cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Design peptide and multi-epitope protein vaccine candidates against monkeypox virus using reverse vaccinology approach: an in-silico study
Creators: name: Jahantigh, Hamid Reza
name: Shahbazi, Behzad
name: Gouklai, Hamed
name: Van der Weken, Hans
name: Gharibi, Zahra
name: Rezaei, Zahra
name: Habibi, Mehri
name: Ahmadi, Khadijeh
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Monkeypox is a zoonotic virus that has recently affected different countries worldwide. On July 23, 2022, the WHO declared the outbreak of monkeypox as a public health emergency of international concern. Surveillance studies conducted in Central Africa in the 1980s and later during outbreaks in the same region showed smallpox vaccines to be clinically somewhat effective against Monkeypox virus. However, there is no specific vaccine against this virus. This research used bioinformatics techniques to establish a novel multi-epitope vaccine candidate against Monkeypox that can induce a strong immune response. Five well-known antigenic proteins (E8L, A30L, A35R, A29L, and B21R) of the virus were picked and assessed as possible immunogenic peptides. Two suitable peptide candidates were selected according to bio-informatics analysis. Based upon in silico evaluation, two multi-epitope vaccine candidates (ALALAR and ALAL) were built with rich-epitope domains consisting of high-ranking T and B-cell epitopes. After predicting and evaluating the 3D structure of the protein candidates, the most efficient 3D models were considered for docking studies with Toll-like receptor 4 (TLR4) and the HLA-A * 11:01, HLA-A*01:01, HLA-A*02:01, HLA-A*03:01, HLA-A*07:02, HLA-A*15:01, HLA-A*30:01 receptors. Subsequently, molecular dynamics (MD) simulation of up to 150 nanoseconds was employed to assess the durability of the interaction of the vaccine candidates with immune receptors. MD studies showed that M5-HLA-A*11:01, ALAL-TLR4, and ALALAR-TLR4 complexes were stable during simulation. Analysis of the in silico outcomes indicates that the M5 peptide and ALAL and ALALAR proteins may be suitable vaccine candidates against the Monkeypox virus. Communicated by Ramaswamy H. Sarma
title: Detection of non-metallic foreign bodies of gastrointestinal tract in emergency pediatric practice.
Creators: name: Hambardzumyan, Andrias
Publisher: name: European Congress of Radiology
Year: 2019
Subjects: subject: Paediatric
subject: Emergency
subject: Gastrointestinal tract
subject: Conventional radiography
subject: CT-High Resolution
subject: Digital radiography
subject: Barium meal
subject: Diagnostic procedure
subject: Complications
subject: Foreign bodies
subject: Image registration

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: Plain radiographs still play an essential role in the assessment of ingested foreign bodies in the pediatric patient: plain films of the neck, chest, and abdomen are very useful in confirming the diagnosis of foreign bodies ingestion because most...
Highly tunable lateral homojunction formed in 2D layered CuInP2S6 via in-plane ionic migration
Creators: name: Zhu, Huanfeng
name: Li, Jialin
name: Chen, Qiang
name: Tang, Wei
name: Fan, Xinyi
name: Li, Fan
name: Li, Linjun
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: As basic building blocks for next-generation information technologies devices, high-quality p-n junctions based on van der Waals (vdW) materials have attracted widespread interest.Compared to traditional two dimensional (2D) heterojunction diodes, the emerging homojunctions are more attractive owing to their intrinsic advantages, such as continuous band alignments and smaller carrier trapping. Here, utilizing the long-range migration of Cu + ions under in-plane electric field, a novel lateral p-n homojunction was constructed in the 2D layered copper indium thiophosphate (CIPS). The symmetric Au/CIPS/Au devices demonstrate an electric-field-driven resistance switching (RS) accompanying by a rectification behavior without any gate control. Moreover, such rectification behavior can be continuously modulated by poling voltage. We deduce that the reversable rectifying RS behavior is governed by the effective lateral build-in potential and the change of the interfacial barrier during the poling process. Furthermore, the CIPS p-n homojuction is evidenced by the photovoltaic effect, with the spectral response extending up to visible region due to the better photogenerated carrier separation efficiency. Our study provides a facile route to fabricate homojuctions through electric-field-driven ionic migration and paves the way towards the use of this method in other vdW materials.
