bluuebunny/crossref_metadata_2025_split huggingface dataset:
RECA plays a dual role in the maintenance of chloroplast genome stability in Physcomitrella patens
Authors: Odahara Masaki , Inouye Takayuki , Nishimura Yoshiki , Sekine Yasuhiko 
Published: September 2015

SummaryChloroplast DNA (cpDNA) encodes essential genes for chloroplast functions, including photosynthesis. Homologous recombination occurs frequently in cpDNA; however, its significance and underlying mechanism remain poorly understood. In this study, we analyzed the role of a nuclear‐encoded chloroplast‐localized homolog of RecA recombinase, which is a key factor in homologous recombination in bacteria, in the moss Physcomitrella patens. Complete knockout (KO) of the P. patens chloroplast RecA homolog RECA2 caused a modest growth defect and conferred sensitivity to methyl methanesulfonate and UV. The KO mutant exhibited low recovery of cpDNA from methyl methanesulfonate damage, suggesting that RECA2 knockout impairs repair of damaged cpDNA. The RECA2 KO mutant also exhibited reduced cpDNA copy number and an elevated level of cpDNA molecule resulting from aberrant recombination between short dispersed repeats (13–63 bp), indicating that the RECA2 KO chloroplast genome was destabilized. Taken together, these data suggest a dual role for RECA2 in the maintenance of chloroplast genome stability: RECA2 suppresses aberrant recombination between short dispersed repeats and promotes repair of damaged DNA.
Transthecal Arthroscopy of the Palmar Distal Interphalangeal Joint in the Horse: A Cadaver Study
Authors: Rubio‐Martínez Luis M. , Bracamonte Jose L. , Tompkins Samantha , Villarino Nicolás F. 
Published: September 2015

ObjectiveTo describe a transthecal approach to the palmar pouch of the distal interphalangeal joint (DIPJ) in horses and compare it with the conventional blind arthroscopic technique.Study DesignEx vivo study.Sample PopulationCadaver forelimbs (n = 26 pairs) from mature horses.MethodsOne limb from each pair was randomly assigned to each arthroscopic approach (conventional or transthecal). The conventional arthroscopic approach was performed as previously described and the transthecal approach was performed through sharp dissection of the distal reflection of the digital flexor tendon sheath (DFTS). The proportion (0–100%) of the navicular bone, palmar aspect of the condyles of the 2nd phalanx, collateral sesamoidean ligaments, and palmar synovial pouches of the DIPJ visualized by each approach was estimated. Limbs were dissected and iatrogenic damage of relevant structures was assessed. Nondirectional Mann–Whitney U‐test was used to compare groups. Significance was set at P < .05.ResultsThe transthecal approach provided greater visualization of the navicular bone (P < .001), palmar aspect of the 2nd phalanx (P < .001), and palmar synovial pouches of the DIPJ (P < .001) than the conventional approach. There were no significant differences in iatrogenic damage between approaches.ConclusionThe transthecal approach provides improved visualization of the palmar aspect of the DIPJ compared to the conventional blind approach and may be useful in nonseptic conditions of the DIPJ. However, because of the creation of communication with the DFTS, use of the transthecal approach for suspected synovial sepsis of the DIPJ may be contraindicated.
Draft Genome Sequence of the Shellfish Larval Probiotic Bacillus pumilus RI06-95
Authors: Hamblin Meagan , Spinard Edward , Gomez-Chiarri Marta , Nelson David R. , Rowley David C. 
Published: September 2015

ABSTRACT

Bacillus pumilus
RI06-95 is a marine bacterium isolated in Narragansett, Rhode Island, which has shown probiotic activity against marine pathogens in larval shellfish. We report the genome of
B. pumilus
RI06-95, which provides insight into the microbe's probiotic ability and may be used in future studies of the probiotic mechanism.
Draft Genome Sequence of Perfluorooctane Acid-Degrading Bacterium Pseudomonas parafulva YAB-1
Authors: Yi Langbo , Tang Chongjian , Peng Qingjing , Peng Qingzhong , Chai Liyuan 
Published: September 2015

