Quantifying Selection Bias from Birth History Estimates of Child Mortality

Thesis (Master's)--University of Washington, 2016-08

Publication Bias

According to the Declaration of Helsinki, as well as the Statement on Public Disclosure of Clinical Trial Results of the World Health Organization, every researcher has the ethical obligation to publish research results on all trials with human participants in a complete and accurate way within 12 months after the end of the trial.1,2 Nevertheless, for several reasons, not all research results are published in an accurate way in case they are released at all. This phenomenon of publication bias may not only create a false impression on the reliability of clinical research business, but it may also affect the evidence of clinical conclusions about the best treatments, which are mostly based on published data and results.

Study of tRNA modifying enzymes and codon usage bias in cancer

Recent evidences indicate that tRNA modifications and tRNA modifying enzymes may play important roles in complex human diseases such as cancer, neurological disorders and mitochondrial-linked diseases. We postulate that expression deregulation of tRNA modifying enzymes affects the level of tRNA modifications and, consequently, their function and the translation efficiency of their tRNA corresponding codons. Due to the degeneracy of the genetic code, most amino acids are encoded by two to six synonymous codons. This degeneracy and the biased usage of synonymous codons cause alterations that can span from protein folding to enhanced translation efficiency of a select gene group. In this work, we focused on cancer and performed a meta-analysis study to compare microarray gene expression profiles, reported by previous studies and evaluate the codon usage of different types of cancer where tRNA modifying enzymes were found de-regulated. A total of 36 different tRNA modifying enzymes were found de-regulated in most cancer datasets analyzed. The codon usage analysis revealed a preference for codons ending in AU for the up-regulated genes, while the down-regulated genes show a preference for GC ending codons. Furthermore, a PCA biplot analysis showed this same tendency. We also analyzed the codon usage of the datasets where the CTU2 tRNA modifying enzyme was found deregulated as this enzyme affects the wobble position (position 34) of specific tRNAs. Our data points to a distinct codon usage pattern between up and downregulated genes in cancer, which might be caused by the deregulation of specific tRNA modifying enzymes. This codon usage bias may augment the transcription and translation efficiency of some genes that otherwise, in a normal situation, would be translated less efficiently.

Investigating bias in recreational fishing surveys: Fishers listed in public telephone directories fish similarly to their unlisted counterparts

Several recent offsite recreational fishing surveys have used public landline telephone directories as a sampling frame. Sampling biases inherent in this method are recognised, but are assumed to be corrected through demographic data expansion. However, the rising prevalence of mobile-only households has potentially increased these biases by skewing raw samples towards households that maintain relatively high levels of coverage in telephone directories. For biases to be corrected through demographic expansion, both the fishing participation rate and fishing activity must be similar among listed and unlisted fishers within each demographic group. In this study, we tested for a difference in the fishing activity of listed and unlisted fishers within demographic groups by comparing their avidity (number of fishing trips per year), as well as the platform used (boat or shore) and species targeted on their most recent fishing trip. 3062 recreational fishers were interviewed at 34 tackle stores across 12 residential regions of Queensland, Australia. For each fisher, data collected included their fishing avidity, the platform used and species targeted on their most recent trip, their gender, age, residential region, and whether their household had a listed telephone number. Although the most avid fishers were younger and less likely to have a listed phone number, cumulative link models revealed that avidity was not affected by an interaction of phone listing status, age group and residential region (p > 0.05). Likewise, binomial generalized linear models revealed that there was no interaction between phone listing, age group and avidity acting on platform (p > 0.05), and platform was not affected by an interaction of phone listing status, age group, and residential region (p > 0.05). Ordination of target species using Bray-Curtis dissimilarity indices found a significant but irrelevant difference (i.e. small effect size) between listed and unlisted fishers (ANOSIM R < 0.05, p < 0.05). These results suggest that, at this time, the fishing activity of listed and unlisted fishers in Queensland is similar within demographic groups. Future research seeking to validate the assumptions of recreational fishing telephone surveys should investigate fishing participation rates of listed and unlisted fishers within demographic groups.

