Computational challenges of systems biology

Progress in the study of biological systems such as the heart, brain, and liver will require computer scientists to work closely with life scientists and mathematicians. Computer science will play a key role in shaping the new discipline of systems biology and addressing the significant computational challenges it poses

Model Orchestration: Addressing the Model Management Challenges of Systems Biology

Biological modelling is an increasingly complex and diverse firld. As well as developing new models for biological phenomena, there is a need to integrate existing models and scale up to investigate higher level behaviour. To achieve this integration, techniques and tools are required to catalogue and understand existing models, and to support the development of new models ready for integration. We describe our approach to this problem and validate the approach with examples

Dressing the Shop Window of Socialism: Gender and Consumption in the Soviet Union in the Era of 'Cultured Trade', 1934-53

By 1953, Soviet consumer culture seemingly depended upon a gendered dichotomy that presented women as the primary consumers and that was reflected in, re-inscribed and reworked by Soviet consumption practices and the discourse of 'cultured trade'. However, the gendered discourse of consumption was neither inevitable nor static throughout the Stalin period. This article argues that the image of women as the paradigmatic consumers was ambiguous in the early years of 'cultured trade' in the 1930s, and indeed men were often featured as the primary shoppers for the home, or at least as equally interested in domestic consumer goods as women. Furthermore, in the era of pro-natalism, both male and female sexual desirability was mobilised in advertising and consumption discourse, arguably to redirect the libidinal urges of the buying public to 'cultured' ends. The fact that this gendered discourse developed over time, and in part in response to the intense upheaval of the SecondWorldWar, contrad icts the argument that the strict separation between male and female consumer spheres discernible by 1953 was part of a deliberate and planned 'Great Retreat' from revolutionary ideals

OC-163 identification of inflammatory bowel disease (IBD) using field asymmetric ion mobility spectrometry (FAIMS)

Introduction Resident colonic bacteria, principally anaerobes and firmicutes, ferment undigested fibre. The resultant volatile organic compounds (VOCs) formed are dissolved in the faeces but also absorbed and excreted in the urine. We have previously shown that electronic nose (E-nose) analysis of urine VOCs distinguishes between Crohn's disease (CD), ulcerative colitis (UC) and healthy volunteers (HV): the underlying principle is pattern recognition of disease-specific “chemical fingerprint”. High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) offers a possible alternative. The underlying principle is separation of VOC chemical components based on their different ion mobilties in high electric fields. We performed a pilot study in the above groups, the patients in remission (Rem) or with active disease (AD), to assess if this technology could achieve separation between the groups. The results were validated against E-nose analysis. Methods 59 subjects were studied; HV n=14, UC (Rem) n=18, UC (AD) n=4; CD (Rem) n=19, CD (AD) n=4. Urine samples (7 ml) in universal containers (25 ml) were heated to 40±0.1 C. The headspace (the air above the sample) was then analysed using FAIMS. The data were analysed by Fisher Discriminant Analysis. Results The technique distinguished between the three groups. Additionally, patients with active disease could be distinguished from those in remission. These results were concordant with E-nose analysis. Conclusion This pilot shows that urine VOCs, analysed by the different approaches of E-nose and FAIMS, the latter a novel application, can distinguish the healthy from those with UC and CD when disease is active or in remission. The two technologies together offer a non-invasive approach to diagnosis and follow-up in inflammatory bowel disease

MAGRITTE: a new multidimensional accelerated general-purpose radiative transfer code

Magritte is a new deterministic radiative transfer code. It is a ray-tracing code that computes the radiation field by solving the radiative transfer equation along a fixed set of rays for each grid cell. Its ray-tracing algorithm is independent of the type of input grid and thus can handle smoothed-particle hydrodynamics (SPH) particles, structured as well as unstructured grids. The radiative transfer solver is highly parallelized and optimized to have well scaling performance on several computer architectures. Magritte also contains separate dedicated modules for chemistry and thermal balance. These enable it to self-consistently model the interdependence between the radiation field and the local thermal and chemical states. The source code for Magritte will be made publically available at github.com/Magritte-code

