Finite Population Inference for Causal Parameters

Thesis (Ph.D.)--University of Washington, 2016-08

Nonparametric Evaluation of Quantitative Traits in Population-Based Association Studies when the Genetic Model is Unknown

Statistical association between a single nucleotide polymorphism (SNP) genotype and a quantitative trait in genome-wide association studies is usually assessed using a linear regression model, or, in the case of non-normally distributed trait values, using the Kruskal-Wallis test. While linear regression models assume an additive mode of inheritance via equi-distant genotype scores, Kruskal-Wallis test merely tests global differences in trait values associated with the three genotype groups. Both approaches thus exhibit suboptimal power when the underlying inheritance mode is dominant or recessive. Furthermore, these tests do not perform well in the common situations when only a few trait values are available in a rare genotype category (disbalance), or when the values associated with the three genotype categories exhibit unequal variance (variance heterogeneity). We propose a maximum test based on Marcus-type multiple contrast test for relative effect sizes. This test allows model-specific testing of either dominant, additive or recessive mode of inheritance, and it is robust against variance heterogeneity. We show how to obtain mode-specific simultaneous confidence intervals for the relative effect sizes to aid in interpreting the biological relevance of the results. Further, we discuss the use of a related all-pairwise comparisons contrast test with range preserving confidence intervals as an alternative to Kruskal-Wallis heterogeneity test. We applied the proposed maximum test to the Bogalusa Heart Study dataset, and gained a remarkable increase in the power to detect association, particularly for rare genotypes. Our simulation study also demonstrated that the proposed non-parametric tests control family-wise error rate in the presence of non-normality and variance heterogeneity contrary to the standard parametric approaches. We provide a publicly available R library nparcomp that can be used to estimate simultaneous confidence intervals or compatible multiplicity-adjusted p-values associated with the proposed maximum test.

Effects of two teaching strategies on the relationship between nursing students’ self-efficacy and performance in BLS/AED

Purpose: Nurses and nursing students are often first responders to in-hospital cardiac arrest events; thus they are expected to perform Basic Life Support (BLS) and use an automated external defibrillator (AED) without delay. The aim of this study was to explore the relationship between nursing students’ self-efficacy and performance before and after receiving a particular training intervention in BLS/AED. Materials and methods: Explanatory correlational study. 177 nursing students received a 4-h training session in BLS/AED after being randomized to either a self-directed (SDG) or an instructor-directed teaching group (IDG).1 A validated self-efficacy scale, the Cardiff Test and Laerdal SkillReporter® software were used to assess students’ self-efficacy and performance in BLS/AED at pre-test, post-test and 3-month retention-test. Independent t-test analysis was performed to compare the differences between groups at pre-test. Pearson coefficient (r) was used to calculate the strength of the relationship between self-efficacy and performance in both groups at pre-test, post-test and retention-test. Results: Independent t-tests analysis showed that there were non-significant differences (p-values > 0.05) between groups for any of the variables measured. At pre-test, results showed that correlation between self-efficacy and performance was moderate for the IDG (r = 0.53; p < 0.05) and the SDG (r = 0.49; p < 0.05). At post-test, correlation between self-efficacy and performance was much higher for the SDG (r = 0.81; p < 0.05) than for the IDG (r = 0.32; p < 0.05), which in fact was weaker than at pre-test. Finally, it was found that whereas the correlation between self-efficacy and performance increased from the post-test to the retention-test to almost reach baseline levels for the ILG (r = 0.52; p < 0.05), it slightly decreased in this phase for the SDG (r = 0.77; p < 0.05). Conclusion: Student-directed strategies may be more effective than instructor-directed strategies at promoting self-assessment and, therefore, may help to improve and maintain the relationship between nursing student self-efficacy and actual ability to perform BLS/AED.

