bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of miR‐146a and miR‐142‐3p as Potential Markers of Freshly Isolated or In Vitro‐Expanded Human Treg cells
Authors: Holmstrøm K. , Pedersen A. E. , Gad M. 
Published: December 2016

AbstractRegulatory CD4+ T cells (Tregs) are pivotal for prevention of autoimmunity. The use of Tregs is therefore of increasing interest in in vitro drug screening assays as well as for a cytotherapy per se against autoimmune disorders. For both purposes, in vitro expansion of peripheral blood Tregs is necessary and there is an increasing need to identify novel markers that can discriminate natural thymic‐derived Tregs (tTregs) from other T cell subsets, and ideally, such markers should be stably expressed during in vitro expansion procedures. We screened for novel miRNAs differentially expressed in tTregs and identified miR‐146a and 142‐3p as possible candidates. We analysed freshly isolated naïve and activated tTregs and non‐Treg subsets after or prior to in vitro expansion. We observed a tTreg‐specific profile of these miRNAs together with FOXP3 and Helios in freshly isolated tTregs, but observed a decline in the same markers in activated tTregs as opposed to naïve tTregs. In vitro‐expanded Tregs could be identified based on FOXP3 expression, but with loss of a discriminate profile for miRNA candidates and a decline in FOXP3 when activated tTregs were expanded. Our data demonstrate miR‐146a and 142‐3p as potential miRNA markers for discrimination between non‐Treg cells and tTregs, but these miRNAs are not stable markers for in vitro‐expanded Treg cells. In addition, the loss of FOXP3 in expansion of activated tTregs has implication for in vitro use of this cell subset in immunopharmacological assays and cytotherapy as FOXP3 is pivotal for suppressive function.
Expression of Toll‐Like Receptors in Peripheral Blood Mononuclear Cells of Patients with Primary Sjögren's Syndrome
Authors: Karlsen M. , Jakobsen K. , Jonsson R. , Hammenfors D. , Hansen T. , Appel S. 
Published: December 2016

AbstractToll‐like receptors (TLRs) are pattern recognition receptors important for the detection of pathogen‐associated molecular patterns. They are localized on cellular membranes, on either the cell surface or the endosomes. Primary Sjögren's syndrome (pSS) is a systemic rheumatic autoimmune disease characterized by lymphocytic infiltrations in exocrine glands resulting in dryness in eyes and mouth. In a majority of patients, autoantibodies against Ro/SSA and/or La/SSB are present. Here we analysed mRNA levels of TLR1‐10 and protein expression levels of most of them in human peripheral blood mononuclear cells from 20 patients with pSS and 20 healthy controls. Patients with pSS showed significantly higher mRNA levels of TLR8 than controls, while transcript levels of TLR9 were significantly lower. At the protein level, patients with pSS expressed significantly less TLR5 and significantly more TLR7 compared with healthy controls. TLR7 and 8 are encoded by genes localized on the X chromosome, which is especially interesting regarding the gender imbalance of pSS. The differential expression of various TLR in PBMC of patients with pSS might contribute to an altered recognition of nucleic acids, eventually resulting in the development of autoimmune disease.
Risk factors for the development of Clostridium difficile infection in adult allogeneic hematopoietic stem cell transplant recipients: A single‐center study in Québec, Canada
Authors: Lavallée Christian , Labbé Annie‐Claude , Talbot Jean‐Daniel , Alonso Carolyn D. , Marr Kieren A. , Cohen Sandra , Laverdière Michel , Dufresne Simon Frédéric 
Published: December 2016

