Choosing between Cox proportional hazards and logistic models for interval-censored data via bootstrap

This work develops a new methodology in order to discriminate models for interval-censored data based on bootstrap residual simulation by observing the deviance difference from one model in relation to another, according to Hinde (1992). Generally, this sort of data can generate a large number of tied observations and, in this case, survival time can be regarded as discrete. Therefore, the Cox proportional hazards model for grouped data (Prentice & Gloeckler, 1978) and the logistic model (Lawless, 1982) can befitted by means of generalized linear models. Whitehead (1989) considered censoring to be an indicative variable with a binomial distribution and fitted the Cox proportional hazards model using complementary log-log as a link function. In addition, a logistic model can be fitted using logit as a link function. The proposed methodology arises as an alternative to the score tests developed by Colosimo et al. (2000), where such models can be obtained for discrete binary data as particular cases from the Aranda-Ordaz distribution asymmetric family. These tests are thus developed with a basis on link functions to generate such a fit. The example that motivates this study was the dataset from an experiment carried out on a flax cultivar planted on four substrata susceptible to the pathogen Fusarium oxysoprum. The response variable, which is the time until blighting, was observed in intervals during 52 days. The results were compared with the model fit and the AIC values.

Integrable aspects of the scaling q-state Potts models I: bound states and bootstrap closure

We discuss the q-state Potts models for q less than or equal to 4, in the scaling regimes close to their critical or tricritical points. Starting from the kink S-matrix elements proposed by Chim and Zamolodchikov, the bootstrap is closed for the scaling regions of all critical points, and for the tricritical points when 4 > q greater than or equal to 2. We also note a curious appearance of the extended last line of Freudenthal's magic square in connection with the Potts models. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Estimation of population profiles of two strains of the fly Megaselia scalaris (Diptera: Phoridae) by bootstrap simulation

A partir de perfis populacionais experimentais de linhagens do díptero forídeo Megaselia scalaris, foi determinado o número mínimo de perfis amostrais que devem ser repetidos, via processo de simulação bootstrap, para se ter uma estimativa confiável do perfil médio populacional e apresentar estimativas do erro-padrão como medida da precisão das simulações realizadas. Os dados originais são provenientes de populações experimentais fundadas com as linhagens SR e R4, com três réplicas cada, e que foram mantidas por 33 semanas pela técnica da transferência seriada em câmara de temperatura constante (25 ± 1,0ºC). A variável usada foi tamanho populacional e o modelo adotado para cada perfíl foi o de um processo estocástico estacionário. Por meio das simulações, os perfis de três populações experimentais foram amplificados, determinando-se, dessa forma, o tamanho mínimo de amostra. Fixado o tamanho de amostra, simulações bootstrap foram realizadas para construção de intervalos de confiança e comparação dos perfis médios populacionais das duas linhagens. Os resultados mostram que com o tamanho de amostra igual a 50 inicia-se o processo de estabilização dos valores médios.

Orthogonal projections and bootstrap resampling procedures in the study of infraspecific variation

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Bootstrap confidence regions for canonical variates: Application to studies of evolutionary differentiation

Theory recently developed to construct confidence regions based on the parametric bootstrap is applied to add inferential information to graphical displays of sample centroids in canonical variate analysis. Problems of morphometric differentiation among subspecies and species are addressed using numerical resampling procedures.

Métodos de bootstrap e aplicações em problemas biológicos

Pós-graduação em Matemática Universitária - IGCE

Intraspecific scaling of arterial blood pressure in the Burmese python

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Autonomic control of heart rate during orthostasis and the importance of orthostatic-tachycardia in the snake Python molurus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Diversidade de Phytophthora parasitica isolados de Citrus usando seqüências de nucleotídeos da região ITS-5.8S rDNA

Realizou-se estudo para caracterização e verificação da diversidade genética de Phytophthora parasitica, agente causador da gomose dos citros. Quatorze isolados de Phytophthora parasitica, provenientes do Estado de São Paulo, foram seqüenciados a partir das regiões internas transcritas (ITS1 e ITS2) do gene 5.8S. Obtiveram-se seqüências de 812 pb a 860 pb que foram comparadas com seqüências de outras espécies de Phytophthora spp depositadas no NCBI. Foram feitos estudos filogenéticos, utilizando-se o método neighbor-joining com 1000 bootstrap e construído o dendrograma mais representativo. Obtiveram-se os resultados de 98,88% a 100% de similaridade genética entre os 14 isolados paulistas, e 99,5% a 98,8% entre estes e a seqüência de P. nicotianae (gi| 8927482) obtida do GenBank NCBI.

Genetic characterization of Brazilian annual Arachis species from sections Arachis and Heteranthae using RAPD markers

The genus Arachis is divided into nine taxonomic sections. Section Arachis is composed of annual and perennial species, while section Heteranthae has only annual species. The objective of this study was to investigate the genetic relationships among 15 Brazilian annual accessions from Arachis and Heteranthae using RAPD markers. Twenty-seven primers were tested, of which nine produced unique fingerprintings for all the accessions studied. A total of 88 polymorphic fragments were scored and the number of fragments per primer varied from 6 to 17 with a mean of 9.8. Two specific markers were identified for species with 2n = 18 chromosomes. The phenogram derived from the RAPD data corroborated the morphological classification. The bootstrap analysis divided the genotypes into two significant clusters. The first cluster contained all the section Arachis species, and the accessions within it were grouped based upon the presence or absence of the 'A' pair and the number of chromosomes. The second cluster grouped all accessions belonging to section Heteranthae.

