cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Overdamped stochastic thermodynamics with multiple reservoirs
Creators: name: Murashita, Yûto
name: Esposito, Massimiliano
Publisher: name: arXiv
Year: 2016
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: After establishing stochastic thermodynamics for underdamped Langevin systems in contact with multiple reservoirs, we derive its overdamped limit using timescale separation techniques. The overdamped theory is different from the naive theory that one obtains when starting from overdamped Langevin or Fokker-Planck dynamics and only coincide with it in presence of a single reservoir. The reason is that the coarse-grained fast momenta dynamics reaches a nonequilibrium state which conducts heat in presence of multiple reservoirs. The underdamped and overdamped theory are both shown to satisfy fundamental fluctuation theorems. Their predictions for the heat statistics are derived analytically for a Brownian particle on a ring in contact with two reservoirs and subjected to a non-conservative force and are shown to coincide in the long-time limit.
description: 18 pages, 1 figure
Electronic and structural study of T315I mutated form in DFG-out conformation of BCR-ABL inhibitors
Creators: name: Pereira, Washington A.
name: Nascimento, Érica C. M.
name: Martins, João B. L.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Hematology

description: In this work, the four main drugs for the treatment of chronic myeloid leukemia were analyzed, being imatinib, dasatinib, nilotinib and ponatinib followed by four derivative molecules of nilotinib and ponatinib. For these derivative molecules, the fluorine atoms were replaced by hydrogen and chlorine atoms in order to shade light to the structural effects on this set of inhibitors. Electronic studies were performed at density functional theory level with the B3LYP functional and 6-311+G(d,p) basis set. The frontier molecular orbitals, gap HOMO-LUMO, and NBO were analyzed and compared to docking studies for mutant T315I tyrosine kinase protein structure code 3IK3, in the DFG-out conformation. Structural similarities were pointed out, such as the presence of groups common to all inhibitors and modifications raised up on new generations of imatinib-based inhibitors. One of them is the trifluoromethyl group present in nilotinib and later included in ponatinib, in addition to the 1-methylpiperazin-1-ium group that is present in imatinib and ponatinib. The frontier molecular orbitals of imatinib and ponatinib are contributing to the same amino acid residues, and the ineffectiveness of imatinib against the T315I mutation was discussed. Communicated by Ramaswamy H. Sarma.
Laser-Induced Electron Diffraction: Alignment Defects and Symmetry Breaking
Creators: name: Nguyen-Dang, T. T.
name: Peters, M.
name: Viau-Trudel, J.
name: Couture-Bienvenue, E.
name: Puthumpally-Joseph, R.
name: Charron, E.
name: Atabek, O.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The fringe pattern that allows geometrical and orbital structure information to be extracted from LIED spectra of symmetric molecules is shown to reflect a symmetry conservation principle. We show that under a field polarization which preserves certain symmetry elements of the molecule, the symmetry character of the initial wave function is conserved during its time-evolution. We present a symmetry analysis of a deviation from a perfect alignment by decomposing the field into a major, symmetry-determining part, and a minor, symmetry breaking, part. This decomposition leads to a corresponding factorization of the time-evolution operator. The formalism is applied to the analysis of the robustness of LIED readings and inversions with respect to deviations from a perfect perpendicular and parallel alignment of a symmetric ABA triatomic molecule. The results indicate a particularly strong stability of the type of LIED spectra associated with the perpendicular alignment situation.
Superior thermal conductivity in suspended bilayer hexagonal boron nitride
Creators: name: Wang, Chengru
name: Guo, Jie
name: Dong, Lan
name: Aiyiti, Adili
name: Xu, Xiangfan
name: Li, Baowen
Publisher: name: arXiv
Year: 2016
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We reported the basal-plane thermal conductivity in exfoliated bilayer hexagonal boron nitride h-BN that was measured using suspended prepatterned microstructures. The h-BN sample suitable for thermal measurements was fabricated by dry-transfer method, whose sample quality, due to less polymer residues on surfaces, is believed to be superior to that of PMMA-mediated samples. The measured room temperature thermal conductivity is around 484 Wm-1K-1(+141 Wm-1K-1/ -24 Wm-1K-1) which exceeds that in bulk h-BN, providing experimental observation of the thickness-dependent thermal conductivity in suspended few-layer h-BN.
description: 10 pages, 3 figures
Production and dynamics of positrons in ultrahigh intensity laser-foil interactions
Creators: name: Kostyukov, I. Yu.
name: Nerush, E. N.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: The electron-positron pair production accompanying interaction of a circularly polarized laser pulse with a foil is studied for laser intensities higher than $10^{24}$W cm$^{-2}$. The laser energy penetrates into the foil due to the effect of the relativistic hole-boring. It is demonstrated that the electron-positron plasma is produced as a result of quantum-electrodynamical cascading in the field of the incident and reflected laser light in front of the foil. The incident and reflected laser light makes up the circularly polarized standing wave in the reference frame of the hole-boring front and the pair density peaks near the nodes and antinodes of the wave. A model based on the particle dynamics with radiation reaction effect near the magnetic nodes is developed. The model predictions are verified by 3D PIC-MC simulations.
Surface modification of prostheses
Creators: name: Gross, Karlis A.
Publisher: name: Monash University
Year: 2022

