cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Principles of Adaptive Sorting Revealed by In Silico Evolution
Creators: name: Lalanne, Jean-Benoît
name: François, Paul
Publisher: name: arXiv
Year: 2013
Subjects: subject: Molecular Networks (q-bio.MN)
subject: FOS: Biological sciences

description: Many biological networks have to filter out useful information from a vast excess of spurious interactions. We use computational evolution to predict design features of networks processing ligand categorization. The important problem of early immune response is considered as a case-study. Rounds of evolution with different constraints uncover elaborations of the same network motif we name adaptive sorting. Corresponding network substructures can be identified in current models of immune recognition. Our work draws a deep analogy between immune recognition and biochemical adaptation.
description: 50 pages, 28 figures, including supplementary information
title: Das Kochen mit Steinen. Ein Beitrag zur Entwicklungsgeschichte der Nahrungszubereitung. Andreas Dittmann. Marburger Studien zur Völkerkunde Bd. 7. Berlin 1990
Creators: name: Schmidt, Martin
Publisher: name: University Library Heidelberg
Year: 2015

description: Rezension zu: Das Kochen mit Steinen. Ein Beitrag zur Entwicklungsgeschichte der Nahrungszubereitung. Andreas Dittmann. Marburger Studien zur Völkerkunde Bd. 7. Berlin 1990. 357 S. mit 11 Karten, 8 Tabellen und 30 Abb., Brosch.
title: Cranial ultrasound findings in congenital CMV infection
Creators: name: Dewachter, Bram
Publisher: name: EURORAD
Year: 2023
Subjects: subject: Paediatric radiology
subject: Neuroradiology brain
subject: Paediatric
subject: Ultrasound
subject: Clinical Cases

description: Clinical History: A one-month-old girl presented for screening cranial ultrasound because of maternal cytomegalovirus (CMV) seroconversion during first trimester of pregnancy and positive urine PCR at birth. 

Her birth was uncomplicated at 39 weeks and 4 days. At one month of age fundoscopy showed no evidence of CMV-retinopathy and behavioural audiometry was normal.

description: 1 month, female
An inverse spectral problem related to the Geng-Xue two-component peakon equation
Creators: name: Lundmark, Hans
name: Szmigielski, Jacek
Publisher: name: arXiv
Year: 2013
Subjects: subject: Spectral Theory (math.SP)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We solve a spectral and an inverse spectral problem arising in the computation of peakon solutions to the two-component PDE derived by Geng and Xue as a generalization of the Novikov and Degasperis-Procesi equations. Like the spectral problems for those equations, this one is of a 'discrete cubic string' type -- a nonselfadjoint generalization of a classical inhomogeneous string -- but presents some interesting novel features: there are two Lax pairs, both of which contribute to the correct complete spectral data, and the solution to the inverse problem can be expressed using quantities related to Cauchy biorthogonal polynomials with two different spectral measures. The latter extends the range of previous applications of Cauchy biorthogonal polynomials to peakons, which featured either two identical, or two closely related, measures. The method used to solve the spectral problem hinges on the hidden presence of oscillatory kernels of Gantmacher-Krein type implying that the spectrum of the boundary value problem is positive and simple. The inverse spectral problem is solved by a method which generalizes, to a nonselfadjoint case, M. G. Krein's solution of the inverse problem for the Stieltjes string.
description: 78 pages, 7 figures. pdfLaTeX + AMS packages + hyperref + TikZ
Impact of renewable and fossil fuel energy consumption on environmental degradation: evidence from USA by nonlinear approaches
Creators: name: Kartal, Mustafa Tevfik
name: Depren, Serpil Kılıç
name: Ayhan, Fatih
name: Depren, Özer
Publisher: name: Taylor & Francis
Year: 2022
Subjects: 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: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: The study investigates impact of energy consumption on environmental degradation at aggregated and disaggregated levels. In this context, the study considers carbon dioxide (CO2) emissions as proxy of environmental degradation, and focuses on the United States of America (USA) as the biggest economy and highest second carbon-emitting country. Moreover, the study uses monthly data between 1989 January and 2021 September and performs nonlinear approaches as Wavelet Coherence (WC), Granger Causality-in-Quantiles (GCQ), and Quantile-on-Quantile Regression (QQR). Besides, Quantile Regression (QR) is used for robustness checks of the QQR. The results show that (i) energy consumption has an important impact on the CO2 emissions in the short, medium and long term, while the impact changes according to times and frequencies; (ii) causal effect exists in almost all quantiles excluding some lower (0.05, 0.25), middle (0.65, 0.70, 0.75, 0.80) and higher (0.95) quantiles, whereas indicator-based results change a bit; (iii) the QR results confirm that the QQR results are robust; (iv) overall, the effects of the energy consumption indicators change according to times, frequencies, quantiles, and aggregated/disaggregated levels. Hence, the empirical outcomes underline the significance of renewable energy consumption in improving environmental quality through limiting CO2 emissions at aggregated and disaggregated levels. The results imply that the USA policymakers should focus on the efforts the decreasing fossil sources and increasing renewable sources through conversion of energy systems to limit CO2 emissions while considering changing impacts of energy consumption at various times, frequencies, quantiles, and aggregated/disaggregated levels.
title: The Gallo-Roman temple »Auf dem Spätzrech« at Schwarzenbach (Lkr. St. Wendel) in Saarland. A pilgrim shrine for Mars Cnabetius in the civitas Treverorum?
Creators: name: Burger, Daniel
Publisher: name: University Library Heidelberg
Year: 2015