Family of Gaussian wavepacket dynamics methods from the perspective of a nonlinear Schrödinger equation
Creators: name: Vaníček, Jiří J. L.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Many approximate solutions of the time-dependent Schrödinger equation can be formulated as exact solutions of a nonlinear Schrödinger equation with an effective Hamiltonian operator depending on the state of the system. We show that several well-known Gaussian wavepacket dynamics methods, such as Heller's original thawed Gaussian approximation or Coalson and Karplus's variational Gaussian approximation, fit into this framework if the effective potential is a quadratic polynomial with state-dependent coefficients. We study such a nonlinear Schrödinger equation in general: in particular, we derive general equations of motion for the Gaussian's parameters, demonstrate the time reversibility and norm conservation, and analyze conservation of the energy, effective energy, and symplectic structure. We also describe efficient geometric integrators of arbitrary even orders of accuracy in the time step for the numerical solution of this nonlinear Schrödinger equation. The general presentation is illustrated by examples of this family of Gaussian wavepacket dynamics, including the variational and nonvariational thawed and frozen Gaussian approximations, and special limits of these methods based on the global harmonic, local harmonic, single-Hessian, local cubic, and single quartic approximations for the potential energy. Without substantially increasing the cost, the proposed single quartic variational thawed Gaussian wavepacket dynamics improves the accuracy over the local cubic approximation and, at the same time, conserves both the effective energy and symplectic structure, in contrast to the much more expensive local quartic approximation. Most results are presented in both Heller's and Hagedorn's parametrizations of the Gaussian wavepacket.
Subfactors of index less than 5, part 4: vines
Creators: name: Penneys, David
name: Tener, James E.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Operator Algebras (math.OA)
subject: FOS: Mathematics
subject: 46L37, 18D10

description: We eliminate 38 infinite families of possible principal graphs as part of the classification of subfactors up to index 5. A number-theoretic result of Calegari-Morrison-Snyder, generalizing Asaeda-Yasuda, reduces each infinite family to a finite number of cases. We provide algorithms for computing the effective constants that are required for this result, and we obtain 28 possible principal graphs. The Ostrik d-number test and an algebraic integer test reduce this list to 7 graphs in the index range (4,5) which actually occur as principal graphs.
description: 17 pages, many figures, minor changes from v1
An overview of intercropping tree/tea plantations in China
Creators: name: Feng, Yutong
Publisher: name: University of British Columbia
Year: 2022

description: The construction of composite tea plantations allows for symbiosis and reciprocity of organisms within the tea plantation, increasing the overall benefits and enriching biodiversity. Cultivation methods that intercrop tea with other species are widespread within China. They are found throughout the provinces, and the intercropping methods vary greatly. However, no article has provided a general overview of them. This thesis is a literature review designed to summarize and analyze all the composite ecological tea gardens. Through a keyword search of all the materials in the current literature database, 223 eligible documents were selected from 10,069 relevant documents in Web of Science Core Collection, UBC Library, and Elsevier Science Direct abstracts. The possible effects of 151 different tea/other species intercropping plantations were summarized and analyzed from six aspects: contained chemical substances in tea leaves substances, microbial environment, ecological environment, multiple ecological niches, prevention of pests and diseases, and soil conditions. Moreover, it was concluded that the advantages of intercropping tea gardens outweighed the disadvantages of monoculture tea gardens. Intercropping tea gardens are more sustainable than regular tea gardens because of the changes and benefits in the above six aspects to varying degrees.
Anderson localization of matter waves in tailored disordered potentials
Creators: name: Piraud, Marie
name: Aspect, Alain
name: Sanchez-Palencia, Laurent
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We show that, in contrast to immediate intuition, Anderson localization of noninteracting particles induced by a disordered potential in free space can increase (i.e., the localization length can decrease) when the particle energy increases, for appropriately tailored disorder correlations. We predict the effect in one, two, and three dimensions, and propose a simple method to observe it using ultracold atoms placed in optical disorder. The increase of localization with the particle energy can serve to discriminate quantum versus classical localization.
LiNbO$_3$ volatile memristors for reservoir computing
Creators: name: Yuanxi, Zhao
name: Wenrui, Duan
name: Huanglong, Li
Publisher: name: arXiv
Year: 2023
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: In conventional digital computers, data and information are represented in binary form and encoded in the steady states of transistors. They are then processed in a quasi-static way. However, with transistors approaching their physical limits and the von Neumann bottleneck, the rate of improvement in computing efficiency has slowed down. Therefore, drawing inspiration from the dynamic and adaptive properties of biological systems, research in neural morphology computing has great potential for development. Memristors, a class of nonlinear resistors with memory function, naturally embody dynamics through their internal electrical processes. This enables nonconventional computing paradigms with enhanced capability and energy efficiency, such as reservoir computing. In this paper, we propose a volatile memristor made of LiNbO3 with nonlinear I-V characteristics and short-term memory function. This memristor is well-suited to be used as a nonlinear node in the storage layer of reservoir computing. With this system, we can achieve the same functionality as traditional reservoir computing with a single device, instead of a large number of interconnected nodes. The collective states of memristors after the application of trains of pulses to the respective memristors are unique for each combination of pulse patterns. This provides a more reliable and efficient way for subsequent output layer classification processing. The system was successfully used to recognize images of Arabic numerals 0-9. This work not only broadens the application scope of materials such as lithium niobate in neural morphology computing but also provides new ideas for developing more efficient neural morphology devices and systems.
