cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Cosmologia e Representação
Creators: name: Ribeiro, Marcelo Byrro
Publisher: name: arXiv
Year: 2013
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: This work presents a brief and non-technical description of the main results and concepts of the modern scientific cosmology, viewing it from an epistemological perspective which allows a dialog with other modes of thinking like e.g. history, philosophy, sociology and religion. This epistemological viewpoint is based on the philosophical theses advanced by Ludwig Boltzmann (1844-1906) which states that scientific theories are nothing more than representations, or images, of nature (arXiv:physics/0701308v1). By being representations one cannot know how nature really is because the intrinsic and indispensable properties that characterize nature are unreachable by science. In other words, the true essences that constitute nature are unknowable. Therefore, all answers proposed by science are partial, simplified and replaceable. Another way of putting forward this viewpoint is to state that all scientific truths are provisional, a result which naturally leads to the conclusion that the same set of phenomena, or scientific questions, may have various answers, or representations. This conclusion is generally known as theoretical pluralism (arXiv:physics/9806011). It is exactly such a plurality for conceiving, or representing, nature that opens the way for a possibly fruitful dialog among the various forms of thinking, since this dialog can take place in the realm of the representations. A few examples taken from cosmology, sociology and theology are discussed in the context of this epistemological framework.
description: 27 pages. Invited talk presented at the XII Symposium of the Brazilian Association for the History of Religions. Text written in Brazilian Portuguese
Si$_3$N$_4$ optomechanical crystals in the resolved-sideband regime
Creators: name: Davanco, Marcelo
name: Ates, Serkan
name: Liu, Yuxiang
name: Srinivasan, Kartik
Publisher: name: arXiv
Year: 2013
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We demonstrate sideband-resolved Si$_3$N$_4$ optomechanical crystals supporting $10^5$ quality factor optical modes at 980 nm, coupled to $\approx4$ GHz frequency mechanical modes with quality factors of $\approx3000$. Optomechanical electromagnetically induced transparency and absorption are observed at room temperature and in atmosphere with intracavity photon numbers of the order of $10^4$.
Infrared evidence of a Slater metal-insulator transition in NaOsO3
Creators: name: Vecchio, Irene Lo
name: Perucchi, Andrea
name: Di Pietro, Paola
name: Limaj, Odeta
name: Schade, Ulrich
name: Sun, Ying
name: Arai, Masao
name: Yamaura, Kazunari
name: Lupi, Stefano
Publisher: name: arXiv
Year: 2013
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The magnetically driven metal-insulator transition (MIT) was predicted by Slater in the fifties. Here a long-range antiferromagnetic (AF) order can open up a gap at the Brillouin electronic band boundary regardless of the Coulomb repulsion magnitude. However, while many low-dimensional organic conductors display evidence for an AF driven MIT, in three-dimensional (3D) systems the Slater MIT still remains elusive. We employ terahertz and infrared spectroscopy to investigate the MIT in the NaOsO3 3D antiferromagnet. From the optical conductivity analysis we find evidence for a continuous opening of the energy gap, whose temperature dependence can be well described in terms of a second order phase transition. The comparison between the experimental Drude spectral weight and the one calculated through Local Density Approximation (LDA) shows that electronic correlations play a limited role in the MIT. All the experimental evidence demonstrates that NaOsO3 is the first known 3D Slater insulator.
description: 4 figures
Suncus occultidens
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Insectivora
Soricidae
Suncus
Suncus occultidens