description: This thesis was scanned from the print manuscript for digital preservation and is copyright the author.
 Researchers can access this thesis by asking their local university, institution or public library to
 make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.
Heavy Exotic Molecules with Charm and Bottom
Creators: name: Liu, Yizhuang
name: Zahed, Ismail
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We revisit the formation of pion-mediated heavy-light exotic molecules with both charm and bottom and their chiral partners under the general strictures of both heavy-quark and chiral symmetry. The chiral exotic partners with good parity formed using the $(0^+, 1^+)$ multiplet are about twice more bound than their primary exotic partners formed using the $(0^-,1^-)$ multiplet. The chiral couplings across the multiplets $(0^\pm, 1^\pm)$ cause the chiral exotic partners to unbind, and the primary exotic molecules to be about twice more bound, for $J\leq 1$. Our multi-channel coupling results show that only the charm isosinglet exotic molecules with $J^{PC}=1^{++}$ binds, which we identify as the reported neutral $X(3872)$. Also, the bottom isotriplet exotic with $J^{PC}=1^{+-}$ binds, which we identify as a mixture of the reported charged exotics $Z^+_b(10610)$ and $Z^+_b(10650)$. The bound isosinglet with $J^{PC}=1^{++}$ is suggested as a possible neutral $X_b(10532)$ not yet reported.
description: 10 pages, 9 figures
New imino-methoxy derivatives: design, synthesis, characterization, antimicrobial activity, DNA interaction and molecular docking studies
Creators: name: Onur, Sultan
name: Çeşme, Mustafa
name: Köse, Muhammet
name: Tümer, Ferhan
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Space Science
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Microbiology
subject: FOS: Biological sciences
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

description: Four new diarylmethylamine imine compounds (5a-5d) were prepared in order to examine their DNA binding properties, antimicrobial activity and molecular docking. The compounds were characterized by the common spectroscopic and analytic methods. Furthermore, solid-state structure of compounds 5a and 5c were determined by single-crystal X-ray diffraction studies. The compounds were then investigated for their DNA binding properties employing UV absorption, fluorescence spectroscopy under the physiological pH condition Tris-HCl buffer at pH 7.4. The compounds 5a-5d showed moderate binding constants with Kb values of 3.56 ± 0.3 × 104, 2.18 ± 0.2 × 105, 1.44 ± 0.3 × 105 and 2.56 ± 0.3 × 104 M−1, respectively. The molecular dockings were performed to investigate the ligand-DNA interactions. The in-silico DNA-compound interaction studies showed that the compounds interact with DNA in groove binding mode. Antimicrobial activity studies of imine compounds were tested against E. coli as bacteria, S. typhimurium, S. aureus, B. cereus, B. subtilis, and C. albicans as fungi. While all compounds show moderate activity against bacteria, no activity against fungi has been investigated. Communicated by Ramaswamy H. Sarma
Professionalising data stewardship: competences, training and communities
Creators: name: Jetten, Mijke
Publisher: name: Zenodo
Year: 2020
Subjects: Data stewardship
Competences
Data stewards
Communities

description: Presentation and recording of Professionalising data stewardship: competences, training and communities by Mijke Jetten (DTL) on November 30, 2020, for the FAIR Convergence Symposium 2020 in the session The Importance of Demand and Environment for Defining Data Stewardship. This includes the NPOS F project, DTL’s own Data Stewardship Interest Group (DSIG), the recently established Research Data Alliance (RDA) Professionalising Data Stewardship Interest Group (PDS IG) and the RDA/LCRDM 23 things project, which collected practical tools for data stewards to use in their daily work.
A finite element investigation of adiabatic shear
Creators: name: Flockhart, Craig J. .
Publisher: name: Monash University
Year: 2022

description: This thesis was scanned from the print manuscript for digital preservation and is copyright the author.
 Researchers can access this thesis by asking their local university, institution or public library to
 make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.
Additional file 1 of The Severity of Chronic Cough Diary (SCCD): development and content validation of a novel patient-reported outcome instrument for evaluating the symptom experience of chronic cough
Creators: name: de la Orden Abad, Margarita
name: Haberland, Claudia
name: Karn, Hayley
name: Skalicky, Anne
name: Hareendran, Asha
Publisher: name: figshare
Year: 2023
Subjects: Medicine
Biotechnology
Science Policy

