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431.
The Class III nucleotide cyclases are found in bacteria, eukaryotes and archaebacteria. Our survey of the bacterial and archaebacterial genome and plasmid sequences identified 193 Class III cyclase genes in only 29 species, of which we predict the majority to be adenylyl cyclases. Interestingly, several putative cyclase genes were found to have non-conserved substrate specifying residues. Ancestors of the eukaryotic C1-C2 domain containing soluble adenylyl cyclases as well as the protist guanylyl cyclases were found in bacteria. Diverse domains were fused to the cyclase domain and phylogenetic analysis indicated that most proteins within a single cluster have similar domain compositions, emphasising the ancient evolutionary origin and versatility of the cyclase domain. 相似文献
432.
Lee I Skinner MA Guo HB Sujan A Pierce M 《The Journal of biological chemistry》2004,279(51):53007-53014
Vacuolar H(+)-ATPase functions as a vacuolar proton pump and is responsible for acidification of intracellular compartments such as the endoplasmic reticulum, Golgi, lysosomes, and endosomes. Previous reports have demonstrated that a 16-kDa subunit (16K) of vacuolar H(+)-ATPase via one of its transmembrane domains, TMD4, strongly associates with beta(1) integrin, affecting beta(1) integrin N-linked glycosylation and inhibiting its function as a matrix adhesion receptor. Because of this dramatic inhibition of beta(1) integrin-mediated HEK-293 cell motility by 16K expression, we investigated the mechanism by which 16 kDa was having this effect. Using HT1080 cells whose alpha(5)beta(1) integrin-mediated adhesion to fibronectin has been extensively studied, the expression of 16 kDa also resulted in reduced cell spreading on fibronectin-coated substrates. A pulse-chase study of beta(1) integrin biosynthesis indicated that 16K expression down-regulated the level of the 110-kDa biosynthetic form of beta(1) integrin (premature form) and, consequently, the level of the 130-kDa form of beta(1) integrin (mature form). Further experiments showed that the normal levels of association between the premature beta(1) integrin form and calnexin were significantly decreased by the expression of either 16 kDa or TMD4. Expression of 16 kDa also resulted in a Triton X-100-insoluble aggregation of an unusual 87-kDa form of beta(1) integrin. Interestingly, both Western blotting and a pulse-chase experiment showed co-immunoprecipitation of calnexin and 16K. These results indicate that 16K expression inhibits beta(1) integrin surface expression and spreading on matrix by a novel mechanism that results in reduced levels of functional beta(1) integrin. 相似文献
433.
Denver DR Morris K Kewalramani A Harris KE Chow A Estes S Lynch M Thomas WK 《Journal of molecular evolution》2004,58(5):584-595
Homopolymeric nucleotide runs, also called mononucleotide microsatellites, are a ubiquitous, dominant, and mutagenic feature of eukaryotic genomes. A clear understanding of the forces that shape patterns of homopolymer evolution, however, is lacking. We provide a focused investigation of the abundance, chromosomal distribution, and mutation spectra of the four strand-specific homopolymer types (A, T, G, C) 8 bp in the genome of Caenorhabditis elegans. A and T homopolymers vastly outnumber G and C HPs, and the run-length distributions of A and T homopolymers differ significantly from G and C homopolymers. A scanning window analysis of homopolymer chromosomal distribution reveals distinct clusters of homopolymer density in autosome arms that are regions of high recombination in C. elegans. Dramatic biases are detected among closely spaced homopolymers; for instance, we observe 994 A homopolymers immediately followed by a T homopolymer (5 to 3) and only 8 instances of T homopolymers directly followed by an A homopolymer. Empirical homopolymer mutation assays in a set of C. elegans mutation-accumulation lines reveal an 20-fold higher mutation rate for G and C homopolymers compared to A and T homopolymers. Nuclear A and T homopolymers are also found to mutate 100-fold more slowly than mitochondrial A and T homopolymers. This integrative approach yields a total nuclear genome-wide homopolymer mutation rate estimate of 1.6 mutations per genome per generation.Novel sequences are deposited in GenBank under accession numbers AY219759–AY219789. 相似文献
434.
A mixed culture of sulfate-reducing bacteria containing the species Desulfovibrio desulfuricans was used to study sulfate-reduction stoichiometry and kinetics using ethanol as the carbon source. Growth yield was lower, and kinetics were slower, for ethanol compared to lactate. Ethanol was converted into acetate and no significant carbon dioxide production was observed. A mathematical model for growth of sulfate-reducing bacteria on ethanol was developed, and simulations of the growth experiments on ethanol were carried out using the model. The pH variation due to sulfate reduction, and hydrogen sulfide production and removal by nitrogen sparging, were examined. The modeling study is distinct from earlier models for systems using sulfate-reducing bacteria in that it considers growth on ethanol, and analyzes pH variations due to the product-formation reactions. 相似文献
435.
436.
Hanyin Cheng Avinash V. Dharmadhikari Sylvia Varland Ning Ma Deepti Domingo Robert Kleyner Alan F. Rope Margaret Yoon Asbjørg Stray-Pedersen Jennifer E. Posey Sarah R. Crews Mohammad K. Eldomery Zeynep Coban Akdemir Andrea M. Lewis Vernon R. Sutton Jill A. Rosenfeld Erin Conboy Katherine Agre Gholson J. Lyon 《American journal of human genetics》2018,102(5):985-994
437.
