New methods for quantification and analysis of quantitative real-time polymerase chain reaction data

Quantitative real-time polymerase chain reaction (qPCR) is a sensitive gene quantitation method that has been widely used in the biological and biomedical fields. The currently used methods for PCR data analysis, including the threshold cycle (CT) method, linear and non-linear model fitting methods, all require subtracting background fluorescence. However, the removal of background fluorescence is usually inaccurate, and therefore can distort results. Here, we propose a new method, the taking-difference linear regression method, to overcome this limitation. Briefly, for each two consecutive PCR cycles, we subtracted the fluorescence in the former cycle from that in the later cycle, transforming the n cycle raw data into n-1 cycle data. Then linear regression was applied to the natural logarithm of the transformed data. Finally, amplification efficiencies and the initial DNA molecular numbers were calculated for each PCR run. To evaluate this new method, we compared it in terms of accuracy and precision with the original linear regression method with three background corrections, being the mean of cycles 1-3, the mean of cycles 3-7, and the minimum. Three criteria, including threshold identification, max R2, and max slope, were employed to search for target data points. Considering that PCR data are time series data, we also applied linear mixed models. Collectively, when the threshold identification criterion was applied and when the linear mixed model was adopted, the taking-difference linear regression method was superior as it gave an accurate estimation of initial DNA amount and a reasonable estimation of PCR amplification efficiencies. When the criteria of max R2 and max slope were used, the original linear regression method gave an accurate estimation of initial DNA amount. Overall, the taking-difference linear regression method avoids the error in subtracting an unknown background and thus it is theoretically more accurate and reliable. This method is easy to perform and the taking-difference strategy can be extended to all current methods for qPCR data analysis.^

Comparación a campo de distintos cultivares de olivo (Olea europaea L.) como hospedadores de Siphoninus phillyreae (Haliday)

La mosca blanca del fresno, Siphoninus phillyreae (Haliday) , es una especie polífaga invasiva que causa graves daños en sus hospedadores, entre ellos el olivo (Olea europaea L.). El uso del hospedador por parte de S. phillyreae fue observado en tres cultivares de olivo (Arauco, Arbequina y Aloreña) en el norte de la provincia de La Rioja (Argentina) durante 2007 y 2008. De cada cultivar se muestrearon seis plantas infestadas y de cada planta se tomaron ocho hojas. De cada hoja se registró la abundancia de adultos y estados inmaduros de la mosca blanca que fueron comparadas entre los cultivares mediante modelos lineales generales y mixtos. Los resultados obtenidos mostraron diferencias significativas entre las densidades de adultos y ninfas de S. phillyreae en los distintos cultivares de olivo analizados. Dichos resultados indican que este insecto realiza un uso diferente de los cultivares de olivo, siendo Arauco y Arbequina las variedades hospedadoras más utilizadas en la zona de estudio.

Genetic diversity among alfalfa genotypes (Medicago sativa L.) of non-dormant cultivars using SSR markers and agronomic traits

The aim of this study was to assess genetic diversity among 40 alfalfa (Medicago sativa L.) genotypes of different non-dormant (FD=8) cultivars. Biomass yield, regrowth speed and reaction to spring black stem, lepto leaf spot, and rust were evaluated. Analyses of variances were performed using a mixed model to examine the agronomic variation among individuals. A principal component analysis on standardized agronomic data was performed. Agronomic data were also used to calculate Gower's distance and UPGMA algorithm. For the molecular analysis, six SSR markers were evaluated and 84 alleles were identified. The genetic distance was estimated using standard Nei's distance. Average standard genetic diversity was 0.843, indicating a high degree of variability among genotypes. Finally, a generalized procrustes analysis was performed to calculate the correlation between molecular and agronomic distance, indicating a 65.4% of consensus. This value is likely related to the low number of individuals included in the study, which might have underestimated the real phenotypic variability among genotypes. Despite the low number of individuals and SSR markers analyzed, this study provides a baseline for future diversity studies to identify genetically distant alfalfa individuals or cultivars.

