Methods for Identifying Regions of Brain Activation Using FMRI Meta-Data

Functional neuroimaging is a relatively young discipline within the neurosciences that has led to significant advances in our understanding of the human brain and progress in neuroscientific research related to public health. Accurately identifying activated regions in the brain showing a strong association with an outcome of interest is crucial in terms of disease prediction and prevention. Functional magnetic resonance imaging (fMRI) is the most widely used method for this type of study as it has the ability to measure and identify the location of changes in tissue perfusion, blood oxygenation, and blood volume. In practice, the three-dimensional brain locations or coordinates of the local maximum of these changes are reported. By nature, fMRIs are noninvasive, slowly becoming more available, have relatively high spatiotemporal resolution, and have the remarkable ability to map the entire network of the brain’s function during the thought process. However, due to their high costs, fMRI studies tend to have a very small number of participants, which cause inflated type II error and lack reproducibility. This gives rise to the need for fMRI meta analyzes, which combines studies in order to increase overall sample size and testing power. In this dissertation, two methods are proposed that aim to identify regions of brain activation using fMRI coordinate-based meta analysis; a spatial Cox process and a mixture of Dirichlet processes model. The first method was motivated by the desire to identify significant regions of brain activation using fMRI coordinate-based meta data. To identify these regions we elected to implement a Bayesian spatial Cox process. We considered two levels of clustering, latent foci center and study activation center, utilizing the Dirichlet process (DP) built into a spatial Cox process used to model the distribution of foci. Commonly used spatial clustering methods model the random variation of the intensity governed by a process such that peaks in these processes would relate to areas of elevated aggregation in the events. However, methods of this type all assume three-dimensional normality, which is inappropriate for fMRI due to the nature of brain functioning and brain structure, and can possibly cause misclassification of foci and increase error in prediction and estimation. We relax this normality assumption and model intensity as a function of distance between the focus and the center of the cluster of foci using Gaussian kernels and the foci center will be identified by the use of a Dirichlet process. Simulation studies were conducted to evaluate the sensitivity and robustness with respect to cluster identification and underlying data distributions. An additional application of the proposed method was applied to an fMRI meta data of emotion foci. Both simulations and real data application produced promising results that highlighted the ability to correctly cluster. The second method was motivated by the spatial Cox process’ inability to statistically distinguish between clusters via a limitation to the Dirichlet process. However, it still aimed to identify significant regions of brain activation. This method modeled the realization of the data as a linear association with the overall mean of the data and adjusts for some study effect. The mean of the data was modeled as a mixture of unknown finite number of components and adjusted for a study effect modeled as a Dirichlet process. Similarly, each component was modeled as a Dirichlet process. Conditional on the mean of the data and some study effect, the distribution of the random error is standard multivariate normal. By modeling the mean as a mixture of Dirichlet processes, this still allows the method flexibility in capturing irregular spatial patterns and relaxes the typical normality assumptions, but can also statistically distinguish between a cluster or a mode within a cluster. The Bayesian framework was again implemented to draw model inferences. Simulation studies were conducted to explore the sensitivity and robustness of the method, but illustrated a mediocre ability to correctly identify clusters. As an additional application, we applied the proposed method to the same fMRI meta data as was done in the first proposed method. The number of clusters identified were significantly lower and cluster centers identified were not in close proximity to any of those identified in the first proposed method. Both simulation studies and real data applications indicate this second proposed method is not sensitive enough to correctly identify clusters

An efficient approach to screening epigenome-wide data

Screening cytosine-phosphate-guanine dinucleotide (CpG) DNA methylation sites in association with some covariate(s) is desired due to high dimensionality. We incorporate surrogate variable analyses (SVAs) into (ordinary or robust) linear regressions and utilize training and testing samples for nested validation to screen CpG sites. SVA is to account for variations in the methylation not explained by the specified covariate(s) and adjust for confounding effects. To make it easier to users, this screening method is built into a user-friendly R package, ttScreening, with efficient algorithms implemented. Various simulations were implemented to examine the robustness and sensitivity of the method compared to the classical approaches controlling for multiple testing: the false discovery rates-based (FDR-based) and the Bonferroni-based methods. The proposed approach in general performs better and has the potential to control both types I and II errors. We applied ttScreening to 383,998 CpG sites in association with maternal smoking, one of the leading factors for cancer risk

The interplay of DNA methylation over time with Th2 pathway genetic variants on asthma risk and temporal asthma transition