description: Supplementary Material 1
Grant proposal: Catalyzing investment in and adoption of open infrastructure for research
Creators: name: Invest In Open Infrastructure
Publisher: name: Zenodo
Year: 2023
Subjects: grant proposals
scholarly communication
open science
open infrastructure

description: Grant proposal submitted by Invest in Open Infrastructure to the Mellon Foundation in 2023-01. From the proposal summary: "We request $1,000,000 USD over 21 months to support the further development and productization of the Catalog of Open Infrastructure Services (COIs) and to test models and strategies for sustaining open infrastructure. Funding will be dedicated in large part to providing technical development and leadership support to scale COIs, with additional convening and research support to help grow the uptake and investment in open infrastructure from for-profits, institutions, and other aligned initiatives. This builds on IOI’s existing efforts to provide targeted, evidence-based guidance, analysis, and strategic support to institutions and funders to improve the resourcing, viability, and sustainability for open technologies that underpin research and scholarship. IOI is a fiscally sponsored project of Code for Science & Society, a leading 501(c)3 that supports a portfolio of projects in the public interest technology and research sectors."
Additional file 2 of The Severity of Chronic Cough Diary (SCCD): development and content validation of a novel patient-reported outcome instrument for evaluating the symptom experience of chronic cough
Creators: name: de la Orden Abad, Margarita
name: Haberland, Claudia
name: Karn, Hayley
name: Skalicky, Anne
name: Hareendran, Asha
Publisher: name: figshare
Year: 2023
Subjects: Medicine
Biotechnology
Science Policy

description: Supplementary Material 2
Spectroscopic, quantum chemical, molecular docking and molecular dynamics investigations of hydroxylic indole-3-pyruvic acid: a potent candidate for nonlinear optical applications and Alzheimer’s drug
Creators: name: Koyambo-Konzapa, Stève-Jonathan
name: Kongbonga, Gilbert Yvon Mbesse
name: R, Premkumar
name: Vamhindi, Berthelot Saïd Duvalier Ramlina
name: Nsangou, Mama
name: Benial, A. Milton Franklin
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Cell 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

description: In this paper, a complete theoretical investigation of hydroxylic indole-3-pyruvic acid (HIPyA) molecule was performed using the DFT quantum chemical, molecular docking and molecular dynamics calculations. The conformational analysis of HIPyA molecule was carried out using density functional theory quantum chemical calculations. The most stable structure of the studied molecule was predicted by means of DFT/B3LYP method with cc-pVTZ basis set. The simulated vibrational frequencies were assigned and proved to be in agreement with the available experimental FT-IR data. The effects of gas phase and solvents on UV-visible spectra of HIPyA molecule were simulated using TD-DFT/B3LYP method with cc-pVTZ basis set. The analysis of the density of states spectrum validates the frontier molecular orbitals results, which reveals the charge transfer interaction in HIPyA molecule. The molecular electrostatic potential surface confirms the electrophilic and nucleophilic reactive sites of the studied molecule. The natural bond orbital analysis evidences the bioactivity of the studied molecule. The obtained first order hyperpolarizability value is 33.596 times greater than urea, which confirms the nonlinear optical activity of HIPyA molecule. The molecular docking analysis reveals that the studied molecule under interest can act as a potent inhibitor against the amyloid β-protein (Aβ) enzyme, which causes the Alzheimer’s disease. The molecular dynamics analysis confirms the reliability of the docking results. Communicated by Ramaswamy H. Sarma
Distribution of Cr atoms in a strained and strain-relaxed Fe89.15Cr10.75 alloy: Mössbauer effect study
Creators: name: Dubiel, S. M.
name: Zukrowski, J.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: A Fe89.15Cr10.75 alloy in a heavily strained (by cold rolling) and strain-relaxed states was studied by means of the conversion electrons Mössbauer spectroscopy (CEMS). Analysis of the spectra in terms of a two-shell model revealed significant differences between the studied samples, in particular, in values of the hyperfine field, a distribution of Cr atoms within the first two neighbor-shells, the latter was expressed in terms of the short-range order parameters, and in the magnetic texture.
description: 9 pages, 3 figures, 10 references. arXiv admin note: text overlap with arXiv:1610.08014
Comments on "Approximate Characterizations for the Gaussian Source Broadcast Distortion Region"
Creators: name: Yu, Lei
name: Li, Houqiang
name: Li, Weiping
Publisher: name: arXiv
Year: 2016
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: Recently, Tian et al. [1] considered joint source-channel coding of transmitting a Gaussian source over $K$-user Gaussian broadcast channel, and derived an outer bound on the admissible distortion region. In [1], they stated "due to its nonlinear form, it appears difficult to determine whether it is always looser than the trivial outer bound in all distortion regimes with bandwidth compression". However, in this correspondence we solve this problem and prove that for the bandwidth expansion case ($K\geq2$), this outer bound is strictly tighter than the trivial outer bound with each user being optimal in the point-to-point setting; while for the bandwidth compression or bandwidth match case, this outer bound actually degenerates to the trivial outer bound. Therefore, our results imply that on one hand, the outer bound given in [1] is nontrivial only for Gaussian broadcast communication ($K\geq2$) with bandwidth expansion; on the other hand, unfortunately, no nontrivial outer bound exists so far for Gaussian broadcast communication ($K\geq2$) with bandwidth compression.
description: To be published in IEEE Transactions on Information Theory
An integrated model for the design of stable meanders
Creators: name: Chong, Irene Ling Ee.
Publisher: name: Monash University
Year: 2022

