bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Cocirculating Varicella-Zoster Virus Genotypes during a Chickenpox Outbreak in Guinea-Bissau
Authors: Depledge Daniel P. , Gray Eleanor R. , Kundu Samit , Cooray Samantha , Poulsen Anja , Aaby Peter , Breuer Judith 
Published: October 2014

ABSTRACT
Varicella-zoster virus (VZV), a double-stranded DNA alphaherpesvirus, is associated with seasonal outbreaks of varicella in nonimmunized populations. Little is known about whether these outbreaks are associated with a single or multiple viral genotypes and whether new mutations rapidly accumulate during transmission. Here, we take advantage of a well-characterized population cohort in Guinea-Bissau and produce a unique set of 23 full-length genome sequences, collected over 7 months from eight households. Comparative sequence analysis reveals that four distinct genotypes cocirculated among the population, three of which were present during the first week of the outbreak, although no patients were coinfected, which indicates that exposure to infectious virus from multiple sources is common during VZV outbreaks. Transmission of VZV was associated with length polymorphisms in the R1 repeat region and the origin of DNA replication. In two cases, these were associated with the formation of distinct lineages and point to the possible coevolution of these loci, despite the lack of any known functional link in VZV or related herpesviruses. We show that these and all other sequenced clade 5 viruses possess a distinct R1 repeat motif that increases the acidity of an ORF11p protein domain and postulate that this has either arisen or been lost following divergence of the major clades. Thus, sequencing of whole VZV genomes collected during an outbreak has provided novel insights into VZV biology, transmission patterns, and (recent) natural history.

IMPORTANCE
VZV is a highly infectious virus and the causative agent of chickenpox and shingles, the latter being particularly associated with the risk of painful complications. Seasonal outbreaks of chickenpox are very common among young children, yet little is known about the dynamics of the virus during person-to-person to transmission or whether multiple distinct viruses seed and/or cocirculate during an outbreak. In this study, we have sequenced chickenpox viruses from an outbreak in Guinea-Bissau that are supported by detailed epidemiological data. Our data show that multiple different virus strains seeded and were maintained throughout the 6-month outbreak period and that viruses transmitted between individuals accumulated new mutations in specific genomic regions. Of particular interest is the potential coevolution of two distinct parts of the genomes and our calculations of the rate of viral mutation, both of which increase our understanding of how VZV evolves over short periods of time in human populations.
Differential Contribution of Adeno-Associated Virus Type 2 Rep Protein Expression and Nucleic Acid Elements to Inhibition of Adenoviral Replication in
cis
and in
trans
Authors: Weger Stefan , Hammer Eva , Heilbronn Regine 
Published: October 2014

ABSTRACT

The helper-dependent adeno-associated virus type 2 (AAV-2) exhibits complex interactions with its helper adenovirus. Whereas AAV-2 is dependent on adenoviral functions for productive replication, it conversely inhibits adenoviral replication, both when its genome is present in
trans
after coinfection with both viruses and when it is present in
cis
, as in the production of recombinant adenovirus (rAd)/AAV-2 hybrid vectors. The notion that AAV-mediated inhibition of adenoviral replication is due predominantly to the expression of the AAV-2 Rep proteins was recently challenged by successful Rep78 expression in a rAd5 vector through recoding of the Rep open reading frame (ORF). We closely analyzed the relative contributions of AAV-2 nucleic acid elements and Rep protein expression to the inhibition of adenoviral replication in both of the above scenarios. When present in
cis
, a sequence element in the 3′ part of the
rep
gene, comprising only the AAV-2 p40 promoter and the AAV-2 intron sequence, which we termed the RIS-Ad, completely blocks adenoviral replication. p5/p19 promoter-driven Rep protein expression, on the other hand, only weakly inhibits rAd/AAV-2 vector propagation, and by inactivation of the RIS-Ad, it is feasible to generate first-generation rAd vectors expressing functional Rep proteins. The RIS-Ad plays no role in the inhibition of adenoviral replication in
trans
in a model closely mimicking AAV-2–Ad coinfection. In this case, expression of the Rep proteins is required, as well as the presence of an amplifiable inverted terminal repeat (ITR)-containing template. Thus, very different AAV-2 elements and mechanisms are involved in inhibition of adenoviral replication during rAd/AAV-2 vector propagation and after Ad-AAV coinfection.

