cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Phase transition in the computational complexity of the shortest common superstring and genome assembly
Creators: name: Fernandez, L. A.
name: Martin-Mayor, V.
name: Yllanes, D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Computational Complexity (cs.CC)
subject: Biological Physics (physics.bio-ph)
subject: Genomics (q-bio.GN)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle formulation. That is, the computing time is believed to grow exponentially with the the problem size in the worst case. Despite this fact, high-throughput technologies and modern algorithms currently allow bioinformaticians to handle datasets of billions of reads. Using methods from statistical mechanics, we address this conundrum by demonstrating the existence of a phase transition in the computational complexity of the problem and showing that practical instances always fall in the 'easy' phase (solvable by polynomial-time algorithms). In addition, we propose a Markov-chain Monte Carlo method that outperforms common deterministic algorithms in the hard regime.
description: 9 pages, 5 figures. Version accepted for publication in Phys. Rev. E
Particle Astrophysics from the Particle Perspective
Creators: name: Dine, Michael
Publisher: name: arXiv
Year: 1993
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In this talk I discuss several topics at the interface of particle physics and astrophysics/cosmology. These include the problem of dark matter and two popular dark matter candidates: axions and neutralinos. I also discuss briefly some recent developments in electroweak baryogenesis, as well as a variety of somewhat more exotic topics: the fate of domain walls, axinos, non-vanishing cosmological constant, and cosmological constraints on models with dynamical supersymmetry breaking. Most of the material is review, however a few of the remarks, especially regarding axion cosmology in the framework of supersymmetry, I believe to be original.
description: Talk presented at the Lepton-Photon Symposium, 1993, some discussion of axions and anthropic principle revised, 34pp, SCIPP 93/31
Fast-growing SMBHs in Fast-growing Galaxies, at High Redshifts: the Role of Major Mergers as Revealed by ALMA
Creators: name: Trakhtenbrot, Benny
name: Lira, Paulina
name: Netzer, Hagai
name: Cicone, Claudia
name: Maiolino, Roberto
name: Shemmer, Ohad
Publisher: name: arXiv
Year: 2018
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present a long-term, multi-wavelength project to understand the epoch of fastest growth of the most massive black holes by using a sample of 40 luminous quasars at z~4.8. These quasars have rather uniform properties, with typical accretion rates and black hole masses of L/L_Edd~0.7 and M_BH~10^9 M_sol. The sample consists of "FIR-bright" sources with a previous Herschel/SPIRE detection, suggesting SFR > 1000 M_sol/yr, as well as of "FIR-faint" sources for which Herschel stacking analysis implies a typical SFR of ~400 M_sol/yr. Six of the quasars have been observed by ALMA in [CII]λ157.74 micron line emission and adjacent rest-frame 150 micron continuum, to study the dusty cold ISM. ALMA detected companion, spectroscopically confirmed sub-mm galaxies (SMGs) for three sources - one FIR-bright and two FIR-faint. The companions are separated by ~14-45 kpc from the quasar hosts, and we interpret them as major galaxy interactions. Our ALMA data therefore clearly support the idea that major mergers may be important drivers for rapid, early SMBH growth. However, the fact that not all high-SFR quasar hosts are accompanied by interacting SMGs, and their ordered gas kinematics observed by ALMA, suggest that other processes may be fueling these systems. Our analysis thus demonstrates the diversity of host galaxy properties and gas accretion mechanisms associated with early and rapid SMBH growth.
description: 5 pages of text, 4 figures. Proceeding of the meeting "Quasars at All Cosmic Epochs" (Padova, April 2017). Published in "Frontiers in Astronomy and Space Science" (available at http://www.frontiersin.org/articles/10.3389/fspas.2017.00049)
A Weil-Petersson Type Metric on the Space of Fano Kaehler-Ricci Solitons
Creators: name: Cao, Huai-Dong
name: Sun, Xiaofeng
name: Zhang, Yingying
Publisher: name: arXiv
Year: 2022
Subjects: subject: Differential Geometry (math.DG)
subject: Complex Variables (math.CV)
subject: FOS: Mathematics
subject: 32G07, 32Q15, 53C55

description: In this paper we define a Weil-Petersson type metric on the space of shrinking Kaehler-Ricci solitons and prove a necessary and sufficient condition on when it is independent of the choices of Kaehler-Ricci soliton metrics. We also show that the Weil-Petersson metric is Kaehler when it defines a metric on the Kuranishi space of small deformations of Fano Kaehler-Ricci solitons. Finally, we establish the first and second order deformation of Fano Kähler-Ricci solitons and show that, essentially, the first effective term in deforming Kaehler-Ricci solitons leads to the Weil-Petersson metric.
description: 16 pages; final version available at the journal cite of JGEA (see the journal reference info below)
Radiation pressure in galactic disks: stability, turbulence, and winds in the single-scattering limit
Creators: name: Wibking, Benjamin D.