BackgroundGenetic effects on asthma of genes in the T-helper 2 (Th2) pathway may interact with epigenetic factors including DNA methylation. We hypothesized that interactions between genetic variants and methylation in genes in this pathway (IL4, IL4R, IL13, GATA3, and STAT6) influence asthma risk, that such influences are age-dependent, and that methylation of some CpG sites changes over time in accordance with asthma transition. We tested these hypotheses in subsamples of girls from a population-based birth cohort established on the Isle of Wight, UK, in 1989.ResultsLogistic regression models were applied to test the interaction effect of DNA methylation and SNP on asthma within each of the five genes. Bootstrapping was used to assess the models identified. From 1,361 models fitted at each age of 10 and 18 years, 8 models, including 4 CpGs and 8 SNPs, showed potential associations with asthma risk. Of the 4 CpGs, methylation of cg26937798 (IL4R) and cg23943829 (IL4) changes between ages 10 and 18 (both higher at 10; P?=?9.14?×?10?6 and 1.07?×?10?5, respectively).At age 10, the odds of asthma tended to decrease as cg12405139 (GATA3) methylation increased (log-OR?=??12.15; P?=?0.049); this effect disappeared by age 18. At age 18, methylation of cg09791102 (IL4R) was associated with higher risk of asthma among subjects with genotype GG compared to AG (P?=?0.003), increased cg26937798 methylation among subjects with rs3024685 (IL4R) genotype AA (P?=?0.003) or rs8832 (IL4R) genotype GG (P?=?0.01) was associated with a lower asthma risk; these CpGs had no effect at age 10. Increasing cg26937798 methylation over time possibly reduced the risk of positive asthma transition (asthma-free at age 10???asthma at age 18; log-OR?=??3.11; P?=?0.069) and increased the likelihood of negative transition (asthma at age 10???asthma-free at age 18; log-OR?=?3.97; P?=?0.074).ConclusionsThe interaction of DNA methylation and SNPs in Th2 pathway genes is likely to contribute to asthma risk. This effect may vary with age. Methylation of some CpGs changed over time, which may influence asthma transition

Alu insertion loci and platyrrhine primate phylogeny

Short INterspersed Elements (SINEs) make very useful phylogenetic markers because the integration of a particular element at a location in the genome is irreversible and of known polarity. These attributes make analysis of SINEs as phylogenetic characters an essentially homoplasy-free affair. Alu elements are primate-specific SINEs that make up a large portion of the human genome and are also widespread in other primates. Using a combination wet-bench and computational approach we recovered 190 Alu insertions, 183 of which are specific to the genomes of nine New World primates. We used these loci to investigate branching order and have produced a cladogram that supports a sister relationship between Atelidae (spider, woolly, and howler monkeys) and Cebidae (marmosets, tamarins, and owl monkeys) and then the joining of this two family clade to Pitheciidae (titi and saki monkeys). The data support these relationships with a homoplasy index of 0.00. In this study, we report one of the largest applications of SINE elements to phylogenetic analysis to date, and the results provide a robust molecular phylogeny for platyrrhine primates. © 2004 Elsevier Inc. All rights reserved

Analysis of the human Alu Ya-lineage

The Alu Ya-lineage is a group of related, short interspersed elements (SINEs) found in primates. This lineage includes subfamilies Ya1-Ya5, Ya5a2 and others. Some of these subfamilies are still actively mobilizing in the human genome. We have analyzed 2482 elements that reside in the human genome draft sequence and focused our analyses on the 2318 human autosomal Ya Alu elements. A total of 1470 autosomal loci were subjected to polymerase chain reaction (PCR)-based assays that allow analysis of individual Ya-lineage Alu elements. About 22% (313/1452) of the Ya-lineage Alu elements were polymorphic for the insertion presence on human autosomes. Less than 0.01% (5/1452) of the Ya-lineage loci analyzed displayed insertions in orthologous loci in non-human primate genomes. DNA sequence analysis of the orthologous inserts showed that the orthologous loci contained older pre-existing Y, Sc or Sq Alu subfamily elements that were the result of parallel forward insertions or involved in gene conversion events in the human lineage. This study is the largest analysis of a group of young , evolutionarily related human subfamilies. The size, evolutionary age and variable allele insertion frequencies of several of these subfamilies makes members of the Ya-lineage useful tools for human population studies and primate phylogenetics. © 2004 Elsevier Ltd. All rights reserved

The combined tensile and torsional behavior of irregular fibers

Most fibers are irregular, and they are often subjected to combined loading conditions during processing and end-use. In this paper, polyester and wool fibers under the combined tensile and torsional loads have been studied for the first time, using the finite element method (FEM). The dimensional irregularities of these fibers are simulated with sine waves of different magnitude and frequency. The breaking load and breaking extension of the fibers at different twist or torsion levels are then calculated from the finite element model. The results indicate that twist and level of fiber irregularity have a major impact on the mechanical properties of the fiber and the effect of the frequency of irregularity is relatively small.<br /

Characterizing the Near-infrared Spectra of Flares from TRAPPIST-1 During JWST Transit Spectroscopy Observations

