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931.
Wrapping things up about virus RNA replication 总被引:5,自引:1,他引:4
Mackenzie J 《Traffic (Copenhagen, Denmark)》2005,6(11):967-977
All single-stranded 'positive-sense' RNA viruses that infect mammalian, insect or plant cells rearrange internal cellular membranes to provide an environment facilitating virus replication. A striking feature of these unique membrane structures is the induction of 70-100 nm vesicles (either free within the cytoplasm, associated with other induced vesicles or bound within a surrounding membrane) harbouring the viral replication complex (RC). Although similar in appearance, the cellular composition of these vesicles appears to vary for different viruses, implying different organelle origins for the intracellular sites of viral RNA replication. Genetic analysis has revealed that induction of these membrane structures can be attributed to a particular viral gene product, usually a non-structural protein. This review will highlight our current knowledge of the formation and composition of virus RCs and describe some of the similarities and differences in RNA-membrane interactions observed between the virus families Flaviviridae and Picornaviridae. 相似文献
932.
Background
Microarray experiments, as well as other genomic analyses, often result in large gene sets containing up to several hundred genes. The biological significance of such sets of genes is, usually, not readily apparent. 相似文献933.
Greaves DK Schreer JF Hammill MO Burns JM 《Physiological and biochemical zoology : PBZ》2005,78(1):9-17
Harbour seals, Phoca vitulina, dive from birth, providing a means of mapping the development of the diving response, and so our objective was to investigate the postpartum development of diving bradycardia. The study was conducted May-July 2000 and 2001 in the St. Lawrence River Estuary (48 degrees 41'N, 68 degrees 01'W). Both depth and heart rate (HR) were remotely recorded during 86,931 dives (ages 2-42 d, n = 15) and only depth for an additional 20,300 dives (combined data covered newborn to 60 d, n = 20). The mean dive depth and mean dive durations were conservative during nursing (2.1 +/- 0.1 m and 0.57 +/- 0.01 min, range = 0-30.9 m and 0-5.9 min, respectively). The HR of neonatal pups during submersion was bimodal, but as days passed, the milder of the two diving HRs disappeared from their diving HR record. By 15 d of age, most of the dive time was spent at the lower diving bradycardia rate. Additionally, this study shows that pups are born with the ability to maintain the lower, more fully developed dive bradycardia during focused diving but do not do so during shorter routine dives. 相似文献
934.
Glycosylation is an important post-translational modification. Analysis of glycopeptides is difficult using collision-induced dissociation, as it typically yields only information about the glycan structure, without any peptide sequence information. We demonstrate here how a 3D-quadrupole ion trap, using the complementary techniques of collision induced dissociation (CID) and electron-transfer dissociation (ETD), can be used to elucidate the glycan structure and peptide sequence of the N-glycosylated peptide from a fractionated tryptic digest of the lectin from the coral tree, Erythina cristagalli. CID experiments on the multiply protonated glycopeptide ions yield, almost exclusively, cleavage at glycosidic bonds, with little peptide backbone fragmentation. ETD reactions of the triply charged glycopeptide cations with either sulfur dioxide or nitrobenzene anions yield cleavage of the peptide backbone with no loss of the glycan structure. These results show that a 3D-quadrupole ion trap can be used to provide glycopeptide amino acid sequence information as well as information about the glycan structure. 相似文献
935.
Randomized sequence databases for tandem mass spectrometry peptide and protein identification 总被引:4,自引:0,他引:4
Tandem mass spectrometry (MS/MS) combined with database searching is currently the most widely used method for high-throughput peptide and protein identification. Many different algorithms, scoring criteria, and statistical models have been used to identify peptides and proteins in complex biological samples, and many studies, including our own, describe the accuracy of these identifications, using at best generic terms such as "high confidence." False positive identification rates for these criteria can vary substantially with changing organisms under study, growth conditions, sequence databases, experimental protocols, and instrumentation; therefore, study-specific methods are needed to estimate the accuracy (false positive rates) of these peptide and protein identifications. We present and evaluate methods for estimating false positive identification rates based on searches of randomized databases (reversed and reshuffled). We examine the use of separate searches of a forward then a randomized database and combined searches of a randomized database appended to a forward sequence database. Estimated error rates from randomized database searches are first compared against actual error rates from MS/MS runs of known protein standards. These methods are then applied to biological samples of the model microorganism Shewanella oneidensis strain MR-1. Based on the results obtained in this study, we recommend the use of use of combined searches of a reshuffled database appended to a forward sequence database as a means providing quantitative estimates of false positive identification rates of peptides and proteins. This will allow researchers to set criteria and thresholds to achieve a desired error rate and provide the scientific community with direct and quantifiable measures of peptide and protein identification accuracy as opposed to vague assessments such as "high confidence." 相似文献
936.
