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991.
Hisashi Mizutani Hideaki Sugawara Ashley M. Buckle Takeshi Sangawa Ken-ichi Miyazono Jun Ohtsuka Koji Nagata Tomoki Shojima Shohei Nosaki Yuqun Xu Delong Wang Xiao Hu Masaru Tanokura Kei Yura 《BMC structural biology》2017,17(1):4
Background
More than 7000 papers related to “protein refolding” have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource – “REFOLDdb” that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest.Results
We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17th, 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/.Conclusion
REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.992.
Hélène Pereira Jean-François Martin Charlotte Joly Jean-Louis Sébédio Estelle Pujos-Guillot 《Metabolomics : Official journal of the Metabolomic Society》2010,6(2):207-218
In order to study the effect of a diet on metabolites found in body fluids such as plasma, we have developed and validated
a UPLC/MS method. While methods using NMR have been well established to analyse different biological tissues, recent studies
have described robust untargeted UPLC-MS methods for plasma analysis. One major concern when profiling plasma is the presence
of an important quantity of proteins which have to be precipitated without any loss of metabolites prior to LC/MS analysis.
The utilization of untargeted approaches in nutritional metabolomics still suffers from the lack of identification of specific
biomarkers. We therefore suggest an alternative method still using a global approach but focusing at the same time on metabolites
previously described in human plasma in order to detect biomarkers of metabolic dysregulations. Thus, to fulfil our objectives,
analytical parameters were tested (i) the anticoagulant type for sample collection, (ii) the protein precipitation method
and (iii) UPLC/MS analytical conditions. Three protein precipitation methods and two anticoagulants were tested and compared.
The method utilizing blood collection on heparin and methanol precipitation was chosen for giving the most reproducible results
while keeping the complexity of the sample. Finally, a validation was proposed to evaluate the stability of this analytical
method applied to a large batch of samples for nutritional metabolomic studies. 相似文献
993.
Yan Liu Zheng-lian Xue Shao-peng Chen Zhou Wang Yong Zhang Wei-liang Gong Zhi-ming Zheng 《Journal of industrial microbiology & biotechnology》2016,43(6):751-760
To enhance the screening efficiency and accuracy of a high-yield menaquinone (vitamin K2, MK) bacterial strain, a novel, quantitative method by fluorescence-activated cell sorting (FACS) was developed. The staining technique was optimized to maximize the differences in fluorescence signals between spontaneous and MK-accumulating cells. The fluorescence carrier rhodamine 123 (Rh123), with its ability to reflect membrane potential, proved to be an appropriate fluorescent dye to connect the MK content with fluorescence signal quantitatively. To promote adequate access of the fluorescent molecule to the target and maintain higher cell survival rates, staining and incubation conditions were optimized. The results showed that 10 % sucrose facilitated uptake of Rh123, while maintaining a certain level of cell viability. The pre-treatment of cells with MgCl2 before staining with Rh123 also improved cell viability. Using FACS, 50 thousands cells can easily be assayed in less than 1 h. The optimized staining protocol yielded a linear response for the mean fluorescence against high performance liquid chromatography-measured MK content. We have developed a novel and useful staining protocol in the high-throughput evaluation of Flavobacterium sp. mutant libraries, using FACS to identify mutants with increased MK-accumulating properties. This study also provides reference for the screening of other industrial microbial strains. 相似文献
994.
The Effect of Sterilization Methods on the Physical Properties of Silk Sericin Scaffolds 总被引:1,自引:0,他引:1
Protein-based biomaterials respond differently to sterilization methods. Since protein is a complex structure, heat, or irradiation
may result in the loss of its physical or biological properties. Recent investigations have shown that sericin, a degumming
silk protein, can be successfully formed into a 3-D scaffolds after mixing with other polymers which can be applied in skin
tissue engineering. The objective of this study was to investigate the effectiveness of ethanol, ethylene oxide (EtO) and
gamma irradiation on the sterilization of sericin scaffolds. The influence of these sterilization methods on the physical
properties such as pore size, scaffold dimensions, swelling and mechanical properties, as well as the amount of sericin released
from sericin/polyvinyl alcohol/glycerin scaffolds, were also investigated. Ethanol treatment was ineffective for sericin scaffold
sterilization whereas gamma irradiation was the most effective technique for scaffold sterilization. Moreover, ethanol also
caused significant changes in pore size resulting from shrinkage of the scaffold. Gamma-irradiated samples exhibited the highest
swelling property, but they also lost the greatest amount of weight after immersion for 24 h compared with scaffolds obtained
from other sterilization methods. The results of the maximum stress test and Young’s modulus showed that gamma-irradiated
and ethanol-treated scaffolds are more flexible than the EtO-treated and untreated scaffolds. The amount of sericin released,
which was related to its collagen promoting effect, was highest from the gamma-irradiated scaffold. The results of this study
indicate that gamma irradiation should have the greatest potential for sterilizing sericin scaffolds for skin tissue engineering. 相似文献
995.
996.