ABSTRACT

Pseudomonas parafulva
YAB-1, isolated from perfluorinated compound-contaminated soil, has the ability to degrade perfluorooctane acid (PFOA) compound. Here, we report the draft genome sequence and annotation of the PFOA-degrading bacterium
P. parafulva
YAB-1. The data provide the basis to investigate the molecular mechanism of PFOA metabolism.
Draft Genome Sequence of Desulfocarbo indianensis SCBM, a New Genus of Sulfate-Reducing Bacteria, Isolated from Water Extracted from an Active Coalbed Methane Gas Well
Authors: An Thuy T. , Picardal Flynn W. 
Published: September 2015

ABSTRACT

We used Illumina MiSeq technology to sequence the whole genome of
Desulfocarbo indianensis
SCBM, a new genus of sulfate-reducing bacteria isolated from a coal bed in Indiana, USA. This draft genome represents the first sequenced genome of the genus
Desulfocarbo
and the second known genome of the order
Desulfarculales
.
Blastomyces Antigen Detection for Diagnosis and Management of Blastomycosis
Authors: Frost Holly M. , Novicki Thomas J. 
Published: September 2015

ABSTRACT

Blastomyces
spp. antigen testing was evaluated over a 10-year period in an area where blastomycosis is endemic. Antigen testing was less sensitive than previously reported, but serial urine testing was useful in monitoring disease resolution or progression. Culture and cytopathology remain the gold standard for diagnosis and exclusion of this infection.
Phenotypic Correlates of HIV-1 Macrophage Tropism
Authors: Arrildt Kathryn T. , LaBranche Celia C. , Joseph Sarah B. , Dukhovlinova Elena N. , Graham William D. , Ping Li-Hua , Schnell Gretja , Sturdevant Christa B. , Kincer Laura P. , Mallewa Macpherson , Heyderman Robert S. , Van Rie Annelies , Cohen Myron S. , Spudich Serena , Price Richard W. , Montefiori David C. , Swanstrom Ronald 
Published: September 2015

ABSTRACT

HIV-1 is typically CCR5 using (R5) and T cell tropic (T-tropic), targeting memory CD4
+
T cells throughout acute and chronic infections. However, viruses can expand into alternative cells types. Macrophage-tropic (M-tropic) HIV-1 variants have evolved to infect macrophages, which have only low levels of surface CD4. Most M-tropic variants have been isolated from the central nervous system during late-stage chronic infection. We used the HIV-1
env
genes of well-defined, subject-matched M-tropic and T-tropic viruses to characterize the phenotypic features of the M-tropic Env protein. We found that, compared to T-tropic viruses, M-tropic viruses infect monocyte-derived macrophages (MDMs) on average 28-fold more efficiently, use low-density CD4 more efficiently, have increased sensitivity to soluble CD4 (sCD4), and show trends toward sensitivity to some CD4 binding site antibodies but no difference in sensitivity to antibodies targeting the CD4-bound conformation. M-tropic viruses also displayed a trend toward resistance to neutralization by monoclonal antibodies targeting the V1/V2 region of Env, suggesting subtle changes in Env protein conformation. The paired M- and T-tropic viruses did not differ in autologous serum neutralization, temperature sensitivity, entry kinetics, intrinsic infectivity, or Env protein incorporation. We also examined viruses with modestly increased CD4 usage. These variants have significant sensitivity to sCD4 and may represent evolutionary intermediates. CD4 usage is strongly correlated with infectivity of MDMs over a wide range of CD4 entry phenotypes. These data suggest that emergence of M-tropic HIV-1 includes multiple steps in which a phenotype of increased sensitivity to sCD4 and enhanced CD4 usage accompany subtle changes in Env conformation.

