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991.
Leuko S Goh F Allen MA Burns BP Walter MR Neilan BA 《Extremophiles : life under extreme conditions》2007,11(1):203-210
Hamelin Pool in Western Australia is one of the two major sites in the world with active marine stromatolite formation. Surrounded
by living smooth and pustular mats, these ancient laminated structures are associated with cyanobacterial communities. Recent
studies have identified a wide diversity of bacteria and archaea in this habitat. By understanding and evaluating the microbial
diversity of this environment we can obtain insights into the formation of early life on Earth, as stromatolites have been
dated in the geological record as far back as 3.5 billion years. Automated ribosomal intergenic spacer analysis (ARISA) patterns
were shown to be a useful method to genetically discriminate halophilic archaea within this environment. Patterns of known
halophilic archaea are consistent, by replicate analysis, and the halophilic strains isolated from stromatolites have novel
intergenic spacer profiles. ARISA–PCR, performed directly on extracted DNA from different sample sites, provided significant
insights into the extent of previous unknown diversity of halophilic archaea within this environment. Cloning and sequence
analysis of the spacer regions obtained from stromatolites confirmed the novel and broad diversity of halophilic archaea in
this environment. 相似文献
992.
Headwater streams are key sites of nutrient and organic matter processing and retention, but little is known about temporal
variability in gross primary production (GPP) and ecosystem respiration (ER) rates as a result of the short duration of most
metabolism measurements in lotic ecosystems. We examined temporal variability and controls on ecosystem metabolism by measuring
daily rates continuously for 2 years in Walker Branch, a first-order deciduous forest stream. Four important scales of temporal
variability in ecosystem metabolism rates were identified: (1) seasonal, (2) day-to-day, (3) episodic (storm-related), and
(4) inter-annual. Seasonal patterns were largely controlled by the leaf phenology and productivity of the deciduous riparian
forest. Walker Branch was strongly net heterotrophic throughout the year with the exception of the open-canopy spring when
GPP and ER rates were co-equal. Day-to-day variability in weather conditions influenced light reaching the streambed, resulting
in high day-to-day variability in GPP particularly during spring (daily light levels explained 84% of the variance in daily
GPP in April). Episodic storms depressed GPP for several days in spring, but increased GPP in autumn by removing leaves shading
the streambed. Storms depressed ER initially, but then stimulated ER to 2–3 times pre-storm levels for several days. Walker
Branch was strongly net heterotrophic in both years of the study, with annual GPP being similar (488 and 519 g O2 m−2 y−1 or 183 and 195 g C m−2 y−1) but annual ER being higher in 2004 than 2005 (−1,645 vs. −1,292 g O2 m−2 y−1 or −617 and −485 g C m−2 y−1). Inter-annual variability in ecosystem metabolism (assessed by comparing 2004 and 2005 rates with previous measurements)
was the result of the storm frequency and timing and the size of the spring macroalgal bloom. Changes in local climate can
have substantial impacts on stream ecosystem metabolism rates and ultimately influence the carbon source and sink properties
of these important ecosystems. 相似文献
993.
994.
Mandy M Cox Sherryll L Layton Tieshan Jiang Kim Cole Billy M Hargis Luc R Berghman Walter G Bottje Young Min Kwon 《BMC biotechnology》2007,7(1):59
Background
A variety of techniques have been described which introduce scarless, site-specific chromosomal mutations. These techniques can be applied to make point mutations or gene deletions as well as insert heterologous DNA into bacterial vectors for vaccine development. Most methods use a multi-step approach that requires cloning and/or designing repeat sequences to facilitate homologous recombination. We have modified previously published techniques to develop a simple, efficient PCR-based method for scarless insertion of DNA into Salmonella enteritidis chromosome. 相似文献995.
The biodistribution of two near-infrared fluorescent agents was assessed in vivo by time-resolved diffuse optical imaging. Bacteriochlorophyll a (BC) and cypate-glysine-arginine-aspartic acid-serine-proline-lysine-OH (Cyp-GRD) were administered separately or combined to mice with subcutaneous xenografts of human breast adenocarcinoma and slow-release estradiol pellets for improved tumor growth. The same excitation (780 nm) and emission (830 nm) wavelengths were used to image the distinct fluorescence lifetime distribution of the fluorescent molecular probes in the mouse cancer model. Fluorescence intensity and lifetime maps were reconstructed after raster-scanning whole-body regions of interest by time-correlated single-photon counting. Each captured temporal point-spread function (TPSF) was deconvolved using both a single and a multiexponental decay model to best determine the measured fluorescence lifetimes. The relative signal from each fluorophore was estimated for any region of interest included in the scanned area. Deconvolution of the individual TPSFs from whole-body fluorescence intensity scans provided corresponding lifetime images for comparing individual component biodistribution. In vivo fluorescence lifetimes were determined to be 0.8 ns (Cyp-GRD) and 2 ns (BC). This study demonstrates that the relative biodistribution of individual fluorophores with similar spectral characteristics can be compartmentalized by using the time-domain fluorescence lifetime gating method. 相似文献
996.
997.
