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"Taylor, Eric"
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Virtual Classrooms
Online college courses are a rapidly expanding feature of higher education, yet little research identifies their effects relative to traditional in-person classes. Using an instrumental variables approach, we find that taking a course online, instead of in-person, reduces student success and progress in college. Grades are lower both for the course taken online and in future courses. Students are less likely to remain enrolled at the university. These estimates are local average treatment effects for students with access to both online and in-person options; for other students, online classes may be the only option for accessing college-level courses.
Journal Article
Regulation of pyruvate metabolism and human disease
Pyruvate is a keystone molecule critical for numerous aspects of eukaryotic and human metabolism. Pyruvate is the end-product of glycolysis, is derived from additional sources in the cellular cytoplasm, and is ultimately destined for transport into mitochondria as a master fuel input undergirding citric acid cycle carbon flux. In mitochondria, pyruvate drives ATP production by oxidative phosphorylation and multiple biosynthetic pathways intersecting the citric acid cycle. Mitochondrial pyruvate metabolism is regulated by many enzymes, including the recently discovered mitochondria pyruvate carrier, pyruvate dehydrogenase, and pyruvate carboxylase, to modulate overall pyruvate carbon flux. Mutations in any of the genes encoding for proteins regulating pyruvate metabolism may lead to disease. Numerous cases have been described. Aberrant pyruvate metabolism plays an especially prominent role in cancer, heart failure, and neurodegeneration. Because most major diseases involve aberrant metabolism, understanding and exploiting pyruvate carbon flux may yield novel treatments that enhance human health.
Journal Article
The Arctic char (Salvelinus alpinus) “complex” in North America revisited
The Arctic char (
Salvelinus alpinus
) species “complex” has fascinated biologists for decades particularly with respect to how many species there are and their geographic distributions. I review recent research on the species complex, focussing on biodiversity within northwestern North America, which indicates (i) what was once considered a single taxon consists of three taxa:
S. alpinus
(Arctic char),
S. malma
(Dolly Varden), and
S. confluentus
(bull trout), (ii) morphological and genetic data indicate that
S. alpinus
and
S. malma
, and
S
.
malma
and
S. confluentus
exist as distinct biological species in sympatry, (iii) sympatric forms of
S. alpinus
exist in Alaska as in other areas of the Holarctic, (iv) Dolly Varden comprises two well-differentiated subspecies,
S. m. malma
and
S. m. lordi
, in the eastern Pacific and the northwestern Canadian Arctic that meet at a contact zone on the southern edge of the Alaska Peninsula, and (v) Dolly Varden and bull trout consist of several population assemblages that have legal status as distinct conservation units under US and Canadian law. This research has significantly revised what constitutes the
S. alpinus
species “complex”, provided insights into the ecology and genetics of co-existence, and promoted conservation assessment that better represents biodiversity within
Salvelinus
. A geographically and genetically comprehensive analysis of relationships among putative taxa of Pan-Pacific
Salvelinus
is still required to better quantify the number of taxa and their origins.
Journal Article
The Effect of Evaluation on Teacher Performance
Teacher performance evaluation has become a dominant theme in school reform efforts. Yet, whether evaluation changes the performance of teachers, the focus of this paper, is unknown. Instead, evaluation has largely been studied as an input to selective dismissal decisions. We study mid-career teachers for whom we observe an objective measure of productivity—value-added to student achievement—before, during, and after evaluation. We find teachers are more productive in post-evaluation years, with the largest improvements among teachers performing relatively poorly ex-ante. The results suggest teachers can gain information from evaluation and subsequently develop new skills, increase long-run effort, or both.
Journal Article
Metabolic and proteomic indications of diabetes progression in human aqueous humor
Diabetes mellitus is a multiorgan systemic disease impacting numerous ocular structures that results in significant ocular morbidity and often results in more frequent corneal and glaucoma surgeries for affected individuals. We hypothesize that the systemic metabolic and proteomic derangement observed in the progression of diabetes influences the composition of the aqueous humor (AH), which ultimately impacts the anterior segment health of the eye. To identify changes associated with diabetes progression, we mapped the metabolite profile and proteome of AH samples from patients with varying severities of type II diabetes (T2DM). Patients were classified as nondiabetic (ND or control), non-insulin-dependent diabetic without advanced features of disease (NAD-ni), insulin-dependent diabetic without advanced features (NAD-i), or diabetic with advanced features (AD). AH samples collected from the anterior chamber during elective ophthalmic surgery were evaluated for metabolite and protein expression changes associated with diabetic severity via gas chromatography/mass spectrometry and ultra-high performance liquid chromatography tandem mass spectrometry, respectively. Metabolic and proteomic pathway analyses were conducted utilizing MetaboAnalyst 4.0 and Ingenuity Pathway Analysis. A total of 14 control, 12 NAD-ni, 4 NAD-I, and 14 AD samples were included for analysis. Elevated levels of several branched amino acids (e.g., valine, leucine, isoleucine), and lipid metabolites (e.g., palmitate) were found only with increasing diabetic severity (i.e., the AD group). Similar proteomic trends were noted in amino acid and fatty acid metabolism and the unfolded protein/stress response. These results represent the first report of both metabolomic and proteomic evaluation of aqueous humor. Diabetes results in metabolic and proteomic perturbations detectable in the AH, and unique changes become manifest as T2DM severity worsens. Changes in AH composition may serve as an indicator of disease severity, risk assessment of anterior segment cells and structures, and potential future therapies.
Journal Article
The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome
Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes-the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.
Journal Article
Parameter Estimation and Identifiability in Kinetic Flux Profiling Models of Metabolism
Metabolic fluxes are the rates of life-sustaining chemical reactions within a cell and metabolites are the components. Determining the changes in these fluxes is crucial to understanding diseases with metabolic causes and consequences. Kinetic flux profiling (KFP) is a method for estimating flux that utilizes data from isotope tracing experiments. In these experiments, the isotope-labeled nutrient is metabolized through a pathway and integrated into the downstream metabolite pools. Measurements of proportion labeled for each metabolite in the pathway are taken at multiple time points and used to fit an ordinary differential equations model with fluxes as parameters. We begin by generalizing the process of converting diagrams of metabolic pathways into mathematical models composed of differential equations and algebraic constraints. The scaled differential equations for proportions of unlabeled metabolite contain parameters related to the metabolic fluxes in the pathway. We investigate flux parameter identifiability given data collected only at the steady state of the differential equation. Next, we give criteria for valid parameter estimations in the case of a large separation of timescales with fast–slow analysis. Bayesian parameter estimation on simulated data from KFP experiments containing both irreversible and reversible reactions illustrates the accuracy and reliability of flux estimations. These analyses provide constraints that serve as guidelines for the design of KFP experiments to estimate metabolic fluxes.
Journal Article