bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multicenter Evaluation of Whole-Blood Epstein-Barr Viral Load Standardization Using the WHO International Standard
Authors: Semenova Touyana , Lupo Julien , Alain Sophie , Perrin-Confort Gwladys , Grossi Laurence , Dimier Julie , Epaulard Olivier , Morand Patrice , Germi Raphaële 
Published: April 2016

ABSTRACT

The first WHO international standard for Epstein-Barr virus (EBV) (WHO EBV standard) for nucleic acid amplification technology (NAT)-based assays was commercialized in January 2012 by the National Institute for Biological Standards and Control. In the study reported here, we compared whole-blood EBV DNA load (EDL) results from 12 French laboratories for seven samples (Quality Controls for Molecular Diagnostics 2013 proficiency panel) in order to determine whether expression in international units reduces interlaboratory variability in whole-blood EDLs. Each testing laboratory used a conversion factor to convert EDL results from copies per milliliter to international units per milliliter. This conversion factor was calculated from the WHO EBV standard according to the protocol described in this study (nine laboratories) or the recommendations of the PCR kit suppliers (three laboratories). The interlaboratory variability in whole-blood EDL results was reduced after standardization of the results using the WHO EBV standard. For the seven samples tested, standard deviations (SD) ranged from 0.41 to 0.55 when the results were expressed in log copies per milliliter, whereas the SD ranged from 0.17 to 0.32 when results were given in log international units per milliliter. Comparing the variance data (
F
test), we showed that the dispersion of whole-blood EDL results was significantly lower when they were expressed in log international units per milliliter (
P
< 0.001 for six of seven samples and
P
< 0.05 for one sample with a low mean EDL of 2.62 log IU/ml). This study showed that the use of the WHO EBV standard could improve the homogeneity of whole-blood EDL results between laboratories as well as the monitoring of patients at high risk of posttransplant lymphoproliferative disorders or other EBV-associated diseases.
Do Staphylococcus epidermidis Genetic Clusters Predict Isolation Sources?
Authors: Tolo Isaiah , Thomas Jonathan C. , Fischer Rebecca S. B. , Brown Eric L. , Gray Barry M. , Robinson D. Ashley 
Published: April 2016

ABSTRACT

Staphylococcus epidermidis
is a ubiquitous colonizer of human skin and a common cause of medical device-associated infections. The extent to which the population genetic structure of
S. epidermidis
distinguishes commensal from pathogenic isolates is unclear. Previously, Bayesian clustering of 437 multilocus sequence types (STs) in the international database revealed a population structure of six genetic clusters (GCs) that may reflect the species' ecology. Here, we first verified the presence of six GCs, including two (GC3 and GC5) with significant admixture, in an updated database of 578 STs. Next, a single nucleotide polymorphism (SNP) assay was developed that accurately assigned 545 (94%) of 578 STs to GCs. Finally, the hypothesis that GCs could distinguish isolation sources was tested by SNP typing and GC assignment of 154 isolates from hospital patients with bacteremia and those with blood culture contaminants and from nonhospital carriage. GC5 was isolated almost exclusively from hospital sources. GC1 and GC6 were isolated from all sources but were overrepresented in isolates from nonhospital and infection sources, respectively. GC2, GC3, and GC4 were relatively rare in this collection. No association was detected between
fdh
-positive isolates (GC2 and GC4) and nonhospital sources. Using a machine learning algorithm, GCs predicted hospital and nonhospital sources with 80% accuracy and predicted infection and contaminant sources with 45% accuracy, which was comparable to the results seen with a combination of five genetic markers (
icaA
, IS
256
,
sesD
[
bhp
],
mecA
, and arginine catabolic mobile element [ACME]). Thus, analysis of population structure with subgenomic data shows the distinction of hospital and nonhospital sources and the near-inseparability of sources within a hospital.
Cell-Free Hepatitis B Virus Capsid Assembly Dependent on the Core Protein C-Terminal Domain and Regulated by Phosphorylation
Authors: Ludgate Laurie , Liu Kuancheng , Luckenbaugh Laurie , Streck Nicholas , Eng Stacey , Voitenleitner Christian , Delaney William E. , Hu Jianming 
Published: April 2016

