cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Predictive local field theory for interacting active Brownian spheres in two spatial dimensions
Creators: name: Bickmann, Jens
name: Wittkowski, Raphael
Publisher: name: arXiv
Year: 2019
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We present a predictive local field theory for the nonequilibrium dynamics of interacting active Brownian particles with a spherical shape in two spatial dimensions. The theory is derived by a rigorous coarse-graining starting from the Langevin equations that describe the trajectories of the individual particles. For maximal accuracy and generality of the theory, it includes configurational order parameters and derivatives up to infinite order. In addition, we discuss possible approximations of the theory and present reduced models that are easier to apply. We show that our theory contains popular models such as Active Model B + as special cases and that it provides explicit expressions for the coefficients occurring in these and other, often phenomenological, models. As a further outcome, the theory yields an analytical expression for the density-dependent mean swimming speed of the particles. To demonstrate an application of the new theory, we analyze a simple reduced model of the lowest nontrivial order in derivatives, which is able to predict the onset of motility-induced phase separation of the particles. By a linear stability analysis, an analytical expression for the spinodal corresponding to motility-induced phase separation is obtained. This expression is evaluated for the case of particles interacting repulsively by a Weeks-Chandler-Anderson potential. The analytical predictions for the spinodal associated with these particles are found to be in very good agreement with the results of Brownian dynamics simulations that are based on the same Langevin equations as our theory. Furthermore, the critical point predicted by our analytical results agrees excellently with recent computational results from the literature.
description: 15 pages, 2 figures, 2 tables
Distributed linear algebra on networks of workstations
Creators: name: Carlin, Peter
Publisher: name: California Institute of Technology
Year: 1994
Subjects: Computer science
Computer Science

