bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetics of Epstein-Barr Virus (EBV) Neutralizing and Virus-Specific Antibodies after Primary Infection with EBV
Authors: Bu Wei , Hayes Gregory M. , Liu Hui , Gemmell Lorraine , Schmeling David O. , Radecki Pierce , Aguilar Fiona , Burbelo Peter D. , Woo Jennifer , Balfour Henry H. , Cohen Jeffrey I. 
Published: February 2016

ABSTRACT
Prospective studies of antibodies to multiple Epstein-Barr virus (EBV) proteins and EBV neutralizing antibodies in the same individuals before, during, and after primary EBV infection have not been reported. We studied antibody responses to EBV in college students who acquired primary EBV infection during prospective surveillance and correlated the kinetics of antibody response with the severity of disease. Neutralizing antibodies and enzyme-linked immunosorbent assay (ELISA) antibodies to gp350, the major target of neutralizing antibody, reached peak levels at medians of 179 and 333 days after the onset of symptoms of infectious mononucleosis, respectively. No clear correlation was found between the severity of the symptoms of infectious mononucleosis and the peak levels of antibody to individual viral proteins or to neutralizing antibody. In summary, we found that titers of neutralizing antibody and antibodies to multiple EBV proteins increase over many months after primary infection with EBV.
Comparison of the Copan eSwab System with an Agar Swab Transport System for Maintenance of Fastidious Anaerobic Bacterium Viability
Authors: Tyrrell Kerin L. , Citron Diane M. , Leoncio Eliza S. , Goldstein Ellie J. C. 
Published: February 2016

ABSTRACTWe compared the eSwab system to a swab with an anaerobic transport semisolid agar system for their capacities to maintain the viability of 20 species of fastidious anaerobes inoculated on the bench and held at ambient or refrigerator temperature for 24 or 48 h. On average, both systems maintained similar viabilities among analogous groups of organisms at both temperatures, although there were quantitative differences among some species.
Evaluation of the Check-Points Check MDR CT103 and CT103 XL Microarray Kits by Use of Preparatory Rapid Cell Lysis
Authors: Cunningham Scott A. , Vasoo Shawn , Patel Robin 
Published: February 2016

ABSTRACT
Using a rapid bacterial lysis method, the Check MDR CT103 and CT103 XL microarrays demonstrated accuracies of 98.1% and 94.2%, respectively, for detection of known resistance genes in 108 multidrug-resistant Gram-negative bacilli. In 45 isolates, 49 previously unrecognized extended-spectrum β-lactamase or plasmid AmpC targets were detected and confirmed by conventional PCR.
VP8, the Major Tegument Protein of Bovine Herpesvirus 1, Interacts with Cellular STAT1 and Inhibits Interferon Beta Signaling
Authors: Afroz Sharmin , Brownlie Robert , Fodje Michel , van Drunen Littel-van den Hurk Sylvia 
Published: February 2016

ABSTRACT

The

U
L
47

gene product, VP8, is the most abundant tegument protein of bovine herpesvirus 1 (BoHV-1). Previously, we demonstrated that a

U
L
47

-deleted BoHV-1 mutant (BoHV1-ΔU
L
47) exhibits 100-fold-reduced virulence
in vitro
and is avirulent
in vivo
. In this study, we demonstrated that VP8 expression or BoHV-1 infection inhibits interferon beta (IFN-β) signaling by using an IFN-α/β-responsive plasmid in a luciferase assay. As transducer and activator of transcription (STAT) is an essential component in the IFN-signaling pathways, the effect of VP8 on STAT was investigated. An interaction between VP8 and STAT1 was established by coimmunoprecipitation assays in both VP8-transfected and BoHV-1-infected cells. Two domains of VP8, amino acids 259 to 482 and 632 to 686, were found to be responsible for its interaction with STAT1. The expression of VP8 did not induce STAT1 ubiquitination or degradation. Moreover, VP8 did not reduce STAT1 tyrosine phosphorylation to downregulate IFN-β signaling. However, the expression of VP8 or a version of VP8 (amino acids 219 to 741) that contains the STAT1-interacting domains but not the nuclear localization signal prevented nuclear accumulation of STAT1. Inhibition of nuclear accumulation of STAT1 also occurred during BoHV-1 infection, while nuclear translocation of STAT1 was observed in BoHV1-ΔU
L
47-infected cells. During BoHV-1 infection, VP8 was detected in the cytoplasm at 2 h postinfection without any
de novo
protein synthesis, at which time STAT1 was already retained in the cytoplasm. These results suggest that viral VP8 downregulates IFN-β signaling early during infection, thus playing a role in overcoming the antiviral response of BoHV-1-infected cells.