name: Thompson, Todd A.
name: Krumholz, Mark R.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: The radiation force on dust grains may be dynamically important in driving turbulence and outflows in rapidly star-forming galaxies. Recent studies focus on the highly optically-thick limit relevant to the densest ultra-luminous galaxies and super star clusters, where reprocessed infrared photons provide the dominant source of electromagnetic momentum. However, even among starburst galaxies, the great majority instead lie in the so-called "single-scattering" limit, where the system is optically-thick to the incident starlight, but optically-thin to the re-radiated infrared. In this paper we present a stability analysis and multidimensional radiation-hydrodynamic simulations exploring the stability and dynamics of isothermal dusty gas columns in this regime. We describe our algorithm for full angle-dependent radiation transport based on the discontinuous Galerkin finite element method. For a range of near-Eddington fluxes, we show that the medium is unstable, producing convective-like motions in a turbulent atmosphere with a scale height significantly inflated compared to the gas pressure scale height and mass-weighted turbulent energy densities of $\sim 0.01-0.1$ of the midplane radiation energy density, corresponding to mass-weighted velocity dispersions of Mach number $\sim 0.5-2$. Extrapolation of our results to optical depths of $10^3$ implies maximum turbulent Mach numbers of $\sim20$. Comparing our results to galaxy-averaged observations, and subject to the approximations of our calculations, we find that radiation pressure does not contribute significantly to the effective supersonic pressure support in star-forming disks, which in general are substantially sub-Eddington. We further examine the time-averaged vertical density profiles in dynamical equilibrium and comment on implications for radiation-pressure-driven galactic winds.
description: 19 pages, 15 figures, submitted to MNRAS. Comments welcome
title: ADCO, Troisième cartulaire de Saint-Étienne de Dijon (XVIe), Cart. 23 (G 127), 310 folios, f. 00515
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2011
name: Petot, Frédéric
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: cartulaire
subject: Corpus Burgundiae Medii Aevi

description: Troisième cartulaire de Saint-Étienne de Dijon (XVIe), Archives départementales de la Côte-d'Or, Cart. 23 (G 127), 310 folios, f. 00515, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Troisième cartulaire de Saint-Étienne de Dijon (XVIe), Archives départementales de la Côte-d'Or, Cart. 23 (G 127), 310 folios, f. 00515, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-project.eu/
description: Provenance: abbaye Saint-Étienne de Dijon
description: Provenance: http://www.wikidata.org/entity/Q15945019
Scaling laws of solar and stellar flares
Creators: name: Aschwanden, Markus J.
name: Stern, Robert A.
name: Güdel, Manuel
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: In this study we compile for the first time comprehensive data sets of solar and stellar flare parameters, including flare peak temperatures T_p, flare peak volume emission measures EM_p, and flare durations t_f from both solar and stellar data, as well as flare length scales L from solar data. Key results are that both the solar and stellar data are consistent with a common scaling law of EM_p ~ T_p^4.7, but the stellar flares exhibit ~250 times higher emission measures (at the same flare peak temperature). For solar flares we observe also systematic trends for the flare length scale L(T_p) ~ T_p^0.9 and the flare duration t_F(T_p) ~ T_p^0.9 as a function of the flare peak temperature. Using the theoretical RTV scaling law and the fractal volume scaling observed for solar flares, i.e., V(L) ~ L^2.4, we predict a scaling law of EM_p ~ T_p^4.3, which is consistent with observations, and a scaling law for electron densities in flare loops, n_p ~ T_p^2/L ~ T_p^1.1. The RTV-predicted electron densities were also found to be consistent with densities inferred from total emission measures, n_p=(EM_p/q_V*V)^1/2, using volume filling factors of q_V=0.03-0.08 constrained by fractal dimensions measured in solar flares. Our results affect also the determination of radiative and conductive cooling times, thermal energies, and frequency distributions of solar and stellar flare energies.
description: 9 Figs., (paper in press, The Astrophsycial Journal)
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing.
