cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2
Creators: name: Ahmed, Sinthyia
name: Mahtarin, Rumana
name: Ahmed, Sayeda Samina
name: Akter, Shaila
name: Islam, Md. Shamiul
name: Mamun, Abdulla Al
name: Islam, Rajib
name: Hossain, Md Nayeem
name: Ali, Md Ackas
name: Sultana, Mossammad U. C.
name: Parves, MD. Rimon
name: Ullah, M. Obayed
name: Halim, Mohammad A.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Computational Biology

description: SARS-CoV-2 virus outbreak poses a major threat to humans worldwide due to its highly contagious nature. In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. The RNA-dependent RNA polymerase is a vital enzyme of coronavirus replication/transcription complex whereas the main protease acts on the proteolysis of replicase polyproteins. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. To explore the dynamic nature of the interaction, 100 ns molecular dynamics (MD) simulation is performed on the selected protein-drug complexes and apo-protein. Binding free energy of the selected drugs is performed by MM/PBSA. Besides docking and dynamics, partial least square (PLS) regression method is applied for the quantitative structure activity relationship to generate and predict the binding energy for drugs. PLS regression satisfactorily predicts the binding energy of the effective antiviral drugs compared to binding energy achieved from molecular docking with a precision of 85%. This study highly recommends researchers to screen these potential drugs in vitro and in vivo against SARS-CoV-2 for further validation of utility. Communicated by Ramaswamy H. Sarma
Application of Traditional Vaccine Development Strategies to SARS-CoV-2
Creators: name: Rando, Halie M.
name: Lordan, Ronan
name: Lee, Alexandra J.
name: Naik, Amruta
name: Wellhausen, Nils
name: Sell, Elizabeth
name: Kolla, Likhitha
name: Consortium, COVID-19 Review
name: Gitter, Anthony
name: Greene, Casey S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Other Quantitative Biology (q-bio.OT)
subject: FOS: Biological sciences

description: Over the past 150 years, vaccines have revolutionized the relationship between people and disease. During the COVID-19 pandemic, technologies such as mRNA vaccines have received attention due to their novelty and successes. However, more traditional vaccine development platforms have also yielded important tools in the worldwide fight against the SARS-CoV-2 virus. A variety of approaches have been used to develop COVID-19 vaccines that are now authorized for use in countries around the world. In this review, we highlight strategies that focus on the viral capsid and outwards, rather than on the nucleic acids inside. These approaches fall into two broad categories: whole-virus vaccines and subunit vaccines. Whole-virus vaccines use the virus itself, either in an inactivated or attenuated state. Subunit vaccines contain instead an isolated, immunogenic component of the virus. Here, we highlight vaccine candidates that apply these approaches against SARS-CoV-2 in different ways. In a companion manuscript, we review the more recent and novel development of nucleic-acid based vaccine technologies. We further consider the role that these COVID-19 vaccine development programs have played in prophylaxis at the global scale. Well-established vaccine technologies have proved especially important to making vaccines accessible in low- and middle-income countries. Vaccine development programs that use established platforms have been undertaken in a much wider range of countries than those using nucleic-acid-based technologies, which have been led by wealthy Western countries. Therefore, these vaccine platforms, though less novel from a biotechnological standpoint, have proven to be extremely important to the management of SARS-CoV-2.
Mid and Far Infrared Photometry of Galactic Planetary Nebulae with the AKARI All Sky Survey
Creators: name: Phillips, J. P.
name: Marquez-Lugo, R. A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We provide mid- and far-infrared photometry of 857 Galactic planetary nebulae (PNe) using data derived from the AKARI All-Sky Survey. These include fluxes at 9 and 18 μm obtained with the Infrared Camera (IRC), and at 65, 90, 140 and 160 μm using the far-Infrared Surveyor (FIS). It is noted that the IR luminosities of the youngest PNe are comparable to the total luminosities of the central stars, and subsequently decline to ~ 5102 L where D > 0.08 pc. This is consistent with an evolution of PNe dust opacities, and appreciable absorption in young and proto-PNe. We also note that whilst there is little evidence for the evolution in IR/radio flux ratios suggested by previous authors. The fall-off in dust temperatures is similar to that determined in previous studies, whilst levels of Ly heating are < 0.5 of the total energy budget of the grains. There appears to be an evolution in the infrared excess (IRE) as nebulae expand, with the largest values occurring in the most compact PNe.
description: 76 pages, 13 figures (1 in color), 2 tables
Physical Confinement and Cell Proximity Increase Cell Migration Rates and Invasiveness: A Mathematical Model of Cancer Cell Invasion through Flexible Channels
Creators: name: Peng, Qiyao
name: Vermolen, Fred J
name: Weihs, Daphne
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cell Behavior (q-bio.CB)
subject: Numerical Analysis (math.NA)
subject: FOS: Biological sciences
subject: FOS: Mathematics

