cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Design, synthesis, and computational studies of benzimidazole derivatives as new antitubercular agents
Creators: name: Yalcin-Ozkat, Gozde
name: Ersan, Ronak H.
name: Ulger, Mahmut
name: Ulger, Seda T.
name: Burmaoglu, Serdar
name: Yildiz, Ilkay
name: Algul, Oztekin
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: The increase in the drug-resistant strains of Mycobacterium tuberculosis has led researchers to new drug targets. The development of new compounds that have effective inhibitory properties with the selective vital structure of Mycobacterium tuberculosis is required in new scientific approaches. The most important of these approaches is the development of inhibitor molecules for Mycobacterium cell wall targets. In this study, first of all, the antitubercular activity of 23 benzimidazole derivatives was experimentally determined. And then molecular docking studies were carried out with 4 different targets: Arabinosyltransferase C (EmbC), Filamentous Temperature Sensitive Mutant Z (FtsZ), Protein Tyrosine Phosphatase B (PtpB), and Decaprenylphosphoryl-β-D-ribose-2′-oxidase (DprE1). It has been determined that benzimidazole derivatives show activity through the DprE1 enzyme. It is known that DprE1, which has an important role in the synthesis of the cell envelope from Arabinogalactan, is also effective in the formation of drug resistance. Due to this feature, the DprE1 enzyme has become an important target for drug development studies. Also, it was chosen as a target for this study. This study aims to identify molecules that inhibit DprE1 for the development of more potent and selective antitubercular drugs. For this purpose, molecular docking studies by AutoDock Vina, and CDOCKER and molecular dynamics (MD) simulations and in silico ADME/Tox analysis were implemented for 23 molecules. The molecules exhibited binding affinity values of less than −8.0 kcal/mol. After determining the compound’s anti-TB activities by a screening test, the best-docked results were detected using compounds 20, 21, and 30. It was found that 21, was the best molecule with its binding affinity value, which was supported by MD simulations and in silico ADME modeling results. Communicated by Ramaswamy H. Sarma.
Experimental access to higher-order Zeeman effects by precision spectroscopy of highly charged ions in a Penning trap
Creators: name: von Lindenfels, D.
name: Wiesel, M.
name: Glazov, D. A.
name: Volotka, A. V.
name: Sokolov, M. M.
name: Shabaev, V. M.
name: Plunien, G.
name: Quint, W.
name: Birkl, G.
name: Martin, A.
name: Vogel, M.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We present an experimental concept and setup for laser-microwave double-resonance spectroscopy of highly charged ions in a Penning trap. Such spectroscopy allows a highly precise measurement of the Zeeman splittings of fine- and hyperfine-structure levels due the magnetic field of the trap. We have performed detailed calculations of the Zeeman effect in the framework of quantum electrodynamics of bound states as present in such highly charged ions. We find that apart from the linear Zeeman effect, second- and third-order Zeeman effects also contribute to the splittings on a level of 10^-4 and 10^-8, respectively, and hence are accessible to a determination within the achievable spectroscopic resolution of the ARTEMIS experiment currently in preparation.
Chern degree functions
Creators: name: Lahoz, Martí
name: Rojas, Andrés
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: We introduce Chern degree functions for complexes of coherent sheaves on a polarized surface, which encode information given by stability conditions on the boundary of the $(α, β)$-plane. We prove that these functions extend to continuous real valued functions and we study their differentiability in terms of stability. For abelian surfaces, Chern degree functions coincide with the cohomological rank functions defined by Jiang-Pareschi. We illustrate in some geometrical situations a general strategy to compute these functions.
description: Minor changes. Final version, to appear in Commun. Contemp. Math
Stability of viscous detonations for Majda's model
Creators: name: Humpherys, Jeffrey
name: Lyng, Gregory
name: Zumbrun, Kevin
Publisher: name: arXiv
Year: 2013
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: Using analytical and numerical Evans-function techniques, we examine the spectral stability of strong-detonation-wave solutions of Majda's scalar model for a reacting gas mixture with an Arrhenius-type ignition function. We introduce an efficient energy estimate to limit possible unstable eigenvalues to a compact region in the unstable complex half plane, and we use a numerical approximation of the Evans function to search for possible unstable eigenvalues in this region. Our results show, for the parameter values tested, that these waves are spectrally stable. Combining these numerical results with the pointwise Green function analysis of Lyng, Raoofi, Texier, & Zumbrun [J. Differential Equations 233 (2007), no. 2, 654-698.], we conclude that these waves are nonlinearly stable. This represents the first demonstration of nonlinear stability for detonation-wave solutions of the Majda model without a smallness assumption. Notably, our results indicate that, for the simplified Majda model, there does not occur, either in a normal parameter range or in the limit of high activation energy, Hopf bifurcation to "galloping" or "pulsating" solutions as is observed in the full reactive Navier-Stokes equations. This answers in the negative a question posed by Majda as to whether the scalar detonation model captures this aspect of detonation behavior.
