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Discovery and affinity maturation of antibody fragments from an unfavorably enriched phage display selection by deep sequencing and machine learning

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Journal of Bioscience and Bioengineering 2025年

作者： Kawada, Sakiya Kurumida, Yoichi Ito, Tomoyuki Nguyen, Thuy Duong Nishi, Hafumi Nakazawa, Hikaru Saito, Yutaka Kameda, Tomoshi Tsuda, Koji Umetsu, Mitsuo Department of Biomolecular Engineering of Engineering Tohoku University 6-6-11 Aoba Aramaki Aoba-ku Sendai 980-8579 Japan Department of Data Science School of Frontier Engineering Kitasato University 1-15-1 Kitazato Minami-ku Kanagawa Sagamihara 252-0373 Japan Artificial Intelligence Research Center National Institute of Advanced Industrial Science and Technology (AIST) 2-4-7 Aomi Koto-ku Tokyo 135-0064 Japan Department of Applied Information Sciences of Information Sciences Tohoku University 6-3-09 Aoba Aramaki Aoba-ku Sendai 980-8579 Japan Tohoku Medical Megabank Organization Tohoku University 2-1 Seiryo-machi Aoba-ku Sendai 980-8573 Japan Faculty of Core Research Ochanomizu University 2-1-1 Ohtsuka Bunkyo-ku Tokyo 112-8610 Japan Department of Computational Biology and Medical Sciences of Frontier Sciences The University of Tokyo 5-1-5 Kashiwanoha Chiba Kashiwa 277-8561 Japan Center for Advanced Intelligence Project RIKEN 1-4-1 Nihombashi Chuo-ku Tokyo 103-0027 Japan Research and Services Division of Materials Data and Integrated Systems National Institute for Materials Science 1-2-1 Sengen Tsukuba Ibaraki 305-0047 Japan

Phage display selection has been used for directed evolution of antibody fragments. However, variants with binding affinity cannot be always identified due to undesirable enrichment of target-unrelated variants in the biopanning process. Here, our goal was to obtain functional variants by deep sequencing and machine learning from a phage display library where functional variants were not appropriately enriched. Deep sequencing of the previously biopanned pools revealed that amplification bias might have prevented the enrichment of target-binding phages. We performed a sequence similarity search based on the deep sequencing analysis so that the influence of bias was decreased, leading to discovery of a variant with binding affinity, which could not be discovered by a conventional screening method alone. We applied machine learning to the deep sequencing data;the machine learning proposed effective mutations for increasing affinity, allowing us to identify a variant with improved affinity (EC50 = 3.46 μM). In summary, we present the possibility of obtaining functional variants even from unfavorably enriched phage libraries by using deep sequencing and machine learning. © 2025 The Society for Biotechnology, Japan

关键词： Clustering analysis Deep sequencing Galectin-3 Machine learning Phage display VHH

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Bottomonium production in heavy-ion collisions using quantum trajectories: Differential observables and momentum anisotropy

arXiv

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arXiv 2021年

作者： Brambilla, Nora Escobedo, Miguel Ángel Strickland, Michael Vairo, Antonio Griend, Peter Vander Weber, Johannes Heinrich Physik-Department Technische Universität München James-Franck-Str. 1 Garching85748 Germany Institute for Advanced Study Technische Universität München Lichtenbergstrasse 2 a Garching85748 Germany Munich Data Science Institute Technische Universität München Walther-von-Dyck-Strasse 10 Garching85748 Germany Universidade de Santiago de Compostela GaliciaE-15782 Spain Department of Physics Kent State University KentOH44242 United States Department of Computational Mathematics Science and Engineering Department of Physics and Astronomy Michigan State University East LansingMI48824 United States Institut für Physik Humboldt-Universität zu Berlin & IRIS Adlershof BerlinD-12489 Germany

We report predictions for the suppression and elliptic flow of the Υ(1S), Υ(2S), and Υ(3S) as a function of centrality and transverse momentum in ultra-relativistic heavy-ion collisions. We obtain our predictions by numerically solving a Lindblad equation for the evolution of the heavy-quarkonium reduced density matrix derived using potential nonrelativistic QCD and the formalism of open quantum systems. To numerically solve the Lindblad equation, we make use of a stochastic unraveling called the quantum trajectories algorithm. This unraveling allows us to solve the Lindblad evolution equation efficiently on large lattices with no angular momentum cutoff. The resulting evolution describes the full 3D quantum and non-abelian evolution of the reduced density matrix for bottomonium states. We expand upon our previous work by treating differential observables and elliptic flow;this is made possible by a newly implemented Monte-Carlo sampling of physical trajectories. Our final results are compared to experimental data collected in √sNN = 5.02 TeV Pb-Pb collisions by the ALICE, ATLAS, and CMS collaborations. © 2021, CC BY.

