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1.
Successful implementation of the Water Framework Directive and achieving its objective of good ecological status of all water bodies depend on the power of the set of monitoring indicators to capture the change in the ecological status of aquatic systems. In this context, testing the robustness and sensitivity of ecological indicators currently used for assessing the status of lotic water bodies is instrumental for the adaptation and further development of assessment methods. This is also a prerequisite for an effective, context-based monitoring system and for improving the quality of the decision making for water bodies. This is particularly challenging in regions where the sets of indicators are under development, the data series are relatively short and data which addresses the individual error sources are lacking. Here we show that hierarchical clusters and ordination analysis provide appropriate tools with which the validity of the ecological status of water bodies set up based on biological multimetric monitoring indices in a small water basin could be tested. We hypothesize that robust and informative monitoring methods classify all water bodies belonging to a single ordination grouping in the same quality class (high, good, moderate, poor or bad). In our case study multimetric biological indicators failed to discriminate between the good and moderate ecological status. Community structure as well as water conductivity and nitrate load were primarily responsible for the observed difference between ordination groupings. Inconsistencies shown in our case study are likely to be induced by insufficient refinement of monitoring schemes and by the constraints existing in the data series and available metadata. We show that multiplication of indicators leads to discrepant interpretation and problematic application. Proposed ordination analysis proves to be a simple and useful tool to detect such discrepancies and support further progress in indicator development. Integrated and longer data and metadata series are needed to refine context-based monitoring methods.  相似文献   
2.
Sterol O-acyltransferase 2 (SOAT2), also known as ACAT2, is the major cholesterol esterifying enzyme in the liver and small intestine (SI). Esterified cholesterol (EC) carried in certain classes of plasma lipoproteins is hydrolyzed by lysosomal acid lipase (LAL) when they are cleared from the circulation. Loss-of-function mutations in LIPA, the gene that encodes LAL, result in Wolman disease (WD) or cholesteryl ester storage disease (CESD). Hepatomegaly and a massive increase in tissue EC levels are hallmark features of both disorders. While these conditions can be corrected with enzyme replacement therapy, the question arose as to what effect the loss of SOAT2 function might have on tissue EC sequestration in LAL-deficient mice. When weaned at 21 days, Lal/:Soat2+/+ mice had a whole liver cholesterol content (mg/organ) of 24.7 mg vs 1.9 mg in Lal+/+:Soat2+/+ littermates, with almost all the excess sterol being esterified. Over the next 31 days, liver cholesterol content in the Lal/:Soat2+/+ mice increased to 145 ± 2 mg but to only 29 ± 2 mg in their Lal/:Soat2/ littermates. The level of EC accumulation in the SI of the Lal/:Soat2/ mice was also much less than in their Lal/:Soat2+/+ littermates. In addition, there was a >70% reduction in plasma transaminase activities in the Lal/:Soat2/ mice. These studies illustrate how the severity of disease in a mouse model for CESD can be substantially ameliorated by elimination of SOAT2 function.  相似文献   
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4.
干细胞是一类具有多向分化潜能的细胞群,如胚胎干细胞(embryonic stem cell,ESC)、诱导多潜能干细胞(induced pluripotent stem cell,i PSC)等,可在特定的条件下向包括视网膜感光细胞在内的多种细胞分化。小分子化合物是一类由组织细胞合成、分泌的小分子多肽类因子,特定的小分子化合物可作用于干细胞诱导其向视网膜感光细胞分化。目前,对干细胞体外培养,通过使用不同的诱导培养方案,探索干细胞向视网膜感光细胞分化的研究成为热点。早期,研究者们主要在共培养条件下采用小分子化合物诱导ESC向视网膜感光细胞分化,随着研究的进展,逐渐开始探索在无共培养条件下小分子化合物诱导ESC向视网膜感光细胞的分化以及小分子化合物诱导i PSC向视网膜感光细胞的分化。本文主要就小分子化合物促进ESC和i PSC向视网膜感光细胞分化的研究进展进行综述。  相似文献   
5.

Background

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.

Results

We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.