description: This thesis describes the development of a portion of a distributed linear algebra library for use
on networks of workstations. The library was designed with special consideration towards three
characteristics of networks of workstations: small numbers of processes, availability of multithreading, and high communication latency. Two aspects of the library are highlighted. First, modifications to message passing primitives to permit their use in a multithreaded environment. Second, modifications to basic linear algebra algorithms to improve their performance on networks of workstations. A model of distributed linear algebra on networks of workstations is developed, and used to predict the performance of the modified algorithms. These predictions are compared to experimental results on several networks of workstations.
Additional file 5: of Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data
Creators: name: Feng, Huijuan
name: Li, Tingting
name: Zhang, Xuegong
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Figure S1. DE gene counts in prostate cancer related GO terms. Figure S2. Enriched KEGG pathways by DE genes. Figure S3. REVIGO treemap for enriched GO terms by DS genes. Figure S4. REVIGO treemap for enriched GO terms by DE and DS kinase genes. Figure S5. Kinase domain and phosphorylation site of CDK5 two protein isoforms. (PDF 836 kb)
Magnetization of a two-dimensional electron gas with a second filled subband
Creators: name: Schaapman, M. R.
name: Zeitler, U.
name: Christianen, P. C. M.
name: Maan, J. C.
name: Reuter, D.
name: Wieck, A. D.
name: Schuh, D.
name: Bichler, M.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We have measured the magnetization of a dual-subband two-dimensional electron gas, confined in a GaAs/AlGaAs heterojunction. In contrast to two-dimensional electron gases with a single subband, we observe non-1/B-periodic, triangularly shaped oscillations of the magnetization with an amplitude significantly less than $1 μ_{\mathrm{B}}^*$ per electron. All three effects are explained by a field dependent self-consistent model, demonstrating the shape of the magnetization is dominated by oscillations in the confining potential. Additionally, at 1 K, we observe small oscillations at magnetic fields where Landau-levels of the two different subbands cross.
description: 4 pages, 4 figures
Back-action cancellation in interferometers by quantum locking
Creators: name: Courty, J. -M.
name: Heidmann, A.
name: Pinard, M.
Publisher: name: arXiv
Year: 2003
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We show that back-action noise in interferometric measurements such as gravitational-waves detectors can be completely suppressed by a local control of mirrors motion. An optomechanical sensor with an optimized measurement strategy is used to monitor mirror displacements. A feedback loop then eliminates radiation-pressure effects without adding noise. This very efficient technique leads to an increased sensitivity for the interferometric measurement, which becomes only limited by phase noise. Back-action cancellation is furthermore insensitive to losses in the interferometer.
description: 4 pages, 3 figures, RevTeX
Outflowing material in the zem = 4.92 BAL QSO SDSS~J160501.21-011220.0
Creators: name: Gupta, Neeraj
name: Srianand, Raghunathan
name: Petitjean, Patrick
name: Ledoux, Cedric
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present the analysis of two BALs seen in the spectrum of the QSO SDSS J160501.21-011220.0. Our UVES spectrum shows two well detached BALs at z(abs)= 4.685 and 4.855. The system at z(abs)= 4.855 covers the background source completely suggesting that the gas is located outside the BLR. On the contrary the system at z(abs)= 4.685 has a covering factor of ~0.9. The observed H I absorption line together with the limits on C II and Si II absorptions suggest that 16
description: 10 pages, 6 figures, to appear in A& A
Additional file 3 of The WUR0000125 PRRS resilience SNP had no apparent effect on pigs’ infectivity and susceptibility in a novel transmission trial
Creators: name: Chase-Topping, Margo
name: Plastow, Graham
name: Dekkers, Jack
name: Li, Yanhua
name: Fang, Ying
name: Gerdts, Volker
name: Van Kessel, Jill
name: Harding, John
name: Opriessnig, Tanja
name: Doeschl-Wilson, Andrea
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 3: Figure S5. Serum PRRSV-2 viral load of the Inoculation pigs after they were exposed to the Shedder pigs.
MOESM1 of Use of gene expression studies to investigate the human immunological response to malaria infection
Creators: name: Hodgson, Susanne
name: Muller, Julius
name: Lockstone, Helen
name: Hill, Adrian
name: Marsh, Kevin
name: Draper, Simon
name: Knight, Julian
Publisher: name: figshare
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1: Figure S1. Flowchart summarizing identification of GEO datasets and publications.
RR Lyrae variables in Galactic globular clusters - I: The observational scenario
Creators: name: Castellani, M.
name: Caputo, F.
name: Castellani, V.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: In this paper we revisit observational data concerning RR Lyrae stars in Galactic globular clusters, presenting frequency histograms of fundamentalized periods for the 32 clusters having more than 12 pulsators with well recognized period and pulsation mode. One finds that the range of fundamentalized periods covered by the variables in a given cluster remains fairly constant in varying the cluster metallicity all over the metallicity range spanned by the cluster sample, with the only two exceptions given by M15 and NGC6441. We conclude that the width in temperature of the RR Lyrae instability strip appears largely independent of the cluster metallicity. At the same time, it appears that the fundamentalized periods are not affected by the predicted variation of pulsators luminosity with metal abundance, indicating the occurrence of a correlated variation in the pulsator mass. We discuss mean periods in a selected sample of statistically significant "RR rich" clusters with no less than 10 RRab and 5 RRc variables. One finds a clear evidence for the well known Oosterhoff dichotomy in the mean period of ab-type variables, together with a similarly clear evidence for a constancy of the mean fundamentalized period in passing from Oosterhoff type II to type I clusters. On this basis, the origin of the Oosterhoff dichotomy is discussed, presenting evidence against a strong dependence of the RR Lyrae luminosity on the metal content.
description: 9 pages, 6 figures. Accepted for publication on A&A
Center of mass integral in canonical general relativity
Creators: name: Baskaran, D.
name: Lau, S. R.
name: Petrov, A. N.
Publisher: name: arXiv
Year: 2003
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: For a two-surface B tending to an infinite--radius round sphere at spatial infinity, we consider the Brown--York boundary integral H_B belonging to the energy sector of the gravitational Hamiltonian. Assuming that the lapse function behaves as N \sim 1 in the limit, we find agreement between H_B and the total Arnowitt--Deser--Misner energy, an agreement first noted by Braden, Brown, Whiting, and York. However, we argue that the Arnowitt--Deser--Misner mass--aspect differs from a gauge invariant mass--aspect by a pure divergence on the unit sphere. We also examine the boundary integral H_B corresponding to the Hamiltonian generator of an asymptotic boost, in which case the lapse N \sim x^k grows like one of the asymptotically Cartesian coordinate functions. Such an integral defines the kth component of the center of mass for a Cauchy surface Σbounded by B. In the large--radius limit, we find agreement between H_B and an integral introduced by Beig and O'Murchadha. Although both H_B and the Beig--O'Murchadha integral are naively divergent, they are in fact finite modulo the Hamiltonian constraint. Furthermore, we examine the relationship between H_B and a certain two--surface integral linear in the spacetime Riemann curvature tensor. Similar integrals featuring the curvature appear in works by Ashtekar and Hansen, Penrose, Goldberg, and Hayward. Within the canonical 3+1 formalism, we define gravitational energy and center--of--mass as certain moments of Riemann curvature.
description: 52 pages, revtex4, uses amsmath and amssymb
Noether currents of locally equivalent symmetries
Creators: name: Brauner, Tomas
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: Local symmetry transformations play an important role for establishing the existence and form of a conserved (Noether) current in systems with a global continuous symmetry. We explain how this fact leads to the existence of linear relations between Noether currents of distinct global symmetries that coincide on the local level, thus generalizing the well-known relationship $\vec L=\vec r\times\vec p$ between momentum $\vec p$ and angular momentum $\vec L$. As a byproduct, we find a natural interpretation for the discrepancy between the canonical and metric energy-momentum tensors in theories of particles with spin. A symmetric energy-momentum tensor can thus be obtained from the Noether procedure without adding any ad hoc corrections or imposing additional constraints such as gauge invariance in Maxwell's electrodynamics.
description: 8 pages; pedagogical exposition of aspects of the Noether theorem in classical field theory; Author's Original of a paper to be published in Physica Scripta
Optimized Computer-Generated Motions for Animation
Creators: name: Goldsmith, Jeff
Publisher: name: California Institute of Technology
Year: 1994
Subjects: Computer Science

