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41.
Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI) network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics. 相似文献
42.
Asiye Başusta Burak Çetinkaya Nuri Başusta 《Zeitschrift fur angewandte Ichthyologie》2020,36(6):888-892
Fish specimens were captured by a commercial bottom trawler at a depth of 50–80 m from Iskenderun Bay (Hatay, Turkey) between December 2017 and May 2018. The bottom trawl gear used was equipped with a 44 mm stretched mesh size net at the cod-end. Blind side and eyed side otolith lengths (OL), otolith breadths (OB) and otolith weights (OW) were measured from each specimen to the nearest 0.001 mm and 0.0001g respectively. A total of 110 fish (43 females and 67 males) were collected. Total length ranged from 20.8 to 28.2 cm and 68.0 to 166.1 g (males) and 21.1 to −28.5 cm and 74.5 to 201.4 g (females). The coefficients of determination between fish weight and otolith weight, and total length and otolith weight (sexes combined) were found as R2 = .7694 (0.77) and R2 = .6274 (0.63), respectively. A moderate positive relationship between the total length-otolith dimensions, and fish weight-otolith dimensions, was also demonstrated. 相似文献
43.
A tentative survey on selected marine fish farms was undertaken to delineate the extent to which infections with Staphylococcus species occur in Turkish aquaculture systems. To determine the presence and the distribution of fish pathogenic staphylococci, representative farm types such as marine cages as well as inland pond farms working with saline-ground water and a large hatchery were selected. Field sampling was performed in a total of 13 commercial fish farms that are located in the most-popular aquaculture sites of Turkey. Samples were taken between October 2013 and August 2014. Almost all size classes of the most commonly marine cultured fish species in Turkey were investigated, including Dicentrarchus labrax, Sparus aurata, Argyrosomus regius, Diplodus puntazzo, Dentex dentex, Onchorhynchus mykiss and Salmo labrax. After a visual check, specimens with various clinical signs were sampled for bacteriological and histopathological investigations. Mixed infections of staphylococci along with Vibrio and Aeromonas representatives were detected in Dicentrarchus labrax, Sparus aurata and Diplodus puntazzo samples obtained from 7 farms. The following pathogens were identified: Staphylococcus. epidermidis, S. aureus, S. capitis subsp. capitis, S. lentus, S. hominis subsp. hominis and S. sciuri subsp. sciuri. Main clinical and histopathological effects of the infections in fishes were revealed. The pathogenicity of some isolates was confirmed with in vivo pathogenicity assay and SDS-PAGE analysis. 相似文献
44.
Ozge Rencuzogulları Pınar Obakan Yerlikaya Ajda Çoker Gürkan Elif Damla Arısan Dilek Telci 《Journal of cellular biochemistry》2020,121(1):508-523
The mortality rate of pancreatic cancer has close parallels to its incidence rate because of limited therapeutics and lack of effective prognosis. Despite various novel chemotherapeutics combinations, the 5-year survival rate is still under 5%. In the current study, we aimed to modulate the aberrantly activated PI3K/AKT pathway and epithelial-mesenchymal transition (EMT) signaling with the treatment of CDK4/6 inhibitor PD-0332991 (palbociclib) in Panc-1 and MiaPaCa-2 pancreatic cancer cells. It was found that PD-0332991 effectively reduced cell viability and proliferation dose-dependently within 24 hours. In addition, PD-0332991 induced cell cycle arrest at the G1 phase by downregulation of aberrant expression of CDK4/6 through the dephosphorylation of Rb in each cell lines. Although PD-0332991 treatment increased epithelial markers and decreased mesenchymal markers, the nuclear translocation of β-catenin was not prevented by PD-0332991 treatment, especially in MiaPaCa-2 cells. Effects of PD-0332991 on the regulation of PI3K/AKT signaling and its downstream targets such as GSK-3 were cell type-dependent. Although the activity of AKT was inhibited in both cell lines, the phosphorylation of GSK-3β at Ser9 increased only in Panc-1. In conclusion, PD-0332991 induced cell cycle arrest and reduced the cell viability of Panc-1 and MiaPaCa-2 cells. However, PD-0332991 differentially affects the regulation of the PI3K/AKT pathway and EMT process in cells due to its distinct influence on Rb and GSK-3/β-catenin signaling. Understanding the effect of PD-0332991 on the aberrantly activated signaling axis may put forward a new therapeutic strategy to reduce the cell viability and metastatic process of pancreatic cancer. 相似文献
45.
46.
An in vitro hair perforation test is used to differentiate isolates of Trichophyton mentagrophytes and Trichophyton rubrum complexes because morphological criteria are insufficient. Here, we performed in vitro hair perforation tests using blond prepubertal hair and albino adult hair to determine whether they differentiate between fungal species. We tested 43 well-characterized dermatophyte strains, Arthroderma spp. [n = 4], Epidermophyton floccosum [n = 1], Microsporum spp. [n = 8], and Trichophyton spp. [n = 30], and examined hair perforation at 3–30 days postinoculation (p.i.). The perforation times were not significantly different between the two hair types (P > 0.05). The T. mentagrophytes complex strains perforated hair 4–5 days p.i., whereas T. rubrum complex strains perforated hair 13–30 days p.i., except for Trichophyton violaceum, which perforated hair after 6–7 days. Thus, the hair perforation test is highly sensitive (100 %) and specific (100 %) for differentiating T. mentagrophytes from T. rubrum complexes 5 days p.i. At 14 and 30 days, the sensitivity and negative predictive value of the test remained unchanged (100 %), but the specificity was reduced (64.3 and 14.3 %, respectively). Consistent with previous reports, we observed “perforating organs” of zoophilic Microsporum canis and geophilic Microsporum gypseum at 4 and 3 days, respectively. This paper offers a “low-cost” and “low-tech” alternative to differentiating dermatophyte species where standard morphological techniques fail and/or where molecular techniques are not a viable option. 相似文献
47.
