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71.
Classifications are generally pictured in the form of hierarchical trees, also called dendrograms. A dendrogram is the graphical
representation of an ultrametric (=cophenetic) matrix; so dendrograms can be compared to one another by comparing their cophenetic
matrices. Three methods used in testing the correlation between matrices corresponding to dendrograms are evaluated. The three
permutational procedures make use of different aspects of the information to compare dendrograms: the Mantel procedure permutes
label positions only; the binary tree methods randomize the topology as well; the double-permutation procedure is based on
all the information included in a dendrogram, that is: topology, label positions, and cluster heights. Theoretical and empirical
investigations of these methods are carried out to evaluate their relative performance. Simulations show that the Mantel test
is too conservative when applied to the comparison of dendrograms; the methods of binary tree comparisons do slightly better;
only the doublepermutation test provides unbiased type I error.
Les arbres utilisés pour illustrés les groupements sont généralement représentés sous la forme de classifications hiérarchiques
ou dendrogrammes. Un dendrogramme représente graphiquement l’information contenue dans la matrice ultramétrique (=cophénétique)
correspondant à la classification. Dès ultramétriques correspondantes. Nous comparons trois méthodes permettant d’évaluer
la signification statistique du coefficient de correlation mesuré entre deux matrices ultramétriques. Ces trois tests par
permutations tiennent compte d’aspects différents pour comparer des dendrogrammes: le test de Mantel permute les feuilles
de l’arbre, les méthodes pour arbres binaires permutent les feuilles et la topologie, alors que la procédure à double permutation
permute les feuilles, la topologie et les niveaux de fusion des dendrogrammes comparés. L’efficacité relative des trois méthodes
est évaluée empiriquement et théoriquement. Nos résultats suggèrent l’utilisation préférentielle du test à double permutation
pour la comparaison de dendrogrammes: le test de Mantel s’avère trop conservateur, tandis que les méthodes pour arbres binaires
ne sont pas toujours adéquates.
This work was supported by NSERC grant no. A7738 to Pierre Legendre and by a NSERC scholarship to F.-J. Lapointe. 相似文献
This work was supported by NSERC grant no. A7738 to Pierre Legendre and by a NSERC scholarship to F.-J. Lapointe. 相似文献
72.
Summary Condensed chromatin shows globules of 300 Å formed by 8 to 10 nucleosomes. Each globule might be an uncoiled turn of a supercoil. This supercoil forms major coils along the fibre.This work was supported by grants from Brazilian CNPq, FAPESP and FEDIB.We thank Dr A. Brunner Jr for the permission to use the electron microscope. 相似文献
73.
The primary goal of this study was to propose an algorithm using mathematical programming to detect earnings management practices. In order to evaluate the ability of this proposed algorithm, the traditional statistical models are used as a benchmark vis‐à‐vis their time series counterparts. As emerging techniques in the area of mathematical programming yield better results, application of suitable models is expected to result in highly performed forecasts. The motivation behind this paper is to develop an algorithm which will succeed in detecting companies that appeal to financial manipulation. The methodology is based on cutting plane formulation using mathematical programming. A sample of 126 Turkish manufacturing firms described over 10 financial ratios and indexes are used for detecting factors associated with false financial statements. The results indicate that the proposed three‐phase cutting plane algorithm outperforms the traditional statistical techniques which are widely used for false financial statement detections. Furthermore, the results indicate that the investigation of financial information can be helpful towards the identification of false financial statements and highlight the importance of financial ratios/indexes such as Days' Sales in Receivables Index (DSRI), Gross Margin Index (GMI), Working Capital Accruals to Total Assets (TATA) and Days to Inventory Index (DINV). Copyright © 2009 John Wiley & Sons, Ltd. 相似文献
74.
Ellinghaus E Ellinghaus D Stuart PE Nair RP Debrus S Raelson JV Belouchi M Fournier H Reinhard C Ding J Li Y Tejasvi T Gudjonsson J Stoll SW Voorhees JJ Lambert S Weidinger S Eberlein B Kunz M Rahman P Gladman DD Gieger C Wichmann HE Karlsen TH Mayr G Albrecht M Kabelitz D Mrowietz U Abecasis GR Elder JT Schreiber S Weichenthal M Franke A 《Nature genetics》2010,42(11):991-995
75.
Pujana MA Han JD Starita LM Stevens KN Tewari M Ahn JS Rennert G Moreno V Kirchhoff T Gold B Assmann V Elshamy WM Rual JF Levine D Rozek LS Gelman RS Gunsalus KC Greenberg RA Sobhian B Bertin N Venkatesan K Ayivi-Guedehoussou N Solé X Hernández P Lázaro C Nathanson KL Weber BL Cusick ME Hill DE Offit K Livingston DM Gruber SB Parvin JD Vidal M 《Nature genetics》2007,39(11):1338-1349
Many cancer-associated genes remain to be identified to clarify the underlying molecular mechanisms of cancer susceptibility and progression. Better understanding is also required of how mutations in cancer genes affect their products in the context of complex cellular networks. Here we have used a network modeling strategy to identify genes potentially associated with higher risk of breast cancer. Starting with four known genes encoding tumor suppressors of breast cancer, we combined gene expression profiling with functional genomic and proteomic (or 'omic') data from various species to generate a network containing 118 genes linked by 866 potential functional associations. This network shows higher connectivity than expected by chance, suggesting that its components function in biologically related pathways. One of the components of the network is HMMR, encoding a centrosome subunit, for which we demonstrate previously unknown functional associations with the breast cancer-associated gene BRCA1. Two case-control studies of incident breast cancer indicate that the HMMR locus is associated with higher risk of breast cancer in humans. Our network modeling strategy should be useful for the discovery of additional cancer-associated genes. 相似文献
76.
