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31.
Tabu search is a meta-heuristic approach that is proven to be useful in solving combinatorial optimization problems. We implement the adaptive memory features of tabu search to refine a multiple sequence alignment. Adaptive memory helps the search process to avoid local optima and explores the solution space economically and effectively without getting trapped into cycles. The algorithm is further enhanced by introducing extended tabu search features such as intensification and diversification. The neighborhoods of a solution are generated stochastically and a consistency-based objective function is employed to measure its quality. The algorithm is tested with the datasets from BAliBASE benchmarking database. We have observed through experiments that tabu search is able to improve the quality of multiple alignments generated by other software such as ClustalW and T-Coffee. The source code of our algorithm is available at http://www.bii.a-star.edu.sg/~tariq/tabu/. 相似文献
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Riaz N Steinberg S Ahmad J Pluzhnikov A Riazuddin S Cox NJ Drayna D 《American journal of human genetics》2005,76(4):647-651
Stuttering is a common and sometimes severe communication disorder, of unknown primary etiology, that exists in populations worldwide. Many types of evidence suggest a genetic contribution to stuttering; however, the complex inheritance of this disorder has hindered identification of these factors. We have employed highly inbred families to increase the power of linkage analysis of this disorder. Forty-four Pakistani families with documented or probable consanguinity, from the city of Lahore and surrounding areas, were included. Each family contained multiple cases of stuttering, which were diagnosed using the Stuttering Severity Instrument. Using the Marshfield Weber 9 marker panel, we performed a genomewide linkage scan focused on affected individuals and their parents. The analysis included 199 genotyped individuals, 144 affected and 55 unaffected. The Pedigree Relationship Statistical Test (PREST) was used to identify pedigrees that required additional specification of inbreeding. Initial nonparametric analysis gave evidence of linkage on chromosomes 1, 5, 7, and 12. Additional genotyping was performed on chromosome 12 to a 5-cM level of resolution, and 16 additional individuals were then included, bringing the number of families to 46. Analysis of the enlarged data set provided consistent evidence of linkage on chromosome 12: the S(homoz) scoring function gave a nonparametric LOD score of 4.61, and a LOD score of 3.51 was obtained using the S(all) scoring function. These results suggest that a locus on chromosome 12q may contain a gene with a large effect in this sample. 相似文献
34.
Atta-ur-Rahman Khalid A Sultana N Ghayur MN Mesaik MA Khan MR Gilani AH Choudhary MI 《Journal of enzyme inhibition and medicinal chemistry》2006,21(6):703-710
During this study, one new coumarin; 7-O-beta-D-glucopyranoside-2H-1-benzopyran-2-one (1) and three quinoline alkaloids; 3-hydroxy, 2, 2, 6-trimethyl-3, 4, 5, 6-tetrahydro-2H-pyrano[3,2-c] quinoline 5-one (2), ribalinine (3) and methyl isoplatydesmine (4) were isolated from the aerial parts of Skimmia laureola and their structures established by spectroscopic studies. Compounds 2-4 were found to be linear mixed type inhibitors of acetylcholinesterase (K(i) = 110.0, 30.0 and 30.0 microM, respectively). Compounds 2 and 3 were also found to be linear mixed type inhibitors of butyrylcholinesterase, while compound 4 was a noncompetitive inhibitor of the enzyme (K(i) = 90.0, 70.0 and 19.0 microM, respectively). The inhibition of acetyl- and butyryl-cholinesterase enzymes persists as the most promising therapeutic strategy for activating the impaired cholinergic functions in Alzheimer's disease and related dementias. Compound 4 also showed dose-dependent spasmolytic activity in the isolated rabbit jejunum intestinal preparation by relaxing the spontaneous (EC50 = 0.1 mg/mL) and K(+)-induced contractions (EC50 = 0.4 mg/mL), suggesting that the spasmolytic effect of compound 4 is mediated through the blockade of voltage-dependent Ca2+ channels. 相似文献
35.
Riaz S Hu R Walker MA 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2012,125(6):1195-1210
This study presents a framework linkage map based on microsatellite markers for Muscadinia rotundifolia (1n?=?20). The mapping population consisted of 206 progeny generated from a cross of two M. rotundifolia varieties, 'Fry' and 'Trayshed'. A total of 884 primers were tested for their ability to amplify markers: 686 amplified and 312 simple sequence repeat (SSR) primer pairs generated 322 polymorphic markers for either one or both parents. The map for the female parent 'Fry' consisted of 212 markers and covered 879?cM on 18 chromosomes. The average distance between the markers was 4.1?cM and chromosome 6 was not represented due to a lack of polymorphic markers. The map for the male parent 'Trayshed' consisted of 191 markers and covered 841?cM on 19 chromosomes. The consensus map consisted of 314 markers on 19 chromosomes with a total distance of 1,088?cM, which represented 66?% of the distance covered by the Vitis vinifera reference linkage map. Marker density varied greatly among chromosomes from 5 to 35 mapped markers. Relatively good synteny was observed across 19 chromosomes based on markers in common with the V. vinifera reference map. Extreme segregation distortion was observed for chromosome 8 and 14 on the female parent map, and 4 on the male parent map. The lack of mapping coverage for the 20th M. rotundifolia chromosome is discussed in relation to possible evolutionary events that led to the reduction in chromosome number from 21 to 19 in the ancestral genome. 相似文献
36.