description: Die Aufarbeitung des gallo-römischen Umgangstempels »Auf dem Spätzrech «erbrachte insgesamt vier Bauphasen. Diesen geht ein nicht funktional einzuordnender späteisenzeitlicher Fundhorizont mit einem Schwerpunkt in den Stufen Lt D2a und D2b voraus. Für die erste Bauphase ist ein hölzerner Vorgängerbau ab der zweiten Hälfte des 1. Jahrhunderts nachgewiesen, während in der Mitte des 2. Jahrhunderts von einem Ausbau in Stein ausgegangen werden kann. Die Phasen 3 und 4 sind zeitlich nicht näher zu bestimmen und können lediglich über den Annexbau definiert werden. Ein Bedeutungsverlust der Anlage ist nach der Mitte des 4. Jahrhunderts festzustellen. Aufgrund von vier Marsstatuetten und einer Weiheinschrift an den gallo-römischen Mars Cnabetius kann von einer Hauptverehrung des Gottes Mars bzw. Mars Cnabetius ausgegangen werden. Sowohl die Statuetten von Apollon und Mars als auch verschiedene Funde, darunter mögliche Gliederweihungen, deuten auf einen Heilkult hin. Die Ausdehnung der Anlage lässt weitere Bebauungen und eine gewisse regionale Bedeutung vermuten.
description: Post-excavation work and analysis of the Gallo-Roman temple »Auf dem Spätzrech« concluded in the distinction of four building phases. They are preceded by a functionally not identifiable find horizon of the Late Iron Age mainly from the periods Lt D2a and D2b. For the first building phase a wooden temple from the second half of the 1st century was identified whereas around the middle of the 2nd century a stone building can be assumed. Chronologically the periods 3 and 4 cannot be defined more precisely and are only identified under consideration of the annex building. After the middle of the 4th century a decreasing importance of the construction is notable. Four Mars figurines and a votive inscription to Mars Cnabetius suggest that Mars or Mars Cnabetius was the principal god worshipped here. Figurines of Apollo and Mars as well as various finds among which there are possible votives of parts of the body indicate that a healing cult was practiced. The extension of the complex points to further buildings and a certain regional importance.
GPfit: An R package for Gaussian Process Model Fitting using a New Optimization Algorithm
Creators: name: MacDonald, Blake
name: Ranjan, Pritam
name: Chipman, Hugh
Publisher: name: arXiv
Year: 2013
Subjects: subject: Computation (stat.CO)
subject: FOS: Computer and information sciences

description: Gaussian process (GP) models are commonly used statistical metamodels for emulating expensive computer simulators. Fitting a GP model can be numerically unstable if any pair of design points in the input space are close together. Ranjan, Haynes, and Karsten (2011) proposed a computationally stable approach for fitting GP models to deterministic computer simulators. They used a genetic algorithm based approach that is robust but computationally intensive for maximizing the likelihood. This paper implements a slightly modified version of the model proposed by Ranjan et al. (2011), as the new R package GPfit. A novel parameterization of the spatial correlation function and a new multi-start gradient based optimization algorithm yield optimization that is robust and typically faster than the genetic algorithm based approach. We present two examples with R codes to illustrate the usage of the main functions in GPfit. Several test functions are used for performance comparison with a popular R package mlegp. GPfit is a free software and distributed under the general public license, as part of the R software project (R Development Core Team 2012).
description: 20 pages, 17 images
The Impact of Phonological Biases on Mispronunciation Sensitivity and Novel Accent Adaptation
Creators: name: Von Holzen, Katie
name: van Ommen, Sandrien
name: White, Katherine S.
name: Nazzi, Thierry
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Successful word recognition requires that listeners attend to differences that are phonemic in the language while also remaining flexible to the variation introduced by different voices and accents. Previous work has demonstrated that American-English-learning 19-month-olds are able to balance these demands: although one-off one-feature mispronunciations typically disrupt English-learning toddlers’ lexical access, they no longer do after toddlers are exposed to a novel accent in which these changes occur systematically. The flexibility to deal with different types of variation may not be the same for toddlers learning different first languages, however, as language structure shapes early phonological biases. We examined French-learning 19-month-olds’ sensitivity and adaptation to a novel accent that shifted either the standard pronunciation of /a/ from [a] to [ɛ] (Experiment 1) or the standard pronunciation of /p/ from [p] to [t] (Experiment 2). In Experiment 1, French-learning toddlers recognized words with /a/ produced as [ɛ], regardless of whether they were previously exposed to an accent that contained this vowel shift or not. In Experiment 2, toddlers did not recognize words with /p/ pronounced as [t] at test unless they were first familiarized with an accent that contained this consonant shift. These findings are consistent with evidence that French-learning toddlers privilege consonants over vowels in lexical processing. Together with previous work, these results demonstrate both differences and similarities in how French- and English-learning children treat variation, in line with their language-specific phonological biases.
Щестовицьке городище
Creators: name: Кучера, Михайло
Publisher: name: figshare
Year: 2022
Subjects: Archaeology