IMPORTANCE
HIV-1 typically replicates in CD4
+
T cells. However, HIV-1 can evolve to infect macrophages, especially within the brain. Understanding how CCR5-using macrophage-tropic viruses evolve and differ from CCR5-using T cell-tropic viruses may provide insights into viral evolution and pathogenesis within the central nervous system. We characterized the HIV-1
env
viral entry gene from subject-matched macrophage-tropic and T cell-tropic viruses to identify entry features of macrophage-tropic viruses. We observed several differences between T cell-tropic and macrophage-tropic Env proteins, including functional differences with host CD4 receptor engagement and possible changes in the CD4 binding site and V1/V2 region. We also identified viruses with phenotypes between that of “true” macrophage-tropic and T cell-tropic viruses, which may represent evolutionary intermediates in a multistep process to macrophage tropism.
Release of Vesicular Stomatitis Virus Spike Protein G-Pseudotyped Lentivirus from the Host Cell Is Impaired upon Low-Density Lipoprotein Receptor Overexpression
Authors: Otahal Alexander , Fuchs Renate , Al-Allaf Faisal A. , Blaas Dieter 
Published: September 2015

ABSTRACT
Production of a vesicular stomatitis virus spike protein G (VSVG)-pseudotyped lentiviral expression vector in HEK293 cells decreased on overexpression of low-density lipoprotein receptor (LDLR) but not that of ICAM1 or TfR1. Reverse transcription-quantitative PCR (RT-qPCR) revealed a reduction in vector RNA as a function of LDLR expression. Decreased syncytium formation suggested diminished surface expression of VSVG. Intracellular VSVG granules colocalized with LDLR, ER-Golgi intermediate compartment protein 53 (ERGIC53), LAMP2, and vimentin but not with GM130 or calnexin, suggesting that VSVG interacts with LDLR within the ERGIC, resulting in rerouting into the aggresome/autophagosome pathway.
Mapping Enterovirus A71 Antigenic Determinants from Viral Evolution
Authors: Huang Sheng-Wen , Tai Ching-Hui , Fonville Judith M. , Lin Chin-Hui , Wang Shih-Min , Liu Ching-Chung , Su Ih-Jen , Smith Derek J. , Wang Jen-Ren 
Published: September 2015

ABSTRACT

Human enterovirus A71 (EV-A71) belongs to the
Enterovirus A
species in the
Picornaviridae
family. Several vaccines against EV-A71, a disease causing severe neurological complications or even death, are currently under development and being tested in clinical trials, and preventative vaccination programs are expected to start soon. To characterize the potential for antigenic change of EV-A71, we compared the sequences of two antigenically diverse genotype B4 and B5 strains of EV-A71 and identified substitutions at residues 98, 145, and 164 in the VP1 capsid protein as antigenic determinants. To examine the effects of these three substitutions on antigenicity, we constructed a series of recombinant viruses containing different mutation combinations at these three residues with a reverse genetics system and then investigated the molecular basis of antigenic changes with antigenic cartography. We found that a novel EV-A71 mutant, containing lysine, glutamine, and glutamic acid at the respective residues 98, 145, and 164 in the VP1 capsid protein, exhibited neutralization reduction against patients' antisera and substantially increased virus binding ability to human cells. These observations indicated that this low-neutralization-reactive EV-A71 VP1-98K/145Q/164E mutant potentially increases viral binding ability and that surveillance studies should look out for these mutants, which could compromise vaccine efficacy.

