bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adverse events appear to unblind clinical trials in irritable bowel syndrome
Authors: Shah E. , Triantafyllou K. , Hana A. A. , Pimentel M. 
Published: December 2013

AbstractBackgroundClinical trial design is challenging in irritable bowel syndrome (IBS) due in part to a high placebo effect. We postulated that the mere presence of an adverse event (AE) may unmask patients in clinical trials who are assigned to the active agent, and this may lead to higher reported efficacy.MethodsWe evaluated therapies receiving at least a Grade 1B from the American College of Gastroenterology Task Force for IBS or which passed recent phase III clinical trials. Therapies with AE data derived from less than 50 patients in each study arm were excluded. Statistically significant excess AE were identified, risk difference was calculated for each AE, and incidence of AE in the treatment arm was reported. We examined the relationship of attributable drug benefit, defined as the reciprocal of number‐needed‐to‐treat found in literature, with various measures of AE incidence.Key ResultsAttributable drug benefit correlated significantly with average AE risk difference, calculated as treatment arm AE incidence minus placebo arm AE incidence (R2 = 0.70, p = 0.039), and also with highest treatment arm AE incidence (R2 = 0.70, p = 0.038) for each therapy. There were also trends toward correlation with average treatment arm AE incidence (R2 = 0.54, p = 0.096) and highest AE risk difference (R2 = 0.63, p = 0.059) for each therapy.Conclusions & InferencesOur study suggests that higher AE incidence on active therapy is associated with more beneficial patient‐reported outcomes in IBS clinical trials. This raises the issue of spontaneous unblinding.
Next‐generation sequencing can reveal in vitro‐generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database
Authors: Holcomb C. L. , Rastrou M. , Williams T. C. , Goodridge D. , Lazaro A. M. , Tilanus M. , Erlich H. A. 
Published: December 2013

AbstractThe high‐resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR ‘crossing over’ between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%–10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence.
The Seventh Pandemic Vibrio cholerae O1 El Tor Isolate in China Has Undergone Genetic Shifts
Authors: Zhang Ping , Li Fengjuan , Liang Weili , Li Jie , Kan Biao , Wang Duochun 
Published: December 2013

ABSTRACT

A total of 330 clinical
Vibrio cholerae
O1 serogroups from China dating between 1961 and 2010 were investigated. By phenotypic biotyping and genetic analysis, during the seventh pandemic of
V. cholerae
O1 in China, the isolates of hybrid biotype (mixed classical phenotypes) were present during the entire1961-2010 period, while El Tor genetic shifts appeared in 1992 and replaced the prototype El Tor from 2002 to 2010.
Interaction of Foot-and-Mouth Disease Virus Nonstructural Protein 3A with Host Protein DCTN3 Is Important for Viral Virulence in Cattle
Authors: Gladue D. P. , O'Donnell V. , Baker-Bransetter R. , Pacheco J. M. , Holinka L. G. , Arzt J. , Pauszek S. , Fernandez-Sainz I. , Fletcher P. , Brocchi E. , Lu Z. , Rodriguez L. L. , Borca M. V. 
Published: December 2013

ABSTRACT
Nonstructural protein 3A of foot-and-mouth disease virus (FMDV) is a partially conserved protein of 153 amino acids in most FMDVs examined to date. The role of 3A in virus growth and virulence within the natural host is not well understood. Using a yeast two-hybrid approach, we identified cellular protein DCTN3 as a specific host binding partner for 3A. DCTN3 is a subunit of the dynactin complex, a cofactor for dynein, a motor protein. The dynactin-dynein duplex has been implicated in several subcellular functions involving intracellular organelle transport. The 3A-DCTN3 interaction identified by the yeast two-hybrid approach was further confirmed in mammalian cells. Overexpression of DCTN3 or proteins known to disrupt dynein, p150/Glued and 50/dynamitin, resulted in decreased FMDV replication in infected cells. We mapped the critical amino acid residues in the 3A protein that mediate the protein interaction with DCTN3 by mutational analysis and, based on that information, we developed a mutant harboring the same mutations in O1 Campos FMDV (O1C3A-PLDGv). Although O1C3A-PLDGv FMDV and its parental virus (O1Cv) grew equally well in LFBK-αvβ6, O1C3A-PLDGv virus exhibited a decreased ability to replicate in primary bovine cell cultures. Importantly, O1C3A-PLDGv virus exhibited a delayed disease in cattle compared to the virulent parental O1Campus (O1Cv). Virus isolated from lesions of animals inoculated with O1C3A-PLDGv virus contained amino acid substitutions in the area of 3A mediating binding to DCTN3. Importantly, 3A protein harboring similar amino acid substitutions regained interaction with DCTN3, supporting the hypothesis that DCTN3 interaction likely contributes to virulence in cattle.