IMPORTANCE
This is the first study to systematically compare the contributions of AAV-2 protein expression and AAV-2 nucleic acid elements to the inhibition of adenoviral replication in rAd/AAV-2 hybrid vector generation and in AAV-2–adenovirus coinfection. This study shows that the two inhibitory processes are very different with regard to AAV-2 functions and the mechanisms involved. Whereas inhibition of rAd/AAV-2 hybrid vector propagation mostly involves a 3′ nucleic acid element in the
rep
gene, inhibition of an adenoviral genome in
trans
requires the Rep proteins and the AAV ITRs. These findings have important implications both for a basic understanding of the AAV replication cycle and for generation of rAd/AAV-2 hybrid vectors expressing the nonstructural and structural proteins of AAV-2.
Linking Pig-Tailed Macaque Major Histocompatibility Complex Class I Haplotypes and Cytotoxic T Lymphocyte Escape Mutations in Simian Immunodeficiency Virus Infection
Authors: Gooneratne Shayarana L. , Alinejad-Rokny Hamid , Ebrahimi Diako , Bohn Patrick S. , Wiseman Roger W. , O'Connor David H. , Davenport Miles P. , Kent Stephen J. 
Published: October 2014

ABSTRACTThe influence of major histocompatibility complex class I (MHC-I) alleles on human immunodeficiency virus (HIV) diversity in humans has been well characterized at the population level. MHC-I alleles likely affect viral diversity in the simian immunodeficiency virus (SIV)-infected pig-tailed macaque (Macaca nemestrina) model, but this is poorly characterized. We studied the evolution of SIV in pig-tailed macaques with a range of MHC-I haplotypes. SIVmac251genomes were amplified from the plasma of 44 pig-tailed macaques infected with SIVmac251at 4 to 10 months after infection and characterized by Illumina deep sequencing. MHC-I typing was performed on cellular RNA using Roche/454 pyrosequencing. MHC-I haplotypes and viral sequence polymorphisms at both individual mutations and groups of mutations spanning 10-amino-acid segments were linked using in-house bioinformatics pipelines, since cytotoxic T lymphocyte (CTL) escape can occur at different amino acids within the same epitope in different animals. The approach successfully identified 6 known CTL escape mutations within 3 Mane-A1*084-restricted epitopes. The approach also identified over 70 new SIV polymorphisms linked to a variety of MHC-I haplotypes. Using functional CD8 T cell assays, we confirmed that one of these associations, a Mane-B028 haplotype-linked mutation in Nef, corresponded to a CTL epitope. We also identified mutations associated with the Mane-B017 haplotype that were previously described to be CTL epitopes restricted by Mamu-B*017:01 in rhesus macaques. This detailed study of pig-tailed macaque MHC-I genetics and SIV polymorphisms will enable a refined level of analysis for future vaccine design and strategies for treatment of HIV infection.IMPORTANCECytotoxic T lymphocytes select for virus escape mutants of HIV and SIV, and this limits the effectiveness of vaccines and immunotherapies against these viruses. Patterns of immune escape variants are similar in HIV type 1-infected human subjects that share the same MHC-I genes, but this has not been studied for SIV infection of macaques. By studying SIV sequence diversity in 44 MHC-typed SIV-infected pigtail macaques, we defined over 70 sites within SIV where mutations were common in macaques sharing particular MHC-I genes. Further, pigtail macaques sharing nearly identical MHC-I genes with rhesus macaques responded to the same CTL epitope and forced immune escape. This allows many reagents developed to study rhesus macaques to also be used to study pigtail macaques. Overall, our study defines sites of immune escape in SIV in pigtailed macaques, and this enables a more refined level of analysis of future vaccine design and strategies for treatment of HIV infection.
Role of the Short Telomeric Repeat Region in Marek's Disease Virus Replication, Genomic Integration, and Lymphomagenesis
Authors: Greco Annachiara , Fester Nadine , Engel Annemarie T. , Kaufer Benedikt B. 
Published: October 2014