Creators: name: Coelho, Luis Pedro
name: Peng, Tao
name: Murphy, Robert
Publisher: name: Carnegie Mellon University
Year: 2010
Subjects: Computational Biology

description: MOTIVATION: Proteins exhibit complex subcellular distributions, which may include localizing in more than one organelle and varying in location depending on the cell physiology. Estimating the amount of protein distributed in each subcellular location is essential for quantitative understanding and modeling of protein dynamics and how they affect cell behaviors. We have previously described automated methods using fluorescent microscope images to determine the fractions of protein fluorescence in various subcellular locations when the basic locations in which a protein can be present are known. As this set of basic locations may be unknown (especially for studies on a proteome-wide scale), we here describe unsupervised methods to identify the fundamental patterns from images of mixed patterns and estimate the fractional composition of them. METHODS: We developed two approaches to the problem, both based on identifying types of objects present in images and representing patterns by frequencies of those object types. One is a basis pursuit method (which is based on a linear mixture model), and the other is based on latent Dirichlet allocation (LDA). For testing both approaches, we used images previously acquired for testing supervised unmixing methods. These images were of cells labeled with various combinations of two organelle-specific probes that had the same fluorescent properties to simulate mixed patterns of subcellular location. RESULTS: We achieved 0.80 and 0.91 correlation between estimated and underlying fractions of the two probes (fundamental patterns) with basis pursuit and LDA approaches, respectively, indicating that our methods can unmix the complex subcellular distribution with reasonably high accuracy. AVAILABILITY: http://murphylab.web.cmu.edu/software.
9 Monate NFDI4Culture
Creators: name: Blümel, Ina
Publisher: name: Kolloquium Wissensinfrastruktur
Year: 2021

description: Dieser Beitrag stellt das Konsortium für Forschungsdaten zu materiellen und immateriellen Kulturgütern (NFDI4Culture) vor. NFDI4Culture - https://nfdi4culture.de/ - ist Teil der Initiative einer Nationalen Forschungsdateninfrastruktur. Folgende Aspekte werden diskutiert: • NFDI und NFDI4Culture - Organisation und Partner • FORSCHUNGSDATEN in NFDI4Culture • Task Areas und Inhalte/Services • Aktivitäten und Community-Building • NFDI und andere nationale sowie internationale Projekte
description: Kolloquium Wissensinfrastruktur, Sommersemester 2021
Dynamical Transition of Operator Size Growth in Quantum Systems Embedded in an Environment
Creators: name: Zhang, Pengfei
name: Yu, Zhenhua
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In closed generic many-body systems, unitary evolution disperses local quantum information into highly non-local objects, resulting in thermalization. Such a process is called information scrambling, whose swiftness is quantified by the operator size growth. However, for quantum systems embedded in an environment, how the couplings to the environment affect the process of information scrambling quests revelation. Here we predict a dynamical transition in quantum systems with all-to-all interactions accompanied by an environment, which separates two phases. In the dissipative phase, information scrambling halts as the operator size decays with time, while in the scrambling phase, dispersion of information persists and the operator size grows and saturates to an $O(N)$ value in the long-time limit with $N$ the number of degrees of freedom of the systems. The transition is driven by the competition between the system intrinsic and environment propelled scramblings and the environment induced dissipation. Our prediction is derived from a general argument based on epidemiological models and demonstrated analytically via solvable Brownian SYK models. We provide further evidence which suggests that the transition is generic to quantum chaotic systems when coupled to an environment. Our study sheds light on the fundamental behavior of quantum systems in the presence of an environment.
description: 6 pages + supplementary material
Four Fermion Processes at Future $e^+e^-$ Colliders as a Probe of New Resonant Structures
Creators: name: Layssac, J.
name: Renard, F. M.
name: Verzegnassi, C.
Publisher: name: arXiv
Year: 1993
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Possible oblique effects from vector particles that are strongly coupled to the known gauge bosons are calculated for the case of final hadronic states produced at future $e^+e^-$ colliders, using a formalism that was recently proposed and that exploits the information and the constraints provided by LEP 1 results. Combining the hadronic channels with the previously analysed leptonic ones we derive improved limits for the masses of the resonances that,in technicolour-like cases, would range from one to two TeV for a 500 GeV linear collider, depending on the assumed theoretical constraints.
description: 11 pages, postscript file of 3 figures appended at the end of the latex file PM/93-34 UTS-DFT-93-28
Orbital Origin of Intrinsic Planar Hall Effect
Creators: name: Wang, Hui
name: Huang, Yue-Xin
name: Liu, Huiying
name: Feng, Xiaolong
name: Zhu, Jiaojiao
name: Wu, Weikang
name: Xiao, Cong
name: Yang, Shengyuan A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Recent experiments reported an antisymmetric planar Hall effect, where the Hall current is odd in the in-plane magnetic field and scales linearly with both electric and magnetic fields applied. Existing theories rely exclusively on a spin origin, which requires spin-orbit coupling to take effect. Here, we develop a general theory for the intrinsic planar Hall effect (IPHE), highlighting a previously unknown orbital mechanism and connecting it to a band geometric quantity -- the anomalous orbital polarizability (AOP). Importantly, the orbital mechanism does not request spin-orbit coupling, so sizable IPHE can occur and is dominated by orbital contribution in systems with weak spin-orbit coupling. Combined with first-principles calculations, we demonstrate our theory with quantitative evaluation for bulk materials $\mathrm{TaSb_{2}}$, $\mathrm{NbAs_{2}}$, and $\mathrm{SrAs_{3}}$. We further show that AOP and its associated orbital IPHE can be greatly enhanced at topological band crossings, offering a new way to probe topological materials.
