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91.
A common issue in bioinformatics is that computational methods often generate a large number of predictions sorted according to certain confidence scores. A key problem is then determining how many predictions must be selected to include most of the true predictions while maintaining reasonably high precision. In nuclear magnetic resonance (NMR)-based protein structure determination, for instance, computational peak picking methods are becoming more and more common, although expert-knowledge remains the method of choice to determine how many peaks among thousands of candidate peaks should be taken into consideration to capture the true peaks. Here, we propose a Benjamini-Hochberg (B-H)-based approach that automatically selects the number of peaks. We formulate the peak selection problem as a multiple testing problem. Given a candidate peak list sorted by either volumes or intensities, we first convert the peaks into -values and then apply the B-H-based algorithm to automatically select the number of peaks. The proposed approach is tested on the state-of-the-art peak picking methods, including WaVPeak [1] and PICKY [2]. Compared with the traditional fixed number-based approach, our approach returns significantly more true peaks. For instance, by combining WaVPeak or PICKY with the proposed method, the missing peak rates are on average reduced by 20% and 26%, respectively, in a benchmark set of 32 spectra extracted from eight proteins. The consensus of the B-H-selected peaks from both WaVPeak and PICKY achieves 88% recall and 83% precision, which significantly outperforms each individual method and the consensus method without using the B-H algorithm. The proposed method can be used as a standard procedure for any peak picking method and straightforwardly applied to some other prediction selection problems in bioinformatics. The source code, documentation and example data of the proposed method is available at http://sfb.kaust.edu.sa/pages/software.aspx. 相似文献
92.
Objectives
There has been increased interest in the possible role of human cytomegalovirus (HCMV) in carcinogenesis during the last decade. HCMV seroprevalence was enhanced in patients with hepatocellular carcinoma (HCC) but a possible relationship between HCC and HCMV infection remained to be assessed. The aim of this work was to investigate the pro-tumor influence of HCMV on primary human hepatocytes (PHH) and HepG2 cells.Methods
Following infection of PHH and HepG2 cells by two different strains of HCMV, we measured the production of IL-6 in culture supernatants by ELISA and the protein levels of STAT3, pSTAT3, JAK, cyclin D1, survivin, p53, p21, and Mdm2 by western Blotting in infected and uninfected cells. Cell proliferation and transformation were investigated using Ki67Ag expression measurement and soft-agar colony formation assay respectively.Results
Infection of HepG2 cells and PHH by HCMV resulted in the production of IL-6 and the subsequent activation of the IL-6R-JAK-STAT3 pathway. HCMV increased the expression of cyclin D1 and survivin. Cell proliferation was enhanced in HepG2 and PHH infected with HCMV, despite a paradoxical overexpression of p53 and p21. More importantly, we observed the formation of colonies in soft agar seeded with PHH infected with HCMV and when we challenged the HepG2 cultures to form tumorspheres, we found that the HCMV-infected cultures formed 2.5-fold more tumorspheres than uninfected cultures.Conclusion
HCMV activated the IL-6-JAK-STAT3 pathway in PHH and HepG2 cells, favored cellular proliferation, induced PHH transformation and enhanced HepG2 tumorsphere formation. Our observations raise the possibility that HCMV infection might be involved in the genesis of hepatocellular carcinoma. 相似文献93.
Narges Abdali Enrico Barth Amir Norouzy Robert Schulz Werner M. Nau Ulrich Kleinekath?fer Andreas Tauch Roland Benz 《PloS one》2013,8(10)
Corynebacterium jeikeium, a resident of human skin, is often associated with multidrug resistant nosocomial infections in immunodepressed patients. C. jeikeium K411 belongs to mycolic acid-containing actinomycetes, the mycolata and contains a channel-forming protein as judged from reconstitution experiments with artificial lipid bilayer experiments. The channel-forming protein was present in detergent treated cell walls and in extracts of whole cells using organic solvents. A gene coding for a 40 amino acid long polypeptide possibly responsible for the pore-forming activity was identified in the known genome of C. jeikeium by its similar chromosomal localization to known porH and porA genes of other Corynebacterium strains. The gene jk0268 was expressed in a porin deficient Corynebacterium glutamicum strain. For purification temporarily histidine-tailed or with a GST-tag at the N-terminus, the homogeneous protein caused channel-forming activity with an average conductance of 1.25 nS in 1M KCl identical to the channels formed by the detergent extracts. Zero-current membrane potential measurements of the voltage dependent channel implied selectivity for anions. This preference is according to single-channel analysis caused by some excess of cationic charges located in the channel lumen formed by oligomeric alpha-helical wheels. The channel has a suggested diameter of 1.4 nm as judged from the permeability of different sized hydrated anions using the Renkin correction factor. Surprisingly, the genome of C. jeikeium contained only one gene coding for a cell wall channel of the PorA/PorH type found in other Corynebacterium species. The possible evolutionary relationship between the heterooligomeric channels formed by certain Corynebacterium strains and the homooligomeric pore of C. jeikeium is discussed. 相似文献
94.