The artistic collaboration resulting in the creation of the ballet "Parade"
Creators: name: Kattner, Elizabeth Marie
Publisher: name: University of Nevada, Las Vegas
Year: 1997

description: The Artistic Collaboration Resulting in the Creation of the Ballet Parade is an examination of the development of Parade for the Ballet Russe. It describes the process by which Jean Cocteau, Pablo Picasso, Erik Satie, and Leonide Massine collaborated under the guidance of Serge Diaghilev. The collaborators' objective was to create a work of "total art" which gave equal attention to visual art, music, and dance. The medium of dance is the primary focus for examination in this thesis, but it cannot be understood without looking at the work of each of the collaborators as well as the political and cultural climate of Paris in 1917. Cocteau's scenario, Picasso's Cubist designs, and Satie's innovative music, along with Massine's choreographic invention, resulted in this work of total art.
Towards an Evolvable Cancer Treatment Simulator
Creators: name: Preen, Richard J.
name: Bull, Larry
name: Adamatzky, Andrew
Publisher: name: arXiv
Year: 2018
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Artificial Intelligence (cs.AI)
subject: Computational Engineering, Finance, and Science (cs.CE)
subject: Multiagent Systems (cs.MA)
subject: FOS: Computer and information sciences

description: The use of high-fidelity computational simulations promises to enable high-throughput hypothesis testing and optimisation of cancer therapies. However, increasing realism comes at the cost of increasing computational requirements. This article explores the use of surrogate-assisted evolutionary algorithms to optimise the targeted delivery of a therapeutic compound to cancerous tumour cells with the multicellular simulator, PhysiCell. The use of both Gaussian process models and multi-layer perceptron neural network surrogate models are investigated. We find that evolutionary algorithms are able to effectively explore the parameter space of biophysical properties within the agent-based simulations, minimising the resulting number of cancerous cells after a period of simulated treatment. Both model-assisted algorithms are found to outperform a standard evolutionary algorithm, demonstrating their ability to perform a more effective search within the very small evaluation budget. This represents the first use of efficient evolutionary algorithms within a high-throughput multicellular computing approach to find therapeutic design optima that maximise tumour regression.
Learning from Nature to Improve the Heat Generation of Iron-Oxide Nanoparticles for Magnetic Hyperthermia Applications
Creators: name: Martinez-Boubeta, Carlos
name: Simeonidis, Konstantinos
name: Makridis, Antonios
name: Angelakeris, Makis
name: Iglesias, Oscar
name: Guardia, Pablo
name: Cabot, Andreu
name: Yedra, Lluis
name: Estrade, Sonia
name: Peiro, Francesca
name: Saghi, Zineb
name: Midgley, Paul A.
name: Conde-Leboran, Ivan
name: Serantes, David
name: Baldomir, Daniel
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The performance of magnetic nanoparticles is intimately entwined with their structure, mean size and magnetic anisotropy. Besides, ensembles offer a unique way of engineering the magnetic response by modifying the strength of the dipolar interactions between particles. Here we report on an experimental and theoretical analysis of magnetic hyperthermia, a rapidly developing technique in medical research and oncology. Experimentally, we demonstrate that single-domain cubic iron oxide particles resembling bacterial magnetosomes have superior magnetic heating efficiency compared to spherical particles of similar sizes. Monte Carlo simulations at the atomic level corroborate the larger anisotropy of the cubic particles in comparison with the spherical ones, thus evidencing the beneficial role of surface anisotropy in the improved heating power. Moreover we establish a quantitative link between the particle assembling, the interactions and the heating properties. This knowledge opens new perspectives for improved hyperthermia, an alternative to conventional cancer therapies.
description: Accepted for publication in Scientific Reports, 52 pages including supporting info, 7+12 figures
Quantum Computing with Majorana Kramers Pairs
Creators: name: Schrade, Constantin
name: Fu, Liang
Publisher: name: arXiv
Year: 2018
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We propose a universal gate set acting on a qubit formed by the degenerate ground states of a Coulomb-blockaded time-reversal invariant topological superconductor island with spatially separated Majorana Kramers pairs: the "Majorana Kramers Qubit". All gate operations are implemented by coupling the Majorana Kramers pairs to conventional superconducting leads. Interestingly, in such an all-superconducting device, the energy gap of the leads provides another layer of protection from quasiparticle poisoning independent of the island charging energy. Moreover, the absence of strong magnetic fields - which typically reduce the superconducting gap size of the island - suggests a unique robustness of our qubit to quasiparticle poisoning due to thermal excitations. Consequently, the Majorana Kramers Qubit should benefit from prolonged coherence times and may provide an alternative route to a Majorana-based quantum computer.