IMPORTANCE
Emerging and reemerging EV-A71 viruses can cause severe neurological etiology, primarily affecting children, especially around Asia-Pacific countries. We identified a set of mutations in EV-A71 that both reduced neutralization activity against humoral immunity in antisera of patients and healthy adults and greatly increased the viral binding ability to cells. These findings provide important insights for EV-A71 antigenic determinants and emphasize the importance of continuous surveillance, especially after EV-A71 vaccination programs begin.
Secondhand smoke exposure (SHS) and health-related quality of life (HRQoL) in Chinese never smokers in Hong Kong
Authors: Chen Jing , Wang Man-Ping , Wang Xin , Viswanath Kasisomayajula , Lam Tai-Hing , Chan Sophia S 
Published: September 2015

ObjectiveThe evidence on the effect of secondhand smoke (SHS) on Health Related Quality of Life (HRQoL) is limited. We examined the relation between SHS and HRQoL among Chinese in Hong Kong.MethodsAdult never smokers from a probability sample of three cross-sectional waves (2010, 2012, 2013) of The Hong Kong Family and Health Information Trends Survey who completed the Cantonese-version of Short-Form 12 Health Survey Questionnaire (SF12v2) were included in the data analysis conducted in 2014. Models were used to examine associations of SHS with SF12 domains and summary scores of Physical (PCS12) and Mental Component (MCS12) with subgroups analysis by SHS locations.ResultsAfter adjustments, SHS was associated with lower scores on all SF12 domains except physical functioning. PCS12 (regress coefficient=−0.76, 95% CI −1.34 to −0.17) and MCS12 (regress coefficient=−1.35, 95% CI −2.06 to −0.64) were lower in those with SHS exposure than those non-exposed. Those exposed to SHS in outdoor public places had lower scores on most SF12 domains and PSC12 and MCS12. SHS exposure in one's home and workplace was associated with lower scores on role physical, body pain and role emotional while SHS exposure in friends’ homes was additionally associated with lower social functioning and mental health scores. Lower MCS12 was associated with SHS exposure at all locations except one's home.ConclusionsOur study showed that SHS exposure, particularly in outdoor public places, was associated with decreased HRQoL. It can provide new evidence for stronger smoke-free policies on public places and promoting smoke-free homes.
Acupuncture for patients with chronic urticaria: a systematic review protocol
Authors: Yao Qin , Ye Yongming , Liu Xiaoxu , Qin Zongshi , Liu Zhishun 
Published: September 2015

IntroductionThis systematic review protocol aims to describe a meta-analysis to assess the effectiveness and safety of acupuncture therapy for patients with chronic urticaria.Methods and analysisWe will electronically search the following databases: the Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, EMBASE, the Web of Science, Traditional Chinese Medicine, China National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature Database (CBM), Chinese Scientific Journal Database (VIP database) and Wan-Fang Database from their inception. Other sources will also be searched, including the reference lists of identified publications and conference proceedings. Any clinical randomised controlled trials related to acupuncture for treating chronic urticaria without restriction of publication status and languages will be included. Study selection, data extraction and assessment of study quality will be performed independently by 2 researchers. Data will be synthesised by either the fixed-effects or random-effects model according to a heterogeneity test. Improvement in pruritus and wheals will be assessed as the primary outcomes. Adverse events, quality of life and the recurrence rate after at least 3 months of the treatment will also be evaluated as secondary outcomes. RevMan V.5.2 statistical software will be used for meta-analysis, if possible. If it is not appropriate for a meta-analysis, then a descriptive analysis or a subgroup analysis will be conducted. The results will be expressed as a risk ratio for dichotomous data and mean difference (MD) or standardised MD for continuous data.Dissemination and ethicsThe protocol of this systematic review will be disseminated in a peer-reviewed journal and presented at relevant conferences. It is not necessary for a formal ethical approval because the data are not individualised.Trial registration numberPROSPERO CRD42015015702.
Health risk of air pollution on people living with major chronic diseases: a Canadian population-based study
Authors: To Teresa , Feldman Laura , Simatovic Jacqueline , Gershon Andrea S , Dell Sharon , Su Jiandong , Foty Richard , Licskai Christopher 
Published: September 2015