description: Кучера, М. П. 1975. Шестовицьке городище. В: Бібіков, С. М. (гол. ред.). Археологія Української РСР. Т. 3. Довженок, В. Й. (відп. ред.). Ранньослов’янський та давньоруський періоди. Ч. 2. Археологія епохи Київської Русі. ІІ: Городища, селища та могильники. Київ: Наукова думка, с. 286–287.
The Influence of Exemplar Variability on Young Children’s Construal of Verb Meaning
Creators: name: Ma, Weiyi
name: Luo, Rufan
name: Golinkoff, Roberta
name: Hirsh-Pasek, Kathy
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Science Policy
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences

description: Verbs serve as the architectural centerpiece of sentences, making verb learning pivotal for language acquisition. Verb learning requires both the formation of a verb-action mapping and the abstraction of relations between an object and its action. Two competing positions have been proposed to explain the process of verb learning: (a) seeing a highly variable range of exemplars allows children to detect and abstract the commonalities across actions—the action invariants; and (b) seeing a less variable range of exemplars enables children to focus on and extract the action invariants. Using manner—a major component of verb meaning in English—as a test case, this study addressed this debate by examining the influence of manner variability on the ability to fast-map new verbs and extend them to novel exemplars in 2-, 3-, and 4-year-old English-speaking children. Results contribute to this debate by showing that high manner variability hindered fast-mapping but facilitated extension to manner variations in the 2- and 3-year-olds. Thus, high exemplar variability may affect verb fast-mapping and extension differently. Furthermore, manner variability did not affect 4-year-olds’ (or adults’) fast-mapping or extension, suggesting that the influence of exemplar variability on verb learning attenuates with age. Finally, manner variability did not affect agent or object extension, revealing a component-specific effect of exemplar variability on verb extension.
Metamaterial Loadings for Waveguide Miniaturization
Creators: name: Odabasi, H.
name: Teixeira, F. L.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Classical Physics (physics.class-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We show that a rectangular metallic waveguide loaded with metamaterial elements consisting of electric-field coupled (ELC) resonators placed at the side walls can operate well below the cutoff frequency of the respective unloaded waveguide. The dispersion diagrams indicate that propagating modes in ELC-loaded waveguides are of forward-type for both TE and TM modes. We also study the dispersion diagram and transmission characteristics of rectangular metallic waveguides simultaneously loaded with ELCs and split ring resonators (SRRs). Such doubly-loaded waveguides can support both forward wave and backward waves, and provide independent control of the propagation characteristics for the respective modes.
description: 13 pages, 7 figures
An ontology-based approach to relax traffic regulation for autonomous vehicle assistance
Creators: name: Morignot, Philippe
name: Nashashibi, Fawzi
Publisher: name: arXiv
Year: 2012
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Traffic regulation must be respected by all vehicles, either human- or computer- driven. However, extreme traffic situations might exhibit practical cases in which a vehicle should safely and reasonably relax traffic regulation, e.g., in order not to be indefinitely blocked and to keep circulating. In this paper, we propose a high-level representation of an automated vehicle, other vehicles and their environment, which can assist drivers in taking such "illegal" but practical relaxation decisions. This high-level representation (an ontology) includes topological knowledge and inference rules, in order to compute the next high-level motion an automated vehicle should take, as assistance to a driver. Results on practical cases are presented.
Computational attributes of protein kinase-C gamma C2-domain & virtual screening for small molecules: elucidation from meta-dynamics simulations & free-energy calculations
Creators: name: Singh, Harvinder
name: Raja, Anupam
name: Shekhar, Nishant
name: Chauhan, Arushi
name: Prakash, Ajay
name: Avti, Pramod
name: Medhi, Bikash
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Epilepsy, a moderate to chronic neuropathological condition, is induced by the acute blockage of synaptic and voltage-gated inhibitory conduction or through the activation of synaptic and voltage-gated excitatory conduction. The regulation of long-term potentiation (LTP) is important in the regulation of epileptic events, and its activity is linked to specific protein kinases. The PKC-γ subtype is a vaguely explored therapeutic target for neurological disorders, but in selected studies, it is proven to be a critical intermediate protein in LTP. This study utilized computational modelling approaches including receptor-based docking, QSAR followed by explicit binding score assessment method MM/GBSA, MM/PBSA (EDA) and MTD simulation-based FES iteration. This was performed to virtually screen the small molecule libraries, which comprised about 2.79 lacs compounds against the Ca2+-binding site of the PKC-γ-C2 regulatory domain. The screened molecules LIG-41 ([4-Oxo-4-(4-phenylmethoxyanilino) butyl] azanium) and LIG-16 (Emixustat) exhibit overall optimal attributes in the above-mentioned parameters. The two leads are expected to inhibit the Ca2+-mediated PKC-γ activity. Communicated by Ramaswamy H. Sarma
Городище на хут. Половецькому
Creators: name: Кучера, Михайло
Publisher: name: figshare
Year: 2019
Subjects: Archaeology

