共查询到20条相似文献,搜索用时 15 毫秒
1.
Thierry-Pascal Baum Vivien Hierle Nicolas Pasqual Fatena Bellahcene Denys Chaume Marie-Paule Lefranc Evelyne Jouvin-Marche Patrice Noël Marche Jacques Demongeot 《BMC bioinformatics》2006,7(1):224-7
Background
Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract. 相似文献2.
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Vadim I. Nazarov Mikhail V. Pogorelyy Ekaterina A. Komech Ivan V. Zvyagin Dmitry A. Bolotin Mikhail Shugay Dmitry M. Chudakov Yury B. Lebedev Ilgar Z. Mamedov 《BMC bioinformatics》2015,16(1)
Background
The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing.Results
Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies.Conclusions
tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network (http://cran.r-project.org/mirrors.html). The source code and development version are available at tcR GitHub (http://imminfo.github.io/tcr/) along with the full documentation and typical usage examples. 相似文献6.
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Background
Thioredoxin reductase (TR) is a redox active protein involved in many cellular processes as part of the thioredoxin system. Presently there are three recognised forms of mammalian thioredoxin reductase designated as TR1, TR3 and TGR, that represent the cytosolic, mitochondrial and novel forms respectively. In this study we elucidated the genomic organisation of the mouse (Txnrd1) and human thioredoxin reductase 1 genes (TXNRD1) through library screening, restriction mapping and database mining. 相似文献8.
Keely G McDonald Matthew R Leach Conway Huang Caihong Wang Rodney D Newberry 《Immunity & ageing : I & A》2011,8(1):1
Background
Immunosenescence is the age-related decline and dysfunction of protective immunity leading to a marked increase in the risk of infections, autoimmune disease, and cancer. The majority of studies have focused on immunosenescence in the systemic immune system; information concerning the effect of aging on intestinal immunity is limited. Isolated lymphoid follicles (ILFs) are newly appreciated dynamic intestinal lymphoid structures that arise from nascent lymphoid tissues, or cryptopatches (CP), in response to local inflammatory stimuli. ILFs promote "homeostatic" responses including the production of antigen-specific IgA, thus playing a key role in mucosal immune protection. ILF dysfunction with aging could contribute to immunosenescence of the mucosal system, and accordingly we examined phenotypic and functional aspects of ILFs from young (2 month old) and aged (2 year old) mice. 相似文献9.
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Feng Tian Huayue Zhang Xinyu Zhang Chi Song Yongjing Xia Yiqing Wu Xiangjun Liu 《BMC bioinformatics》2007,8(1):285
Background
The study of microRNAs (miRNAs) is attracting great considerations. Recent studies revealed that miRNAs play as important regulators of gene expression and some even as cancer players or inhibitors. Many studies try to discover new miRNAs and reveal the miRNA expression profile in cancer using a SAGE-based total RNA clone method. However, the data processing of this method is labor-intensive with several different biological databases and more than ten data processing steps involved. 相似文献11.
Martinez M Ono N Planutiene M Planutis K Nelson EL Holcombe RF 《Cancer cell international》2012,12(1):2
Background
Advanced cancer and chemotherapy are both associated with immune system suppression. We initiated a clinical trial in patients receiving chemotherapy for metastatic colorectal cancer to determine if administration of GM-CSF in this setting was immunostimulatory. 相似文献12.
IMGT-Choreography for immunogenetics and immunoinformatics 总被引:1,自引:0,他引:1
Lefranc MP Clement O Kaas Q Duprat E Chastellan P Coelho I Combres K Ginestoux C Giudicelli V Chaume D Lefranc G 《In silico biology》2005,5(1):45-60
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. IMGT-Choreography will further increase the IMGT leadership in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr. 相似文献
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Hsi-Hsien Hsu Wei-Syun Hu Yueh-Min Lin Wei-Wen Kuo Li-Mien Chen Wei-Kung Chen Jin-Ming Hwang Fuu-Jen Tsai Chung-Jung Liu Chih-Yang Huang 《Journal of biomedical science》2011,18(1):61
Background
Epidemiological studies demonstrate that the incidence and mortality rates of colorectal cancer in women are lower than in men. However, it is unknown if 17β-estradiol treatment is sufficient to inhibit prostaglandin E2 (PGE2)-induced cellular motility in human colon cancer cells. 相似文献14.