Davis Jose Steven E. Weitzel Walter A. Baase Miya M. Michael Peter H. von?Hippel 《Nucleic acids research》2015,43(19):9291-9305
We here use our site-specific base analog mapping approach to study the interactions and binding equilibria of cooperatively-bound clusters of the single-stranded DNA binding protein (gp32) of the T4 DNA replication complex with longer ssDNA (and dsDNA) lattices. We show that in cooperatively bound clusters the binding free energy appears to be equi-partitioned between the gp32 monomers of the cluster, so that all bind to the ssDNA lattice with comparable affinity, but also that the outer domains of the gp32 monomers at the ends of the cluster can fluctuate on and off the lattice and that the clusters of gp32 monomers can slide along the ssDNA. We also show that at very low binding densities gp32 monomers bind to the ssDNA lattice at random, but that cooperatively bound gp32 clusters bind preferentially at the 5′-end of the ssDNA lattice. We use these results and the gp32 monomer-binding results of the companion paper to propose a detailed model for how gp32 might bind to and interact with ssDNA lattices in its various binding modes, and also consider how these clusters might interact with other components of the T4 DNA replication complex. 相似文献
998.
Daniela M. Russo Patricia L. Abdian Diana M. Posadas Alan Williams Nicolás Vozza Walter Giordano Elmar Kannenberg J. Allan Downie Angeles Zorreguieta 《Applied and environmental microbiology》2015,81(3):1013-1023
The formation of biofilms is an important survival strategy allowing rhizobia to live on soil particles and plant roots. Within the microcolonies of the biofilm developed by Rhizobium leguminosarum, rhizobial cells interact tightly through lateral and polar connections, forming organized and compact cell aggregates. These microcolonies are embedded in a biofilm matrix, whose main component is the acidic exopolysaccharide (EPS). Our work shows that the O-chain core region of the R. leguminosarum lipopolysaccharide (LPS) (which stretches out of the cell surface) strongly influences bacterial adhesive properties and cell-cell cohesion. Mutants defective in the O chain or O-chain core moiety developed premature microcolonies in which lateral bacterial contacts were greatly reduced. Furthermore, cell-cell interactions within the microcolonies of the LPS mutants were mediated mostly through their poles, resulting in a biofilm with an altered three-dimensional structure and increased thickness. In addition, on the root epidermis and on root hairs, O-antigen core-defective strains showed altered biofilm patterns with the typical microcolony compaction impaired. Taken together, these results indicate that the surface-exposed moiety of the LPS is crucial for proper cell-to-cell interactions and for the formation of robust biofilms on different surfaces. 相似文献
999.
Xiaoxi B. Lin Christopher T. Lohans Rebbeca Duar Jinshui Zheng John C. Vederas Jens Walter Michael G?nzle 《Applied and environmental microbiology》2015,81(6):2032-2041
Reutericyclin is a unique antimicrobial tetramic acid produced by some strains of Lactobacillus reuteri. This study aimed to identify the genetic determinants of reutericyclin biosynthesis. Comparisons of the genomes of reutericyclin-producing L. reuteri strains with those of non-reutericyclin-producing strains identified a genomic island of 14 open reading frames (ORFs) including genes coding for a nonribosomal peptide synthetase (NRPS), a polyketide synthase (PKS), homologues of PhlA, PhlB, and PhlC, and putative transport and regulatory proteins. The protein encoded by rtcN is composed of a condensation domain, an adenylation domain likely specific for d-leucine, and a thiolation domain. rtcK codes for a PKS that is composed of a ketosynthase domain, an acyl-carrier protein domain, and a thioesterase domain. The products of rtcA, rtcB, and rtcC are homologous to the diacetylphloroglucinol-biosynthetic proteins PhlABC and may acetylate the tetramic acid moiety produced by RtcN and RtcK, forming reutericyclin. Deletion of rtcN or rtcABC in L. reuteri TMW1.656 abrogated reutericyclin production but did not affect resistance to reutericyclin. Genes coding for transport and regulatory proteins could be deleted only in the reutericyclin-negative L. reuteri strain TMW1.656ΔrtcN, and these deletions eliminated reutericyclin resistance. The genomic analyses suggest that the reutericyclin genomic island was horizontally acquired from an unknown source during a unique event. The combination of PhlABC homologues with both an NRPS and a PKS has also been identified in the lactic acid bacteria Streptococcus mutans and Lactobacillus plantarum, suggesting that the genes in these organisms and those in L. reuteri share an evolutionary origin. 相似文献
1000.
Magda Budzowska Thomas GW Graham Alexandra Sobeck Shou Waga Johannes C Walter 《The EMBO journal》2015,34(14):1971-1985
DNA interstrand cross‐links (ICLs) are repaired in S phase by a complex, multistep mechanism involving translesion DNA polymerases. After replication forks collide with an ICL, the leading strand approaches to within one nucleotide of the ICL (“approach”), a nucleotide is inserted across from the unhooked lesion (“insertion”), and the leading strand is extended beyond the lesion (“extension”). How DNA polymerases bypass the ICL is incompletely understood. Here, we use repair of a site‐specific ICL in Xenopus egg extracts to study the mechanism of lesion bypass. Deep sequencing of ICL repair products showed that the approach and extension steps are largely error‐free. However, a short mutagenic tract is introduced in the vicinity of the lesion, with a maximum mutation frequency of ~1%. Our data further suggest that approach is performed by a replicative polymerase, while extension involves a complex of Rev1 and DNA polymerase ζ. Rev1–pol ζ recruitment requires the Fanconi anemia core complex but not FancI–FancD2. Our results begin to illuminate how lesion bypass is integrated with chromosomal DNA replication to limit ICL repair‐associated mutagenesis. 相似文献