description: Кучера, М. П. 1975. Городище на хут. Половецькому. В: Бібіков, С. М. (гол. ред.). Археологія Української РСР. Т. 3. Довженок, В. Й. (відп. ред.). Ранньослов’янський та давньоруський періоди. Ч. 2. Археологія епохи Київської Русі. ІІ: Городища, селища та могильники. Київ: Наукова думка, с. 287–288.
Prospects for the use of macrocyclic photosensitizers for inactivation of SARS-CoV-2: selection of compounds leaders based on the molecular docking data
Creators: name: Gubarev, Yury A.
name: Lebedeva, Natalia Sh.
name: Yurina, Elena S.
name: Mamardashvili, Galina M.
name: Zaitceva, Svetlana V.
name: Zdanovich, Sergey A.
name: Koifman, Oskar I.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: 60506 Virology

description: The treatment of coronavirus COVID-19, like other viral diseases, is currently underdeveloped. This fact necessitates the search for new drugs and treatment methods that will effectively disrupt the life cycle of the virus. A big problem in the therapy of viral diseases is the ability of viruses to evade the host's immune response. We suppose that the search for drugs that can change the evasiveness of the virus from the immune response of the host is a very promising strategy, as it can help the body to cope with the infection. Protein SARS-CoV-2 ORF8 is one of the key proteins that can suppress antiviral immunity. This paper considers the available information on the structure and functioning of ORF8, as well as the results of molecular docking of ORF8 to a wide range of tetrapyrrole macroheterocyclic compounds capable of generating reactive oxygen species upon photoirradiation. This principle of photoinactivation of biosubstrates underlies the methods of photodynamic therapy of cancer. Application of photoinactivation of drug-resistant forms of bacteria and some viruses can be useful in the fight against COVID-19 and other viral infections. In this work, the structure of ORF8 complexes with macrocyclic compounds is considered in detail, the dependence of their binding affinity on the nature of macrocycles and the nature of peripheral substituents is analyzed and spectral studies of the binding of ORF8 to chlorin is performed. This paper is a part of a large project to investigate the possibility of using macrocyclic compounds for the treatment of viral diseases. Communicated by Ramaswamy H. Sarma
Generating far-field orbital angular momenta from near-field optical chirality
Creators: name: Gorodetski, Yuri
name: Drezet, Aurélien
name: Genet, Cyriaque
name: Ebbesen, Thomas W.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We demonstrate that nanostructures carefully designed on both sides of a thin suspended metallic membrane couple light into a chiral near field and transmit vortex beams through a central aperture that connects the two sides of the membrane. We show how far-field orbital angular momentum (OAM) indices can be tailored through nanostructure designs. We reveal the crucial importance of OAM selection rules imposed by the central aperture and derive OAM summation rules in perfect agreement with experimental data.
description: 5 pages, 4 figures
Stationary States and Asymptotic Behaviour of Aggregation Models with Nonlinear Local Repulsion
Creators: name: Burger, Martin
name: Fetecau, Razvan
name: Huang, Yanghong
Publisher: name: arXiv
Year: 2013
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We consider a continuum aggregation model with nonlinear local repulsion given by a degenerate power-law diffusion with general exponent. The steady states and their properties in one dimension are studied both analytically and numerically, suggesting that the quadratic diffusion is a critical case. The focus is on finite-size, monotone and compactly supported equilibria. We also investigate numerically the long time asymptotics of the model by simulations of the evolution equation. Issues such as metastability and local/ global stability are studied in connection to the gradient flow formulation of the model.
Concept of Separation Management for UAS in the U-space
Creators: name: Claramunt-Puchol, Cecilia
name: Vera-Vélez, Norberto
name: Balbastre-Tejedor, Juan Vicente
Publisher: name: Zenodo
Year: 2022
Subjects: separation management
U-space
UTM
separation minima
TLS
Target Level of Safety
UAS
Drone
SESAR