Efeito da administração da hormona PGF2α nos problemas pós-parto, mais concretamente na retenção placentária em bovinos leiteiros

Dissertação de Mestrado em Engenharia Zootécnica/Produção Animal

Child Abuse and Mental Disorders in Iranian Adolescents

Background: Child abuse is a serious social health problem all over the world with important adverse effects. Objectives: The aim of this study was to extend our understanding of the relation between mental disorders and child abuse. Materials and Methods: The study was designed as a cross-sectional survey on 700 students in secondary schools using multiple cluster sampling in Yazd, Iran in 2013. We applied 2 self reported questionnaires: DASS (depression anxiety stress scales)-42 for assessing mental disorders (anxiety, stress and depression) and a standard self-reported valid and reliable questionnaire for recording child abuse information in neglect, psychological, physical and sexual domains. The collected data was analyzed using SPSS software. P-values < 0.05 were considered as significant. Results: There was a statically significant correlation between mental disorder and child abuse score (Spearman rho: 0.2; P-value < 0.001). The highest correlations between mental disorders and child abuse were found in psychological domain, Spearman’s rho coefficients were 0.46, 0.41 and 0.36 for depression, anxiety and stress respectively (P-value < 0.001). Based on the results of logistic regression for mental disorder, females, last born adolescents and subjects with drug or alcohol abuser parents had mental disorder odds of 3, 0.4 and 1.9 times compared to others; and severe psychological abuse, being severely neglected and having sexual abuse had odds 90, 1.6 and 1.5 respectively in another model. Conclusions: Programming for mandatory reporting of child abuse by physicians and all health care givers e.g. those attending schools or health centers, in order to prevent or reduce its detrimental effects is useful and success in preventing child abuse could lead to reductions in the prevalence of mental disorders.

Modelagem matemática para o transporte de partículas sujeitas a múltiplos mecanismos de retenção

Discrepancies between classical model predictions and experimental data for deep bed filtration have been reported by various authors. In order to understand these discrepancies, an analytic continuum model for deep bed filtration is proposed. In this model, a filter coefficient is attributed to each distinct retention mechanism (straining, diffusion, gravity interception, etc.). It was shown that these coefficients generally cannot be merged into an effective filter coefficient, as considered in the classical model. Furthermore, the derived analytic solutions for the proposed model were applied for fitting experimental data, and a very good agreement between experimental data and proposed model predictions were obtained. Comparison of the obtained results with empirical correlations allowed identifying the dominant retention mechanisms. In addition, it was shown that the larger the ratio of particle to pore sizes, the more intensive the straining mechanism and the larger the discrepancies between experimental data and classical model predictions. The classical model and proposed model were compared via statistical analysis. The obtained p values allow concluding that the proposed model should be preferred especially when straining plays an important role. In addition, deep bed filtration with finite retention capacity was studied. This work also involves the study of filtration of particles through porous media with a finite capacity of filtration. It was observed, in this case, that is necessary to consider changes in the boundary conditions through time evolution. It was obtained a solution for such a model using different functions of filtration coefficients. Besides that, it was shown how to build a solution for any filtration coefficient. It was seen that, even considering the same filtration coefficient, the classic model and the one here propposed, show different predictions for the concentration of particles retained in the porous media and for the suspended particles at the exit of the media

A Retrospective-Longitudinal Examination of the Relationship between Apportionment of Seat Time in Community-College Algebra Courses and Student Academic Performance

During the past decade, there has been a dramatic increase by postsecondary institutions in providing academic programs and course offerings in a multitude of formats and venues (Biemiller, 2009; Kucsera & Zimmaro, 2010; Lang, 2009; Mangan, 2008). Strategies pertaining to reapportionment of course-delivery seat time have been a major facet of these institutional initiatives; most notably, within many open-door 2-year colleges. Often, these enrollment-management decisions are driven by the desire to increase market-share, optimize the usage of finite facility capacity, and contain costs, especially during these economically turbulent times. So, while enrollments have surged to the point where nearly one in three 18-to-24 year-old U.S. undergraduates are community college students (Pew Research Center, 2009), graduation rates, on average, still remain distressingly low (Complete College America, 2011). Among the learning-theory constructs related to seat-time reapportionment efforts is the cognitive phenomenon commonly referred to as the spacing effect, the degree to which learning is enhanced by a series of shorter, separated sessions as opposed to fewer, more massed episodes. This ex post facto study explored whether seat time in a postsecondary developmental-level algebra course is significantly related to: course success; course-enrollment persistence; and, longitudinally, the time to successfully complete a general-education-level mathematics course. Hierarchical logistic regression and discrete-time survival analysis were used to perform a multi-level, multivariable analysis of a student cohort (N = 3,284) enrolled at a large, multi-campus, urban community college. The subjects were retrospectively tracked over a 2-year longitudinal period. The study found that students in long seat-time classes tended to withdraw earlier and more often than did their peers in short seat-time classes (p < .05). Additionally, a model comprised of nine statistically significant covariates (all with p-values less than .01) was constructed. However, no longitudinal seat-time group differences were detected nor was there sufficient statistical evidence to conclude that seat time was predictive of developmental-level course success. A principal aim of this study was to demonstrate—to educational leaders, researchers, and institutional-research/business-intelligence professionals—the advantages and computational practicability of survival analysis, an underused but more powerful way to investigate changes in students over time.