Lynch RL Konicek BW McNulty AM Hanna KR Lewis JE Neubauer BL Graff JR 《Molecular cancer research : MCR》2005,3(3):163-169
937.
Bedell JA Budiman MA Nunberg A Citek RW Robbins D Jones J Flick E Rholfing T Fries J Bradford K McMenamy J Smith M Holeman H Roe BA Wiley G Korf IF Rabinowicz PD Lakey N McCombie WR Jeddeloh JA Martienssen RA 《PLoS biology》2005,3(1):e13
938.
Antigen-engaged B cells undergo chemotaxis toward the T zone and form motile conjugates with helper T cells 总被引:4,自引:1,他引:3
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Okada T Miller MJ Parker I Krummel MF Neighbors M Hartley SB O'Garra A Cahalan MD Cyster JG 《PLoS biology》2005,3(6):e150
Interactions between B and T cells are essential for most antibody responses, but the dynamics of these interactions are poorly understood. By two-photon microscopy of intact lymph nodes, we show that upon exposure to antigen, B cells migrate with directional preference toward the B-zone–T-zone boundary in a CCR7-dependent manner, through a region that exhibits a CCR7-ligand gradient. Initially the B cells show reduced motility, but after 1 d, motility is increased to approximately 9 μm/min. Antigen-engaged B cells pair with antigen-specific helper T cells for 10 to more than 60 min, whereas non-antigen-specific interactions last less than 10 min. B cell–T cell conjugates are highly dynamic and migrate extensively, being led by B cells. B cells occasionally contact more than one T cell, whereas T cells are strictly monogamous in their interactions. These findings provide evidence of lymphocyte chemotaxis in vivo, and they begin to define the spatiotemporal cellular dynamics associated with T cell–dependent antibody responses. 相似文献
939.
Yano JK Hsu MH Griffin KJ Stout CD Johnson EF 《Nature structural & molecular biology》2005,12(9):822-823
Human microsomal cytochrome P450 2A6 (CYP2A6) contributes extensively to nicotine detoxication but also activates tobacco-specific procarcinogens to mutagenic products. The CYP2A6 structure shows a compact, hydrophobic active site with one hydrogen bond donor, Asn297, that orients coumarin for regioselective oxidation. The inhibitor methoxsalen effectively fills the active site cavity without substantially perturbing the structure. The structure should aid the design of inhibitors to reduce smoking and tobacco-related cancers. 相似文献
940.
McMahon SA Miller JL Lawton JA Kerkow DE Hodes A Marti-Renom MA Doulatov S Narayanan E Sali A Miller JF Ghosh P 《Nature structural & molecular biology》2005,12(10):886-892
Only few instances are known of protein folds that tolerate massive sequence variation for the sake of binding diversity. The most extensively characterized is the immunoglobulin fold. We now add to this the C-type lectin (CLec) fold, as found in the major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein of Bordetella bacteriophage. Variation in Mtd, with its approximately 10(13) possible sequences, enables phage adaptation to Bordetella spp. Mtd is an intertwined, pyramid-shaped trimer, with variable residues organized by its CLec fold into discrete receptor-binding sites. The CLec fold provides a highly static scaffold for combinatorial display of variable residues, probably reflecting a different evolutionary solution for balancing diversity against stability from that in the immunoglobulin fold. Mtd variants are biased toward the receptor pertactin, and there is evidence that the CLec fold is used broadly for sequence variation by related retroelements. 相似文献