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91.
Identifying DNA splice sites using hypernetworks with artificial molecular evolution 总被引:3,自引:0,他引:3
Identifying DNA splice sites is a main task of gene hunting. We introduce the hyper-network architecture as a novel method for finding DNA splice sites. The hypernetwork architecture is a biologically inspired information processing system composed of networks of molecules forming cells, and a number of cells forming a tissue or organism. Its learning is based on molecular evolution. DNA examples taken from GenBank were translated into binary strings and fed into a hypernetwork for training. We performed experiments to explore the generalization performance of hypernetwork learning in this data set by two-fold cross validation. The hypernetwork generalization performance was comparable to well known classification algorithms. With the best hypernetwork obtained, including local information and heuristic rules, we built a system (HyperExon) to obtain splice site candidates. The HyperExon system outperformed leading splice recognition systems in the list of sequences tested. 相似文献
92.
Giron-Michel J Azzi S Khawam K Mortier E Caignard A Devocelle A Ferrini S Croce M François H Lecru L Charpentier B Chouaib S Azzarone B Eid P 《PloS one》2012,7(2):e31624
The ability of Interleukin-15 (IL-15) to activate many immune antitumor mechanisms renders the cytokine a good candidate for the therapy of solid tumors, particularly renal cell carcinoma. Although IL-15 is being currently used in clinical trials, the function of the cytokine on kidney's components has not been extensively studied; we thus investigated the role of IL-15 on normal and tumor renal epithelial cells. Herein, we analyzed the expression and the biological functions of IL-15 in normal renal proximal tubuli (RPTEC) and in their neoplastic counterparts, the renal clear cell carcinomas (RCC). This study shows that RPTEC express a functional heterotrimeric IL-15Rαβγc complex whose stimulation with physiologic concentrations of rhIL-15 is sufficient to inhibit epithelial mesenchymal transition (EMT) commitment preserving E-cadherin expression. Indeed, IL-15 is not only a survival factor for epithelial cells, but it can also preserve the renal epithelial phenotype through the γc-signaling pathway, demonstrating that the cytokine possess a wide range of action in epithelial homeostasis. In contrast, in RCC in vitro and in vivo studies reveal a defect in the expression of γc-receptor and JAK3 associated kinase, which strongly impacts IL-15 signaling. Indeed, in the absence of the γc/JAK3 couple we demonstrate the assembly of an unprecedented functional high affinity IL-15Rαβ heterodimer, that in response to physiologic concentrations of IL-15, triggers an unbalanced signal causing the down-regulation of the tumor suppressor gene E-cadherin, favoring RCC EMT process. Remarkably, the rescue of IL-15/γc-dependent signaling (STAT5), by co-transfecting γc and JAK3 in RCC, inhibits EMT reversion. In conclusion, these data highlight the central role of IL-15 and γc-receptor signaling in renal homeostasis through the control of E-cadherin expression and preservation of epithelial phenotype both in RPTEC (up-regulation) and RCC (down-regulation). 相似文献
93.
94.
Maximiliano Rapanelli Sergio Eduardo Lew Luciana Romina Frick Bonifacio Silvano Zanutto 《PloS one》2010,5(1)
The plasticity in the medial Prefrontal Cortex (mPFC) of rodents or lateral prefrontal cortex in non human primates (lPFC), plays a key role neural circuits involved in learning and memory. Several genes, like brain-derived neurotrophic factor (BDNF), cAMP response element binding (CREB), Synapsin I, Calcium/calmodulin-dependent protein kinase II (CamKII), activity-regulated cytoskeleton-associated protein (Arc), c-jun and c-fos have been related to plasticity processes. We analysed differential expression of related plasticity genes and immediate early genes in the mPFC of rats during learning an operant conditioning task. Incompletely and completely trained animals were studied because of the distinct events predicted by our computational model at different learning stages. During learning an operant conditioning task, we measured changes in the mRNA levels by Real-Time RT-PCR during learning; expression of these markers associated to plasticity was incremented while learning and such increments began to decline when the task was learned. The plasticity changes in the lPFC during learning predicted by the model matched up with those of the representative gene BDNF. Herein, we showed for the first time that plasticity in the mPFC in rats during learning of an operant conditioning is higher while learning than when the task is learned, using an integrative approach of a computational model and gene expression. 相似文献
95.