ABSTRACT

Multiple subunits of the hepatitis B virus (HBV) core protein (HBc) assemble into an icosahedral capsid that packages the viral pregenomic RNA (pgRNA). The N-terminal domain (NTD) of HBc is sufficient for capsid assembly, in the absence of pgRNA or any other viral or host factors, under conditions of high HBc and/or salt concentrations. The C-terminal domain (CTD) is deemed dispensable for capsid assembly although it is essential for pgRNA packaging. We report here that HBc expressed in a mammalian cell lysate, rabbit reticulocyte lysate (RRL), was able to assemble into capsids when (low-nanomolar) HBc concentrations mimicked those achieved under conditions of viral replication
in vivo
and were far below those used previously for capsid assembly
in vitro
. Furthermore, at physiologically low HBc concentrations in RRL, the NTD was insufficient for capsid assembly and the CTD was also required. The CTD likely facilitated assembly under these conditions via RNA binding and protein-protein interactions. Moreover, the CTD underwent phosphorylation and dephosphorylation events in RRL similar to those seen
in vivo
which regulated capsid assembly. Importantly, the NTD alone also failed to accumulate in mammalian cells, likely resulting from its failure to assemble efficiently. Coexpression of the full-length HBc rescued NTD assembly in RRL as well as NTD expression and assembly in mammalian cells, resulting in the formation of mosaic capsids containing both full-length HBc and the NTD. These results have important implications for HBV assembly during replication and provide a facile cell-free system to study capsid assembly under physiologically relevant conditions, including its modulation by host factors.

IMPORTANCE
Hepatitis B virus (HBV) is an important global human pathogen and the main cause of liver cancer worldwide. An essential component of HBV is the spherical capsid composed of multiple copies of a single protein, the core protein (HBc). We have developed a mammalian cell-free system in which HBc is expressed at physiological (low) concentrations and assembles into capsids under near-physiological conditions. In this cell-free system, as in mammalian cells, capsid assembly depends on the C-terminal domain (CTD) of HBc, in contrast to other assembly systems in which HBc assembles into capsids independently of the CTD under conditions of nonphysiological protein and salt concentrations. Furthermore, the phosphorylation state of the CTD regulates capsid assembly and RNA encapsidation in the cell-free system in a manner similar to that seen in mammalian cells. This system will facilitate detailed studies on capsid assembly and RNA encapsidation under physiological conditions and identification of antiviral agents that target HBc.
Dynamic Nucleolar Targeting of Dengue Virus Polymerase NS5 in Response to Extracellular pH
Authors: Fraser Johanna E. , Rawlinson Stephen M. , Heaton Steven M. , Jans David A. 
Published: April 2016

ABSTRACT
The nucleolar subcompartment of the nucleus is increasingly recognized as an important target of RNA viruses. Here we document for the first time the ability of dengue virus (DENV) polymerase, nonstructural protein 5 (NS5), to accumulate within the nucleolus of infected cells and to target green fluorescent protein (GFP) to the nucleolus of live transfected cells. Intriguingly, NS5 exchange between the nucleus and nucleolus is dynamically modulated by extracellular pH, responding rapidly and reversibly to pH change, in contrast to GFP alone or other nucleolar and non-nucleolar targeted protein controls. The minimal pH-sensitive nucleolar targeting region (pHNTR), sufficient to target GFP to the nucleolus in a pH-sensitive fashion, was mapped to NS5 residues 1 to 244, with mutation of key hydrophobic residues, Leu-165, Leu-167, and Val-168, abolishing pHNTR function in NS5-transfected cells, and severely attenuating DENV growth in infected cells. This is the first report of a viral protein whose nucleolar targeting ability is rapidly modulated by extracellular stimuli, suggesting that DENV has the ability to detect and respond dynamically to the extracellular environment.

IMPORTANCE
Infections by dengue virus (DENV) threaten 40% of the world's population yet there is no approved vaccine or antiviral therapeutic to treat infections. Understanding the molecular details that govern effective viral replication is key for the development of novel antiviral strategies. Here, we describe for the first time dynamic trafficking of DENV nonstructural protein 5 (NS5) to the subnuclear compartment, the nucleolus. We demonstrate that NS5's targeting to the nucleolus occurs in response to acidic pH, identify the key amino acid residues within NS5 that are responsible, and demonstrate that their mutation severely impairs production of infectious DENV. Overall, this study identifies a unique subcellular trafficking event and suggests that DENV is able to detect and respond dynamically to environmental changes.
Assembly of Lipoic Acid on Its Cognate Enzymes: an Extraordinary and Essential Biosynthetic Pathway
Authors: Cronan John E. 
Published: April 2016

