Atypical hemispheric specialization for faces in infants at risk for autism spectrum disorder

Among the many experimental findings that tend to distinguish those with and without autism spectrum disorder (ASD) are face processing deficits, reduced hemispheric specialization, and atypical neurostructural and functional connectivity. To investigate the earliest manifestations of these features, we examined lateralization of event-related gamma-band coherence to faces during the first year of life in infants at high risk for autism (HRA; defined as having an older sibling with ASD) who were compared with low-risk comparison (LRC) infants, defined as having no family history of ASD. Participants included 49 HRA and 46 LRC infants who contributed a total of 127 data sets at 6 and 12 months. Electroencephalography was recorded while infants viewed images of familiar/unfamiliar faces. Event-related gamma-band (30-50 Hz) phase coherence between anterior-posterior electrode pairs for left and right hemispheres was computed. Developmental trajectories for lateralization of intra-hemispheric coherence were significantly different in HRA and LRC infants: by 12 months, HRA infants showed significantly greater leftward lateralization compared with LRC infants who showed rightward lateralization. Preliminary results indicate that infants who later met criteria for ASD were those that showed the greatest leftward lateralization. HRA infants demonstrate an aberrant pattern of leftward lateralization of intra-hemispheric coherence by the end of the first year of life, suggesting that the network specialized for face processing may develop atypically. Further, infants with the greatest leftward asymmetry at 12 months where those that later met criteria for ASD, providing support to the growing body of evidence that atypical hemispheric specialization may be an early neurobiological marker for ASD.R01 DC010290 - NIDCD NIH HHS; R01-DC010290 - NIDCD NIH HH

Gamma power in rural Pakistani children: links to executive function and verbal ability

Children in low- and middle-income countries are at high risk of cognitive deficits due to environmental deprivation that compromises brain development. Despite the high prevalence of unrealized cognitive potential, very little is known about neural correlates of cognition in this population. We assessed resting EEG power and cognitive ability in 105 highly disadvantaged 48-month-old children in rural Pakistan. An increase in EEG power in gamma frequency bands (21–30 Hz and 31–45 Hz) was associated with better executive function. For girls, EEG gamma power also related to higher verbal IQ. This study identifies EEG gamma power as a neural marker of cognitive function in disadvantaged children in low- and middle-income countries. Elevated gamma power may be a particularly important protective factor for girls, who may experience greater deprivation due to gender inequality.This research was supported by Grand Challenges Canada Saving Brains Initiative Grant 0061-03. The preparation of this article also was supported by a Scholar's Award from the William T. Grant Foundation to Jelena Obradovic. (0061-03 - Grand Challenges Canada Saving Brains Initiative; William T. Grant Foundation)Published versio

ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest.

Next-generation sequencing technology (NGS) enables the discovery of nearly all genetic variants present in a genome. A subset of these variants, however, may have poor sequencing quality due to limitations in NGS or variant callers. In genetic studies that analyze a large number of sequenced individuals, it is critical to detect and remove those variants with poor quality as they may cause spurious findings. In this paper, we present ForestQC, a statistical tool for performing quality control on variants identified from NGS data by combining a traditional filtering approach and a machine learning approach. Our software uses the information on sequencing quality, such as sequencing depth, genotyping quality, and GC contents, to predict whether a particular variant is likely to be false-positive. To evaluate ForestQC, we applied it to two whole-genome sequencing datasets where one dataset consists of related individuals from families while the other consists of unrelated individuals. Results indicate that ForestQC outperforms widely used methods for performing quality control on variants such as VQSR of GATK by considerably improving the quality of variants to be included in the analysis. ForestQC is also very efficient, and hence can be applied to large sequencing datasets. We conclude that combining a machine learning algorithm trained with sequencing quality information and the filtering approach is a practical approach to perform quality control on genetic variants from sequencing data

AtomSim: web-deployed atomistic dynamics simulator

AtomSim, a collection of interfaces for computational crystallography simulations, has been developed. It uses forcefield-based dynamics through physics engines such as the General Utility Lattice Program, and can be integrated into larger computational frameworks such as the Virtual Neutron Facility for processing its dynamics into scattering functions, dynamical functions etc. It is also available as a Google App Engine-hosted web-deployed interface. Examples of a quartz molecular dynamics run and a hafnium dioxide phonon calculation are presented

Functional connectivity in the first year of life in infants at-risk for autism: a preliminary near-infrared spectroscopy study

