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51.
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
52.
53.
Grégoire Masliah Pierre Barraud Frédéric H. -T. Allain 《Cellular and molecular life sciences : CMLS》2013,70(11):1875-1895
The double-stranded RNA binding domain (dsRBD) is a small protein domain of 65–70 amino acids adopting an αβββα fold, whose central property is to bind to double-stranded RNA (dsRNA). This domain is present in proteins implicated in many aspects of cellular life, including antiviral response, RNA editing, RNA processing, RNA transport and, last but not least, RNA silencing. Even though proteins containing dsRBDs can bind to very specific dsRNA targets in vivo, the binding of dsRBDs to dsRNA is commonly believed to be shape-dependent rather than sequence-specific. Interestingly, recent structural information on dsRNA recognition by dsRBDs opens the possibility that this domain performs a direct readout of RNA sequence in the minor groove, allowing a global reconsideration of the principles describing dsRNA recognition by dsRBDs. We review in this article the current structural and molecular knowledge on dsRBDs, emphasizing the intricate relationship between the amino acid sequence, the structure of the domain and its RNA recognition capacity. We especially focus on the molecular determinants of dsRNA recognition and describe how sequence discrimination can be achieved by this type of domain. 相似文献
54.
Identification of the gene responsible for methylmalonic aciduria and homocystinuria, cblC type 总被引:10,自引:0,他引:10
Lerner-Ellis JP Tirone JC Pawelek PD Doré C Atkinson JL Watkins D Morel CF Fujiwara TM Moras E Hosack AR Dunbar GV Antonicka H Forgetta V Dobson CM Leclerc D Gravel RA Shoubridge EA Coulton JW Lepage P Rommens JM Morgan K Rosenblatt DS 《Nature genetics》2006,38(1):93-100
Methylmalonic aciduria and homocystinuria, cblC type (OMIM 277400), is the most common inborn error of vitamin B(12) (cobalamin) metabolism, with about 250 known cases. Affected individuals have developmental, hematological, neurological, metabolic, ophthalmologic and dermatologic clinical findings. Although considered a disease of infancy or childhood, some individuals develop symptoms in adulthood. The cblC locus was mapped to chromosome region 1p by linkage analysis. We refined the chromosomal interval using homozygosity mapping and haplotype analyses and identified the MMACHC gene. In 204 individuals, 42 different mutations were identified, many consistent with a loss of function of the protein product. One mutation, 271dupA, accounted for 40% of all disease alleles. Transduction of wild-type MMACHC into immortalized cblC fibroblast cell lines corrected the cellular phenotype. Molecular modeling predicts that the C-terminal region of the gene product folds similarly to TonB, a bacterial protein involved in energy transduction for cobalamin uptake. 相似文献
55.
Beukelaers P Vandenbosch R Caron N Nguyen L Moonen G Malgrange B 《Cellular and molecular life sciences : CMLS》2012,69(9):1493-1503
The adult brain most probably reaches its highest degree of plasticity with the lifelong generation and integration of new
neurons in the hippocampus and olfactory system. Neural precursor cells (NPCs) residing both in the subgranular zone of the
dentate gyrus and in the subventricular zone of the lateral ventricles continuously generate neurons that populate the dentate
gyrus and the olfactory bulb, respectively. The regulation of NPC proliferation in the adult brain has been widely investigated
in the past few years. Yet, the intrinsic cell cycle machinery underlying NPC proliferation remains largely unexplored. In
this review, we discuss the cell cycle components that are involved in the regulation of NPC proliferation in both neurogenic
areas of the adult brain. 相似文献
56.
Willer CJ Sanna S Jackson AU Scuteri A Bonnycastle LL Clarke R Heath SC Timpson NJ Najjar SS Stringham HM Strait J Duren WL Maschio A Busonero F Mulas A Albai G Swift AJ Morken MA Narisu N Bennett D Parish S Shen H Galan P Meneton P Hercberg S Zelenika D Chen WM Li Y Scott LJ Scheet PA Sundvall J Watanabe RM Nagaraja R Ebrahim S Lawlor DA Ben-Shlomo Y Davey-Smith G Shuldiner AR Collins R Bergman RN Uda M Tuomilehto J Cao A Collins FS Lakatta E Lathrop GM Boehnke M Schlessinger D Mohlke KL 《Nature genetics》2008,40(2):161-169
To identify genetic variants influencing plasma lipid concentrations, we first used genotype imputation and meta-analysis to combine three genome-wide scans totaling 8,816 individuals and comprising 6,068 individuals specific to our study (1,874 individuals from the FUSION study of type 2 diabetes and 4,184 individuals from the SardiNIA study of aging-associated variables) and 2,758 individuals from the Diabetes Genetics Initiative, reported in a companion study in this issue. We subsequently examined promising signals in 11,569 additional individuals. Overall, we identify strongly associated variants in eleven loci previously implicated in lipid metabolism (ABCA1, the APOA5-APOA4-APOC3-APOA1 and APOE-APOC clusters, APOB, CETP, GCKR, LDLR, LPL, LIPC, LIPG and PCSK9) and also in several newly identified loci (near MVK-MMAB and GALNT2, with variants primarily associated with high-density lipoprotein (HDL) cholesterol; near SORT1, with variants primarily associated with low-density lipoprotein (LDL) cholesterol; near TRIB1, MLXIPL and ANGPTL3, with variants primarily associated with triglycerides; and a locus encompassing several genes near NCAN, with variants strongly associated with both triglycerides and LDL cholesterol). Notably, the 11 independent variants associated with increased LDL cholesterol concentrations in our study also showed increased frequency in a sample of coronary artery disease cases versus controls. 相似文献
57.
Assouad has shown that a real-valued distance d = (dij)1 ≤ i < j ≤ n is isometrically embeddable in ℓ1space if and only if it belongs to the cut cone on n points. Determining if this condition holds is NP-complete. We use Assouad's
result in a constructive column generation algorithm for ℓ1-embeddability. The subproblem is an unconstrained 0-1 quadratic program, solved by Tabu Search and Variable Neighborhood
Search heuristics as well as by an exact enumerative algorithm. Computational results are reported. Several ways to approximate
a distance which is not ℓ1-embeddable by another one which is are also studied. 相似文献
58.
一种求解带有阻塞限制的混合流水车间的禁忌搜索算法 总被引:3,自引:0,他引:3
针对带有阻塞限制的混合流水车间调度问题,提出一种禁忌搜索算法和优先级规则相结合的方法.开发了启发式调度算法求出问题初始解,应用禁忌搜索算法对工件在第一级的排序进行优化,采用优先级规则进行其他级工件的排序.实验结果表明,该方法大大缩减了搜索空间,能够较好地解决此类调度问题. 相似文献
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60.