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21.
Given a sequenceA and regular expressionR, theapproximate regular expression matching problem is to find a sequence matchingR whose optimal alignment withA is the highest scoring of all such sequences. This paper develops an algorithm to solve the problem in timeO(MN), whereM andN are the lengths ofA andR. Thus, the time requirement is asymptotically no worse than for the simpler problem of aligning two fixed sequences. Our
method is superior to an earlier algorithm by Wagner and Seiferas in several ways. First, it treats real-valued costs, in
addition to integer costs, with no loss of asymptotic efficiency. Second, it requires onlyO(N) space to deliver just the score of the best alignment. Finally, its structure permits implementation techniques that make
it extremely fast in practice. We extend the method to accommodate gap penalties, as required for typical applications in
molecular biology, and further refine it to search for substrings ofA that strongly align with a sequence inR, as required for typical data base searches. We also show how to deliver an optimal alignment betweenA andR in onlyO(N+logM) space usingO(MN logM) time. Finally, anO(MN(M+N)+N
2logN) time algorithm is presented for alignment scoring schemes where the cost of a gap is an arbitrary increasing function of
its length. 相似文献
22.
Physiological Characterization of Dicarboxylate-Induced Pleomorphic Forms of Bradyrhizobium japonicum 总被引:1,自引:0,他引:1 下载免费PDF全文
When Bradyrhizobium japonicum I-110 was transferred into medium containing 40 mM succinate or 40 mM fumarate, over 90% of the bacteria acquired a swollen, pleomorphic form similar to that of bacteroids. The induction of pleomorphism was dependent on the carbon substrate and concentration but was independent of the hydrogen ion and sodium ion concentration. Cell extracts of rod-shaped and pleomorphic cells contained enzymes required for sugar catabolism and gluconeogenesis. Variations in these enzyme profiles were correlated with the carbon source used and not with the conversion to the bacteroid-like morphology. Rod-shaped cells cultured on glucose or 10 mM succinate transported glucose and succinate; however, the pleomorphic cells behaved similarly to symbiotic bacteroids in that they lacked the ability to transport glucose and transported succinate at lower rates than did rod-shaped cells. 相似文献
23.
Helicopters can be used to collect water samples from many lakes over a wide geographic area within a relatively short time period. Here we report the results from an experiment in which sequential water samples from a lake were collected first from a nonmotorized boat and then immediately afterward from a helicopter. No significant differences were found between the means of the measurement of 20 chemical parameters for the two methods of collection. When compared to obtaining samples from a boat, collection of samples from a helicopter platform had no effect on the content of the water samples. 相似文献
24.
Sidney L. Vail Oliver D. Dailey Eugene J. Blanchard Armand B. Pepperman James L. Riopel 《Journal of Plant Growth Regulation》1990,9(1-3):77-83
Strigol and some of its synthetic precursors and analogs are known to be germination stimulants for broomrape (Orobanche ramosa) and witchweed (Striga asiatica). Fifteen synthetic terpenoids, similar in structure to one of the four rings of the strigol molecule, were evaluated in two bioassays as seed germination stimulants with broomrape, and nine were found to be active. Five of the more active compounds contained ester groups. Whereas the study was intended primarily to evaluate forced germination of broomrape by aqueous solutions, the results are almost qualitatively identical for broomrape and witchweed. Monocyclic compounds with chemical structures similar to two of the rings of strigol have now been shown to possess significant bioactivity as germination stimulants.Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the U.S. Department of Agriculture and does not imply its approval to the exclusion of other products or vendors that may also be suitable. 相似文献
25.
S D Varfolomeev 《Biokhimii?a (Moscow, Russia)》1988,53(10):1677-1683
The kinetic regularities characterizing the behaviour of enzyme-receptor systems underlying molecular mechanisms of transmission and transformation of current information at the cellular level are reviewed. The properties of receptors as molecular detectors responsible for chemical signal "recognition" are described, and the efficiency of enzyme-substrate and effector-receptor interactions is compared. The heterogeneity of receptor populations and kinetic approaches to their discrimination are considered. The principal mechanisms and problems of chemical signal amplification in coupled enzymatic reactions are discussed. The major properties of the ligand-receptor system and its relation to gene expression in receptors as well as mechanisms of cell response "quenching" are reviewed. Some kinetic regularities of desensitization of enzyme-receptor systems are discussed in terms of present-day concepts on desensitization as inactivation of enzyme-receptor systems in the reaction course. 相似文献
26.
