bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Chemokine-Like Viral Protein Enhances Alpha Interferon Production by Plasmacytoid Dendritic Cells but Delays CD8+T Cell Activation and Impairs Viral Clearance
Authors: Wikstrom Matthew E. , Fleming Peter , Comerford Iain , McColl Shaun R. , Andoniou Christopher E. , Degli-Esposti Mariapia A. 
Published: May 2013

ABSTRACTMurine cytomegalovirus encodes numerous proteins that act on a variety of pathways to modulate the innate and adaptive immune responses. Here, we demonstrate that a chemokine-like protein encoded by murine cytomegalovirus activates the early innate immune response and delays adaptive immunity, thereby impairing viral clearance. The protein, m131/129 (also known as MCK-2), is not required to establish infection in the spleen; however, a mutant virus lacking m131/129 was cleared more rapidly from this organ. In the absence of m131/129 expression, there was enhanced activation of dendritic cells (DC), and virus-specific CD8+T cells were recruited into the immune response earlier. Viral mutants lacking m131/129 elicited weaker production of alpha interferon (IFN-α) at 40 h postinfection, indicating that this protein exerts its effects during early rounds of viral replication in the spleen. Furthermore, while wild-type and mutant viruses activated plasmacytoid dendritic cells (pDC) equally at this time, as measured by the upregulation of costimulatory molecules, the presence of m131/129 stimulated more pDC to secrete IFN-α, accounting for the stronger IFN-α response than from the wild-type virus. These data provide evidence for a novel immunomodulatory function of a viral chemokine and expose the multifunctionality of immune evasion proteins. In addition, these results broaden our understanding of the interplay between innate and adaptive immunity.
Specific Amino Acid Substitutions in the S Protein Prevent Its Excretion
In Vitro
and May Contribute to Occult Hepatitis B Virus Infection
Authors: Biswas Subhajit , Candotti Daniel , Allain Jean-Pierre 
Published: May 2013

ABSTRACT

Occult hepatitis B virus (HBV) infection (OBI) is defined as low plasma level of HBV DNA with undetectable HBV surface antigen (HBsAg) outside the preseroconversion window period. The mechanisms leading to OBI remain largely unknown. The potential role of specific amino acid substitutions in the S protein from OBI in HBsAg production and excretion was examined
in vitro
. HBsAg was quantified in culture supernatants and cell extracts of HuH-7 cells transiently transfected with plasmids containing the S gene of eight HBsAg
+
controls and 18 OBI clones. The intracellular (IC)/extracellular (EC) HBsAg production ratio was ∼1.0 for the majority of controls. Three IC/EC HBsAg patterns were observed in OBI strains clones: pattern 1, an IC/EC ratio of 1.0, was found in 5/18 OBI clones, pattern 2, detectable IC but low or undetectable EC HBsAg (IC/EC, 7.0 to 800), was found in 6/18 OBIs, and pattern 3, low or undetectable IC and EC HBsAg, was found in 7/18 clones. Intracellular immunofluorescence staining showed that in pattern 2, HBsAg was concentrated around the nucleus, suggesting retention in the endoplasmic reticulum. The substitution M75T, Y100S, or P178R was present in 4/6 pattern 2 OBI clones. Site-directed-mutagenesis-corrected mutations reversed HBsAg excretion to pattern 1 and, when introduced into a control clone, induced pattern 2 except for Y100S. In a control and several OBIs, variants of a given quasispecies expressed HBsAg according to different patterns. However, the P178R substitution present in all cloned sequences of two OBI strains may contribute significantly to the OBI phenotype.
Accessory Genes Confer a High Replication Rate to Virulent Feline Immunodeficiency Virus
Authors: Troyer Ryan M. , Thompson Jesse , Elder John H. , VandeWoude Sue 
Published: May 2013

