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11.
Muhammad Usman Shujaat Khan Seongyong Park Jeong-A Lee 《Current issues in molecular biology》2021,43(3):1489
It is of utmost importance to develop a computational method for accurate prediction of antioxidants, as they play a vital role in the prevention of several diseases caused by oxidative stress. In this correspondence, we present an effective computational methodology based on the notion of deep latent space encoding. A deep neural network classifier fused with an auto-encoder learns class labels in a pruned latent space. This strategy has eliminated the need to separately develop classifier and the feature selection model, allowing the standalone model to effectively harness discriminating feature space and perform improved predictions. A thorough analytical study has been presented alongwith the PCA/tSNE visualization and PCA-GCNR scores to show the discriminating power of the proposed method. The proposed method showed a high MCC value of 0.43 and a balanced accuracy of 76.2%, which is superior to the existing models. The model has been evaluated on an independent dataset during which it outperformed the contemporary methods by correctly identifying the novel proteins with an accuracy of 95%. 相似文献
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13.
Zahoor Ahmad Ejaz Ahmad Waraich Muhammad Zia ur Rehman Muhammad Ashar Ayub Muhammad Usman Hesham Alharby Atif Bamagoos Celaleddin Barutçular Muhammad Ali Raza Fatih Çiğ Ayman El Sabagh 《Phyton》2021,90(2):503-514
Water is essential for the growth period of crops; however, water unavailability badly affects the growth and physiological attributes of crops, which considerably reduced the yield and yield components in crops. Therefore, a pot
experiment was conducted to investigate the effect of foliar phosphorus (P) on morphological, gas exchange, biochemical traits, and phosphorus use efficiency (PUE) of maize (Zea mays L.) hybrids grown under normal as well as water
deficit situations at the Department of Agronomy, University of Agriculture Faisalabad, Pakistan in 2014. Two different
treatments (control and P @ 8 kg ha−1
) and four hybrids (Hycorn, 31P41, 65625, and 32B33) of maize were tested by
using a randomized complete block design (RCBD) with three replications. Results showed that the water stress caused
a remarkable decline in total soluble protein (9.7%), photosynthetic rate (9.4%) and transpiration rate (13.4%), stomatal
conductance (10.2%), and internal CO2 rate (20.4%) comparative to well-watered control. An increase of 37.1%, 36.8%,
and 24.5% were recorded for proline, total soluble sugar, and total free amino acid, respectively. However, foliar P
application minimized the negative impact of drought by improving plant growth, physio-biochemical attributes,
and PUE in maize plants under water stress conditions. Among the hybrids tested, the hybrid 6525 performed better
both under stress and non-stress conditions. These outcomes confirmed that the exogenous application of P improved
drought stress tolerance by modulating growth, physio-biochemical attributes, and PUE of maize hybrids. 相似文献
14.
Létuvé S Kozhich A Arouche N Grandsaigne M Reed J Dombret MC Kiener PA Aubier M Coyle AJ Pretolani M 《Journal of immunology (Baltimore, Md. : 1950)》2008,181(7):5167-5173
YKL-40 is a chitin-binding protein that is elevated in patients with various inflammatory conditions associated with ongoing remodeling. We investigated whether the levels of YKL-40 were up-regulated in the circulation and the airways of patients with chronic obstructive pulmonary disease (COPD), and whether it promoted the production of inflammatory mediators from macrophages. Serum, bronchoalveolar lavage (BAL), bronchial biopsies, lung tissue specimens, and alveolar macrophages from never-smokers (n = 15), smokers without COPD (n = 20), and smokers with COPD (n = 30) were assessed for YKL-40 levels and immunolocalization. In addition, YKL-40-induced mediator release from alveolar macrophages was examined. We found that smokers with COPD had elevated levels of YKL-40 in serum (p = 0.027) and BAL (p = 0.007), more YKL-40-positive cells in bronchial biopsies (p = 0.03), and a greater proportion of alveolar macrophages expressing YKL-40 than smokers without COPD or never-smokers. YKL-40 levels in serum and BAL were associated with airflow obstruction (pre-beta(2) agonist forced expiratory volume in 1 s, r(s) = -0.3892, p = 0.0072 and r(s) = -0.5491, p < 0.0001, respectively) and impaired diffusion lung capacity (transfer factor of the lung for carbon monoxide, r(s) = -0.4667, p = 0.002 and r(s) = -0.3854, p = 0.0045, respectively). TNF-alpha stimulated YKL-40 synthesis in alveolar macrophages from smokers with COPD, and exposure of these cells to YKL-40 promoted the release of IL-8, MCP-1, MIP-1alpha, and metalloproteinase-9. We conclude that YKL-40 is up-regulated in COPD, in which it may contribute to tissue inflammation and remodeling by sustaining the synthesis of proinflammatory and fibrogenic chemokines and of metalloproteinases by alveolar macrophages. 相似文献
15.