Compact routing in fault-tolerant distributed systems
Creators: name: Lawrence, James Edward
Publisher: name: University of Nevada, Las Vegas
Year: 1997

description: A compact routing algorithm is a routing algorithm which reduces the space complexity of all-pairs shortest path routing. Compact routing protocols in distributed systems have been studied extensively as an attractive alternative to the traditional method of all-pairs shortest path routing. The use of compact routing protocols have several advantages. Compact routing schemes are not only more memory-efficient, but provide faster routing table lookup, more efficient broadcast scheme, and allow for a more scalable network. These routing schemes still maintain optimal or near-optimal routing paths. However, most of the compact routing protocols are not fault-tolerant. This thesis will first report the recent developments in the compact routing research. Several new methods for compact routing in fault-tolerant distributed systems will be presented and analyzed. The most important feature of the algorithms presented in this thesis is that they are self-stabilizing. The self-stabilization paradigm has been shown to be the most unified and all-inclusive approach to the design of fault-tolerant system. Additionally, these algorithms will address and solve several problems left unsolved by previous works. Relabelable and non-relabelable networks will be considered for both specific and arbitrary topologies.
Finite genome length corrections for the mean fitness and gene probabilities in evolution models
Creators: name: Kirakosyan, Zara
name: Saakian, David B.
name: Hu, Chin Kun
Publisher: name: arXiv
Year: 2012
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Using the Hamilton-Jacobi equation approach to study genomes of length $L$, we obtain 1/L corrections for the steady state population distributions and mean fitness functions for horizontal gene transfer model, as well as for the diploid evolution model with general fitness landscapes. Our numerical solutions confirm the obtained analytic equations. Our method could be applied to the general case of nonlinear Markov models.
description: 8 pages
Luminescence studies of binding affinity of vildagliptin with bovine serum albumin
Creators: name: Verma, Piyush
name: Kaur, Lajpreet
name: Aswal, Priyanka
name: Singh, Anju
name: Ojha, Himanshu
name: Rahman, Afreen Jahan
name: Singhal, Rahul
name: Tiwari, Anjani K.
name: Pathak, Mallika
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: Vildagliptin (VDG)is a frontier drug for diabetes mellitus. It is prescribed both in the monotherapy as well as in an amalgamation with other antidiabetic drugs. Drug-serum protein binding is an essential parameter which influences ADME properties of the drug. In current study, binding of VDG with serum protein (bovine serum albumin: BSA) was investigated using multi-spectroscopic techniques. A computational approach was also employed to identify the binding affinity of VDG with BSA at both Sudlow I and II sites. An enzyme activity assay specific for esterase was also investigated to know the post-binding consequences of VDG with BSA. Fluorescence spectra of BSA samples treated with VDG shows static quenching with binding parameters for VDG-BSA complex show single class of equivalent binding stoichiometry(n = 1.331) and binding constant 1.1 x 104M−1 at 298.15 K. The binding constant indicates important role of non-polar interactions in the binding process. Fluorescence resonance energy transfer (FRET) analysis of VDG absorption spectra and emission spectrum of BSA confirmed no significant resonance in energy transfer. Synchronous fluorescence of BSA after binding with VDG show maximum changes in emission intensity at tryptophan (Trp) residues. Post binding with VDG, BSA conformation changes as suggested by circular dichorism (CD) spectra of BSA and this lead to enhanced protein stability as indicated by a thermal melting curve of BSA. Communicated by Ramaswamy H. Sarma
IMAGO: A family photo album dataset for a socio-historical analysis of the twentieth century
Creators: name: Stacchio, Lorenzo
name: Angeli, Alessia
name: Lisanti, Giuseppe
name: Calanca, Daniela
name: Marfia, Gustavo
Publisher: name: arXiv
Year: 2020
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Computers and Society (cs.CY)
subject: Multimedia (cs.MM)
subject: FOS: Computer and information sciences

description: Although one of the most popular practices in photography since the end of the 19th century, an increase in scholarly interest in family photo albums dates back to the early 1980s. Such collections of photos may reveal sociological and historical insights regarding specific cultures and times. They are, however, in most cases scattered among private homes and only available on paper or photographic film, thus making their analysis by academics such as historians, social-cultural anthropologists and cultural theorists very cumbersome. In this paper, we analyze the IMAGO dataset including photos belonging to family albums assembled at the University of Bologna's Rimini campus since 2004. Following a deep learning-based approach, the IMAGO dataset has offered the opportunity of experimenting with photos taken between year 1845 and year 2009, with the goals of assessing the dates and the socio-historical contexts of the images, without use of any other sources of information. Exceeding our initial expectations, such analysis has revealed its merit not only in terms of the performance of the approach adopted in this work, but also in terms of the foreseeable implications and use for the benefit of socio-historical research. To the best of our knowledge, this is the first work that moves along this path in literature.
