206 research outputs found
Likelihood methods to infer balancing selection under K-allele models /by Erkan Ozge Buzbas.
No full textA balanced pattern in the allele frequencies of polymorphic loci is a potential sign of selection, particularly of overdominance. Although this type of selection is of some interest in population genetics, there exist no likelihood based approaches specifically tailored to make inference on selection intensity. To fill this gap, we present likelihood methods to estimate selection intensity under k-allele models with overdominance.;The stationary distribution of allele frequencies under a variety of Wright-Fisher k-allele models with selection and parent independent mutation is well studied. However, the statistical properties of maximum likelihood estimates of parameters under these models are not well understood. We show that under each of these models, there is a point in data space which carries the strongest possible signal for selection, yet, at this point, the likelihood is unbounded. This result remains valid even if all of the mutation parameters are assumed to be known. Therefore, standard simulation approaches used to approximate the sampling distribution of the maximum likelihood estimate produce numerically unstable results in the presence of substantial selection.;We describe the Bayesian alternative where the posterior distribution tends to produce more accurate and reliable interval estimates for the selection intensity at a locus. In particular, we present methods for single locus and multiple loci k -allele models, including a case where there is epistasis between loci. For the multiple loci model without epistasis, we assume a hierarchical setup between loci to estimate the posterior distribution of the mean selection intensity in a multi locus region of the genome. For the epistatic case, we focus on two types of epistasis: synergistic (antagonistic), where the fitness of the genotype decreases more (less) severely in comparison to the case of independence between loci. We estimate the posterior distribution of the selection intensity for a group of epistatically interacting loci using recent theoretical developments. We provide methods to generate data and to test for independence between loci under selection. Simulated data are used to validate the methods and real data at the Human Leukocyte Antigen loci are analyzed to illustrate an application.Thesis (Ph. D., Bioinformatics and Computational Biology)--University of Idaho, May 2009
Can biophysical models of pelagic larval dispersal explain the observed population structure; case studies from the Gulf of Alaska
No full textNumerous marine fish species have a characteristic pelagic larval dispersal stage. Understanding how this life history strategy affects the observed population structure of the adult groups and the adaptive potential of the species as a whole is therefore of paramount importance. In this study, I initially apply RAD-seq genomic analysis to examine the young of the year aggregates of Pacific ocean perch (Sebastes alutus) collected in 2014 and 2015 in the eastern Gulf of Alaska. I discover that these samples, even from the same haul, contain distinct genetic population mixtures indicating pelagic life stage sympatry. I also discover differences in selection strength between the two years, indicating that the maintenance of a portfolio of adaptive alleles may provide resilience of populations to natural environmental variability, where each adult cohort’s genetic composition is influenced by the environmental conditions experienced during their first year at sea. The apparent disconnect between pelagic stage sympatry and adult stage allopatry motivated the development of a stochastic spatio-temporal genetic model to understand the effect of biophysical dispersal on the population structure. Here, I develop the spatio-temporal genetic model utilizing a dispersal matrix and an allele frequency matrix which is then tracked over a number of generations. I then validate the genetic model with a suite of eight synthetic dispersal matrices and examine the inference via isolation by distance regression, STRUCTURE admixture analysis, and principal component analysis. This lead to unique insight into how each of these commonly used inference methods differs in their ability to differentiate among the synthetic candidate models. I then propose a log likelihood model selection framework based on the beta distribution as a viable alternate to determine which of the candidate dispersal models best explain the observed population structure based on pairwise F_ST values. Finally, I demonstrate the application of the newly developed spatio-temporal genetic model to calculate the expected population structure for three fish species in the Gulf of Alaska, namely, Pacific ocean perch (Sebastes alutus), arrowtooth flounder (Atheresthes stomias), and Pacific cod (Gadus macrocephalus). I use a biophysical dispersal matrix based on the Regional Ocean Modeling System (ROMS) and species specific ontogenic life stage behavior combined in a previously developed mode, the Dispersal Model for Early Life History Stages (DisMELS) to calculate the expected genetic differentiation. I then describe the expected population structure for these three species and apply the PCA, STRUCTURE admixture, and IBD regression inference. This is followed by the comparison of Pacific ocean perch and Pacific cod biophysical model based expected population structure and the observed genetic datasets which reconciles previously contradictory studies. I also demonstrate the application of this spatio-temporal genetic model to determine optimal sampling strategy in the log likelihood model selection framework. The results presented here also suggest that the biophysical based dispersal may be the primary driver behind the observed population structure in the marine species with life history strategies characterized by pelagic larval dispersal.doctoral, Ph.D., Bioinformatics & Computational Biology -- University of Idaho - College of Graduate Studies, 2022-0
