cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Polyhedral Gauss Sums, and polytopes with symmetry
Creators: name: Malikiosis, Romanos-Diogenes
name: Robins, Sinai
name: Zhang, Yichi
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: Metric Geometry (math.MG)
subject: FOS: Mathematics
subject: 11L05, 52C22, 05B45, 52B10, 52B15, 51M20

description: We define certain natural finite sums of $n$'th roots of unity, called $G_P(n)$, that are associated to each convex integer polytope $P$, and which generalize the classical $1$-dimensional Gauss sum $G(n)$ defined over $\mathbb Z/ {n \mathbb Z}$, to higher dimensional abelian groups and integer polytopes. We consider the finite Weyl group $\mathcal{W}$, generated by the reflections with respect to the coordinate hyperplanes, as well as all permutations of the coordinates; further, we let $\mathcal G$ be the group generated by $\mathcal{W}$ as well as all integer translations in $\mathbb Z^d$. We prove that if $P$ multi-tiles $\mathbb R^d$ under the action of $\mathcal G$, then we have the closed form $G_P(n) = \text{vol}(P) G(n)^d$. Conversely, we also prove that if $P$ is a lattice tetrahedron in $\mathbb R^3$, of volume $1/6$, such that $G_P(n) = \text{vol}(P) G(n)^d$, for $n \in \{ 1,2,3,4 \}$, then there is an element $g$ in $\mathcal G$ such that $g(P)$ is the fundamental tetrahedron with vertices $(0,0,0)$, $(1, 0, 0)$, $(1,1,0)$, $(1,1,1)$.
description: 18 pages, 2 figures
Anemia in people on second line antiretroviral treatment in Lilongwe, Malawi: a cross-sectional study
Creators: name: Broadhurst, Richard
name: Tembo, Petros
name: Rosenberg, Nora E
name: Stanley, Christopher C
name: Lim, Robertino
name: Flick, Robert
name: Ngongondo, McNeil
name: Ongubo, Dennis
name: Speight, Colin
name: Hosseinipour, Mina
Publisher: name: BioMed Central
Year: 2018

description: Abstract Background Anemia is common among people living with HIV infection and is frequently associated with poor quality of life and poor prognosis. It has been well described in antiretroviral naïve individuals and those on non-nucleoside reverse transcriptase inhibitor-based first line antiretroviral therapy (ART) regimens. However there is limited information on anemia for ART experienced individuals on protease inhibitor-based second line ART regimens in resource limited settings. Our objective was to describe the prevalence and risk factors of anemia in this ART experienced population in Malawi. Methods We conducted a cross-sectional study using routine facility data at two HIV clinics in Lilongwe, Malawi. The analysis included individuals receiving protease inhibitor-based second line ART. Clinical and laboratory data were collected at routine clinic visits. We used descriptive statistics, two-sample t-tests and multivariate logistic regression for data analysis. Results Three hundred seventy-seven records were included in this analysis (37% male, median age 41 years, median CD4 count 415 cells/μL). The prevalence of anemia was 125/377 (33.2%) − mild, moderate and severe anemia was 17.5%, 13.8%, and 1.9% respectively. Female participants had a higher prevalence than male participants (43.6% vs. 15.7%, p < 0.001). In multivariate logistic regression, female sex (adjusted odds ratio (aOR) 5.3; 95% CI 2.9–9.5) and a CD4 count <200 cell/ul (aOR 3.1; 95%CI 1.6–6.0) were associated with increased risk of having anemia while a BMI ≥30 kg/m2 (aOR 0.8; 95% CI 0.6–1.0) and being on ART for more than 10 years (aOR 0.4; 95% CI 0.2–0.9) were associated with reduced risk of anemia. Being on a zidovudine- containing ART regimen was not associated with anemia. Conclusion Anemia is common in people on second line ART in Lilongwe, Malawi. Screening for anemia in this population would be a useful strategy; especially for female patients, those who are underweight and have a low CD4 cell counts.
title: Hallazgos radiológicos de los Tumores Carcinoides Abdominales: Nuestra experiencia en 3 años.
Creators: name: Gómez Gil, Marta Elena
Publisher: name: Sociedad Española de Radiología Médica
Year: 2014
Subjects: subject: Abdomen
subject: Gastrointestinal tract
subject: MR
subject: CT

description: Objetivos Material y método Resultados Conclusiones Bibliografía
description: Objetivos: Realizar una revisión de las manifestaciones radiológicas del tumor carcinoide de origen abdominal con las diferentes técnicas de imagen (ecografía, TC y...