IMPORTANCE
Since VP8 is the most abundant protein in BoHV-1 virions and thus may be released in large amounts into the host cell immediately upon infection, we proposed that it might have a function in the establishment of conditions suitable for viral replication. Indeed, while nonessential
in vitro
, it is critical for BoHV-1 replication
in vivo
. In this study, we determined that VP8 plays a role in downregulation of the antiviral host response by inhibiting IFN-β signaling. VP8 interacted with and prevented nuclear accumulation of STAT1 at 2 h postinfection in the absence of
de novo
viral protein synthesis. Two domains of VP8, amino acids 259 to 482 and 632 to 686, were found to be responsible for this interaction. These results provide a new functional role for VP8 in BoHV-1 infection and a potential explanation for the lack of viral replication of the

U
L
47

deletion mutant in cattle.
The Proteolytic Activation of (H3N2) Influenza A Virus Hemagglutinin Is Facilitated by Different Type II Transmembrane Serine Proteases
Authors: Kühn Nora , Bergmann Silke , Kösterke Nadine , Lambertz Ruth L. O. , Keppner Anna , van den Brand Judith M. A. , Pöhlmann Stefan , Weiß Siegfried , Hummler Edith , Hatesuer Bastian , Schughart Klaus 
Published: February 2016

ABSTRACT

Cleavage of influenza virus hemagglutinin (HA) by host cell proteases is necessary for viral activation and infectivity. In humans and mice, members of the type II transmembrane protease family (TTSP), e.g., TMPRSS2, TMPRSS4, and TMPRSS11d (HAT), have been shown to cleave influenza virus HA for viral activation and infectivity
in vitro
. Recently, we reported that inactivation of a single HA-activating protease gene,
Tmprss2
, in knockout mice inhibits the spread of H1N1 influenza viruses. However, after infection of
Tmprss2
knockout mice with an H3N2 influenza virus, only a slight increase in survival was observed, and mice still lost body weight. In this study, we investigated an additional trypsin-like protease, TMPRSS4. Both TMPRSS2 and TMPRSS4 are expressed in the same cell types of the mouse lung. Deletion of
Tmprss4
alone in knockout mice does not protect them from body weight loss and death upon infection with H3N2 influenza virus. In contrast,
Tmprss2
−/−
Tmprss4
−/−
double-knockout mice showed a remarkably reduced virus spread and lung pathology, in addition to reduced body weight loss and mortality. Thus, our results identified TMPRSS4 as a second host cell protease that, in addition to TMPRSS2, is able to activate the HA of H3N2 influenza virus
in vivo
.

IMPORTANCE
Influenza epidemics and recurring pandemics are responsible for significant global morbidity and mortality. Due to high variability of the virus genome, resistance to available antiviral drugs is frequently observed, and new targets for treatment of influenza are needed. Host cell factors essential for processing of the virus hemagglutinin represent very suitable drug targets because the virus is dependent on these host factors for replication. We reported previously that
Tmprss2
-deficient mice are protected against H1N1 virus infections, but only marginal protection against H3N2 virus infections was observed. Here we show that deletion of two host protease genes,
Tmprss2
and
Tmprss4
, strongly reduced viral spread as well as lung pathology and resulted in increased survival after H3N2 virus infection. Thus, TMPRSS4 represents another host cell factor that is involved in cleavage activation of H3N2 influenza viruses
in vivo
.
Linear Epitopes in Vaccinia Virus A27 Are Targets of Protective Antibodies Induced by Vaccination against Smallpox
Authors: Kaever Thomas , Matho Michael H. , Meng Xiangzhi , Crickard Lindsay , Schlossman Andrew , Xiang Yan , Crotty Shane , Peters Bjoern , Zajonc Dirk M. 
Published: February 2016

