cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Actin associated intercellular adhesion junctions in the mammalian testis
Creators: name: Pfeiffer, David Carl
Publisher: name: University of British Columbia
Year: 2010

description: In the mammalian seminiferous epithelium, the cytoplasm of Sertoli cells adjacent to sites of intercellular attachment exhibits unique structural attributes. In each of these regions, a layer of hexagonally packed actin filaments lies situated between a cistern of endoplasmic reticulum and the plasma membrane. The filament layer together with the reticulum and adjacent plasma membrane are collectively termed an "ectoplasmic specialization". Ectoplasmic specializations occur in apical Sertoli cell regions at sites of attachment to spermatids and basally at sites of attachment to adjacent Sertoli cells. Ectoplasmic specializations have been hypothesized to be actin associated intercellular adhesion junctions. If this is true, molecular components that characterize actin associated adhesion junctions in general should be present in ectoplasmic specializations. In this study, I tested this prediction in two ways. First, I investigated whether or not the protein vinculin is co-distributed with actin filament bundles in ectoplasmic specializations of the ground squirrel. Second, I immunologically probed ectoplasmic specializations for three cell adhesion molecules (CAMs) that are commonly found in regions of intercellular adhesion in other tissues. My results indicate that vinculin is co-distributed with actin in Sertoli cell regions attached to spermatids. These data are consistent with the conclusion that vinculin is a component of ectoplasmic specializations and, therefore, with the hypothesis that the latter structures are a form of actin associated adhesion junction. Experiments using probes for the CAMs indicate that E-cadherin, A-CAM and N-CAM are probably not present in ectoplasmic specializations. The adhesion molecule at these sites may be a different member of the known CAMs or an as yet unidentified CAM. Based on data presented here and elsewhere indicating that ectoplasmic specializations are a form of actin associated adhesion junction, I describe the elaborate changes that occur in constituent filament bundles at sites of attachment to spermatids of the ground squirrel and interprete them in the context of the adhesion hypothesis. During the course of the co-localization studies described above, I observed that vinculin and actin are co-distributed at certain sites of intercellular attachment between interstitial cells of Leydig in the ground squirrel testis. Moreover, at the ultrastructural level I found these sites correspond to microfilament rich junction regions. These observations are consistent with the conclusion that actin associated intercellular adhesion junctions exist between interstitial cells of Leydig in the ground squirrel testis.
Effective bath model for arrays of coupled non-Hermitian nanoresonators
Creators: name: Vinel, Vincent
name: Li, Zejian
name: Borne, Adrien
name: Bensemhoun, Adrien
name: Favero, Ivan
name: Ciuti, Cristiano
name: Leo, Giuseppe
Publisher: name: arXiv
Year: 2021
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Nanophotonics systems have recently been studied under the perspective of non-Hermitian physics. Given their potential for wavefront control, nonlinear optics and quantum optics, it is crucial to develop predictive tools to assist their design. We present here a simple model relying on the coupling to an effective bath consisting of a continuum of modes to describe systems of coupled resonators, and test it on dielectric nanocylinder chains accessible to experiments. The effective coupling constants, which depend non-trivially on the distance between resonators, are extracted from numerical simulations in the case of just two coupled elements. The model predicts successfully the dispersive and reactive nature of modes for configurations with multiple resonators, as validated by numerical solutions. It can be applied to larger systems, which are hardly solvable with finite-element approaches.
description: 5 pages, 3 figures, published in Optics Express
Variation of the Fine-Structure Constant from the de Sitter Invariant Special Relativity
Creators: name: Chen, Shao-Xia
name: Xiao, Neng-Chao
name: Yan, Mu-Lin
Publisher: name: arXiv
Year: 2007
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: There are obvious discrepancies among various experimental constraints on the variation of the fine-structure constant, $α$. We attempt to discuss the issue in the framework of de Sitter invariant Special Relativity (${\cal SR}_{c,R}$) and to present a possible solution to the disagreement. In addition, on the basis of the observational data and the discussions presented in this Letter, we derive a rough theoretical estimate of the radius of the Universe.
description: 8 pages, no figures
Discovery of potent DNMT1 inhibitors against sickle cell disease using structural-based virtual screening, MM-GBSA and molecular dynamics simulation-based approaches
Creators: name: Ala, Chandu
name: Joshi, Renuka Parshuram
name: Gupta, Pragya
name: Ramalingam, Sivaprakash
name: Sankaranarayanan, Murugesan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer

description: Sickle cell disease (SCD) is an autosomal recessive genetic disorder affecting millions of people worldwide. A reversible and selective DNMT1 inhibitor, GSK3482364, has been known to decrease the overall methylation activity of DNMT1, resulting in the increase of HbF levels and percentage of HbF-expressing erythrocytes in an in vitro and in vivo model. In this study, a structure-based virtual screening was done with GSK3685032, a co-crystalized ligand of DNMT1 (PDB ID: 6X9K) with an IC50 value of 0.036 μM and identified 3988 compounds from three databases (ChEMBL, PubChem and Drug Bank). Using this screening method, we identified around 15 compounds with XP docking scores greater than −8 kcal/mol. Further, prime MM-GBSA calculations have been performed and found compound SCHEMBL19716714 with the highest binding free energy of −83.31 kcal/mol. Finally, four compounds were identified based on glide energy and ΔG bind scores that have the most binding with DG7, DG19, DG20 bases and Lys1535, His1507, Trp1510, Ser1230, which were required for the target enzyme inhibition. Furthermore, molecular dynamics simulation studies of top ligands validate the stability of the docked complexes by examining root mean square deviations, root mean square fluctuations, solvent accessible surface area, and radius of gyration graphs from simulation trajectories. These findings suggest that the top four hit compounds may be capable of inhibiting DNMT1 and that additional in vitro and in vivo studies will be essential to prove the clinical effectiveness of the selected lead compounds. Communicated by Ramaswamy H. Sarma
Cape Gardiner Civic Association Correspondence, 1964
Creators: name: Hammer, Leon I.
Publisher: name: Unknown
Year: 1964
Subjects: Springs
East Hampton
Correspondence
Organizations
Capes (Coasts)

description: These letters are from the Cape Gardiner Civic Association from October 1964 to February 1966. The majority of them are authored directly by the association's President, Leon I. Hammer, M. D.
description: This material was lent to the Long Island Collection by the Springs Historical Society Library for digitization purposes.
Island may not save the information paradox of Liouville black holes
Creators: name: Li, Ran
name: Wang, Xuanhua
name: Wang, Jin
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: By using the quantum extremal island formula, we perform a simple calculation of the generalized entanglement entropy of Hawking radiation from the two dimensional Liouville black hole. No reasonable island was found when extremizing the generalized entropy. We explain qualitatively the reason why the page curve cannot be reproduced in the present model. This suggests that the islands may not necessarily save the information paradox for the Liouville black holes.
description: Some clarifications added, conclusion unchanged. Comments are welcome
Bandwidth-control orbital-selective delocalization of 4f electrons in epitaxial Ce films
Creators: name: Wu, Yi
name: Fang, Yuan
name: Li, Peng
name: Xiao, Zhiguang
name: Zheng, Hao
name: Yuan, Huiqiu
name: Cao, Chao
name: Yang, Yi-feng
name: Liu, Yang
Publisher: name: arXiv
Year: 2021
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The 4f-electron delocalization plays a key role in the low-temperature properties of rare-earth metals and intermetallics, including heavy fermions and mix-valent compounds, and is normally realized by the many-body Kondo coupling between 4f and conduction electrons. Due to the large onsite Coulomb repulsion of 4f electrons, the bandwidth-control Mott-type delocalization, commonly observed in d-electron systems, is difficult in 4f-electron systems and remains elusive in spectroscopic experiments. Here we demonstrate that the bandwidth-control orbital-selective delocalization of 4f electrons can be realized in epitaxial Ce films by thermal annealing, which results in a metastable surface phase with a reduced layer spacing. The resulting quasiparticle bands exhibit large dispersion with exclusive 4f character near E_F and extend reasonably far below the Fermi energy, which can be explained from the Mott physics. The experimental quasiparticle dispersion agrees surprisingly well with density-functional theory calculation and also exhibits unusual temperature dependence, which could be a direct consequence of the delicate interplay between the bandwidth-control Mott physics and the coexisting Kondo hybridization. Our work therefore opens up the opportunity to study the interaction between two well-known localization-delocalization mechanisms in correlation physics, i.e., Kondo vs Mott, which can be important for a fundamental understanding of 4f-electron systems.
description: Nature Communications (accepted)
Particle acceleration in strong MHD turbulence
Creators: name: Lemoine, Martin
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Nonthermal acceleration of particles in magnetohydrodynamic (MHD) turbulence plays a central role in a wide variety of astrophysical sites. This physics is addressed here in the context of a strong turbulence, composed of coherent structures rather than waves, beyond the realm of quasilinear theory. The present description tracks the momentum of the particle through a sequence of frames in which the electric field vanishes, in the spirit of the original Fermi scenario. It connects the sources of energy gain (or loss) to the gradients of the velocity of the magnetic field lines, in particular the acceleration and the shear of their velocity flow projected along the field line direction, as well as their compression in the transverse plane. Those velocity gradients are subject to strong intermittency: they are spatially localized and their strengths obey power law distributions, as demonstrated through direct measurements in the incompressible MHD simulation of the Johns Hopkins University database. This intermittency impacts the acceleration process in a significant way, which opens up prospects for a rich phenomenology. In particular, the momentum distribution, which is here captured through an analytical random walk model, displays extended power law tails with soft-to-hard evolution in time, in general agreement with recent kinetic numerical simulations. Extensions to this description and possible avenues of exploration are discussed.
description: Matches published version (PRD)
Development of Multi-Alkali Antimonides Photocathodes for High-Brightness RF Photoinjectors
Creators: name: Mohanty, Sandeep
name: Guerini Rocco, Giorgio
name: Hillert, Wolfgang
name: Krasilnikov, Mikhail
name: Michelato, Paolo
name: Monaco, Laura
name: Oppelt, Anne
name: Pagani, Carlo
name: Qian, Houjun
name: Sertore, Daniele
name: Stephan, Frank
Publisher: name: Deutsches Elektronen-Synchrotron, DESY, Hamburg
Year: 2021
Subjects: Accelerator Physics
MC2: Photon Sources and Electron Accelerators

