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991.
992.
Fabiano Tófoli de Araújo Victor M. Bolanos-Garcia Cristiane T. Pereira Mario Sanches Elisa E. Oshiro Rita C. C. Ferreira Dimitri Y. Chigardze Jo?o Alexandre Gon?alves Barbosa Luís Carlos de Souza Ferreira Celso E. Benedetti Tom L. Blundell Andrea Balan 《PloS one》2013,8(11)
Background
The uptake of sulphur-containing compounds plays a pivotal role in the physiology of bacteria that live in aerobic soils where organosulfur compounds such as sulphonates and sulphate esters represent more than 95% of the available sulphur. Until now, no information has been available on the uptake of sulphonates by bacterial plant pathogens, particularly those of the Xanthomonas genus, which encompasses several pathogenic species. In the present study, we characterised the alkanesulphonate uptake system (Ssu) of Xanthomonas axonopodis pv. citri 306 strain (X. citri), the etiological agent of citrus canker.Methodology/Principal Findings
A single operon-like gene cluster (ssuEDACB) that encodes both the sulphur uptake system and enzymes involved in desulphurisation was detected in the genomes of X. citri and of the closely related species. We characterised X. citri SsuA protein, a periplasmic alkanesulphonate-binding protein that, together with SsuC and SsuB, defines the alkanesulphonate uptake system. The crystal structure of SsuA bound to MOPS, MES and HEPES, which is herein described for the first time, provides evidence for the importance of a conserved dipole in sulphate group coordination, identifies specific amino acids interacting with the sulphate group and shows the presence of a rather large binding pocket that explains the rather wide range of molecules recognised by the protein. Isolation of an isogenic ssuA-knockout derivative of the X. citri 306 strain showed that disruption of alkanesulphonate uptake affects both xanthan gum production and generation of canker lesions in sweet orange leaves.Conclusions/Significance
The present study unravels unique structural and functional features of the X. citri SsuA protein and provides the first experimental evidence that an ABC uptake system affects the virulence of this phytopathogen. 相似文献993.
Christina R?hr Martin Kerick Axel Fischer Alexander Kühn Karl Kashofer Bernd Timmermann Andriani Daskalaki Thomas Meinel Dmitriy Drichel Stefan T. B?rno Anja Nowka Sylvia Krobitsch Alice C. McHardy Christina Kratsch Tim Becker Andrea Wunderlich Christian Barmeyer Christian Viertler Kurt Zatloukal Christoph Wierling Hans Lehrach Michal R. Schweiger 《PloS one》2013,8(7)
MiRNAs are discussed as diagnostic and therapeutic molecules. However, effective miRNA drug treatments with miRNAs are, so far, hampered by the complexity of the miRNA networks. To identify potential miRNA drugs in colorectal cancer, we profiled miRNA and mRNA expression in matching normal, tumor and metastasis tissues of eight patients by Illumina sequencing. We validated six miRNAs in a large tissue screen containing 16 additional tumor entities and identified miRNA-1, miRNA-129, miRNA-497 and miRNA-215 as constantly de-regulated within the majority of cancers. Of these, we investigated miRNA-1 as representative in a systems-biology simulation of cellular cancer models implemented in PyBioS and assessed the effects of depletion as well as overexpression in terms of miRNA-1 as a potential treatment option. In this system, miRNA-1 treatment reverted the disease phenotype with different effectiveness among the patients. Scoring the gene expression changes obtained through mRNA-Seq from the same patients we show that the combination of deep sequencing and systems biological modeling can help to identify patient-specific responses to miRNA treatments. We present this data as guideline for future pre-clinical assessments of new and personalized therapeutic options. 相似文献
994.
Christian Milani Arancha Hevia Elena Foroni Sabrina Duranti Francesca Turroni Gabriele Andrea Lugli Borja Sanchez Rebeca Martín Miguel Gueimonde Douwe van Sinderen Abelardo Margolles Marco Ventura 《PloS one》2013,8(7)
Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota. 相似文献
995.