description: Suncus occultidens (Hollister, 1913). Proc. U.S. Nat. Mus., 46:303. TYPE LOCALITY: Philippine Isis., Panay, Iloilo. DISTRIBUTION: Mindanao, Panay Isl., Negros IsL (Philippine Isis.). ISIS NUMBER: 5301403007020010001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Insectivora, pp. 58-106 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 100, DOI: 10.5281/zenodo.7353001
Splitting up method for the 2D stochastic Navier-Stokes equations
Creators: name: Bessaih, Hakima
name: Brzezniak, Zdzislaw
name: Millet, Annie
Publisher: name: arXiv
Year: 2013
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: In this paper, we deal with the convergence of an iterative scheme for the 2-D stochastic Navier-Stokes Equations on the torus suggested by the Lie-Trotter product formulas for stochastic differential equations of parabolic type. The stochastic system is split into two problems which are simpler for numerical computations. An estimate of the approximation error is given either with periodic boundary conditions. In particular, we prove that the strong speed of the convergence in probability is almost $1/2$. This is shown by means of an $L^2(Ω,P)$ convergence localized on a set of arbitrary large probability. The assumptions on the diffusion coefficient depend on the fact that some multiple of the Laplace operator is present or not with the multiplicative stochastic term. Note that if one of the splitting steps only contains the stochastic integral, then the diffusion coefficient may not contain any gradient of the solution.
Divergence of the Long Wavelength Collective Diffusion Coefficient in Quasi-one and Quasi-two Dimensional Colloid Suspensions
Creators: name: Lin, Binhua
name: Cui, Bianxiao
name: Xu, Xinliang
name: Zangi, Ronen
name: Diamant, Haim
name: Rice, Stuart A.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We report the results of experimental studies of the short time-long wavelength behavior of collective particle displacements in quasi-one-dimensional and quasi-two-dimensional colloid suspensions. Our results are represented by the behavior of the hydrodynamic function H(q) that relates the effective collective diffusion coefficient, D_e(q) with the static structure factor S(q) and the self-diffusion coefficient of isolated particles D_0: H(q)=D_e(q)S(q)/D_0. We find an apparent divergence of H(q) as q->0 with the form H(q) proportional to q^-gamma, 1.70 we infer that D_e(q) does. We provide evidence that this divergence arises from the interplay of boundary conditions on the flow of the carrier liquid and many-body hydrodynamic interactions between colloid particles that affect the long wavelength behavior of the particle collective diffusion coefficient in the suspension. We speculate that in the q1D and q2D systems studied the divergence of H(q) might be associated with a q-dependent partial slip boundary condition, specifically an effective slip length that increases with decreasing q. We also verify, using data from the work of Lin, Rice and Weitz (J. Chem. Phys. 99, 9585 (1993)), the prediction by Bleibel et al (arXiv:1305.3715), that D_e(q) for a monolayer of colloid particles constrained to lie in the interface between two fluids diverges as 1/q as q->0. The verification of that prediction, which is based on an analysis that allows two-dimensional colloid motion embedded in three-dimensional suspending fluid motion, supports the contention that the boundary conditions that define a q2D system play a very important role in determining the long wavelength behavior of the collective diffusion coefficient.
Molecular dynamics simulation and pharmacokinetics studies of ombuin and quercetin against human pancreatic α-amylase
Creators: name: Kikiowo, Babatomiwa
name: Ahmad, Iqrar
name: Alade, Adebowale A.
name: Ijatuyi, Taiwo T.
name: Iwaloye, Opeyemi
name: Patel, Harun M.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Diabetes mellitus (DM) is a group of metabolic disorders characterised by chronic hyperglycaemia. DM is currently one of the top ten causes of death in humans. Chronic hyperglycaemia in DM leads to long-term damage and failure of different organs in the body. Type 2 DM (T2D) is the most common DM form, characterised by peripheral insulin resistance, relative insulin deficiency, impaired hepatic glucose production regulation and pancreatic β cell dysfunction. The human pancreatic α-amylase (HPA) inhibitor is currently one of the most effective methods developed to inhibit hyperglycaemia in T2D patients. However, the current standard drug available, acarbose, has been associated with severe side effects following prolonged use in patients. Therefore, an alternative drug capable of effectively inhibiting HPA with minimal side effects is required. Based on our previous study, we further explored the therapeutic potential of quercetin and ombuin via molecular dynamics (MD) simulation. The Desmond Simulation Package was used to run 100-ns MD simulations to examine the steady nature and conformational stability of the ligand–HPA complexes. Post-simulation molecular mechanics-generalised born surface area (MM-GBSA) analysis of HPA’s binding free energy with quercetin and ombuin was explored. The lead compounds’ drug-likeness, absorption, distribution, metabolism and elimination properties were also studied using the SwissADME tool. These results indicate that quercetin and ombuin have great potential as anti-DM drugs with more favourable properties than acarbose. Communicated by Ramaswamy H. Sarma
Suncus palawanensis
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Insectivora
Soricidae
Suncus
Suncus palawanensis

