Hasil untuk "q-bio.TO"

Stephen D. Turner

Summary Genome-wide association studies (GWAS) have identified thousands of human trait-associated single nucleotide polymorphisms. Here, I describe a freely available R package for visualizing GWAS results using Q-Q and manhattan plots. The qqman package enables the flexible creation of manhattan plots, both genome-wide and for single chromosomes, with optional highlighting of SNPs of interest. Availability qqman is released under the GNU General Public License, and is freely available on the Comprehensive R Archive Network (http://cran.r-project.org/package=qqman). The source code is available on GitHub (https://github.com/stephenturner/qqman). Contact turner@virginia.edu

Y. Shao, Zhengting Gan, E. Epifanovsky et al.

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

F. Shayan

While the mixed method approach has attracted much attention over the past few years in the field of educational research, including educational technology, Q-methodology, which encapsulates the advantages of both the quantitative and qualitative methods, has not yet entered the mainstream of scholarly educational technology research into human subjectivity and remains unfamiliar to most researchers. Based on more than 16 years of applying Q-methodology in a diverse range of studies, Watts and Stenner’s Doing Q Methodological Research is a step-by-step procedure that covers both the theory and pragmatism of gathering, analysing, interpreting, and publishing a Q-study.

Anderson Cs, E. Heeley, Y. Huang et al.

G. Aad, T. Abajyan, B. Abbott et al.

F. An, J. Bai, A. Balantekin et al.

The Daya Bay Reactor Neutrino Experiment has measured a nonzero value for the neutrino mixing angle θ(13) with a significance of 5.2 standard deviations. Antineutrinos from six 2.9 GWth reactors were detected in six antineutrino detectors deployed in two near (flux-weighted baseline 470 m and 576 m) and one far (1648 m) underground experimental halls. With a 43,000 ton-GWth-day live-time exposure in 55 days, 10,416 (80,376) electron-antineutrino candidates were detected at the far hall (near halls). The ratio of the observed to expected number of antineutrinos at the far hall is R=0.940±0.011(stat.)±0.004(syst.). A rate-only analysis finds sin(2)2θ(13)=0.092±0.016(stat.)±0.005(syst.) in a three-neutrino framework.

M. Grabherr, B. Haas, Moran Yassour et al.

Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.

S. Chatrchyan, G. Hmayakyan, V. Khachatryan et al.

Huy Q. Nguyen

The author discusses some basic questions in fluid dynamics. He describes Newton's contribution to fluid dynamics in the second volume of the Principia. He presents a brief review of fluid dynamics since Newton, and discusses the nature and content of physics curricula in schools and universities. He also outlines some aspects of modern research.

M. Adams, S. Celniker, R. Holt et al.

Neil Genzlinger

W. Jin, Qifan Yang, L. Chang et al.

Driven by narrow-linewidth bench-top lasers, coherent optical systems spanning optical communications, metrology and sensing provide unrivalled performance. To transfer these capabilities from the laboratory to the real world, a key missing ingredient is a mass-produced integrated laser with superior coherence. Here, we bridge conventional semiconductor lasers and coherent optical systems using CMOS-foundry-fabricated microresonators with a high Q factor of over 260 million and finesse over 42,000. A five-orders-of-magnitude noise reduction in the pump laser is demonstrated, enabling a frequency noise of 0.2 Hz2 Hz−1 to be achieved in an electrically pumped integrated laser, with a corresponding short-term linewidth of 1.2 Hz. Moreover, the same configuration is shown to relieve the dispersion requirements for microcomb generation that have handicapped certain nonlinear platforms. The simultaneous realization of this high Q factor, highly coherent lasers and frequency combs using foundry-based technologies paves the way for volume manufacturing of a wide range of coherent optical systems. Using CMOS-ready ultra-high-Q microresonators, a highly coherent electrically pumped integrated laser with frequency noise of 0.2 Hz2 Hz−1, corresponding to a short-term linewidth of 1.2 Hz, is demonstrated. The device configuration is also found to relieve the dispersion requirements for microcomb generation that have limited certain nonlinear platforms.

A. Sirunyan, A. Tumasyan, W. Adam et al.

New sets of CMS underlying-event parameters (“tunes”) are presented for the pythia8 event generator. These tunes use the NNPDF3.1 parton distribution functions (PDFs) at leading (LO), next-to-leading (NLO), or next-to-next-to-leading (NNLO) orders in perturbative quantum chromodynamics, and the strong coupling evolution at LO or NLO. Measurements of charged-particle multiplicity and transverse momentum densities at various hadron collision energies are fit simultaneously to determine the parameters of the tunes. Comparisons of the predictions of the new tunes are provided for observables sensitive to the event shapes at LEP, global underlying event, soft multiparton interactions, and double-parton scattering contributions. In addition, comparisons are made for observables measured in various specific processes, such as multijet, Drell–Yan, and top quark-antiquark pair production including jet substructure observables. The simulation of the underlying event provided by the new tunes is interfaced to a higher-order matrix-element calculation. For the first time, predictions from pythia8 obtained with tunes based on NLO or NNLO PDFs are shown to reliably describe minimum-bias and underlying-event data with a similar level of agreement to predictions from tunes using LO PDF sets.