description: 12th International Particle Accelerator Conference, IPAC'21, Campinas, Brazil, 24 May 2021 - 28 May 2021; doi:10.18429/JACOW-IPAC2021-TUPAB034
description: Multi-alkali antimonide-based photocathodes are suitable candidate for the electron sources of next-generation high brightness RF photoinjectors due to their excellent photoemissive properties especially, like low thermal emittances and high sensitivity to visible light. The former stands out, paving the way towards CW operations. Based on the previous successful development of Cesium Telluride photocathodes, we are now channelling our efforts toward an R activity focused on KCsSb and NaKSb(Cs) photocathodes. Parallel to that R activity, we have installed a new dedicated photocathode production system at the INFN-LASA to start the preparation of these photocathodes for their test in the PITZ photoinjector at DESY in Zeuthen. In this paper, detailed experimental results obtained from the KCsSb, along with a preliminary result from the NaKSb(Cs) photocathode material as well as the status of the overall project are presented.
MOESM14 of Mutation of 4-coumarate: coenzyme A ligase 1 gene affects lignin biosynthesis and increases the cell wall digestibility in maize brown midrib5 mutants
Creators: name: Xiong, Wangdan
name: Wu, Zhenying
name: Liu, Yuchen
name: Li, Yu
name: Su, Kunlong
name: Bai, Zetao
name: Guo, Siyi
name: Hu, Zhubing
name: Zhang, Zhiming
name: Bao, Yan
name: Sun, Juan
name: Yang, Guofeng
name: Fu, Chunxiang
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Information Systems not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: Additional file 14: Fig. S6. SDS-PAGE analysis of recombinant AtUGT84A1, ZmUGT84A-1, and UGT84A-2 proteins.
Phase I and II Archaeological Testing at the Talbot County Women’s Club, 18 Talbot Lane, Easton, Maryland, 18TA439
Creators: name: Jenkins, Tracy H.
name: Leone, Mark P.
Publisher: name: Digital Repository at the University of Maryland
Year: 2013
Subjects: Talbot County Women’s Club
Easton, Maryland
18TA439
archaeological excavation

