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141.
Gabriel Minarik Gabriela Repiska Michaela Hyblova Emilia Nagyova Katarina Soltys Jaroslav Budis Frantisek Duris Rastislav Sysak Maria Gerykova Bujalkova Barbora Vlkova-Izrael Orsolya Biro Balint Nagy Tomas Szemes 《PloS one》2015,10(12)
Objectives
The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods.Methods
Samples from 130 pregnant women were analyzed by whole genome sequencing on benchtop NGS systems Ion Torrent PGM and MiSeq. The targeted yield of 3 million raw reads on each platform was used for z score calculation. The impact of in silico and physical size selection on analytical performance of the test was studied.Results
Using a z score value of 3 as the cut-off, 98.11% - 100% (104-106/106) specificity and 100% (24/24) sensitivity and 99.06% - 100% (105-106/106) specificity and 100% (24/24) sensitivity were observed for Ion Torrent PGM and MiSeq, respectively. After in silico based size selection both platforms reached 100% specificity and sensitivity. Following the physical size selection z scores of tested trisomic samples increased significantly—p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively.Conclusions
Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on high-to-ultrahigh throughput NGS systems. The in silico size selection led to higher specificity of the test. Physical size selection performed on isolated DNA led to significant increase in z scores. The observed results could represent a basis for increasing of cost effectiveness of the test and thus help with its penetration worldwide. 相似文献142.
143.
Carolina I. Cura Tomas Duffy Raúl H. Lucero Margarita Bisio Julie Péneau Matilde Jimenez-Coello Eva Calabuig María J. Gimenez Edward Valencia Ayala Sonia A. Kjos José Santalla Susan M. Mahaney Nelly M. Cayo Claudia Nagel Laura Barcán Edith S. Málaga Machaca Karla Y. Acosta Viana Laurent Brutus Susana B. Ocampo Christine Aznar Cesar A. Cuba Cuba Ricardo E. Gürtler Janine M. Ramsey Isabela Ribeiro John L. VandeBerg Zaida E. Yadon Antonio Osuna Alejandro G. Schijman 《PLoS neglected tropical diseases》2015,9(5)
Background
Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR).Methods/Principal Findings
The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm.Conclusions/Significance
Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production. 相似文献144.
Background/Objectives
Inflammation and oxidative stress are central in many disease states. The major anti-oxidative enzymes contain selenium. The selenium intake in Europe is low, and supplementation with selenium and coenzyme Q10, important anti-oxidants, was evaluated in a previous study. The aim of this study was to evaluate response on the inflammatory biomarkers C-reactive protein, and sP-selectin, and their possible impact on cardiovascular mortality.Subjects/Methods
437 elderly individuals were included in the study. Clinical examination, echocardiography, electrocardiography and blood samples were drawn. The intervention time was 48 months, and median follow-up was 5.2 years. The effects on inflammation/atherosclerosis were evaluated through analyses of CRP and sP-selectin. Evaluations of the effect of the intervention was performed using repeated measures of variance. All mortality was registered, and endpoints of mortality were assessed by Kaplan-Meier plots.Results
The placebo group showed a CRP level of 4.8 ng/mL at the start, and 5.1 ng/mL at the study end. The active supplementation group showed a CRP level of 4.1 ng/mL at the start, and 2.1 ng/mL at the study end. SP-selectin exhibited a level of 56.6 mg/mL at the start in the placebo group and 72.3 mg/mL at the study end, and in the active group the corresponding figures were 55.9 mg/mL and 58.0 mg/mL. A significantly smaller increase was demonstrated through repeated measurements of the two biomarkers in those on active supplementation. Active supplementation showed an effect on the CRP and sP-selectin levels, irrespective of the biomarker levels. Reduced cardiovascular mortality was demonstrated in both those with high and low levels of CRP and sP-selectin in the active supplementation group.Conclusion
CRP and sP-selectin showed significant changes reflecting effects on inflammation and atherosclerosis in those given selenium and coenzyme Q10 combined. A reduced cardiovascular mortality could be demonstrated in the active group, irrespective of biomarker level. This result should be regarded as hypothesis-generating, and it is hoped it will stimulate more research in the area. 相似文献145.
