niryuu/sni-each-converted huggingface dataset:
Background: We undertook a 2X2 factorial, randomized controlled trial (RCT) to assess whether vitamin D 3 supplementation (10,000 international units per week) versus placebo and gargling versus no gargling could prevent viral, clinical upper respiratory tract infection (URTI) in university students. Methods: We randomized 600 students into 4 treatment arms: 1) vitamin D 3 and gargling, 2) placebo and gargling, 3) vitamin D 3 and no gargling, and 4) placebo and no gargling. Students completed weekly electronic surveys and submitted self-collected mid-turbinate nasal flocked swabs during September and October in 2010 or 2011. Symptomatic students also completed an electronic symptom diary. The primary and secondary outcomes were the occurrence of symptomatic clinical URTI and laboratory confirmed URTI respectively. Results: Of 600 participants, 471 (78.5%) completed all surveys while 43 (7.2%) completed none; 150 (25.0%) reported clinical URTI. Seventy participants (23.3%) randomized to vitamin D 3 reported clinical URTI compared to 80 (26.7%) randomized to placebo (RR:0.79, CI 95 :0.61-1.03, p = 0.09). Eighty-five participants (28.3%) randomized to gargling reported clinical URTI compared to 65 participants (21.7%) randomized to the no gargling arm (RR:1.3, CI 95 :0.92-1.57, p = 0.19). Laboratory testing identified 70 infections (46.7 per 100 URTIs). Vitamin D 3 treatment was associated with a significantly lower risk for laboratory confirmed URTI (RR: 0.54, CI 95 :0.34-0.84, p = 0.007) and with a significantly lower mean viral load measured as log 10 viral copies/mL (mean difference: −0.89, CI 95: -1.7, −0.06, p = 0.04). Fewer students assigned to gargling experienced laboratory confirmed URTI, however this was not statistically significant (RR:0.82, CI 95 :0.53-1.26, p = 0.36). Conclusions: These results suggest that vitamin D 3 is a promising intervention for the prevention of URTI. Vitamin D 3 significantly reduced the risk of laboratory confirmed URTI and may reduce the risk of clinical infections. Trial registration: Clinical Trials Registration: NCT01158560.
Output: Vitamin D 3 and gargling for the prevention of upper respiratory tract infections: a randomized controlled trial
Outbreaks of gastroenteritis may lead to serious disruption when many persons are absent from work or school. The illness may be life-threatening, particularly in the very young and very old. Control of gastroenteritis associated with microbial infection is therefore an important aspect of preventive medicine. Laboratory investigations are necessary to establish the source of an outbreak, to determine whether chemotherapy is necessary as it is in, for example, Giardia lamblia infection and to identify long-term changes in the pattern of infections related to altered dietary habits and other social factors. In this survey we draw attention to the many infective agents which have to be considered in the investigation of cases and outbreaks of gastroenteritis. The examination of faecal samples in the microbiology laboratory is becoming increasingly complex requiring as it does the use of additional new techniques for previously unrecognised bacterial, viral and protozoal causes of gastroenteritis including, in the last two decades, Campylobacter, Clostridiurn difficile, rotavirus, Norwalk virus and Cryptosporidium. These investigations are however expensive and in the face of increasing pressure to economise, it is of paramount importance that the best use should be made of the resources available. To this end we make recommendations about the information that should accompany faecal and other samples submitted to the laboratory from outbreaks of gastroenteritis.
Output: Investigating Gastroenteritis: The Merseyside Experience 1983-1987
Viral infection induces translocation of the nucleolar protein GLTSCR2 from the nucleus to the cytoplasm, resulting in attenuation of the type I interferon IFN-b. Addressing the role of GLTSCR2 in viral replication, we detect that knocking down GLTSCR2 by shRNAs results in significant suppression of viral replication in mammalian and chicken cells. Injection of chicken embryo with the GLTSCR2-specific shRNA-1370 simultaneously or 24 h prior to infection with Newcastle disease virus (NDV) substantially reduces viral replication in chicken embryo fibroblasts. Injection of shRNA-1370 into chicken embryo also reduces the replication of avian influenza virus (AIV). In contrast, GLTSCR2-derived protein G4-T, forming ahelical dimers, increases replication of seven various DNA and RNA viruses in cells. Our studies reveal that alteration of the function of cellular GLTSCR2 plays a role in supporting viral replication. GLTSCR2 should be seriously considered as a therapeutic target for developing broad spectrum antiviral agents to effectively control viral infection.