Phylogenetic relationships within the speciose family Characidae (Teleostei: Ostariophysi: Characiformes) based on multilocus analysis and extensive ingroup sampling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pulmonary receptors in reptiles: discharge patterns of receptor populations in snakes versus turtles

This study examines the effects of lung inflation/deflation with and without CO2 on the entire population of pulmonary receptors in the vagus nerve in two species of snakes and two species of turtles. We asked the question, how does the response of the entire mixed population of pulmonary stretch receptors (PSR) and intrapulmonary chemoreceptors (IPC) in species possessing both differ from that in species with only PSR? This was studied under conditions of artificial ventilation with the secondary goal of extending observations on the presence/absence of IPC to a further three species. Our results indirectly illustrate the presence of IPC in the Burmese python and South American rattlesnake but not the side necked turtle, adding support to the hypothesis that IPC first arose in diapsid reptiles. In both species of snake, CO2-sensitive discharge (presumably from IPC) predominated almost to the exclusion of CO2-insensitive discharge (presumably arising from PSR) while the opposite was true for both species of turtle. The data suggest that for animals breathing air under conditions of normal metabolism there is little to distinguish between the discharge profiles of the total population of receptors arising from the lungs in the different groups. Interestingly, however, under conditions of elevated environmental CO2 most volume-related feedback from the lungs is abolished in the two species of snakes, while under conditions of elevated metabolic CO2, it is estimated that volume feedback from the lungs would be enhanced in these same species.

The role of nitric oxide in regulation of the cardiovascular system in reptiles

The roles that nitric oxide (NO) plays in the cardiovascular system of reptiles are reviewed, with particular emphasis on its effects on central vascular blood flows in the systemic and pulmonary circulations. New data is presented that describes the effects on hemodynamic variables in varanid lizards of exogenously administered NO via the nitric oxide donor sodium nitroprusside (SNP) and, preliminary data on the effects of SNP inhibition of nitric oxide synthase (NOS) by L-nitroarginine methyl ester (L-NAME). Furthermore. on hemodynamic variables in the tegu lizard are presented. The findings are compared with previously published data from Our laboratory on three other species of reptiles: pythons (Skovgaard, N., Galli, G., Taylor, E.W., Conlon, J.M., Wang.. T., 2005. Hemodynamic effects of python neuropeptide gamma in the anesthetized python, Python regius. Regul. Pept. 18, 15-26), rattlesnakes (Galli, G., Skovgaard, N., Abe, A.S., Taylor, E.W., Wang, T., 2005. The role of nitric oxide in the regulation of the systemic and the pulmonary vasculature of the rattlesnake, Crotalus durissus terrificus. J. Comp. Physiol. 175B, 201-208) and turtles (Crossley, D.A., Wang, T., Altimiras, J., 2000. Role of nitric oxide in the systemic and pulmonary circulation of anesthetized turtles (Trachemys scripta). J. Exp. Zool. 286, 683-689). These five species of reptiles possess different combinations of division of the heart and structural complexity of the lungs. Comparison of their responses to NO donors and NOS inhibitors may reveal whether the potential contribution of NO to vascular tone correlates with pulmonary complexity and/or with blood pressure. All existing studies oil reptiles have clearly established a potential role for NO in regulating vascular tone in the systemic circulation and NO may be important for maintaining basal systemic vascular tone in varanid lizards, pythons and turtles, through a continuous release of NO. In contrast., the pulmonary circulation is less responsive to NO donors or NOS inhibitors, and it was only in pythons and varanid lizards that the lungs responded to SNP. Both species have a functionally separated heart, so it is possible that NO may exert a larger role in species with low pulmonary blood pressures, irrespective of lung complexity. (C) 2005 Elsevier B.V. All rights reserved.

Minimal volume regulation after shrinkage of red blood cells from five species of reptiles

Red blood cells (RBCs) from most vertebrates restore volume upon hypertonic shrinkage and the mechanisms underlying this regulatory volume increase (RVI) have been studied extensively in these cells. Despite the phylogenetically interesting position of reptiles, very little is known about their red cell function. The present study demonstrates that oxygenated RBCs in all major groups of reptiles exhibit no or a very reduced RVI upon -25% calculated hyperosmotic shrinkage. Thus, RBCs from the snakes Crotalus durissus and Python regius, the turtle Trachemys scripta and the alligator Alligator mississippiensis showed no statistically significant RVI within 120 min after shrinkage, while the lizard Tupinambis merianae showed 22% volume recovery after 120 min. Amiloride (10(-4) M) and bumetanide (10(-5) M) had no effect on the RVI in T merianae, indicating no involvement of the Na(+)/H(+) exchanger (NHE) or the Na(+)/K(+)/2Cl(-) co-transporter (NKCC) or insentive transporters. Deoxygenation of RBCs from A. mississippiensis and T merianae did not significantly affect RVI upon shrinkage. Deoxygenation per se of red blood cells from T merianae elicited a slow volume increase, but the mechanism was not characterized. It seems, therefore, that the RVI response based on NHE activation was lost among the early sauropsids that gave rise to modern reptiles and birds, while it was retained in mammals. An RVI response has then reappeared in birds, but based on activation of the NKCC. Alternatively, the absence of the RVI response may represent the most ancient condition, and could have evolved several times within vertebrates. (C) 2008 Elsevier B.V. All rights reserved.