Structural and Pharmacological Characterisation of Splice Isoforms of the Pituitary Adenylate Cyclase-Activating Polypeptide Type 1 (PAC1) Receptor
Creators: name: LU, JESSICA JUEXI
Publisher: name: Monash University
Year: 2023
Subjects: Structural biology (incl. macromolecular modelling)
Basic pharmacology
Proteins and peptides
Receptors and membrane biology

description: The pituitary adenylate cyclase-activating polypeptide type 1 receptor (PAC1R) is a promising drug target for the treatment of numerous central nervous system disorders where there is significant unmet clinical need. This may, in part, be due to the existence of multiple PAC1R splice isoforms, from alternative splicing in the N-terminal extracellular domain (ECD) and intracellular loop 3 (ICL3) regions. These regions may be important for ligand recognition and transducer coupling and activation of PAC1R, hence the pharmacological profiles of the N-terminal ECD and ICL3 PAC1R splice isoforms and structural determinants of select PAC1R N-terminal ECD splice isoforms were investigated.
Seamless GPU acceleration for C++ based physics with the Metal Shading Language on Apple's M series unified chips
Creators: name: Gebraad, Lars
name: Fichtner, Andreas
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: The M series of chips produced by Apple have proven a capable and power-efficient alternative to mainstream Intel and AMD x86 processors for everyday tasks. Additionally, the unified design integrating the central processing and graphics processing unit, have allowed these M series chips to excel at many tasks with heavy graphical requirements without the need for a discrete graphical processing unit (GPU), and in some cases even outperforming discrete GPUs. In this work, we show how the M series chips can be leveraged using the Metal Shading Language (MSL) to accelerate typical array operations in C++. More importantly, we show how the usage of MSL avoids the typical complexity of CUDA or OpenACC memory management, by allowing the central processing unit (CPU) and GPU to work in unified memory. We demonstrate how performant the M series chips are on standard one-dimensional and two-dimensional array operations such as array addition, SAXPY and finite difference stencils, with respect to serial and OpenMP accelerated CPU code. The reduced complexity of implementing MSL also allows us to accelerate an existing elastic wave equation solver (originally based on OpenMP accelerated C++) using MSL, with minimal effort, while retaining all CPU and OpenMP functionality. The resulting performance gain of simulating the wave equation is near an order of magnitude for specific settings. This gain attained from using MSL is similar to other GPU-accelerated wave-propagation codes with respect to their CPU variants, but does not come at much increased programming complexity that prohibits the typical scientific programmer to leverage these accelerators. This result shows how unified processing units can be a valuable tool to seismologists and computational scientists in general, lowering the bar to writing performant codes that leverage modern GPUs.
Convergence and local-to-global results for $p$-superminimizers on quasiopen sets
Creators: name: Björn, Anders
name: Björn, Jana
name: Latvala, Visa
Publisher: name: arXiv
Year: 2022
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: Primary: 31E05, Secondary: 30L99, 31C40, 35J92

description: In this paper, several convergence results for fine $p$-(super)minimizers on quasiopen sets in metric spaces are obtained. For this purpose, we deduce a Caccioppoli-type inequality and local-to-global principles for fine $p$-(super)minimizers on quasiopen sets. A substantial part of these considerations is to show that the functions belong to a suitable local fine Sobolev space. We prove our results for a complete metric space equipped with a doubling measure supporting a $p$-Poincaré inequality with $1
description: arXiv admin note: text overlap with arXiv:2106.13738
title: Radioembolización en el tratamiento de Hepatocarcinomas. Experiencia propia.
Creators: name: Pérez Enguix, Daniel
Publisher: name: Sociedad Española de Radiología Médica
Year: 2014
Subjects: subject: Neoplasia
subject: Radioembolisation
subject: CT
subject: SPECT-CT
subject: Catheter arteriography
subject: Oncology
subject: Interventional vascular
subject: Liver

description: Objetivos Material y método Resultados Conclusiones Bibliografía
description: Objetivos: El HCC es la sexta neoplasia en incidencia mundial, constituyéndose como la tercera causa de muerte por cáncer. Tan sólo un 20% de los nuevos casos diagnosticados pueden tratarse con intención curativa. La radioembolización viene empleándose...
Development of Active Correlation Technique
Creators: name: Tsyganov, Y. S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: With reaching to extremely high intensities of heavy-ion beams new requirements for the detection system of the Dubna Gas-Filled Recoil Separator (DGFRS) will definitely be set. One of the challenges is how to apply the active correlations method to suppress beam associated background products without significant losses in the whole long-term experiment efficiency value. Different scenarios and equations to develop the method according this requirement are under consideration in the present paper. The execution time to estimate the dead time parameter associated with the optimal choice of the life-time parameter is presented.
