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281.
Isabel Ferrera Ramon Massana Vanessa Balagué Carles Pedrós-Alió Olga Sánchez Jordi Mas 《Biofouling》2013,29(3):349-357
Phototrophic biofilms are used in a variety of biotechnological and industrial processes. Understanding their structure, ie microbial composition, is a necessary step for understanding their function and, ultimately, for the success of their application. DNA analysis methods can be used to obtain information on the taxonomic composition and relative abundance of the biofilm members. The potential bias introduced by DNA extraction methods in the study of the diversity of a complex phototrophic sulfide-oxidizing biofilm was examined. The efficiency of eight different DNA extraction methods combining physical, mechanical and chemical procedures was assessed. Methods were compared in terms of extraction efficiency, measured by DNA quantification, and detectable diversity (16S rRNA genes recovered), evaluated by denaturing gradient gel electrophoresis (DGGE). Significant differences were found in DNA yields ranging from 116 ± 12 to 1893 ± 96 ng of DNA. The different DGGE fingerprints ranged from 7 to 12 bands. Methods including phenol–chloroform extraction after enzymatic lysis resulted in the greatest DNA yields and detectable diversity. Additionally, two methods showing similar yields and retrieved diversity were compared by cloning and sequencing. Clones belonging to members of the Alpha-, Beta- and Gamma- proteobacteria, Bacteroidetes, Cyanobacteria and to the Firmicutes were recovered from both libraries. However, when bead-beating was applied, clones belonging to the Deltaproteobacteria were also recovered, as well as plastid signatures. Phenol–chloroform extraction after bead-beating and enzymatic lysis was therefore considered to be the most suitable method for DNA extraction from such highly diverse phototrophic biofilms. 相似文献
282.
283.
Ying L. Chen Vanessa M. Dunbabin Johannes A. Postma Art J. Diggle Kadambot H. M. Siddique Zed Rengel 《Plant and Soil》2013,372(1-2):319-337
Background & Aims
Searching for root traits underpinning efficient nutrient acquisition has received increased attention in modern breeding programs aimed at improved crop productivity. Root models provide an opportunity to investigate root-soil interactions through representing the relationships between rooting traits and the non-uniform supply of soil resources. This study used simulation modelling to predict and identify phenotypic plasticity, root growth responses and phosphorus (P) use efficiency of contrasting Lupinus angustifolius genotypes to localised soil P in a glasshouse.Methods
Two L. angustifolius genotypes with contrasting root systems were grown in cylindrical columns containing uniform soil with three P treatments (nil and 20 mg P kg?1 either top-dressed or banded) in the glasshouse. Computer simulations were carried out with root architecture model ROOTMAP which was parameterized with root architectural data from an earlier published hydroponic phenotyping study.Results
The experimental and simulated results showed that plants supplied with banded P had the largest root system and the greatest P-uptake efficiency. The P addition significantly stimulated root branching in the topsoil, whereas plants with nil P had relatively deeper roots. Genotype-dependent root growth plasticity in response to P supply was shown, with the greatest response to banded P.Conclusions
Both experimental and simulation outcomes demonstrated that 1) root hairs and root proliferation increased plant P acquisition and were more beneficial in the localised P fertilisation scenario, 2) placing P deeper in the soil might be a more effective fertilisation method with greater P uptake than top dressing, and 3) the combination of P foraging strategies (including root architecture, root hairs and root growth plasticity) is important for efficient P acquisition from a localised source of fertiliser P. 相似文献284.
The palaeoecological visibility of historical human impact on natural ecosystems in tropical East Africa is strongly impeded by an overriding dominant signature of climate change at decadal‐to‐millennial time scales. Better knowledge of the relative magnitude and timing of present and past human impact and climate variability is, however, instrumental to properly assess the resilience, and recovery potential, of East Africa's natural ecosystems. Here, we briefly review comprehensive previous attempts to assess past ecosystem responses to climate change and human impact. We further discuss some key issues of climate‐human‐ecosystem relationships in a multidisciplinary framework and address some future challenges and outcomes, which may pave the way to a better understanding of past climate‐human‐ecosystem interaction‐ in tropical Africa. 相似文献
285.
