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1.
Transforming growth factor-β (TGF-β) signaling has been prominently implicated in the pathogenesis of vascular remodeling, especially the initiation and progression of flow-induced vascular remodeling. Smooth muscle cells (SMCs) are the principal resident cells in arterial wall and are critical for arterial remodeling. However, the role of TGF-β signaling in SMC for flow-induced vascular remodeling remains unknown. Therefore, the goal of our study was to determine the effect of TGF-β pathway in SMC for vascular remodeling, by using a genetical smooth muscle-specific (SM-specific) TGF-β type II receptor (Tgfbr2) deletion mice model. Mice deficient in the expression of Tgfbr2 (MyhCre.Tgfbr2f/f) and their corresponding wild-type background mice (MyhCre.Tgfbr2WT/WT) underwent partial ligation of left common carotid artery for 1, 2, or 4 weeks. Then the carotid arteries were harvested and indicated that the disruption of Tgfbr2 in SMC provided prominent inhibition of vascular remodeling. And the thickening of carotid media, proliferation of SMC, infiltration of macrophage, and expression of matrix metalloproteinase (MMP) were all significantly attenuated in Tgfbr2 disruption mice. Our study demonstrated, for the first time, that the TGF-β signaling in SMC plays an essential role in flow-induced vascular remodeling and disruption can prevent this process.  相似文献   
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We combine total internal reflection fluorescence structured illumination microscopy with spatiotemporal image correlation spectroscopy to quantify the flow velocities and directionality of filamentous-actin at the T cell immunological synapse. These techniques demonstrate it is possible to image retrograde flow of filamentous-actin at superresolution and provide flow quantification in the form of velocity histograms and flow vector maps. The flow was found to be retrograde and radially directed throughout the periphery of T-cells during synapse formation.Many biological processes are now being visualized with the use of superresolution fluorescence microscopy techniques. However, localization-based techniques primarily rely on fixed or slow moving samples to permit the collection of structural information. The 10-fold gains in resolution afforded by these superresolution techniques are usually possible through sacrificing the factors that originally made microscopy such a powerful tool: the ability to image live cells. In the case of stimulated emission depletion imaging, the scanning approach associated with this technique may fail to detect faster molecular events when imaging whole cellular regions.Structured illumination microscopy (SIM) is an alternative to these methods (1). It increases the resolution of conventional fluorescence microscopy twofold; it has the advantage of using a wide-field system, providing fast acquisition speeds of whole cells with relatively low laser powers; and it is compatible with standard fluorophores. By using a physical grating to produce interference patterns from a laser, periodic illumination is created. This patterned illumination causes information from higher spatial frequencies to be downmodulated (i.e., shifted) into the optical transfer function (support region) of the lens, resulting in higher-resolution spatial information being captured than is ordinarily obtainable.To quantify the directional motion of intracellular molecules, spatiotemporal image correlation spectroscopy (STICS (2)) was applied. Using spatial image correlation in time, STICS measures the similarity of pixels with those surrounding in lagging frames via a correlation function. The correlation function provides information on both flow velocities and directionality, while discounting static structures through the immobile object filter, achieved by subtracting a moving average of pixel intensities.The formation of an immunological synapse between T cells and antigen-presenting cells is a process requiring many dynamic (3) and subdiffraction-limited clustering events (4–6) to take place. The polymerization of actin is important for the spreading of cells over their target antigen-presenting cells (7), as well as cell mobility and migration (8). Retrograde flow of densely meshed cortical actin is observed at the basal membrane of synapse-forming T cells, where it may have a role in the corralling and clustering of signaling molecules at the plasma membrane (9), as well as at the leading edge of migrating cells (10). Filamentous actin is an extremely dynamic (7), densely packed, and thin (7-nm) structure (11,12).Here, we perform STICS on SIM data acquired on a total internal reflection fluorescence (TIRF) microscope system, which generated an evanescent field of 75-nm depth for excitation. To our knowledge, this is the first demonstration of an image correlation approach to quantify molecular dynamics on subresolution length scales using wide-field microscopy. To demonstrate the technique, we analyze two-dimensional actin flows in CD4+ T cells during immunological synapse formation, performed after cross-linking of antigen T cell receptors on a coverslip coated with specific antibodies.Fig. 1 a shows a schematic of the TIRF SIM setup. Excitation light (488 nm) passes through a polarizing module and then a phase-grating block, producing diffracted beams. These are then passed through a diffraction filter module to isolate the −1 and +1 order laser beams. These first-order laser beams are angled through the objective to produce total internal reflection conditions at the glass-water interface. The two evanescent waves interfere at the sample, producing structured illumination. The setup then produces lateral and rotational shifts through three orientations, producing nine raw images containing higher spatial frequencies than can normally be acquired by an objective using standard light microscopy. Fig. 1 b demonstrates the increased resolution