Motion compensated images using Rgb data
Creators: name: Jeon, Jin Ah
Publisher: name: University of Nevada, Las Vegas
Year: 1997

description: A motion compensation algorithm correcting not only for translation but also for rotation, scaling, and shearing, is investigated in this thesis. Our work also includes noise detection and noise compensation due to the variation of the light. The probability distribution of the noise is investigated. The variation of the light could occur due to the voltage variation or due to the sunlight variation in the presence of clouds, or other reasons. Practical results have also been obtained by applying our theory to moving pictures.
Dynamical Properties of the Mukhanov-Sasaki Hamiltonian in the context of adiabatic vacua and the Lewis-Riesenfeld invariant
Creators: name: Fahn, Max Joseph
name: Giesel, Kristina
name: Kobler, Michael
Publisher: name: arXiv
Year: 2018
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We use the method of the Lewis-Riesenfeld invariant to analyze the dynamical properties of the Mukhanov-Sasaki Hamiltonian and, following this approach, investigate whether we can obtain possible candidates for initial states in the context of inflation considering a quasi-de Sitter spacetime. Our main interest lies in the question to which extent these already well-established methods at the classical and quantum level for finitely many degrees of freedom can be generalized to field theory. As our results show, a straightforward generalization does in general not lead to a unitary operator on Fock space that implements the corresponding time-dependent canonical transformation associated with the Lewis-Riesenfeld invariant. The action of this operator can be rewritten as a time-dependent Bogoliubov transformation and we show that its generalization to Fock space has to be chosen appropriately in order that the Shale-Stinespring condition is not violated, where we also compare our results to already existing ones in the literature. Furthermore, our analysis relates the Ermakov differential equation that plays the role of an auxiliary equation, whose solution is necessary to construct the Lewis-Riesenfeld invariant, as well as the corresponding time-dependent canonical transformation to the defining differential equation for adiabatic vacua. Therefore, a given solution of the Ermakov equation directly yields a full solution to the differential equation for adiabatic vacua involving no truncation at some adiabatic order. As a consequence, we can interpret our result obtained here as a kind of non-squeezed Bunch-Davies mode, where the term non-squeezed refers to a possible residual squeezing that can be involved in the unitary operator for certain choices of the Bogoliubov map.
description: 40 pages, 5 figures, minor changes: slightly rewrote the introduction, extended the discussion on the infrared modes, corrected typos and added references
Political violence in Argentina during the 1970s
Creators: name: Kazemi, Arya Bardo
Publisher: name: University of Nevada, Las Vegas
Year: 1997

description: The topic of this thesis is a historical study of selected controversial topics within the broader phenomenon of political violence in Argentina during the decade of the 1970s. A historical background from 1930 until 1969 (of the events and political problems in Argentina) which prompted the formation of armed guerrilla movements in order to create political change, is outlined in the first chapter. The growth of the guerrilla movements and the evolution of their respective political ideologies during the years 1970-75 are discussed in the second chapter, which also discusses the relative success of the guerrillas in their armed actions; The third chapter examines the most debated aspects of political violence in Argentina during the 1970s: the legitimacy of the Argentine military's illegal and covert crackdown on "subversion" in the second half of the decade (1975-79). Whether the military's campaign was a random attack against any opposition to the military government, which came to power in March of 1976, or a necessary, publicly supported form of bringing peace back to a country seemingly on the verge of anarchy. Although no definite conclusion can be drawn upon these issues, I raise various estimates and critique each group's methodology; This paper relies heavily on primary sources such as personal interviews and official documents as well as the latest published revelations on the topics which I compiled during my nine month stay in Argentina (January until September, 1995), in order to give a first hand, non-biased perspective on the topic. The conclusion, however, is based partly on my personal observations on the issue of the military's brutal campaign.
