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781.
The general Markov model (GMM) of nucleotide substitution does not assume the evolutionary process to be stationary, reversible, or homogeneous. The GMM can be simplified by assuming the evolutionary process to be stationary. A stationary GMM is appropriate for analyses of phylogenetic data sets that are compositionally homogeneous; a data set is considered to be compositionally homogeneous if a statistical test does not detect significant differences in the marginal distributions of the sequences. Though the general time-reversible (GTR) model assumes stationarity, it also assumes reversibility and homogeneity. We propose two new stationary and nonhomogeneous models--one constrains the GMM to be reversible, whereas the other does not. The two models, coupled with the GTR model, comprise a set of nested models that can be used to test the assumptions of reversibility and homogeneity for stationary processes. The two models are extended to incorporate invariable sites and used to analyze a seven-taxon hominoid data set that displays compositional homogeneity. We show that within the class of stationary models, a nonhomogeneous model fits the hominoid data better than the GTR model. We note that if one considers a wider set of models that are not constrained to be stationary, then an even better fit can be obtained for the hominoid data. However, the methods for reducing model complexity from an extremely large set of nonstationary models are yet to be developed. 相似文献
782.
Rocha LA 《Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences》2011,42(3):328-343
This paper begins with a discussion of the scientia sexualis/ars erotica distinction, which Foucault first advances in History of Sexuality Vol. 1, and which has been employed by many scholars to do a variety of analytical work. Though Foucault has expressed his doubts regarding his conceptualization of the differences between Western and Eastern discourses of desire, he never entirely disowns the distinction. In fact, Foucault remains convinced that China must have an ars erotica. I will explore Foucault’s sources of authority. To this end, I introduce the work of famous Dutch sinologist Robert Hans van Gulik, who published the tremendously influential Sexual Life in Ancient China in 1961, and also explore Joseph Needham’s view on Chinese sex. I argue that, Foucault, in his fierce polemic against the “Repressive Hypothesis”, himself imagined a utopian Other where pleasure and desire were organised differently. I end on a discuss on Orientalism and the project of “Sinography” of comparative literature scholars Haun Saussy, Eric Hayot and others. 相似文献
783.
Jackson WM Lozito TP Djouad F Kuhn NZ Nesti LJ Tuan RS 《Journal of cellular and molecular medicine》2011,15(11):2377-2388
Mesenchymal stem cell (MSC) therapy is a promising approach to promote tissue regeneration by either differentiating the MSCs into the desired cell type or by using their trophic functions to promote endogenous tissue repair. These strategies of regenerative medicine are limited by the availability of MSCs at the point of clinical care. Our laboratory has recently identified multipotent mesenchymal progenitor cells (MPCs) in traumatically injured muscle tissue, and the objective of this study was to compare these cells to a typical population of bone marrow derived MSCs. Our hypothesis was that the MPCs exhibit multilineage differentiation and expression of trophic properties that make functionally them equivalent to bone marrow derived MSCs for tissue regeneration therapies. Quantitative evaluation of their proliferation, metabolic activity, expression of characteristic cell-surface markers and baseline gene expression profile demonstrate substantial similarity between the two cell types. The MPCs were capable of differentiation into osteoblasts, adipocytes and chondrocytes, but they appeared to demonstrate limited lineage commitment compared to the bone marrow derived MSCs. The MPCs also exhibited trophic (i.e. immunoregulatory and pro-angiogenic) properties that were comparable to those of MSCs. These results suggest that the traumatized muscle derived MPCs may not be a direct substitute for bone marrow derived MSCs. However, because of their availability and abundance, particularly following orthopaedic injuries when traumatized muscle is available to harvest autologous cells, MPCs are a promising cell source for regenerative medicine therapies designed to take advantage of their trophic properties. 相似文献
784.
785.
Anton D. van Staden Tiaan D. J. Heunis Leon M. T. Dicks 《Probiotics and antimicrobial proteins》2011,3(2):119-124
Maxillofacial and craniofacial surgery is on the increase, which exposes more patients at risk of acquiring microbial infections. The use of antibiotic-loaded calcium phosphate bone cements has been shown to reduce the incidence of infection. A marked increase in antibiotic-resistant pathogens, including multidrug-resistant pathogens, has been reported. This has led to the investigation of various compounds as alternatives to conventional treatments. In this paper, we report on the incorporation and release of a broad-spectrum class II antimicrobial peptide, bacteriocin ST4SA produced by Enterococcus mundtii, into a calcium orthophosphate-based bone cement. Our results suggest class II bacteriocins may be incorporated into self-setting bone cements to produce implants with antimicrobial activity over extended periods of time. 相似文献
786.