关键词： Quantum chemistry

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Scaling up the lattice dynamics of amorphous materials by orders of magnitude

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Physical Review B 2020年第2期102卷 024108-024108页

作者： Ivan Kriuchevskyi Vladimir V. Palyulin Rico Milkus Robert M. Elder Timothy W. Sirk Alessio Zaccone Department of Physics “A. Pontremoli” University of Milan via Celoria 16 20133 Milan Italy Centre for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Nobelya Ulitsa 3 Moscow 121205 Russia Department of Chemical Engineering and Biotechnology University of Cambridge Cambridge CB3 0AS United Kingdom Polymers Branch U.S. Army Research Laboratory Aberdeen Proving Ground Maryland 20783 USA Bennett Aerospace Inc. Cary North Carolina 27518 USA Center for Devices and Radiological Health U.S. Food and Drug Administration Silver Spring Maryland 20903 USA

We generalize the nonaffine theory of viscoelasticity for use with large, well-sampled systems of arbitrary chemical complexity. Having in mind predictions of mechanical and vibrational properties of amorphous systems with atomistic resolution, we propose an extension of the kernel polynomial method (KPM) for the computation of the vibrational density of states and the eigenmodes, including the Γ correlator of the affine force field, which is a key ingredient of lattice-dynamic calculations of viscoelasticity. We show that the results converge well to the solution obtained by direct diagonalization (DD) of the Hessian (dynamical) matrix. As is well known, the DD approach has prohibitively high computational requirements for systems with N=104 atoms or larger. Instead, the KPM approach developed here allows one to scale up lattice dynamic calculations of real materials up to 106 atoms, with a hugely more favorable (linear) scaling of computation time and memory consumption with N.

关键词： Dissipative dynamics Lattice dynamics Mechanical deformation Amorphous materials Polydisperse materials Polymer glasses Random & disordered media Viscoelasticity Molecular dynamics Numerical techniques

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What affects the performance of POD for the simulation of heat transfer through building component?

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Journal of Physics: Conference Series 2021年第1期2069卷

作者： Tianfeng Hou Staf Roels Hans Janssen KU Leuven Department of Civil Engineering Building Physics Section 3001 Leuven Belgium Data Assimilation Research Team RIKEN Center for Computational Science Kobe Japan RIKEN Prediction Science Laboratory Kobe Japan RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program Kobe Japan

The capability of the proper orthogonal decomposition for the simulation of heat transfer in building components is investigated via three applications: linear heat transfer (not coupled to mass transfer), mildly non-linear heat transfer (coupled to air and moisture transfer (hygroscopic)) and highly non-linear heat transfer (coupled to moisture transfer (capillary)). It is shown that increasing non-linearity leads to an increasing number of required construction modes. To further investigate the reason for this degrading performance of POD, the singular values' decay progress from the different training snapshots is addressed in this paper. The results confirm that a fast decay of the singular values implies a high interrelation of the snapshots and a better performance of the POD method.

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Most of the photons that reionized the Universe came from dwarf galaxies

