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51.
Malte Buchholz Tatjana Honstein Sandra Kirchhoff Ramona Kreider Harald Schmidt Bence Sipos Thomas M. Gress 《PloS one》2015,10(4)
In order to foster the systematic identification of novel genes with important functional roles in pancreatic cancer, we have devised a multi-stage screening strategy to provide a rational basis for the selection of highly relevant novel candidate genes based on the results of functional high-content analyses. The workflow comprised three consecutive stages: 1) serial gene expression profiling analyses of primary human pancreatic tissues as well as a number of in vivo and in vitro models of tumor-relevant characteristics in order to identify genes with conspicuous expression patterns; 2) use of ‘reverse transfection array’ technology for large-scale parallelized functional analyses of potential candidate genes in cell-based assays; and 3) selection of individual candidate genes for further in-depth examination of their cellular roles. A total of 14 genes, among them 8 from “druggable” gene families, were classified as high priority candidates for individual functional characterization. As an example to demonstrate the validity of the approach, comprehensive functional data on candidate gene ADRBK1/GRK2, which has previously not been implicated in pancreatic cancer, is presented. 相似文献
52.
Alexander Ziegler Malte Ogurreck Thomas Steinke Felix Beckmann Steffen Prohaska Andreas Ziegler 《Biology direct》2010,5(1):45
Abstract
Advances in digital data acquisition, analysis, and storage have revolutionized the work in many biological disciplines such as genomics, molecular phylogenetics, and structural biology, but have not yet found satisfactory acceptance in morphology. Improvements in non-invasive imaging and three-dimensional visualization techniques, however, permit high-throughput analyses also of whole biological specimens, including museum material. These developments pave the way towards a digital era in morphology. Using sea urchins (Echinodermata: Echinoidea), we provide examples illustrating the power of these techniques. However, remote visualization, the creation of a specialized database, and the implementation of standardized, world-wide accepted data deposition practices prior to publication are essential to cope with the foreseeable exponential increase in digital morphological data. 相似文献53.
Clutch size control in capital breeders such as large waterfowl has been much debated. Some studies have concluded that clutch size in ducks is determined before the start of laying and does not change in response to egg additions or removals. The response, however, may depend on the timing of tests, and experiments may have been too late for females to alter the number of eggs. We here study clutch size responses to predation of first and second eggs in the common eider, using protein fingerprinting of egg albumen to verify that the same female continues laying in the nest after predation. Sixty of 79 females with early egg predation (one or both of the two first eggs) deserted the nest. Among the 19 females that stayed and continued laying, the mean number of eggs produced was 4.4, significantly higher than the 3.7 in non-predated nests. The staying females had similar egg size and clutch initiation date as females that deserted, and their body mass and clutch initiation date was similar to that of females whose clutches were not predated. Even capital-breeding common eiders may therefore be indeterminate layers, as many females in which early eggs are removed lay more eggs than others. A previous study has shown that they can reduce their laying if eggs are added. Our results add to increasing evidence that ducks have more flexible egg production than previously thought. 相似文献
54.
Mona Hoppenrath Malte Elbrächter Hannelore Halliger Reinoud P. T. Koeman Alexander Krakhmalnyy Barbara Surek Katrin Erler Bernd Luckas 《Helgoland Marine Research》2007,61(3):157-165
Thecadinium yashimaense was recorded for the first time in France, Great Britain, The Netherlands, and Germany. The invasion and establishment of
the species in the German Bight was documented reliably and is presented here. The geographic expansion of the species from
the North Pacific to the North Atlantic Ocean is discussed. This bloom-forming, marine, sand-dwelling dinoflagellate was shown
to be non-toxic. Also Thecadinium kofoidii, the type species of the genus, was analyzed for potential toxin production and turned out to be non-toxic as well. 相似文献
55.
