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131.
Cimmaruta Chiara Citro Valentina Andreotti Giuseppina Liguori Ludovica Cubellis Maria Vittoria Hay Mele Bruno 《BMC bioinformatics》2018,19(15):433-46
Background
Severity gradation of missense mutations is a big challenge for exome annotation. Predictors of deleteriousness that are most frequently used to filter variants found by next generation sequencing, produce qualitative predictions, but also numerical scores. It has never been tested if these scores correlate with disease severity.Results
wANNOVAR, a popular tool that can generate several different types of deleteriousness-prediction scores, was tested on Fabry disease. This pathology, which is caused by a deficit of lysosomal alpha-galactosidase, has a very large genotypic and phenotypic spectrum and offers the possibility of associating a quantitative measure of the damage caused by mutations to the functioning of the enzyme in the cells. Some predictors, and in particular VEST3 and PolyPhen2 provide scores that correlate with the severity of lysosomal alpha-galactosidase mutations in a statistically significant way.Conclusions
Sorting disease mutations by severity is possible and offers advantages over binary classification. Dataset for testing and training in silico predictors can be obtained by transient transfection and evaluation of residual activity of mutants in cell extracts. This approach consents to quantitative data for severe, mild and non pathological variants.132.
133.
134.
Timm Konold A Robin Sayers Amanda Sach Gemma E Bone Steven van Winden Gerald AH Wells Marion M Simmons Michael J Stack Angus Wear Steve AC Hawkins 《BMC veterinary research》2010,6(1):53
Background
Various clinical protocols have been developed to aid in the clinical diagnosis of classical bovine spongiform encephalopathy (BSE), which is confirmed by postmortem examinations based on vacuolation and accumulation of disease-associated prion protein (PrPd) in the brain. The present study investigated the occurrence and progression of sixty selected clinical signs and behaviour combinations in 513 experimentally exposed cattle subsequently categorised postmortem as confirmed or unconfirmed BSE cases. Appropriate undosed or saline inoculated controls were examined similarly and the data analysed to explore the possible occurrence of BSE-specific clinical expression in animals unconfirmed by postmortem examinations. 相似文献135.
Inflammation, genetics, and ischemic heart disease: focus on the major histocompatibility complex (MHC) genes 总被引:4,自引:0,他引:4
BACKGROUND: Increasing data suggest that ischemic heart disease (IHD) shares several characteristics with common inflammatory diseases (such as rheumatoid arthritis), in which the pathogenetic role of inflammatory gene polymorphisms is well established. Variants in the genes for the major histocompatibility complex (MHC) molecules on the short arm of chromosome 6 show profound "linkage disequilibrium", leading to the formation of "haplotypes", i.e., frozen blocks of alleles travelling together through generations. DESIGN: We performed a review of published studies linking IHD with gene polymorphisms of the MHC molecules tumor necrosis factor (TNF)-alpha and -beta, the class II DR human leukocyte antigens, heat shock protein 70-1, hemochromatosis related gene, and complement C4. RESULTS: The emerging data are quite conflicting and do not provide definitive evidence for a role of these gene variants in the pathogenesis of IHD; a possible exception is the G252A and polymorphism in the TNF-beta gene (also known as lymphotoxin-alpha) which, in a comprehensive genome-scan linkage analysis of unrelated Japanese, but not in a smaller German population, was linked to myocardial infarction. However, some important biases appear, e.g. different study design and variable linkage disequilibrium among different populations. CONCLUSIONS: Preliminary positive results should encourage future studies to focus on clinical models of IHD with well-codified inflammatory components, using novel methods (such as haplotype analysis) to assess gene polymorphisms and their clinical effect. 相似文献
136.
Giuseppina Andreotti Valentina Citro Agostina De Crescenzo Pierangelo Orlando Marco Cammisa Antonella Correra Maria Vittoria Cubellis 《Orphanet journal of rare diseases》2011,6(1):66
Background
Fabry disease is a rare disorder caused by a large variety of mutations in the gene encoding lysosomal alpha-galactosidase. Many of these mutations are unique to individual families. Fabry disease can be treated with enzyme replacement therapy, but a promising novel strategy relies on small molecules, so called "pharmacological chaperones", which can be administered orally. Unfortunately only 42% of genotypes respond to pharmacological chaperones.Results
A procedure to predict which genotypes responsive to pharmacological chaperones in Fabry disease has been recently proposed. The method uses a position-specific substitution matrix to score the mutations. Using this method, we have screened public databases for predictable responsive cases and selected nine representative mutations as yet untested with pharmacological chaperones. Mutant lysosomal alpha galactosidases were produced by site directed mutagenesis and expressed in mammalian cells. Seven out of nine mutations responded to pharmacological chaperones. Nineteen other mutations that were tested with pharmacological chaperones, but were not included in the training of the predictive method, were gathered from literature and analyzed in silico. In this set all five mutations predicted to be positive were responsive to pharmacological chaperones, bringing the percentage of responsive mutations among those predicted to be positive and not used to train the classifier to 86% (12/14). This figure differs significantly from the percentage of responsive cases observed among all the Fabry mutants tested so far.Conclusions
In this paper we provide experimental support to an "in silico" method designed to predict missense mutations in the gene encoding lysosomal alpha galactosidase responsive to pharmacological chaperones. We demonstrated that responsive mutations can be predicted with a low percentage of false positive cases. Most of the mutations tested to validate the method were described in the literature as associated to classic or mild classic phenotype. The analysis can provide a guideline for the therapy with pharmacological chaperones supported by experimental results obtained in vitro. We are aware that our results were obtained in vitro and cannot be translated straightforwardly into benefit for patients, but need to be validated by clinical trials.137.