Output: Cellular protein GLTSCR2: A valuable target for the development of broad-spectrum antivirals
Paramyxovirus infections can be detected worldwide with some emerging zoonotic viruses and currently there are no specific therapeutic treatments or vaccines available for many of these diseases. Recent studies have demonstrated that peptides derived from the two heptad repeat regions (HR1 and HR2) of paramyxovirus fusion proteins could be used as inhibitors of virus fusion. The mechanism underlying this activity is in accordance with that of class I virus fusion proteins, of which human immunodeficiency virus (HIV) and influenza virus fusion proteins are members. For class I virus fusion proteins, the HR1 fragment binds to HR2 to form a six-helix bundle with three HR1 fragments forming the central coiled bundle surrounded by three coiled HR2 fragments in the post fusion conformational state (fusion core). It is hypothesized that the introduced exogenous HR1 or HR2 can compete against their endogenous counterparts, which results in fusion inhibition. Using Newcastle disease virus (NDV) as a model, we designed several protein inhibitors, denoted HR212 as well asHR121 and 5-Helix, which could bind the HR1 or HR2 region of fusion protein, respectively. All the proteins were expressed and purified using a GST-fusion expression system in Escherichia coli. The HR212 or GST-HR212 protein, which binds the HR1 peptide in vitro, displayed inhibitory activity against NDV-mediated cell fusion, while the HR121 and 5-Helix proteins, which bind the HR2 peptide in vitro, inhibited virus fusion from the avirulent NDV strain when added before the cleavage of the fusion protein. These results showed that the designed HR212, HR121 or 5-Helix protein could serve as specific antiviral agents. These data provide additional insight into the difference between the virulent and avirulent strains of NDV. q 2005 Published by Elsevier Ltd.
Output: Design and Characterization of Viral Polypeptide Inhibitors Targeting Newcastle Disease Virus Fusion
The Shortest Common Supersequence Problem asks to obtain a shortest string that is a supersequence of every member of a given set of strings. It has applications, among others, in data compression and oligonucleotide microarray production. The problem is NP-hard, and the existing exact solutions are impractical for large instances. In this paper, a new beam search algorithm is proposed for the problem, which employs a probabilistic heuristic and uses the dominance property to further prune the search space. The proposed algorithm is compared with three recent algorithms proposed for the problem on both random and biological sequences, outperforming them all by quickly providing solutions of higher average quality in all the experimental cases. The Java source and binary files of the proposed IBS_SCS algorithm and our implementation of the DR algorithm and all the random and real datasets used in this paper are freely available upon request.
Output: Bahri), f.tabataba@ec.iut.ac.ir (F.S. Tabataba)
Enterovirus D68 (EV-D68) is an emerging pathogen that recently caused a large outbreak of severe respiratory disease in the United States and other countries. Little is known about the relationship between EV-D68 virus and host cells. In this study, we assessed the effect of the host cell cycle on EV-D68 viral production, as well as the ability of EV-D68 to manipulate host cell cycle progression. The results suggest that synchronization in G0/G1 phase, but not S phase, promotes viral production, while synchronization in G2/M inhibits viral production. Both an early EV-D68 isolate and currently circulating strains of EV-D68 can manipulate the host cell cycle to arrest cells in the G0/G1 phase, thus providing favorable conditions for virus production. Cell cycle regulation by EV-D68 was associated with corresponding effects on the expression of cyclins and CDKs, which were observed at the level of the protein and/or mRNA. Furthermore, the viral non-structural protein 3D of EV-D68 prevents progression from G0/G1 to S. Interestingly, another member of the Picornaviridae family, EV-A71, differs from EV-D68 in that G0/G1 synchronization inhibits, rather than promotes, EV-A71 viral replication. However, these viruses are similar in that G2/M synchronization inhibits the production and activity of both viruses, which is suggestive of a common therapeutic target for both types of enterovirus. These results further clarify the pathogenic mechanisms of enteroviruses and provide a potential strategy for the treatment and prevention of EV-D68-related disease.
Output: Human Enterovirus 68 Interferes with the Host Cell Cycle to Facilitate Viral Production
Acute respiratory distress syndrome (ARDS) can be associated with various disorders. Among these, coronavirus infection may cause life-threatening severe acute respiratory syndrome (SARS). In this review, we present animal models and techniques for the study of ARDS, and discuss the roles and possible mechanisms of various chemical factors, including nitric oxide (NO). Our early work revealed that cerebral compression elicits severe hemorrhagic pulmonary edema (PE), leading to central sympathetic activation that results in systemic vasoconstriction. The consequence of systemic vasoconstriction is volume and pressure loading in the pulmonary circulation. Vasodilators, but not oxidant radical scavengers, are effective in the prevention of centrogenic PE. In isolated perfused lung, exogenous and endogenous NO enhances lung injury following air embolism and ischemia/reperfusion. In contrast, NO synthase (NOS) inhibitors reverse such lung injury. Although NO is important in maintaining vasodilator tone, hypoxiainduced pulmonary vasoconstriction is accompanied by an increase instead of a decrease in NO release. In animal and isolated lung studies, endotoxin produces acute lung injury that is associated with increases in cytokines and inducible NOS mRNA expression, suggesting that NO is toxic to the lung in endotoxin shock. Recently, we reported several rare cases that indicate that ARDS in patients with Japanese B encephalitis, lymphangitis with breast cancer and fat embolism is caused by different mechanisms. Our early and recent studies on ARDS and PE may provide information for clinical practice and the understanding of the pathogenesis of SARS.