Beakcheol Jang, Myeonghwi Kim, Gaspard Harerimana et al.

Q-learning is arguably one of the most applied representative reinforcement learning approaches and one of the off-policy strategies. Since the emergence of Q-learning, many studies have described its uses in reinforcement learning and artificial intelligence problems. However, there is an information gap as to how these powerful algorithms can be leveraged and incorporated into general artificial intelligence workflow. Early Q-learning algorithms were unsatisfactory in several aspects and covered a narrow range of applications. It has also been observed that sometimes, this rather powerful algorithm learns unrealistically and overestimates the action values hence abating the overall performance. Recently with the general advances of machine learning, more variants of Q-learning like Deep Q-learning which combines basic Q learning with deep neural networks have been discovered and applied extensively. In this paper, we thoroughly explain how Q-learning evolved by unraveling the mathematical complexities behind it as well its flow from reinforcement learning family of algorithms. Improved variants are fully described, and we categorize Q-learning algorithms into single-agent and multi-agent approaches. Finally, we thoroughly investigate up-to-date research trends and key applications that leverage Q-learning algorithms.

Zhuojun Liu, Yi Xu, Ye Lin et al.

Sharp electromagnetic resonances play an essential role in physics in general and optics in particular. The last decades have witnessed the successful developments of high-quality (Q) resonances in microcavities operating below the light line, which however is fundamentally challenging to access from free space. Alternatively, metasurface-based bound states in the continuum (BICs) offer a complementary solution of creating high-Q resonances in devices operating above the light line, yet the experimentally demonstrated Q factors under normal excitations are still limited. Here, we present the realizations of quasi-BIC under normal excitation with a record Q factor up to 18 511 by engineering the symmetry properties and the number of the unit cells in all-dielectric metasurface platforms. The high-Q quasi-BICs exhibit exceptionally high conversion efficiency for the third harmonic generation and even enable the second harmonic generation in Si metasurfaces. Such ultrasharp resonances achieved in this work may immediately boost the performances of BICs in a plethora of fundamental research and device applications, e.g., cavity QED, biosensing, nanolasing, and quantum light generations.

H. M. Srivastava, H. M. Srivastava, H. M. Srivastava

L. C. R. Aaij, A. Abdelmotteleb, C. Beteta et al.

Conventional, hadronic matter consists of baryons and mesons made of three quarks and a quark–antiquark pair, respectively1,2. Here, we report the observation of a hadronic state containing four quarks in the Large Hadron Collider beauty experiment. This so-called tetraquark contains two charm quarks, a u¯\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\overline{{{{{u}}}}}$$\end{document} and a d¯\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\overline{{{{{d}}}}}$$\end{document} quark. This exotic state has a mass of approximately 3,875 MeV and manifests as a narrow peak in the mass spectrum of D0D0π+ mesons just below the D*+D0 mass threshold. The near-threshold mass together with the narrow width reveals the resonance nature of the state. The LHCb Collaboration reports the observation of an exotic, narrow, tetraquark state that contains two charm quarks, an up antiquark and a down antiquark.

L. C. R. Aaij, C. Beteta, T. Ackernley et al.

Using proton-proton collision data at centre-of-mass energies of s=7,8 and 13TeV recorded by the LHCb experiment at the Large Hadron Collider, corresponding to an integrated luminosity of 9fb-1, the invariant mass spectrum of J/ψ pairs is studied. A narrow structure around 6.9GeV/c2 matching the lineshape of a resonance and a broad structure just above twice the J/ψ mass are observed. The deviation of the data from nonresonant J/ψ-pair production is above five standard deviations in the mass region between 6.2 and 7.4GeV/c2, covering predicted masses of states composed of four charm quarks. The mass and natural width of the narrow X(6900) structure are measured assuming a Breit-Wigner lineshape.

M. Todisco, Héctor Delgado, N. Evans

Lavinia Heisenberg

Recent years have witnessed a rise in interest in the geometrical trinity of General Relativity and its extensions. This interest has been fuelled by novel insights into the nature of gravity, the possibility to address computational and conceptual questions -- such as the determination of black hole entropy or the definition of gravitational energy-momentum -- from a new perspective. In particular, $f(Q)$ gravity has also inspired numerous works on black holes, wormholes, and cosmology. In the latter case, $f(Q)$ models have the potential to elucidate phenomena in both early and late-time cosmology without necessitating the inclusion of dark energy, the inflaton field, or dark matter. Particularly noteworthy is the role of $f(Q)$ theories in addressing cosmological tensions, presenting exciting possibilities for reshaping our understanding of gravity and its manifestations in cosmology. The emergence of intriguing new black hole solutions and the potential existence of wormhole solutions suggest the presence of novel physics within the realm of strong gravity. These phenomena have become increasingly measurable only in recent times, opening up exciting avenues for further exploration and discovery. This review is tailored to students and researchers alike. It offers a self-contained and pedagogical introduction to metric-affine geometry--The mathematical foundation and indispensable tool upon which the geometrical trinity of General Relativity as well as its various extensions are built.