AbstractBackgroundClostridium difficile infection (CDI) is a significant complication of allogeneic hematopoietic stem cell transplantation (allo‐HSCT). Our primary objective was to determine risk factors for the development of CDI during the first year following allo‐HSCT.MethodsA matched case–control study nested in a cohort of allo‐HSCT at a single hospital in Montréal, Québec, Canada, was conducted from 2002 through 2011.ResultsSixty‐five of 760 patients who underwent allo‐HSCT between 2002 and 2011 developed CDI, representing an incidence of 8.6%. We selected 123 controls matched for year of transplant for risk factor analyses. In the multivariable analysis, receipt of trimethoprim‐sulfamethoxazole (TMP‐SMX) prior to transplantation (adjusted odds ratio [aOR] 0.07, 95% confidence interval [CI] 0.02‐0.27), mucositis (aOR 5.90, 95% CI 2.08‐16.72), and reactivation of cytomegalovirus (CMV) (aOR 6.17, 95% CI 2.17‐17.57) and of other Herpesviridae viruses (aOR 3.04, 95% CI 1.13‐8.16) were the variables that remained statistically associated with CDI. High‐risk antibiotic use in the late post‐transplant period (aOR 7.63, 95% CI 2.14‐27.22) was associated with development of late CDI.ConclusionThis study revealed reactivation of CMV and other Herpesviridae viruses as novel risk factors for CDI. Administration of TMP‐SMX prior to transplantation was independently associated with a decreased risk of CDI. Early and late CDI after HSCT may have distinct risk factors.
Risk factors and epidemiology of Clostridium difficile infection in hematopoietic stem cell transplant recipients during the peritransplant period
Authors: Aldrete Sol del Mar , Kraft Colleen S. , Magee Matthew J. , Chan Austin , Hutcherson Don , Langston Amelia A. , Greenwell Brian I. , Burd Eileen M. , Friedman‐Moraco Rachel 
Published: December 2016

AbstractBackgroundHematopoietic stem cell transplant (HSCT) recipients represent a high‐risk group for developing Clostridium difficile (CD) infection (CDI). We aimed to identify specific risk factors for CDI in an HSCT patient population during the peritransplant period.MethodsWe performed a case–control study within a cohort of HSCT patients who received a transplant from November 2010 to March 2013. Cases had a clinical presentation compatible with CDI and a positive stool sample Xpert® C. difficile test. Controls were CDI negative and matched on age, gender, and transplant type. Peritransplant period was defined as −30 days or time of stem cell mobilization maneuver to 30 days post transplant in autologous SCT or 90 days post transplant in allogeneic SCT.ResultsOf 781 HSCTs performed during the study period, 650 (83.2%) had a stool sample submitted for CD testing. Eight‐six (13.2%) cases with CDI were identified. Most of the cases were diagnosed within a week after transplantation (median of 5 days). In adjusted analysis, prior hospitalization (odds ratio [OR]: 2.01, 95% confidence interval [CI] 1.2‐3.36), prior cephalosporin administration (OR 2.72, 95% CI: 1.54‐4.83), and prior chemotherapy (OR: 3.26, 95% CI: 1.92‐5.5) were significantly associated with CDI.ConclusionsHospitalization, and prior antibiotic and chemotherapy use are risk factors that are not easily modifiable, which emphasizes the need to start investigating preventive or prophylactic strategies in this high‐risk population.
The mitochondrial complexome of Arabidopsis thaliana
Authors: Senkler Jennifer , Senkler Michael , Eubel Holger , Hildebrandt Tatjana , Lengwenus Christian , Schertl Peter , Schwarzländer Markus , Wagner Stephan , Wittig Ilka , Braun Hans‐Peter 
Published: December 2016

SummaryMitochondria are central to cellular metabolism and energy conversion. In plants they also enable photosynthesis through additional components and functional flexibility. A majority of those processes relies on the assembly of individual proteins to larger protein complexes, some of which operate as large molecular machines. There has been a strong interest in the makeup and function of mitochondrial protein complexes and protein–protein interactions in plants, but the experimental approaches used typically suffer from selectivity or bias. Here, we present a complexome profiling analysis for leaf mitochondria of the model plant Arabidopsis thaliana for the systematic characterization of protein assemblies. Purified organelle extracts were separated by 1D Blue native (BN) PAGE, a resulting gel lane was dissected into 70 slices (complexome fractions) and proteins in each slice were identified by label free quantitative shot‐gun proteomics. Overall, 1359 unique proteins were identified, which were, on average, present in 17 complexome fractions each. Quantitative profiles of proteins along the BN gel lane were aligned by similarity, allowing us to visualize protein assemblies. The data allow re‐annotating the subunit compositions of OXPHOS complexes, identifying assembly intermediates of OXPHOS complexes and assemblies of alternative respiratory oxidoreductases. Several protein complexes were discovered that have not yet been reported in plants, such as a 530 kDa Tat complex, 460 and 1000 kDa SAM complexes, a calcium ion uniporter complex (150 kDa) and several PPR protein complexes. We have set up a tailored online resource (https://complexomemap.de/at_mito_leaves) to deposit the data and to allow straightforward access and custom data analyses.
Maintaining the factory: the roles of the unfolded protein response in cellular homeostasis in plants
Authors: Angelos Evan , Ruberti Cristina , Kim Sang‐Jin , Brandizzi Federica 
Published: December 2016

SummaryMuch like a factory, the endoplasmic reticulum (ER) assembles simple cellular building blocks into complex molecular machines known as proteins. In order to protect the delicate protein folding process and ensure the proper cellular delivery of protein products under environmental stresses, eukaryotes have evolved a set of signaling mechanisms known as the unfolded protein response (UPR) to increase the folding capacity of the ER. This process is particularly important in plants, because their sessile nature commands adaptation for survival rather than escape from stress. As such, plants make special use of the UPR, and evidence indicates that the master regulators and downstream effectors of the UPR have distinct roles in mediating cellular processes that affect organism growth and development as well as stress responses. In this review we outline recent developments in this field that support a strong relevance of the UPR to many areas of plant life.
Seed dormancy and soil seedbank of the invasive weed Chenopodium hybridum in north‐western China
Authors: Hu X W , Pan J , Min D D , Fan Y , Ding X Y , Fan S G , Baskin C C , Baskin J M 
Published: December 2016

SummarySeed dormancy and persistence in the soil seedbank play a key role in timing of germination and seedling emergence of weeds; thus, knowledge of these traits is required for effective weed management. We investigated seed dormancy and seed persistence on/in soil of Chenopodium hybridum, an annual invasive weed in north‐western China. Fresh seeds are physiologically dormant. Sulphuric acid scarification, mechanical scarification and cold stratification significantly increased germination percentages, whereas dry storage and treatments with plant growth regulators or nitrate had no effect. Dormancy was alleviated by piercing the seed coat but not the pericarp. Pre‐treatment of seeds collected in 2012 and 2013 with sulphuric acid for 30 min increased germination from 0% to 66% and 62% respectively. Effect of cold stratification on seed germination varied with soil moisture content (MC) and duration of treatment; seeds stratified in soil with 12% MC for 2 months germinated to 39%. Burial duration, burial depth and their interaction had significant effects on seed dormancy and seed viability. Dormancy in fresh seeds was released from October to February, and seeds re‐entered dormancy in April. Seed viability decreased with time for seeds on the soil surface and for those buried at a depth of 5 cm, and 39% and 10%, respectively, were viable after 22 months. Thus, C. hybridum can form at least a short‐lived persistent soil seedbank.
Modeling Stochastic Variability in the Numbers of Surviving Salmonella enterica, Enterohemorrhagic Escherichia coli, and Listeria monocytogenes Cells at the Single-Cell Level in a Desiccated Environment
Authors: Koyama Kento , Hokunan Hidekazu , Hasegawa Mayumi , Kawamura Shuso , Koseki Shigenobu 
Published: December 2016

ABSTRACT

Despite effective inactivation procedures, small numbers of bacterial cells may still remain in food samples. The risk that bacteria will survive these procedures has not been estimated precisely because deterministic models cannot be used to describe the uncertain behavior of bacterial populations. We used the Poisson distribution as a representative probability distribution to estimate the variability in bacterial numbers during the inactivation process. Strains of four serotypes of
Salmonella enterica
, three serotypes of enterohemorrhagic
Escherichia coli
, and one serotype of
Listeria monocytogenes
were evaluated for survival. We prepared bacterial cell numbers following a Poisson distribution (indicated by the parameter λ, which was equal to 2) and plated the cells in 96-well microplates, which were stored in a desiccated environment at 10% to 20% relative humidity and at 5, 15, and 25°C. The survival or death of the bacterial cells in each well was confirmed by adding tryptic soy broth as an enrichment culture. Changes in the Poisson distribution parameter during the inactivation process, which represent the variability in the numbers of surviving bacteria, were described by nonlinear regression with an exponential function based on a Weibull distribution. We also examined random changes in the number of surviving bacteria using a random number generator and computer simulations to determine whether the number of surviving bacteria followed a Poisson distribution during the bacterial death process by use of the Poisson process. For small initial cell numbers, more than 80% of the simulated distributions (λ = 2 or 10) followed a Poisson distribution. The results demonstrate that variability in the number of surviving bacteria can be described as a Poisson distribution by use of the model developed by use of the Poisson process.

IMPORTANCE
We developed a model to enable the quantitative assessment of bacterial survivors of inactivation procedures because the presence of even one bacterium can cause foodborne disease. The results demonstrate that the variability in the numbers of surviving bacteria was described as a Poisson distribution by use of the model developed by use of the Poisson process. Description of the number of surviving bacteria as a probability distribution rather than as the point estimates used in a deterministic approach can provide a more realistic estimation of risk. The probability model should be useful for estimating the quantitative risk of bacterial survival during inactivation.
Association between meteorological factors and bacillary dysentery incidence in Chaoyang city, China: an ecological study
Authors: Zhao Yang , Zhu Yaxin , Zhu Zhiwei , Qu Bo 
Published: December 2016

ObjectivesTo quantify the relationship between meteorological factors and bacillary dysentery incidence.DesignEcological study.SettingWe collected bacillary dysentery incidences and meteorological data of Chaoyang city from the year 1981 to 2010. The climate in this city was a typical northern temperate continental monsoon. All meteorological factors in this study were divided into 4 latent factors: temperature, humidity, sunshine and airflow. Structural equation modelling was used to analyse the relationship between meteorological factors and the incidence of bacillary dysentery.MaterialIncidences of bacillary dysentery were obtained from the Center for Disease Control and Prevention of Chaoyang city, and meteorological data were collected from the Bureau of Meteorology in Chaoyang city.Primary outcome measuresThe indexes including χ2, root mean square error of approximation (RMSEA), comparative fit index (CFI), standardised root mean square residual (SRMR) and goodness-of-fit index (GFI) were used to evaluate the goodness-of-fit of the theoretical model to the data. The factor loads were used to explore quantitative relationship between bacillary dysentery incidences and meteorological factors.ResultsThe goodness-of-fit results of the model showing that RMSEA=0.08, GFI=0.84, CFI=0.88, SRMR=0.06 and the χ2value is 231.95 (p=0.0) with 15 degrees of freedom. Temperature and humidity factors had positive correlations with incidence of bacillary dysentery, with the factor load of 0.59 and 0.78, respectively. Sunshine had a negative correlation with bacillary dysentery incidence, with a factor load of −0.15.ConclusionsHumidity and temperature should be given greater consideration in bacillary dysentery prevention measures for northern temperate continental monsoon climates, such as that of Chaoyang.
Effectiveness of medicines authentication technology to detect counterfeit, recalled and expired medicines: a two-stage quantitative secondary care study
Authors: Naughton Bernard , Roberts Lindsey , Dopson Sue , Chapman Stephen , Brindley David 
Published: December 2016

ObjectivesTo identify the authentication and detection rate of serialised medicines using medicines authentication technology.Design and intervention4192 serialised medicines were entered into a hospital dispensary over two separate 8-week stages in 2015. Medicines were authenticated using secure external database cross-checking, triggered by the scanning of a two-dimensional data matrix with a unit specific 12-digit serial code. 4% of medicines included were preprogrammed with a message to identify the product as either expired, pack recalled, product recalled or counterfeit.SettingA site within a large UK National Health Service teaching hospital trust.ParticipantsAccredited checking staff, pharmacists and dispensers in a pharmacy department.Primary outcome measuresAuthentication and detection rate of counterfeit expired and recalled medicines.ResultsThe operational detection rate of counterfeit, recalled and expired medicines scanned as a combined group was 81.4% (stage 1 (S1)) and 87% (stage 2 (S2)). The technology's technical detection rate (TDR) was 100%; however, not all medicines were scanned and of those that were scanned not all that generated a warning message were quarantined. Owing to an operational authentication rate (OAR) of 66.3% (over both stages), only 31.8% of counterfeit medicines, 58% of recalled drugs and 64% of expired medicines were detected as a proportion of those entered into the study. Response times (RTs) of 152 ms (S1) and 165 ms (S2) were recorded, meeting the falsified medicines directive-mandated 300 ms limit.ConclusionsTDRs and RTs were not a limiting factor in this study. The suboptimal OAR poses significant quality and safety issues with this detection approach. Authentication at the checking stage, however, demonstrated higher OARs. There is a need for further qualitative research to establish the reasons for less than absolute authentication and detection rates in the hospital environment to improve this technology in preparation for the incumbent European Union regulative deadline.
Ultrasonographic reference values for peripheral nerves and nerve roots in the normal population of children and adolescents: study protocol for an observational-prospective trial
Authors: Rasenack Maria , Décard Bernhard F , Schädelin Sabine , Grimm Alexander , Fischer Dirk , Hafner Patricia 
Published: December 2016

BackgroundHigh-resolution ultrasonography is a new and promising technique to evaluate peripheral and spinal nerves. Its validity as a diagnostic tool in neurological diseases has been demonstrated in adults. Up to now no reference values have been published in children and adolescents although this technique would be ideal in this population as it is fast and non-invasive.Methods/designOur aim is to generate ultrasonographic reference values for several peripheral nerves (median, ulnar, radial, tibial, sural, peroneal and tibial nerve) as well as for the spinal nerves C5 and C6 and the vagus nerve in children and adolescents. In an observational prospective study, we will recruit 205 children and adolescents aged between ≥2 and ≤18 years without neuromuscular symptoms/signs and without a history of neuromuscular disease. After the collection of demographic and anthropometric data (height, weight, body mass index, age, gender and handedness) and a neurologic examination, a high-resolution ultrasonography of peripheral and spinal nerves at several anatomic landmarks will be performed. These data will be used to estimate age-dependent percentile curves and to evaluate inter-rater, intrarater and interequipment reliability of the measurements.Ethics and disseminationThis study was approved by the local ethics committee (EKNZ 2015-210). The findings from this study will be disseminated through peer-reviewed publications and conference presentations.Trial registration numberNCT02570802, pre-results publication.
Genetic polymorphisms ofUTS2rs2890565 Ser89Asn in cardiac hypertrophy in Chinese Han population
Authors: Zhao Jing , Jiang Jie , Wang Jie , Liu Lin , Han Xiao-Ning , Chu Song-Yun , Xue Lin , Ding Wen-Hui 
Published: December 2016

ABSTRACTObjectiveCardiac hypertrophy is the heart’s response to a variety of extrinsic and intrinsic stimuli, some of which might finally lead up to a maladaptive state. Clinical evidence, in vitro and in vivo studies have implicated urotensin II (U-II/UTS2) in the development of cardiac hypertrophy, contributing to the (patho)-physiological regulation of cardiovascular homeostasis in humans. Several genes are associated with left ventricular hypertrophy; considering these, our objective was to evaluate the possible role of UTS2 gene polymorphisms (Thr21Met and Ser89Asn) in the genetic susceptibility to cardiac hypertrophy in a Chinese population.MethodsA case-control study was designed to compare the distribution of alleles and genotypes between three groups: case group 1 (subjects with hypertension and cardiac hypertrophy, n=265), case group 2 (subjects with hypertension, without cardiac hypertrophy, n=768), and the control group (subjects neither with hypertension nor with cardiac hypertrophy, n=416). The detection of UTS2 gene polymorphisms was achieved with the PCR restriction fragment length polymorphism technique.ResultsWe did not identify statistically significant differences between the three groups, neither with regard to the frequency of genotype/variant at the Ser89Asn locus nor at the Thr21Met locus. When stratified by sex, differences in genotype distribution of polymorphism Ser89Asn were only seen in female subjects in both the additive tested inheritance model (OR=0.507, 95% CI 0.249 to 1.032, p=0.032) and the recessive tested inheritance model (OR=0.475, 95% CI 0.239 to 0.945, p=0.034) between case group 2 (subjects with hypertension, without cardiac hypertrophy) and the control group (subjects neither with hypertension nor with cardiac hypertrophy). When stratified by sex, for female subjects with cardiac hypertrophy, we identified statistically significant differences in left ventricular posterior wall thickness for variant genotypes at the Ser89Asn locus (AA vs GG: 1.2500 (1.2000, 1.3750) vs 1.2500 (1.2000, 1.3750), p=0.03) and (AG+AA vs GG: 1.2000 (1.2000, 1.3000) vs 1.2000 (1.1000, 1.2000), p=0.01).ConclusionsSer89Asn (S89N) polymorphisms of the UTS2 gene were associated with hypertension in a Chinese female population. Additionally, we demonstrated that genotype Asn89Asn was associated with left ventricular posterior wall thickness for subjects with hypertension and cardiac hypertrophy in a Chinese female population.