cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Uniform Penalty inversion of two-dimensional NMR Relaxation data
Creators: name: Bortolotti, V.
name: Brown, R. J. S.
name: Fantazzini, P.
name: Landi, G.
name: Zama, F.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: The inversion of two-dimensional NMR data is an ill-posed problem related to the numerical computation of the inverse Laplace transform. In this paper we present the 2DUPEN algorithm that extends the Uniform Penalty (UPEN) algorithm [Borgia, Brown, Fantazzini, {\em Journal of Magnetic Resonance}, 1998] to two-dimensional data. The UPEN algorithm, defined for the inversion of one-dimensional NMR relaxation data, uses Tikhonov-like regularization and optionally non-negativity constraints in order to implement locally adapted regularization. In this paper, we analyze the regularization properties of this approach. Moreover, we extend the one-dimensional UPEN algorithm to the two-dimensional case and present an efficient implementation based on the Newton Projection method. Without any a-priori information on the noise norm, 2DUPEN automatically computes the locally adapted regularization parameters and the distribution of the unknown NMR parameters by using variable smoothing. Results of numerical experiments on simulated and real data are presented in order to illustrate the potential of the proposed method in reconstructing peaks and flat regions with the same accuracy.
New hybrids based on benzimidazole and diazepine moieties: design, synthesis, characterization, molecular docking studies and their in vitro interactions with benzodiazepine receptors
Creators: name: Takhti, Samaneh
name: Pordel, Mehdi
name: Bozorgmehr, Mohammad Reza
name: Davoodnia, Abolghasem
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biochemistry
Physical Sciences not elsewhere classified
Medicine
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: Benzodiazepines are one of the most widely prescribed pharmacologic agents in the world. They are employed for numerous indications, including anxiety, insomnia, muscle relaxation, relief from spasticity caused by central nervous system pathology and epilepsy. In this work, we have synthesized some new hybrids based on benzimidazole and diazepine scaffolds from the reaction of suitable benzimidazole derivatives with glycine. NMR spectra, IR and mass as well as elemental analyses approved the structure of the title compounds. In vitro interactions of the title compounds were also examined on recombinant benzodiazepine receptors (αxβ2/3γ2, x = 1–3, 5) expressed in HEK293 cells. The results indicated that the title compounds exhibited suitable affinity for α1β2 γ2 subtype (Ki = 16–29 nM). To achieve deeper insight into their interactions with benzodiazepine receptors, molecular dynamics simulation was employed. According to the results obtained from the molecular dynamics simulation, Pro85, Leu103, Pro101, Gln102, Ile79, Ser80, Pro17, Leu82 and Val84 interact with the most potent ligand by hydrophobic interactions and Asp86 and Leu87 interact with the ligand by hydrogen bond interactions. Communicated by Ramaswamy H. Sarma
Quantum gates and architecture for the quantum simulation of the Fermi-Hubbard model
Creators: name: Dallaire-Demers, Pierre-Luc
name: Wilhelm, Frank K.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum computers are the ideal platform for quantum simulations. Given enough coherent operations and qubits, such machines can be leveraged to simulate strongly correlated materials, where intricate quantum effects give rise to counter-intuitive macroscopic phenomena such as high-temperature superconductivity. In this paper, we provide a gate decomposition and an architecture for a quantum simulator used to simulate the Fermi-Hubbard model in a hybrid variational quantum-classical algorithm. We propose a simple planar implementation-independent layout of qubits that can also be used to simulate more general fermionic systems. By working through a concrete application, we show the gate decomposition used to simulate the Hamiltonian of a cluster of the Fermi-Hubbard model. We briefly analyze the Trotter-Suzuki errors and estimate the scaling properties of the algorithm for more complex applications.
description: 13 pages, 10 figures
In silico approaches and in vitro assays identify a coumarin derivative as antiviral potential against SARS-CoV-2
Creators: name: da Silva Gomes, Gabriel Felix
name: Camargo, Priscila Goes
name: de Santiago-Silva, Kaio Maciel
name: Suzukawa, Helena Tiemi
name: da Silva Ribeiro, Ana Paula Sotero
name: Orsato, Alexandre
name: Nakazato, Gerson
name: Yamada-Ogatta, Sueli Fumie
name: Faccin-Galhardi, Ligia Carla
name: da Silva Lima, Camilo Henrique
name: de Lima Ferreira Bispo, Marcelle
name: Perez, Carla Cristina
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: COVID-19, a disease caused by SARS-CoV-2, was declared a pandemic in 2020 and created a global crisis in health systems, with more than 545 million confirmed cases and 6.33 million deaths. In this sense, this work aims to identify possible inhibitors of the SARS-CoV-2 RdRp enzyme using in silico approaches. RdRp is a crucial enzyme in the replication and assembly cycle of new viral particles and a critical pharmacological target in the treatment of COVID-19. We performed a virtual screening based on molecular docking from our in-house chemical library, which contains a diversity of 313 structures from different chemical classes. Nine compounds were selected since they showed important interactions with the active site from RdRp. Next, the ADME-Tox in silico predictions served as a filter and selected the three most promising compounds: a coumarin LMed-052, a hydantoin LMed-087, and a guanidine LMed-250. Molecular dynamics simulations revealed details such as changes in the positions of ligands and catalytic residues during the simulations compared to the complex from molecular docking studies. Binding free energy analysis was performed using the MMGBSA method, demonstrating that LMed-052 and LMed-087 have better affinities for the RdRp by energetic contributions to the stability of the complexes when compared to LMed-250. Furthermore, LMed-052 showed significant in vitro inhibition against MHV-3, decreasing 99% of viral titers. Finally, these findings are useful to guide structural modifications aiming to improve the potential of these compounds to act as inhibitors of SARS-CoV-2. Communicated by Ramaswamy H. Sarma
In silico designed microtubule-stabilizer drugs against tauopathy in Alzheimer’s disease
Creators: name: Sarukhanyan, Edita
name: Dandekar, Thomas
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Microtubules are the main building blocks of the cytoskeleton that maintain the shape of the cell. Microtubule-associated proteins, such as Tau protein, facilitate their plasticity in cells. Highly phosphorylated Tau has weak affinity to microtubule and, hence, high probability of aggregation into neurofibrillary tangles (tauopathy). Alzheimer’s disease evolves when Tau proteins are abnormally phosphorylated. To prevent tauopathy in Alzheimer’s disease, we designed drugs de novo targeting them in silico to the phosphorylated Tau-microtubule complexes. Our molecular docking (AutoDock, MOE, GOLD) and molecular dynamics (GROMACS, 2019.6) simulation results revealed compound 23 (C12H28N4O5) as a potential drug candidate, since it can bind (-11.1 kcal/mol by AutoDock) and fix not only phosphorylated Tau on the surface of microtubules, but also prevent their aggregation into bundles. In addition, compound 23 has shown its ability to de-bundle already grouped phosphorylated peptides into single pieces. Communicated by Ramaswamy H. Sarma
Improved bounds on the diameter of lattice polytopes
Creators: name: Deza, Antoine
name: Pournin, Lionel
Publisher: name: arXiv
Year: 2016
Subjects: subject: Metric Geometry (math.MG)
subject: Combinatorics (math.CO)
subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: We show that the largest possible diameter $δ(d,k)$ of a $d$-dimensional polytope whose vertices have integer coordinates ranging between $0$ and $k$ is at most $kd-\lceil2d/3\rceil$ when $k\geq3$. In addition, we show that $δ(4,3)=8$. This substantiates the conjecture whereby $δ(d,k)$ is at most $\lfloor(k+1)d/2\rfloor$ and is achieved by a Minkowski sum of lattice vectors.
description: 14 pages, 1 figure
The twofold diabatization of the KRb $(1\sim 2)^1Π$ complex in the framework of \emph{ab initio} and deperturbation approaches
Creators: name: Kozlov, S. V.
name: Pazyuk, E. A.
name: Stolyarov, A. V.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Atomic and Molecular Clusters (physics.atm-clus)
subject: FOS: Physical sciences