48.
Halil Erhan Eroğlu Neslihan Şimşek Murat Koç Ergin Hamzaoğlu 《Plant Systematics and Evolution》2013,299(1):67-73
Karyotypic characters, mitotic metaphase chromosomes, monoploid idiograms and karyograms of Minuartia anatolica (Boiss.) Woronow var. phrygia (Bornm.) McNeill, Minuartia anatolica (Boiss.) Woronow var. scleranthoides (Boiss. & Noe) McNeill, Minuartia corymbulosa (Boiss. & Balansa) McNeill var. gypsophilloides McNeill and Minuartia aksoyi M.Koç & Hamzao?lu were investigated for the first time. Analysis of somatic metaphases showed that the chromosome numbers and the formulas of these taxa were 2n = 24 = 14m + 6sm + 4st for Minuartia anatolica var. phrygia, 2n = 14 = 6m + 8sm for Minuartia anatolica var. scleranthoides, 2n = 14 = 6m + 4sm + 4st for Minuartia corymbulosa var. gypsophilloides and 2n = 30 = 14m + 10sm + 6st for Minuartia aksoyi. No satellites were observed in the karyotypes of these taxa. Karyotype asymmetry was estimated by many different methods, namely the Stebbins classification, the karyotype asymmetry index (As K %), the total form percent (TF %), the Rec and Syi indices, the intrachromosomal asymmetry index (A1) and interchromosomal asymmetry index (A2), the dispersion index (DI), the degree of asymmetry of karyotype (A index) and the asymmetry index (AI). 相似文献
49.
We present a new molecular dynamics method for studying the dynamics of open systems. The method couples a classical system to a chemical potential reservior. In the formulation, following the extended system dynamics approach, we introduce a variable, v to represent the coupling to the chemical potential reservoir. The new variable governs the dynamics of the variation of number of particles in the system. The number of particles is determined by taking the integer part of v. The fractional part of the new variable is used to scale the potential energy and the kinetic energy of an additional particle: i.e., we introduce a fractional particle. We give the ansatz Lagrangians and equations of motion for both the isothermal and the adiabatic forms of grand molecular dynamics. The averages calculated over the trajectories generated by these equations of motion represent the classical grand canonical ensemble (μVT) and the constant chemical potential adiabatic ensemble (μVL) averages, respectively. The microcanonical phase space densities of the adiabatic and isothermal forms the molecular dynamics method are shown to be equivalent to adiabatic constant chemical potential ensemble, and grand canonical ensemble partition functions. We also discuss the extension to multi-component systems, molecular fluids, ionic solutions and the problems and solutions associated with the implementation of the method. The statistical expressions for thermodynamic functions such as specific heat; adiabatic bulk modulus, Grüneissen parameter and number fluctuations are derived. These expressions are used to analyse trajectories of constant chemical potential systems. 相似文献
50.
Duygu İnci Özgür Vatan Yunus Zorlu Nilüfer Çinkılıç 《Journal of biomolecular structure & dynamics》2013,31(15):3878-3901
New binary copper(II) complexes – [Cu(4-mphen)2(NO3)]NO3·H2O (1), [Cu(5-mphen)2 (NO3)]NO3·H2O (2), the known complex [Cu(dmphen)2(NO3)]NO3 (3) and [Cu(tmphen)2 (NO3)]NO3·H2O (4) - (4-mphen: 4-methyl-1,10-phenanthroline, 5-mphen: 5-methyl-1,10-phenanthroline, dmphen: 4,7-dimethyl-1,10-phenanthroline, tmphen: 3,4,7,8-tetramethyl-1,10-phenanthroline), have been synthesized and characterized by CHN analysis, ESI-MS, FTIR and single-crystal X-ray diffraction techniques. Interaction of these complexes with calf thymus DNA (CT-DNA) has been investigated by absorption spectral titration, ethidium bromide (EB) and Hoechst 33,258 displacement assay and thermal denaturation measurement. These complexes cleaved pUC19 plasmid DNA in the absence and presence of an external agent. Notably, in the presence of H2O2 as an activator, the cleavage abilities of these complexes are obviously enhanced at low concentration. Addition of hydroxyl radical scavengers like DMSO shows significant inhibition of the DNA cleavage activity of these complexes. BSA quenching mechanism was investigated with regard to the type of quenching, binding constant, number of binding locations and the thermodynamic parameters. The experimental results suggested that the probable quenching mechanism was an unusual static process and hydrophobic forces play a dominant role. The CT-DNA and BSA binding efficiencies of these complexes follow the order: 4 > 3 > 1 > 2. Furthermore, in vitro cytotoxicities of these complexes on tumor cells lines (Caco-2, MCF-7 and A549) and healthy cell line (BEAS-2B) showed that these complexes exhibited anticancer activity with low IC50 values. The effect of hydrophobicity of the methyl-substituted phenanthrolines on DNA and protein binding activities of these complexes is discussed. 相似文献