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81.
Annette Masuch Kathrin Budde Gabi Kastenmüller Anna Artati Jerzy Adamski Henry Vlzke Matthias Nauck Maik Pietzner 《Journal of cellular and molecular medicine》2019,23(8):5144-5153
Metabolomics studies now approach large sample sizes and the health characterization of the study population often include complete blood count (CBC) results. Upon careful interpretation the CBC aids diagnosis and provides insight into the health status of the patient within a clinical setting. Uncovering metabolic signatures associated with parameters of the CBC in apparently healthy individuals may facilitate interpretation of metabolomics studies in general and related to diseases. For this purpose 879 subjects from the population‐based Study of Health in Pomerania (SHIP)‐TREND were included. Using metabolomics data resulting from mass‐spectrometry based measurements in plasma samples associations of specific CBC parameters with metabolites were determined by linear regression models. In total, 118 metabolites significantly associated with at least one of the CBC parameters. Strongest associations were observed with metabolites of heme degradation and energy production/consumption. Inverse association seen with mean corpuscular volume and mean corpuscular haemoglobin comprised metabolites potentially related to kidney function. The presently identified metabolic signatures are likely derived from the general function and formation/elimination of blood cells. The wealth of associated metabolites strongly argues to consider CBC in the interpretation of metabolomics studies, in particular if mutual effects on those parameters by the disease of interest are known. 相似文献
82.
It is well proved that the probability that a protein interacts with itself is higher than that it interacts with another protein. It has been recently shown that the probability of interaction is also higher for proteins with significant sequence similarity. In this paper we show that proteins sharing identical PFAM domains interact more often than expected by chance in Saccharomyces cerevisiae and Escherichia coli. We also analyze the variety of domain interfaces used by homologous proteins to interact and show that the overrepresentation of interactions between homological proteins is not caused by small number of pairs of identical "sticky domains" shared between interacting proteins. 相似文献
83.
Dyguda-Kazimierowicz E Sokalski WA Leszczyński J 《Journal of molecular modeling》2007,13(6-7):839-849
The subject of this study was an analysis of the role of active site residues in the phosphoryl transfer reaction catalyzed
by 4-methyl-5-β-hydroxyethylthiazole kinase (ThiK). The ThiK-catalyzed reaction is of special interest due to the lack of
a highly conserved aspartate residue serving as a catalytic base. ONIOM(B3LYP:PM3) models of stationary points along the reaction
pathway consisted of reactants, two magnesium ions and several highly conserved ThiK active site residues. The results indicate
that an SN2-like mechanism of ThiK, with γ-phosphate acting as an alcohol-activating base is reasonable. Geometries of substrates, transition
state and products were utilized in the non-empirical analysis of the physical nature of catalytic interactions taking place
in the ThiK active site. The role of particular residues was investigated in terms of their ability to preferentially stabilize
the transition state relative to substrates (differential transition state stabilization, DTSS) or products (differential
product stabilization, DPS). It seems that Mg2, Glu126 and Cys198 play a major catalytic role, whereas Mg1 and the same Cys198
are responsible for product release. It is remarkable that no dominant role of an electrostatic term in the interactions involved
in catalytic activity is observed for product release. Determination of catalytic fields expressing differential electrostatic
potential of the transition state with respect to substrates revealed the optimal electrostatic features of an ideal catalyst
for the studied reaction. The predicted catalytic environment is in agreement with experimental data showing increased catalytic
activity of ThiK upon mutation of Cys198 to aspartate.
Figure Catalytic fields for ThiK-catalyzed reaction juxtaposed with the positions of active site residues of a model system. Magnesium
ions are considered part of the transition state/reactants. The surface of constant electronic density is colored according
to differential electrostatic potential of transition state with respect to reactants. The sign of the differential potential
reflects the electrostatic properties of a complementary molecular environment. Red (green) color denotes regions where a negative (positive) charge would be optimal for catalytic activity 相似文献
84.
Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin 总被引:1,自引:0,他引:1
Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed. 相似文献
85.
Hao Jie Wong Nuradilla Mohamad-Fauzi Mohammed Rizman-Idid Peter Convey Jerzy Smykla Siti Aisyah Alias 《Environmental microbiology》2022,24(7):3164-3180
Solar radiation regulates most biological activities on Earth. Prolonged exposure to solar UV radiation can cause deleterious effects by inducing two major types of DNA damage, namely, cyclobutane pyrimidine dimers (CPDs) and pyrimidine 6-4 pyrimidone photoproducts. These lesions may be repaired by the photoreactivation (Phr) and nucleotide excision repair (NER) pathways; however, the principal UV-induced DNA repair pathway is not known in the fungal genus Pseudogymnoascus. In this study, we demonstrated that an unweighted UV-B dosage of 1.6 kJ m−2 d−1 significantly reduced fungal growth rates (by between 22% and 35%) and inhibited conidia production in a 10 d exposure. The comparison of two DNA repair conditions, light or dark, which respectively induced photoreactivation (Phr) and NER, showed that the UV-B-induced CPDs were repaired significantly more rapidly in light than in dark conditions. The expression levels of two DNA repair genes, RAD2 and PHR1 (encoding a protein in NER and Phr respectively), demonstrated that NER rather than Phr was primarily activated for repairing UV-B-induced DNA damage in these Pseudogymnoascus strains. In contrast, Phr was inhibited after exposure to UV-B radiation, suggesting that PHR1 may have other functional roles. We present the first study to examine the capability of the Arctic and Antarctic Pseudogymnoascus sp. to perform photoreactivation and/or NER via RT-qPCR approaches, and also clarify the effects of light on UV-B-induced DNA damage repair in vivo by quantifying cyclobutene pyrimidine dimers and pyrimidine 6-4 pyrimidone photoproducts. Physiological response data, including relative growth rate, pigmentation and conidia production in these Pseudogymnoascus isolates exposed to UV-B radiation are also presented. 相似文献
86.