ObjectivesThe objective of this study was to use health administrative and environmental data to quantify the effects of ambient air pollution on health service use among those with chronic diseases. We hypothesised that health service use would be higher among those with more exposure to air pollution as measured by the Air Quality Health Index (AQHI).SettingHealth administrative data was used to quantify health service use at the primary (physician office visits) and secondary (emergency department visits, hospitalisations) level of care in Ontario, Canada.ParticipantsWe included individuals who resided in Ontario, Canada, from 2003 to 2010, who were ever diagnosed with one of 11 major chronic diseases.Outcome measuresRate ratios (RR) from Poisson regression models were used to estimate the short-term impact of incremental unit increases in AQHI, nitrogen dioxide (NO2; 10 ppb), fine particulate matter (PM2.5; 10 µg/m3) and ozone (O3; 10 ppb) on health services use among individuals with each disease. We adjusted for age, sex, day of the week, temperature, season, year, socioeconomic status and region of residence.ResultsIncreases in outpatient visits ranged from 1% to 5% for every unit increase in the 10-point AQHI scale, corresponding to an increase of about 15 000 outpatient visits on a day with poor versus good air quality. The greatest increases in outpatient visits were for individuals with non-lung cancers (AQHI:RR=1.05; NO2:RR=1.14; p<0.0001) and COPD (AQHI:RR=1.05; NO2:RR=1.12; p<0.0001) and in hospitalisations, for individuals with diabetes (AQHI:RR=1.04; NO2:RR=1.07; p<0.0001) and COPD (AQHI:RR=1.03; NO2:RR=1.09; p<1.001). The impact remained 2 days after peak AQHI levels.ConclusionsAmong individuals with chronic diseases, health service use increased with higher levels of exposure to air pollution, as measured by the AQHI. Future research would do well to measure the utility of targeted air quality advisories based on the AQHI to reduce associated health service use.
Improving data management practices in the Portuguese HIV/AIDS surveillance system during a time of public sector austerity
Authors: Shivaji Tara , Cortes Martins Helena 
Published: September 2015

AbstractIn a climate of public sector austerity, the demand for accurate information about disease epidemiology rises as health program managers try to align spending to health needs. A policy of case re-notification to improve HIV information quality resulted in a nine-fold increase in the number of case reports received in 2013 by the Portuguese HIV surveillance office.We used value stream mapping to introduce improvements to data processing practices, identify and reduce waste. Two cycles of improvement were trialled. Before intervention, processing time was nine minutes and 28 seconds (95%CI 8:53-10:58) per report. Two months post intervention, it was six minutes and 34 seconds (95% CI 6:25-6:43). One year after the start of the project, processing time was five minutes and 20 seconds (95% CI 1:46-8:52).
Origin of ferroelectric phase transition in SbOxS1−xI mixed crystals
Authors: Audzijonis A. , Žigas L. , Žaltauskas R. , Sereika R. 
Published: September 2015

The dependence of the potential energy [Formula: see text] of Sb atoms on [Formula: see text] symmetry normal coordinates for [Formula: see text] crystal in ferroelectric phase with a varying mixture [Formula: see text] is investigated in the current paper. The potential energy of Sb atoms is characterized by a high anharmonicity within the temperature range 295–377 K. The large anharmonicity of the potential energy [Formula: see text] implies that [Formula: see text] crystals exhibit intermediate behavior between displacement and order–disorder type phase transitions. The phase transition temperature [Formula: see text] depends on the mixture composition [Formula: see text].
Krüppel-like Factor 4 Blocks Hepatocellular Carcinoma Dedifferentiation and Progression through Activation of Hepatocyte Nuclear Factor-6
Authors: Sun Hongcheng , Tang Huamei , Xie Dacheng , Jia Zhiliang , Ma Zhenyu , Wei Daoyan , Mishra Lopa , Gao Yong , Zheng Shaojiang , Xie Keping , Peng Zhihai 
Published: September 2015

