Consistent Energy-based Atomistic/Continuum Coupling for Two-body Potentials in Three Dimensions

Very few works exist to date on development of a consistent energy-based coupling of atomistic and continuum models of materials in more than one dimension. The difficulty in constructing such a coupling consists in defining a coupled energy whose minimizers are free from uncontrollable errors on the atomistic/continuum interface. In this paper a consistent coupling in three dimensions is proposed. The main achievement of this work is to identify and efficiently treat a modified Cauchy-Born continuum model which can be coupled to the exact atomistic model. The convergence and stability of the method is confirmed with numerical tests.Comment: 29 pages, 1 Matlab code. Typos corrected, exposition improve

Regulation of smooth muscle contraction by monomeric non‐RhoA GTPases

Smooth muscle contraction in the cardiovascular system, airways, prostate and lower urinary tract is involved in the pathophysiology of many diseases, including cardiovascular and obstructive lung disease plus lower urinary tract symptoms, which are associated with high prevalence of morbidity and mortality. This prominent clinical role of smooth muscle tone has led to the molecular mechanisms involved being subjected to extensive research. In general smooth muscle contraction is promoted by three major signalling pathways, including the monomeric GTPase RhoA pathway. However, emerging evidence suggests that monomeric GTPases other than RhoA may be involved in signal transduction in smooth muscle contraction, including Rac GTPases, cell division control protein 42 homologue, adenosine ribosylation factor 6, Ras, Rap1b and Rab GTPases. Here, we review these emerging functions of non‐RhoA GTPases in smooth muscle contraction, which has now become increasingly more evident and constitutes an emerging and innovative research area of high clinical relevance

Transmural intestinal wall permeability in severe ischemia after enteral protease inhibition.

In intestinal ischemia, inflammatory mediators in the small intestine's lumen such as food byproducts, bacteria, and digestive enzymes leak into the peritoneal space, lymph, and circulation, but the mechanisms by which the intestinal wall permeability initially increases are not well defined. We hypothesize that wall protease activity (independent of luminal proteases) and apoptosis contribute to the increased transmural permeability of the intestine's wall in an acutely ischemic small intestine. To model intestinal ischemia, the proximal jejunum to the distal ileum in the rat was excised, the lumen was rapidly flushed with saline to remove luminal contents, sectioned into equal length segments, and filled with a tracer (fluorescein) in saline, glucose, or protease inhibitors. The transmural fluorescein transport was determined over 2 hours. Villi structure and epithelial junctional proteins were analyzed. After ischemia, there was increased transmural permeability, loss of villi structure, and destruction of epithelial proteins. Supplementation with luminal glucose preserved the epithelium and significantly attenuated permeability and villi damage. Matrix metalloproteinase (MMP) inhibitors (doxycycline, GM 6001), and serine protease inhibitor (tranexamic acid) in the lumen, significantly reduced the fluorescein transport compared to saline for 90 min of ischemia. Based on these results, we tested in an in-vivo model of hemorrhagic shock (90 min 30 mmHg, 3 hours observation) for intestinal lesion formation. Single enteral interventions (saline, glucose, tranexamic acid) did not prevent intestinal lesions, while the combination of enteral glucose and tranexamic acid prevented lesion formation after hemorrhagic shock. The results suggest that apoptotic and protease mediated breakdown cause increased permeability and damage to the intestinal wall. Metabolic support in the lumen of an ischemic intestine with glucose reduces the transport from the lumen across the wall and enteral proteolytic inhibition attenuates tissue breakdown. These combined interventions ameliorate lesion formation in the small intestine after hemorrhagic shock

Non-local signatures of the chiral magnetic effect in Dirac semimetal Bi0.97_{0.97}Sb0.03_{0.03}

The field of topological materials science has recently been focussing on three-dimensional Dirac semimetals, which exhibit robust Dirac phases in the bulk. However, the absence of characteristic surface states in accidental Dirac semimetals (DSM) makes it difficult to experimentally verify claims about the topological nature using commonly used surface-sensitive techniques. The chiral magnetic effect (CME), which originates from the Weyl nodes, causes an $\textbf{E}\cdot\textbf{B}$-dependent chiral charge polarization, which manifests itself as negative magnetoresistance. We exploit the extended lifetime of the chirally polarized charge and study the CME through both local and non-local measurements in Hall bar structures fabricated from single crystalline flakes of the DSM Bi$_{0.97}$Sb$_{0.03}$. From the non-local measurement results we find a chiral charge relaxation time which is over one order of magnitude larger than the Drude transport lifetime, underlining the topological nature of Bi$_{0.97}$Sb$_{0.03}$.Comment: 6 pages, 6 figures + 7 pages of supplemental materia

