth cellís granules was evaluated. Lyzozyme was immunohistochemically detected in the granules of Paneth cells from day 283 of pregnancy in all the small intestinal sections of the studied fetuses. In newborn alpacas Paneth cells were initially found in the duodenum, but the following days (days 18-21 after birth) they were also found in the ileum. Their size gradually increased after birth, but then no significant differences were found. In adult alpacas the number was lower than offsprings. We suggest that Paneth cells early differentiate in the small intestine of alpacas, and the increase in their number during the first two weeks of life strongly support their possible involvement in the intestinal defensive functions against the enteric diseases that occur during the lactancy stage.
Output: Characterization of paneth cells in alpacas (Vicugna pacos, Mammalia, Camelidae)