bluuebunny/crossref_metadata_2025_split huggingface dataset:
What constitutes an Arabian Helicobacter pylori? Lessons from comparative genomics
Authors: Kumar Narender , Albert M. John , Al Abkal Hanan , Siddique Iqbal , Ahmed Niyaz 
Published: June 2016

AbstractBackgroundHelicobacter pylori, the human gastric pathogen, causes a variety of gastric diseases ranging from mild gastritis to gastric cancer. While the studies on H. pylori are dominated by those based on either East Asian or Western strains, information regarding H. pylori strains prevalent in the Middle East remains scarce. Therefore, we carried out whole‐genome sequencing and comparative analysis of three H. pylori strains isolated from three native Arab, Kuwaiti patients.Materials and MethodsH. pylori strains were sequenced using Illumina platform. The sequence reads were filtered and draft genomes were assembled and annotated. Various pathogenicity‐associated regions and phages present within the genomes were identified. Phylogenetic analysis was carried out to determine the genetic relatedness of Kuwaiti strains to various lineages of H. pylori. The core genome content and virulence‐related genes were analyzed to assess the pathogenic potential.ResultsThe three genomes clustered along with HpEurope strains in the phylogenetic tree comprising various H. pylori lineages. A total of 1187 genes spread among various functional classes were identified in the core genome analysis. The three genomes possessed a complete cagPAI and also retained most of the known outer membrane proteins as well as virulence‐related genes. The cagA gene in all three strains consisted of an AB‐C type EPIYA motif.ConclusionsThe comparative genomic analysis of Kuwaiti H. pylori strains revealed a European ancestry and a high pathogenic potential.
Reductions in all‐cause and cause‐specific mortality among HIV‐infected individuals receiving antiretroviral therapy in British Columbia, Canada: 2001–2012
Authors: Cheung CC , Ding E , Sereda P , Yip B , Lourenco L , Barrios R , Montaner JSG , Hogg RS , Lima V , Moore DM 
Published: June 2016

ObjectivesSince 2006, the British Columbia HIV/AIDS Drug Treatment Program (DTP) has expanded enrolment and dramatically increased its number of participants. We examined the effect this expansion has had on the underlying cause of death in HIV‐infected individuals.MethodsWe analysed data from participants aged 18 years and older in the DTP to measure 2‐year mortality rates and causes of death from 2001 to 2012. We conducted tests of trend for all‐cause and cause‐specific mortality, and compared demographics and characteristics of individuals. Cox proportional hazard models were used to determine the risk of death.ResultsA total of 8185 participants received antiretroviral therapy (ART) during the study period. Mortality declined from 3.88 per 100 person‐years (PY) in 2001‐2002 to 2.15 per 100 PY in 2011‐2012 (P = 0.02). There were significant decreases in HIV‐related deaths (2.34 to 0.56 per 100 PY; P = 0.02) and deaths attributable to chronic liver disease (0.20 to 0.09 per 100 PY; P = 0.01), cardiovascular disease (0.24 to 0.05 per 100 PY; P = 0.03) and suicides (0.47 to 0 per 100 PY; P = 0.003). Multivariate models, adjusted for age, gender, history of injecting drug use, AIDS diagnoses and baseline CD4 cell counts, demonstrated that initiation of ART in all time periods after 2001‐2002 was independently associated with reduced mortality (P < 0.001).ConclusionsWe observed declines in HIV‐related mortality and certain non‐HIV‐related causes of death among participants in the BC DTP from 2001 to 2012. These findings suggest that there may be broader benefits to the increasingly liberal HIV treatment guidelines, including reductions in death caused by cardiovascular disease and chronic liver disease.
Expression of FOXM1 and related proteins in breast cancer molecular subtypes
Authors: Lee Jeong‐Ju , Lee Hee Jin , Son Byung‐Ho , Kim Sung‐Bae , Ahn Jin‐Hee , Ahn Seung Do , Cho Eun Yoon , Gong Gyungyub 
Published: June 2016

