Inversion of Sequence of Diffusion and Density Anomalies in Core-Softened Systems

In this paper we present a simulation study of water-like anomalies in core-softened system introduced in our previous publications. We investigate the anomalous regions for a system with the same functional form of the potential but with different parameters and show that the order of the region of anomalous diffusion and the region of density anomaly is inverted with increasing the width of the repulsive shoulder.Comment: 8 pages, 10 figure

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.

Integrating single nucleotide polymorphism (SNP) p-values from genome-wide association studies (GWAS) across genes and pathways is a strategy to improve statistical power and gain biological insight. Here, we present Pascal (Pathway scoring algorithm), a powerful tool for computing gene and pathway scores from SNP-phenotype association summary statistics. For gene score computation, we implemented analytic and efficient numerical solutions to calculate test statistics. We examined in particular the sum and the maximum of chi-squared statistics, which measure the strongest and the average association signals per gene, respectively. For pathway scoring, we use a modified Fisher method, which offers not only significant power improvement over more traditional enrichment strategies, but also eliminates the problem of arbitrary threshold selection inherent in any binary membership based pathway enrichment approach. We demonstrate the marked increase in power by analyzing summary statistics from dozens of large meta-studies for various traits. Our extensive testing indicates that our method not only excels in rigorous type I error control, but also results in more biologically meaningful discoveries

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility.

To better understand genome regulation, it is important to uncover the role of transcription factors in the process of chromatin structure establishment and maintenance. Here we present a data-driven approach to systematically characterise transcription factors that are relevant for this process. Our method uses a linear mixed modelling approach to combine datasets of transcription factor binding motif enrichments in open chromatin and gene expression across the same set of cell lines. Applying this approach to the ENCODE dataset, we confirm already known and imply numerous novel transcription factors that play a role in the establishment or maintenance of open chromatin. In particular, our approach rediscovers many factors that have been annotated as pioneer factors

Genome-Wide Analysis Reveals Novel Regulators of Growth in Drosophila melanogaster.

Organismal size depends on the interplay between genetic and environmental factors. Genome-wide association (GWA) analyses in humans have implied many genes in the control of height but suffer from the inability to control the environment. Genetic analyses in Drosophila have identified conserved signaling pathways controlling size; however, how these pathways control phenotypic diversity is unclear. We performed GWA of size traits using the Drosophila Genetic Reference Panel of inbred, sequenced lines. We find that the top associated variants differ between traits and sexes; do not map to canonical growth pathway genes, but can be linked to these by epistasis analysis; and are enriched for genes and putative enhancers. Performing GWA on well-studied developmental traits under controlled conditions expands our understanding of developmental processes underlying phenotypic diversity

Performance Bottlenecks in Digital Movie Systems

Digital movie systems offer great perspectives for multimedia applications. But the large amounts of data involved and the demand for isochronous transmission and playback are also great challenges for the designers of a new generation of file systems, database systems, operating systems, window systems, video encoder/decoder and networks. Today's research prototypes of digital movie systems suffer from severe performance bottlenecks, resulting in small movie windows, low frame rates or bad image quality (or all of these!). We consider the performance problem to be the most important problem with digital movie systems, preventing their widespread use today. In this paper we address performance issues of digital movie systems from a practical perspective. We report on performance experience gained with the XMovie system and new algorithms and protocols to overcome some of these bottlenecks

eXtended Color Cell Compression -- A Runtime-efficient Compression Scheme for Software Video

Multimedia applications require a compression and decompression scheme for digital video. The standardized and widely used techniques JPEG and MPEG provide very good compression ratios, but are computationally quite complex and demanding. We propose to use an extension to the much simpler Color Cell Compression scheme as an alternative. Our extension includes the use of variable block sizes, the reuse of color index values from previously encoded blocks, and Huffman encoding of the stream of blocks. We present experimental results showing that our scheme provides much better runtime performance than MPEG, at the cost of a slightly inferior compression ratio. It is thus especially suited for software videos in high-speed networks

