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51.
Sheng-Da Zhang Claire-Lise Santini Wei-Jia Zhang Valérie Barbe Sophie Mangenot Charlotte Guyomar Marc Garel Hai-Tao Chen Xue-Gong Li Qun-Jian Yin Yuan Zhao Jean Armengaud Jean-Charles Gaillard Séverine Martini Nathalie Pradel Claude Vidaud François Alberto Claudine Médigue Christian Tamburini Long-Fei Wu 《Extremophiles : life under extreme conditions》2016,20(3):301-310
Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantial eco-physiological diversity including free-living, symbiotic and piezophilic life styles. Genomic characteristics underlying this variability across species are poorly understood. Here we carried out genomic and physiological analysis of Photobacterium phosphoreum strain ANT-2200, the first deep-sea luminous bacterium of which the genome has been sequenced. Using optical mapping we updated the genomic data and reassembled it into two chromosomes and a large plasmid. Genomic analysis revealed a versatile energy metabolic potential and physiological analysis confirmed its growth capacity by deriving energy from fermentation of glucose or maltose, by respiration with formate as electron donor and trimethlyamine N-oxide (TMAO), nitrate or fumarate as electron acceptors, or by chemo-organo-heterotrophic growth in rich media. Despite that it was isolated at a site with saturated dissolved oxygen, the ANT-2200 strain possesses four gene clusters coding for typical anaerobic enzymes, the TMAO reductases. Elevated hydrostatic pressure enhances the TMAO reductase activity, mainly due to the increase of isoenzyme TorA1. The high copy number of the TMAO reductase isoenzymes and pressure-enhanced activity might imply a strategy developed by bacteria to adapt to deep-sea habitats where the instant TMAO availability may increase with depth. 相似文献
52.
The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure prediction and protein design. It is a difficult problem due to its combinatorial nature. We study the performance of an “MMGBSA” energy function, implemented in our protein design program Proteus, which combines molecular mechanics terms, a Generalized Born and Surface Area (GBSA) solvent model, with approximations that make the model pairwise additive. Proteus is not a competitor to specialized side chain prediction programs due to its cost, but it allows protein design applications, where side chain prediction is an important step and MMGBSA an effective energy model. We predict the side chain conformations for 18 proteins. The side chains are first predicted individually, with the rest of the protein in its crystallographic conformation. Next, all side chains are predicted together. The contributions of individual energy terms are evaluated and various parameterizations are compared. We find that the GB and SA terms, with an appropriate choice of the dielectric constant and surface energy coefficients, are beneficial for single side chain predictions. For the prediction of all side chains, however, errors due to the pairwise additive approximation overcome the improvement brought by these terms. We also show the crucial contribution of side chain minimization to alleviate the rigid rotamer approximation. Even without GB and SA terms, we obtain accuracies comparable to SCWRL4, a specialized side chain prediction program. In particular, we obtain a better RMSD than SCWRL4 for core residues (at a higher cost), despite our simpler rotamer library. Proteins 2016; 84:803–819. © 2016 Wiley Periodicals, Inc. 相似文献
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Félix-Faure Jim Gaillard Jérémie Descloux Stéphane Chanudet Vincent Poirel Alain Baudoin Jean-Marc Avrillier Jean-Noël Millery Annie Dambrine Etienne 《Ecosystems》2019,22(2):312-330
Ecosystems - When a water reservoir is created, the pre-existing soils and vegetation are flooded. Here, we took advantage of the complete emptying of the Sarrans Reservoir, which was flooded... 相似文献
55.
FXR-deficiency confers increased susceptibility to torpor 总被引:1,自引:0,他引:1
Cariou B Bouchaert E Abdelkarim M Dumont J Caron S Fruchart JC Burcelin R Kuipers F Staels B 《FEBS letters》2007,581(27):5191-5198
The role of the nuclear receptor FXR in adaptive thermogenesis was investigated using FXR-deficient mice. Despite elevated serum bile acid concentrations and increased mRNA expression profiles of thermogenic genes in brown adipose tissue, FXR-deficiency did not alter energy expenditure under basal conditions. However, FXR-deficiency accelerated the fasting-induced entry into torpor in a leptin-dependent manner. FXR-deficient mice were also extremely cold-intolerant. These altered responses may be linked to a more rapid decrease in plasma concentrations of metabolic fuels (glucose, triglycerides) thus impairing uncoupling protein 1-driven thermogenesis. These results identify FXR as a modulator of energy homeostasis. 相似文献
56.