arXiv

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arXiv 2023年

作者： Atek, Hakim Labbé, Ivo Furtak, Lukas J. Chemerynska, Iryna Fujimoto, Seiji Setton, David J. Miller, Tim B. Oesch, Pascal Bezanson, Rachel Price, Sedona H. Dayal, Pratika Zitrin, Adi Kokorev, Vasily Weaver, John R. Brammer, Gabriel van Dokkum, Pieter Williams, Christina C. Cutler, Sam E. Feldmann, Robert Fudamoto, Yoshinobu Greene, Jenny E. Leja, Joel Maseda, Michael V. Muzzin, Adam Pan, Richard Papovich, Casey Nelson, Erica J. Nanayakkara, Themiya Stark, Daniel P. Stefanon, Mauro Suess, Katherine A. Wang, Bingjie Whitaker, Katherine E. Institut d’Astrophysique de Paris CNRS Sorbonne Université 98bis Boulevard Arago Paris75014 France Centre for Astrophysics and Supercomputing Swinburne University of Technology MelbourneVIC3122 Australia Physics Department Ben-Gurion University of the Negev P.O. Box 653 Be’er-Sheva84105 Israel Department of Astronomy The University of Texas at Austin AustinTX78712 United States Department of Physics and Astronomy PITT PACC University of Pittsburgh PittsburghPA15260 United States Department of Physics & Astronomy Northwestern University IL60201 United States Department of Astronomy University of Geneva Chemin Pegasi 51 Versoix1290 Switzerland Niels Bohr Institute University of Copenhagen Jagtvej 128 København NDK-2200 Denmark Kapteyn Astronomical Institute University of Groningen P.O. Box 800 Groningen9700 AV Netherlands Department of Astronomy University of Massachusetts AmherstMA01003 United States Department of Astronomy Yale University New HavenCT06511 United States NSF’s National Optical-Infrared Astronomy Research Laboratory 950 N. Cherry Avenue TucsonAZ85719 United States Steward Observatory University of Arizona TucsonAZ85721 United States Department of Astrophysical Sciences Princeton University 4 Ivy Lane PrincetonNJ08544 United States Institute for Computational Science University of Zurich ZurichCH-8057 Switzerland Waseda Research Institute for Science and Engineering Faculty of Science and Engineering Waseda University 3-4-1 Okubo Shinjuku Tokyo169-8555 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo Japan Department of Astronomy & Astrophysics The Pennsylvania State University University ParkPA16802 United States Institute for Computational & Data Sciences The Pennsylvania State University University ParkPA16802 United States Institute for Gravitation and the Cosmos The Pennsylvania State University University ParkPA16802 United States Department of Astronomy Universi

The identification of sources driving cosmic reionization, a major phase transition from neutral Hydrogen to ionized plasma around 600-800 Myr after the Big Bang,1, 2, 3 has been a matter of intense debate.4 Some models suggest that high ionizing emissivity and escape fractions (fesc) from quasars support their role in driving cosmic reionization.8, 9 Others propose that the high fesc values from bright galaxies generates sufficient ionizing radiation to drive this process.5 Finally, a few studies suggest that the number density of faint galaxies, when combined with a stellar-mass-dependent model of ionizing efficiency and fesc can effectively dominate cosmic reionization.6, 7 However, so far, low-mass galaxies have eluded comprehensive spectroscopic studies owing to their extreme faintness. Here we report an analysis of eight ultra-faint galaxies (in a very small field) during the epoch of reionization with absolute magnitudes between MUV ∼ −17 to −15 mag (down to 0.005 L★10, 11). We find that faint galaxies during the Universe’s first billion years produce ionizing photons with log(ξion/ Hz erg−1) =25.80 ± 0.14, a factor of 4 higher than commonly assumed values.22 If this field is representative of the large scale distribution of faint galaxies, the rate of ionizing photons exceeds that needed for reionization, even for escape fractions of order five per cent. © 2023, CC BY.

关键词： Galaxies

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Detecting anomalous citation groups in journal networks

arXiv

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arXiv 2020年

作者： Kojaku, Sadamori Livan, Giacomo Masuda, Naoki Luddy School of Informatics Computing and Engineering Indiana University BloomingtonIN47408 United States Department of Computer Science University College London LondonWC1E 6EA United Kingdom Systemic Risk Centre London School of Economics and Political Science LondonWC2A 2AE United Kingdom Department of Mathematics University at Buffalo State University of New York BuffaloNY United States Computational and Data-Enabled Science and Engineering Program University at Buffalo State University of New York BuffaloNY14260-2900 United States Faculty of Science and Engineering Waseda University Tokyo169-8555 Japan

The ever-increasing competitiveness in the academic publishing market incentivizes journal editors to pursue higher impact factors. This translates into journals becoming more selective, and, ultimately, into higher publication standards. However, the fixation on higher impact factors leads some journals to artificially boost impact factors through the coordinated effort of a "citation cartel" of journals. "Citation cartel" behavior has become increasingly common in recent years, with several instances being reported. Here, we propose an algorithm—-named CIDRE—to detect anomalous groups of journals that exchange citations at excessively high rates when compared against a null model that accounts for scientific communities and journal size. CIDRE detects more than half of the journals suspended from Journal Citation Reports due to anomalous citation behavior in the year of suspension or in advance. Furthermore, CIDRE detects many new anomalous groups, where the impact factors of the member journals are lifted substantially higher by the citations from other member journals. We describe a number of such examples in detail and discuss the implications of our findings with regard to the current academic climate. Copyright © 2020, The Authors. All rights reserved.