ABSTRACTFeline immunodeficiency virus (FIV) is a lentivirus that causes AIDS in domestic cats, similar to human immunodeficiency virus (HIV)/AIDS in humans. The FIV accessory protein Vif abrogates the inhibition of infection by cat APOBEC3 restriction factors. FIV also encodes a multifunctional OrfA accessory protein that has characteristics similar to HIV Tat, Vpu, Vpr, and Nef. To examine the role ofvifandorfAaccessory genes in FIV replication and pathogenicity, we generated chimeras between two FIV molecular clones with divergent disease potentials: a highly pathogenic isolate that replicates rapidlyin vitroand is associated with significant immunopathologyin vivo, FIV-C36 (referred to here as high-virulence FIV [HV-FIV]), and a less-pathogenic strain, FIV-PPR (referred to here as low-virulence FIV [LV-FIV]). Using PCR-driven overlap extension, we produced viruses in whichvif,orfA, or both genes from virulent HV-FIV replaced equivalent genes in LV-FIV. The generation of these chimeras is more straightforward in FIV than in primate lentiviruses, since FIV accessory gene open reading frames have very little overlap with other genes. All three chimeric viruses exhibited increased replication kineticsin vitrocompared to the replication kinetics of LV-FIV. Chimeras containing HV-Vif or Vif/OrfA had replication rates equivalent to those of the virulent HV-FIV parental virus. Furthermore, small interfering RNA knockdown of feline APOBEC3 genes resulted in equalization of replication rates between LV-FIV and LV-FIV encoding HV-FIV Vif. These findings demonstrate that Vif-APOBEC interactions play a key role in controlling the replication and pathogenicity of this immunodeficiency-inducing virus in its native host species and that accessory genes act as mediators of lentiviral strain-specific virulence.
Hepatitis C Virus Infection Upregulates CD55 Expression on the Hepatocyte Surface and Promotes Association with Virus Particles
Authors: Mazumdar Budhaditya , Kim Hangeun , Meyer Keith , Bose Sandip K. , Di Bisceglie Adrian M. , Ray Ratna B. , Diamond Michael S. , Atkinson John P. , Ray Ranjit 
Published: May 2013

ABSTRACTCD55 limits excessive complement activation on the host cell surface by accelerating the decay of C3 convertases. In this study, we observed that hepatitis C virus (HCV) infection of hepatocytes or HCV core protein expression in transfected hepatocytes upregulated CD55 expression at the mRNA and protein levels. Further analysis suggested that the HCV core protein or full-length (FL) genome enhanced CD55 promoter activity in a luciferase-based assay, which was further augmented in the presence of interleukin-6. Mutation of the CREB or SP-1 binding site on the CD55 promoter impaired HCV core protein-mediated upregulation of CD55. HCV-infected or core protein-transfected Huh7.5 cells displayed greater viability in the presence of CD81 and CD55 antibodies and complement. Biochemical analysis revealed that CD55 was associated with cell culture-grown HCV after purification by sucrose density gradient ultracentrifugation. Consistent with this, a polyclonal antibody to CD55 captured cell culture-grown HCV. Blocking antibodies against CD55 or virus envelope glycoproteins in the presence of normal human serum as a source of complement inhibited HCV infection. The inhibition was enhanced in the presence of both the antibodies and serum complement. Collectively, these results suggest that HCV induces and associates with a negative regulator of the complement pathway, a likely mechanism for immune evasion.
Crystal Structure of the Avian Astrovirus Capsid Spike
Authors: DuBois Rebecca M. , Freiden Pamela , Marvin Shauna , Reddivari Muralidhar , Heath Richard J. , White Stephen W. , Schultz-Cherry Stacey 
Published: May 2013

ABSTRACT
Astroviruses are small, nonenveloped, single-stranded RNA viruses that cause diarrhea in a wide variety of mammals and birds. On the surface of the viral capsid are globular spikes that are thought to be involved in attachment to host cells. To understand the basis of species specificity, we investigated the structure of an avian astrovirus capsid spike and compared it to a previously reported human astrovirus capsid spike structure. Here we report the crystal structure of the turkey astrovirus 2 (TAstV-2) capsid surface spike domain, determined to 1.5-Å resolution, and identify three conserved patches on the surface of the spike that are candidate avian receptor-binding sites. Surprisingly, the overall TAstV-2 capsid spike structure is unique, with only distant structural similarities to the human astrovirus capsid spike and other viral capsid spikes. There is an absence of conserved putative receptor-binding sites between the human and avian spikes. However, there is evidence for carbohydrate-binding sites in both human and avian spikes, and studies with human astrovirus 1 (HAstV-1) suggest a minor role in infection for chondroitin sulfate but not heparin. Overall, our structural and functional studies provide new insights into astrovirus host cell entry, species specificity, and evolution.
Does contact with a podiatrist prevent the occurrence of a lower extremity amputation in people with diabetes? A systematic review and meta-analysis
Authors: Buckley C M , Perry I J , Bradley C P , Kearney P M 
Published: May 2013