Dive depth and dive duration data of male southern elephant seals from Marion Island between 2004 and 2008 with links to datasets

We describe the habitat use of 22 male southern elephant seals (Mirounga leonina) satellite tagged at Marion Island between 2004 and 2008. While a few areas of increased utilization appeared to be associated with areas of shallower bathymetry (such as sea-floor ridges and fracture zones), seals in our study did not target other areas of shallow bathymetry within close proximity to Marion Island. Rather, most elephant seals foraged pelagically over very deep water where much variation was evident in diel vertical migration strategies. These strategies resulted in generally deeper and longer dives than what has been reported for male elephant seals from other colonies. No significant differences were recorded for dive durations or dive depths between adults and sub-adults. However, younger animals displayed a positive relationship between dive durations and age, as well as between dive depths and age, while these relationships became negative for older animals. Mixed model outputs suggested that seals increased their aerobic fitness as migrations progressed, enabling them to undertake longer dives. We conclude that Marion Island male elephant seals exhibit much variability in dive strategy and are seemingly capable of exploiting a range of different prey types occurring in various depth layers.

At surface behaviour, dive depth and dive duration and associated hydrographic data of adult male southern elephant seals from King George Island from expedition JUB2010 with links to datasets

Understanding the distribution and foraging ecology of major consumers within pelagic systems, specifically in relation to physical parameters, can be important for the management of bentho-pelagic systems undergoing rapid change associated with global climate change and other anthropogenic disturbances such as fishing (i.e., the Antarctic Peninsula and Scotia Sea). We tracked 11 adult male southern elephant seals (Mirounga leonina), during their five-month post-moult foraging migrations from King George Island (Isla 25 de Mayo), northern Antarctic Peninsula, using tags capable of recording and transmitting behavioural data and in situ temperature and salinity data. Seals foraged mostly within the Weddell-Scotia Confluence, while a few foraged along the western Antarctic Peninsula shelf of the Bellingshausen Sea. Mixed model outputs suggest that the at-sea behaviour of seals was associated with a number of environmental parameters, especially seafloor depth, sea-ice concentrations and the temperature structure of the water column. Seals increased dive bottom times and travelled at slower speeds in shallower areas and areas with increased sea-ice concentrations. Changes in dive depth and durations, as well as relative amount of time spent during the bottom phases of dives, were observed in relation to differences in overall temperature gradient, likely as a response to vertical changes in prey distribution associated with temperature stratification in the water column. Our results illustrate the likely complex influences of bathymetry, hydrography and sea ice on the behaviour of male southern elephant seals in a changing environment and highlight the need for region-specific approaches to studying environmental influences on behaviour.

Noninvasive monitoring of serial changes in pulmonary vascular resistance and acute vasodilator testing using cardiac magnetic resonance

Objectives The study sought to evaluate the ability of cardiac magnetic resonance (CMR) to monitor acute and long-term changes in pulmonary vascular resistance (PVR) noninvasively. Background PVR monitoring during the follow-up of patients with pulmonary hypertension (PH) and the response to vasodilator testing require invasive right heart catheterization. Methods An experimental study in pigs was designed to evaluate the ability of CMR to monitor: 1) an acute increase in PVR generated by acute pulmonary embolization (n = 10); 2) serial changes in PVR in chronic PH (n = 22); and 3) changes in PVR during vasodilator testing in chronic PH (n = 10). CMR studies were performed with simultaneous hemodynamic assessment using a CMR-compatible Swan-Ganz catheter. Average flow velocity in the main pulmonary artery (PA) was quantified with phase contrast imaging. Pearson correlation and mixed model analysis were used to correlate changes in PVR with changes in CMR-quantified PA velocity. Additionally, PVR was estimated from CMR data (PA velocity and right ventricular ejection fraction) using a formula previously validated. Results Changes in PA velocity strongly and inversely correlated with acute increases in PVR induced by pulmonary embolization (r = –0.92), serial PVR fluctuations in chronic PH (r = –0.89), and acute reductions during vasodilator testing (r = –0.89, p ≤ 0.01 for all). CMR-estimated PVR showed adequate agreement with invasive PVR (mean bias –1.1 Wood units,; 95% confidence interval: –5.9 to 3.7) and changes in both indices correlated strongly (r = 0.86, p < 0.01). Conclusions CMR allows for noninvasive monitoring of acute and chronic changes in PVR in PH. This capability may be valuable in the evaluation and follow-up of patients with PH.