ABSTRACT
Vaccinia virus (VACV) A27 is a target for viral neutralization and part of the Dryvax smallpox vaccine. A27 is one of the three glycosaminoglycan (GAG) adhesion molecules and binds to heparan sulfate. To understand the function of anti-A27 antibodies, especially their protective capacity and their interaction with A27, we generated and subsequently characterized 7 murine monoclonal antibodies (MAbs), which fell into 4 distinct epitope groups (groups I to IV). The MAbs in three groups (groups I, III, and IV) bound to linear peptides, while the MAbs in group II bound only to VACV lysate and recombinant A27, suggesting that they recognized a conformational and discontinuous epitope. Only group I antibodies neutralized the mature virion in a complement-dependent manner and protected against VACV challenge, while a group II MAb partially protected against VACV challenge but did not neutralize the mature virion. The epitope for group I MAbs was mapped to a region adjacent to the GAG binding site, a finding which suggests that group I MAbs could potentially interfere with the cellular adhesion of A27. We further determined the crystal structure of the neutralizing group I MAb 1G6, as well as the nonneutralizing group IV MAb 8E3, bound to the corresponding linear epitope-containing peptides. Both the light and the heavy chains of the antibodies are important in binding to their antigens. For both antibodies, the L1 loop seems to dominate the overall polar interactions with the antigen, while for MAb 8E3, the light chain generally appears to make more contacts with the antigen.

IMPORTANCE
Vaccinia virus is a powerful model to study antibody responses upon vaccination, since its use as the smallpox vaccine led to the eradication of one of the world's greatest killers. The immunodominant antigens that elicit the protective antibodies are known, yet for many of these antigens, little information about their precise interaction with antibodies is available. In an attempt to better understand the interplay between the antibodies and their antigens, we generated and functionally characterized a panel of anti-A27 antibodies and studied their interaction with the epitope using X-ray crystallography. We identified one protective antibody that binds adjacent to the heparan sulfate binding site of A27, likely affecting ligand binding. Analysis of the antibody-antigen interaction supports a model in which antibodies that can interfere with the functional activity of the antigen are more likely to confer protection than those that bind at the extremities of the antigen.
Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies
Authors: Kaplan Gilad , Roitburd-Berman Anna , Lewis George K. , Gershoni Jonathan M. 
Published: February 2016

ABSTRACT

The HIV envelope binds cellular CD4 and undergoes a range of conformational changes that lead to membrane fusion and delivery of the viral nucleocapsid into the cellular cytoplasm. This binding to CD4 reveals cryptic and highly conserved epitopes, the molecular nature of which is still not fully understood. The atomic structures of CD4 complexed with gp120 core molecules (a form of gp120 in which the V1, V2, and V3 loops and N and C termini have been truncated) have indicated that a hallmark feature of the CD4-bound conformation is the bridging sheet minidomain. Variations in the orientation of the bridging sheet hairpins have been revealed when CD4-liganded gp120 was compared to CD4-unliganded trimeric envelope structures. Hence, there appears to be a number of conformational transitions possible in HIV-1 monomeric gp120 that are affected by CD4 binding. The spectrum of CD4-bound conformations has been interrogated in this study by using a well-characterized panel of conditional, CD4-induced (CD4i) monoclonal antibodies (MAbs) that bind HIV-1 gp120 and its mutations under various conditions. Two distinct CD4i epitopes of the outer domain were studied: the first comprises the bridging sheet, while the second contains elements of the V2 loop. Furthermore, we show that the unliganded extended monomeric core of gp120 (core
e
) assumes an intermediate CD4i conformation in solution that further undergoes detectable rearrangements upon association with CD4. These discoveries impact both accepted paradigms concerning gp120 structure and the field of HIV immunogen design.

IMPORTANCE
Elucidation of the conformational transitions that the HIV-1 envelope protein undergoes during the course of entry into CD4
+
cells is fundamental to our understanding of HIV biology. The binding of CD4 triggers a range of gp120 structural rearrangements that could present targets for future drug design and development of preventive vaccines. Here we have systematically interrogated and scrutinized these conformational transitions using a panel of antibody probes that share a specific preference for the CD4i conformations. These have been employed to study a collection of gp120 mutations and truncations. Through these analyses, we propose 4 distinct sequential steps in CD4i transitions of gp120 conformations, each defined by antibody specificities and structural requirements of the HIV envelope monomer. As a result, we not only provide new insights into this dynamic process but also define probes to further investigate HIV infection.
How do scientists perceive the current publication culture? A qualitative focus group interview study among Dutch biomedical researchers
Authors: Tijdink J K , Schipper K , Bouter L M , Maclaine Pont P , de Jonge J , Smulders Y M 
Published: February 2016