Karin E. van Straaten Jong Bum Ko Rajendra Jagdhane Shazia Anjum David R. J. Palmer David A. R. Sanders 《The Journal of biological chemistry》2013,288(47):34121-34130
NtdA from Bacillus subtilis is a sugar aminotransferase that catalyzes the pyridoxal phosphate-dependent equatorial transamination of 3-oxo-α-d-glucose 6-phosphate to form α-d-kanosamine 6-phosphate. The crystal structure of NtdA shows that NtdA shares the common aspartate aminotransferase fold (Type 1) with residues from both monomers forming the active site. The crystal structures of NtdA alone, co-crystallized with the product α-d-kanosamine 6-phosphate, and incubated with the amine donor glutamate reveal three key structures in the mechanistic pathway of NtdA. The structure of NtdA alone reveals the internal aldimine form of NtdA with the cofactor pyridoxal phosphate covalently attached to Lys-247. The addition of glutamate results in formation of pyridoxamine phosphate. Co-crystallization with kanosamine 6-phosphate results in the formation of the external aldimine. Only α-d-kanosamine 6-phosphate is observed in the active site of NtdA, not the β-anomer. A comparison of the structure and sequence of NtdA with other sugar aminotransferases enables us to propose that the VIβ family of aminotransferases should be divided into subfamilies based on the catalytic lysine motif. 相似文献
286.
Leticia Ramos de Arvelos Vanessa Custódio Afonso Rocha Gabriela Pereira Felix Cleine Chagas da Cunha Morun Bernardino Neto Mario da Silva Garrote Filho Conceição de Fátima Pinheiro Elmiro Santos Resende Nilson Penha-Silva 《The Journal of membrane biology》2013,246(3):231-242
The stability of the erythrocyte membrane, which is essential for the maintenance of cell functions, occurs in a critical region of fluidity, which depends largely on its composition and the composition and characteristics of the medium. As the composition of the erythrocyte membrane is influenced by several blood variables, the stability of the erythrocyte membrane must have relations with them. The present study aimed to evaluate, by bivariate and multivariate statistical analyses, the correlations and causal relationships between hematologic and biochemical variables and the stability of the erythrocyte membrane against the chaotropic action of ethanol. The validity of this type of analysis depends on the homogeneity of the population and on the variability of the studied parameters, conditions that can be filled by patients who undergo bariatric surgery by the technique of Roux-en-Y gastric bypass since they will suffer feeding restrictions that have great impact on their blood composition. Pathway analysis revealed that an increase in hemoglobin leads to decreased stability of the cell, probably through a process mediated by an increase in mean corpuscular volume. Furthermore, an increase in the mean corpuscular hemoglobin (MCH) leads to an increase in erythrocyte membrane stability, probably because higher values of MCH are associated with smaller quantities of red blood cells and a larger contact area between the cell membrane and ethanol present in the medium. 相似文献
287.
Kristen L. Leslie Gyun Jee Song Stacey Barrick Vanessa L. Wehbi Jean-Pierre Vilardaga Philip M. Bauer Alessandro Bisello 《The Journal of biological chemistry》2013,288(51):36426-36436
The interaction between vascular cells and macrophages is critical during vascular remodeling. Here we report that the scaffolding protein, ezrin-binding phosphoprotein 50 (EBP50), is a central regulator of macrophage and vascular smooth muscle cells (VSMC) function. EBP50 is up-regulated in intimal VSMC following endoluminal injury and promotes neointima formation. However, the mechanisms underlying these effects are not fully understood. Because of the fundamental role that inflammation plays in vascular diseases, we hypothesized that EBP50 mediates macrophage activation and the response of vessels to inflammation. Indeed, EBP50 expression increased in primary macrophages and VSMC, and in the aorta of mice, upon treatment with LPS or TNFα. This increase was nuclear factor-κB (NF-κB)-dependent. Conversely, activation of NF-κB was impaired in EBP50-null VSMC and macrophages. We found that inflammatory stimuli promote the formation of an EBP50-PKCζ complex at the cell membrane that induces NF-κB signaling. Macrophage activation and vascular inflammation after acute LPS treatment were reduced in EBP50-null cells and mice as compared with WT. Furthermore, macrophage recruitment to vascular lesions was significantly reduced in EBP50 knock-out mice. Thus, EBP50 and NF-κB participate in a feed-forward loop leading to increased macrophage activation and enhanced response of vascular cells to inflammation. 相似文献
288.