description: Cancer cell migration between different body parts is the driving force behind cancer metastasis, which is the main cause of mortality of patients. Migration of cancer cells often proceeds by penetration through narrow cavities in locally stiff, yet flexible tissues. In our previous work, we developed a model for cell geometry evolution during invasion, which we extend here to investigate whether leader and follower (cancer) cells that only interact mechanically can benefit from sequential transmigration through narrow micro-channels and cavities. We consider two cases of cells sequentially migrating through a flexible channel: leader and follower cells being closely adjacent or distant. Using Wilcoxon's signed-rank test on the data collected from Monte Carlo simulations, we conclude that the modelled transmigration speed for the follower cell is significantly larger than for the leader cell when cells are distant, i.e. follower cells transmigrate after the leader has completed the crossing. Furthermore, it appears that there exists an optimum with respect to the width of the channel such that cell moves fastest. On the other hand, in the case of closely adjacent cells, effectively performing collective migration, the leader cell moves $12\%$ faster since the follower cell pushes it. This work shows that mechanical interactions between cells can increase the net transmigration speed of cancer cells, resulting in increased invasiveness. In other words, interaction between cancer cells can accelerate metastatic invasion.
Screening and identification of secondary metabolites in the bark of Bauhinia variegata to treat Alzheimer’s disease by using molecular docking and molecular dynamics simulations
Creators: name: Khare, Noopur
name: Maheshwari, Sanjiv Kumar
name: Jha, Abhimanyu Kumar
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
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
subject: Computational Biology

description: Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE) acts as a promising protein targets for which drug as an inhibitor can be designed to treat Alzheimer’s Disease. Different flavonoids and alkaloids of Bauhinia variegata were used as an inhibitor to target the protein. The current in silico study was carried out to explore the binding patterns of flavanoids and alkaloids against Acetylcholinesterase (PDB ID: 4PQE) and Butyrylcholinesterase (PDB ID: 1P0I) using molecular docking and molecular dynamics simulations approach. Molecular docking result shows that Dihydroquercetin (CID:439533) binds with the active region of AChE and BChE. Using molsoft, molinspiration, and pkCSM all the properties of the candidate were analyzed. The best compound Dihydroquercetin was compared with Donepezil drug through molecular dynamic simulation studies. The analysis of Molecular Dynamics Simulations showed that AChE and AChE-Dihydroquercetin complex became stable at 3000 ps and there was little conformational change in BChE and BChE-Dihydroquercetin complex. The in silico study finally predicts that Dihydroquercetin may act as a good inhibitor for treating Alzheimer’s disease and further in vitro and in vivo studies may prove its therapeutic potential. Communicated by Ramaswamy H. Sarma
Effect of anisotropy on the field induced quantum critical properties of the three dimensional s=1/2 Heisenberg model
Creators: name: Rezania, H.
name: Langari, A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The field induced quantum critical properties of the three dimensional spin-1/2 anisotropic antiferromagnetic Heisenberg model has been studied. We have investigated the quantum phase transition between the spiral order and field induced ferromagnetic order by means of Bose-Einstein condensation of magnons in terms of a bosonic representation. The effect of in-plane anisotropy on the critical properties has been studied via the bosonic model by Green's function approach. We have found an analytic expression for the gap exponent in addition to numerical results for the critical magnetic field in terms of anisotropy parameter. The in-plane anisotropy breaks the U(1) symmetry explicitly which changes the universal behavior by a drastic change on the gap exponent. Moreover, the critical magnetic field depends strongly on the in-plane anisotropies. The divergence of the transverse structure factor at the antiferromagnetic wave vector confirms the onset of the magnetic order which scales with the negative value of gap exponent as the magnetic field approaches the critical one. The transverse staggered magnetization as an order parameter vanishes with exponent $β=0.5$ when the magnetic field reaches its critical value in low field region.
description: 9 pages and 2 figures
Resistance to BET inhibitors in lung adenocarcinoma is mediated through casein kinase 2 phosphorylation of BRD4
Creators: name: Calder, Jack
Publisher: name: University of British Columbia
Year: 2018