description: Suncus palawanensis (Taylor, 1934). Philippine Monogr. Bur. Sci. Manila, 30:78. TYPE LOCALITY: Philippine Isis., Palawan, Taytay. DISTRIBUTION: Palawan (Philippine Isis.). ISIS NUMBER: 5301403007020012001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Insectivora, pp. 58-106 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 100, DOI: 10.5281/zenodo.7353001
Existence and regularity of solution for a Stochastic Cahn-Hilliard/Allen-Cahn equation with unbounded noise diffusion
Creators: name: Antonopoulou, Dimitra C.
name: Karali, Geogia
name: Millet, Annie
Publisher: name: arXiv
Year: 2013
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: The Cahn-Hilliard/Allen-Cahn equation with noise is a simplified mean field model of stochastic microscopic dynamics associated with adsorption and desorption-spin flip mechanisms in the context of surface processes. For such an equation we consider a multiplicative space-time white noise with diffusion coefficient of sub-linear growth. Using technics from semigroup theory, we prove existence, and path regularity of stochastic solution depending on that of the initial condition. Our results are also valid for the stochastic Cahn-Hilliard equation with unbounded noise diffusion, for which previous results were established only in the framework of a bounded diffusion coefficient. We prove that the path regularity of stochastic solution depends on that of the initial condition, and are identical to those proved for the stochastic Cahn-Hilliard equation and a bounded noise diffusion coefficient. If the initial condition vanishes, they are strictly less than 2-d/2 in space and 1/2-d/8 in time. As expected from the theory of parabolic operators in the sense of Petrovski, the bi-Laplacian operator seems to be dominant in the combined model.
Effects of Bridge Functions on Radial Distribution Functions of Liquid Water
Creators: name: Tanaka, Shigenori
name: Nakano, Miki
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: In this report the radial distribution functions (RDFs) of liquid water are calculated on the basis of the classical density functional theory combined with the reference interaction site model for molecular liquids. The bridge functions, which are neglected in the hypernetted-chain (HNC) approximation, are taken into account through the density expansion for the Helmholtz free energy functional up to the third order. A factorization approximation to the ternary direct correlation functions in terms of the site-site pair correlation functions is then employed in the expression of the bridge functions, thus leading to a closed set of integral equations for the determination of the RDFs. It is confirmed through numerical calculations that incorporation of the oxygen-oxygen bridge function substantially improves the poor descriptions by the HNC approximation at room temperature, e.g., for the second peak of the oxygen-oxygen RDF.
description: 2 figures, Interdisciplinary Sciences: Computational Life Sciences (2014)
Molecular insights into the in silico discovery of corilagin from Terminalia chebula as a potential dual inhibitor of SARS-CoV-2 structural proteins
Creators: name: Pradeep, Sushma
name: Patil, Shashank M
name: Dharmashekara, Chandan
name: Jain, Anisha
name: Ramu, Ramith
name: Shirahatti, Prithvi S
name: Mandal, Subhankar P
name: Reddy, Pruthvish
name: Srinivasa, Chandrashekar
name: Patil, Sharanagouda S
name: Ortega-Castro, Joaqúın
name: Frau, Juan
name: Flores-Holgúın, Norma
name: Shivamallu, Chandan
name: Kollur, Shiva Prasad
name: Glossman-Mitnik, Daniel
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biophysics
Biochemistry
Medicine
Molecular Biology
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer
Virology

description: The spike (S) glycoprotein and nucleocapsid (N) proteins are the crucial pathogenic proteins of the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) virus during its interaction with the host. Even FDA-approved drugs like dexamethasone and grazoprevir are not able to curb the viral progression inside the host and are reported with adverse effects on body metabolism. In this context, we aim to report corilagin a novel, potential dual inhibitor of S and N proteins from Terminalia chebula. The bioactive compounds of T. chebula were subjected to a series of computational investigations including molecular docking simulations, molecular dynamics (MD) simulations, binding free energy calculations, and PASS pharmacological analysis. The results obtained from these studies revealed that corilagin was highly interactive with the S (-8.9 kcal/mol) and N (-9.2 kcal/mol) proteins, thereby showing dual inhibition activity. It was also found to be stable enough to induce biological activity inside the inhibitor binding pocket of the target enzymes throughout the dynamics simulation run for 100 ns. This is also confirmed by the changes in the protein conformations, evaluated using free energy landscapes. Outcomes from this investigation identify corilagin as the lead potential dual inhibitor of S and N proteins of SARS-CoV-2, which could be taken for biological studies in near future. Communicated by Ramaswamy H. Sarma
Additional file 2 of Context matters in genomic data sharing: a qualitative investigation into responses from the Australian public
Creators: name: Warren, Vanessa
name: Critchley, Christine
name: McWhirter, Rebekah
name: Walshe, Jarrod
name: Nicol, Dianne
Publisher: name: figshare
Year: 2024
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: Additional file 2. Title: Full survey instrument. Description: Full text of the survey instrument presented to respondents.
Minimal Distance of Propositional Models
Creators: name: Behrisch, Mike
name: Hermann, Miki
name: Mengel, Stefan
name: Salzer, Gernot
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computational Complexity (cs.CC)
subject: FOS: Computer and information sciences

description: We investigate the complexity of three optimization problems in Boolean propositional logic related to information theory: Given a conjunctive formula over a set of relations, find a satisfying assignment with minimal Hamming distance to a given assignment that satisfies the formula ($\mathsf{NeareastOtherSolution}$, $\mathsf{NOSol}$) or that does not need to satisfy it ($\mathsf{NearestSolution}$, $\mathsf{NSol}$). The third problem asks for two satisfying assignments with a minimal Hamming distance among all such assignments ($\mathsf{MinSolutionDistance}$, $\mathsf{MSD}$). For all three problems we give complete classifications with respect to the relations admitted in the formula. We give polynomial time algorithms for several classes of constraint languages. For all other cases we prove hardness or completeness regarding APX, APX, NPO, or equivalence to well-known hard optimization problems.
Algebraic degrees of stretch factors in mapping class groups
Creators: name: Shin, Hyunshik
Publisher: name: arXiv
Year: 2014
Subjects: subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57M50, 57M15