Paraoxonase is an HDL-associated enzyme that plays a preventive role against oxidative stress, which is thought to contribute
to cancer development. PON1 activity varies widely among individuals, which is in part related to two common nonsynonymous
polymorphisms in the PON1 gene (Q192R and L55M). The polymorphisms in PON1 have been implicated in cancer risk. However, results
from the studies to date have been conflicting. To clarify the association, a meta-analysis was performed for 7,073 cases
and 9,520 controls from 25 published case–control studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used
to assess the strength of the association. Significant associations between PON1-L55M but not Q192R polymorphism and total
cancer were observed from all the comparisons. In stratified analyses, PON1-55M allele was a risk factor for breast cancer.
Similarly, increased risk was observed for prostate cancer (OR = 1.18, 95% CI: 1.01–1.36, P
heterogeneity = 0.260) and Caucasian population (OR = 1.18, 95% CI: 1.02–1.38, P
heterogeneity = 0.1) of the LM genotype, compared with the LL genotype. For PON1-Q192R polymorphism, PON1-192R allele was a decreased risk
factor for cancer in the Asian group (RR vs QQ: OR = 0.61, 95% CI: 0.38–0.98, P
heterogeneity = 0.268; QR vs QQ: OR = 0.71, 95% CI: 0.52–0.96, P
heterogeneity = 0.130; RR + QR vs QQ: OR = 0.71, 95% CI: 0.53–0.95, P
heterogeneity = 0.135). Although some modest bias could not be eliminated, this meta-analysis suggests that the PON1-55M allele is a risk factor for the development of cancer, in particular for breast cancer. Future studies with larger sample
sizes are warranted to further evaluate these associations. 相似文献
996.
Peng Wang Yongzhong Xing Zhikang Li Sibin Yu 《Molecular breeding : new strategies in plant improvement》2012,29(4):903-913
To facilitate marker-assisted transfer of desirable genes for improvement of yield traits, we used a set of backcross recombinant
inbred lines (BRIL) derived from two elite parental lines, ‘Zhenshan97’ and ‘93-11’, to resolve a quantitative trait loci
(QTL) cluster for heading date and yield-related traits in rice. Four main-effect QTL (qHD6.1, qHD6.2, qHD7, and qHD8) and four epistatic QTL affecting heading date in the BRIL were detected in two experimental trials. The major QTL (qHD8) was confirmed in three heterogeneous inbred families (HIF) that segregated for this target region, and narrowed down to
a 20-kb segment in a large HIF-derived population. qHD8 was found to interact with qHD7 and had a pleiotropic effect responsible for heading date and yield components. To test usability of the identified QTL in
rice improvement, we further developed near-isogenic lines (NIL) containing one or more target genes by marker-assisted transfer
of ‘93-11’ alleles at qHD8, qHD7, and qHD6.1, and the GS3 gene for grain size into ‘Zhenshan97’. The pyramid line NIL(qHD8 + GS3) had higher yield potential, longer grains, and a more suitable heading date than ‘Zhenshan97’. Comparison of the NIL showed
existence of epistasis between alleles at different loci and background effect on qHD8, which are very important for pyramiding of desirable alleles at the target QTL. These results will be particularly useful
not only to understand the genetic basis of yield-related traits but also to improve the efficiency of marker-assisted selection
for favorable loci in rice breeding programs. 相似文献
997.
Georgia E. Knauss Walter G. Joyce Tyler R. Lyson Dean Pearson 《Pal?ontologische Zeitschrift》2011,85(2):125-142
A nearly complete turtle shell from the Late Cretaceous (Maastrichtian) Hell Creek Formation of Slope County, North Dakota,
represents the most complete remains to date of a Mesozoic kinosternoid turtle and a new species, Hoplochelys clark nov. sp. The new taxon is diagnosable from other representatives of Hoplochelys by the plesiomorphic placement of the humeral/femoral sulcus behind the hyo/hypoplastral suture and the autapomorphic development
of an interrupted median (neural) keel. All six previously named Paleocene (Puercan and Torrejonian) representatives of Hoplochelys lack diagnostic characters and are synonymized as Hoplochelys crassa. A phylogenetic analysis reveals that Hoplochelys spp. and Agomphus pectoralis are most parsimoniously placed within Kinosternoidea along the phylogenetic stem of the extant Mesoamerican River Turtle
Dermatemys mawii, extending that taxon’s stem lineage from the early Eocene to the late Maastrichtian. The two primary crown lineages of Kinosternoidea
are thus known from the Mesozoic and split prior to the late Campanian. The presence of a thickened cruciform plastron, true
costiform processes, only three inframarginals, and the reduction of the medial contact of the abdominals are synapomorphies
of Chelydroidea, the clade formed by Chelydridae and Kinosternoidae. 相似文献
998.