description: We performed a diabatization of the mutually perturbed $1^1Π$ and $2^1Π$ states of KRb based on both electronic structure calculation and direct coupled-channel deperturbation analysis of experimental energies. The potential energy curves (PECs) of the diabatic states and their scalar coupling were constructed from the \textit{ab initio} adiabatic PECs by analytically integrating the radial $\langle ψ_1^{ad}|\partial /\partial R|ψ_2^{ad}\rangle$ matrix element obtained by a finite-difference method. The diabatic potentials and electronic coupling function were refined by the least squares fitting of the rovibronic termvalues of the $1^1Π\sim 2^1Π$ complex. The empirical PECs combined with the coupling function as well as the diabatized spin-orbit coupling and transition dipole matrix elements are useful for further deperturbation treatment of both singlet and triplet states manifold.
DFT analysis on the adsorption of melamine in Ga12-N12/P12 nanocages: solvent effects, SERS analysis, reactivity properties
Creators: name: Al-Otaibi, Jamelah S.
name: Mary, Y. Sheena
name: Mary, Shyma
name: Mondal, Asmita
name: Acharjee, Nivedita
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: Due to its negative effects on people, melamine contamination in food products are detected and filtered. Amongst several sensory schemes for the screening of melamine poisoning, one of the most promising techniques is the use of nanomaterial based sensing for real time applicability in industries. In the current work, we have looked into the way melamine binds to Ga12-N12/P12 nanocages. Surface-enhanced Raman scattering (SERS), a successful spectroscopic technique is used to monitor melamine. Density functional theoretical (DFT) computations were used to study the sensing properties of melamine (Me) with Ga12-N12/P12 nanocages. Reactivity and Mulliken charge analyses show charge transfer from melamine to nanocage. Me-Ga12-N12 and Me-Ga12P12 clusters have adsorption energies of −47.54 and −33.12 kcal/mol, respectively. All nanocage-Me systems have a significant increase in polarizability. The electron densities revealed non-covalent interactions in the adsorbed systems. All adsorption energies in aqueous media are negative, indicating an attractive and exothermic reaction, with maximum value in water for Me-Ga12N12 and in acetone for Me-Ga12P12. Evidence of SERS is observed due to the enhancement of different vibrational modes. Communicated by Ramaswamy H. Sarma
A comment on power-law inflation with a dark radiation component
Creators: name: Di Valentino, Eleonora
name: Bouchet, Francois R.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Tram et al. 2016 recently pointed out that power-law inflation in presence of a dark radiation component may relieve the 3.3 sigma tension which exists within standard LCDM between the determination of the local value of the Hubble constant by Riess et al. (2016) and the value derived from CMB anisotropy data by the Planck collaboration. In this comment, we simply point out that this interesting proposal does not help in solving the $σ_8$ tension between the Planck data and, e.g., the weak lensing measurements. Moreover, when the latest constraints on the reionization optical depth obtained from Planck HFI data are included in the analysis, the $H_0$ tension reappears and this scenario looses appeal.
description: 5 pages, 4 figures
Disordered regions endow structural flexibility to shell proteins and function towards shell–enzyme interactions in 1,2-propanediol utilization microcompartment
Creators: name: Kumar, Gaurav
name: Hazra, Jagadish Prasad
name: Sinha, Sharmistha
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Astronomical and Space Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Hematology
subject: Computational Biology

