Hasil untuk "q-bio.BM"

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

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.

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.

K. Sørensen, S. van den Broucke, J. Pelikan et al.

BackgroundSeveral measurement tools have been developed to measure health literacy. The tools vary in their approach and design, but few have focused on comprehensive health literacy in populations. This paper describes the design and development of the European Health Literacy Survey Questionnaire (HLS-EU-Q), an innovative, comprehensive tool to measure health literacy in populations.MethodsBased on a conceptual model and definition, the process involved item development, pre-testing, field-testing, external consultation, plain language check, and translation from English to Bulgarian, Dutch, German, Greek, Polish, and Spanish.ResultsThe development process resulted in the HLS-EU-Q, which entailed two sections, a core health literacy section and a section on determinants and outcomes associated to health literacy. The health literacy section included 47 items addressing self-reported difficulties in accessing, understanding, appraising and applying information in tasks concerning decisions making in healthcare, disease prevention, and health promotion. The second section included items related to, health behaviour, health status, health service use, community participation, socio-demographic and socio-economic factors.ConclusionsBy illuminating the detailed steps in the design and development process of the HLS-EU-Q, it is the aim to provide a deeper understanding of its purpose, its capability and its limitations for others using the tool. By stimulating a wide application it is the vision that HLS-EU-Q will be validated in more countries to enhance the understanding of health literacy in different populations.

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.

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.

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

Jesse Clifton, Eric B. Laber

Q-learning, originally an incremental algorithm for estimating an optimal decision strategy in an infinite-horizon decision problem, now refers to a general class of reinforcement learning methods widely used in statistics and artificial intelligence. In the context of personalized medicine, finite-horizon Q-learning is the workhorse for estimating optimal treatment strategies, known as treatment regimes. Infinite-horizon Q-learning is also increasingly relevant in the growing field of mobile health. In computer science, Q-learning methods have achieved remarkable performance in domains such as game-playing and robotics. In this article, we ( a) review the history of Q-learning in computer science and statistics, ( b) formalize finite-horizon Q-learning within the potential outcomes framework and discuss the inferential difficulties for which it is infamous, and ( c) review variants of infinite-horizon Q-learning and the exploration-exploitation problem, which arises in decision problems with a long time horizon. We close by discussing issues arising with the use of Q-learning in practice, including arguments for combining Q-learning with direct-search methods; sample size considerations for sequential, multiple assignment randomized trials; and possibilities for combining Q-learning with model-based methods.

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. V. Rybin, K. Koshelev, Z. Sadrieva et al.

Recent progress in nanoscale optical physics is associated with the development of a new branch of nanophotonics exploring strong Mie resonances in dielectric nanoparticles with a high refractive index. The high-index resonant dielectric nanostructures form building blocks for novel photonic metadevices with low losses and advanced functionalities. However, unlike extensively studied cavities in photonic crystals, such dielectric resonators demonstrate low quality factors (Q factors). Here, we uncover a novel mechanism for achieving giant Q factors of subwavelength nanoscale resonators by realizing the regime of bound states in the continuum. In contrast to the previously suggested multilayer structures with zero permittivity, we reveal strong mode coupling and Fano resonances in homogeneous high-index dielectric finite-length nanorods resulting in high-Q factors at the nanoscale. Thus, high-index dielectric resonators represent the simplest example of nanophotonic supercavities, expanding substantially the range of applications of all-dielectric resonant nanophotonics and meta-optics.

M. Todisco, Héctor Delgado, N. Evans

Fotios Anagnostopoulos, S. Basilakos, E. Saridakis

Fotios K. Anagnostopoulos, Spyros Basilakos, 3 and Emmanuel N. Saridakis 4, 5 Department of Physics, National & Kapodistrian University of Athens, Zografou Campus GR 157 73, Athens, Greece National Observatory of Athens, Lofos Nymfon, 11852 Athens, Greece Academy of Athens, Research Center for Astronomy and Applied Mathematics, Soranou Efesiou 4, 11527, Athens, Greece CAS Key Laboratory for Researches in Galaxies and Cosmology, Department of Astronomy, University of Science and Technology of China, Hefei, Anhui 230026, P.R. China School of Astronomy, School of Physical Sciences, University of Science and Technology of China, Hefei 230026, P.R. China

John Schulman, P. Abbeel, Xi Chen

Two of the leading approaches for model-free reinforcement learning are policy gradient methods and $Q$-learning methods. $Q$-learning methods can be effective and sample-efficient when they work, however, it is not well-understood why they work, since empirically, the $Q$-values they estimate are very inaccurate. A partial explanation may be that $Q$-learning methods are secretly implementing policy gradient updates: we show that there is a precise equivalence between $Q$-learning and policy gradient methods in the setting of entropy-regularized reinforcement learning, that "soft" (entropy-regularized) $Q$-learning is exactly equivalent to a policy gradient method. We also point out a connection between $Q$-learning methods and natural policy gradient methods. Experimentally, we explore the entropy-regularized versions of $Q$-learning and policy gradients, and we find them to perform as well as (or slightly better than) the standard variants on the Atari benchmark. We also show that the equivalence holds in practical settings by constructing a $Q$-learning method that closely matches the learning dynamics of A3C without using a target network or $\epsilon$-greedy exploration schedule.

Divyansh Garg, Shuvam Chakraborty, Chris Cundy et al.

In many sequential decision-making problems (e.g., robotics control, game playing, sequential prediction), human or expert data is available containing useful information about the task. However, imitation learning (IL) from a small amount of expert data can be challenging in high-dimensional environments with complex dynamics. Behavioral cloning is a simple method that is widely used due to its simplicity of implementation and stable convergence but doesn't utilize any information involving the environment's dynamics. Many existing methods that exploit dynamics information are difficult to train in practice due to an adversarial optimization process over reward and policy approximators or biased, high variance gradient estimators. We introduce a method for dynamics-aware IL which avoids adversarial training by learning a single Q-function, implicitly representing both reward and policy. On standard benchmarks, the implicitly learned rewards show a high positive correlation with the ground-truth rewards, illustrating our method can also be used for inverse reinforcement learning (IRL). Our method, Inverse soft-Q learning (IQ-Learn) obtains state-of-the-art results in offline and online imitation learning settings, significantly outperforming existing methods both in the number of required environment interactions and scalability in high-dimensional spaces, often by more than 3x.

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.