cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Phenomenology of TMDs
Creators: name: Melis, Stefano
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We present a review of current Transverse Momentum Dependent (TMD) phenomenology focusing our attention on the unpolarized TMD parton distribution function and the Sivers function. The paper introduces and comments about the new Collins-Soper-Sterman (CSS) TMD evolution formalism. We make use of a selection of results obtained by several groups to illustrate the achievements and the failures of the simple Gaussian approach and the TMD CSS evolution formalism.
description: 10 pages, 5 figures, to appear in the proceedings of the TRANSVERSITY 2014, Chia, Italy, 9-13 June, 2014
Memristive Networks: from Graph Theory to Statistical Physics
Creators: name: Zegarac, Ana
name: Caravelli, Francesco
Publisher: name: arXiv
Year: 2019
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: We provide an introduction to a very specific toy model of memristive networks, for which an exact differential equation for the internal memory which contains the Kirchhoff laws is known. In particular, we highlight how the circuit topology enters the dynamics via an analysis of directed graph. We try to highlight in particular the connection between the asymptotic states of memristors and the Ising model, and the relation to the dynamics and statics of disordered systems.
description: 7 pages double columns; invited EPL Perspectives paper
Anomalous Pressure Dependence of magnetic Ordering Temperature in Tb to 141 GPa: Comparison with Gd and Dy
Creators: name: Lim, J.
name: Fabbris, G.
name: Haskel, D.
name: Schilling, J. S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: In previous studies the pressure dependence of the magnetic ordering temperature $T_{\text{o}}$ of Dy was found to exhibit a sharp increase above its volume collapse pressure of 73 GPa, appearing to reach temperatures well above ambient at 157 GPa. In a search for a second such lanthanide, electrical resistivity measurements were carried out on neighboring Tb to 141 GPa over the temperature range 3.8 - 295 K. Below Tb's volume collapse pressure of 53 GPa, the pressure dependence $T_{\text{o}}(P)$ mirrors that of both Dy and Gd. However, at higher pressures $T_{\text{o}}(P)$ for Tb becomes highly anomalous. This result, together with the very strong suppression of superconductivity by dilute Tb ions in Y, suggests that extreme pressure transports Tb into an unconventional magnetic state with an anomalously high magnetic ordering temperature.
Application of high throughput in vitro metabolomics for hepatotoxicity mode of action characterization and mechanistic-anchored point of departure derivation: a case study with nitrofurantoin
Creators: name: Ramirez-Hincapie, Sabina
name: Birk, Barbara
name: Ternes, Philipp
name: Giri, Varun
name: Zickgraf, Franziska Maria
name: Haake, Volker
name: Herold, Michael
name: Kamp, Hennicke
name: Driemert, Peter
name: Landsiedel, Robert
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: Metabolomics in vitro
subject: High throughput
subject: Nitrofurantoin
subject: Hepatotoxicity
subject: New approach methodologies
subject: Next generation risk assessment
subject: Point of departure
subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften

description: Omics techniques have been increasingly recognized as promising tools for Next Generation Risk Assessment. Targeted metabolomics offer the advantage of providing readily interpretable mechanistic information about perturbed biological pathways. In this study, a high-throughput LC–MS/MS-based broad targeted metabolomics system was applied to study nitrofurantoin metabolic dynamics over time and concentration and to provide a mechanistic-anchored approach for point of departure (PoD) derivation. Upon nitrofurantoin exposure at five concentrations (7.5 µM, 15 µM, 20 µM, 30 µM and 120 µM) and four time points (3, 6, 24 and 48 h), the intracellular metabolome of HepG2 cells was evaluated. In total, 256 uniquely identified metabolites were measured, annotated, and allocated in 13 different metabolite classes. Principal component analysis (PCA) and univariate statistical analysis showed clear metabolome-based time and concentration effects. Mechanistic information evidenced the differential activation of cellular pathways indicative of early adaptive and hepatotoxic response. At low concentrations, effects were seen mainly in the energy and lipid metabolism, in the mid concentration range, the activation of the antioxidant cellular response was evidenced by increased levels of glutathione (GSH) and metabolites from the de novo GSH synthesis pathway. At the highest concentrations, the depletion of GSH, together with alternations reflective of mitochondrial impairments, were indicative of a hepatotoxic response. Finally, a metabolomics-based PoD was derived by multivariate PCA using the whole set of measured metabolites. This approach allows using the entire dataset and derive PoD that can be mechanistically anchored to established key events. Our results show the suitability of high throughput targeted metabolomics to investigate mechanisms of hepatoxicity and derive point of departures that can be linked to existing adverse outcome pathways and contribute to the development of new ones.