Effective Lagrangian approach to fermion electric dipole moments induced by a CP--violating $WWγ$ vertex
Creators: name: Novales--Sanchez, H.
name: Toscano, J. J.
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The one--loop contribution of the two CP--violating components of the $WWγ$ vertex, $ \tildeκ_γW^+_μW^-_ν\tilde{F}^{μν}$ and $(\tildeλ_γ/ m^2_W)W^+_{μν}W^{-ν}_{\ ρ}\tilde{F}^{ρμ}$, on the electric dipole moment (EDM) of fermions is calculated using dimensional regularization and its impact at low energies reexamined in the light of the decoupling theorem. The Ward identities satisfied by these couplings are derived by adopting a $SU_L(2)\times U_Y(1)$--invariant approach and their implications in radiative corrections discussed. Previous results on $\tildeκ_γ$, whose bound is updated to $|\tildeκ_γ| <5.2\times 10^{-5}$, are reproduced, but disagreement with those existing for $\tildeλ_γ$ is found. In particular, the upper bound $|\tildeλ_γ|<1.9\times10^{-2}$ is found from the limit on the neutron EDM, which is more than 2 orders of magnitude less stringent than that of previous results. It is argued that this difference between the $\tildeκ_γ$ and $\tildeλ_γ$ bounds is the one that might be expected in accordance with the decoupling theorem. This argument is reinforced by analyzing careful the low--energy behavior of the loop functions. The upper bounds on the $W$ EDM, $|d_W|<6.2\times 10^{-21} e\cdot cm$, and the magnetic quadrupole moment, $|\tilde{Q}_W|<3\times 10^{-36} e\cdot cm^2$, are derived. The EDM of the second and third families of quarks and charged leptons are estimated. In particular, EDM as large as $ 10^{-20} e\cdot cm$ and $10^{-21} e\cdot cm$ are found for the $t$ and $b$ quarks, respectively.
description: 14 pages and 2 figures
A simple approach to the chaos-order contributions in nuclear spectra
Creators: name: Magner, A. G.
name: Levon, A. I.
name: Radionov, S. V.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Nuclear Theory (nucl-th)
subject: Chaotic Dynamics (nlin.CD)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: The simple one-parameter nearest neighbor-spacing distribution (NNSD) is suggested for statistical analysis of nuclear spectra. This distribution is derived within the Wigner-Dyson approach in the linear approximation for the level repulsion density of quantum states. The obtained NNSD gives the individual information on the Wigner and Poisson contributions in agreement with that of the statistical experimental distributions of collective states in deformed nuclei. Using this NNSD, one finds that the symmetry breaking due to the fixing of projections of the angular momentum of collective states enhances a chaos as a shift of the NNSD from the Poisson to Wigner distribution behavior.
description: 6 pages, 3 figures. arXiv admin note: text overlap with arXiv:1711.01848
Der Uni-Dienst 'Teamchat 2.0' im Kontext der UB
Creators: name: Schirrwagen, Jochen
Publisher: name: Kolloquium Wissensinfrastruktur
Year: 2021

description: Im Frühjahr 2021 wurde an der Universität Bielefeld der Instant Messaging Dienst Matrix eingeführt, der als Teamchat 2.0 den Vorgänger RocketChat abgelöst hat. Teamchat 2.0 nutzt die Software-App Element als plattformübergreifenden Client, der Chat, IP-Telefonie und Video-Telefonie über die Matrix-Protokolle ermöglicht. Nach einer kurzen Einführung in Matrix und Element werden die im Vorfeld und spontan gestellten Fragen der Kolleginnen und Kollegen aufgegriffen. Draüberhinaus soll Ziel der Veranstaltung sein zu erörtern, wie 'Teamchat 2.0' für die Kommunikation innerhalb der UB zwischen MitarbetierInnen und Abteilungen effektiv genutzt werden kann.
description: Kolloquium Wissensinfrastruktur, Sommersemester 2021
Der ORCID-DE Monitor
Creators: name: Summann, Friedrich
name: Gagla-Dietz, Stephanie
name: Wolf, Sebastian
Publisher: name: Kolloquium Wissensinfrastruktur
Year: 2021

description: Die UB Bielefeld hat im Rahmen des DFG-Projektes "ORCID DE 2 – Konsolidierung der ORCID-Informationsinfrastruktur in Deutschland“ im Rahmen eines Arbeitspaktes den ORCID DE Monitor entwickelt. Dieser stellt vorliegende Daten aus dem BASE- und Crossref-Umfeld, von GND, ORCID-Konsortium Deutschland und ORCID, Inc zur Verbreitung und Nutzung der ORCID iD zusammen und ermöglicht darauf basierende Auswertungen. Diese Anwendung wird zum Bibliothekartag in Bremen produktiv geschaltet. Der Kolloquiumsvortrag skizziert die technische Infrastruktur und stellt an konkreten Beispielen die entwickelte Endnutzeroberfläche vor.