description: This thesis was scanned from the print manuscript for digital preservation and is copyright the author.
 Researchers can access this thesis by asking their local university, institution or public library to
 make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.
Uma rede de colaboração para os repositórios digitais brasileiros
Creators: name: Sousa, Juliana
name: Silva, Tatyane Guedes Martins da
name: Sena, Priscila Machado Borges
name: Segundo, Washington
name: Amaro, Bianca
Publisher: name: Zenodo
Year: 2023

description: Apresentação realizada na sessão "Pecha Kucha I" da 14ª Conferência Lusófona de Ciência Aberta, Natal Brasil, de 18 a 21 de setembro de 2023.
Additional file 2 of Smoking-related dysregulation of plasma circulating microRNAs: the Rotterdam study
Creators: name: Karabegović, Irma
name: Maas, Silvana C. E.
name: Shuai, Yu
name: Ikram, M. Arfan
name: Stricker, Bruno
name: Aerts, Joachim
name: Brusselle, Guy
name: Lahousse, Lies
name: Voortman, Trudy
name: Ghanbari, Mohsen
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Molecular Biology
subject: Biotechnology
classificationCode: 69999
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
classificationCode: 111714
subject: Mental Health

description: Additional file 2: Fig. S1. Provides the distribution of the top 10 significantly associated miRNAs with current versus never smoking status; Fig. S2. Provides a Volcano plot depicting the results from current versus former smokers analysis, where current smoking was a reference; Fig. S3. Depicts boxplots of all 41 smoking miRNAs with their expression levels across different smoking cessation categories, while Fig. S4. Depicts the enrichment plot for the smoking associated miRNAs in the KEGG pathways.
Automated attribution and credit for data: connecting publication to data–and data to data creators
Creators: name: Stall, Shelley
name: Specht, Alison
name: Mouquet, Nicolas
name: Mouillot, David
Publisher: name: Zenodo
Year: 2019
Subjects: protected areas
data sharing
incentives
credit
transnational

