Sensitive and accurate detection of copy number variants using read depth of coverage

Methods for the direct detection of copy number variation (CNV) genome-wide have become effective instruments for identifying genetic risk factors for disease. The application of next-generation sequencing platforms to genetic studies promises to improve sensitivity to detect CNVs as well as inversions, indels, and SNPs. New computational approaches are needed to systematically detect these variants from genome sequence data. Existing sequence-based approaches for CNV detection are primarily based on paired-end read mapping (PEM) as reported previously by Tuzun et al. and Korbel et al. Due to limitations of the PEM approach, some classes of CNVs are difficult to ascertain, including large insertions and variants located within complex genomic regions. To overcome these limitations, we developed a method for CNV detection using read depth of coverage. Event-wise testing (EWT) is a method based on significance testing. In contrast to standard segmentation algorithms that typically operate by performing likelihood evaluation for every point in the genome, EWT works on intervals of data points, rapidly searching for specific classes of events. Overall false-positive rate is controlled by testing the significance of each possible event and adjusting for multiple testing. Deletions and duplications detected in an individual genome by EWT are examined across multiple genomes to identify polymorphism between individuals. We estimated error rates using simulations based on real data, and we applied EWT to the analysis of chromosome 1 from paired-end shotgun sequence data (30x) on five individuals. Our results suggest that analysis of read depth is an effective approach for the detection of CNVs, and it captures structural variants that are refractory to established PEM-based methods

Towards the digitalisation of porous energy materials: evolution of digital approaches for microstructural design

Porous energy materials are essential components of many energy devices and systems, the development of which have been long plagued by two main challenges. The first is the ‘curse of dimensionality’, i.e. the complex structure–property relationships of energy materials are largely determined by a high-dimensional parameter space. The second challenge is the low efficiency of optimisation/discovery techniques for new energy materials. Digitalisation of porous energy materials is currently being considered as one of the most promising solutions to tackle these issues by transforming all material information into the digital space using reconstruction and imaging data and fusing this with various computational methods. With the help of material digitalisation, the rapid characterisation, the prediction of properties, and the autonomous optimisation of new energy materials can be achieved by using advanced mathematical algorithms. In this paper, we review the evolution of these computational and digital approaches and their typical applications in studying various porous energy materials and devices. Particularly, we address the recent progress of artificial intelligence (AI) in porous energy materials and highlight the successful application of several deep learning methods in microstructural reconstruction and generation, property prediction, and the performance optimisation of energy materials in service. We also provide a perspective on the potential of deep learning methods in achieving autonomous optimisation and discovery of new porous energy materials based on advanced computational modelling and AI techniques

Changes in mangrove vegetation area and character in a war and land use change affected region of Vietnam (Mui Ca Mau) over six decades

Aerial photographs and satellite images have been used to determine land cover changes during the period 1953 to 2011 in the Mui Ca Mau, Vietnam, especially in relation to changes in the mangrove area. The mangrove area declined drastically from approximately 71,345 ha in 1953 to 33,083 ha in 1992, then rose to 46,712 ha in 2011. Loss due to herbicide attacks during the Vietnam War, overexploitation, and conversion into agriculture and aquaculture encouraged by land management policies are being partially counteracted by natural regeneration and replanting, especially a gradual increase in plantations as part of integrated mangrove-shrimp farming systems. The nature of the mangrove vegetation has markedly been transformed over this period. The results are valuable for management planning to understand and improve the contribution of mangrove forests to the provision of ecosystem services and resources, local livelihood and global interest

Market based approaches for food safety and animal health interventions in smallholder pig systems: the case of Vietnam

Food safety and animal health concerns place rising burdens on smallholder pig production in Viet Nam, both in terms of negatively affecting livelihoods and profitability as well as reducing consumer confidence in pork. While reducing the incidence of pig disease and improving the safety of pork products are potentially important public goods, it is critical to take into account the tradeoffs between improved animal health and food safety outcomes and their associated costs

B Physics at the Tevatron: Run II and Beyond

This report provides a comprehensive overview of the prospects for B physics at the Tevatron. The work was carried out during a series of workshops starting in September 1999. There were four working groups: 1) CP Violation, 2) Rare and Semileptonic Decays, 3) Mixing and Lifetimes, 4) Production, Fragmentation and Spectroscopy. The report also includes introductory chapters on theoretical and experimental tools emphasizing aspects of B physics specific to hadron colliders, as well as overviews of the CDF, D0, and BTeV detectors, and a Summary.Comment: 583 pages. Further information on the workshops, including transparencies, can be found at the workshop's homepage: http://www-theory.lbl.gov/Brun2/. The report is also available in 2-up http://www-theory.lbl.gov/Brun2/report/report2.ps.gz or chapter-by-chapter http://www-theory.lbl.gov/Brun2/report