Information and the evolution of codon bias

The informational properties of biological systems are the subject of much debate and research. I present a general argument in favor of the existence and central importance of information in organisms, followed by a case study of the genetic code (specifically, codon bias) and the translation system from the perspective of information. The codon biases of 831 Bacteria and Archeae are analyzed and modeled as points in a 64-dimensional statistical space. The major results are that (1) codon bias evolution does not follow canonical patterns, and (2) the use of coding space in organsims is a subset of the total possible coding space. These findings imply that codon bias is a unique adaptive mechanism that owes its existence to organisms' use of information in representing genes, and that there is a particularly biological character to the resulting biased coding and information use.

Aniseikonia tests: The role of viewing mode, response bias, and size-color illusions.

PURPOSE To identify the factors responsible for the poor validity of the most common aniseikonia tests, which involve size comparisons of red-green stimuli presented haploscopically. METHODS Aniseikonia was induced by afocal size lenses placed before one eye. Observers compared the sizes of semicircles presented haploscopically via color filters. The main factor under study was viewing mode (free viewing versus short presentations under central fixation). To eliminate response bias, a three-response format allowed observers to respond if the left, the right, or neither semicircle appeared larger than the other. To control decisional (criterion) bias, measurements were taken with the lens-magnified stimulus placed on the left and on the right. To control for size-color illusions, measurements were made with color filters in both arrangements before the eyes and under binocular vision (without color filters). RESULTS Free viewing resulted in a systematic underestimation of lens-induced aniseikonia that was absent with short presentations. Significant size-color illusions and decisional biases were found that would be mistaken for aniseikonia unless appropriate action is taken. CONCLUSIONS To improve their validity, aniseikonia tests should use short presentations and include control conditions to prevent contamination from decisional/response biases. If anaglyphs are used, presence of size-color illusions must be checked for. TRANSLATIONAL RELEVANCE We identified optimal conditions for administration of aniseikonia tests and appropriate action for differential diagnosis of aniseikonia in the presence of response biases or size-color illusions. Our study has clinical implications for aniseikonia management.

Using a CGE Model to Identify the Policy Trade-Off between Unemployment and Inflation: The Efficient Phillips Curve

This paper provides a new reading of a classical economic relation: the short-run Phillips curve. Our point is that, when dealing with inflation and unemployment, policy-making can be understood as a multicriteria decisionmaking problem. Hence, we use so-called multiobjective programming in connection with a computable general equilibrium (CGE) model to determine the combinations of policy instruments that provide efficient combinations of inflation and unemployment. This approach results in an alternative version of the Phillips curve labelled as efficient Phillips curve. Our aim is to present an application of CGE models to a new area of research that can be especially useful when addressing policy exercises with real data. We apply our methodological proposal within a particular regional economy, Andalusia, in the south of Spain. This tool can give some keys for policy advice and policy implementation in the fight against unemployment and inflation.

Der Anti-Bias-Ansatz als Methode politischer Erwachsenenbildung

Vorurteile, Macht und Diskriminierung sind die zentralen Themen des Anti-Bias-Ansatzes, der Diskriminierung auf zwischenmenschlicher, struktureller und gesellschaftlich-kultureller Ebene berücksichtigt. Die eigene Verwobenheit in Machtverhältnisse und damit verbundene Erfahrungen von Diskriminierung und Privilegierung sind dabei der Ausgangspunkt des Lernens. Vision ist eine vorurteilsbewusste, diskriminierungskritische und machtsensible Gesellschaft. Der vorliegende Beitrag stellt den Anti-Bias-Ansatz als Methode politischer Erwachsenenbildung vor. Hierfür werden die (Macht-)Mechanismen der Entstehung, Verinnerlichung und Reproduktion von Vorurteilen und Diskriminierung beleuchtet und wird die Intersektionalität (Überkreuzung) verschiedener Differenzlinien ausgemacht und aufgedeckt. Den Abschluss bildet ein Beispiel konkreter Umsetzung. (DIPF/Orig.)

