How dsDNA breathing enhances its flexibility and instability on short length scales

We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the duplex and also forks at the ends, with the size distributions independent of the contour length. We find that these local denaturations at a physiological temperature, despite their rare and transient presence, can lower the persistence length drastically for a short DNA segment in agreement with experiment

ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest.

Next-generation sequencing technology (NGS) enables the discovery of nearly all genetic variants present in a genome. A subset of these variants, however, may have poor sequencing quality due to limitations in NGS or variant callers. In genetic studies that analyze a large number of sequenced individuals, it is critical to detect and remove those variants with poor quality as they may cause spurious findings. In this paper, we present ForestQC, a statistical tool for performing quality control on variants identified from NGS data by combining a traditional filtering approach and a machine learning approach. Our software uses the information on sequencing quality, such as sequencing depth, genotyping quality, and GC contents, to predict whether a particular variant is likely to be false-positive. To evaluate ForestQC, we applied it to two whole-genome sequencing datasets where one dataset consists of related individuals from families while the other consists of unrelated individuals. Results indicate that ForestQC outperforms widely used methods for performing quality control on variants such as VQSR of GATK by considerably improving the quality of variants to be included in the analysis. ForestQC is also very efficient, and hence can be applied to large sequencing datasets. We conclude that combining a machine learning algorithm trained with sequencing quality information and the filtering approach is a practical approach to perform quality control on genetic variants from sequencing data

Paper-Based Flexible Electrode Using Chemically-Modified Graphene and Functionalized Multiwalled Carbon Nanotube Composites for Electrophysiological Signal Sensing

Flexible paper-based physiological sensor electrodes were developed using chemically-modified graphene (CG) and carboxylic-functionalized multiwalled carbon nanotube composites (f@MWCNTs). A solvothermal process with additional treatment was conducted to synthesize CG and f@MWCNTs to make CG-f@MWCNT composites. The composite was sonicated in an appropriate solvent to make a uniform suspension, and then it was drop cast on a nylon membrane in a vacuum filter. A number of batches (0%~35% f@MWCNTs) were prepared to investigate the performance of the physical characteristics. The 25% f@MWCNT-loaded composite showed the best adhesion on the paper substrate. The surface topography and chemical bonding of the proposed CG-f@MWCNT electrodes were characterized by scanning electron microscopy (SEM) and Raman spectroscopy, respectively. The average sheet resistance of the 25% CG-f@MWCNT electrode was determined to be 75 Ω/⬜ , and it showed a skin contact impedance of 45.12 kΩ at 100 Hz. Electrocardiogram (ECG) signals were recorded from the chest and fingertips of healthy adults using the proposed electrodes. The CG-f@MWCNT electrodes demonstrated comfortability and a high sensitivity for electrocardiogram signal detection

The Period Variation of and a Spot Model for the Eclipsing Binary AR Bootis

New CCD photometric observations of the eclipsing system AR Boo were obtained from February 2006 to April 2008. The star's photometric properties are derived from detailed studies of the period variability and of all available light curves. We find that over about 56 years the orbital period of the system has varied due to a combination of an upward parabola and a sinusoid rather than in a monotonic fashion. Mass transfer from the less massive primary to the more massive secondary component is likely responsible for at least a significant part of the secular period change. The cyclical variation with a period of 7.57 yrs and a semi-amplitude of 0.0015 d can be produced either by a light-travel-time effect due to an unseen companion with a scaled mass of $M_3 \sin i_3$=0.081 $M_\odot$ or by a magnetic period modulation in the secondary star. Historical light curves of AR Boo, as well as our own, display season-to-season light variability, which are best modeled by including both a cool spot and a hot one on the secondary star. We think that the spots express magnetic dynamo-related activity and offer limited support for preferring the magnetic interpretation of the 7.57-year cycle over the third-body understanding. Our solutions confirm that AR Boo belongs to the W-subtype contact binary class, consisting of a hotter, less massive primary star with a spectral type of G9 and a companion of spectral type K1.Comment: 30 pages, including 6 figures and 9 tables, accepted for publication in A

A literature search tool for intelligent extraction of disease-associated genes

Objective: To extract disorder-associated genes from the scientific literature in PubMed with greater sensitivity for literature-based support than existing methods. Methods: We developed a PubMed query to retrieve disorder-related, original research articles. Then we applied a rule-based text-mining algorithm with keyword matching to extract target disorders, genes with significant results, and the type of study described by the article. Results: We compared our resulting candidate disorder genes and supporting references with existing databases. We demonstrated that our candidate gene set covers nearly all genes in manually curated databases, and that the references supporting the disorder–gene link are more extensive and accurate than other general purpose gene-to-disorder association databases. Conclusions: We implemented a novel publication search tool to find target articles, specifically focused on links between disorders and genotypes. Through comparison against gold-standard manually updated gene–disorder databases and comparison with automated databases of similar functionality we show that our tool can search through the entirety of PubMed to extract the main gene findings for human diseases rapidly and accurately