description: Kolloquium Wissensinfrastruktur, Sommersemester 2021
Behavior of Ising Spin Glasses in a Magnetic Field
Creators: name: Jorg, Thomas
name: Katzgraber, Helmut G.
name: Krzakala, Florent
Publisher: name: arXiv
Year: 2007
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We study the existence of a spin-glass phase in a field using Monte Carlo simulations performed along a nontrivial path in the field--temperature plane that must cross any putative de Almeida-Thouless instability line. The method is first tested on the Ising spin glass on a Bethe lattice where the instability line separating the spin glass from the paramagnetic state is also computed analytically. While the instability line is reproduced by our simulations on the mean-field Bethe lattice, no such instability line can be found numerically for the short-range three-dimensional model.
description: 4 pages, 4 figures
Robust optimality and duality for composite uncertain multiobjective optimization in Asplund spaces with its applications
Creators: name: Saadati, Maryam
name: Oveisiha, Morteza
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics
subject: 49K99, 65K10, 90C29, 90C46

description: This article is devoted to investigate a nonsmooth/nonconvex uncertain multiobjective optimization problem with composition fields (CUP) for brevity) over arbitrary Asplund spaces. Employing some advanced techniques of variational analysis and generalized differentiation, we establish necessary optimality conditions for weakly robust efficient solutions of (CUP) in terms of the limiting subdifferential. Sufficient conditions for the existence of (weakly) robust efficient solutions to such a problem are also driven under the new concept of pseudo-quasi convexity for composite functions. We formulate a Mond-Weir-type robust dual problem to the primal problem (CUP), and explore weak, strong, and converse duality properties. In addition, the obtained results are applied to an approximate uncertain multiobjective problem and a composite uncertain multiobjective problem with linear operators.
description: arXiv admin note: substantial text overlap with arXiv:2105.14366, arXiv:2205.01145
Protein subcellular location pattern classification in cellular images using latent discriminative models.
Creators: name: Jieyue  Li
name: Xiong, Liang
name: Schneider, Jeff
name: Murphy, Robert
Publisher: name: Carnegie Mellon University
Year: 2014
Subjects: Computational Biology

description: MOTIVATION: Knowledge of the subcellular location of a protein is crucial for understanding its functions. The subcellular pattern of a protein is typically represented as the set of cellular components in which it is located, and an important task is to determine this set from microscope images. In this article, we address this classification problem using confocal immunofluorescence images from the Human Protein Atlas (HPA) project. The HPA contains images of cells stained for many proteins; each is also stained for three reference components, but there are many other components that are invisible. Given one such cell, the task is to classify the pattern type of the stained protein. We first randomly select local image regions within the cells, and then extract various carefully designed features from these regions. This region-based approach enables us to explicitly study the relationship between proteins and different cell components, as well as the interactions between these components. To achieve these two goals, we propose two discriminative models that extend logistic regression with structured latent variables. The first model allows the same protein pattern class to be expressed differently according to the underlying components in different regions. The second model further captures the spatial dependencies between the components within the same cell so that we can better infer these components. To learn these models, we propose a fast approximate algorithm for inference, and then use gradient-based methods to maximize the data likelihood. RESULTS: In the experiments, we show that the proposed models help improve the classification accuracies on synthetic data and real cellular images. The best overall accuracy we report in this article for classifying 942 proteins into 13 classes of patterns is about 84.6%, which to our knowledge is the best so far. In addition, the dependencies learned are consistent with prior knowledge of cell organization. AVAILABILITY: http://murphylab.web.cmu.edu/software/.
Quantum-Dynamical Semigroups and the Church of the Larger Hilbert Space
Creators: name: Ende, Frederik vom
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: Functional Analysis (math.FA)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: In this work we investigate Stinespring dilations of quantum-dynamical semigroups, which are known to exist by means of a constructive proof given by Davies in the early 70s. We show that if the semigroup describes an open system, that is, if it does not consist of only unitary channels, then the evolution of the dilated closed system has to be generated by an unbounded Hamiltonian; subsequently the environment has to correspond to an infinite-dimensional Hilbert space, regardless of the original system. Moreover, we prove that the second derivative of Stinespring dilations with a bounded total Hamiltonian yields the dissipative part of some quantum-dynamical semigroup -- and vice versa. In particular this characterizes the generators of quantum-dynamical semigroups via Stinespring dilations.
description: 9+9 pages
The chiral transition on a 24^3x10 lattice with N_f=2 clover sea quarks studied by overlap valence quarks
Creators: name: Weinberg, V.
name: Ilgenfritz, E. -M.
name: Koller, K.
name: Koma, Y.
name: Nakamura, Y.
name: Schierholz, G.
name: Streuer, T.