Abecasis G Tam PK Bustamante CD Ostrander EA Scherer SW Chanock SJ Kwok PY Brookes AJ 《Nature genetics》2007,39(2):153-155
The eighth annual Human Genome Variation Meeting was held in September 2006 in the Hong Kong Special Administrative Region, China. The meeting highlighted recent advances in characterization of genetic variation, including genome-wide association studies and structural variation. 相似文献
77.
Sun L Rommens JM Corvol H Li W Li X Chiang TA Lin F Dorfman R Busson PF Parekh RV Zelenika D Blackman SM Corey M Doshi VK Henderson L Naughton KM O'Neal WK Pace RG Stonebraker JR Wood SD Wright FA Zielenski J Clement A Drumm ML Boëlle PY Cutting GR Knowles MR Durie PR Strug LJ 《Nature genetics》2012,44(5):562-569
Variants associated with meconium ileus in cystic fibrosis were identified in 3,763 affected individuals by genome-wide association study (GWAS). Five SNPs at two loci near SLC6A14 at Xq23-24 (minimum P = 1.28 × 10(-12) at rs3788766) and SLC26A9 at 1q32.1 (minimum P = 9.88 × 10(-9) at rs4077468) accounted for ~5% of phenotypic variability and were replicated in an independent sample of affected individuals (n = 2,372; P = 0.001 and 0.0001, respectively). By incorporating the knowledge that disease-causing mutations in CFTR alter electrolyte and fluid flux across surface epithelium into a hypothesis-driven GWAS (GWAS-HD), we identified associations with the same SNPs in SLC6A14 and SLC26A9 and established evidence for the involvement of SNPs in a third solute carrier gene, SLC9A3. In addition, GWAS-HD provided evidence of association between meconium ileus and multiple genes encoding constituents of the apical plasma membrane where CFTR resides (P = 0.0002; testing of 155 apical membrane genes jointly and in replication, P = 0.022). These findings suggest that modulating activities of apical membrane constituents could complement current therapeutic paradigms for cystic fibrosis. 相似文献
78.
Identification of ten loci associated with height highlights new biological pathways in human growth 总被引:1,自引:0,他引:1
Lettre G Jackson AU Gieger C Schumacher FR Berndt SI Sanna S Eyheramendy S Voight BF Butler JL Guiducci C Illig T Hackett R Heid IM Jacobs KB Lyssenko V Uda M;Diabetes Genetics Initiative;FUSION;KORA;Prostate Lung Colorectal Ovarian Cancer Screening Trial;Nurses' Health Study;SardiNIA Boehnke M Chanock SJ Groop LC Hu FB Isomaa B Kraft P Peltonen L Salomaa V Schlessinger D Hunter DJ Hayes RB Abecasis GR Wichmann HE Mohlke KL Hirschhorn JN 《Nature genetics》2008,40(5):584-591
Height is a classic polygenic trait, reflecting the combined influence of multiple as-yet-undiscovered genetic factors. We carried out a meta-analysis of genome-wide association study data of height from 15,821 individuals at 2.2 million SNPs, and followed up the strongest findings in >10,000 subjects. Ten newly identified and two previously reported loci were strongly associated with variation in height (P values from 4 x 10(-7) to 8 x 10(-22)). Together, these 12 loci account for approximately 2% of the population variation in height. Individuals with < or =8 height-increasing alleles and > or =16 height-increasing alleles differ in height by approximately 3.5 cm. The newly identified loci, along with several additional loci with strongly suggestive associations, encompass both strong biological candidates and unexpected genes, and highlight several pathways (let-7 targets, chromatin remodeling proteins and Hedgehog signaling) as important regulators of human stature. These results expand the picture of the biological regulation of human height and of the genetic architecture of this classical complex trait. 相似文献
79.
Meriem El Ghachi Nicole Howe Rodolphe Auger Alexandre Lambion Annick Guiseppi François Delbrassine Guillaume Manat Sophie Roure Sabine Peslier Eric Sauvage Lutz Vogeley Juan-Carlos Rengifo-Gonzalez Paulette Charlier Dominique Mengin-Lecreulx Maryline Foglino Thierry Touzé Martin Caffrey Frédéric Kerff 《Cellular and molecular life sciences : CMLS》2017,74(12):2319-2332
Type 2 phosphatidic acid phosphatases (PAP2s) can be either soluble or integral membrane enzymes. In bacteria, integral membrane PAP2s play major roles in the metabolisms of glycerophospholipids, undecaprenyl-phosphate (C55-P) lipid carrier and lipopolysaccharides. By in vivo functional experiments and biochemical characterization we show that the membrane PAP2 coded by the Bacillus subtilis yodM gene is the principal phosphatidylglycerol phosphate (PGP) phosphatase of B. subtilis. We also confirm that this enzyme, renamed bsPgpB, has a weaker activity on C55-PP. Moreover, we solved the crystal structure of bsPgpB at 2.25 Å resolution, with tungstate (a phosphate analog) in the active site. The structure reveals two lipid chains in the active site vicinity, allowing for PGP substrate modeling and molecular dynamic simulation. Site-directed mutagenesis confirmed the residues important for substrate specificity, providing a basis for predicting the lipids preferentially dephosphorylated by membrane PAP2s. 相似文献
80.