description: We explicitly construct pseudo-Anosov maps on the closed surface of genus $g$ with orientable foliations whose stretch factor $λ$ is a Salem number with algebraic degree $2g$. Using this result, we show that there is a pseudo-Anosov map whose stretch factor has algebraic degree $d$, for each positive even integer $d$ such that $d \leq g$.
description: 19 pages, 5 figures; The revision contains new proof by Coxeter theory as suggested by the referee. Final version. To appear in AGT
A uniform area law for the entanglement of eigenstates in the disordered XY chain
Creators: name: Abdul-Rahman, Houssam
name: Stolz, Günter
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: Spectral Theory (math.SP)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 82B44

description: We consider the isotropic or anisotropic XY spin chain in the presence of a transversal random magnetic field, with parameters given by random variables. It is shown that eigenfunction correlator localization of the corresponding effective one-particle Hamiltonian implies a uniform area law bound in expectation for the bipartite entanglement entropy of all eigenstates of the XY chain, i.e. a form of many-body localization at all energies. Here entanglement with respect to arbitrary connected subchains of the chain can be considered. Applications where the required eigenfunction correlator bounds are known include the isotropic XY chain in random field as well as the anisotropic chain in strong or strongly disordered random field.
description: 28 pages, v2: changes in introduction after feedback received, some references added, v3: some improvements and updates, main results unchanged
Additional file 1 of Patients' use of Danish emergency medical services before and during the COVID-19 pandemic: a register-based study
Creators: name: Lindskou, Tim Alex
name: Bogh, Søren Bie
name: Kløjgaard, Torben Anders
name: Fløjstrup, Marianne
name: Folke, Fredrik
name: Væggemose, Ulla
name: Christensen, Helle Collatz
name: Christensen, Erika Frischknecht
name: Brabrand, Mikkel
name: Mikkelsen, Søren
Publisher: name: figshare
Year: 2024
Subjects: Medicine
Neuroscience
Developmental Biology
Cancer
Mental Health
Computational Biology

description: Additional file 1: Table S1. Primary dispatch category according to the Danish Index for Emergency Care. δ = Percentage decrease/increase of Danish Index for Emergency Care criteria for 2019 compared to 2020 in patients to whom a Danish Index for Emergency Care criteria was assigned at the emergency call. Table S2. Diagnoses assigned within the hospital. δ = Percentage decrease/increase of ICD-10 main chapters for 2019 compared to 2020 in patients transported to a hospital.
Absolute binding free energies of the antiviral peptide ATN-161 with protein targets of SARS-CoV-2
Creators: name: Silva, Rudielson Santos
name: Souza, Lucas Miguel Pereira
name: Costa, Rayla Kelly Magalhães
name: Souza, Felipe Rodrigues
name: Pimentel, André Silva
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Cell Biology
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: The interactions of the antiviral pentapeptide ATN-161 with the closed and open conformations of the α5β1 integrin, the SARS-CoV-2 major protease, and the omicron variant spike protein complexed with hACE2 were studied using molecular docking and molecular dynamics simulation. Molecular docking was performed to obtain ATN-161 binding poses with these studied protein targets. Subsequently, molecular dynamics simulations were performed to verify the ligand stability at the binding site of each protein target. Pulling simulations, umbrella sampling, and weighted histogram analysis method were used to obtain the potential of mean force of each system and calculate the Gibbs free energy of binding for the ATN-161 peptide in each binding site of these protein targets. The results showed that ATN-161 binds to α5β1 integrin in its active and inactive form, binds weakly to the omicron variant spike protein complexed with hACE2, and strongly binds to the main protease target. Communicated by Ramaswamy H. Sarma
Landau damping in a collisionless dipolar Bose gas
Creators: name: Natu, Stefan S.
name: Wilson, Ryan M.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We present a theory for the Landau damping of low energy quasi-particles in a collisionless, quasi-2D dipolar Bose gas and produce expressions for the damping rate in uniform and non-uniform systems. Using simple energy-momentum conservation arguments, we show that in the homogeneous system, the nature of the low energy dispersion in a dipolar Bose gas severely inhibits Landau damping of long wave-length excitations. For a gas with contact and dipolar interactions, the damping rate for phonons tends to decrease with increasing dipolar interactions; for strong dipole-dipole interactions, phonons are virtually undamped over a broad range of temperature. The damping rate for maxon-roton excitations is found to be significantly larger than the damping rate for phonons.
description: 11 pages, 4 figures
A perturbation density functional theory for the competition between inter and intramolecular association
Creators: name: Marshall, B. D.
name: Garcia-Cuellar, A. J.
name: Chapman, W. G.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Using the framework of Wertheim's thermodynamic perturbation theory we develop the first density functional theory which accounts for intramolecular association in chain molecules. To test the theory new Monte Carlo simulations are performed at a fluid solid interface for a 4 segment chain which can both intra and intermolecularly associate. The theory and simulation results are found to be in excellent agreement. It is shown that the inclusion of intramolecular association can have profound effects on interfacial properties such as interfacial tension and the partition coefficient.
Suncus remyi Brosset, DuBost and Heim de Balsac 1965
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Insectivora
Soricidae
Suncus
Suncus remyi