Association of SNPs in LCP1 and CTIF with hearing in 11 year old children:findings from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort and the G-EAR consortium

BACKGROUND: The genetic basis of hearing loss in humans is relatively poorly understood. In recent years, experimental approaches including laboratory studies of early onset hearing loss in inbred mouse strains, or proteomic analyses of hair cells or hair bundles, have suggested new candidate molecules involved in hearing function. However, the relevance of these genes/gene products to hearing function in humans remains unknown. We investigated whether single nucleotide polymorphisms (SNPs) in the human orthologues of genes of interest arising from the above-mentioned studies correlate with hearing function in children. METHODS: 577 SNPs from 13 genes were each analysed by linear regression against averaged high (3, 4 and 8 kHz) or low frequency (0.5, 1 and 2 kHz) audiometry data from 4970 children in the Avon Longitudinal Study of Parents and Children (ALSPAC) birth-cohort at age eleven years. Genes found to contain SNPs with low p-values were then investigated in 3417 adults in the G-EAR study of hearing. RESULTS: Genotypic data were available in ALSPAC for a total of 577 SNPs from 13 genes of interest. Two SNPs approached sample-wide significance (pre-specified at p = 0.00014): rs12959910 in CBP80/20-dependent translation initiation factor (CTIF) for averaged high frequency hearing (p = 0.00079, β = 0.61 dB per minor allele); and rs10492452 in L-plastin (LCP1) for averaged low frequency hearing (p = 0.00056, β = 0.45 dB). For low frequencies, rs9567638 in LCP1 also enhanced hearing in females (p = 0.0011, β = -1.76 dB; males p = 0.23, β = 0.61 dB, likelihood-ratio test p = 0.006). SNPs in LCP1 and CTIF were then examined against low and high frequency hearing data for adults in G-EAR. Although the ALSPAC results were not replicated, a SNP in LCP1, rs17601960, is in strong LD with rs9967638, and was associated with enhanced low frequency hearing in adult females in G-EAR (p = 0.00084). CONCLUSIONS: There was evidence to suggest that multiple SNPs in CTIF may contribute a small detrimental effect to hearing, and that a sex-specific locus in LCP1 is protective of hearing. No individual SNPs reached sample-wide significance in both ALSPAC and G-EAR. This is the first report of a possible association between LCP1 and hearing function.

An in-depth characterisation of neonatal seizures by early continuous video-EEG analysis

Introduction Seizures are harmful to the neonatal brain; this compels many clinicians and researchers to persevere further in optimizing every aspects of managing neonatal seizures. Aims To delineate the seizure profile between non-cooled versus cooled neonates with hypoxic-ischaemic encephalopathy (HIE), in neonates with stroke, the response of seizure burden to phenobarbitone and to quantify the degree of electroclinical dissociation (ECD) of seizures. Methods The multichannel video-EEG was used in this research study as the gold standard to detect seizures, allowing accurate quantification of seizure burden to be ascertained in term neonates. The entire EEG recording for each neonate was independently reviewed by at least 1 experienced neurophysiologist. Data were expressed in medians and interquartile ranges. Linear mixed models results were presented as mean (95% confidence interval); p values <0.05 were deemed as significant. Results Seizure burden in cooled neonates was lower than in non-cooled neonates [60(39-224) vs 203(141-406) minutes; p=0.027]. Seizure burden was reduced in cooled neonates with moderate HIE [49(26-89) vs 162(97-262) minutes; p=0.020] when compared with severe HIE. In neonates with stroke, the background pattern showed suppression over the infarcted side and seizures demonstrated a characteristic pattern. Compared with 10 mg/kg, phenobarbitone doses at 20 mg/kg reduced seizure burden (p=0.004). Seizure burden was reduced within 1 hour of phenobarbitone administration [mean (95% confidence interval): -14(-20 to -8) minutes/hour; p<0.001], but seizures returned to pre-treatment levels within 4 hours (p=0.064). The ECD index in cooled, non-cooled neonates with HIE, stroke and in neonates with other diagnoses were 88%, 94%, 64% and 75% respectively. Conclusions Further research exploring the treatment effects on seizure burden in the neonatal brain is required. A change to our current treatment strategy is warranted as we continue to strive for more effective seizure control, anchored with use of the multichannel EEG as the surveillance tool.