We present the first analysis of JWST near-infrared spectroscopy of stellar flares from TRAPPIST-1 during transits of rocky exoplanets. Four flares were observed from 0.6--2.8 $\mu$m with NIRISS and 0.6--3.5 $\mu$m with NIRSpec during transits of TRAPPIST-1b, f, and g. We discover P$\alpha$ and Br$\beta$ line emission and characterize flare continuum at wavelengths from 1--3.5 $\mu$m for the first time. Observed lines include H$\alpha$, P$\alpha$-P$\epsilon$, Br$\beta$, He I $\lambda$0.7062$\mu$m, two Ca II infrared triplet (IRT) lines, and the He I IRT. We observe a reversed Paschen decrement from P$\alpha$-P$\gamma$ alongside changes in the light curve shapes of these lines. The continuum of all four flares is well-described by blackbody emission with an effective temperature below 5300 K, lower than temperatures typically observed at optical wavelengths. The 0.6--1 $\mu$m spectra were convolved with the TESS response, enabling us to measure the flare rate of TRAPPIST-1 in the TESS bandpass. We find flares of 10$^{30}$ erg large enough to impact transit spectra occur at a rate of 3.6$\substack{+2.1 \\ -1.3}$ flare d$^{-1}$, $\sim$10$\times$ higher than previous predictions from K2. We measure the amount of flare contamination at 2 $\mu$m for the TRAPPIST-1b and f transits to be 500$\pm$450 and 2100$\pm$400 ppm, respectively. We find up to 80% of flare contamination can be removed, with mitigation most effective from 1.0--2.4 $\mu$m. These results suggest transits affected by flares may still be useful for atmospheric characterization efforts.Comment: 29 pages, 17 figures, 3 tables, accepted to The Astrophysical Journa

Folate Status of Reproductive Age Women and Neural Tube Defect Risk: The Effect of Long-Term Folic Acid Supplementation at Doses of 140 µg and 400 µg per Day

Primary prevention of most folate-responsive neural tube defects (NTDs) may not require 400 μg folic acid/day but may be achieved by attaining a high maternal folate status. Using RBC folate ≥906 nmol/L as a marker for NTD risk reduction, the study aimed to determine the change in blood folate concentrations in reproductive age women in response to long-term folic acid supplementation at 400 µg/day and 140 µg/day (dose designed to mimic the average daily folic acid intake received from New Zealand’s proposed mandatory bread fortification program). Participants were randomly assigned to a daily folic acid supplement of 140 µg (n = 49), 400 µg (n = 48) or placebo (n = 47) for 40 weeks. RBC folate concentrations were measured at baseline, and after 6, 12, 29 and 40 weeks. At 40 weeks, the overall prevalence of having a RBC folate <906 nmol/L decreased to 18% and 35% in the 400 µg and 140 µg groups, respectively, while remaining relatively unchanged at 58% in the placebo group. After 40 weeks, there was no evidence of a difference in RBC folate between the two treatment groups (P = 0.340), nor was there evidence of a difference in the odds of a RBC folate <906 nmol/L (P = 0.078). In conclusion, the average daily intake of folic acid received from the proposed fortification program would increase RBC folate concentrations in reproductive age women to levels associated with a low risk of NTDs

Altered multisensory temporal integration in obesity

Eating is a multisensory behavior. The act of placing food in the mouth provides us with a variety of sensory information, including gustatory, olfactory, somatosensory, visual, and auditory. Evidence suggests altered eating behavior in obesity. Nonetheless, multisensory integration in obesity has been scantily investigated so far. Starting from this gap in the literature, we seek to provide the first comprehensive investigation of multisensory integration in obesity. Twenty male obese participants and twenty male healthy-weight participants took part in the study aimed at describing the multisensory temporal binding window (TBW). The TBW is defined as the range of stimulus onset asynchrony in which multiple sensory inputs have a high probability of being integrated. To investigate possible multisensory temporal processing deficits in obesity, we investigated performance in two multisensory audiovisual temporal tasks, namely simultaneity judgment and temporal order judgment. Results showed a wider TBW in obese participants as compared to healthy-weight controls. This holds true for both the simultaneity judgment and the temporal order judgment tasks. An explanatory hypothesis would regard the effect of metabolic alterations and low-grade inflammatory state, clinically observed in obesity, on the temporal organization of brain ongoing activity, which one of the neural mechanisms enabling multisensory integration

Evidence for a Two-Metal-Ion Mechanism in the Cytidyltransferase KdsB, an Enzyme Involved in Lipopolysaccharide Biosynthesis

Lipopolysaccharide (LPS) is located on the surface of Gram-negative bacteria and is responsible for maintaining outer membrane stability, which is a prerequisite for cell survival. Furthermore, it represents an important barrier against hostile environmental factors such as antimicrobial peptides and the complement cascade during Gram-negative infections. The sugar 3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) is an integral part of LPS and plays a key role in LPS functionality. Prior to its incorporation into the LPS molecule, Kdo has to be activated by the CMP-Kdo synthetase (CKS). Based on the presence of a single Mg2+ ion in the active site, detailed models of the reaction mechanism of CKS have been developed previously. Recently, a two-metal-ion hypothesis suggested the involvement of two Mg2+ ions in Kdo activation. To further investigate the mechanistic aspects of Kdo activation, we kinetically characterized the CKS from the hyperthermophilic organism Aquifex aeolicus. In addition, we determined the crystal structure of this enzyme at a resolution of 2.10 Å and provide evidence that two Mg2+ ions are part of the active site of the enzyme