Relevant examples of polyglycosylating exo-glycosidases were reported among enzymes of marine origin (Aplysia fasciata, Geobacillus, and Pecten maximus). Herein we describe the enzymatic polyglucosylation of a chromane-methanol (2-hydroxymethyl-2,5,7,8-tetramethylchroman-6-ol)
performed by using the α-d-glucosidase from the sea hare Aplysia fasciata. New di-, tri-, and tetrasaccharide derivatives were synthesized and their antioxidant activities were evaluated by DPPH test.
High enzymatic substrate conversion was assessed by NMR spectroscopy, and the products were easily purified. These findings
suggest that the proposed procedure is an effective process both for the molecular diversity of products and for the peculiar
stereochemistry of the enzyme. At the beginning of the enzymatic reaction, only (S)-diastereomer of the monoglucoside was obtained. The isomaltoside was the most abundant disaccharide obtained and showed
a radical scavenging activity similar to that of the chromane-methanol. The disaccharide can be considered a new hydrosoluble
antioxidant agent useful for various technological applications (cosmetics, food industry, etc.). A relationship between the
interglycosidic linkage present in disaccharides and trisaccharides and their scavenging activity was also pointed out. 相似文献
138.
Mass spectrometry coupled to liquid chromatography (LC-MS and LC-MS/MS) is commonly used to analyze the protein content of biological samples in large scale studies, enabling quantitation and identification of proteins and peptides using a wide range of experimental protocols, algorithms, and statistical models to analyze the data. Currently it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists for peptide identification algorithms but data that represents a ground truth for the evaluation of LC-MS data is limited. Hence there have been attempts to simulate such data in a controlled fashion to evaluate and compare algorithms. We present MSSimulator, a simulation software for LC-MS and LC-MS/MS experiments. Starting from a list of proteins from a FASTA file, the simulation will perform in-silico digestion, retention time prediction, ionization filtering, and raw signal simulation (including MS/MS), while providing many options to change the properties of the resulting data like elution profile shape, resolution and sampling rate. Several protocols for SILAC, iTRAQ or MS(E) are available, in addition to the usual label-free approach, making MSSimulator the most comprehensive simulator for LC-MS and LC-MS/MS data. 相似文献
139.
Stella Koutros Sonja I. Berndt Kathryn Hughes Barry Gabriella Andreotti Jane A. Hoppin Dale P. Sandler Meredith Yeager Laurie A. Burdett Jeffrey Yuenger Michael C. R. Alavanja Laura E. Beane Freeman 《PloS one》2013,8(4)
Uncovering SNP (single nucleotide polymorphisms)-environment interactions can generate new hypotheses about the function of poorly characterized genetic variants and environmental factors, like pesticides. We evaluated SNP-environment interactions between 30 confirmed prostate cancer susceptibility loci and 45 pesticides and prostate cancer risk in 776 cases and 1,444 controls in the Agricultural Health Study. We used unconditional logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Multiplicative SNP-pesticide interactions were calculated using a likelihood ratio test. After correction for multiple tests using the False Discovery Rate method, two interactions remained noteworthy. Among men carrying two T alleles at rs2710647 in EH domain binding protein 1 (EHBP1) SNP, the risk of prostate cancer in those with high malathion use was 3.43 times those with no use (95% CI: 1.44–8.15) (P-interaction = 0.003). Among men carrying two A alleles at rs7679673 in TET2, the risk of prostate cancer associated with high aldrin use was 3.67 times those with no use (95% CI: 1.43, 9.41) (P-interaction = 0.006). In contrast, associations were null for other genotypes. Although additional studies are needed and the exact mechanisms are unknown, this study suggests known genetic susceptibility loci may modify the risk between pesticide use and prostate cancer. 相似文献
140.
Gabriella d'Ettorre Silvia Baroncelli Luca Micci Giancarlo Ceccarelli Mauro Andreotti Prachi Sharma Gianfranco Fanello Fausto Fiocca Eugenio Nelson Cavallari Noemi Giustini Alessandra Mallano Clementina M. Galluzzo Stefano Vella Claudio M. Mastroianni Guido Silvestri Mirko Paiardini Vincenzo Vullo 《PloS one》2014,9(10)