description: 58 pages, in Chinese language, 58 figures
Detection Loophole in Bell experiments: How post-selected local correlations can look non-local
Creators: name: Branciard, Cyril
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A common problem in Bell type experiments is the well-known detection loophole: if the detection efficiencies are not perfect and if one simply post-selects the conclusive events, one might observe a violation of a Bell inequality, even though a local model could have explained the experimental results. In this paper, we analyze the set of all post-selected correlations that can be explained by a local model, and show that it forms a polytope, larger than the Bell local polytope. We characterize the facets of this post-selected local polytope in the CHSH scenario, where two parties have binary inputs and outcomes. Our approach gives new insights on the detection loophole problem.
description: 9 pages, 3 figures
Long-range communication between transmembrane- and nucleotide-binding domains does not depend on drug binding to mutant P-glycoprotein
Creators: name: Bonito, Cátia A.
name: Ferreira, Ricardo J.
name: Ferreira, Maria-José U.
name: Gillet, Jean-Pierre
name: Cordeiro, M. Natália D. S.
name: dos Santos, Daniel J. V. A.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Biological Sciences not elsewhere classified
subject: Computational Biology

description: In this study, the impact of four P-gp mutations (G185V, G830V, F978A and ΔF335) on drug-binding and efflux-related signal-transmission mechanism was comprehensively evaluated in the presence of ligands within the drug-binding pocket (DBP), experimentally related with changes in their drug efflux profiles. The severe repacking of the transmembrane helices (TMH), induced by mutations and exacerbated by the presence of ligands, indicates that P-gp is sensitive to perturbations in the transmembrane region. Alterations on drug-binding were also observed as a consequence of the TMH repacking, but were not always correlated with alterations on ligands binding mode and/or binding affinity. Finally, and although all P-gp variants holo systems showed considerable changes in the intracellular coupling helices/nucleotide-binding domain (ICH-NBD) interactions, they seem to be primarily induced by the mutation itself rather than by the presence of ligands within the DBP. The data further suggest that the changes in drug efflux experimentally reported are mostly related with changes on drug specificity rather than effects on signal-transmission mechanism. We also hypothesize that an increase in the drug-binding affinity may also be related with the decreased drug efflux, while minor changes in binding affinities are possibly related with the increased drug efflux observed in transfected cells. Communicated by Ramaswamy H. Sarma
Compositeness of $T_{cc}$ and $X(3872)$ by considering decay and coupled-channels effects
Creators: name: Kinugawa, Tomona
name: Hyodo, Tetsuo
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The compositeness of weakly bound states is discussed using the effective field theory from the viewpoint of the low-energy universality. We introduce a model with coupling of the single-channel scattering to the bare state, and study the compositeness of the bound state by varying the bare state energy. In contrast to the naive expectation that the near-threshold states are dominated by the molecular structure, we demonstrate that a non-composite state can always be realized even with a small binding energy. At the same time, however, it is shown that a fine tuning is necessary to obtain the non-composite weakly bound state. In other words, the probability of finding a model with the composite dominant state becomes larger with the decrease of the binding energy in accordance with the low-energy universality. For the application to exotic hadrons, we then discuss the modification of the compositeness due to the decay and coupled-channels effects. We quantitatively show that these contributions suppress the compositeness, because of the increase of the fraction of other components. Finally, as examples of near-threshold exotic hadrons, the structures of $T_{cc}$ and $X(3872)$ are studied by evaluating the compositeness. We find the importance of the coupled-channels and decay contributions for the structures of $T_{cc}$ and $X(3872)$, respectively.
description: 19 pages, 14 figures, published version
On the integrality of Witten-Reshetikhin-Turaev 3-manifold invariants
Creators: name: Beliakova, Anna
name: Chen, Qi
name: Le, Thang
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Algebra (math.QA)
subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 57M27, 57M25

description: We prove that the SU(2) and SO(3) Witten-Reshetikhin-Turaev invariants of any 3-manifold with any colored link inside at any root of unity are algebraic integers.