description: Lung cancer is the leading cause of cancer related death in both men and women worldwide, mainly due to the lack of effective therapies. The development of specific chemical compounds that target epigenetic post-translational modifications has recently emerged as an excellent approach for validating new treatment strategies for diseases that have complex underlying mechanisms. JQ1 is a small-molecule inhibitor of the bromodomain and extraterminal (BET) family proteins, which function as important reader molecules of acetylated histones and recruit transcriptional activators to specific promoter sites. In many cancer lines the down-regulation of MYC, a known oncogenic transcription factor and contributor to the pathogenesis in certain cancer types, has been linked to BET inhibitor (BETi) treatment. In addition, resistance to BETis has only been examined in MYC-dependent cancers, with all forms of resistance involving re-expression of MYC, through several mechanisms. Previously, our lab has shown that lung adenocarcinoma (LAC) cells are inhibited by JQ1 through a mechanism independent of MYC down-regulation, identifying FOSL1 as a mediator of response. This suggests that the epigenetic landscape of cells from different origins and differentiation states influences response to JQ1. Therefore, I aim to investigate how LAC cells, independent of MYC down-regulation, acquire resistance to BET inhibition, to elucidate mechanisms of primary resistance and potential treatment strategies for LAC. Here, I establish resistance in two JQ1 sensitive LAC cell lines and demonstrate that MYC levels were not significantly altered, nor was FOSL1 expression reactivated in resistant lines, indicating a novel mechanism of resistance. Interestingly, resistant lines were still dependent on the BET protein BRD4, as demonstrated by siRNA knockdown, suggesting that BRD4 may drive resistance through regulating gene transcription independent of its acetyl-binding domain. Both resistant lines showed increased levels of phosphorylated BRD4, and also up-regulation of casein kinase 2 (CK2), a kinase previously shown to phosphorylate BRD4. Furthermore, combining JQ1 with a CK2 inhibitor showed synergistic effects in both resistant lines, with treatment leading to decreased levels of pBRD4. Overall, we have determined that LAC cells develop JQ1 resistance through mechanisms independent of MYC, identifying CK2 phosphorylation of BRD4 as a likely mechanism of resistance.
The VLA-COSMOS Survey. IV. Deep Data and Joint Catalog
Creators: name: Schinnerer, Eva
name: Sargent, M. T.
name: Bondi, M.
name: Smolcic, V.
name: Datta, A.
name: Carilli, C. L.
name: Bertoldi, F.
name: Blain, A.
name: Ciliegi, P.
name: Koekemoer, A. M.
name: Scoville, N. Z.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In the context of the VLA-COSMOS Deep project additional VLA A array observations at 1.4 GHz were obtained for the central degree of the COSMOS field and combined with the existing data from the VLA-COSMOS Large project. A newly constructed Deep mosaic with a resolution of 2.5" was used to search for sources down to 4 sigma with 1 sigma ~ 12 microJy/beam in the central 50'x50'. This new catalog is combined with the catalog from the Large project (obtained at 1.5"x1.4" resolution) to construct a new Joint catalog. All sources listed in the new Joint catalog have peak flux densities of >5 sigma at 1.5" and/or 2.5" resolution to account for the fact that a significant fraction of sources at these low flux levels are expected to be slighty resolved at 1.5" resolution. All properties listed in the Joint catalog such as peak flux density, integrated flux density and source size are determined in the 2.5" resolution Deep image. In addition, the Joint catalog contains 43 newly identified multi-component sources.
description: 34 pages, 20 figures (3 at reduced resolution). Accepted for publication in ApJS.
Visualizing the Passage of Time with Video Temporal Pyramids
Creators: name: Swift, Melissa E.
name: Ayers, Wyatt
name: Pallanck, Sophie
name: Wehrwein, Scott
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Image and Video Processing (eess.IV)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: I.5.4; I.4.8

description: What can we learn about a scene by watching it for months or years? A video recorded over a long timespan will depict interesting phenomena at multiple timescales, but identifying and viewing them presents a challenge. The video is too long to watch in full, and some occurrences are too slow to experience in real-time, such as glacial retreat. Timelapse videography is a common approach to summarizing long videos and visualizing slow timescales. However, a timelapse is limited to a single chosen temporal frequency, and often appears flickery due to aliasing and temporal discontinuities between frames. In this paper, we propose Video Temporal Pyramids, a technique that addresses these limitations and expands the possibilities for visualizing the passage of time. Inspired by spatial image pyramids from computer vision, we developed an algorithm that builds video pyramids in the temporal domain. Each level of a Video Temporal Pyramid visualizes a different timescale; for instance, videos from the monthly timescale are usually good for visualizing seasonal changes, while videos from the one-minute timescale are best for visualizing sunrise or the movement of clouds across the sky. To help explore the different pyramid levels, we also propose a Video Spectrogram to visualize the amount of activity across the entire pyramid, providing a holistic overview of the scene dynamics and the ability to explore and discover phenomena across time and timescales. To demonstrate our approach, we have built Video Temporal Pyramids from ten outdoor scenes, each containing months or years of data. We compare Video Temporal Pyramid layers to naive timelapse and find that our pyramids enable alias-free viewing of longer-term changes. We also demonstrate that the Video Spectrogram facilitates exploration and discovery of phenomena across pyramid levels, by enabling both overview and detail-focused perspectives.
description: 11 pages, 9 figures, accepted for presentation at IEEE VIS 2022, will be published in conference proceedings, supplementary material and more can be found on our project page at https://fw.cs.wwu.edu/~wehrwes/TemporalPyramids
title: Comparative bacterial genomics and fish vaccinology: genomic and phenotypic analysis of Vibrio anguillarum isolated from lumpfish (Cyclopterus lumpus) and vaccine evaluation in sablefish (Anoplopoma fimbria) against Aeromonas salmonicida
Creators: name: Vasquez Solis De Ovando, Jose Ignacio
Publisher: name: Memorial University of Newfoundland
Year: 2020

