cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Identification of bioactive molecule from Withania somnifera (Ashwagandha) as SARS-CoV-2 main protease inhibitor
Creators: name: Tripathi, Manish Kumar
name: Pushpendra Singh
name: Sharma, Sujata
name: Tej P. Singh
name: A. S. Ethayathulla
name: Kaur, Punit
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: SARS-CoV-2 is the causative agent of COVID-19 and has been declared as pandemic disease by World Health Organization. Lack of targeted therapeutics and vaccines for COVID-2019 have triggered the scientific community to develop new vaccines or drugs against this novel virus. Many synthetic compounds and antimalarial drugs are undergoing clinical trials. The traditional medical practitioners widely use Indian medicinal plant Withania somnifera (Ashwagandha) natural constituents, called withanolides for curing various diseases. The main protease (Mpro) of SARS-CoV-2 plays a vital role in disease propagation by processing the polyproteins which are required for its replication. Hence, it denotes a significant target for drug discovery. In the present study, we evaluate the potential of 40 natural chemical constituents of Ashwagandha to explore a possible inhibitor against main protease of SARS-CoV-2 by adopting the computational approach. The docking study revealed that four constituents of Ashwagandha; Withanoside II (-11.30 Kcal/mol), Withanoside IV (-11.02 Kcal/mol), Withanoside V (-8.96 Kcal/mol) and Sitoindoside IX (-8.37 Kcal/mol) exhibited the highest docking energy among the selected natural constituents. Further, MD simulation study of 100 ns predicts Withanoside V possess strong binding affinity and hydrogen-bonding interactions with the protein active site and indicates its stability in the active site. The binding free energy score also correlates with the highest score of −87.01 ± 5.01 Kcal/mol as compared to other selected compounds. In conclusion, our study suggests that Withanoside V in Ashwagandha may be serve as a potential inhibitor against Mpro of SARS-CoV-2 to combat COVID-19 and may have an antiviral effect on nCoV. Communicated by Ramaswamy H. Sarma
Multi-GPU Performance Optimization of a CFD Code using OpenACC on Different Platforms
Creators: name: Xue, Weicheng
name: Roy, Christopher J.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Performance (cs.PF)
subject: FOS: Computer and information sciences

description: This paper investigates the multi-GPU performance of a 3D buoyancy driven cavity solver using MPI and OpenACC directives on different platforms. The paper shows that decomposing the total problem in different dimensions affects the strong scaling performance significantly for the GPU. Without proper performance optimizations, it is shown that 1D domain decomposition scales poorly on multiple GPUs due to the noncontiguous memory access. The performance using whatever decompositions can be benefited from a series of performance optimizations in the paper. Since the buoyancy driven cavity code is latency-bounded on the clusters examined, a series of optimizations both agnostic and tailored to the platforms are designed to reduce the latency cost and improve memory throughput between hosts and devices efficiently. First, the parallel message packing/unpacking strategy developed for noncontiguous data movement between hosts and devices improves the overall performance by about a factor of 2. Second, transferring different data based on the stencil sizes for different variables further reduces the communication overhead. These two optimizations are general enough to be beneficial to stencil computations having ghost changes on all of the clusters tested. Third, GPUDirect is used to improve the communication on clusters which have the hardware and software support for direct communication between GPUs without staging CPU's memory. Finally, overlapping the communication and computations is shown to be not efficient on multi-GPUs if only using MPI or MPI+OpenACC. Although we believe our implementation has revealed enough overlap, the actual running does not utilize the overlap well due to a lack of asynchronous progression.
A Higher-dimensional Origin of the Inverted Mass Hierarchy for Neutrino
Creators: name: Tanimoto, M.
name: Yanagida, T.
Publisher: name: arXiv
Year: 2005
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present successful lepton mass matrices with an inverted mass hierarchy for neutrinos, which follow from a geometrical structure of a (1+5) dimensional space-time where two extra dimensions are compactified on the T^2/Z_3 orbifold. A 5^* and a right-handed neutrino N in each family are localized on each of the equivalent three fixed points of the orbifold while three 10's and Higgs doublets H_u and H_d live in the bulk. An S_3 family symmetry is assumed on three 5^*'s and on three N's, since the three fixed points are equivalent to one another. The Higgs field ϕresponsible for the B-L breaking is localized on one of the three fixed points, which generates the inverted hierarchy for the neutrino masses. The baryon asymmetry is well explained in the non-thermal leptogenesis via inflaton decay. We emphasize that the present model predicts the effective neutrino mass, _{ee}, responsible for neutrinoless double beta decays as _{ee}\simeq 50 meV. This will be accessible to future experiments.
description: 15 pages
Prediction of the Curie temperature considering the dependence of the phonon free energy on magnetic states
Creators: name: Tanaka, Tomonori
name: Gohda, Yoshihiro
Publisher: name: arXiv
Year: 2020
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Prediction of the Curie temperature is of significant importance for the design of ferromagnetic materials. Even though the Curie temperature has been estimated using the Heisenberg model, magnetic exchange coupling parameters widely used is thus far based on first-principles calculations at zero temperature. In the explicit consideration of temperature effects, it is important to minimise the total free energy, because the magnetic and phonon free energies correlate with each other. Here, we propose a first-principles thermodynamic approach to minimise the total free energy considering both the influences of magnetism on phonons and the feedback effect from phonons to magnetism. By applying our scheme to bcc Fe, we find a significant reduction of the Curie temperature due to the feedback effect. This result inevitably enforces us to change our convention as follows: we should use exchange coupling constants for the disordered local moment state, not for the ferromagnetic state, in the prediction of the Curie temperature. Our results not only change the fundamental understanding of finite-temperature magnetism but also provide a general framework to predict the Curie temperature more accurately.
Livestock, Liberalization and Democracy: Constraints and Opportunities for Rural Livestock Producers in a Reforming Uganda
Creators: name: Turner, Robin L.
name: Turner, Robin L.
Publisher: name: Unknown
Year: 2005
Subjects: Livestock Production/Industries

