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41.
The Brazilian Atlantic Forest is a Biodiversity Hotspot, yet many biological groups in this biome are poorly known. We compiled
information on the diversity of Atlantic Forest tiger moths (Arctiidae) and assessed the resemblance among localities, whether
arctiid assemblages are concordant with major vegetation types, and the importance of environmental factors in structuring
the variation among assemblages. Additionally, we developed a procedure composed of subsampling and procrustean analysis to
assess the robustness of the results from community composition ordinations when localities differ in species richness. To
do this, we built a database from specimens deposited in the ten most important Brazilian entomological collections, and mapped
species richness in one-degree latitude/longitude grid cells. We employed Principal Coordinates Analysis to assess similarities
among the best-sampled localities. We obtained 8,667 records including 1,193 species, representing 60 and 20% of the estimated
Brazilian and Neotropical faunas, respectively. Our subsampling procedure indicated that the ordination was not greatly affected
by differences in species richness, and was congruent with major vegetation types. Lowland localities on the seacoast were
quite distinct in species composition. A second group included localities in montane areas in the southeast part of the biome.
The last group included localities in the southern region and those with Araucaria forests, and was associated with long distances
from the ocean, even distribution of precipitation throughout the year, and large annual temperature ranges. 相似文献
42.
Mónica Serrano Nicolas Kint Fátima C. Pereira Laure Saujet Pierre Boudry Bruno Dupuy Adriano O. Henriques Isabelle Martin-Verstraete 《PLoS genetics》2016,12(9)
The strict anaerobe Clostridium difficile is the most common cause of nosocomial diarrhea, and the oxygen-resistant spores that it forms have a central role in the infectious cycle. The late stages of sporulation require the mother cell regulatory protein σK. In Bacillus subtilis, the onset of σK activity requires both excision of a prophage-like element (skinBs) inserted in the sigK gene and proteolytical removal of an inhibitory pro-sequence. Importantly, the rearrangement is restricted to the mother cell because the skinBs recombinase is produced specifically in this cell. In C. difficile, σK lacks a pro-sequence but a skinCd element is present. The product of the skinCd gene CD1231 shares similarity with large serine recombinases. We show that CD1231 is necessary for sporulation and skinCd excision. However, contrary to B. subtilis, expression of CD1231 is observed in vegetative cells and in both sporangial compartments. Nevertheless, we show that skinCd excision is under the control of mother cell regulatory proteins σE and SpoIIID. We then demonstrate that σE and SpoIIID control the expression of the skinCd gene CD1234, and that this gene is required for sporulation and skinCd excision. CD1231 and CD1234 appear to interact and both proteins are required for skinCd excision while only CD1231 is necessary for skinCd integration. Thus, CD1234 is a recombination directionality factor that delays and restricts skinCd excision to the terminal mother cell. Finally, while the skinCd element is not essential for sporulation, deletion of skinCd results in premature activity of σK and in spores with altered surface layers. Thus, skinCd excision is a key element controlling the onset of σK activity and the fidelity of spore development. 相似文献
43.
Dragisic C Ashkenazi E Bede L Honzák M Killeen T Paglia A Semroc B Savy C 《Journal of industrial microbiology & biotechnology》2011,38(2):371-374
Increasingly, government regulations, voluntary standards, and company guidelines require that biofuel production complies with sustainability criteria. For some stakeholders, however, compliance with these criteria may seem complex, costly, or unfeasible. What exiting tools, then, might facilitate compliance with a variety of biofuel-related sustainability criteria? This paper presents four existing tools and methodologies that can help stakeholders assess (and mitigate) potential risks associated with feedstock production, and can thus facilitate compliance with requirements under different requirement systems. These include the Integrated Biodiversity Assessment Tool (IBAT), the ARtificial Intelligence for Ecosystem Services (ARIES) tool, the Responsible Cultivation Areas (RCA) methodology, and the related Biofuels + Forest Carbon (Biofuel + FC) methodology. 相似文献
44.
