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111.
Eissenberg JC 《Methods (San Diego, Calif.)》2006,40(4):360-364
Knowing the genomic distribution of chromosomal proteins and of histone modifications provides essential insight into function. The giant polytene chromosomes of the Drosophila larval salivary glands provide a high-resolution genomic map with a resolution exceeded only by chromatin immunoprecipitation. Immunofluorescence localization of chromosomal proteins and specific post-translational modifications of histones is a simple and rapid tool for the functional genomics of chromosomal proteins. 相似文献
112.
Gause M Webber HA Misulovin Z Haller G Rollins RA Eissenberg JC Bickel SE Dorsett D 《Chromosoma》2008,117(1):51-66
Drosophila Nipped-B is an essential protein that has multiple functions. It facilitates expression of homeobox genes and is also required
for sister chromatid cohesion. Nipped-B is conserved from yeast to man, and its orthologs also play roles in deoxyribonucleic
acid repair and meiosis. Mutation of the human ortholog, Nipped-B-Like (NIPBL), causes Cornelia de Lange syndrome (CdLS),
associated with multiple developmental defects. The Nipped-B protein family is required for the cohesin complex that mediates
sister chromatid cohesion to bind to chromosomes. A key question, therefore, is whether the Nipped-B family regulates gene
expression, meiosis, and development by controlling cohesin. To gain insights into Nipped-B’s functions, we compared the effects
of several Nipped-B mutations on gene expression, sister chromatid cohesion, and meiosis. We also examined association of Nipped-B and cohesin
with somatic and meiotic chromosomes by immunostaining. Missense Nipped-B alleles affecting the same HEAT repeat motifs as CdLS-causing NIPBL mutations have intermediate effects on both gene expression and mitotic chromatid cohesion, linking these two functions and
the role of NIPBL in human development. Nipped-B colocalizes extensively with cohesin on chromosomes in both somatic and meiotic
cells and is present in soluble complexes with cohesin subunits in nuclear extracts. In meiosis, Nipped-B also colocalizes
with the synaptonemal complex and contributes to maintenance of meiotic chromosome cores. These results support the idea that
direct regulation of cohesin function underlies the diverse functions of Nipped-B and its orthologs.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
Gause, Webber, and Misulovin provided equal contributions. 相似文献
113.
Laurie L Baker Rodrigo Wiff JC Quiroz Andrés Flores Renato Céspedes Mauricio A. Barrientos Vilma Ojeda Claudio Gatica 《Environmental Biology of Fishes》2014,97(10):1083-1093
The pink cusk-eel (Genypterus blacodes), a benthic-demersal fish confined to the southern hemisphere, supports an important commercial fishery in Chile where it is exploited over an extensive geographic area. Although the fishery was originally divided into a northern (41º28′–47º00′S) and southern (47º00′–57º00′S) zone for the purposes of fisheries management, recent studies have reported significant differences in life history parameters between these zones. Individuals from the southern zone reached larger asymptotic sizes and possessed higher survival rates compared to the northern zone. We estimate and compare the gonadosomatic index (GSI), shape of the maturity ogive, and length at 50 % maturity (L 50%) of female G. blacodes between management zones and across time using biological data collected from the industrial fleet between 1985 and 2009. Females in the northern zone had higher monthly mean GSI than females in the southern zone. Our analyses also revealed L 50% to be significantly higher in the southern zone than in the northern zone from 1985 to 2009. The significant differences in life-history traits between fishery management zones agree with the trade-offs predicted by Charnov’s life history theory. Together these results provide additional support for the hypothesis that two separate stocks exist and suggest that females from the northern zone have developed a life-history strategy, which favours early maturation and a proportionally greater investment in reproduction than females from the southern zone. 相似文献
114.