Background
Thyroid hormone receptors TRα1, TRβ1 and TRβ2 are broadly expressed and exert a pleiotropic influence on many developmental and homeostatic processes. Extensive genetic studies in mice precisely defined their respective function.Scope of review
The purpose of the review is to discuss two puzzling issues:- –
- The isoform specificity problem: the different functions of TRα1, TRβ1 and TRβ2 might reflect either their different distribution in tissues or differences in the receptor intrinsic properties.
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- The cell-specificity problem: one would expect that different cell types share a common repertoire of TR target genes, but current knowledge does not support this assumption. How TR function is affected by the cellular context is an unsolved question.
Major conclusions
Mouse genetics support a balanced contribution of expression pattern and receptor intrinsic properties in defining the receptor respective functions. The molecular mechanisms sustaining cell specific response remain hypothetical and based on studies performed with other nuclear receptors.General significance
The isoform-specificity and cell-specificity questions have many implications for clinical research, drug development, and endocrine disruptor studies. This article is part of a Special Issue entitled Thyroid hormone signalling. 相似文献15.
Regina Lindborg Tibor Hartel Aveliina Helm Elisabeth Prangel Ttriin Reitalu Raimon Ripoll-Bosch 《应用植被学》2023,26(2):e12729
Question
Semi-natural grasslands (SNG) are important for maintaining biodiversity and ecological processes in farmland. Current pasture-based livestock production mainly occurs on intensified grasslands (IG) that have been agronomically improved. Although it is documented that SNG and IG differ in terms of plant diversity, their ability to provide ecosystem services (ES) in farmland is less explored. Here, we review the role of SNG and IG in delivering ES, illustrate their trade-offs and synergies, and examine how ES can be assessed by using plant traits and functional richness.Results
We found that SNG generate a wider range of ES than IG. Trade-offs exist between ES that appear more pronounced in IG between high biomass production and other ES. SNG are good in providing habitat for biodiversity, supporting pollination and cultural services. SNG also have a significantly wider range of plant functional traits and a higher functional richness, suggesting that the potential to supply ES in SNG is partly driven by higher number of species and their functional diversity.Conclusion
Clearer trade-offs were found in IG compared with SNG, supported both by the literature and the functional richness. This suggests that functional knowledge could be a good complement to understand the mechanisms behind ES generation and could help with tailoring grassland management to sustain biodiversity, ecological functions and ES. Although both IG and SNG are likely needed for the long-term sustainability of food production, both could aim for a more balanced generation of ES, increasing biodiversity and functional redundancy at the landscape scale. 相似文献16.
Julia Mascherbauer Andreas A. Kammerlander Beatrice A. Marzluf Alexandra Graf Alfred Kocher Diana Bonderman 《PloS one》2015,10(8)
Background
The prognostic significance of tricuspid regurgitation (TR) and right ventricular (RV) function in patients undergoing aortic valve replacement (AVR) for severe aortic stenosis (AS) is unknown. The aim of the present study was to evaluate the impact of TR and RV systolic dysfunction on early and late mortality in this setting.Methods
This was a prospective single-center observational study. 465 consecutive patients who were referred to AVR for severe AS were investigated. Significant TR was defined as TR≥moderate by transthoracic echocardiography.Results
At baseline, significant TR was present in 26 (5.6%) patients. Patients with TR presented with a higher EuroSCORE I (p = 0.001), a higher incidence of previous cardiac surgery (p<0.001), pulmonary hypertension (p = 0.003), more dilated RVs (p = 0.001), and more frequent RV dysfunction (p = 0.001). Patients were followed for an average of 5.2 (±2.8 SD) years. By multivariable Cox regression analysis TR (p = 0.014), RV dysfunction (p = 0.046), age (p = 0.001) and concomitant coronary artery bypass graft surgery (CABG, p = 0.003) were independently associated with overall mortality. By Kaplan-Meier analysis, survival rates were significantly worse in patients with significant than with non-significant TR (log rank p = 0.001).Conclusions
TR, RV dysfunction, age, and concomitant CABG are associated with outcome in patients undergoing AVR for severe AS. This finding underlines the importance of a thorough echocardiographic evaluation with particular consideration of the right heart in these patients. 相似文献17.
