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Identifying interaction sites in "Recalcitrant" proteins: Predicted protein and RNA binding sites in REV proteins of HIV-1 and EIAV agree with experimental data

Identifying interaction sites in "Recalcitrant" proteins: Pr...

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11th Pacific Symposium on Biocomputing 2006, PSB 2006

作者： Terribllini, Michael Lee, Jae-Hyung Yan, Changhui Jernigan, Robert L. Carpenter, Susan Honavar, Vasant Dobbs, Drena Bioinformatics and Computational Biology Graduate Program LH. Baker Center for Bioinformatics and Biological Statistics Iowa State University Ames IA 50010 United States Department of Computer Science Iowa State University Ames IA 50010 United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50010 United States Department of Genetics Development and Cell Biology Iowa State University Ames IA 50010 United States Artificial Intelligence Research Laboratory Center for Computational Intelligence Learning and Discovery Iowa State University Ames IA 50010 United States Department of Veterinary Microbiology and Pathology Washington State University Pullman WA. 99164 United States

ISBN: (纸本)9812564632

Protein-protein and protein nucleic acid interactions are vitally important for a wide range of biological processes, including regulation or gene expression, protein synthesis, and replication and assembly of many viruses. We have developed machine learning approaches for predicting which amino acids of a protein participate in its interactions with other proteins and/or nucleic acids, using only the proiein sequence as input. In this paper, we describe an application of classifiers trained on datasets of well-characterized protein-protein and protein-RNA complexes for which experimental structures are available. We apply these classifiers to the problem of predicting protein and RNA binding sites in the sequence of a clinically important protein for which the structure is not known: the regulatory protein Rev, essential for the replication of HIV-I and other lentiviruses. We compare our predictions with published biochemical, genetic and partial structural information for HIV-1 and EIAV Rev and with our own published experimental mapping of RNA binding sites in EIAV Rev. The predicted and experimentally determined binding sites are in very good agreement. The ability to predict reliably the residues of a protein that directly contribute to specific binding events - without the requirement for structural information regarding either the protein or complexes in which it participates - can potentially generate new disease intervention strategies.

关键词： Binding sites

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Undersampled Magnetic Resonance Image Reconstructions Based on a Combination of U-Nets and L1, L2, and TV Optimizations

Undersampled Magnetic Resonance Image Reconstructions Based ...

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IEEE International Workshop on Imaging Systems and Techniques (IST)

作者： Aline A.S. Thomaz Jonathan A.S. Lima Cristiano J. Miosso Mylé ne C.Q. Farias Andrey S. Krylov Yong Ding Department of Electrical Engineering University of Brasilia (UnB) Brasilia Brazil Biomedical Engineering Graduate Program University of Brasilia (UnB) Brasilia Brazil Faculty of Computational Mathematics and Cybernetics Lomonosov Moscow State University Moscow Russia College of Information Science and Electronic Engineering Zhejiang University Zhejiang China

Magnetic Resonance Imaging (MRI) plays a major role in the diagnosis of several diseases. However, the acquisition of measurements in the k-space domain, which is the basis for image reconstruction, takes a long time compared to other imaging modalities and is comparatively costly. In this context, undersampled MRI reconstruction is an approach for decreasing the acquisition duration and the exam's final cost. With this objective, both Compressed Sensing (CS) and Deep Learning (DL) provide techniques for generating good quality MRI images from undersampled measurements. In this paper, we combine CS and DL methods in order to investigate the potential increase in image quality over each isolated approach. We use reconstructions from from highly undersampled MRI signals using two CS approaches, the L1 and total minimizations, as inputs to a U-Net. We also use, for comparison, the reconstructions from the same undersampled signals using L2 minimization, and also test them as inputs to a U-net. The goal is to evaluate whether the the U-Net can improve the results of the CS reconstructions after learning from degraded and original image pairs. Our experimental results suggest that the combination of L1 or TV minimization with U-Nets can improve reconstruction, in terms of objective image quality, over each technique used in isolation.