Frank Maldarelli Mary Kearney Sarah Palmer Robert Stephens JoAnn Mican Michael A. Polis Richard T. Davey Joseph Kovacs Wei Shao Diane Rock-Kress Julia A. Metcalf Catherine Rehm Sarah E. Greer Daniel L. Lucey Kristen Danley Harvey Alter John W. Mellors John M. Coffin 《Journal of virology》2013,87(18):10313-10323
HIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIV pro-pol to assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n = 22) or multiple, longitudinal (n = 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift. 相似文献
289.
Gabriel Capella Machado Daniela Vanessa Moris Thales Domingos Arantes Luciane Regina Franciscone Silva Raquel Cordeiro Theodoro Rinaldo P?ncio Mendes Adriana Pardini Vicentini Eduardo Bagagli 《Memórias do Instituto Oswaldo Cruz》2013,108(5):637-643
We aimed to evaluate whether the occurrence of cryptic species of
Paracoccidioides brasiliensis, S1, PS2, PS3 and
Paracoccidioides lutzii, has implications in the
immunodiagnosis of paracoccidioidomycosis (PCM). Small quantities of the antigen
gp43 were found in culture filtrates of P. lutzii strains and
this molecule appeared to be more variable within P. lutzii
because the synonymous-nonsynonymous mutation rate was lower, indicating an
evolutionary process different from that of the remaining genotypes. The
production of gp43 also varied between isolates belonging to the same species,
indicating that speciation events are important, but not sufficient to fully
explain the diversity in the production of this antigen. The culture filtrate
antigen AgEpm83, which was obtained from a PS3 isolate, showed large quantities
of gp43 and reactivity by immunodiffusion assays, similar to the standard
antigen (AgB-339) from an S1 isolate. Furthermore, AgEpm83 was capable of
serologically differentiating five serum samples from patients from the Botucatu
and Jundiaí regions. These patients had confirmed PCM but, were non-reactive to
the standard antigen, thus demonstrating an alternative for serological
diagnosis in regions in which S1 and PS2 occur. We also emphasise that it is not
advisable to use a single antigen preparation to diagnose PCM, a disease that is
caused by highly diverse pathogens. 相似文献
290.
Rosane Dias Costa Vanessa Amaral Mendon?a Frederico Marianetti Soriani Sandra Lyon Rachel Adriana Penido Ana Maria Duarte Dias Costa Marina Dias Costa Fabio de Souza Terra Mauro Martins Teixeira Carlos Mauricio de Figueiredo Antunes Antonio Lúcio Teixeira 《Memórias do Instituto Oswaldo Cruz》2013,108(8):1051-1056
Leprosy is an infectious and contagious spectral disease accompanied by a series of
immunological events triggered by the host response to the aetiologic agent,
Mycobacterium leprae . The induction and maintenance of the
immune/inflammatory response in leprosy are linked to multiple cell interactions and
soluble factors, primarily through the action of cytokines. The purpose of the
present study was to evaluate the serum levels of tumour necrosis factor (TNF)-α and
its soluble receptors (sTNF-R1 and sTNF-R2) in leprosy patients at different stages
of multidrug treatment (MDT) in comparison with non-infected individuals and to
determine their role as putative biomarkers of the severity of leprosy or the
treatment response. ELISA was used to measure the levels of these molecules in 30
healthy controls and 37 leprosy patients at the time of diagnosis and during and
after MDT. Our results showed increases in the serum levels of TNF-α and sTNF-R2 in
infected individuals in comparison with controls. The levels of TNF-α, but not
sTNF-R2, decreased with treatment. The current results corroborate previous reports
of elevated serum levels of TNF-α in leprosy and suggest a role for sTNF-R2 in the
control of this cytokine during MDT. 相似文献