Coxeter factorizations with generalized Jucys-Murphy weights and Matrix Tree theorems for reflection groups
Creators: name: Chapuy, Guillaume
name: Douvropoulos, Theo
Publisher: name: arXiv
Year: 2020
Subjects: subject: Combinatorics (math.CO)
subject: Representation Theory (math.RT)
subject: Spectral Theory (math.SP)
subject: FOS: Mathematics
subject: 05E99 (Primary) 05A15, 05C05, 20C99, 20F55, 47A99 (Secondary)

description: We prove universal (case-free) formulas for the weighted enumeration of factorizations of Coxeter elements into products of reflections valid in any well-generated reflection group $W$, in terms of the spectrum of an associated operator, the $W$-Laplacian. This covers in particular all finite Coxeter groups. The results of this paper include generalizations of the Matrix Tree and Matrix Forest theorems to reflection groups, and cover reduced (shortest length) as well as arbitrary length factorizations. Our formulas are relative to a choice of weighting system that consists of $n$ free scalar parameters and is defined in terms of a tower of parabolic subgroups. To study such systems we introduce (a class of) variants of the Jucys-Murphy elements for every group, from which we define a new notion of `tower equivalence' of virtual characters. A main technical point is to prove the tower equivalence between virtual characters naturally appearing in the problem, and exterior products of the reflection representation of $W$. Finally we study how this $W$-Laplacian matrix we introduce can be used in other problems in Coxeter combinatorics. We explain how it defines analogues of trees for $W$ and how it relates them to Coxeter factorizations, we give new numerological identities between the Coxeter number of $W$ and those of its parabolic subgroups, and finally, when $W$ is a Weyl group, we produce a new, explicit formula for the volume of the corresponding root zonotope.
description: v2: 59 pages, Lemma 7.2 corrected
Structures and dynamics of peptide and peptidomimetic inhibitors bound to the NS2B-NS3 protease of the ZIKA virus
Creators: name: Pant, S.
name: Bhattacharya, G.
name: Jena, N.R
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Infections caused by the Zika virus (ZIKV) have detrimental effects on human health, in particular on infants. As no potent drug or vaccine is available to date to contain this viral disease, it is necessary to design inhibitors that can target the NS2B-NS3 protease of the ZIKV, which is mainly responsible for the proliferation of the virus inside the host cells . Here, molecular dynamics (MD) simulation and molecular mechanics energies combined with the generalized Born and surface area continuum solvation model (MM/GBSA) are used to understand the binding modes and stabilities of R, KR, KKR, WKR, WKKR, YKKR, and FKKR peptide inhibitors bound to the NS3-NS2B protease. The results are compared with the corresponding results obtained for covalent (compound 1) and non-covalent (compound 4*) peptidomimetic inhibitors . It is revealed that peptide inhibitors can bind strongly with the ZIKV protease with the ΔGbind ranging from −12 kcal/mol to −73 kcal/mol. Among these peptides, YKKR is found to make the most stable complex with the protease and fully occupy the electrostatically active substrate binding site. Hence, it would inhibit the protease activities of ZIKV strongly. The residue-wise decomposition of ΔGbind indicates that Asp75, Asp129, Tyr130, Ser135, Gly151, Asn152, Glys153, and Tyr161 of NS3 and Ser81, Asp83, and Phe84 of NS2B play a prominent role in the inhibitor binding. Therefore, any future design of inhibitors should be aimed to target these residues. The activities of the NS2B-NS3 protease of the ZIKV can be inhibited by the peptide inhibitor YKKR. Communicated by Ramaswamy H. Sarma
An Old Disk That Can Still Form a Planetary System
Creators: name: Bergin, Edwin A.
name: Cleeves, L. Ilsedore
name: Gorti, Uma
name: Zhang, Ke
name: Blake, Geoffrey A.
name: Green, Joel D.
name: Andrews, Sean M.
name: Evans, Neal J.
name: Henning, Thomas
name: Oberg, Karin
name: Pontoppidan, Klaus
name: Qi, Chunhua
name: Salyk, Colette
name: van Dishoeck, Ewine F.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: From the masses of planets orbiting our Sun, and relative elemental abundances, it is estimated that at birth our Solar System required a minimum disk mass of ~0.01 solar masses within ~100 AU of the star. The main constituent, gaseous molecular hydrogen, does not emit from the disk mass reservoir, so the most common measure of the disk mass is dust thermal emission and lines of gaseous carbon monoxide. Carbon monoxide emission generally probes the disk surface, while the conversion from dust emission to gas mass requires knowledge of the grain properties and gas-to-dust mass ratio, which likely differ from their interstellar values. Thus, mass estimates vary by orders of magnitude, as exemplified by the relatively old (3--10 Myr) star TW Hya, with estimates ranging from 0.0005 to 0.06 solar masses. Here we report the detection the fundamental rotational transition of hydrogen deuteride, HD, toward TW Hya. HD is a good tracer of disk gas because it follows the distribution of molecular hydrogen and its emission is sensitive to the total mass. The HD detection, combined with existing observations and detailed models, implies a disk mass >0.05 solar masses, enough to form a planetary system like our own.