Outpatient follow-up during the first year after heart transplantation, is it feasible?

First year follow-up after heart transplantation requires invasive tests. Although patients used to be hospitalized for this purpose, ambulatory invasive procedures now offer the possibility of outpatient follow-up. The feasibility and security of this strategy is unknown. From 2007 we transitioned to outpatient follow-up. We have retrospectively reviewed the clinical course of the outpatient group (2007 to 2014) and an inpatient group (2000–2006). Basal characteristics, hospital stay, infections, rejection episodes and vascular complications were evaluated. 87 patients had Inpatient Follow-up (IF) and 98 Outpatient Follow-up (OF). Basal characteristics were similar, with significant differences in immunosuppression (tacrolimus IF 44.8% vs. OF 90.8%, and mycophenolate IF 86.2% vs OF 100%, both p values < 0.001) and age (IF 52 ± 11.5 years vs. OF 56.1 ± 11 years, p = 0.016). In the OF group more clinical visits were performed (IF 10 vs. OF 13, p < 0.001) while hospital stay was lower (IF 23 days vs. OF 3 days, p < 0.001). The rate of infection, rejection, and vascular complications was similar. No difference was found in 1-year mortality (IF 2.3% vs. 1.0%, p = 0.60). First year post-cardiac transplantation outpatient follow-up seems to be feasible and safe in terms of infection, rejection, vascular complications and mortality.

Outpatient follow-up during the first year after heart transplantation, is it feasible?

First year follow-up after heart transplantation requires invasive tests. Although patients used to be hospitalized for this purpose, ambulatory invasive procedures now offer the possibility of outpatient follow-up. The feasibility and security of this strategy is unknown. From 2007 we transitioned to outpatient follow-up. We have retrospectively reviewed the clinical course of the outpatient group (2007 to 2014) and an inpatient group (2000–2006). Basal characteristics, hospital stay, infections, rejection episodes and vascular complications were evaluated. 87 patients had Inpatient Follow-up (IF) and 98 Outpatient Follow-up (OF). Basal characteristics were similar, with significant differences in immunosuppression (tacrolimus IF 44.8% vs. OF 90.8%, and mycophenolate IF 86.2% vs OF 100%, both p values < 0.001) and age (IF 52 ± 11.5 years vs. OF 56.1 ± 11 years, p = 0.016). In the OF group more clinical visits were performed (IF 10 vs. OF 13, p < 0.001) while hospital stay was lower (IF 23 days vs. OF 3 days, p < 0.001). The rate of infection, rejection, and vascular complications was similar. No difference was found in 1-year mortality (IF 2.3% vs. 1.0%, p = 0.60). First year post-cardiac transplantation outpatient follow-up seems to be feasible and safe in terms of infection, rejection, vascular complications and mortality.

Efecto del consumo concomitante de inhibidores de bomba protones y levotiroxina : revisión sistemática y metaanálisis