Output: Biomedical Science Review Acute Respiratory Distress Syndrome
We collected serum samples from 50 healthy blood donors (Cohort A) as negative controls Sanquin Blood Bank (Rotterdam, the Netherlands) obtained written informed consent for research use. We assessed specificity using cohorts B and C, which consisted of 145 serum specimens from patients confirmed by RT-PCR to be positive for human respiratory infections. Those included samples from persons recently infected with 13 different respiratory viruses, or with acute IgM-positive CMV and EBV infection, which are known to be cross-reactive in serologic assays; as well as Mycoplasma pneumoniae. Because MERS has no pathognomonic signs distinguishing it from other respiratory infections, cohort B, including 85 samples from acute non-HCoV respiratory infections, was used to assess specificity in acute cases. To further evaluate specificity, cohort C included serum samples from acute to convalescent HCoV-NL63, 229E, and -OC43 patients. Furthermore, we assessed Cohorts D-G were used to evaluate sensitivity of the different platforms. Serologically identified MERS-CoV-infected mild and asymptomatic persons with camel contact (D1) and healthy donors (D2) from Qatar characterized in an earlier study (1) constituted cohort D. Serial serum samples from 2 RT-PCRdiagnosed MERS-CoV case-patients imported to the Netherlands (2) were used as positive controls and to evaluate antibody kinetics; these were 15 serum samples from patient 1, ranging 4-228 days postdiagnosis (dpd), and 13 from patient 2, ranging 1-44 dpd. These 28 samples were categorized into cohorts E (<14 dpd, acute phase) and F (>14 dpd, convalescent phase).
Output: Sensitive and Specific Detection of Low- Level Antibody Responses in Mild Middle East Respiratory Syndrome Coronavirus Infections Serum Samples
Amyloid fibril formation has long been studied because of the variety of proteins that are capable of adopting this structure despite sharing little sequence homology. This makes amyloid fibrils a challenging focus for inhibition studies because the peptides and proteins that form amyloid fibrils cannot be targeted based on a sequence motif. Most peptide inhibitors that target specific amyloidogenic proteins rely heavily on sequence recognition to ensure that the inhibitory peptide is able to bind its target. This approach is limited to targeting one amyloidogenic protein at a time. However, there is increasing evidence of cross-reactivity between amyloidforming polypeptides. It has therefore become more useful to study the similarities between these proteins that goes beyond their sequence homology. Indeed, the observation that amyloidogenic proteins adopt similar secondary structures along the pathway to fibril formation opens the way to an interesting investigation: the development of inhibitors that could be universal amyloid traps. The review below will analyze two specific amyloidogenic proteins, α-synuclein and human amylin, and introduce a small number of peptides that have been shown to be capable of inhibiting the amyloidogenesis of both of these very dissimilar polypeptides. Some of the inhibitory peptide motifs may indeed, be applicable to Aβ and other amyloidogenic systems.
Output: Pre-structured hydrophobic peptide β-strands: A universal amyloid trap?
To analyze the proteins interacting with the severe acute respiratory syndrome coronavirus (SARS-CoV) envelope (E) protein, a SARS-CoV was engineered including two tags associated to the E protein. Using this virus, complexes of SARS-CoV E and other proteins were purified using a tandem affinity purification system. Several viral and cell proteins including spike, membrane, non-structural protein 3 (nsp3), dynein heavy chain, fatty acid synthase and transmembrane protein 43 bound E protein. In the present work, we focused on the binding of E protein to nsp3 in infected cells and cell-free systems. This interaction was mediated by the N-terminal acidic domain of nsp3. Moreover, nsp3 and E protein colocalized during the infection. It was shown that E protein was ubiquitinated in vitro and in cell culture, suggesting that the interaction between nsp3 and E protein may play a role in the E protein ubiquitination status and therefore on its turnover.
Output: The envelope protein of severe acute respiratory syndrome coronavirus interacts with the non-structural protein 3 and is ubiquitinated
HIV-1 Tat protein is an important pathogenic factor in HIV-1-associated neurological diseases. One hallmark of HIV-1 infection of the central nervous system (CNS) is astrocytosis, which is characterized by elevated GFAP expression in astrocytes. We have shown that Tat activates GFAP expression in astrocytes (Zhou, et al., Mol. Cell. Neurosci. 27:296, 2004) and that GFAP is an important regulator of Tat neurotoxicity (Zou, et. al., Am. J. Pathol. 171:1293 , 2007 . However, the underlying mechanisms for Tat-mediated GFAP up-regulation are not understood. In the current study, we reported concurrent up-regulation of adenovirus E1a-associated 300 kDa protein p300 and GFAP in Tat-expressing human astroytoma cells and primary astrocytes. We showed that p300 was indeed induced by Tat expression and HIV-1 infection and that the induction occurred at the transcriptional level through the cis-acting elements of early growth response 1 (Egr-1) within its promoter. Using siRNA, we further showed that p300 regulated both constitutive and Tat-mediated GFAP expression. Moreover, we showed that ectopic expression of p300 potentiated Tat transactivation activity and increased proliferation of HIV-1-infected astrocytes, but had little effect on HIV-1 replication in these cells. Taken together, these results demonstrate for the first time that Tat is a positive regulator of p300 expression, which in turn regulates GFAP expression, and suggest that the Tat-Egr-1-p300-GFAP axis likely contributes to Tat neurotoxicity and predisposes astrocytes to be an HIV-1 sanctuary in the CNS.
