Heteropolymer Sequence Design and Preferential Solvation of Hydrophilic Monomers: One More Application of Random Energy Model

In this paper, we study the role of surface of the globule and the role of interactions with the solvent for designed sequence heteropolymers using random energy model (REM). We investigate the ground state energy and surface monomer composition distribution. By comparing the freezing transition in random and designed sequence heteropolymers, we discuss the effects of design. Based on our results, we are able to show under which conditions solvation effect improves the quality of sequence design. Finally, we study sequence space entropy and discuss the number of available sequences as a function of imposed requirements for the design quality

Telescoper: de novo assembly of highly repetitive regions.

MotivationWith advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo assemblies from short-reads remains challenging, primarily because of the complex repeat structures found in the genomes of most higher organisms. The telomeric regions of many genomes are particularly difficult to assemble, though much could be gained from the study of these regions, as their evolution has not been fully characterized and they have been linked to aging.ResultsIn this article, we tackle the problem of assembling highly repetitive regions by developing a novel algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. Our algorithm, Telescoper, uses short- and long-insert libraries in an integrated way throughout the assembly process. Results on real and simulated data demonstrate that our approach can effectively resolve much of the complex repeat structures found in the telomeres of yeast genomes, especially when longer long-insert libraries are used.AvailabilityTelescoper is publicly available for download at sourceforge.net/p/[email protected] informationSupplementary data are available at Bioinformatics online

On the poverty of a priorism: technology, surveillance in the workplace and employee responses

Many debates about surveillance at work are framed by a set of a priori assumptions about the nature of the employment relationship that inhibits efforts to understand the complexity of employee responses to the spread of new technology at work. In particular, the debate about the prevalence of resistance is hamstrung from the outset by the assumption that all apparently non-compliant acts, whether intentional or not, are to be counted as acts of resistance. Against this background this paper seeks to redress the balance by reviewing results from an ethnographic study of surveillance-capable technologies in a number of British workplaces. It argues for greater attention to be paid to the empirical character of the social relations at work in and through which technologies are deployed and in the context of which employee responses are played out

SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad-hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. Results: We propose SMaSH, a benchmarking methodology for evaluating human genome variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes, and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on this benchmarking data. Moreover, we illustrate the utility of SMaSH to evaluate the performance of some leading single nucleotide polymorphism (SNP), indel, and structural variant calling algorithms. Availability: We provide free and open access online to the SMaSH toolkit, along with detailed documentation, at smash.cs.berkeley.edu

Two-photon spin injection in semiconductors

A comparison is made between the degree of spin polarization of electrons excited by one- and two-photon absorption of circularly polarized light in bulk zincblende semiconductors. Time- and polarization-resolved experiments in (001)-oriented GaAs reveal an initial degree of spin polarization of 49% for both one- and two-photon spin injection at wavelengths of 775 and 1550 nm, in agreement with theory. The macroscopic symmetry and microscopic theory for two-photon spin injection are reviewed, and the latter is generalized to account for spin-splitting of the bands. The degree of spin polarization of one- and two-photon optical orientation need not be equal, as shown by calculations of spectra for GaAs, InP, GaSb, InSb, and ZnSe using a 14x14 k.p Hamiltonian including remote band effects. By including the higher conduction bands in the calculation, cubic anisotropy and the role of allowed-allowed transitions can be investigated. The allowed-allowed transitions do not conserve angular momentum and can cause a high degree of spin polarization close to the band edge; a value of 78% is calculated in GaSb, but by varying the material parameters it could be as high as 100%. The selection rules for spin injection from allowed-allowed transitions are presented, and interband spin-orbit coupling is found to play an important role.Comment: 12 pages including 7 figure

Extracting surface representations from rim curves

LNCS v. 3852 is the conference proceedings of ACCV 2006In this paper, we design and implement a novel method for constructing a mixed triangle/quadrangle mesh from the 3D space curves (rims) estimated from the profiles of an object in an image sequence without knowing the original 3D topology of the object. To this aim, a contour data structure for representing visual hull, which is different from that for CT/MRI, is introduced. In this paper, we (1) solve the "branching structure" problem by introducing some additional "directed edge", and (2) extract a triangle/ quadrangle closed mesh from the contour structure with an algorithm based on dynamic programming. Both theoretical demonstration and real world results show that our proposed method has sufficient robustness with respect to the complex topology of the object, and the extracted mesh is of high quality. © Springer-Verlag Berlin Heidelberg 2006.postprintThe 7th Asian Conference on Computer Vision (ACCV 2006), Hyderabad, India, 13-16 January 2006. In Lecture Notes in Computer Science, 2006, v. 3852, p. 732-74

Визначення кількості рослинних антиоксидантів для захисту гірких хмелевих речовин від окисної деструкції

Досліджено кінетику окиснення гірких речовин водного розчину екстракту хмелю у прискорених умовах з різною концентрацією антиоксидантів із рослинної сировини. Визначено ефективну концентрацію антиоксидантів із кори дубу, трави звіробою та трави м'яти.Kinetics of bitter matters in aquatic solution of hope extract in speed-up terms with different concentration of antioxidants from the digister are investigated. Certainly effective concentration of antioxidants from the bark oak, st-john's-wort herbares and mint herbares are determinated

Integrating Murine Gene Expression Studies to Understand Obstructive Lung Disease due to Chronic Inhaled Endotoxin

Rationale: Endotoxin is a near ubiquitous environmental exposure that that has been associated with both asthma and chronic obstructive pulmonary disease (COPD). These obstructive lung diseases have a complex pathophysiology, making them difficult to study comprehensively in the context of endotoxin. Genome-wide gene expression studies have been used to identify a molecular snapshot of the response to environmental exposures. Identification of differentially expressed genes shared across all published murine models of chronic inhaled endotoxin will provide insight into the biology underlying endotoxin-associated lung disease. Methods: We identified three published murine models with gene expression profiling after repeated low-dose inhaled endotoxin. All array data from these experiments were re-analyzed, annotated consistently, and tested for shared genes found to be differentially expressed. Additional functional comparison was conducted by testing for significant enrichment of differentially expressed genes in known pathways. The importance of this gene signature in smoking-related lung disease was assessed using hierarchical clustering in an independent experiment where mice were exposed to endotoxin, smoke, and endotoxin plus smoke. Results: A 101-gene signature was detected in three murine models, more than expected by chance. The three model systems exhibit additional similarity beyond shared genes when compared at the pathway level, with increasing enrichment of inflammatory pathways associated with longer duration of endotoxin exposure. Genes and pathways important in both asthma and COPD were shared across all endotoxin models. Mice exposed to endotoxin, smoke, and smoke plus endotoxin were accurately classified with the endotoxin gene signature. Conclusions: Despite the differences in laboratory, duration of exposure, and strain of mouse used in three experimental models of chronic inhaled endotoxin, surprising similarities in gene expression were observed. The endotoxin component of tobacco smoke may play an important role in disease development