SUMMARY

Although the structure of lipoic acid and its role in bacterial metabolism were clear over 50 years ago, it is only in the past decade that the pathways of biosynthesis of this universally conserved cofactor have become understood. Unlike most cofactors, lipoic acid must be covalently bound to its cognate enzyme proteins (the 2-oxoacid dehydrogenases and the glycine cleavage system) in order to function in central metabolism. Indeed, the cofactor is assembled on its cognate proteins rather than being assembled and subsequently attached as in the typical pathway, like that of biotin attachment. The first lipoate biosynthetic pathway determined was that of
Escherichia coli
, which utilizes two enzymes to form the active lipoylated protein from a fatty acid biosynthetic intermediate. Recently, a more complex pathway requiring four proteins was discovered in
Bacillus subtilis
, which is probably an evolutionary relic. This pathway requires the H protein of the glycine cleavage system of single-carbon metabolism to form active (lipoyl) 2-oxoacid dehydrogenases. The bacterial pathways inform the lipoate pathways of eukaryotic organisms. Plants use the
E. coli
pathway, whereas mammals and fungi probably use the
B. subtilis
pathway. The lipoate metabolism enzymes (except those of sulfur insertion) are members of PFAM family PF03099 (the cofactor transferase family). Although these enzymes share some sequence similarity, they catalyze three markedly distinct enzyme reactions, making the usual assignment of function based on alignments prone to frequent mistaken annotations. This state of affairs has possibly clouded the interpretation of one of the disorders of human lipoate metabolism.
Psychosocial factors associated with outcomes of sports injury rehabilitation in competitive athletes: a mixed studies systematic review
Authors: Forsdyke Dale , Smith Andy , Jones Michelle , Gledhill Adam 
Published: April 2016

BackgroundThe prime focus of research on sports injury has been on physical factors. This is despite our understanding that when an athlete sustains an injury it has psychosocial as well as physical impacts. Psychosocial factors have been suggested as prognostic influences on the outcomes of rehabilitation. The aim of this work was to address the question: are psychosocial factors associated with sports injury rehabilitation outcomes in competitive athletes?Study designMixed studies systematic review (PROSPERO reg.CRD42014008667).MethodElectronic database and bibliographic searching was undertaken from the earliest entry until 1 June 2015. Studies that included injured competitive athletes, psychosocial factors and a sports injury rehabilitation outcome were reviewed by the authors. A quality appraisal of the studies was undertaken to establish the risk of reporting bias.Results25 studies were evaluated that included 942 injured competitive athletes were appraised and synthesised. Twenty studies had not been included in previous reviews. The mean methodological quality of the studies was 59% (moderate risk of reporting bias). Convergent thematic analysis uncovered three core themes across the studies: (1) emotion associated with rehabilitation outcomes; (2) cognitions associated with rehabilitation outcomes; and (3) behaviours associated with rehabilitation outcomes. Injury and performance-related fears, anxiety and confidence were associated with rehabilitation outcomes. There is gender-related, age-related and injury-related bias in the reviewed literature.ConclusionsPsychosocial factors were associated with a range of sports injury rehabilitation outcomes. Practitioners need to recognise that an injured athlete's thoughts, feelings and actions may influence the outcome of rehabilitation.
Availability and provision of emergency obstetric care under a public–private partnership in three districts of Gujarat, India: lessons for Universal Health Coverage
Authors: Iyer V , Sidney K , Mehta R , Mavalankar D 
Published: April 2016

ObjectiveThe state of Gujarat in India (population 60 million) has implemented a public–private partnership (PPP) with private obstetricians called the Chiranjeevi Yojana (CY) since 2006. This study investigated the adequacy of basic and comprehensive emergency obstetric care (BEmOC and CEmOC) services through the public and private sectors with reference to the United Nations (UN) guidelines.DesignA cross-sectional facility survey was conducted in three districts.ResultsA total of 300 facilities, 151 public and 149 private, had provided obstetric services to a total of 53 896 births in the past 6 months. Nearly half, 135 facilities (104 public and 31 private), individually reported <10 births per month (low load), and, as a group, reported only 4% of all births in the past 6 months. The remaining 165 high-load facilities consisted of 23 (3 public; 20 private) full CEmOC, 66 (1; 65) ‘potential’ CEmOC, 12 (3; 9) BEmOC and 57 (40; 17) non-EmOC facilities. All the three districts exceeded the UN recommendation for EmOC availability by 3.3 to 11.3 times. Free provision, through both public and PPP facilities, ranged from 1.42 to 3.43. The actual performance was nearly double the recommendation for CEmOC but inadequate for BEmOC.ConclusionsPublic sector EmOC availability and provision is negligible. Private sector availability is well beyond the recommended UN norms. The CY programme has resulted in increased availability and provision of EmOC services. However, the overall provision of EmOC is compromised due to the poor performance of BEmOC functions and clustering of private facilities in towns.
Methotrexate Hepatotoxicity in Psoriatics: Report of 104 Patients from Nova Scotia, with Analysis of Risks from Obesity, Diabetes and Alcohol Consumption During Long Term Follow‐Up
Authors: Malatjalian DA , Ross JB , Williams CN , Colwell SJ , Eastwood BJ 
Published: April 2016

