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961.
962.
Park SJ Park BJ Jung MY Kim SJ Chae JC Roh Y Forwick M Yoon HI Rhee SK 《Microbial ecology》2011,62(3):537-548
Increases in global temperatures have been shown to enhance glacier melting in the Arctic region. Here, we have evaluated
the effects of meltwater runoff on the microbial communities of coastal marine sediment located along a transect of Temelfjorden,
in Svalbard. As close to the glacier front, the sediment properties were clearly influenced by deglaciation. Denaturing gradient
gel electrophoresis profiles showed that the sediment microbial communities of the stations of glacier front (stations 188–178)
were distinguishable from that of outer fjord region (station 176). Canonical correspondence analysis indicated that total
carbon and calcium carbonate in sediment and chlorophyll a in bottom water were key factors driving the change of microbial
communities. Analysis of 16S rRNA gene clone libraries suggested that microbial diversity was higher within the glacier–proximal
zone (station 188) directly affected by the runoffs than in the outer fjord region. While the crenarchaeotal group I.1a dominated
at station 176 (62%), Marine Benthic Group-B and other Crenarchaeota groups were proportionally abundant. With regard to the
bacterial community, alpha-Proteobacteria and Flavobacteria lineages prevailed (60%) at station 188, whereas delta-Proteobacteria (largely sulfate-reducers) predominated (32%) at station 176. Considering no clone sequences related to sulfate-reducers,
station 188 may be more oxic compared to station 176. The distance-wise compositional variation in the microbial communities
is attributable to their adaptations to the sediment environments which are differentially affected by melting glaciers. 相似文献
963.
Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm
The discovery of genomic structural variants (SVs), such as copy number variants (CNVs), is essential to understand genetic variation of human populations and complex diseases. Over recent years, the advent of new high-throughput sequencing (HTS) platforms has opened many opportunities for SVs discovery, and a very promising approach consists in measuring the depth of coverage (DOC) of reads aligned to the human reference genome. At present, few computational methods have been developed for the analysis of DOC data and all of these methods allow to analyse only one sample at time. For these reasons, we developed a novel algorithm (JointSLM) that allows to detect common CNVs among individuals by analysing DOC data from multiple samples simultaneously. We test JointSLM performance on synthetic and real data and we show its unprecedented resolution that enables the detection of recurrent CNV regions as small as 500 bp in size. When we apply JointSLM to analyse chromosome one of eight genomes with different ancestry, we identify 3000 regions with recurrent CNVs of different frequency and size: hierarchical clustering on these regions segregates the eight individuals in two groups that reflect their ancestry, demonstrating the potential utility of JointSLM for population genetics studies. 相似文献
964.
965.
Peptide nucleic acids (PNA) are one of the most widely used synthetic DNA mimics where the four bases are attached to a N-(2-aminoethyl)glycine (aeg) backbone instead of the negative-charged phosphate backbone in DNA. We have developed a chimeric PNA (chiPNA), in which a chiral GNA-like γ(3)T monomer is incorporated into aegPNA backbone. The base pair opening kinetics of the aegPNA:DNA and chiPNA:DNA hybrid duplexes were studied by NMR hydrogen exchange experiments. This study revealed that the aegPNA:DNA hybrid is much more stable duplex and is less dynamic compared to DNA duplex, meaning that base pairs are opened and reclosed much more slowly. The site-specific incorporation of γ(3)T monomer in the aegPNA:DNA hybrid can destabilize a specific base pair and its neighbors, maintaining the thermal stabilities and dynamic properties of other base pairs. Our hydrogen exchange study firstly revealed the unique kinetic features of base pairs in the aegPNA:DNA and chiPNA:DNA hybrids, which will provide an insight into the development of methodology for specific DNA recognition using PNA fragments. 相似文献
966.
967.
