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101.
102.
Emily R. Davenport Darren A. Cusanovich Katelyn Michelini Luis B. Barreiro Carole Ober Yoav Gilad 《PloS one》2015,10(11)
The bacterial composition of the human fecal microbiome is influenced by many lifestyle factors, notably diet. It is less clear, however, what role host genetics plays in dictating the composition of bacteria living in the gut. In this study, we examined the association of ~200K host genotypes with the relative abundance of fecal bacterial taxa in a founder population, the Hutterites, during two seasons (n = 91 summer, n = 93 winter, n = 57 individuals collected in both). These individuals live and eat communally, minimizing variation due to environmental exposures, including diet, which could potentially mask small genetic effects. Using a GWAS approach that takes into account the relatedness between subjects, we identified at least 8 bacterial taxa whose abundances were associated with single nucleotide polymorphisms in the host genome in each season (at genome-wide FDR of 20%). For example, we identified an association between a taxon known to affect obesity (genus Akkermansia) and a variant near PLD1, a gene previously associated with body mass index. Moreover, we replicate a previously reported association from a quantitative trait locus (QTL) mapping study of fecal microbiome abundance in mice (genus Lactococcus, rs3747113, P = 3.13 x 10−7). Finally, based on the significance distribution of the associated microbiome QTLs in our study with respect to chromatin accessibility profiles, we identified tissues in which host genetic variation may be acting to influence bacterial abundance in the gut. 相似文献
103.
Lila Kari Kathleen A. Hill Abu S. Sayem Rallis Karamichalis Nathaniel Bryans Katelyn Davis Nikesh S. Dattani 《PloS one》2015,10(5)
We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to k (herein k = 9) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal, the Denisovan, and the chimp), and that the sequence most different from it in this dataset belongs to a cucumber. 相似文献
104.
Shanique A. Young Katelyn E. McCabe Alena Bartakova Joe Delaney Donald P. Pizzo Robert O. Newbury Judith A. Varner David D. Schlaepfer Dwayne G. Stupack 《PloS one》2015,10(5)
High-risk neuroblastoma is associated with an overall survival rate of 30–50%. Neuroblastoma-expressed cell adhesion receptors of the integrin family impact cell adhesion, migration, proliferation and survival. Integrin α4 is essential for neural crest cell motility during development, is highly expressed on leukocytes, and is critical for transendothelial migration. Thus, cancer cells that express this receptor may exhibit increased metastatic potential. We show that α4 expression in human and murine neuroblastoma cell lines selectively enhances in vitro interaction with the alternatively spliced connecting segment 1 of fibronectin, as well as vascular cell adhesion molecule-1 and increases migration. Integrin α4 expression enhanced experimental metastasis in a syngeneic tumor model, reconstituting a pattern of organ involvement similar to that seen in patients. Accordingly, antagonism of integrin α4 blocked metastasis, suggesting adhesive function of the integrin is required. However, adhesive function was not sufficient, as mutants of integrin α4 that conserved the matrix-adhesive and promigratory function in vitro were compromised in their metastatic capacity in vivo. Clinically, integrin α4 is more frequently expressed in non-MYNC amplified tumors, and is selectively associated with poor prognosis in this subset of disease. These results reveal an unexpected role for integrin α4 in neuroblastoma dissemination and identify α4 as a potential prognostic indicator and therapeutic target. 相似文献
105.
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107.
Tuckett Quenton M. Lawson Katelyn M. Lipscomb Taylor N. Hill Jeffrey E. Daniel Wesley M. Siders Zachary A. 《Hydrobiologia》2021,848(20):4731-4745
Hydrobiologia - Livebearers in the family Poeciliidae are some of the most widely introduced fishes. Native poeciliid translocations within the U.S. are mostly due to deliberate stocking for... 相似文献
108.
109.
Katelyn Hamilton Celine T. Goulet Emily M. Drummond Anna F. Senior Mellesa Schroder Michael G. Gardner Geoffrey M. While David G. Chapple 《Austral ecology》2021,46(1):8-19
The rapid changes in altitude, and associated habitat, of mountain ecosystems make them ideal natural laboratories for testing the effect of environmental heterogeneity on species assemblage. Our understanding of the sensitivity of Australian reptiles to elevational clines is limited. We examined lizard distribution across three elevation zones (montane, subalpine and alpine), spanning from 900 to 1840 m above sea level, in the Australian alps. We aimed to examine how elevation influences species diversity and abundance, and ectoparasite load, and whether species alter their habitat use amongst different elevational zones. Active searches were conducted across the elevation zones to identify lizard community structure (at least 16 species) across elevational zones, along with skink habitat preferences and the ectoparasite load. Skink diversity and abundance were negatively correlated with increased elevation. The alpine zone had significantly lower diversity and abundance of skinks. Habitat use differed amongst both elevations and species. Ectoparasite prevalence was also significantly diminished in the alpine zone. Ectoparasites only infected a subset of the skink community, with ectoparasite load increasing as the active season progressed. This study provides evidence of the complex interplay between elevation and species diversity, as well as the differences in ectoparasite pressure along elevational gradients in the Australian alps. 相似文献
110.
Quenneville CE Dunning CE 《Computer methods in biomechanics and biomedical engineering》2011,14(2):205-212
Finite element (FE) models can allow computer simulations of impact loading, providing a useful companion to cadaveric testing. These models allow injury evaluations to be conducted under a variety of conditions, but must be validated against experimental data. An FE model of a cadaveric tibia was developed using geometry from CT scans, and the quality of the mesh was evaluated. Loading and boundary conditions from experimental tests were simulated, and the model was optimised to best represent the response of natural bone to impacts. The model was shown to have good agreement for impact force, duration, impulse and strain during simulation of three non-injurious and one injurious axial impact when compared with experimental test data for the specimen. Failure criteria were evaluated for their ability to predict fracture. This model of the tibia can be used for future injury prediction assessment studies. 相似文献