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Search Results: 1 - 10 of 303053 matches for " Timothy J. White "
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Photomechanical Response of Composite Structures Built from Azobenzene Liquid Crystal Polymer Networks
Kyung Min Lee,Timothy J. White
Polymers , 2011, DOI: 10.3390/polym3031447
Abstract: Optically directed shape adaptive responses have been sought after for many decades in photoresponsive polymeric materials. A number of recent examinations have elucidated elucidated the unique opportunities of photomechanical responses realized in azobenzene-functionalized liquid crystalline polymer networks (both elastomers and glasses). This work summarizes and contrasts the photomechanical response of glassy polydomain, monodomain, and twisted nematic azo-LCN materials to blue-green irradiation. Building from this summary, the combinatorial photomechanical response observed upon irradiation of composite cantilevers is examined. Large scale shape adaptations are realized, with novel responses that may be of potential use in future employment of these materials in actuation.
Compressing DNA sequence databases with coil
W Timothy J White, Michael D Hendy
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-242
Abstract: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database.coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.The advent of the Sanger sequencing method enabled DNA sequence data to be collected and manipulated on computers, paving the way for explosive growth in the new field of bioinformatics. Publicly available DNA sequence databases such as GenBank play a crucial role in collecting and disseminating the raw data needed by researchers in the field. This database currently contains 168 Gb of sequence data [1] section 2.2.8, and is expected to continue to grow at an exponential rate, doubling in size roughly every 14 months [2]. The volume of data being dealt with now presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv compression [3] (e.g. with gzip [4]). Unfortunately this approach rarely achieves good compression ratios: typically, gzip fails to match the "compression" a
Beyond Reasonable Doubt: Evolution from DNA Sequences
W. Timothy J. White, Bojian Zhong, David Penny
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0069924
Abstract: We demonstrate quantitatively that, as predicted by evolutionary theory, sequences of homologous proteins from different species converge as we go further and further back in time. The converse, a non-evolutionary model can be expressed as probabilities, and the test works for chloroplast, nuclear and mitochondrial sequences, as well as for sequences that diverged at different time depths. Even on our conservative test, the probability that chance could produce the observed levels of ancestral convergence for just one of the eight datasets of 51 proteins is ≈1×10?19 and combined over 8 datasets is ≈1×10?132. By comparison, there are about 1080 protons in the universe, hence the probability that the sequences could have been produced by a process involving unrelated ancestral sequences is about 1050 lower than picking, among all protons, the same proton at random twice in a row. A non-evolutionary control model shows no convergence, and only a small number of parameters are required to account for the observations. It is time that that researchers insisted that doubters put up testable alternatives to evolution.
Evolution of Prolate Molecular Clouds at HII Boundaries: I. Formation of fragment-core structures
Timothy M. Kinnear,Jingqi Miao,Glenn J. White,Simon Goodwin
Physics , 2014, DOI: 10.1093/mnras/stu1510
Abstract: The evolution of a prolate cloud at an Hii boundary is investigated using Smoothed Particle Hydrodynamics (SPH). The prolate molecular clouds in our investigation are set with their semi-major axis perpendicular to the radiative direction of a plane parallel ionising Extreme Ultraviolet (EUV) flux. Simulations on three high mass prolate clouds reveal that EUV radiation can trigger distinctive high density core formation embedded in a final linear structure. This contrasts with results of the previous work in which only an isotropic Far Ultraviolet (FUV) interstellar background flux was applied. A systematic investigation on a group of prolate clouds of equal mass but different initial densities and geometric shapes finds that the distribution of the cores over the final linear structure changes with the initial conditions of the prolate cloud and the strength of the EUV radiation flux. These highly condensed cores may either scatter over the full length of the final linear structure or form two groups of high density cores at two foci, depending on the value of the ionising radiation penetration depth d_EUV, the ratio of the physical ionising radiation penetration depth to the minor axis of the cloud. Data anlysis on the total mass of the high density cores and the core formation time finds that the potential for EUV radiation triggered star formation efficiency is higher in prolate clouds with shallow ionisation penetration depth and intermediate major to minor axial ratio, for the physical environments investigated. Finally, it is suggested that the various fragment-core structures observed at Hii boundaries may result from the interaction between ionising radiation and pre-existing prolate clouds of different initial geometrical and physical conditions.
Encoding Gaussian curvature in glassy and elastomeric liquid crystal polymer networks
Cyrus Mostajeran,Taylor H. Ware,Timothy J. White
Physics , 2015,
Abstract: Considerable recent attention has been given to the study of shape formation using modern responsive materials that can be preprogrammed to undergo spatially inhomogeneous local deformations. In particular, nematic liquid crystal polymer networks offer exciting possibilities in this context. In this paper, we discuss the generation of Gaussian curvature in thin nematic sheets using smooth in-plane director fields patterned across the surface. We highlight specific patterns which encode constant Gaussian curvature of prescribed sign and magnitude and present experimental results which appear to support the theoretical predictions. Specifically, we provide experimental evidence for the realization of positive and negative Gaussian curvature in glassy and elastomeric liquid crystal polymer networks through the stimulation of smoothly varying in-plane director fields.