CHARACTERIZING A NOVEL GENETIC LOCUS ASSOCIATED WITH FAMILIAL CO-OCCURRENCE OF THORACIC AORTIC ANEURYSMS AND INTRACRANIAL ANEURYSMS

The Mendelian inheritance of genetic mutations can lead to adult-onset cardiovascular disease. Several genetic loci have been mapped for the familial form of Thoracic Aortic Aneurysms (TAA), and many causal mutations have been identified for this disease. Intracranial Aneurysms (ICA) also show linkage heterogeneity, but no mutations have been identified causing familial ICA alone. Here, we characterized a large family (TAA288) with an autosomal dominant pattern of inherited aneurysms. It is intriguing that female patients predominantly present with ICA and male patients predominantly with TAA in this family. To identify a causal mutation in this family, a genome-wide linkage analysis was previously performed on nine members of this family using the 50k GenChips Hind array from Affymetrix. This analysis eventually identified a single disease-segregating locus, on chromosome 5p15. We build upon this previous analysis in this study, hypothesizing that a genetic mutation inherited in this locus leads to the sex-specific phenotype of TAA and ICA in this family First we refined the boundaries of the 5p15 disease linked locus down to the genomic coordinates 5p15: 3,424,465- 6,312,925 (GRCh37/hg19 Assembly). This locus was named the TAA288 critical interval. Next, we sequenced candidate genes within the TAA288 critical interval. The selection of genes was simplified by the relatively small number of well-characterized genetic elements within the region. Seeking novel or rare disease-segregating variants, we initially observed a single point alteration in the metalloproteinase gene ADAMTS16 fulfilling this criteria. This variant was later classified as a low-frequency population polymorphism (rs72647757), but we continued to explore the potential role of the ADAMTS16 as the cause of disease in TAA288. We observed that fibroblasts cultured from TAA288 patients consistently upregulated the expression of this gene more strongly compared to matched control fibroblasts when treated with the cytokine TGF-β1, though there was some variation in the exact nature of this expression. We also observed evidence that this protein is expressed at elevated levels in aortic aneurysm tissue from patients with mutations in the gene TGFBR2 and Marfan syndrome, shown by immunohistochemical detection of this protein

Detection of Genes Influencing Chronic and Mendelian Disease via Loss-Of-Function Variation

A typical human exome harbors dozens of loss-of-function (LOF) variants predicted to severely disrupt or abolish gene function. These variants are enriched at the extremely rare end of the allele frequency spectrum (\u3c 0.1%), suggesting purifying selection against these sites. However, most previous population-based sequencing studies have not included analysis of genotype-phenotype relationships with LOF variants. Thus, the contribution of LOF variation to health and disease within the general population remains largely uncharacterized. Using whole exome sequence from 8,554 participants in the Atherosclerosis Risk in Communities (ARIC) study, we explored the impact of LOF variation on a broad spectrum of human phenotypes. First, we selected 20 common chronic disease risk factor phenotypes and performed gene-based association tests. Analysis of this sample verified two relationships in well-studied genes (PCSK9 and APOC3) and identified eight new loci. Novel relationships included elevated fasting glucose in heterozygous carriers of LOF variation in TXNDC5, which encodes a biomarker for type 1 diabetes progression, and apparent recessive effects of C1QTNF8 on serum magnesium levels. Next, we explored the effect of LOF variation on 308 small molecular metabolites, observing 8 significant genotype-phenotype associations. We highlight the relationship between serum histidine and HAL, a gene essential to histidine catabolism, demonstrating the biologically interpretability of associations with molecular metabolite targets. Finally, we explore the impact of LOF variation on a rare birth defect by comparing sequence from 342 unrelated left ventricular outflow tract obstruction (LVOTO) cases to ARIC sequence, identifying genes harboring case-exclusive LOF mutations. Comparison to an a priori list of cardiac candidate genes revealed 28 genes potentially related to LVOTO, including 22 not previously associated with a human disorder. Genotype validation in these samples revealed diverse inheritance patterns, including 9 confirmed de novo variants (ACVR1, JARID2, KMT2D, NF1, NR2F2, PLRG1, SMURF1, TBX20, and ZEB2). The analytical strategy presented here highlights the role of biologically-informed annotation on large-scale human genetic studies. The genes identified by these methods may have applications in disease prediction and drug development, and future genome studies will continue to refine our understanding of the scope of genetic variation affecting human health and disease