description: Suncus remyi Brosset, DuBost and Heim de Balsac, 1965. Biologia Gabon., 1:170. TYPE LOCALITY: Gabon, Makokou. DISTRIBUTION: Belinga and Makokou (Gabon). ISIS NUMBER: 5301403007020013001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Insectivora, pp. 58-106 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 101, DOI: 10.5281/zenodo.7353001
Schreiben, Worinnen Alle Umbstände enthalten Die Bey dem Todte Des Monsieur Claude Brousson, Dieners U. H. u. H. J. Observiret und von Mons. ... an einem seiner guten Freunde aus Montpeiller berichtet worden; 1699
Creators: name: Brousson, Claude
name: L., J. D.
Publisher: name: Universitätsbibliothek der Ludwig-Maximilians-Universität München
Year: 2012

description: Vorlageform des Erscheinungsvermerks: Erlang, Druckts Johann Friederich Regelein. Anno 1699.
A comprehensive computer simulation insight into inhibitory mechanisms of EGCG and NQTrp ligands on amyloid-beta assemblies as the Alzheimer’s disease insignia
Creators: name: Zahraee, Hamed
name: Arab, Seyed Shahriar
name: Khoshbin, Zahra
name: Bozorgmehr, Mohammad Reza
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biophysics
Biochemistry
Cell Biology
Molecular Biology
Neuroscience
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified

description: Amyloid-β peptide with predominant presence in the senile plaques is the most common agent for Alzheimer’s disease (AD) incidence. Assembly of the amyloid-β(1-42) (Aβ1-42) isoform is known as the main reason for the AD appearance. Epigallocatechin gallate (EGCG) and 1,4-naphthoquinone-2-yl-L-tryptophan (NQTrp) are two small molecules that inhibit the formation of the Aβ1-42 fibrils. The present study provides molecular insight to clarify the inhibitory mechanisms of the EGCG and NQTrp ligands on the Aβ1-42 assemblies by using molecular dynamics (MD) simulation. Hence, nine different Aβ1-42-containing systems including the monomer, dimer, and hexamer of Aβ1-42 considering each of them in a media with no ligands, in the presence of one EGCG ligand, and in the presence of one EGCG ligand were studied with a simulation time of 1 µs for each system. The precise investigation of the peptide-ligand distance, conformational factor (Pi), solvent accessible surface area (SASA), dictionary of secondary structure (DSSP), and Lys28-Ala42 salt bridge analyses confirmed that the hydroxyl-rich structure of the EGCG ligand applied its inhibitory effect on the aggregation of the peptides indirectly by involving water molecules. While the hydroxyl-free structure of the NQTrp ligand exposed its inhibitory effect through a direct interaction with the Aβ1-42 peptides. Besides, reduced density gradient (RDG) analysis clarified the hydrogen bonding interactions as the dominant ones for the peptide-EGCG systems, and also, steric and van der Waals interactions for the peptide-NQTrp systems. Communicated by Ramaswamy H. Sarma
Suncus stoliczkanus
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Insectivora
Soricidae
Suncus
Suncus stoliczkanus