description: This paper explores the policy environment surrounding livestock policy improvements in Uganda, with a view to identify opportunities for pro-poor interventions and reforms. The paper reviews challenges facing livestock producers and analyzes the broad political economic context in which livestock sector dynamics are situated. A review of the livestock sector highlights the constraints facing poor rural livestock producers based on: missing or inadequate infrastructure; the small size of the domestic market and limited capacity to service international markets; the complex political environment; violent conflict between the Lord's Resistance Army, the government, and civilians; predation by cattle rustlers and restrictions on political participation. Although neoliberal reform rhetoric pervades policy discourse, many civil servants are sceptical about this approach. The concluding section outlines several interventions that could improve the livelihoods of poor rural livestock producers in Uganda. Working within the dominant neoliberal reform context, the proposed interventions seek to reduce barriers to producer benefit and improve the functioning of livestock markets. In particular, information provision, investment in infrastructure, and development of measurable indicators of how reforms affect poor Ugandans could have substantial impact.
Projective symmetry group classifications of quantum spin liquids on the simple cubic, body centered cubic, and face centered cubic lattices
Creators: name: Sonnenschein, Jonas
name: Chauhan, Aishwarya
name: Iqbal, Yasir
name: Reuther, Johannes
Publisher: name: arXiv
Year: 2020
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We perform extensive classifications of $\mathbb{Z}_2$ quantum spin liquids on the simple cubic, body centered cubic, and face centered cubic lattices using a spin-rotation invariant fermionic projective symmetry group approach. Taking into account that all three lattices share the same point group $O_h$, we apply an efficient gauge where the classification for the simple cubic lattice can be partially carried over to the other two lattices. We identify hundreds of projective representations for each of the three lattices, however, when constructing short-range mean-field models for the fermionic partons (spinons) these phases collapse to only very few relevant cases. We self-consistently calculate the corresponding mean-field parameters for frustrated Heisenberg models on all three lattices with up to third neighbor spin interactions and discuss the spinon dispersions, ground state energies and dynamical spin structure factors. Our results indicate that phases with non-uniform spinon hopping or pairing amplitudes are energetically favored. An unusual situation is identified for the fcc lattice where the spinon dispersion minimizing the mean-field energy features a network of symmetry protected line-like zero modes in reciprocal space. We further discuss characteristic fingerprints of these phases in the dynamical spin structure factor which may help to identify and distinguish them in future numerical or experimental studies.
Chaotic Cryptographic Scheme Based on Composition Maps
Creators: name: Behnia, S.
name: Akhshani, A.
name: Akhavan, A.
name: Mahmodi, H.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: In recent years, a growing number of cryptosystems based on chaos have been proposed. But most of them encountered many problems such as small key space and weak security. In the present paper, a new kind of chaotic cryptosystem based on Composition of Trigonometric Chaotic Maps is proposed. These maps which are defined as ratios of polynomials of degree N, have interesting properties such as invariant measure, ergodicity, variable chaotic region with respect to the control parameters and ability to construct composition form of maps. We have used a composition of chaotic map to shuffle the position of image pixels. Another composition of chaotic map is used in diffusion process. According to the performed analysis, the introduced algorithm can satisfy the required performances such as high level security, large key space and the acceptable encryption speed.
description: 23 pages, 15 figures
Klamroth, Erich, Der Gedanke der ewigen Schöpfung bei Nikolai Berdiajew
Creators: name: Schaeder, Hildegard
Publisher: name: Ökumenische Rundschau
Year: 2025