description: in print for Lett. to ECHAYA 2015
${\rm f}_{0}(980)$ production in inelastic pp collisions at $\sqrt{s} = 5.02$ TeV
Creators: name: ALICE Collaboration
Publisher: name: arXiv
Year: 2022
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The measurement of the production of ${\rm f}_{0}(980)$ in inelastic pp collisions at $\sqrt{s} = 5.02$ TeV is presented. This is the first reported measurement of inclusive ${\rm f}_{0}(980)$ yield at LHC energies. The production is measured at midrapidity, $|y| < 0.5$, in a wide transverse momentum range, $0 < p_{\rm T} < 16$ GeV/$c$, by reconstructing the resonance in the ${\rm f}_{0}(980) \rightarrow π^{+}π^{-}$ hadronic decay channel using the ALICE detector. The $p_{\rm T}$-differential yields are compared to those of pions, protons and $ϕ$ mesons as well as to predictions from the HERWIG 7.2 QCD-inspired Monte Carlo event generator and calculations from a coalescence model that uses the AMPT model as an input. The ratio of the $p_{\rm T}$-integrated yield of ${\rm f}_{0}(980)$ relative to pions is compared to measurements in ${\rm e}^{+}{\rm e}^{-}$ and pp collisions at lower energies and predictions from statistical hadronisation models and HERWIG 7.2. A mild collision energy dependence of the ${\rm f}_{0}(980)$ to pion production is observed in pp collisions from SPS to LHC energies. All considered models underpredict the $p_{\rm T}$-integrated $2{\rm f}_{0}(980)/(π^{+}+π^{-})$ ratio. The prediction from the canonical statistical hadronisation model assuming a zero total strangeness content of ${\rm f}_{0}(980)$ is consistent with the data within 1.9$σ$ and is the closest to the data. The results provide an essential reference for future measurements of the particle yield and nuclear modification in p$-$Pb and Pb$-$Pb collisions, which have been proposed to be instrumental to probe the elusive nature and quark composition of the ${\rm f}_{0}(980)$ scalar meson.
description: 23 pages, 5 captioned figures, 1 table, authors from page 18, published version, figures at http://alice-publications.web.cern.ch/node/8276
Non-parametric estimation of Fisher information from real data
Creators: name: Shemesh, Omri Har
name: Quax, Rick
name: Miñano, Borja
name: Hoekstra, Alfons G.
name: Sloot, Peter M. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computation (stat.CO)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: The Fisher Information matrix is a widely used measure for applications ranging from statistical inference, information geometry, experiment design, to the study of criticality in biological systems. Yet there is no commonly accepted non-parametric algorithm to estimate it from real data. In this rapid communication we show how to accurately estimate the Fisher information in a nonparametric way. We also develop a numerical procedure to minimize the errors by choosing the interval of the finite difference scheme necessary to compute the derivatives in the definition of the Fisher information. Our method uses the recently published "Density Estimation using Field Theory" algorithm to compute the probability density functions for continuous densities. We use the Fisher information of the normal distribution to validate our method and as an example we compute the temperature component of the Fisher Information Matrix in the two dimensional Ising model and show that it obeys the expected relation to the heat capacity and therefore peaks at the phase transition at the correct critical temperature.
description: 6 pages, 5 figures
Comparative short-term safety of bolus versus maintenance iron dosing in hemodialysis patients: a replication study
Creators: name: Brookhart, M. Alan
name: Kshirsagar, Abhijit
name: Ellis, Alan R
name: Wang, Lily
name: Freburger, Janet K
Publisher: name: BioMed Central Ltd
Year: 2014

description: Abstract Background Recent research has reported that patients receiving bolus (frequent large doses to achieve iron repletion) versus maintenance dosing of iron have an increased short-term risk of infection, but a similar risk of cardiovascular events. We sought to determine whether these findings could be replicated using the same methods and a different data source. Methods Clinical data from 6,605 patients of a small U.S. dialysis provider merged with Medicare claims data were examined. Iron dosing patterns (bolus, maintenance, no iron) were identified during 1-month exposure periods and cardiovascular and infection-related outcomes were assessed during 3-month follow-up periods. The effects of bolus versus maintenance dosing were assessed using Cox proportional hazards regression analyses to estimate hazard ratios and semiparametric additive risk models to estimate hazard rate differences, controlling for demographic and clinical characteristics, laboratory values and medications, and comorbidities. Results 48,050 exposure/follow-up periods were examined. 13.9 percent of the exposure periods were bolus dosing, 49.3 percent were maintenance dosing, and the remainder were no iron use. All of the adjusted hazard ratios were >1.00 for the infection-related outcomes, suggesting that bolus dosing increases the risk of these events. The effects were greatest for hospitalized for infection of any major organ system (hazard ratio 1.13 (1.03, 1.24)) and use of intravenous antibiotics (hazard ratio 1.08 (1.02, 1.15). When examining the subgroup of individuals with catheters, the hazard ratios for the infection-related outcomes were generally greater than in the overall sample. There was little association between type of dosing practice and cardiovascular outcomes. Conclusions Results of this study provide further evidence of the association between bolus dosing and increased infection risk, particularly in the subgroup of patients with a catheter, and of the lack of an association between dosing practices and cardiovascular outcomes.
Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics
Creators: name: Borrell, Enric Ribera
name: Quer, Jannes
name: Richter, Lorenz
name: Schütte, Christof
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics
subject: 49-XX, 62-XX, 68-XX

description: Sampling rare events in metastable dynamical systems is often a computationally expensive task and one needs to resort to enhanced sampling methods such as importance sampling. Since we can formulate the problem of finding optimal importance sampling controls as a stochastic optimization problem, this then brings additional numerical challenges and the convergence of corresponding algorithms might as well suffer from metastabilty. In this article, we address this issue by combining systematic control approaches with the heuristic adaptive metadynamics method. Crucially, we approximate the importance sampling control by a neural network, which makes the algorithm in principle feasible for high-dimensional applications. We can numerically demonstrate in relevant metastable problems that our algorithm is more effective than previous attempts and that only the combination of the two approaches leads to a satisfying convergence and therefore to an efficient sampling in certain metastable settings.
Fake gaps in AdS_3/CFT_2
Creators: name: Belin, Alexandre
name: Castro, Alejandra
name: Hung, Ling-Yan
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We discuss properties of interpolating geometries in three dimensional gravity in the presence of a chiral anomaly. This anomaly, which introduces an unbalance between left and right central charges, is protected under RG flows. For this simple reason it is impossible to gap a system with such an anomaly. Our goal is to discuss how holography captures this basic and robust feature. We demonstrate the absence of a mass gap by analysing the linearized spectrum and holographic entanglement entropy of these backgrounds in the context of AdS$_3$/CFT$_2$.
description: 22 pages + Appendices, v2 bibliography fixed + references added
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences
Creators: name: Guan, Xiaojun
Publisher: name: BioMed Central Ltd
Year: 2012

description: Abstract Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.
Colonoscopy 3D Video Dataset with Paired Depth from 2D-3D Registration
Creators: name: Bobrow, Taylor L.
name: Golhar, Mayank
name: Vijayan, Rohan
name: Akshintala, Venkata S.
name: Garcia, Juan R.
name: Durr, Nicholas J.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Screening colonoscopy is an important clinical application for several 3D computer vision techniques, including depth estimation, surface reconstruction, and missing region detection. However, the development, evaluation, and comparison of these techniques in real colonoscopy videos remain largely qualitative due to the difficulty of acquiring ground truth data. In this work, we present a Colonoscopy 3D Video Dataset (C3VD) acquired with a high definition clinical colonoscope and high-fidelity colon models for benchmarking computer vision methods in colonoscopy. We introduce a novel multimodal 2D-3D registration technique to register optical video sequences with ground truth rendered views of a known 3D model. The different modalities are registered by transforming optical images to depth maps with a Generative Adversarial Network and aligning edge features with an evolutionary optimizer. This registration method achieves an average translation error of 0.321 millimeters and an average rotation error of 0.159 degrees in simulation experiments where error-free ground truth is available. The method also leverages video information, improving registration accuracy by 55.6% for translation and 60.4% for rotation compared to single frame registration. 22 short video sequences were registered to generate 10,015 total frames with paired ground truth depth, surface normals, optical flow, occlusion, six degree-of-freedom pose, coverage maps, and 3D models. The dataset also includes screening videos acquired by a gastroenterologist with paired ground truth pose and 3D surface models. The dataset and registration source code are available at durr.jhu.edu/C3VD.
title: Acoustic Crystallization of 2D Colloidal Crystals
Creators: name: Menath, Johannes
name: Mohammadi, Reza
name: Grauer, Jens Christian
name: Deters, Claudius
name: Böhm, Maike
name: Liebchen, Benno
name: Janssen, Liesbeth M. C.
name: Löwen, Hartmut
name: Vogel, Nicolas
Publisher: name: Wiley-VCH
Year: 2023

description: 2D colloidal crystallization provides a simple strategy to produce defined nanostructure arrays over macroscopic areas. Regularity and long‐range order of such crystals is essential to ensure functionality, but difficult to achieve in self‐assembling systems. Here, a simple loudspeaker setup for the acoustic crystallization of 2D colloidal crystals (ACDC) of polystyrene, microgels, and core–shell particles at liquid interfaces is introduced. This setup anneals an interfacial colloidal monolayer and affords an increase in average grain size by almost two orders of magnitude. The order is characterized via the structural color of the colloidal crystal, the acoustic annealing process is optimized via the frequency and the amplitude of the applied sound wave, and its efficiency is rationalized via the surface coverage‐dependent interactions within the interfacial colloidal monolayer. Computer simulations show that multiple rearrangement mechanisms at different length scales, from the local motion around voids to grain boundary movements via consecutive particle rotations around common centers, collude to remove defects. The experimentally simple ACDC process, paired with the demonstrated applicability toward complex particle systems, provides access to highly defined nanostructure arrays for a wide range of research communities.
