bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zika Virus Testing Considerations: Lessons Learned from the First 80 Real-Time Reverse Transcription-PCR-Positive Cases Diagnosed in New York State
Authors: St. George Kirsten , Sohi Inderbir S. , Dufort Elizabeth M. , Dean Amy B. , White Jennifer L. , Limberger Ronald , Sommer Jamie N. , Ostrowski Stephanie , Wong Susan J. , Backenson P. Bryon , Kuhles Daniel , Blog Debra , Taylor Jill , Hutton Brad , Zucker Howard A. 
Published: December 2016

ABSTRACT
The performance and interpretation of laboratory tests for Zika virus (ZKV) continue to be evaluated. Serology is cross-reactive, laborious, and frequently difficult to interpret, and serum was initially solely recommended for molecular diagnosis. ZKV testing was initiated in January 2016 in New York State for symptomatic patients, pregnant women, their infants, and patients with Guillain-Barré syndrome who had traveled to areas with ZKV transmission. Subsequently, eligibility was expanded to pregnant women with sexual partners with similar travel histories. Serum and urine collected within 4 weeks of symptom onset or within 6 weeks of travel were tested with real-time reverse transcription-PCR (RT-PCR) assays targeting the ZKV envelope and NS2B genes. In this review of lessons learned from the first 80 positive cases in NYS, ZKV RNA was detected in urine only in 50 patients, in serum only in 19 patients, and in both samples concurrently in 11 patients, with average viral loads in urine a log higher than those in serum. Among 93 positive samples from the 80 patients, 41 were positive on both gene assays, 52 were positive on the envelope only, and none were positive on the NS2B only. Of the 80 infected patients, test results for 74 (93%) would have defined their infection status as not detected or equivocal if the requirement for positive results from two assay targets (two-target-positive requirement) in the initial federal guidance to public health laboratories was enforced, if urine was not tested, or if the extended eligibility time for molecular testing was not implemented. These changes facilitated more extensive molecular diagnosis of ZKV, reducing reliance on time-consuming and potentially inconclusive serology.
Emergence of
mmpT5
Variants during Bedaquiline Treatment of Mycobacterium intracellulare Lung Disease
Authors: Alexander David C. , Vasireddy Ravikiran , Vasireddy Sruthi , Philley Julie V. , Brown-Elliott Barbara A. , Perry Benjamin J. , Griffith David E. , Benwill Jeana L. , Cameron Andrew D. S. , Wallace Richard J. 
Published: December 2016

ABSTRACT

Bedaquiline (BDQ), a diarylquinoline antibiotic that targets ATP synthase, is effective for the treatment of
Mycobacterium tuberculosis
infections that no longer respond to conventional drugs. While investigating the off-label use of BDQ as salvage therapy, seven of 13 patients with
Mycobacterium intracellulare
lung disease had an initial microbiological response and then relapsed. Whole-genome comparison of pretreatment and relapse isolates of
M. intracellulare
uncovered mutations in a previously uncharacterized locus,
mmpT5
. Preliminary analysis suggested similarities between
mmpT5
and the
mmpR5
locus, which is associated with low-level BDQ resistance in
M. tuberculosis
. Both genes encode transcriptional regulators and are adjacent to orthologs of the
mmpS5-mmpL5
drug efflux operon. However, MmpT5 belongs to the TetR superfamily, whereas MmpR5 is a MarR family protein. Targeted sequencing uncovered nonsynonymous
mmpT5
mutations in isolates from all seven relapse cases, including two pretreatment isolates. In contrast, only two relapse patient isolates had nonsynonymous changes in ATP synthase subunit c (
atpE
), the primary target of BDQ. Susceptibility testing indicated that
mmpT5
mutations are associated with modest 2- to 8-fold increases in MICs for BDQ and clofazimine, whereas one
atpE
mutant exhibited a 50-fold increase in MIC for BDQ. Bedaquiline shows potential for the treatment of
M. intracellulare
lung disease, but optimization of treatment regimens is required to prevent the emergence of
mmpT5
variants and microbiological relapse.
Mice Expressing Minimally Humanized CD81 and Occludin Genes Support Hepatitis C Virus Uptake
In Vivo
Authors: Ding Qiang , von Schaewen Markus , Hrebikova Gabriela , Heller Brigitte , Sandmann Lisa , Plaas Mario , Ploss Alexander 
Published: December 2016