description: Suncus stoliczkanus (Anderson, 1877). J. Asiat. Soc. Bengal, 46:270. TYPE LOCALITY: India, Bombay. DISTRIBUTION: Pakistan; India; Nepal. Bangladesh (RGVG). ISIS NUMBER: 5301403007020015001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Insectivora, pp. 58-106 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 101, DOI: 10.5281/zenodo.7353001
Fast and numerically stable circle fit
Creators: name: Abdul-Rahman, Houssam
name: Chernov, Nikolai
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: We develop a new algorithm for fitting circles that does not have drawbacks commonly found in existing circle fits. Our fit achieves ultimate accuracy (to machine precision), avoids divergence, and is numerically stable even when fitting circles get arbitrary large. Lastly, our algorithm takes less than 10 iterations to converge, on average.
description: 16 pages
Molecular dynamics simulation and pharmacokinetics studies of ombuin and quercetin against human pancreatic α-amylase
Creators: name: Kikiowo, Babatomiwa
name: Ahmad, Iqrar
name: Alade, Adebowale A.
name: Ijatuyi, Taiwo
name: Iwaloye, Opeyemi
name: Patel, Harun M.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Diabetes mellitus (DM) is a group of metabolic disorders characterised by chronic hyperglycaemia. DM is currently one of the top ten causes of death in humans. Chronic hyperglycaemia in DM leads to long-term damage and failure of different organs in the body. Type 2 DM (T2D) is the most common DM form, characterised by peripheral insulin resistance, relative insulin deficiency, impaired hepatic glucose production regulation and pancreatic β cell dysfunction. The human pancreatic α-amylase (HPA) inhibitor is currently one of the most effective methods developed to inhibit hyperglycaemia in T2D patients. However, the current standard drug available, acarbose, has been associated with severe side effects following prolonged use in patients. Therefore, an alternative drug capable of effectively inhibiting HPA with minimal side effects is required. Based on our previous study, we further explored the therapeutic potential of quercetin and ombuin via molecular dynamics (MD) simulation. The Desmond Simulation Package was used to run 100-ns MD simulations to examine the steady nature and conformational stability of the ligand–HPA complexes. Post-simulation molecular mechanics-generalised born surface area (MM-GBSA) analysis of HPA’s binding free energy with quercetin and ombuin was explored. The lead compounds’ drug-likeness, absorption, distribution, metabolism and elimination properties were also studied using the SwissADME tool. These results indicate that quercetin and ombuin have great potential as anti-DM drugs with more favourable properties than acarbose. Communicated by Ramaswamy H. Sarma
Inhibitory effect of gallic acid from Thunbergia mysorensis against α-glucosidase, α-amylase, aldose reductase and their interaction: Inhibition kinetics and molecular simulations
Creators: name: Kokila, N. R.
name: Mahesh, B.
name: Ramu, Ramith
name: Mruthunjaya, K.
name: Bettadaiah, B. K.
name: Madhyastha, Harishkumar
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: In this exploration, we assessed the antihyperglycaemic properties of methanol extract of flowers of Thunbergia mysorensis (MeT) against α-glucosidase, α-amylase and aldose reductase enzymes for the effective management of postprandial hyperglycemia. Hyperglycemia occurs when the body lacks enough insulin or is unable to correctly utilize it. MeT inhibited both the carbohydrate digestive enzymes (α-glucosidase and α-amylase) and aldose reductase, which are vital for the therapeutic control of postprandial hyperglycaemia. MeT was also found to have significant antioxidant activity. Using several spectroscopic approaches, the primary active component found in MeT was identified as gallic acid. With low Ki values, gallic acid significantly inhibited α-glucosidase (30.86 µg/mL) and α-amylase (6.50 µg/mL). Also, MeT and gallic acid both inhibited aldose reductase effectively, corresponding to an IC50 value of 3.31 and 3.05 µg/mL. Our findings imply that the presence of polyphenol compounds (identified via HPLC analysis) is more likely to be responsible for the antihyperglycaemic role exhibited by MeT via the inhibition of α-glucosidase and the polyol pathway. Further, gallic acid interacted with the key residues of the active sites of α-glucosidase (−6.4 kcal/mol), α-amylase (−5.8 kcal/mol) and aldose reductase (−5.8 kcal/mol) as observed in the protein-ligand docking. It was also predicted that gallic acid was stable inside the binding pockets of the target enzymes during molecular dynamics simulation. Overall, gallic acid derived from MeT via bioassay-guided isolation emerges as a natural antidiabetic drug and can be taken into in vivo and clinical studies shortly. Communicated by Ramaswamy H. Sarma
Invariant types in NIP theories
Creators: name: Simon, Pierre
Publisher: name: arXiv
Year: 2014
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03C45

description: We study invariant types in NIP theories. Amongst other things: we prove a definable version of the (p,q)-theorem in theories of small or medium directionality; we construct a canonical retraction from the space of M-invariant types to that of M-finitely satisfiable types; we show some amalgamation results for invariant types and list a number of open questions.
description: Small changes made
Galois theory for semiclones
Creators: name: Behrisch, Mike
Publisher: name: arXiv
Year: 2015
Subjects: subject: Rings and Algebras (math.RA)
subject: Logic (math.LO)
subject: FOS: Mathematics
subject: Primary: 08A40, Secondary: 08A02, 08A99