description: Although aquaculture is the fastest growing food-producing industry in the world, it is negatively impacted by parasites and infectious diseases. Bacterial infections are the most important diseases of emergent Canadian aquaculture species such as lumpfish (Cyclopterus lumpus) and sablefish (Anoplopoma fimbria). Aeromonas salmonicida and Vibrio anguillarum, both Gram-negative pathogens, are the most prevalent infectious diseases agents affecting lumpfish aquaculture in the North Atlantic, meanwhile A. salmonicida is the most common pathogen in the sablefish aquaculture industry in the Pacific coast. Comparative genomic analysis of V. anguillarum and A. salmonicida isolates from lumpfish and sablefish outbreaks, respectively, can provide insights into bacterial evolution and virulence, and contribute to effective vaccine design programs. Currently, there are no commercial vaccines available specifically for lumpfish against V. anguillarum, and for sablefish against A. salmonicida. Therefore, the objectives of this study were to: i) analyze the genome and phenotype of V. anguillarum strain J360 isolated from infected lumpfish (Chapter 2); and ii) develop an infection model for atypical A. salmonicida strain J410 in sablefish to evaluate commercial vaccines and an autogenous vaccine (Chapter 3)
Latent Signal Models: Learning Compact Representations of Signal Evolution for Improved Time-Resolved, Multi-contrast MRI
Creators: name: Arefeen, Yamin
name: Xu, Junshen
name: Zhang, Molin
name: Dong, Zijing
name: Wang, Fuyixue
name: White, Jacob
name: Bilgic, Berkin
name: Adalsteinsson, Elfar
Publisher: name: arXiv
Year: 2022
Subjects: subject: Signal Processing (eess.SP)
subject: Medical Physics (physics.med-ph)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Physical sciences

description: Purpose: Training auto-encoders on simulated signal evolution and inserting the decoder into the forward model improves reconstructions through more compact, Bloch-equation-based representations of signal in comparison to linear subspaces. Methods: Building on model-based nonlinear and linear subspace techniques that enable reconstruction of signal dynamics, we train auto-encoders on dictionaries of simulated signal evolution to learn more compact, non-linear, latent representations. The proposed Latent Signal Model framework inserts the decoder portion of the auto-encoder into the forward model and directly reconstructs the latent representation. Latent Signal Models essentially serve as a proxy for fast and feasible differentiation through the Bloch-equations used to simulate signal. This work performs experiments in the context of T2-shuffling, gradient echo EPTI, and MPRAGE-shuffling. We compare how efficiently auto-encoders represent signal evolution in comparison to linear subspaces. Simulation and in-vivo experiments then evaluate if reducing degrees of freedom by inserting the decoder into the forward model improves reconstructions in comparison to subspace constraints. Results: An auto-encoder with one real latent variable represents FSE, EPTI, and MPRAGE signal evolution as well as linear subspaces characterized by four basis vectors. In simulated/in-vivo T2-shuffling and in-vivo EPTI experiments, the proposed framework achieves consistent quantitative NRMSE and qualitative improvement over linear approaches. From qualitative evaluation, the proposed approach yields images with reduced blurring and noise amplification in MPRAGE shuffling experiments. Conclusion: Directly solving for non-linear latent representations of signal evolution improves time-resolved MRI reconstructions through reduced degrees of freedom.
Room-Temperature Electron Spin Transport in a Highly Doped Si Channel
Creators: name: Suzuki, Toshio
name: Sasaki, Tomoyuki
name: Oikawa, Tohru
name: Shiraishi, Masashi
name: Noguchi, Yoshishige Suzuki andn Kiyoshi
Publisher: name: arXiv
Year: 2011
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report on the first demonstration of generating a spin current and spin transport in a highly doped Si channel at room temperature (RT) using a four-terminal lateral device with a spin injector and a detector consisting of an Fe/MgO tunnel barrier. Spin current was generated using a nonlocal technique, and spin injection signals and Hanle-type spin precession were successfully detected at 300 K, thus proving spin injection with the elimination of spurious signals. The spin diffusion length and its lifetime at RT were estimated to be 0.6 ïm and 1.3 ns by the Hanle-type spin precession, respectively.
description: 14 pages, 4 Figures
Forward light-by-light scattering and electromagnetic correction to hadronic vacuum polarization
Creators: name: Biloshytskyi, Volodymyr
name: Chao, En-Hung
name: Gérardin, Antoine
name: Green, Jeremy R.
name: Hagelstein, Franziska
name: Meyer, Harvey B.
name: Parrino, Julian
name: Pascalutsa, Vladimir
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Lattice QCD calculations of the hadronic vacuum polarization (HVP) have reached a precision where the electromagnetic (e.m.) correction can no longer be neglected. This correction is both computationally challenging and hard to validate, as it leads to ultraviolet (UV) divergences and to sizeable infrared (IR) effects associated with the massless photon. While we precisely determine the UV divergence using the operator-product expansion, we propose to introduce a separation scale $Λ\sim400\;$MeV into the internal photon propagator, whereby the calculation splits into a short-distance part, regulated in the UV by the lattice and in the IR by the scale $Λ$, and a UV-finite long-distance part to be treated with coordinate-space methods, thereby avoiding power-law finite-size effects altogether. In order to predict the long-distance part, we express the UV-regulated e.m. correction to the HVP via the forward hadronic light-by-light (HLbL) scattering amplitude and relate the latter via a dispersive sum rule to $γ^*γ^*$ fusion cross-sections. Having tested the relation by reproducing the two-loop QED vacuum polarization (VP) from the tree-level $γ^*γ^*\to e^+e^-$ cross-section, we predict the expected lattice-QCD integrand resulting from the $γ^*γ^*\toπ^0$ process.
description: 29 pages, 6 figures; text matches the published version
Evaluation of biomolecular interactions and cytotoxic activity of organometallic binuclear Ru(II) complexes of ferrocenyl thiosemicarbazones
Creators: name: Khanvilkar, Priyanka
name: Dash, Soumya R.
name: Vohra, Alisagar
name: Devkar, Ranjitsinh
name: Chakraborty, Debjani
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Cell Biology
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: Cancer