Additional file 1 of Using optimal control to understand complex metabolic pathways
Creators: name: Tsiantis, Nikolaos
name: Banga, Julio R.
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Computational Biology

description: Additional file 1. Solution details for case study LPN3B.
Theoretical evaluation on the temperature dependence of magnetic anisotropy constants of Nd2Fe14B - Effects of exchange field and crystal field strength -
Creators: name: Sasaki, Ryo
name: Miura, Daisuke
name: Sakuma, Akimasa
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: To identify the possible mechanism of coercivity (Hc) degradation of Nd-Fe-B sintered magnets, we study the roles of the exchange field acting on the 4f electrons in Nd ions and theoretically investigate how the variation of the exchange field affects the values of the magnetic anisotropy constants K1 and K2. We find that, with decreasing exchange field strength, both values decrease as a result of the lower asphericity of the 4f electron cloud, indicating that the local anisotropy constants might become small around the grain boundaries where the exchange fields are decreased owing to the smaller coordination number.
description: 7 pages, 4 figures
On the (K.2) supercongruence of Van Hamme
Creators: name: Osburn, Robert
name: Zudilin, Wadim
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: Primary: 11B65, Secondary: 33C20, 33F10

description: We prove the last remaining case of the original 13 Ramanujan-type supercongruence conjectures due to Van Hamme from 1997. The proof utilizes classical congruences and a WZ pair due to Guillera. Additionally, we mention some future directions concerning this type of supercongruence.
description: 6 pages, to appear in the Journal of Mathematical Analysis and Applications
Identification of Threat Regions From a Dynamic Occupancy Grid Map for Situation-Aware Environment Perception
Creators: name: Henning, Matti
name: Strohbeck, Jan
name: Buchholz, Michael
name: Dietmayer, Klaus
Publisher: name: arXiv
Year: 2022
Subjects: subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: The advance towards higher levels of automation within the field of automated driving is accompanied by increasing requirements for the operational safety of vehicles. Induced by the limitation of computational resources, trade-offs between the computational complexity of algorithms and their potential to ensure safe operation of automated vehicles are often encountered. Situation-aware environment perception presents one promising example, where computational resources are distributed to regions within the perception area that are relevant for the task of the automated vehicle. While prior map knowledge is often leveraged to identify relevant regions, in this work, we present a lightweight identification of safety-relevant regions that relies solely on online information. We show that our approach enables safe vehicle operation in critical scenarios, while retaining the benefits of non-uniformly distributed resources within the environment perception.
description: Accepted for publication at the 25th IEEE International Conference on Intelligent Transportation Systems 2022. V2: added IEEE copyright notice V3: Added DOI
Edge states and integer quantum Hall effect in topological insulator thin films
Creators: name: Zhang, Song-Bo
name: Lu, Hai-Zhou
name: Shen, Shun-Qing
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The integer quantum Hall effect is a topological state of quantum matter in two dimensions, and has recently been observed in three-dimensional topological insulator thin films. Here we study the Landau levels and edge states of surface Dirac fermions in topological insulators under strong magnetic field. We examine the formation of the quantum plateaux of the Hall conductance and find two different patterns, in one pattern the filling number covers all integers while only odd integers in the other. We focus on the quantum plateau closest to zero energy and demonstrate the breakdown of the quantum spin Hall effect resulting from structure inversion asymmetry. The phase diagrams of the quantum Hall states are presented as functions of magnetic field, gate voltage and chemical potential. This work establishes an intuitive picture of the edge states to understand the integer quantum Hall effect for Dirac electrons in topological insulator thin films.
description: 10 pages, 5 figures
Designing $π$-stacked molecular structures to control heat transport through molecular junctions
Creators: name: Kiršanskas, Gediminas
name: Li, Qian
name: Flensberg, Karsten
name: Solomon, Gemma C.