description: We present a Galois theory connecting finitary operations with pairs of finitary relations one of which is contained in the other. The Galois closed sets on both sides are characterised as locally closed subuniverses of the full iterative function algebra (semiclones) and relation pair clones, respectively. Moreover, we describe the modified closure operators if only functions and relation pairs of a certain bounded arity, respectively, are considered.
description: 38 pages; supported by the Austrian Science Fund (FWF) under grant I836-N23
Entanglement Dynamics of Disordered Quantum XY Chains
Creators: name: Abdul-Rahman, Houssam
name: Nachtergaele, Bruno
name: Sims, Robert
name: Stolz, Günter
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 82B44

description: We consider the dynamics of the quantum XY chain with disorder under the general assumption that the expectation of the eigenfunction correlator of the associated one-particle Hamiltonian satisfies a decay estimate typical of Anderson localization. We show that, starting from a broad class of product initial states, entanglement remains bounded for all times. For the XX chain, we also derive bounds on the particle transport which, in particular, show that the density profile of initial states that consist of fully occupied and empty intervals, only have significant dynamics near the edges of those intervals, uniformly for all times.
description: 22 pages, final version, to appear in Lett. Math. Phys
Directly measuring single molecule heterogeneity using force spectroscopy
Creators: name: Hinczewski, Michael
name: Hyeon, Changbong
name: Thirumalai, D.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Biomolecules (q-bio.BM)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with random interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Though we now have proof of functional heterogeneity in a handful of systems---enzymes, motors, adhesion complexes---identifying and measuring it remains a formidable challenge. Here we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single molecule techniques: AFM or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This results in a single parameter, quantifying the degree of heterogeneity, and also leads to bounds on the equilibration and conformational interconversion timescales. Surveying ten published datasets, we find heterogeneity in five of them, all with interconversion rates slower than 10 s$^{-1}$. Moreover, we identify two systems where additional data at realizable pulling velocities is likely to find a theoretically predicted, but so far unobserved cross-over regime between heterogeneous and non-heterogeneous behavior. The significance of this regime is that it will allow far more precise estimates of the slow conformational switching times, one of the least understood aspects of functional heterogeneity.
description: Main text: 13 pages, 6 figures; SI: 9 pages, 6 figures
Suncus varilla
Creators: name: Honacki, James H.
name: Kinman, Kenneth E.
name: Koeppl, James W.
Publisher: name: Zenodo
Year: 1982
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Insectivora
Soricidae
Suncus
Suncus varilla

description: Suncus varilla (Thomas, 1895). Ann. Mag. Nat. Hist., ser. 6, 16:54. TYPE LOCALITY: South Africa, Cape Prov., East London. DISTRIBUTION: South Africa; N.E. Zimbabwe; Tanzania; E. Zaire; Malawi; Zambia. COMMENT: Includes minor, natalensis, orangiae, tulbaghensis, and warreni; see Heim de Balsac and Meester, 1977, Part 1:6. Gureev, 1979:383, listed orangiae and warreni as distinct species without comment. ISIS NUMBER: 5301403007020016001.
description: Published as part of James H. Honacki, Kenneth E. Kinman & James W. Koeppl, 1982, Order Insectivora, pp. 58-106 in Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA :Alien Press, Inc. & The Association of Systematics Collections on page 101, DOI: 10.5281/zenodo.7353001
description: {"references": ["Heim de Balsac, H., and J. Meester. 1977. Order Insectivora. Part 1. Pp. 1 - 29, in The mammals of Africa: An identification manual (J. Meester and H. W. Setzer, eds.). [issued 22 Aug 1977]. Smithsonian Institution Press, Washington, D. C., not continuously paginated.", "Gureev, A. A. 1979. Fauna SSSR, Mlekopitayutschie, tom. 4, vyp. 2. Nasekomoyadnye ... [Fauna of the USSR, Mammals, vol. 4, pt. 2. Insectivores (Mammalia, Insectivora)]. Nauka, Leningrad, 501 pp. (in Russian)."]}
Simulation Model Of Functional Stability Of Business Processes
Creators: name: Monakhov, Yuri
name: Fayman, Olga
Publisher: name: arXiv
Year: 2013
Subjects: subject: Other Computer Science (cs.OH)
subject: FOS: Computer and information sciences

description: Functioning of business processes of high-tech enterprise is in a constant interaction with the environment. Herewith a wide range of such interaction represents a variety of conflicts affecting the achievement of the goals of business processes. All these things lead to the disruption of functioning of business processes. That's why modern enterprises should have mechanisms to provide a new property of business processes - ability to maintain and/or restore functions in various adverse effects. This property is called functional stability of business processes (FSBP). In this article we offer, showcase and test the new approach to assessing the results of business process re-engineering by simulating their functional stability before and after re-engineering.
description: 10 pages, 12 figures
Motor control by precisely timed spike patterns
Creators: name: Srivastava, Kyle H.
name: Holmes, Caroline M.
name: Vellema, Michiel
name: Pack, Andrea
name: Elemans, Coen P. H.
name: Nemenman, Ilya
name: Sober, Samuel J.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Biological sciences