Liu Y Gibson J Wheeler J Kwee LC Santiago-Turla CM Akafo SK Lichter PR Gaasterland DE Moroi SE Challa P Herndon LW Girkin CA Budenz DL Richards JE Allingham RR Hauser MA 《PloS one》2011,6(11):e27134
DNA copy number variants (CNVs) have been reported in many human diseases including autism and schizophrenia. Primary Open Angle Glaucoma (POAG) is a complex adult-onset disorder characterized by progressive optic neuropathy and vision loss. Previous studies have identified rare CNVs in POAG; however, their low frequencies prevented formal association testing. We present here the association between POAG risk and a heterozygous deletion in the galactosylceramidase gene (GALC). This CNV was initially identified in a dataset containing 71 Caucasian POAG cases and 478 ethnically matched controls obtained from dbGAP (study accession phs000126.v1.p1.) (p = 0.017, fisher's exact test). It was validated with array comparative genomic hybridization (arrayCGH) and realtime PCR, and replicated in an independent POAG dataset containing 959 cases and 1852 controls (p = 0.021, OR (odds ratio) = 3.5, 95% CI -1.1-12.0). Evidence for association was strengthened when the discovery and replication datasets were combined (p = 0.002; OR = 5.0, 95% CI 1.6-16.4). Several deletions with different endpoints were identified by array CGH of POAG patients. Homozygous deletions that eliminate GALC enzymatic activity cause Krabbe disease, a recessive Mendelian disorder of childhood displaying bilateral optic neuropathy and vision loss. Our findings suggest that heterozygous deletions that reduce GALC activity are a novel mechanism increasing risk of POAG. This is the first report of a statistically-significant association of a CNV with POAG risk, contributing to a growing body of evidence that CNVs play an important role in complex, inherited disorders. Our findings suggest an attractive biomarker and potential therapeutic target for patients with this form of POAG. 相似文献
787.
Armand AS Laziz I Djeghloul D Lécolle S Bertrand AT Biondi O De Windt LJ Chanoine C 《PloS one》2011,6(11):e27283
Apoptosis Inducing Factor (AIF) is a highly conserved, ubiquitous flavoprotein localized in the mitochondrial intermembrane space. In vivo, AIF provides protection against neuronal and cardiomyocyte apoptosis induced by oxidative stress. Conversely in vitro, AIF has been demonstrated to have a pro-apoptotic role upon induction of the mitochondrial death pathway, once AIF translocates to the nucleus where it facilitates chromatin condensation and large scale DNA fragmentation. Given that the aif hypomorphic harlequin (Hq) mutant mouse model displays severe sarcopenia, we examined skeletal muscle from the aif hypomorphic mice in more detail. Adult AIF-deficient skeletal myofibers display oxidative stress and a severe form of atrophy, associated with a loss of myonuclei and a fast to slow fiber type switch, both in "slow" muscles such as soleus, as well as in "fast" muscles such as extensor digitorum longus, most likely resulting from an increase of MEF2 activity. This fiber type switch was conserved in regenerated soleus and EDL muscles of Hq mice subjected to cardiotoxin injection. In addition, muscle regeneration in soleus and EDL muscles of Hq mice was severely delayed. Freshly cultured myofibers, soleus and EDL muscle sections from Hq mice displayed a decreased satellite cell pool, which could be rescued by pretreating aif hypomorphic mice with the manganese-salen free radical scavenger EUK-8. Satellite cell activation seems to be abnormally long in Hq primary culture compared to controls. However, AIF deficiency did not affect myoblast cell proliferation and differentiation. Thus, AIF protects skeletal muscles against oxidative stress-induced damage probably by protecting satellite cells against oxidative stress and maintaining skeletal muscle stem cell number and activation. 相似文献
788.