name: Leijnse, Martin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We propose and analyze a new way of using $π$ stacking to design molecular junctions that either enhance or suppress a phononic heat current, but at the same time remain conductors for an electric current. Such functionality is highly desirable in thermoelectric energy converters, as well as in other electronic components where heat dissipation should be minimized or maximized. We suggest a molecular design consisting of two masses coupled to each other with one mass coupled to each lead. By having a small coupling (spring constant) between the masses, it is possible to either reduce, or perhaps more surprisingly enhance the phonon conductance. We investigate a simple model system to identify optimal parameter regimes and then use first principle calculations to extract model parameters for a number of specific molecular realizations, confirming that our proposal can indeed be realized using standard molecular building blocks.
description: 5 pages + supplemental material, 3 figures
Absorption of Fermionic Dark Matter by Nuclear Targets
Creators: name: Dror, Jeff A.
name: Elor, Gilly
name: McGehee, Robert
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Absorption of fermionic dark matter leads to a range of distinct and novel signatures at dark matter direct detection and neutrino experiments. We study the possible signals from fermionic absorption by nuclear targets, which we divide into two classes of four Fermi operators: neutral and charged current. In the neutral current signal, dark matter is absorbed by a target nucleus and a neutrino is emitted. This results in a characteristically different nuclear recoil energy spectrum from that of elastic scattering. The charged current channel leads to induced $β$ decays in isotopes which are stable in vacuum as well as shifts of the kinematic endpoint of $ β$ spectra in unstable isotopes. To confirm the possibility of observing these signals in light of other constraints, we introduce UV completions of example higher dimensional operators that lead to fermionic absorption signals and study their phenomenology. Most prominently, dark matter which exhibits fermionic absorption signals is necessarily unstable leading to stringent bounds from indirect detection searches. Nevertheless, we find a large viable parameter space in which dark matter is sufficiently long lived and detectable in current and future experiments.
description: 30 pages plus appendices, 8 figures, 3 tables. v2: published in JHEP with minor revisions (no change to results)
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies
Creators: name: Matentzoglu, Nicolas
name: Goutte-Gattat, Damien
name: Tan, Shawn Zheng Kai
name: Balhoff, James P.
name: Carbon, Seth
name: Caron, Anita R.
name: Duncan, William D.
name: Flack, Joe E.
name: Haendel, Melissa
name: Harris, Nomi L.
name: Hogan, William R
name: Hoyt, Charles Tapley
name: Jackson, Rebecca C.
name: Kim, HyeongSik
name: Kir, Huseyin
name: Larralde, Martin
name: McMurry, Julie A.
name: Overton, James A.
name: Peters, Bjoern
name: Pilgrim, Clare
name: Stefancsik, Ray
name: Robb, Sofia MC
name: Toro, Sabrina
name: Vasilevsky, Nicole A
name: Walls, Ramona
name: Mungall, Christopher J.
name: Osumi-Sutherland, David
Publisher: name: arXiv
Year: 2022
Subjects: subject: Databases (cs.DB)
subject: FOS: Computer and information sciences

description: Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking, and dependency management. To manage these processes, a diverse set of tools is required, from command line utilities to powerful ontology engineering environments such as ROBOT. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardising release practices and metadata, and establishing shared quality standards, are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardised, customisable, and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice, and describe how we envision it driving standardisation efforts in our community.
description: 19 pages, 2 supplementary tables, 1 supplementary figure
Some new CAT(0) free-by-cyclic groups
Creators: name: Lyman, Rylee Alanza
Publisher: name: arXiv
Year: 2019
Subjects: subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 20F65 (Primary) 20F67, 20E08, 57M07 (Secondary)

description: We show the existence of several new infinite families of polynomially-growing automorphisms of free groups whose mapping tori are CAT(0) free-by-cyclic groups. Such mapping tori are thick, and thus not relatively hyperbolic. These are the first families comprising infinitely many examples for each rank of the nonabelian free group; they contrast strongly with Gersten's example of a thick free-by-cyclic group which cannot be a subgroup of a CAT(0) group.
description: 7 pages, 2 figures; v2: the original paper has been split in two, with the other half (containing construction of train track maps on graphs of groups) to appear; v3: minor revisions according to referee comments
Additional file 3 of Using optimal control to understand complex metabolic pathways
Creators: name: Tsiantis, Nikolaos
name: Banga, Julio R.
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Computational Biology

description: Additional file 3. Solution details for case study BSUB.
New findings of Prototherium ausetanum (Mammalia, Pan-Sirenia) from paving stones in Girona (Catalonia, Spain)?
Creators: name: Voss, Manja
name: Hampe, Oliver
name: Mahlow, Kristin
name: Vilanova, Joan C.