Frédéric D Chevalier Claudia LL Valentim Philip T LoVerde Timothy JC Anderson 《BMC genomics》2014,15(1)
Background
Identification of parasite genes that underlie traits such as drug resistance and host specificity is challenging using classical linkage mapping approaches. Extreme QTL (X-QTL) methods, originally developed by rodent malaria and yeast researchers, promise to increase the power and simplify logistics of linkage mapping in experimental crosses of schistosomes (or other helminth parasites), because many 1000s of progeny can be analysed, phenotyping is not required, and progeny pools rather than individuals are genotyped. We explored the utility of this method for mapping a drug resistance gene in the human parasitic fluke Schistosoma mansoni.Results
We staged a genetic cross between oxamniquine sensitive and resistant parasites, then between two F1 progeny, to generate multiple F2 progeny. One group of F2s infecting hamsters was treated with oxamniquine, while a second group was left untreated. We used exome capture to reduce the size of the genome (from 363 Mb to 15 Mb) and exomes from pooled F2 progeny (treated males, untreated males, treated females, untreated females) and the two parent parasites were sequenced to high read depth (mean = 95-366×) and allele frequencies at 14,489 variants compared. We observed dramatic enrichment of alleles from the resistant parent in a small region of chromosome 6 in drug-treated male and female pools (combined analysis: = 11.07, p = 8.74 × 10-29). This region contains Smp_089320 a gene encoding a sulfotransferase recently implicated in oxamniquine resistance using classical linkage mapping methods.Conclusions
These results (a) demonstrate the utility of exome capture for generating reduced representation libraries in Schistosoma mansoni, and (b) provide proof-of-principle that X-QTL methods can be successfully applied to an important human helminth. The combination of these methods will simplify linkage analysis of biomedically or biologically important traits in this parasite.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-617) contains supplementary material, which is available to authorized users. 相似文献115.
Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations
Jose L Gualdrón Duarte Rodolfo JC Cantet Ronald O Bates Catherine W Ernst Nancy E Raney Juan P Steibel 《BMC bioinformatics》2014,15(1)
Background
Currently, association studies are analysed using statistical mixed models, with marker effects estimated by a linear transformation of genomic breeding values. The variances of marker effects are needed when performing the tests of association. However, approaches used to estimate the parameters rely on a prior variance or on a constant estimate of the additive variance. Alternatively, we propose a standardized test of association using the variance of each marker effect, which generally differ among each other. Random breeding values from a mixed model including fixed effects and a genomic covariance matrix are linearly transformed to estimate the marker effects.Results
The standardized test was neither conservative nor liberal with respect to type I error rate (false-positives), compared to a similar test using Predictor Error Variance, a method that was too conservative. Furthermore, genomic predictions are solved efficiently by the procedure, and the p-values are virtually identical to those calculated from tests for one marker effect at a time. Moreover, the standardized test reduces computing time and memory requirements.The following steps are used to locate genome segments displaying strong association. The marker with the highest − log(p-value) in each chromosome is selected, and the segment is expanded one Mb upstream and one Mb downstream of the marker. A genomic matrix is calculated using the information from those markers only, which is used as the variance-covariance of the segment effects in a model that also includes fixed effects and random genomic breeding values. The likelihood ratio is then calculated to test for the effect in every chromosome against a reduced model with fixed effects and genomic breeding values. In a case study with pigs, a significant segment from chromosome 6 explained 11% of total genetic variance.Conclusions
The standardized test of marker effects using their own variance helps in detecting specific genomic regions involved in the additive variance, and in reducing false positives. Moreover, genome scanning of candidate segments can be used in meta-analyses of genome-wide association studies, as it enables the detection of specific genome regions that affect an economically relevant trait when using multiple populations.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-246) contains supplementary material, which is available to authorized users. 相似文献116.
Background
The complex societies of ants and other social insects rely on sophisticated chemical communication. Two families of small soluble proteins, the odorant binding and chemosensory proteins (OBPs and CSPs), are believed to be important in insect chemosensation. To better understand the role of these proteins in ant olfaction, we examined their evolution and expression across the ants using phylogenetics and sex- and tissue-specific RNA-seq.Results
We find that subsets of both OBPs and CSPs are expressed in the antennae, contradicting the previous hypothesis that CSPs have replaced OBPs in ant olfaction. Both protein families have several highly conserved clades with a single ortholog in all eusocial hymenopterans, as well as clades with more dynamic evolution and many taxon-specific radiations. The dynamically evolving OBPs and CSPs have been hypothesized to function in chemical communication. Intriguingly, we find that seven members of the conserved clades are expressed specifically in the antennae of the clonal raider ant Cerapachys biroi, whereas only one dynamically evolving CSP is antenna specific. The orthologs of the conserved, antenna-specific C. biroi genes are also expressed in antennae of the ants Camponotus floridanus and Harpegnathos saltator, indicating that antenna-specific expression of these OBPs and CSPs is conserved across ants. Most members of the dynamically evolving clades in both protein families are expressed primarily in non-chemosensory tissues and thus likely do not fulfill chemosensory functions.Conclusions
Our results identify candidate OBPs and CSPs that are likely involved in conserved aspects of ant olfaction, and suggest that OBPs and CSPs may not rapidly evolve to recognize species-specific signals.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-718) contains supplementary material, which is available to authorized users. 相似文献117.