description: Computer programmers working on computer animation have long been trying to solve the problem of how to move objects in user-desired ways with a minimum of user interaction. Objects moving from one place to another move along a path often determined by a spline. We would like to be able to allow the user a specify a characteristic of the object's motion and the animation system to choose a motion path that evidences that characteristic. We develop an approach using constrained optimization that will create paths. Some interesting motions have been found. We describe the effects obtainable from this method so that an animator can sensibly choose between them. We found that minimization of the covariant acceleration of all the points in a body leads to motion that is attractive. This motion seems to cause the moving body to anticipate its motion path in order to prevent sudden moves. It also seems to create very fluid-appearing motions because it tries to avoid sharp turns and sudden stops.
MOESM2 of Re-estimating the changes and ranges of forest biomass carbon in China during the past 40â€‰years
Creators: name: Xiaolu Zhou
name: Xiangdong Lei
name: Caixia Liu
name: Huabing Huang
name: Zhou, Carl
name: Changhui Peng
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: Additional file 2. Parameters and wood densities.
A complex network approach to political analysis: application to the Brazilian Chamber of Deputies
Creators: name: Brito, Ana C. M.
name: Silva, Filipi N.
name: Amancio, Diego R.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: In this paper, we introduce a network-based methodology to study how clusters represented by political entities evolve over time. We constructed networks of voting data from the Brazilian Chamber of Deputies, where deputies are nodes and edges are represented by voting similarity among deputies. The Brazilian Chamber of deputies is characterized by a multi-party political system. Thus, we would expect a broad spectrum of ideas to be represented. Our results, however, revealed that plurality of ideas is not present at all: the effective number of communities representing ideas based on agreement/disagreement in propositions is about 3 over the entire studied time span. The obtained results also revealed different patterns of coalitions between distinct parties. Finally, we also found signs of early party isolation before presidential impeachment proceedings effectively started. We believe that the proposed framework could be used to complement the study of political dynamics and even applied in similar social networks where individuals are organized in a complex manner.
description: All network visualizations are available from https://filipinascimento.github.io/politiciannetworks
MOESM1 of Rapid evaluation for health and social care innovations: challenges for “quick wins” using interrupted time series
Creators: name: McCarthy, Andrew
name: McMeekin, Peter
name: Haining, Shona
name: Bainbridge, Lesley
name: Laing, Claire
name: Gray, Joanne
Publisher: name: figshare
Year: 2019
Subjects: subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. PP (probability-probability) plots of normality.
Platynaspis ocellimaculata Pang & Mao 1979
Creators: name: Poorani, J.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Coccinellidae
Platynaspis
Platynaspis ocellimaculata

description: Platynaspis ocellimaculata Pang­&­Mao
Platynaspis ocellimaculata Pang & Mao, 1979: 95.— Canepari 1997: 20.
Pang & Mao (1979) described it from China and Canepari (1997) recorded it from Nepal. Ren et al. (2009) illustrated the habitus and the male genitalia.
­ Distribution. Nepal. China.
description: Published as part of Poorani, J., 2023, A review of Platynaspini (Coleoptera: Coccinellidae) of the Indian subcontinent, including description of a new genus from north-eastern India and Bangladesh, pp. 301-328 in Zootaxa 5256 (4) on page 317, DOI: 10.11646/zootaxa.5256.4.1, http://zenodo.org/record/7755142
A Hierarchical Design Rule Checker
Creators: name: Whitney, Telle
Publisher: name: California Institute of Technology
Year: 1981
Subjects: Computer Science