Climatic factors control rodent seed predation in Pinus pinea L. stands in Central Spain

- Context: Pinus pinea L. presents serious problems of natural regeneration in managed forest of Central Spain. The species exhibits specific traits linked to frugivore activity. Therefore, information on plant–animal interactions may be crucial to understand regeneration failure. - Aims: Determining the spatio-temporal pattern of P. pinea seed predation by Apodemus sylvaticus L. and the factors involved. Exploring the importance of A. sylvaticus L. as a disperser of P. pinea. Identifying other frugivores and their seasonal patterns. - Methods: An intensive 24-month seed predation trial was carried out. The probability of seeds escaping predation was modelled through a zero-inflated binomial mixed model. Experiments on seed dispersal by A. sylvaticus were conducted. Cameras were set up to identify other potential frugivores. - Results: Decreasing rodent population in summer and masting enhances seed survival. Seeds were exploited more rapidly nearby parent trees and shelters. A. sylvaticus dispersal activity was found to be scarce. Corvids marginally preyed upon P. pinea seeds. - Conclusions: Survival of P. pinea seeds is climate-controlled through the timing of the dry period together with masting occurrence. Should germination not take place during the survival period, establishment may be limited. A. sylvaticus mediated dispersal does not modify the seed shadow. Seasonality of corvid activity points to a role of corvids in dispersal.

Identidade profissional: como se veem os professores na escola atual

Dissertação apresentada para a obtenção do grau de mestre em Ciências da Educação - área de Supervisão e Orientação Pegagógica

On the magnitude of the electrostatic contribution to ligand-DNA interactions.

A model based on the nonlinear Poisson-Boltzmann equation is used to study the electrostatic contribution to the binding free energy of a simple intercalating ligand, 3,8-diamino-6-phenylphenanthridine, to DNA. We find that the nonlinear Poisson-Boltzmann model accurately describes both the absolute magnitude of the pKa shift of 3,8-diamino-6-phenylphenanthridine observed upon intercalation and its variation with bulk salt concentration. Since the pKa shift is directly related to the total electrostatic binding free energy of the charged and neutral forms of the ligand, the accuracy of the calculations implies that the electrostatic contributions to binding are accurately predicted as well. Based on our results, we have developed a general physical description of the electrostatic contribution to ligand-DNA binding in which the electrostatic binding free energy is described as a balance between the coulombic attraction of a ligand to DNA and the disruption of solvent upon binding. Long-range coulombic forces associated with highly charged nucleic acids provide a strong driving force for the interaction of cationic ligands with DNA. These favorable electrostatic interactions are, however, largely compensated for by unfavorable changes in the solvation of both the ligand and the DNA upon binding. The formation of a ligand-DNA complex removes both charged and polar groups at the binding interface from pure solvent while it displaces salt from around the nucleic acid. As a result, the total electrostatic binding free energy is quite small. Consequently, nonpolar interactions, such as tight packing and hydrophobic forces, must play a significant role in ligand-DNA stability.

