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71.
The transgeneticist's toolbox: novel methods for the targeted modification of eukaryotic genomes 总被引:1,自引:0,他引:1
Bode J Schlake T Iber M Schübeler D Seibler J Snezhkov E Nikolaev L 《Biological chemistry》2000,381(9-10):801-813
Classical techniques for gene transfer into mammalian cells involve tedious screening procedures to identify transgenic clones or animals with the appropriate level and stability of expression or with the correct developmental patterns. These first generation technologies are clearly inadequate for complex genetic strategies by which gene regulation can be studied in its entire complexity. While site-specific insertions can principally be achieved by homologous recombination or by adapting the recombination apparatus from phages or yeast, these methods usually lack the required efficiency or they perturb expression patterns by the co-insertion of prokaryotic vector parts. Virtually all of these problems can be overcome by recombinase-mediated cassette exchange (RMCE) techniques which cleanly replace a resident cassette that is flanked by two hetero-specific recombination target sites for a second cassette with the analogous design, presented on a targeting vector. After illustrating the fundamentals of site-specific recombination by selected experiments, the authors (arranged in the chronological order of their contribution) will describe their efforts to develop RMCE into a method of wide applicability. Further developments that have been initiated utilizing the particular potential of the RMCE principle will be outlined. 相似文献
72.
Two new bisnaphthalene compounds, sphaerolone (1) and dihydrosphaerolone (2), together with 2-hydroxyjuglone (9), were isolated from the culture broth of a Sphaeropsidales sp. (strain F-24'707) after inhibition of the regular proceeding 1,8-dihydroxynaphthalene (DHN) biosynthesis with tricyclazole. The structures of 1 and 2 were established by detailed spectroscopic analysis and present novel bisnaphthalenes. The biosynthetic origin of 1 and 2 as dimerization products of 1,3,8-trihydroxynaphthalene, an intermediate of the DHN biosynthesis, is discussed. 相似文献
73.
Sommerhoff CP Bode W Matschiner G Bergner A Fritz H 《Biochimica et biophysica acta》2000,1477(1-2):75-89
Tryptases, the predominant proteins of human mast cells, have been implicated as pathogenetic mediators of allergic and inflammatory conditions, most notably asthma. Until recently, the fascinating properties that distinguish tryptases among the serine proteinases, particularly their activity as a heparin-stabilized tetramer, resistance to most proteinaceous inhibitors, and preference for peptidergic over macromolecular substrates presented a riddle. This review solves this riddle with the help of the crystal structure of the human beta(2)-tryptase tetramer, but also indicates controversies between the unique quaternary architecture and some experimental data. 相似文献
74.
Gerard H. Bode Karin E. Pickl Maria Sanchez-Purrà Berta Albaiges Salvador Borrós Andy J. G. P?tgens Christoph Schmitz Frank M. Sinner Mario Losen Harry W. M. Steinbusch Hans-Georg Frank Pilar Martinez-Martinez European NanoBioPharmaceutics Research Initiative 《PloS one》2015,10(5)
AimsThe aim of the current study was to develop a method to detect peptide-linked nanoparticles in blood plasma.ResultsThe ELISA based method for the detection of FITC labeled peptides had a detection limit of 1 ng/mL. We were able to accurately measure peptides bound to pentafluorophenyl methacrylate nanoparticles in blood plasma of rats, and similar results were obtained by LC/MS.ConclusionsWe detected FITC-labeled peptides on pentafluorophenyl methacrylate nanoparticles after injection in vivo. This method can be extended to detect nanoparticles with different chemical compositions. 相似文献
75.