description: This thesis describes a new approach to the problem of Geometrical Design Rule Checking (DRC). Previous DRC implementations have dealt with fully instantiated geometrical artwork. As the complexity of VLSI increases, it becomes infeasible to analyze the vast amounts of information present in a fully instantiated design. The
DRC algorithm presented here introduces an approach that exploits the structural
hierarchy of a design in order to reduce the computational complexity of the
geometrical tests that need to be made. The technique described is also applicable to
other types of design checking such as circuit extraction, functional verification
and electrical rule verification.

A new DRC algorithm has been developed that, by making use of the structure
inherent in a hierarchical design, eliminates many redundant design rule checks.
In this approach there are two places where possible design rule violations may
occur. The first is within a symbol definition. The second is the area where two
symbols interact. The algorithm checks a given definition only once, and then examines how interactions within each new environment where the definition is placed modify the original definition. A note is made after each interaction has been scrutinized, so that a duplicate situation will not be rechecked.

An implementation of the hierarchical DRC algorithm has been written at Caltech.
This implementation extracts a minimal number of pairwise geometrical
comparisons needed to check the entire design. The program accepts as in put a
design description in the Caltech Intermediate Form (CIF). The output of the program is currently a fully instantiated version of those portions of the geometry
that need to be checked in order to check the entire design.

A means of expressing the designer's intent through the design description is
required. Current DRC's deal with geometrical artwork exclusively. Most of the
difficult design rules are involved in the checking of devices. Rather than
restricting the designer to the use of geometry, the idea of a primitive element is
introduced. A primitive element is defined to be anything that cannot be broken
down into sub-elements. A design defined using primitive elements conveys more
of the functional structure than a purely geometric definition.
Homophily on social networks changes evolutionary advantage in competitive information diffusion
Creators: name: Liu, Longzhao
name: Wang, Xin
name: Zheng, Yi
name: Fang, Wenyi
name: Tang, Shaoting
name: Zheng, Zhiming
Publisher: name: arXiv
Year: 2019
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Competitive information diffusion on large-scale social networks reveals fundamental characteristics of rumor contagions and has profound influence on public opinion formation. There has been growing interest in exploring dynamical mechanisms of the competing evolutions recently. Nevertheless, the impacts of population homophily, which determines powerful collective human behaviors, remains unclear. In this paper, we incorporate homophily effects into a modified competitive ignorant-spreader-ignorant (SIS) rumor diffusion model with generalized population preference. Using microscopic Markov chain approach, we first derive the phase diagram of competing diffusion results and examine how competitive information spreads and evolves on social networks. We then explore the detailed effects of homophily, which is modeled by a rewiring mechanism. Results show that homophily promotes the formation of divided "echo chambers" and protects the disadvantaged information from extinction, which further changes or even reverses the evolutionary advantage, i.e., the difference of final proportions of the competitive information. We highlight the conclusion that the reversals may happen only when the initially disadvantaged information has stronger transmission ability, owning diffusion advantage over the other one. Our framework provides profound insight into competing dynamics with population homophily, which may pave ways for further controlling misinformation and guiding public belief systems. Moreover, the reversing condition sheds light on designing effective competing strategies in many real scenarios.
MOESM2 of Rapid evaluation for health and social care innovations: challenges for “quick wins” using interrupted time series
Creators: name: McCarthy, Andrew
name: McMeekin, Peter
name: Haining, Shona
name: Bainbridge, Lesley
name: Laing, Claire
name: Gray, Joanne
Publisher: name: figshare
Year: 2019
Subjects: subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2. Tests for heteroscedasticity and autocorrelation A&E attendances.
MOESM1 of Re-estimating the changes and ranges of forest biomass carbon in China during the past 40â€‰years
Creators: name: Xiaolu Zhou
name: Xiangdong Lei
name: Caixia Liu
name: Huabing Huang
name: Zhou, Carl
name: Changhui Peng
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified

description: Additional file 1. Measurements of volume and biomass in China.
An experimental investigation of high-shear-strain-rate behavior of metals
Creators: name: Deshpande, Nitin
Publisher: name: California Institute of Technology
Year: 1999
Subjects: Aeronautics

description: NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.