description: The University of Maryland, College Park, Archaeology in Annapolis Project, conducted
Phase I and II archaeological excavations of the Talbot County Women’s Club (TCWC) in
Easton, Maryland, from July 8th through July 26th, 2013. This site is located at 18 Talbot Lane.
The Women’s Club granted permission for this excavation as a part of The Hill Community
Project to document and publicize the history of the Easton neighborhood known as The Hill and
of the community of free African Americans that coalesced around this neighborhood in the
nineteenth century. Following on the heels of the 2012 successful public excavation of the
Home of the Family of the Buffalo Soldier (HFBS), this second public excavation within The
Hill Community Project sought more information on early members of the free black community
and on the material conditions of tenants living on The Hill in the eighteenth, nineteenth, and
twentieth centuries. It also continued archaeologists’ efforts at the HFBS to test the capability of
archaeological sites of bringing together people of different backgrounds to forge a more open,
civil discourse about the past. To these ends, archaeologists conducted a shovel test pit (STP)
survey of yard spaces at the Women’s Club and opened seven test units to further investigate
activity areas and construction phases, while maintaining a public dig site.
While the HFBS excavation focused on African-American landowners from 1879 to
2002, the Women’s Club excavation focuses on the non-landowners who lived here from the late
eighteenth to early twentieth centuries in order to highlight the diversity of experiences among
neighborhood residents through the years. These residents included enslaved and free African
Americans in the nineteenth century and tenants of unknown ethnic background in the late
nineteenth and early twentieth centuries. Today, upwards of two thirds of the residents of The
Hill rent their homes. The high rate of tenancy has been identified as a major contributor toward
the gentrification processes that currently threaten the integrity of the African American
community by pushing black families from dilapidating homes and demolishing historic
community and racial landmarks in attempts to remove blight from the neighborhood.
Excavations at the Women’s Club therefore sought more information on the material conditions
of tenancy and the ways in which community can exist even without home-ownership. The most
promising archaeological materials for addressing these questions at the Women’s Club are a
nineteenth-century kitchen used by both enslaved and free cooks and a sheet midden created by
the several families renting the property from 1891-1946.
Analysis of medication patterns for pediatric asthma patients in emergency department: Does the sequence placement of glucocorticoids administration matter?
Creators: name: Jang, Hoon
name: Ozkaynak, Mustafa
name: Amura, Claudia R.
name: Ayer, Turgay
name: Sills, Marion R.
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Evolutionary Biology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Objectives: Timely glucocorticoid administration is associated with decreased admission rate and is thus a common quality metric for ED asthma care; less is known about the impact of the timing of glucocorticoids in the context of the sequence of asthma medications administered. Therefore, we investigated the distribution of asthma medication sequences in one ED and analyzed the effect of the sequence placement of glucocorticoids administration on treatment outcomes. Methods: A retrospective study using five-year electronic health record data obtained from an academic urban children’s hospital ED was conducted. We clustered the sequences of medication administration using an exact string-matching algorithm to identify the most frequently used asthma medication sequences. Then, we used the identified patterns to perform statistical tests to examine the effect of the sequence placement of glucocorticoids administration on the outcomes length-of-stay and ED disposition. Results: A total of 4,844 encounters were included in our study. The ten most common treatment sequences accounted for 43% of all encounters. Stratified analyses confirmed that treatment sequences pattern was correlated with patient severity, but ED crowding does not impact treatment sequences. In multivariable models, glucocorticoids administration earlier in the treatment sequence was associated with shorter length of stay and lower hospital admission rates. Conclusions: By analyzing medication sequence patterns for the ED encounter of pediatric asthma, we found that the earlier sequence placement of glucocorticoids administration is associated with improved outcomes. Our findings can help inform quality improvement and clinical guideline development related to ED asthma care for children.
MOESM1 of Mutation of 4-coumarate: coenzyme A ligase 1 gene affects lignin biosynthesis and increases the cell wall digestibility in maize brown midrib5 mutants
Creators: name: Xiong, Wangdan
name: Wu, Zhenying
name: Liu, Yuchen
name: Li, Yu
name: Su, Kunlong
name: Bai, Zetao
name: Guo, Siyi
name: Hu, Zhubing
name: Zhang, Zhiming
name: Bao, Yan
name: Sun, Juan
name: Yang, Guofeng
name: Fu, Chunxiang
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: Additional file 1: Table S1. The SSR markers used in this study.
Analysis of developing chick Gallus domesticus spinal cord proteins using two dimensional gel electrophoresis
Creators: name: Ethell, Douglas Wayne
Publisher: name: University of British Columbia
Year: 2010

description: Several recent experiments on developing chick spinal cord have established a time window when the developing spinal cord changes from a permissive to a restrictive environment for regeneration. This time window occurs during embryonic days 13-14 (E13-E14) of chick development. Recent experiments in adult rat, have found two proteins that actively inhibit axonal regeneration. This study has sought possible inhibitory proteins, in chicks, correlating to this temporal change. Proteins continuously present after this change (E14-E20) but not before (E11) were identified. Two-dimensional gel electrophoresis was used for separatation of the proteins. Seven protein spots of interest demonstrated this correlative late-expressing neural protein (LNP) profile. Although the functions of these proteins could not be ascertained in this study, further investigation is warranted.
A heuristic algorithm to select genes potentially regulated by methylation
Creators: name: Sanchez-Pla, Alex
name: Miró, Berta
name: Carmona, Francesc
name: Bazzoco, Sarah
name: Corro, Diego Arango Del
Publisher: name: F1000 Research Limited
Year: 2019

description: Methylation of CpG dinucleotides in the promoter of genes involved in the oncogenic process is considered a key process contributing to tumour initiation and/or progression. Methylation often acts by inhibiting the expression of the gene, that is the more methylated is the gene the less it is expressed, but if methylation is absent or low then any values of expression, high or low, can be found. This suggests that a way to select genes regulated by methylation may be looking for patterns in the relation between gene expression and methylation consistent with this form of regulation, such as L-shapes. In a previous work [1] we compared several methods ((i) Negative Correlation (ii) Selection Based on Conditional Mutual information and (iii) Clustering based on Splines Regression) to select L-shaped genes and tested them on an ongoing study on colon cancer. The CMI method proved to be a good approach but it has two main drawbacks: it works well mainly when the sample size is big (hundreds more than dozens), and (ii) It selects well-defined patterns but fails when these are less clear. In this work, we propose a heuristic algorithm that mimics the process of visually selecting an L-shape. The algorithm works by decomposing the scatterplot region on a 3x3 grid and assigning a minimum and maximum percentage of points and weight to each sub-region, allowing for a flexible selection on a variety of shapes. We have tested the method against CMI and naïve correlation on several public and private datasets and, despite not being able to quantify its accuracy -because no dataset with “TRUE” L-shaped genes is available- its performance seems to be very good especially due to its flexibility. The method is available as an R package and as a Shiny application both available from github (http://github.com/alexsanchezpla). Integrative analysis to select genes regulated by methylation in a cancer colon study Trends in Mathematics. 2017 |. DOI:10.1007/978-3-319-55639-0_9.
Nagy-Foias type functional models of nondissipative operators in parabolic domains
Creators: name: Yakubovich, Dmitry V.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Functional Analysis (math.FA)
subject: Spectral Theory (math.SP)
subject: FOS: Mathematics
subject: 47A45, 47A48, 47B44