SummaryForkhead box (FOX) proteins constitute an extended family of transcriptional regulators. FOXM1 is ubiquitously expressed in cells undergoing proliferation, and overexpression of FOXM1 is associated with poor prognosis in various malignant tumours. FOXM1 and FOXO3a are often transcriptionally antagonistic. FOXO3a plays a critical tumour‐suppressive role in breast cancer. FOXO activity is modulated by its acetylation status, which is regulated by class III histone deacetylases (sirtuins; also known as SIRTs). This study evaluated the role of FOX proteins and their regulators in each molecular subtype of breast cancer. Immunohistochemical expressions of FOXM1, FOXO3a, SIRT1 and SIRT6 were evaluated in tissue microarray blocks containing 688 consecutive breast cancer samples. Mean expression levels were used to categorize tumours according to the expression of each protein (high or low). High expression of FOXM1 was significantly correlated with high SIRT1 and SIRT6 expression, higher histologic grade and triple‐negative breast cancer (TNBC). High expression of nuclear FOXO3a and nuclear SIRT1 was correlated with a lower histologic grade and the hormone receptor‐positive/HER2‐negative subtype. In survival analysis, FOXM1 was an independent adverse prognostic factor for disease‐free and overall survival in the hormone receptor‐positive/HER2‐negative subtype but not in the HER2‐positive subtype or TNBC. In conclusion, although high FOXM1 expression was noted in the TNBC subtype, it had no prognostic impact in TNBC. However, it had prognostic significance in the hormone receptor‐positive/HER2‐negative subtype.
Identification of a new HLA‐G allele, HLA‐G*01:19, by cloning and phasing
Authors: Wang W. Y. , Tian W. 
Published: June 2016

SummaryA new HLA‐G allelic variant, HLA‐G*01:19, was identified in a southern Chinese Han population by polymerase chain reaction–sequence‐based typing (PCR‐SBT), cloning and phasing. HLA‐G*01:19 differs from HLA‐G*01:04:01 by a nonsynonymous cytosine at position 99 in exon 2, resulting in amino acid change from valine to leucine at codon 34 of the mature HLA‐G molecule.
Multiparametric magnetic resonance imaging and active surveillance: How to better select insignificant prostate cancer?
Authors: Porpiglia Francesco , Cantiello Francesco , De Luca Stefano , De Pascale Agostino , Manfredi Matteo , Mele Fabrizio , Bollito Enrico , Cirillo Stefano , Damiano Rocco , Russo Filippo 
Published: June 2016

ObjectivesTo evaluate the role of multiparametric magnetic resonance imaging in improving the predictive accuracy of the Prostate Cancer Research International: Active Surveillance and Epstein criteria for active surveillance in prostate cancer.MethodsA retrospective study was carried out with 126 prostate cancer patients treated with robot‐assisted radical prostatectomy, but eligible for active surveillance according to the Prostate Cancer Research International: Active Surveillance criteria; 63 patients were also eligible according to the Epstein criteria. All patients underwent preoperative multiparametric magnetic resonance imaging, after at least 6 weeks from biopsy. The images from the multiparametric magnetic resonance imaging were assessed, and diagrams showing prostate sextants were used to designate regions of abnormalities within the prostate. Findings in the prostate were assigned to one of five categories according the Prostate Imaging‐Reporting and Data System guidelines (v1.0), and considered positive for prostate cancer if the final Prostate Imaging‐Reporting and Data System guidelines were >3 and negative if ≤3. Multivariate logistic regression analysis was carried out to evaluate the gain in accuracy of the Prostate Cancer Research International: Active Surveillance and Epstein criteria when added to multiparametric magnetic resonance imaging. Decision curve analysis was carried out to identify the net benefit of each model.ResultsThe inclusion of multiparametric magnetic resonance imaging to the Epstein criteria and the Prostate Cancer Research International: Active Surveillance multivariate model significantly increased their accuracy in predicting pathologically‐confirmed insignificant prostate cancer by 7% and 5%, respectively. At the decision curve analysis evaluation, the model including the Prostate Cancer Research International: Active Surveillance criteria and multiparametric magnetic resonance imaging improved the clinical risk prediction over the other models.ConclusionsThe present findings suggest that multiparametric magnetic resonance imaging is able to increase the predictive accuracy of Prostate Cancer Research International: Active Surveillance and Epstein criteria to identify prostate cancer patients eligible for active surveillance.
Macrophages transfer antigens to dendritic cells by releasing exosomes containing dead‐cell‐associated antigens partially through a ceramide‐dependent pathway to enhance CD4+ T‐cell responses
Authors: Xu Yingping , Liu Yi , Yang Chunqing , Kang Li , Wang Meixiang , Hu Jingxia , He Hao , Song Wengang , Tang Hua 
Published: June 2016