Mahim Khan Muhammad Qasim Usman Ali Ashfaq Sobia Idrees Masoud Shah 《Bioinformation》2013,9(14):710-714
Background:
HCV has become a leading cause of liver cirrhosis and hepatocellular carcinoma and is a major health concern worldwide. To date,
there is no vaccine available in the market to tackle this disease, therefore there is a strong need to develop antiviral compounds
that can target all genotypes of HCV with the same efficiency. Medicinal plants have low cost and are less toxic therefore, extracts
of medicinal plants can serve as important antiviral agents against HCV. This study was designed to screen phytochemicals of
Accacia nilotica to find a potent drug candidate that can inhibit HCV infection effectively.Results:
Docking of NS3/4A protease and Flavonoids of Accacia nilotica revealed that most of the flavonoids bound deeply with the active
site of NS3/4A protease. Compound 01 showed a high ranking on docking score. All other compounds also showed reliable
docking scores and had interactions with the binding cavity of NS3/4A protease, suggesting them as a potent drug candidate to
block HCV replication.Conclusion:
To recognize binding interactions of Accacia nilotica phytochemicals with NS3/4A protease, molecular docking was performed to
find potential inhibitor against NS3/4A protease of HCV. After post docking analysis, important interactions were found between
active compounds and active site of NS3/4A protease. It can be concluded from the study that phytochemicals of Accacia nilotica
may serve as a potential drug candidate with relatively simple structural changes against HCV NS3/4A protease. 相似文献
16.
Nassim Vakhide 《Archives Of Phytopathology And Plant Protection》2013,46(3):355-365
The greenbug, Schizaphis graminum (Rondani) (Hemiptera: Aphididae) has been known as a major pest of small grains, particularly wheat, worldwide. In this study, the effect of new wheat cultivar (Pishgam) for cold regions on biological characteristics of greenbug was investigated in a greenhouse at 25 ± 2 °C, 55 ± 10% relative humidity and a photoperiod of 16:8 h (L:D). The raw data were analysed based on the age-stage, two-sex life table. The intrinsic rate of increase (r), the finite rate of increase (λ), the net reproduction rate (R0) and the mean generation time (T) of greenbug were 0.313 ± 0.0019, 1.36 ± 0.0027 females/female/day, 83.33 ± 0.331 females/female and 14.11 ± 0.09 days, respectively. The life expectancy of a nymph is 43.57 days. The maximum reproductive value of females is on the 16th day which coincides with the total pre-reproduction period counted from birth. Hence, the present results may provide helpful information for comprehensive IPM programme of greenbug on this variety in cold regions of Iran. Result revealed that nymphal survival rate of the aphid was 100% on studied cultivar like that on sensitive host plant cultivar. 相似文献
17.