description: A functional model for nondissipative unbounded perturbations of an unbounded self-adjoint operator on a Hilbert space X is constructed. This model is analogous to the Nagy--Foias model of dissipative operators, but it is linearly similar and not unitarily equivalent to the operator. It is attached to a domain of parabolic type, instead of a half-plane. The transformation map from X to the model space and the analogue of the characteristic function are given explicitly. All usual consequences of the Nagy--Foias construction (the H-infty calculus, the commutant lifting, etc.) hold true in our context.
description: 31 pages
On Fox quotients of arbitrary group algebras
Creators: name: Hartl, Manfred
Publisher: name: arXiv
Year: 2007
Subjects: subject: Group Theory (math.GR)
subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: 20C07 (Primary) 20J05, 17B35 (Secondary)

description: For a group $G$, N-series $\cal G$ of $G$ and commutative ring $R$ let $I^n_{R,\cal G}(G)$, $n\ge 0$, denote the filtration of the group algebra $R(G)$ induced by $\cal G$, and $I_R(G)$ its augmentation ideal. For subgroups $H$ of $G$, left ideals $J$ of $R(H)$ and right $H$-submodules $M$ of $I_Z(G)$ the quotients $I_R(G)J/MJ$ are studied by homological methods, notably for $M= I_Z(G)I_Z(H)$, $I_Z(H)I_Z(G) + I_Z([H,G])Z(G)$ and $Z(G)I_Z(N) +I^n_{Z,\cal G}(G)$ with $N \lhd G$ where the group $I_R(G)J/MJ$ is completely determined for $n=2$. The groups $I^{n-1}_{Z,\cal G}(G)I_Z(H)/I^n_{Z,\cal G}(G)I_Z(H)$ are studied and explicitly computed for $n\le 3$ in terms of enveloping rings of certain graded Lie rings and of torsion products of abelian groups.
description: 44 pages; introduction and notation improved, some minor errors corrected
Neutron scattering study of the kagome metal Sc3Mn3Al7Si5
Creators: name: Li, X. Y.
name: Reig-i-Plessis, D.
name: Liu, P. -F.
name: Wu, S.
name: Wang, B. -T.
name: Hallas, A. M.
name: Stone, M. B.
name: Broholm, C.
name: Aronson, M. C.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Sc3Mn3Al7Si5 is a rare example of a correlated metal in which the Mn moments form a kagome lattice. The absence of magnetic ordering to the lowest temperatures suggests that geometrical frustration of magnetic interactions may lead to strong magnetic fluctuations. We have performed inelastic neutron scattering measurements on Sc3Mn3Al7Si5, finding that phonon scattering dominates for energies from ~20 - 50 meV. These results are in good agreement with ab initio calculations of the phonon dispersions and densities of states, and as well reproduce the measured specific heat. A weak magnetic signal was detected at energies less than ~10 meV, present only at the lowest temperatures. The magnetic signal is broad and quasielastic, as expected for metallic paramagnets.
Capacity of a condenser whose plates are circular arcs
Creators: name: Karp, D.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Complex Variables (math.CV)
subject: FOS: Mathematics
subject: 31A15, 30C85

description: We find an asymptotic formula for the conformal capacity of a plane condenser both plate of which are concentric circular arcs as the distance between them vanishes. This result generalizes the formula for the capacity of parallel linear plate condenser found by Simonenko and Chekulaeva in 1972 and sheds light on the problem of finding an asymptotic formula for the capacity of condenser whose plates are arbitrary parallel curves. This problem was posed and partially solved by R. Kühnau in 1998.
description: 15 pages, 1 figure
Magnetic impurities at quantum critical points: large-$N$ expansion and SPT connections
Creators: name: Liu, Shang
name: Shapourian, Hassan
name: Vishwanath, Ashvin
name: Metlitski, Max A.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: In symmetry protected topological (SPT) phases, the combination of symmetries and a bulk gap stabilizes protected modes at surfaces or at topological defects. Understanding the fate of these modes at a quantum critical point, when the protecting symmetries are on the verge of being broken, is an outstanding problem. This interplay of topology and criticality must incorporate both the bulk dynamics of critical points, often described by nontrivial conformal field theories, and SPT physics. Here, we study the simplest nontrivial setting - that of a 0+1 dimensional topological mode - a quantum spin - coupled to a 2+1D critical bulk. Using the large-$N$ technique we solve a series of models which, as a consequence of topology, demonstrate intermediate coupling fixed points. We compare our results to previous numerical simulations and find good agreement. We also point out intriguing connections to generalized Kondo problems and Sachdev-Ye-Kitaev (SYK) models. In particular, we show that a Luttinger theorem derived for the complex SYK models, that relates the charge density to particle-hole asymmetry, also holds in our setting. These results should help stimulate further analytical study of the interplay between SPT physics and quantum criticality.
description: Published version. Only minor modifications compared to v1. Main text 19 pages, 8 figures
Hydroxamic acid derivatives as selective HDAC3 inhibitors: computer-aided drug design strategies
Creators: name: Patel, Preeti
name: Shrivastava, Sushant Kumar
name: Sharma, Piyoosh
name: Kurmi, Balak Das
name: Shirbhate, Ekta
name: Rajak, Harish
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Molecular Biology
Pharmacology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified

description: Histone deacetylases (HDACs) are critical epigenetic drug targets that have gained significant attention in the scientific community for the treatment of cancer. The currently marketed HDAC inhibitors lack selectivity for the various HDAC isoenzymes. Here, we describe our protocol for the discovery of novel potential hydroxamic acid based HDAC3 inhibitors through pharmacophore modeling, virtual screening, docking, molecular dynamics (MD) simulation and toxicity studies. The ten pharmacophore hypotheses were established, and their reliability was validated by different ROC (receiving operator curve) analysis. Among them, the best model (Hypothesis 9 or RRRA) was employed for searching SCHEMBL, ZINC and MolPort database to screen out hit molecules as selective HDAC3 inhibitors, followed by different docking stages. MD simulation (50 ns) and MMGBSA study were performed to study the stability of ligand binding modes and with the help of trajectory analysis, to calculate the ligand-receptor complex RMSD (root-mean-square deviation), RMSF (root-mean-square fluctuation) and H-bond distance, etc. Finally, in-silico toxicity studies were performed on top screened molecules and compared with reference drug SAHA and established structure-activity relationship (SAR). The results indicated that compound 31, with high inhibitory potency and less toxicity (probability value 0.418), is suitable for further experimental analysis. Communicated by Ramaswamy H. Sarma Pharmacophore modeling and virtual screening were performed with hydroxamic acid derivatives as HDAC3 inhibitors. MD simulation was performed for 50 ns time duration for selected protein-ligand complexes. SAR and toxicity studies (using TOPKAT tool) were performed. The results of these studies might be valuable in the further design and development of more potent HDAC3 inhibitors.
Deliverable 3.2 - Epidemiological status of Mediterranean farmed fish
Creators: name: Padrós, Francesc
name: Constenla, Maria
name: Casal, Jordi
name: Fioravanti, Marialetizia
name: Ciulli, Sara
name: Gustinelli, Andrea
name: Caffara, Monica
name: Acosta, Felix
name: Sitjà-Bobadilla, Ariadna
name: Palenzuela, Oswaldo
name: Rigos, George
name: Marino, Giovanna
name: Petochi, Tommaso
Publisher: name: Zenodo
Year: 2020