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: 3D-visualisation
subject: CT-scanning
subject: Eocene
subject: morphology
subject: taxonomy
subject: urban fossil
subject: 500 Naturwissenschaften und Mathematik::560 Fossilien, Paläontologie::560 Paläontologie, Paläozoologie

description: Taxonomic and morphological approaches on Eocene sirenians from Catalonia (Spain) benefit from a newly discovered specimen found in a quite unusual locality, the pedestrian zone in the city of Girona. Two fossil-bearing limestone slabs from middle Eocene (Bartonian) layers of a quarry in the wider surrounding area north-west of Barcelona, were CT-scanned in the Clínica Girona to enhance more detailed investigations. Post-processing of the scans and, as far as possible, 3D-reconstruction of the preserved elements in the slabs was performed at Museum für Naturkunde Berlin. Thereby, a skull of a Dugong specimen was used as a reference point. Based on the combined analysis of macroscopic and CT-data, the specimen most likely represents Prototherium ausetanum Balaguer & Alba, 2016 and complements the available information of the holotype and hitherto only known specimen of that species. The Girona specimen is an adult, but small individual that corroborates P. ausetanum as a generally small-sized species compared to other known Prototherium taxa.
Subspace Estimation from Unbalanced and Incomplete Data Matrices: $\ell_{2,\infty}$ Statistical Guarantees
Creators: name: Cai, Changxiao
name: Li, Gen
name: Chi, Yuejie
name: Poor, H. Vincent
name: Chen, Yuxin
Publisher: name: arXiv
Year: 2019
Subjects: subject: Statistics Theory (math.ST)
subject: Information Theory (cs.IT)
subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: This paper is concerned with estimating the column space of an unknown low-rank matrix $\boldsymbol{A}^{\star}\in\mathbb{R}^{d_{1}\times d_{2}}$, given noisy and partial observations of its entries. There is no shortage of scenarios where the observations -- while being too noisy to support faithful recovery of the entire matrix -- still convey sufficient information to enable reliable estimation of the column space of interest. This is particularly evident and crucial for the highly unbalanced case where the column dimension $d_{2}$ far exceeds the row dimension $d_{1}$, which is the focal point of the current paper. We investigate an efficient spectral method, which operates upon the sample Gram matrix with diagonal deletion. While this algorithmic idea has been studied before, we establish new statistical guarantees for this method in terms of both $\ell_{2}$ and $\ell_{2,\infty}$ estimation accuracy, which improve upon prior results if $d_{2}$ is substantially larger than $d_{1}$. To illustrate the effectiveness of our findings, we derive matching minimax lower bounds with respect to the noise levels, and develop consequences of our general theory for three applications of practical importance: (1) tensor completion from noisy data, (2) covariance estimation / principal component analysis with missing data, and (3) community recovery in bipartite graphs. Our theory leads to improved performance guarantees for all three cases.
description: Accepted to Annals of Statistics
On geodesics with negative energies in the ergoregions of dirty black holes
Creators: name: Zaslavskii, O. B.
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We consider behavior of equatorial geodesics with the negative energy in the ergoregion of a generic rotating "dirty" (surrounded by matter) black hole. It is shown that under very simple and generic conditions on the metric coefficients, there are no such circular orbits. This entails that such geodesic must originate and terminate under the event horizon. These results generalize the observation made for the Kerr metric in A. A. Grib, Yu. V. Pavlov, and V. D. Vertogradov, Mod. Phys. Lett. 29, 1450110 (2014) [arXiv:1304.7360].
description: 6 pages
Les Houches 2021: Physics at TeV Colliders: Report on the Standard Model Precision Wishlist
Creators: name: Huss, Alexander
name: Huston, Joey
name: Jones, Stephen
name: Pellen, Mathieu
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Les Houches activities in 2021 were truncated due to the lack of an in-person component. However, given the rapid progress in the field, and the restart of the LHC, we wanted to continue the bi-yearly tradition of updating the standard model precision wishlist. If nothing else, this will keep us from having even more work to do at Les Houches 2023.
description: 81 pages, 4 tables, 848 references. Matches published version
Using pERK immunostaining to quantify neuronal activity induced by stress in zebrafish larvae
Creators: name: Corradi, Laura
name: Zaupa, Margherita
name: Sawamiphak, Suphansa
name: Filosa, Alessandro
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: Microscopy
subject: Model organisms
subject: Neuroscience
subject: Behavior
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: The larval zebrafish has emerged as a very useful model organism to study the neuronal circuits controlling neuroendocrine and behavioral responses to stress. This protocol describes how to expose zebrafish larvae to hyperosmotic stress and test whether candidate populations of neurons are activated or inhibited by the stressor using a relatively rapid immunofluorescence staining approach. This approach takes advantage of the phosphorylation of the extracellular signal-regulated kinase (ERK) upon neuronal activation. For complete details on the use and execution of this protocol, please refer to Corradi et al. (2022).