Juuti-Uusitalo K Klunder LJ Sjollema KA Mackovicova K Ohgaki R Hoekstra D Dekker J van Ijzendoorn SC 《PloS one》2011,6(8):e22967
Background
The cytokines TNF (TNFSF2) and IFNγ are important mediators of inflammatory bowel diseases and contribute to enhanced intestinal epithelial permeability by stimulating apoptosis and/or disrupting tight junctions. Apoptosis and tight junctions are also important for epithelial tissue morphogenesis, but the effect of TNF and IFNγ on the process of intestinal epithelial morphogenesis is unknown.Methods/Principal Findings
We have employed a three-dimensional cell culture system, reproducing in vivo-like multicellular organization of intestinal epithelial cells, to study the effect of TNF on intestinal epithelial morphogenesis and permeability. We show that human intestinal epithelial cells in three-dimensional culture assembled into luminal spheres consisting of a single layer of cells with structural, internal, and planar cell polarity. Exposure of preformed luminal spheres to TNF or IFNγ enhanced paracellular permeability, but via distinctive mechanisms. Thus, while both TNF and IFNγ, albeit in a distinguishable manner, induced the displacement of selected tight junction proteins, only TNF increased paracellular permeability via caspase-driven apoptosis and cell shedding. Infliximab and adalumimab inhibited these effects of TNF. Moreover, we demonstrate that TNF via its stimulatory effect on apoptosis fundamentally alters the process of intestinal epithelial morphogenesis, which contributes to the de novo generation of intestinal epithelial monolayers with increased permeability. Also IFNγ contributes to the de novo formation of monolayers with increased permeability, but in a manner that does not involve apoptosis.Conclusions
Our study provides an optimized 3D model system for the integrated analysis of (real-time) intestinal epithelial paracellular permeability and morphogenesis, and reveals apoptosis as a pivotal mechanism underlying the enhanced permeability and altered morphogenesis in response to TNF, but not IFNγ. 相似文献789.
Schijman AG Bisio M Orellana L Sued M Duffy T Mejia Jaramillo AM Cura C Auter F Veron V Qvarnstrom Y Deborggraeve S Hijar G Zulantay I Lucero RH Velazquez E Tellez T Sanchez Leon Z Galvão L Nolder D Monje Rumi M Levi JE Ramirez JD Zorrilla P Flores M Jercic MI Crisante G Añez N De Castro AM Gonzalez CI Acosta Viana K Yachelini P Torrico F Robello C Diosque P Triana Chavez O Aznar C Russomando G Büscher P Assal A Guhl F Sosa Estani S DaSilva A Britto C Luquetti A Ladzins J 《PLoS neglected tropical diseases》2011,5(1):e931
Background
A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation.Methodology/Findings
An international collaborative study was launched by expert PCR laboratories from 16 countries. Currently used strategies were challenged against serial dilutions of purified DNA from stocks representing T. cruzi discrete typing units (DTU) I, IV and VI (set A), human blood spiked with parasite cells (set B) and Guanidine Hidrochloride-EDTA blood samples from 32 seropositive and 10 seronegative patients from Southern Cone countries (set C). Forty eight PCR tests were reported for set A and 44 for sets B and C; 28 targeted minicircle DNA (kDNA), 13 satellite DNA (Sat-DNA) and the remainder low copy number sequences. In set A, commercial master mixes and Sat-DNA Real Time PCR showed better specificity, but kDNA-PCR was more sensitive to detect DTU I DNA. In set B, commercial DNA extraction kits presented better specificity than solvent extraction protocols. Sat-DNA PCR tests had higher specificity, with sensitivities of 0.05–0.5 parasites/mL whereas specific kDNA tests detected 5.10−3 par/mL. Sixteen specific and coherent methods had a Good Performance in both sets A and B (10 fg/µl of DNA from all stocks, 5 par/mL spiked blood). The median values of sensitivities, specificities and accuracies obtained in testing the Set C samples with the 16 tests determined to be good performing by analyzing Sets A and B samples varied considerably. Out of them, four methods depicted the best performing parameters in all three sets of samples, detecting at least 10 fg/µl for each DNA stock, 0.5 par/mL and a sensitivity between 83.3–94.4%, specificity of 85–95%, accuracy of 86.8–89.5% and kappa index of 0.7–0.8 compared to consensus PCR reports of the 16 good performing tests and 63–69%, 100%, 71.4–76.2% and 0.4–0.5, respectively compared to serodiagnosis. Method LbD2 used solvent extraction followed by Sybr-Green based Real time PCR targeted to Sat-DNA; method LbD3 used solvent DNA extraction followed by conventional PCR targeted to Sat-DNA. The third method (LbF1) used glass fiber column based DNA extraction followed by TaqMan Real Time PCR targeted to Sat-DNA (cruzi 1/cruzi 2 and cruzi 3 TaqMan probe) and the fourth method (LbQ) used solvent DNA extraction followed by conventional hot-start PCR targeted to kDNA (primer pairs 121/122). These four methods were further evaluated at the coordinating laboratory in a subset of human blood samples, confirming the performance obtained by the participating laboratories.Conclusion/Significance
This study represents a first crucial step towards international validation of PCR procedures for detection of T. cruzi in human blood samples. 相似文献790.
Sales AM Ponce de Leon A Düppre NC Hacker MA Nery JA Sarno EN Penna ML 《PLoS neglected tropical diseases》2011,5(3):e1013