description: As many other farming activities, aquatic animals and particularly finfish can be affected by several infectious and non-infectious diseases. The specific diseases and pathogens or other causes triggering the development of these diseases, since there are usually multifactorial, can be related to a number of different factors: characteristics of the infectious agents, affected fish species or genetic susceptibility, environment and environmental conditions, geographical parameters, and farming systems amongst others.
Significant improvement of flux pinning and irreversibility field in nano-Carbon doped MgB2 superconductor
Creators: name: Mudgel, Monika
name: Awanaa, V. P. S.
name: Kishana, H.
name: Bhalla, G. L.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We report the synthesis and variation of superconductivity parameters such as transition temperature Tc, upper critical field Hc, critical current density Jc, irreversibility field Hirr and flux pinning parameter (Fp) for the MgB2-xCx system with nano-Carbon doping up to x=0.20. Carbon substitutes successfully on boron site and results in significant enhancement of Hirr and Jc(H). Resistivity measurements reveal a continuous decrease in Tc under zero applied field, while the same improves remarkably at higher fields with an increase in nano-C content for MgB2-xCx system. The irreversibility field value (Hirr) is 7.6 & 6.6 Tesla at 5 and 10K respectively for the pristine sample, which is enhanced to 13.4 and 11.0 Tesla for x = .08 sample at same temperatures. Compared to undoped sample, critical current density (Jc) for the x=0.08 nano-Carbon doped sample is increased by a factor of 24 at 10K at 6 Tesla field.
description: 14 pages Text+Figs; Comments/suggestions welcome (awana@mail.nplindia.ernet.in)
Pulsars as Astrophysical Laboratories for Nuclear and Particle Physics
Creators: name: Weber, F.
name: Negreiros, R.
name: Rosenfield, P.
name: Stejner, M.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: A forefront area of research concerns the exploration of the properties of hadronic matter under extreme conditions of temperature and density, and the determination of the equation of state--the relation between pressure, temperature and density--of such matter. Experimentally, relativistic heavy-ion collision experiments enable physicists to cast a brief glance at hot and ultra-dense matter for times as little as about $10^{-22}$ seconds. Complementary to this, the matter that exists in the cores of neutron stars, observed as radio pulsars, X-ray pulsars, and magnetars, is at low temperatures but compressed permanently to ultra-high densities that may be more than an order of magnitude higher than the density of atomic nuclei. This makes pulsars superb astrophysical laboratories for medium and high-energy nuclear physics, as discussed in this paper.
description: 10 pages, 13 figures; Paper presented at the International School Of Nuclear Physics, 28th Course: Radioactive Beams, Nuclear Dynamics and Astrophysics, Erice-Sicily, 16-24 September 2006; to be published in Prog. Part. Nucl. Phys
COVID-19 detection using deep convolutional neural networks and binary-differential-algorithm-based feature selection on X-ray images
Creators: name: Iraji, Mohammad Saber
name: Feizi-Derakhshi, Mohammad-Reza
name: Tanha, Jafar
Publisher: name: arXiv
Year: 2021
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: The new Coronavirus is spreading rapidly, and it has taken the lives of many people so far. The virus has destructive effects on the human lung, and early detection is very important. Deep Convolution neural networks are such powerful tools in classifying images. Therefore, in this paper, a hybrid approach based on a deep network is presented. Feature vectors were extracted by applying a deep convolution neural network on the images, and useful features were selected by the binary differential meta-heuristic algorithm. These optimized features were given to the SVM classifier. A database consisting of three categories of images such as COVID-19, pneumonia, and healthy included in 1092 X-ray samples was considered. The proposed method achieved an accuracy of 99.43%, a sensitivity of 99.16%, and a specificity of 99.57%. Our results demonstrate that the suggested approach is better than recent studies on COVID-19 detection with X-ray images.
description: This is a preprint of an article published in "Complexity". The final authenticated version is available online at: https://www.hindawi.com/journals/complexity/2021/9973277/
Schottky-barrier double-walled carbon nanotube field-effect transistors
Creators: name: Wang, Shidong
name: Grifoni, Milena
Publisher: name: arXiv
Year: 2007
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate electronic transport properties of Schottky-barrier field-effect transistors (FET) based on double-walled carbon nanotubes (DWNT) with a semiconducting outer shell and a metallic inner one. These kind of DWNT-FET show asymmetries of the $I$-$V$ characteristics and threshold voltages due to the electron-hole asymmetry of the Schottky barrier. The presence of the metallic inner shell induces a large effective band gap, which is one order of magnitude larger than that due to the semiconducting shell alone of a single-walled carbon nanotube FET.
description: 4 pages, 3 figures. Published form
Fragment-based design and MD simulations of human papilloma virus-16 E6 protein inhibitors
Creators: name: Vemula, Vani
name: Marudamuthu, Amarnath Satheesh
name: Prasad, Sanjay
name: M, Suman B
name: E, Mamatha S
name: A, Swathi
name: Seal, Priyanka
name: Alagumuthu, Manikandan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: The main objective of this study is to screen potential small molecule inhibitors against HPV (Human Papilloma Virus)-16 E6 protein (HPV16 E6P) using a fragment-based approach. Twenty-six natural HPV inhibitors were selected based on the review of the literature. Among them, Luteolin was selected as the reference compound. These 26 compounds were used to generate novel inhibitors against HPV16 E6P. Fragment script and BREED of Schrodinger software were used to build novel inhibitor molecules. The result in 817 novel molecules was docked into the active binding site of HPV E6 protein and the top ten compounds were screened based on binding affinity compared to Luteolin for further study. Compounds Cpd5, Cpd7, and Cpd10 were the most potent inhibitors of HPV16 E6P and these were non-toxic and showed high Gastrointestinal (GI) absorption and positive drug-likeness score. Complexes of these compounds were stable in the 200 ns Molecular Dynamics (MD) simulation. These 3 HPV16 E6P inhibitors could be the lead molecules as new drugs for HPV-related diseases. Communicated by Ramaswamy H. Sarma
Quantum scaling laws in the onset of dynamical delocalization
Creators: name: Chabé, Julien
name: Lignier, Hans
name: Cavalcante, Hugo L. D. De Souza
name: Delande, Dominique
name: Szriftgiser, Pascal
name: Garreau, Jean Claude
Publisher: name: arXiv
Year: 2006
Subjects: subject: Quantum Physics (quant-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: Chaotic Dynamics (nlin.CD)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We study the destruction of dynamical localization, experimentally observed in an atomic realization of the kicked rotor, by a deterministic Hamiltonian perturbation, with a temporal periodicity incommensurate with the principal driving. We show that the destruction is gradual, with well defined scaling laws for the various classical and quantum parameters, in sharp contrast with predictions based on the analogy with Anderson localization.
description: 3 pages, revtex4
Scaling Dialogic Peer Feedback via Learning Analytics and Scripts
Creators: name: Er, Erkan
name: Dimitriadis, Yannis
name: Gasevic, Dragan
Publisher: name: Zenodo
Year: 2019
Subjects: feedback
peer feedback
dialogue
learning analytics

