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51.
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Dynamic treatment regimes (DTRs) consist of a sequence of decision rules, one per stage of intervention, that aim to recommend effective treatments for individual patients according to patient information history. DTRs can be estimated from models which include interactions between treatment and a (typically small) number of covariates which are often chosen a priori. However, with increasingly large and complex data being collected, it can be difficult to know which prognostic factors might be relevant in the treatment rule. Therefore, a more data-driven approach to select these covariates might improve the estimated decision rules and simplify models to make them easier to interpret. We propose a variable selection method for DTR estimation using penalized dynamic weighted least squares. Our method has the strong heredity property, that is, an interaction term can be included in the model only if the corresponding main terms have also been selected. We show our method has both the double robustness property and the oracle property theoretically; and the newly proposed method compares favorably with other variable selection approaches in numerical studies. We further illustrate the proposed method on data from the Sequenced Treatment Alternatives to Relieve Depression study. 相似文献
53.
Gill raker variation and the feeding niche of some temperate and tropical freshwater fishes 总被引:1,自引:0,他引:1
G. Eric E Moodie 《Environmental Biology of Fishes》1985,13(1):71-76
Synopsis Variability in the mean number of gill rakers was examined in 17 tropical (Panama) and 16 temperate (Canada) freshwater fishes. Ranges for an additional 16 temperate species were obtained from the literature. Variance in gill raker number within species was significantly greater in the tropical species. The tropical species also showed significantly greater dispersion of the species means when among-species variation was compared to an overall mean for each latitude. The reduced among-species variation observed in the temperate species appears to result from a scarcity of high raker means in small, stream species of Canada. This study offers no evidence for the existence of greater feeding specialization among small, primarily stream fishes in the neotropics. The data suggest that the food resource spectrum utilized by these species may be shorter at the higher latitudes examined. 相似文献
54.
T Jelinek A D Catling C W Reuter S A Moodie A Wolfman M J Weber 《Molecular and cellular biology》1994,14(12):8212-8218
Recent studies have demonstrated the existence of a physical complex containing p21ras (RAS), p74raf-1 (RAF-1), and MEK-1. Although it is clear that formation of this complex depends on the activation state of RAS, it is not known whether this complex is regulated by the activation state of the cell and whether MEK-2 is also present in the complex. To analyze the regulation and specificity of this complex, we utilized immobilized RAS to probe lysates of cultured NIH 3T3 fibroblasts and analyzed the proteins complexing with RAS following serum starvation or stimulation. Complex formation among RAS, RAF-1, and MEK-1 was dependent only on RAS:GMP-PNP and not on cell stimulation. Incubations of lysates with immobilized RAS depleted all RAF-1 from the lysate but bound only a small fraction of cytosolic MEK-1, and further MEK-1 could bind immobilized RAS only if exogenous RAF-1 was added to the lysate. This indicates that binding of MEK-1 to RAS depends on the presence of RAF-1 or an equivalent protein. In contrast to MEK-1, MEK-2 was not detected in the RAS signalling complex. A proline-rich region of MEK-1 containing a phosphorylation site appears to be essential for signalling complex formation. Consistent with the preferential binding of MEK-1 to RAS:RAF-1, the basal activity of MEK-1 in v-ras-transformed cells was found to be elevated sixfold, whereas MEK-2 was elevated only twofold, suggesting that the RAS signalling pathway favors MEK-1 activation. 相似文献
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56.
TOSHIHIRO TOKIWA DAVID MODRÝ AKIRA ITO KATEŘINA POMAJBÍKOVÁ KLÁRA J. PETRŽELKOVÁ SOICHI IMAI 《The Journal of eukaryotic microbiology》2010,57(2):115-120
ABSTRACT. Troglocorys cava n. g., n. sp. is described from the feces of wild eastern chimpanzee, Pan troglodytes schweinfurthii, in Uganda. This new species has a spherical body with a frontal lobe, a long vestibulum, a cytoproct located at the posterior dorsal side of the body, an ovoid macronucleus, a contractile vacuole near the cytoproct, and a large concavity on the left surface of the body. Buccal ciliature is non‐retractable and consists of three ciliary zones: an adoral zone surrounding the vestibular opening, a dorso‐adoral zone extending transversely at the basis of the frontal lobe, and a vestibular zone longitudinally extending in a gently spiral curve to line the surface of the vestibulum. Two non‐retractable somatic ciliary zones comprise arches over the body surface: a short dorsal ciliary arch extending transversely at the basis of the frontal lobe and a wide C‐shaped left ciliary arch in the left concavity. Because of the presence of three ciliary zones in the non‐retractable buccal ciliature, the present genus might be a member of the family Blepharocorythidae, but the large left concavity and the C‐shaped left ciliary arch are unique, such structures have never been described from other blepharocorythids. 相似文献
57.
Frank T Bergmann Richard Adams Stuart Moodie Jonathan Cooper Mihai Glont Martin Golebiewski Michael Hucka Camille Laibe Andrew K Miller David P Nickerson Brett G Olivier Nicolas Rodriguez Herbert M Sauro Martin Scharm Stian Soiland-Reyes Dagmar Waltemath Florent Yvon Nicolas Le Novère 《BMC bioinformatics》2014,15(1)
Background
With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result.Results
We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software.Conclusions
The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0369-z) contains supplementary material, which is available to authorized users. 相似文献58.
59.
Grimes GR Wen TQ Mewissen M Baxter RM Moodie S Beattie JS Ghazal P 《Bioinformatics (Oxford, England)》2006,22(16):2055-2057
SUMMARY: PDQ Wizard automates the process of interrogating biomedical references using large lists of genes, proteins or free text. Using the principle of linkage through co-citation biologists can mine PubMed with these proteins or genes to identify relationships within a biological field of interest. In addition, PDQ Wizard provides novel features to define more specific relationships, highlight key publications describing those activities and relationships, and enhance protein queries. PDQ Wizard also outputs a metric that can be used for prioritization of genes and proteins for further research. AVAILABILITY: PDQ Wizard is freely available from http://www.gti.ed.ac.uk/pdqwizard/. 相似文献
60.
Lyle R. McKinnon Sean M. Hughes Stephen C. De Rosa Jeffrey A. Martinson Jill Plants Kirsten E. Brady Pamela P. Gumbi Devin J. Adams Lucia Vojtech Christine G. Galloway Michael Fialkow Gretchen Lentz Dayong Gao Zhiquan Shu Billy Nyanga Preston Izulla Joshua Kimani Steve Kimwaki Alfred Bere Zoe Moodie Alan L. Landay Jo-Ann S. Passmore Rupert Kaul Richard M. Novak M. Juliana McElrath Florian Hladik 《PloS one》2014,9(1)