Evidence of Bottom-Trapped Currents in the Kuroshio Extension Region

As part of the Kuroshio Extension System Study, observations from five current meter moorings reveal that the abyssal currents are weakly bottom intensified. In the framework of linear quasigeostrophic flow, the best fitted vertical trapping depths range from 8 to 15 km in the absence of steep topography, but one mooring near an isolated seamount exhibited vertical trapping that was more pronounced and energetic with a vertical trapping depth of 5 km. The ratios of current speeds and geostrophic pressure streamfunctions at the sea surface compared to the bottom are 88% in the absence of steep topography, 63% near an isolated seamount, and overall on average 83% of their value at a reference depth of 5300 m. It is hypothesized that weakly depth-dependent eddies impinging upon topographic features introduce to the flow the horizontal length scales of the topography, and these smaller lateral scales are subject to bottom intensification

Autworks: a Cross-Disease Network Biology Application for Autism and Related Disorders

Background: The genetic etiology of autism is heterogeneous. Multiple disorders share genotypic and phenotypic traits with autism. Network based cross-disorder analysis can aid in the understanding and characterization of the molecular pathology of autism, but there are few tools that enable us to conduct cross-disorder analysis and to visualize the results. Description: We have designed Autworks as a web portal to bring together gene interaction and gene-disease association data on autism to enable network construction, visualization, network comparisons with numerous other related neurological conditions and disorders. Users may examine the structure of gene interactions within a set of disorder-associated genes, compare networks of disorder/disease genes with those of other disorders/diseases, and upload their own sets for comparative analysis. Conclusions: Autworks is a web application that provides an easy-to-use resource for researchers of varied backgrounds to analyze the autism gene network structure within and between disorders

Efficient terahertz generation in highly nonlinear organic crystal HMB-TMS

We report on generation of strong and broadband terahertz (THz) pulses via collinearly phase-matched optical rectification of near-infrared femtosecond pulses in the organic nonlinear optical HMB-TMS (2-(4-hydroxy-3-methoxystyryl)-3-methylbenzo[d]thiazol-3-ium 2,4,6-trimethylbenzenesulfonate) single crystals which exhibit optimal molecular orientation and large macroscopic optical nonlinearity for efficient THz wave generation. Single-cycle THz pulses with a peak electric field strength of 0.66 MV/cm and a bandwidth from 0.1 to 5.4 THz are achieved from an HMB-TMS crystal with only a 2-mm clear aperture pumped by 1350 nm pulses at moderate fluences. The generated THz energy is about 1 µJ and the corresponding pump-to-THz energy conversion efficiency reaches 0.23%.United States. Office of Naval Research (N00014-13-1-0509)United States. Office of Naval Research. Defense University Research Instrumentation Program (N00014-15-1-2879)Samsung Global Research Outreach ProgramNational Research Foundation of Korea (No. 2016R1A2B4011050National Research Foundation of Korea (No. 2014R1A5A1009799)National Research Foundation of Korea (No. 2015K1A3A1A14004646)National Research Foundation of Korea (No. 2009-0093826

The First Comprehensive Photometric Study of the Algol-type System CL Aurigae

We present the first extensive photometric results of CL Aur from our BVRI CCD photometry made on 22 nights from 2003 November through 2005 February. Fifteen new timings of minimum light were obtained. During the past 104 years, the orbital period has varied due to a periodic oscillation superposed on a continuous period increase. The period and semi-amplitude of the oscillation are about 21.6 yrs and 0.0133 d, respectively. This detail is interpreted as a light-travel-time effect due to a low-luminosity K-type star gravitationally bound to the CL Aur close system. Our photometric study indicates that CL Aur is a relatively short-period Algol-type binary with values of q=0.602 and i=88$^\circ$.2. Mass transfer from the secondary to the primary eclipsing component is at least partly responsible for the observed secular period change with a rate of dP/dt = +1.4$\times10^{-7}$ d yr$^{-1}$. A cool spot model has been calculated but we think that an alternative hot-spot model resulting from a gas stream impact on the hot star is more reasonable despite two difficulties with the explanation. Absolute dimensions of the eclipsing system are deduced and its present state is compared with tracks for single star and conservative close binary evolution. Finally, we examine the possible reconciliation of two different calculations of the luminosity of the hot spot and a re-interpretation of the secular term of the period variability.Comment: 26 pages, including 5 figures and 9 tables, accepted for publication in A