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Overlap fermions are particularly well suited to study the finite temperature dynamics of the chiral symmetry restoration transition of QCD, which might be just an analytic crossover. Using gauge field configurations on a 24^3x10 lattice with N_f=2 flavours of dynamical Wilson-clover quarks generated by the DIK collaboration, we compute the lowest 50 eigenmodes of the overlap Dirac operator and try to locate the transition by fermionic means. We analyse the spectral density, local chirality and localisation properties of the low-lying modes and illustrate the changing topological and (anti-) selfdual structure of the underlying gauge fields across the transition.
description: 7 pages, 6 figures, talk presented at the XXVth International Symposium on Lattice Field Theory, July 30 - August 4 2007, Regensburg, Germany
Predicting protein interactions via parsimonious network history inference.
Creators: name: Patro, Rob
name: Kingsford, Carl
Publisher: name: Carnegie Mellon University
Year: 2011
Subjects: Computational Biology

description: MOTIVATION: Reconstruction of the network-level evolutionary history of protein-protein interactions provides a principled way to relate interactions in several present-day networks. Here, we present a general framework for inferring such histories and demonstrate how it can be used to determine what interactions existed in the ancestral networks, which present-day interactions we might expect to exist based on evolutionary evidence and what information extant networks contain about the order of ancestral protein duplications. RESULTS: Our framework characterizes the space of likely parsimonious network histories. It results in a structure that can be used to find probabilities for a number of events associated with the histories. The framework is based on a directed hypergraph formulation of dynamic programming that we extend to enumerate many optimal and near-optimal solutions. The algorithm is applied to reconstructing ancestral interactions among bZIP transcription factors, imputing missing present-day interactions among the bZIPs and among proteins from five herpes viruses, and determining relative protein duplication order in the bZIP family. Our approach more accurately reconstructs ancestral interactions than existing approaches. In cross-validation tests, we find that our approach ranks the majority of the left-out present-day interactions among the top 2 and 17% of possible edges for the bZIP and herpes networks, respectively, making it a competitive approach for edge imputation. It also estimates relative bZIP protein duplication orders, using only interaction data and phylogenetic tree topology, which are significantly correlated with sequence-based estimates. AVAILABILITY: The algorithm is implemented in C++, is open source and is available at http://www.cs.cmu.edu/ckingsf/software/parana2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Establishing and storing of deterministic quantum entanglement among three distant atomic ensembles
Creators: name: Yan, Zhihui
name: Wu, Liang
name: Jia, Xiaojun
name: Liu, Yanhong
name: Deng, Ruijie
name: Li, Shujing
name: Wang, Hai
name: Xie, Changde
name: Peng, Kunchi
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: It is crucial for physical realization of quantum information networks to first establish entanglement among multiple space-separated quantum memories and then at a user-controlled moment to transfer the stored entanglement to quantum channels for distribution and conveyance of information. Here we present an experimental demonstration on generation, storage and transfer of deterministic quantum entanglement among three spatially separated atomic ensembles. The off-line prepared multipartite entanglement of optical modes is mapped into three distant atomic ensembles to establish entanglement of atomic spin waves via electromagnetically-induced-transparency light-matter interaction. Then the stored atomic entanglement is transferred into a tripartite quadrature entangled state of light, which is space-separated and can be dynamically allocated to three quantum channels for conveying quantum information. The existence of entanglement among released three optical modes verifies that the system has capacity of preserving multipartite entanglement. The presented protocol can be directly extended to larger quantum networks with more nodes.
title: Nonnuclear Hyper/Ultraluminous X-Ray Sources in the Starbursting Cartwheel Ring Galaxy
Creators: name: Gao, Y
name: Wang, QD
name: Appleton, PN
name: Lucas, RA
Publisher: name: University of Massachusetts Amherst
Year: 2003
Subjects: subject: galaxies: active; galaxies: individual (Cartwheel
subject: VV 784); galaxies: interactions; galaxies: starburst; X-rays: galaxies
subject: Astrophysics and Astronomy

description: This is the pre-published version harvested from ArXiv. The published version is located at http://iopscience.iop.org/1538-4357/596/2/L171/
description: We report the Chandra/ACIS-S detection of more than 20 ultraluminous X-ray sources (ULXs; L0.5-10 keV 3 × 1039 ergs s-1) in the Cartwheel collisional ring galaxy system, of which over a dozen are located in the outer active star-forming ring. A remarkable hyperluminous X-ray source (HLX; L0.5-10 keV 1041 ergs s-1 assuming isotropic radiation), which dominates the X-ray emission from the Cartwheel ring, is located in the same segment of the ring as most ULXs. These powerful H/ULXs appear to be coincident with giant H II region complexes, young star clusters, and radio and mid-infrared hot spots: all strong indicators of recent massive star formation. The X-ray spectra show that H/ULXs have similar properties as those of the most luminous ULXs found in the nearest starbursts and galaxy mergers such as the Antennae galaxies and M82. The close association between the X-ray sources and the starbursting ring strongly suggests that the H/ULXs are intimately associated with the production and rapid evolution of short-lived massive stars. The observations represent the most extreme X-ray luminosities discovered to date associated with star-forming regions—rivaling the X-ray luminosities usually associated with active galactic nuclei.
