bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasmacytoid Dendritic Cells Mediate Synergistic Effects of HIV and Lipopolysaccharide on CD27+IgD–Memory B Cell Apoptosis
Authors: Zhang Lumin , Luo Zhenwu , Sieg Scott F. , Funderburg Nicholas T. , Yu Xiaocong , Fu Pingfu , Wu Hao , Jiao Yanmei , Gao Yong , Greenspan Neil S. , Harding Clifford V. , Kilby J. Michael , Li Zihai , Lederman Michael M. , Jiang Wei 
Published: July 2014

ABSTRACTThe effects of heightened microbial translocation on B cells during HIV infection are unknown. We examined thein vitroeffects of HIV and lipopolysaccharide (LPS) on apoptosis of CD27+IgD−memory B (mB) cells from healthy controls.In vivoanalysis was conducted on a cohort of 82 HIV+donors and 60 healthy controls.In vitroexposure of peripheral blood mononuclear cells (PBMCs) to LPS and HIV led to mB cell death via the Fas/Fas ligand (FasL) pathway. Plasmacytoid dendritic cells (pDCs) produced FasL in response to HIV via binding to CD4 and chemokine coreceptors. HIV and LPS increased Fas expression on mB cells in PBMCs, which was dependent on the presence of pDCs and monocytes. Furthermore, mB cells purified from PBMCs and pretreated with both HIV and LPS were more sensitive to apoptosis when cocultured with HIV-treated pDCs. Blocking the interferon receptor (IFNR) prevented HIV-stimulated FasL production in pDCs, HIV-plus-LPS-induced Fas expression, and apoptosis of mB cells.In vivoorex vivo, HIV+donors have higher levels of plasma LPS, Fas expression on mB cells, and mB cell apoptosis than controls. Correspondingly, in HIV+donors, but not in controls, a positive correlation was found between plasma FasL and HIV RNA levels and between Fas expression on mB cells and plasma LPS levels. This work reveals a novel mechanism of mB cell apoptosis mediated by LPS and HIV through the Fas/FasL pathway, with key involvement of pDCs and type I IFN, suggesting a role for microbial translocation in HIV pathogenesis.IMPORTANCEThis study demonstrates that lipopolysaccharide (LPS) and type I interferon (IFN) play an important role in memory B cell apoptosis in HIV infection. It reveals a previously unrecognized role of microbial translocation in HIV pathogenesis.
Rational Design of Human Metapneumovirus Live Attenuated Vaccine Candidates by Inhibiting Viral mRNA Cap Methyltransferase
Authors: Zhang Yu , Wei Yongwei , Zhang Xiaodong , Cai Hui , Niewiesk Stefan , Li Jianrong 
Published: July 2014

ABSTRACT

The paramyxoviruses human respiratory syncytial virus (hRSV), human metapneumovirus (hMPV), and human parainfluenza virus type 3 (hPIV3) are responsible for the majority of pediatric respiratory diseases and inflict significant economic loss, health care costs, and emotional burdens. Despite major efforts, there are no vaccines available for these viruses. The conserved region VI (CR VI) of the large (L) polymerase proteins of paramyxoviruses catalyzes methyltransferase (MTase) activities that typically methylate viral mRNAs at positions guanine N-7 (G-N-7) and ribose 2′-O. In this study, we generated a panel of recombinant hMPVs carrying mutations in the
S
-adenosylmethionine (SAM) binding site in CR VI of L protein. These recombinant viruses were specifically defective in ribose 2′-O methylation but not G-N-7 methylation and were genetically stable and highly attenuated in cell culture and viral replication in the upper and lower respiratory tracts of cotton rats. Importantly, vaccination of cotton rats with these recombinant hMPVs (rhMPVs) with defective MTases triggered a high level of neutralizing antibody, and the rats were completely protected from challenge with wild-type rhMPV. Collectively, our results indicate that (i) amino acid residues in the SAM binding site in the hMPV L protein are essential for 2′-O methylation and (ii) inhibition of mRNA cap MTase can serve as a novel target to rationally design live attenuated vaccines for hMPV and perhaps other paramyxoviruses, such as hRSV and hPIV3.