description: 16 pages, 3 figures. Pre-editorial version of paper published in Nature. Full version can be found at http://www.nature.com.proxy.lib.umich.edu/nature/journal/v493/n7434/full/nature11805.html
Targeting two potential sites of SARS-CoV-2 main protease through computational drug repurposing
Creators: name: Prakash, Archisha
name: Borkotoky, Subhomoi
name: Dubey, Vikash Kumar
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Before the rise of SARS-CoV-2, emergence of different coronaviruses such as SARS-CoV and MERS-CoV has been reported that indicates possibility of the future novel pathogen from the coronavirus family at a pandemic level. In this context, explicit studies on identifying inhibitors focused on the coronavirus life cycle, are immensely important. The main protease is critical for the life cycle of coronaviruses. Majority of the work done on the inhibitor studies on the catalytically active dimeric SARS-CoV-2 main protease (Mpro), primarily focussed on the catalytic site of a single protomer, with a few targeting the dimeric site. In this study, we have exploited the FDA-approved drugs, for a computational drug repurposing study against the Mpro. A virtual screening approach was employed with docking and molecular dynamics (MD) methods. Out of 1576, FDA-approved compounds, our study suggests three compounds: netupitant, paliperidone and vilazodone as possible inhibitors with a potential to inhibit both sites (monomeric and dimeric) of the Mpro. These compounds were found to be stable during the MD simulations and their post simulation binding energies were also correlated for both the targeted sites, suggesting equal binding capacity. This unique efficiency of the reported compounds might support further experimental studies on developing inhibitors against SARS-CoV-2 main protease. Communicated by Ramaswamy H. Sarma
Braiding properties of worldline configurations in hardcore lattice bosons
Creators: name: Lingua, Fabio
name: Wang, Wei
name: Shpani, Liana
name: Capogrosso-Sansone, Barbara
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In this manuscript, we study braiding properties of worldline configurations for a variety of ground-states of hardcore Bose-Hubbard models in two dimensions. Configurations are collections of particle paths and result from the path-integral formulation of statistical mechanics. For hard-core bosons, configurations can be seen as geometric braids and therefore can be assigned a certain topological structure, i.e. a way to classify braiding events among worldlines. By means of Monte Carlo calculations, we study superfluid phase and a variety of insulating phases and observe that ground-states of different quantum phases correspond to different probability distributions of braiding properties.
description: 11 pages, 5 figures. The current version focuses on the discussion of braiding properties of worldline configurations. The study of phase transitions and permutation cycles has been moved to a new manuscript: arXiv:1912.00080. The current manuscript has been accepted for publication on Scientific Reports
Autoencoding with a Classifier System
Creators: name: Preen, Richard J.
name: Wilson, Stewart W.
name: Bull, Larry
Publisher: name: arXiv
Year: 2019
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Artificial Intelligence (cs.AI)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Autoencoders are data-specific compression algorithms learned automatically from examples. The predominant approach has been to construct single large global models that cover the domain. However, training and evaluating models of increasing size comes at the price of additional time and computational cost. Conditional computation, sparsity, and model pruning techniques can reduce these costs while maintaining performance. Learning classifier systems (LCS) are a framework for adaptively subdividing input spaces into an ensemble of simpler local approximations that together cover the domain. LCS perform conditional computation through the use of a population of individual gating/guarding components, each associated with a local approximation. This article explores the use of an LCS to adaptively decompose the input domain into a collection of small autoencoders where local solutions of different complexity may emerge. In addition to benefits in convergence time and computational cost, it is shown possible to reduce code size as well as the resulting decoder computational cost when compared with the global model equivalent.
Bayesian statistical framework for identifying strongly lensed gravitational-wave signals
Creators: name: Lo, Rico K. L.
name: Hernandez, Ignacio Magana
Publisher: name: arXiv
Year: 2021
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: It is expected that gravitational waves, similar to electromagnetic waves, can be gravitationally lensed by intervening matters, producing multiple instances of the same signal arriving at different times from different apparent luminosity distances with different phase shifts compared to the un-lensed signal due to lensing. If unaccounted for, these lensed signals will masquerade as separate systems with higher mass and lower redshift. Here we present a Bayesian statistical framework for identifying strongly-lensed gravitational-wave signals that incorporates astrophysical information and accounts for selection effects. We also propose a two-step hierarchical analysis for more efficient computations of the probabilities and inferences of source parameters free from bias introduced by lensing. We show with examples on how changing the astrophysical models could shift one's interpretation on the origin of the observed gravitational waves, and possibly lead to indisputable evidence of strong lensing of the observed waves. In addition, we demonstrate the improvement in the sky localization of the source of the lensed signals, and in some cases the identification of the Morse indices of the lensed signals. If confirmed, lensed gravitational waves will allow us to probe the Universe at higher redshift, and to constrain the polarization contents of the waves with fewer detectors.
description: 26 pages, 14 figures
New styrylquinoxaline: synthesis, structural, biological evaluation, ADMET prediction and molecular docking investigations
Creators: name: Mortada, Salma
name: Missioui, Mohcine
name: Guerrab, Walid
name: Demirtaş, Güneş
name: Mague, Joel T.