The ethoxy chains of short ethoxy chain nonylphenol (NPEOav2.0, containing average 2.0 ethoxy units) were dehydrogenated by cell-free extracts from Ensifer sp. strain AS08 grown on a basal medium supplemented with NPEOav2.0. The reaction was coupled with the reduction in 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide and phenazine
methosulfate. The enzyme (NPEOav2.0 dehydrogenase; NPEO-DH) was purified to homogeneity with a yield of 20% and a 56-fold increase in specific activity. The
molecular mass of the native enzyme was 120 kDa, consisting of two identical monomer units (60 kDa). The gene encoding NPEO-DH
was cloned, which consisted of 1,659 bp, corresponding to a protein of 553 amino acid residues. The deduced amino acid sequence
agreed with the N-terminal amino acid sequence of the purified NPEO-DH. The presence of a flavin adenine dinucleotide (FAD)-binding
motif and glucose–methanol–choline (GMC) oxidoreductase signature motifs strongly suggested that the enzyme belongs to the
GMC oxidoreductase family. The protein exhibited homology (40–45% identity) with several polyethylene glycol dehydrogenases
(PEG-DHs) of this family, but the identity was lower than those (approximately 58%) among known PEG-DHs. The substrate-binding
domain was more hydrophobic compared with those of glucose oxidase and PEG-DHs. The recombinant protein had the same molecular
mass as the purified NPEO-DH and dehydrogenated PEG400-2000, NPEOav2.0 and its components, and NPEOav10, but only slight or no activity was found using diethylene glycol, triethylene glycol, and
PEG200.
English edition: The paper was edited by a native speaker through American Journal Experts (). 相似文献
999.
Salmonella typhimurium AhpC is a founding member of the peroxiredoxin family, a ubiquitous group of cysteine-based peroxidases with high reactivity toward hydrogen peroxide, organic hydroperoxides, and peroxynitrite. For all of the peroxiredoxins, the catalytic cysteine, referred to as the peroxidatic cysteine (C(P)), acts as a nucleophile in attacking the peroxide substrate, forming a cysteine sulfenic acid at the active site. Because thiolates are far stronger nucleophiles than thiol groups, it is generally accepted that cysteine-based peroxidases should exhibit pK(a) values lower than an unperturbed value of 8.3-8.5. In this investigation, several independent approaches were used to assess the pK(a) of the two cysteinyl residues of AhpC. Methods using two different iodoacetamide derivatives yielded unperturbed pK(a) values (7.9-8.7) for both cysteines, apparently due to reactivity with the wrong conformation of C(P) (i.e., locally unfolded and flipped out of the active site), as supported by X-ray crystallographic analyses. A functional pK(a) of 5.94 +/- 0.10 presumably reflecting the titration of C(P) within the fully folded active site was obtained by measuring AhpC competition with horseradish peroxidase for hydrogen peroxide; this value is quite similar to that obtained by analyzing the pH dependence of the epsilon(240) of wild-type AhpC (5.84 +/- 0.02) and similar to those obtained for two typical 2-cysteine peroxiredoxins from Saccharomyces cerevisiae (5.4 and 6.0). Thus, the pK(a) value of AhpC balances the need for a deprotonated thiol (at pH 7, approximately 90% of the C(P) would be deprotonated) with the fact that thiolates with higher pK(a) values are stronger nucleophiles. 相似文献
1000.
Meghann Ryan Peter Kochunov Laura M. Rowland Braxton D. Mitchell S. Andrea Wijtenburg Els Fieremans Jelle Veraart Dmitry S. Novikov Xiaoming Du Bhim Adhikari Feven Fisseha Heather Bruce Joshua Chiappelli Hemalatha Sampath Seth Ament Jeffrey O'Connell Alan R. Shuldiner L. Elliot Hong 《Obesity (Silver Spring, Md.)》2017,25(11):1876-1880