BACKGROUND AND DESIGN: Methotrexate (MTX) hepatotoxicity in psoriatic patients is well recognized, but there are discrepancies in the reported incidence and associated risk factors. This retrospective study describes 104 Nova Scotian patients with psoriasis seen between 1979 and 1990. Patients received MTX over one to 11 years (mean 3.38), with baseline and annual follow‐up liver biopsies. Clinical data were obtained by chart review. Statistical analysis evaluated the risks associated with obesity, diabetes, alcohol consumption and duration of therapy, with the histological grade of liver biopsies.RESULTS: Of the 104 patients, 35 were obese, 10 were diabetic and 37 occasionally consumed alcohol. At the end of the study, 21 patients had developed severe hepatic fibrosis (grade IIIB), and three developed liver cirrhosis (grade IV). Significant risk of severe hepatotoxicity is related to diabetes (P=0.02) but not to obesity (P=0.12) or alcohol consumption (P=0.12). All patients with cirrhosis took MTX for two years in standard doses of 20 to 25 mg/week.CONCLUSIONS: In this first Canadian study evaluating MTX hepatotoxicity in psoriatics, the incidence of severe hepatotoxicity is high: 23.1% (24 of 104 patients). This study shows that diabetic patients are particularly at increased risk of MTX hepatotoxicity. Occasional alcohol consumption is not associated with increased risk. Three patients who developed cirrhosis over two years of standard MTX therapy may represent a subset of psoriatics with increased hepatic susceptibility to MTX. Another three patients whose severe hepatic fibrosis had regressed upon discontinuation of MTX, but who developed accelerated recurrence of the severe hepatic fibrosis upon resumption of MTX therapy, also suggest the possibility of unusual sensitivity to the drug. These cases emphasize the need for continuing surveillance, with regular liver biopsies, of psoriatic patients on MTX.
Increased Prevalence of Celiac Disease in Girls with Turner Syndrome Detected Using Antibodies to Endomysium and Tissue Transglutaminase
Authors: Gillett PM , Gillett HR , Israel DM , Metzger DL , Stewart L , Chanoine J-P , Freeman HJ 
Published: April 2016

OBJECTIVE: To establish the prevalence of celiac disease (CD) in girls with Turner syndrome (TS) in British Columbia.METHODS: Forty‐five girls with TS were prospectively screened for CD using blinded testing with the current ’gold standard’ ‐ immunoglobulin A (IgA) endomysium antibody (EmA) and the novel IgA tissue transglutaminase antibody (tTG). Those with positive results were offered small bowel biopsies, and a gluten‐free diet was recommended if CD was confirmed.RESULTS: One asymptomatic prepubertal East Indian girl was positive for EmA, had an elevated tTG concentration of 560 U/mL and histological evidence of CD. Seven girls were negative for EmA but had elevated tTG concentrations (175 to 250 U/mL); five were white, one was Asian and one was East Indian. Small bowel biopsies were performed on three girls, and the histologies were normal. The remaining four patients declined biopsy.CONCLUSIONS: One girl with TS was identified with CD from 45 screened, giving an overall biopsy‐confirmed prevalence of 2.2%. This study confirms previous observations placing girls with TS at higher risk for CD and suggests a similar high prevalence in British Columbia.
Do NSAIDs Prevent Colorectal Cancer?
Authors: Arber Nadir 
Published: April 2016