description: A fundamental problem in neuroscience is to understand how sequences of action potentials ("spikes") encode information about sensory signals and motor outputs. Although traditional theories of neural coding assume that information is conveyed by the total number of spikes fired (spike rate), recent studies of sensory and motor activity have shown that far more information is carried by the millisecond-scale timing patterns of action potentials (spike timing). However, it is unknown whether or how subtle differences in spike timing drive differences in perception or behavior, leaving it unclear whether the information carried by spike timing actually plays a causal role in brain function. Here we demonstrate how a precise spike timing code is read out downstream by the muscles to control behavior. We provide both correlative and causal evidence to show that the nervous system uses millisecond-scale variations in the timing of spikes within multi-spike patterns to regulate a relatively simple behavior - respiration in the Bengalese finch, a songbird. These findings suggest that a fundamental assumption of current theories of motor coding requires revision, and that significant improvements in applications, such as neural prosthetic devices, can be achieved by using precise spike timing information.
description: 48 pages, 16 figures
Potential inhibitors of FemC to combat Staphylococcus aureus: virtual screening, molecular docking, dynamics simulation, and MM-PBSA analysis
Creators: name: Rathi, Ravi
Publisher: name: Taylor & Francis
Year: 2022
Subjects: Biophysics
Biochemistry
Cell Biology
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer
Hematology

description: FemC is a methicillin resistance factor involved in the alterations of peptidoglycan and glutamine synthesis in Staphylococcus aureus. To identify the potent antibacterial agents, antibacterial molecules were screened against the predicted and validated FemC model. Based on docking scores, presence of essential interactions with active site residues of FemC, pharmacokinetic, and ADMET properties, six candidates were shortlisted and subjected to molecular dynamics to evaluate the stability of FemC-ligand complexes. Further, per residue decomposition analysis and Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis confirmed that S15, M16, S17, R31, R43, Q47, K48 and R49 of FemC played a vital role in the formation of lower energy stable FemC-inhibitor(s) complexes. Therefore, in the present study, the reported six molecules (Z317461228, Z92241701, Z30923155, Z30202349, Z2609517102 and Z92470167) may pave the path to design the scaffold of novel potent antimicrobials against S. aureus. Communicated by Ramaswamy H. Sarma
title: Melchioris Breleri Philosophiae Magistri, et P.C. Polyglottophili Schediasmatvm Ivvenilivm Prodromus; 1611
title: Ad Dominum Janum Christophorvm Graetervm Amicum Meum Magnum, et Ex Recentioribus Sinceriorem
titleType: Subtitle
Creators: name: Breler, Melchior
Publisher: name: Universitätsbibliothek der Ludwig-Maximilians-Universität München
Year: 2012

description: Text und Druck identisch mit: Breler, Melchior: Schediasmatum Iuvenilium Manipulus unus. - Altorfii, 1611 (ohne beigef. Werk). - Bogensignatur A1 - A6
Additional file 1 of Surface and deep learning: a blended learning approach in preclinical years of medical school
Creators: name: Khong, Mei Li
name: Tanner, Julian Alexander
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Astronomical and Space Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Science Policy
subject: Mental Health

description: Supplementary Material 1. Additional file 1: R-SPQ-2F questionnaire.
Evolutionary consequences of behavioral diversity
Creators: name: Stewart, Alexander J.
name: Parsons, Todd L.
name: Plotkin, Joshua B.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Iterated games provide a framework to describe social interactions among groups of individuals. Recent work stimulated by the discovery of "zero-determinant" strategies has rapidly expanded our ability to analyze such interactions. This body of work has primarily focused on games in which players face a simple binary choice, to "cooperate" or "defect". Real individuals, however, often exhibit behavioral diversity, varying their input to a social interaction both qualitatively and quantitatively. Here we explore how access to a greater diversity of behavioral choices impacts the evolution of social dynamics in finite populations. We show that, in public goods games, some two-choice strategies can nonetheless resist invasion by all possible multi-choice invaders, even while engaging in relatively little punishment. We also show that access to greater behavioral choice results in more "rugged " fitness landscapes, with populations able to stabilize cooperation at multiple levels of investment, such that choice facilitates cooperation when returns on investments are low, but hinders cooperation when returns on investments are high. Finally, we analyze iterated rock-paper-scissors games, whose non-transitive payoff structure means unilateral control is difficult and zero-determinant strategies do not exist in general. Despite this, we find that a large portion of multi-choice strategies can invade and resist invasion by strategies that lack behavioral diversity -- so that even well-mixed populations will tend to evolve behavioral diversity.
description: 26 pages, 4 figures