description: This poster is an introduction to PARSEC and its goals which include developing an: • Improved understanding of the impact of PAs on local communities across a broad range of bio-geographical domains, cultural divides, and historic land-use practices. • Improved decision-making capacity of managers to predict and mitigate the effects of natural protected areas on local populations. • Improved recommendations and skills for research data management by researchers. • Improve the adoption of ORCID by the repository infrastructure community for authoritative attribution. • Develop a new cross-domain tool for researchers to obtain credit for their data, as well as for their publications.
description: This research is a product of the PARSEC consortium funded by the Belmont Forum as part of its Collaborative Research Action (CRA) on Science-Driven e-Infrastructures Innovation (SEI) with funding from the Agence Nationale de Research (ANR), France, the Japan Science and Technology Agency (JST), the Sao Paulo Research Foundation (FAPESP) and the US National Science Foundation (NSF) grant number 1929464, with support from the synthesis centre CESAB of the French Foundation for Research on Biodiversity.
Coherence and stiffness of spin waves in diluted ferromagnets
Creators: name: Turek, Ilja
name: Kudrnovsky, Josef
name: Drchal, Vaclav
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We present results of a numerical analysis of magnon spectra in supercells simulating two-dimensional and bulk random diluted ferromagnets with long-ranged pair exchange interactions. We show that low-energy spectral regions for these strongly disordered systems contain a coherent component leading to interference phenomena manifested by a pronounced sensitivity of the lowest excitation energies to the adopted boundary conditions. The dependence of configuration averages of these excitation energies on the supercell size can be used for an efficient determination of the spin-wave stiffness D. The developed formalism is applied to the ferromagnetic Mn-doped GaAs semiconductor with optional incorporation of phosphorus; the obtained concentration trends of D are found in reasonable agreement with recent experiments. Moreover, a relation of the spin stiffness to the Curie temperature Tc has been studied for Mn-doped GaAs and GaN semiconductors. It is found that the ratio Tc/D exhibits qualitatively the same dependence on Mn concentration in both systems.
description: 7 pages, 7 figures, accepted in Phys. Rev. B
Polymorphisms at site 469 of B-RAF protein associated with skin melanoma may be correlated with dabrafenib resistance: An in silico study
Creators: name: Chatterjee, Samadrita
name: Chakraborty, Rajkumar
name: Hasija, Yasha
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Melanoma is a type of skin cancer. Numerous genes and their proteins are strongly associated with melanoma susceptibility. This study aims to use an in silico method to identify genetic variants in the melanoma susceptibility gene. The COSMIC database was queried for genes and cross-referenced with three environment–gene interaction databases (EGP, SeattleSNPs and CTD) to identify shared genes. The majority of approved skin melanoma drugs were found to act on the protein serine/threonine-protein kinase (B-RAF) encoded by the BRAF gene, which was also present in all three referenced databases. Comprehensive computational analysis was performed to predict deleterious genetic variants associated with skin melanoma, and the nsSNPs G469V and G469E were prioritized based on their predicted deleterious effects. Molecular dynamic simulation analysis of the B-RAF protein mutants G469V and G469E reveals that variations in the amino acid conformation at the drug binding site result in inconsistency in drug interaction. Additionally, this analysis showed that the G469V and G469E mutants have lower binding energy for dabrafenib than the wild type. The population with the highest frequency of each deleterious and pathogenic variant has been determined. The study's findings would support the development of more effective treatment strategies for skin melanoma. Communicated by Ramaswamy H. Sarma
Sulfur and few-layer graphene interaction under thermal treatments
Creators: name: Bautista-Flores, C.
name: Arellano-Peraza, J. S.
name: Sato-Berrú, R. Y.
name: Camps, E.
name: Mendoza, D.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: In this work we study sulfur confined between two multilayer graphene films under thermal treatments by means of electrical and Raman spectroscopy characterization. We found some similarities between the electrical behavior and differential scanning calorimetry of sulfur immersed into nanoporous anodic alumina template during sulfur phase transitions, this suggests that sulfur has a different thermal behavior when it is in confining conditions compared to the free state. In addition, multilayer graphene was exposed to sulfur vapors at 500 °C to induce chemical reaction. This method effectively produced covalent bonding between sulfur and multilayer graphene and a p-type doping of about 2x10^13 cm^-2 in charge concentration. Finally, based on first principle calculations we speculate on the existence of a new bidimensional structure of sulfur.
description: 7 pages, 6 figures
An insight into the binding mechanism of Viprinin and its morpholine and piperidine derivatives with HIV-1 Vpr: molecular dynamics simulation, principal component analysis and binding free energy calculation study
Creators: name: Majumder, Satyabrata
name: Giri, Kalyan
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: FOS: Biological sciences
subject: Computational Biology

description: HIV-1 Vpr is an accessory protein responsible for a plethora of functions inside the host cell to promote viral pathogenesis. One of the major functions of Vpr is the G2 cell cycle arrest. Among several small molecule inhibitors, Viprinin, a coumarin derivative, has been shown to specifically inhibit the G2 cell cycle arrest activity of Vpr thus making it an excellent choice for a lead molecule to design antiretroviral drug. But the exact mechanism of binding of the Viprinin and its two potent derivatives with Vpr is still not understood. In this study with combined molecular docking, molecular dynamics simulation, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method, Principal component analysis and Umbrella sampling simulation, we have explored the binding mechanism of Viprinin and its two derivatives with Vpr. MM-PBSA and Umbrella sampling calculations suggest that Viprinin and ViprininD1 have higher binding energy than ViprininD2. Molecular dynamics simulation shows that the ligands are not very stable inside the initial binding pocket and various hydrophobic interactions are responsible to hold the ligands with Vpr. Vpr backbone Principle Component Analysis (PCA) shows various unique essential motions of Vpr bound with Viprinin and its two derivatives. This study may give detailed insight of the mode of binding of the specified compounds at atomic scale and provide valuable information about the possibility of using these compounds as a potent Vpr inhibitor. Communicated by Ramaswamy H. Sarma
Fundamental Physics With Cosmic High-Energy Gamma Rays
Creators: name: De Angelis, Alessandro
Publisher: name: arXiv
Year: 2016
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: High-energy photons (above the MeV) are a powerful probe for astrophysics and for fundamental physics under extreme conditions. During the recent years, our knowledge of the high-energy gamma-ray sky has impressively progressed thanks to the advent of new detectors for cosmic gamma rays, at ground (H.E.S.S., MAGIC, VERITAS, HAWC) and in space (AGILE, Fermi). This presentation reviews the present status of the studies of fundamental physics problems with high-energy gamma rays, and discusses the expected experimental developments.
description: Invited Talk at the 6th International Symposium on High-Energy Gamma-Ray Astronomy (Gamma2016), Heidelberg, July 2016
Research across Disciplinary boundaries: Data Challenges and Solutions in the Environmental and Social Sciences
Creators: name: Specht, Alison
name: Machicao, Jeaneth
name: Stall, Shelley
name: Vellenich, Danton Ferreira
name: Correa, Pedro Pizzigati
Publisher: name: Zenodo
Year: 2020
Subjects: geographical boundaries
data types
scale diversity
data workflow
data management

