Replication of linkage at chromosome 20p13 and identification of suggestive sex-differential risk loci for autism spectrum disorder.

BackgroundAutism spectrum disorders (ASDs) are male-biased and genetically heterogeneous. While sequencing of sporadic cases has identified de novo risk variants, the heritable genetic contribution and mechanisms driving the male bias are less understood. Here, we aimed to identify familial and sex-differential risk loci in the largest available, uniformly ascertained, densely genotyped sample of multiplex ASD families from the Autism Genetics Resource Exchange (AGRE), and to compare results with earlier findings from AGRE.MethodsFrom a total sample of 1,008 multiplex families, we performed genome-wide, non-parametric linkage analysis in a discovery sample of 847 families, and separately on subsets of families with only male, affected children (male-only, MO) or with at least one female, affected child (female-containing, FC). Loci showing evidence for suggestive linkage (logarithm of odds ≥2.2) in this discovery sample, or in previous AGRE samples, were re-evaluated in an extension study utilizing all 1,008 available families. For regions with genome-wide significant linkage signal in the discovery stage, those families not included in the corresponding discovery sample were then evaluated for independent replication of linkage. Association testing of common single nucleotide polymorphisms (SNPs) was also performed within suggestive linkage regions.ResultsWe observed an independent replication of previously observed linkage at chromosome 20p13 (P < 0.01), while loci at 6q27 and 8q13.2 showed suggestive linkage in our extended sample. Suggestive sex-differential linkage was observed at 1p31.3 (MO), 8p21.2 (FC), and 8p12 (FC) in our discovery sample, and the MO signal at 1p31.3 was supported in our expanded sample. No sex-differential signals met replication criteria, and no common SNPs were significantly associated with ASD within any identified linkage regions.ConclusionsWith few exceptions, analyses of subsets of families from the AGRE cohort identify different risk loci, consistent with extreme locus heterogeneity in ASD. Large samples appear to yield more consistent results, and sex-stratified analyses facilitate the identification of sex-differential risk loci, suggesting that linkage analyses in large cohorts are useful for identifying heritable risk loci. Additional work, such as targeted re-sequencing, is needed to identify the specific variants within these loci that are responsible for increasing ASD risk

The development of models to predict melting and pyrolysis point data associated with several hundred thousand compounds mined from PATENTS

BACKGROUND: Melting point (MP) is an important property in regards to the solubility of chemical compounds. Its prediction from chemical structure remains a highly challenging task for quantitative structure-activity relationship studies. Success in this area of research critically depends on the availability of high quality MP data as well as accurate chemical structure representations in order to develop models. Currently, available datasets for MP predictions have been limited to around 50k molecules while lots more data are routinely generated following the synthesis of novel materials. Significant amounts of MP data are freely available within the patent literature and, if it were available in the appropriate form, could potentially be used to develop predictive models. RESULTS: We have developed a pipeline for the automated extraction and annotation of chemical data from published PATENTS. Almost 300,000 data points have been collected and used to develop models to predict melting and pyrolysis (decomposition) points using tools available on the OCHEM modeling platform (http://ochem.eu). A number of technical challenges were simultaneously solved to develop models based on these data. These included the handing of sparse data matrices with >200,000,000,000 entries and parallel calculations using 32 × 6 cores per task using 13 descriptor sets totaling more than 700,000 descriptors. We showed that models developed using data collected from PATENTS had similar or better prediction accuracy compared to the highly curated data used in previous publications. The separation of data for chemicals that decomposed rather than melting, from compounds that did undergo a normal melting transition, was performed and models for both pyrolysis and MPs were developed. The accuracy of the consensus MP models for molecules from the drug-like region of chemical space was similar to their estimated experimental accuracy, 32 °C. Last but not least, important structural features related to the pyrolysis of chemicals were identified, and a model to predict whether a compound will decompose instead of melting was developed. CONCLUSIONS: We have shown that automated tools for the analysis of chemical information have reached a mature stage allowing for the extraction and collection of high quality data to enable the development of structure-activity relationship models. The developed models and data are publicly available at http://ochem.eu/article/99826