Vav1 is necessary for PU.1 mediated upmodulation of miR‐29b in acute myeloid leukaemia‐derived cells
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96.
Claudia Pacelli Ruth A. Bryan Silvano Onofri Laura Selbmann Laura Zucconi Igor Shuryak Ekaterina Dadachova 《Fungal biology》2018,122(12):1222-1227
Despite living organisms are not exposed to acute ionizing radiation under natural conditions, some exhibit a high radiation resistance. Understanding this phenomenon is important for assessing the impact of radiation-related accidents, occupational exposures and space missions. In this context, in this study we analyzed the effect of gamma rays on the Antarctic cryptoendolithic melanized fungus Friedmanniomyces endolithicus CCFEE 5208 and demonstrated its resistance to acute doses of gamma radiation (up to 400 Gy), accompanied by increase in metabolic activity. 相似文献
97.
Targeting the phosphatidylinositol 3‐kinase/Akt/mechanistic target of rapamycin signaling pathway in B‐lineage acute lymphoblastic leukemia: An update
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98.
99.
Facheng Ye Gaia Crippa Lucia Angiolini Uwe Brand GianCarlo Capitani Maggie Cusack Claudio Garbelli Erika Griesshaber Elizabeth Harper Wolfgang Schmahl 《Journal of structural biology》2018,201(3):221-236
Shells of brachiopods are excellent archives for environmental reconstructions in the recent and distant past as their microstructure and geochemistry respond to climate and environmental forcings. We studied the morphology and size of the basic structural unit, the secondary layer fibre, of the shells of several extant brachiopod taxa to derive a model correlating microstructural patterns to environmental conditions. Twenty-one adult specimens of six recent brachiopod species adapted to different environmental conditions, from Antarctica, to New Zealand, to the Mediterranean Sea, were chosen for microstructural analysis using SEM, TEM and EBSD. We conclude that: 1) there is no significant difference in the shape and size of the fibres between ventral and dorsal valves, 2) there is an ontogenetic trend in the shape and size of the fibres, as they become larger, wider, and flatter with increasing age. This indicates that the fibrous layer produced in the later stages of growth, which is recommended by the literature to be the best material for geochemical analyses, has a different morphostructure and probably a lower organic content than that produced earlier in life.In two species of the same genus living in seawater with different temperature and carbonate saturation state, a relationship emerged between the microstructure and environmental conditions. Fibres of the polar Liothyrella uva tend to be smaller, rounder and less convex than those of the temperate Liothyrella neozelanica, suggesting a relationship between microstructural size, shell organic matter content, ambient seawater temperature and calcite saturation state. 相似文献
100.
Luca M. Neri Caterina Cinti Spartaco Santi Marco Marchisio Silvano Capitani Nadir M. Maraldi 《Histochemistry and cell biology》1997,107(2):97-104
DNA sequences digested by HaeIII and reconstructed by in situ nick translation employing digoxigenin-labelled nucleotides are usually revealed either by
horseradish peroxidase or FITC fluorescence. To obtain a significant improvement in terms of resolution, sensitivity and specificity,
colloidal gold has been used instead of FITC (as the reporter molecule) to reveal the labelled DNA. Colloidal gold and propidium
iodide were visualised by employing the reflectance mode and the 488-nm laser line of a confocal laser scanning microscope.
In chromosomes, the fluorescent reaction pattern showed diffuse areas of labelling in which it was impossible to identify
any specific kind of banding along the arms. In some chromosomes and, in particular, 1 and 9, a C-negative banding due to
the negativity of the centromeric areas was seen. A more accurate localisation on chromosomes, including telomeric regions,
often organised in spot pairs that resembled an R-like banding, was detected using 1-nm colloidal gold. A fine labelling was
also demonstrated in nuclei, especially at their peripheral heterochromatin. The non-fading properties of colloidal gold combined
with visualisation by reflectance confocal laser scanning microscopy demonstrated the possibility of obtaining a higher spatial
resolution than when using conventional fluorophores or higher laser wavelength. This improved way to study the localization
of HaeIII digestion sites in single chromosomes and in interphase nuclei made the reaction a valuable tool for the detection of
antigens or of specific DNA sequences in biological preparations.
Accepted: 5 September 1996 相似文献