Cynthia CH Khoo Joseph Piper Irma Sanchez-Vargas Ken E Olson Alexander WE Franz 《BMC microbiology》2010,10(1):130
Background
The RNA interference (RNAi) pathway acts as an innate antiviral immune response in Aedes aegypti, modulating arbovirus infection of mosquitoes. Sindbis virus (SINV; family: Togaviridae, genus: Alphavirus) is an arbovirus that infects Ae. aegypti in the laboratory. SINV strain TR339 encounters a midgut escape barrier (MEB) during infection of Ae. aegypti. The nature of this barrier is not well understood. To investigate the role of the midgut as the central organ determining vector competence for arboviruses, we generated transgenic mosquitoes in which the RNAi pathway was impaired in midgut tissue of bloodfed females. We used these mosquitoes to reveal effects of RNAi impairment in the midgut on SINV replication, midgut infection and dissemination efficiencies, and mosquito longevity. 相似文献18.
R. Jansen B. R. van Klarenbosch M. J. Cramer R. C. A. Meijer P. H. M. Westendorp H. W. J. Meijburg J. J. J. Bucx S. A. J. Chamuleau J. Kluin 《Netherlands heart journal》2018,26(11):552-561
Background
In patients with mild to moderate functional tricuspid regurgitation (TR) and absence of right ventricular dysfunction or tricuspid annulus (TA) dilatation, there is currently no indication for concomitant tricuspid valve (TV) repair during elective mitral valve (MV) surgery. However, long-term results are conflicting. Here, we sought to determine the clinical outcome of this cohort, the rate of TR progression after MV surgery and the role of MV aetiology.Methods
Patients for elective MV surgery without concomitant TV repair were retrospectively analysed with longitudinal echocardiographic and clinical follow-up, focusing on TR progression and MV aetiology. Linear regression analysis was performed for change in TR at follow-up, using pre-determined variables and confounders.Results
In total 204 patients without TV repair were analysed. Development of more than moderate TR after a median of 3.1 [1.6–4.6] years was rarely seen: only in 2 out of 161 patients (1.2%) with known TR grade at follow-up. Overall, median preoperative and late postoperative TR grade were equal (p?=?0.116). Subanalysis showed no significant difference in MV aetiology subgroups. Preoperative TR grade and male gender were inversely correlated to change in TR. Mortality was not influenced by the 1?year postoperative TR severity.Conclusion
Our data showed that in a study population of patients with mild to moderate TR undergoing MV surgery without concomitant TV repair, significant late TR was rarely seen. Based on our study, it is safe to waive concomitant TV repair in this specific patient cohort.19.
The association of garlic with Helicobacter pylori infection and gastric cancer risk: A systematic review and meta‐analysis
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Background
Garlic may be protective against Helicobacter pylori infection and gastric cancer development. We conducted this study to quantitatively update evidence on garlic intake and gastric cancer with the inclusion of most recent cohort studies and qualitatively summarize epidemiological studies of garlic consumption and Helicobacter pylori infection.Materials and Methods
PubMed, Embase, MEDLINE, and Cochrane Library were searched on April 2018. We conducted a meta‐analysis to determine whether garlic intake reduced gastric cancer risk using random‐effect models and a systematic review to summarize evidence on the association between garlic consumption and Helicobacter pylori infection. Risk of bias was assessed using tools of Cochrane risk of bias and Robins‐I for randomized and nonrandomized studies, respectively.Results
Meta‐analysis of 18 studies (142 921 subjects) demonstrated high garlic consumption (as comparing the highest category to the lowest) was associated with a reduced gastric cancer risk (OR = 0.51, 95% CI = 0.44‐0.57). This association became nonsignificant if only derived from the prospective studies (OR = 0.95, 95% CI = 0.66‐1.24). Thirteen studies (4889 participants) were included in the systematic review for garlic consumption and Helicobacter pylori infection; ten of which found no significant results. The majority of these studies were poor in quality given the small sample size and high risk of bias.Conclusions
Pooled evidence, mainly from case‐control studies, suggested a significant inverse association of garlic intake with gastric cancer risk. Given the limitations of included studies, current epidemiological evidence is not sufficient to reach any definite conclusion regarding the association of garlic with Helicobacter pylori infection. 相似文献20.
Titus MA Zeithaml B Kantor B Li X Haack K Moore DT Wilson EM Mohler JL Kafri T 《PloS one》2012,7(1):e30192