87.
This article presents the results of studies on the pyrenes of selected European brambles belonging to different subgenera and sections of the genus Rubus. Differences between the pyrenes of particular species are mainly visible in their shape, size and the outer endocarp sculpture. Numerous SEM photographs revealed that the differentiation of the endocarp surface is due to variations in a thin layer of transition sclereids developing between the outer endocarp and a mesocarp parenchyma. The endocarp structure of the genus Rubus can be used in determining some species belonging to different subgenera, even if generally its significance in the taxonomy of the European Rubus is limited. 相似文献
88.
Jerzy K. Kulski David S. Dunn Silvana Gaudieri Takashi Shiina Hidetoshi Inoko 《Journal of molecular evolution》2001,53(6):642-650
The human CD1 proteins belong to a lipid-glycolipid antigen-presenting gene family and are related in structure and function to the MHC class I molecules. Previous mapping and DNA hybridization studies have shown that five linked genes located within a cluster on human chromosome 1q22-23 encode the CD1 protein family. We have analyzed the complete genomic sequence of the human CD1 gene cluster and found that the five active genes are distributed over 175,600 nucleotides and separated by four expanded intervening genomic regions (IGRs) ranging in length between 20 and 68 kb. The IGRs are composed mostly of retroelements including five full-length L1 PA sequences and various pseudogenes. Some L1 sequences have acted as receptors for other subtypes or families of retroelements. Alu molecular clocks that have evolved during primate history are found distributed within the HLA class I duplicated segments (duplicons) but not within the duplicons of CD1. Phylogeny of the alpha3 domain of the class I-like superfamily of proteins shows that the CD1 cluster is well separated from HLA class I by a number of superfamily members including MIC (PERB11), HFE, Zn-alpha2-GP, FcRn, and MR1. Phylogenetically, the human CD1 sequences are interspersed by CD1 sequences from other mammalian species, whereas the human HLA class I sequences cluster together and are separated from the other mammalian sequences. Genomic and phylogenetic analyses support the view that the human CD1 gene copies were duplicated prior to the evolution of primates and the bulk of the HLA class I genes found in humans. In contrast to the HLA class I genomic structure, the human CD1 duplicons are smaller in size, they lack Alu clocks, and they are interrupted by IGRs at least 4 to 14 times longer than the CD1 genes themselves. The IGRs seem to have been created as "buffer zones" to protect the CD1 genes from disruption by transposable elements. 相似文献
89.
Kaleczyc J Timmermans JP Majewski M Lakomy M Scheuermann DW 《Histochemistry and cell biology》1999,111(3):217-228
Immunohistochemical studies have been performed to investigate the occurrence and coexistence of two catecholamine-synthesising
enzymes, tyrosine hydroxylase and dopamine-β-hydroxylase, and several neuropeptides, including neuropeptide Y, vasoactive
intestinal polypeptide, Leu5-enkephalin, somatostatin, calcitonin gene-related peptide and substance P, in nerve fibres supplying porcine accessory genital
glands, the seminal vesicles, prostate (body and the disseminated part) and bulbourethral glands. Three major populations
of nerve fibres supplying non-vascular elements of the glands have been distinguished (from the largest to the smallest one):
(1) noradrenergic fibres, the majority of which contain Leu5-enkephalin, neuropeptide Y or, to a lesser extent, somatostatin, (2) non-noradrenergic, putative cholinergic fibres containing
vasoactive intestinal polypeptide, neuropeptide Y and/or somatostatin and, (3) non-noradrenergic, presumably sensory fibres,
containing calcitonin gene-related peptide and substance P. Whilst the coexistence patterns within nerves supplying particular
glands are similar, the density of innervation varies between the organs. The innervation of the seminal vesicles and prostatic
body is more developed than that of the disseminated part of the prostate and bulbourethral glands. The majority of noradrenergic
fibres related to blood vessels contain neuropeptide Y only, while the non-noradrenergic nerves contain mainly vasoactive
intestinal polypeptide. The possible function and origin of particular nerve fibre populations are discussed.
Accepted: 16 November 1998 相似文献
90.
We have found that in isolated spinach thylakoids, plastoquinone-pool (PQ-pool), after its photoreduction, undergoes dark-reoxidation with the half-time of 1/2 = 43 ± 3 s. To explain the observed rates of PQ-pool reoxidation, a nonenzymatic plastoquinol (PQH2) autoxidation under molecular oxygen and an enzymatic oxidation by the low-potential form of cytochrome b-559 (cyt. b-559LP), as the postulated PQ-oxidase in chlororespiration, were investigated. It was found that the autoxidation rate of PQH2 in organic solvents and liposomes was too low to account for the observed oxidation rate of PQH2 in thylakoids. The rate of cyt. b-559LP autoxidation in isolated Photosystem II was found to be similar (1/2 = 26 ± 5 s) to that of the PQ-pool. This suggests that the LP form of cyt. b-559 is probably responsible for the PQ-oxidase activity observed during chlororespiration. 相似文献