Output: Involvement of p300 in constitutive and HIV-1 Tat-activated expression of glial fibrillary acidic protein in astrocytes
Background: On-site vaccination arrangements were introduced in 2005 to improve influenza vaccination rate among employees of a 1500-bed tertiary hospital in Singapore. Methods: On-site arrangements include mobile teams to 3 distant departments and same-service area vaccination for employees at 4 service areas. Results: Influenza vaccination rate in 2005 was 66.4% (versus 56.8% in 2004, odds ratio 1.50, 95% confidence interval 1.39-1.62). Employees who attended on-site arrangements had higher influenza vaccination rate (97.0%). Conclusion: On-site vaccination arrangements improved influenza vaccination rate among hospital employees. (Am J Infect Control 2007;35:481-3.) 
Output: On-site influenza vaccination arrangements improved influenza vaccination rate of employees of a tertiary hospital in Singapore
In this contribution, the classification of protein binding sites using the physicochemical properties exposed to their pockets is presented. We recently introduced Cavbase, a method for describing and comparing protein binding pockets on the basis of the geometrical and physicochemical properties of their active sites. Here, we present algorithmic and methodological enhancements in the Cavbase property description and in the cavity comparison step. We give examples of the Cavbase similarity analysis detecting pronounced similarities in the binding sites of proteins unrelated in sequence. A similarity search using SARS M pro protease subpockets as queries retrieved ligands and ligand fragments accommodated in a physicochemical environment similar to that of the query. This allowed the characterization of the protease recognition pockets and the identification of molecular building blocks that can be incorporated into novel antiviral compounds. A cluster analysis procedure for the functional classification of binding pockets was implemented and calibrated using a diverse set of enzyme binding sites. Two relevant protein families, the a-carbonic anhydrases and the protein kinases, are used to demonstrate the scope of our cluster approach. We propose a relevant classification of both protein families, on the basis of the binding motifs in their active sites. The classification provides a new perspective on functional properties across a protein family and is able to highlight features important for potency and selectivity. Furthermore, this information can be used to identify possible cross-reactivities among proteins due to similarities in their binding sites.
Output: From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase Keywords: protein binding pockets; classification of protein binding pockets; cluster analysis of protein binding pockets; protein kinases; SARS protease
We studied the genetic diversity, geographical structure, infection prevalence, and age-associated prevalence among camels at the largest entry port of camels from Africa into the Arabian Peninsula. Methods In this prospective genomic study, we took nasal samples from camels imported from Sudan and Djibouti into the Port of Jeddah in Jeddah, Saudi Arabia, over an almost 2-year period and local Arabian camels over 2 months in the year after surveillance of the port. We determined the prevalence of MERS-CoV infection, age-associated patterns of infection, and undertook phylogeographical and migration analyses to determine intercountry virus transmission after local lineage establishment. We compared all virological characteristics between the local and imported cohorts. We compared major gene deletions between African and Arabian strains of the virus. Reproductive numbers were inferred with Bayesian birth death skyline analyses. Between Aug 10, 2016, and May 3, 2018, we collected samples from 1196 imported camels, of which 868 originated from Sudan and 328 from Djibouti, and between May 1, and June 25, 2018, we collected samples from 472 local camels, of which 189 were from Riyadh and 283 were from Jeddah, Saudi Arabia. Virus prevalence was higher in local camels than in imported camels (224 [47·5%] of 472 vs 157 [13·1%] of 1196; p<0·0001). Infection prevalence peaked among camels older than 1 year and aged up to 2 years in both groups, with 255 (66·9%) of 381 positive cases in this age group. Although the overall geographical distribution of the virus corresponded with the phylogenetic tree topology, some virus exchange was observed between countries corresponding with trade routes in the region. East and west African strains of the virus appear to be geographically separated, with an origin of west African strains in east Africa. African strains of the virus were not re-sampled in Saudi Arabia despite sampling approximately 1 year after importation from Africa. All local Arabian samples contained strains of the virus that belong to a novel recombinant clade (NRC) first detected in 2014 in Saudi Arabia. Reproduction number estimates informed by the sequences suggest sustained endemicity of NRC, with a mean R e of 1·16. Interpretation Despite frequent imports of MERS-CoV with camels from Africa, African lineages of MERS-CoV do not establish themselves in Saudi Arabia. Arabian strains of the virus should be tested for changes in virulence and transmissibility.
Output: Enzootic patterns of Middle East respiratory syndrome coronavirus in imported African and local Arabian dromedary camels: a prospective genomic study
View is a key factor that influences property price. Previous studies represent view either by simple pictorial description of a scene, or by rather sophisticated mathematical methods. Both hinder proper allocation of a premium for different view obstruction levels for high-rise high-density urban environments. View obstruction level and the applicable premium are useful information for stakeholders of the property market for making optimum decisions. Accordingly, there is a need to develop a simple parameter for assessing view obstruction level. While view is difficult to define, reference is made to law cases which often settle view disputes by the extent of daylight obstruction. Shading mask is typically used to assess availability of daylight outside a residential unit and hence is an ideal parameter for assessing view obstruction. Computation of shading mask values (SMK) is a very complex task that needs meticulous site surveys, 3D drafting skills, and computer simulations. They are too effort intensive for stakeholders. This paper summarizes the relevant considerations and the case studies conducted to establish the average angle of unobstructed sky (q) as a simple parameter to represent mean SMK for assessing view obstruction. Correlation analysis of mean SMK of 708 case study residential units determined by the detailed computer simulation method and the corresponding angle of unobstructed sky showed that the latter can be used to assess view obstruction adequately close to simulation predictions. Given average angle of unobstructed sky can easily be determined based on the geometrical primitives of a residential unit, this can enable future allocation of a premium for different view obstruction levels for stakeholders.