description: This document describes the Concept of Operations (ConOps) of a separation management service in the U-space. The document contains the final version of the ConOps developed to capture the conclusions drawn from the BUBBLES workshops, as well as from the validation exercises and to define BUBBLES as a SESAR solution, following the indications provided by SJU. In addition to that, this document covers the review of the BUBBLES SESAR solution for separation management that the research team conducted to align it with the guidelines from the SESAR ConOps Coordination Cell. Lastly, this document also updates the regulatory context described in previous editions by addressing the impact of the Implementing Regulation (IR) published by the European Commission in April 2021 (CIR 2021/664, CIR 2021/665 and CIR 2021/666).
A stochastic diffusion process for the Dirichlet distribution
Creators: name: Bakosi, J.
name: Ristorcelli, J. R.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mathematical Physics (math-ph)
subject: Probability (math.PR)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: G.3
subject: 60G10

description: The method of potential solutions of Fokker-Planck equations is used to develop a transport equation for the joint probability of N coupled stochastic variables with the Dirichlet distribution as its asymptotic solution. To ensure a bounded sample space, a coupled nonlinear diffusion process is required: the Wiener-processes in the equivalent system of stochastic differential equations are multiplicative with coefficients dependent on all the stochastic variables. Individual samples of a discrete ensemble, obtained from the stochastic process, satisfy a unit-sum constraint at all times. The process may be used to represent realizations of a fluctuating ensemble of N variables subject to a conservation principle. Similar to the multivariate Wright-Fisher process, whose invariant is also Dirichlet, the univariate case yields a process whose invariant is the beta distribution. As a test of the results, Monte-Carlo simulations are used to evolve numerical ensembles toward the invariant Dirichlet distribution.
description: Accepted in International Journal of Stochastic Analysis, March 1, 2013
Identification of dual active sites in Caenorhabditis elegans GANA-1 protein: an ortholog of the human α-GAL a and α-NAGA enzymes
Creators: name: Cheong, Clerance Su Yee
name: Khan, Shafi Ullah
name: Ahmed, Nafees
name: Narayanan, Kumaran
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Fabry disease (FD) is caused by a defective α-galactosidase A (α-GAL A) enzyme responsible for breaking down globotriaosylceramide (Gb3). To develop affordable therapeutics, more effort is needed to obtain insights into the underlying mechanism of FD and understanding human α-GAL A structure and function in related animal models. We adopted C. elegans as a model to elucidate the sequence and 3D structure of its GANA-1 enzyme and compared it to human α-GAL A. We constructed GANA-1 3D structure by homology modelling and validated the quality of the predicted GANA-1 structure, followed by computational docking of human ligands. The GANA-1 protein shared sequence similarities up to 42.1% with the human α-GAL A in silico and had dual active sites. GANA-1 homology modelling showed that 11 out of 13 amino acids in the first active site of GANA-1 protein overlapped with the human α-GAL A active site, indicating the prospect for substrate cross-reaction. Computational molecular docking using human ligands like Gb3 (first pocket), 4-nitrophenyl-α-D-galactopyranoside (second pocket), α-galactose (second pocket), and N-acetyl-D-galactosamine (second pocket) showed negative binding energy. This revealed that the ligands were able to bind within both GANA-1 active sites, mimicking the human α-GAL A and α-NAGA enzymes. We identified human compounds with adequate docking scores, predicting robust interactions with the GANA-1 active site. Our data suggested that the C. elegans GANA-1 enzyme may possess structural and functional similarities to human α-GAL A, including an intrinsic capability to metabolize Gb3 deposits. Communicated by Ramaswamy H. Sarma
Weak turbulence in two-dimensional magnetohydrodynamics
Creators: name: Tronko, Natalia
name: Nazarenko, Sergey V.
name: Galtier, Sebastien
Publisher: name: arXiv
Year: 2012
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: A weak wave turbulence theory is developed for two-dimensional (2D) magnetohydrodynamics (MHD). We derive and analyze the kinetic equation describing the three-wave interactions of pseudo-Alfvén waves. Our analysis is greatly helped by the fortunate fact that in 2D the wave-kinetic equation is integrable. In contrast with the 3D case, in 2D the wave interactions are nonlocal. Another distinct feature is that strong derivatives of spectra tend to appear in the region of small parallel (i.e. along the uniform magnetic field direction) wavenumbers leading to a breakdown of the weak turbulence description in this region. We develop a qualitative theory beyond weak turbulence describing subsequent evolution and formation of a steady state.
The Eclipsing Binary Cepheid OGLE-LMC-CEP-0227 in the Large Magellanic Cloud: pulsation modelling of light and radial velocity curves
Creators: name: Marconi, M.
name: Molinaro, R.
name: Bono, G.
name: Pietrzynski, G.
name: Gieren, W.
name: Pilecki, B.
name: Stellingwerf, R. F.
name: Graczyk, D.
name: Smolec, R.
name: Konorski, P.
name: Suchomska, K.
name: Gorski, M.
name: Karczmarek, P.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We performed a new and accurate fit of light and radial velocity curves of the Large Magellanic Cloud (LMC) Cepheid --OGLE-LMC-CEP-0227-- belonging to a detached double-lined eclipsing binary system. We computed several sets of nonlinear, convective models covering a broad range in stellar mass, effective temperature and in chemical composition. The comparison between theory and observations indicates that current theoretical framework accounts for luminosity --V and I band-- and radial velocity variations over the entire pulsation cycle. Predicted pulsation mass --M=4.14+-0.06 Mo-- and mean effective temperature --Te=6100+-50 K-- do agree with observed estimates with an accuracy better than 1 sigma. The same outcome applies, on average, to the luminosity amplitudes and to the mean radius. We find that the best fit solution requires a chemical composition that is more metal--poor than typical LMC Cepheids (Z=0.004 vs 0.008) and slightly helium enhanced (Y=0.27 vs 0.25), but the sensitivity to He abundance is quite limited. Finally, the best fit model reddening --E(V-I)=0.171+-0.015 mag-- and the true distance modulus corrected for the barycenter of the LMC --mu_{0,LMC}=18.50+-0.02+-0.10 (syst) mag--, agree quite well with similar estimates in the recent literature.
description: Accepted for publication on Astrophysical Journal Letters
Evidence for a high pKa of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach
Creators: name: Capone, Matteo
name: Zanetti-Polzi, Laura
name: Leonzi, Ilenia
name: Spreti, Nicoletta
name: Daidone, Isabella
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
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
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Computational Biology