Avinash Kaur Ritu Das Mayank Rai Nigam Ravikrishnan Elangovan Deepal Pandya Sandeep Jha Dinesh Kalyanasundaram 《Indian journal of microbiology》2018,58(3):381-392
A limit of detection of 200 CFU/mL of Salmonella typhi spiked in various sample matrices were achieved in 30 min. The sample matrices were raw/unprocessed milk, commercially available milk, juice from packed bottles, fresh juice from carts, potable water, turbid water and calf serum. The complete protocol comprised of three steps: (a) cell lysis (b) nucleic acid amplification and (c) an in situ optical detection. The cell lysis was carried out using a simple heating based protocol, while the loop-mediated isothermal amplification of DNA was carried out by an in-house designed and fabricated system. The developed system consists of an aluminum block fitted with two cartridge heaters along with a thermocouple. The system was coupled to a light source and spectrometer for a simultaneous in situ detection. Primers specific for STY2879 gene were used to amplify the nucleic acid sequence, isolated from S. typhi cells. The protocol involves 15 min of cell lysis and DNA isolation followed by 15 min for isothermal amplification and simultaneous detection. No cross-reactivity of the primers were observed at 106 CFU/mL of Escherichia coli, Vibrio cholerae, Salmonella typhimurium, Salmonella paratyphi A, Pseudomonas aeruginosa, Bacillus cereus, Lysteria monocytogenes, Clostridium botulinum, Staphylococcus aureus and Salmonella havana. In addition, the system was able to detect S. typhi of 200 CFU/mL in a concoction of 106 CFU/mL of E. coli, 106 CFU/mL of V. cholerae, and 106 CFU/mL of hepatocyte-derived cellular carcinoma HUH7 cells. The proposed rapid diagnostic system shows a promising future in the field of food and medical diagnostics. 相似文献
438.
Avinash H. Udayashankar Shibina Noorjahan Nirmala Srikantia K. Ravindra Babu Sandeep Muzumder 《Reports of Practical Oncology and Radiotherapy》2018,23(4):233-241
Aim
To identify the most reproducible technique of patient positioning and immobilization during pelvic radiotherapy.Background
Radiotherapy plays an important role in the treatment of pelvic malignancies. Errors in positioning of patient are an integral component of treatment. The present study compares two methods of immobilization with no immobilization with an aim of identifying the most reproducible method.Materials and methods
65 consecutive patients receiving pelvic external beam radiotherapy were retrospectively analyzed. 30, 21 and 14 patients were treated with no-immobilization with a leg separator, whole body vacuum bag cushion (VBC) and six point aquaplast immobilization system, respectively. The systematic error, random error and the planning target volume (PTV) margins were calculated for all the three techniques and statistically analyzed.Results
The systematic errors were the highest in the VBC and random errors were the highest in the aquaplast group. Both systematic and random errors were the lowest in patients treated with no-immobilization. 3D Systematic error (mm, mean ± 1SD) was 4.31 ± 3.84, 3.39 ± 1.71 and 2.42 ± 0.97 for VBC, aquaplast and no-immobilization, respectively. 3D random error (mm, 1SD) was 2.96, 3.59 and 1.39 for VBC, aquaplast and no-immobilization, respectively. The differences were statistically significant between all the three groups. The calculated PTV margins were the smallest for the no-immobilization technique with 4.56, 4.69 and 4.59 mm, respectively, in x, y and z axes, respectively.Conclusions
Among the three techniques, no-immobilization technique with leg separator was the most reproducible technique with the smallest PTV margins. For obvious reasons, this technique is the least time consuming and most economically viable in developing countries. 相似文献439.
Ece?D. Gamsiz Emma?W. Viscidi Abbie?M. Frederick Shailender Nagpal Stephan?J. Sanders Michael?T. Murtha Michael Schmidt Simons Simplex Collection Genetics Consortium Elizabeth?W. Triche Daniel?H. Geschwind Matthew?W. State Sorin Istrail Edwin?H. Cook Jr. Bernie Devlin Eric?M. Morrow 《American journal of human genetics》2013,93(1):103-109
Intellectual disability (ID), often attributed to autosomal-recessive mutations, occurs in 40% of autism spectrum disorders (ASDs). For this reason, we conducted a genome-wide analysis of runs of homozygosity (ROH) in simplex ASD-affected families consisting of a proband diagnosed with ASD and at least one unaffected sibling. In these families, probands with an IQ ≤ 70 show more ROH than their unaffected siblings, whereas probands with an IQ > 70 do not show this excess. Although ASD is far more common in males than in females, the proportion of females increases with decreasing IQ. Our data do support an association between ROH burden and autism diagnosis in girls; however, we are not able to show that this effect is independent of low IQ. We have also discovered several autism candidate genes on the basis of finding (1) a single gene that is within an ROH interval and that is recurrent in autism or (2) a gene that is within an autism ROH block and that harbors a homozygous, rare deleterious variant upon analysis of exome-sequencing data. In summary, our data suggest a distinct genetic architecture for participants with autism and co-occurring intellectual disability and that this architecture could involve a role for recessively inherited loci for this autism subgroup. 相似文献
440.