Mycoplasma bovis pneumonia in cattle has been epidemic in China since 2008. To investigate M. bovis pathogenesis, we completed genome sequencing of strain HB0801 isolated from a lesioned bovine lung from Hubei, China. The genomic plasticity was determined by comparing HB0801 with M. bovis strain ATCC? 25523?/PG45 from cow mastitis milk, Chinese strain Hubei-1 from lesioned lung tissue, and 16 other Mycoplasmas species. Compared to PG45, the genome size of HB0801 was reduced by 11.7 kb. Furthermore, a large chromosome inversion (580 kb) was confirmed in all Chinese isolates including HB0801, HB1007, a strain from cow mastitis milk, and Hubei-1. In addition, the variable surface lipoproteins (vsp) gene cluster existed in HB0801, but contained less than half of the genes, and had poor identity to that in PG45, but they had conserved structures. Further inter-strain comparisons revealed other mechanisms of gene acquisition and loss in HB0801 that primarily involved insertion sequence (IS) elements, integrative conjugative element, restriction and modification systems, and some lipoproteins and transmembrane proteins. Subsequently, PG45 and HB0801 virulence in cattle was compared. Results indicated that both strains were pathogenic to cattle. The scores of gross pathological assessment for the control group, and the PG45- and HB0801-infected groups were 3, 13 and 9, respectively. Meanwhile the scores of lung lesion for these three groups were 36, 70, and 69, respectively. In addition, immunohistochemistry detection demonstrated that both strains were similarly distributed in lungs and lymph nodes. Although PG45 showed slightly higher virulence in calves than HB0801, there was no statistical difference between the strains (P>0.05). Compared to Hubei-1, a total of 122 SNP loci were disclosed in HB0801. In conclusion, although genomic plasticity was thought to be an evolutionary advantage, it did not apparently affect virulence of M. bovis strains in cattle. 相似文献
37.
Arundo donax (giant reed) is an aggressive invasive weed of riparian habitats throughout the southern half of the United States from California to Maryland. Native to Asia, the species is believed to have been initially introduced into North America from the Mediterranean region although subsequent introductions were from multiple regions. To provide insight into the potential for biological control of A. donax, genetic variation in plants sampled from a wide geographical area in the United States was analyzed using Sequence Related Amplification Polymorphism (SRAP) and transposable element (TE)-based molecular markers. Invasive individuals from 15 states as well as four populations in southern France were genetically fingerprinted using 10 SRAP and 12 TE-based primer combinations. With the exception of simple mutations detected in four plants, A. donax exhibited a single multilocus DNA fingerprint indicating a single genetic clone. The genetic uniformity of invasive A. donax suggests that classical biological control of the species could be successful. A lack of genetic diversity in the invaded range simplifies identification of native source populations to search for natural enemies that could be used as biocontrol agents. 相似文献
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39.
Nazia Riaz Romana Idress Sadia Habib Iqbal Azam El-Nasir MA Lalani 《Translational oncology》2018,11(4):920-929
BACKGROUND: Androgen receptor (AR) has emerged as a significant prognostic marker in early breast cancer (BCa). Association of AR with cancer stem cell (CSC) markers in BCa is unknown. Aim of the present study was to evaluate the immunohistochemical expression of AR, CD44, CD24 and ALDH1 in a cohort of Pakistani patients diagnosed with invasive BCa and to correlate the expression with 5- year disease free survival. PATIENTS AND METHODS: We evaluated immunohistochemical expression AR, CD44, CD24 and ALDH1 in formalin fixed paraffin embedded archival blocks of 166 cases of primary invasive BCa (stage I-III) and correlated the expression with clinicopathological variables and outcome using univariable and multivariable analysis. Survival data was computed by Kaplan Meier curves. RESULTS: Expression of AR was observed in 62.7% tumors whereas CD44, CD24 and ALDH1 were expressed in 61.4%, 44% and 30.1% tumors, respectively. AR expression was significantly associated with T1-T2 tumors, lower grade, estrogen and progesterone receptor expression (P < .05) and remained an independent prognostic indicator in multivariable analysis (adjusted HR 0.33, 95% CI 0.13–0.81; P = .016). Significant association was observed between concordant expression of AR and CD24 (P = .001) with a favorable impact on survival (P = .007) whereas expression of CSC phenotypes (CD44+, CD44+/CD24? and ALDH1+) did not correlate with adverse outcome (P > .05). However, AR expression retained the association with better prognosis even in patients whose tumors exhibited a CSC phenotype. CONCLUSIONS: Expression of AR and CD24 in stage I-III invasive BCa correlates with favorable clinicopathological features and delineates a subgroup of patients with better disease-free survival. 相似文献
40.
Lei Yan Muhammad Riaz Xiuwen Wu Yuhan Wang Chenqing Du Cuncang Jiang 《Acta Physiologiae Plantarum》2018,40(2):33
It has been reported that aluminum (Al) toxicity is a major limiting factor for plant growth and production on acidic soils. Boron (B) is indispensable micronutrient for normal growth of higher plants, and its addition could alleviate Al toxicity. The rape seedlings were grown under three B (0.25, 25 and 500 μM) and two Al concentrations [0 (?Al) and 100 μM (+Al) as AlCl3·6H2O]. The results indicated that Al stress severely hampered root elongation and root activity at 0.25 μM B while the normal (25 μM) and excess (500 μM) B improved the biomass of rape seedlings under Al exposure. Additionally, normal and excess B treatment reduced accumulation of Al in the roots and leaves under Al toxicity, which was also confirmed by hematoxylin with light staining. This indicates that both normal and excess B could alleviate Al toxicity. Furthermore, it also decreased the contents of malondialdehyde and soluble protein under Al toxicity. Likewise, superoxide dismutase activity (SOD) improved by 97.82 and 131.96% in the roots, and 168 and 119.88% in the leaves at 25 and 500 µM B, respectively, while the peroxidase and catalase activities dropped as a result of Al stress. The study results demonstrated that appropriate B application is necessary to avoid the harmful consequences of Al toxicity in rape seedlings. 相似文献