IMPORTANCE
The objective of this study was to understand the possible role of a FMD virus protein 3A, in causing disease in cattle. We have found that the cellular protein, DCTN3, is a specific binding partner for 3A. It was shown that manipulation of DCTN3 has a profound effect in virus replication. We developed a FMDV mutant virus that could not bind DCTN3. This mutant virus exhibited a delayed disease in cattle compared to the parental strain highlighting the role of the 3A-DCTN3 interaction in virulence in cattle. Interestingly, virus isolated from lesions of animals inoculated with mutant virus contained mutations in the area of 3A that allowed binding to DCTN3. This highlights the importance of the 3A-DCTN3 interaction in FMD virus virulence and provides possible mechanisms of virus attenuation for the development of improved FMD vaccines.
Mechanism of Neutralization of Herpes Simplex Virus by Antibodies Directed at the Fusion Domain of Glycoprotein B
Authors: Cairns Tina M. , Fontana Juan , Huang Zhen-Yu , Whitbeck J. Charles , Atanasiu Doina , Rao Samhita , Shelly Spencer S. , Lou Huan , Ponce de Leon Manuel , Steven Alasdair C. , Eisenberg Roselyn J. , Cohen Gary H. 
Published: December 2013

ABSTRACTGlycoprotein B (gB), the fusogen of herpes simplex virus (HSV), is a class III fusion protein with a trimeric ectodomain of known structure for the postfusion state. Seen by negative-staining electron microscopy, it presents as a rod with three lobes (base, middle, and crown). gB has four functional regions (FR), defined by the physical location of epitopes recognized by anti-gB neutralizing monoclonal antibodies (MAbs). Located in the base, FR1 contains two internal fusion loops (FLs) and is the site of gB-lipid interaction (the fusion domain). Many of the MAbs to FR1 are neutralizing, block cell-cell fusion, and prevent the association of gB with lipid, suggesting that these MAbs affect FL function. Here we characterize FR1 epitopes by using electron microscopy to visualize purified Fab-gB ectodomain complexes, thus confirming the locations of several epitopes and localizing those of MAbs DL16 and SS63. We also generated MAb-resistant viruses in order to localize the SS55 epitope precisely. Because none of the epitopes of our anti-FR1 MAbs mapped to the FLs, we hyperimmunized rabbits with FL1 or FL2 peptides to generate polyclonal antibodies (PAbs). While the anti-FL1 PAb failed to bind gB, the anti-FL2 PAb had neutralizing activity, implying that the FLs become exposed during virus entry. Unexpectedly, the anti-FL2 PAb (and the anti-FR1 MAbs) bound to liposome-associated gB, suggesting that their epitopes are accessible even when the FLs engage lipid. These studies provide possible mechanisms of action for HSV neutralization and insight into how gB FR1 contributes to viral fusion.IMPORTANCEFor herpesviruses, such as HSV, entry into a target cell involves transfer of the capsid-encased genome of the virus to the target cell after fusion of the lipid envelope of the virus with a lipid membrane of the host. Virus-encoded glycoproteins in the envelope are responsible for fusion. Antibodies to these glycoproteins are important biological tools, providing a way of examining how fusion works. Here we used electron microscopy and other techniques to study a panel of anti-gB antibodies. Some, with virus-neutralizing activity, impair gB-lipid association. We also generated a peptide antibody against one of the gB fusion loops; its properties provide insight into the way the fusion loops function as gB transits from its prefusion form to an active fusogen.
Epigenetic Regulation of HIV-1 Latency in Astrocytes
Authors: Narasipura Srinivas D. , Kim Stephanie , Al-Harthi Lena 
Published: December 2013