name: Faouzi, My El Abbes
name: Ramli, Youssef
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Computational Biology

description: The organic compound (E)-3-(4-methylstyryl)quinoxalin-2(1H)-one (SQO) with molecular formula C17H14N2O was synthesized and analyzed using single crystal X-ray diffraction, 1H, 13C NMR and FTIR spectroscopic techniques. The geometric parameters of the molecule was optimized by density-functional theory (DFT) choosing B3LYP with 6-31++G(d,p) basis set. For compatibility, the theoretical structure and experimental structure were overlapped with each other. Frontier molecular orbitals of the title compound were made, and energy gap between HOMO and LUMO was calculated. Molecular electrostatic potential map was generated finding electrophilic and nucleophilic attack centers using DFT method. Hirshfeld surface analysis (HSA) confirms active regions at the circumference of N1 atoms and O1 atoms that form intermolecular N1—H1···O1 hydrogen bond. The acute oral toxicity study was carried out according to OECD guideline, which approve that the compound SQO was non-toxic. In addition, this quinoxaline derivative was evaluated for its in vitro antidiabetic activity against α-glucosidase and α-amylase enzymes and for antioxidant activity by utilizing several tests as 1,1-diphenyl-2-picryl hydrazyl, (2,2′-azino-bis(3-ethyl benzthiazoline-6-sulfonicacid), reducing power test (FRAP) and hydrogen peroxide activity H2O2. The molecular docking studies were performed to investigate the antidiabetic activity of SQO and compared with the experimental results. SQO is a potent antidiabetic from both the experimental and molecular docking results. Finally, the physicochemical, pharmacokinetic and toxicological properties of SQO have been evaluated by using in silico absorption, distribution, metabolism, excretion and toxicity analysis prediction.
Stein fillable contact 3-manifolds and positive open books of genus one
Creators: name: Lisca, Paolo
Publisher: name: arXiv
Year: 2013
Subjects: subject: Symplectic Geometry (math.SG)
subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57R17, 57R57

description: A two-dimensional open book (S,h) determines a closed, oriented three-manifold Y(S,h) and a contact structure C(S,h) on Y(S,h). The contact structure C(S,h) is Stein fillable if h is positive, i.e. h can be written as a product of right-handed Dehn twists. Work of Wendl implies that when S has genus zero the converse statement holds, that is if C(S,h) is Stein fillable then h is positive. On the other hand, results by Wand and by Baker, Etnyre and Van Horn-Morris imply the existence of counterexamples to the converse statement with S of arbitrary genus strictly greater than one. The main purpose of this paper is to prove the converse statement under the assumption that S is a one-holed torus and Y(S,h) is a Heegaard Floer L-space.
description: 12 pages, 3 figures
Before we can find a model, we must forget about perfection
Creators: name: Dobrev, Dimiter
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (cs.LG)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: With Reinforcement Learning we assume that a model of the world does exist. We assume furthermore that the model in question is perfect (i.e. it describes the world completely and unambiguously). This article will demonstrate that it does not make sense to search for the perfect model because this model is too complicated and practically impossible to find. We will show that we should abandon the pursuit of perfection and pursue Event-Driven (ED) models instead. These models are generalization of Markov Decision Process (MDP) models. This generalization is essential because nothing can be found without it. Rather than a single MDP, we will aim to find a raft of neat simple ED models each one describing a simple dependency or property. In other words, we will replace the search for a singular and complex perfect model with a search for a large number of simple models.
Time-Domain Audio Source Separation Based on Wave-U-Net Combined with Discrete Wavelet Transform
Creators: name: Nakamura, Tomohiko
name: Saruwatari, Hiroshi
Publisher: name: arXiv
Year: 2020
Subjects: subject: Sound (cs.SD)
subject: Machine Learning (cs.LG)
subject: Multimedia (cs.MM)
subject: Audio and Speech Processing (eess.AS)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: We propose a time-domain audio source separation method using down-sampling (DS) and up-sampling (US) layers based on a discrete wavelet transform (DWT). The proposed method is based on one of the state-of-the-art deep neural networks, Wave-U-Net, which successively down-samples and up-samples feature maps. We find that this architecture resembles that of multiresolution analysis, and reveal that the DS layers of Wave-U-Net cause aliasing and may discard information useful for the separation. Although the effects of these problems may be reduced by training, to achieve a more reliable source separation method, we should design DS layers capable of overcoming the problems. With this belief, focusing on the fact that the DWT has an anti-aliasing filter and the perfect reconstruction property, we design the proposed layers. Experiments on music source separation show the efficacy of the proposed method and the importance of simultaneously considering the anti-aliasing filters and the perfect reconstruction property.
description: 5 pages, to appear in IEEE International Conference on Acoustics, Speech, and Signal Processing 2020 (ICASSP 2020)
Parallel and perpendicular turbulence correlation length in the TJ-II Stellarator
Creators: name: van Milligen, B. Ph.