ABSTRACT

Marek's disease virus (MDV) is a cell-associated alphaherpesvirus that causes generalized polyneuritis and T-cell lymphomas in chickens. MDV is able to integrate its genome into host telomeres, but the mechanism of integration is poorly understood. The MDV genome harbors two arrays of telomeric repeats (TMR) at the ends of its linear genome: multiple telomeric repeats (mTMR), with a variable number of up to 100 repeats, and short telomeric repeats (sTMR), with a fixed number of 6 repeats. The mTMR have recently been shown to play an important role in MDV integration and tumor formation; however, the functions of the sTMR have remained unknown. In this study, we demonstrate that deletion of the sTMR in the MDV genome abrogates virus replication, while extensive mutation of the sTMR does not, indicating that the presence of the sTMR but not the sTMR sequence itself is important. Furthermore, we generated a panel of truncation mutants to determine the minimal length of the sTMR and observed a direct correlation between sTMR length and MDV replication. To address the role of sTMR in MDV replication, integration, and tumorigenesis, sTMR sequences were replaced by a scrambled repeated sequence (vsTMR_mut). vsTMR_mut replicated comparably to parental and revertant viruses
in vitro. In vivo
, however, a significant reduction in disease and tumor incidence was observed in chickens infected with vsTMR_mut that also correlated with a reduced number of viral integration sites in tumor cells. Taken together, our data demonstrate that the sTMR play a central role in MDV genome replication, pathogenesis, and MDV-induced tumor formation.

IMPORTANCE
Marek's disease virus (MDV) is a highly oncogenic alphaherpesvirus that infects chickens and causes high economic losses in the poultry industry. MDV integrates its genetic material into host telomeres, a process that is crucial for efficient tumor formation. The MDV genome harbors two arrays of telomeric repeats (TMR) at the ends of its linear genome that are identical to host telomeres and that are termed mTMR and sTMR. mTMR have been recently shown to be involved in MDV integration, while the functions of sTMR remain unknown. Here, we demonstrate that the presence and length of sTMR sequence, but not the exact nucleotide sequence, are crucial for MDV replication. Furthermore, the sTMR contribute to the high integration frequency of MDV and are important for MDV pathogenesis and tumor formation. As a number of herpesviruses harbor arrays of telomeric repeats (TMR), MDV serves as a model to determine the role of the herpesvirus TMR in replication, integration, and pathogenesis.
Prevalence, nature and predictors of prescribing errors in mental health hospitals: a prospective multicentre study
Authors: Keers Richard N , Williams Steven D , Vattakatuchery Joe J , Brown Petra , Miller Joan , Prescott Lorraine , Ashcroft Darren M 
Published: October 2014

ObjectiveTo determine the prevalence, nature and predictors of prescribing errors (PEs) in three mental health hospitals.SettingInpatient units in three National Health Service (NHS) mental health hospitals in the North West of England.ParticipantsTrained clinical pharmacists prospectively recorded the number of PEs in newly written or omitted prescription items screened during their routine work on 10 data collection days. A multidisciplinary panel reviewed PE data using established methods to confirm (1) the presence of a PE, (2) the type of PE and (3) whether errors were clinically relevant and likely to cause harm.Primary outcome measuresFrequency, nature and predictors of PEs.ResultsOf 4427 screened prescription items, 281 were found to have one or more PEs (error rate 6.3% (95% CI 5.6 to 7.1%)). Multivariate analysis revealed that specialty trainees (OR 1.23 (1.01 to 1.51)) and staff grade psychiatrists (OR 1.50 (1.05 to 2.13)) were more likely to make PEs when compared to foundation year (FY) one doctors, and that specialty trainees and consultant psychiatrists were twice as likely to make clinically relevant PEs (OR 2.61 (2.11 to 3.22) and 2.03 (1.66 to 2.50), respectively) compared to FY one staff. Prescription items screened during the prescription chart rewrite (OR 0.52 (0.33 to 0.82)) or at discharge (OR 0.87 (0.79 to 0.97)) were less likely to be associated with PEs than items assessed during inpatient stay, although they were more likely to be associated with clinically relevant PEs (OR 2.27 (1.72 to 2.99) and 4.23 (3.68 to 4.87), respectively). Prescription items screened at hospital admission were five times more likely (OR 5.39 (2.72 to 10.69)) to be associated with clinically relevant errors than those screened during patient stay.ConclusionsPEs may be more common in mental health hospitals than previously reported and important targets to minimise these errors have been identified.
Starting early: integration of self-management support into an acute stroke service
Authors: Mäkelä Petra , Gawned Sara , Jones Fiona 
Published: October 2014

