Epigenetic markings acquired in early life may have phenotypic consequences later in development through their role in transcriptional regulation with relevance to the developmental origins of ...diseases including obesity. The goal of this study was to investigate whether DNA methylation levels at birth are associated with body size later in childhood.
A study design involving two birth cohorts was used to conduct transcription profiling followed by DNA methylation analysis in peripheral blood. Gene expression analysis was undertaken in 24 individuals whose biological samples and clinical data were collected at a mean ± standard deviation (SD) age of 12.35 (0.95) years, the upper and lower tertiles of body mass index (BMI) were compared with a mean (SD) BMI difference of 9.86 (2.37) kg/m(2). This generated a panel of differentially expressed genes for DNA methylation analysis which was then undertaken in cord blood DNA in 178 individuals with body composition data prospectively collected at a mean (SD) age of 9.83 (0.23) years. Twenty-nine differentially expressed genes (>1.2-fold and p<10(-4)) were analysed to determine DNA methylation levels at 1-3 sites per gene. Five genes were unmethylated and DNA methylation in the remaining 24 genes was analysed using linear regression with bootstrapping. Methylation in 9 of the 24 (37.5%) genes studied was associated with at least one index of body composition (BMI, fat mass, lean mass, height) at age 9 years, although only one of these associations remained after correction for multiple testing (ALPL with height, p(Corrected) = 0.017).
DNA methylation patterns in cord blood show some association with altered gene expression, body size and composition in childhood. The observed relationship is correlative and despite suggestion of a mechanistic epigenetic link between in utero life and later phenotype, further investigation is required to establish causality.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
There has been growing interest in using statistical methods to analyze data and estimate effect size indices from studies that use single-case designs (SCDs), as a complement to traditional visual ...inspection methods. The validity of a statistical method rests on whether its assumptions are plausible representations of the process by which the data were collected, yet there is evidence that some assumptions—particularly regarding normality of error distributions—may be inappropriate for single-case data. To develop more appropriate modeling assumptions and statistical methods, researchers must attend to the features of real SCD data. In this study, we examine several features of SCDs with behavioral outcome measures in order to inform development of statistical methods. Drawing on a corpus of over 300 studies, including approximately 1,800 cases, from seven systematic reviews that cover a range of interventions and outcome constructs, we report the distribution of study designs, distribution of outcome measurement procedures, and features of baseline outcome data distributions for the most common types of measurements used in single-case research. We discuss implications for the development of more realistic assumptions regarding outcome distributions in SCD studies, as well as the design of Monte Carlo simulation studies evaluating the performance of statistical analysis techniques for SCD data.
The dynamics of reductive genome evolution for eukaryotes living inside other eukaryotic cells are poorly understood compared to well-studied model systems involving obligate intracellular bacteria. ...Here we present 8.5 Mb of sequence from the genome of the microsporidian Trachipleistophora hominis, isolated from an HIV/AIDS patient, which is an outgroup to the smaller compacted-genome species that primarily inform ideas of evolutionary mode for these enormously successful obligate intracellular parasites. Our data provide detailed information on the gene content, genome architecture and intergenic regions of a larger microsporidian genome, while comparative analyses allowed us to infer genomic features and metabolism of the common ancestor of the species investigated. Gene length reduction and massive loss of metabolic capacity in the common ancestor was accompanied by the evolution of novel microsporidian-specific protein families, whose conservation among microsporidians, against a background of reductive evolution, suggests they may have important functions in their parasitic lifestyle. The ancestor had already lost many metabolic pathways but retained glycolysis and the pentose phosphate pathway to provide cytosolic ATP and reduced coenzymes, and it had a minimal mitochondrion (mitosome) making Fe-S clusters but not ATP. It possessed bacterial-like nucleotide transport proteins as a key innovation for stealing host-generated ATP, the machinery for RNAi, key elements of the early secretory pathway, canonical eukaryotic as well as microsporidian-specific regulatory elements, a diversity of repetitive and transposable elements, and relatively low average gene density. Microsporidian genome evolution thus appears to have proceeded in at least two major steps: an ancestral remodelling of the proteome upon transition to intracellular parasitism that involved reduction but also selective expansion, followed by a secondary compaction of genome architecture in some, but not all, lineages.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Single-case designs are a class of repeated measures experiments used to evaluate the effects of interventions for small or specialized populations, such as individuals with low-incidence ...disabilities. There has been growing interest in systematic reviews and syntheses of evidence from single-case designs, but there remains a need to further develop appropriate statistical models and effect sizes for data from the designs. We propose a novel model for single-case data that exhibit nonlinear time trends created by an intervention that produces gradual effects, which build up and dissipate over time. The model expresses a structural relationship between a pattern of treatment assignment and an outcome variable, making it appropriate for both treatment reversal and multiple baseline designs. It is formulated as a generalized linear model so that it can be applied to outcomes measured as frequency counts or proportions, both of which are commonly used in single-case research, while providing readily interpretable effect size estimates such as log response ratios or log odds ratios. We demonstrate the gradual effects model by applying it to data from a single-case study and examine the performance of proposed estimation methods in a Monte Carlo simulation of frequency count data.