description: Four new ferrocenyl substituted thiosemicarbazone ligands (L1–L4) and their corresponding binuclear ruthenium(II) arene complexes of the general type [(η6-p cym)(L)Ru(μ-im)Ru(L)(η6-p-cym)]Cl (C1–C4) and [(η6-p cym)(L)Ru(μ-azpy)Ru(L)(η6-p-cym)]Cl2 (C5–C8) (cym = cymene, im = imidazole, azpy = 4,4′-azopyridine) have been synthesized and characterized. The structures of the complexes were established through DFT calculations and geometry optimization. The interactions of the binuclear complexes with DNA were investigated by absorption, emission and viscosity studies which indicated that the complexes bind to DNA via intercalation. Meanwhile, the interaction of complexes with the protein, bovine serum albumin (BSA), has also been studied using fluorescence emission spectroscopy. The experimental results show that the binuclear complexes exhibit good binding propensities to BSA. The complexes can quench the intrinsic fluorescence of BSA remarkably through a static or dynamic quenching process. In addition, the in vitro cytotoxicity of complexes C1–C8 against HeLa cell line was assayed which showed lower IC50 values indicating their higher cytotoxicity and potency in killing the cancer cells at low concentrations. Communicated by Ramaswamy H. Sarma
Phase separation transition in anti-ferromagnetically interacting particle systems
Creators: name: Kundu, Anasuya
name: Mohanty, P. K.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: One dimensional non-equilibrium systems with short-range interaction can undergo phase transitions from homogeneous states to phase separated states as interaction ($ε$) among particles is increased. One of the model systems where such transition has been observed is the extended Katz-Lebowitz-Spohn (KLS) model with ferro-magnetically interacting particles at $ε=4/5$. Here, the system remains homogeneous for small interaction strength ($ε<4/5$), and for anti-feromagnetic interactions ($ε<0$). We show that the phase separation transitions can also occur in anti-ferromagnetic systems if interaction among particles depends explicitly on the size of the block ($n$) they belong to. We study this transition in detail for a specific case $ε= δ/n$, where phase separation occurs for $δ< -1$.
description: 4 pages, 5 figures
Происхождение древнерусского прикладного искуства
Creators: name: Орлов, Руслан
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 430101
subject: Archaeological science