description: Intrinsically disordered regions in proteins have been functionally linked to the protein–protein interactions and genesis of several membraneless organelles. Depending on their residual makeup, hydrophobicity or charge distribution they may remain in extended form or may assume certain conformations upon biding to a partner protein or peptide. The present work investigates the distribution and potential roles of disordered regions in the integral proteins of 1,2-propanediol utilization microcompartments. We use bioinformatics tools to identify the probable disordered regions in the shell proteins and enzyme of the 1,2-propanediol utilization microcompartment. Using a combination of computational modelling and biochemical techniques we elucidate the role of disordered terminal regions of a major shell protein and enzyme. Our findings throw light on the importance of disordered regions in the self-assembly, providing flexibility to shell protein and mediating its interaction with a native enzyme. Communicated by Ramaswamy H. Sarma
Numerical matrix method for quantum periodic potentials
Creators: name: Vot, Felipe Le
name: Meléndez, Juan J.
name: Yuste, Santos Bravo
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: 81-01, 81-08

description: A numerical matrix methodology is applied to quantum problems with periodic potentials. The procedure consists essentially in replacing the true potential by an alternative one, restricted by an infinite square well, and in expressing the wave functions as finite superpositions of eigenfunctions of the infinite well. A matrix eigenvalue equation then yields the energy levels of the periodic potential within an acceptable accuracy. The methodology has been successfully used to deal with problems based on the well-known Kronig-Penney (KP) model. Besides the original model, these problems are a dimerized KP solid, a KP solid containing a surface, and a KP solid under an external field. A short list of additional problems that can be solved with this procedure is presented.
description: 9 pages, 12 figures, Ref. 9 differs from the one appearing in the AJP paper
Elimination of Numerical Cherenkov Instability in flowing-plasma Particle-In-Cell simulations by using Galilean coordinates
Creators: name: Lehe, Remi
name: Kirchen, Manuel
name: Godfrey, Brendan B.
name: Maier, Andreas R.
name: Vay, Jean-Luc
Publisher: name: arXiv
Year: 2016
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Particle-In-Cell (PIC) simulations of relativistic flowing plasmas are of key interest to several fields of physics (including e.g. laser-wakefield acceleration, when viewed in a Lorentz-boosted frame), but remain sometimes infeasible due to the well-known numerical Cherenkov instability (NCI). In this article, we show that, for a plasma drifting at a uniform relativistic velocity, the NCI can be eliminated by simply integrating the PIC equations in Galilean coordinates that follow the plasma (also sometimes known as comoving coordinates) within a spectral analytical framework. The elimination of the NCI is verified empirically and confirmed by a theoretical analysis of the instability. Moreover, it is shown that this method is applicable both to Cartesian geometry and to cylindrical geometry with azimuthal Fourier decomposition.
description: 18 pages, 6 figures
Properties of Magnetic Tongues over a Solar Cycle
Creators: name: Poisson, M.
name: Démoulin, P.
name: Fuentes, M. López
name: Mandrini, C. H.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The photospheric spatial distribution of the main magnetic polarities of bipolar active regions (ARs) presents during their emergence deformations are known as magnetic tongues. They are attributed to the presence of twist in the toroidal magnetic flux-tubes that form the ARs. The aim of this article is to study the twist of newly emerged ARs from the evolution of magnetic tongues observed in photospheric line-of-sight magnetograms. We apply the procedure described by Poisson et al. (2015, Solar Phys. 290, 727) to ARs observed over the full Solar Cycle 23 and the beginning of Cycle 24. Our results show that the hemispherical rule obtained using the tongues as a proxy of the twist has a weak sign-dominance (53 % in the southern hemisphere and 58 % in the northern hemisphere). By defining the variation of the tongue angle, we characterize the strength of the magnetic tongues during different phases of the AR emergence. We find that there is a tendency of the tongues to be stronger during the beginning of the emergence and to become weaker as the AR reaches its maximum magnetic flux. We compare this evolution with the emergence of a toroidal flux-rope model with non-uniform twist. The variety of evolution of the tongues in the analyzed ARs can only be reproduced when using a broad range of twist profiles, in particular having a large variety of twist gradient in the direction vertical to the photosphere. Although the analytical model used is a special case, selected to minimize the complexity of the problem, the results obtained set new observational constraints to theoretical models of flux-rope emergence that form bipolar ARs.