ObjectiveTo investigate the biomedical scientist's perception of the prevailing publication culture.DesignQualitative focus group interview study.SettingFour university medical centres in the Netherlands.ParticipantsThree randomly selected groups of biomedical scientists (PhD, postdoctoral staff members and full professors).Main outcome measuresMain themes for discussion were selected by participants.ResultsFrequently perceived detrimental effects of contemporary publication culture were the strong focus on citation measures (like the Journal Impact Factor and the H-index), gift and ghost authorships and the order of authors, the peer review process, competition, the funding system and publication bias. These themes were generally associated with detrimental and undesirable effects on publication practices and on the validity of reported results. Furthermore, senior scientists tended to display a more cynical perception of the publication culture than their junior colleagues. However, even among the PhD students and the postdoctoral fellows, the sentiment was quite negative. Positive perceptions of specific features of contemporary scientific and publication culture were rare.ConclusionsOur findings suggest that the current publication culture leads to negative sentiments, counterproductive stress levels and, most importantly, to questionable research practices among junior and senior biomedical scientists.
Treatment of faecal incontinence using allogeneic-adipose-derived mesenchymal stem cells: a study protocol for a pilot randomised controlled trial
Authors: Park Eun Jung , Kang Jeonghyun , Baik Seung Hyuk 
Published: February 2016

IntroductionFaecal incontinence is a distressing condition with recurrent uncontrolled passage of faecal material. Although faecal incontinence may cause psychological depression and social isolation, previous treatments have been limited. Recently, regenerative treatment has been developed using mesenchymal stem cells. Especially, there are possibilities that adipose-tissue-derived stem cells can be effective to treat a degenerated anal sphincter that is causing faecal incontinence. Therefore, this study aimed to investigate the safety and efficacy of using allogeneic-adipose-derived mesenchymal stem cells in the treatment of the anal sphincter of patients with faecal incontinence.Methods and analysisThis study is a randomised, prospective, dose escalation, placebo-controlled, single-blinded, single-centre trial with two parallel groups. The safety test is performed by an injection of allogeneic-adipose-derived mesenchymal stem cells (ALLO-ASCs) into the anal sphincter with dose escalation (3×107, 6×107and 9×107cells, sequentially). After confirming the safety of the stem cells, an efficacy test is performed by this dose in the experimental group. The experimental group will receive ALLO-ASCs mixed with fibrin glue into the anal sphincter, and the placebo group will receive 0.9% normal saline injection mixed with fibrin glue. The primary end point is to assess the safety of ALLO-ASCs after the injection into the anal sphincter, and the secondary end point is to compare the efficacy of ALLO-ASC injection with fibrin glue in patients with faecal incontinence.Ethics and disseminationThe study protocol was approved by the Ministry of Food and Drug Safety and the Ministry of Health & Welfare, in the Republic of Korea. The informed consent form was approved by the institutional review board of Gangnam Severance Hospital (IRB approval number 3-2014-0271). Dissemination of the results will be presented at a conference and in peer-reviewed publications.Trial registration numberNCT02384499; Pre-results.
Using Monte Carlo simulation to assess variability and uncertainty of tobacco consumption in a city by sewage epidemiology
Authors: Wang De-Gao , Dong Qian-Qian , Du Juan , Yang Shuo , Zhang Yun-Jie , Na Guang-Shui , Ferguson Stuart G , Wang Zhuang , Zheng Tong 
Published: February 2016