Shima Rajaei Saeed Karima Hessam Sepasi Tehrani Somayeh Shateri Somayeh Mahmoodi Baram Meisam Mahdavi Farzad Mokhtari Alimohammad Alimohammadi Abbas Tafakhori Abolfazl Amiri Vajiheh Aghamollaii Hamid Fatemi Masoumeh Rajabibazl Farzad Kobarfard Ali Gorji 《Journal of neurochemistry》2020,155(2):207-224
95.
Parthenium poses serious threat to modern crop production system and
necessitate evaluating control practices for its effective management. Efficacy of
different weed control practices for controlling parthenium was explored in conventional and deep tillage systems in the field conditions. Hand hoeing (20 and
35 days after emergence), S-Metolachlor (pre-emergence herbicide), sorghum
straw mulch @ 5 tons ha-1 and combination of hand hoeing and sorghum straw
mulch (hand hoeing at 20 and straw mulch at 35 days after emergence) were used
as weed control practice. Weedy check where no weed control measure was
applied was also included in this experiment for comparison. Results concluded
that the all weed management treatments significantly reduced parthenium density, its fresh and dry biomass during both the years of study as compared to weedy check. Maximum sunflower achene yield was recorded in hand hoeing (20 and
35 days after emergence) in combination with deep tillage. So, mold bold plough
used for the purpose of deep tillage should be encouraged for better control of
parthenium and higher achene yield of sunflower crop (3293.3 kg ha-1 in 2017
and 3221.3 kg ha-1 in 2018). Moreover, is also inferred that total dose of herbicide
might be reduced by using hoeing and mulching in an integrated way. 相似文献
96.
Mohd Amir Taj Mohammad Kartikay Prasad Gulam Mustafa Hasan Vijay Kumar Ravins Dohare 《Journal of biomolecular structure & dynamics》2020,38(15):4625-4634
Communicated by Ramaswamy H. Sarma 相似文献
97.
Ghazizadeh Hamideh Rezaei Majid Avan Amir Fazilati Mohammad Pasdar Alireza Tavallaie Shima Kazemi Elham Seyedi Seyed Mohammad Reza Ferns Gordon A. Azimi-Nezhad Mohsen Ghayour-Mobarhan Majid 《Molecular biology reports》2020,47(2):867-875
Molecular Biology Reports - Metabolic syndrome (MetS) is associated with a pro-inflammatory state and endothelial dysfunction that places subjects with MetS at a higher risk of atherosclerosis.... 相似文献
98.
Roshankhah Shiva Abdolmaleki Amir Salahshoor Mohammad Reza 《Molecular biology reports》2020,47(8):6053-6065
Molecular Biology Reports - Mercuric chloride (MC) is a complex substance which is capable to produce free radicals. Middle Eastern Phoenix dactylifera (MEPD) is a flowering plant of palm family... 相似文献
99.
Reza Jafarzadeh-Esfehani Seyed Mostafa Parizadeh Amirsaeed Sabeti Aghabozorgi Negar Yavari Ariane Sadr-Nabavi Seyed Alireza Parizadeh Maryam Ghandehari Afsane Javanbakht Afsaneh Rezaei-Kalat Seyed Mahdi Hassanian Mohammad Vojdanparast Gordon A. Ferns Majid Khazaei Amir Avan 《Journal of cellular physiology》2020,235(10):6393-6403
Venous and arterial thrombosis are conditions that have a considerable burden if left untreated. The hypoxia-induced by the occluded vessel can disrupt the circulation of any organ, the cornerstone of treating thrombosis is rapid diagnosis and appropriate treatment. Diagnosis of thrombosis may be made by using laboratory tests or imaging techniques in individuals who have clinical manifestations of a thrombotic event. The use of serum micro ribonucleic acids (RNAs) has recently been applied to the diagnosis of thrombosis. These small RNA molecules are emerging as new diagnostic markers but have had very limited applications in vascular disease. Most of the articles provided various microRNAs with different levels of accuracy. However, there remains a lack of an appropriate panel of the most specific microRNA in the literature. The purpose of the present review was to summarize the existing data on the use of microRNAs as a diagnostic biomarker for venous thrombosis. 相似文献