In silico designed microtubule-stabilizer drugs against tauopathy in Alzheimer’s disease
Creators: name: Sarukhanyan, Edita
name: Dandekar, Thomas
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Microtubules are the main building blocks of the cytoskeleton that maintain the shape of the cell. Microtubule-associated proteins, such as Tau protein, facilitate their plasticity in cells. Highly phosphorylated Tau has weak affinity to microtubule and, hence, high probability of aggregation into neurofibrillary tangles (tauopathy). Alzheimer’s disease evolves when Tau proteins are abnormally phosphorylated. To prevent tauopathy in Alzheimer’s disease, we designed drugs de novo targeting them in silico to the phosphorylated Tau-microtubule complexes. Our molecular docking (AutoDock, MOE, GOLD) and molecular dynamics (GROMACS, 2019.6) simulation results revealed compound 23 (C12H28N4O5) as a potential drug candidate, since it can bind (-11.1 kcal/mol by AutoDock) and fix not only phosphorylated Tau on the surface of microtubules, but also prevent their aggregation into bundles. In addition, compound 23 has shown its ability to de-bundle already grouped phosphorylated peptides into single pieces. Communicated by Ramaswamy H. Sarma
Computational prediction of B and T-cell epitopes of Kyasanur Forest Disease virus marker proteins towards the development of precise diagnosis and potent subunit vaccine
Creators: name: Hafeez, Sayad
name: Achur, Rajeshwara
name: Kiran, S. K.
name: Thippeswamy, N. B.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Kyasanur Forest Disease (KFD), also known as ‘monkey fever’, caused by KFD Virus (KFDV), is a highly neglected tropical disease endemic to Western Ghat region of Karnataka, India. Recently, KFD, which is fatal for both monkeys and humans with a mortality rate of 2–10% has been found to spread from its epicenter to neighboring districts and states also. The current ELISA based KFD detection method is very non-specific due to cross-reactivity with other flaviviruses. Further, presently available formalin-inactivated vaccine has been found to be less effective leading to disease susceptibility and severity. To address these, the present study was aimed at predicting the potent specific B and T-cell epitopes of KFDV immunogenic marker proteins using diverse computational tools aiming at developing precise diagnostic method and an effective subunit vaccine. Here, we have chosen E, NS1 and NS5 proteins as markers of KFDV by taking into account of their differential and non-overlapping sequences with selected arboviruses. Based on the linear and nonlinear epitope prediction tools and important biophysical parameters, we identified three potential linear and ten nonlinear B-cell epitopes. We also predicted T-cell epitope peptides which binds to MHC class-I and class-II receptors for the effective T-cell activation. Thus, our molecular docking and molecular dynamics simulation analysis has identified six different TH-cell epitopes based on the distribution frequency of MHC-II haplotypes in the human population and one TC-cell epitope from NS5 protein that has maximum interaction with class-I MHC. Overall, we have successfully identified potential B and T-cell epitope marker peptides present in the envelope and two non-structural proteins. Communicated by Ramaswamy H. Sarma
Inhibition of the predicted allosteric site of the SARS-CoV-2 main protease through flavonoids
Creators: name: Kubra, Bibi
name: Badshah, Syed Lal
name: Faisal, Shah
name: Sharaf, Mohamed
name: Emwas, Abdul-Hamid
name: Jaremko, Mariusz
name: Abdalla, Mohnad
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Since its emergence in 2019, coronavirus infection (COVID-19) has become a global pandemic and killed several million people worldwide. Even though several types of vaccines are available against the COVID-19 virus, SARS-CoV-2, new strains are emerging that pose a constant danger to vaccine effectiveness. In this computational study, we identified and predicted potent allosteric inhibitors of the SARS-CoV-2 main protease (Mpro). Via molecular docking and simulations, more than 100 distinct flavonoids were docked with the allosteric site of Mpro. Docking experiments revealed four top hit compounds (Hesperidin, Schaftoside, Brickellin, and Marein) that bound strongly to the Mpro predicted allosteric site. Simulation analyses further revealed that these continually interacted with the enzyme’s allosteric region throughout the simulation time. ADMET and Lipinski drug likenesses were calculated to indicate the therapeutic value of the top four hits: They were non-toxic and exhibited high human intestinal absorption concentrations. These novel allosteric site inhibitors provide a higher chance of drugging SARS-CoV2 Mpro due to the rapid mutation rate of the viral enzyme’s active sites. Our findings provide a new avenue for developing novel allosteric inhibitors of SARS-CoV-2 Mpro. Communicated by Ramaswamy H. Sarma
Bulk flow scaling for turbulent channel and pipe flows
Creators: name: Chen, Xi
name: Hussain, Fazle
name: She, Zhen-Su
Publisher: name: arXiv
Year: 2016
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences
subject: 76F40

