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2.
G J Blomquist M A Major J B Lok 《Biochemical and biophysical research communications》1975,64(1):43-50
The biosynthesis of 3-methylalkanes was investigated in the cockroach . Between 0.2 and 0.3 percent of the labelled acetate and propionate injected into the insect was incorporated into the cuticular hydrocarbons, compared to 0.01 percent for labelled isoleucine. Twenty-three ± four percent of the [2-14C]acetate, 42 ± 3 and 44 ± 4 percent of the [2-14C] and [3-14C]propionate, and 75 ± 5 percent of the [1-14C]propionate incorporated into the cuticular hydrocarbons was found in 3-methylpentacosane. These results indicate that propionate serves as the source of the branching methyl group, suggesting a pathway in which this precursor is incorporated during the penultimate step in 3-methylalkane biosynthesis in insects. 相似文献
3.
Victor A. Kostyuchenko Qian Zhang Joanne L. Tan Thiam-Seng Ng Shee-Mei Lok 《Journal of virology》2013,87(13):7700-7707
Dengue virus is a major human pathogen that has four serotypes (DENV1 to -4). Here we report the cryoelectron microscopy (cryo-EM) structures of immature and mature DENV1 at 6- and 4.5-Å resolution, respectively. The subnanometer-resolution maps allow accurate placement of all of the surface proteins. Although the immature and mature viruses showed vastly different surface protein organizations, the envelope protein transmembrane (E-TM) regions remain in similar positions. The pivotal role of the E-TM regions leads to the identification of the start and end positions of all surface proteins during maturation. 相似文献
4.
Guntur Fibriansah Thiam-Seng Ng Victor A. Kostyuchenko Jaime Lee Sumarlin Lee Jiaqi Wang Shee-Mei Lok 《Journal of virology》2013,87(13):7585-7592
Previous binding studies of antibodies that recognized a partially or fully hidden epitope suggest that insect cell-derived dengue virus undergoes structural changes at an elevated temperature. This was confirmed by our cryo-electron microscopy images of dengue virus incubated at 37°C, where viruses change their surface from smooth to rough. Here we present the cryo-electron microscopy structures of dengue virus at 37°C. Image analysis showed four classes of particles. The three-dimensional (3D) map of one of these classes, representing half of the imaged virus population, shows that the E protein shell has expanded and there is a hole at the 3-fold vertices. Fitting E protein structures into the map suggests that all of the interdimeric and some intradimeric E protein interactions are weakened. The accessibility of some previously found cryptic epitopes on this class of particles is discussed. 相似文献
5.
Shabana Vohra Maria Musgaard Luet‐Lok Wong Weihong Zhou Philip C. Biggin 《Protein science : a publication of the Protein Society》2013,22(9):1218-1229
The recent crystal structures of CYP101D2, a cytochrome P450 protein from the oligotrophic bacterium Novosphingobium aromaticivorans DSM12444 revealed that both the native (substrate‐free) and camphor‐soaked forms have open conformations. Furthermore, two other potential camphor‐binding sites were also identified from electron densities in the camphor‐soaked structure, one being located in the access channel and the other in a cavity on the surface near the F‐helix side of the F‐G loop termed the substrate recognition site. These latter sites may be key intermediate positions on the pathway for substrate access to or product egress from the active site. Here, we show via the use of unbiased atomistic molecular dynamics simulations that despite the open conformation of the native and camphor‐bound crystal structures, the underlying dynamics of CYP101D2 appear to be very similar to other CYP proteins. Simulations of the native structure demonstrated that the protein is capable of sampling many different conformational substates. At the same time, simulations with the camphor positioned at various locations within the access channel or recognition site show that movement towards the active site or towards bulk solvent can readily occur on a short timescale, thus confirming many previously reported in silico studies using steered molecular dynamics. The simulations also demonstrate how the fluctuations of an aromatic gate appear to control access to the active site. Finally, comparison of camphor‐bound simulations with the native simulations suggests that the fluctuations can be of similar level and thus are more representative of the conformational selection model rather than induced fit. 相似文献
6.