Increasing Intake of an Unfamiliar Vegetable in Preschool Children Through Learning Using Storybooks and Sensory Play: A Cluster Randomized Trial

Background: Most children eat fewer vegetables than recommended. Storybooks and sensory play may increase vegetable intake. Objective: This study tested the effects on intake of learning about an unfamiliar vegetable (celeriac) through storybooks and sensory play. It was predicted that an illustrated, congruent storybook would increase intake of celeriac compared to an incongruent storybook (carrot); and that adding congruent sensory play with celeriac to the storybook would produce a synergistic effect on intake of celeriac. Design: Children from 12 UK preschools were randomly assigned by clusters to four intervention conditions using a 2×2 factorial design. The factors were vegetable congruency (sensory play and/or storybook were congruent, or incongruent [carrot] with celeriac) and intervention type (storybook only or storybook combined with sensory play). Participants/setting: Three hundred and thirty-seven children aged 2 to 5 years were recruited to take part in November 2017. Intervention: Over a 2-week period, children in all four conditions were read a vegetable storybook featuring celeriac or carrot. In addition, two conditions received sensory play with either carrot or celeriac added to the storybook method. Main outcome measures: Intake of the unfamiliar vegetable (celeriac) was measured at baseline and after the 2-week intervention. Statistical analysis performed: Complex samples logistic regression and general linear modeling were performed to examine group differences at post-intervention. Results: Children receiving the congruent (celeriac) storybook had higher odds of eating celeriac compared to children who received the incongruent (carrot) storybook. Receiving congruent sensory play increased the odds of eating celeriac, whereas receiving incongruent sensory play did not. From the 267 children who completed both baseline and post-intervention assessments, 85 ate no celeriac at baseline and were classed as non-eaters. Sensory play (congruent or incongruent) increased the odds of eating some celeriac in non-eaters compared to storybook only conditions. Conclusions: Congruency between storybook and vegetable increased intake; sensory play with celeriac increased the likelihood of eating celeriac. Storybooks and sensory play are simple interventions to increase willingness to try an unfamiliar vegetable

Characterization of the glass transition in vitreous silica by temperature scanning small-angle X-ray scattering

The temperature dependence of the x-ray scattering in the region below the first sharp diffraction peak was measured for silica glasses with low and high OH content (GE-124 and Corning 7980). Data were obtained upon scanning the temperature at 10, 40 and 80 K/min between 400 K and 1820 K. The measurements resolve, for the first time, the hysteresis between heating and cooling through the glass transition for silica glass, and the data have a better signal to noise ratio than previous light scattering and differential thermal analysis data. For the glass with the higher hydroxyl concentration the glass transition is broader and at a lower temperature. Fits of the data to the Adam-Gibbs-Fulcher equation provide updated kinetic parameters for this very strong glass. The temperature derivative of the observed X-ray scattering matches that of light scattering to within 14%.Comment: EurophysicsLetters, in pres

Random walks near Rokhsar-Kivelson points

There is a class of quantum Hamiltonians known as Rokhsar-Kivelson(RK)-Hamiltonians for which static ground state properties can be obtained by evaluating thermal expectation values for classical models. The ground state of an RK-Hamiltonian is known explicitly, and its dynamical properties can be obtained by performing a classical Monte Carlo simulation. We discuss the details of a Diffusion Monte Carlo method that is a good tool for studying statics and dynamics of perturbed RK-Hamiltonians without time discretization errors. As a general result we point out that the relation between the quantum dynamics and classical Monte Carlo simulations for RK-Hamiltonians follows from the known fact that the imaginary-time evolution operator that describes optimal importance sampling, in which the exact ground state is used as guiding function, is Markovian. Thus quantum dynamics can be studied by a classical Monte Carlo simulation for any Hamiltonian that is free of the sign problem provided its ground state is known explicitly.Comment: 12 pages, 9 figures, RevTe