description: 30 pages
Structural-based design of HD-TAC7 PROteolysis TArgeting chimeras (PROTACs) candidate transformations to abrogate SARS-CoV-2 infection
Creators: name: Zahid, Sana
name: Ali, Yasir
name: Rashid, Sajid
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for about 672 million infections and 6.85 million deaths worldwide. Upon SARS-CoV-2 infection, Histone deacetylases (HDACs) hyperactivate the pro-inflammatory response resulting in stimulation of Acetyl-Coenzyme A and cholesterol for viral entry. HDAC3 inhibition results in the anti-inflammatory activity and reduction of pro-inflammatory cytokines that may restrict COVID-19 progression. Here, we have designed 44 conformational ensembles of previously known HD-TAC7 by enumerating torsions of dihedral angles tested for their binding preferences against HDAC3. Through scrutinizing their placements at active site and binding affinities, three hits were isolated. Cereblon (CRBN) is a well-known E3 ligase that facilitates Proteolysis Targeting Chimeras (PROTACs) targeting. Three entities, including HDAC3-binding moiety (4-acetamido-N-(2-amino-4 fluorophenyl) benzamide), a 6-carbon linker, and CRBN binding ligand (pomalidomide) were assembled to design 4 PROTACs followed by energy minimization and docking against HDAC3 and CRBN, respectively. Subsequent molecular dynamics (MD) and free energy analyses corroborated similar binding trends and favorable energy values. Among all cases, Met88, GLu106, Pro352, Trp380 and Trp388 residues of CRBN, and Pro23, Arg28, Lys194, Phe199, Leu266, Thr299 and Ile346 residues of HDAC3 were engaged in PROTAC binding. Thus, conformational dynamics of both HDAC3 and CRBN moieties are essential for the placement of PROTAC, resulting in target degradation. Overall, the proposed bifunctional small molecules may effectively target HDAC3, stimulating innate immune response to restrict COVID-19 hyperinflammation. This study supports the basis for designing new PROTACs by limiting the conformational search space that may prove more efficient for targeting the protein of interest. Communicated by Ramaswamy H. Sarma
Simulating the quantum Fourier transform, Grover's algorithm, and the quantum counting algorithm with limited entanglement using tensor-networks
Creators: name: Niedermeier, Marcel
name: Lado, Jose L.
name: Flindt, Christian
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: Quantum algorithms reformulate computational problems as quantum evolutions in a large Hilbert space. Most quantum algorithms assume that the time-evolution is perfectly unitary and that the full Hilbert space is available. However, in practice, the available entanglement may be limited, leading to a reduced fidelity of the quantum algorithms. To simulate the execution of quantum algorithms with limited entanglement, tensor-network methods provide a useful framework, since they allow us to restrict the entanglement in a quantum circuit. Thus, we here use tensor-networks to analyze the fidelity of the quantum Fourier transform, Grover's algorithm, and the quantum counting algorithm as the entanglement is reduced, and we map out the entanglement that is generated during the execution of each algorithm. In all three cases, we find that the algorithms can be executed with high fidelity even if the entanglement is somewhat reduced. Our results are promising for the execution of these algorithms on future quantum computers, and our simulation method based on tensor networks may also be applied to other quantum algorithms.
description: 16 pages, 13 figures
Somali Research and Education Repository – Quick «How-To»
Creators: name: Ahmed, Mohamed Ali
Publisher: name: SORER
Year: 2020
Subjects: Open-Acess
Open-Data
How-to
Quick-guide
SORER
SomaliREN

description: This document is a quick guide on the use of the Somali Research and Education Repository (SORER) from the user point of view. Accessing SORER, creating ORCID ID, content upload, community management, and user support are briefly well explained.
Skyrme crystals, nuclear matter and compact stars
Creators: name: Adam, Christoph
name: Martin-Caro, Alberto Garcia
name: Huidobro, Miguel
name: Wereszczynski, Andrzej
Publisher: name: arXiv
Year: 2023
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: A general review of the crystalline solutions of the generalized Skyrme model and their application to the study of cold nuclear matter at finite density and the Equation of State (EOS) of neutron stars is presented. For the relevant range of densities, the ground state of the Skyrme model in the three torus is shown to correspond to configurations with different symmetries, with a sequence of phase transitions between such configurations. The effects of nonzero finite isospin asymmetry are taken into account by the canonical quantization of isospin collective coordinates, and some thermodynamical and nuclear observables (such as the symmetry energy) are computed as a function of the density. We also explore the extension of the model to accommodate strange degrees of freedom, and find a first order transition for the condensation of kaons in the Skyrme crystal background in a thermodynamically consistent, non-perturbative way. Finally, an approximate EOS of dense matter is constructed by fitting the free parameters of the model to some nuclear observables close to saturation density, which are particularly relevant for the description of nuclear matter. The resulting neutron star mass-radius curves already reasonably satisfy current astrophysical constraints.
description: 54 pages, 28 figures, review
Entanglement of a Quantum Optical Elliptic Vortex
Creators: name: Bandyopadhyay, Abir
name: Prabhakar, Shashi
name: Singh, Ravindra Pratap
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We calculate the entanglement of a generalized elliptical vortex formed by quantized radiation field, using Wigner quasiprobability distribution function for such states. We find a critical squeezing parameter above which the entanglement is less for higher vorticity, which is counter intuitive.