obtained from TIRF SIM. Shown are the collected Fourier frequencies compared to those of a conventional microscope (dotted red line). Resolution was also measured using sparse 100-nm diameter fluorescent beads. Fig. 1 c shows a magnified image of these beads from which a line profile was obtained (yellow arrow). The full width at half-maximum of this profile (Fig. 1 d) gives a lateral resolution for the system of 120 nm.Open in a separate windowFigure 1(a) Schematic of the TIRF SIM setup. (b) Demonstration of the doubling of spatial resolution of collected frequencies through a Fourier transform (superimposed red circle demonstrating regular spatial frequency limits). (c) SIM reconstructed image of 100-nm bead (scale bar 0.5 μm). (d) (Plotted line) Bead showing full width at half-maximum of 120 nm.We then applied STICS analysis to quantify actin flow in T cell synapses acquired using TIRF SIM (Fig. 2). Fig. 2 a shows a schematic of the STICS analysis. From the raw data, immobile objects are first filtered by subtracting a moving average of the pixel values. Vector maps were obtained from correlation analysis of the time-series as previously published in Hebert et al. (2) and Brown et al. (13). Fig. 2 b shows a reconstructed TIRF SIM image of a mature T cell immunological synapse, representative of a time-point derived from the time series acquired at 1.28 fps (see Movie S1 in the Supporting Material). From this reconstructed image, two representative regions have been selected. In these regions, pseudo-colored actin flow vectors are overlaid onto the fluorescence intensity image. These range in magnitude from 0.01 μm/min (blue) to 5.61 μm/min (red). It can be observed that all flow vectors are directed radially toward the synapse center. A histogram of this flow is shown in Fig. 2 c. The histogram shows a peak retrograde flow velocity of 1.91 ± 1.27 μm/min. These data are representative of n = 7 T-cell synapses imaged by TIRF SIM.Open in a separate windowFigure 2(a) STICS analysis, performed by isolating mobile from immobile structures through a moving average filter (i) and binning a subset of pixels into blocks of superpixels (ii); the STICS software correlates spatial fluorescence fluctuations through time (iii). The code then outputs vector maps showing directionality and flow velocities. (b) TIRF SIM image of actin flow in a T cell 5 min after contact with a stimulatory coverslip. (Zoomed regions) Retrograde actin flow at the synapse periphery. (c) Histograms showing flow speed statistics of vectors from T-cell synapses (n = 7).  相似文献   
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Despite a strong increase in research on seamounts and oceanic islands ecology and biogeography, many basic aspects of their biodiversity are still unknown. In the southwestern Atlantic, the Vitória-Trindade Seamount Chain (VTC) extends ca. 1,200 km offshore the Brazilian continental shelf, from the Vitória seamount to the oceanic islands of Trindade and Martin Vaz. For a long time, most of the biological information available regarded its islands. Our study presents and analyzes an extensive database on the VTC fish biodiversity, built on data compiled from literature and recent scientific expeditions that assessed both shallow to mesophotic environments. A total of 273 species were recorded, 211 of which occur on seamounts and 173 at the islands. New records for seamounts or islands include 191 reef fish species and 64 depth range extensions. The structure of fish assemblages was similar between islands and seamounts, not differing in species geographic distribution, trophic composition, or spawning strategies. Main differences were related to endemism, higher at the islands, and to the number of endangered species, higher at the seamounts. Since unregulated fishing activities are common in the region, and mining activities are expected to drastically increase in the near future (carbonates on seamount summits and metals on slopes), this unique biodiversity needs urgent attention and management.  相似文献   
7.
Exposure to lower-than-therapeutic levels of anti-tuberculosis drugs is likely to cause selection of resistant strains of Mycobacterium tuberculosis and treatment failure. The first-line anti-tuberculosis (TB) regimen consists of rifampicin, isoniazid, pyrazinamide, and ethambutol, and correct management reduces risk of TB relapse and development of drug resistance. In this study we aimed to investigate the effect of standard of care plus nutritional supplementation versus standard care on the pharmacokinetics of isoniazid, pyrazinamide and ethambutol among sputum smear positive TB patients with and without HIV. In a clinical trial in 100 Tanzanian TB patients, with or without HIV infection, drug concentrations were determined at 1 week and 2 months post initiation of anti-TB medication. Data was analysed using population pharmacokinetic modelling. The effect of body size was described using allometric scaling, and the effects of nutritional supplementation, HIV, age, sex, CD4+ count, weight-adjusted dose, NAT2 genotype, and time on TB treatment were investigated. The kinetics of all drugs was well characterised using first-order elimination and transit compartment absorption, with isoniazid and ethambutol described by two-compartment disposition models, and pyrazinamide by a one-compartment model. Patients with a slow NAT2 genotype had higher isoniazid exposure and a lower estimate of oral clearance (15.5 L/h) than rapid/intermediate NAT2 genotype (26.1 L/h). Pyrazinamide clearance had an estimated typical value of 3.32 L/h, and it was found to increase with time on treatment, with a 16.3% increase after the first 2 months of anti-TB treatment. The typical clearance of ethambutol was estimated to be 40.7 L/h, and was found to decrease with age, at a rate of 1.41% per year. Neither HIV status nor nutritional supplementations were found to affect the pharmacokinetics of these drugs in our cohort of patients.  相似文献   
8.