ObjectiveTo determine the effect of contact with a podiatrist on the occurrence of Lower Extremity Amputation (LEA) in people with diabetes.Design and data sourcesWe conducted a systematic review of available literature on the effect of contact with a podiatrist on the risk of LEA in people with diabetes. Eligible studies, published in English, were identified through searches of PubMed, CINAHL, EMBASE and Cochrane databases. The key terms, ‘podiatry’, ‘amputation’ and ‘diabetes’, were searched as Medical Subject Heading terms. Reference lists of selected papers were hand-searched for additional articles. No date restrictions were imposed.Study selectionPublished randomised and analytical observational studies of the effect of contact with a podiatrist on the risk of LEA in people with diabetes were included. Cross-sectional studies, review articles, chart reviews and case series were excluded. Two reviewers independently assessed titles, abstracts and full articles to identify eligible studies and extracted data related to the study design, characteristics of participants, interventions, outcomes, control for confounding factors and risk estimates.AnalysisMeta-analysis was performed separately for randomised and non-randomised studies. Relative risks (RRs) with 95% CIs were estimated with fixed and random effects models as appropriate.ResultsSix studies met the inclusion criteria and five provided data included in meta-analysis. The identified studies were heterogenous in design and included people with diabetes at both low and high risk of amputation. Contact with a podiatrist did not significantly affect the RR of LEA in a meta-analysis of available data from randomised controlled trials (RCTs); (1.41, 95% CI 0.20 to 9.78, 2 RCTs) or from cohort studies; (0.73, 95% CI 0.39 to 1.33, 3 Cohort studies with four substudies in one cohort).ConclusionsThere are very limited data available on the effect of contact with a podiatrist on the risk of LEA in people with diabetes.
Patients’ subjective assessment of the duration of cataract surgery: a case series
Authors: Rothschild Pierre-Raphael , Grabar Sophie , Le Dû Brivael , Temstet Cyril , Rostaqui Olga , Brézin Antoine P 
Published: May 2013

ObjectivesSurgery duration is a source of preoperative anxiety for patients undergoing cataract surgery. To better inform patients, we evaluated the agreement between objective and patient-perceived surgery durations.DesignCase series.SettingPublic teaching university hospital (Paris, France).ParticipantsDuring the study period, 368 cataract surgery cases performed on 285 patients were included, 85 cases were excluded from the final analysis. All patients who had uneventful phacoemulsification were included. Cases with any significant intraoperative adverse event or cases requiring additional anaesthesia other than topical were excluded. Resident performed cases were also excluded.Primary and secondary outcomesProcedures were timed (objective duration) and patients were asked, immediately afterwards, to assess the duration of their surgery (patient-assessed duration). The agreement between objective and patient-assessed durations as well as influencing factors was studied.ResultsMean objective duration (13.9±5 min) and patient-assessed duration (15.3±6.9 min) were significantly correlated (Spearman's r=0.452, p<0.0001). Furthermore, Bland-Altman analysis and the intraclass correlation coefficient (0.341, 95% CI 0.23 to 0.44) were quite in agreement. On univariate analysis, senior-performed procedures were significantly shorter than those performed by juniors (13.4 vs 17.8 min, p=0.0001). Pain was recorded as ‘no sensation’ (31.5% of the cases), ‘mild sensation’ (41%), ‘moderate pain’ (23.3%), ‘intense pain’ (3.5%) and ‘unbearable pain’ (0.7%). Groups with high pain score had significantly longer procedures (p<0.001). Multivariate analysis revealed that the only independent factors associated with both the objective and patient-assessed durations of surgery were surgeon's experience and pain-score.ConclusionsIn our study, patients’ estimated and real duration of the surgery showed moderate agreement, suggesting that emotions associated with eye surgery under topical anaesthesia did not dramatically hinder the patients’ perception of time. However, the benefit of preoperative counselling regarding the duration of surgery will need further evaluation.
Synergistic Induction of Adaptive Antitumor Immunity by Codelivery of Antigen with α-Galactosylceramide on Exosomes
Authors: Gehrmann Ulf , Hiltbrunner Stefanie , Georgoudaki Anna-Maria , Karlsson Mikael C. , Näslund Tanja I. , Gabrielsson Susanne 
Published: May 2013