Additional file 2 of Using optimal control to understand complex metabolic pathways
Creators: name: Tsiantis, Nikolaos
name: Banga, Julio R.
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Computational Biology

description: Additional file 2. Solution details for case study SC.
Global properties of vector fields on compact Lie groups in Komatsu classes. II. Normal forms
Creators: name: Kirilov, Alexandre
name: de Moraes, Wagner Augusto Almeida
name: Ruzhansky, Michael
Publisher: name: arXiv
Year: 2019
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: Primary 35R03, 34C20, Secondary 35H10, 22E30

description: Let $G_1$ and $G_2$ be compact Lie groups, $X_1 \in \mathfrak{g}_1$, $X_2 \in \mathfrak{g}_2$ and consider the operator \begin{equation*} L_{aq} = X_1 + a(x_1)X_2 + q(x_1,x_2), \end{equation*} where $a$ and $q$ are ultradifferentiable functions in the sense of Komatsu, and $a$ is real-valued. We characterize completely the global hypoellipticity and the global solvability of $L_{aq}$ in the sense of Komatsu. For this, we present a conjugation between $L_{aq}$ and a constant-coefficient operator that preserves these global properties in Komatsu classes. We also present examples of globally hypoelliptic and globally solvable operators on $\mathbb{T}^1\times \mathbb{S}^3$ and $\mathbb{S}^3\times \mathbb{S}^3$ in the sense of Komatsu. In particular, we give examples of differential operators which are not globally $C^\infty$-solvable, but are globally solvable in Gevrey spaces.
description: 23 pages. arXiv admin note: text overlap with arXiv:1910.01922, arXiv:1910.00059
Dark matter from primordial black holes would hold charge
Creators: name: Araya, Ignacio J.
name: Padilla, Nelson D.
name: Rubio, Marcelo E.
name: Sureda, Joaquín
name: Magaña, Juan
name: Osorio, Loreto
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We explore the possibility that primordial black holes (PBHs) contain electric charge down to the present day. We find that PBHs should hold a non-zero net charge at their formation, due to either Poisson fluctuations at horizon crossing or high-energy particle collisions. Although initial charge configurations are subject to fast discharge processes through particle accretion or quantum particle emission, we show that maximally rotating PBHs could produce magnetic fields able to shield them from discharge. Moreover, given that electrons are the lightest and fastest charge carriers, we show that the plasma within virialised dark matter haloes can endow PBHs with net negative charge. We report charge-to-mass ratios between $10^{-31}\,C/\mbox{kg}$ and $10^{-15}\,C/\mbox{kg}$ for PBHs within the mass windows that allow them to constitute the entirety of the dark matter in the Universe.
description: 25 pages, 6 figures, accepted in JCAP
Combined shared and distributed memory ab-initio computations of molecular-hydrogen systems in the correlated state: process pool solution and two-level parallelism
Creators: name: Biborski, Andrzej
name: Kądzielawa, Andrzej P.
name: Spałek, Józef
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: An efficient computational scheme devised for investigations of ground state properties of the electronically correlated systems is presented. As an example, $(H_{2})_{n}$ chain is considered with the long-range electron-electron interactions taken into account. The implemented procedure covers: (i) single-particle Wannier wave-function basis construction in the correlated state, (ii) microscopic parameters calculation, and (iii) ground state energy optimization. The optimization loop is based on highly effective process-pool solution - specific root-workers approach. The hierarchical, two-level parallelism was applied: both shared (by use of Open Multi-Processing) and distributed (by use of Message Passing Interface) memory models were utilized. We discuss in detail the feature that such approach results in a substantial increase of the calculation speed reaching factor of $300$ for the fully parallelized solution.
description: 14 pages, 10 figures, 1 table
RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein–RNA Cross-Linking/Mass Spectrometry Data
Creators: name: Sarnowski, Chris P.