The present study investigated the mechanical behavior of metals under high-shear-strain-rates and large shear strains. Numerical and experimental investigation of different specimen geometries for shear testing of materials was carried out. Results of numerical simulations showed that shear stress-strain curves calculated from boundary measurement of load and displacement did not match with the constitutive law for the material. The yield stress for the shear stress-strain curve from the boundary measurement was considerably lower than that of the constitutive law whereas hardening exponent was almost the same for two curves. Considerable bending was observed in the shear zone. The results from the boundary measurements were close to the constitutive law for H specimen, an analogue of axisymmetric top hat specimen with top replaced by tool steel punch. A planar version of axisymmetric top hat specimen geometry was studied using finite element analysis. The plane specimen was chosen since it is suitable for temperature measurements in the shear zone. In order to reduce the bending, three types of constraints were considered in the experiments.

Quasi-static and high strain rate experiments were carried out on different geometries in the strain rate range, 10[...] to 10[...] s[...]. Relatively rate insensitive material, 2024-T3 aluminum was used to establish the relationship between numerical and experimental results. Experimental results for the axisymmetric top hat specimen were found to be in good agreement with the finite element results, but there was discrepancy between the stress-strain curve from the boundary measurements and the constitutive law.  Shear stress-strain curve from the quasi-static test for the plane specimen with external constraint reproduced the results of numerical simulation. A planar specimen with built-in constraint was fabricated using wire EDM. Both quasi-static and high strain rate results matched with the numerical simulation of the same specimen geometry. High shear strains of the order of 1.5 were reached in the experiments on the Kolsky pressure bar. Some amount of thermal softening was observed in high strain rate experiments.

It was concluded that both numerical simulations and experiments are required in order to obtain accurate constitutive behavior of the material using top hat specimen geometries. A relationship can be established between the numerical tests and the experiments by conducting the experiments at strain rates where the constitutive behavior of the metal is well known. This relationship then can be used to predict the constitutive law at higher strain rates from the experimental data obtained at high strain rates.
The study of conformational dynamics of choline import mediated by a bacterial membrane transport protein using modelling and non-equilibrium simulations
Creators: name: T Mathew, Alen
name: Mehdipour, AhmedReza
Publisher: name: Zenodo
Year: 2023

description: LicB is a bacterial membrane choline transporter that plays a crucial role in virulence features & antibiotic resistance in S. pneumonia. Invitro studies involving inactivation of the licb gene, lead to nonviable S. pneumonia suggesting the therapeutic potential of targeting LicB, but currently the exact mechanism by which LicB imports choline into the bacterial cytoplasmic space is unknown.Objectives: Our objective is to explore the conformational changes of LicB during the choline import by reconstructing the free energy landscape of LicB to explain the thermodynamics & kinetics of the transport cycle. To achieve our objective, we are using a set of computational techniques like biomolecular simulations coupled with enhanced sampling techniques. Using homology modelling approaches and non-equilibrium simulation techniques like steered molecular dynamics (SMD) & targeted MD (TMD), we will generate intermediate states, such as the inward-open, which are yet to be identified experimentally. Later, techniques like Markov state modelling & transition path sampling are used to explore the kinetics of the protein conformational changes during the transport cycle.Through our microseconds long unbiased simulation of the protein, we verified the stability of the experimentally identified intermediate structures of the protein. Later we were able to generate other intermediate structures like inward open, choline-bound outward open, which are yet to be identified experimentally, using a combination of Alphafold based predictions, homology modelling of evolutionary similar proteins and non-equilibrium simulations like SMD & TMD. We have identified a suitable way of generating intermediate structures of proteins involved in membrane transport cycle using a combination of modelling and non-equilibrium simulations. Next step involves identifying the free energy and kinetics associated with the transport cycle which will help in designing drugs targeting LicB against S. pneumonia.
ShapeBots: Shape-changing Swarm Robots
Creators: name: Suzuki, Ryo
name: Zheng, Clement
name: Kakehi, Yasuaki
name: Yeh, Tom
name: Do, Ellen Yi-Luen
name: Gross, Mark D.
name: Leithinger, Daniel
Publisher: name: arXiv
Year: 2019
Subjects: subject: Robotics (cs.RO)
subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: We introduce shape-changing swarm robots. A swarm of self-transformable robots can both individually and collectively change their configuration to display information, actuate objects, act as tangible controllers, visualize data, and provide physical affordances. ShapeBots is a concept prototype of shape-changing swarm robots. Each robot can change its shape by leveraging small linear actuators that are thin (2.5 cm) and highly extendable (up to 20cm) in both horizontal and vertical directions. The modular design of each actuator enables various shapes and geometries of self-transformation. We illustrate potential application scenarios and discuss how this type of interface opens up possibilities for the future of ubiquitous and distributed shape-changing interfaces.
description: UIST 2019
Graviton Mass, Quintessence and Oscillatory Character of the Universe Evolution
Creators: name: Gershtein, S. S.
name: Logunov, A. A.
name: Mestvirishvili, M. A.
name: Tkachenko, N. P.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: It is shown that using the relativistic field theory of gravity (RTG) and measured value of $Ω_{tot}$ one can obtain the upper limit on the graviton mass with 95%C.L.: $m\leq 1.6\cdot 10^{-66}$ [g]; within the $(1σ)$ range its probable value is $m_{g}= 1.3\cdot 10^{-66}$ [g]. It is pointed out that according to RTG the presence of the quintessence is necessary to explain the Universe accelerated expansion. Experimental data on the Universe age and dark matter density allow one to determine the range of possible values of the $ν$ parameter in the equation of quintessence state and indicate characteristic time, which corresponds to the beginning and cessation of the accelerated expansion epoch, as well as the time period of the maximal expansion, which corresponds to the half-period of the oscillatory evolution of the Universe.
description: 17 pages, 4 jpeg figures
Exploring caveolae's role in oxygen "buffering" through coarse-grained molecular dynamics.
Creators: name: Davoudi, Samaneh
name: Ghysels, An
Publisher: name: Zenodo
Year: 2023