AbstractExosomes and the invariant NKT (iNKT) immune cell ligand α-galactosylceramide (αGC) may offer novel tools for cancer immunotherapy. In this study, we investigated whether exosomes loaded with αGC can activate iNKT cells and potentiate a cancer-specific adaptive immune response. αGC loaded exosomes readily activated iNKT cells both in vitro and in vivo. Exosomes loaded with αGC plus the model antigen ovalbumin (OVA) induced potent NK and γδ T-cell innate immune responses, and they also synergistically amplified T- and B-cell responses that were OVA specific. In contrast to soluble αGC, which anergizes iNKT cells, we found that αGC/OVA-loaded exosomes did not induce iNKT cell anergy but were more potent than soluble αGC + OVA in inducing adaptive immune responses. In an OVA-expressing mouse model of melanoma, treatment of tumor-bearing mice with αGC/OVA-loaded exosomes decreased tumor growth, increased antigen-specific CD8+ T-cell tumor infiltration, and increased median survival, relative to control mice immunized with soluble αGC + OVA alone. Notably, an additional injection of αGC/OVA-loaded exosomes further augmented the treatment effects. Our findings show that exosomes loaded with protein antigen and αGC will activate adaptive immunity in the absence of triggering iNKT-cell anergy, supporting their application in the design of a broad variety of cancer immunotherapy trials. Cancer Res; 73(13); 3865–76. ©2013 AACR.
Targeting FGFR with Dovitinib (TKI258): Preclinical and Clinical Data in Breast Cancer
Authors: André Fabrice , Bachelot Thomas , Campone Mario , Dalenc Florence , Perez-Garcia Jose M. , Hurvitz Sara A. , Turner Nicholas , Rugo Hope , Smith John W. , Deudon Stephanie , Shi Michael , Zhang Yong , Kay Andrea , Graus Porta Diana , Yovine Alejandro , Baselga José 
Published: May 2013

Abstract
Purpose: Fibroblast growth factor receptor 1 (FGFR1) and FGFR2 amplifications are observed in approximately 10% of breast cancers and are related to poor outcomes. We evaluated whether dovitinib (TKI258), an inhibitor of FGFR1, FGFR2, and FGFR3, presented antitumor activity in FGFR-amplified breast cancers.
Experimental Design: Preclinical activity of dovitinib was evaluated in both breast cancer cell lines and an FGFR1-amplified xenograft model (HBCx2). Dovitinib was then evaluated in a phase II trial that included 4 groups of patients with human EGF receptor 2–negative metastatic breast cancer on the basis of FGFR1 amplification and hormone receptor (HR) status. FGFR1 amplification was assessed by silver in situ hybridization. Preplanned retrospective analyses assessed predictive value of FGFR1, FGFR2, and FGF3 amplifications by quantitative PCR (qPCR).
Results: Dovitinib monotherapy inhibits proliferation in FGFR1- and FGFR2-amplified, but not FGFR-normal, breast cancer cell lines. Dovitinib also inhibits tumor growth in FGFR1-amplified breast cancer xenografts. Eighty-one patients were enrolled in the trial. Unconfirmed response or stable disease for more than 6 months was observed in 5 (25%) and 1 (3%) patient(s) with FGFR1-amplified/HR-positive and FGFR1-nonamplified/HR-positive breast cancer. When qPCR-identified amplifications in FGFR1, FGFR2, or FGF3 were grouped to define an FGF pathway–amplified breast cancer in HR-positive patients, the mean reduction in target lesions was 21.1% compared with a 12.0% increase in patients who did not present with FGF pathway–amplified breast cancer.
Conclusion: Dovitinib showed antitumor activity in FGFR-amplified breast cancer cell lines and may have activity in breast cancers with FGF pathway amplification. Clin Cancer Res; 19(13); 3693–702. ©2013 AACR.
Abstract A12: Chromatin accessibility reveals insight into androgen receptor activation and transcriptional specificity
Authors: Tewari Alok , Yardimci Galip , Shibata Yoichiro , Sheffield Nathan , Song Lingyun , Taylor Barry , Coetzee Gerhard , Furey Terrence , Crawford Gregory , Febbo Phillip 
Published: May 2013