Stephanie Nikolaus Christina Bode Erik Taal Harald E. Vonkeman Cees A. W. Glas Mart A. F. J. van de Laar 《PloS one》2015,10(12)
Objective
Multidimensional computerized adaptive testing enables precise measurements of patient-reported outcomes at an individual level across different dimensions. This study examined the construct validity of a multidimensional computerized adaptive test (CAT) for fatigue in rheumatoid arthritis (RA).Methods
The ‘CAT Fatigue RA’ was constructed based on a previously calibrated item bank. It contains 196 items and three dimensions: ‘severity’, ‘impact’ and ‘variability’ of fatigue. The CAT was administered to 166 patients with RA. They also completed a traditional, multidimensional fatigue questionnaire (BRAF-MDQ) and the SF-36 in order to examine the CAT’s construct validity. A priori criterion for construct validity was that 75% of the correlations between the CAT dimensions and the subscales of the other questionnaires were as expected. Furthermore, comprehensive use of the item bank, measurement precision and score distribution were investigated.Results
The a priori criterion for construct validity was supported for two of the three CAT dimensions (severity and impact but not for variability). For severity and impact, 87% of the correlations with the subscales of the well-established questionnaires were as expected but for variability, 53% of the hypothesised relations were found. Eighty-nine percent of the items were selected between one and 137 times for CAT administrations. Measurement precision was excellent for the severity and impact dimensions, with more than 90% of the CAT administrations reaching a standard error below 0.32. The variability dimension showed good measurement precision with 90% of the CAT administrations reaching a standard error below 0.44. No floor- or ceiling-effects were found for the three dimensions.Conclusion
The CAT Fatigue RA showed good construct validity and excellent measurement precision on the dimensions severity and impact. The dimension variability had less ideal measurement characteristics, pointing to the need to recalibrate the CAT item bank with a two-dimensional model, solely consisting of severity and impact. 相似文献76.
Light has a profound influence on ochratoxin biosynthesis by Penicillia. When incubated under constant daylight of a certain
intensity, ochratoxin A biosynthesis is decreased by about 20–30% compared to incubation under constant darkness. Under day/night
oscillation, the ochratoxin A polyketide synthase gene, a key gene of the ochratoxin A biosynthesis pathway, is rhythmically
expressed, and moreover, the amount of ochratoxin also oscillates between the amounts produced either during constant darkness
or during constant light. This indicates a partial degradation of ochratoxin A (20–30%) under light conditions until a certain
lower limit is reached. This behavior is dependent on the light intensity. At 1,600 Lux, only weak effects could be observed;
however, at 2,800 Lux, the effects became significant. After growth under constant light conditions, Penicillium produced ochratoxin B at amounts which are 5 times higher than after growth in constant dark or in alternating light/dark
conditions. Growth experiments in the dark on medium with increasing amounts of ochratoxin A revealed that externally applied
ochratoxin is moderately toxic. However, if the same growth experiments are carried out under light conditions, the growth
inhibiting activity of ochratoxin A is greatly increased, indicating that light amplifies the toxic activity of ochratoxin.
Because of the oscillation of the concentration of ochratoxin A during night and day incubation, Penicillium seems to have developed an adaptive mechanism to reduce the amount of ochratoxin A during daylight below a toxic level. 相似文献
77.
Fiki AE Metabteb GE Bellebna C Wartmann T Bode R Gellissen G Kunze G 《Applied microbiology and biotechnology》2007,74(6):1292-1299
The yeast Arxula
adeninivorans provides an attractive expression platform and can be exploited as gene source for biotechnologically interesting proteins.
In the following study, a striking example for the combination of both aspects is presented. The transaldolase-encoding A. adeninivorans ATAL gene, including its promoter and terminator elements, was isolated and characterized. The gene includes a coding sequence
of 963 bp encoding a putative 321 amino acid protein of 35.0 kDa. The enzyme characteristics analyzed from isolates of native
strains and recombinant strains overexpressing the ATAL gene revealed a molecular mass of ca. 140 kDa corresponding to a tetrameric structure, a pH optimum of ca. 5.5, and a temperature
optimum of 20°C. The preferred substrates for the enzyme include d-erythrose-4-phosphate and d-fructose-6-phosphate, whereas d-glyceraldehyde is not converted. The ATAL expression level under salt-free conditions was observed to increase in media supplemented with 5% NaCl rendering the ATAL promoter attractive for moderate heterologous gene expression under high-salt conditions. Its suitability was assessed for
the expression of a human serum albumin (HSA) reporter gene. 相似文献
78.