description: Ökumenische Rundschau, Bd. 14 Nr. 2 (1965): Ökumenische Rundschau, Band 14, Heft 2
The role of the let-268 and spc-1 genes in the early stages of muscle development in Caenorhabditis elegans
Creators: name: Norman, Kenneth Rich
Publisher: name: University of British Columbia
Year: 2009

description: Myogenesis in Caenorhabditis elegans is composed of several stages: the generation of presumptive myoblasts; the migration of these cells dorsally and ventrally from their lateral position to form the muscle quadrants; the accumulation of muscle specific proteins in these cells; the polarization of the cells; and, finally, the organization of sarcomeres and attachment structures within the cells. The goal of this thesis work has been to identify genes involved in this process. From a mutant screen designed to identify mutations that disrupt muscle development during C. elegans embryogenesis, eight mutations have been isolated and placed into five distinct classes. Two of the mutants identified in this screen have been characterized in greater detail and the affected genes have been cloned. One of the mutants, let-268 (a class IV mutant), encodes a procollagen processing enzyme, procollagen lysyl hydroxylase, required for post-translational modifications of collagen. In let-268 mutants the processing and secretion of type IV collagen is disrupted. An examination of the body wall muscle in these mutant animals reveals normal myofilament assembly prior to contraction. However, once body wall muscle contraction commences the muscle cells separate from the underlying epidermal layer (hypodermis) and the myofilaments become disorganized. These observations indicate that type IV collagen is required in the basement membrane for mechanical support and not for organogenesis of the body wall muscle. The other mutant examined in greater detail is spc-1 (class V mutant), spc-1 encodes the only α spectrin gene in the C. elegans genome. Animals lacking functional α spectrin die just after hatching and have defects in myofilament organization. More specifically, when compared to myofilaments in wild type animals, the myofilaments in the mutant animals are abnormally oriented relative to the longitudinal axis of the embryo. In cross section, the myofilaments appear to be loosely associated with the sarcolemma as compared to wild type. In addition, analysis of the basement membrane and the hypodermis of spc-1(ra409) mutants provides evidence that the body wall muscle directs where the basement membrane is established and signals the hypodermis to determine where muscle anchoring structures are assembled in this tissue.
Complete chemical shift assignment and molecular modeling studies of two chromene derivatives as potential leads for new anticancer drugs
Creators: name: Santana, Priscila Ivo Rubim De
name: Neto, Denise Cristian Ferreira
name: Goncalves, Arlan Da Silva
name: Almeida, Joyce Sobreiro Francisco Diz De
name: Tanos Celmar Costa França
name: Figueroa-Villar, José Daniel
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology

description: The compounds 7-chloro-9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one (5) and 5-[-7-chloro-2,4-dioxo-1H, 2H, 3H, 4H, 5H-chromeno[2,3-d]pyrimidin-5-yl)]-1,3-diazinane-2,4,6-trione (7), were synthesized from dimedone and barbituric acid and had their three-dimensional structures and precise chemical shifts assignments obtained by Nuclear Magnetic Resonance (NMR) from 1H, 13C, APT, COSY, HSQC, and HMBC spectra. Additional HOMO-LUMO DFT calculations corroborated the NMR results and pointed to the most stable stereoisomers of each compound. Besides, further docking and molecular dynamic studies suggest that the stereoisomers (9S)-7-chloro-9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one, and 5-[(5S)-7-chloro-2,4-dioxo-1H, 2H, 3H, 4H, 5H-chromeno[2,3-d]pyrimidin-5-yl)]-1,3-diazinane-2,4,6-trione of these compounds may act as DNA intercalators and qualify as potential leads for the development of new anticancer drugs. Communicated by Ramaswamy H. Sarma
Domain structures and the transitional state of ordering in long-period stacking ordered (LPSO) structures in Mg-Al-Gd alloy
Creators: name: Gu, Xin-Fu
name: Furuhara, Tadashi
name: Chen, Leng
name: Yang, Ping
Publisher: name: arXiv
Year: 2020
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The transitional state of ordering in the long-period stacking ordered (LPSO) structure in Mg-Al-Gd alloy has been investigated by scanning transmission electron microscopy. It is found that the domains are the origin of observed transitional state. Three new patterns of clusters at this state can be fully explained by the superimposition of L12 type clusters located in different domains. The domains are further verified by different tilted views. Growth of preferred domains during ageing process will result in final ordered LPSO structure. Based on the idea of domains, less ordered LPSO structure in other dilute alloys can be also understood.
title: Aprendizagem entre pares: mentorado num curso de português língua estrangeira
Creators: name: Estrela, Antónia
name: Ferreira, Patrícia
name: Boléo, Ana
Publisher: name: Escola Superior de Educação, Instituto Politécnico de Lisboa
Year: 2021