Output: Developing a simplified parameter for assessing view obstruction in high-rise high-density urban environment
The observations that Lymphopenia is common in severe acute respiratory syndrome (SARS) patients and that peripheral blood mononuclear cell (PBMC) could be infected by SARS-CoV indicate that PBMC could be useful in identifying the gene expression profile in convalescent patients and tracing the host response to SARS-CoV infection. In this study, the altered genes expressions in the PBMC of convalescent SARS patients were investigated with suppression subtractive hybridization (SSH). We found that genes encoded by mitochondrial DNA (mtDNA) were obviously upregulated, while mitochondria were now found to be closely connected with antiviral immunity. The identification of a viral gene, M, in SSH cDNA library shows the long-term existence of SARS-CoV in vivo. In addition, some oxidative stress sensitive genes, heat shock proteins, transcription factors, and cytokines showed remarkable elevation. Thin-section electron microscope shows increased lysosome-like granule and mitochondria in PBMC of patients. These results provide important intracellular clue for tracing host response to SARS-CoV infection and suggest a role of mitochondria in that process.
Output: Upregulation of Mitochondrial Gene Expression in PBMC from Convalescent SARS Patients
29 Background: Our understanding of the corona virus disease 2019 (COVID-19) continues to 30 evolve. However, there are many unknowns about its epidemiology. 31 Purpose: To synthesize the number of deaths from confirmed COVID-19 cases, incubation 32 period, as well as time from onset of COVID-19 symptoms to first medical visit, ICU admission, 33 recovery and death of COVID-19. Data Synthesis: Out of 1675 non-duplicate studies identified, 57 were included. Pooled mean 41 incubation period was 5.84 (99% CI: 4.83, 6.85) days. Pooled mean number of days from the 42 onset of COVID-19 symptoms to first clinical visit was 4.82 (95% CI: 3.48, 6.15), ICU admission 43 was 10.48 (95% CI: 9.80, 11.16), recovery was 17.76 (95% CI: 12.64, 22.87), and until death 44 was 15.93 (95% CI: 13.07, 18.79). Pooled probability of COVID-19-related death was 0.02 (95% 45 CI: 0.02, 0.03). 46 Limitations: Studies are observational and findings are mainly based on studies that recruited 47 patient from clinics and hospitals and so may be biased toward more severe cases. 48 We found that the incubation period and lag between the onset of symptoms and diagnosis 50 of COVID-19 is longer than other respiratory viral infections including MERS and SARS; 51 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not peer-reviewed) The copyright holder for this preprint .
Output: Epidemiological Characteristics of COVID-19; a Systemic Review and Meta-Analysis 1
Polyomaviruses (PyVs) are known to infect a wide range of vertebrates and invertebrates and are associated with a broad spectrum of diseases, including cancers, particularly in immune-suppressed hosts. A novel polyomavirus, designated rat polyomavirus 2 (RatPyV2), was identified from a breeding colony of rats having X-linked severe combined immunodeficiency. Using a human panpolyomavirus immunohistochemistry test (P-PIT), RatPyV2 was initially detected in the parotid salivary gland of a colony member. Rolling circle amplification using DNA from harderian and parotid glands identified a novel 5.1-kb polyomavirus genome closely related to human Washington University (WU) and Karolinska Institute (KI) and vole polyomaviruses but notably divergent from Rattus norvegicus PyV1 (RnorPyV1; also designated RatPyV1). Further screening showed RatPyV2 inclusion body infection in the lung epithelium and variably in other respiratory, reproductive, and glandular tissues of 12/12 (100%) rats. IMPORTANCE Although P-PIT was developed to detect diseases associated with known human polyomaviruses, the identification of a new polyomavirus in rats suggests that it may have utility as a broad-based screen for new, as well as known polyomaviruses. Our findings suggest that RatPyV2 may be a commensal infection of laboratory rats that can lead to disseminated disease in T cell immune-deficient rats. Infection of the X-SCID rats with RatPyV2 and Pneumocystis carinii is a potential model for coinfection pathogenesis and treatment options during transplant preclinical studies.