ABSTRACT

Hepatitis C virus (HCV) causes chronic infections in at least 150 million individuals worldwide. HCV has a narrow host range and robustly infects only humans and chimpanzees. The underlying mechanisms for this narrow host range are incompletely understood. At the level of entry, differences in the amino acid sequences between the human and mouse orthologues of two essential host factors, the tetraspanin CD81 and the tight junction protein occludin (OCLN), explain, at least in part, HCV's limited ability to enter mouse hepatocytes. We have previously shown that adenoviral or transgenic overexpression of human CD81 and OCLN facilitates HCV uptake into mouse hepatocytes
in vitro
and
in vivo
. In efforts to refine these models, we constructed knock-in mice in which the second extracellular loops of CD81 and OCLN were replaced with the respective human sequences, which contain the determinants that are critical for HCV uptake. We demonstrate that the humanized CD81 and OCLN were expressed at physiological levels in a tissue-appropriate fashion. Mice bearing the humanized alleles formed normal tight junctions and did not exhibit any immunologic abnormalities, indicating that interactions with their physiological ligands were intact. HCV entry factor knock-in mice take up HCV with an efficiency similar to that in mice expressing HCV entry factors transgenically or adenovirally, demonstrating the utility of this model for studying HCV infection
in vivo
.

IMPORTANCE
At least 150 million individuals are chronically infected with hepatitis C virus (HCV). Chronic hepatitis C can result in progressive liver disease and liver cancer. New antiviral treatments can cure HCV in the majority of patients, but a vaccine remains elusive. To gain a better understanding of the processes culminating in liver failure and cancer and to prioritize vaccine candidates more efficiently, small-animal models are needed. Here, we describe the characterization of a new mouse model in which the parts of two host factors that are essential for HCV uptake, CD81 and occludin (OCLN), which differ between mice and humans, were humanized. We demonstrate that such minimally humanized mice develop normally, express the modified genes at physiological levels, and support HCV uptake. This model is of considerable utility for studying viral entry in the three-dimensional context of the liver and to test approaches aimed at preventing HCV entry.
Lassa Virus Cell Entry Reveals New Aspects of Virus-Host Cell Interaction
Authors: Torriani Giulia , Galan-Navarro Clara , Kunz Stefan 
Published: December 2016

ABSTRACT
Viral entry represents the first step of every viral infection and is a determinant for the host range and disease potential of a virus. Here, we review the latest developments on cell entry of the highly pathogenic Old World arenavirus Lassa virus, providing novel insights into the complex virus-host cell interaction of this important human pathogen. We will cover new discoveries on the molecular mechanisms of receptor recognition, endocytosis, and the use of late endosomal entry factors.
Promising Role of Toll-Like Receptor 8 Agonist in Concert with Prostratin for Activation of Silent HIV
Authors: Rochat M. A. , Schlaepfer E. , Speck R. F. 
Published: December 2016

ABSTRACTThe persistence of latently HIV-infected cells in patients under combined antiretroviral treatment (cART) remains the major hurdle for HIV eradication. Thus far, individual compounds have not been sufficiently potent to reactivate latent virus and guarantee its eliminationin vivo. Thus, we hypothesized that transcriptional enhancers, in concert with compounds triggering the innate immune system, are more efficient in reversing latency by creating a Th1 supportive milieu that acts against latently HIV-infected cells at various levels. To test our hypothesis, we screened six compounds on a coculture of latently infected cells (J-lat) and monocyte-derived dendritic cells (MDDCs). The protein kinase C (PKC) agonist prostratin, with a Toll-like receptor 8 (TLR8) agonist, resulted in greater reversion of HIV latency than any single compound. This combinatorial approach led to a drastic phenotypic and functional maturation of the MDDCs. Tumor necrosis factor (TNF) and cell-cell interactions were crucial for the greater reversion observed. Similarly, we found a greater potency of the combination of prostratin and TLR8 agonist in reversing HIV latency when applying it to primary cells of HIV-infected patients. Thus, we demonstrate here the synergistic interplay between TLR8-matured MDDCs and compounds acting directly on latently HIV-infected cells, targeting different mechanisms of latency, by triggering various signaling pathways. Moreover, TLR8 triggering may reverse exhaustion of HIV-specific cytotoxic T lymphocytes that might be essential for killing or constraining the latently infected cells.IMPORTANCECuring HIV is the Holy Grail. The so-called “shock and kill” strategy relies on drug-mediated reversion of HIV latency and the subsequent death of those cells under combined antiretroviral treatment. So far, no compound achieves efficient reversal of latency or eliminates this latent reservoir. The compounds may not target all of the latency mechanisms in all latently infected cells. Moreover, HIV-associated exhaustion of the immune system hinders the efficient elimination of the reactivated cells. In this study, we demonstrated synergistic latency reversion by combining agonists for protein kinase C and Toll-like receptor 8 in a coculture of latently infected cells with myeloid dendritic cells. The drug prostratin stimulates directly the transcriptional machinery of latently infected cells, and the TLR8 agonist acts indirectly by maturing dendritic cells. These findings highlight the importance of the immune system and its activation, in combination with direct-acting compounds, to reverse latency.
Histidine 375 Modulates CD4 Binding in HIV-1 CRF01_AE Envelope Glycoproteins
Authors: Zoubchenok Daria , Veillette Maxime , Prévost Jérémie , Sanders-Buell Eric , Wagh Kshitij , Korber Bette , Chenine Agnès L. , Finzi Andrés 
Published: December 2016