AbstractSelf-management support following stroke is rare, despite emerging evidence for impact on patient outcomes. The promotion of a common approach to self-management support across a stroke pathway requires collaboration between professionals. To date, the feasibility of self-management support in acute stroke settings has not been evaluated.The Bridges stroke self-management package (SMP) is based on self-efficacy principles. It is delivered by professionals and supported by a patient-held workbook. The aim of this project was to introduce the Bridges stroke SMP to the multidisciplinary staff of a London hyperacute and acute stroke unit.The ‘Plan Do Study Act’ (PDSA) cycle guided iterative stages of project development, with normalisation process theory helping to embed the intervention into existing ways of working. Questionnaires explored attitudes, beliefs and experiences of the staff who were integrating self-management support into ways of working in the acute stroke setting.Self-management support training was delivered to a total of 46 multidisciplinary stroke staff. Of the staff who attended the follow-up training, 66% had implemented Bridges self-management support with patients since initial training, and 100% felt their practice had changed. Questionnaire findings demonstrated that staff attitudes and beliefs had changed following training, particularly regarding ownership and type of rehabilitation goals set, and prioritisation of self-management support within acute stroke care.Staff initiated an audit of washing and dressing practices pre- and post-training. This was designed to evaluate the number of occasions when techniques were used by staff to facilitate patients’ independence and self-management. They found that the number of occasions featuring optimum practice went from 54% at baseline to 63% at three months post-training.This project demonstrated the feasibility of integrating self-management support into an acute stroke setting. Further work is required to evaluate sustainability of the Bridges stroke SMP, to understand the barriers and opportunities involved in engaging all professional groups in integrated self-management support in acute stroke settings, and to assess patient reported outcomes.
TGFβ Receptor 1: An Immune Susceptibility Gene in HPV-Associated Cancer
Authors: Levovitz Chaya , Chen Dan , Ivansson Emma , Gyllensten Ulf , Finnigan John P. , Alshawish Sara , Zhang Weijia , Schadt Eric E. , Posner Marshal R. , Genden Eric M. , Boffetta Paolo , Sikora Andrew G. 
Published: October 2014

Abstract
Only a minority of those exposed to human papillomavirus (HPV) develop HPV-related cervical and oropharyngeal cancer. Because host immunity affects infection and progression to cancer, we tested the hypothesis that genetic variation in immune-related genes is a determinant of susceptibility to oropharyngeal cancer and other HPV-associated cancers by performing a multitier integrative computational analysis with oropharyngeal cancer data from a head and neck cancer genome-wide association study (GWAS). Independent analyses, including single-gene, gene-interconnectivity, protein–protein interaction, gene expression, and pathway analysis, identified immune genes and pathways significantly associated with oropharyngeal cancer. TGFβR1, which intersected all tiers of analysis and thus selected for validation, replicated significantly in the head and neck cancer GWAS limited to HPV-seropositive cases and an independent cervical cancer GWAS. The TGFβR1 containing p38–MAPK pathway was significantly associated with oropharyngeal cancer and cervical cancer, and TGFβR1 was overexpressed in oropharyngeal cancer, cervical cancer, and HPV+ head and neck cancer tumors. These concordant analyses implicate TGFβR1 signaling as a process dysregulated across HPV-related cancers. This study demonstrates that genetic variation in immune-related genes is associated with susceptibility to oropharyngeal cancer and implicates TGFβR1/TGFβ signaling in the development of both oropharyngeal cancer and cervical cancer. Better understanding of the immunogenetic basis of susceptibility to HPV-associated cancers may provide insight into host/virus interactions and immune processes dysregulated in the minority of HPV-exposed individuals who progress to cancer. Cancer Res; 74(23); 6833–44. ©2014 AACR.
Levosimendan exerts anti-inflammatory effects on cardiac myocytes and endothelial cells in vitro
Authors: Krychtiuk Konstantin A. , Watzke Lukas , Kaun Christoph , Buchberger Elisabeth , Hofer-Warbinek Renate , Demyanets Svitlana , Pisoni Julia , Kastl Stefan P. , Rauscher Sabine , Gröger Marion , Aliabadi Arezu , Zuckermann Andreas , Maurer Gerald , Martin Rainer de , Huber Kurt , Speidl Walter S. , Wojta Johann 
Published: October 2014

