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991.
Salt bridges can play important roles in protein structure and function and have stabilizing and destabilizing effects in protein folding. ESBRI is a software available as web tool which analyses the salt bridges in a protein structure, starting from the atomic coordinates. In the case of protein complexes, the salt bridges between protein chains can be evaluated, as well as those among specific charged amino acids and the different protein subunits, in order to obtain useful information regard the protein-protein interaction.  相似文献   
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994.
The Cansiglio Forest, situated in the Veneto Prealps, is of particular naturalistic and landscape interest, going back to the times of the Most Serene Republic of Venice. Its long silvicultural tradition, which is now even more “near to nature”, remains unaltered. Over the last century there has been a considerable increase in the number of ungulates. This is partly due to prohibition of hunting since the beginning of the 20th century throughout the territory. It has therefore become necessary to survey forest regeneration, to ascertain whether deer pressure hampers silvicultural goals and also to investigate which factors are most involved. A review of management plans over the last 30 years identified areas in which regeneration is present, where transects were subsequently sampled. Inside every transect, all saplings (over 50 cm) were measured for diameter and height and monitored for degree and type of damage (browsing, debarking, fraying). Using the CART statistical method, the following key factors were singled out: species, proving that fir is the most frequently selected sapling; silvicultural system, clarifying that the regeneration of uneven-aged stands is more subject to damage; aspect, locating more damage in the southern and eastern areas, probably because they are more often frequented by deer. High densities of deer endanger fir survival, reduce biodiversity, and affect forest economy, limiting silvicultural choices, so that culling ungulate populations seems to be necessary.  相似文献   
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996.
The introduction of an iodine atom on the vanillyl moiety of nonivamide causes a switch in the vanilloid activity (TRPV1 antagonism versus TRPV1 desensitization) and nullifies the aversive properties of capsaicinoids. In the present study we investigated the effect of iodination in the vanillyl moiety on the antioxidant activity of capsaicinoids. To this aim, we have compared the protective effects of nonivamide and three iododerivatives, 2-iodononivamide (2IN), 5-iodononivamide (5IN), and 6-iodononivamide (6IN) in a series of in vitro models of lipid oxidation, namely the autoxidation and the FeCl3-mediated oxidation of linoleic acid at 37 °C and the thermal (140 °C), solvent-free oxidation of cholesterol. All tested compounds could protect linoleic acid and cholesterol against oxidative degradation, the order of potency being: nonivamide > 5IN > 6IN ≈ 2IN. Our results show that, in general, the introduction of an iodine atom on the vanillyl moiety of nonivamide causes a decrease in the antioxidant activity, and this effect is sensitive to the position of iodine on the aromatic ring, with 5IN substantially retaining the efficacy of nonivamide to protect linoleic and cholesterol against free radical attack. Moreover, the pre-treatment with 5IN, at noncytotoxic concentrations, significantly preserved LDL from Cu2+-induced oxidative damage at 37 °C for 2 h, inhibiting the reduction of polyunsaturated fatty acids and cholesterol and the increase of their oxidative products. The results of the present work suggest that 5IN exerts useful antioxidant properties in different in vitro systems of lipid peroxidation. This, coupled to its lacks of pungency and TRPV1 inhibiting properties, qualifies this phenolic compound as an attractive candidate for further investigations in vivo.  相似文献   
997.
Sobel and Randle (2009) challenge several methodological choices in the comparative study of the evolution of reproductive isolation in Mediterranean deceptive orchids of Scopece et al. (2007) including the species concept used and the selection of taxa, together with the perceived comparison of clades of different ages. They further criticize that pollinator information was taken from the literature and that two different methods were used to estimate pollinator specificity in food-deceptive and sexually deceptive orchids, respectively. Here we reply to these challenges.  相似文献   
998.
Fibroblast growth factors (FGFs) exert basic functions both during embryonic development and in the adult. The expression of FGFs and their receptors has been reported in mammalian retinas, although information on the organization of the FGF system is still incomplete. Here, we report a detailed double-label immunohistochemical investigation of the localization patterns of FGF1 and its receptors FGFR1 and FGFR2 in adult and early postnatal mouse retinas. In adult retinas, FGF1 is localized to ganglion cells, horizontal cells, and photoreceptor inner and outer segments. FGFR1 is found in ganglion cells and Müller cells, whereas FGFR2 is primarily located in ganglion cells, the nuclei of Müller cells, and glycine-containing amacrine cells. During postnatal development, the patterns of FGF1, FGFR1, and FGFR2 immunostaining are similar to those in the adult, although transient FGF1-expressing cells have been detected in the proximal inner nuclear layer before eye opening. These patterns are consistent with a major involvement of FGF1, FGFR1, and FGFR2 in ganglion cell maturation (during development) and survival (in the adult). Moreover, FGF1 may affect amacrine cell development, whereas Müller cells appear to be regulated via both FGFR1 and FGFR2 throughout postnatal life. In immature retinas, large numbers of amacrine cells, including those containing calbindin and glycine, display both FGF1 and FGFR2 immunoreactivities in their nuclei, suggesting an action of FGF1 on FGFR2 leading to the maturation of these amacrine cells during a restricted period of postnatal development. This work was supported by funding from the Italian Ministry of Education.  相似文献   
999.
The availability of the human genome sequence and progress in sequencing and bioinformatic technologies have enabled genome-wide investigation of somatic mutations in human cancers. This article briefly reviews challenges arising in the statistical analysis of mutational data of this kind. A first challenge is that of designing studies that efficiently allocate sequencing resources. We show that this can be addressed by two-stage designs and demonstrate via simulations that even relatively small studies can produce lists of candidate cancer genes that are highly informative for future research efforts. A second challenge is to distinguish mutated genes that are selected for by cancer (drivers) from mutated genes that have no role in the development of cancer and simply happened to mutate (passengers). We suggest that this question is best approached as a classification problem and discuss some of the difficulties of more traditional testing-based approaches. A third challenge is to identify biologic processes affected by the driver genes. This can be pursued by gene set analyses. These can reliably identify functional groups and pathways that are enriched for mutated genes even when the individual genes involved in those pathways or sets are not mutated at sufficient frequencies to provide conclusive evidence as drivers.  相似文献   
1000.
Pim1 belongs to a family of serine/threonine kinases, which is involved in the control of cell growth, differentiation, and apoptosis. Pim1 plays a pivotal role in cytokine signaling and is implicated in the development of a large number of tumors, representing a very attractive target for anticancer therapy. In this work, we applied a virtual screening protocol aimed at identifying small molecules able to inhibit Pim1 activity. The search of novel inhibitors was performed through a structure-based molecular modeling approach, taking advantage of the availability of the three-dimensional crystal structure of inhibitors bound to Pim1. Starting from the knowledge of protein–ligand complexes, the software LigandScout was used to generate pharmacophoric models, in turn used as queries to perform a virtual screening of databases, followed by docking experiments. As a result, a restricted set of candidates for biological testing was identified. Finally, among the six compounds selected as potential inhibitors of Pim1, two candidates endowed with a significant activity against Pim1 emerged. Interestingly, one of these compounds has a chemical scaffold different from inhibitors previously identified.  相似文献   
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