description: Accepted in Physics Letters A. Proof corrected version. 11 pages including 2 figs
Offline Uncertainty Sampling in Data-driven Stochastic MPC
Creators: name: Teutsch, Johannes
name: Kerz, Sebastian
name: Brüdigam, Tim
name: Wollherr, Dirk
name: Leibold, Marion
Publisher: name: arXiv
Year: 2023
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In this work, we exploit an offline-sampling based strategy for the constrained data-driven predictive control of an unknown linear system subject to random measurement noise. The strategy uses only past measured, potentially noisy data in a non-parametric system representation and does not require any prior model identification. The approximation of chance constraints using uncertainty sampling leads to efficient constraint tightening. Under mild assumptions, robust recursive feasibility and closed-loop constraint satisfaction is shown. In a simulation example, we provide evidence for the improved control performance of the proposed control scheme in comparison to a purely robust data-driven predictive control approach.
description: This work has been accepted for presentation at IFAC World Congress 2023
Parent experiences of the primary to secondary school transition for their child with autism spectrum disorder
Creators: name: Yli-Renko, Teija Kristiina
Publisher: name: University of British Columbia
Year: 2022

description: The transition from primary to secondary school for children with autism spectrum disorder (ASD) can be a time of stress and challenges for the student and their family (Stack et al., 2021). When advocating for support for their child, the parent is faced with many decisions and concerns about how to assist their child as they transition to an unfamiliar environment. Limited literature on this period of transition necessitates further research that explicates the experience of transition for these families. As such, the study captures the perceptions of parents who have a child with ASD who is transitioning from primary to mainstream secondary school. The study builds on the survey by Ravenscroft and colleagues (2017) and uses an adapted form of their instrument to study the population of students with ASD in the context of British Columbia schools. The current study surveyed parents to elicit ratings related to key elements of their experience of planning for and implementation of transition with their child. Further, the study included additional elements that are intended to inform the literature on the impacts of the COVID-19 pandemic restrictions and mandatory quarantines on the parent (and family) experiences of transition planning and process. The results of this study provide a preliminary representation of current parent and family experiences of transition planning and its outcomes and can be interpreted in the context of proposed frameworks for transition success provided in the literature, mainly aspects related to inclusion, membership, and belonging (IMB) in the secondary school environment, as well as parental involvement (PI). These two variables contributed to the prediction of transition success with respect to parent satisfaction, or child adjustment outcomes. These findings provide an initial representation of transition planning and outcome in a Canadian context and may well contribute findings that can inform educational policy and practice.
Lawsonia inermis flower aqueous extract expressed better anti-alpha-glucosidase and anti-acetylcholinesterase activity and their molecular dynamics
Creators: name: Shahanaj, Ismail
name: Ramakrishnan, Jaganathan
name: Poomani, Kumaradhas
name: Devarajan, Natarajan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Lawsonia inermis (henna) has been used in traditional medicine throughout the world and biological property of its flower has been least explored. In the present study, the phytochemical characterization and biological activity (in vitro radical scavenging activity, anti-alpha glucosidase and anti-acetylcholinesterase) of aqueous extract prepared from henna flower (HFAE) was carried out by both Qualitative and quantitative phytochemical analysis and Fourier-transform infrared spectroscopy revealed the functional group of the phytoconstituents such as phenolics, flavonoids, saponin, tannins and glycosides. The phytochemicals present in HFAE was preliminary identified by liquid chromatography/electrospray ionization tandem mass spectrometry. The HFAE showed potent in vitro antioxidant activity and the HFAE inhibited mammalian α-glucosidase (IC50 = 129.1 ± 5.3 µg/ml; Ki = 38.92 µg/ml) and acetylcholinesterase (AChE; IC50 = 137.77 ± 3.5 µg/ml; Ki = 35.71 µg/ml) activity by competitive manner. In silico molecular docking analysis revealed the interaction of active constituents identified in HFAE with human α-glucosidase and AChE. Molecular dynamics simulation for 100 ns showed the stable binding of top two ligand/enzyme complexes with lowest binding energy such as 1,2,3,6-Tetrakis-O-galloyl-beta-D-glucose (TGBG)/human α-glucosidase, Kaempferol 3-glucoside-7-rhamnoside (KGR)/α-glucosidase, agrimonolide 6-O-β-D-glucopyranoside (AMLG)/human AChE and KGR/AChE. Through MM/GBSA analysis, the binding energy for TGBG/human α-glucosidase, KGR/α-glucosidase, AMLG/human AChE and KGR/AChE was found to be −46.3216, −28.5772, −45.0077 and −47.0956 kcal/mol, respectively. Altogether, HFAE showed an excellent antioxidant, anti-alpha glucosidase and anti-AChE activity under in vitro. This study suggest HFAE with remarkable biological activities could be further explored for therapeutics against type 2 diabetes and diabetes-associated cognitive decline. Communicated by Ramaswamy H. Sarma
An Online Adaptation Strategy for Direct Data-driven Control
Creators: name: Teutsch, Johannes
name: Ellmaier, Sebastian
name: Kerz, Sebastian
name: Wollherr, Dirk
name: Leibold, Marion
Publisher: name: arXiv
Year: 2023
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: The fundamental lemma from behavioral systems theory yields a data-driven non-parametric system representation that has shown great potential for the data-efficient control of unknown linear and weakly nonlinear systems, even in the presence of measurement noise. In this work, we strive to extend the applicability of this paradigm to more strongly nonlinear systems by updating the system representation during control. Unlike existing approaches, our method does not impose suitable excitation to the control inputs, but runs as an observer parallel to the controller. Whenever a rank condition is deemed to be fulfilled, the system representation is updated using newly available datapoints. In a reference tracking simulation of a two-link robotic arm, we showcase the performance of the proposed strategy in a predictive control framework.
