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21.
Massive parallel analysis of
the binding specificity of histone-like protein HU to single- and
double-stranded DNA with generic oligodeoxyribonucleotide microchips 总被引:7,自引:4,他引:3
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Alexander S. Krylov Olga A. Zasedateleva Dmitry V. Prokopenko Josette Rouviere-Yaniv Andrei D. Mirzabekov 《Nucleic acids research》2001,29(12):2654-2660
A generic hexadeoxyribonucleotide microchip has been applied to test the DNA-binding properties of HU histone-like bacterial protein, which is known to have a low sequence specificity. All 4096 hexamers flanked within 8mers by degenerate bases at both the 3′- and 5′-ends were immobilized within the 100 × 100 × 20 mm polyacrylamide gel pads of the microchip. Single-stranded immobilized oligonucleotides were converted in some experiments to the double-stranded form by hybridization with a specified mixture of 8mers. The DNA interaction with HU was characterized by three type of measurements: (i) binding of FITC-labeled HU to microchip oligonucleotides; (ii) melting curves of complexes of labeled HU with single-stranded microchip oligonucleotides; (iii) the effect of HU binding on melting curves of microchip double-stranded DNA labeled with another fluorescent dye, Texas Red. Large numbers of measurements of these parameters were carried out in parallel for all or many generic microchip elements in real time with a multi-wavelength fluorescence microscope. Statistical analysis of these data suggests some preference for HU binding to G/C-rich single-stranded oligonucleotides. HU complexes with double-stranded microchip 8mers can be divided into two groups in which HU binding either increased the melting temperature (Tm) of duplexes or decreased it. The stabilized duplexes showed some preference for presence of the sequence motifs AAG, AGA and AAGA. In the second type of complex, enriched with A/T base pairs, the destabilization effect was higher for longer stretches of A/T duplexes. Binding of HU to labeled duplexes in the second type of complex caused some decrease in fluorescence. This decrease also correlates with the higher A/T content and lower Tm. The results demonstrate that generic microchips could be an efficient approach in analysis of sequence specificity of proteins. 相似文献
22.
Usdin K; Chevret P; Catzeflis FM; Verona R; Furano AV 《Molecular biology and evolution》1995,12(1):73-82
The single most difficult problem in phylogenetic analysis is deciding
whether a shared taxonomic character is due to common ancestry or one that
appeared independently due to convergence, parallelism, or reversion to an
ancestral state. Mammalian L1 retrotransposons undergo periodic
amplifications in which multiple copies of the elements are interspersed in
the genome. Because these elements apparently are transmitted only by
inheritance and are retained in the genome, a shared L1 amplification event
can only be an inherited ancestral character. We propose that L1
amplification events can be an excellent tool for analyzing mammalian
evolution and demonstrate here how we addressed several refractory problems
in rodent systematics using L1 DNA as a taxonomic character.
相似文献
23.
D. O. Fesenko T. V. Nasedkina A. V. Chudinov D. V. Prokopenko R. A. Yurasov A. S. Zasedatelev 《Molecular Biology》2005,39(1):84-89
A method was developed for producing cell biochips on the basis of calcium alginate. Cell immobilization in microvolumes of nontoxic alginate gel under mild conditions extended the range of testable micro-organisms. The possibility of studying the intracellular processes with alginate gel biochips was demonstrated in model experiments with Escherichia coli, Bordetella bronchiseptica, and Saccharomyces cerevisiae. Cell biochips proved to be suitable for simultaneous monitoring of nucleic acid and protein syntheses with two fluorescent dyes. The effect of chloramphenicol on nucleic acid synthesis was studied with five bacterial strains. Inducible synthesis of the green fluorescence protein (EGFP) in E. coli cells was monitored with the use of biochips. The level of EGFP synthesis correlated with the inductor concentration in the medium.Translated from Molekulyarnaya Biologiya, Vol. 39, No. 1, 2005, pp. 96–102.Original Russian Text Copyright © 2005 by Fesenko, Nasedkina, Chudinov, Prokopenko, Yurasov, Zasedatelev. 相似文献
24.
The activity of myeloperoxidase (MPO) was studied in chorionic and placental tissues of women with miscarriage. The MPO level reached the maximum during the first trimester both in normal pregnancy and in the case of spontaneous abortion. During gestation, the MPO level decreased in the placental tissues independently of the enzyme location. The MPO levels in the placenta during the first and second trimesters were higher in the case of spontaneous abortion than in an uncomplicated pregnancy. In the third trimester, the MPO level in the placenta was significantly lower in the case of miscarriage than in normal pregnancy ending with childbirth at term. The results suggest a close correlation between the MPO level in the placenta and the possible pregnancy outcome. 相似文献
25.
P G Prokopenko S A Borisenko O V Makarov T I Reshetova M V Fomina 《Biulleten' eksperimental'no? biologii i meditsiny》1991,111(5):528-530
Immunoenzymatic method for the determination of new ovarian-metastatic antigen-8 in human blood serum was worked out. OMA-8 level was studied in blood serum of 40 healthy women, 40 healthy men, 16 neonates, 33 pregnant women, 103 patients with genital tumours. It was found out that OMA-8 level in blood serum of healthy women changed between 2 to 15.4 micrograms/l, in men between 5-17.0 microgramS/l. OMA-8 concentration higher than 15.4 micrograms/ was considered elevated. The elevated OMA-8 level was marked in neonates (100%) and in pregnant (39.3%). High level was discovered in the amniotic fluid. 相似文献
26.