name: Götze, Michael
name: Leitner, Alexander
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: cross-linking mass spectrometry
subject: protein−RNA interactions
subject: ribonucleoproteins
subject: XL-MS
subject: XL-MS software
subject: false discovery rate estimation
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Cross-linking and mass spectrometry (XL-MS) workflows are increasingly popular techniques for generating low-resolution structural information about interacting biomolecules. xQuest is an established software package for analysis of protein–protein XL-MS data, supporting stable isotope-labeled cross-linking reagents. Resultant paired peaks in mass spectra aid sensitivity and specificity of data analysis. The recently developed cross-linking of isotope-labeled RNA and mass spectrometry (CLIR-MS) approach extends the XL-MS concept to protein–RNA interactions, also employing isotope-labeled cross-link (XL) species to facilitate data analysis. Data from CLIR-MS experiments are broadly compatible with core xQuest functionality, but the required analysis approach for this novel data type presents several technical challenges not optimally served by the original xQuest package. Here we introduce RNxQuest, a Python package extension for xQuest, which automates the analysis approach required for CLIR-MS data, providing bespoke, state-of-the-art processing and visualization functionality for this novel data type. Using functions included with RNxQuest, we evaluate three false discovery rate control approaches for CLIR-MS data. We demonstrate the versatility of the RNxQuest-enabled data analysis pipeline by also reanalyzing published protein–RNA XL-MS data sets that lack isotope-labeled RNA. This study demonstrates that RNxQuest provides a sensitive and specific data analysis pipeline for detection of isotope-labeled XLs in protein–RNA XL-MS experiments.
Multi-kink topological terms and charge-binding domain-wall condensation induced symmetry-protected topological states: Beyond Chern-Simons/BF theory
Creators: name: Gu, Zheng-Cheng
name: Wang, Juven C.
name: Wen, Xiao-Gang
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum-disordering a discrete-symmetry breaking state by condensing domain-walls can lead to a trivial symmetric insulator state. In this work, we show that if we bind a 1D representation of the symmetry (such as a charge) to the intersection point of several domain walls, condensing such modified domain-walls can lead to a non-trivial symmetry-protected topological (SPT) state. This result is obtained by showing that the modified domain-wall condensed state has a non-trivial SPT invariant -- the symmetry-twist dependent partition function. We propose two different kinds of field theories that can describe the above mentioned SPT states. The first one is a Ginzburg-Landau-type non-linear sigma model theory, but with an additional multi-kink domain-wall topological term. Such theory has an anomalous $U^k(1)$ symmetry but an anomaly-free $Z_N^k$ symmetry. The second one is a gauge theory, which is beyond Abelian Chern-Simons/BF gauge theories. We argue that the two field theories are equivalent at low energies. After coupling to the symmetry twists, both theories produce the desired SPT invariant.
description: 22 pages, 8 figures, symmetry transformaition for the Ginzburg-Landau NL$\sigma$M is added in the introduction part, references added
SnapperGPS: Open Hardware for Energy-Efficient, Low-Cost Wildlife Location Tracking with Snapshot GNSS
Creators: name: Beuchert, Jonas
name: Matthes, Amanda
name: Rogers, Alex
Publisher: name: arXiv
Year: 2022
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Location tracking with global navigation satellite systems (GNSS), such as the GPS, is used in many applications, including the tracking of wild animals for research. Snapshot GNSS is a technique that only requires milliseconds of satellite signals to infer the position of a receiver. This is ideal for low-power applications such as animal tracking. However, there are few existing snapshot systems, none of which is open source. To address this, we developed SnapperGPS, a fully open-source, low-cost, and low-power location tracking system designed for wildlife tracking. SnapperGPS comprises three parts, all of which are open-source: (i) a small, low-cost, and low-power receiver; (ii) a web application to configure the receiver via USB; and (iii) a cloud-based platform for processing recorded data. This paper presents the hardware side of this project. The total component cost of the receiver is under $30, making it feasible for field work with restricted budgets and low recovery rates. The receiver records very short and low-resolution samples resulting in particularly low power consumption, outperforming existing systems. It can run for more than a year on a 40 mAh battery. We evaluated SnapperGPS in controlled static and dynamic tests in a semi-urban environment where it achieved median errors of 12 m. Additionally, SnapperGPS has already been deployed for two wildlife tracking studies on sea turtles and sea birds.