Long-read sequencing can overcome the weaknesses of short reads in the assembly of eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We ...generated Pacific Biosciences (PacBio) long-read data of the genomes of three relatives of the model plant
and assembled all three genomes into only a few hundred contigs. To improve the contiguities of these assemblies, we generated BioNano Genomics optical mapping and Dovetail Genomics chromosome conformation capture data for genome scaffolding. Despite their technical differences, optical mapping and chromosome conformation capture performed similarly and doubled N50 values. After improving both integration methods, assembly contiguity reached chromosome-arm-levels. We rigorously assessed the quality of contigs and scaffolds using Illumina mate-pair libraries and genetic map information. This showed that PacBio assemblies have high sequence accuracy but can contain several misassemblies, which join unlinked regions of the genome. Most, but not all, of these misjoints were removed during the integration of the optical mapping and chromosome conformation capture data. Even though none of the centromeres were fully assembled, the scaffolds revealed large parts of some centromeric regions, even including some of the heterochromatic regions, which are not present in gold standard reference sequences.
Exhibiting Heritage Swan, Daniel C.; Chudak, Aleksandr
Museum anthropology review,
10/2022, Letnik:
16, Številka:
1-2
Journal Article
Recenzirano
Odprti dostop
This project report discusses the 2018 Centennial Commemoration of the Native American Church State of Oklahoma (NAC-OK). Chartered in 1918 the NAC-OK is an intertribal organization dedicated to the ...protection of the First Amendment rights of its members to use peyote as a holy sacrament. The Centennial Committee of the NAC-OK invited the University of Oklahoma’s Sam Noble Museum to collaborate on an interpretive exhibition on the history of the NAC-OK. The Committee and the museum employed a methodology grounded in shared authority to integrate community driven content with established museum processes for exhibition development. This approach allowed the museum to produce the exhibition through the museum’s established workflow while privileging community interpretation and design.
Children in rural communities consume more energy-dense foods relative to their urban peers. Identifying effective interventions for improving energy intake patterns are needed to address these ...geographic disparities. The primary aim of this study was to harness the benefits of physical activity on children’s executive functioning to see if these improvements lead to acute changes in eating behaviors. In a randomized crossover design, 91 preadolescent (8-10y; M age = 9.48 ± 0.85; 50.5% female; 85.7% White, 9.9% Multiracial, 9.9% Hispanic) children (86% rural) completed a 20-minute physical activity condition (moderate intensity walking) and time-matched sedentary condition (reading and/or coloring) ~ 14 days apart. Immediately following each condition, participants completed a behavioral inhibition task and then eating behaviors (total energy intake, relative energy intake, snack intake) were measured during a multi-array buffet test meal. After adjusting for period and order effects, body fat (measured via DXA), and depressive symptoms, participants experienced significant small improvements in their behavioral inhibition following the physical activity versus sedentary condition (
p
= 0.04, Hedge’s g = 0.198). Eating behaviors did not vary by condition, nor did improvements in behavioral inhibition function as a mediator (
p
s > 0.09). Thus, in preadolescent children, small improvements in behavioral inhibition from physical activity do not produce acute improvements in energy intake. Additional research is needed to clarify whether the duration and/or intensity of physical activity sessions would produce different results in this age group, and whether intervention approaches and corresponding mechanisms of change vary by individual factors, like age and degree of food cue responsivity.
In single-case experimental design (SCED) research, researchers often choose when to start treatment based on whether the baseline data collected so far are stable, using what is called a ...response-guided design. There is evidence that response-guided designs are common, and researchers have described a variety of criteria for assessing stability. With many of these criteria, making judgments about stability could yield data with limited variability, which may have consequences for statistical inference and effect size estimates. However, little research has examined the impact of response-guided design on the resulting data. Drawing on both applied and methodological research, we describe several algorithms as models for response-guided design. We use simulation methods to assess how using a response-guided design impacts the baseline data pattern. The simulations generate baseline data in the form of frequency counts, a common type of outcome in SCEDs. Most of the response-guided algorithms we identified lead to baselines with approximately unbiased mean levels, but nearly all of them lead to underestimates in the baseline variance. We discuss implications for the use of response-guided designs in practice and for the plausibility of specific algorithms as representations of actual research practice.
Partial interval recording (PIR) is a procedure for collecting measurements during direct observation of behavior. It is used in several areas of educational and psychological research, particularly ...in connection with single-case research. Measurements collected using partial interval recording suffer from construct invalidity because they are not readily interpretable in terms of the underlying characteristics of the behavior. Using an alternating renewal process model for the behavior under observation, we demonstrate that ignoring the construct invalidity of PIR data can produce misleading inferences, such as inferring that an intervention reduces the prevalence of an undesirable behavior when in fact it has the opposite effect. We then propose four different methods for analyzing PIR summary measurements, each of which can be used to draw inferences about interpretable behavioral parameters. We demonstrate the methods by applying them to data from two single-case studies of problem behavior.
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