Jodï
Creators: Rosés Labrada, Jorge Emilio
Publisher: name: University of Alberta Library
Year: 2023

This book chapter offers an overview of the grammar of Jodï, an Amazonian language spoken in Venezuela. It appears in Volume 1 Language Isolates I: Aikanã to Kandozi-Shapra of the multivolume handbook "Amazonian Languages, An International Handbook" edited by Pattie Epps and Lev Michael and published by De Gruyter. The DOI link is: https://doi.org/10.1515/9783110419405-012
Charge dynamics and "in plane" magnetic field I: Rashba-Dresselhauss interaction, Majorana fermions and Aharonov-Casher theorems
Creators: name: Cirilo-Lombardo, Diego Julio
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The 2-dimensional charge transport with parallel (in plane) magnetic field is considered from the physical and mathematical point of view. To this end, we start with the magnetic field parallel to the plane of charge transport, in sharp contrast to the configuration described by the theorems of Aharonov and Casher where the magnetic field is perpendicular. We explicitly show that the specific form of the arising equation enforce the respective field solution to fulfil the Majorana condition. Consequently, as soon any physical system is represented by this equation, the rise of fields with Majorana type behaviour is immediately explained and predicted. In addition, there exists a quantized particular phase that removes the action of the vector potential producing interesting effects. Such new effects are able to explain due the geometrical framework introduced, several phenomenological results recently obtained in the area of spintronics and quantum electronic devices. The quantum ring as spin filter is worked out in this framework and also the case of the quantum Hall effect.
description: Accepted in International Journal of Geometric Methods in Modern Physics (IJGMMP) Vol. 12 (2015), no figures. General references added, english improved. arXiv admin note: text overlap with arXiv:quant-ph/0701076, arXiv:1302.3641 by other authors
Ballistic macroscopic fluctuation theory
Creators: name: Doyon, Benjamin
name: Perfetto, Gabriele
name: Sasamoto, Tomohiro
name: Yoshimura, Takato
Publisher: name: arXiv
Year: 2022
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We introduce a new universal framework describing fluctuations and correlations in quantum and classical many-body systems, at the Euler hydrodynamic scale of space and time. The framework adapts the ideas of the conventional macroscopic fluctuation theory (MFT) to systems that support ballistic transport. The resulting "ballistic MFT" (BMFT) is solely based on the Euler hydrodynamics data of the many-body system. Within this framework, mesoscopic observables are classical random variables depending only on the fluctuating conserved densities, and Euler-scale fluctuations are obtained by deterministically transporting thermodynamic fluctuations via the Euler hydrodynamics. Using the BMFT, we show that long-range correlations in space generically develop over time from long-wavelength inhomogeneous initial states in interacting models. This result, which we verify by numerical calculations, challenges the long-held paradigm that at the Euler scale, fluid cells may be considered uncorrelated. We also show that the Gallavotti-Cohen fluctuation theorem for non-equilibrium ballistic transport follows purely from time-reversal invariance of the Euler hydrodynamics. We check the validity of the BMFT by applying it to integrable systems, and in particular the hard-rod gas, with extensive simulations that confirm our analytical results.
description: v1: 47 pages, 5 figures. v2: 48 pages, 5 figures; generalized proof of the GCFT and the conclusion slightly expanded. v3: 80 pages, 5 figures; single column ver
Band bending inversion in Bi$_2$Se$_3$ nanostructures
Creators: name: Veyrat, Louis
name: Iacovella, Fabrice
name: Dufouleur, Joseph
name: Nowka, Christian
name: Funke, Hannes
name: Yang, Ming
name: Escoffier, Walter
name: Goiran, Michel
name: Buechner, Bernd
name: Hampel, Silke
name: Giraud, Romain
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Shubnikov-de-Haas oscillations were studied under high magnetic field in Bi$_2$Se$_3$ nanostructures grown by Chemical Vapor Transport, for different bulk carrier densities ranging from $3\times10^{19}\text{cm}^{-3}$ to $6\times10^{17}\text{cm}^{-3}$. The contribution of topological surface states to electrical transport can be identified and separated from bulk carriers and massive two-dimensional electron gas. Band bending is investigated, and a crossover from upward to downward band bending is found at low bulk density, as a result of a competition between bulk and interface doping. These results highlight the need to control electrical doping both in the bulk and at interfaces in order to study only topological surface states.
description: 6 pages, 4 figures
Enhancement of mobility in an interacting colloidal system under feedback control
Creators: name: Gernert, Robert
name: Klapp, Sabine H. L.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Feedback control schemes are a promising way to manipulate transport properties of driven colloidal suspensions. In the present article we suggest a feedback scheme to enhance the collective transport of colloidal particles with repulsive interactions through a one-dimensional tilted washboard potential. The control is modelled by a harmonic confining potential, mimicking an optical "trap", with the center of this trap moving with the (instantaneous) mean particle position. Our theoretical analysis is based on the Smoluchowski equation combined with Dynamical Density Functional Theory (DDFT) for systems with hard-core or ultra-soft (Gaussian) interactions. For either type of interaction we find that the feedback control can lead to an enhancement of the mobility by several orders of magnitude relative to the uncontrolled case. The largest effects occur for intermediate stiffness of the trap and large particle numbers. Moreover, in some regions of the parameter space the feedback control induces oscillations of the mean velocity. Finally, we show that the enhancement of mobility is robust against a small time delay in implementing the feedback control.