Output: Identification and Characterization of Novel Rat Polyomavirus 2 in a Colony of X-SCID Rats by P-PIT assay
The objectives of this study were to evaluate the effects of free-access acidified milk replacer feeding on the pre-and postweaning health of dairy and veal calves. Individually housed calves were systematically assigned at birth to 1 of 2 feeding programs: free-access feeding (ad libitum) of acidified milk replacer (ACD, n = 249) or traditional restricted feeding (3 L fed twice daily) of milk replacer (RES, n = 249). Calves were fed milk replacer containing 24% crude protein and 18% fat. Acidified milk replacer was prepared to a target pH between 4.0 and 4.5 using formic acid. Calves were weaned off milk replacer at approximately 6 wk of age. Weaning occurred over 5 d, and during this weaning period, ACD calves had access to milk replacer for 12 h/d and RES calves were offered only one feeding of milk replacer (3 L) daily. Calves were monitored daily for signs of disease. Fecal consistency scores were assigned each week from birth until weaning. A subset of calves was systematically selected for fecal sampling at 3 time points between 7 and 27 d of age. Fecal samples were analyzed for enterotoxigenic Escherichia coli F5, Cryptosporidium parvum, rotavirus, and coronavirus. Hip width, hip height, body length, heart girth, and body weight were measured at birth and weaning. Postweaning body weight measurements were collected from the heifers at approximately 8 mo of age. Postweaning body weight and carcass grading information was collected from the veal calves at slaughter once a live weight between 300 and 350 kg had been achieved. The odds of ACD calves being treated for a preweaning disease event tended to be lower than that of the RES calves (1.2 vs. 5.2%, respectively). Preweaning mortality, postweaning disease treatment, and postweaning mortality did not differ between feeding treatments. The ACD feeding treatment supported greater preweaning average daily gain (0.59 vs. 0.43 kg/d) and structural growth than RES feeding. Postweaning average daily gain and carcass characteristics were similar for ACD and RES calves. These results indicate that free-access acidified milk replacer feeding tended to support improved health, and greater body weight gain and structural growth during the preweaning period; these effects did not persist in the postweaning period. The growth advantage observed before weaning in the ACD calves likely disappeared due to the weaning methods used.
Output: Clinical trial on the effects of a free-access acidified milk replacer feeding program on the health and growth of dairy replacement heifers and veal calves
Eukaryotes and bacteria can be infected with a wide variety of RNA viruses. On average, these pathogens share little sequence similarity and use different replication and transcription strategies. Nevertheless, the members of nearly all RNA virus families depend on the activity of a virally encoded RNA-dependent polymerase for the condensation of nucleotide triphosphates. This review provides an overview of our current understanding of the viral RNAdependent polymerase structure and the biochemistry and biophysics that is involved in replicating and transcribing the genetic material of RNA viruses.
Output: Common and unique features of viral RNA-dependent polymerases
a b s t r a c t 2-Deoxy-a-D-ribose-1-phosphate is of great interest as it is involved in the biosynthesis and/or catabolic degradation of several nucleoside analogues of biological and therapeutic relevance. However due to the lack of a stabilising group at its 2-position, it is difficult to synthesize stable prodrugs of this compound. In order to overcome this lack of stability, the synthesis of carbasugar analogues of 2-deoxyribose-1phosphate was envisioned. Herein the preparation of a series of prodrugs of two carbocyclic analogues of 2-deoxyribose-1-phosphate using the phosphoramidate ProTide technology, along with their biological evaluation against HIV and cancer cell proliferation, is reported.
Output: Synthesis and biological evaluation of phosphoramidate prodrugs of two analogues of 2-deoxy-D-ribose-1-phosphate directed to the discovery of two carbasugars as new potential anti-HIV leads
YopH is a bacterial protein tyrosine phosphatase, which is essential for the viability and pathogenic virulence of the plague-causing Yersinia sp. bacteria. Inactivation of YopH activity would lead to the loss of bacterial pathogenicity. We have studied the inhibitory properties of aurintricarboxylic acid (ATA) against YopH phosphatase and found that at nanomolar concentrations ATA reversibly decreases the activity of YopH. Computational docking studies indicated that in all binding poses ATA binds in the YopH active site. Molecular dynamics simulations showed that in the predicted binding pose, ATA binds to the essential Cys403 and Arg409 residues in the active site and has a stronger binding affinity than the natural substrate (pTyr). The cyclic voltammetry experiments suggest that ATA reacts remarkably strongly with molecular oxygen. Additionally, the electrochemical reduction of ATA in the presence of a negative potential from -2.0 to 2.5 V generates a current signal, which is observed for hydrogen peroxide. Here we showed that ATA indicates a unique mechanism of YopH inactivation due to a redox process. We proposed that the potent inhibitory properties of ATA are a result of its strong binding in the YopH active site and in situ generation of hydrogen peroxide near catalytic cysteine residue.
Output: Redox process is crucial for inhibitory properties of aurintricarboxylic acid against activity of YopH: virulence factor of Yersinia pestis
The plague is an infectious bacterial disease having a high fatality rate without treatment. It has occurred in three huge pandemics since the 6 th century with millions of deaths and numerous smaller epidemics and sporadic cases. Referring to specific clinical symptoms of pulmonary plague the disease became known as the Black Death. This pandemic probably originated in central Asia and began spreading westward along major trade routes. Upon the arrival in the eastern Mediterranean the disease quickly spread especially by sea traffic to Italy, Greece and France and later throughout Europe by land. Until the 18 th century many European cities were frequently affected by other great plague epidemics. The worldwide spread of the third pandemic began when the plague reached Hong Kong and Canton in the year 1894. The gram-negative coccobacillus now designated as Yersinia pestis has been discovered as the causative agent of plague in this Hong Kong outbreak. In the following years the role of rats and fleas and their detailed role in the transmission of plague has been discovered and experimentally verified. Today the plague is still endemic in many countries of the world.