IMPORTANCE
Human paramyxoviruses, including hRSV, hMPV, and hPIV3, cause the majority of acute upper and lower respiratory tract infections in humans, particularly in infants, children, the elderly, and immunocompromised individuals. Currently, there is no licensed vaccine available. A formalin-inactivated vaccine is not suitable for these viruses because it causes enhanced lung damage upon reinfection with the same virus. A live attenuated vaccine is the most promising vaccine strategy for human paramyxoviruses. However, it remains a challenge to identify an attenuated virus strain that has an optimal balance between attenuation and immunogenicity. Using reverse genetics, we generated a panel of recombinant hMPVs that were specifically defective in ribose 2′-O methyltransferase (MTase) but not G-N-7 MTase. These MTase-defective hMPVs were genetically stable and sufficiently attenuated but retained high immunogenicity. This work highlights a critical role of 2′-O MTase in paramyxovirus replication and pathogenesis and a new avenue for the development of safe and efficacious live attenuated vaccines for hMPV and other human paramyxoviruses.
Immunodominance Changes as a Function of the Infecting Dengue Virus Serotype and Primary versus Secondary Infection
Authors: Weiskopf Daniela , Angelo Michael A. , Sidney John , Peters Bjoern , Shresta Sujan , Sette Alessandro 
Published: July 2014

ABSTRACTDengue virus (DENV) is the causative agent of dengue fever (DF). This disease can be caused by any of four DENV serotypes (DENV1 to -4) which share 67 to 75% sequence homology with one another. The effect of subsequent infections with different serotypes on the T cell repertoire is not fully understood. We utilized mice transgenic for human leukocyte antigens (HLA) lacking the alpha/beta interferon (IFN-α/β) receptor to study responses to heterologous DENV infection. First, we defined the primary T cell response to DENV3 in the context of a wide range of HLA molecules. The primary DENV3 immune response recognized epitopes derived from all 10 DENV proteins, with a significant fraction of the response specific for structural proteins. This is in contrast to primary DENV2 infection, in which structural proteins are a minor component of the response, suggesting differential antigen immunodominance as a function of the infecting serotype. We next investigated the effect of secondary heterologous DENV infection on the T cell repertoire. In the case of both DENV2/3 and DENV3/2 heterologous infections, recognition of conserved/cross-reactive epitopes was either constant or expanded compared to that in homologous infection. Furthermore, in heterologous infection, previous infection with a different serotype impaired the development of responses directed to serotype-specific but not conserved epitopes. Thus, a detrimental effect of previous heterotypic responses might not be due to dysfunctional and weakly cross-reactive epitopes dominating the response. Rather, responses to the original serotype might limit the magnitude of responses directed against epitopes that are either cross-reactive to or specific for the most recently infecting serotype.IMPORTANCEDENV transmission occurs in more than 100 countries and is an increasing public health problem in tropical and subtropical regions. At present, no effective antiviral therapy or licensed vaccine exists, and treatment is largely supportive in nature. Disease can be caused by any of the four DENV serotypes (DENV1 to -4), which share a high degree of sequence homology with one another. In this study, we have addressed the question of how the T cell repertoire changes as a function of infections with different serotypes and of subsequent heterologous secondary infections. This is of particular interest in the field of dengue viruses, in which secondary infections with different DENV serotypes increase the risk of severe disease. Our results on the evolution of the immune response after primary and secondary infections provide new insights into HLA-restricted T cell responses against DENV relevant for the design of a vaccine against DENV.
Contribution of Silent Mutations to Thermal Adaptation of RNA Bacteriophage Qβ
Authors: Kashiwagi Akiko , Sugawara Ryu , Sano Tsushima Fumie , Kumagai Tomofumi , Yomo Tetsuya 
Published: July 2014

ABSTRACT
Changes in protein function and other biological properties, such as RNA structure, are crucial for adaptation of organisms to novel or inhibitory environments. To investigate how mutations that do not alter amino acid sequence may be positively selected, we performed a thermal adaptation experiment using the single-stranded RNA bacteriophage Qβ in which the culture temperature was increased from 37.2°C to 41.2°C and finally to an inhibitory temperature of 43.6°C in a stepwise manner in three independent lines. Whole-genome analysis revealed 31 mutations, including 14 mutations that did not result in amino acid sequence alterations, in this thermal adaptation. Eight of the 31 mutations were observed in all three lines. Reconstruction and fitness analyses of Qβ strains containing only mutations observed in all three lines indicated that five mutations that did not result in amino acid sequence changes but increased the amplification ratio appeared in the course of adaptation to growth at 41.2°C. Moreover, these mutations provided a suitable genetic background for subsequent mutations, altering the fitness contribution from deleterious to beneficial. These results clearly showed that mutations that do not alter the amino acid sequence play important roles in adaptation of this single-stranded RNA virus to elevated temperature.

