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81.
Luzyanina T Mrusek S Edwards JT Roose D Ehl S Bocharov G 《Journal of mathematical biology》2007,54(1):57-89
CFSE based tracking of the lymphocyte proliferation using flow cytometry is a powerful experimental technique in immunology
allowing for the tracing of labelled cell populations over time in terms of the number of divisions cells undergone. Interpretation
and understanding of such population data can be greatly improved through the use of mathematical modelling. We apply a heterogenous
linear compartmental model, described by a system of ordinary differential equations similar to those proposed by Kendall.
This model allows division number-dependent rates of cell proliferation and death and describes the rate of changes in the
numbers of cells having undergone j divisions. The experimental data set that we specifically analyze specifies the following characteristics of the kinetics
of PHA-induced human T lymphocyte proliferation assay in vitroL (1) the total number of live cells, (2) the total number of
dead but not disintegrated cells and (3) the number of cells divided j times. Following the maximum likelihood approach for data fitting, we estimate the model parameters which, in particular,
present the CTL birth- and death rate “functions”. It is the first study of CFSE labelling data which convincingly shows that
the lymphocyte proliferation and death both in vitro and in vivo are division number dependent. For the first time, the confidence
in the estimated parameter values is analyzed by comparing three major methods: the technique based on the variance–covariance
matrix, the profile-likelihood-based approach and the bootstrap technique. We compare results and performance of these methods
with respect to their robustness and computational cost. We show that for evaluating mathematical models of differing complexity
the information-theoretic approach, based upon indicators measuring the information loss for a particular model (Kullback–Leibler
information), provides a consistent basis. We specifically discuss methodological and computational difficulties in parameter
identification with CFSE data, e.g. the loss of confidence in the parameter estimates starting around the sixth division.
Overall, our study suggests that the heterogeneity inherent in cell kinetics should be explicitly incorporated into the structure
of mathematical models.
相似文献
82.
Non-CpG methylation occurring in the context of CNG sequences is found in plants at a large number of genomic loci. However, there is still little information available about non-CpG methylation in mammals. Efficient methods that would allow detection of scarcely localized methylated sites in small quantities of DNA are required to elucidate the biological role of non-CpG methylation in both plants and animals. In this study, we tested a new whole genome approach to identify sites of CCWGG methylation (W is A or T), a particular case of CNG methylation, in genomic DNA. This technique is based on digestion of DNAs with methylation-sensitive restriction endonucleases EcoRII-C and AjnI. Short DNAs flanking methylated CCWGG sites (tags) are selectively purified and assembled in tandem arrays of up to nine tags. This allows high-throughput sequencing of tags, identification of flanking regions, and their exact positions in the genome. In this study, we tested specificity and efficiency of the approach. 相似文献
83.
Li MH Tapio I Vilkki J Ivanova Z Kiselyova T Marzanov N Cinkulov M Stojanović S Ammosov I Popov R Kantanen J 《Molecular ecology》2007,16(18):3839-3853
We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian-based clustering approach, we identified a genetic distinctness between populations of modern commercial origin and those of native origin. Our data suggested that northern European Russia represents the most heavily colonized area by modern commercial cattle. Further genetic mixture analyses based on individual assignment tests found that native Red Steppe cattle were also employed in the historical breeding practices in Eastern Europe, most probably for incorporating their strong and extensive adaptability. In analysis of molecular variance, within-population differences accounted for approximately 90% of the genetic variation. Despite some correspondence between geographical proximity and genetic similarity, genetic differentiation was observed to be significantly associated with the difference in breeding purpose among the European populations (percentage of variance among groups and significance: 2.99%, P = 0.02). Our findings give unique genetic insight into the historical patterns of cattle breeding practices in the former Soviet Union. The results identify the neighbouring Near Eastern regions such as the Balkan, the Caucasus and Ukraine, and the isolated Far Eastern Siberia as areas of 'genetic endemism', where cattle populations should be given conservation priority. The results will also be of importance for cost-effective management of their future utilization. 相似文献
84.
Andreeva AV Kutuzov MA Voyno-Yasenetskaya TA 《American journal of physiology. Lung cellular and molecular physiology》2007,293(2):L259-L271
Molecular mechanisms of surfactant delivery to the air/liquid interface in the lung, which is crucial to lower the surface tension, have been studied for more than two decades. Lung surfactant is synthesized in the alveolar type II cells. Its delivery to the cell surface is preceded by surfactant component synthesis, packaging into specialized organelles termed lamellar bodies, delivery to the apical plasma membrane and fusion. Secreted surfactant undergoes reuptake, intracellular processing, and finally resecretion of recycled material. This review focuses on the mechanisms of delivery of surfactant components to and their secretion from lamellar bodies. Lamellar bodies-independent secretion is also considered. Signal transduction pathways involved in regulation of these processes are discussed as well as disorders associated with their malfunction. 相似文献
85.
Alexandrova LA Jasko MV Belobritskaya EE Chudinov AV Mityaeva ON Nasedkina TV Zasedatelev AS Kukhanova MK 《Bioconjugate chemistry》2007,18(3):886-893
A simple and convenient method for incorporation of fluorescent or ligand groups into 3'-termini of DNA fragments is proposed. A set of triphosphoric acid monoesters bearing fluorescent groups or biotin attached to the triphosphate fragment through linkers of different lengths and structures was synthesized. All the compounds were substrates for calf thymus terminal deoxynucleotidyltransferase and were used for incorporation of marker groups into 3'-termini of DNA fragments. The compounds were successfully applied for DNA labeling during post-PCR target preparation for microarray analysis. 相似文献
86.