Malte C. Ebach Antonio G. Valdecasas Quentin D. Wheeler 《Cladistics : the international journal of the Willi Hennig Society》2011,27(5):550-557
There has been much discussion of the “taxonomic impediment”. This phrase confuses two kinds of impediment: an impediment to end users imposed by lack of reliable information; and impediments to taxonomy itself, which vary from insufficient funding to low citation rates of taxonomic monographs. In order to resolve both these types of impediment, taxonomy needs to be revitalized through funding and training taxonomists, as well as investing in taxonomic revisions and monographs rather than technological surrogates such as DNA barcoding.© The Willi Hennig Society 2011. 相似文献
56.
Bachmann M Hennemann H Xing PX Hoffmann I Möröy T 《The Journal of biological chemistry》2004,279(46):48319-48328
The Pim-1 oncogene encodes a serine-threonine kinase that relays signals from cytokine receptors and contributes to the formation of lymphoid tumors when expressed at high levels. Here we show that the protein kinase Cdc25 C-associated kinase 1 (C-TAK1) is a binding partner and a substrate of Pim-1. A physical interaction of Pim-1 and C-TAK1 could be shown biochemically and in yeast two-hybrid assays. Immunofluorescence experiments suggested that Pim-1.C-TAK1 complexes are predominantly cytoplasmic. When transiently transfected, Pim-1 was also found in the nucleus and could recruit C-TAK1 to this compartment. Both Pim-1 and C-TAK1 underwent autophosphorylation, but only Pim-1 was able to phosphorylate C-TAK1 but not vice versa. Mass spectrometry analysis of C-TAK1 suggested that the sites of autophosphorylation and Pim-1-mediated phosphorylation are distinct and not overlapping. Phosphorylation by Pim-1 decreased C-TAK1 kinase activity significantly, in particular its ability to phosphorylate and inactivate Cdc25C, a protein that actively promotes cell cycle progression at the G(2)/M phase. Hence our findings directly suggest a novel role for Pim-1 as a positive regulator at the G(2)/M transition of the cell cycle. 相似文献
57.
Vollmar P Kullmann JS Thilo B Claussen MC Rothhammer V Jacobi H Sellner J Nessler S Korn T Hemmer B 《Journal of immunology (Baltimore, Md. : 1950)》2010,185(10):6338-6347
Active immunization with amyloid-β (Aβ) peptide 1-42 reverses amyloid plaque deposition in the CNS of patients with Alzheimer's disease and in amyloid precursor protein transgenic mice. However, this treatment may also cause severe, life-threatening meningoencephalitis. Physiological responses to immunization with Aβ(1-42) are poorly understood. In this study, we characterized cognitive and immunological consequences of Aβ(1-42)/CFA immunization in C57BL/6 mice. In contrast to mice immunized with myelin oligodendrocyte glycoprotein (MOG)(35-55)/CFA or CFA alone, Aβ(1-42)/CFA immunization resulted in impaired exploratory activity, habituation learning, and spatial-learning abilities in the open field. As morphological substrate of this neurocognitive phenotype, we identified a disseminated, nonfocal immune cell infiltrate in the CNS of Aβ(1-42)/CFA-immunized animals. In contrast to MOG(35-55)/CFA and PBS/CFA controls, the majority of infiltrating cells in Aβ(1-42)/CFA-immunized mice were CD11b(+)CD14(+) and CD45(high), indicating their blood-borne monocyte/macrophage origin. Immunization with Aβ(1-42)/CFA was significantly more potent than immunization with MOG(35-55)/CFA or CFA alone in activating macrophages in the secondary lymphoid compartment and peripheral tissues. Studies with TLR2/4-deficient mice revealed that the TLR2/4 pathway mediated the Aβ(1-42)-dependent proinflammatory cytokine release from cells of the innate immune system. In line with this, TLR2/4 knockout mice were protected from cognitive impairment upon immunization with Aβ(1-42)/CFA. Thus, this study identifies adjuvant effects of Aβ(1-42), which result in a clinically relevant neurocognitive phenotype highlighting potential risks of Aβ immunotherapy. 相似文献
58.