Marcadores prognósticos em recém-nascidos portadores de mielomeningocele

Introdução: Pacientes com mielomeningocele apresentam elevada mortalidade e desenvolvem déficits neurológicos que ocorrem, primariamente, pelo desenvolvimento anormal da medula e de raízes nervosas e, secundariamente, por complicações adquiridas no período pós-natal. O desafio no cuidado desses pacientes é o reconhecimento precoce dos recém-nascidos de risco para evolução desfavorável a fim de estabelecer estratégias terapêuticas individualizadas. Objetivo: Este estudo tem como objetivo identificar marcadores prognósticos de curto prazo para recém-nascidos com mielomeningocele. As características anatômicas do defeito medular e da sua correção neurocirúrgica foram analisadas para esta finalidade. Métodos: Foi realizado um estudo de coorte retrospectiva com 70 pacientes com mielomeningocele em topografia torácica, lombar ou sacral nascidos entre janeiro de 2007 a dezembro de 2013 no Centro Neonatal do Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. Pacientes com infecção congênita, anomalias cromossômicas e outras malformações maiores não relacionadas à mielomeningocele foram excluídos da análise. As características anatômicas da mielomeningocele e a sua correção neurocirúrgica foram analisadas quanto aos seguintes desfechos: reanimação neonatal, tempo de internação, necessidade de derivação ventricular, deiscência da ferida operatória, infecção da ferida operatória, infecção do sistema nervoso central e sepse. Para a análise bivariada dos desfechos qualitativos com os fatores de interesse foram empregados testes do qui-quadrado e exato de Fisher. Para a análise do desfecho quantitativo, tempo de internação hospitalar, foram empregados testes de Mann-Whitney. Foram estimados os riscos relativos e os respectivos intervalos com 95% de confiança. Foram desenvolvidos modelos de regressão linear múltipla para os desfechos quantitativos e regressão de Poisson para os desfechos qualitativos. Resultados: Durante o período do estudo 12.559 recém-nascidos foram admitidos no Centro Neonatal do Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. Oitenta pacientes foram diagnosticados com mielomeningocele, com incidência de 6,4 casos para cada 1.000 nascidos vivos. Dez pacientes foram excluídos da análise devido à mielomeningocele em topografia cervical (n = 1), à cardiopatia congênita (n = 4), à trissomia do cromossomo 13 (n = 1), à onfalocele (n = 3) e à encefalocele (n = 1). Ocorreram três óbitos (4,28%). Mielomeningocele extensa foi associada a infecção do sistema nervoso central, a complicação de ferida operatória e a maior tempo de internação hospitalar. Os pacientes com mielomeningocele em topografia torácica apresentaram tempo de internação, em média, 39 dias maior que aqueles com defeito em topografia lombar ou sacral. Houve maior necessidade de reanimação em sala de parto entre os pacientes com macrocrania ao nascer. A correção cirúrgica realizada após 48 horas de vida aumentou em 5,7 vezes o risco de infecção do sistema nervoso central. Entre os pacientes operados nas primeiras 48 horas de vida não foi observado benefício adicional na correção cirúrgica realizada em \"tempo zero\". A ausência de hidrocefalia antenatal foi um marcador de bom prognóstico. Nestes pacientes, a combinação dos desfechos necessidade de derivação ventricular, complicações infecciosas, complicações de ferida operatória e reanimação em sala de parto foi 70% menos frequente. Conclusão: Este estudo permitiu identificar marcadores prognósticos de curto prazo em recém-nascidos com mielomeningocele. Os defeitos medulares extensos e a correção cirúrgica após 48 horas de vida influenciaram negativamente na evolução de curto prazo. As lesões extensas foram associadas a maiores taxas de infecção do sistema nervoso central, a complicações de ferida operatória e a internação hospitalar prolongada. A correção cirúrgica realizada após 48 horas de vida aumentou significativamente a ocorrência de infecção do sistema nervoso central. Ausência de hidrocefalia antenatal foi associada a menor número de complicações nos primeiros dias de vida