description: Candida antarctica Lipase B (CALB) is a paradigm for the family of lipases. At pH 7, the optimal pH for catalysis, the protonation state of an aspartic acid of the active site (Asp134) could not be conclusively assigned. In fact, the pKa estimate provided by a widely used computational tool, namely PropKa, that predicts pKa values of ionizable groups in proteins based on the crystallographic structure, is only slightly above 7 (pKa = 7.25). This, along with the lack of an experimental evaluation, makes the assignment of its protonation state at neutral pH challenging. Here, we calculate the pKa of Asp134 by means of a fully atomistic multiscale computational approach based on classical molecular dynamics (MD) simulation and the perturbed matrix method (PMM), namely the MD-PMM approach. MD-PMM is able to take into account the dynamics of the system and, at the same time, to treat the deprotonation step at the quantum level. The calculations provide a pKa value of 8.9 ± 1.1, hence suggesting that Asp134 in CALB should be protonated at neutral, and even at slightly basic, pH. Communicated by Ramaswamy H. Sarma
Загальна характеристика городищ
Creators: name: Кучера, Михайло
Publisher: name: figshare
Year: 2022
Subjects: Archaeology

description: Кучера, М. П. 1975. Загальна характеристика городищ. В: Бібіков, С. М. (гол. ред.). Археологія Української РСР. Т. 3. Довженок, В. Й. (відп. ред.). Ранньослов’янський та давньоруський періоди. Ч. 2. Археологія епохи Київської Русі. ІІ: Городища, селища та могильники. Київ: Наукова думка, с. 289–295.
title: Die App „Weltbrand 1914“ der SUB Hamburg – Ein Werkstattbericht
Creators: name: Trapp, Markus
Publisher: name: University Library Heidelberg
Year: 2015

description: Wie kommt eine wissenschaftliche Bibliothek dazu, eine App entwickeln zu lassen, auf der 100 Jahre alte Zeitungsseiten der Hamburger Nachrichten gelesen werden können, in denen auf Volltextebene recherchiert werden kann und die einen Einblick in Fotos gibt, die zu Beginn des Ersten Weltkrieges veröffentlicht wurden? Wie ist die Vorgeschichte der Tablet-App für iOS und Android, wie ist die SUB Hamburg an diese Aufgabe herangegangen und wie hat sie das Projekt zusammen mit dem Hamburger Softwareunternehmen CCS realisiert? Auf diese Fragen gibt der folgende Werkstattbericht eine Antwort und liefert auch ein erstes persönliches Zwischenfazit von einem der Projektbeteiligten.
description: Informationspraxis, Bd. 1, Nr. 1 (2015), Beginn und Erscheinungsfrequenz: Nummer: 1, Jahr: 2014, Ausgaben pro Band: 4, Bände pro Jahr: 1
Energy-conserving discontinuous Galerkin methods for the Vlasov-Ampère system
Creators: name: Cheng, Yingda
name: Christlieb, Andrew J.
name: Zhong, Xinghui
Publisher: name: arXiv
Year: 2013
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: In this paper, we propose energy-conserving numerical schemes for the Vlasov-Ampère (VA) systems. The VA system is a model used to describe the evolution of probability density function of charged particles under self consistent electric field in plasmas. It conserves many physical quantities, including the total energy which is comprised of the kinetic and electric energy. Unlike the total particle number conservation, the total energy conservation is challenging to achieve. For simulations in longer time ranges, negligence of this fact could cause unphysical results, such as plasma self heating or cooling. In this paper, we develop the first Eulerian solvers that can preserve fully discrete total energy conservation. The main components of our solvers include explicit or implicit energy-conserving temporal discretizations, an energy-conserving operator splitting for the VA equation and discontinuous Galerkin finite element methods for the spatial discretizations. We validate our schemes by rigorous derivations and benchmark numerical examples such as Landau damping, two-stream instability and bump-on-tail instability.
Drug repurposing against the RNA-dependent RNA polymerase domain of dengue serotype 3 by virtual screening and molecular dynamics simulations
Creators: name: Gangopadhyay, Aditi
name: Saha, Achintya
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
subject: Cancer