$IRIS^{2+}$: A comprehensive database of stratified thermodynamic models in the low solar atmosphere
Creators: name: Dalda, Alberto Sainz
name: Agrawal, Aaryan
name: De Pontieu, Bart
name: Gosic, M.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Our knowledge of the low solar atmosphere, i.e., the photosphere and chromosphere, is based on the knowledge gained from the observations and the theoretical and numerical modeling of these layers. In this sense, the thermodynamical and magnetic semi-empirical models of the solar atmosphere have significantly contributed to the advance in the understanding of the physics of the Sun. In the past, many of these models have been used as a reference that helps us to, e.g., constrain the theoretical and numerical modeling, or to verify the goodness of physical parameters obtained from the inversion of the spectral lines. Nevertheless, semi-empirical models are quite limited by the assumptions that are inherent to the approach and do not necessarily provide an accurate view of the instantaneous and local thermodynamic conditions in the solar atmosphere. In this work, we provide an extensive collection of thermodynamic model atmospheres for active regions (ARs) obtained from the simultaneous inversion of 6 lines sensitive to changes in the thermodynamical conditions in the chromosphere, and another 6 lines sensitive to changes in the thermodynamical conditions in the photospere. These inversions were made using 320 representative profiles (RP) obtained by clustering the profiles in the umbra, penumbra, pore-like, plage, and surrounding quiet-sun in 126 active regions. Due to the simultaneous inversion of the selected lines, the resulting representative model atmosphere (RMA) samples the thermodynamics from the bottom of the photosphere to the top of the chromosphere. As a result, this database, named $IRIS^{2+}$ and formed by $40,320$ RP-RMA pairs, represents the most comprehensive collection of stratified-in-optical-depth thermodynamic models of the low solar atmosphere.
description: 11 pages, 6 figures and 2 tables
Parameter discovery in stochastic biological models using simulated annealing and statistical model checking.
Creators: name: Faraz  Hussain
name: Jha, Sumit Kumar
name: Susmit  Jha
name: Langmead, Christopher J.
Publisher: name: Carnegie Mellon University
Year: 2015
Subjects: Computational Biology

description: Stochastic models are increasingly used to study the behaviour of biochemical systems. While the structure of such models is often readily available from first principles, unknown quantitative features of the model are incorporated into the model as parameters. Algorithmic discovery of parameter values from experimentally observed facts remains a challenge for the computational systems biology community. We present a new parameter discovery algorithm that uses simulated annealing, sequential hypothesis testing, and statistical model checking to learn the parameters in a stochastic model. We apply our technique to a model of glucose and insulin metabolism used for in-silico validation of artificial pancreata and demonstrate its effectiveness by developing parallel CUDA-based implementation for parameter synthesis in this model.
Non-Standard Neutrino Interactions : Obviating Oscillation Experiments
Creators: name: Choudhury, Debajyoti
name: Ghosh, Kirtiman
name: Niyogi, Saurabh
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Searching for non-standard neutrino interactions, as a means for discovering physics beyond the Standard Model, has one of the key goals of dedicated neutrino experiments, current and future. We demonstrate here that much of the parameter space accessible to such experiments is already ruled out by the RUN II data of the Large Hadron Collider experiment.
description: 5 pages, 2 figures
Deconstructing Little Strings with $\mathcal{N}=1$ Gauge Theories on Ellipsoids
Creators: name: Hayling, Joseph
name: Panerai, Rodolfo
name: Papageorgakis, Constantinos
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: A formula was recently proposed for the perturbative partition function of certain $\mathcal N=1$ gauge theories on the round four-sphere, using an analytic-continuation argument in the number of dimensions. These partition functions are not currently accessible via the usual supersymmetric-localisation technique. We provide a natural refinement of this result to the case of the ellipsoid. We then use it to write down the perturbative partition function of an $\mathcal N=1$ toroidal-quiver theory (a double orbifold of $\mathcal N=4$ super Yang-Mills) and show that, in the deconstruction limit, it reproduces the zero-winding contributions to the BPS partition function of (1,1) Little String Theory wrapping an emergent torus. We therefore successfully test both the expressions for the $\mathcal N=1$ partition functions, as well as the relationship between the toroidal-quiver theory and Little String Theory through dimensional deconstruction.
