1,818 research outputs found
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
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
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 âchemical fingerprintâ. 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 (7â
ml) in universal containers (25â
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
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 2Ă2 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
In situ measurements of density fluctuations and compressibility in silica glass as a function of temperature and thermal history
In this paper, small-angle X-ray scattering measurements are used to
determine the different compressibility contributions, as well as the
isothermal compressibility, in thermal equilibrium in silica glasses having
different thermal histories. Using two different methods of analysis, in the
supercooled liquid and in the glassy state, we obtain respectively the
temperature and fictive temperature dependences of the isotheraml
compressibility. The values obtained in the glass and supercooled liquid states
are very close to each other. They agree with previous determinations of the
literature. The compressibility in the glass state slightly decreases with
increasing fictive temperature. The relaxational part of the compressibility is
also calculated and compared to previous determinations. We discussed the small
differences between the different determinations
Testing the durability of limestone for Cathedral façade restoration
This research aimed to specify an optimum replacement stone for Truro Cathedral. A variety of petrographically and visually similar material to the original Bath stone was initially selected. The stones were subjected to three different durability tests; Sodium sulphate crystallisation and large scale testing with both accelerated and climatic freeze-thaw cyclic loading. The most suitable stone was determined as the one with the best performance characteristics overall
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
A Caching Scheme to Accelerate Kinetic Monte Carlo Simulations of Catalytic Reactions
Kinetic Monte Carlo (KMC) simulations have been instrumental in advancing our fundamental understanding of heterogeneously catalyzed reactions, with particular emphasis on structure sensitivity, ensemble effects, and the interplay between adlayer structure and adsorbate-adsorbate lateral interactions in shaping the observed kinetics. Yet, the computational cost of KMC remains high, thereby motivating the development of acceleration schemes that would improve the simulation effciency. We present an exact such scheme, which implements a caching algorithm along with shared-memory parallelization to improve the computational performance of simulations incorporating long-range adsorbate-adsorbate lateral interactions. This scheme is based on caching information about the energetic interaction patterns associated with the products of each possible lattice process (adsorption, desorption, reaction etc). Thus, every time a reaction occurs ("ongoing reaction") it enables fast updates of the rate constants of "affected reactions", i.e. possible reactions in the region of influence of the "ongoing reaction". Benchmarks on KMC simulations of NOx oxidation/reduction, yield acceleration factors of up to 20Ă when comparing single-thread runs without caching to runs on 16 threads with caching, for simulations with a cluster expansion Hamiltonian that incorporates up to 8th nearest-neighbor interactions
- âŠ