description: Dengue is an arboviral disease caused by the dengue flavivirus. The NS5 protein of flaviviruses is a potential therapeutic target, and comprises an RNA-dependent RNA polymerase (RDRP) domain that catalyses viral replication. The aim of this study was to repurpose FDA-approved drugs against the RDRP domain of dengue virus serotype 3 (DENV3) using structure-based virtual screening and molecular dynamics (MD) simulations. The FDA-approved drugs were screened against the RDRP domain of DENV3 using a two-step docking-based screening approach with Glide SP and Glide XP. For comparison, four reported DENV3 RDRP inhibitors were docked as standards. The hitlist was screened based on the docking score of the inhibitor with the lowest docking score (PubChem ID: 118797902; reported IC50 value: 0.34 µM). Five hits with docking scores and Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) energy lower than those of 118797902 were selected. The stability of the hit-receptor complexes was investigated using 100 ns MD simulations in an explicit solvent. The results of MD simulations demonstrated that polydatin and betiatide remained stably bound to the receptor, and formed stable interactions with the RDRP domain of DENV3. The hit-receptor interactions were comparable to those of 118797902. The average Prime MM-GBSA energy of polydatin and betiatide was lower than that of 118797902 during simulation, indicating that their binding affinity to DENV3 RDRP was higher than that of the standard. The results of this study may aid in the development of serotype-selective drugs against dengue in the future. Communicated by Ramaswamy H. Sarma
Energy levels of Th+ between 7.3 and 8.3 eV
Creators: name: Herrera-Sancho, O. A.
name: Nemitz, N.
name: Okhapkin, M. V.
name: Peik, E.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Using resonant two-step laser excitation of trapped 232Th+ ions, we observe 43 previously unknown energy levels within the energy range from 7.3 to 8.3 eV. The high density of states promises a strongly enhanced electronic bridge excitation of the 229mTh nuclear state that is expected in this energy range. From the observation of resonantly enhanced three-photon ionization of Th+, the second ionization potential of thorium can be inferred to lie within the range between 11.9 and 12.3 eV. Pulsed laser radiation in a wide wavelength range from 237 to 289 nm is found to provide efficient photodissociation of molecular ions that are formed in reactions of Th+ with impurities in the buffer gas, leading to a significantly increased storage time for Th+ in the ion trap.
description: 7 pages, 6 figures
Towards community standards in Adaptive Feedback Microscopy
Creators: name: Balazs, B.
name: Bischof, J.
name: Camacho, R.
name: Gunkel, M.
name: Halavatyi, A.
name: Norlin, N.
name: Pfander, C.
name: Schaden, H.
name: Sisamakis, E.
name: Tewinkel, M.
name: Thomas, L.
Publisher: name: Zenodo
Year: 2023
Subjects: feedback microscopy
smart microscopy
adaptive feedback microscopy
microscope controle

description: While there are several software solutions for microscopy control that can be used to implement smart-microscopy workflows, there is no reference specification on what functionalities are needed, or how these workflows could be implemented. To facilitate the development of smart-microscopy applications, and enable their execution across imaging-systems with similar modalities, we, the Smart Microscopy Working Group, are working to establish such a standard specification and to put forth desired workflows, then in dialog we find functionality requirements, reach common terminologies, and share these with the community for feedback and improvement. The working group is composed of participants from both academia and industry, meeting regularly online with the support of the Euro-BioImaging Industry Board.
description: The poster was presented at ELMI 2023 in Noordwijk, Netherlands.
title: Wohl dem, der Gönner hat! Zum Neuankauf eines Roentgen-Möbels durch den Fördererkreis
Creators: name: Krutisch, Petra
Publisher: name: University Library Heidelberg
Year: 2015

description: KulturGut : aus der Forschung des Germanischen Nationalmuseums, Nr. 2 (2004): KulturGut : aus der Forschung des Germanischen Nationalmuseums, Beginn und Erscheinungsfrequenz: Jahr: 2004
title: Modischer Durchblick. Designer-Damenbrillen der achtziger Jahre als Neuzugänge
Creators: name: Korbacher, Dagmar
Publisher: name: University Library Heidelberg
Year: 2015

