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991.
Stijn Vanderzande Niek Hias Daniel Edge-Garza Evelyne Costes Mark W. Davey Johan Keulemans 《Tree Genetics & Genomes》2016,12(5):87
Well-feathered apple trees are essential for commercial orchards to optimize yields. However, most cultivars do not form these sylleptic branches readily in commercial nurseries due to high apical dominance. Several treatments exist to promote their formation in the nurseries, one of which is heading. However, not all cultivars are expected to react similarly to these treatments. We studied the branching response of 155 genotypes following heading and its relation to other architectural traits as a function of the cultivar’s genetic background. Trees were grown for two consecutive years after grafting in a nursery, and the main axes were headed in the winter following growth in year 1. After heading, a single shoot was retained when growth resumed in the second year. Plant architectural traits such as growth of the main shoot, internode length, sylleptic branching, etc. were measured before and after heading and were statistically compared using a mixed model. This model showed the effect of heading for all architectural traits studied. In addition significant genotype and genotype × treatment interactions were found. In general, genotypes that showed a more vigorous growth during the first year also reacted more vigorously to heading. Accounting for the genetic substructure of this collection, no clear distinction in tree response could be found except in a small group of individuals that belonged to an F1 mapping population. This study shows that heading is not favorable for all genotypes to promote sufficient sylleptic branching and that other methods are needed to promote branching in these accessions. 相似文献
992.
Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root‐associated fungi mirrors plant succession in two glacial chronosequences 下载免费PDF全文
Marie Davey Rakel Blaalid Unni Vik Tor Carlsen Håvard Kauserud Pernille B. Eidesen 《Environmental microbiology》2015,17(8):2777-2790
Glacier chronosequences are important sites for primary succession studies and have yielded well‐defined primary succession models for plants that identify environmental resistance as an important determinant of the successional trajectory. Whether plant‐associated fungal communities follow those same successional trajectories and also respond to environmental resistance is an open question. In this study, 454 amplicon pyrosequencing was used to compare the root‐associated fungal communities of the ectomycorrhizal (ECM) herb Bistorta vivipara along two primary succession gradients with different environmental resistance (alpine versus arctic) and different successional trajectories in the vascular plant communities (directional replacement versus directional non‐replacement). At both sites, the root‐associated fungal communities were dominated by ECM basidiomycetes and community composition shifted with increasing time since deglaciation. However, the fungal community's successional trajectory mirrored the pattern observed in the surrounding plant community at both sites: the alpine site displayed a directional‐replacement successional trajectory, and the arctic site displayed a directional‐non‐replacement successional trajectory. This suggests that, like in plant communities, environmental resistance is key in determining succession patterns in root‐associated fungi. The need for further replicated study, including in other host species, is emphasized. 相似文献
993.
Stephen J. Hadfield Justin A. Pachebat Martin T. Swain Guy Robinson Simon JS Cameron Jenna Alexander Matthew J. Hegarty Kristin Elwin Rachel M. Chalmers 《BMC genomics》2015,16(1)
Background
Whole genome sequencing (WGS) of Cryptosporidium spp. has previously relied on propagation of the parasite in animals to generate enough oocysts from which to extract DNA of sufficient quantity and purity for analysis. We have developed and validated a method for preparation of genomic Cryptosporidium DNA suitable for WGS directly from human stool samples and used it to generate 10 high-quality whole Cryptosporidium genome assemblies. Our method uses a combination of salt flotation, immunomagnetic separation (IMS), and surface sterilisation of oocysts prior to DNA extraction, with subsequent use of the transposome-based Nextera XT kit to generate libraries for sequencing on Illumina platforms. IMS was found to be superior to caesium chloride density centrifugation for purification of oocysts from small volume stool samples and for reducing levels of contaminant DNA.Results
The IMS-based method was used initially to sequence whole genomes of Cryptosporidium hominis gp60 subtype IbA10G2 and Cryptosporidium parvum gp60 subtype IIaA19G1R2 from small amounts of stool left over from diagnostic testing of clinical cases of cryptosporidiosis. The C. parvum isolate was sequenced to a mean depth of 51.8X with reads covering 100 % of the bases of the C. parvum Iowa II reference genome (Bioproject PRJNA 15586), while the C. hominis isolate was sequenced to a mean depth of 34.7X with reads covering 98 % of the bases of the C. hominis TU502 v1 reference genome (Bioproject PRJNA 15585).The method was then applied to a further 17 stools, successfully generating another eight new whole genome sequences, of which two were C. hominis (gp60 subtypes IbA10G2 and IaA14R3) and six C. parvum (gp60 subtypes IIaA15G2R1 from three samples, and one each of IIaA17G1R1, IIaA18G2R1, and IIdA22G1), demonstrating the utility of this method to sequence Cryptosporidium genomes directly from clinical samples. This development is especially important as it reduces the requirement to propagate Cryptosporidium oocysts in animal models prior to genome sequencing.Conclusion
This represents the first report of high-quality whole genome sequencing of Cryptosporidium isolates prepared directly from human stool samples. 相似文献994.