ObjectiveTo use Monte Carlo simulation to assess the uncertainty and variability of tobacco consumption through wastewater analysis in a city.MethodsA total of 11 wastewater treatment plants (WWTPs) (serving 2.2 million people; approximately 83% of urban population in Dalian) were selected and sampled. By detection and quantification of principal metabolites of nicotine, cotinine (COT) and trans-3′-hydroxycotinine (OH-COT), in raw wastewater, back calculation of tobacco use in the population of WWTPs can be realised.ResultsCOT and OH-COT were detected in the entire set of samples with an average concentration of 2.33±0.30 and 2.76±0.91 µg/L, respectively. The mass load of absorbed NIC during the sampling period ranged from 0.25 to 4.22 mg/day/capita with an average of 1.92 mg/day/capita. Using these data, we estimated that smokers in the sampling area consumed an average of 14.6 cigarettes per day for active smoker. Uncertainty and variability analysis by Monte Carlo simulation were used to refine this estimate: the procedure concluded that smokers in Dalian smoked between 10 and 27 cigarettes per day. This estimate showed good agreement with estimates from epidemiological research.ConclusionsSewage-based epidemiology may be a useful additional tool for the large-scale monitoring of patterns of tobacco use. Probabilistic methods can be used to strengthen the reliability of estimated use generated from wastewater analysis.
ERK and AKT phosphorylation status in lung cancer and emphysema using nanocapillary isoelectric focusing
Authors: Crosbie Philip A J , Crosbie Emma J , Aspinall-O'Dea Mark , Walker Michael , Harrison Rebecca , Pernemalm Maria , Shah Rajesh , Joseph Leena , Booton Richard , Pierce Andrew , Whetton Anthony D 
Published: February 2016

BackgroundEmphysema is an independent risk factor for the development of lung cancer in smokers. Activation of oncogenic signalling proteins AKT and ERK by phosphorylation has an established role in the development of lung cancer and has also been implicated in the pathogenesis of emphysema. The aim of this study was to compare the protein level and phosphorylation status of AKT and ERK in paired lung cancer and emphysema tissue using a highly sensitive phosphoprotein analysis approach.MethodsAn antibody-based, nanocapillary isoelectric focusing (cIEF) assay was used to determine the relative quantities and phosphorylation status of AKT and ERK in tumour and matched lung tissue from patients, with or without evidence of emphysema, undergoing curative resection for non-small cell lung cancer.Results20 patients with adenocarcinoma (n=9) or squamous cell carcinoma (n=11) of the lung were included (mean age 67.3 years (SD 7.5, range 47–80 years)), 12 were men and all were current (n=10) or former smokers (n=10). Paired macroscopically normal lung tissue was either histologically normal (n=7) or showed emphysema (n=13). Total and phosphorylated AKT levels were fourfold (p=0.0001) and fivefold (p=0.001) higher in tumour compared with matched lung, respectively. There was no correlation with tumour histology, stage or differentiation; however, total AKT signal in tumour was significantly correlated with fluorodeoxyglucose avidity on positron emission tomography-CT scan (r=0.53, p=0.035). Total ERK was not differentially expressed, but doubly phosphorylated (activated) ERK was threefold higher in emphysema (23.5%, SD 9.2) than either matched tumour (8.8%, SD 8.6) or normal lung tissue (8.3%, SD 9.0) and correlated with the histological severity of emphysema (p=0.005).ConclusionscIEF offers opportunities for quantifying subtle shifts in the phosphorylation status of oncoproteins in nanogram amounts of lung tissue. ERK activation is a feature of emphysema.
Building a taxonomy of integrated palliative care initiatives: results from a focus group
Authors: Ewert Benjamin , Hodiamont Farina , van Wijngaarden Jeroen , Payne Sheila , Groot Marieke , Hasselaar Jeroen , Menten Johann , Radbruch Lukas 
Published: February 2016

BackgroundEmpirical evidence suggests that integrated palliative care (IPC) increases the quality of care for palliative patients and supports professional caregivers. Existing IPC initiatives in Europe vary in their design and are hardly comparable. InSuP-C, a European Union research project, aimed to build a taxonomy of IPC initiatives applicable across diseases, healthcare sectors and systems.MethodsThe taxonomy of IPC initiatives was developed in cooperation with an international and multidisciplinary focus group of 18 experts. Subsequently, a consensus meeting of 10 experts revised a preliminary taxonomy and adopted the final classification system.ResultsConsisting of eight categories, with two to four items each, the taxonomy covers the process and structure of IPC initiatives. If two items in at least one category apply to an initiative, a minimum level of integration is assumed to have been reached. Categories range from thetype of initiative(items:pathway, modelorguideline) to patients’key contact(items:non-pc specialist, pc specialist,general practitioner). Experts recommended the inclusion of two new categories:level of care(items:primary, secondaryortertiary) indicating at which stage palliative care is integrated andprimary focus of interventiondescribing IPC givers’ different roles (items:treating function, advising/consulting or training) in the care process.ConclusionsEmpirical studies are required to investigate how the taxonomy is used in practice and whether it covers the reality of patients in need of palliative care. The InSuP-C project will test this taxonomy empirically in selected initiatives using IPC.