description: This work has been accepted for presentation at IFAC World Congress 2023
Minimum-length deformed quantization of a free field on de Sitter background and corrections to the inflaton perturbations
Creators: name: Maziashvili, Michael
Publisher: name: arXiv
Year: 2011
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The effect of string and quantum gravity inspired minimum-length deformed quantization on a free, massless scalar field is studied on de Sitter background at the level of second quantization. Analytic solution of a field operator is obtained to the first order in deformation parameter. Using this solution we then estimate the two point and four point correlation functions (with respect to the Bunch-Davies vacuum). The field operator shows up a non-linear dependence on creation and annihilation operators, therefore the perturbation spectrum proves to be non-Gaussian. The correction to the power spectrum is of the same order as obtained previously in a similar study that incorporates the minimum-length deformed momentum operator into the first quantization picture and then proceeds in the standard way for second quantization. The non-Gaussianity comes at the level of four point correlation function; its magnitude appears to be suppressed by the factor $\sim\exp(-6N)$, where $N$ is the number of e-foldings.
description: 14 pages, clarifying remark added
Computational analysis of structural and functional evaluation of the deleterious missense variants in the human CTLA4 gene
Creators: name: Bouqdayr, Meryem
name: Abbad, Anass
name: Baba, Hanâ
name: Saih, Asmae
name: Wakrim, Lahcen
name: Kettani, Anass
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mental Health

description: CTLA-4 is an immune checkpoint receptor that negatively regulates the T-cell function expressed after T-cell activation to break the immune response. The current study predicted the genomic analysis to explore the functional variations of missense SNPs in the human CTLA4 gene using PolyPhen2, SIFT, PANTHER, PROVEAN, Fathmm, Mutation Assessor, PhD-SNP, SNPs&GO, SNAP2, and MutPred2. Phylogenetic conservation protein was predicted by ConSurf. Protein structural analysis was carried out by I-Mutant3, MUpro, iStable2, PremPS, and ERIS servers. Molecular dynamics trajectory analysis (RMSD, RMSF, Rg, SASA, H-bonds, and PCA) was performed to analyze the dynamic behavior of native and mutant CTLA-4 at the atomic level. Our in-silico analysis suggested that C58S, G118R, P137Q, P137R, P137L, P138T, and G146L variants were predicted to be the most deleterious missense variants and highly conserved residues. Moreover, the molecular dynamics analysis proposed a decrease in the protein stability and compactness with the P137R and P138T highlighting the impact of these variants on the function of the CTLA-4 protein. Communicated by Ramaswamy H. Sarma
Evaluation of the size effect of hydrophobic ring substitution on 9-O position of berberine on DNA binding
Creators: name: Khatun, Munira
name: Jana, Gopal Chandra
name: Nayim, Sk
name: Dhal, Asima
name: Patra, Anirudha
name: Hossain, Maidul
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Medicine
Molecular Biology
Pharmacology
Chemical Sciences not elsewhere classified
Cancer

description: The interaction of deoxyribonucleic acid (DNA) with medicinally significant small molecules has long piqued the interest of researchers because its applications are directly related to the discovery of new classes of drugs. Keeping this in mind, here we report berberine derivatives and their interaction with calf thymus DNA (CT-DNA). In this report we discussed on the structural perspectives and thermodynamic characteristics of the interaction of four 9-O-substituted berberines (BRDR1 to BRDR4) with CT-DNA. The binding affinity of BRDR–DNA complexes increased with increasing the cycloalkane ring size of the substitution except BRDR2. The binding constant value obtained from UV–Visible spectral analysis was 1.12 × 106 for BRDR1, 0.37 × 106 for BRDR2, 1.72 × 106 for BRDR3 and 3.20 × 106 for BRDR4. Ferrocyanide quenching experiments revealed unequivocally that the analogues except BRDR2 had a partly intercalative binding to DNA. From the ITC experiment it was found that the bindings of BRDR1, BRDR3 and BRDR4 to DNA was favoured by negative enthalpy and positive entropy while BRDR2 was driven by positive enthalpy and positive entropy. In all cases the hydrophobic interaction plays a crucial role. Thus, the complete multispectroscopic and thermodynamic binding studies may be useful for new drug design and development. Communicated by Ramaswamy H. Sarma
Relativistic approach for the determination of nuclear and neutron star properties in consideration of PREX-II results
Creators: name: Thakur, Virender
name: Kumar, Raj
name: Kumar, Pankaj
name: Kumar, Mukul
name: Mondal, C.