Schäfer C Parlesak A Eckoldt J Bode C Bode JC März W Winkler K 《Journal of lipid research》2007,48(7):1550-1558
The reduction of cardiovascular mortality associated with moderate alcohol consumption is chiefly thought to be mediated by an increase of high density lipoprotein cholesterol (HDL-CH). This study highlights additional qualitative changes of HDL that might augment this antiatherogenic effect. In 279 healthy men, alcohol and nutrient consumption were evaluated. Groups 1 (n=62), 2 (n=172), and 3 (n=45) comprised subjects with alcohol consumption of 0-5.0, 5.1-30.0, and 30.1-75 g/day, respectively. Lipid analysis was performed in nonfractionated and fractionated plasma, including subfractions HDL(2a), HDL(2b), and HDL(3). No difference in LDL-cholesterol was observed. Compared with group 1, groups 2 and 3 exhibited significant increases of HDL-CH (group 1, 44 +/- 10 mg/dl; group 2, 51 +/- 11 mg/dl; group 3, 55 +/- 11 mg/dl; mean +/- SD, P<0.0005), accompanied by enhanced lipidation of HDL (increase of the HDL(2)-CH/HDL(3)-CH ratio). Moreover, phospholipid enrichment of HDL occurred in alcohol consumers, whereas the ratios between other HDL components remained constant. Multivariate analysis revealed alcohol to have the foremost statistical influence on changes of the HDL fraction, followed by body mass index and physical activity level. The increased lipidation of HDL found in alcohol consumers might augment the antiatherogenic effect of HDL-CH increase. In addition, the phospholipid enrichment of HDL might reduce the inflammatory response of atherogenesis. 相似文献
79.
Tochowicz A Maskos K Huber R Oltenfreiter R Dive V Yiotakis A Zanda M Pourmotabbed T Bode W Goettig P 《Journal of molecular biology》2007,371(4):989-1006
Human matrix metalloproteinase 9 (MMP-9), also called gelatinase B, is particularly involved in inflammatory processes, bone remodelling and wound healing, but is also implicated in pathological processes such as rheumatoid arthritis, atherosclerosis, tumour growth, and metastasis. We have prepared the inactive E402Q mutant of the truncated catalytic domain of human MMP-9 and co-crystallized it with active site-directed synthetic inhibitors of different binding types. Here, we present the X-ray structures of five MMP-9 complexes with gelatinase-specific, tight binding inhibitors: a phosphinic acid (AM-409), a pyrimidine-2,4,6-trione (RO-206-0222), two carboxylate (An-1 and MJ-24), and a trifluoromethyl hydroxamic acid inhibitor (MS-560). These compounds bind by making a compromise between optimal coordination of the catalytic zinc, favourable hydrogen bond formation in the active-site cleft, and accommodation of their large hydrophobic P1' groups in the slightly flexible S1' cavity, which exhibits distinct rotational conformations of the Pro421 carbonyl group in each complex. In all these structures, the side-chain of Arg424 located at the bottom of the S1' cavity is not defined in the electron density beyond C(gamma), indicating its mobility. However, we suggest that the mobile Arg424 side-chain partially blocks the S1' cavity, which might explain the weaker binding of most inhibitors with a long P1' side-chain for MMP-9 compared with the closely related MMP-2 (gelatinase A), which exhibits a short threonine side-chain at the equivalent position. These novel structural details should facilitate the design of more selective MMP-9 inhibitors. 相似文献
80.
Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays 总被引:1,自引:0,他引:1
Tembe W Zavaljevski N Bode E Chase C Geyer J Wasieloski L Benson G Reifman J 《Bioinformatics (Oxford, England)》2007,23(1):5-13
MOTIVATION: Advances in DNA microarray technology and computational methods have unlocked new opportunities to identify 'DNA fingerprints', i.e. oligonucleotide sequences that uniquely identify a specific genome. We present an integrated approach for the computational identification of DNA fingerprints for design of microarray-based pathogen diagnostic assays. We provide a quantifiable definition of a DNA fingerprint stated both from a computational as well as an experimental point of view, and the analytical proof that all in silico fingerprints satisfying the stated definition are found using our approach. RESULTS: The presented computational approach is implemented in an integrated high-performance computing (HPC) software tool for oligonucleotide fingerprint identification termed TOFI. We employed TOFI to identify in silico DNA fingerprints for several bacteria and plasmid sequences, which were then experimentally evaluated as potential probes for microarray-based diagnostic assays. Results and analysis of approximately 150 in silico DNA fingerprints for Yersinia pestis and 250 fingerprints for Francisella tularensis are presented. AVAILABILITY: The implemented algorithm is available upon request. 相似文献