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921.
Ina Kycia Srikanth Kudithipudi Raluca Tamas Goran Kungulovski Arunkumar Dhayalan Albert Jeltsch 《Journal of molecular biology》2014
PHF1 associates with the Polycomb repressive complex 2 and it was demonstrated to stimulate its H3K27-trimethylation activity. We studied the interaction of the PHF1 Tudor domain with modified histone peptides and found that it recognizes H3K36me3 and H3tK27me3 (on the histone variant H3t) and that it uses the same trimethyllysine binding pocket for the interaction with both peptides. Since both peptide sequences are very different, this result indicates that reading domains can have dual specificities. Sub-nuclear localization studies of full-length PHF1 in human HEK293 cells revealed that it co-localizes with K27me3, but not with K36me3, and that this co-localization depends on the trimethyllysine binding pocket indicating that K27me3 is an in vivo target for the PHF1 Tudor domain. Our data suggest that PHF1 binds to H3tK27me3 in human chromatin, and H3t has a more general role in Polycomb regulation. 相似文献
922.
Douglas?J. Swartz Leo Mok Sri?K. Botta Anukriti Singh Guillermo?A. Altenberg Ina?L. Urbatsch 《Bioscience reports》2014,34(3)
Pgp (P-glycoprotein) is a prototype ABC (ATP-binding-cassette) transporter involved in multidrug resistance of cancer. We used directed evolution to replace six cytoplasmic Cys (cysteine) residues in Pgp with all 20 standard amino acids and selected for active mutants. From a pool of 75000 transformants for each block of three Cys, we identified multiple mutants that preserved drug resistance and yeast mating activity. The most frequent substitutions were glycine and serine for Cys427 (24 and 20%, respectively) and Cys1070 (37 and 25%) of the Walker A motifs in the NBDs (nucleotide-binding domains), Cys1223 in NBD2 (25 and 8%) and Cys638 in the linker region (24 and 16%), whereas close-by Cys669 tolerated glycine (16%) and alanine (14%), but not serine (absent). Cys1121 in NBD2 showed a clear preference for positively charged arginine (38%) suggesting a salt bridge with Glu269 in the ICL2 (intracellular loop 2) may stabilize domain interactions. In contrast, three Cys residues in transmembrane α-helices could be successfully replaced by alanine. The resulting CL (Cys-less) Pgp was fully active in yeast cells, and purified proteins displayed drug-stimulated ATPase activities indistinguishable from WT (wild-type) Pgp. Overall, directed evolution identified site-specific, non-conservative Cys substitutions that allowed building of a robust CL Pgp, an invaluable new tool for future functional and structural studies, and that may guide the construction of other CL proteins where alanine and serine have proven unsuccessful. 相似文献
923.
Gareth D. Westrop Ina Georg Graham H. Coombs 《The Journal of biological chemistry》2009,284(48):33485-33494
Trichomonas vaginalis is a protozoan parasite of humans that is able to synthesize cysteine de novo using cysteine synthase but does not produce glutathione. In this study, high pressure liquid chromatography analysis confirmed that cysteine is the major intracellular redox buffer by showing that T. vaginalis contains high levels of cysteine (∼600 μm) comprising more than 70% of the total thiols detected. To investigate possible mechanisms for the regulation of cysteine levels in T. vaginalis, we have characterized enzymes of the mercaptopyruvate pathway. This consists of an aspartate aminotransferase (TvAspAT1), which transaminates cysteine to form 3-mercaptopyruvate (3-MP), and mercaptopyruvate sulfurtransferase (TvMST), which transfers the sulfur of 3-MP to a nucleophilic acceptor, generating pyruvate. TvMST has high activity with 3-MP as a sulfur donor and can use several thiol compounds as sulfur acceptor substrates. Our analysis indicated that TvMST has a kcat/Km for reduced thioredoxin of 6.2 × 107 m−1 s−1, more than 100-fold higher than that observed for β-mercaptoethanol and cysteine, suggesting that thioredoxin is a preferred substrate for TvMST. Thiol trapping and mass spectrometry provided direct evidence for the formation of thioredoxin persulfide as a product of this reaction. The thioredoxin persulfide could serve a biological function such as the transfer of the persulfide to a target protein or the sequestered release of sulfide for biosynthesis. Changes in MST activity of T. vaginalis in response to variation in the supply of exogenous cysteine are suggestive of a role for the mercaptopyruvate pathway in the removal of excess intracellular cysteine, redox homeostasis, and antioxidant defense. 相似文献
924.