Search for right-handed W bosons in top quark decay

We present a measurement of the fraction f+ of right-handed W bosons produced in top quark decays, based on a candidate sample of $t\bar{t}$ events in the lepton+jets decay mode. These data correspond to an integrated luminosity of 230pb^-1, collected by the DO detector at the Fermilab Tevatron $p\bar{p}$ Collider at sqrt(s)=1.96 TeV. We use a constrained fit to reconstruct the kinematics of the $t\bar{t}$ and decay products, which allows for the measurement of the leptonic decay angle $\theta^*$ for each event. By comparing the $\cos\theta^*$ distribution from the data with those for the expected background and signal for various values of f+, we find f+=0.00+-0.13(stat)+-0.07(syst). This measurement is consistent with the standard model prediction of f+=3.6x10^-4.Comment: Submitted to Physical Review D Rapid Communications 7 pages, 3 figure

Measurement of the Lifetime Difference in the B_s^0 System

We present a study of the decay B_s^0 -> J/psi phi We obtain the CP-odd fraction in the final state at time zero, R_perp = 0.16 +/- 0.10 (stat) +/- 0.02 (syst), the average lifetime of the (B_s, B_sbar) system, tau (B_s^0) =1.39^{+0.13}_{-0.16} (stat) ^{+0.01}_{-0.02} (syst) ps, and the relative width difference between the heavy and light mass eigenstates, Delta Gamma/Gamma = (Gamma_L - Gamma_H)/Gamma =0.24^{+0.28}_{-0.38} (stat) ^{+0.03}_{-0.04} (syst). With the additional constraint from the world average of the B_s^0$lifetime measurements using semileptonic decays, we find tau (B_s^0)= 1.39 +/- 0.06 ~ps and Delta Gamma/\Gamma = 0.25^{+0.14}_{-0.15}. For the ratio of the B_s^0 and B^0 lifetimes we obtain tau(B_s^0)/tau(B^0)} = 0.91 +/- 0.09 (stat) +/- 0.003 (syst).Comment: submitted to Phys. Rev. Lett. FERMILAB-PUB-05-324-

Measurement of Semileptonic Branching Fractions of B Mesons to Narrow D** States

Using the data accumulated in 2002-2004 with the DO detector in proton-antiproton collisions at the Fermilab Tevatron collider with centre-of-mass energy 1.96 TeV, the branching fractions of the decays B -> \bar{D}_1^0(2420) \mu^+ \nu_\mu X and B -> \bar{D}_2^{*0}(2460) \mu^+ \nu_\mu X and their ratio have been measured: BR(\bar{b}->B) \cdot BR(B-> \bar{D}_1^0 \mu^+ \nu_\mu X) \cdot BR(\bar{D}_1^0 -> D*- pi+) = (0.087+-0.007(stat)+-0.014(syst))%; BR(\bar{b}->B)\cdot BR(B->D_2^{*0} \mu^+ \nu_\mu X) \cdot BR(\bar{D}_2^{*0} -> D*- \pi^+) = (0.035+-0.007(stat)+-0.008(syst))%; and (BR(B -> \bar{D}_2^{*0} \mu^+ \nu_\mu X)BR(D2*0->D*- pi+)) / (BR(B -> \bar{D}_1^{0} \mu^+ \nu_\mu X)\cdot BR(\bar{D}_1^{0}->D*- \pi^+)) = 0.39+-0.09(stat)+-0.12(syst), where the charge conjugated states are always implied.Comment: submitted to Phys. Rev. Let

Search for Large Extra Spatial Dimensions in Dimuon Production with the D0 Detector

We present the results of a search for the effects of large extra spatial dimensions in $p{\bar p}$ collisions at $\sqrt{s} =$ 1.96 TeV in events containing a pair of energetic muons. The data correspond to 246 \ipb of integrated luminosity collected by the \D0 experiment at the Fermilab Tevatron Collider. Good agreement with the expected background was found, yielding no evidence for large extra dimensions. We set 95% C.L. lower limits on the fundamental Planck scale between 0.85 TeV and 1.27 TeV within several formalisms. These are the most stringent limits achieved in the dimuon channel to date.Comment: 8 pages, 3 figures, 1 table. Published in Phys. Rev. Lett. Minor changes in v2 to match the published versio