Background: Autism spectrum disorder (ASD) has been called a “developmental disconnection syndrome,” however the majority of the research examining connectivity in ASD has been conducted exclusively with older children and adults. Yet, prior ASD research suggests that perturbations in neurodevelopmental trajectories begin as early as the first year of life. Prospective longitudinal studies of infants at risk for ASD may provide a window into the emergence of these aberrant patterns of connectivity. The current study employed functional connectivity near-infrared spectroscopy (NIRS) in order to examine the development of intra- and inter-hemispheric functional connectivity in high- and low-risk infants across the first year of life. Methods: NIRS data were collected from 27 infants at high risk for autism (HRA) and 37 low-risk comparison (LRC) infants who contributed a total of 116 data sets at 3-, 6-, 9-, and 12-months. At each time point, HRA and LRC groups were matched on age, sex, head circumference, and Mullen Scales of Early Learning scores. Regions of interest (ROI) were selected from anterior and posterior locations of each hemisphere. The average time course for each ROI was calculated and correlations for each ROI pair were computed. Differences in functional connectivity were examined in a cross-sectional manner. Results: At 3-months, HRA infants showed increased overall functional connectivity compared to LRC infants. This was the result of increased connectivity for intra- and inter-hemispheric ROI pairs. No significant differences were found between HRA and LRC infants at 6- and 9-months. However, by 12-months, HRA infants showed decreased connectivity relative to LRC infants. Conclusions: Our preliminary results suggest that atypical functional connectivity may exist within the first year of life in HRA infants, providing support to the growing body of evidence that aberrant patterns of connectivity may be a potential endophenotype for ASD

Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury.

Background:Recent studies have demonstrated the vital influence of commensal microbial communities on human health. The central role of the gut in the response to injury is well described; however, no prior studies have used culture-independent profiling techniques to characterize the gut microbiome after severe trauma. We hypothesized that in critically injured patients, the gut microbiome would undergo significant compositional changes in the first 72 hours after injury. Methods:Trauma stool samples were prospectively collected via digital rectal examination at the time of presentation (0 hour). Patients admitted to the intensive care unit (n=12) had additional stool samples collected at 24 hours and/or 72 hours. Uninjured patients served as controls (n=10). DNA was extracted from stool samples and 16S rRNA-targeted PCR amplification was performed; amplicons were sequenced and binned into operational taxonomic units (OTUs; 97% sequence similarity). Diversity was analyzed using principle coordinates analyses, and negative binomial regression was used to determine significantly enriched OTUs. Results:Critically injured patients had a median Injury Severity Score of 27 and suffered polytrauma. At baseline (0 hour), there were no detectable differences in gut microbial community diversity between injured and uninjured patients. Injured patients developed changes in gut microbiome composition within 72 hours, characterized by significant alterations in phylogenetic composition and taxon relative abundance. Members of the bacterial orders Bacteroidales, Fusobacteriales and Verrucomicrobiales were depleted during 72 hours, whereas Clostridiales and Enterococcus members enriched significantly. Discussion:In this initial study of the gut microbiome after trauma, we demonstrate that significant changes in phylogenetic composition and relative abundance occur in the first 72 hours after injury. This rapid change in intestinal microbiota represents a critical phenomenon that may influence outcomes after severe trauma. A better understanding of the nature of these postinjury changes may lead to the ability to intervene in otherwise pathological clinical trajectories. Level of evidence:III. Study type:Prognostic/epidemiological

Examining the Effect of Varying Dilutions of Octopamine on the Gut Microbiome of Lab-raised and Wild Acheta Domesticus By Brandon Nelson University of Puget Sound Biology

For my research I am comparing the gut microbiome of lab raised A. Domesticus that are given various levels of Octopamine, a stress hormone, and comparing that to the gut microbiome of wild cricket types. Crickets are a widely used organism across the world for various experiments as both subject and feed. Knowing how the gut microbiome of these crickets is affected by various levels of stress will allow us to better take care of these crickets. This could also help us determine if there are any diseases that lab raised crickets may be susceptible to. A large part of this research has been exploratory, finding various bacteria from frass samples. This project uses genomic DNA extraction kits, PCR, nanodrop, and other microbiology techniques

The Beast Inside Your Head: A Look at Mental Health Issues in Samoa

Mental illness remains a very controversial and prevalent problem for the entire world, especially the Pacific. This study examines some prevalent mental health issues and looks at how suicide, youth, alcohol, and prison correlate with mental health issues and illness in Samoa. It also looks at the Mental Health Unit (MHU) at National Hospital and programs implemented to help Samoans suffering within the four areas of mental health researched. Quantitative data from international organizations, government bureaus, and surveys, helps describe the current status of mental health issues in Samoa. One hundred twenty four surveys (124) were distributed about mental health awareness and what people deemed as the best way to treat mental illness. Interviews and observations rounded out the study. Results show most Samoans understand mental health and its importance. Analysis also suggests that Samoa is progressing in clinical terms and treatment of mental illness, as well as being proactive in mental health education. Overall, this research documents the programs that the National Hospital provides in terms of mental health treatment and education to communities. Ke

Untangling the Conceptual Isssues Raised in Reydon and Scholz’s Critique of Organizational Ecology and Darwinian Populations

Reydon and Scholz raise doubts about the Darwinian status of organizational ecology by arguing that Darwinian principles are not applicable to organizational populations. Although their critique of organizational ecology’s typological essentialism is correct, they go on to reject the Darwinian status of organizational populations. This paper claims that the distinction between replicators and interactors, raised in modern philosophy of biology but not discussed by Reydon and Scholz, points the way forward for organizational ecologists. It is possible to conceptualise evolving Darwinian populations providing the inheritance mechanism is appropriately specified. By this approach, adaptation and selection are no longer dichotomised, and the evolutionary significance of knowledge transmission is highlightedPeer reviewe