description: We report a theory deriving bulk flow scaling for canonical wall-bounded flows. The theory accounts for the symmetries of boundary geometry (flat plate channel versus circular pipe) by a variational calculation for a large-scale energy length, which characterizes its bulk flow scaling by a simple exponent, i.e. $m=4$ for channel and 5 for pipe. The predicted mean velocity shows excellent agreement with several dozen sets of quality empirical data for a wide range of the Reynolds number (Re), with a universal bulk flow constant $κ\approx0.45$. Predictions for dissipation and turbulent transport in the bulk flow are also given, awaiting data verification.
description: 4 pages, 4 figures
Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations
Creators: name: Guo, Chuan
name: Li, Qinxuan
name: Xiao, Jiujia
name: Ma, Feng
name: Xia, Xun
name: Shi, Mingsong
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biophysics
Space Science
Medicine
Molecular Biology
Pharmacology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Computational Biology

description: Focal adhesion kinase (FAK) belongs to the nonreceptor tyrosine kinases, which selectively phosphorylate tyrosine residues on substrate proteins. FAK is associated with bladder, esophageal, gastric, neck, breast, ovarian and lung cancers. Thus, FAK has been considered as a potential target for tumor treatment. Currently, there are six adenosine triphosphate (ATP)-competitive FAK inhibitors tested in clinical trials but no approved inhibitors targeting FAK. Defactinib (VS-6063) is a second-generation FAK inhibitor with an IC50 of 0.6 nM. The binding model of VS-6063 with FAK may provide a reference model for developing new antitumor FAK-targeting drugs. In this study, the VS-6063/FAK binding model was constructed using ensemble docking and molecular dynamics simulations. Furthermore, the molecular mechanics/generalized Born (GB) surface area (MM/GBSA) method was employed to estimate the binding free energy between VS-6063 and FAK. The key residues involved in VS-6063/FAK binding were also determined using per-residue energy decomposition analysis. Based on the binding model, VS-6063 could be separated into seven regions to enhance its binding affinity with FAK. Meanwhile, 60 novel defactinib-based compounds were designed and verified using ensemble docking. Overall, the present study improves our understanding of the binding mechanism of human FAK with VS-6063 and provides new insights into future drug designs targeting FAK. Communicated by Ramaswamy H. Sarma
Equilibrium states on operator algebras associated to self-similar actions of groupoids on graphs
Creators: name: Laca, Marcelo
name: Raeburn, Iain
name: Ramagge, Jacqui
name: Whittaker, Michael F.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Operator Algebras (math.OA)
subject: Dynamical Systems (math.DS)
subject: Group Theory (math.GR)
subject: FOS: Mathematics