description: 10 pages, 10 figures
Asteroseismology of solar-type stars with K2
Creators: name: Chaplin, W. J.
name: Lund, M. N.
name: Handberg, R.
name: Basu, S.
name: Buchhave, L. A.
name: Campante, T. L.
name: Davies, G. R.
name: Huber, D.
name: Latham, D. W.
name: Latham, C. A.
name: Serenelli, A.
name: Antia, H. M.
name: Appourchaux, T.
name: Ball, W. H.
name: Benomar, O.
name: Casagrande, L.
name: Christensen-Dalsgaard, J.
name: Coelho, H. R.
name: Creevey, O. L.
name: Elsworth, Y.
name: Garc, R. A.
name: Gaulme, P.
name: Hekker, S.
name: Kallinger, T.
name: Karoff, C.
name: Kawaler, S. D.
name: Kjeldsen, H.
name: Lundkvist, M. S.
name: Marcadon, F.
name: Mathur, S.
name: Miglio, A.
name: Mosser, B.
name: R, C.
name: Roxburgh, I. W.
name: Aguirre, V. Silva
name: Stello, D.
name: Verma, K.
name: White, T. R.
name: Bedding, T. R.
name: Barclay, T.
name: Buzasi, D. L.
name: Deheuvels, S.
name: Gizon, L.
name: Houdek, G.
name: Howell, S. B.
name: Salabert, D.
name: Soderblom, D. R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present the first detections by the NASA K2 Mission of oscillations in solar-type stars, using short-cadence data collected during K2 Campaign\,1 (C1). We understand the asteroseismic detection thresholds for C1-like levels of photometric performance, and we can detect oscillations in subgiants having dominant oscillation frequencies around $1000\,\rm μHz$. Changes to the operation of the fine-guidance sensors are expected to give significant improvements in the high-frequency performance from C3 onwards. A reduction in the excess high-frequency noise by a factor of two-and-a-half in amplitude would bring main-sequence stars with dominant oscillation frequencies as high as ${\simeq 2500}\,\rm μHz$ into play as potential asteroseismic targets for K2.
description: Accepted for publication in PASP; 16 pages, 2 figures
Effect of gate voltage on spin transport along $α$-helical protein
Creators: name: Pan, Ting-Rui
name: Guo, Ai-Min
name: Sun, Qing-Feng
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Recently, the chiral-induced spin selectivity in molecular systems has attracted extensive interest among the scientific communities. Here, we investigate the effect of the gate voltage on spin-selective electron transport through the $α$-helical peptide/protein molecule contacted by two nonmagnetic electrodes. Based on an effective model Hamiltonian and the Landauer-Büttiker formula, we calculate the conductance and the spin polarization under an external electric field which is perpendicular to the helix axis of the $α$-helical peptide/protein molecule. Our results indicate that both the magnitude and the direction of the gate field have a significant effect on the conductance and the spin polarization. The spin filtration efficiency can be improved by properly tuning the gate voltage, especially in the case of strong dephasing regime. And the spin polarization increases monotonically with the molecular length without the gate voltage, which is consistent with the recent experiment, and presents oscillating behavior in the presence of the gate voltage. In addition, the spin selectivity is robust against the dephasing, the on-site energy disorder, and the space angle disorder under the gate voltage. Our results could motivate further experimental and theoretical works on the chiral-based spin selectivity in molecular systems.
description: 8 pages, 7 figures
Transcriptional response of rat frontal cortex following acute In Vivo exposure to the pyrethroid insecticides permethrin and deltamethrin
Creators: name: Li, Zhen
name: Wright, Fred A.
name: Harrill, Joshua A
Publisher: name: BioMed Central Ltd
Year: 2008

description: Abstract Background Pyrethroids are neurotoxic pesticides that interact with membrane bound ion channels in neurons and disrupt nerve function. The purpose of this study was to characterize and explore changes in gene expression that occur in the rat frontal cortex, an area of CNS affected by pyrethroids, following an acute low-dose exposure. Results Rats were acutely exposed to either deltamethrin (0.3 - 3 mg/kg) or permethrin (1 - 100 mg/kg) followed by collection of cortical tissue at 6 hours. The doses used range from those that cause minimal signs of intoxication at the behavioral level to doses well below apparent no effect levels in the whole animal. A statistical framework based on Parallel linear (SAM) and isotonic regression (PIR) methods identified 95 and 53 probe sets as dose-responsive. The PIR analysis was most sensitive for detecting transcripts with changes in expression at the NOAEL dose. A sub-set of genes (Camk1g, Ddc, Gpd3, c-fos and Egr1) was then confirmed by qRT-PCR and examined in a time course study. Changes in mRNA levels were typically less than 3-fold in magnitude across all components of the study. The responses observed are consistent with pyrethroids producing increased neuronal excitation in the cortex following a low-dose in vivo exposure. In addition, Significance Analysis of Function and Expression (SAFE) identified significantly enriched gene categories common for both pyrethroids, including some relating to branching morphogenesis. Exposure of primary cortical cell cultures to both compounds resulted in an increase (~25%) in the number of neurite branch points, supporting the results of the SAFE analysis. Conclusion In the present study, pyrethroids induced changes in gene expression in the frontal cortex near the threshold for decreases in ambulatory motor activity in vivo. The penalized regression methods performed similarly in detecting dose-dependent changes in gene transcription. Finally, SAFE analysis of gene expression data identified branching morphogenesis as a biological process sensitive to pyrethroids and subsequent in vitro experiments confirmed this predicted effect. The novel findings regarding pyrethroid effects on branching morphogenesis indicate these compounds may act as developmental neurotoxicants that affect normal neuronal morphology.