Empirical evidence of bias in the design of experimental stroke studies: a metaepidemiologic approach

Background and Purpose: At least part of the failure in the transition from experimental to clinical studies in stroke has been attributed to the imprecision introduced by problems in the design of experimental stroke studies. Using a metaepidemiologic approach, we addressed the effect of randomization, blinding, and use of comorbid animals on the estimate of how effectively therapeutic interventions reduce infarct size. Methods: Electronic and manual searches were performed to identify meta-analyses that described interventions in experimental stroke. For each meta-analysis thus identified, a reanalysis was conducted to estimate the impact of various quality items on the estimate of efficacy, and these estimates were combined in a meta meta-analysis to obtain a summary measure of the impact of the various design characteristics. Results: Thirteen meta-analyses that described outcomes in 15 635 animals were included. Studies that included unblinded induction of ischemia reported effect sizes 13.1% (95% CI, 26.4% to 0.2%) greater than studies that included blinding, and studies that included healthy animals instead of animals with comorbidities overstated the effect size by 11.5% (95% CI, 21.2% to 1.8%). No significant effect was found for randomization, blinded outcome assessment, or high aggregate CAMARADES quality score. Conclusions: We provide empirical evidence of bias in the design of studies, with studies that included unblinded induction of ischemia or healthy animals overestimating the effectiveness of the intervention. This bias could account for the failure in the transition from bench to bedside of stroke therapies.

Méthodes de Bootstrap pour les modèles à facteurs

Cette thèse développe des méthodes bootstrap pour les modèles à facteurs qui sont couram- ment utilisés pour générer des prévisions depuis l'article pionnier de Stock et Watson (2002) sur les indices de diffusion. Ces modèles tolèrent l'inclusion d'un grand nombre de variables macroéconomiques et financières comme prédicteurs, une caractéristique utile pour inclure di- verses informations disponibles aux agents économiques. Ma thèse propose donc des outils éco- nométriques qui améliorent l'inférence dans les modèles à facteurs utilisant des facteurs latents extraits d'un large panel de prédicteurs observés. Il est subdivisé en trois chapitres complémen- taires dont les deux premiers en collaboration avec Sílvia Gonçalves et Benoit Perron. Dans le premier article, nous étudions comment les méthodes bootstrap peuvent être utilisées pour faire de l'inférence dans les modèles de prévision pour un horizon de h périodes dans le futur. Pour ce faire, il examine l'inférence bootstrap dans un contexte de régression augmentée de facteurs où les erreurs pourraient être autocorrélées. Il généralise les résultats de Gonçalves et Perron (2014) et propose puis justifie deux approches basées sur les résidus : le block wild bootstrap et le dependent wild bootstrap. Nos simulations montrent une amélioration des taux de couverture des intervalles de confiance des coefficients estimés en utilisant ces approches comparativement à la théorie asymptotique et au wild bootstrap en présence de corrélation sérielle dans les erreurs de régression. Le deuxième chapitre propose des méthodes bootstrap pour la construction des intervalles de prévision permettant de relâcher l'hypothèse de normalité des innovations. Nous y propo- sons des intervalles de prédiction bootstrap pour une observation h périodes dans le futur et sa moyenne conditionnelle. Nous supposons que ces prévisions sont faites en utilisant un ensemble de facteurs extraits d'un large panel de variables. Parce que nous traitons ces facteurs comme latents, nos prévisions dépendent à la fois des facteurs estimés et les coefficients de régres- sion estimés. Sous des conditions de régularité, Bai et Ng (2006) ont proposé la construction d'intervalles asymptotiques sous l'hypothèse de Gaussianité des innovations. Le bootstrap nous permet de relâcher cette hypothèse et de construire des intervalles de prédiction valides sous des hypothèses plus générales. En outre, même en supposant la Gaussianité, le bootstrap conduit à des intervalles plus précis dans les cas où la dimension transversale est relativement faible car il prend en considération le biais de l'estimateur des moindres carrés ordinaires comme le montre une étude récente de Gonçalves et Perron (2014). Dans le troisième chapitre, nous suggérons des procédures de sélection convergentes pour les regressions augmentées de facteurs en échantillons finis. Nous démontrons premièrement que la méthode de validation croisée usuelle est non-convergente mais que sa généralisation, la validation croisée «leave-d-out» sélectionne le plus petit ensemble de facteurs estimés pour l'espace généré par les vraies facteurs. Le deuxième critère dont nous montrons également la validité généralise l'approximation bootstrap de Shao (1996) pour les regressions augmentées de facteurs. Les simulations montrent une amélioration de la probabilité de sélectionner par- cimonieusement les facteurs estimés comparativement aux méthodes de sélection disponibles. L'application empirique revisite la relation entre les facteurs macroéconomiques et financiers, et l'excès de rendement sur le marché boursier américain. Parmi les facteurs estimés à partir d'un large panel de données macroéconomiques et financières des États Unis, les facteurs fortement correlés aux écarts de taux d'intérêt et les facteurs de Fama-French ont un bon pouvoir prédictif pour les excès de rendement.