description: No contexto educativo, a inclusão deve ser pensada para todos os alunos numa perspetiva de os levar a fazer aprendizagens ricas e diversificadas que venham contribuir para o seu crescimento humano, social e académico. Neste sentido, e visando uma integração mais plena dos alunos Erasmus que frequentam os cursos de Português Língua Estrangeira do Centro de Línguas e Cultura do Instituto Politécnico de Lisboa (CLiC-IPL), delineou-se um programa de mentorado que visou pôr lado a lado estudantes estrangeiros e estudantes portugueses, dado que entendemos como pertinente o apoio interpares, potenciado pelos benefícios de uma relação próxima, cujos comportamentos de modelagem (Bandura, 1969) poderão facilitar a promoção de uma boa adaptação dos novos estudantes nos primeiros momentos de vivência numa dada instituição (Welling, 1997).
Data-Driven Multi-Objective Controller Optimization for a Magnetically-Levitated Nanopositioning System
Creators: name: Li, Xiaocong
name: Zhu, Haiyue
name: Ma, Jun
name: Teo, Tat Joo
name: Teo, Chek Sing
name: Tomizuka, Masayoshi
name: Lee, Tong Heng
Publisher: name: arXiv
Year: 2020
Subjects: subject: Systems and Control (eess.SY)
subject: Robotics (cs.RO)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: The performance achieved with traditional model-based control system design approaches typically relies heavily upon accurate modeling of the motion dynamics. However, modeling the true dynamics of present-day increasingly complex systems can be an extremely challenging task; and the usually necessary practical approximations often render the automation system to operate in a non-optimal condition. This problem can be greatly aggravated in the case of a multi-axis magnetically-levitated nanopositioning system where the fully floating behavior and multi-axis coupling make extremely accurate identification of the motion dynamics largely impossible. On the other hand, in many related industrial automation applications, e.g., the scanning process with the maglev system, repetitive motions are involved which could generate a large amount of motion data under non-optimal conditions. These motion data essentially contain rich information; therefore, the possibility exists to develop an intelligent automation system to learn from these motion data and to drive the system to operate towards optimality in a data-driven manner. Along this line then, this paper proposes a data-driven controller optimization approach that learns from the past non-optimal motion data to iteratively improve the motion control performance. Specifically, a novel data-driven multi-objective optimization approach is proposed that is able to automatically estimate the gradient and Hessian purely based on the measured motion data; the multi-objective cost function is suitably designed to take into account both smooth and accurate trajectory tracking. Experiments are then conducted on the maglev nanopositioning system to demonstrate the effectiveness of the proposed method, and the results show rather clearly the practical appeal of our methodology for related complex robotic systems with no accurate model available.
description: 11 pages, 11 figures, to appear in IEEE/ASME Transactions on Mechatronics
Supplementary material from The slave trade and the origins of matrilineal kinship
Creators: name: Lowes, Sara
name: Nunn, Nathan
Publisher: name: The Royal Society
Year: 2024
Subjects: classificationCode: 310499
subject: Evolutionary biology not elsewhere classified
classificationCode: 310901
subject: Animal behaviour