IMPORTANCE
Recent studies using whole-genome analysis technology suggested the importance of mutations that do not alter the amino acid sequence for adaptation of organisms to novel environmental conditions. It is necessary to investigate how these mutations may be positively selected and to determine to what degree such mutations that do not alter amino acid sequences contribute to adaptive evolution. Here, we report the roles of these silent mutations in thermal adaptation of RNA bacteriophage Qβ based on experimental evolution during which Qβ showed adaptation to growth at an inhibitory temperature. Intriguingly, four synonymous mutations and one mutation in the untranslated region that spread widely in the Qβ population during the adaptation process at moderately high temperature provided a suitable genetic background to alter the fitness contribution of subsequent mutations from deleterious to beneficial at a higher temperature.
Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting
Authors: Cotten Matthew , Petrova Velislava , Phan My V. T. , Rabaa Maia A. , Watson Simon J. , Ong Swee Hoe , Kellam Paul , Baker Stephen 
Published: July 2014

ABSTRACT

Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. Norovirus infections can be severe and can be initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission and evolution. To address this need, we have developed a whole-genome deep-sequencing method that generates entire genome sequences from small amounts of clinical specimens. This novel approach employs an algorithm for reverse transcription and PCR amplification primer design using all of the publically available norovirus sequence data. Deep sequencing and
de novo
assembly were used to generate norovirus genomes from a large set of diarrheal patients attending three hospitals in Ho Chi Minh City, Vietnam, over a 2.5-year period. Positive-selection analysis and direct examination of protein changes in the virus over time identified codons in the regions encoding proteins VP1, p48 (NS1-2), and p22 (NS4) under positive selection and expands the known targets of norovirus evolutionary pressure.

IMPORTANCE
The high transmissibility and rapid evolutionary rate of norovirus, combined with a short-lived host immune responses, are thought to be the reasons why the virus causes the majority of pediatric viral diarrhea cases. The evolutionary patterns of this RNA virus have been described in detail for only a portion of the virus genome and never for a virus from a detailed urban tropical setting. We provide a detailed sequence description of the noroviruses circulating in three Ho Chi Minh City hospitals over a 2.5-year period. This study identified patterns of virus change in known sites of host immune response and identified three additional regions of the virus genome under selection that were not previously recognized. In addition, the method described here provides a robust full-genome sequencing platform for community-based virus surveillance.
HIV-1 Infection Leads to Increased Transcription of Human Endogenous Retrovirus HERV-K (HML-2) ProvirusesIn Vivobut Not to Increased Virion Production
Authors: Bhardwaj Neeru , Maldarelli Frank , Mellors John , Coffin John M. 
Published: July 2014

ABSTRACTRecent studies suggest that human endogenous retrovirus group K (HERV-K) provirus expression plays a role in the pathogenesis of HIV-1 infection. In particular, RNA from the HML-2 subgroup of HERV-K proviruses has been reported to be highly expressed at the cellular level and detectable in the plasma of HIV-1-infected patients, suggestive of virion production and, perhaps, replication. In this study, we developed an HML-2-specific quantitative-PCR assay that detects 51 of the 89 known HML-2 proviruses in the human genome. Plasma and peripheral blood mononuclear cells (PBMCs) from HIV-negative controls and HIV-1-infected patients were collected for analysis of HML-2 RNA expression. Contrary to previous reports, we did not detect high levels of HML-2 RNA in the plasma of HIV-1-infected patients, but we did observe a significant increase of HML-2 RNA in total PBMCs compared to HIV-negative controls. The level of HML-2 expression in PBMCs does not appear to be related to patient use of antiretrovirals or to HIV-1 plasma RNA, cellular RNA, or cellular DNA levels. To investigate the source of HML-2 RNA expression, patient PBMCs were sorted into CD3+CD4+, CD3+CD8+, CD3−CD14+, and CD3−CD20+cell subsets and then analyzed for HML-2 RNA levels. No single cell subset was enriched for HML-2 RNA expression in HIV-1-infected patients, but there appears to be substantial variability in the level of HML-2 expression depending on the cell type.IMPORTANCEHere, we report that human endogenous retrovirus group K (HERV-K) (HML-2) proviruses are expressed at significantly higher levels in peripheral blood mononuclear cells (PBMCs) from patients with HIV-1 infection than in those from uninfected individuals. However, contrary to previous reports, this expression did not lead to detectable virions in the plasma of these patients. In addition, we found that HML-2 proviruses were expressed in multiple blood cell types from HIV-1-infected individuals, and the magnitude of HML-2 expression was not related to HIV-1 disease markers in this patient cohort. These findings may have implications for HML-2-based therapies targeting HIV-1 infection.
Stability Determinants of Murine Cytomegalovirus Long Noncoding RNA7.2
Authors: Schwarz Toni M. , Kulesza Caroline A. 
Published: July 2014