Muhammad Muzammal Adeel Muhammad Qasim Usman Ali Ashfaq Muhammad Shareef Masoud Mahmood ur Rehman Muhammad Tahir ul Qamar Muhammad Rizwan Javed 《Bioinformation》2014,10(7):454-459
Computational tools occupy the prime position in the analysis of large volume of post-genomic data. These tools have advantage
over the wet lab experiments in terms of high coverage, cost and time. Breast cancer is the most common cancer in females
worldwide. It is a genetically heterogeneous disorder and many genes are involved in the pathway of the disease. Mutations in
metastasis suppressor gene are the major cause of the disease. In this study, the effects of mutations in breast cancer metastasis
suppressor 1gene upon protein structure and function were examined by means of computational tools and information from
databases.This study can be useful to predict the potential effect of every allelic variant, devise new biological experiments and to
interpret and predict the patho-physiological impact of new mutations or non-synonymous polymorphisms. 相似文献
18.
Shadia Beaini Youakim Saliba Joelle Hajal Viviane Smayra Jules-Joel Bakhos Najat Joubran Dania Chelala Nassim Fares 《Journal of cellular physiology》2019,234(6):9616-9630
Salt-sensitive hypertension is a major risk factor for renal impairment leading to chronic kidney disease. High-salt diet leads to hypertonic skin interstitial volume retention enhancing the activation of the tonicity-responsive enhancer-binding protein (TonEBP) within macrophages leading to vascular endothelial growth factor C (VEGF-C) secretion and NOS3 modulation. This promotes skin lymphangiogenesis and blood pressure regulation. Whether VEGF-C administration enhances renal and skin lymphangiogenesis and attenuates renal damage in salt-sensitive hypertension remains to be elucidated. Hypertension was induced in BALB/c mice by a high-salt diet. VEGF-C was administered subcutaneously to high-salt-treated mice as well as control animals. Analyses of kidney injury, inflammation, fibrosis, and biochemical markers were performed in vivo. VEGF-C reduced plasma inflammatory markers in salt-treated mice. In addition, VEGF-C exhibited a renal anti-inflammatory effect with the induction of macrophage M2 phenotype, followed by reductions in interstitial fibrosis. Antioxidant enzymes within the kidney as well as urinary RNA/DNA damage markers were all revelatory of abolished oxidative stress under VEGF-C. Furthermore, VEGF-C decreased the urinary albumin/creatinine ratio and blood pressure as well as glomerular and tubular damages. These improvements were associated with enhanced TonEBP, NOS3, and lymphangiogenesis within the kidney and skin. Our data show that VEGF-C administration plays a major role in preserving renal histology and reducing blood pressure. VEGF-C might constitute an interesting potential therapeutic target for improving renal remodeling in salt-sensitive hypertension. 相似文献
19.
Peptides are preferred for designing inhibitors because of their high activity and specificity. Seven cyclopentapeptide inhibitors were designed in this study against dengue virus type 2 (DEN-2) NS3-NS2B protease: CKRRC, CGRRC, CRGRC, CRTRC, CTRRC, CKRKC and CRRKC. Docking analysis was performed to study the enzyme-inhibitor binding interactions. The free energy binding and estimated Ki values for all the inhibitors were found to be small (within micromolar range), indicating that the inhibitors bind considerably well to the binding site. The results showed that the cyclopentapeptide CKRKC was the best peptide inhibitor candidate with estimated free binding energy of -8.39 kcal/mol and Ki of 0.707 μM when compared to the standard inhibitor Bz-Nle-Lys-Arg-Arg-H that has been experimentally tested and shown to exhibit Ki value of 5.8 μM. Several modes of weak interactions were observed between the cyclopentapeptide CKRKC and the active site of DEN-2 NS3-NS2B protease. Thus, the cyclopentapeptide is proposed as a potential inhibitor to the NS3-NS2B protease activities of DEN-2. While these preliminary results are promising, further experimental investigation is necessary to validate the results. 相似文献
20.
The orphan G protein-coupled receptor GPR40 is activated by medium and long chain fatty acids 总被引:21,自引:0,他引:21