ABSTRACT
The envelope glycoproteins (Envs) from human immunodeficiency virus type 1 (HIV-1) mediate viral entry. The binding of the HIV-1 gp120 glycoprotein to CD4 triggers conformational changes in gp120 that allow high-affinity binding to its coreceptors. In contrast to all other Envs from the same phylogenetic group, M, which possess a serine (S) at position 375, those from CRF01_AE strains possess a histidine (H) at this location. This residue is part of the Phe43 cavity, where residue 43 of CD4 (a phenylalanine) engages with gp120. Here we evaluated the functional consequences of replacing this residue in two CRF01_AE Envs (CM244 and 92TH023) by a serine. We observed that reversion of amino acid 375 to a serine (H375S) resulted in a loss of functionality of both CRF01_AE Envs as measured by a dramatic loss in infectivity and ability to mediate cell-to-cell fusion. While no effects on processing or trimer stability of these variants were observed, decreased functionality could be linked to a major defect in CD4 binding induced by the replacement of H375 by a serine. Importantly, mutations of residues 61 (layer 1), 105 and 108 (layer 2), and 474 to 476 (layer 3) of the CRF01_AE gp120 inner domain layers to the consensus residues present in group M restored CD4 binding and wild-type levels of infectivity and cell-to-cell fusion. These results suggest a functional coevolution between the Phe43 cavity and the gp120 inner domain layers. Altogether, our observations describe the functional importance of amino acid 375H in CRF01_AE envelopes.

IMPORTANCE
A highly conserved serine located at position 375 in group M is replaced by a histidine in CRF01_AE Envs. Here we show that H375 is required for efficient CRF01_AE Env binding to CD4. Moreover, this work suggests that specific residues of the gp120 inner domain layers have coevolved with H375 in order to maintain its ability to mediate viral entry.
Temperature-Sensitive Live-Attenuated Canine Influenza Virus H3N8 Vaccine
Authors: Nogales Aitor , Rodriguez Laura , Chauché Caroline , Huang Kai , Reilly Emma C. , Topham David J. , Murcia Pablo R. , Parrish Colin R. , Martínez-Sobrido Luis 
Published: December 2016

ABSTRACT

Canine influenza is a respiratory disease of dogs caused by canine influenza virus (CIV). CIV subtypes responsible for influenza in dogs include H3N8, which originated from the transfer of H3N8 equine influenza virus to dogs; and the H3N2 CIV, which is an avian-origin virus that adapted to infect dogs. Influenza infections are most effectively prevented through vaccination to reduce transmission and future infection. Currently, only inactivated influenza vaccines (IIVs) are available for the prevention of CIV in dogs. However, the efficacy of IIVs is suboptimal, and novel approaches are necessary for the prevention of disease caused by this canine respiratory pathogen. Using reverse genetics techniques, we have developed a live-attenuated CIV vaccine (LACIV) for the prevention of H3N8 CIV. The H3N8 LACIV replicates efficiently in canine cells at 33°C but is impaired at temperatures of 37 to 39°C and was attenuated compared to wild-type H3N8 CIV
in vivo
and
ex vivo
. The LACIV was able to induce protection against H3N8 CIV challenge with a single intranasal inoculation in mice. Immunogenicity and protection efficacy were better than that observed with a commercial CIV H3N8 IIV but provided limited cross-reactive immunity and heterologous protection against H3N2 CIV. These results demonstrate the feasibility of implementing a LAIV approach for the prevention and control of H3N8 CIV in dogs and suggest the need for a new LAIV for the control of H3N2 CIV.

