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131.
This study compares the relative influences of physiography and anthropogenic pressures on river biota at catchment, riparian corridor, and reach scales. Environmental data, catchment and riparian corridor land use, anthropogenic modifications and biological data were compiled for 301 French sites sampled from 2005 to 2008. First, relationships between anthropogenic pressures and fish and macroinvertebrate assemblages were analysed using redundancy analysis. Second, the influences of physiography and the three scales of human pressures on biological assemblages were measured using variance partitioning. Distributions of fish and macroinvertebrate taxa along the pressure gradients agreed with bio-ecological knowledge. At the reach scale, assemblage variability among the 301 French sites was related to the presence of an impoundment and to poor water quality, while at larger scales it was linked to a gradient from forest to agricultural covers. In addition, a large proportion of the explained variability in assemblage composition was related to complex interactions among factors (~40%) and to physiographic variables (~30%). Furthermore, our results highlight that catchment land use better reflects local water quality impairments than hydromorphological degradations. Finally, this study supports the idea that human pressure effects on river communities are linked at several spatial scales and must be considered jointly. 相似文献
132.
Angela Feechan Claire Anderson Laurent Torregrosa Angelica Jermakow Pere Mestre Sabine Wiedemann‐Merdinoglu Didier Merdinoglu Amanda R. Walker Lance Cadle‐Davidson Bruce Reisch Sebastien Aubourg Nadia Bentahar Bipna Shrestha Alain Bouquet Anne‐Françoise Adam‐Blondon Mark R. Thomas Ian B. Dry 《The Plant journal : for cell and molecular biology》2013,76(4):661-674
The most economically important diseases of grapevine cultivation worldwide are caused by the fungal pathogen powdery mildew (Erysiphe necator syn. Uncinula necator) and the oomycete pathogen downy mildew (Plasmopara viticola). Currently, grapegrowers rely heavily on the use of agrochemicals to minimize the potentially devastating impact of these pathogens on grape yield and quality. The wild North American grapevine species Muscadinia rotundifolia was recognized as early as 1889 to be resistant to both powdery and downy mildew. We have now mapped resistance to these two mildew pathogens in M. rotundifolia to a single locus on chromosome 12 that contains a family of seven TIR‐NB‐LRR genes. We further demonstrate that two highly homologous (86% amino acid identity) members of this gene family confer strong resistance to these unrelated pathogens following genetic transformation into susceptible Vitis vinifera winegrape cultivars. These two genes, designated r esistance to P lasmopara v iticola (MrRPV1) are the first resistance genes to be cloned from a grapevine species. Both MrRUN1 and MrRPV1 were found to confer resistance to multiple powdery and downy mildew isolates from France, North America and Australia; however, a single powdery mildew isolate collected from the south‐eastern region of North America, to which M. rotundifolia is native, was capable of breaking MrRUN1‐mediated resistance. Comparisons of gene organization and coding sequences between M. rotundifolia and the cultivated grapevine V. vinifera at the MrRUN1/MrRPV1 locus revealed a high level of synteny, suggesting that the TIR‐NB‐LRR genes at this locus share a common ancestor. 相似文献
133.
Background
Accurate QTL mapping is a prerequisite in the search for causative mutations. Bayesian genomic selection models that analyse many markers simultaneously should provide more accurate QTL detection results than single-marker models. Our objectives were to (a) evaluate by simulation the influence of heritability, number of QTL and number of records on the accuracy of QTL mapping with Bayes Cπ and Bayes C; (b) estimate the QTL status (homozygous vs. heterozygous) of the individuals analysed. This study focussed on the ten largest detected QTL, assuming they are candidates for further characterization.Methods
Our simulations were based on a true dairy cattle population genotyped for 38 277 phased markers. Some of these markers were considered biallelic QTL and used to generate corresponding phenotypes. Different numbers of records (4387 and 1500), heritability values (0.1, 0.4 and 0.7) and numbers of QTL (10, 100 and 1000) were studied. QTL detection was based on the posterior inclusion probability for individual markers, or on the sum of the posterior inclusion probabilities for consecutive markers, estimated using Bayes C or Bayes Cπ. The QTL status of the individuals was derived from the contrast between the sums of the SNP allelic effects of their chromosomal segments.Results
The proportion of markers with null effect (π) frequently did not reach convergence, leading to poor results for Bayes Cπ in QTL detection. Fixing π led to better results. Detection of the largest QTL was most accurate for medium to high heritability, for low to moderate numbers of QTL, and with a large number of records. The QTL status was accurately inferred when the distribution of the contrast between chromosomal segment effects was bimodal.Conclusions
QTL detection is feasible with Bayes C. For QTL detection, it is recommended to use a large dataset and to focus on highly heritable traits and on the largest QTL. QTL statuses were inferred based on the distribution of the contrast between chromosomal segment effects. 相似文献134.
