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Background
Almost 16,000 human long non-coding RNA (lncRNA) genes have been identified in the GENCODE project. However, the function of most of them remains to be discovered. The function of lncRNAs and other novel genes can be predicted by identifying significantly enriched annotation terms in already annotated genes that are co-expressed with the lncRNAs. However, such approaches are sensitive to the methods that are used to estimate the level of co-expression.Results
We have tested and compared two well-known statistical metrics (Pearson and Spearman) and two geometrical metrics (Sobolev and Fisher) for identification of the co-expressed genes, using experimental expression data across 19 normal human tissues. We have also used a benchmarking approach based on semantic similarity to evaluate how well these methods are able to predict annotation terms, using a well-annotated set of protein-coding genes.Conclusion
This work shows that geometrical metrics, in particular in combination with the statistical metrics, will predict annotation terms more efficiently than traditional approaches. Tests on selected lncRNAs confirm that it is possible to predict the function of these genes given a reliable set of expression data. The software used for this investigation is freely available.83.
Elahe Seyed Hosseini Rezvan Moniri Yasaman Dasteh Goli Hamed Haddad Kashani 《Probiotics and antimicrobial proteins》2016,8(4):202-210
Therapeutic LysK-CHAP is a potent anti-staphylococcal protein that could be utilized as an antibiotic substitute. Intein-mediated protein purification is a reasonable and cost-effective method that is most recently used for recombinant therapeutic protein production. Intein (INT) is the internal parts of the protein that can be separated from the immature protein during protein splicing process. This sequence requires no specific enzyme or cofactor for separation. INT sequence and their characteristic of self-cleavage by thiol induction, temperature, and pH changes are used for protein purification. The current study presents the expression of CHAPK262 domain of LysK gene that is fused with INT/chitin-binding sequence while evaluating its purification procedure and antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). The coding gene sequence of LysK-CHAP (CHAPK262) in pET22-b was amplified with polymerase chain reaction (PCR); the digested product was then cloned into the pTXB1 vector. Electrophoresis confirmed the cloning accuracy of the gene. The pTXB1-CHAPK262 plasmid was transformed to the Escherichia coli ER2566 (E. coli ER2566) expression strain and analyzed for expression of the recombinant protein by SDS-PAGE and Western blotting methods. Finally, CHAPK262 was purified by chitin affinity column using INT tag technology and confirmed by SDS-PAGE. Lytic activity of the purified protein was investigated by disk diffusion method. Cloning of CHAPK262 into the pTXB1 vector, which comprised INT/chitin-binding sequence, was successfully achieved. The SDS-PAGE data also revealed successful expression of the CHAPK262-INT fusion protein and Western blotting method validated the accuracy of the protein. Moreover, purification of CHAPK262 protein was induced by dithiothreitol (DTT) and confirmed by SDS-PAGE. Finally, inhibition zone in MRAS culture medium confirmed antibacterial activity of the protein. Application of intein-mediated antibacterial protein is an appropriate and streamlined method for one-step purification of CHAPK262 as a therapeutic and antibacterial protein. Self-cleaving tags like intein are cost-effective and could be used as a proper purification method for industrial purposes. 相似文献
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Marcel GA van der Heijden Susanne de Bruin Ludo Luckerhoff Richard SP van Logtestijn Klaus Schlaeppi 《The ISME journal》2016,10(2):389-399
Highly diverse microbial assemblages colonize plant roots. It is still poorly understood whether different members of this root microbiome act synergistically by supplying different services (for example, different limiting nutrients) to plants and plant communities. In order to test this, we manipulated the presence of two widespread plant root symbionts, arbuscular mycorrhizal fungi and nitrogen-fixing rhizobia bacteria in model grassland communities established in axenic microcosms. Here, we demonstrate that both symbionts complement each other resulting in increased plant diversity, enhanced seedling recruitment and improved nutrient acquisition compared with a single symbiont situation. Legume seedlings obtained up to 15-fold higher productivity if they formed an association with both symbionts, opposed to productivity they reached with only one symbiont. Our results reveal the importance of functional diversity of symbionts and demonstrate that different members of the root microbiome can complement each other in acquiring different limiting nutrients and in driving important ecosystem functions. 相似文献
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Chizari Atieh Hassanpour Rezvan Karimi-haghighi Saeideh Azizbeigi Ronak Mesgar Somaye Mousavi Zahra Haghparast Abbas 《Neurochemical research》2022,47(6):1565-1573
Neurochemical Research - Insulin receptors are distributed in the whole brain, including different parts of the reward circuit that modulate dopamine as the primary neurotransmitter implicated in... 相似文献
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Mona Pourjafar Massoud Saidijam Katayoon Etemadi Rezvan Najafi 《Biotechnology letters》2017,39(8):1263-1268
Objectives
To investigate the effect of all-trans retinoic acid (ATRA) on caspase 3 activity, matrix metalloproteinase 2 (MMP-2), and MMP-9 expression and activity as well as in vitro rat bone marrow-derived mesenchymal stem cells (MSCs) migration.Results
The expression of the MMP-2/-9 was at least five times higher in ATRA-treated MSCs (P < 0.001), and MMP-2/-9 activity was enhanced with increasing doses compared to the control MSCs. The caspase three activity was attenuated by ATRA preconditioning. Scratch test showed that ATRA could promote the migration capacity of the MSCs compared to the untreated MSCs in a dose-dependent manner.Conclusion
ATRA increases the in vitro migration capacity of the MSCs through stimulating the expression and activity of MMP-2/-9 and inhibiting caspase three enzyme activity.90.
Rahil Eftekhari Rezvan Esmaeili Reza Mirzaei Katayoon Bidad Stacy de Lima Maryam Ajami Hedayatollah Shirzad Jamshid Hadjati Keivan Majidzadeh-A 《Cancer cell international》2017,17(1):123