There is increasing evidence to suggest that acetylsalicylic acid (ASA) and other nonsteroidal anti-inflammatory drugs (NSAIDs) reduce the risk of colorectal cancer. This observation is supported by animal studies that show fewer tumours per animal and fewer animals with tumours after administration of several different NSAIDs. Studies in humans consistently support this hypothesis. Intervention data from familial adenomatosis coli establish that the process of human colonic adenoma polyp formation is affected. Supportive evidence comes from 21 of 23 human studies -- both case-control and cohort. The reduced risk has been found in men and women, for cancers of the colon and the rectum and for the use of both ASA and the other NSAIDs. Earlier detection of lesions as a result of drug-induced bleeding does not seem to account for these findings. The molecular mechanisms responsible for the chemopreventive action of this class of drugs is not completely established. Protection may affect several pathways, including cell cycle arrest and induction of apoptosis. Because of the consistency of epidemiological, clinical and experimental data, there is no need for further placebo trials. At the same time, there is a need to establish the dose, duration and frequency of use required for cancer-preventive activity.
Does the Depth of Gastric Ulceration Influence a Modified Dual Therapy with Amoxicilin and Lansoprazole forHelicobacter pylori-Positive Gastric Ulcer?
Authors: Okai Takashi , Ohtsubo Koushiro , Sakai Junta , Watanabe Hiroyuki , Motoo Yoshiharu , Kawashima Atsuhiro , Norio Sawabu 
Published: April 2016

PURPOSE: To clarify whether the depth of ulceration evaluated by endoscopic ultrasonography (EUS) influences a modified dual therapy with amoxicillin and lansoprazole for the treatment ofHelicobacter pylori-positive patients with gastric ulcer.PATIENTS AND METHODS: Twenty-two consecutive cases of gastric ulcer (nine superficial ulcers and 13 deep ulcers) inH pylori-positive patients were studied. Ten of 22 patients received a two-week eradication therapy with amoxicillin 1500 mg/day, lansoprazole 30 mg/day and a new antiulcer agent with features in common with sucralfate, ecabet sodium, 2.0 g/day. They continued to receive the same doses of lansoprazole and ecabet sodium for the next six weeks. The other 12 patients received the same therapy except for those who underwent the four-week amoxicillin treatment. All patients underwent EUS both at the start of the study and eight weeks later. They then received ecabet sodium alone for the next six months as a maintenance therapy, followed by a six-month interval with no treatment. The final endoscopy was done one year afterH pylorieradication therapy was completed to evaluateH pyloristatus and ulcer recurrence.RESULTS: The rates of endoscopic healing andH pylorieradication in the nine patients with superficial ulcer were 100%, irrespective of the period of amoxicillin treatment. In contrast, the rates of endoscopic evidence of healing andH pylorieradication in the 13 patients with deep ulcer were different for each period of amoxicillin treatment; that is, the rates of reduction in ulcer determined by echo andH pylorieradication in the four patients treated with the two-week amoxicillin course were significantly lower (P=0.03) than those in the nine patients treated with the four-week course.CONCLUSION: Ulcer depth is likely to influence the success of amoxicillin treatment forH pylori-positive patients with gastric ulcer.
Acid-Induced Esophageal Shortening in Humans: A Cause for Hiatus Hernia?
Authors: Dunne Donal P , Paterson William G 
Published: April 2016

BACKGROUND: Hiatus hernia and gastroesophageal reflux disease commonly coexist, and there is pathophysiological evidence that the presence of a hiatus hernia contributes to abnormal acid reflux. However, the cause of hiatus hernia remains unclear. In an animal model, it has been shown that acute acid injury to the esophagus results in esophageal shortening, raising the possibility that reflux esophagitis per se can contribute to the formation of hiatus hernia by inducing esophageal shortening.AIM: To determine whether luminal acid produces esophageal shortening in humans.METHODS: Twelve volunteers were each studied on two occasions, one week apart, in a double-blind, crossover trial. The location of the lower esophageal sphincter (LES), as well as the LES resting pressure and axial length were determined at baseline and then again after 20 min of either acid or saline perfusion.RESULTS: Acid perfusion did not induce significant changes in resting LES pressure but resulted in proximal migration of the LES (ie, esophageal shortening) by an average of 0.5 cm, with the largest proximal migration being 1.8 cm. In contrast, saline perfusion resulted in slight distal migration of the LES (ie, esophageal lengthening).CONCLUSIONS: Intraluminal acid perfusion causes longitudinal axis shortening of the esophagus and suggests that gastroesophageal acid reflux may contribute to the cause of hiatus hernia.