description: The "oxygen paradox" refers to the intricate interplay between two contrasting biological processes involving oxygen (O2) as a reactant. O2 is vital for aerobic metabolism, acting as a fuel for oxidative phosphorylation within mitochondria. However, an excessive supply of O2 can lead to the generation of reactive species that harm cellular health. Therefore, maintaining O2 homeostasis becomes crucial, requiring a delicate balance that prioritizes the former process while minimizing the latter. In earlier research, a hypothesis was proposed centered around specialized membrane invaginations called caveolae. These unique structures exhibit a curved morphology and are rich in cholesterol. It was postulated that caveolae play a pivotal role in regulating O2 levels within cells by efficiently absorbing O2 and attenuating its release to the mitochondria. However, the exact mechanism through which caveolae contribute to O2 buffering remains unclear, presenting an intriguing research question. To address this knowledge gap, our primary objective is to investigate how specific structural characteristics of caveolae, such as membrane curvature and cholesterol content, influence the local O2 abundance and membrane permeability. To accurately simulate a curved membrane resembling caveolae, we employed coarse grained molecular dynamics (MD) simulations. After conducting a comprehensive set of tests, we carefully selected one of the CG beads to serve as the CG O2 model. Liposomes of varying sizes were created to represent different levels of curvature, composed of phosphatidylcholine (POPC) and cholesterol. This approach allows us to observe associated changes in the O2 free energy profile and membrane permeability. By unraveling the influence of membrane curvature and cholesterol content on local O2 abundance and membrane permeability, we aim to deepen our understanding of the underlying mechanisms governing O2 homeostasis. Ultimately, this enhanced knowledge may pave the way for the development of novel therapeutic approaches targeting O2-related disorders and conditions.
Bio26_art8.pdf
Creators: name: Fraga Delfino Kunz, Camile
name: Marta Rodrigues de Souza, Juliana
name: Frederico da C. A. Meyer, João
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 490199
subject: Applied mathematics not elsewhere classified

description: The objective of this study was to assess the impact of data separation treatment on the estimation of the diffusion/dispersal coefficient in ecological and epidemiological problems. In a previous study, a method for estimating the diffusion coefficient was developed and validated under the assumption of a single focal point of relevant events. The validation of this method relied on simulation techniques for diffusivity-based data. In the present study, we extend this approach by considering cases with two geographically distinct focal points. Two different data generation experiments were conducted and analyzed in detail using the K-means clustering algorithm. Finally, a practical application is presented, focusing on avian influenza in Nigeria, where two different clustering algorithms were used to process latitude and longitude data.
A methodology for eliciting user-implicit knowledge of word categories for use in connection with a speech-driven word processor
Creators: name: Bentley, Catherine
Publisher: name: Loughborough University
Year: 2021
Subjects: subject: 89999 Information and Computing Sciences not elsewhere classified
subject: FOS: Computer and information sciences