description: Matrilineal kinship systems—where descent is traced through mothers only—are present all over the world but are most concentrated in sub-Saharan Africa. We explore the relationship between exposure to Africa’s external slave trades, during which millions of people were shipped from the continent during a 400-year period, and the evolution of matrilineal kinship. Scholars have hypothesized that matrilineal kinship, which is well-suited to incorporating new members, maintaining lineage continuity and insulating children from the removal of parents (particularly fathers), was an adaptive response to the slave trades. Motivated by this, we test for a connection between the slave trades and matrilineal kinship by combining historical data on an ethnic group’s exposure to the slave trades and the presence of matrilineal kinship following the end of the trades. We find that the slave trades are positively associated with the subsequent presence of matrilineal kinship. The result is robust to a variety of measures of exposure to the slave trades, the inclusion of additional covariates, sensitivity analyses that remove outliers, and an instrumental variables estimator that uses a group’s historical distance from the coast as an instrument. We also find evidence of a complementarity between polygyny and matrilineal kinship, which were both social responses to the disruption of the trades.This article is part of the theme issue ‘Social norm change: from evolution to policy intervention’.
The Sensitivity of Multidimensional Nova Calculations to the Outer Boundary Conditions
Creators: name: Glasner, S. Ami
name: Livne, Eli
name: Truran, James W.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Multidimensional reactive flow models of accreted hydrogen rich envelopes on top of degenerate cold white dwarfs are very effective tools for the study of critical, non spherically symmetric, behaviors during the early stages of nova outbursts. Such models can shed light both on the mechanism responsible for the heavy element enrichment observed to characterize nova envelope matter and on the role of perturbations during the early stages of ignition of the runaway. The complexity of convective reactive flow in multi-dimensions makes the computational model itself complex and sensitive to the details of the numerics. In this study, we demonstrate that the imposed outer boundary condition can have a dramatic effect on the solution. Several commonly used choices for the outer boundary conditions are examined. It is shown that the solutions obtained from Lagrangian simulations, where the envelope is allowed to expand and mass is being conserved, are consistent with spherically symmetric solutions. In Eulerian schemes which utilize an outer boundary condition of free outflow, the outburst can be artificially quenched.
description: 12 Pages 3 figures; Accepted for publication in the Astrophysical Journal
Unbiased determination of the proton structure function F_2^p with faithful uncertainty estimation
Creators: name: The NNPDF Collaboration
name: Del Debbio, Luigi
name: Forte, Stefano
name: Latorre, Jose I.
name: Piccione, Andrea
name: Rojo, Joan
Publisher: name: arXiv
Year: 2005
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We construct a parametrization of the deep-inelastic structure function of the proton F_2 based on all available experimental information from charged lepton deep-inelastic scattering experiments. The parametrization effectively provides a bias-free determination of the probability measure in the space of structure functions, which retains information on experimental errors and correlations. The result is obtained in the form of a Monte Carlo sample of neural networks trained on an ensemble of replicas of the experimental data. We discuss in detail the techniques required for the construction of bias-free parameterizations of large amounts of structure function data, in view of future applications to the determination of parton distributions based on the same method.
description: 19 pages, 8 figures. Corrected treatment of normalization uncertainties. Tables 3-6 and Figures 3-7 updated, eqs 13-14 added
Dual equivalence between self-dual and topologically massive $B\wedge F$ models coupled to matter in $3+1$ dimensions
Creators: name: Maluf, R. V.
name: Silveira, F. A. G.
name: Silva, J. E. G.
name: Almeida, C. A. S.
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this work, we revisit the duality between a self-dual non-gauge invariant theory and a topological massive theory in $3+1$ dimensions. The self-dual Lagrangian is composed by a vector field and an antisymmetric field tensor whereas the topological massive Lagrangian is build using a $B \wedge F$ term. Though the Lagrangians are quite different, they yield to equations of motion that are connected by a simple dual mapping among the fields. We discuss this duality by analyzing the degrees of freedom in both theories and comparing their propagating modes at the classical level. Moreover, we employ the master action method to obtain a fundamental Lagrangian that interpolates between these two theories and makes evident the role of the topological $B \wedge F$ term in the duality relation. By coupling these theories with matter fields, we show that the duality holds provided a Thirring-like term is included. In addition, we use the master action in order to probe the duality upon the quantized fields. We carried out a functional integration of the fields and compared the resulting effective Lagrangians.
description: 21 pages
Supplementary material from The slave trade and the origins of matrilineal kinship
Creators: name: Lowes, Sara
name: Nunn, Nathan
Publisher: name: The Royal Society
Year: 2023
Subjects: classificationCode: 310499
subject: Evolutionary biology not elsewhere classified
classificationCode: 310901
subject: Animal behaviour

description: Matrilineal kinship systems—where descent is traced through mothers only—are present all over the world but are most concentrated in sub-Saharan Africa. We explore the relationship between exposure to Africa’s external slave trades, during which millions of people were shipped from the continent during a 400-year period and the evolution of matrilineal kinship. Scholars have hypothesized that matrilineal kinship, which is well-suited to incorporating new members, maintaining lineage continuity and insulating children from the removal of parents (particularly fathers), was an adaptive response to the slave trades. Motivated by this, we test for a connection between the slave trades and matrilineal kinship by combining historical data on an ethnic group’s exposure to the slave trades and the presence of matrilineal kinship following the end of the trades. We find that the slave trades are positively associated with the subsequent presence of matrilineal kinship. The result is robust to a variety of measures of exposure to the slave trades, the inclusion of additional covariates, sensitivity analyses that remove outliers, and an IV estimator that uses a group’s historical distance from the coast as an instrument. We also find evidence of a complementarity between polygyny and matrilineal kinship, which were both social responses to the disruption of the trades.This article is part of the theme issue ‘Social norm change: from evolution to policy intervention’.
Modifying the acidic tail of High Mobility Group B1 for designing Salmo salar TLR5 agonist peptides
Creators: name: Vásquez-Suárez, Aleikar
name: Muñoz-Flores, Carolina
name: Roa, Francisco
name: Castillo, Carolina
name: Romero, Alex
name: Parra, Natalie
name: Sandoval, Felipe
name: Macaya, Luis
name: Gutiérrez, Nicolás
name: González, Iván
name: Lamazares, Emilio
name: Astuya, Allison
name: Starck, María Francisca
name: Ortega, Leonardo
name: Villegas, Milton F.
name: Agurto, Niza
name: Montesino, Raquel
name: Sánchez, Oliberto
name: Valenzuela, Ariel
name: Toledo, Jorge R.
name: Acosta, Jannel
Publisher: name: Zenodo
Year: 2023