SummaryDefects in rapid clearance of apoptotic cells lead to an accumulation of dead cells (late apoptotic or secondary necrotic cells), which results in an aberrant immune response. However, little is known about whether and how macrophages (Mφs) cooperate with dendritic cells (DCs) in the presentation of dead‐cell‐associated antigens in this process. By transferring high numbers of dead cells to mimic a failure of apoptotic cell clearance in vivo, we found that Mφs and neutrophils were the predominant phagocytes in the uptake of dead cells in the spleen. Moreover, both Mφs and DCs were required for an optimal CD4+ T‐cell response triggered by dead‐cell‐associated antigens. Importantly, although Mφs alone had a poor capacity for antigen presentation, they could transfer phagocytosed antigens to DCs for potent antigen presentation to enhance T‐cell responses. Finally, we found that exosomes released from Mφs acted as a transmitter to convey antigens to DCs partially in a ceramide‐dependent manner, since treatment with the neutral sphingomyelinase inhibitor GW4869 and spiroepoxide resulted in a significant reduction of T‐cell proliferation in vitro and in vivo. These findings point to a novel pathway of cross‐talk between Mφs and DCs, which will be helpful to explain possible mechanisms for autoimmune diseases characterized by increased rates of apoptosis.
MicroRNAs regulate T‐cell production of interleukin‐9 and identify hypoxia‐inducible factor‐2α as an important regulator of T helper 9 and regulatory T‐cell differentiation
Authors: Singh Yogesh , Garden Oliver A. , Lang Florian , Cobb Bradley S. 
Published: June 2016

SummaryMicroRNAs (miRNAs) regulate many aspects of helper T cell (Th) development and function. Here we found that they are required for the suppression of interleukin‐9 (IL‐9) expression in Th9 cells and other Th subsets. Two highly related miRNAs (miR‐15b and miR‐16) that we previously found to play an important role in regulatory T (Treg) cell differentiation were capable of suppressing IL‐9 expression when they were over‐expressed in Th9 cells. We used these miRNAs as tools to identify novel regulators of IL‐9 expression and found that they could regulate the expression of Epas1, which encodes hypoxia‐inducible factor (HIF)‐2α. HIF proteins regulate metabolic pathway usage that is important in determining appropriate Th differentiation. The related protein, HIF‐1α enhances Th17 differentiation and inhibits Treg cell differentiation. Here we found that HIF‐2α was required for IL‐9 expression in Th9 cells, but its expression was not sufficient in other Th subsets. Furthermore, HIF‐2α suppressed Treg cell differentiation like HIF‐1α, demonstrating both similar and distinct roles of the HIF proteins in Th differentiation and adding a further dimension to their function. Ironically, even though miR‐15b and miR‐16 suppressed HIF‐2α expression in Treg cells, inhibiting their function in Treg cells did not lead to an increase in IL‐9 expression. Therefore, the physiologically relevant miRNAs that regulate IL‐9 expression in Treg cells and other subsets remain unknown. Nevertheless, the analysis of miR‐15b and miR‐16 function led to the discovery of the importance of HIF‐2α so this work demonstrated the utility of studying miRNA function to identify novel regulatory pathways in helper T‐cell development.
Characteristics of IT artifacts: a systems thinking‐based framework for delineating and theorizing IT artifacts
Authors: Matook Sabine , Brown Susan A. 
Published: June 2016

AbstractThe information technology artifact (ITA) has been suggested as the core of information systems (IS) research, and the research community has been encouraged to deeply engage with the ITA. Various studies highlight, however, that the ITA continues to receive only limited attention and thus, little foundation exists for IS researchers to delineate and theorize about the ITAs studied. In this paper, we develop a framework that can be utilized as a language for articulating and theorizing the ITA in IS research. Our framework builds on the multi‐faceted theoretical paradigm of systems thinking from which we derive several concepts and appropriate them to the context at hand, resulting in a seven‐dimensional framework of characteristics for ITAs. In a literature survey of research on enterprise systems and enterprise resource planning systems in top IS journals, we show how ITA characteristics are currently included to present details of the relevant ITA instance and identify theoretical relationships between ITA characteristics and outcomes. We conclude the study by demonstrating the use of the ITA framework for delineating and theorizing the ITA in IS research.
Strong dominance of functional alleles over gene deletions in both intensely growing and deeply starved yeast cells
Authors: Marek A. , Korona R. 
Published: June 2016