Inference on admixture fractions in a mechanistic model of recurrent admixture
No full textInternational audienc
Minimum Viable Experiment to Replicate
No full textReplication experiments purport to independently validate claims from previous research or provide some diagnostic evidence about their reliability. In practice, this value of replication experiments is often taken for granted. Our research shows that in replication experiments, practice often does not live up to theory. Most replication experiments in practice are confounded and their results multiply determined, hence uninterpretable. These results can be driven by the true data generating mechanism, issues present in the original experiment, discrepancies between the original and the replication experiment, new issues introduced in the replication experiment, or combinations of any of these factors. The answers we are looking for with regard to the true state of nature require a rigorous and meticulous investigative process of eliminating errors and singling out elementary or pure cases. In this paper, we introduce the idea of a minimum viable experiment that needs to be identified in practice for replication results to be clearly interpretable. Most experiments are not replication-ready and before striving to replicate a given result, we need theoretical precision or systematic exploration to discover empirical regularities
Minimum Viable Experiment to Replicate
No full textReplication experiments purport to independently validate claims from previous research or provide some diagnostic evidence about their reliability. In practice, this value of replication experiments is often taken for granted. Our research shows that in replication experiments, practice often does not live up to theory. Most replication experiments in practice are confounded and their results multiply determined, hence uninterpretable. These results can be driven by the true data generating mechanism, issues present in the original experiment, discrepancies between the original and the replication experiment, new issues introduced in the replication experiment, or combinations of any of these factors. The answers we are looking for with regard to the true state of nature require a rigorous and meticulous investigative process of eliminating errors and singling out elementary or pure cases. In this paper, we introduce the idea of a minimum viable experiment that needs to be identified in practice for replication results to be clearly interpretable. Most experiments are not replication-ready and before striving to replicate a given result, we need theoretical precision or systematic exploration to discover empirical regularities
Static and dynamic properties of CN/Cu(001) surfaces and oxidation, dissociation and bimolecular debarboxylation of isocyanate species adsorbed on Cu(001)
No full textThis dissertation presents an outlines my investigations of static and dynamic properties of adsorbed cyanide (CN) and isocyanate (-NCO) species as well as some of their chemistries. Surface bound CN-containing species have not previously been studied extensively, partially due to the inapplicability of fundamental e-beam based surface analysis techniques for investigations. I had the opportunity in my studies to employ multiple surface probing techniques, i.e. HAS, XPS, NEXAFS, TPD and RAIRS, to compile and cross-examine information from CN, –NCO, and derived species, adsorbed on the Cu(001) surface. While angle resolved He atom scattering (HAS) was employed to identify and investigate the ordered superstructure of CN/Cu(001) surfaces, TOF-HAS was employed to investigate its dynamic properties. The CN/Cu(001) surface induced unprecedented simultaneous coherent He diffraction with a large “classical” multiphonon backscattered He intensity. A superstructure is implied that contains both rigidly bound CN species, which maintain the long range c(10x6) translational symmetry, together with bound highly-dynamic CN species that exhibit large thermally induced displacements. The NEXAFS measurements suggest multiple spatial binding configurations for the adsorbed CN moieties. In addition, TPD spectra of C2N2 desorption from CN/Cu(001) surface were analyzed, using my newly developed method, to determine the activation energies for desorption as a function of CN coverage. There are two reactions of NCO species examined in my studies. The first is the newly discovered mutual reaction between NCO species. This type of interaction had not been seen before, as it is essentially difficult to prepare pure NCO/metallic surfaces. Copper was chosen as a substrate as HNCO exposures of Cu(001) at RT, followed by spontaneous H2 desorption, do produce NCO only surfaces. A thermal treatment of the surface, at 573K, leads to a bimolecular decarboxylation of NCO, leaving a carbodimide species (NCN) on the surface. The sp-hybridized linear NCN moieties, which are bound nearly parallel to the substrate, show high thermal stability. The second reaction of NCO, which I have studied, is its oxidation. In particular, the effect of CN coadsorbates on the oxidation of NCO was studied. It was found that the presence of CN catalyzes a dissociation reaction of NCO species on Cu(001).Ph. D.Includes bibliographical referencesby Erkan Ziya Ciftlikl
Statistics in Service of Metascience: Measuring Replication Distance with Reproducibility Rate