Estudios afirman que la acidez gástrica es importante en la absorción de levotiroxina (LT4) con resultados controversiales sobre la interacción entre inhibidores de bomba de protones (IBP) y LT4. El objetivo del estudio fue establecer el efecto del uso concomitante de LT4 e IBP en los niveles de TSH en pacientes adultos con hipotiroidismo primario. Se realizó una revisión sistemática mediante búsqueda en Medline, Embase, Lilacs, Bireme, Scielo, Cochrane y Universidad de York, Access Pharmacy, Google Scholar, Dialnet y Opengray. La búsqueda no se limito por lenguaje. Se evaluó el efecto en la diferencia de medias de TSH luego del consumo de LT4 y luego del consumo concomitante con IBP. Se hizo un metaanálisis, análisis de subgrupos y análisis de sensibilidad utilizando el programa Review Manager 5.3. Se eligieron 5 artículos para el análisis cualitativo y 3 para el metaanálisis. La calidad de los estudios fue buena y el riesgo de sesgos bajo. La diferencia de medias obtenida fue 0.21 mUI/L (IC95%: 0.02-0.40; p=0.03; I2:0%). En el análisis de subgrupos en pacientes mayores de 55 años la diferencia de medias fue 0.21 mUI/L (IC95%: 0.01-0.40; p=0.27; I2:19%). En el análisis de sensibilidad se excluyo el estudio con mayor muestra y la diferencia de medias fue 0.49 mUI/L (IC95%: -0.12 a 1.11; p=0.12; I2:0%). La diferencia de medias de TSH luego del consumo concomitante no se considera clínicamente significativa pues no representa riesgo para el paciente. Son necesarios estudios clínicos aleatorizados y evaluar el efecto en los niveles de T4 libre.

Haplotype distribution of five nuclear genes based on network genealogies and Bayesian inference indicates that Trypanosoma cruzi hybrid strains are polyphyletic

Chagas disease is still a major public health problem in Latin America. Its causative agent, Trypanosoma cruzi, can be typed into three major groups, T. cruzi I, T. cruzi II and hybrids. These groups each have specific genetic characteristics and epidemiological distributions. Several highly virulent strains are found in the hybrid group; their origin is still a matter of debate. The null hypothesis is that the hybrids are of polyphyletic origin, evolving independently from various hybridization events. The alternative hypothesis is that all extant hybrid strains originated from a single hybridization event. We sequenced both alleles of genes encoding EF-1 alpha, actin and SSU rDNA of 26 T. cruzi strains and DHFR-TS and TR of 12 strains. This information was used for network genealogy analysis and Bayesian phylogenies. We found T. cruzi I and T. cruzi II to be monophyletic and that all hybrids had different combinations of T. cruzi I and T. cruzi II haplotypes plus hybrid-specific haplotypes. Bootstrap values (networks) and posterior probabilities (Bayesian phylogenies) of clades supporting the monophyly of hybrids were far below the 95% confidence interval, indicating that the hybrid group is polyphyletic. We hypothesize that T. cruzi I and T. cruzi II are two different species and that the hybrids are extant representatives of independent events of genome hybridization, which sporadically have sufficient fitness to impact on the epidemiology of Chagas disease.

Using Bayesian networks with rule extraction to infer the risk of weed infestation in a corn-crop

This paper describes the modeling of a weed infestation risk inference system that implements a collaborative inference scheme based on rules extracted from two Bayesian network classifiers. The first Bayesian classifier infers a categorical variable value for the weed-crop competitiveness using as input categorical variables for the total density of weeds and corresponding proportions of narrow and broad-leaved weeds. The inferred categorical variable values for the weed-crop competitiveness along with three other categorical variables extracted from estimated maps for the weed seed production and weed coverage are then used as input for a second Bayesian network classifier to infer categorical variables values for the risk of infestation. Weed biomass and yield loss data samples are used to learn the probability relationship among the nodes of the first and second Bayesian classifiers in a supervised fashion, respectively. For comparison purposes, two types of Bayesian network structures are considered, namely an expert-based Bayesian classifier and a naive Bayes classifier. The inference system focused on the knowledge interpretation by translating a Bayesian classifier into a set of classification rules. The results obtained for the risk inference in a corn-crop field are presented and discussed. (C) 2009 Elsevier Ltd. All rights reserved.

Multicollinearity and financial constraint in investment decisions: a Bayesian generalized ridge regression

This paper addresses the investment decisions considering the presence of financial constraints of 373 large Brazilian firms from 1997 to 2004, using panel data. A Bayesian econometric model was used considering ridge regression for multicollinearity problems among the variables in the model. Prior distributions are assumed for the parameters, classifying the model into random or fixed effects. We used a Bayesian approach to estimate the parameters, considering normal and Student t distributions for the error and assumed that the initial values for the lagged dependent variable are not fixed, but generated by a random process. The recursive predictive density criterion was used for model comparisons. Twenty models were tested and the results indicated that multicollinearity does influence the value of the estimated parameters. Controlling for capital intensity, financial constraints are found to be more important for capital-intensive firms, probably due to their lower profitability indexes, higher fixed costs and higher degree of property diversification.