Output: The history of the plague and the research on the causative agent Yersinia pestis
Positive-stranded viruses synthesize their RNA in membrane-bound organelles, but it is not clear how this benefits the virus or the host. For coronaviruses, these organelles take the form of double-membrane vesicles (DMVs) interconnected by a convoluted membrane network. We used electron microscopy to identify murine coronaviruses with mutations in nsp3 and nsp14 that replicated normally while producing only half the normal amount of DMVs under low-temperature growth conditions. Viruses with mutations in nsp5 and nsp16 produced small DMVs but also replicated normally. Quantitative reverse transcriptase PCR (RT-PCR) confirmed that the most strongly affected of these, the nsp3 mutant, produced more viral RNA than wild-type virus. Competitive growth assays were carried out in both continuous and primary cells to better understand the contribution of DMVs to viral fitness. Surprisingly, several viruses that produced fewer or smaller DMVs showed a higher fitness than wild-type virus at the reduced temperature, suggesting that larger and more numerous DMVs do not necessarily confer a competitive advantage in primary or continuous cell culture. For the first time, this directly demonstrates that replication and organelle formation may be, at least in part, studied separately during infection with positive-stranded RNA virus. DMVs is why they exist in the first place. In this study, we looked at thousands of infected cells and identified two coronavirus mutants that made half as many organelles as normal and two others that made typical numbers but smaller organelles. Despite differences in DMV size and number, all four mutants replicated as efficiently as wild-type virus. To better understand the relative importance of replicative organelles, we carried out competitive fitness experiments. None of these viruses was found to be significantly less fit than wild-type, and two were actually fitter in tests in two kinds of cells. This suggests that viruses have evolved to have tremendous plasticity in the ability to form membraneassociated replication complexes and that large and numerous DMVs are not exclusively associated with efficient coronavirus replication. Citation Al-Mulla HMN, Turrell L, Smith NM, Payne L, Baliji S, Züst R, Thiel V, Baker SC, Siddell SG, Neuman BW. 2014. Competitive fitness in coronaviruses is not correlated with size or number of double-membrane vesicles under reduced-temperature growth conditions. mBio 5(2):e01107-13.
Output: Competitive Fitness in Coronaviruses Is Not Correlated with Size or Number of Double-Membrane Vesicles under Reduced-Temperature Growth Conditions
A 26-year-old male with a past medical history of Crohn's disease, in remission for more than 10 years, presented to the Medical Intensive Care Unit (MICU) with diarrhea, hematuria, left-sided pulmonary infiltrates, transaminitis, and rapid-onset respiratory failure with acute kidney injury (AKI). The patient was well until 7 days prior to ICU admission, when he developed severe non-bloody diarrhea, approximately 20 times daily. Three days prior, he presented to an emergency department (ED) and was sent home after rehydration with normal saline with a reportedly normal chest x-ray (CXR). Two days prior, he presented to his primary care provider with continued diarrhea and fever to 39.4 °C, and he was sent home with anti-diarrheal medications. One day prior, he returned to the ED with chest tightness, shortness of breath, and cough productive of dark sputum, and he was found to have a new left-sided infiltrate on CXR, consistent with a pneumonia. He also reported dark urine and anorexia. He denied nausea, vomiting, abdominal pain, rash, or dysuria. In the ED, he was noted to be febrile with a temperature of 40.6 °C, tachycardic with a heart rate of 140 beats per minute, tachypneic with a respiratory rate of 29 breaths per minute and blood pressure of 115/65 mmHg, and hypoxic with an oxygen saturation of 93% on 4 L per minute of oxygen supplementation. He was transitioned to bilevel positive airway pressure (BIPAP) due to his increased work of breathing and hypoxia and received empiric antibiotic therapy and steroids, including intravenous (IV) ceftriaxone, azithromycin, and linezolid. He was then transferred to the University of Chicago Medicine MICU. His respiratory status worsened, and after about 5 h he was intubated. The patient had eaten no recent restaurant foods and had no known sick contacts. He worked as a pipe fitter. He denied having pets, unusual hobbies, or travel within the previous 6 months. On physical examination, his heart rate was 150 beats per minute, blood pressure 100/50 mmHg, temperature 39.1 °C, and respiratory rate 28 breaths per minute. He was intubated and sedated. He did not have any cervical adenopathy, and his conjunctivae were injected. His pulmonary exam demonstrated crackles bilaterally, and cardiovascular exam revealed a normal S1 and S2 with no murmurs. Pulses were equal, but capillary refill was slow, approximately 3 s. Abdominal exam showed normal liver and spleen to palpation and was nontender. He did not have any rashes. Initial serum laboratory results on transfer to the MICU included white blood cell (WBC) count of 11,900/μL (92% neutrophils, 3% lymphocytes), hemoglobin of 14.1 g/dL, and platelet count of 195,000/μL. The basic metabolic panel was within
Output: Diarrhea Leads to Pneumonia and Hematuria in the Intensive Care Unit
The goal of this study was to determine whether the use of nesting material or polycarbonate shelters, as enrichment devices would have an impact on endpoints commonly measured during the conduct of the National Toxicology Program (NTP) 13-week studies. The study design was consistent with the NTP 13-week toxicity studies. Harlan Sprague Dawley (HSD) rats and their offspring, and B6C3F1/N mice were assigned to control (unenriched) and enriched experimental groups. Body weight, food and water consumption, behavioral observations, fecal content, clinical pathology, gross pathology, organ weights, and histopathology were evaluated. Enriched male mice and male and female rats exhibited decreased feed intake without a subsequent decrease in body weight; this may have been the result of the nesting material reducing the effect of cold stress thereby allowing for more efficient use of feed. There were statistical differences in some hematological parameters, however these were not considered physiologically relevant since all values were within the normal range. Gross pathology and histopathological findings were background changes and were not considered enrichment-related. Nesting material and shelters were used frequently and consistently and allowed animals to display species typical behavior. There was no significant impact on commonly measured endpoints in HSD rats and B6C3F1/N mice given enrichment devices.