ABSTRACT
Cytomegalovirus is a ubiquitous herpesvirus that persistently replicates in glandular epithelial tissue. Murine cytomegalovirus expresses a 7.2-kb-long noncoding RNA (RNA7.2) that is a determinant of viral persistence in the salivary gland. RNA7.2 is an extremely long-lived intron, yet the basis of its stability is unknown. We present data that localize key sequence determinants of RNA stability to the 3′ end of RNA7.2 and suggest that stability is a result of sustained lariat conformation.
Inhibition of Phosphorylated-STAT1 Nuclear Translocation and Antiviral Protein Expression in Human Brain Vascular Adventitial Fibroblasts Infected with Varicella-Zoster Virus
Authors: Nagel Maria A. , James Stephanie F. , Traktinskiy Igor , Wyborny Ann , Choe Alexander , Rempel April , Baird Nicholas L. , Gilden Don 
Published: July 2014

ABSTRACT
In varicella-zoster virus (VZV)-infected primary human brain vascular adventitial fibroblasts (BRAFs), levels of beta interferon (IFN-β,) STAT1, and STAT2 transcripts as well as STAT1 and STAT2 protein were decreased. IFN-α transcript levels were increased but not secreted IFN-α protein levels. Compared to IFN-α-treated control results, in VZV-infected BRAFs, phosphorylated STAT1 did not translocate to the nucleus, resulting in impaired downstream expression of interferon-inducible antiviral Mx1. Overall, VZV interference with the type I interferon pathway may promote virus persistence in cerebral arteries.
Performance of the Medtronic Sentrino continuous glucose management (CGM) system in the cardiac intensive care unit
Authors: Kosiborod Mikhail , Gottlieb Rebecca K , Sekella Julie A , Peterman Diane , Grodzinsky Anna , Kennedy Paul , Borkon Michael A 
Published: July 2014

BackgroundMaintaining glucose in the target range, while avoiding hypoglycemia, is challenging in critically ill patients. We investigated the performance and safety of Medtronic Sentrino, a newly developed continuous glucose management (CGM) system for critically ill adults.MethodsThis was a prospective, single-center, single-arm, open-label study in adult patients with cardiac ICU admission. Sentrino subcutaneous glucose sensors were inserted into patients’ thigh with planned study participation of 72 h. Sensor glucose results were displayed, and the system's alerts and alarms fully enabled. Reference blood glucose was collected from central venous catheter and analyzed with a blood gas analyzer. Treatment decisions were made independently of sensor glucose values, according to the existing standard of care.ResultsA total of 21 patients were enrolled; all successfully completed the study. Sensor glucose values were displayed 96% of the time, and 870 paired blood glucose–sensor glucose points were analyzed. Overall mean absolute relative difference (MARD) was 12.8% (95% CI 11.9% to 13.6%). No clinically significant differences in accuracy were seen within subgroups of hemodynamic status (MARD 12.3% and 13.1% for compromised vs stable hemodynamics). Consensus grid analysis showed >99% of sensor glucose values within A/B zones. No device or study-related adverse events were reported. 100% of clinicians found Sentrino easy to use after two patients.ConclusionsIn our single-center experience, Sentrino CGM system demonstrated good accuracy and reliability, with no device-related adverse events in critically ill cardiac patients, and was easy to use and integrate in the cardiac ICU.Trial registration numberNCT01763567.
Association of napping and night-time sleep with impaired glucose regulation, insulin resistance and glycated haemoglobin in Chinese middle-aged adults with no diabetes: a cross-sectional study
Authors: Baoying Huang , Hongjie Chen , Changsheng Qiu , Peijian Wu , Qingfei Lin , Yinghua Lin , Huibin Huang , Jixing Liang , Liantao Li , Ling Chen , Kaka Tang , Zichun Chen , Lixiang Lin , Jieli Lu , Yufang Bi , Guang Ning , Penli Zhu , Junping Wen , Gang Chen 
Published: July 2014