description: Орлов Р.С. Происхождение древнерусского прикладного искуства — VI Міжнародний конгрес слов’янської археології: Тези доповідей української делегації. - Київ, 1996. - С.94-97.The origin of ancient Rus applied art
Quantum Mixed State Compiling
Creators: name: Ezzell, Nic
name: Ball, Elliott M.
name: Siddiqui, Aliza U.
name: Wilde, Mark M.
name: Sornborger, Andrew T.
name: Coles, Patrick J.
name: Holmes, Zoë
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The task of learning a quantum circuit to prepare a given mixed state is a fundamental quantum subroutine. We present a variational quantum algorithm (VQA) to learn mixed states which is suitable for near-term hardware. Our algorithm represents a generalization of previous VQAs that aimed at learning preparation circuits for pure states. We consider two different ansätze for compiling the target state; the first is based on learning a purification of the state and the second on representing it as a convex combination of pure states. In both cases, the resources required to store and manipulate the compiled state grow with the rank of the approximation. Thus, by learning a lower rank approximation of the target state, our algorithm provides a means of compressing a state for more efficient processing. As a byproduct of our algorithm, one effectively learns the principal components of the target state, and hence our algorithm further provides a new method for principal component analysis. We investigate the efficacy of our algorithm through extensive numerical implementations, showing that typical random states and thermal states of many body systems may be learnt this way. Additionally, we demonstrate on quantum hardware how our algorithm can be used to study hardware noise-induced states.
description: 17 main + 17 appendix pages, 6 main + 9 appendix figures
Suppression of Kelvon-induced decay of quantized vortices in oblate Bose-Einstein Condensates
Creators: name: Rooney, S. J.
name: Blakie, P. B.
name: Anderson, B. P.
name: Bradley, A. S.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the Kelvin mode excitations on a vortex line in a three-dimensional trapped Bose-Einstein condensate at finite temperature. Our stochastic Gross-Pitaevskii simulations show that the activation of these modes can be suppressed by tightening the confinement along the direction of the vortex line, leading to a strong suppression in the vortex decay rate as the system enters a regime of two-dimensional vortex dynamics. As the system approaches the condensation transition temperature we find that the vortex decay rate is strongly sensitive to dimensionality and temperature, observing a large enhancement for quasi-two-dimensional traps. Three-dimensional simulations of the recent vortex dipole decay experiment of Neely et al. [Phys. Rev. Lett. 104, 160401 (2010)] confirm two-dimensional vortex dynamics, and predict a dipole lifetime consistent with experimental observations and suppression of Kelvon-induced vortex decay in highly oblate condensates.
description: 8 pages, 8 figures
Arbitrary-order non-linear contribution to self-steepening
Creators: name: Kasparian, J.
name: Béjot, P.
name: Wolf, J. -P.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Based on the recently published generalized Miller formula, we derive the spectral dependence of the contribution of arbitrary-order non-linear indices to the group-velocity index. We show that in the context of laser filamentation in gases all experimentally-accessible orders (up to the $9^{th}$-order non-linear susceptibility $χ^{(9)}$ in air and $χ^{(11)}$ in argon) have contributions of alternative signs and similar magnitudes. Moreover, we show both analytically and numerically that the dispersion term of the non-linear indices must be considered when computing the intensity-dependent group velocity.
description: 10 pages, 3 figures (14 panels)
EU-Turkey Relations in the Midst of a Global Storm
Creators: name: Morillas, Pol
name: Sökmen, Melike Janine
name: Ünver, Akın
Publisher: name: Zenodo
Year: 2017
Subjects: European Union; Turkey; EU-Turkey Relations; Emerging Powers; International Order; Russia; Populism; Authoritarianism; Foreign Policy; US Foreign Policy; Transformation

description: FEUTURE Online Paper No. 7

This paper presents the global movements, trends and actors driving EU-Turkey relations: namely, the global shift of power, the declining liberal international order and the rise of authoritarianism, populism, the new US foreign policy under Trump and Russia’s rise under Putin. It analyzes the impact of these drivers on the EU and Turkey respectively, and proposes the most likely scenario on the future of EU-Turkey relations under this constellation of drivers. It argues that the transformations at the global level have diminished the capacity of the EU to act as a “force for good” in international affairs which, coupled with Turkey’s will to emerge as a global actor, is likely to increase conflictual dynamics between both actors.
description: This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 692976. This publication reflects the views only of the authors, and the Commission cannot be held responsible for any use which may be made of the information contained therein.
From language learners to bilingual providers : second language socialization of bilingual mothers in South Korea
Creators: name: Sohn, Bong-Gi
Publisher: name: University of British Columbia
Year: 2018