description: Based on the structural knowledge of TLR5 surface using blind docking platforms, a series of peptides derived from HMGB1 truncated acidic tail from Salmo salar was designed TLR5 agonistic. Also, a template peptide with the wild type C-terminal acidic tail sequence as reference was included (SsOri). Peptide binding poses complexed on TLR5 ectodomain model from each algorithm were filtrated based on docking scoring functions and predicted theoretical binding affinity of complex.
Assessing the impact of a multinational corporation on local social capital : a case study of a semiconductor company in the Philippines
Creators: name: Mochrie, Clare
Publisher: name: University of British Columbia
Year: 2009

description: This research explores how a multinational corporation (MNC) in the Philippines impacts on the social relations and integration of its host community in Baguio City. A lens of social capital is used to assess how the company influences local social patterns and networks, and in doing so, affects the community's capacity for development. Although emerging theories of development emphasize the importance of social linkages, little is known about how MNCs impact on these dynamics. Therefore, this study looks at the American subsidiary of Texas Instruments in the Philippines (TIPI) to determine whether it fosters relations within the local community that will support positive modes of development, or is shaping social networks that will stand to impede the community's achievement of its development goals. MNCs are first discussed generally in the context of globalization and the political economy of the Philippines. The paper then focuses on how this particular company operates in Baguio City. It is shown how, guided by principles of corporate social responsibility and contemporary ideologies of business, this widely accredited corporation builds community amongst its employees. How TIPI affects relations in the greater community of Baguio City is also explored and the implications for community development, as predicted by social capital theory, are discussed. In summary, it was found that while TIPI fosters social capital among its employees, it stands to inhibit social connections at a broader scope within the community. In that these community-wide networks are an important component of a community's development and planning capacity, the research suggests that TIPI, despite being socially responsible, does not represent a positive force for the community's development from the perspective of social capital. Several suggestions for policy and governance are provided by which the community might better ensure that MNCs foster positive development.
Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1)
Creators: name: Menezes, Gabriela De Lima
name: Silva, Roosevelt Alves Da
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer

description: Non-structural protein 1 (nsp1) is found in all Betacoronavirus genus, an important viral group that causes severe respiratory human diseases. This protein has significant role in pathogenesis and it is considered a probably major virulence factor. As it is absent in humans, it becomes an interesting target of study, especially when it comes to the rational search for drugs, since it increases the specificity of the target and reduces possible adverse effects that may be caused to the patient. Using approaches in silico we seek to study the behavior of nsp1 in solution to obtain its most stable conformation and find possible drugs with affinity to all of them. For this purpose, complete model of nsp1 of SARS-CoV-2 were predicted and its stability analyzed by molecular dynamics simulations in five different replicas. After main pocket validation using two control drugs and the main conformations of nsp1, molecular docking based on virtual screening were performed to identify novel potential inhibitors from DrugBank database. It has been found 16 molecules in common to all five nsp1 replica conformations. Three of them was ranked as the best compounds among them and showed better energy score than control molecules that have in vitro activity against nsp1 from SARS-CoV-2. The results pointed out here suggest new potential drugs for therapy to aid the rational drug search against COVID-19. Communicated by Ramaswamy H. Sarma
Constrained Dynamics: Generalized Lie Symmetries, Singular Lagrangians, and the Passage to Hamiltonian Mechanics
Creators: name: Speliotopoulos, Achilles D.
Publisher: name: arXiv
Year: 2020
Subjects: subject: Mathematical Physics (math-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: Guided by the symmetries of the Euler-Lagrange equations of motion, a study of the constrained dynamics of singular Lagrangians is presented. We find that these equations of motion admit a generalized Lie symmetry, and on the Lagrangian phase space the generators of this symmetry lie in the kernel of the Lagrangian two-form. Solutions of the energy equation\textemdash called second-order, Euler-Lagrange vector fields (SOELVFs)\textemdash with integral flows that have this symmetry are determined. Importantly, while second-order, Lagrangian vector fields are not such a solution, it is always possible to construct from them a SOELVF that is. We find that all SOELVFs are projectable to the Hamiltonian phase space, as are all the dynamical structures in the Lagrangian phase space needed for their evolution. In particular, the primary Hamiltonian constraints can be constructed from vectors that lie in the kernel of the Lagrangian two-form, and with this construction, we show that the Lagrangian constraint algorithm for the SOELVF is equivalent to the stability analysis of the total Hamiltonian. Importantly, the end result of this stability analysis gives a Hamiltonian vector field that is the projection of the SOELVF obtained from the Lagrangian constraint algorithm. The Lagrangian and Hamiltonian formulations of mechanics for singular Lagrangians are in this way equivalent.
description: 45 pages. Published paper is open access, and can be found either at the Journal of Physics Communications website or at the DOI below
Fingerprint-based similarity search identified p-anisidine as an anticancer agent in HeLa and a prospective phytochemical ETV1 transcription factor inhibitor
Creators: name: Ambily Nath IV
name: Achuthsankar S. Nair
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Plant Biology