IMPORTANCE
Two influenza A virus subtypes has been reported in dogs in the last 16 years: the canine influenza viruses (CIV) H3N8 and H3N2 of equine and avian origins, respectively. To date, only inactivated influenza vaccines (IIVs) are available to prevent CIV infections. Here, we report the generation of a recombinant, temperature-sensitive H3N8 CIV as a live-attenuated influenza vaccine (LAIV), which was attenuated in mice and dog tracheal, explants compared to CIV H3N8 wild type. A single dose of H3N8 LACIV showed immunogenicity and protection against a homologous challenge that was better than that conferred with an H3N8 IIV, demonstrating the feasibility of implementing a LAIV approach for the improved control of H3N8 CIV infections in dogs.
Is body mass index associated with patellofemoral pain and patellofemoral osteoarthritis? A systematic review and meta-regression and analysis
Authors: Hart Harvi F , Barton Christian J , Khan Karim M , Riel Henrik , Crossley Kay M 
Published: December 2016

BackgroundPatellofemoral pain (PFP) occurs frequently, and may be related to patellofemoral osteoarthritis (PFOA). Obesity is associated with increased risk of knee OA. This systematic review involves a meta-regression and analysis to determine the relationship between body mass index (BMI) and PFP and PFOA, and to determine the link between BMI and interventional outcomes.MethodsWe searched seven electronic databases and reference lists of relevant papers and systematic reviews, for cross-sectional, prospective, human-based observational and interventional studies reporting BMI in individuals with PFP or PFOA compared to healthy controls. Two independent reviewers appraised methodological quality (epidemiological appraisal instrument). Where possible, data from prospective studies were pooled to conduct meta-regression and case–control, and intervention studies to conduct meta-analysis using the following categories: adolescents with PFP, adults with PFP and PFOA.Results52 studies were included. We found greater BMI in adults with PFP (standardised mean difference: 0.24, 95% CI 0.12 to 0.36) and PFOA (0.73, 0.46 to 0.99) compared to healthy controls, but not in adolescents with PFP (−0.19, −0.56 to 0.18). We also observed statistical trends (p<0.10) towards higher BMI being a predictor for development of PFP in adults (0.34, −0.04 to 0.71). No significant link between BMI and intervention outcomes in adults with PFP was identified.ConclusionsHigher BMI is present in PFP and PFOA, but not in adolescents with PFP.PROSPERO registration numberCRD42015024812.
Hydration education: developing, piloting and evaluating a hydration education package for general practitioners
Authors: McCotter L , Douglas P , Laur C , Gandy J , Fitzpatrick L , Rajput-Ray M , Ray S 
Published: December 2016

ObjectivesTo (1) assess the hydration knowledge, attitudes and practices (KAP) of doctors; (2) develop an evidence-based training package; and (3) evaluate the impact of the training package.DesignEducational intervention with impact evaluation.SettingCambridgeshire, UK.ParticipantsGeneral practitioners (GPs (primary care physicians)).InterventionsHydration and healthcare training.Main outcome measuresHydration KAP score before and immediately after the training session.ResultsKnowledge gaps of doctors identified before the teaching were the definition of dehydration, European Food Safety Authority water intake recommendations, water content of the human body and proportion of water from food and drink. A face-to-face teaching package was developed on findings from the KAP survey and literature search. 54 questionnaires were completed before and immediately after two training sessions with GPs. Following the training, total hydration KAP scores increased significantly (p<0.001; median (25th, 75th centiles); 32 (29, 34)). Attendees rated the session as excellent or good (90%) and reported the training was likely to influence their professional practice (100%).ConclusionsThe training package will continue to be developed and adapted, with increased focus on follow-up strategies as well as integration into medical curricula and standards of practice. However, further research is required in the area of hydration care to allow policymakers to incorporate hydration awareness and care with greater precision in local and national policies.
Development of a brief measure of intimate partner violence experiences: the Composite Abuse Scale (Revised)—Short Form (CASR-SF)
Authors: Ford-Gilboe Marilyn , Wathen C Nadine , Varcoe Colleen , MacMillan Harriet L , Scott-Storey Kelly , Mantler Tara , Hegarty Kelsey , Perrin Nancy 
Published: December 2016