Free boundary problem for a gas bubble in a liquid, and exponential stability of the manifold of spherically symmetric equilibria
Creators: name: Lai, Chen-Chih
name: Weinstein, Michael I.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We consider the dynamics of a gas bubble immersed in an incompressible fluid of fixed temperature, and focus on the relaxation of an expanding and contracting spherically symmetric bubble due to thermal effects. We study two models, both systems of PDEs with an evolving free boundary: the full mathematical model as well as an approximate model, arising for example in the study of sonoluminescence. For fixed physical parameters (surface tension of the gas-liquid interface, liquid viscosity, thermal conductivity of the gas, etc.), both models share a family of spherically symmetric equilibria, smoothly parametrized by the mass of the gas bubble. Our main result concerns the approximate model. We prove the nonlinear asymptotic stability of the manifold of equilibria with respect to small spherically symmetric perturbations. The rate of convergence is exponential in time. To prove this result we first prove a weak form of nonlinear asymptotic stability -- with no explicit rate of time-decay -- using the energy dissipation law, and then, via a center manifold analysis, bootstrap the weak time-decay to exponential time-decay. We also study the uniqueness of the family of spherically symmetric equilibria within each model. The family of spherically symmetric equilibria captures all regular spherically symmetric equilibria of the approximate system. However within the full model, this family is embedded in a larger family of spherically symmetric solutions. For the approximate system, we prove that all equilibrium bubbles are spherically symmetric, by an application of Alexandrov's theorem on closed surfaces of constant mean curvature.
description: Regularity assumption is needed in part (2) of Proposition 4.3. In other words, the family of spherically symmetric equilibria captures all "regular" spherically symmetric equilibria of the approximate system
Destruction of surface states of ($d_{zx}+id_{yz}$)-wave superconductor by surface roughness: application to Sr$_2$RuO$_4$
Creators: name: Suzuki, Shu-Ichiro
name: Ikegaya, Satoshi
name: Golubov, Alexander A.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The fragility of the chiral surface current of ($d_{zx}+id_{yz}$)-wave superconductor, a potential candidate for Sr$_2$RuO$_4$, against surface roughness is demonstrated utilizing the quasiclassical Eilenberger theory. Comparing the chiral surface currents of ($d_{zx}+id_{yz}$)-wave and ($p_{x}+ip_{y}$)-wave pairings, we conclude the chiral current for ($d_{zx}+id_{yz}$)-wave SC is much more fragile than that for the ($p_x+ip_y$)-wave one. The difference can be understood in terms of the orbital symmetry of the odd-frequency Cooper pairs arising at the surface. Our results show the ($d_{zx}+id_{yz}$)-wave scenario can explain the null spontaneous magnetization in Sr$_2$RuO$_4$ experiments.
description: 6 pages, 5 figures
Hypersymmetry bounds and three-dimensional higher-spin black holes
Creators: name: Henneaux, Marc
name: Perez, Alfredo
name: Tempo, David
name: Troncoso, Ricardo
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We investigate the hypersymmetry bounds on the higher spin black hole parameters that follow from the asymptotic symmetry superalgebra in higher-spin anti-de Sitter gravity in three spacetime dimensions. We consider anti-de Sitter hypergravity for which the analysis is most transparent. This is a $osp(1\vert 4) \oplus osp(1\vert 4)$ Chern-Simons theory which contains, besides a spin-$2$ field, a spin-$4$ field and a spin-$5/2$ field. The asymptotic symmetry superalgebra is then the direct sum of two-copies of the hypersymmetric extension $W_{(2,\frac52,4)}$ of $W_{(2,4)}$, which contains fermionic generators of conformal weight $5/2$ and bosonic generators of conformal weight $4$ in addition to the Virasoro generators. Following standard methods, we derive bounds on the conserved charges from the anticommutator of the hypersymmetry generators. The hypersymmetry bounds are nonlinear and are saturated by the hypersymmetric black holes, which turn out to possess $1/4$-hypersymmetry and to be "extreme", where extremality can be defined in terms of the entropy: extreme black holes are those that fulfill the extremality bounds beyond which the entropy ceases to be a real function of the black hole parameters. We also extend the analysis to other $sp(4)$-solitonic solutions which are maximally (hyper)symmetric.