Holographic representation of local bulk operators

The Lorentzian AdS/CFT correspondence implies a map between local operators in supergravity and non-local operators in the CFT. By explicit computation we construct CFT operators which are dual to local bulk fields in the semiclassical limit. The computation is done for general dimension in global, Poincare and Rindler coordinates. We find that the CFT operators can be taken to have compact support in a region of the complexified boundary whose size is set by the bulk radial position. We show that at finite N the number of independent commuting operators localized within a bulk volume saturates the holographic bound.Comment: 36 pages, LaTeX, 4 eps figure

Constructing local bulk observables in interacting AdS/CFT

Local operators in the bulk of AdS can be represented as smeared operators in the dual CFT. We show how to construct these bulk observables by requiring that the bulk operators commute at spacelike separation. This extends our previous work by taking interactions into account. Large-N factorization plays a key role in the construction. We show diagrammatically how this procedure is related to bulk Feynman diagrams.Comment: 41 pages, LaTeX. v2: reference correcte

Transcriptomic analysis of autistic brain reveals convergent molecular pathology.

Autism spectrum disorder (ASD) is a common, highly heritable neurodevelopmental condition characterized by marked genetic heterogeneity. Thus, a fundamental question is whether autism represents an aetiologically heterogeneous disorder in which the myriad genetic or environmental risk factors perturb common underlying molecular pathways in the brain. Here, we demonstrate consistent differences in transcriptome organization between autistic and normal brain by gene co-expression network analysis. Remarkably, regional patterns of gene expression that typically distinguish frontal and temporal cortex are significantly attenuated in the ASD brain, suggesting abnormalities in cortical patterning. We further identify discrete modules of co-expressed genes associated with autism: a neuronal module enriched for known autism susceptibility genes, including the neuronal specific splicing factor A2BP1 (also known as FOX1), and a module enriched for immune genes and glial markers. Using high-throughput RNA sequencing we demonstrate dysregulated splicing of A2BP1-dependent alternative exons in the ASD brain. Moreover, using a published autism genome-wide association study (GWAS) data set, we show that the neuronal module is enriched for genetically associated variants, providing independent support for the causal involvement of these genes in autism. In contrast, the immune-glial module showed no enrichment for autism GWAS signals, indicating a non-genetic aetiology for this process. Collectively, our results provide strong evidence for convergent molecular abnormalities in ASD, and implicate transcriptional and splicing dysregulation as underlying mechanisms of neuronal dysfunction in this disorder

Local bulk operators in AdS/CFT: a boundary view of horizons and locality

We develop the representation of local bulk fields in AdS by non-local operators on the boundary, working in the semiclassical limit and using AdS_2 as our main example. In global coordinates we show that the boundary operator has support only at points which are spacelike separated from the bulk point. We construct boundary operators that represent local bulk operators inserted behind the horizon of the Poincare patch and inside the Rindler horizon of a two dimensional black hole. We show that these operators respect bulk locality and comment on the generalization of our construction to higher dimensional AdS black holes.Comment: 28 pages, 4 figures, late

Access, Socioeconomic Environment, and Death from COVID-19 in Nebraska

Our study assesses whether factors related to healthcare access in the first year of the pandemic affect mortality and length of stay (LOS). Our cohort study examined hospitalized patients at Nebraska Medicine between April and October 2020 who were tested for SARS-CoV-2 and had a charted sepsis related diagnostic code. Multivariate logistic was used to analyze the odds of mortality and linear regression was used to calculate the parameter estimates of LOS associated with COVID-19 status, age, gender, race/ethnicity, median household income, admission month, and residential distance from definitive care. Among 475 admissions, the odds of mortality is greater among those with older age (OR: 1.04, 95% CI: 1.02-1.07) and residence in an area with low median household income (OR: 2.11, 95% CI: 0.52-8.57), however, the relationship between mortality and wealth was not statistically significant. Those with non-COVID-19 sepsis had longer LOS (Parameter Estimate: -5.11, adjusted 95% CI: -7.92 to -2.30). Distance from definitive care had trends toward worse outcomes (Parameter Estimate: 0.164, adjusted 95% CI: -1.39 to 1.97). Physical and social aspects of access to care are linked to poorer COVID-19 outcomes. Non-COVID-19 healthcare outcomes may be negatively impacted in the pandemic. Strategies to advance patient-centered outcomes in vulnerable populations should account for varied aspects (socioeconomic, residential setting, rural populations, racial, and ethnic factors). Indirect impacts of the pandemic on non-COVID-19 health outcomes require further study

How Do Collegiate Sport Clubs Achieve Organizational Effectiveness?