Good laboratory practice: preventing introduction of bias at the bench

Background and Purpose—As a research community, we have failed to demonstrate that drugs which show substantial efficacy in animal models of cerebral ischemia can also improve outcome in human stroke. Summary of Review—Accumulating evidence suggests this may be due, at least in part, to problems in the design, conduct and reporting of animal experiments which create a systematic bias resulting in the overstatement of neuroprotective efficacy. Conclusions—Here, we set out a series of measures to reduce bias in the design, conduct and reporting of animal experiments modeling human stroke.

Inflation and the personal distribution of income in Portugal.

Doutoramento em Economia.

Bia’s smile: an health education instrument on cleft lip and palate

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited.

Bias-induced threshold voltages shifts in thin-film organic transistors

An investigation into the stability of metal-insulator-semiconductor (MIS) transistors based on alpha-sexithiophene is reported. In particular, the kinetics of the threshold voltage shift upon application of a gate bias has been determined. The kinetics follow stretched-hyperbola-type behavior, in agreement with the formalism developed to explain metastability in amorphous-silicon thin-film transistors. Using this model, quantification of device stability is possible. Temperature-dependent measurements show that there are two processes involved in the threshold voltage shift, one occurring at Tapproximate to220 K and the other at Tapproximate to300 K. The latter process is found to be sample dependent. This suggests a relation between device stability and processing parameters. (C) 2004 American Institute of Physics.

SAMPLING BIAS IN EVALUATING THE PROBABILITY OF SEISMICALLY INDUCED SOIL LIQUEFACTION WITH SPT & CPT CASE HISTORIES

Several deterministic and probabilistic methods are used to evaluate the probability of seismically induced liquefaction of a soil. The probabilistic models usually possess some uncertainty in that model and uncertainties in the parameters used to develop that model. These model uncertainties vary from one statistical model to another. Most of the model uncertainties are epistemic, and can be addressed through appropriate knowledge of the statistical model. One such epistemic model uncertainty in evaluating liquefaction potential using a probabilistic model such as logistic regression is sampling bias. Sampling bias is the difference between the class distribution in the sample used for developing the statistical model and the true population distribution of liquefaction and non-liquefaction instances. Recent studies have shown that sampling bias can significantly affect the predicted probability using a statistical model. To address this epistemic uncertainty, a new approach was developed for evaluating the probability of seismically-induced soil liquefaction, in which a logistic regression model in combination with Hosmer-Lemeshow statistic was used. This approach was used to estimate the population (true) distribution of liquefaction to non-liquefaction instances of standard penetration test (SPT) and cone penetration test (CPT) based most updated case histories. Apart from this, other model uncertainties such as distribution of explanatory variables and significance of explanatory variables were also addressed using KS test and Wald statistic respectively. Moreover, based on estimated population distribution, logistic regression equations were proposed to calculate the probability of liquefaction for both SPT and CPT based case history. Additionally, the proposed probability curves were compared with existing probability curves based on SPT and CPT case histories.