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991.
Thomas Riedel Anne Fiebig James Han Marcel Huntemann Stefan Spring J?rn Petersen Natalia N. Ivanova Victor Markowitz Tanja Woyke Markus G?ker Nikos C. Kyrpides Hans-Peter Klenk 《Standards in genomic sciences》2014,9(3):855-865
Wenxinia marina Ying et al. 2007 is the type species of the genus Wenxinia, a representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, isolated from oilfield sediments of the South China Sea. This family was shown to harbor the most abundant bacteria especially from coastal and polar waters, but was also found in microbial mats, sediments and attached to different kind of surfaces.Here we describe the features of W. marina strain HY34T together with the genome sequence and annotation of strain DSM 24838T and novel aspects of its phenotype. The 4,181,754 bp containing genome sequence encodes 4,047 protein-coding genes and 59 RNA genes. The genome of W. marina DSM 24838T was sequenced as part of the activities of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project funded by the DoE and the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG). 相似文献
992.
Wayne Reeve Ross Ballard Elizabeth Drew Rui Tian Lambert Br?u Lynne Goodwin Marcel Huntemann James Han Reddy Tatiparthi Amy Chen Konstantinos Mavrommatis Victor Markowitz Krishna Palaniappan Natalia Ivanova Amrita Pati Tanja Woyke Nikos Kyrpides 《Standards in genomic sciences》2014,9(3):602-613
Ensifer meliloti strain RRI128 is an aerobic, motile, Gram-negative, non-spore-forming rod. RRI128 was isolated from a nodule recovered from the roots of barrel medic (Medicago truncatula) grown in the greenhouse and inoculated with soil collected from Victoria, Australia. The strain is used in commercial inoculants in Australia. RRI128 nodulates and forms an effective symbiosis with a diverse range of lucerne cultivars (Medicago sativa) and several species of annual medic (M. truncatula, Medicago littoralis and Medicago tornata), but forms an ineffective symbiosis with Medicago polymorpha. Here we describe the features of E. meliloti strain RRI128, together with genome sequence information and annotation. The 6,900,273 bp draft genome is arranged into 156 scaffolds of 157 contigs, contains 6,683 protein-coding genes and 87 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. 相似文献
993.
Mikkel Z. Ankarfeldt Lars ?ngquist Tanja Stocks Marianne U. Jakobsen Kim Overvad Jytte Halkj?r Wim H. M. Saris Arne Astrup Thorkild I. A. S?rensen 《PloS one》2014,9(7)
Background/Objectives
Physiological evidence indicates that high-protein diets reduce caloric intake and increase thermogenic response, which may prevent weight gain and regain after weight loss. Clinical trials have shown such effects, whereas observational cohort studies suggest an association between greater protein intake and weight gain. In both types of studies the results are based on average weight changes, and show considerable diversity in both directions. This study investigates whether the discrepancy in the evidence could be due to recruitment of overweight and obese individuals into clinical trials.Subjects/Methods
Data were available from the European Diet, Obesity and Genes (DiOGenes) post-weight-loss weight-maintenance trial and the Danish Diet, Cancer and Health (DCH) cohort. Participants of the DCH cohort were matched with participants from the DiOGenes trial on gender, diet, and body characteristics. Different subsets of the DCH-participants, comparable with the trial participants, were analyzed for weight maintenance according to the randomization status (high or low protein) of the matched trial participants.Results
Trial participants were generally heavier, had larger waist circumference and larger fat mass than the participants in the entire DCH cohort. A better weight maintenance in the high-protein group compared to the low protein group was observed in the subgroups of the DCH cohort matching body characteristics of the trial participants.Conclusion
This modified observational study, minimized the differences between the RCT and observational data with regard to dietary intake, participant characteristics and statistical analysis. Compared with low protein diet the high protein diet was associated with better weight maintenance when individuals with greater body mass index and waist circumference were analyzed. Selecting subsets of large-scale observational cohort studies with similar characteristics as participants in clinical trials may reconcile the otherwise conflicting results. 相似文献994.
Brandon K. Swan Mark D. Chaffin Manuel Martinez-Garcia Hilary G. Morrison Erin K. Field Nicole J. Poulton E. Dashiell P. Masland Christopher C. Harris Alexander Sczyrba Patrick S. G. Chain Sergey Koren Tanja Woyke Ramunas Stepanauskas 《PloS one》2014,9(4)
Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures. 相似文献
995.
996.
Tip-enhanced Raman scattering (TERS) enables the label-free investigation of biochemical interfaces with nanometer lateral resolution by combining the benefits of the intrinsic molecular specificity of Raman spectroscopy, the sensitivity because of signal enhancing capabilities of plasmonic nanoparticles, and the precision of scanning probe microscopy. The structural differentiation of constituents based on inherent molecular information is possible even down to a few nanometer spatial resolution and consequently, nucleobases, proteins, lipids, and carbohydrates can be identified and localized in a single measurement. This has been shown in the last few years for different biological samples ranging from single DNA strand investigations to cell membrane studies. 相似文献
997.