description: In the context of unprecedented globalization and migration flows, South Korea, known for promoting the modern nation-state’s ‘one-nation, one-language’ ideology, has undergone recalibration of its national identity and language ideologies. Since the mid-2000s, the South Korean government has developed a dual contradictory bilingual framework—assimilative Korean as a Second Language and celebratory multilingual development—particularly for damunhwa (multicultural) families consisting of international marriages between Korean men and foreign women and their children. Despite the government’s enthusiastic development of language policy, little is known of the grounds on which this bilingual initiative was established and how it is practiced in families. Adopting an approach that Bronson and Watson-Gegeo (2008) have called “language socialization as topic,” this qualitative study employed a document analysis and interviews to investigate the representational practices of foreign mothers across their lifespan in South Korea. I first address how the national-level language policy guides the regulation of foreign mothers’ four linear life trajectories: marriage, migration, childbirth and education, and home economics. Findings from the policy analysis represent the government’s (1) emphasis on damunhwa mothers’ exclusive use of Korean, (2) selective recommendation of heritage/foreign language for nationalistic purposes, and (3) discouragement of heritage language use in damunhwa families. They also demonstrate the government’s lack of concern with the roles of Korean fathers in family language socialization. The four damunhwa mothers in this study—from Japan, China, Vietnam, and Kyrgyzstan—presented their survival stories on learning to become dedicated mothers who are expected to use Korean with their children. Their narratives also demonstrate how the linguistic hierarchy is exacerbated and how they are demoralized in their bilingual workplaces. The mothers’ stated promotion of heritage languages often serves instrumental purposes rather than fostering bilingual and bicultural identities. These findings explain how damunhwa mothers have become the heart of linguistic nationalism in globalized times for South Korea, where the government has failed to recognize the fundamental importance of the situated nature of multilingual socialization of families. Through illuminating what has been neglected by policy makers, this dissertation calls for more equitable and gender-sensitive approaches to bilingual education in transnational and translingual times.
The Universal Time-Dependent Ginzburg-Landau theory
Creators: name: Kapustin, Anton
name: Mrini, Luke
Publisher: name: arXiv
Year: 2022
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study the hydrodynamics of superconductors within the framework of Schwinger-Keldysh Effective Field Theory. We show that in the vicinity of the superconducting phase transition the most general leading-order EFT satisfying the local Kubo-Martin-Schwinger condition is described by a version of the Time-Dependent Ginzburg-Landau (TDGL) equations augmented with stochastic terms. This version of TDGL is applicable in the gapless regime independently of any microscopic details. Within this approach, it is possible to include systematically the effects of non-uniform temperature and heat conductivity, as well as explicit or spontaneous breaking of time reversal. We also introduce a thermal version of the Josephson relation and use it to construct an exotic hydrodynamics describing a phase of matter where heat can flow without dissipation.
description: v2: 35 pages, version published in Physical Review B
X-ray coronae in simulations of disc galaxy formation
Creators: name: Crain, Robert A.
name: McCarthy, Ian G.
name: Frenk, Carlos S.
name: Theuns, Tom
name: Schaye, Joop
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The existence of X-ray luminous gaseous coronae around massive disc galaxies is a long-standing prediction of galaxy formation theory in the cold dark matter cosmogony. This prediction has garnered little observational support, with non-detections commonplace and detections for only a relatively small number of galaxies which are much less luminous than expected. We investigate the coronal properties of a large sample of bright, disc-dominated galaxies extracted from the GIMIC suite of cosmological hydrodynamic simulations recently presented by Crain et al. Remarkably, the simulations reproduce the observed scalings of X-ray luminosity with K-band luminosity and star formation rate and, when account is taken of the density structure of the halo, with disc rotation velocity as well. Most of the star formation in the simulated galaxies (which have realistic stellar mass fractions) is fuelled by gas cooling from a quasi-hydrostatic hot corona. However, these coronae are more diffuse, and of a lower luminosity, than predicted by the analytic models of White & Frenk because of a substantial increase in entropy at z ~ 1-3. Both the removal of low entropy gas by star formation and energy injection from supernovae contribute to this increase in entropy, but the latter is dominant for halo masses M_200
description: 21 pages, 16 figures. Accepted for publication in MNRAS. Accompanying visualisations at http://pulsar.swin.edu.au/~rcrain/webpages/X-ray_coronae.html
Zeeman ratchets: pure spin current generation in mesoscopic conductors with non-uniform magnetic fields
Creators: name: Scheid, Matthias
name: Bercioux, Dario
name: Richter, Klaus
Publisher: name: Universität Regensburg
Year: 2007
Subjects: subject: 530 Physik

description: We consider the possibility to employ a quantum wire realized in a two-dimensional electron gas (2DEG) as a spin ratchet. We show that a net spin current without accompanying net charge transport can be induced in the nonlinear regime by an unbiased external driving via an ac voltage applied between the contacts at the ends of the quantum wire. To achieve this, we make use of the coupling of the electron spin to inhomogeneous magnetic fields created by ferromagnetic stripes patterned on the semiconductor heterostructure that harbors the 2DEG. Using recursive Green function techniques, we numerically study two different set-ups, consisting of one and two ferromagnetic stripes, respectively.
Prospecting for new catechol-O-methyltransferase (COMT) inhibitors as a potential treatment for Parkinson’s disease: a study by molecular dynamics and structure-based virtual screening
Creators: name: da Silva, Iasmin Ramos
name: Parise, Michelle Rocha
name: Pereira, Maristela
name: da Silva, Roosevelt Alves
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Computational Biology