name: Huang, Kaixuan
name: Hu, Jinniu
name: Agrawal, B. K.
name: Dhiman, Shashi K.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The bulk properties of nuclear matter and neutron stars with the newly generated relativistic interaction DBHP are investigated which provides an opportunity to modify the coupling parameters keeping in view the finite nuclei, nuclear matter, PREX-II data for neutron skin thickness in $^{208}$Pb and astrophysical constraints. The relativistic interaction has been generated by including all possible self and mixed interactions between $σ$, $ω$, and $ρ$-meson up to the quartic order satisfying the naturalness behavior of parameters. A covariance analysis is performed to assess the statistical uncertainties on the model parameters and observables of interest along with correlations amongst them. We obtained a value of neutron skin thickness for $^{208}$Pb nucleus $Δr_{np}$ = 0.24 $\pm$ 0.02 fm. The maximum gravitational mass of neutron star and radius corresponding to the canonical mass ($R_{1.4}$) come out to be 2.03 $\pm$ 0.04 M$\odot$ and 13.39 $\pm$ 0.41 km respectively. The dimensionless tidal deformability, $Λ$ for a neutron star is also analyzed.
description: 12 pages, 10 Figures. arXiv admin note: substantial text overlap with arXiv:2305.05937
In silico analysis of dietary polyphenols and their gut microbial metabolites suggest inhibition of SARS-CoV-2 infection, replication, and host inflammatory mediators
Creators: name: Mezhibovsky, Esther
name: Hoang, Skyler H.
name: Szeto, Samantha
name: Roopchand, Diana E.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: The outcome of SARS-CoV-2 infection ranges from asymptomatic to severe COVID-19 and death resulting from an exaggerated immune response termed cytokine storm. Epidemiological data have associated consumption of a high-quality plant-based diet with decreased incidence and severity of COVID-19. Dietary polyphenols and their microbial metabolites (MMs) have anti-viral and anti-inflammatory activities. Autodock Vina and Yasara were used in molecular docking and dynamics studies to investigate potential interactions of 7 parent polyphenols (PPs) and 11 MMs with the α- and Omicron variants of the SARS-CoV-2 spike glycoprotein (SGP), papain-like pro-tease (PLpro) and 3 chymotrypsin-like protease (3CLpro), as well as host inflammatory mediators including complement component 5a (C5a), C5a receptor (C5aR), and C-C chemokine receptor type 5 (CCR5). PPs and MMs interacted to varying degrees with residues on target viral and host inflammatory proteins showing potential as competitive inhibitors. Based on these in silico findings, PPs and MMs may inhibit SARS-CoV-2 infection, replication, and/or modulate host immunity in the gut or periphery. Such inhibition may explain why people that consume a high-quality plant-based diet have less incidence and severity of COVID-19. Communicated by Ramaswamy H. Sarma
Generation of coherent phonons in bismuth by ultrashort laser pulses in the visible and NIR: displacive versus impulsive excitation mechanism
Creators: name: Melnikov, A. A.
name: Misochko, O. V.