995.
Darnell DK Kaur S Stanislaw S Davey S Konieczka JH Yatskievych TA Antin PB 《Cytogenetic and genome research》2007,117(1-4):30-35
An important and ongoing focus of biomedical and agricultural avian research is to understand gene function, which for a significant fraction of genes remains unknown. A first step is to determine when and where genes are expressed during development and in the adult. Whole mount in situ hybridization gives precise spatial and temporal resolution of gene expression throughout an embryo, and a comprehensive analysis and centralized repository of in situ hybridization information would provide a valuable research tool. The GEISHA project (gallus expression in situ hybridization analysis) was initiated to explore the utility of using high-throughput in situ hybridization as a means for gene discovery and annotation in chicken embryos, and to provide a unified repository for in situ hybridization information. This report describes the design and implementation of a new GEISHA database and user interface (www.geisha.arizona.edu), and illustrates its utility for researchers in the biomedical and poultry science communities. Results obtained from a high throughput screen of microRNA expression in chicken embryos are also presented. 相似文献
996.
The least understood components of the DNA damage checkpoint are the DNA damage sensors. Genetic studies of Schizosaccharomyces pombe identified six yeast genes, Rad3, Rad17, Rad9, Rad1, Hus1, and Rad26, which encode proteins thought to sense DNA damage and activate the checkpoint-signaling cascade. It has been suggested that Rad9, Rad1 and Hus1 make a heterotrimeric complex forming a PCNA-like structure. In order to carry out structural and biophysical studies of the complex and its associated proteins, the cDNAs encoding full length human Rad9, Rad1 and Hus1 were cloned together into the pET28a vector using a one-step ligation procedure. Here we report successful tri-cistronic cloning, overexpression and purification of this three-protein complex using a single hexa-histidine tag. The trimeric protein complex of Rad9, Rad1 and Hus1 was purified to near homogeneity, yielding approximately 10mg of protein from one liter of Escherichia coli culture. 相似文献
997.
998.
Changes in paracrine interleukin-2 requirement, CCR7 expression, frequency, and cytokine secretion of human immunodeficiency virus-specific CD4+ T cells are a consequence of antigen load 下载免费PDF全文
Tilton JC Luskin MR Johnson AJ Manion M Hallahan CW Metcalf JA McLaughlin M Davey RT Connors M 《Journal of virology》2007,81(6):2713-2725
Virus-specific CD4+ T-cell responses are thought to be required for the induction and maintenance of many effective CD8+ T-cell and B-cell immune responses in experimental animals and humans. Although the presence of human immunodeficiency virus (HIV)-specific CD4+ T cells has been documented in patients at all stages of HIV infection, many fundamental questions regarding their frequency and function remain. A 10-color, 12-parameter flow cytometric panel was utilized to examine the frequency, memory phenotype (CD27, CCR7, and CD45RA), and cytokine production (interleukin-2 [IL-2], gamma interferon, and tumor necrosis factor alpha) of CD4+ T cells specific for HIV antigens as well as for adenovirus, Epstein-Barr virus (EBV), influenza H1N1 virus, influenza H3N2 virus, cytomegalovirus, varicella-zoster virus (VZV), and tetanus toxoid in normal controls, long-term nonprogressors (LTNP), and HIV-infected patients with progressive disease on or off therapy. The HIV-specific CD4+ T-cell responses in LTNP and patients on therapy were similar in frequency, phenotype, and cytokine production to responses directed against adenovirus, EBV, influenza virus, and VZV. HIV-specific CD4+ T cells from patients off antiretroviral therapy demonstrated a shift towards a CCR7(-) CD45RA(-) phenotype and a reduced percentage of IL-2-producing cells. The alterations in cytokine production during HIV viremia were found to be intrinsic to the HIV-specific CD4+ T cells and caused a requirement for IL-2 supplied exogenously for proliferation to occur. These observations suggest that many previously described changes in HIV-specific CD4+ T-cell function and phenotype are a consequence of high levels of antigen in viremic patients. In addition, defects in function and phenotype of HIV-specific CD4+ T cells are not readily discernible in the context of antiretroviral therapy but rather are similar to responses to other viruses. 相似文献
999.
1000.
Kebede Deribe Jorge Cano Melanie J. Newport Nick Golding Rachel L. Pullan Heven Sime Abeba Gebretsadik Ashenafi Assefa Amha Kebede Asrat Hailu Maria P. Rebollo Oumer Shafi Moses J. Bockarie Abraham Aseffa Simon I. Hay Richard Reithinger Fikre Enquselassie Gail Davey Simon J. Brooker 《PLoS neglected tropical diseases》2015,9(7)