ABSTRACT
HIV infiltrates the brain at early times postinfection and remains latent within astrocytes and macrophages. Because astrocytes are the most abundant cell type in the brain, we evaluated epigenetic regulation of HIV latency in astrocytes. We have shown that class I histone deacetylases (HDACs) and a lysine-specific histone methyltransferase, SU(VAR)3-9, play a significant role in silencing of HIV transcription in astrocytes. Our studies add to a growing body of evidence demonstrating that astrocytes are a reservoir for HIV.
Analysis of T Cell Responses during Active Varicella-Zoster Virus Reactivation in Human Ganglia
Authors: Steain Megan , Sutherland Jeremy P. , Rodriguez Michael , Cunningham Anthony L. , Slobedman Barry , Abendroth Allison 
Published: December 2013

ABSTRACT

Varicella-zoster virus (VZV) is responsible for both varicella (chickenpox) and herpes zoster (shingles). During varicella, the virus establishes latency within the sensory ganglia and can reactivate to cause herpes zoster, but the immune responses that occur in ganglia during herpes zoster have not previously been defined. We examined ganglia obtained from individuals who, at the time of death, had active herpes zoster. Ganglia innervating the site of the cutaneous herpes zoster rash showed evidence of necrosis, secondary to vasculitis, or localized hemorrhage. Despite this, there was limited evidence of VZV antigen expression, although a large inflammatory infiltrate was observed. Characterization of the infiltrating T cells showed a large number of infiltrating CD4
+
T cells and cytolytic CD8
+
T cells. Many of the infiltrating T cells were closely associated with neurons within the reactivated ganglia, yet there was little evidence of T cell-induced neuronal apoptosis. Notably, an upregulation in the expression of major histocompatibility complex class I (MHC-I) and MHC-II molecules was observed on satellite glial cells, implying these cells play an active role in directing the immune response during herpes zoster. This is the first detailed characterization of the interaction between T cells and neuronal cells within ganglia obtained from patients suffering herpes zoster at the time of death and provides evidence that CD4
+
and cytolytic CD8
+
T cell responses play an important role in controlling VZV replication in ganglia during active herpes zoster.

IMPORTANCE
VZV is responsible for both varicella (chickenpox) and herpes zoster (shingles). During varicella, the virus establishes a life-long dormant infection within the sensory ganglia and can reawaken to cause herpes zoster, but the immune responses that occur in ganglia during herpes zoster have not previously been defined. We examined ganglia obtained from individuals who, at the time of death, had active herpes zoster. We found that specific T cell subsets are likely to play an important role in controlling VZV replication in ganglia during active herpes zoster.
Poor adherence of randomised trials in surgery to CONSORT guidelines for non-pharmacological treatments (NPT): a cross-sectional study
Authors: Nagendran Myura , Harding Daniel , Teo Wendy , Camm Christian , Maruthappu Mahiben , McCulloch Peter , Hopewell Sally 
Published: December 2013

ObjectiveTo systematically assess adherence of randomised trials in surgery to Consolidated Standards of Reporting Trials (CONSORT) guidelines for non-pharmacological treatments (NPT). Surgical trials are considered more difficult to design and execute than pharmacological trials. Furthermore, the original CONSORT statement does not address some aspects that are vital to the transparent reporting of surgical trials. The CONSORT-NPT extension was designed to address these issues but adherence in medical and surgical journals has not been assessed.DesignCross-sectional study.SampleWe identified eight general medical and eight surgical journals, indexed in PubMed and published in 2011, with the highest impact factors in their respective categories.Main outcomesAdherence to CONSORT statement and CONSORT-NPT extension items.ResultsWe identified 54 surgical trials (22 published in medical journals and 32 in surgical journals). There were eight items for which there was less than 30% overall compliance (seven were specific to the CONSORT-NPT extension). These seven items are related to: a full description of the care providers, centres and blinding status in the abstract (n=7/54, 13%), eligibility criteria for centres performing the interventions (n=13/54, 24%), how adherence of care providers with the protocol was assessed or enhanced (n=7/54, 13%), how clustering by care providers or centres was addressed as it relates to sample size (n=3/54, 6%), how care providers were allocated to each group (n=9/54, 17%), how clustering by care providers or centres was addressed as it relates to statistical methods (n=2/54, 4%), a description of care providers (case volume, qualification, expertise, etc) and centres (volume) in each group (n=0/54, 0%).ConclusionsAdherence of surgical trials to CONSORT-NPT extension items is much poorer than to the standard CONSORT statement. Adherence also appears to be superior in general medical journals compared with surgical journals. Raising awareness and conducting qualitative research to identify areas for specific intervention will be important going forward.
Rationale and design of the PRognostic Importance of MIcrovascular Dysfunction in asymptomatic patients with Aortic Stenosis (PRIMID-AS): a multicentre observational study with blinded investigations
Authors: Singh Anvesha , Ford Ian , Greenwood John P , Khan Jamal N , Uddin Akhlaque , Berry Colin , Neubauer Stefan , Prendergast Bernard , Jerosch-Herold Michael , Williams Bryan , Samani Nilesh J , McCann Gerry P 
Published: December 2013