AbstractPrevious studies with diploid yeast have shown that the deletion of one allele at a single locus typically has little impact on fitness under conditions promoting fast growth. Here, we confirm and quantify this finding. The strong dominance of functional over nonfunctional alleles is predicted by the metabolic control theory which assumes that the cell is a system of metabolic fluxes and that the total metabolic rate is equivalent to fitness. To test whether these requirements are critical, we tested dominance under conditions of long‐term starvation when metabolism is low and thus the metabolic activities of proteins are likely inadequate or imbalanced. More fundamentally, the central assumption of the model, that high metabolic rate translates into high fitness, appears implausible. Contrary to these conjectures, we found that the mean rate of survival of starving heterozygotes was affected only slightly more than was the mean rate of growth under good conditions. Under none of the two treatments the central prediction of the model, that fitness of heterozygous strains is higher for the enzymatic proteins than for nonenzymatic ones, was confirmed. Our data add to growing uncertainty whether the metabolic control theory is sufficient to explain the remarkable ubiquity of strong genetic dominance.
A brief history of topographical anatomy
Authors: Standring Susan 
Published: June 2016

AbstractThis brief history of topographical anatomy begins with Egyptian medical papyri and the works known collectively as the Greco‐Arabian canon, the time line then moves on to the excitement of discovery that characterised the Renaissance, the increasing regulatory and legislative frameworks introduced in the 18th and 19th centuries, and ends with a consideration of the impact of technology that epitomises the period from the late 19th century to the present day. This paper is based on a lecture I gave at the Winter Meeting of the Anatomical Society in Cambridge in December 2015, when I was awarded the Anatomical Society Medal.
Application effect of sterile normal saline ice for post‐partum hemorrhage at the time of cesarean delivery: A retrospective review
Authors: Cheng Wenjing , Wang Qiushi , Zhang Zhenyu 
Published: June 2016

AbstractAimPost‐partum hemorrhage (PPH) is a common complication of cesarean sections (CS) and affects maternal and newborn health. We used a new method to control bleeding and compared its efficacy with conventional methods.MethodsEighty‐six women who experienced PPH with volume of bleeding over 1000 mL in CS between January 2008 and January 2012 were chosen as samples. Thirty‐three underwent the new method in which normal saline ice blocks are placed in the uterus, and 53 underwent the conventional method. We evaluated blood loss, volume of transfusion and complications.ResultsPatients who were treated with ice blocks had better hemostatic efficacy than those who underwent the conventional method (1450 ± 251.9 mL vs 1800 ± 278.9 mL; P < 0.001); they also had less blood transfusion (806.1 ± 242.3 mL vs 1222.6 ± 308.0 mL; P < 0.001), lower rate of hysterectomy and infection (3.03% vs 5.66%; P = 0.971; 0% vs 7.55%; P = 0.276), and shorter duration of hospital stay (5.3 ± 0.5 days vs 7.6 ± 3.0 days; P < 0.001).ConclusionPPH in CS can be treated with peeled sterile normal saline ice blocks, a simple and reliable method for stopping bleeding. Nonetheless, there needs to be a large randomized control trial for confirmation.
Effectiveness of medical self‐experience counseling in pregnant women after echocardiographic detection of a suspected fetal heart anomaly: A longitudinal study
Authors: Zhu Mei , Liang Hao , Feng Juan , Wang Zhengjun , Wang Wei , Zhou Yanhui 
Published: June 2016

AbstractAimThe purpose of this longitudinal study was to assess maternal psychological responses after echocardiographic detection of a suspected fetal heart anomaly and to evaluate a medical self‐experience counseling intervention in improving psychological responses.MethodsA total of 751 women were referred to Shandong Provincial Hospital, Jinan during May 2014 and April 2015. To analyze the psychological impact on the mothers, the groups were divided into mild, intermediate and severe, according to heart defect severity. State–Trait Anxiety Inventory (STAI) and Beck Depression Inventory II (BDI‐II) questionnaires were distributed in three steps: first evaluation, after the diagnostic examination; second evaluation, two weeks after step one, both study and control groups underwent routine psychological counseling; third evaluation, two weeks after step two, study groups underwent self‐experience counseling and controls underwent routine counseling. Anxiety and depression scores and above clinical cut‐off percentages in the subgroups were calculated and compared.ResultsThe severity of anxiety and depression was not significantly relieved with the alleviative type of suspicious heart abnormality. State‐STAI and BDI‐II scores and above clinical cut‐off percentages were statistically different between steps 2 and 3 in intermediate and mild mothers. Women in control groups did not exhibit obvious relief of anxiety and depression.ConclusionWomen pregnant with fetuses with mild or intermediate fetal heart abnormalities presented heightened levels of depression and anxiety when compared with mothers pregnant with fetuses with severe heart disease. Medical self‐experience counseling played an important role in relieving anxiety and depression in these mothers.
Relationship between Fas and Fas Ligand gene polymorphisms and pre‐eclampsia
Authors: Masoumi Elham , Tavakkol‐Afshari Jalil , Nikpoor Amin Reza , Ghaffari‐Nazari Haniyeh , Tahaghoghi‐hajghorbani Sahar , Jalali Seyed Amir 
Published: June 2016