Norbert Meyer Jan W Dallinga Sarah Janine Nuss Edwin JC Moonen Joep JBN van Berkel Cezmi Akdis Frederik Jan van Schooten Günter Menz 《Respiratory research》2014,15(1)
Background
Several classifications of adult asthma patients using cluster analyses based on clinical and demographic information has resulted in clinical phenotypic clusters that do not address molecular mechanisms. Volatile organic compounds (VOC) in exhaled air are released during inflammation in response to oxidative stress as a result of activated leukocytes. VOC profiles in exhaled air could distinguish between asthma patients and healthy subjects. In this study, we aimed to classify new asthma endotypes by combining inflammatory mechanisms investigated by VOC profiles in exhaled air and clinical information of asthma patients.Methods
Breath samples were analyzed for VOC profiles by gas chromatography–mass spectrometry from asthma patients (n = 195) and healthy controls (n = 40). A total of 945 determined compounds were subjected to discriminant analysis to find those that could discriminate healthy from asthmatic subjects. 2-step cluster analysis based on clinical information and VOCs in exhaled air were used to form asthma endotypes.Results
We identified 16 VOCs, which could distinguish between healthy and asthma subjects with a sensitivity of 100% and a specificity of 91.1%. Cluster analysis based on VOCs in exhaled air and the clinical parameters FEV1, FEV1 change after 3 weeks of hospitalization, allergic sensitization, Junipers symptoms score and asthma medications resulted in the formation of 7 different asthma endotype clusters. We identified asthma clusters with different VOC profiles but similar clinical characteristics and endotypes with similar VOC profiles, but distinct clinical characteristics.Conclusion
This study demonstrates that both, clinical presentation of asthma and inflammatory mechanisms in the airways should be considered for classification of asthma subtypes.Electronic supplementary material
The online version of this article (doi:10.1186/s12931-014-0136-8) contains supplementary material, which is available to authorized users. 相似文献118.
Background
Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. 相似文献119.
Eissenberg JC Lee MG Schneider J Ilvarsonn A Shiekhattar R Shilatifard A 《Nature structural & molecular biology》2007,14(4):344-346
Histone H3 Lys4 (H3K4) is methylated by yeast Set1-COMPASS and its mammalian homolog, the MLL complex. Human JARID1d can demethylate trimethyl-H3K4 (H3K4me3). We identified Drosophila melanogaster little imaginal discs (Lid) as the JARID1d homolog. We report that Lid knockdown using RNA interference results in a specific genome-wide increase in H3K4me3 levels without affecting other patterns of H3 methylation, and results in an altered distribution of the chromo-helicase protein Chd1. 相似文献
120.
H Pojski? JC Pagaduan F Babaji? E U?i?anin M Muratovi? M Tomljanovi? 《Biology of sport / Institute of Sport》2015,32(2):129-134
The aim of the present study was to compare the effects of different warm-up interventions on jump, sprint and agility performance in collegiate soccer players. Twenty-one healthy male college soccer players (age: 20.14 ± 1.65 years; body height: 179.9 ± 8.34 cm; body mass: 74.4 ± 13.0 kg; % body fat: 9.45 ± 4.8) participated in the study. Subjects underwent four different randomized warm-up protocols separated by at least 48 hours. The warm-up schemes were: 1. no conditioning contraction protocol (NCC); 2. dynamic stretching (DS); 3. prolonged intermittent low-intensity isometric exercise (ST); and, 4. ST with an additional external load equal to 30% of body weight (ST + 30% BW). All interventions were preceded by a general warm-up. Results from one-way repeated measures ANOVA demonstrated a significant difference in countermovement jump (CMJ) at F(3,60) = 10.2, ηρ2 = 0.337, p < 0.01. Post hoc analysis revealed a significant difference in CMJ performance in DS when compared to NCC and ST + 30% BW. No significant difference in CMJ was observed between DS and ST. CMJ scores in NCC, ST, and ST + 30% BW were non-significant. There was a significant difference in speed; F(3, 60) = 6.61, ηρ2 = 0.248, p < 0.01. Post hoc analysis revealed significantly better time in DS than NCC and ST. However, no difference in speed was observed between DS and ST + 30% BW. Similarly, speed was similar in NCC, ST and ST + 30% BW. A significant difference in agility performance was also observed; F(3, 60) = 24.1, ηρ2= 0.546, p < 0.01. Post hoc analysis revealed significantly greater performance gains in DS than NCC. No significant difference in agility was observed in DS, ST and ST + 30% BW. In conclusion, a prolonged intermittent low-intensity isometric protocol using bodyweight only showed similar benefits with dynamic stretching in countermovement jump performance. When the same isometric condition with additional load equal to 30% of bodyweight was applied, effects in speed and agility were similar to dynamic stretching. 相似文献