Fast image deconvolution for enhancement of the resolution in the video rate terahertz imaging

International audienceA fast image deconvolution algorithm is used to demonstrate the resolution enhancement of video rate camera acquired Terahertz images. Our algorithm is based on variable splitting technique with the use of a family of sparsity inducing regularizers for the first time in an image deconvolution application, it is also suitable for practical applications in industry with computationally constrained conditions. The results of the proposed process provide substantial enhancement on the quality and resolution of THz images

Modelling trace metal background to evaluate anthropogenic contamination in arable soils of south-western France

The trace metal (TM) content in arable soils has been monitored across a region of France characterised by a large proportion of calcareous soils. Within this particular geological context, the objectives were to first determine the natural levels of trace metals in the soils and secondly, to assess which sites were significantly contaminated. Because no universal contamination assessment method is currently available, four different methods were applied and compared in order to facilitate the best diagnosis of contamination. First, the TM geochemical background was determined by using basic descriptive statistics and linear regression models calculated with semi-conservative major elements as predictors. The natural concentrations of trace metals varied greatly due to the high soil heterogeneity encountered on the regional scale and were more-or-less accurately modelled according to the considered TM. Second, the basic descriptive statistics and the linear regression methods were then compared with the enrichment factor (EF) method and multivariate analysis (PCA), in order to evaluate whether the concentrations measured in soils were abnormally high or not. The advantages and disadvantages of each method were discussed and their results used to identify the most probable contamination cases, the influence of the soils characteristics, as well as the agricultural land cover. The basic descriptive method was good as a first and easy approach to describe the TM ambient concentrations, but may misinterpret the natural anomalies as contaminations. Based on geochemical associations, the linear regression method provided more realistic results even if the relationships between major and trace metals were not significant for the most mobile TM. The EF method was useful to identify high point source contaminations, but it was not suitable when considering a large dataset of low TM concentrations. Finally, the PCA method was a good preliminary tool for the description of the global TM concentrations in a studied area, but it could only give indication on the highest contaminated points. By comparing the results of the different methods in the studied region, we estimated that 24% of the arable soils were contaminated by at least one trace metal, mainly Cu in vineyards/orchards and Cd, Pb and/or Zn in grazing lands. In addition, the calcareous soils exhibited globally higher natural and anthropogenic TM concentrations than non-calcareous soils, probably because of the lower TM mobility at alkaline pH

Excitations of incoherent spin-waves due to spin-transfer torque

As predicted by Slonczewski and Berger, the possibility of exciting microwave oscillations in a nanomagnet by a spin-polarized current has been recently demonstrated. This observation opens very important perspectives of applications in RF components. However, some unresolved inconsistencies are found when interpreting the magnetization dynamics results within the coherent spin-torque model (CSM). In some cases, the telegraph noise caused by spin-currents could not be described quantitatively by the CSM. This led to controversies about the need of an effective magnetic temperature model (ETM). Here we interpret the experimental results of Kiselev et al. [Nature 425, 380 (2003)] using micromagnetic simulations. We point out the key role played by incoherent spin-waves excitation due to spin-transfer effects. The incoherence is caused by the spatial inhomogeneities of the local fields, generating a distribution of local precession frequencies. It results in telegraph noise at zero temperature associated with transitions between attraction wells in phase space.Comment: Nature Materials advance online publication, 7 November 200

High-Throughput Analysis of Promoter Occupancy Reveals New Targets for Arx, a Gene Mutated in Mental Retardation and Interneuronopathies

Genetic investigations of X-linked intellectual disabilities have implicated the ARX (Aristaless-related homeobox) gene in a wide spectrum of disorders extending from phenotypes characterised by severe neuronal migration defects such as lissencephaly, to mild or moderate forms of mental retardation without apparent brain abnormalities but with associated features of dystonia and epilepsy. Analysis of Arx spatio-temporal localisation profile in mouse revealed expression in telencephalic structures, mainly restricted to populations of GABAergic neurons at all stages of development. Furthermore, studies of the effects of ARX loss of function in humans and animal models revealed varying defects, suggesting multiple roles of this gene during brain development. However, to date, little is known about how ARX functions as a transcription factor and the nature of its targets. To better understand its role, we combined chromatin immunoprecipitation and mRNA expression with microarray analysis and identified a total of 1006 gene promoters bound by Arx in transfected neuroblastoma (N2a) cells and in mouse embryonic brain. Approximately 24% of Arx-bound genes were found to show expression changes following Arx overexpression or knock-down. Several of the Arx target genes we identified are known to be important for a variety of functions in brain development and some of them suggest new functions for Arx. Overall, these results identified multiple new candidate targets for Arx and should help to better understand the pathophysiological mechanisms of intellectual disability and epilepsy associated with ARX mutations

A Multi-Sample Based Method for Identifying Common CNVs in Normal Human Genomic Structure Using High-Resolution aCGH Data