description: We consider self-similar actions of groupoids on the path spaces of finite directed graphs, and construct examples of such self-similar actions using a suitable notion of graph automaton. Self-similar groupoid actions have a Cuntz-Pimsner algebra and a Toeplitz algebra, both of which carry natural dynamics lifted from the gauge actions. We study the equilibrium states (the KMS states) on the resulting dynamical systems. Above a critical inverse temperature, the KMS states on the Toeplitz algebra are parametrised by the traces on the full $C^*$-algebra of the groupoid, and we describe a program for finding such traces. The critical inverse temperature is the logarithm of the spectral radius of the incidence matrix of the graph, and at the critical temperature the KMS states on the Toeplitz algebra factor through states of the Cuntz-Pimsner algebra. Under a verifiable hypothesis on the self-similar action, there is a unique KMS state on the Cuntz-Pimsner algebra. We discuss an explicit method of computing the values of this KMS state, and illustrate with examples.
description: 48 pages
title:   Some Kentucky clays, including kaolinic, plastic and fire clays
title:  clays in several parts of Kentucky, with some account of sands, marls and limestones
titleType: Subtitle
Creators: name: Foerste, Aug
name: Gardner, James H.
Publisher: name: Kentucky Geological Survey, University of Kentucky
Year: 2023
Subjects: classificationCode: 1.5
subject: FOS: Earth and related environmental sciences

description: The bulletin is preliminary in character and is offered now simply in order to meet the urgent calls for all information concerning our clays that is at present available. A more comprehensive report, in which not only the geology and distribution of our clays, but also their technological values, will be given, will follow in due course.

Data for such a bulletin are being gathered as rapidly as circumstances will permit. Among the clays upon which more field work is required are some of those associated with the coals and Conglomerate Measures of the Eastern Coalfield; those in other Lower Carbon­iferous regions than are included in this bulletin; those on the western rim of the Ordovician (Lower Silurian), and in parts of the Western Coalfield; while those of the Jackson's Purchase region are to be studied in greater detail. It is believed that another year of field work will yield results sufficient to develop the lines along which technological work may be most profit­ably carried.
description: Kentucky Geological Survey, ser. 3, Bulletin 6, 223p.
description: Part I

    1. The Kaolins and Plastic Clays on the Eastern Rim of the Western Coalfield, by J. H. Gardner, pp 7 - 63
    2. Clays in the Red River Valley, by J. H. Gardner, pp 64 - 79
    3. Clays and Sands of Jackson's Purchase, by J. H. Gardner, pp 80 - 123
    4. Some Clays in the Western Lead, Zinc and Spar District/Clays in Crittenden and Livingston County, by F. Julius Fohs

Part II

    Silurian Clays, with notes on clays of the Waverly and Irvine Formations, by Aug. F. Foerste, pp 143 - 178

Part III

    Miscellaneous Analyses of Kentucky Clays and Marls, compiled by Jas. H. Gardner, pp 179 - 223
Heterogeneous nucleation and heat flux avalanches in La(Fe,Si)$_{13}$ magnetocaloric compounds near the critical point
Creators: name: Bennati, C.
name: Gozzelino, L.
name: Olivetti, E. S.
name: Basso, V.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The phase transformation kinetics of LaFe$_{11.41}$Mn$_{0.30}$Si$_{1.29}$-H$_{1.65}$ magnetocaloric compound is addressed by low rate calorimetry experiments. Scans at 1 mK/s show that its first order phase transitions are made by multiple heat fllux avalanches. Getting very close to the critical point, the step-like discontinuous behavior associated with avalanches is smoothed out and thermal hysteresis disappears. This result is confirmed by magneto-resistivity measurements and allows to measure accurate values of the zero field hysteresis ($ΔT_{hyst}$ = 0.37 K) and of the critical field (H$_c$ = 1.19 T). The number and magnitude of heat flux avalanches change with magnetic field, showing the interplay between the intrinsic energy barrier between phases and the microstructural disorder of the sample.
description: 5 pages, 4 figures
Design, synthesis and molecular docking and ADME studies of novel hydrazone derivatives for AChE inhibitory, BBB permeability and antioxidant effects
Creators: name: Osmaniye, Derya
name: Ahmad, Iqrar
name: Sağlık, Begüm Nurpelin
name: Levent, Serkan
name: Patel, Harun M.
name: Ozkay, Yusuf
name: Kaplancıklı, Zafer Asım
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Medicine
Neuroscience
Pharmacology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified

description: Alzheimer’s disease (AD) is a progressive and fatal neurodegenerative disease that is characterized by memory and cognitive impairments that predominantly affects the elderly and is the most common cause of dementia. As is known, the AChE enzyme consists of two parts. In this work, 10 new hydrazones (3a–3j) were designed and synthesized. Naphthalene, indole, benzofuran and benzothiophene rings were used to interact with the PAS region. 4-fluorophenyl and 4-fluorobenzyl structures were preferred for interaction with the CAS region. In biological activity studies, the AChE and BChE inhibitory potentials of all compounds were evaluated using the in vitro Ellman method. The biological evaluation showed that compounds 3i and 3j displayed significant activity against AChE. The compounds 3i and 3j displayed IC50 values of 0.034 and 0.027 µM against AChE, respectively. The reference drug donepezil (IC50 = 0.021 µM) also displayed a significant inhibition against AChE. In addition, the antioxidant activities of the compounds were also evaluated. Derivatives 3i and 3j, which emerged active from both in vitro activity studies, were subjected to in vitro PAMPA tests to determine BBB permeability. Further docking simulation also revealed that these compounds (3i, 3j and donepezil) interacted with the enzyme active site in a similar manner to donepezil. A few parameters derived from MD simulation trajectories were computed and validated for the protein-ligand complex’s stability under the dynamic conditions. Communicated by Ramaswamy H. Sarma
Anisotropic Heisenberg form of RKKY interaction in the one-dimensional spin-polarized electron gas
Creators: name: Valizadeh, M. M.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We study the indirect exchange interaction between two localized magnetic moments, known as Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction, in a one-dimensional spin-polarized electron gas. We find explicit expressions for each term of this interaction, study their oscillatory behaviors as a function of the distance between two magnetic moments, $R$, and compare them with the known results for RKKY interaction in the case of one-dimensional standard electron gas. We show this interaction can be written in an anisotropic Heisenberg form, $E(\vec R)=λ^2χ_{xx}(S_{1x}S_{2x}+S_{1y}S_{2y})+λ^2χ_{zz}\, S_{1z}S_{2z}$, coming from broken time-reversal symmetry of the host material.
description: International Journal of Modern Physics B, 2016
Effects of exchange-correlation potentials on the density functional description of C_60 versus C_240 photoionization
Creators: name: Choi, Jinwoo
name: Chang, EonHo
name: Anstine, Dylan M.
name: Madjet, Mohamed El-Amine
name: Chakraborty, Himadri S.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Atomic and Molecular Clusters (physics.atm-clus)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We study the photoionization properties of the C_60 versus C_240 molecule in a spherical jellium frame of density functional method. Two different approximations to the exchange-correlation (xc) functional are used: (i) The Gunnerson-Lundqvist parametrization [Phys. Rev. B 13, 4274 (1976)] with an explicit correction for the electron self-interaction (SIC) and (ii) a gradient-dependent augmentation of (i) by using the van Leeuwen and Baerends model potential [Phys. Rev. A 49, 2421 (1994)], in lieu of SIC, to implicitly restore electrons' asymptotic properties. Ground state results from the two schemes for both molecules show differences in the shapes of mean-field potentials and bound-level properties. The choice of a xc scheme also significantly alters the dipole single-photoionization cross sections obtained by an abinitio method that incorporates linear-response dynamical correlations. Differences in the structures and ionization responses between C_60 and C_240 uncover the effect of molecular size on the underlying physics. Analysis indicates that the collective plasmon resonances with the gradient-based xc-option produce results noticeably closer to the experimental data available for C_60.
description: 10 pages, 7 figures, submitted
Supplementary Table 2 HRADM GP
Creators: name: Soliman, Heithem
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 320209
subject: Gastroenterology and hepatology
classificationCode: 320899
subject: Medical physiology not elsewhere classified

description: Supplementary table 2 for article "Physiologic characterization of gastric emptying with high-resolution antropyloroduodenal manometry"
Analysis of Chromosome 20 - A Study
Creators: name: Ausmees, Kristiina
name: John, Pushpam Aji
Publisher: name: arXiv
Year: 2016
Subjects: subject: Genomics (q-bio.GN)
subject: FOS: Biological sciences

description: Since the arrival of next-generation sequencing technologies the amount of genetic sequencing data has increased dramatically. This has has fueled an increase in human genetics research. At the same time, with the recent advent of technologies in processing large data sets, lot of these technologies are proving valuable and efficient in analyzing these huge datasets. In this paper we use some of these technologies to analyze genetic sequencing data of 1000 Genomes Project,produce and evaluate a framework to process the sequencing data thereof and look into structural variations with respect to population groups.
description: 6 pages, 7 figures
Stochastic Dynamics of Extended Objects in Driven Systems II: Current Quantization in the Low-Temperature Limit
Creators: name: Catanzaro, Michael J.
name: Chernyak, Vladimir Y.
name: Klein, John R.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 82C31, 82C05, 55B45, 55C05