description: Dialogic peer feedback is a challenge to design and implement when learning takes place at scale. For proper implementation of dialogic feedback among large learning cohorts, peers’ interactions and learning activities need to be framed and systematized within a solid theoretical perspective. This paper presents a theoretical model of dialogic peer feedback, consisting of three interconnected phases. This model incorporates learning analytics and scripts to support individual and collaborative regulatory processes involved in each phase.
UAV Communications for Sustainable Federated Learning
Creators: name: Pham, Quoc-Viet
name: Zeng, Ming
name: Ruby, Rukhsana
name: Huynh-The, Thien
name: Hwang, Won-Joo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Federated learning (FL), invented by Google in 2016, has become a hot research trend. However, enabling FL in wireless networks has to overcome the limited battery challenge of mobile users. In this regard, we propose to apply unmanned aerial vehicle (UAV)-empowered wireless power transfer to enable sustainable FL-based wireless networks. The objective is to maximize the UAV transmit power efficiency, via a joint optimization of transmission time and bandwidth allocation, power control, and the UAV placement. Directly solving the formulated problem is challenging, due to the coupling of variables. Hence, we leverage the decomposition technique and a successive convex approximation approach to develop an efficient algorithm, namely UAV for sustainable FL (UAV-SFL). Finally, simulations illustrate the potential of our proposed UAV-SFL approach in providing a sustainable solution for FL-based wireless networks, and in reducing the UAV transmit power by 32.95%, 63.18%, and 78.81% compared with the benchmarks.
description: Accepted by IEEE Vehicular Technology correspondence 2021
Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity
Creators: name: Khan, Sadaf
name: Naeem, Aabgeena
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Medicine
Pharmacology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Hematology
Computational Biology

description: This study investigates the ability of bovine serum albumin (BSA) to act as an extracellular chaperone (EC) on human hemoglobin (Hb) at a pH of 7.4. The best temperature for studying this behavior was determined by analyzing Hb’s aggregation kinetics at multiple temperatures. 55 °C was chosen as the optimal temperature for forming Hb amyloids. BSA was then tested at various concentrations (20–100 μM) to assess its chaperone-like activity on Hb at 55 °C. At a concentration of 100 μM, BSA exhibits chaperone-like activity with a client protein:BSA ratio of 1:10. The high ratio implies that the chaperone activity of BSA is favored by the effects of macromolecular crowding. The results showed that BSA has the potential to inhibit Hb’s dissociation into alpha and beta subunits and protein aggregation by inhibiting secondary nucleation. BSA also causes the depolymerization of fibrils over time. The results were validated using molecular docking and all-atom molecular dynamics simulations. MD analysis such as RMSD, RMSF, Rg, SASA, Hydrogen bond, PCA, Free energy landscape (FEL) revealed that the stability of hemoglobin is greater when it is bound to BSA compared to unbound state. The study suggests that BSA can potentially bind to Hb dimers and reduce excitonic interactions, which reduces Hb aggregation. These results are consistent with the aggregation kinetics experiments. Communicated by Ramaswamy H. Sarma
Recovery from exhaustive exercise in rainbow trout white muscle : a model for studies of the control of energy metabolism in vivo
Creators: name: Schulte, Patricia Marita
Publisher: name: University of British Columbia
Year: 2010

description: Recovery from exhaustive exercise in the white muscle of rainbow trout (Oncorhynchus mykiss) was used to examine the role of the adenylates in the control of energy metabolism and to assess the validity of equilibrium models of the behaviour of the high energy phosphates. The difficulty of obtaining muscle samples from fish makes detailed analysis of the behaviour of the labile high energy phosphates complex. The use of a new sampling procedure, the infusion of a lethal dose of anaesthetic via an indwelling cannula, minimized this problem. At exhaustion [ATP] and [PCr] were depressed by 75 and 80% respectively relative to the resting values. [ATP] depletion was mirrored by a stoichiometric increase in [IMP]. During recovery [PCr] returned to the resting level within 2 hours, but [ATP] recovery was slow and not complete until 24 hours post exercise. In contrast, energy charge and RATP(the proportion of the free adenylate pool phosphorylated to ATP) were, if anything, higher than the resting values by 2 hours post exercise. Therefore, [ATP] and energy status can be dissociated in tissues like fish white muscle because of the action of the purine nucleotide cycle. At 2 hours post exercise the calculated free ADP concentration dropped to less than one tenth the value at rest. As a result the [ATP] / [ADP] free ratio increased by nearly 6 fold. This condition may be required for glycogen resynthesis from lactate in muscle. Several similar equilibrium models of the behaviour of the adenylates and PCr were applied to the fish white muscle system. In general, the models well describe the relationship between the high energy phosphates. However, the definition of the high energy phosphate pool introduces some complications since this includes the total [ATP]. Because of the action of AMP deaminase the [ATP] concentration can change without measurable changes in the energy status, which is not considered in any of the models. As long as the extent of IMP formation is known the models can be applied, but since the formation of IMP may vary from fish to fish or with exercise regime the models lose much of their predictive power.