BACKGROUND: It is difficult to identify copy number variations (CNV) in normal human genomic data due to noise and non-linear relationships between different genomic regions and signal intensity. A high-resolution array comparative genomic hybridization (aCGH) containing 42 million probes, which is very large compared to previous arrays, was recently published. Most existing CNV detection algorithms do not work well because of noise associated with the large amount of input data and because most of the current methods were not designed to analyze normal human samples. Normal human genome analysis often requires a joint approach across multiple samples. However, the majority of existing methods can only identify CNVs from a single sample. METHODOLOGY AND PRINCIPAL FINDINGS: We developed a multi-sample-based genomic variations detector (MGVD) that uses segmentation to identify common breakpoints across multiple samples and a k-means-based clustering strategy. Unlike previous methods, MGVD simultaneously considers multiple samples with different genomic intensities and identifies CNVs and CNV zones (CNVZs); CNVZ is a more precise measure of the location of a genomic variant than the CNV region (CNVR). CONCLUSIONS AND SIGNIFICANCE: We designed a specialized algorithm to detect common CNVs from extremely high-resolution multi-sample aCGH data. MGVD showed high sensitivity and a low false discovery rate for a simulated data set, and outperformed most current methods when real, high-resolution HapMap datasets were analyzed. MGVD also had the fastest runtime compared to the other algorithms evaluated when actual, high-resolution aCGH data were analyzed. The CNVZs identified by MGVD can be used in association studies for revealing relationships between phenotypes and genomic aberrations. Our algorithm was developed with standard C++ and is available in Linux and MS Windows format in the STL library. It is freely available at: http://embio.yonsei.ac.kr/~Park/mgvd.php

Intracranial Aneurysm Classifier Using Phenotypic Factors: An International Pooled Analysis

Intracranial aneurysms (IAs) are usually asymptomatic with a low risk of rupture, but consequences of aneurysmal subarachnoid hemorrhage (aSAH) are severe. Identifying IAs at risk of rupture has important clinical and socio-economic consequences. The goal of this study was to assess the effect of patient and IA characteristics on the likelihood of IA being diagnosed incidentally versus ruptured. Patients were recruited at 21 international centers. Seven phenotypic patient characteristics and three IA characteristics were recorded. The analyzed cohort included 7992 patients. Multivariate analysis demonstrated that: (1) IA location is the strongest factor associated with IA rupture status at diagnosis; (2) Risk factor awareness (hypertension, smoking) increases the likelihood of being diagnosed with unruptured IA; (3) Patients with ruptured IAs in high-risk locations tend to be older, and their IAs are smaller; (4) Smokers with ruptured IAs tend to be younger, and their IAs are larger; (5) Female patients with ruptured IAs tend to be older, and their IAs are smaller; (6) IA size and age at rupture correlate. The assessment of associations regarding patient and IA characteristics with IA rupture allows us to refine IA disease models and provide data to develop risk instruments for clinicians to support personalized decision-making

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Genome-wide association analyses identify new Brugada syndrome risk loci and highlight a new mechanism of sodium channel regulation in disease susceptibility.

Brugada syndrome (BrS) is a cardiac arrhythmia disorder associated with sudden death in young adults. With the exception of SCN5A, encoding the cardiac sodium channel Na1.5, susceptibility genes remain largely unknown. Here we performed a genome-wide association meta-analysis comprising 2,820 unrelated cases with BrS and 10,001 controls, and identified 21 association signals at 12 loci (10 new). Single nucleotide polymorphism (SNP)-heritability estimates indicate a strong polygenic influence. Polygenic risk score analyses based on the 21 susceptibility variants demonstrate varying cumulative contribution of common risk alleles among different patient subgroups, as well as genetic associations with cardiac electrical traits and disorders in the general population. The predominance of cardiac transcription factor loci indicates that transcriptional regulation is a key feature of BrS pathogenesis. Furthermore, functional studies conducted on MAPRE2, encoding the microtubule plus-end binding protein EB2, point to microtubule-related trafficking effects on Na1.5 expression as a new underlying molecular mechanism. Taken together, these findings broaden our understanding of the genetic architecture of BrS and provide new insights into its molecular underpinnings

Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as novel risk factors for Alzheimers Disease

The genetic component of Alzheimer’s disease (AD) has been mainly assessed using Genome Wide Association Studies (GWAS), which do not capture the risk contributed by rare variants. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals —16,036 AD cases and 16,522 controls— in a two-stage analysis. Next to known genes TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Next to these genes, the rare variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential driver genes in AD-GWAS loci. Rare damaging variants in these genes, and in particular loss-of-function variants, have a large effect on AD-risk, and they are enriched in early onset AD cases. The newly identified AD-associated genes provide additional evidence for a major role for APP-processing, Aβ-aggregation, lipid metabolism and microglial function in AD