ObjectivesApproaches to measuring intimate partner violence (IPV) in populations often privilege physical violence, with poor assessment of other experiences. This has led to underestimating the scope and impact of IPV. The aim of this study was to develop a brief, reliable and valid self-report measure of IPV that adequately captures its complexity.DesignMixed-methods instrument development and psychometric testing to evolve a brief version of the Composite Abuse Scale (CAS) using secondary data analysis and expert feedback.SettingData from 5 Canadian IPV studies; feedback from international IPV experts.Participants31 international IPV experts including academic researchers, service providers and policy actors rated CAS items via an online survey. Pooled data from 6278 adult Canadian women were used for scale development.Primary/secondary outcome measuresScale reliability and validity; robustness of subscales assessing different IPV experiences.ResultsA 15-item version of the CAS has been developed (Composite Abuse Scale (Revised)—Short Form, CASR-SF), including 12 items developed from the original CAS and 3 items suggested through expert consultation and the evolving literature. Items cover 3 abuse domains: physical, sexual and psychological, with questions asked to assess lifetime, recent and current exposure, and abuse frequency. Factor loadings for the final 3-factor solution ranged from 0.81 to 0.91 for the 6 psychological abuse items, 0.63 to 0.92 for the 4 physical abuse items, and 0.85 and 0.93 for the 2 sexual abuse items. Moderate correlations were observed between the CASR-SF and measures of depression, post-traumatic stress disorder and coercive control. Internal consistency of the CASR-SF was 0.942. These reliability and validity estimates were comparable to those obtained for the original 30-item CAS.ConclusionsThe CASR-SF is brief self-report measure of IPV experiences among women that has demonstrated initial reliability and validity and is suitable for use in population studies or other studies. Additional validation of the 15-item scale with diverse samples is required.
Molecular mechanism(s) involved in differential expression of vitamin C transporters along the intestinal tract
Authors: Subramanian Veedamali S. , Srinivasan Padmanabhan , Wildman Alexis J. , Marchant Jonathan S. , Said Hamid M. 
Published: December 2016

Mammalian cells utilize two transporters for the uptake of ascorbic acid (AA), Na+-dependent vitamin C transporter SVCT-1 and SVCT-2. In the intestine, these transporters are involved in AA absorption and are expressed at the apical and basolateral membrane domains of the polarized epithelia, respectively. Little is known about the differential expression of these two transporters along the anterior-posterior axis of the intestinal tract and the molecular mechanism(s) that dictate this pattern of expression. We used mouse and human intestinal cDNAs to address these issues. The results showed a significantly lower rate of carrier-mediated AA uptake by mouse colon than jejunum. This was associated with a significantly lower level of expression of SVCT-1 and SVCT-2 at the protein, mRNA, and heterogeneous nuclear RNA (hnRNA) levels in the colon than the jejunum, implying the involvement of transcriptional mechanism(s). Similarly, expression levels of SVCT-1 and SVCT-2 mRNA and hnRNA were significantly lower in human colon. We also examined the levels of expression of hepatocyte nuclear factor 1α and specificity protein 1, which drive transcription of the Slc23a1 and Slc23a2 promoters, respectively, and found them to be markedly lower in the colon. Furthermore, significantly lower levels of the activating markers for histone (H3) modifications [H3 trimethylation of lysine 4 (H3K4me3) and H3 triacetylation of lysine 9 (H3K9ac)] were observed in the Slc23a1 and Slc23a2 promoters in the colon. These findings show, for the first time, that SVCT-1 and SVCT-2 are differentially expressed along the intestinal tract and that this pattern of expression is, at least in part, mediated via transcriptional/epigenetic mechanisms. NEW & NOTEWORTHY Our findings show, for the first time, that transporters of the water-soluble vitamin ascorbic acid (i.e., the vitamin C transporters SVCT-1 and SVCT-2) are differentially expressed along the length of the intestinal tract and that the pattern of expression is mediated, at least in part, by transcriptional and epigenetic mechanism(s) affecting both Slc23a1 and Slc23a2 genes.