关键词： Image quality TV Magnetic resonance imaging Magnetic resonance Minimization Time measurement Sensors

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Asymmetric profiles observed in the recombination of Bi79+: A benchmark for relativistic theories involving interference

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Physical Review A 2009年第1期80卷 014503-014503页

作者： Nobuyuki Nakamura Anthony P. Kavanagh Hirofumi Watanabe Hiroyuki A. Sakaue Yueming Li Daiji Kato Fred J. Currell Xiao-Min Tong Tsutomu Watanabe Shunsuke Ohtani Institute for Laser Science The University of Electro-Communications Chofu Tokyo 182-8585 Japan Queen’s University Belfast Belfast BT7 1NN United Kingdom Chubu University Kasugai-shi Aichi 487-8501 Japan National Institute for Fusion Science Toki Gifu 509-5292 Japan Institute of Applied Physics and Computational Mathematics P.O. Box 8009 Beijing 100088 China Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba Tsukuba Ibaraki 305-8573 Japan Center for Computational Sciences University of Tsukuba Tsukuba Ibaraki 305-8577 Japan

Asymmetric profiles have been observed in the recombination cross section of Be-like Bi obtained by measuring the electron energy dependence of the ion abundance ratio in an electron-beam ion trap. In contrast to the previous x-ray measurements, the present measurement gives the integrated recombination cross section with higher statistical quality, which provides a benchmark to test the relativistic theory involving the interference between the resonant and continuum states. The comparison with our theoretical study shows that the Breit interaction plays an important role in this case.

关键词： Benchmarking

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Gaussian Process Port-Hamiltonian Systems: Bayesian Learning with Physics Prior

arXiv

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arXiv 2023年

作者： Beckers, Thomas Seidman, Jacob Perdikaris, Paris Pappas, George J. Department of Electrical and Systems Engineering University of Pennsylvania PhiladelphiaPA19104 United States graduate program in Applied Mathematics and Computational Science University of Pennsylvania PhiladelphiaPA19104 United States Department of Mechanical Engineering and Applied Mechanics University of Pennsylvania PhiladelphiaPA19104 United States

Data-driven approaches achieve remarkable results for the modeling of complex dynamics based on collected data. However, these models often neglect basic physical principles which determine the behavior of any real-world system. This omission is unfavorable in two ways: The models are not as data-efficient as they could be by incorporating physical prior knowledge, and the model itself might not be physically correct. We propose Gaussian Process Port-Hamiltonian systems (GP-PHS) as a physics-informed Bayesian learning approach with uncertainty quantification. The Bayesian nature of GP-PHS uses collected data to form a distribution over all possible Hamiltonians instead of a single point estimate. Due to the underlying physics model, a GP-PHS generates passive systems with respect to designated inputs and outputs. Further, the proposed approach preserves the compositional nature of Port-Hamiltonian systems. © 2023, CC BY-NC-ND.

关键词： Hamiltonians

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The use of research activities as learning instrument in electrical engineering and computer science graduations

The use of research activities as learning instrument in ele...

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Frontiers in Education (FIE) Conference

作者： C.A.P.S. Martins M.B. Carvalho C.V. Pousa D.O. Penha Computer Science Department and Graduate Program in Electrical Engineering (PPGEE) Computational and Digital System Laboratoty (LSDC) Pontifical Catholic University of Minas Gerais Belo Horizonte Minas Gerais Brazil PUC-Minas PPGEE LSDC Belo Horizonte Minas Gerais Brazil Computer Science Department LSDC PUC-Minas Belo Horizonte Minas Gerais Brazil

In this paper we analyze the use of research activities as learning instrument in electrical engineering and computer science. This pedagogic approach was applied in undergraduate disciplines, undergraduate teaching assistance and undergraduate research projects. Our main goals are optimize the learning process using research and motivate the use of research activities as learning instrument.

关键词： Instruments Computer science Education Performance analysis Electrical engineering Learning systems Proposals Humans Microprocessors Cache memory

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Dynamical charge structure factor of a one-dimensional ionic Hubbard model in the low-energy region

arXiv

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arXiv 2018年

作者： Komaki, Yuhei Iwase, Yuma Yanagimatsu, Shogo Muta, Yoshiyuki Maeshima, Nobuya Hino, Ken-ichi Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba Tsukuba Ibaraki305-8573 Japan College of Engineering Sciences University of Tsukuba Tsukuba305-8573 Japan Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan Division of Materials Science University of Tsukuba Tsukuba305-8573 Japan

We present a numerical study of the charge dynamical structure factor N(k, ω) of a one-dimensional (1D) ionic Hubbard model in the Mott insulator (MI) phase. We show that the low-energy spectrum of N(k, ω) is expressed in terms of the spin operators for the spin degrees of freedom. Numerical results for the spin degrees of freedom, obtained by the Lanczos diagonalization method, well reproduce the low-energy spectrum of N(k, ω) of the 1D ionic Hubbard model. In addition, we show that these spectral peaks probe the dispersion of the spin-singlet excitations of the system and are observed in the wide parameter region of the MI phase. Copyright © 2018, The Authors. All rights reserved.