关键词： Publishing

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Cosmological phase-space analysis of f(G)-theories of gravity

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Journal of High Energy Astrophysics 2025年 47卷

作者： Papagiannopoulos, Giannis Luongo, Orlando Leon, Genly Paliathanasis, Andronikos Department of Physics National & Kapodistrian University of Athens Zografou Campus GR Athens 157 73 Greece School of Science and Technology University of Camerino Via Madonna delle Carceri Camerino 62032 Italy Department of Nanoscale Science and Engineering University at Albany-SUNY Albany 12222 NY United States INAF - Osservatorio Astronomico di Brera Milano Italy Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Perugia Perugia 06123 Italy Al-Farabi Kazakh National University Al-Farabi av. 71 Almaty 050040 Kazakhstan Departamento de Matemáticas Universidad Católica del Norte Avda. Angamos 0610 Casilla 1280 Antofagasta Chile Department of Mathematics Faculty of Applied Sciences Durban University of Technology Durban 4000 South Africa School for Data Science and Computational Thinking Department of Mathematical Sciences Stellenbosch University Stellenbosch 7602 South Africa

The impact of topological terms that modify the Hilbert-Einstein action is here explored by virtue of a further f(G) contribution. In particular, we investigate the phase-space stability and critical points of an equivalent scalar field representation that makes use of a massive field, whose potential is function of the topological correction. To do so, we introduce to the gravitational Action Integral a Lagrange multiplier and model the modified Friedmann equations by virtue of new non-dimensional variables. We single out dimensionless variables that permit a priori the Hubble rate change of sign, enabling regions in which the Hubble parameter either vanishes or becomes negative. In this respect, we thus analyze the various possibilities associated with a universe characterized by such topological contributions and find the attractors, saddle points and regions of stability, in general. The overall analysis is carried out considering the exponential potential first and then shifting to more complicated cases, where the underlying variables do not simplify. We compute the eigenvalues of our coupled differential equations and, accordingly, the stability of the system, in both a spatially-flat and non-flat universe. Quite remarkably, regardless of the spatial curvature, we show that a stable de Sitter-like phase that can model current time appears only a small fraction of the entire phase-space, suggesting that the model under exam is unlikely in describing the whole universe dynamics, i.e., the topological terms appear disfavored in framing the entire evolution of the universe. © 2025 The Author(s)

关键词： Equilibrium points f(G)-gravity Gauss-Bonnet

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An extreme test case for planet formation: a close-in Neptune orbiting an ultracool star

arXiv

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arXiv 2023年

作者： Stefánsson, Guðmundur Mahadevan, Suvrath Miguel, Yamila Robertson, Paul Delamer, Megan Kanodia, Shubham Cañas, Caleb Winn, Joshua Ninan, Joe Terrien, Ryan Holcomb, Rae Ford, Eric Zawadzki, Brianna Bowler, Brendan P. Bender, Chad Cochran, William Diddams, Scott Endl, Michael Fredrick, Connor Halverson, Samuel Hearty, Fred Hill, Gary J. Lin, Andrea Metcalf, Andrew Monson, Andrew Ramsey, Lawrence Roy, Arpita Schwab, Christian Wright, Jason Zeimann, Gregory Princeton University Department of Astrophysical Sciences United States Department of Astronomy & Astrophysics The Pennsylvania State University United States Center for Exoplanets and Habitable Worlds The Pennsylvania State University United States ETH Zurich Institute for Particle Physics & Astrophysics Switzerland Leiden Observatory University of Leiden Netherlands SRON Netherlands Institute for Space Research Netherlands Department of Physics & Astronomy University of California Irvine United States Earth and Planets Laboratory Carnegie Institution for Science United States NASA Goddard Space Flight Center United States Department of Astronomy & Astrophysics Tata Institute of Fundamental Research India Carleton College United States Center for Astrostatistics The Pennsylvania State University United States Institute for Computational & Data Sciences The Pennsylvania State University United States Department of Astronomy The University of Texas at Austin AustinTX78712 United States Steward Observatory The University of Arizona United States Center for Planetary Systems Habitability and McDonald Observatory UT Austin United States Electrical Computer and Energy Engineering University of Colorado United States National Institute of Standards & Technology United States Department of Physics University of Colorado United States Jet Propulsion Laboratory California Institute of Technology United States McDonald Observatory UT Austin United States Space Vehicles Directorate Air Force Research Laboratory United States Space Telescope Science Institute United States Department of Physics and Astronomy Johns Hopkins University United States School of Mathematical and Physical Sciences Macquarie University Australia Penn State Extraterrestrial Intelligence Center The Pennsylvania State University United States Hobby-Eberly Telescope University of Texas Austin AustinTX78712 United States

In current theories of planet formation, close-orbiting planets as massive as Neptune are expected to be very rare around low-mass stars. We report the discovery of a Neptune-mass planet orbiting the 'ultracool' star LHS 3154, which is nine times less massive than the Sun. The planet's orbital period is 3.7 days and its minimum mass is 13.2 Earth masses, giving it the largest known planet-to-star mass ratio among short-period planets ( Copyright © 2023, The Authors. All rights reserved.