Tess V. Clendenen Justin Rendleman Wenzhen Ge Karen L. Koenig Isaac Wirgin Diane Currie Roy E. Shore Tomas Kirchhoff Anne Zeleniuch-Jacquotte 《PloS one》2015,10(8)
Background
Large epidemiologic studies have the potential to make valuable contributions to the assessment of gene-environment interactions because they prospectively collected detailed exposure data. Some of these studies, however, have only serum or plasma samples as a low quantity source of DNA.Methods
We examined whether DNA isolated from serum can be used to reliably and accurately genotype single nucleotide polymorphisms (SNPs) using Sequenom multiplex SNP genotyping technology. We genotyped 81 SNPs using samples from 158 participants in the NYU Women’s Health Study. Each participant had DNA from serum and at least one paired DNA sample isolated from a high quality source of DNA, i.e. clots and/or cell precipitates, for comparison.Results
We observed that 60 of the 81 SNPs (74%) had high call frequencies (≥95%) using DNA from serum, only slightly lower than the 85% of SNPs with high call frequencies in DNA from clots or cell precipitates. Of the 57 SNPs with high call frequencies for serum, clot, and cell precipitate DNA, 54 (95%) had highly concordant (>98%) genotype calls across all three sample types. High purity was not a critical factor to successful genotyping.Conclusions
Our results suggest that this multiplex SNP genotyping method can be used reliably on DNA from serum in large-scale epidemiologic studies. 相似文献146.
An individual-based, mass-spring modeling framework has been developed to investigate the effect of cell properties on the structure of biofilms and microbial aggregates through Lagrangian modeling. Key features that distinguish this model are variable cell morphology described by a collection of particles connected by springs and a mechanical representation of deformable intracellular, intercellular, and cell-substratum links. A first case study describes the colony formation of a rod-shaped species on a planar substratum. This case shows the importance of mechanical interactions in a community of growing and dividing rod-shaped cells (i.e., bacilli). Cell-substratum links promote formation of mounds as opposed to single-layer biofilms, whereas filial links affect the roundness of the biofilm. A second case study describes the formation of flocs and development of external filaments in a mixed-culture activated sludge community. It is shown by modeling that distinct cell-cell links, microbial morphology, and growth kinetics can lead to excessive filamentous proliferation and interfloc bridging, possible causes for detrimental sludge bulking. This methodology has been extended to more advanced microbial morphologies such as filament branching and proves to be a very powerful tool in determining how fundamental controlling mechanisms determine diverse microbial colony architectures. 相似文献
147.
148.
149.
Martin Welin J?rg Günter Grossmann Susanne Flodin Tomas Nyman P?l Stenmark Lionel Trésaugues Tetyana Kotenyova Ida Johansson P?r Nordlund Lari Lehti? 《Nucleic acids research》2010,38(20):7308-7319
Human purine de novo synthesis pathway contains several multi-functional enzymes, one of which, tri-functional GART, contains three enzymatic activities in a single polypeptide chain. We have solved structures of two domains bearing separate catalytic functions: glycinamide ribonucleotide synthetase and aminoimidazole ribonucleotide synthetase. Structures are compared with those of homologous enzymes from prokaryotes and analyzed in terms of the catalytic mechanism. We also report small angle X-ray scattering models for the full-length protein. These models are consistent with the enzyme forming a dimer through the middle domain. The protein has an approximate seesaw geometry where terminal enzyme units display high mobility owing to flexible linker segments. This resilient seesaw shape may facilitate internal substrate/product transfer or forwarding to other enzymes in the pathway. 相似文献
150.
Avery O. Tatters Harris I. Muhlstein Carmelo R. Tomas 《Journal of applied phycology》2010,22(4):435-442
Blooms of the toxic dinoflagellate, Karenia brevis, occur annually along the Gulf coast of Florida. Other species, like Karenia selliformis, are at times found in association. Hemolytic activity, the ability to lyse red blood cells, of two K. brevis clones (SP3 non-toxic (N-tox) and SP3 super toxic (S-tox)) from the Gulf of Mexico and a single clone of K. selliformis from New Zealand was investigated throughout a growth cycle. Activity is reported as effective concentration (EC50) values, the quantitative measure of hemolysis of human erythrocytes expressed as cell numbers. Both cells and media of K. selliformis cultures consistently produced potent levels of hemolysis (maximum EC50 = 4.88 × 103 cells) from inoculation until the population declined 35 days later. For SP3 N-tox and S-tox, no hemolytic activity was detectable
until day 26 of sampling. The media of both SP3 N-tox and SP3 S-tox cultures consistently contained non-detectable or low
levels of hemolysis compared to K. selliformis. Maximum EC50s for the SP3 clones were 1.80 × 106 and 1.97 × 106 cells, respectively. The experimental EC50 values observed represent ecologically relevant cell densities for K. selliformis, but not for the K. brevis clones. In addition, the hemolytic activity of gymnodimine A and various PbTx derivatives was examined in this study. Our
findings indicate that the hemolytic capability of these dinoflagellates, especially K. selliformis, represents an additional component of toxicity aside from their already recognized toxins and that this activity may play
a larger role than was previously considered. The purpose of this study was to extend the knowledge of the biology and toxicology
of species within the genus Karenia. 相似文献