description: This presentation was given at the International Symposium on Data Science in 2020, sponsored by The Science Council of Japan, the Japanese Research Organisation of Information and Systems, The Joint Support Centre for Data Science Research, the World Data System, ORCID and the National Institute of Information and Communications Technology (NICT). In this presentation we focussed on three challenges we have encountered In PARSEC to date: (i) blending data across difference scales, (ii) working together across geographical boundaries (and how we can develop that), and (iii) ensuring the data management of the project is of international standard. After describing the project and the broad challenges presented by the different data-types we shall be dealing with, we presented a possible workflow from Google Drive -> Open Science Framework -> Amazon Web Services -> publication, and our progress on the Data and Digital Objects Management Plan
description: This research is a product of the PARSEC consortium funded by the Belmont Forum as part of its Collaborative Research Action (CRA) on Science-Driven e-Infrastructures Innovation (SEI) with funding from the Agence Nationale de Research (ANR), France, the Japan Science and Technology Agency (JST), the Sao Paulo Research Foundation (FAPESP) and the US National Science Foundation (NSF) grant number 1929464, with support from the synthesis centre CESAB of the French Foundation for Research on Biodiversity.
Convergence of the solutions of the discounted equation: the discrete case
Creators: name: Davini, Andrea
name: Fathi, Albert
name: Iturriaga, Renato
name: Zavidovique, Maxime
Publisher: name: arXiv
Year: 2016
Subjects: subject: Optimization and Control (math.OC)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We derive a discrete version of the results of our previous work. If $M$ is a compact metric space, $c : M\times M \to \mathbb R$ a continuous cost function and $λ\in (0,1)$, the unique solution to the discrete $λ$-discounted equation is the only function $u_λ: M\to \mathbb R$ such that $$\forall x\in M, \quad u_λ(x) = \min_{y\in M} λu_λ(y) + c(y,x).$$ We prove that there exists a unique constant $α\in \mathbb R$ such that the family of $u_λ+α/(1-λ)$ is bounded as $λ\to 1$ and that for this $α$, the family uniformly converges to a function $u_0 : M\to \mathbb R$ which then verifies $$\forall x\in X, \quad u_0(x) = \min_{y\in X}u_0(y) + c(y,x)+α.$$ The proofs make use of Discrete Weak KAM theory. We also characterize $u_0$ in terms of Peierls barrier and projected Mather measures.
description: 15 pages
R3PACK WP1 D7.1 Communication and advocacy action plan and DOMP
Creators: name: Dolce, Federica
name: Pilot, Louise
name: Alvarez, Carla Valeiras
name: Schott, Elodie
Publisher: name: Zenodo
Year: 2022
Subjects: Communication
Data outputs
Advocacy
Action plan

description: This document initial objectif is to provide all R3PACK project partners with an outline that covers: (1) the target groups the project seeks to impact, (2) the main messages of the project, (3) the actions to be carried out to reach them, (4) the general and specific obligations regarding Dissemination and Communication of the project that all partners must be aware of and (5) the Advocacy Strategy.
Jitter in cascaded digital communications links employing constrained stuffing
Creators: name: Warner, Michael.
Publisher: name: Monash University
Year: 2022

description: This thesis was scanned from the print manuscript for digital preservation and is copyright the author.
 Researchers can access this thesis by asking their local university, institution or public library to
 make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.
Science Requirements and Trade-offs for the MOSAIC Instrument for the European ELT
Creators: name: Evans, C. J.
name: Puech, M.
name: Rodrigues, M.
name: Barbuy, B.
name: Cuby, J. -G.
name: Dalton, G.
name: Fitzsimons, E.
name: Hammer, F.
name: Jagourel, P.
name: Kaper, L.
name: Morris, S. L.
name: Morris, T. J.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Building on the comprehensive White Paper on the scientific case for multi-object spectroscopy on the European ELT, we present the top-level instrument requirements that are being used in the Phase A design study of the MOSAIC concept. The assembled cases span the full range of E-ELT science and generally require either 'high multiplex' or 'high definition' observations to best exploit the excellent sensitivity and spatial performance of the telescope. We highlight some of the science studies that are now being used in trade-off studies to inform the capabilities of MOSAIC and its technical design.
description: 12 pages, in Ground-based and Airborne Instrumentation for Astronomy VI, 2016, Proc. SPIE 9908, 9J
Evaluating the Benefits of Smart Stormwater Systems: Unley Case Study
Creators: name: Thyer, Mark
name: Maier, Holger
name: Di Matteo, Michael
Publisher: name: The University of Adelaide
Year: 2022
Subjects: Water resources engineering