Sequence comparison with concave weighting functions 总被引:2,自引:0,他引:2
We consider efficient methods for computing a difference metric between two sequences of symbols, where the cost of an operation
to insert or delete a block of symbols is a concave function of the block's length. Alternatively, sequences can be optimally
aligned when gap penalties are a concave function of the gap length. Two algorithms based on the ‘candidate list paradigm’
first used by Waterman (1984) are presented. The first computes significantly more parsimonious candidate lists than Waterman's
method. The second method refines the first to the point of guaranteeingO(N
2
lgN) worst-case time complexity, and under certain conditionsO(N
2). Experimental data show how various properties of the comparison problem affect the methods' relative performance. A number
of extensions are discussed, among them a technique for constructing optimal alignments inO(N) space in expectation. This variation gives a practical method for comparing long amino sequences on a small computer.
This work was supported in part by NSF Grant DCR-8511455. 相似文献
27.
Optimal alignments in linear space 总被引:40,自引:0,他引:40
Space, not time, is often the limiting factor when computingoptimal sequence alignments, and a number of recent papers inthe biology literature have proposed space-saving strategies.However, a 1975 computer science paper by Hirschberg presenteda method that is superior to the new proposals, both in theoryand in practice. The goal of this paper is to give Hirschberg'sidea the visibility it deserves by developing a linear-spaceversion of Gotoh's algorithm, which accommodates affine gappenalties. A portable C-software package implementing this algorithmis available on the BIONET free of charge.
Received on October 14, 1987; accepted on December 19, 1987 相似文献
28.
Eugene M. Rinchik Terry Magnuson Bernadette Holdener-Kenny Gavin Kelsey Albert Bianchi Claudio J. Conti Fran?ois Chartier Kathryn A. Brown Stephen D. M. Brown Josephine Peters 《Mammalian genome》1992,3(Z1):S104-S120
Chair of Committee for Mouse Chromosome 7 相似文献
29.
Comparison of the roles of Ostracods and Cladocerans in regulating community structure and metabolism in freshwater microcosms 总被引:1,自引:1,他引:0
Laboratory microcosms were used to compare the effects of the littoral ostracod Cypridopsis vidua and the planktonic cladoceran Daphnia magna on community structure and metabolism. Filter-feeding by cladocerans, both in the presence and absence of ostracods, greatly
reduced the abundance of planktonic algae when D. magna reached peak density around day 50; rotifers and euglenids were then limited to flocculent matter on the container bottom.
Both net production and community respiration rates decreased as community composition changed. Microcosms containing ostracods
as the only microcrustacean showed little reduction in total algal numbers but the otherwise dominant alga, Scenedesmus spp., was replaced by Ankistrodesmus spp. when peak ostracod density was reached around day 100. Rotifers were completely eliminated but euglenids were able to
coexist with ostracods. Ostracods impacted community metabolism less than cladocerans, but depressed respiration slightly
more than net production. 相似文献
30.
Cloning and expression of a tylosin resistance gene from a tylosin-producing strain of Streptomyces fradiae 总被引:1,自引:0,他引:1
Virginia A. Birmingham Karen L. Cox Jeffrey L. Larson Scott E. Fishman Charles L. Hershberger Eugene T. Seno 《Molecular & general genetics : MGG》1986,204(3):532-539
Summary A gene conferring high-level resistance to tylosin in Streptomyces lividans and Streptomyces griseofuscus was cloned from a tylosin-producing strain of Streptomyces fradiae. The tylosin-resistance (Tylr) gene (tlrA) was isolated on five overlapping DNA fragments which contained a common 2.6 Kb KpnI fragment. The KpnI fragment contained all of the information required for the expression of the Tylr phenotype in S. lividans and S. griseofuscus. Southern hybridization indicated that the sequence conferring tylosin resistance was present on the same 5 kb SalI fragment in genomic DNA from S. fradiae and several tylosin-sensitive (Tyls) mutants. The cloned tlrA gene failed to restore tylosin resistance in two Tyls mutants derived by protoplast formation and regeneration, and it restored partial resistance in a Tyls mutant obtained by N-methyl-N-nitro-N-nitrosoguanidine (MNNG) mutagenesis. The tlrA gene conferred resistance to tylosin, carbomycin, niddamycin, vernamycin-B and, to some degree, lincomycin in S. griseofuscus, but it had no effect on sensitivity to streptomycin or spectinomycin, suggesting that the cloned gene is an MLS (macrolide, lincosamide, streptogramin-B)-resistance gene. Twenty-eight kb of S. fradiae DNA surrounding the tlrA gene was isolated from a genomic library in bacteriophage Charon 4. Introduction of these DNA sequence into S. fradiae mutants blocked at different steps in tylosin biosynthesis failed to restore tylosin production, suggesting that the cloned Tylr gene is not closely linked to tylosin biosynthetic genes. 相似文献