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1.
Irena Zupanič Pajnič Carlo Previderè Tomaž Zupanc Martina Zanon Paolo Fattorini 《Electrophoresis》2022,43(13-14):1521-1530
The recent introduction of polymerase chain reaction (PCR)-massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR-MPS could generate “isometric drop-ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR-MPS analyses). As expected, several well-known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology. 相似文献
2.
Nucleic acids dye Goldview is widely used in agarose gel electrophoresis (AGE). However, in this study, a sample of multiplasmid DNA (multi-pDNA) stained with Goldview analyzed by AGE showed its instability at low temperature. Three types of DNA samples were analyzed, including linear DNA (ladder), single-plasmid DNA (single-pDNA), and multi-pDNA, electrophoretic conditions were optimized by adjusting the dye, the buffer, and the temperature (1–50°C). The results showed that the light intensity of Gelred is 2.2-times higher than that of Goldview in staining multi-pDNA. Compared with the single-pDNA and the linear DNA, the multi-pDNA stained with Goldview was greatly affected by temperature. This short communication indicated that Gelred is a highly applicable dye for analyzing multiplasmid samples. The degree and the way of binding of Goldview to multi-pDNA are greatly affected by temperature. 相似文献
3.
《印度化学会志》2022,99(12):100799
A charge transfer hydrogen bonded complex was prepared and experimentally explored in an acetonitrile (ACN) medium between the proton acceptor (electron donor) 2, 3-Diamino-5-bromopyridine and the proton donor (electron acceptor) chloranilic acid. The stoichiometry of the charge transfer complex is 1:1. The Benesi-Hildebrand equation is used to calculate the molar absorptivity (εCT), association constant (KCT) and other spectroscopic physical characteristics. The solid compound was synthesized and studied using several spectroscopic methods. The presence of charge and proton transfers in the resultant complex was supported by 1H NMR, FT-IR and SEM-EDX investigations. The complex DNA binding ability was investigated using electron absorption spectroscopy, and the CT complex binding mechanism is intercalative. The intrinsic binding constant (Kb) value is 5.2 × 106M?1. The good binding affinity of the CT complex makes it potentially suitable for usage as a pharmaceutical in the future. Molecular docking calculations have been performed between CT complex and DNA (ID = 1BNA) to study the CT-DNA interaction theoretically. To corroborate the experimental findings, calculations based on DFT were carried out in the gas and PCM analysis where the existence of charge and hydrogen transfers. Finally, good agreement between experimental and theoretical computations was observed confirming that the basis set used is appropriate for the system under examination. 相似文献
4.
Prof. Arivazhagan Rajendran Kirankumar Krishnamurthy Seojeong Park Prof. Eiji Nakata Prof. Youngjoo Kwon Prof. Takashi Morii 《Chemistry (Weinheim an der Bergstrasse, Germany)》2022,28(22):e202200108
DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions. 相似文献
5.
Fan Xuemei Liu Yandan Fan Xinhui Nan Yue Su Lingling Wang Shumin Wang Yimeng Wang Xiangting 《分析试验室》2022,(9):1029-1033
N and S co-doped graphene quantum dotsNS-GQDswith excellent fluorescence properties were synthesized by hydrothermal method using citrate and thiourea as ingredientsand were characterized. The fluorescence signal was notably reduced in the presence of single stranded DNAssDNAsince ssDNA can adsorb on the surface of NS-GQDs through p-p stacking interaction. Whereas a significantly restored fluorescence signal was observed in the presence of bleomycinowing to the irreversible cleavage of ssDNA by bleomycin with Fe2+ as cofactor. Thusa fluorescence sensor for bleomycin detection was developed. The linear range was from 1.8 to 1200 nmol/L and the detection limit was 0.25 nmol/L. The method was used to detect bleomycin content in human serum samples with satisfactory results. © 2022, Youke Publishing Co.,Ltd. All rights reserved. 相似文献
6.
7.
《Arabian Journal of Chemistry》2022,15(8):103953
In this study, ultrasound-assisted extraction of polyphenols from C. cicadae was optimized by response surface methodology (RSM). The optimized conditions were determined as extraction time of 39 min, liquid-to-solid ratio of 1:29 g/mL, extraction temperature of 69 °C and ethanol concentration of 55% with a yield of 21.9 mg gallic acid equivalent/g dry weight. Four resins were used for polyphenol purification. D101 resin had the highest ratio of adsorption and was further applied in polyphenol purification test. A total of 19 different phenolic compounds were identified by LC-MS, including 12 phenolic acids and 7 organic acids. In addition, C. cicadae polyphenols displayed higher antioxidant activity in vitro and anti-aging activity of C. elegans in vivo. Lastly, C. cicadae polyphenols showed the potential to protect DNA from oxidative damage. Overall, our results suggest that polyphenols from C. cicadae may be considered as novel sources of anti-oxidation, anti-aging and recommended as reagents to protect DNA from oxidative damage in food and pharmaceutical industries. 相似文献
8.
Elaina P. Boyle Dr. Levan Lomidze Prof. Dr. Karin Musier-Forsyth Prof. Dr. Besik Kankia 《ChemistryOpen》2022,11(2):e202100276
Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K+ or Sr2+. TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines. 相似文献
9.
通过3,3′-((乙烷-1,2-二基双(2-甲基吡啶杂氮二基)双(亚甲基))双(2-羟基-5-甲基苯甲醛)与2-羟基-1,3-丙二胺的缩合反应得到一种具有双吡啶悬臂的双核锰配合物。通过X射线单晶衍射确定了该配合物结构,结果显示其分子式为[Mn2(C37H43N6O6)]·(ClO4)2。该配合物属于单斜晶系,P21/c空间群,晶胞参数为:a=1.096 50(19) nm, b=1.419 5(3) nm, c=3.109 4(5) nm, β=108.153(5)°。进一步分析表明两个二价锰离子分别与(Namine)2(Nimine)2O3和(Nimine)2O4体系配位,它们与配位原子形成的几何构型分别是十面体和扭曲的八面体。两个中心锰离子距离为0.331 6 nm,由酚氧原子和醋酸根共同桥联。另外,本文也利用伏安法和黏度法对该配合物与小牛胸腺DNA的结合能力进行研究,实验结果表明它们之间的结合方式为弱的插入作用。 相似文献
10.