关键词： Numerical methods

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Linkages of the 2022 Unprecedented Global Heatwave Events to Triple-Dip La Niña

Linkages of the 2022 Unprecedented Global Heatwave Events to...

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IEEE International Symposium on Geoscience and Remote Sensing (IGARSS)

作者： Sachi Perera Joshua B. Fisher Mohamed Allali Hesham El-Askary Computational and Data Sciences Graduate Program Schmid College of Science and Technology Chapman University Orange CA USA Earth Systems Science and Data Solution Lab Chapman University Orange CA USA Schmid College of Science and Technology Chapman University Orange CA USA Fowler School of Engineering Chapman University Orange CA USA Department of Environmental Sciences Faculty of Science Alexandria University Alexandria Egypt

ISBN: (数字)9798350360325

ISBN: (纸本)9798350360332

Heatwaves are influenced significantly by El Niño-Southern Oscillation (ENSO), which alters temperature and precipitation patterns throughout the world. Since 2020, we have witnessed a "triple dip" La Niña conditions persisting for three consecutive years resulting in severe weather and climate driven events globally. In this study, we identified the dominant frequency of Niño 3.4 Sea Surface Temperature (SST) signals and correlated them with regions experiencing unprecedented heat waves in 2022, namely, the Indian Ocean, the North Atlantic around England and Spain, and the Mediterranean Sea. The signal's power spectrum and its three highest power components are determined based on the signal's Singular Spectrum Analysis (SSA) for each region. Furthermore, the power spectrum coherence (PSC) of Niño 3.4 and other study regions is obtained to determine whether ENSO and heatwaves are linked. We find that Niño 3.4 and the Indian Ocean have the same dominant frequency for the highest power received, indicating ENSO's influence on the Indian heat wave. Additionally, we discovered that in March 2022, the Jet stream is essential in bringing warm Arctic waves southward, passing through Niño 3.4 and India. Furthermore, we found that no other region shared the dominant frequency of the Niño 3.4 region.

关键词： Heating systems Couplings Sea surface Precipitation Surface waves Indian Ocean Geoscience and remote sensing

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Irregular oscillatory patterns in the early-time region of coherent phonon generation in silicon

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Physical Review B 2017年第12期96卷 125204-125204页

作者： Yohei Watanabe Ken-ichi Hino Muneaki Hase Nobuya Maeshima Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba Tsukuba Ibaraki 305-8573 Japan Division of Materials Science Faculty of Pure and Applied Sciences University of Tsukuba Tsukuba 305-8573 Japan Center for Computational Sciences University of Tsukuba Tsukuba 305-8577 Japan Division of Applied Physics Faculty of Pure and Applied Sciences University of Tsukuba Tsukuba 305-8573 Japan

Coherent phonon (CP) generation in an undoped Si crystal is theoretically investigated to shed light on unexplored quantum-mechanical effects in the early-time region immediately after the irradiation of ultrashort laser pulses. We examine time signals attributed to an induced charge density of an ionic core, placing the focus on the effects of the Rabi frequency Ω0cv on the signals; this frequency corresponds to the peak electric-field of the pulse. It is found that at specific Ω0cv's, where the energy of plasmon caused by photoexcited carriers coincides with the longitudinal-optical phonon energy, the energetically resonant interaction between these two modes leads to striking anticrossings, revealing irregular oscillations with anomalously enhanced amplitudes in the observed time signals. Also, the oscillatory pattern is subject to the Rabi flopping of the excited carrier density that is controlled by Ω0cv. These findings show that the early-time region is enriched with quantum-mechanical effects inherent in the CP generation, though experimental signals are more or less masked by the so-called coherent artifact due to nonlinear optical effects.

关键词： Electron-phonon coupling Optical phonons Plasma oscillations Ultrafast phenomena Elemental semiconductors Optical absorption spectroscopy

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Exploring the mutation tendency of a specific region in the virus taxonomic groups using data mining techniques

Exploring the mutation tendency of a specific region in the ...