On the energy demands of small appliances in homes

Understanding the use of electrical appliances in households is crucial for improving the accuracy of electricity and energy loads forecasts. In particular, bottom-up techniques provide a powerful tool, not only for predicting demands considering socio-demographic characteristics of the occupants, but also to better resolve and implement demand side management strategies in homes. With this purpose, a study of the temporal energy use of low-load appliances (meaning those whose annual energy share is individually negligible but relevant when considered as a group) has been carried out, with the longer term objective of finding a parsimonious approach to modelling them, and which considers an appropriate aggregation of appliances. In this work, a discrete-time stochastic process has been implemented for a specific classification of low-load appliances. More precisely, a time-inhomogeneous Markov chain has been used to model energy variations over time for four different categories of appliances and its prediction capabilities have been tested and compared

Key Amino Acids in the Bacterial (6-4) Photolyase PhrB from Agrobacterium fabrum

Photolyases can repair pyrimidine dimers on the DNA that are formed during UV irradiation. PhrB from Agrobacterium fabrum represents a new group of prokaryotic (6–4) photolyases which contain an iron-sulfur cluster and a DMRL chromophore. We performed site-directed mutagenesis in order to assess the role of particular amino acid residues in photorepair and photoreduction, during which the FAD chromophore converts from the oxidized to the enzymatically active, reduced form. Our study showed that Trp342 and Trp390 serve as electron transmitters. In the H366A mutant repair activity was lost, which points to a significant role of His366 in the protonation of the lesion, as discussed for the homolog in eukaryotic (6–4) photolyases. Mutants on cysteines that coordinate the Fe-S cluster of PhrB were either insoluble or not expressed. The same result was found for proteins with a truncated C-terminus, in which one of the Fe-S binding cysteines was mutated and for expression in minimal medium with limited Fe concentrations. We therefore assume that the Fe-S cluster is required for protein stability. We further mutated conserved tyrosines that are located between the DNA lesion and the Fe-S cluster. Mutagenesis results showed that Tyr424 was essential for lesion binding and repair, and Tyr430 was required for efficient repair. The results point to an important function of highly conserved tyrosines in prokaryotic (6–4) photolyase

Three-nucleon mechanisms in photoreactions

The $^{12}$C$(\gamma,ppn)$ reaction has been measured for E$_{\gamma}$=150-800 MeV in the first study of this reaction in a target heavier than $^3$He. The experimental data are compared to a microscopic many body calculation. The model, which predicts that the largest contribution to the reaction arises from final state interactions following an initial pion production process, overestimates the measured cross sections and there are strong indications that the overestimate arises in this two-step process. The selection of suitable kinematic conditions strongly suppresses this two-step contribution leaving cross sections in which up to half the yield is predicted to arise from the absorption of the photon on three interacting nucleons and which agree with the model. The results indicate $(\gamma,3N)$ measurements on nuclei may be a valuable tool for obtaining information on the nuclear three-body interaction.Comment: 5 pages, 3 figure

Ontology-Based Integration of Streaming and Static Relational Data with Optique

An important application of semantic technologies in industry has been the formalisation of information models usingOWL 2 ontologies and the use of RDF for storing and exchanging application data. Moreover, legacy data can be virtualised asRDF using ontologies following the ontology-based data access (OBDA) approach. In all these applications, it is important toprovide domain experts with query formulation tools for expressing their information needs in terms of queries over ontologies. Inthis work, we present such a tool, OptiqueVQS, which is designed based on our experience with OBDA applications in Statoil andSiemens and on best HCI practices for interdisciplinary engineering environments. OptiqueVQS implements a number of uniquetechniques distinguishing it from analogous query formulation systems. In particular, it exploits ontology projection techniquesto enable graph-based navigation over an ontology during query construction. Secondly, while OptiqueVQS is primarily ontologydriven, it exploits sampled data to enhance selection of data values for some data attributes. Finally, OptiqueVQS is built onwell-grounded requirements, design rationale, and quality attributes. We evaluated OptiqueVQS with both domain experts andcasual users and qualitatively compared our system against prominent visual systems for ontology-driven query formulation andexploration of semantic data. OptiqueVQS is available online and can be downloaded together with an example OBDA scenario