IntroductionAortic stenosis (AS) is the commonest valve disorder in the developed world requiring surgery. Surgery in patients with severe asymptomatic AS remains controversial. Exercise testing can identify asymptomatic patients at increased risk of death and symptom development, but with limited specificity, especially in older adults. Cardiac MRI (CMR), including myocardial perfusion reserve (MPR) may be a novel imaging biomarker in AS.Aims(1) To improve risk stratification in asymptomatic patients with AS and (2) to determine whether MPR is a better predictor of outcome than exercise testing and brain natriuretic peptide (BNP).Method/designMulticentre, prospective observational study in the UK, comparing MPR with exercise testing and BNP (with blinded CMR analysis) for predicting outcome.Population170 asymptomatic patients with moderate-to-severe AS, who would be considered for aortic valve replacement (AVR).Primary outcomeComposite of: typical symptoms necessitating referral for AVR and major adverse cardiovascular events. Follow-up: 12–30 months (minimum 12 months).Primary hypothesisMPR will be a better predictor of outcome than exercise testing and BNP.Ethics/disseminationThe study has full ethical approval and is actively recruiting patients. Data collection will be completed in November 2014 and the study results will be submitted for publication within 6 months of completion.ClinicalTrials.gov identifierNCT01658345.
Correlation of AOL recanalization, TIMI reperfusion and TICI reperfusion with infarct growth and clinical outcome
Authors: Marks Michael P , Lansberg Maarten G , Mlynash Michael , Kemp Stephanie , McTaggart Ryan , Zaharchuk Greg , Bammer Roland , Albers Gregory W 
Published: December 2013

ObjectiveTo understand how three commonly used measures of endovascular therapy correlate with clinical outcome and infarct growth.MethodsProspectively enrolled patients underwent baseline MRI and started endovascular therapy within 12 h of stroke onset. The final angiogram was given a primary arterial occlusive lesion (AOL) recanalization score (0–3), a Thrombolysis in Myocardial Infarction (TIMI) score (0–3) and a Thrombolysis in Cerebral Infarction (TICI) score (0–3). The scores were dichotomized into poor revascularization (AOL 0–2, TIMI 0–1 and TICI 0–2a) versus good revascularization (AOL 3, TIMI 2–3, TICI 2b–3). Patients were classified according to whether or not they had target mismatch (TMM). Good outcome was defined as a 90-day modified Rankin Scale score of 0–2.ResultsEndovascular treatment was attempted in 100. A good outcome was achieved in 57% of patients with a TICI score of 2b–3 and in 24% of patients with a TICI score of 0–2a (p=0.001). Patients with TIMI scores of 2–3 and an AOL score of 3 had lower rates of good outcome (44% and 47%, respectively), which were not significantly better than those with TIMI scores of 0–1 or AOL scores of 0–2. In patients with TMM, these rates of good outcome improved with all the scoring systems and were significantly better for TIMI and TICI scores. Patients with a TICI score of 2a had rates of good functional outcome and lesion growth which were not different from those with TICI scores of 0–1 but were significantly worse than those with TICI scores of 2b–3.ConclusionsTIMI 2–3 and TICI 2b–3 reperfusion scores demonstrated improved outcome in patients with tissue mismatch with a small infarct core and a larger hypoperfused region but AOL scores did not. Patients with a TICI score of 2a had a poorer outcome and more lesion growth than those with TICI scores of 2b–3.
The Final Stage of Gravitationally Collapsed Thick Matter Layers
Authors: Nicolini Piero , Orlandi Alessio , Spallucci Euro 
Published: December 2013