Corneal Biomechanics, Retinal Nerve Fiber Layer, and Optic Disc in Children

Purpose: To evaluate the possible associations between corneal biomechanical parameters, optic disc morphology, and retinal nerve fiber layer (RNFL) thickness in healthy white Spanish children. Methods: This cross-sectional study included 100 myopic children and 99 emmetropic children as a control group, ranging in age from 6 to 17 years. The Ocular Response Analyzer was used to measure corneal hysteresis (CH) and corneal resistance factor. The optic disc morphology and RNFL thickness were assessed using posterior segment optical coherence tomography (Cirrus HD-OCT). The axial length was measured using an IOLMaster, whereas the central corneal thickness was measured by anterior segment optical coherence tomography (Visante OCT). Results: The mean (±SD) age and spherical equivalent were 12.11 (±2.76) years and −3.32 (±2.32) diopters for the myopic group and 11.88 (±2.97) years and +0.34 (±0.41) diopters for the emmetropic group. In a multivariable mixed-model analysis in myopic children, the average RNFL thickness and rim area correlated positively with CH (p = 0.007 and p = 0.001, respectively), whereas the average cup-to-disc area ratio correlated negatively with CH (p = 0.01). We did not observe correlation between RNFL thickness and axial length (p = 0.05). Corneal resistance factor was only positively correlated with the rim area (p = 0.001). The central corneal thickness did not correlate with the optic nerve parameters or with RNFL thickness. These associations were not found in the emmetropic group (p > 0.05 for all). Conclusions: The corneal biomechanics characterized with the Ocular Response Analyzer system are correlated with the optic disc profile and RNFL thickness in myopic children. Low CH values may indicate a reduction in the viscous dampening properties of the cornea and the sclera, especially in myopic children.

Identidade profissional: como se veem os professores na escola atual

Dissertação apresentada para a obtenção do grau de mestre em Ciências da Educação - área de Supervisão e Orientação Pegagógica

Modelling inpatient length of stay by a hierarchical mixture regression via the EM algorithm

The modelling of inpatient length of stay (LOS) has important implications in health care studies. Finite mixture distributions are usually used to model the heterogeneous LOS distribution, due to a certain proportion of patients sustaining-a longer stay. However, the morbidity data are collected from hospitals, observations clustered within the same hospital are often correlated. The generalized linear mixed model approach is adopted to accommodate the inherent correlation via unobservable random effects. An EM algorithm is developed to obtain residual maximum quasi-likelihood estimation. The proposed hierarchical mixture regression approach enables the identification and assessment of factors influencing the long-stay proportion and the LOS for the long-stay patient subgroup. A neonatal LOS data set is used for illustration, (C) 2003 Elsevier Science Ltd. All rights reserved.

Feeding ecology of the fish ectoparasite Gnathia sp. (Crustacea: Isopoda) from the Great Barrier Reef, and its implications for fish cleaning behaviour

The feeding rate of a parasitic gnathiid isopod on fish was examined. Individual fish, Hemigymnus melapterus, were exposed to gnathiid larvae and sampled after 5, 10, 30, 60, and 240 min. I recorded whether larvae had an engorged gut, an engorged gut containing red material, or had dropped off the fish after having completed engorgement; variation among sampling times and larval stages was analyzed using generalized linear mixed model analyses. The likelihood that larvae had an engorged gut increased with time and varied with larval stage. First stage (1.45 mm) larvae. After 30 min, however, most (>93%) larvae had an engorged gut regardless of their larval stage. The likelihood of red material in the gut of third stage larvae increased over time (46% after 30 min, 70% after 60 min, and 86% after 240 min) while that of first and second stage larvae remained relatively low (

Analysis of Melanoma Onset: Assessing Familial Aggregation by Using Estimating Equations and Fitting Variance Components via Bayesian Random Effects Models

We investigate whether relative contributions of genetic and shared environmental factors are associated with an increased risk in melanoma. Data from the Queensland Familial Melanoma Project comprising 15,907 subjects arising from 1912 families were analyzed to estimate the additive genetic, common and unique environmental contributions to variation in the age at onset of melanoma. Two complementary approaches for analyzing correlated time-to-onset family data were considered: the generalized estimating equations (GEE) method in which one can estimate relationship-specific dependence simultaneously with regression coefficients that describe the average population response to changing covariates; and a subject-specific Bayesian mixed model in which heterogeneity in regression parameters is explicitly modeled and the different components of variation may be estimated directly. The proportional hazards and Weibull models were utilized, as both produce natural frameworks for estimating relative risks while adjusting for simultaneous effects of other covariates. A simple Markov Chain Monte Carlo method for covariate imputation of missing data was used and the actual implementation of the Bayesian model was based on Gibbs sampling using the free ware package BUGS. In addition, we also used a Bayesian model to investigate the relative contribution of genetic and environmental effects on the expression of naevi and freckles, which are known risk factors for melanoma.