No full textMotivated by the recent putative reproducibility crisis, we discuss the relationship between the replicability of scientific studies, the reproducibility of results obtained in these replications, and the philosophy of statistics. Our approach focuses on challenges in specifying scientific studies for scientific inference via statistical inference and is complementary to classical discussions in the philosophy of statistics. We particularly consider the challenges in replicating studies exactly, using the notion of the idealized experiment. We argue against treating reproducibility as an inherently desirable property of scientific results, and in favor of viewing it as a tool to measure the distance between an original study and its replications. To sensibly study the implications of replicability and results reproducibility on inference, such a measure of replication distance is needed. We present an effort to delineate such a framework here, addressing some challenges in capturing the components of scientific studies while identifying others as ongoing issues. We illustrate our measure of replication distance by simulations using a toy example. Rather than replications, we present purposefully planned modifications as an appropriate tool to inform scientific inquiry. Our ability to measure replication distance serves scientists in their search for replication-ready studies. We believe that likelihood-based and evidential approaches may play a critical role towards building statistics that effectively serve the practical needs of science
Effect of size and slenderness on the axial-compressive behavior of basalt FRP-confined predamaged concrete
No full textTo investigate the size and slenderness effect on the axial-compressive behavior of basalt fiber-reinforced polymer (BFRP)-confined predamaged concrete, five groups of concrete cylinders with different sizes and slenderness ratios were designed and tested. The cylinders were axially preloaded to three predamage levels, then repaired using BFRP, and reloaded. The results showed that the concrete predamage had an adverse effect on the ultimate strength and initial elastic modulus of BFRP-confined concrete. Except for the smallest specimens affected by the wall effect, the initial analysis found that the ultimate strength of BFRP-confined concrete decreased with an increase in size and slenderness ratio, and the size and slenderness effect decreased with an increase in BFRP confining pressure, while these increased with the severity of concrete predamage. However, there was no obvious size or slenderness effect on the ultimate strain of BFRP-confined concrete. Through multifactorial analysis, it was confirmed that the ultimate strength of BFRP-confined undamaged and predamaged concrete was influenced by the slenderness. Considering the effect of size, slenderness, and predamage, monotonic and cyclic models were developed for BFRP-confined concrete. Finally, a uniaxial material object was added into OpenSees to provide an effective numerical material model for theoretical analyses and engineering applications. © 2021 American Society of Civil Engineers.The present research was supported by the National Natural Science Foundation of China (Grant No. 51878268) and the Natural Science Foundation of Hunan Province, China (Grant No. 2020JJ4195).
Part of this research was completed by the first author in collaboration with the third and fourth authors during his one-year visit to Ohio State University. The first author acknowledges the State Scholarship Fund of China Scholarship Council (Grant No. 201606135057) for supporting this work and his research visit to the United States
Rigorous exploration in a model-centric science via epistemic iteration
No full textUrgent attention is needed to address generalizability problems in psychology. However, the current dominant paradigm, which centers dichotomous results and rapid discoveries, may not provide the solution. Instead, we propose a paradigm shift towards a model-centric approach, which can aid in understanding the sources of generalizability and promote systematic exploration. In a model-centric paradigm, scientific activity involves iteratively building and refining theoretical, empirical, and statistical models that communicate with each other. This approach is organic, transparent, and efficient in addressing generalizability issues. We illustrate the nature of scientific activity in a model-centric system and its potential for advancing the field of psychology
A Comparison of the Ballistic Performances of Various Microstructures in Mil-A Armor Steel
No full textKonca, Erkan/0000-0001-8943-091XDue to their advantageous properties, there is a growing interest in developing armor steels containing fully or partially bainitic microstructures. In this study, bainitic and martensitic microstructures were obtained in rolled homogeneous armor (RHA) steel samples and their ballistic protection performances were investigated. RHA (MIL-A-12560) steel samples were subjected to isothermal heat treatments at three different temperatures, where one temperature (360 degrees C) was above the martensite formation start (Ms) temperature of 336 degrees C while the other two (320 degrees C and 270 degrees C) were below. For the assessment of the ballistic protection performance, the kinetic energy losses of the 12.7 mm bullets fired at the test samples were determined. The promising nature of the bainite microstructure was confirmed as the sample isothermally treated at 360 degrees C provided approximately 10% higher ballistic protection as compared to the regular RHA sample of tempered martensite microstructure. However, the ballistic performances of the isothermally treated samples decreased as the treatment temperature went below the Ms temperature. Following the ballistic tests, hardness measurements, impact tests at -40 degrees C, and macro- and microstructural examinations of the samples were performed. No correlation was found between the hardness and impact energies of the samples and their ballistic performances.ROKETSAN Missile Industries Inc. (Ankara, Turkey)This research was funded by ROKETSAN Missile Industries Inc. (Ankara, Turkey). The APC was paid for by the author
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