Yi SS Hwang IK Kim DW Shin JH Nam SM Choi JH Lee CH Won MH Seong JK Yoon YS 《Neurochemical research》2011,36(1):117-128
Because it appears that oxidative stress and inflammation are implicated with disease pathogenesis in the diabetic brain,
many researchers have used streptozotocin (STZ)-induced diabetic animals to study superoxide production and the effects of
superoxide scavengers like Cu,Zn-superoxide dismutase (SOD1). However, many studies have been conducted without considering
temporal changes after STZ injection. Interestingly, though SOD activities were not significantly different among the groups,
SOD1 and 4-hydroxy-2-nonenal (4-HNE) immunoreactivities were significantly enhanced at 3 weeks after an STZ injection (STZ3w)
versus only marginal levels in sham controls, whereas microglial activity was remarkably reduced in injected rats at this
time. However, SOD1 immunoreactivity and microglial activities were only at the sham level at STZ4w. The present study provides
important information concerning cell damage by ROS generated by STZ. Microglial response was found to be inactivated at STZ3w
and neuronal cells (NeuN) showed a non-significant tendency to be reduced in number at STZ4w except in the dentate gyrus.
We speculated that the above oxidative stress-related events should be accomplished at STZ3w in the brains of STZ-induced
diabetes animal models. Therefore, the aim of the present study was to investigate chronological changes in SOD1 immunoreactivity
associated with lipid peroxidation and inflammatory responses in the hippocampi of STZ-induced type I diabetic rats. 相似文献
968.
Overcoming the recalcitrance in lignocellulosic biomass for efficient hydrolysis of the polysaccharides cellulose and hemicellulose to fermentable sugars is a research priority for the transition from a fossilfuel-based economy to a renewable carbohydrate economy. Methylglucuronoxylans (MeGXn) are the major components of hemicellulose in woody biofuel crops. Here, we describe efficient production of the GH10 xylanase Xyl10B from Thermotoga maritima in transplastomic plants and demonstrate exceptional stability and catalytic activities of the in planta produced enzyme. Fully expanded leaves from homotransplastomic plants contained enzymatically active Xyl10B at a level of 11-15% of their total soluble protein. Transplastomic plants and their seed progeny were morphologically indistinguishable from non-transgenic plants. Catalytic activity of in planta produced Xyl10B was detected with poplar, sweetgum and birchwood xylan substrates following incubation between 40 and 90 °C and was also stable in dry and stored leaves. Optimal yields of Xyl10B were obtained from dry leaves if crude protein extraction was performed at 85 °C. The transplastomic plant derived Xyl10B showed exceptional catalytic activity and enabled the complete hydrolysis of MeGXn to fermentable sugars with the help of a single accessory enzyme (α-glucuronidase) as revealed by the sugar release assay. Even without this accessory enzyme, the majority of MeGXn was hydrolyzed by the transplastomic plant-derived Xyl10B to fermentable xylose and xylobiose. 相似文献
969.
Yoon HY Kales SC Luo R Lipkowitz S Randazzo PA 《Biology of the cell / under the auspices of the European Cell Biology Organization》2011,103(4):171-184
Background information. ARAP1 is an Arf (ADP‐ribosylation factor)‐directed GAP (GTPase‐activating protein) that inhibits the trafficking of EGFR (epidermal growth factor receptor) to the early endosome. To further understand the function of ARAP1, we sought to identify proteins that interact with ARAP1. Results. Here we report that ARAP1 associates with the CIN85 (Cbl‐interacting protein of 85 kDa). Arg86 and Arg90 of ARAP1 and the SH3 (Src homology 3) domains of CIN85 are necessary for the interaction. We found that a mutant of ARAP1 with reduced affinity for CIN85 does not efficiently rescue the effect of reduced ARAP1 expression on EGFR trafficking to the early endosome. Reduced expression of CIN85 has a similar effect as reduced expression of ARAP1 on traffic of the EGFR. Cbl proteins regulate the endocytic trafficking of the EGFR by mediating ubiquitination of the EGFR. Overexpression of ARAP1 reduced ubiquitination of the EGFR by Cbl and slowed Cbl‐dependent degradation of the EGFR. Reduced expression of ARAP1 accelerated degradation of EGFR but did not affect the level of ubiquitination of the receptor that was detected. Conclusion. ARAP1 interaction with CIN85 regulates endocytic trafficking of the EGFR and affects ubiquitination of EGFR. We propose a model in which the ARAP1‐CIN85 complex drives exit of EGF—EGFR–Cbl complex from a pre‐early endosome into a pathway distinct from the early endosome/lysosome pathway. 相似文献
970.