Marta Coll Philippe Cury Ernesto Azzurro Michel Bariche Giorgos Bayadas Jose Maria Bellido Christian Chaboud Joachim Claudet Abdel-Fattah El-Sayed Didier Gascuel Leyla Knittweis Carlo Pipitone Yianna Samuel-Rhoads Said Taleb Sergi Tudela Audrey Valls 《Reviews in Fish Biology and Fisheries》2013,23(4):415-434
135.
Kenza Mokhtar‐Jamaï Rafel Coma Jinliang Wang Frederic Zuberer Jean‐Pierre Féral Didier Aurelle 《Ecology and evolution》2013,3(6):1765-1779
Dispersal and mating features strongly influence the evolutionary dynamics and the spatial genetic structure (SGS) of marine populations. For the first time in a marine invertebrate, we examined individual reproductive success, by conducting larval paternity assignments after a natural spawning event, combined with a small‐scale SGS analysis within a population of the gorgonian Paramuricea clavata. Thirty four percent of the larvae were sired by male colonies surrounding the brooding female colonies, revealing that the bulk of the mating was accomplished by males from outside the studied area. Male success increased with male height and decreased with increasing male to female distance. The parentage analyses, with a strong level of self‐recruitment (25%), unveiled the occurrence of a complex family structure at a small spatial scale, consistent with the limited larval dispersal of this species. However, no evidence of small scale SGS was revealed despite this family structure. Furthermore, temporal genetic structure was not observed, which appears to be related to the rather large effective population size. The low level of inbreeding found suggests a pattern of random mating in this species, which disagrees with expectations that limited larval dispersal should lead to biparental inbreeding. Surface brooding and investment in sexual reproduction in P. clavata contribute to multiple paternity (on average 6.4 fathers were assigned per brood), which enhance genetic diversity of the brood. Several factors may have contributed to the lack of biparental inbreeding in our study such as (i) the lack of sperm limitation at a small scale, (ii) multiple paternity, and (iii) the large effective population size. Thus, our results indicate that limited larval dispersal and complex family structure do not necessarily lead to biparental inbreeding and SGS. In the framework of conservation purposes, our results suggested that colony size, proximity among colonies and the population size should be taken into consideration for restoration projects. 相似文献
136.
Adam Ahanchédé José E. F. Alfaya L. W. Andersen Didier Azam Ma. Anita M. Bautista Anne‐Laure Besnard Gregorio Bigatti Anthony Bouétard Marie‐Agnès Coutellec Eben‐Ezer B. K. Ewédjè Reiko Fuseya Ricardo GarcÍa‐Jiménez M. Haratian Olivier J. Hardy L.‐E. Holm Casey W. Hoy Eriko Koshimizu V. Loeschcke Violeta López‐Márquez Carlos A. Machado Annie Machordom C. Marchi Andrew P. Michel Claire Micheneau Omprakash Mittapalli Takahiro Nagai Nobuaki Okamoto Ying Pan F. Panitz N. Safaie Takashi Sakamoto B. Sharifnabi En‐Wei Tian Hui Yu 《Molecular ecology resources》2013,13(1):158-159
This article documents the addition of 83 microsatellite marker loci and 96 pairs of single‐nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bembidion lampros, Inimicus japonicus, Lymnaea stagnalis, Panopea abbreviata, Pentadesma butyracea, Sycoscapter hirticola and Thanatephorus cucumeris (anamorph: Rhizoctonia solani). These loci were cross‐tested on the following species: Pentadesma grandifolia and Pentadesma reyndersii. This article also documents the addition of 96 sequencing primer pairs and 88 allele‐specific primers or probes for Plutella xylostella. 相似文献
137.