Xingjun Fan Jianye Zhang Mathilde Theves Christopher Strauch Ina Nemet Xiaoqin Liu Juan Qian Frank J. Giblin Vincent M. Monnier 《The Journal of biological chemistry》2009,284(50):34618-34627
Oxidative mechanisms during nuclear sclerosis of the lens are poorly understood, in particular metal-catalyzed oxidation. The lysyl oxidation product adipic semialdehyde (allysine, ALL) and its oxidized end-product 2-aminoadipic acid (2-AAA) were determined as a function of age and presence of diabetes. Surprisingly, whereas both ALL and 2-AAA increased with age and strongly correlated with cataract grade and protein absorbance at 350 nm, only ALL formation but not 2-AAA was increased by diabetes. To clarify the mechanism of oxidation, rabbit lenses were treated with hyperbaric oxygen (HBO) for 48 h, and proteins were analyzed by gas and liquid chromatography mass spectrometry for ALL, 2-AAA, and multiple glycation products. Upon exposure to HBO, rabbit lenses were swollen, and nuclei were yellow. Protein-bound ALL increased 8-fold in the nuclear protein fractions versus controls. A dramatic increase in methyl-glyoxal hydroimidazolone and carboxyethyl-lysine but no increase of 2-AAA occurred, suggesting more drastic conditions are needed to oxidize ALL into 2-AAA. Indeed the latter formed only upon depletion of glutathione and was catalyzed by H2O2. Neither carboxymethyl-lysine nor glyoxal hydroimidazolone, two markers of glyco-/lipoxidation, nor markers of lenticular glycemia (fructose-lysine, glucospane) were elevated by HBO, excluding significant lipid peroxidation and glucose involvement. The findings strongly implicate dicarbonyl/metal catalyzed oxidation of lysine to allysine, whereby low GSH combined with ascorbate-derived H2O2 likely contributes toward 2-AAA formation, since virtually no 2-AAA formed in the presence of methylglyoxal instead of ascorbate. An important translational conclusion is that chelating agents might help delay nuclear sclerosis. 相似文献
925.
926.
927.
Background
Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. 相似文献928.
929.
QTL and candidate genes for fecundity in sows 总被引:1,自引:0,他引:1
Fecundity in pigs is a trait of major economic interest but low heritability. For the improvement of fecundity, genetic markers for selection are desirable and therefore, several searches for genetic variation influencing fecundity have been performed. The aim of this review is to compare and to evaluate all published QTL analyses and candidate gene approaches concerning reproductive traits in sows. For this purpose, we present a comprehensive cytogenetic map comprising 54 QTL and 11 candidate genes with influence on reproductive traits. The evaluation and comparison of the results showed similarities, but also marked differences among studies. Reasons for different results are multicausal and are due to differences between resource populations, number of evaluated animals, mating systems, measured phenotypical traits and environmental influences. We could show that chromosome 8 and to a lower extend chromosome 7 are the most important chromosomes with regard to reproductive traits in pigs. For further research, fine mapping of the identified QTL regions is necessary in order to confirm and to narrow the most likely chromosomal intervals. Although difficult to perform, an advance would be a standardization of the experimental setup in particular, in respect to the collection of phenotypic data. Furthermore, we suggest to publish the information on further identified QTL and candidate genes as comprehensive and accurate as possible in order to allow a more transparent comparison and collation of the results. 相似文献
930.
Statistical multivariate metabolite profiling for aiding biomarker pattern detection and mechanistic interpretations in GC/MS based metabolomics 总被引:1,自引:0,他引:1
Elin Pohjanen Elin Thysell Johan Lindberg Ina Schuppe-Koistinen Thomas Moritz Pär Jonsson Henrik Antti 《Metabolomics : Official journal of the Metabolomic Society》2006,2(4):257-268
A strategy for robust and reliable mechanistic statistical modelling of metabolic responses in relation to drug induced toxicity
is presented. The suggested approach addresses two cases commonly occurring within metabonomic toxicology studies, namely;
1) A pre-defined hypothesis about the biological mechanism exists and 2) No such hypothesis exists. GC/MS data from a liver
toxicity study consisting of rat urine from control rats and rats exposed to a proprietary AstraZeneca compound were resolved
by means of hierarchical multivariate curve resolution (H-MCR) generating 287 resolved chromatographic profiles with corresponding
mass spectra. Filtering according to significance in relation to drug exposure rendered in 210 compound profiles, which were
subjected to further statistical analysis following correction to account for the control variation over time. These dose
related metabolite traces were then used as new observations in the subsequent analyses. For case 1, a multivariate approach,
named Target Batch Analysis, based on OPLS regression was applied to correlate all metabolite traces to one or more key metabolites
involved in the pre-defined hypothesis. For case 2, principal component analysis (PCA) was combined with hierarchical cluster
analysis (HCA) to create a robust and interpretable framework for unbiased mechanistic screening. Both the Target Batch Analysis
and the unbiased approach were cross-verified using the other method to ensure that the results did match in terms of detected
metabolite traces. This was also the case, implying that this is a working concept for clustering of metabolites in relation
to their toxicity induced dynamic profiles regardless if there is a pre-existing hypothesis or not. For each of the methods
the detected metabolites were subjected to identification by means of data base comparison as well as verification in the
raw data. The proposed strategy should be seen as a general approach for facilitating mechanistic modelling and interpretations
in metabolomic studies. 相似文献