Abstract
Epigenetic mechanisms such as chromatin accessibility and histone modifications impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of prostate cancer initiation and progression, acts primarily through ligand-activated transcription of target genes. By combining deep sequencing with DNase I hypersensitivity analysis (DNase-seq) and RNA analysis (mRNA-seq) we assessed genome-wide chromatin structure and transcription and combined this data with publicly available AR chromatin immunoprecipitation data (AR ChIP-seq). We find that 72% of DNase I hypersensitive sites (DHS) overlap each other before and after androgen in LNCaP cells. Interestingly, in regions of increased chromatin accessibility with androgen induction, the canonical AR DNA recognition motif is enriched. Comparing identified DHS to AR binding sites from three different data sets consistently reveals that 50% of AR binding overlaps a DHS in induced cells. Of those sites with both DHS and AR binding, approximately half are available prior to androgen induction (i.e., “primed”) and half open in response to androgen stimulation. This contrasts with the glucocorticoid receptor (GR), which was recently reported to bind to DNA primarily in regions that are accessible to nuclease cleavage prior to ligand activation. Our mRNA-seq analysis discovered 339 genes regulated by AR activation (FDR &lt; 0.05), including 16 of the 19 most commonly identified AR-mediated genes in several other studies. Importantly, we find that regions of increased chromatin accessibility are significantly associated with genes identified as AR-regulated by mRNA-seq. Finally, base pair resolution of the DNase-seq signal reveals distinct footprinting patterns associated with the AR-DNA interaction. Analysis of chromatin structure, AR binding, and transcription prior to and following androgen induction demonstrates that AR activation by ligand induces genome-wide changes in chromatin accessibility, these changes correspond to AR binding to the genome, and they impact AR-mediated transcriptional response. These findings suggest that interaction between the AR and DNA alters chromatin structure and transcriptional specificity.
Citation Format: Alok Tewari, Galip Yardimci, Yoichiro Shibata, Nathan Sheffield, Lingyun Song, Barry Taylor, Gerhard Coetzee, Terrence Furey, Gregory Crawford, Phillip Febbo. Chromatin accessibility reveals insight into androgen receptor activation and transcriptional specificity [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr A12.
Abstract A34: Critical and reciprocal regulation of SLUG-KLF4 and SLUG-miR-1/miR-200b in TGFβ-initiated prostate cancer EMT
Authors: Liu Yen-Nien , Martin Philip , Kelly Kathleen , Yin Juan Juan , Abou-Kheir Wassim , Hynes Paul , Fang Lei , Casey Orla , Yi Ming , Seng Victoria , Tillman Heather 
Published: May 2013

Abstract
Epithelial-mesenchymal transition (EMT) is implicated in various pathological processes within the prostate, including benign prostate hyperplasia (BPH) and prostate cancer progression. However, an ordered sequence of signaling events initiating carcinoma-associated EMT has not been established. We have used a mouse model of Pten and TP53 null prostate adenocarcinoma, which undergoes progressive TGFβ-dependent EMT leading eventually to sarcomtoid carcinoma formation. Sarcomatoid carcinomas are characterized by various mesenchymal lineages and bone formation.
In this model, SLUG is the dominant regulator of EMT initiation in vitro and in vivo. Depletion of Slug inhibited EMT. We determined that TGFβ-stimulated KLF4 degradation is the mechanism of SLUG induction, and the introduction of a degradation-resistant mutant of KLF4 inhibited EMT. We show that KLF4 and another epithelial determinant, FOXA1, are direct transcriptional inhibitors of SLUG expression in mouse and human prostate cancer cells. In addition, SLUG-dependent binding of polycomb repressive complexes to the Klf4 and Foxa1 promoters was demonstrated to inhibit transcription of these epithelial transcription factors, suggesting that SLUG expression helps to consolidate mesenchymal commitment. Analysis of tissue arrays demonstrated decreased KLF4 and increased SLUG expression in advanced stage primary prostate cancer, substantiating the involvement of the EMT signaling events described in model systems.
As microRNAs are pleiotropic regulators of differentiation and tumorigenesis, we evaluated miR expression associated with tumorigenesis and EMT. Mir-1 and mir-200 were reduced with progression of prostate adenocarcinoma, and we identified Slug as one of the phylogenetically-conserved targets of these miRs. We established that SLUG is a direct repressor of miR-1 and miR-200 transcription. Thus, SLUG and miR-1/miR-200 act in a self-reinforcing regulatory loop leading to amplification of EMT. Depletion of Slug inhibited EMT during tumorigenesis, while forced expression of miR-1 or miR-200 inhibited both EMT and tumorigenesis in human and mouse model systems. Various miR targets were analyzed, and our findings suggest that miR-1 has roles in regulating EMT and mesenchymal differentiation through Slug and functions in tumor-suppressive programs by regulating additional targets.
Citation Format: Yen-Nien Liu, Philip Martin, Kathleen Kelly, Juan Juan Yin, Wassim Abou-Kheir, Paul Hynes, Lei Fang, Orla Casey, Ming Yi, Victoria Seng, Heather Tillman. Critical and reciprocal regulation of SLUG-KLF4 and SLUG-miR-1/miR-200b in TGFβ-initiated prostate cancer EMT [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr A34.