Issam Arrouss Fariba Nemati Fernando Roncal Marie Wislez Karim Dorgham David Vallerand Nathalie Rabbe Narjesse Karboul Fran?oise Carlotti Jeronimo Bravo Dominique Mazier Didier Decaudin Angelita Rebollo 《PloS one》2013,8(4)
Purpose
PP2A is a serine/threonine phosphatase critical to physiological processes, including apoptosis. Cell penetrating peptides are molecules that can translocate into cells without causing membrane damage. Our goal was to develop cell-penetrating fusion peptides specifically designed to disrupt the caspase-9/PP2A interaction and evaluate their therapeutic potential in vitro and in vivo.Experimental Design
We generated a peptide containing a penetrating sequence associated to the interaction motif between human caspase-9 and PP2A (DPT-C9h), in order to target their association. Using tumour cell lines, primary human cells and primary human breast cancer (BC) xenografts, we investigated the capacity of DPT-C9h to provoke apoptosis in vitro and inhibition of tumour growth (TGI) in vivo. DPT-C9h was intraperitonealy administered at doses from 1 to 25 mg/kg/day for 5 weeks. Relative Tumour Volume (RTV) was calculated.Results
We demonstrated that DPT-C9h specifically target caspase-9/PP2A interaction in vitro and in vivo and induced caspase-9-dependent apoptosis in cancer cell lines. DPT-C9h also induced significant TGI in BC xenografts models. The mouse-specific peptide DPT-C9 also induced TGI in lung (K-Ras model) and breast cancer (PyMT) models. DPT-C9h has a specific effect on transformed B cells isolated from chronic lymphocytic leukemia patients without any effect on primary healthy cells. Finally, neither toxicity nor immunogenic responses were observed.Conclusion
Using the cell-penetrating peptides blocking caspase-9/PP2A interactions, we have demonstrated that DPT-C9h had a strong therapeutic effect in vitro and in vivo in mouse models of tumour progression. 相似文献138.
139.
Marcos Ramos da Silva Didier Clément Karina Peres Gramacho Wilson Reis Monteiro Xavier Argout Claire Lanaud Uilson Lopes 《Tree Genetics & Genomes》2016,12(3):62
Sexual compatibility limits the production of cacao plantations, being an important selection criterion in breeding programs. However, the current method for characterizing compatibility, based on the frequency of flower setting after controlled pollination, is time consuming, requiring a long time to identify self-compatible individuals. The identification of molecular markers in genomic regions can be an alternative to allow early selection of self-compatible plants. The present study aimed to identify SNP markers associated with sexual compatibility in cacao, by utilizing genome-wide association (GWAS) mapping. A population of 295 individuals mostly from third-generation breeding populations, but also founder clones, was used. This population was phenotypically characterized by hand pollinating 8199 flowers and evaluating the flower retention 15 days after pollination. In addition, leaf samples of each individual were collected and DNA extracted for genotyping by sequencing, generating 5301 SNP markers after cleaning. Genome-wide association mapping analysis was performed using Synbreed, GCTA, and TASSEL softwares. Significant markers associated to incompatibility, likely in strong linkage disequilibrium, were found within a region of 196 kb, in the proximal end of chromosome 4, suggesting the existence of a major gene in that region. However, this result should be validated in a larger population, considering that only 295 trees were used here. When the SNP effects were treated as random in the estimation process, many other regions in the genome appears to be involved with sexual incompatibility in cacao. Candidate genes were found not only in the proximal end of chromosome 4 but also spread in several other regions of the genome. 相似文献
140.
Quantitative assessment of methyl‐esterification and other side reactions in a standard propionylation protocol for detection of histone modifications 下载免费PDF全文
Veerle Paternoster Anders Valdemar Edhager Christian Sibbersen Anders Lade Nielsen Anders Dupont Børglum Jane Hvarregaard Christensen Johan Palmfeldt 《Proteomics》2016,16(14):2059-2063
Histone modifications play an important role in regulating chromatin stability and gene expression, but to date, investigating them remains challenging. In order to obtain peptides suitable for MS‐based analysis, chemical derivatization of N‐terminus and lysine residues by propionic anhydride is commonly performed. Several side reactions (methyl‐esterification, amidation, solvolysis, overpropionylation, and missed propionylation) during propionylation protocols have been described, yet their relative abundances remain vague. Because methyl‐esterification could interfere with correct interpretation of the modification pattern, it is essential to take measures to avoid it. Here we present in‐depth quantitative analyses of methyl‐esterification and the other side reactions in a standard propionylation protocol containing methanol, and when replacing methanol with isopropanol or acetonitrile. We show that the use of alternative solvents can eliminate methyl‐esterification and that even though other side reactions are not prevented, their contribution can be kept relatively small. We also show that replacing methanol can be of importance also in other proteomics methods, such as mixed cation exchange, using methanol under acidic conditions. 相似文献