Eftimie R Dushoff J Bridle BW Bramson JL Earn DJ 《Bulletin of mathematical biology》2011,73(12):2932-2961
Recent advances in virology, gene therapy, and molecular and cell biology have provided insight into the mechanisms through
which viruses can boost the anti-tumor immune response, or can infect and directly kill tumor cells. A recent experimental
report (Bridle et al. in Molec. Ther. 18(8):1430–1439, 2010) showed that a sequential treatment approach that involves two viruses that carry the same tumor antigen leads to an improved
anti-tumor response compared to the effect of each virus alone. In this article, we derive a mathematical model to investigate
the anti-tumor effect of two viruses, and their interactions with the immune cells. We discuss the conditions necessary for
permanent tumor elimination and, in this context, we stress the importance of investigating the long-term effect of non-linear
interactions. In particular, we discuss multi-stability and multi-instability, two complex phenomena that can cause abrupt
transitions between different states in biological and physical systems. In the context of cancer immunotherapies, the transitions
between a tumor-free and a tumor-present state have so far been associated with the multi-stability phenomenon. Here, we show
that multi-instability can also cause the system to switch from one state to the other. In addition, we show that the multi-stability
is driven by the immune response, while the multi-instability is driven by the presence of the virus. 相似文献
997.
Hernández-Hernández A Rincón-Arano H Recillas-Targa F Ortiz R Valdes-Quezada C Echeverría OM Benavente R Vázquez-Nin GH 《Chromosoma》2008,117(1):77-87
The synaptonemal complex (SC) is an evolutionarily conserved structure that mediates synapsis of homologous chromosomes during
meiotic prophase I. Previous studies have established that the chromatin of homologous chromosomes is organized in loops that
are attached to the lateral elements (LEs) of the SC. The characterization of the genomic sequences associated with LEs of
the SC represents an important step toward understanding meiotic chromosome organization and function. To isolate these genomic
sequences, we performed chromatin immunoprecipitation assays in rat spermatocytes using an antibody against SYCP3, a major
structural component of the LEs of the SC. Our results demonstrated the reproducible and exclusive isolation of repeat deoxyribonucleic
acid (DNA) sequences, in particular long interspersed elements, short interspersed elements, long terminal direct repeats,
satellite, and simple repeats. The association of these repeat sequences to the LEs of the SC was confirmed by in situ hybridization
of meiotic nuclei shown by both light and electron microscopy. Signals were also detected over the chromatin surrounding SCs
and in small loops protruding from the lateral elements into the SC central region. We propose that genomic repeat DNA sequences
play a key role in anchoring the chromosome to the protein scaffold of the SC.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
998.
Effects of high temperature coupled with high light on the balance between photooxidation and photoprotection in the sun-exposed peel of apple 总被引:4,自引:1,他引:4
The sun-exposed peel of 'Gala' apple with or without sunburn was compared in terms of photooxidation and photoprotection, and a controlled experiment was conducted to probe the initial responses of PSII to high light and high temperature. The content of carotenoids, lutein and xanthophylls on a chlorophyll basis was higher in the sunburned peel although they were lower expressed on a peel area basis. Significant loss of beta-carotene and neoxanthin was observed relative to chlorophylls in the sunburned peel. O(2) evolution rates and the activity of key enzymes in the Calvin cycle were lower in the sunburned peel, but the activity of these enzymes decreased to a lesser extent than the O(2) evolution rates. The activity of antioxidant enzymes in the ascorbate-glutathione cycle and the level of total ascorbate, total glutathione, and reduced glutathione were higher in the sunburned peel. However, the sunburned peel had higher H(2)O(2) and malondialdehyde contents. Fruit peels treated with high temperature (45 degrees C) alone showed a clear "K" step in their chlorophyll fluorescence transients whereas high temperature coupled with high light (1,600 mumol m(-2) s(-1)) led to the disappearance of the "K" step and a further decrease in F (V)/F (M) (similar to what was observed in the sunburned peel). We conclude that high temperature coupled with high light damages the PSII complexes at both the donor and acceptor sides. Although both the xanthophyll cycle and the antioxidant system are up-regulated in response to the photooxidative stress, this up-regulation does not provide enough protection against the photooxidation. 相似文献
999.
We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (Mb) whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects. 相似文献
1000.
ATP-binding cassette (ABC) transporters serve as importers and exporters for a wide variety of solutes in both prokaryotes
and eukaryotes, and are implicated in microbial drug resistance and a number of significant human genetic disorders. Initial
crystal structures of the soluble nucleotide binding domains (NBDs) of ABC transporters, while a significant step towards
understanding the coupling of ATP binding and hydrolysis to transport, presented researchers with important questions surrounding
the role of the signature sequence residues, the composition of the nucleotide binding sites, and the mode of NBD dimerization
during the transport reaction cycle. Recent studies have begun to address these concerns. This mini-review summarizes the
biochemical and structural characterizations of two archaebacterial NBDs from Methanocaldococcus jannaschii, MJ0796 and MJ1267, and offers current perspectives on the functional mechanism of ABC transporters. 相似文献