AbstractAimIn normal pregnancy, the Th1 subtype, responsible for the production of inflammatory cytokines, is reduced, and the Th2 subtype is increased to prohibit inflammation. In pre‐eclampsia, the Th1 cell population is increased; thus, subsequent inflammation and trophoblast destruction occur. Polymorphisms in the Fas and Fas Ligand (FasL) promoter regions can influence Fas and FasL expression and accused to increase of Th1 subtype.MethodsDNA samples from 153 pregnant women with pre‐eclampsia and 140 controls were genotyped through polymerase chain reaction‐restriction fragment length polymorphism. A Fisher's exact test was used to compare the distribution of individual polymorphisms.ResultsFas‐1377 AA, AG and GG genotypes were observed in 2.61%, 18.30% and 79.08% in the pre‐eclampsia group opposed to 0%, 27.14% and 72.85% in the control group (P = 0.037), respectively. Fas‐670 AA, AG and GG genotypes were observed in 37.9%, 41.8% and 20.3% of pre‐eclampsia patients compared with 33.6%, 50.7% and 15.7% in healthy pregnant women (P = 0.291), respectively. No statically significant differences in the FasL‐844 genotype were observed between the groups (P = 0.69).ConclusionThe Fas‐1377G > A polymorphism is associated with a higher risk of pre‐eclampsia.
Two Tests for Ex Ante Moral Hazard in a Market for Automobile Insurance
Authors: Rowell David , Nghiem Son , Connelly Luke B 
Published: June 2016

AbstractEmpirically separating the phenomena of moral hazard and adverse selection in insurance markets has occupied researchers in this field for decades. Recently, the potential benefits of using survey data instead of claims data to control for the different dimensions of private information when testing for evidence of asymmetric information have been explored in the insurance literature. This article extends that approach to present two tests for ex ante moral hazard in a market for automobile insurance. In this article we specify (1) a recursive model and (2) an instrumental variables model to address endogeneity with respect to policy selection in cross‐sectional road traffic crash (RTC) survey data. We report a statistically significant ex ante moral hazard effect with both models. This result is then subjected to a falsification test, whereby the analysis is repeated in subsamples of at‐fault and not‐at‐fault RTCs. Our antitest produces no evidence of ex ante moral hazard in the sub‐sample of not‐at‐fault RTCs, in which the true moral hazard may reasonably be assumed to be zero, thus supporting the interpretation of the results of our two models. Our extension of the existing literature via these two specifications may have useful analogs in other insurance markets for which survey data are available.
Site fidelity, residency, and abundance of bottlenose dolphins (Tursiopssp.) in Adelaide's coastal waters, South Australia
Authors: Zanardo Nikki , Parra Guido J. , Möller Luciana M. 
Published: June 2016

AbstractLittle is known about the ecology and behavior of southern Australian bottlenose dolphins (Tursiopssp.). This hinders assessment of their conservation status and informed decision‐making concerning their management. We used boat‐based surveys and photo‐identification data to investigate site fidelity, residency patterns, and the abundance of southern Australian bottlenose dolphins in Adelaide's coastal waters. Sighting rates and site fidelity varied amongst individuals, and agglomerative hierarchical cluster analysis led to the categorization of individuals into one of three groups: occasional visitors, seasonal residents, or year‐round residents. Lagged identification rates indicated that these dolphins used the study area regularly from year to year following a model of emigration and reimmigration. Abundance estimates obtained from multisample closed capture‐recapture models ranged from 95 individuals (SE± 45.20) in winter 2013 to 239 (SE± 54.91) in summer 2014. The varying levels of site fidelity and residency, and the relatively high number of dolphins found throughout the study area highlights the Adelaide metropolitan coast as an important habitat for bottlenose dolphins. As these dolphins also appear to spend considerable time outside the study area, future research, conservation, and management efforts on this population must take into account anthropogenic activities within Adelaide's coastal waters and their adjacencies.