Transparent thin film polarizing and optical control systems
Nelson V. Tabiryan,Sarik R. Nersisyan,Timothy J. White,Timothy J. Bunning
AIP Advances , 2011, DOI: 10.1063/1.3609965
Abstract: We show that a diffractive waveplate can be combined with a phase retardation film for fully converting light of arbitrary polarization state into a polarized light. Incorporating a photonic bandgap layer into a system of such polarizers that unify different polarization states in the input light into a single polarization state at its output, rather than absorbing or reflecting half of it, we developed and demonstrated a polarization-independent optical controller capable of switching between transmittive and reflective states. The transition between those states is smoothly controlled with low-voltage and low-power sources. Using versatile fabrication methods, this “universally polarizing optical controller” can be integrated into a thin package compatible with a variety of display, spatial light modulation, optical communication, imaging and other photonics systems.
A comparison of Bayesian and Fourier methods for frequency determination in asteroseismology
Timothy R. White,Brendon J. Brewer,Timothy R. Bedding,Dennis Stello,Hans Kjeldsen
Physics , 2010, DOI: 10.1553/cia161s39
Abstract: Bayesian methods are becoming more widely used in asteroseismic analysis. In particular, they are being used to determine oscillation frequencies, which are also commonly found by Fourier analysis. It is important to establish whether the Bayesian methods provide an improvement on Fourier methods. We compare, using simulated data, the standard iterative sine-wave fitting method against a Markov Chain Monte Carlo (MCMC) code that has been introduced to infer purely the frequencies of oscillation modes (Brewer et al. 2007). A uniform prior probability distribution function is used for the MCMC method. We find the methods do equally well at determining the correct oscillation frequencies, although the Bayesian method is able to highlight the possibility of a misidentification due to aliasing, which can be useful. In general, we suggest that the least computationally intensive method is preferable.
Computational Identification of Four Spliceosomal snRNAs from the Deep-Branching Eukaryote Giardia intestinalis
Xiaowei Sylvia Chen, W. Timothy J. White, Lesley J. Collins, David Penny
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003106
Abstract: RNAs processing other RNAs is very general in eukaryotes, but is not clear to what extent it is ancestral to eukaryotes. Here we focus on pre-mRNA splicing, one of the most important RNA-processing mechanisms in eukaryotes. In most eukaryotes splicing is predominantly catalysed by the major spliceosome complex, which consists of five uridine-rich small nuclear RNAs (U-snRNAs) and over 200 proteins in humans. Three major spliceosomal introns have been found experimentally in Giardia; one Giardia U-snRNA (U5) and a number of spliceosomal proteins have also been identified. However, because of the low sequence similarity between the Giardia ncRNAs and those of other eukaryotes, the other U-snRNAs of Giardia had not been found. Using two computational methods, candidates for Giardia U1, U2, U4 and U6 snRNAs were identified in this study and shown by RT-PCR to be expressed. We found that identifying a U2 candidate helped identify U6 and U4 based on interactions between them. Secondary structural modelling of the Giardia U-snRNA candidates revealed typical features of eukaryotic U-snRNAs. We demonstrate a successful approach to combine computational and experimental methods to identify expected ncRNAs in a highly divergent protist genome. Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes.
Calculating asteroseismic diagrams for solar-like oscillations
Timothy R. White,Timothy R. Bedding,Dennis Stello,J?rgen Christensen-Dalsgaard,Daniel Huber,Hans Kjeldsen
Physics , 2011, DOI: 10.1088/0004-637X/743/2/161
Abstract: With the success of the Kepler and CoRoT missions, the number of stars with detected solar-like oscillations has increased by several orders of magnitude, for the first time we are able to perform large-scale ensemble asteroseismology of these stars. In preparation for this golden age of asteroseismology we have computed expected values of various asteroseismic observables from models of varying mass and metallicity. The relationships between these asteroseismic observables, such as the separations between mode frequencies, are able to significantly constrain estimates of the ages and masses of these stars. We investigate the scaling relation between the large frequency separation, Delta nu, and mean stellar density. Furthermore we present model evolutionary tracks for several asteroseismic diagrams. We have extended the so-called C-D diagram beyond the main sequence to the subgiants and the red-giant branch. We also consider another asteroseismic diagram, the epsilon diagram, which is more sensitive to variations in stellar properties at the subgiant stages and can aid in determining the correct mode identification. The recent discovery of gravity-mode period spacings in red giants forms the basis for a third asteroseismic diagram. We compare the evolutionary model tracks in these asteroseismic diagrams with results from pre-Kepler studies of solar-like oscillations, and early results from Kepler.
What Is the Optimal Therapy for Patients with H5N1 Influenza?
Nicholas J. White ,Robert G. Webster ,Elena A. Govorkova,Timothy M. Uyeki
PLOS Medicine , 2009, DOI: 10.1371/journal.pmed.1000091
Abstract: Background to the debate In a 2007 article in PLoS Medicine [10], Holger J. Schünemann and colleagues described a new process used by the World Health Organization for rapidly developing clinical management guidelines in emergency situations. These situations include outbreaks of emerging infectious diseases. The authors discussed how they developed such a “rapid advice” guideline for the pharmacological management of avian influenza A (H5N1) virus infection. The guideline recommends giving the antiviral drug oseltamivir at a dose of 75 mg twice daily for five days. In this Debate, Nicholas White argues that such dosing is inadequate, Robert Webster and Elena Govorkova say that combination antiviral therapy should be used, and Tim Uyeki reminds us that clinical care of patients with H5N1 entails much more than antiviral treatment. These issues may also apply to therapy of patients hospitalized with severe disease due to novel swine-origin influenza A (H1N1) virus infection.
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