description: A methodology for eliciting user-implicit knowledge of word categories for use in connection with a speech-driven word processor
Multiple Embedded Eigenstates in Nonlocal Plasmonic Nanostructures
Creators: name: Silva, Solange V.
name: Morgado, Tiago A.
name: Silveirinha, Mario G.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Trapping light in open cavities is a long sought "holy grail" of nanophotonics. Plasmonic materials may offer a unique opportunity in this context, as they may fully suppress the radiation loss and enable the observation of spatially localized light states with infinite lifetime in an open system. Here, we investigate how the spatial dispersion effects, e.g., caused by the electron-electron interactions in a metal, affect the trapped eigenstates. Heuristically, one may expect that the repulsive-type electron-electron interactions should act against light localization, and thereby that they should have a negative impact on the formation of the embedded eigenstates. Surprisingly, here we find that the nonlocality of the material response creates new degrees of freedom and relaxes the requirements for the observation of trapped light. In particular, a zero-permittivity condition is no longer mandatory and the same resonator shell can potentially suppress the radiation loss at multiple frequencies.
Commutants of von Neumann Modules, Representations of B^a(E) and Other Topics Related to Product Systems of Hilbert Modules
Creators: name: Skeide, Michael
Publisher: name: arXiv
Year: 2003
Subjects: subject: Operator Algebras (math.OA)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 46L55; 46L53; 60J25; 46L08; 81S25

description: We review some of our results from the theory of product systems of Hilbert modules. We explain that the product systems obtained from a CP-semigroup in a paper by Bhat and Skeide and in a paper by Muhly and Solel are commutants of each other. Then we use this new commutant technique to construct product systems from E_0-semigroups on B^a(E) where E is a strongly full von Neumann module. (This improves the construction from a paper by Skeide for Hilbert modules where existence of a unit vector is required.) Finally, we point out that the Arveson system of a CP-semigroup constructed by Powers from two spatial E_0-semigroups is the product of the corresponding spatial Arveson systems as defined (for Hilbert modules) in a paper by Skeide. It need not coincide with the tensor product of Arveson systems.
description: To appear in Proceedings of ``Advances in Quantum Dynamics'', Mount Holyoke, 2002
Can the impact of grey literature be assessed An investigation of UK government publications cited by articles and books (Appendices)
Creators: name: Bickley, Matthew
name: Kayvan Kousha
name: Thelwall, Mike
Publisher: name: figshare
Year: 2019
Subjects: subject: 80705 Informetrics
subject: FOS: Media and communications
subject: 80704 Information Retrieval and Web Search

description: Appendices (1-7) to the journal contribution (Scientometrics - decision pending):
"Can citation impact of grey literature be assessed? An investigation of UK government publications cited by articles and books"
Activated carbon processed from Citrus sinensis: Synthesis, characterization and application for adsorption-based separation of toxic pesticides from soils
Creators: name: Palwasha Gul
name: Khuram Shahzad Ahmad
name: Ali, Daoud
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: peels activated carbon synthesis was done by means of sulfuric acid activation. Activated carbon was analysed by SEM, XRD, UV-Vis and FT-IR. Two concentrations of pesticides; Thiencarbazone-methyl, Isopyrazam and Zoxamide were separated from ten agricultural and contaminated soils. Removal potential was evaluated for a time span of 3 and 6 hours. Maximum elimination was detected in soil S5 (65% and 92% for 5 mg/L and 7.5 mg/L, respectively) for Thiencarbazone-methyl, 89% and 96% for Isopyrazam and 84% and 88% for Zoxamide. Results of the current work supports the efficient removal achieved with the prepared activated carbon.
Particle emission and gravitational radiation from cosmic strings: observational constraints
Creators: name: Auclair, P.
name: Steer, D. A.
name: Vachaspati, T.
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We account for particle emission and gravitational radiation from cosmic string loops to determine their effect on the loop distribution and observational signatures of strings. The effect of particle emission is that the number density of loops no longer scales. This results in a high frequency cutoff on the stochastic gravitational wave background, but we show that the expected cutoff is outside the range of current and planned detectors. Particle emission from string loops also produces a diffuse gamma ray background that is sensitive to the presence of kinks and cusps on the loops. However, both for kinks and cusps, and with mild assumptions about particle physics interactions, current diffuse gamma-ray background observations do not constrain $Gμ$.
description: 14 pages, 7 figures
Anomalous dimensions of quark masses in the three-loop approximation
Creators: name: Tarasov, O. V.
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The results of calculation of the three-loop radiative correction to the renormalization constant of fermion masses for non-abelian gauge theory interacting with fermions are presented. Dimensional regularization and the 't Hooft minimal subtraction scheme are used. The method of calculation is described in detail. The renormalization group function $γ_m$ determining the behavior of the effective mass of fermions is presented. The anomalous dimensions of fermions for QED and QCD up to three loops are given. All calculations were performed on a computer with the help of the SCHOOONSCHIP system for analytical manipulations. The present text was published in 1982 as a JINR Communication, JINR-P2-82-900 (in russian).
description: 11 pages,
The Origins and Evolutions of the EU's Enlargement and Neighbourhood Policies in the Area of Democracy Promotion
Creators: name: Delcour, Laure
name: Pollozhani, Lura
name: Bieber, Florian
name: Burmester, Isabell
name: Dandashly, Assem
name: Kmezic, Marko
name: Noutcheva, Gergana
Publisher: name: Zenodo
Year: 2024

