Bioclipse-R: integrating management and visualization of life science data with statistical analysis

SUMMARY: Bioclipse, a graphical workbench for the life sciences, provides functionality for managing and visualizing life science data. We introduce Bioclipse-R, which integrates Bioclipse and the statistical programming language R. The synergy between Bioclipse and R is demonstrated by the construction of a decision support system for anticancer drug screening and mutagenicity prediction, which shows how Bioclipse-R can be used to perform complex tasks from within a single software system. Availability and implementation: Bioclipse-R is implemented as a set of Java plug-ins for Bioclipse based on the R-package rj. Source code and binary packages are available from https://github.com/bioclipse and http://www.bioclipse.net/bioclipse-r, respectively. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Social physique anxiety and physical activity in early adolescent girls : the influence of maturation and physical activity motives

This study considered the influence of maturation on social physique anxiety (SPA), the relationship between SPA and current and future physical activity (PA) levels and the influence of motives for physical activity on this relationship in early adolescent girls (n=162; mean age=11.80±0.33 years). Participants completed the Pubertal Development Scale, the modified Social Physique Anxiety Scale and the Motives for Physical Activity Scale at baseline and the Physical Activity Questionnaire for Older Children at baseline and 6 months later. The girls became less active across the 6 months and girls in the early stages of maturation had significantly lower SPA than the girls in the middle and late stages of maturation. SPA was not related to current or future physical activity in the sample as a whole. Cluster analysis identified four groups with different motive profiles and the High Appearance and Fitness group demonstrated a moderate negative relationship between SPA and PA at phase 1, whereas the other groups did not. These findings indicate that SPA may increase with maturation and the relationship between SPA and PA is dependent on reasons for being active. For girls who are motivated to be active primarily by body-related reasons SPA is likely to lead to lower levels of PA

Dynamic Scaling of Ion-Sputtered Surfaces

We derive a stochastic nonlinear equation to describe the evolution and scaling properties of surfaces eroded by ion bombardment. The coefficients appearing in the equation can be calculated explicitly in terms of the physical parameters characterizing the sputtering process. We find that transitions may take place between various scaling behaviors when experimental parameters such as the angle of incidence of the incoming ions or their average penetration depth, are varied.Comment: 13 pages, Revtex, 2 figure

Renormalization Group Analysis of a Noisy Kuramoto-Sivashinsky Equation

We have analyzed the Kuramoto-Sivashinsky equation with a stochastic noise term through a dynamic renormalization group calculation. For a system in which the lattice spacing is smaller than the typical wavelength of the linear instability occurring in the system, the large-distance and long-time behavior of this equation is the same as for the Kardar-Parisi-Zhang equation in one and two spatial dimensions. For the $d=2$ case the agreement is only qualitative. On the other hand, when coarse-graining on larger scales the asymptotic flow depends on the initial values of the parameters.Comment: 8 pages, 5 figures, revte

Skills, attitudes and uptake of evidence-based practice: a cross-sectional study of chiropractors in the Swedish Chiropractic Association.

BackgroundEvidence-based practice (EBP) is integral to the delivery of high-quality health care. Chiropractic has been a licensed health profession in Sweden since 1989, but little is known of the uptake of EBP in this professional group. This study explored the self-reported skills, attitudes and uptake of EBP, and the enablers and barriers of EBP uptake, among licensed chiropractors in Sweden.MethodsLicensed chiropractors (n = 172) of the Swedish Chiropractic Association (Legitimerade Kiropraktorers Riksorganisation) were invited to participate in an anonymous online questionnaire, using the Evidence-Based Practice Attitude and Utilisation Survey (EBASE) in February 2019.ResultsFifty-six (33%) chiropractors completed the survey. Participants were predominantly male, aged 30-49 years, held a Master's degree, and had received their highest qualification and practiced chiropractic for over a decade. Chiropractors rated their EBP skill-level mostly in the moderate to moderate-high range. The majority of chiropractors reported positive attitudes towards EBP, with most agreeing or strongly agreeing that EBP is necessary in the practice of chiropractic, and that EBP assists in making decisions about patient care. Chiropractors reported an average level of engagement in EBP activities. All participants indicated professional literature and research findings were useful in their day-to-day chiropractic practice. The main perceived enabler of EBP uptake was internet access in the workplace, whereas the main barrier to EBP uptake was lack of clinical evidence in chiropractic.ConclusionsParticipating chiropractors of the Swedish Chiropractic Association were generally favourable of EBP, though only reported modest levels of EBP-related skills and engagement in EBP activities. Our findings suggest future studies investigating interventions focussed on improving chiropractors' skills and uptake of EBP are warranted

van der Waals interaction in nanotube bundles : consequences on vibrational modes