SummaryLevosimendan is a positive inotropic drug for the treatment of acute decompensated heart failure (HF). Clinical trials showed that levosimendan was particularly effective in HF due to myocardial infarction. Myocardial necrosis induces a strong inflammatory response, involving chemoattractants guiding polymorphonuclear neutrophils (PMN) into the infarcted myocardial tissue. Our aim was to examine whether levosimendan exhibits anti-inflammatory effects on human adult cardiac myocytes (HACM) and human heart microvascular endothelial cells (HHMEC). Cardiac myocytes and endothelial cells were stimulated with interleukin-1β (IL)-1β (200 U/ml) and treated with levosimendan (0.1–10 μM) for 2–48 hours. IL-1β strongly induced expression of IL-6 and IL-8 in HACM and E-selectin and intercellular adhesion molecule-1 (ICAM-1) in HHMEC and human umbilical vein endothelial cells (HUVEC). Treatment with levosimendan strongly attenuated IL-1β-induced expression of IL-6 and IL-8 in HACM as well as E-selectin and ICAM-1 in ECs. Levosimendan treatment further reduced adhesion of PMN to activated endothelial cells under both static and flow conditions by approximately 50 %. Incubation with 5-hydroxydecanoic acid, a selective blocker of mitochondrial ATP-dependent potassium channels, partly abolished the above seen anti-inflammatory effects. Additionally, levosimendan strongly diminished IL-1β-induced reactive oxygen species and nuclear factor-κB (NF-κB) activity through inhibition of S536 phosphorylation. In conclusion, levosimendan exhibits anti-inflammatory effects on cardiac myocytes and endothelial cells in vitro. These findings could explain, at least in part, the beneficial effects of levosimendan after myocardial infarction.
Longitudinal Assessment of Concurrent Changes in Left Ventricular Ejection Fraction and Left Ventricular Myocardial Tissue Characteristics After Administration of Cardiotoxic Chemotherapies Using T1-Weighted and T2-Weighted Cardiovascular Magnetic Resonance
Authors: Jordan Jennifer H. , D’Agostino Ralph B. , Hamilton Craig A. , Vasu Sujethra , Hall Michael E. , Kitzman Dalane W. , Thohan Vinay , Lawrence Julia A. , Ellis Leslie R. , Lash Timothy L. , Hundley W. Gregory 
Published: October 2014

Background—
In a murine anthracycline-related cardiotoxicity model, increases in cardiovascular magnetic resonance myocardial contrast-enhanced T1-weighted signal intensity are associated with myocellular injury and decreases with left ventricular ejection fraction. We sought to determine whether T1- and T2-weighted measures of signal intensity associate with decreases in left ventricular ejection fraction in human subjects receiving potentially cardiotoxic chemotherapy.

Methods and Results—

In 65 individuals with breast cancer (n=51) or a hematologic malignancy (n=14), we measured left ventricular volumes, ejection fraction, and contrast-enhanced T1-weighted and T2-weighted signal intensity before and 3 months after initiating potentially cardiotoxic chemotherapy using blinded, unpaired analysis of cardiovascular magnetic resonance images. Participants were aged 51±12 years, of whom 55% received an anthracycline, 38% received a monoclonal antibody, and 6% received an antimicrotubule agent. Overall, left ventricular ejection fraction decreased from 57±6% to 54±7% (
P
<0.001) because of an increase in end-systolic volume (
P
<0.05). T1-weighted signal intensities also increased from 14.1±5.1 to 15.9±6.8 (
P
<0.05), with baseline values trending higher among individuals who received chemotherapy before study enrollment (
P
=0.06). Changes in T1-weighted signal intensity did not differ within the 17 LV myocardial segments (
P
=0.97). Myocardial edema quantified from T2-weighted images did not change significantly after 3 months (
P
=0.70).

Conclusions—
Concordant with previous animal studies, cardiovascular magnetic resonance measures of contrast-enhanced T1-weighted signal intensity occur commensurate with small but significant left ventricular ejection fraction declines 3 months after the receipt of potentially cardiotoxic chemotherapy. These data indicate that changes in T1-weighted signal intensity may serve as an early marker of subclinical injury related to the administration of potentially cardiotoxic chemotherapy in human subjects.