关键词： Planets

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SATVAM: Toward an IoT Cyber-Infrastructure for Low-Cost Urban Air Quality Monitoring

SATVAM: Toward an IoT Cyber-Infrastructure for Low-Cost Urba...

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IEEE International Conference on e-science and Grid Computing

作者： Yogesh Simmhan Srijith Nair Sumit Monga Ravi Sahu Kuldeep Dixit Ronak Sutaria Brijesh Mishra Anamika Sharma Anand SVR Malati Hegde Rajesh Zele Sachchida N. Tripathi Department of Computational and Data Sciences Indian Institute of Science Bangalore India Department of Electrical Communication Engineering Indian Institute of Science Bangalore India Departments of Civil Engineering & Earth Sciences Indian Institute of Technology Kanpur India Centre for Urban Science & Engineering Indian Institute of Technology Bombay India Department of Electrical Engineering Indian Institute of Technology Bombay India

ISBN: (数字)9781728124513

ISBN: (纸本)9781728124520

Air pollution is a public health emergency in large cities. The availability of commodity sensors and the advent of Internet of Things (IoT) enable the deployment of a city-wide network of 1000's of low-cost real-time air quality monitors to help manage this challenge. This needs to be supported by an IoT cyber-infrastructure for reliable and scalable data acquisition from the edge to the Cloud. The low accuracy of such sensors also motivates the need for data-driven calibration models that can accurately predict the science variables from the raw sensor signals. Here, we offer our experiences with designing and deploying such an IoT software platform and calibration models, and validate it through a pilot field deployment at two mega-cities, Delhi and Mumbai. Our edge data service is able to even-out the differential bandwidths from the sensing devices and to the Cloud repository, and recover from transient failures. Our analytical models reduce the errors of the sensors from a best-case of 63% using the factory baseline to as low as 21%, and substantially advances the state-of-the-art in this domain.

关键词： Sensors Cloud computing Monitoring Air quality Calibration Logic gates Pollution measurement

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Do cities have a unique magnetic pulse?

arXiv

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arXiv 2022年

作者： Dumont, Vincent Bowen, Trevor A. Roglans, Roger Dobler, Gregory Sharma, Mohit S. Karpf, Andy Bale, Stuart D. Wickenbrock, Arne Zhivun, Elena Kornack, Tom Wurtele, Jonathan S. Budker, Dmitry Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department Of Physics University Of California BerkeleyCA94720-7300 United States Space Sciences Laboratory University Of California BerkeleyCA94720-7300 United States Biden School Of Public Policy And Administration University Of Delaware NewarkDE19716 United States Department Of Physics And Astronomy University Of Delaware NewarkDE19716 United States Data Science Institute University Of Delaware NewarkDE19713 United States Center For Urban Science And Progress New York University BrooklynNY11201 United States Civil And Urban Engineering Tandon School Of Engineering New York University BrooklynNY11201 United States Institut Für Physik Universität Mainz Staudingerweg 7 Mainz55128 Germany Helmholtz Institut Mainz Staudingerweg 18 Mainz55128 Germany Twinleaf LLC 300 Deer Creek Drive PlainsboroNJ08536 United States Johannes Gutenberg-Universität Mainz Mainz55128 Germany Helmholtz Institut Mainz Mainz55128 Germany

We present a comparative analysis of urban magnetic fields between two American cities: Berkeley (California) and Brooklyn Borough of New York City (New York). Our analysis uses data taken over a four-week period during which magnetic field data were continuously recorded using a fluxgate magnetometer of 70 pT/√ Hz sensitivity. We identified significant differences in the magnetic signatures. In particular, we noticed that Berkeley reaches a near-zero magnetic field activity at night whereas magnetic activity in Brooklyn continues during nighttime. We also present auxiliary measurements acquired using magnetoresistive vector magnetometers (VMR), with sensitivity of 300 pT/√ Hz, and demonstrate how cross-correlation, and frequency-domain analysis, combined with data filtering can be used to extract urban magnetometry signals and study local anthropogenic activities. Finally, we discuss the potential of using magnetometer networks to characterize the global magnetic field of cities and give directions for future development. Copyright © 2022, The Authors. All rights reserved.

关键词： Magnetometers

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