We have developed a pair-potential approach for the evaluation of van der Waals interaction between carbon nanotubes in bundles. Starting from a continuum model, we show that the intertube modes range from $5 cm^{-1}$ to $60 cm^{-1}$. Using a non-orthogonal tight-binding approximation for describing the covalent intra-tube bonding in addition, we confirme a slight chiral dependance of the breathing mode frequency and we found that this breathing mode frequency increase by $\sim$ 10 % if the nanotube lie inside a bundle as compared to the isolated tube.Comment: 5 pages, 2 figure

Physiologically Based Pharmacokinetic (PBPK) Modeling of Metabolic Pathways of Bromochloromethane in Rats

Bromochloromethane (BCM) is a volatile compound and a by-product of disinfection of water by chlorination. Physiologically based pharmacokinetic (PBPK) models are used in risk assessment applications. An updated PBPK model for BCM is generated and applied to hypotheses testing calibrated using vapor uptake data. The two different metabolic hypotheses examined are (1) a two-pathway model using both CYP2E1 and glutathione transferase enzymes and (2) a two-binding site model where metabolism can occur on one enzyme, CYP2E1. Our computer simulations show that both hypotheses describe the experimental data in a similar manner. The two pathway results were comparable to previously reported values (Vmax⁡ = 3.8 mg/hour, Km = 0.35 mg/liter, and kGST = 4.7 /hour). The two binding site results were Vmax⁡1 = 3.7 mg/hour, Km⁡1 = 0.3 mg/hour, CL2 = 0.047 liter/hour. In addition, we explore the sensitivity of different parameters for each model using our obtained optimized values

Hole Hopping through Tryptophan in Cytochrome P450

Electron-transfer kinetics have been measured in four conjugates of cytochrome P450 with surface-bound Ru-photosensitizers. The conjugates are constructed with enzymes from Bacillus megaterium (CYP102A1) and Sulfolobus acidocaldarius (CYP119). A W96 residue lies in the path between Ru and the heme in CYP102A1, whereas H76 is present at the analogous location in CYP119. Two additional conjugates have been prepared with (CYP102A1)W96H and (CYP119)H76W mutant enzymes. Heme oxidation by photochemically generated Ru^(3+) leads to P450 compound II formation when a tryptophan residue is in the path between Ru and the heme; no heme oxidation is observed when histidine occupies this position. The data indicate that heme oxidation proceeds via two-step tunneling through a tryptophan radical intermediate. In contrast, heme reduction by photochemically generated Ru+ proceeds in a single electron tunneling step with closely similar rate constants for all four conjugates

Stochastic Model for Surface Erosion Via Ion-Sputtering: Dynamical Evolution from Ripple Morphology to Rough Morphology

Surfaces eroded by ion-sputtering are sometimes observed to develop morphologies which are either ripple (periodic), or rough (non-periodic). We introduce a discrete stochastic model that allows us to interpret these experimental observations within a unified framework. We find that a periodic ripple morphology characterizes the initial stages of the evolution, whereas the surface displays self-affine scaling in the later time regime. Further, we argue that the stochastic continuum equation describing the surface height is a noisy version of the Kuramoto-Sivashinsky equation.Comment: 4 pages, 7 postscript figs., Revtex, to appear in Phys. Rev. Let

Precision scans of the pixel cell response of double sided 3D pixel detectors to pion and x-ray beams

hree-dimensional (3D) silicon sensors offer potential advantages over standard planar sensors for radiation hardness in future high energy physics experiments and reduced charge-sharing for X-ray applications, but may introduce inefficiencies due to the columnar electrodes. These inefficiencies are probed by studying variations in response across a unit pixel cell in a 55μm pitch double-sided 3D pixel sensor bump bonded to TimePix and Medipix2 readout ASICs. Two complementary characterisation techniques are discussed: the first uses a custom built telescope and a 120GeV pion beam from the Super Proton Synchrotron (SPS) at CERN; the second employs a novel technique to illuminate the sensor with a micro-focused synchrotron X-ray beam at the Diamond Light Source, UK. For a pion beam incident perpendicular to the sensor plane an overall pixel efficiency of 93.0±0.5% is measured. After a 10o rotation of the device the effect of the columnar region becomes negligible and the overall efficiency rises to 99.8±0.5%. The double-sided 3D sensor shows significantly reduced charge sharing to neighbouring pixels compared to the planar device. The charge sharing results obtained from the X-ray beam study of the 3D sensor are shown to agree with a simple simulation in which charge diffusion is neglected. The devices tested are found to be compatible with having a region in which no charge is collected centred on the electrode columns and of radius 7.6±0.6μm. Charge collection above and below the columnar electrodes in the double-sided 3D sensor is observed