name: Chekalin, S. V.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We have applied femtosecond pump-probe technique with variable pump wavelength to study coherent lattice dynamics in Bi single crystal. Comparison of the coherent amplitude as a function of pump photon energy for two different in symmetry Eg and A1g phonon modes with respective spontaneous resonance Raman profiles reveals that their generation mechanisms are quite distinct. We show that displacive excitation, which is the main mechanism for the generation of coherent A1g phonons, cannot be reduced to the Raman scattering responsible for the generation of lower symmetry coherent lattice modes
description: 11 pages, 8 figures. This paper is accepted for publication in Physics Letters A
Decentralized Governance for Virtual Community(DeGov4VC): Optimal Policy Design of Human-plant Symbiosis Co-creation
Creators: name: Xiang, Yan
name: Fan, Qianhui
name: Qian, Kejiang
name: Li, Jiajie
name: Tang, Yuying
name: Gao, Ze
Publisher: name: arXiv
Year: 2023
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Does the decentralized nature of user behavior in interactive virtual communities help create rules promoting user engagement? Through scenarios like planting, this framework suggests a new paradigm for mutual influence that allows users to impact communities' political decisions. Sixteen participants in the first round of interviews were involved in the framework's creation. Then we developed and implemented our framework in the community with the help of other stakeholders. This proof-of-concept creates user groups using information from users' daily activities as input and grows the green plants in a virtual environment. Finally, we involved AI agents and stakeholders in the framework test and iterations. Our study's user evaluation of a few key stakeholders demonstrates how our strategy enhances user viscosity and experience. Via human-planting ecosystems in a virtual community, this research gives a fresh viewpoint on decentralized governance and an engaging method for co-creating interactive ecological communities.
description: Accepted In Designing Interactive Systems Conference (DIS Companion 23), July 10-14, 2023, Pittsburgh, PA, USA. ACM, New York, NY, USA, 7 pages
PRODIGEES Researcher Flow Chart
Creators: name: Stewart, Benjamin
name: Reiners, Wulf
Publisher: name: Zenodo
Year: 2021
Subjects: staff
deliverables
guide

description: The PRODIGEES Researcher Flow Chart is each staff member's guiding document for their PRODIGEES secondment. The PRODIGEES Researcher Flow Chart details all of the required actions, deliverables and goals of a PRODIGEES staff member, as well as where to download the necessary documents and to whom to submit them when completed.
description: Horizon 2020 MSCA-RISE, Grant Agreement #873119
Multiconfigurational quantum chemistry: The CASPT2 method
Creators: name: Battaglia, Stefano
name: Galván, Ignacio Fdez.
name: Lindh, Roland
Publisher: name: arXiv
Year: 2023
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Computational Physics (physics.comp-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: This chapter presents the theory behind the CASPT2 method and its adaptation to a multi-state formalism. The chapter starts with an introduction of the theory of the CASPT2 method - an application of Rayleigh-Schrödinger perturbation theory applied to multiconfigurational reference function - as it was originally presented. In particular, we discuss the nature of the reference Hamiltonian and the first-order interacting space. This is followed by some detailed discussion with respect to the intruder state problem and various shift techniques to address this problem. Afterwards a longer review on alternative reference Hamiltonians, which to some degree or completely remove the intruder state problem, is put forward. Subsequently the presently proposed multi-state versions of the CASPT2 method are discussed in some detail. The chapter is concluded with a review of different benchmark assessments of the accuracy of the method and a qualified suggestion on the future development potentials of the approach.
description: This is a post-peer-review, pre-copyedit version of a chapter accepted and published in the book "Theoretical and Computational Photochemistry"
Onset of a conceptual outline map to get a hold on the jungle of cluster analysis
Creators: name: Van Mechelen, Iven
name: Hennig, Christian
name: Kiers, Henk A. L.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Other Statistics (stat.OT)
subject: FOS: Computer and information sciences
subject: 62H30

description: The domain of cluster analysis is a meeting point for a very rich multidisciplinary encounter, with cluster-analytic methods being studied and developed in discrete mathematics, numerical analysis, statistics, data analysis, data science, and computer science (including machine learning, data mining, and knowledge discovery), to name but a few. The other side of the coin, however, is that the domain suffers from a major accessibility problem as well as from the fact that it is rife with division across many pretty isolated islands. As a way out, the present paper offers a thorough and in-depth review of the clustering domain as a whole under the form of an outline map based on an overarching conceptual framework and a common language. With this framework we wish to contribute to structuring the clustering domain, to characterizing methods that have often been developed and studied in quite different contexts, to identifying links between methods, and to introducing a frame of reference for optimally setting up cluster analyses in data-analytic practice.
description: 43 pages, 4 figures
Holography and Entanglement in Flat Spacetime
Creators: name: Li, Wei
name: Takayanagi, Tadashi
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We propose a holographic correspondence of the flat spacetime based on the behavior of the entanglement entropy and the correlation functions. The holographic dual theory turns out to be highly non-local. We argue that after most part of the space is traced out, the reduced density matrix gives the maximal entropy and the correlation functions become trivial. We present a toy model for this holographic dual using a non-local scalar field theory that reproduces the same property of the entanglement entropy. Our conjecture is consistent with the entropy of Schwarzschild black holes in asymptotically flat spacetimes.
description: 5 pages, 1 figure; to appear in Phys. Rev. Lett