description: There is significant promise for the use of smart, distributed stormwater storage for addressing a range of challenges associated with integrated urban water management, includingFlood control via peak flow reductions and/or reduced infrastructure costsWater for urban greening and coolingImproving the quality of receiving waters.This study assessed the benefits and costs of a range of stormwater storage options, including smart operation, for urban stormwater systems The benefits assessed include peak overland flow reduction, water re-use potential and water quality impacts. Results were compared with more traditionally used pipe upgrades. The case study catchment was located in the City of Unley, Adelaide, South Australia. The key conclusions were:Passive distributed storages optimised using machine learning achieves similar peak flow reduction as end-of-system storage with reduced storage size and cost and is easier to implement.
Cost savings were 30%-44% compared to an equivalent pipe upgradeSmart distributed storage with ‘before storm control’ achieves a similar peak flow reduction at similar cost as pipe upgrade with additional water reuse and water quality benefits
Cost and peak flow reductions were similar to an equivalent pipe upgrade of approx. 550m to 700m length with the additional benefits of potential water reuse volume of 3.1 ML/year and water quality benefits with reduced total suspended solids (51%), phosphorus (27%) and nitrogen (9%).Smart distributed storages with ‘during storm’ real-time control provide significant potential for additional peak flow reductions or cost savings through storage size reductions.
Further development is required for this technology to be used in practice.Machine learning / artificial intelligence optimisation methods played an essential role for identifying the optimal location, sizing and operating rules for the distributed storage options.
Due to the high number of potential locations, sizes and operating rules a traditional trial and error design approach would be far slower and unlikely to achieve a similar outcome.
Teacher Educators' Perspectives on Multicultural Teacher Education in the BSEd Social Studies Program of Western Mindanao State University
Creators: name: Kunting, Arayana F.
Publisher: name: Zenodo
Year: 2015
Subjects: Education
Social Studies
Multicultural education

description: Abstract This study looks into the perspectives on multicultural education of teacher educators in the Bachelor in Secondary Education (BSEd) major in Social Studies program of the Western Mindanao State University (WMSU). The research questions are 1) What are the teacher educators’ perspectives (i.e., knowledge, beliefs, and attitudes) on multicultural education? and 2) What factors account for the teacher educators’ perspectives on multicultural education? Using a qualitative methodology consisting of a survey of 13 teacher educators handling the professional education courses in the BSEd Social Studies program, interviews of nine of these teacher educators, and an analysis of the program prospectus and course syllabi, the study finds that the teacher educators as a whole have a positive conception of and attitudes towards multicultural education. There is also a consensus among the teacher educators regarding the relevance of multicultural education in the Philippine context and the need to integrate it in pre-service teacher education. However, the teacher educators’ practice of multicultural education appears to be limited due to lack of formal training in multicultural education at the pre-service and in-service level, and lack of other forms of support for faculty, such as relevant teaching resources and adequate time to plan course delivery. At present, the teacher educators’ practice of multicultural education in their teaching is anchored only on a positive attitude and prior knowledge obtained through personal experiences. But as a group, they are confronted with constraints to implementing multicultural education that require a more holistic and systematic response at the program and institutional level. The study’s findings imply the need for WSMU’s BSEd Social Studies program to have a well-articulated vision for preparing pre-service teachers for teaching in multicultural contexts, which should then be reflected in a systematic infusion of multicultural education in the BSEd Social Studies curriculum. This requires the inclusion of courses specifically on multicultural education and the integration of topics related to multicultural education in the other courses, and the adaptation of appropriate pedagogies for developing the skills and dispositions needed for teaching culturally diverse learners and according to multicultural education principles. The study’s findings also indicate that a comprehensive professional development program in multicultural education is needed for both the faculty and administrators of WMSU’s BSEd Social Studies program. This would include a formal orientation to multicultural education theory and practice, training in multicultural education pedagogies and course design, and avenues for critical reflection on and collaboration in multicultural teacher education.
description: Masters Thesis
Accuracy and precision of binding free energy prediction for a tacrine related lead inhibitor of acetylcholinesterase with an arsenal of supercomputerized molecular modelling methods: a comparative study
Creators: name: Dolezal, Rafael
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Computational Biology