Abstract An efficient alternative which makes use of the reliable 3J1′2′. value to derive the endocyclic torsion angle constraints is proposed in this study. Based on the information embedded in the two plots, (i) the vicinal proton-proton J-couplings, 3J1′2′., 3J1′2″., 3J2′3′., 3J2”3′ and 3J3′4′ against the pseudorotation phase angle, and (ii) 3J1′2″, 3J2′3′., 3J2″3′ and 3J3′4′ against 3J1′2′; using the calculated J-couplings obtained for a range of sugar geometries of deoxyribose ring in nucleosides and nucleotides encountered along the pseudorotation itinerary [J. van Wijk, B.D. Huckriede, J.H. Ippel and C. Altona, Methods Enzymol. 211, 286–306 (1992)], it is suggested that the vicinal 3J1′2′ possesses structural information other than the vicinal torsion angle φ1′2′. This study is divided into two parts. In Part I, a correlation diagram between the endocyclic torsion angles vi (i=0,1,2,3,4) and the restrained vicinal torsion angle φ1′2′ is obtained through the use of the J-coupling restrained molecular mechanics (JrMM) protocol. The established φ1′2′.-vi correlation shows vi can be deduced from the reliable 3J1′2′. value and it forms the basis for developing an alternative protocol to derive endocyclic torsion angle constraints. In Part II of this series, extensive testing demonstrating the validity of the JrMM protocol to derive Vi for defining the sugar geometry of solution DNA molecules is presented. 相似文献
7.
Electrolyte filtration arises due to the presence of fixed charges in cartilage extracellular matrix glycosaminoglycans (GAGs). Commonly assumed negligible, it can be important for design and interpretation of streaming potential measurements and modeling assumptions. To quantify the scale of this phenomenon, chloride ion concentration in exudate of compressed cartilage was measured by Mohr’s titration and explant GAG content was colorimetrically assayed. Pilot studies indicated that an appropriate strain rate for experiments was 8 × 10−3 s−1 to eliminate concerns of exudate evaporation and explant damage (at low and high strain rates, respectively). Exudate chloride concentration of explants equilibrated in 1× PBS was significantly (p < 0.05) lower than the bath chloride concentration at strains of 37.5, 50, and 62.5%, with clear dependence on strain magnitude. Exudate chloride concentration was also significantly lower than that of the bath when 50% strain was applied after equilibration in 0.5, 1, and 2× PBS, with a trend for an increase in this relative difference with decreasing bath concentration (p = 0.065 between 0.5 and 2× PBS). Decreasing exudate chloride concentration correlated negatively with increasing postcompression GAG concentration. No difference between exudate chloride concentration and bath chloride concentration was ever observed for compression of uncharged agarose gel controls. Findings show that exudate from compressed cartilage is dilute relative to the bath due to the presence of matrix fixed charges, and this difference can generate diffusion potentials external to the explant, which may affect streaming potential measurements particularly under conditions of low strain rates and high strains. 相似文献
8.
Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km2 region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes (=wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete. 相似文献
9.
In recent years, PCR-based pyrosequencing of 16S rRNA genes has continuously increased our understanding of complex microbial communities in various environments of the Earth. However, there is always concern on the potential biases of diversity determination using different 16S rRNA gene primer sets and covered regions. Here, we first report how bacterial 16S rRNA gene pyrotags derived from a series of different primer sets resulted in the biased diversity metrics. In total, 14 types of pyrotags were obtained from two-end pyrosequencing of 7 amplicon pools generated by 7 primer sets paired by 1 of 4 forward primers (V1F, V3F, V5F, and V7F) and 1 of 4 reverse primers (V2R, V4R, V6R, and V9R), respectively. The results revealed that: i) the activated sludge exhibited a large bacterial diversity that represented a broad range of bacterial populations and served as a good sample in this methodology research; ii) diversity metrics highly depended on the selected primer sets and covered regions; iii) paired pyrotags obtained from two-end pyrosequencing of each short amplicon displayed different diversity metrics; iv) relative abundance analysis indicated the sequencing depth affected the determination of rare bacteria but not abundant bacteria; v) the primer set of V1F and V2R significantly underestimated the diversity of activated sludge; and vi) the primer set of V3F and V4R was highly recommended for future studies due to its advantages over other primer sets. All of these findings highlight the significance of this methodology research and offer a valuable reference for peer researchers working on microbial diversity determination. 相似文献
10.
Roel J. T. Mocking Anja Lok Johanna Assies Maarten W. J. Koeter Ieke Visser Henricus G. Ruhé Claudi L. H. Bockting Aart H. Schene 《PloS one》2013,8(12)