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11.
DNAase I hypersensitive sites may be correlated with genomic regions of large structural variation 总被引:7,自引:0,他引:7
Helical-twist, roll and torsion-angle variations calculated by the Calladine (1982)-Dickerson (1983) rules were scanned along several nucleotide sequences for which DNAase I cleavage data are available. It has been shown that for short synthetic oligomers DNAase I cuts preferentially at positions of high helical twist (Dickerson & Drew, 1981; Lomonossoff et al., 1981). Our calculations indicate that DNAase I sensitive and hypersensitive sites in chromatin are correlated with regions of successive, large, helical-twist angle variations from regular B-DNA. In many cases these regions exhibit large variations in base-pair roll and backbone torsion angles as well. It has been suggested that DNAase I cuts in the vicinity of cruciforms. However, it was recently demonstrated by Courey & Wang (1983) and Gellert et al. (1983) that such cruciform formation in a negatively supercoiled DNA is kinetically forbidden under physiological conditions. We thus propose that clustering of large twist-angle (and/or roll and backbone torsion angle) variations may be among the conformational features recognized by the enzyme. Specific cuts can then preferentially occur at base-pair steps with high helical twists. 相似文献
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Zolotarev Yu. A. Dadayan A. K. Kozik V. S. Nagaev I. Yu. Azev V. N. Gorbunova E. Yu. Mustaeva L. G. Bogachouk A. P. Lipkin V. M. Myasoedov N. F. 《Russian Journal of Bioorganic Chemistry》2020,46(6):1044-1051
Russian Journal of Bioorganic Chemistry - The HLDF-6 hexapeptide corresponded to the 41–46 (TGENHR) fragment of the Human Leukemia Differentiation Factor (HLDF) and exhibited a wide spectrum... 相似文献
14.
Cora E. Lewis John P. Bantle Alain G. Bertoni George Blackburn Frederick L. Brancati George A. Bray Lawrence J. Cheskin Jeffrey M. Curtis Caitlin Egan Mary Evans John P. Foreyt Siran Ghazarian Bethany Barone Gibbs Stephen P. Glasser Edward W. Gregg Helen P. Hazuda Louise Hesson James O. Hill Edward S. Horton Van S. Hubbard John M. Jakicic Robert W. Jeffery Karen C. Johnson Steven E. Kahn Abbas E. Kitabchi Dalane Kitzman William C. Knowler Edward Lipkin Sara Michaels Maria G. Montez David M. Nathan Ebenezer Nyenwe Jennifer Patricio Anne Peters Xavier Pi‐Sunyer Henry Pownall David M. Reboussin Donna H. Ryan Thomas A. Wadden Lynne E. Wagenknecht Holly Wyatt Rena R. Wing Susan Z. Yanovski 《Obesity (Silver Spring, Md.)》2020,28(2):247-258
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Pengcheng Bu Kai-Yuan Chen Joyce Huan Chen Lihua Wang Jewell Walters Yong Jun Shin Julian P. Goerger Jian Sun Mavee Witherspoon Nikolai Rakhilin Jiahe Li Herman Yang Jeff Milsom Sang Lee Warren Zipfel Moonsoo M. Jin Zeynep H. Gümüş Steven M. Lipkin Xiling Shen 《Cell Stem Cell》2013,12(5):602-615
Highlights? miR-34a regulates colon cancer stem cell asymmetric division ? miR-34a generates a sharp threshold response ? miR-34a converts Notch signaling into a toggle switch ? Binary Notch levels specify self-renewal versus differentiation 相似文献
17.
The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease
Ehud Lipkin Maria Giuseppina Strillacci Harel Eitam Moran Yishay Fausta Schiavini Morris Soller Alessandro Bagnato Ariel Shabtay 《PloS one》2016,11(4)
Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle, caused by multiple pathogens that become more virulent in response to stress. As clinical signs often go undetected and various preventive strategies failed, identification of genes affecting BRD is essential for selection for resistance. Selective DNA pooling (SDP) was applied in a genome wide association study (GWAS) to map BRD QTLs in Israeli Holstein male calves. Kosher scoring of lung adhesions was used to allocate 122 and 62 animals to High (Glatt Kosher) and Low (Non-Kosher) resistant groups, respectively. Genotyping was performed using the Illumina BovineHD BeadChip according to the Infinium protocol. Moving average of -logP was used to map QTLs and Log drop was used to define their boundaries (QTLRs). The combined procedure was efficient for high resolution mapping. Nineteen QTLRs distributed over 13 autosomes were found, some overlapping previous studies. The QTLRs contain polymorphic functional and expression candidate genes to affect kosher status, with putative immunological and wound healing activities. Kosher phenotyping was shown to be a reliable means to map QTLs affecting BRD morbidity. 相似文献
18.