Borgwardt KM Gretton A Rasch MJ Kriegel HP Schölkopf B Smola AJ 《Bioinformatics (Oxford, England)》2006,22(14):e49-e57
MOTIVATION: Many problems in data integration in bioinformatics can be posed as one common question: Are two sets of observations generated by the same distribution? We propose a kernel-based statistical test for this problem, based on the fact that two distributions are different if and only if there exists at least one function having different expectation on the two distributions. Consequently we use the maximum discrepancy between function means as the basis of a test statistic. The Maximum Mean Discrepancy (MMD) can take advantage of the kernel trick, which allows us to apply it not only to vectors, but strings, sequences, graphs, and other common structured data types arising in molecular biology. RESULTS: We study the practical feasibility of an MMD-based test on three central data integration tasks: Testing cross-platform comparability of microarray data, cancer diagnosis, and data-content based schema matching for two different protein function classification schemas. In all of these experiments, including high-dimensional ones, MMD is very accurate in finding samples that were generated from the same distribution, and outperforms its best competitors. Conclusions: We have defined a novel statistical test of whether two samples are from the same distribution, compatible with both multivariate and structured data, that is fast, easy to implement, and works well, as confirmed by our experiments. AVAILABILITY: http://www.dbs.ifi.lmu.de/~borgward/MMD. 相似文献
59.
MOTIVATION: Analyses of genomic signatures are gaining attention as they allow studies of species-specific relationships without involving alignments of homologous sequences. A na?ve Bayesian classifier was built to discriminate between different bacterial compositions of short oligomers, also known as DNA words. The classifier has proven successful in identifying foreign genes in Neisseria meningitis. In this study we extend the classifier approach using either a fixed higher order Markov model (Mk) or a variable length Markov model (VLMk). RESULTS: We propose a simple algorithm to lock a variable length Markov model to a certain number of parameters and show that the use of Markov models greatly increases the flexibility and accuracy in prediction to that of a na?ve model. We also test the integrity of classifiers in terms of false-negatives and give estimates of the minimal sizes of training data. We end the report by proposing a method to reject a false hypothesis of horizontal gene transfer. AVAILABILITY: Software and Supplementary information available at www.cs.chalmers.se/~dalevi/genetic_sign_classifiers/. 相似文献
60.
Totzeck M Hendgen-Cotta UB Rammos C Petrescu AM Meyer C Balzer J Kelm M Rassaf T 《Nitric oxide》2012,26(4):211-216
Myoglobin is presumably the most studied protein in biology. Its functional properties as a dioxygen storage and facilitator of dioxygen transport are widely acknowledged. Experimental evidence also implicates an essential role for myoglobin in the heart in regulating nitric oxide homeostasis. Under normoxia, oxygenated myoglobin can scavenge excessive nitric oxide, while under hypoxia, deoxygenated myoglobin can reduce nitrite, an oxidative product of nitric oxide, to bioactive nitric oxide. Myoglobin-driven nitrite reduction can protect the heart from ischemia and reperfusion injury. While horse and mouse myoglobin have been previously described to reduce nitrite under these conditions, a comparable activity has not been detected in human myoglobin. We here show that human myoglobin is a fully functional nitrite reductase. To study the role of human myoglobin for nitric oxide homeostasis we used repeated photometric wavelength scans and chemiluminescence based experiments. The results revealed that oxygenated human myoglobin reacts with nitrite-derived nitric oxide to form ferric myoglobin and that deoxygenated human myoglobin acts as a nitrite reductase in vitro and in situ. Rates of both nitric oxide scavenging and nitrite reduction were significantly higher in human compared to horse myoglobin. These data extend the existing knowledge about the functional properties of human myoglobin and are the basis for further translational studies towards the importance of myoglobin for nitric oxide metabolism in humans. 相似文献