description: Nowadays, advanced computational chemistry methods offer various strategies for revealing prospective hit structures in drug development essentially through accurate binding free energy predictions. After the era of molecular docking and quantitative structure-activity relationships, much interest has been lately oriented to perturbed molecular dynamic approaches like replica exchange with solute tempering and free energy perturbation (REST/FEP) and the potential of the mean force with adaptive biasing and accelerated weight histograms (PMF/AWH). Both of these receptor-based techniques can exploit exascale CPU&GPU supercomputers to achieve high throughput performance. In this fundamental study, we have compared the predictive power of a panel of supercomputerized molecular modelling methods to distinguish the major binding modes and the corresponding binding free energies of a promising tacrine related potential antialzheimerics in human acetylcholinesterase. The binding free energies were estimated using flexible molecular docking, molecular mechanics/generalized Born surface area/Poisson-Boltzmann surface area (MM/GBSA/PBSA), transmutation REST/FEP with 12 x 5 ns/λ windows, annihilation FEP with 20 x 5 ns/λ steps, PMF with weight histogram analysis method (WHAM) and 40 x 5 ns samples, and PMF/AWH with 10 x 100 ns replicas. Confrontation of the classical approaches such as canonical molecular dynamics and molecular docking with alchemical calculations and steered molecular dynamics enabled us to show how large errors in ΔG predictions can be expected if these in silico methods are employed in the elucidation of a common case of enzyme inhibition. Communicated by Ramaswamy H. Sarma
Additional file 1 of Estimation of migraine prevalence considering active and inactive states across different age groups
Creators: name: Piccininni, Marco
name: Brinks, Ralph
name: Rohmann, Jessica L.
name: Kurth, Tobias
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Immunology
subject: FOS: Clinical medicine
classificationCode: 19999
subject: Mathematical Sciences not elsewhere classified
subject: Science Policy

description: Additional file 1: Appendix A. Methods details and sensitivity analysis results.
Expert system development and application to the design of plain journal bearings
Creators: name: Brennan, John.
Publisher: name: Monash University
Year: 2022

description: This thesis was scanned from the print manuscript for digital preservation and is copyright the author.
 Researchers can access this thesis by asking their local university, institution or public library to
 make a request on their behalf. Monash staff and postgraduate students can use the link in the References field.
Preprints na ciência da computação: um estudo preliminar
Creators: name: Castilho, Rosane Teles Lins
name: Príncipe, Eloisa
Publisher: name: Zenodo
Year: 2023

description: Apresentação realizada na sessão "Pecha Kucha I" da 14ª Conferência Lusófona de Ciência Aberta, Natal Brasil, de 18 a 21 de setembro de 2023.
A First-Principles Comparative Study of Lithium, Sodium, and Magnesium Storage in Pure and Gallium-Doped Germanium: Competition between Interstitial and Substitutional Sites
Creators: name: Legrain, Fleur
name: Manzhos, Sergei
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Thermodynamics and kinetics of Li, Na, and Mg storage in Ge is studied ab initio. The most stable configurations can consist of tetrahedral, substitutional, or a combination of the two types of sites. In the dilute limit, Li, Na prefer interstitial, while Mg prefers substitutional sites. At higher concentrations of Li, Na, and Mg, there is a combination of interstitial and substitutional sites. This is an important finding, as previous ab initio studies of alloying type electrode materials ignored substitutional sites. Insertion energies computed at dilute concentration (x = 1/64) show that Na and Mg insertion are not thermodynamically favored in Ge vs formation of bulk Na and Mg, as opposed to Li insertion which is favored. We investigate the effect of p-doping of Ge (with Ga) on the thermodynamics and find that it considerably lowers the defect formation energies associated with the insertion of Li/Na/Mg at tetrahedral sites. On the other hand, the energetics associated with Li/Na/Mg insertion at substitutional sites are not significantly affected. In addition, we compute the migration energy barriers for Li/Na/Mg diffusion between two tetrahedral sites (0.38/0.79/0.66 eV), between two substitutional sites (0.77/0.93/1.83 eV), and between two sites of different type (2.15/1.75/0.85 eV).
Additional file 1 of Extracellular vesicle-associated tyrosine kinase-like orphan receptors ROR1 and ROR2 promote breast cancer progression
Creators: name: Irmer, Barnabas
name: Efing, Janes
name: Reitnauer, Lea Elisabeth
name: Angenendt, Allegra
name: Heinrichs, Saskia
name: Schubert, Antonia
name: Schulz, Matthias
name: Binder, Claudia
name: Tio, Joke
name: Hansen, Uwe
name: Geyer, Christiane
name: Gerwing, Mirjam
name: Bleckmann, Annalen
name: Menck, Kerstin
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
classificationCode: 39999
subject: Chemical Sciences not elsewhere classified
subject: Cancer

description: Additional file 1.