In the presence of aminimal length, physical objects cannot collapse to an infinite density, singular, matter point. In this paper, we consider the possible final stage of the gravitational collapse of “thick” matter layers. The energy momentum tensor we choose to model these shell-like objects is a proper modification of the source for “noncommutative geometry inspired,” regular black holes. By using higher momenta of Gaussian distribution to localize matter at finite distance from the origin, we obtain new solutions of the Einstein equation which smoothly interpolates between Minkowski’s geometry near the center of the shell and Schwarzschild’s spacetime far away from the matter layer. The metric is curvature singularity free. Black hole type solutions exist only for “heavy” shells; that is,M ≥Me, whereMeis the mass of the extremal configuration. We determine the Hawking temperature and a modified area law taking into account the extended nature of the source.
SIRT1 Limits the Function and Fate of Myeloid-Derived Suppressor Cells in Tumors by Orchestrating HIF-1α–Dependent Glycolysis
Authors: Liu Guangwei , Bi Yujing , Shen Bo , Yang Hui , Zhang Yan , Wang Xiao , Liu Huanrong , Lu Yun , Liao Jiongbo , Chen Xi , Chu Yiwei 
Published: December 2013

Abstract
Myeloid-derived suppressor cells (MDSC) display an immature phenotype that may assume a classically activated (M1) or alternatively activated phenotype (M2) in tumors. In this study, we investigated metabolic mechanisms underlying the differentiation of MDSCs into M1 or M2 myeloid lineage and their effect on cancer pathophysiology. We found that SIRT1 deficiency in MDSCs directs a specific switch to M1 lineage when cells enter the periphery from bone marrow, decreasing the suppressive function in favor of a proinflammatory M1 phenotype associated with tumor cell attack. Glycolytic activation through the mTOR–hypoxia-inducible factor-1α (HIF-1α) pathway was required for differentiation to the M1 phenotype, which conferred protection against tumors. Our results define the essential nature of a SIRT1–mTOR/HIF-1α glycolytic pathway in determining MDSC differentiation, with implications for metabolic reprogramming as a cancer therapeutic approach. Cancer Res; 74(3); 727–37. ©2013 AACR.
Genetic Profiling to Determine Risk of Relapse-Free Survival in High-Risk Localized Prostate Cancer
Authors: Barnett Christine M. , Heinrich Michael C. , Lim Jeong , Nelson Dylan , Beadling Carol , Warrick Andrea , Neff Tanaya , Higano Celestia S. , Garzotto Mark , Qian David , Corless Christopher L. , Thomas George V. , Beer Tomasz M. 
Published: December 2013

Abstract
Purpose: The characterization of actionable mutations in human tumors is a prerequisite for the development of individualized, targeted therapy. We examined the prevalence of potentially therapeutically actionable mutations in patients with high-risk clinically localized prostate cancer.
Experimental Design: Forty-eight samples of formalin-fixed paraffin-embedded prostatectomy tissue from a neoadjuvant chemotherapy trial were analyzed. DNA extracted from microdissected tumor was analyzed for 643 common solid tumor mutations in 53 genes using mass spectroscopy–based sequencing. In addition, PTEN loss and erythroblast transformation-specific–related gene (ERC) translocations were examined using immunohistochemistry (IHC) in associated tissue microarrays. Association with relapse during 5 years of follow-up was examined in exploratory analyses of the potential clinical relevance of the genetic alterations.
Results: Of the 40 tumors evaluable for mutations, 10% had point mutations in potentially actionable cancer genes. Of the 47 tumors evaluable for IHC, 36% had PTEN loss and 40% had ERG rearrangement. Individual mutations were not frequent enough to determine associations with relapse. Using Kaplan–Meier analysis with a log-rank test, the 16 patients who had PTEN loss had a significantly shorter median relapse-free survival, 19 versus 106 months (P = 0.01).
Conclusions: This study confirms that point mutations in the most common cancer regulatory genes in prostate cancer are rare. However, the PIK3CA/AKT pathway was mutated in 10% of our samples. Although point mutations alone did not have a statistically significant association with relapse, PTEN loss was associated with an increased relapse in high-risk prostate cancer treated with chemotherapy followed by surgery. Clin Cancer Res; 20(5); 1306–12. ©2013 AACR.