Galkin O Bentley AA Gupta S Compton BA Mazumder B Kinzy TG Merrick WC Hatzoglou M Pestova TV Hellen CU Komar AA 《RNA (New York, N.Y.)》2007,13(12):2116-2128
Ribosomal protein (rp) S5 belongs to a family of ribosomal proteins that includes bacterial rpS7. rpS5 forms part of the exit (E) site on the 40S ribosomal subunit and is essential for yeast viability. Human rpS5 is 67% identical and 79% similar to Saccharomyces cerevisiae rpS5 but lacks a negatively charged (pI approximately 3.27) 21 amino acid long N-terminal extension that is present in fungi. Here we report that replacement of yeast rpS5 with its human homolog yielded a viable yeast strain with a 20%-25% decrease in growth rate. This replacement also resulted in a moderate increase in the heavy polyribosomal components in the mutant strain, suggesting either translation elongation or termination defects, and in a reduction in the polyribosomal association of the elongation factors eEF3 and eEF1A. In addition, the mutant strain was characterized by moderate increases in +1 and -1 programmed frameshifting and hyperaccurate recognition of the UAA stop codon. The activities of the cricket paralysis virus (CrPV) IRES and two mammalian cellular IRESs (CAT-1 and SNAT-2) were also increased in the mutant strain. Consistently, the rpS5 replacement led to enhanced direct interaction between the CrPV IRES and the mutant yeast ribosomes. Taken together, these data indicate that rpS5 plays an important role in maintaining the accuracy of translation in eukaryotes and suggest that the negatively charged N-terminal extension of yeast rpS5 might affect the ribosomal recruitment of specific mRNAs. 相似文献
87.
Stenoien DL Knyushko TV Londono MP Opresko LK Mayer MU Brady ST Squier TC Bigelow DJ 《American journal of physiology. Cell physiology》2007,292(6):C2084-C2094
Phospholamban (PLB) associates with the Ca2+-ATPase in sarcoplasmic reticulum (SR) membranes to permit the modulation of contraction in response to -adrenergic signaling. To understand how coordinated changes in the abundance and intracellular trafficking of PLB and the Ca2+-ATPase contribute to the maturation of functional muscle, we measured changes in abundance, location, and turnover of endogenous and tagged proteins in myoblasts and during their differentiation. We found that PLB is constitutively expressed in both myoblasts and differentiated myotubes, whereas abundance increases of the Ca2+-ATPase coincide with the formation of differentiated myotubes. We observed that PLB is primarily present in highly mobile vesicular structures outside the endoplasmic reticulum, irrespective of the expression of the Ca2+-ATPase, indicating that PLB targeting is regulated through vesicle trafficking. Moreover, using pulse-chase methods, we observed that in myoblasts, PLB is trafficked through directed transport through the Golgi to the plasma membrane before endosome-mediated internalization. The observed trafficking of PLB to the plasma membrane suggests an important role for PLB during muscle differentiation, which is distinct from its previously recognized role in the regulation of the Ca2+-ATPase. sarco(endo)plasmic reticulum calcium-adenosine triphosphatase; differentiation; C2C12 myocytes; vesicle trafficking 相似文献
88.
Qian W Zhukov T Song D Tockman MS 《Analytical and quantitative cytology and histology / the International Academy of Cytology [and] American Society of Cytology》2007,29(2):103-111
OBJECTIVE: To present a set of novel computerized analysis algorithms to construct a computer-aided cytologic diagnosis (CACD) system to differentiate lung cancer biomarkers and identify cancer cells in the tissue-based specimen images. STUDY DESIGN: Molecular methods, including application of cancer-specific markers, may prove to be complementary to cytology diagnosis, especially when they are combined with CACD system for biomarker assessment. We trained a novel CACD system to recognize expression of the cancer biomarkers histone H2AX in lung cancer cells and then tested the accuracy of this system to distinguish resected lung cancer from preneoplastic and normal tissues. The major characteristics of CACD algorithms is to adapt detection parameters according to cellular image contents. Our newly developed wavelet transform is able to adaptively select different resolution and orientation features based on image content requirements. RESULTS: Visual, statistical and quantitative results as CACD performance evaluation are presented in this paper. CONCLUSION: The presented algorithms and CACD system for cellular feature enhancement, segmentation and classification are very important in distinguishing benign and malignant lesions. 相似文献
89.
Ponimaskin E Voyno-Yasenetskaya T Richter DW Schachner M Dityatev A 《Molecular neurobiology》2007,35(3):278-287
Several neurotransmitters including serotonin and glutamate have been shown to be involved in many aspects of neural development,
such as neurite outgrowth, regulation of neuronal morphology, growth cone motility and dendritic spine shape and density,
in addition to their well-established role in neuronal communication. This review focuses on recent advances in our understanding
of the molecular mechanisms underlying neurotransmitter-induced changes in neuronal morphology. In the first part of the review,
we introduce the roles of small GTPases of the Rho family in morphogenic signaling in neurons and discuss signaling pathways,
which may link serotonin, operating as a soluble guidance factor, and the Rho GTPase machinery, controlling neuronal morphology
and motility. In the second part of the review, we focus on glutamate-induced neuroplasticity and discuss the evidence on
involvement of Rho and Ras GTPases in functional and structural synaptic plasticity triggered by the activation of glutamate
receptors. 相似文献
90.