description: KulturGut : aus der Forschung des Germanischen Nationalmuseums, Nr. 3 (2004): KulturGut : aus der Forschung des Germanischen Nationalmuseums, Beginn und Erscheinungsfrequenz: Jahr: 2004
Identification of phytochemicals from Eclipta alba and assess their potentiality against Hepatitis C virus envelope glycoprotein: virtual screening, docking, and molecular dynamics simulation study
Creators: name: Moharana, Maheswata
name: Pattanayak, Subrat Kumar
name: Khan, Fahmida
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
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
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Hepatitis C virus has a major role in spreading chronic liver disease and hepatocellular carcinoma. Factors such as high costs, pharmacological side effects, and the development of drug resistance strains require the development of new and potentially effective antiviral to treat the various stages of Hepatitis C. Bioactive chemicals have been extracted from medicinal plants and are utilized by humans for the goal of maintaining a healthy lifestyle. The goal of this work is to recognize phytochemicals from Eclipta alba and assess their potentiality activity against the hepatitis C virus envelope glycoprotein using in silico approaches. Phytochemicals from Eclipta alba were virtually screened by Auto dock raccoon and 12 compounds were selected for molecular docking to probe the active binding site. The top two compounds based on the binding score like ecliptalbine and oleanolic acid with HCV E2 glycoprotein exhibit binding energy −8.88 and −8.02 kcal/mol, respectively. The chemicals' usefulness was reinforced by positive pharmacokinetic data. The phytocompounds were identified as potent HCV inhibitors based on the drug likeness and ADMET properties. Both ecliptalbine and oleanolic acid underwent molecular dynamics simulations to determine features such as RMSD, RMSF, SASA, hydrogen-bond number, and MM-PBSA-based binding free energy. From the molecular docking and molecular dynamics simulation study revealed that oleanolic acid obtained from Eclipta alba can be used as inhibitors against Hepatitis C. The identified inhibitor from our study will be study in vitro and in vivo studies to check their efficacy against Hepatitis C. Communicated by Ramaswamy H. Sarma
title: Bezwungene Dämonen. Zwei Konsolen von der Nürnberger Sebalduskirche
Creators: name: Kammel, Frank Matthias
Publisher: name: University Library Heidelberg
Year: 2015

description: KulturGut : aus der Forschung des Germanischen Nationalmuseums, Nr. 4 (2005): KulturGut : aus der Forschung des Germanischen Nationalmuseums, Beginn und Erscheinungsfrequenz: Jahr: 2004
Селища
Creators: name: Кучера, Михайло
Publisher: name: figshare
Year: 2019
Subjects: Archaeology

description: Кучера, М. П. 1975. Селища. В: Бібіков, С. М. (гол. ред.). Археологія Української РСР. Т. 3. Довженок, В. Й. (відп. ред.). Ранньослов’янський та давньоруський періоди. Ч. 2. Археологія епохи Київської Русі. ІІ: Городища, селища та могильники. Київ: Наукова думка, с. 295–297.
title: Inhalt / Aktuelle Ausstellungen / Impressum
Creators: name: Redaktion, Die
Publisher: name: University Library Heidelberg
Year: 2015

description: KulturGut : aus der Forschung des Germanischen Nationalmuseums, Nr. 6 (2005): KulturGut : aus der Forschung des Germanischen Nationalmuseums, Beginn und Erscheinungsfrequenz: Jahr: 2004
An Examination of the Spectral Variability in NGC 1365 with Suzaku
Creators: name: Brenneman, L. W.
name: Risaliti, G.
name: Elvis, M.
name: Nardini, E.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present jointly analyzed data from three deep Suzaku observations of NGC 1365. These high signal-to-noise spectra enable us to examine the nature of this variable, obscured AGN in unprecedented detail on timescales ranging from hours to years. We find that, in addition to the power-law continuum and absorption from ionized gas seen in most AGN, inner disk reflection and variable absorption from neutral gas within the Broad Emission Line Region are both necessary components in all three observations. We confirm the clumpy nature of the cold absorbing gas, though we note that occultations of the inner disk and corona are much more pronounced in the high-flux state (2008) than in the low-flux state (2010) of the source. The onset and duration of the "dips" in the X-ray light curve in 2010 are both significantly longer than in 2008, however, indicating that either the distance to the gas from the black hole is larger, or that the nature of the gas has changed between epochs. We also note significant variations in the power-law flux over timescales similar to the cold absorber, both within and between the three observations. The warm absorber does not vary significantly within observations, but does show variations in column density of a factor of more than 10 on timescales less than 2 weeks that seem unrelated to the changes in the continuum, reflection or cold absorber. By assuming a uniform iron abundance for the reflection and absorption, we have also established that an iron abundance of roughly 3.5 times the solar value is sufficient to model the broad-band spectrum without invoking an additional partial-covering absorber. Such a measurement is consistent with previous published constraints from the 2008 Suzaku observation alone, and with results from other Seyfert AGN in the literature.
description: 19 pages, 11 figures, accepted for publication in MNRAS