Abstract
Purpose: Tumor differentiation is a behavioral index for hepatocellular carcinoma (HCC) and a prognostic factor for patients with HCC who undergo orthotopic liver transplantation (OLT). However, the molecular basis for HCC differentiation and prognostic value of the underlying molecules that regulate HCC differentiation are unclear. In this study, we defined a potential driver pathway for HCC differentiation and prognostication.
Experimental Design: The regulation and function of Krüppel-like factor 4 (KLF4) and hepatocyte nuclear factor-6 (HNF-6) in HCC differentiation was evaluated using human tissues, molecular and cell biology, and animal models, and its prognostic significance was determined according to its impact on patient survival.
Results: There was a direct relationship between the expression levels of KLF4 and HNF6 in HCC. Reduced KLF4 or HNF6 expression correlated with high HCC grade. Poorly differentiated HCC cells had lower expression of KLF4 or HNF6 and differentiation-associated markers than did well-differentiated cells. Elevated KLF4 of HNF6 expression induced differentiation of poorly differentiated hepatoma cells. Mechanistically, KLF4 trans-activated HNF-6 expression. Restored HNF-6 expression upregulated expression of differentiation-associated markers and inhibited HCC cell migration and invasion, whereas HNF-6 knockdown did the opposite. Loss of KLF4 expression in primary HCC correlated with reduced overall survival and shortened relapse-free survival durations after OLT. Combination of KLF4 expression and the Milan criteria improved prognostication for HCC after OLT.
Conclusions: The dysregulated KLF4/HNF-6 pathway drives dedifferentition and progression of HCC, and KLF4 is a biomarker for accurate prognostication of patients with HCC treated by OLT when integrated with the Milan Criteria. Clin Cancer Res; 22(2); 502–12. ©2015 AACR.
VEGF gene promoter polymorphisms and risk of VTE in chemotherapy-treated cancer patients
Authors: Palmirotta Raffaele , Riondino Silvia , Marchis Maria Laura De , Nardecchia Antonella , Formica Vincenzo , Ferroni Patrizia , Guadagni Fiorella , Roselli Mario 
Published: September 2015

SummaryAmong the possible genetic contributors to cancer-related venous thromboembolism (VTE), vascular endothelial growth factor (VEGFA) could play an important role, as an imbalance of the VEGFA system (either disease-related or drug-induced) may result in a disturbance of vascular homeostasis. Thus, this study was designed to investigate the predictive role of eight different VEGFA gene promoter single nucleotide polymorphisms (SNPs) for a first VTE episode in cancer out-patients undergoing chemotherapy. To this purpose, VEGFA gene promoter polymorphisms were analysed in 297 cancer patients using polymerase chain reaction amplification and direct DNA sequencing analysis. One hundred forty unrelated healthy subjects from the same geographical area were also analysed in order to evaluate and compare genotype/haplotype frequencies in our ethnicity. VTE occurred in 26 (9 %) of cancer patients with a median time-to-event of 3.4 months. Association analyses showed that –1154G/A polymorphism was significantly associated with the risk of chemotherapy-triggered VTE, with the A allele exerting a protective role both in the overall population (hazard ratio [HR]: 0.21; 95 % confidence interval [CI]: 0.07–0.58) or in bevacizumab-treated metastatic patients (HR: 0.09, 95 %CI: 0.01–0.86) in whom VEGFA –1154AA genotype also conferred a reduced risk of early progression (HR: 0.58, 95 %CI: 0.34–0.98). These results suggest that VEGFA may represent a candidate gene contributing to VTE development in chemotherapy treated cancer patients and that –1154G/A SNP might provide useful clinical information on the efficacy and toxicity of bevacizumab in metastatic patients. Validation studies are needed for translation into clinical practice.Note: This study has been presented in part at the Congress on Controversies in Thrombosis & Haemostasis, Berlin, Germany, October 30-November 1, 2014.