Zolotarev Yu. A. Dadayan A. K. Kozik V. S. Shram S. I. Azev V. N. Bogachouk A. P. Lipkin V. M. Myasoedov N. F. 《Russian Journal of Bioorganic Chemistry》2019,45(6):514-521
Russian Journal of Bioorganic Chemistry - Pharmacokinetics of the promising antitumor peptide HLDF-6-AA (Ac-ThrGlyGluAsnHisArg-NH2) was studied using its uniformly tritiated derivative. Experiments... 相似文献
19.
Korolkova YV Kozlov SA Lipkin AV Pluzhnikov KA Hadley JK Filippov AK Brown DA Angelo K Strøbaek D Jespersen T Olesen SP Jensen BS Grishin EV 《The Journal of biological chemistry》2001,276(13):9868-9876
The isolation of the peptide inhibitor of M-type K(+) current, BeKm-1, from the venom of the Central Asian scorpion Buthus eupeus has been described previously (Fillipov A. K., Kozlov, S. A., Pluzhnikov, K. A., Grishin, E. V., and Brown, D. A. (1996) FEBS Lett. 384, 277-280). Here we report the cloning, expression, and selectivity of BeKm-1. A full-length cDNA of 365 nucleotides encoding the precursor of BeKm-1 was isolated using the rapid amplification of cDNA ends polymerase chain reaction technique from mRNA obtained from scorpion telsons. Sequence analysis of the cDNA revealed that the precursor contains a signal peptide of 21 amino acid residues. The mature toxin consists of 36 amino acid residues. BeKm-1 belongs to the family of scorpion venom potassium channel blockers and represents a new subgroup of these toxins. The recombinant BeKm-1 was produced as a Protein A fusion product in the periplasm of Escherichia coli. After cleavage and high performance liquid chromatography purification, recombinant BeKm-1 displayed the same properties as the native toxin. Three BeKm-1 mutants (R27K, F32K, and R27K/F32K) were generated, purified, and characterized. Recombinant wild-type BeKm-1 and the three mutants partly inhibited the native M-like current in NG108-15 at 100 nm. The effect of the recombinant BeKm-1 on different K(+) channels was also studied. BeKm-1 inhibited hERG1 channels with an IC(50) of 3.3 nm, but had no effect at 100 nm on hEAG, hSK1, rSK2, hIK, hBK, KCNQ1/KCNE1, KCNQ2/KCNQ3, KCNQ4 channels, and minimal effect on rELK1. Thus, BeKm-1 was shown to be a novel specific blocker of hERG1 potassium channels. 相似文献
20.
Permiakov SE Senin II Uverskiĭ VN Cherskaia AM Shul'ga-Morskoĭ SV Zinchenko DV Alekseev AM Zargarov AA Lipkin VM Filippov PP 《Bioorganicheskaia khimiia》1999,25(10):742-746
The molecule of photoreceptor Ca(2+)-binding protein recoverin contains four potential Ca(2+)-binding sites of the EF-hand type, but only two of them (the second and the third) can actually bind calcium ions. We studied the interaction of Ca2+ with recoverin and its mutant forms containing point amino acid substitutions at the working Ca(2+)-binding sites by measuring the intrinsic protein fluorescence and found that the substitution of Gln for Glu residues chelating Ca2+ in one (the second or the third) or simultaneously in both (the second and the third) Ca(2+)-binding sites changes the affinity of the protein to Ca2+ ions in different ways. The Gln for Glu121 substitution in the third site and the simultaneous Gln substitutions in the second (for Glu85) and in the third (for Glu121) sites result in the complete loss of the capability of recoverin for a strong binding of Ca(2+)-ions. On the other hand, the Gln for Glu85 substitution only in the second site moderately affects its affinity to the cation. Hence, we assumed that recoverin successively binds Ca(2+)-ions: the second site is filled with the cation only after the third site has been filled. The binding constants for the third and the second Ca(2+)-binding sites of recoverin determined by spectrofluorimetric titration are 3.7 x 10(6) and 3.1 x 10(5) M-1, respectively. 相似文献