description: Driven Langevin processes have appeared in a variety of fields due to the relevance of natural phenomena having both deterministic and stochastic effects. The stochastic currents and fluxes in these systems provide a convenient set of observables to describe their non-equilibrium steady states. Here we consider stochastic motion of a (k - 1)-dimensional object, which sweeps out a k-dimensional trajectory, and gives rise to a higher k-dimensional current. By employing the low-temperature (low-noise) limit, we reduce the problem to a discrete Markov chain model on a CW complex, a topological construction which generalizes the notion of a graph. This reduction allows the mean fluxes and currents of the process to be expressed in terms of solutions to the discrete Supersymmetric Fokker-Planck (SFP) equation. Taking the adiabatic limit, we show that generic driving leads to rational quantization of the generated higher dimensional current. The latter is achieved by implementing the recently developed tools, coined the higher-dimensional Kirchhoff tree and co-tree theorems. This extends the study of motion of extended objects in the continuous setting performed in the prequel to this manuscript.
description: To appear in Chemical Physics
Supplementary Table 2 HRADM Gastroparesis
Creators: name: Soliman, Heithem
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 320209
subject: Gastroenterology and hepatology
classificationCode: 320899
subject: Medical physiology not elsewhere classified

description: Supplementary table 2 for article "Physiologic characterization of gastric emptying with high-resolution antropyloroduodenal manometry"
Hyperspectral Subspace Identification Using SURE
Creators: name: Rasti, Behnood
name: Ulfarsson, Magnus O.
name: Sveinsson, Johannes R.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Remote sensing hyperspectral sensors collect large volumes of high dimensional spectral and spatial data. However, due to spectral and spatial redundancy the true hyperspectral signal lies on a subspace of much lower dimension than the original data. The identification of the signal subspace is a very important first step for most hyperspectral algorithms. In this paper we investigate the important problem of identifying the hyperspectral signal subspace by minimizing the mean squared error (MSE) between the true signal and an estimate of the signal. Since the MSE is uncomputable in practice, due to its dependency on the true signal, we propose a method based on the Stein's unbiased risk estimator (SURE) that provides an unbiased estimate of the MSE. The resulting method is simple and fully automatic and we evaluate it using both simulated and real hyperspectral data sets. Experimental results shows that our proposed method compares well to recent state-of-the-art subspace identification methods.
description: Technical Report. A shorten version of this paper has been published in the IEEE Geoscience and Remote Sensing Letters
Supplementary Table 1 HRADM GP
Creators: name: Soliman, Heithem
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 320899
subject: Medical physiology not elsewhere classified
classificationCode: 320209
subject: Gastroenterology and hepatology

description: Supplementary Table 1 for "Physiologic characterization of gastric emptying with high-resolution antropyloroduodenal manometry"
Schur-Weyl Duality for Heisenberg Cosets
Creators: name: Creutzig, Thomas
name: Kanade, Shashank
name: Linshaw, Andrew R.
name: Ridout, David
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Algebra (math.QA)
subject: High Energy Physics - Theory (hep-th)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 17B69 (Primary), 13A50 (Secondary)

description: Let $V$ be a simple vertex operator algebra containing a rank $n$ Heisenberg vertex algebra $H$ and let $C=\text{Com}\left( {H}, {V}\right)$ be the coset of ${H}$ in ${V}$. Assuming that the representation categories of interest are vertex tensor categories in the sense of Huang, Lepowsky and Zhang, a Schur-Weyl type duality for both simple and indecomposable but reducible modules is proven. Families of vertex algebra extensions of ${C}$ are found and every simple ${C}$-module is shown to be contained in at least one ${V}$-module. A corollary of this is that if ${V}$ is rational and $C_2$-cofinite and CFT-type, and $\text{Com}\left( {C}, {V}\right)$ is a rational lattice vertex operator algebra, then so is ${C}$. These results are illustrated with many examples and the $C_1$-cofiniteness of certain interesting classes of modules is established.
description: 41 pages
Supplementary Table 1 HRADM gastroparesis.docx
Creators: name: Soliman, Heithem
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 320899
subject: Medical physiology not elsewhere classified
classificationCode: 320209
subject: Gastroenterology and hepatology

description: Supplementary Table 1 for "Physiologic characterization of gastric emptying with high-resolution antropyloroduodenal manometry"
Stochastic Dynamics of Extended Objects in Driven Systems: I. Higher-Dimensional Currents in the Continuous Setting
Creators: name: Catanzaro, Michael J.
name: Chernyak, Vladimir Y.
name: Klein, John R.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 82C31, 82C05, 55B45, 55C05

description: The probability distributions, as well as the mean values of stochastic currents and fluxes, associated with a driven Langevin process, provide a good and topologically protected measure of how far a stochastic system is driven out of equilibrium. By viewing a Langevin process on a compact oriented manifold of arbitrary dimension m as a theory of a random vector field associated with the environment, we are able to consider stochastic motion of higher-dimensional objects, which allow new observables, called higher-dimensional currents, to be introduced. These higher dimensional currents arise by counting intersections of a k-dimensional trajectory, produced by a evolving (k-1)-dimensional cycle, with a reference cross section, represented by a cycle of complimentary dimension (m - k). We further express the mean fluxes in terms of the solutions of the Supersymmetric Fokker-Planck (SFP), thus generalizing the corresponding well-known expressions for the conventional currents.