Output: Impact of Environmental Enrichment Devices on NTP In Vivo Studies
Although the initial outbreaks of the deadly coronavirus that causes severe acute respiratory syndrome (SARS-CoV) were controlled by public health measures, the development of vaccines and antiviral agents for SARS-CoV is essential for improving control and treatment of future outbreaks. One potential target for SARS-CoV antiviral drug development is the 3C-like protease (3CLpro). This enzyme is an attractive target since it is essential for viral replication, and since there are now a number of high resolution x-ray structures of SARS-CoV 3CLpro available making structure-based drug-design possible. As a result, SARS-CoV 3CLpro has become the focus of numerous drug discovery efforts worldwide, but as a consequence, a variety of different 3CLpro expression constructs and kinetic assays have been independently developed making evaluation and comparison between potential inhibitors problematic. Here, we review the literature focusing on different SARS-CoV 3CLpro expression constructs and assays used to measure enzymatic activity. Moreover, we provide experimental evidence showing that the activity of 3CLpro enzymatic is significantly reduced when non-native sequences or affinity-tags are added to the N-or C-termini of the enzyme, or when the enzyme used in assays is at concentrations below the equilibrium dissociation constant of the 3CLpro dimer. We demonstrate for the first time the utility of a highly sensitive and novel Alexa488-QSY7 FRET-based peptide substrate designed for routine analysis and high-throughput screening, and show that kinetic constants determined from FRET-based assays that are uncorrected for inner-filter effects can lead to artifacts. Finally, we evaluated the effects of common assay components including DTT, NaCl, EDTA and DMSO on enzymatic activity, and we recommend standardized assay conditions and constructs for routine SARS-CoV 3CLpro assays to facilitate direct comparisons between SARS-CoV 3CLpro inhibitors under development worldwide.
Output: Evaluating the 3C-like protease activity of SARS-Coronavirus: Recommendations for Standardized Assays for Drug Discovery NIH Public Access
Due to variations in serotypes among different strains of avian infectious bronchitis viruses (IBV), vaccination of chicks with imported vaccines fails to protect them from IBV infections in Taiwan. Therefore, we develop attenuated vaccines from local strains in Taiwan. A Taiwan Group I (TW I) strain was passaged 74 times through specific pathogen-free (SPF) chicken embryonated eggs, and then tested in SPF chickens. The attenuated vaccine was not pathogenic in 1-week-old chicks, had a neutralization index (NI) of greater than 4.4 and efficacy of 90% when inoculated birds were challenged with a field IBV strain. Similar results were obtained for a vaccine made from a Taiwan Group II IBV strain. Additionally, the TW I attenuated vaccine strain had no reversion to virulence after five back passages in chicks. In conclusion, these attenuated vaccines have potential for controlling local Taiwanese IBV infections in chickens.
Output: Development of attenuated vaccines from Taiwanese infectious bronchitis virus strains
Multiple sclerosis (MS) is a debilitating disease of the central nervous system (CNS) that has been extensively studied using the animal model experimental autoimmune encephalomyelitis (EAE). It is believed that CD4 + T lymphocytes play an important role in the pathogenesis of this disease by mediating the demyelination of neuronal axons via secretion of proinflammatory cytokines resulting in the clinical manifestations. Although a great deal of information has been gained in the last several decades about the cells involved in the inflammatory and disease mediating process, important questions have remained unanswered. It has long been held that initial neuroantigen presentation and T cell activation events occur in the immune periphery and then translocate to the CNS. However, an increasing body of evidence suggests that antigen (Ag) presentation might initiate within the CNS itself. Importantly, it has remained unresolved which antigen presenting cells (APCs) in the CNS are the first to acquire and present neuroantigens during EAE/MS to T cells, and what the conditions are under which this takes place, ie, whether this occurs in the healthy CNS or only during inflammatory conditions and what the related cytokine microenvironment is comprised of. In particular, the central role of interferon-g as a primary mediator of CNS pathology during EAE has been challenged by the emergence of Th17 cells producing interleukin-17. This review describes our current understanding of potential APCs in the CNS and the contribution of these and other CNS-resident cells to disease pathology. Additionally, we discuss the question of where Ag presentation is initiated and under what conditions neuroantigens are made available to APCs with special emphasis on which cytokines may be important in this process.
Output: The Critical Role of Antigen-Presentation-Induced Cytokine Crosstalk in the Central Nervous System in Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis