bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes
Authors: Basnet Ram Kumar , Moreno-Pachon Natalia , Lin Ke , Bucher Johan , Visser Richard G F , Maliepaard Chris , Bonnema Guusje 
Published: December 2013

AbstractBackgroundBrassicaseeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverseB. rapamorphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study inB. rapaseed.ResultsSeed developmental stages were similar in developing seeds of pak choi and yellow sarson ofB. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes inB. rapais at later developmental stages than in the related speciesB. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 “gene modules”, of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds ofBrassicaseeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putativecis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways.ConclusionsThis is the first study of genome-wide profiling of transcript abundance during seed development inB. rapa. The identification of key physiological events, major expression patterns, and putativecis-regulatory elements provides useful information to construct gene regulatory networks inB. rapadeveloping seeds and provides a starting point for a genetical genomics study of seed quality traits.
Morphogenesis-regulated localization of protein kinase A to genomic sites in Candida albicans
Authors: Schaekel Alida , Desai Prashant R , Ernst Joachim F 
Published: December 2013

Abstract

Background
The human fungal pathogen Candida albicans is able to undergo morphogenesis from a yeast to a hyphal growth form. Protein kinase A (PKA) isoforms Tpk1 and Tpk2 promote hyphal growth in a signalling pathway via the transcription factor Efg1.

Results

C. albicans strains producing epitope-tagged Tpk1 or Tpk2 were used in genome-wide chromatin immunoprecipitation on chip (ChIP chip) to reveal genomic binding sites. During yeast growth, both PKA isoforms were situated primarily within ORFs but moved to promoter regions shortly after hyphal induction. Binding sequences for Tpk2 greatly exceeded Tpk1 sites and did not coincide with binding of the PKA regulatory subunit Bcy1. Consensus binding sequences for Tpk2 within ORFs included ACCAC and CAGCA motifs that appeared to bias codon usage within the binding regions. Promoter residency of Tpk2 correlated with the transcript level of the corresponding gene during hyphal morphogenesis and occurred near Efg1 binding sites, mainly on genes encoding regulators of morphogenesis.

Conclusions
PKA isoforms change their genomic binding sites from ORF to promoter regions during yeast-hyphal morphogenesis. Tpk2 binds preferentially to promoters of genes encoding regulators of cellular morphogenesis.
Translational profiling in childhood acute lymphoblastic leukemia: no evidence for glucocorticoid regulation of mRNA translation
Authors: Aneichyk Tatsiana , Bindreither Daniel , Mantinger Christine , Grazio Daniela , Goetsch Katrin , Kofler Reinhard , Rainer Johannes 
Published: December 2013

AbstractBackgroundGlucocorticoids (GCs) are natural stress induced steroid hormones causing cell cycle arrest and cell death in lymphoid tissues. Therefore they are the central component in the treatment of lymphoid malignancies, in particular childhood acute lymphoblastic leukemia (chALL). GCs act mainlyviaregulating gene transcription, which has been intensively studied by us and others. GC control of mRNA translation has also been reported but has never been assessed systematically. In this study we investigate the effect of GCs on mRNA translation on a genome-wide scale.ResultsChildhood T- (CCRF-CEM) and precursor B-ALL (NALM6) cells were exposed to GCs and subjected to “translational profiling”, a technique combining sucrose-gradient fractionation followed by Affymetrix Exon microarray analysis of mRNA from different fractions, to assess the translational efficiency of the expressed genes. Analysis of GC regulation in ribosome-bound fractionsversustranscriptional regulation revealed no significant differences, i.e., GC did not entail a significant shift between ribosomal bound and unbound mRNAs.ConclusionsIn the present study we analyzed for the first time possible effects of GC on the translational efficiency of expressed genes in two chALL model systems employing whole genome polysome profiling. Our results did not reveal significant differences in translational efficiency of expressed genes thereby arguing against a potential widespread regulatory effect of GCs on translation at least in the investigatedin vitrosystems.
Hyperosmotic response of streptococcus mutans: from microscopic physiology to transcriptomic profile
Authors: Liu Chengcheng , Niu Yulong , Zhou Xuedong , Zhang Keke , Cheng Lei , Li Mingyun , Li Yuqing , Wang Renke , Yang Yi , Xu Xin 
Published: December 2013

Abstract

Background
Oral streptococci metabolize carbohydrate to produce organic acids, which not only decrease the environmental pH, but also increase osmolality of dental plaque fluid due to tooth demineralization and consequent calcium and phosphate accumulation. Despite these unfavorable environmental changes, the bacteria continue to thrive. The aim of this study was to obtain a global view on strategies taken by Streptococcus mutans to deal with physiologically relevant elevated osmolality, and perseveres within a cariogenic dental plaque.

Results
We investigated phenotypic change of S. mutans biofilm upon hyperosmotic challenge. We found that the hyperosmotic condition was able to initiate S. mutans biofilm dispersal by reducing both microbial content and extracellular polysaccharides matrix. We then used whole-genome microarray with quantitative RT-PCR validation to systemically investigate the underlying molecular machineries of this bacterium in response to the hyperosmotic stimuli. Among those identified 40 deferentially regulated genes, down-regulation of gtfB and comC were believed to be responsible for the observed biofilm dispersal. Further analysis of microarray data showed significant up-regulation of genes and pathways involved in carbohydrate metabolism. Specific genes involved in heat shock response and acid tolerance were also upregulated, indicating potential cross-talk between hyperosmotic and other environmental stress.

Conclusions
Hyperosmotic condition induces significant stress response on S. mutans at both phenotypic and transcriptomic levels. In the meantime, it may take full advantage of these environmental stimuli to better fit the fluctuating environments within oral cavity, and thus emerges as numeric-predominant bacterium under cariogenic conditions.
A high-throughput virus-induced gene silencing protocol identifies genes involved in multi-stress tolerance
Authors: Ramegowda Venkategowda , Senthil-kumar Muthappa , Udayakumar Makarla , Mysore Kirankumar S 
Published: December 2013

Abstract

Background
Understanding the function of a particular gene under various stresses is important for engineering plants for broad-spectrum stress tolerance. Although virus-induced gene silencing (VIGS) has been used to characterize genes involved in abiotic stress tolerance, currently available gene silencing and stress imposition methodology at the whole plant level is not suitable for high-throughput functional analyses of genes. This demands a robust and reliable methodology for characterizing genes involved in abiotic and multi-stress tolerance.

Results
Our methodology employs VIGS-based gene silencing in leaf disks combined with simple stress imposition and effect quantification methodologies for easy and faster characterization of genes involved in abiotic and multi-stress tolerance. By subjecting leaf disks from gene-silenced plants to various abiotic stresses and inoculating silenced plants with various pathogens, we show the involvement of several genes for multi-stress tolerance. In addition, we demonstrate that VIGS can be used to characterize genes involved in thermotolerance. Our results also showed the functional relevance of NtEDS1 in abiotic stress, NbRBX1 and NbCTR1 in oxidative stress; NtRAR1 and NtNPR1 in salinity stress; NbSOS1 and NbHSP101 in biotic stress; and NtEDS1, NbETR1, NbWRKY2 and NbMYC2 in thermotolerance.

Conclusions
In addition to widening the application of VIGS, we developed a robust, easy and high-throughput methodology for functional characterization of genes involved in multi-stress tolerance.
The reproductive strategy of a pollinator-limited Himalayan plant, Incarvillea mairei(Bignoniaceae)
Authors: Ai Honglian , Zhou Wei , Xu Kun , Wang Hong , Li Dezhu 
Published: December 2013

Abstract

Background
Plants may adapt to alpine habitats by specialization in the reproductive strategy and functional aspects of their flowers and pollination systems. Alpine habitats reduce the opportunities for cross-pollination in a relatively high proportion of alpine plant species, and self-pollination may be favored in these adverse conditions. Here, we investigated the mating system and pollination of Incarvillea mairei, a perennial Himalayan herb typically found at altitudes between 3000 and 4500 m.

Results
Analyses of floral morphology, observation of plant-pollinator interactions, and hand pollination experiments were conducted in three natural populations. Outcrossing rates and effective numbers of pollen donors were assessed in 45 open-pollinated families by using progeny analysis based on seven microsatellite markers. Incarvillea mairei displayed a set of apparently specialized floral traits, the stigma is sensitive to touch and close immediately and its reopening allows a second opportunity for the receipt of pollen. The species is fully self-compatible but employs a predominantly outcrossing mating system according to parentage analysis (tm > 0.9). Fruit set was low (26.3%), whereas seed set was high (67.2%), indicating that this species suffers pollinator limitation. Its main effective pollinator was Halictus sp., and visitation frequency was low.

Conclusions
Floral features such as having a sensitive stigma and anther-prongs, in conjunction with pollinator behavior, function together contributing to a set of unique reproductive adaptations that enhance outcrossing success. The increased floral longevity and high pollination efficiency operated as compensatory mechanisms to counteract low pollinator visitation frequency.
A survey of Preventive Measures Used and their Impact on Central Line-Associated Bloodstream Infections (CLABSI) in Intensive Care Units (SPIN-BACC)
Authors: Gonzales Milagros , Rocher Isabelle , Fortin Élise , Fontela Patricia , Kaouache Mohammed , Tremblay Claude , Frenette Charles , Quach Caroline 
Published: December 2013

Abstract

Background
The Quebec central line-associated bloodstream infections (CLABSI) in intensive care units (ICUs) Surveillance Program saw a decrease in CLABSI rates in most ICUs. Given the surveillance trends observed in recent years, we aimed to determine what preventive measures have been implemented, if compliance to measures was monitored and its impact on CLABSI incidence rates.

Methods
All hospitals participating in the Quebec healthcare-associated infections surveillance program (SPIN-BACC – n = 48) received a 77-question survey about preventive measures implemented and monitored in their ICU. The questionnaire was validated for construct, content, face validity, and reliability. We used Poisson regression to measure the association between compliance monitoring to preventive measures and CLABSI rates.

Results
Forty-two (88%) eligible hospitals completed the survey. Two components from the maximum barrier precautions were used less optimally: cap (88%) and full sterile body drape (71%). Preventive measures reported included daily review of catheter need (79%) and evaluation of insertion site for the presence of inflammation (90%). Two hospitals rewired lines even if an infection was suspected or documented.
In adult ICUs, there was a statistically significant greater decrease in CLABSI rates in ICUs that monitored compliance to preventive insertion measures, after adjusting for teaching status and the number of hospital beds (p = 0.036).

Conclusions
Hospitals participating to the SPIN-BACC program follow recommendations for CLABSI prevention, but only a minority locally monitor their application. Compliance monitoring of preventive measures for catheter insertion was associated with a decrease in CLABSI incidence rates.
Incarceration is associated with used syringe lending among active injection drug users with detectable plasma HIV-1 RNA: a longitudinal analysis
Authors: Milloy M-J , Kerr Thomas , Salters Kate , Samji Hasina , Guillemi Silvia , Montaner Julio , Wood Evan 
Published: December 2013

Abstract

Background
Informed by recent studies demonstrating the central role of plasma HIV-1 RNA viral load (VL) on HIV transmission, interventions to employ HIV antiretroviral treatment as prevention (TasP) are underway. To optimize these efforts, evidence is needed to identify factors associated with both non-suppressed VL and HIV risk behaviours. Thus, we sought to assess the possible role played by exposure to correctional facilities on VL non-suppression and used syringe lending among HIV-seropositive people who use injection drugs (PWID).

Methods
We used data from the ACCESS study, a community-recruited prospective cohort. We used longitudinal multivariate mixed-effects analyses to estimate the relationship between incarceration and plasma HIV-1 RNA > 500 copies/mL among antiretroviral therapy (ART)-exposed active PWID and, during periods of non-suppression, the relationship between incarceration and used syringe lending.

Results
Between May 1996 and March 2012, 657 ART-exposed PWID were recruited. Incarceration was independently associated with higher odds of VL non-suppression (Adjusted Odds Ratio [AOR] = 1.54, 95% Confidence Interval [95% CI]: 1.10, 2.16). In a separate multivariate model restricted to periods of VL non-suppression, incarceration was independently associated with lending used syringes (AOR = 1.81, 95% CI: 1.03, 3.18).

Conclusions
The current findings demonstrate that incarceration is associated with used syringe lending among active PWID with detectable plasma HIV-1 RNA. Our results provide a possible pathway for the commonly observed association between incarceration and increased risk of HIV transmission. Our results suggest that alternatives to incarceration of non-violent PWID and evidence-based combination HIV prevention interventions for PWID within correctional facilities are urgently needed.
Influence of FTO variants on obesity, inflammation and cardiovascular disease risk biomarkers in Spanish children: a case–control multicentre study
Authors: Olza Josune , Ruperez Azahara I , Gil-Campos Mercedes , Leis Rosaura , Fernandez-Orth Dietmar , Tojo Rafael , Cañete Ramon , Gil Angel , Aguilera Concepcion M 
Published: December 2013

Abstract

Background
Variants in the FTO gene have been associated with obesity in children, but this association has not been shown with other biomarkers. We assessed the association of 52 FTO polymorphisms, spanning the whole gene, with obesity and estimated the influence of these polymorphisms on anthropometric, clinical and metabolic parameters as well as inflammation and cardiovascular disease (CVD) risk biomarkers among Spanish children.

Methods
A multicentre case–control study was conducted in 534 children (292 obese and 242 with normal-BMI). Anthropometric, clinical, metabolic, inflammation and CVD risk markers were compared using the Student’s t-test for unpaired samples. The genotype relative risk was assessed by comparing the obese and normal-BMI group, calculating the odds ratio. The association of each SNP with phenotypic parameters was analysed using either logistic or linear regression analysis.

Results
All anthropometric, clinical and metabolic factors as well as inflammatory and CVD risk biomarkers were higher in the obese than in the normal-BMI group, except adiponectin and HDL-c that were lower, and glucose, LDL-c, and metalloproteinase-9 that did not show difference. Four polymorphisms (rs9935401, rs9939609, rs9928094 and rs9930333) were positively associated with obesity and in linkage disequilibrium between each other; the haplotype including the risk alleles of these polymorphisms showed a high risk for obesity. The rs8061518 was negatively associated with obesity and the haplotype including this SNP and rs3826169, rs17818902 and rs7190053 showed a decreased risk for obesity. Additionally, the rs8061518 was associated with weight, diastolic blood pressure, insulin, homeostatic model assessment of insulin resistance, leptin, and active plasminogen inhibitor activator-1 after sex and age adjustment; however, after an additional BMI adjustment, this polymorphism remained associated only with leptin.

Conclusions
We validated the previous reported association of genetic variability in intron 1 of the FTO gene with the risk of obesity and found no association with other related traits in this region of the gene. We have observed strong statistical evidence for an association of rs8061518 in intron 3 of the gene with decreased risk of obesity and low concentration of leptin.
Infusion of autologous bone marrow mononuclear cells leads to transient reduction in proteinuria in treatment refractory patients with Idiopathic membranous nephropathy
Authors: Sengupta Upal , Kumar Vinod , Yadav Ashok K , Marwaha Neelam , Kohli Harbir S , Sakhuja Vinay , Jha Vivekanand 
Published: December 2013

Abstract

Background
The current treatment options for idiopathic membranous nephropathy (IMN) carry significant toxicity. In this prospective, observational pilot study, we used single time infusion of bone marrow derived autologous mononuclear cells (MNCs) in adult patients with treatment refractory IMN.

Methods
Twelve patients of biopsy proven IMN who had failed a cyclical 6-month regimen of steroid and cyclophosphamide were enrolled in the study. Bone-marrow was harvested from the iliac crest and underwent processing to isolate MNCs. Cells were counted and subjected to viability testing before being infused through a peripheral vein on the same day. After the infusion, subjects were followed up monthly for the next six months. Supportive treatment including angiotensin antagonists and statins was continued throughout the study period.

Result
The proteinuria, serum albumin and creatinine values at entry were 2.97 ± 0.6 gm/1.73 m2/d, 2.27 ± 1.1 gm/l and 0.9 ± 0.8 mg/dl respectively. There was a reduction in proteinuria (p < 0.0001), and increase in serum albumin (p = 0.001) at 1 month, with 64% of the subjects showing >50% reduction in proteinuria. However, the response was ill sustained. At 6 months, only 2 patients had >50% reduction. Serum creatinine remained stable throughout the study period. No infusion related side effects were noted.

Conclusion
Autologous mononuclear cell infusion leads to transitory reduction in proteinuria and improvement in serum albumin in treatment refractory IMN. This effect, however, is transient. Whether this can be overcome by repeated infusion of cultured mesenchymal cells needs to be investigated.
Predicting risk of mortality in dialysis patients: a retrospective cohort study evaluating the prognostic value of a simple chest X-ray
Authors: Bohn Ethan , Tangri Navdeep , Gali Brent , Henderson Blair , Sood Manish M , Komenda Paul , Rigatto Claudio 
Published: December 2013

Abstract

Background
Clinical outcomes of dialysis patients are variable, and improved knowledge of prognosis would inform decisions regarding patient management. We assessed the value of simple, chest X-ray derived measures of cardiac size (cardiothoracic ratio (CTR)) and vascular calcification (Aortic Arch Calcification (AAC)), in predicting death and improving multivariable prognostic models in a prevalent cohort of hemodialysis patients.

Methods
Eight hundred and twenty-four dialysis patients with one or more postero-anterior (PA) chest X-ray were included in the study. Using a validated calcification score, the AAC was graded from 0 to 3. Cox proportional hazards models were used to assess the association between AAC score, CTR, and mortality. AAC was treated as a categorical variable with 4 levels (0,1,2, or 3). Age, race, diabetes, and heart failure were adjusted for in the multivariable analysis. The criterion for statistical significance was p<0.05.

Results
The median CTR of the sample was 0.53 [IQR=0.48,0.58] with calcification scores as follows: 0 (54%), 1 (24%), 2 (17%), and 3 (5%). Of 824 patients, 152 (18%) died during follow-up. Age, sex, race, duration of dialysis, diabetes, heart failure, ischemic heart disease and baseline serum creatinine and phosphate were included in a base Cox model. Both CTR (HR 1.78[1.40,2.27] per 0.1 unit change), area under the curve (AUC)=0.60[0.55,0.65], and AAC (AAC 3 vs 0 HR 4.35[2.38,7.66], AAC 2 vs 0 HR 2.22[1.41,3.49], AAC 1 vs 0 HR 2.43[1.64,3.61]), AUC=0.63[0.58,0.68]) were associated with death in univariate Cox analysis. CTR remained significant after adjustment for base model variables (adjusted HR 1.46[1.11,1.92]), but did not increase the AUC of the base model (0.71[0.66,0.76] vs. 0.71[0.66,0.76]) and did not improve net reclassification performance (NRI=0). AAC also remained significant on multivariable analysis, but did not improve net reclassification (NRI=0). All ranges were based on 95% confidence intervals.

Conclusions
Neither CTR nor AAC assessed on chest x-ray improved prediction of mortality in this prevalent cohort of dialysis patients. Our data do not support the clinical utility of X-ray measures of cardiac size and vascular calcification for the purpose of mortality prediction in prevalent hemodialysis patients. More advanced imaging techniques may be needed to improve prognostication in this population.