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IEEE International Conference on Big Data

作者： Mikyung Je Myeongji Cho Yoon Jung Kim Hyeon S. Son Interdisciplinary Graduate Program in Bioinformatics College of Natural Science Seoul National University Seoul Republic of Korea Division of Bio IT Honam National Institute of Biological Resources Mokpo Republic of Korea Lab. of Computational Virology & Viroinformatics Graduate School of Public Health Seoul National University Seoul Republic of Korea Institute of Health and Environment Seoul National University Seoul Republic of Korea

ISBN: (纸本)9781665480468

The GDNQ motif is mainly found in nonsegmented (-)ssRNA viruses and plays a role in the catalytic and polymerase activity pathways. However, in some recently reported dsRNA mycoviruses, the GDNQ motif of the (-)ssRNA virus group is found instead of the GDD motif commonly found in the dsRNA virus group. Therefore, in this study, data mining techniques were used to explore the mutation tendency of a specific region in the virus taxonomic groups. Viral protein sequences were obtained from the NCBI Virus data repository, and the performance of several known string-searching algorithms (BF, KMP, and BM) was evaluated to establish an optimal strategy for extracting useful information from sequence big data. Then, the pattern-matching performance of the algorithm was tested to detect whether the conserved region sequence was a common motif type or a mutated motif type. As a result of the analysis, it was confirmed that the BF method produced the fastest results. However, the BM method recorded higher accuracy. Through the virus mutation tendency derived from the analysis results, it was confirmed that 7.1% of dsRNA viruses had a mutated motif type based on the total data analyzed and that it was relatively recent that ssRNA virus motif variants began to be discovered in dsRNA viruses. It is expected that additional in-depth analysis of the host range and infection route of viruses with the mutation will help understand the evolution of dsRNA and ssRNA mycoviruses.

关键词： Proteins Big Data Data mining Polymers Viruses (medical)

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Global variations in critical drought thresholds that impact vegetation

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National science Review 2023年第5期10卷 180-193页

作者： Xiangyi Li Shilong Piao Chris Huntingford Josep Pe?uelas Hui Yang Hao Xu Anping Chen Pierre Friedlingstein Trevor F.Keenan Stephen Sitch Xuhui Wang Jakob Zscheischler Miguel D.Mahecha Sino-French Institute for Earth System Science College of Urban and Environmental SciencesPeking University Key Laboratory of Alpine Ecology and Biodiversity Institute of Tibetan Plateau ResearchCenter for Excellence in Tibetan Earth ScienceChinese Academy of Sciences UK Centre for Ecology and Hydrology CSIC Global Ecology Unit CREAF-CSIC-UAB CREAF Cerdanyola de Vallès Department of Biogeochemical Integration Max Planck Institute for Biogeochemistry Department of Biology Colorado State University Graduate Degree Program in Ecology Colorado State University Department of Mathematics College of Engineering Mathematics and Physical SciencesUniversity of Exeter Laboratoire de Météorologie Dynamique Institut Pierre-Simon LaplaceCNRS-ENS-UPMC-XDépartement de GeósciencesEcole Normale Superieure Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Department of Environmental Science Policy&ManagementUniversity of California Berkeley Department of Geography College of Life and Environmental SciencesUniversity of Exeter Department of Computational Hydrosystems Helmholtz Centre for Environmental Research—Ufz Remote Sensing Centre for Earth System Research Leipzig University

Identifying the thresholds of drought that,if crossed,suppress vegetation functioning is vital for accurate quantification of how land ecosystems respond to climate variability and *** present a globally applicable framework to identify drought thresholds for vegetation responses to different levels of known soil-moisture deficits using four remotely sensed vegetation proxies spanning *** thresholds identified represent critical inflection points for changing vegetation responses from highly resistant to highly vulnerable in response to drought stress,and as a warning signal for substantial vegetation *** thresholds varied geographically,with much lower percentiles of soil-moisture anomalies in vegetated areas covered by more forests,corresponding to a comparably stronger capacity to mitigate soil water deficit stress in forested ***,those lower thresholds are detected in more humid ***-of-the-art land models,however,overestimated thresholds of soil moisture(*** drought impacts),especially in more humid areas with higher forest covers and arid areas with few forest *** on climate model projections,we predict that the risk of vegetation damage will increase by the end of the twenty-first century in some hotspots like East Asia,Europe,Amazon,southern Australia and eastern and southern *** data-based results will inform projections on future drought impacts on terrestrial ecosystems and provide an effective tool for drought management.

关键词： drought threshold inflection points vegetation response soil moisture drought impacts

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