description: Overexpression of E26 transformation-specific (ETS) PEA3 subfamily transcription factor (TF) ETV1 is reportedly oncogenic and metastatic in several cancers. Albeit, a few synthetic small molecule inhibitors of ETV1 have been identified to date. In this context, we hereby proposed a phytochemical lead development scheme to gather inhibitor scaffolds for ETV1. A fingerprint-based similarity search was conducted to screen plant compounds structurally similar to known ETV1 perturbagens. At default cutoffs, 20 compounds were retrieved whose pharmacokinetic, docking, and scaffold analysis rendered eight compounds for final evaluation in HeLa cells by MTT assay. CID7732 (p-anisidine) belonging to the subclass aminophenyl ethers was emerged as a promising anticancer agent with an IC50 of 27.769 µg/mL. This is the first natural product-based chemical hunt carried out for ETV1 repressors. Communicated by Ramaswamy H. Sarma
Realization of graded-simple algebras as loop algebras
Creators: name: Allison, Bruce
name: Berman, Stephen
name: Faulkner, John
name: Pianzola, Arturo
Publisher: name: arXiv
Year: 2005
Subjects: subject: Rings and Algebras (math.RA)
subject: Quantum Algebra (math.QA)
subject: Representation Theory (math.RT)
subject: FOS: Mathematics
subject: 16W50, 17B70, 17B65, 17B67

description: Multiloop algebras determined by $n$ commuting algebra automorphisms of finite order are natural generalizations of the classical loop algebras that are used to realize affine Kac-Moody Lie algebras. In this paper, we obtain necessary and sufficient conditions for a $Z^n$-graded algebra to be realized as a multiloop algebra based on a finite dimensional simple algebra over an algebraically closed field of characteristic 0. We also obtain necessary and sufficient conditions for two such multiloop algebras to be graded-isomorphic, up to automorphism of the grading group. We prove these facts as consequences of corresponding results for a generalization of the multiloop construction. This more general setting allows us to work naturally and conveniently with arbitrary grading groups and arbitrary base fields.
description: 31 pages. Corrected typos and added minor clarifications. Accepted in Forum Mathematicum
The motion of a shock wave through a non-uniform one-dimensional medium in the case of arbitrary equation of state
Creators: name: Serov, Serge A.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: General Physics (physics.gen-ph)
subject: FOS: Physical sciences

description: The derivation of the equation of one-dimensional movement of a solitary shock wave is given. This derivation shows, that the differential equation of movement of a solitary plane shock wave in the channel with variable area, is exact, if simplifying assumptions, made during derivation, are realized. But these assumptions in plane geometry it is possible to realize only approximately; situation with spherical and cylindrical shock waves is opposite.
description: 11 pages, 1 figure, 1 table
The Activity Reaction Core and Plasticity of Metabolic Networks
Creators: name: Almaas, E.
name: Oltvai, Z. N.
name: Barabasi, A. -L.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Cell Behavior (q-bio.CB)
subject: Quantitative Methods (q-bio.QM)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses (FBA) have proved highly successful in analyzing the capabilities of cellular metabolism, including its capacity to predict deletion phenotypes, the ability to calculate the relative flux values of metabolic reactions and the properties of alternate optimal growth states. Here, we use FBA to thoroughly assess the activity of the Escherichia coli, Helicobacter pylori, and Saccharomyces cerevisiae metabolism in 30,000 diverse simulated environments. We identify a set of metabolic reactions forming a connected metabolic core that carry non-zero fluxes under all growth conditions, and whose flux variations are highly correlated. Furthermore, we find that the enzymes catalyzing the core reactions display a considerably higher fraction of phenotypic essentiality and evolutionary conservation than those catalyzing non-core reactions. Cellular metabolism is characterized by a large number of species-specific conditionally-active reactions organized around an evolutionary conserved always active metabolic core. Finally, we find that most current antibiotics interfering with the bacterial metabolism target the core enzymes, indicating that our findings may have important implications for antimicrobial drug target discovery.
description: 21 pages, 4 figures, supp. mat. available at http://www.nd.edu/~networks
Reclaiming The Lost Glory
Creators: name: RODRIGUES, TENSING CARLOS
Publisher: name: figshare
Year: 2021
Subjects: History

