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81.
Estimating temporal trends in spatially structured populations has a critical role to play in understanding regional changes in biological populations and developing management strategies. Designing effective monitoring programmes to estimate these trends requires important decisions to be made about how to allocate sampling effort among spatial replicates (i.e. number of sites) and temporal replicates (i.e. how often to survey) to minimise uncertainty in trend estimates. In particular, the optimal mix of spatial and temporal replicates is likely to depend upon the spatial and temporal correlations in population dynamics. Although there has been considerable interest in the ecological literature on understanding spatial and temporal correlations in species’ population dynamics, little attention has been paid to its consequences for monitoring design. We address this issue using model‐based survey design to identify the optimal allocation of sampling effort among spatial and temporal replicates for estimating population trends under different levels of spatial and temporal correlation. Based on linear trends, we show that how we should allocate sampling effort among spatial and temporal replicates depends crucially on the spatial and temporal correlations in population dynamics, environmental variation, observation error and the spatial variation in temporal trends. When spatial correlation is low and temporal correlation is high, the best option is likely to be to sample many sites infrequently, particularly when observation error and/or spatial variation in temporal trends are high. When spatial correlation is high and temporal correlation is low, the best option is likely to be to sample few sites frequently, particularly when observation error and/or spatial variation in temporal trends are low. When abundances are spatially independent, it is always preferable to maximise spatial replication. This provides important insights into how spatio‐temporal monitoring programmes should be designed to estimate temporal trends in spatially structured populations. 相似文献
82.
Jonathan B. Puritz Mikhail V. Matz Robert J. Toonen Jesse N. Weber Daniel I. Bolnick Christopher E. Bird 《Molecular ecology》2014,23(24):5937-5942
We are writing in response to the population and phylogenomics meeting review by Andrews & Luikart ( 2014 ) entitled ‘Recent novel approaches for population genomics data analysis’. Restriction‐site‐associated DNA (RAD) sequencing has become a powerful and useful approach in molecular ecology, with several different published methods now available to molecular ecologists, none of which can be considered the best option in all situations. A&L report that the original RAD protocol of Miller et al. ( 2007 ) and Baird et al. ( 2008 ) is superior to all other RAD variants because putative PCR duplicates can be identified (see Baxter et al. 2011 ), thereby reducing the impact of PCR artefacts on allele frequency estimates (Andrews & Luikart 2014 ). In response, we (i) challenge the assertion that the original RAD protocol minimizes the impact of PCR artefacts relative to that of other RAD protocols, (ii) present additional biases in RADseq that are at least as important as PCR artefacts in selecting a RAD protocol and (iii) highlight the strengths and weaknesses of four different approaches to RADseq which are a representative sample of all RAD variants: the original RAD protocol (mbRAD, Miller et al. 2007 ; Baird et al. 2008 ), double digest RAD (ddRAD, Peterson et al. 2012 ), ezRAD (Toonen et al. 2013 ) and 2bRAD (Wang et al. 2012 ). With an understanding of the strengths and weaknesses of different RAD protocols, researchers can make a more informed decision when selecting a RAD protocol. 相似文献
83.
Gordon S. A. B. Stewart Sharon Lubinsky-Mink Clive G. Jackson Aliza Cassel Jonathan Kuhn 《Plasmid》1986,15(3):172-181
During the construction of the Messing pUC plasmid series, the rop(rom) gene of pBR322 which mediates the activity of RNAI was deleted. This has resulted in an elevated copy number for the pUC plasmids which makes the expression of beta-galactosidase activity constitutive in a host containing the Iqtss lac repressor. We describe the construction of a new series of vectors which retain the pUC multiple cloning site (MCS) but in which copy number control has been recovered. In addition, the lac alpha/lac promoter expression region has been inserted into a HpaI cassette. This facilitates the movement of recombinant DNA clones within the MCS. It also increases the complementation activity of the lac alpha peptide by an order of magnitude, allowing selection of recombinants by their Lac- phenotype on MacConkey agar. 相似文献
84.