Adriano de Paula Sabino Daniel Dias Ribeiro Caroline Pereira Domingheti Danyelle Romana Alves Rios Luci Maria SantAna Dusse Maria das Graças Carvalho Ana Paula Fernandes 《Molecular biology reports》2014,41(3):1771-1777
Recent studies have demonstrated association between ABO blood system and thrombosis, indicating that individuals belonging to non-O blood groups (A, B or AB) present an increased risk of venous thrombosis, heart disease, and ischemic stroke (IS) as compared to O blood group carriers. In this study, we investigated the frequency of ABO blood group polymorphisms and its association with IS and peripheral arterial disease. Significant differences were observed for O1 (OR 0.57, 95 % CI 0.35–0.95, p < 0.05) and O2 (OR 3.47, 95 % CI 1.15–10.28, p < 0.05) alleles among IS patients while significant differences were observed for B phenotype (26.3 vs 9.5 %, OR 3.42, 95 % CI 1.32–8.76, p = 0.01, patients vs controls, respectively) and alleles A1 (OR 0.31, 95 % CI 0.11–0.84, p < 0.05), O2 (OR 4.61, 95 % CI 1.59–13.23, p < 0.01) and B (OR 3.42, 95 % CI 1.62–7.13, p < 0.001) alleles for PAD patients. O1 allele was an independent variable (OR 0.27, 95 % CI 0.12–0.57, p < 0.001) for IS patients. These data suggest the relationship of non-O blood groups in pathogenesis of thrombosis events and a possible protective effect of O blood group. 相似文献
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47.
Pablo Moreno Stephan Beisken Bhavana Harsha Venkatesh Muthukrishnan Ilinca Tudose Adriano Dekker Stefanie Dornfeldt Franziska Taruttis Ivo Grosse Janna Hastings Steffen Neumann Christoph Steinbeck 《BMC bioinformatics》2015,16(1)
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48.
Coelho AC Boisvert S Mukherjee A Leprohon P Corbeil J Ouellette M 《PLoS neglected tropical diseases》2012,6(2):e1512
Background
Miltefosine (MF) is the first oral compound used in the chemotherapy against leishmaniasis. Since the mechanism of action of this drug and the targets of MF in Leishmania are unclear, we generated in a step-by-step manner Leishmania major promastigote mutants highly resistant to MF. Two of the mutants were submitted to a short-read whole genome sequencing for identifying potential genes associated with MF resistance.Methods/Principal Findings
Analysis of the genome assemblies revealed several independent point mutations in a P-type ATPase involved in phospholipid translocation. Mutations in two other proteins—pyridoxal kinase and α-adaptin like protein—were also observed in independent mutants. The role of these proteins in the MF resistance was evaluated by gene transfection and gene disruption and both the P-type ATPase and pyridoxal kinase were implicated in MF susceptibility. The study also highlighted that resistance can be highly heterogeneous at the population level with individual clones derived from this population differing both in terms of genotypes but also susceptibility phenotypes.Conclusions/Significance
Whole genome sequencing was used to pinpoint known and new resistance markers associated with MF resistance in the protozoan parasite Leishmania. The study also demonstrated the polyclonal nature of a resistant population with individual cells with varying susceptibilities and genotypes. 相似文献49.
Microinjection of DNA constructs into fertilized mouse oocytes typically results in random transgene integration at a single genomic locus. The resulting transgenic founders can be used to establish hemizygous transgenic mouse lines. However, practical and experimental reasons often require that such lines be bred to homozygosity. Transgene zygosity can be determined by progeny testing assays which are expensive and time-consuming, by quantitative Southern blotting which is labor-intensive, or by quantitative PCR (qPCR) which requires transgene-specific design. Here, we describe a zygosity assessment procedure based on fluorescent in situ hybridization (zyFISH). The zyFISH protocol entails the detection of transgenic loci by FISH and the concomitant assignment of homozygosity using a concise and unbiased scoring system. The method requires small volumes of blood, is scalable to at least 40 determinations per assay, and produces results entirely consistent with the progeny testing assay. This combination of reliability, simplicity and cost-effectiveness makes zyFISH a method of choice for transgenic mouse zygosity determinations. 相似文献
50.