description: Miranda was not the only family from the new Christian brāmhaṇ nobiliarchy that rose to prominence within the first few centuries of the advent of the Portuguese. Not long after Pedro Joaquim de Miranda (1791-1845) was promoted as Administrador Fiscal of the Novas Conquistas, Vicente João de Figueiredo was appointed as the Administrador Particular of the three ‘províncias’ of Canacona, Bally and Chondravadi, in 1841. Vicente João de Figueiredo too was from Loutulim, and a distant cousin of Pedro Joaquim de Miranda; the latter’s paternal great-grandmother (circa middle of 17th century) was from the Figueiredo family.
Magnetoconductivity oscillations induced by intersubband excitation in a degenerate 2D electron gas
Creators: name: Monarkha, Yuriy
Publisher: name: arXiv
Year: 2020
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: Magnetoconductivity oscillations and absolute negative conductivity induced by nonequilibrium populations of excited subbands in a degenerate multisubband two-dimensional electron system are studied theoretically. The displacement from equilibrium, which can be caused by resonant microwave excitation or by any other reason, is assumed to be such that electron distributions can no longer be described by a single Fermi level. In this case, in addition to the well-known conductivity peaks occurring at the Shubnikov-de Haas conditions and small peaks of normal intersubband scattering, sign-changing oscillations with a different shape are shown to be possible. We found also that even a small fraction of electrons transferred to the excited subband can lead to negative conductivity effects.
Dynamics and allostery of Zika virus non-structural protein 5 methyltransferase
Creators: name: Chagas, Marcelo
name: Rocha, Willian
name: Moraes, Adolfo
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Cancer
subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: The methyltransferase (MTase) domain of non-structural protein 5 (NS5) plays a fundamental role in flaviviruses replication, and its inhibition is a strategy for antiviral development. MTase methylates viral RNA cap at guanine N-7 and the ribose 2'OH of the first adenosine. Many structures of Zika virus (ZIKV) and other flaviviruses MTases bound to cofactors, substrates and inhibitor candidates have been solved. Still, the dynamical modulation of MTase binding and catalytic activity yet needs to be clarified. Here, we investigated the structural dynamics of ZIKV NS5 MTase domain free and bound to Guanosine-5'-triphosphate (GTP) and S-Adenosyl-Lmethionine (SAM), to identify the molecular dynamics changes related to ligand binding and methyl transfer reaction. We have observed that the binding of the GTP and SAM individually and GTP-SAM in the ternary complex has induced allostery in the RNA binding site, showing the complexity of ZIKV MTase conformational equilibrium and its impact on viral RNA recognition. We also mapped in molecular dynamics trajectories, conformations of GTP guanine moiety that mimics guanine orientations visualized in human-specific N-methyltransferase structures solved by X-ray crystallography. It is the first time that N-7 methylation-prone guanine orientation has been proposed and modeled in flavivirus MTase. Communicated by Ramaswamy H. Sarma
Copolymer adsorption kinetics at a selective liquid-liquid interface: Scaling theory and computer experiment
Creators: name: Corsi, Andrea
name: Milchev, Andrey
name: Rostiashvili, Vakhtang G.
name: Vilgis, Thomas A.
Publisher: name: arXiv
Year: 2005
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We consider the adsorption kinetics of a regular block-copolymer of total length $N$ and block size $M$ at a selective liquid-liquid interface in the limit of strong localization. We propose a simple analytic theory based on scaling considerations which describes the relaxation of the initial coil into a flat-shaped layer. The characteristic times for attaining equilibrium values of the gyration radius components perpendicular and parallel to the interface are predicted to scale with chain length $N$ and block length $M$ as $τ_{\perp} \propto M^{1+2ν}$ (here $ν\approx 0.6$ is the Flory exponent) and as $τ_{\parallel} \propto N^2$, although initially the rate of coil flattening is expected to decrease with block size as $\propto M^{-1}$. Since typically $N\gg M$ for multiblock copolymers, our results suggest that the flattening dynamics proceeds faster perpendicular rather than parallel to the interface. We also demonstrate that these scaling predictions agree well with the results of extensive Monte Carlo simulations of the localization dynamics.
description: 4 pages, 4 figures, submited to Europhys. Lett