Shibin Gao Carlos Martinez Debra J. Skinner Alan F. Krivanek Jonathan H. Crouch Yunbi Xu 《Molecular breeding : new strategies in plant improvement》2008,22(3):477-494
Leaf collection from the field, labeling and tracking back to the source plants after genotyping are rate limiting steps in
leaf DNA-based genotyping. In this study, an optimized genotyping method using endosperm DNA sampled from single maize seeds
was developed, which can be used to replace leaf DNA-based genotyping for both genetic studies and breeding applications.
A similar approach is likely to be suitable for all plants with relatively large seeds. Part of the endosperm was excised
from imbibed maize seeds and DNA extracted in 96-tube plates using individuals from eight F2 populations and seven inbreds. The quality of the resultant DNA was functionally comparable to DNA extracted from leaf tissue.
Extraction from 30 mg of endosperm yields 3–10 μg DNA, which is sufficient for analysis of 200–400 agarose-gel PCR-based markers,
with the potential for several million chip-based SNP marker analyses. By comparing endosperm DNA and leaf DNA for individuals
from an F2 population, genotyping errors caused by pericarp contamination and hetero-fertilization were found to average 3.8 and 0.6%,
respectively. Endosperm sampling did not affect germination rates under controlled conditions, although under normal field
conditions the germination rate, seedling establishment, and growth vigor were significantly lower than that of non-sampled
controls for some genotypes. However, careful field management can compensate for these effects. Seed DNA-based genotyping
lowered costs by 24.6% compared to leaf DNA-based genotyping due to reduced field plantings and labor costs. A substantial
advantage of this approach is that it can be used to select desirable genotypes before planting. As such it provides an opportunity
for dramatic improvements in the efficiency and selective gain of breeding systems based on optimum combinations of marker-assisted
selection and phenotypic selection within and between generations. 相似文献
85.
The effects of K+ concentration, light intensity and CO2 levels on the volume of Commelina communis L. guard cell protoplasts were studied. Two degrees of swelling response were observed, both dependent on an external supply of K+ , but not necessarily on the supply of a permeant anion. The presence of K+ itself, independent of light or CO2 level, stimulated swelling at a relatively slow rate. When K+ , light and low CO2 conditions were supplied together, the swelling was relatively rapid and of high magnitude. The rapid swelling was specific for K+ and Rb+ giving a half maximal effect after 2 h at a KCl concentration of about 18 mmol m−3 . The addition of CaCl2 at 1 mol m−3 inhibited K+ -dependent swelling under all conditions tested. The response to light and low CO2 levels by Commelina guard cell protoplasts is thought to reflect a high degree of physiological integrity. 相似文献
86.
Ai H Lvov YM Mills DK Jennings M Alexander JS Jones SA 《Cell biochemistry and biophysics》2003,38(2):103-114
A recently developed method for surface modification, layer-by-layer (LbL) assembly, has been applied to silicone, and its
ability to encourage endothelial cell growth and control cell growth patterns has been examined. The surfaces studied consisted
of a precursor, with alternating cationic polyethyleneimine (PEI) and anionic sodium polystyrene sulfonate (PSS) layers followed
by alternating gelatin and poly-d-lysine (PDL) layers. Film growth increased linearly with the number of layers. Each PSS/PEI bilayer was 3 nm thick, and each
gelatin/PDL bilayer was 5 nm thick. All layers were more hydrophilic than the unmodified silicone rubber surface, as determined
from contact angle measurements. The contact angle was primarily dictated by the outermost layer. Of the coatings studied,
gelatin was the most hydrophilic. A film of (PSS/PEI)4/(gelatin/PDL)4/ gelatin was highly favorable for cell adhesion and growth, in contrast to films of (PSS/PEI)8 or (PSS/PEI)8/PSS. Cell growth patterns were successfully controlled by selective deposition of microspheres on silicone rubber, using
microcontact printing with a silicone stamp. Cell adhesion was confined to the region of microsphere deposition. These results
demonstrate that the LbL self-assembly technique provides a general approach to coat and selectively deposit films with nanometer
thickness on silicone rubber. Furthermore, they show that this method is a viable technique for controlling cellular adhesion
and growth. 相似文献
87.