name: Fraguas, A. Lopez
name: Pedrosa, M. A.
name: Hidalgo, C.
name: de Aguilera, A. Martín
name: Ascasíbar, E.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Long range correlations were measured using two remote reciprocating Langmuir probe systems at TJ-II. The influence of the rotational transform on the correlation was studied by scanning the magnetic configuration. A simple drift wave correlation model, assuming an exponential decay of the correlation with different correlation lengths in the directions parallel and perpendicular to the field lines, was found to describe the observations well at low densities. The experiment was repeated at gradually higher densities, and an additional correlation was detected at a critical value of the density. In accordance with previous work, this additional correlation was ascribed to zonal flows associated with a confinement transition. Thus, the total long range correlation is found to be a sum of the drift wave and zonal flow contributions.
description: 15 pages, 8 figures
Random-walk shielding-potential viscosity model for warm dense metals
Creators: name: Cheng, Yuqing
name: Liu, Haifeng
name: Hou, Yong
name: Meng, Xujun
name: Li, Qiong
name: Liu, Yu
name: Gao, Xingyu
name: Yuan, Jianmin
name: Song, Haifeng
name: Wang, Jianguo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We develop a novel model, called the ``random-walk shielding-potential viscosity model'' (RWSP-VM) that introduces the statistics of random-walk ions and the Debye shielding effect to describe the viscosities of warm dense metals. The viscosities of several metals with low to high atomic number (Be, Al, Fe, and U) are calculated using the analytical expression of RWSP-VM. Additionally, we simulate the viscosities of Fe and Be by employing the Langevin molecular dynamics (MD) and classical MD, while the MD data for Al and U are obtained from a previous work. The results of the RWSP-VM are in good agreement with the MD results, which validates the proposed model. Furthermore, we compare the RWSP-VM with the one-component plasma model and Yukawa viscosity model and show that the three models yield results in excellent agreement with each other in the regime where the RWSP-VM is applicable. These results indicate that the RWSP-VM is a universal, accurate, and highly efficient model for calculating the viscosity of metals in the warm dense state. The code of the proposed RWSP-VM is provided, and it is envisaged that it will have broad application prospects in numerous fields.
description: 12 pages, 13 figures
Sorting probability of Catalan posets
Creators: name: Chan, Swee Hong
name: Pak, Igor
name: Panova, Greta
Publisher: name: arXiv
Year: 2020
Subjects: subject: Combinatorics (math.CO)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 05A16, 06A07, 60C05

description: We show that the sorting probability of the Catalan poset} $P_n$ satisfies $δ(P_n)= O \bigl(n^{-5/4}\bigr)$.
description: 10 pages, 6 figures
VIRTUAL REALITY AND ITS POTENTIAL IN IMMERSIVE ENGLISH LANGUAGE LEARNING EXPERIENCES
Creators: name: Abduxalilova, Sevaraxon
name: Tilovxo'jayeva, Asila
name: Yusupova, Gulruxsor
Publisher: name: Zenodo
Year: 2023

description: Virtual Reality (VR) has the potential to revolutionize immersive English language learning experiences. By creating virtual environments that simulate real-life scenarios, VR can provide learners with an immersive and interactive language learning experience. Learners can practice their English skills in a realistic and engaging way, interacting with virtual characters and objects. This technology allows learners to improve their listening, speaking, and communication skills by providing a safe and supportive environment for language practice. VR also offers the opportunity for personalized learning experiences, allowing learners to set their own pace and choose activities that match their learning needs and preferences. Overall, VR has the potential to enhance language learning by providing a dynamic and engaging platform for learners to explore and experience the English language in a unique and interactive way.
Novel min-max reformulations of Linear Inverse Problems
Creators: name: Sheriff, Mohammed Rayyan
name: Chatterjee, Debasish
Publisher: name: arXiv
Year: 2020
Subjects: subject: Optimization and Control (math.OC)
subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: In this article, we dwell into the class of so-called ill-posed Linear Inverse Problems (LIP) which simply refers to the task of recovering the entire signal from its relatively few random linear measurements. Such problems arise in a variety of settings with applications ranging from medical image processing, recommender systems, etc. We propose a slightly generalized version of the error constrained linear inverse problem and obtain a novel and equivalent convex-concave min-max reformulation by providing an exposition to its convex geometry. Saddle points of the min-max problem are completely characterized in terms of a solution to the LIP, and vice versa. Applying simple saddle point seeking ascend-descent type algorithms to solve the min-max problems provides novel and simple algorithms to find a solution to the LIP. Moreover, the reformulation of an LIP as the min-max problem provided in this article is crucial in developing methods to solve the dictionary learning problem with almost sure recovery constraints.