ObjectiveTo assess associations between napping and night-time sleep duration with impaired glucose regulation, insulin resistance (IR) and glycated haemoglobin (HbA1c).DesignCross-sectional study.SettingFujian Province, China, from June 2011 to January 2012.ParticipantsThis study enrolled 9028 participants aged 40–65 years. Data of 7568 participants with no diabetes were included for analysis. Type 2 diabetes was defined applying WHO criteria.Outcome measuresParticipants’ daytime napping and night-time sleep duration data were collected using a standardised self-reported Chinese-language questionnaire about sleep frequency and quality. Anthropometric and laboratory parameters were also measured. IR was defined as a HOMA-IR index value >2.50. ORs and 95% CIs were derived from multivariate logistic regression models.ResultsParticipants (mean age 51.1±7.0 years) included 3060 males and 4508 females with average night-time sleep of 7.9 h. A higher proportion of males napped than females. After adjustment for potential confounders, ORs for HbA1c >6.0% were 1.28 and 1.26 for those napping ≤1 h and >1 h (p=0.002 and p=0.018), respectively. Statistically significant differences in IR between nappers and non-nappers were only marginal clinically. Odds for HbA1c >6.0% were significantly lower in participants with longer night-time sleep durations than in the reference group (>8 h vs 6–8 h). Odds for IR were significantly lower in participants whose night-time sleep hours deviated from the reference group (<6 h, >8 h vs 6–8 h)ConclusionsChinese middle-aged adults with no diabetes who napped had higher HbA1c and IR; those with shorter night-time sleep durations had increased HbA1c. Night-time sleep hours that are either <6 or >8 tend to be associated with lower odds for IR. Further studies are necessary to determine the underlying clinical significance and mechanisms behind these associations.
The Sight Loss and Vision Priority Setting Partnership (SLV-PSP): overview and results of the research prioritisation survey process
Authors: Rowe Fiona , Wormald Richard , Cable Richard , Acton Michele , Bonstein Karen , Bowen Michael , Bronze Carol , Bunce Catey , Conroy Dolores , Cowan Katherine , Evans Kathy , Fenton Mark , Giles Heather , Gordon Iris , Halfhide Louise , Harper Robert , Lightstone Anita , Votruba Marcela , Waterman Heather , Zekite Antra 
Published: July 2014

ObjectivesThe Sight Loss and Vision Priority Setting Partnership aimed to identify research priorities relating to sight loss and vision through consultation with patients, carers and clinicians. These priorities can be used to inform funding bodies’ decisions and enhance the case for additional research funding.DesignProspective survey with support from the James Lind Alliance.SettingUK-wide National Health Service (NHS) and non-NHS.ParticipantsPatients, carers and eye health professionals. Academic researchers were excluded solely from the prioritisation process. The survey was disseminated by patient groups, professional bodies, at conferences and through the media, and was available for completion online, by phone, by post and by alternative formats (Braille and audio).Outcome measurePeople were asked to submit the questions about prevention, diagnosis and treatment of sight loss and eye conditions that they most wanted to see answered by research. Returned survey questions were reviewed by a data assessment group. Priorities were established across eye disease categories at final workshops.Results2220 people responded generating 4461 submissions. Sixty-five per cent of respondents had sight loss and/or an eye condition. Following initial data analysis, 686 submissions remained which were circulated for interim prioritisation (excluding cataract and ocular cancer questions) to 446 patients/carers and 218 professionals. The remaining 346 questions were discussed at final prioritisation workshops to reach agreement of top questions per category.ConclusionsThe exercise engaged a diverse community of stakeholders generating a wide range of conditions and research questions. Top priority questions were established across 12 eye disease categories.