description: 26 pages
Gabor fusion frames generated by difference sets
Creators: name: Bojarovska, Irena
name: Paternostro, Victoria
Publisher: name: arXiv
Year: 2015
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 42C15, 42A38, 94A12, 65T50

description: Collections of time- and frequency-shifts of suitably chosen generators (Alltop or random vectors) proved successful for many applications in sparse recovery and related fields. It was shown in \cite{xia2005achieving} that taking a characteristic function of a difference set as a generator, and considering only the frequency shifts, gives an equaingular tight frame for the subspace they span. In this paper, we investigate the system of all $N^2$ time- and frequency-shifts of a difference set in dimension $N$ via the mutual coherence, and compare numerically its sparse recovery effectiveness with Alltop and random generators. We further view this Gabor system as a fusion frame, show that it is optimally sparse, and moreover an equidistant tight fusion frame, i.e. it is an optimal Grassmannian packing.
description: 14 pages, 3 figures
Differential Hanbury-Brown-Twiss for an exact hydrodynamic model with rotation
Creators: name: Velle, S.
name: Csernai, L. P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study an exact rotating and expanding solution of the fluid dynamical model of heavy ion reactions, that take into account the rate of slowing down of the rotation due to the longitudinal and transverse expansion of the system. The parameters of the model are set on the basis of realistic 3+1D fluid dynamical calculation at TeV energies, where the rotation is enhanced by the build up of the Kelvin Helmholtz Instability in the flow.
description: 4 Pages, 7 figures, to be published in PRC
Discussion of the Gear-Gupta-Leimkuhler method for impacting mechanical systems
Creators: name: Schoeder, Svenja
name: Ulbrich, Heinz
name: Schindler, Thorsten
Publisher: name: arXiv
Year: 2015
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: In multibody simulation, the Gear-Gupta-Leimkuhler method for only persistent contacts enforces constraints on position and velocity level at the same time. It yields a robust numerical discretization of differential algebraic equations avoiding the drift-off effect. In this work, we carry over these benefits to impacting mechanical systems with unilateral constraints. For this kind of a mechanical system, adding the position level constraint to a timestepping scheme on velocity level even maintains physical consistency of the impulsive discretization. Hence, we propose a timestepping scheme based on Moreau's midpoint rule which enables to achieve not only compliance of the impact law but also of the non-penetration constraint. The choice of a decoupled and consecutive evaluation of the respective constraints can be interpreted as a not energy-consistent projection to the non-penetration constraint at the end of each time step. It is the implicit coupling of position and velocity level which yields satisfactory results. An implicit evaluation of the right hand side improves stability properties without additional cost. With the prox function formulation, the overall set of nonsmooth equations is solved by a Newton scheme. Results from simulations of a slider-crank mechanism with unilateral constraints demonstrate the capability of our approach.
Stochastic models of stem cells and their descendants under different criticality assumptions
Creators: name: Nguyen, Nam H.
name: Kimmel, Marek
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Science Policy

description: We study time continuous branching processes with exponentially distributed lifetimes, with two types of cells that proliferate according to binary fission. A range of possible system dynamics are considered, each of which is characterized by the mutation rate of the original cells and the survival probability of the altered cells’ progeny. For each system, we derive a closed-form expression for the joint probability generating function of cell counts, and perform asymptotic analysis on the behaviors of the cell population with particular focus on probability of extinction. Part of our results confirms known properties of branching processes using a different approach while other are original. While the model is best suited for modeling the fate of differentiating stem cells, we discuss other scenarios in which these system dynamics may be applicable in real life. We also discuss the history of the subject.
Dynamical traps in Wang-Landau sampling of continuous systems: Mechanism and solution
Creators: name: Koh, Yang Wei
name: Sim, Adelene Y. L.
name: Lee, Hwee Kuan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study the mechanism behind dynamical trappings experienced during Wang-Landau sampling of continuous systems reported by several authors. Trapping is caused by the random walker coming close to a local energy extremum, although the mechanism is different from that of critical slowing down encountered in conventional molecular dynamics or Monte Carlo simulations. When trapped, the random walker misses entire or even several stages of Wang-Landau modification factor reduction, leading to inadequate sampling of configuration space and a rough density-of-states even though the modification factor has been reduced to very small values. Trapping is dependent on specific systems, the choice of energy bins, and Monte Carlo step size, making it highly unpredictable. A general, simple, and effective solution is proposed where the configurations of multiple parallel Wang-Landau trajectories are inter-swapped to prevent trapping. We also explain why swapping frees the random walker from such traps. The efficacy of the proposed algorithm is demonstrated.