Conclusions

BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0486-3) contains supplementary material, which is available to authorized users.  相似文献   
6.
Small nucleolar RNAs (snoRNAs) guide nucleotide modifications of cellular RNAs in the nucleus. We previously showed that box C/D snoRNAs from the Rpl13a locus are unexpected mediators of physiologic oxidative stress, independent of their predicted ribosomal RNA modifications. Here we demonstrate that oxidative stress induced by doxorubicin causes rapid cytoplasmic accumulation of the Rpl13a snoRNAs through a mechanism that requires superoxide and a nuclear splice variant of NADPH oxidase. RNA-sequencing analysis reveals that box C/D snoRNAs as a class are present in the cytoplasm, where their levels are dynamically regulated by NADPH oxidase. These findings suggest that snoRNAs may orchestrate the response to environmental stress through molecular interactions outside of the nucleus.  相似文献   
7.
Oviparously developing embryos of the brine shrimp, Artemia, arrest at gastrulation and are released from females as cysts before entering diapause, a state of dormancy and stress tolerance. Diapause is terminated by an external signal, and growth resumes if conditions are permissible. However, if circumstances are unfavorable, cysts enter quiescence, a dormant stage that continues as long as adverse conditions persist. Artemia embryos in diapause and quiescence are remarkably resistant to environmental and physiological stressors, withstanding desiccation, cold, heat, oxidation, ultraviolet radiation, and years of anoxia at ambient temperature when fully hydrated. Cysts have adapted to stress in several ways; they are surrounded by a rigid cell wall impermeable to most chemical compounds and which functions as a shield against ultraviolet radiation. Artemia cysts contain large amounts of trehalose, a non-reducing sugar thought to preserve membranes and proteins during desiccation by replacing water molecules and/or contributing to vitrification. Late embryogenesis abundant proteins similar to those in seeds and other anhydrobiotic organisms are found in cysts, and they safeguard cell organelles and proteins during desiccation. Artemia cysts contain abundant amounts of p26, a small heat shock protein, and artemin, a ferritin homologue, both ATP-independent molecular chaperones important in stress tolerance. The evidence provided in this review supports the conclusion that it is the interplay of these protective elements that make Artemia one of the most stress tolerant of all metazoan organisms.  相似文献   
8.
The Montagne Noire (southern France) possesses one of the most complete Cambrian successions in the western peri-Gondwana margin and might provide a good stratigraphic reference for both regional charts and international correlations. However, to date, the lower Cambrian succession of the northern Montagne Noire has been supposed to be devoid of biostratigraphically significant fossils. The complex tectonostratigraphic framework of the area (a range divided into Axial Zone, northern and southern Montagne Noire) exacerbated problems related to regional correlations and palaeogeographic reconstructions. As a result, the chronostratigraphic context of the lower Cambrian of northern Montagne Noire is still uncertain and stratigraphic reports have broadly relied on putative lithostratigraphic correlations with the southern Montagne Noire. The purpose of this study is to characterise, for the first time, the fossil record of carbonate beds and lenses of the northern Montagne Noire occurring at the top of the siliciclastic-dominated Marcory Formation, in order to provide regional bio- and chronostratigraphic constraints on lower Cambrian strata. Moreover, this study is aimed at improving international chronostratigraphic correlation. Carbonate beds and lenses cropping out along the Orque Cliff, in the Mélagues thrust slice, were investigated. They yielded a faunal assemblage constituted of molluscs (Igorella cf. ungulata and Igorella moncereti n. sp.), hyoliths (Conotheca brevica), chancelloriids (Archiasterella cf. pentactina and Allonnia sp.) and tommotiids (Lapworthella rete). L. rete is recorded in upper Meishucunian (Cambrian Stage 3) strata of the Yangtze Platform (South China) where it is used as index fossil of the Cambrian Stage 3 Sinosachites flabelliformisTannuolina zhangwentangi Assemblage Zone. Therefore, the presence of this tommotiid provides evidence that the studied carbonate beds and lenses are Cambrian Age 3 (Atdabanian according to the Siberian chart). The upper part of the Marcory Formation in the Mélagues slice, dated as Cambrian Stage 3, might represent a lateral equivalent of the mixed (carbonate-siliciclastic) Pardailhan Formation defined in the southern Montagne Noire.  相似文献   
9.
The small intestine (SI) is the second-greatest source of HDL in mice. However, the selective evaluation of SI-derived HDL (SI-HDL) has been difficult because even the origin of HDL obtained in vivo from the intestinal lymph duct of anesthetized rodents is doubtful. To shed light on this question, we have developed a novel in situ perfusion technique using surgically isolated mouse SI, with which the possible filtration of plasma HDL into the SI lymph duct can be prevented. With the developed method, we studied the characteristics of and mechanism for the production and regulation of SI-HDL. Nascent HDL particles were detected in SI lymph perfusates in WT mice, but not in ABCA1 KO mice. SI-HDL had a high protein content and was smaller than plasma HDL. SI-HDL was rich in TG and apo AIV compared with HDL in liver perfusates. SI-HDL was increased by high-fat diets and reduced in apo E KO mice. In conclusion, with our in situ perfusion model that enables the selective evaluation of SI-HDL, we demonstrated that ABCA1 plays an important role in intestinal HDL production, and SI-HDL is small, dense, rich in apo AIV, and regulated by nutritional and genetic factors.  相似文献   
10.
The toxin Doc from the phd/doc toxin-antitoxin module targets the cellular translation machinery and is inhibited by its antitoxin partner Phd. Here we show that Phd also functions as a chaperone, keeping Doc in an active, correctly folded conformation. In the absence of Phd, Doc exists in a relatively expanded state that is prone to dimerization through domain swapping with its active site loop acting as hinge region. The domain-swapped dimer is not capable of arresting protein synthesis in vitro, whereas the Doc monomer is. Upon binding to Phd, Doc becomes more compact and is secured in its monomeric state with a neutralized active site.  相似文献   
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