Background

Voids and cavities in the native protein structure determine the pressure unfolding of proteins. In addition, the volume changes due to the interaction of newly exposed atoms with solvent upon protein unfolding also contribute to the pressure unfolding of proteins. Quantitative understanding of these effects is important for predicting and designing proteins with predefined response to changes in hydrostatic pressure using computational approaches. The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for separate calculations.

Results

We developed ProteinVolume, a highly robust and easy-to-use tool to compute geometric volumes of proteins. ProteinVolume generates the molecular surface of a protein and uses an innovative flood-fill algorithm to calculate the individual components of the molecular surface volume, van der Waals and intramolecular void volumes. ProteinVolume is user friendly and is available as a web-server or a platform-independent command-line version.

Conclusions

ProteinVolume is a highly accurate and fast application to interrogate geometric volumes of proteins. ProteinVolume is a free web server available on http://gmlab.bio.rpi.edu. Free-standing platform-independent Java-based ProteinVolume executable is also freely available at this web site.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0531-2) contains supplementary material, which is available to authorized users.  相似文献   
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The hydrocarbons preserved in an Archean rock were extracted, and their composition and distribution in consecutive slices from the outside to the inside of the rock were examined. The 2.7 Ga rock was collected from the Fortescue Group in the Pilbara region, Western Australia. The bitumen I (solvent‐extracted rock) and bitumen II (solvent‐extracted hydrochloric acid‐treated rock) fractions have different hydrocarbon compositions. Bitumen I contains only trace amounts of aliphatic hydrocarbons and virtually no aromatic hydrocarbons. In contrast, bitumen II contains abundant aliphatic and aromatic hydrocarbons. The difference seems to reflect the weathering history and preservational environment of the investigated rock. Aliphatic hydrocarbons in bitumen I are considered to be mainly from later hydrocarbon inputs, after initial deposition and burial, and are therefore not indigenous. The lack of aromatic hydrocarbons in bitumen I suggests a severe weathering environment since uplift and exposure of the rock at the Earth's surface in the Cenozoic. On the other hand, the high abundance of aromatic hydrocarbons in bitumen II suggests that bitumen II hydrocarbons have been physically isolated from removal by their encapsulation within carbonate minerals. The richness of aromatic hydrocarbons and the relative scarcity of aliphatic hydrocarbons may reflect the original compositions of organic materials biosynthesised in ancient organisms in the Archean era, or the high thermal maturity of the rock. Cyanobacterial biomarkers were observed in the surficial slices of the rock, which may indicate that endolithic cyanobacteria inhabited the surface outcrop. The distribution of aliphatic and aromatic hydrocarbons implies a high thermal maturity, which is consistent with the lack of any specific biomarkers, such as hopanes and steranes, and the prehnite–pumpellyite facies metamorphic grade.  相似文献   
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