description: Parkinson’s disease (PD) is a neurodegenerative, chronic, and progressive disease, common in the elderly. The catechol-O-methyltransferase (COMT) is a monomeric enzyme involved in dopamine (DA) degradation, the neurotransmitter in deficit in patients with PD. The reference treatment of PD consists of levodopa (L-dopa) administration, which is the precursor of DA. The inhibition of COMT is an adjuvant treatment in PD since it keeps DA levels constant. The goal of this study was to identify drug candidates capable of inhibiting COMT for the treatment of PD and identify important fragments of these molecules. Initially, we analyzed the flexibility of COMT and defined its main conformations in solution regarding the absence (system I) and presence of the S-adenosyl-L-methionine (SAM) cofactor (system II) through molecular dynamics (MD) simulations. Two regions in these structures were selected for molecular docking, firstly the entire cavity where the cofactor and substrates are bound and secondly the specific biding region of the enzyme substrates. Based on the conformations of the MD, the virtual screening (VS) was performed against FDA Approved and Zinc Natural Products databases aiming at the selection of the best compounds. Subsequently, the absorption, distribution, metabolization, excretion, and toxicity (ADMET) properties, as well as drug-score and drug-likeness indexes of the most promising compounds were analyzed. After a detailed analysis of the compounds selected by structure-based VS, it was possible to highlight the fragments most frequently involved in their stability: 2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole, 9H-Benz(c)indole(3,2,1-ij)(1,5)naphthyridin-9-one and (10R,13S)-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17dodecahydrocyclopenta[a]phenanthren-3-one. The identification of these potential fragments is essential for the prospection of more specific inhibitors against COMT using the technique of Fragment-based lead discovery (FBLD). Besides, this study allowed us to identify the potential COMT inhibitors through a complete understanding of molecular-level interactions based on the flexibility of this protein. Communicated by Ramaswamy H. Sarma
Turkish and European Identity Constructions in the 1946-1999 Period
Creators: name: Aydın-Düzgit, Senem
name: Chovanec, Johanna
name: Gülmez, Seçkin Barış
name: Rumelili, Bahar
name: Topal, Alp Eren
Publisher: name: Zenodo
Year: 2018
Subjects: European Union; Turkey; EU-Turkey relations; Identity Politics; Identity Construction; 1946-1999; Critical Discourse Analysis; CDA; Representation; Newspaper; Nationalism; Citizenship

description: FEUTURE Online Paper No. 15

This FEUTURE paper focuses on Turkey’s and Europe’s perceptions of each other in identity and cultural terms between 1946 and 1999. It identifies the identity representations developed by both sides in response to key selected political and cultural drivers of this period by subjecting selected newspaper articles and editorials as well as popular journals in Europe and Turkey to Critical Discourse Analysis (CDA). Identity representations are then discussed in relation to the pre-identified focal issues in the relationship; namely nationalism, status in international society, civilisation and state-citizen relations. The study finds that mutual identity representations in Turkey and Europe continue to be contested in this period. Yet, a growing convergence of English, French, and German representations of Turkey is observed on the European side whereas divergence of representations of Europe grows on the Turkish front. While the establishment of the conception of multiple civilizations in both Europe and Turkey as well as the rise of nationalism in both contexts make it harder to justify policies aiming at convergence throughout this period, it is observed that the rise of identity representations that focus on state-citizen relations have consistently supported convergence and that European identity representations that focus on Europe’s status in international society have generally supported cooperation with Turkey in this period. Conversely, Turkish identity representations focusing on Turkey’s status in international society have become polarized and were employed in ways that justified both conflict and cooperation/convergence with Europe.
description: This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 692976. This publication reflects the views only of the authors, and the Commission cannot be held responsible for any use which may be made of the information contained therein.
Structured Negativity: A physically realizable measure of entanglement based on structural physical approximation
Creators: name: Kumari, Anu
name: Adhikari, Satyabrata
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantification of entanglement is one of the most important problem in quantum information theory. In this work, we will study this problem by defining a physically realizable measure of entanglement for any arbitrary dimensional bipartite system $ρ$, which we named as structured negativity $(N_S(ρ))$. We have shown that the introduced measure satisfies the properties of a valid entanglement monotone. We also have established an inequality that relate negativity and the structured negativity. For $d\otimes d$ dimensional state, we conjecture from the result obtained in this work that negativity coincide with the structured negativity when the number of negative eigenvalues of the partially transposed matrix is equal to $\frac{d(d-1)}{2}$. Moreover, we proved that the structured negativity not only implementable in the laboratory but also a better measure of entanglement in comparison to negativity. In few cases, we obtain that structure negativity gives better result than the lower bound of the concurrence obtained by Albeverio [Phys. Rev. Lett. \textbf{95}, 040504 (2005)].
description: 8 pages, 5 figures, Accepted in Annals of Physics