Rotival M Zeller T Wild PS Maouche S Szymczak S Schillert A Castagné R Deiseroth A Proust C Brocheton J Godefroy T Perret C Germain M Eleftheriadis M Sinning CR Schnabel RB Lubos E Lackner KJ Rossmann H Münzel T Rendon A;Cardiogenics Consortium Erdmann J Deloukas P Hengstenberg C Diemert P Montalescot G Ouwehand WH Samani NJ Schunkert H Tregouet DA Ziegler A Goodall AH Cambien F Tiret L Blankenberg S 《PLoS genetics》2011,7(12):e1002367
998.
Li Zhang Michael Buerke Michael Lautenschläger Li Chen Adrian Frister Axel Schlitt Tanja Luther Nan Song Britt Hofmann Stefan Rose‐John Rolf‐Edgar Silber Ursula Müller‐Werdan Karl Werdan 《Journal of cellular and molecular medicine》2011,15(4):994-1004
Inflammatory pathways are involved in the development of atherosclerosis. Interaction of vessel wall cells and invading monocytes by cytokines may trigger local inflammatory processes. 3‐Hydroxy‐3‐methylglutaryl coenzyme A reductase inhibitors (statins) are standard medications used in cardiovascular diseases. They are thought to have anti‐inflammatory capacities, in addition to their lipid‐lowering effects. We investigated the anti‐inflammatory effect of statins in the cytokine‐mediated‐interaction‐model of human vascular smooth muscle cells (SMC) and human mononuclear cells (MNC). In this atherosclerosis‐related inflammatory model LPS (lipopolysaccharide, endotoxin), as well as high mobility group box 1 stimulation resulted in synergistic (i.e. over‐additive) IL‐6 (interleukin‐6) production as measured in ELISA. Recombinant IL‐1, tumour necrosis factor‐α and IL‐6 mediated the synergistic IL‐6 production. The standard anti‐inflammatory drugs aspirin and indomethacin (Indo) reduced the synergistic IL‐6 production by 60%. Simvastatin, atorvastatin, fluvastatin or pravastatin reduced the IL‐6 production by 53%, 50%, 64% and 60%, respectively. The inhibition by the statins was dose dependent. Combination of statins with aspirin and/or Indo resulted in complete inhibition of the synergistic IL‐6 production. The same inhibitors blocked STAT3 phosphorylation, providing evidence for an autocrine role of IL‐6 in the synergism. MNC from volunteers after 5 day aspirin or simvastatin administration showed no decreased IL‐6 production, probably due to drug removal during MNC isolation. Taken together, the data show that anti‐inflammatory functions (here shown for statins) can be sensitively and reproducibly determined in this novel SMC/MNC coculture model. These data implicate that statins have the capacity to affect atherosclerosis by regulating cytokine‐mediated innate inflammatory pathways in the vessel wall. 相似文献
999.
Allozyme variation has been and continues to be a major source of information on the level of genetic variation among plant
species. Deciphering the molecular basis of electrophoretic variation is essential for understanding the forces affecting
the protein level variation. In this study, the relationship between allozyme heterozygosity and nucleotide diversity in plants
is investigated among and within species. Allozyme and nucleotide diversity in 27 plant species was reviewed. At the multilocus
level, the two methods are congruent: a clear correlation between the two measures of genetic diversity among plant species
was observed, strengthening the view that effective population size is the major determinant of genome-wide diversity. Nucleotide
diversity at six allozyme coding genes (6pgdB, aco, gdh, gotC, mdhA, and mdhB) in conifer Pinus sylvestris was investigated jointly with electrophoretic data. Single non-synonymous charge-changing mutations were found together with
electrophoretic alleles that consequently were mutationally unique. Synonymous site nucleotide diversity (point estimate of
θ
W—0.009 per bp) and silent site divergence from Pinus pinaster at allozyme coding loci were at comparable levels with other loci in the species. Linkage disequilibrium was extensive compared
to earlier estimates from P. sylvestris and other trees, spanning several kilobases. Allozyme coding genes had an excess of closely related haplotypes whose frequency
has recently increased possibly as a result of partial selective sweeps or balancing selection, but complex demographic effects
cannot be excluded. 相似文献
1000.
The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes 总被引:1,自引:0,他引:1
van Passel MW Kant R Zoetendal EG Plugge CM Derrien M Malfatti SA Chain PS Woyke T Palva A de Vos WM Smidt H 《PloS one》2011,6(3):e16876