description: The development of the European integration project asserted the importance of liberal democracy as one of the pillars of the European Union (EU). It has also been a key building block of foreign policy, through the enlargement process and European Neighbourhood Policy (ENP). The EU’s democracy promotion agenda has been largely successful in central and eastern Europe however, it has been put to the test in both the Western Balkans (WB) and the Eastern neighbourhood (EN), where the EU has struggled to promote sustainable democratisation. EU democracy promotion policies have been implemented in a rapidly changing international, regional and domestic environment, characterised by democratic breakthroughs and setbacks, as well as the influence of non-western actors. Democratic advances, such as those achieved as part of protest movements and colour revolutions, have sometimes been followed by reversals. Likewise, democratic backsliding trends have in some cases been turned around, raising hopes for the fate of liberal democracy in the WB and EN regions.

This paper first investigates the risks and uncertainties that have affected the EU's democracy promotion in the WB6 and EN3 over the last 30 - 35 years. It then examines the control power tools the EU has used and the innovations and improvisations it has employed in response to the dynamic and complex nature of the political landscape in these regions.
Automated Wiring Analysis of Integrated Circuit  Geometric Data
Creators: name: Lang, Charles Richard
Publisher: name: California Institute of Technology
Year: 1979
Subjects: Computer Science
computer science

description: Methods are presented by which wiring data of an NMOS integrated circuit may be extracted from its mask information. The procedures involved utilize the capabilities of a general purpose polygon package. The polygon operations are defined to enhance their use in this application, however the package is suitable for other uses such as, design rule checking. The analysis is performed on hierarchical symbol definitions of mask geometry. The geometry is presumed to be described in CIF 2.0 (Caltech Intermediate Form). The analysis attempts to recognize three basic types of structures in the geometry:

1)	Transistor devices (and capacitors)
2)	Local interconnection structures and
3)	Global interconnection structures

Definitions are put forth for the distinction of global and local wires. The data extracted from the symbol geometry is the percent utilization of each symbol's area by each of the three types of structures. The purpose behind the extraction of this data is its use in the development and evaluation of wiring models for custom NMOS IC design. Two approaches are presented which extract such data. The first is heuristic and depends on built-in assumptions of how the NMOS process is generally used. This technique loses accuracy if a design style falls outside of these assumptions. The second technique is a method by which the topology of design may be extracted from the geometry. The geometric objects, from which devices and interconnections are made, are preserved, such that the wiring information can be obtained precisely. This method is complex and requires considerable computation, however, the topology extracted may also be used to verify the geometric data against the original design topology.
Do We Need Stars to Reionize the Universe at High Redshifts? Early Reionization by Decaying Heavy Sterile Neutrinos
Creators: name: Hansen, Steen H.
name: Haiman, Zoltan
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: A remarkable result of the Wilkinson Microwave Anisotropy Probe (WMAP) observations is that the universe was significantly reionized at large redshifts. The standard explanation is that massive stars formed early and reionized the universe around redshift z=17. Here we explore an alternative possibility, in which the universe was reionized in two steps. An early boost of reionization is provided by a decaying sterile neutrino, whose decay products, relativistic electrons, result in partial ionization of the smooth gas. We demonstrate that a neutrino with a mass of m_nu ~ 200 MeV and a decay time of t ~ 4 * 10^{15} s can account for the electron scattering optical depth tau=0.16 measured by WMAP without violating existing astrophysical limits on the cosmic microwave and gamma ray backgrounds. Reionization is then completed by subsequent star formation at lower redshifts. This scenario alleviates constraints on structure formation models with reduced small-scale power, such as those with a running or tilted scalar index, or warm dark matter models.
description: Improved the discussion of electron-CMB interaction; describe the reionization process in more detail; conclusions unchanged; few references added (as accepted by ApJ)