Effect of a staphylococcaL infection on the development of an immune response after physical loading
The infection of rats with staphylococci enhances the suppressing effect of physical loading on the development of immune response induced by the injection of sheep red blood cells. Intensive physical loading is accompanied by the release of the substance activating the function of splenic suppressor cells into the blood. Staphylococcal infection increases the action of the serum substance of rats performing physical work on splenic suppressor cells, as well as on the action of the suppressor factor released by these cells on immunocompetent cells. 相似文献
27.
Emanuele Crosato Li Jiang Valentin Lecheval Joseph T. Lizier X. Rosalind Wang Pierre Tichit Guy Theraulaz Mikhail Prokopenko 《Swarm Intelligence》2018,12(4):283-305
Quantifying distributed information processing is crucial to understanding collective motion in animal groups. Recent studies have begun to apply rigorous methods based on information theory to quantify such distributed computation. Following this perspective, we use transfer entropy to quantify dynamic information flows locally in space and time across a school of fish during directional changes around a circular tank, i.e., U-turns. This analysis reveals peaks in information flows during collective U-turns and identifies two different flows: an informative flow (positive transfer entropy) from fish that have already turned to fish that are turning, and a misinformative flow (negative transfer entropy) from fish that have not turned yet to fish that are turning. We also reveal that the information flows are related to relative position and alignment between fish and identify spatial patterns of information and misinformation cascades. This study offers several methodological contributions and we expect further application of these methodologies to reveal intricacies of self-organisation in other animal groups and active matter in general. 相似文献
28.
R Alan Harris Dorottya Nagy-Szakal Sabina AV Mir Eibe Frank Reka Szigeti Jess L Kaplan Jiri Bronsky Antone Opekun George D Ferry Harland Winter Richard Kellermayer 《Epigenetics》2014,9(8):1131-1137
Inflammatory bowel diseases (IBD) are emerging globally, indicating that environmental factors may be important in their pathogenesis. Colonic mucosal epigenetic changes, such as DNA methylation, can occur in response to the environment and have been implicated in IBD pathology. However, mucosal DNA methylation has not been examined in treatment-naïve patients. We studied DNA methylation in untreated, left sided colonic biopsy specimens using the Infinium HumanMethylation450 BeadChip array. We analyzed 22 control (C) patients, 15 untreated Crohn’s disease (CD) patients, and 9 untreated ulcerative colitis (UC) patients from two cohorts. Samples obtained at the time of clinical remission from two of the treatment-naïve UC patients were also included into the analysis. UC-specific gene expression was interrogated in a subset of adjacent samples (5 C and 5 UC) using the Affymetrix GeneChip PrimeView Human Gene Expression Arrays. Only treatment-naïve UC separated from control. One-hundred-and-twenty genes with significant expression change in UC (> 2-fold, P < 0.05) were associated with differentially methylated regions (DMRs). Epigenetically associated gene expression changes (including gene expression changes in the IFITM1, ITGB2, S100A9, SLPI, SAA1, and STAT3 genes) were linked to colonic mucosal immune and defense responses. These findings underscore the relationship between epigenetic changes and inflammation in pediatric treatment-naïve UC and may have potential etiologic, diagnostic, and therapeutic relevance for IBD. 相似文献
29.
Dmitry Prokopenko Julian Hecker Edwin Silverman Markus M. N?then Matthias Schmid Christoph Lange Heide Loehlein Fier 《PloS one》2015,10(6)
One of the main caveats of association studies is the possible affection by bias due to population stratification. Existing methods rely on model-based approaches like structure and ADMIXTURE or on principal component analysis like EIGENSTRAT. Here we provide a novel visualization technique and describe the problem of population substructure from a graph-theoretical point of view. We group the sequenced individuals into triads, which depict the relational structure, on the basis of a predefined pairwise similarity measure. We then merge the triads into a network and apply community detection algorithms in order to identify homogeneous subgroups or communities, which can further be incorporated as covariates into logistic regression. We apply our method to populations from different continents in the 1000 Genomes Project and evaluate the type 1 error based on the empirical p-values. The application to 1000 Genomes data suggests that the network approach provides a very fine resolution of the underlying ancestral population structure. Besides we show in simulations, that in the presence of discrete population structures, our developed approach maintains the type 1 error more precisely than existing approaches. 相似文献
30.
Terrilitin is studied for its effect on proteolytic activity of blood and formation of immunostimulating factors by spleen cells. The preparation is shown to induce isolation of the immunostimulating factor (molecular mass 10-15 kDalton) from the spleen cells. The preparation is destroyed by trypsin and RNAase and is stable to the action of lysozyme. Spleen cell factor of the animals with administered terrilitin increases general antiproteolytic activity of the blood serum and concentration of alpha 2-macroglobulins. At the same time, it decreases the general proteolytic activity and callicrein activity of blood serum for syngenic animals. 相似文献