Enzyme activation for organic solvents made easy 总被引:1,自引:0,他引:1
Enzymes are highly selective catalysts that perform intricate chemistries at ambient temperatures and pressures. Although water is the solvent of life, it is a poor solvent for most synthetic organic reactions and, therefore, most chemists avoid aqueous solutions for synthetic applications. However, when removed from the aqueous environment and placed in an organic solvent, enzyme activity is reduced greatly. Here, we present a general overview of recent efforts to activate enzymes for use in nonaqueous media, giving particular focus to the use of simple salts as additives that result in significant biocatalytic improvements. 相似文献
88.
The skeletal muscle Ca(2+) release channel/ryanodine receptor (RyR1) contains approximately 50 thiols per subunit. These thiols have been grouped according to their reactivity/responsiveness toward NO, O(2), and glutathione, but the molecular mechanism enabling redox active molecules to modulate channel activity is poorly understood. In the case of NO, very low concentrations (submicromolar) activate RyR1 by S-nitrosylation of a single cysteine residue (Cys-3635), which resides within a calmodulin binding domain. S-Nitrosylation of Cys-3635 only takes place at physiological tissue O(2) tension (pO(2); i.e. approximately 10 mm Hg) but not at pO(2) approximately 150 mm Hg. Two explanations have been offered for the loss of RyR1 responsiveness to NO at ambient pO(2), i.e. Cys-3635 is oxidized by O(2) versus O(2) subserves an allosteric function (Eu, J. P., Sun, J. H., Xu, L., Stamler, J. S., and Meissner, G. (2000) Cell 102, 499-509). Here we report that the NO donors NOC-12 and S-nitrosoglutathione both activate RyR1 by release of NO but do so independently of pO(2). Moreover, NOC-12 activates the channel by S-nitrosylation of Cys-3635 and thereby reverses channel inhibition by calmodulin. In contrast, S-nitrosoglutathione activates RyR1 by oxidation and S-nitrosylation of thiols other than Cys-3635 (and calmodulin is not involved). Our results suggest that the effect of pO(2) on RyR1 S-nitrosylation is exerted through an allosteric mechanism. 相似文献
89.
Current methods of prediction of protein conformation are reviewedand the algorithms on which they rely are presented. For non-homologousproteins and after cross-validation the reported methods exhibita probability index, i.e. the per cent of correctly predictedresidues per predicted residues, of 6365% with a standarddeviation of the order of 7% for three conformational stateshelix,ß-strand and coil. This present limitation in theaccuracy of predictions that use only the information of thelocal sequence can be related essentially to the effect of long-rangeinteractions specific for each protein family. The methods basedon sequence similarity can improve the accuracy of predictionby expressing explicitly the homology of the protein to be predictedwith proteins in the database. In these circumstances the probabilityindex can reach 87% with a standard deviation of 6.6%. Thisproperty can be used for modeling homologous proteins by aidingin amino acid sequence alignments. The prediction of the tertiarystructure of a protein is still limited to the case of modelinga structure based on the known three-dimensional structure ofa homologous protein. 相似文献
90.
Zhang Y Zhou Y Schweizer U Savaskan NE Hua D Kipnis J Hatfield DL Gladyshev VN 《The Journal of biological chemistry》2008,283(4):2427-2438
Although dietary selenium (Se) deficiency results in phenotypes associated with selenoprotein depletion in various organs, the brain is protected from Se loss. To address the basis for the critical role of Se in brain function, we carried out comparative gene expression analyses for the complete selenoproteome and associated biosynthetic factors. Using the Allen Brain Atlas, we evaluated 159 regions of adult mouse brain and provided experimental analyses of selected selenoproteins. All 24 selenoprotein mRNAs were expressed in the mouse brain. Most strikingly, neurons in olfactory bulb, hippocampus, cerebral cortex, and cerebellar cortex were exceptionally rich in selenoprotein gene expression, in particular in GPx4, SelK, SelM, SelW, and Sep15. Over half of the selenoprotein genes were also expressed in the choroid plexus. A unique expression pattern was observed for one of the highly expressed selenoprotein genes, SelP, which we suggest to provide neurons with Se. Cluster analysis of the expression data linked certain selenoproteins and selenocysteine machinery genes and suggested functional linkages among selenoproteins, such as that between SelM and Sep15. Overall, this study suggests that the main functions of selenium in mammals are confined to certain neurons in the brain. 相似文献