description: 6 pages; v2: typos corrected and references added; v3: minor clarifications added; v4 typo corrected and references added
On the ODE/IM correspondence for minimal models
Creators: name: Dorey, Patrick
name: Dunning, Clare
name: Gliozzi, Ferdinando
name: Tateo, Roberto
Publisher: name: arXiv
Year: 2007
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: Quantum Algebra (math.QA)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Within the framework of the ODE/IM correspondence, we show that the minimal conformal field theories with c<1 emerge naturally from the monodromy properties of certain families of ordinary differential equations.
description: 12 pages, 3 figures; typos corrected and reference added
Learning Sequence Determinants of Protein:protein Interaction Specificity with Sparse Graphical Models.
Creators: name: Hetunandan  Kamisetty
name: Bornika  Ghosh
name: Langmead, Christopher J.
name: Bailey-Kellogg, Chris
Publisher: name: Carnegie Mellon University
Year: 2012
Subjects: Computational Biology

description: In studying the strength and specificity of interaction between members of two protein families, key questions center on which pairs of possible partners actually interact, how well they interact, and why they interact while others do not. The advent of large-scale experimental studies of interactions between members of a target family and a diverse set of possible interaction partners offers the opportunity to address these questions. We develop here a method, DgSpi (Data-driven Graphical models of Specificity in Protein:protein Interactions), for learning and using graphical models that explicitly represent the amino acid basis for interaction specificity (why) and extend earlier classification-oriented approaches (which) to predict the ΔG of binding (how well). We demonstrate the effectiveness of our approach in analyzing and predicting interactions between a set of 82 PDZ recognition modules, against a panel of 217 possible peptide partners, based on data from MacBeath and colleagues. Our predicted ΔG values are highly predictive of the experimentally measured ones, reaching correlation coefficients of 0.69 in 10-fold cross-validation and 0.63 in leave-one-PDZ-out cross-validation. Furthermore, the model serves as a compact representation of amino acid constraints underlying the interactions, enabling protein-level ΔG predictions to be naturally understood in terms of residue-level constraints. Finally, as a generative model, DgSpi readily enables the design of new interacting partners, and we demonstrate that designed ligands are novel and diverse.
EAGER: The FAIR Island Project for Place-based Open Science
Creators: name: Praetzellis, Maria
name: Chodacki, John
name: Davies, Neil
name: Robinson, Erin
name: Buys, Matthew
name: Nancarrow, Catherine
Publisher: name: Zenodo
Year: 2021
Subjects: data management plan
open science
research data management

description: National Science Foundation EAGER grant proposal. PIs: John Chodacki (Principal Investigator), Neil Davies (Co-Principal Investigator), Erin Robinson (Co-Principal Investigator), Matthew Buys (Co-Principal Investigator). This exploratory project will test FAIR (Findable, Accessible, Interoperable, and Reusable) data principles for Open Science purposes in a comprehensive manner for field station data gathering on the Pacific atoll of Tetiaroa. This project is a timely opportunity to leverage the new field station on the atoll of Tetiaroa which has close ties to U.S. institutions through the University of California, including a nearby NSF Long Term Ecological Research (LTER) site, as well as international research programs.

 Place-based data have a unique quality in that they span the sciences and humanities with time and space (geolocation) acting as foundational metadata used to assign data to “place” (or nested “places”). The FAIR Island Project will build interoperability between pieces of critical research infrastructure -- Data Management Plans (DMPs), research practice, DOIs, and publications contributing to the advancement and adoption of Open Science.
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome IX, Cart. 193 (11 H 78), f. 0090v
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome IX, Archives départementales de la Côte-d'Or, Cart. 193 (11 H 78), f. 0090v, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome IX, Archives départementales de la Côte-d'Or, Cart. 193 (11 H 78), f. 0090v, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
Adaptive Quantum Optics with Spatially Entangled Photon Pairs
Creators: name: Defienne, Hugo
name: Reichert, Matthew
name: Fleischer, Jason W.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Light shaping facilitates the preparation and detection of optical states and underlies many applications in communications, computing, and imaging. In this Letter, we generalize light shaping to the quantum domain. We show that patterns of phase modulation for classical laser light can also shape higher orders of spatial coherence, allowing deterministic tailoring of high-dimensional quantum entanglement. By modulating spatially entangled photon pairs, we create periodic, topological, and random patterns of quantum illumination, without effect on intensity. We then structure the quantum illumination to simultaneously compensate for entanglement that has been randomized by a scattering medium and to characterize the medium's properties via a quantum measurement of the optical memory effect. The results demonstrate fundamental aspects of spatial coherence and open the field of adaptive quantum optics.