Nathaniel Valière Christophe Bonenfant Carole Toïgo Gordon Luikart Jean-Michel Gaillard François Klein 《Conservation Genetics》2007,8(1):69-78
Population size information is critical for managing endangered or harvested populations. Population size can now be estimated
from non-invasive genetic sampling. However, pitfalls remain such as genotyping errors (allele dropout and false alleles at
microsatellite loci). To evaluate the feasibility of non-invasive sampling (e.g., for population size estimation), a pilot
study is required. Here, we present a pilot study consisting of (i) a genetic step to test loci amplification and to estimate
allele frequencies and genotyping error rates when using faecal DNA, and (ii) a simulation step to quantify and minimise the
effects of errors on estimates of population size. The pilot study was conducted on a population of red deer in a fenced natural
area of 5440 ha, in France. Twelve microsatellite loci were tested for amplification and genotyping errors. The genotyping
error rates for microsatellite loci were 0–0.83 (mean=0.2) for allele dropout rates and 0–0.14 (mean=0.02) for false allele
rates, comparable to rates encountered in other non-invasive studies. Simulation results suggest we must conduct 6 PCR amplifications
per sample (per locus) to achieve approximately 97% correct genotypes. The 3% error rate appears to have little influence
on the accuracy and precision of population size estimation. This paper illustrates the importance of conducting a pilot study
(including genotyping and simulations) when using non-invasive sampling to study threatened or managed populations. 相似文献
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58.
Daniel Duran Xue Zeng Sheng Chih Jin Jungmin Choi Carol Nelson-Williams Bogdan Yatsula Jonathan Gaillard Charuta Gavankar Furey Qiongshi Lu Andrew T. Timberlake Weilai Dong Michelle A. Sorscher Erin Loring Jennifer Klein August Allocco Ava Hunt Sierra Conine Jason K. Karimy Kristopher T. Kahle 《Neuron》2019,101(3):429-443.e4
59.
Pierre-Yves Jean-Charles Vishwaesh Rajiv Subhodeep Sarker Sangoh Han Yushi Bai Ali Masoudi Sudha K. Shenoy 《The Journal of biological chemistry》2022,298(5)
Arrestins and their yeast homologs, arrestin-related trafficking adaptors (ARTs), share a stretch of 29 amino acids called the ART motif. However, the functionality of that motif is unknown. We now report that deleting this motif prevents agonist-induced ubiquitination of β-arrestin2 (β-arr2) and blocks its association with activated G protein–coupled receptors (GPCRs). Within the ART motif, we have identified a conserved phenylalanine residue, Phe116, that is critical for the formation of β-arr2–GPCR complexes. β-arr2 Phe116Ala mutant has negligible effect on blunting β2-adrenergic receptor–induced cAMP generation unlike β-arr2, which promotes rapid desensitization. Furthermore, available structures for inactive and inositol hexakisphosphate 6–activated forms of bovine β-arr2 revealed that Phe116 is ensconced in a hydrophobic pocket, whereas the adjacent Phe117 and Phe118 residues are not. Mutagenesis of Phe117 and Phe118, but not Phe116, preserves GPCR interaction of β-arr2. Surprisingly, Phe116 is dispensable for the association of β-arr2 with its non-GPCR partners. β-arr2 Phe116Ala mutant presents a significantly reduced protein half-life compared with β-arr2 and undergoes constitutive Lys-48-linked polyubiquitination, which tags proteins for proteasomal degradation. We also found that Phe116 is critical for agonist-dependent β-arr2 ubiquitination with Lys-63-polyubiquitin linkages that are known mediators of protein scaffolding and signal transduction. Finally, we have shown that β-arr2 Phe116Ala interaction with activated β2-adrenergic receptor can be rescued with an in-frame fusion of ubiquitin. Taken together, we conclude that Phe116 preserves structural stability of β-arr2, regulates the formation of β-arr2–GPCR complexes that inhibit G protein signaling, and promotes subsequent ubiquitin-dependent β-arr2 localization and trafficking. 相似文献
60.