A greater understanding of the organizational processes of sport clubs can inform strategies to improve clubs’ organizational effectiveness. This study examined whether sport club capacity and activities influence the organizational effectiveness of collegiate sport clubs. Sport club members (n = 201) completed a questionnaire, with secondary data collected from the university. Regression analysis found club operations, club fiscal responsibility, frequency of club practice, and frequency of competitions significantly, positively predict organizational effectiveness. Comparatively, club human capital and facility quality significantly, negatively predict organizational effectiveness. These results have implications relating to club training, mentorship, resource allocation, and club activities

p53 and NF- B Coregulate Proinflammatory Gene Responses in Human Macrophages

Macrophages are sentinel immune cells that survey the tissue microenvironment, releasing cytokines in response to both exogenous insults and endogenous events such as tumorigenesis. Macrophages mediate tumor surveillance and therapy-induced tumor regression; however, tumor-associated macrophages (TAM) and their products may also promote tumor progression. Whereas NF-κB is prominent in macrophage-initiated inflammatory responses, little is known about the role of p53 in macrophage responses to environmental challenge, including chemotherapy or in TAMs. Here, we report that NF-κB and p53, which generally have opposing effects in cancer cells, coregulate induction of proinflammatory genes in primary human monocytes and macrophages. Using Nutlin-3 as a tool, we demonstrate that p53 and NF-κB rapidly and highly induce interleukin ( IL )- 6 by binding to its promoter. Transcriptome analysis revealed global p53/NF-κB co-regulation of immune response genes, including several chemokines, which effectively induced human neutrophil migration. In addition, we show that p53, activated by tumor cell paracrine factors, induces high basal levels of macrophage IL-6 in a TAM model system [tumor-conditioned macrophages (TCM)]. Compared with normal macrophages, TCMs exhibited higher p53 levels, enhanced p53 binding to the IL-6 promoter, and reduced IL-6 levels upon p53 inhibition. Taken together, we describe a mechanism by which human macrophages integrate signals through p53 and NF-κB to drive proinflammatory cytokine induction. Our results implicate a novel role for macrophage p53 in conditioning the tumor microenvironment and suggest a potential mechanism by which p53-activating chemotherapeutics, acting upon p53-sufficient macrophages and precursor monocytes, may indirectly impact tumors lacking functional p53. Cancer Res; 74(8); 2182–92. ©2014 AACR

Transgenic overexpression of γ-cytoplasmic actin protects against eccentric contraction-induced force loss in mdx mice

<p>Abstract</p> <p>Background</p> <p>γ-cytoplasmic (γ-_cyto) actin levels are elevated in dystrophin-deficient <it>mdx </it>mouse skeletal muscle. The purpose of this study was to determine whether further elevation of γ-_cytoactin levels improve or exacerbate the dystrophic phenotype of <it>mdx </it>mice.</p> <p>Methods</p> <p>We transgenically overexpressed γ-_cytoactin, specifically in skeletal muscle of mdx mice (<it>mdx</it>-TG), and compared skeletal muscle pathology and force-generating capacity between <it>mdx </it>and <it>mdx</it>-TG mice at different ages. We investigated the mechanism by which γ-_cytoactin provides protection from force loss by studying the role of calcium channels and stretch-activated channels in isolated skeletal muscles and muscle fibers. Analysis of variance or independent <it>t</it>-tests were used to detect statistical differences between groups.</p> <p>Results</p> <p>Levels of γ-_cytoactin in <it>mdx</it>-TG skeletal muscle were elevated 200-fold compared to <it>mdx </it>skeletal muscle and incorporated into thin filaments. Overexpression of γ-_cytoactin had little effect on most parameters of <it>mdx </it>muscle pathology. However, γ-_cytoactin provided statistically significant protection against force loss during eccentric contractions. Store-operated calcium entry across the sarcolemma did not differ between <it>mdx </it>fibers compared to wild-type fibers. Additionally, the omission of extracellular calcium or the addition of streptomycin to block stretch-activated channels did not improve the force-generating capacity of isolated extensor digitorum longus muscles from <it>mdx </it>mice during eccentric contractions.</p> <p>Conclusions</p> <p>The data presented in this study indicate that upregulation of γ-_cytoactin in dystrophic skeletal muscle can attenuate force loss during eccentric contractions and that the mechanism is independent of activation of stretch-activated channels and the accumulation of extracellular calcium.</p