description: 17 pages, 9 figures, published in the Journal of Open Hardware (JOH)
Nonconvex Low-Rank Tensor Completion from Noisy Data
Creators: name: Cai, Changxiao
name: Li, Gen
name: Poor, H. Vincent
name: Chen, Yuxin
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (cs.LG)
subject: Information Theory (cs.IT)
subject: Optimization and Control (math.OC)
subject: Statistics Theory (math.ST)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: We study a noisy tensor completion problem of broad practical interest, namely, the reconstruction of a low-rank tensor from highly incomplete and randomly corrupted observations of its entries. While a variety of prior work has been dedicated to this problem, prior algorithms either are computationally too expensive for large-scale applications, or come with sub-optimal statistical guarantees. Focusing on "incoherent" and well-conditioned tensors of a constant CP rank, we propose a two-stage nonconvex algorithm -- (vanilla) gradient descent following a rough initialization -- that achieves the best of both worlds. Specifically, the proposed nonconvex algorithm faithfully completes the tensor and retrieves all individual tensor factors within nearly linear time, while at the same time enjoying near-optimal statistical guarantees (i.e. minimal sample complexity and optimal estimation accuracy). The estimation errors are evenly spread out across all entries, thus achieving optimal $\ell_{\infty}$ statistical accuracy. We have also discussed how to extend our approach to accommodate asymmetric tensors. The insight conveyed through our analysis of nonconvex optimization might have implications for other tensor estimation problems.
description: Accepted to Operations Research
Hybrid convergence of Kähler-Einstein measures
Creators: name: Pille-Schneider, Léonard
Publisher: name: arXiv
Year: 2019
Subjects: subject: Differential Geometry (math.DG)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: We compute the hybrid limit (in the sense of Boucksom-Jonsson) of the family of Kähler-Einstein volume forms on a degeneration of canonically polarized manifolds. The limit measure is a weighted sum of Dirac masses at divisorial valuations, determined by the natural algebro-geometric limit of the family. We also make some remarks on the non-archimedean Monge-Ampère operator and hybrid continuity of Kähler-Einstein potentials in this context.
Searches for massive neutrinos with mechanical quantum sensors
Creators: name: Carney, Daniel
name: Leach, Kyle G.
name: Moore, David C.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: Instrumentation and Detectors (physics.ins-det)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The development of quantum optomechanics now allows mechanical sensors with femtogram masses to be controlled and measured in the quantum regime. If the mechanical element contains isotopes that undergo nuclear decay, measuring the recoil of the sensor following the decay allows reconstruction of the total momentum of all emitted particles, including any neutral particles that may escape detection in traditional detectors. As an example, for weak nuclear decays the momentum of the emitted neutrino can be reconstructed on an event-by-event basis. We present the concept that a single nanometer-scale, optically levitated sensor operated with sensitivity near the standard quantum limit can search for heavy sterile neutrinos in the keV-MeV mass range with sensitivity significantly beyond existing constraints. We also comment on the possibility that mechanical sensors operated well into the quantum regime might ultimately reach the sensitivities required to provide an absolute measurement of the mass of the light neutrino states.
description: 11 pages + refs, 7 figures. v2: published version (+ an appendix containing a quantum model of the 3-body decay in a nanosphere)
Memristive and tunneling effects in 3D interconnected silver nanowires
Creators: name: Chopin, Chloé
name: De Wergifosse, Simon
name: Marchal, Nicolas
name: Van Velthem, Pascal
name: Piraux, Luc
name: Araujo, Flavio Abreu
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Due to their memristive properties nanowire networks are very promising for neuromorphic computing applications. Indeed, the resistance of such systems can evolve with the input voltage or current as it confers a synaptic behaviour to the device. Here, we propose a network of silver nanowires (Ag-NWs) which are grown in a nanopourous membrane with interconnected nanopores by electrodeposition. This bottom-up approach fabrication method gives a conducting network with a 3D architecture and a high density of Ag-NWs. The resulting 3D interconnected Ag-NW network exhibits a high initial resistance as well as a memristive behavior. It is expected to arise from the creation and the destruction of conducting silver filaments inside the Ag-NW network. Moreover, after several cycles of measurement, the resistance of the network switches from a high resistance regime, in the GOhm range, with a tunnel conduction to a low resistance regime, in the kOhm range.
description: 8 pages, 5 figures
Nanostructure Investigations of Nonlinear Differential Conductance in NdNiO$_3$ Thin Films
Creators: name: Hardy, Will J.
name: Ji, Heng
name: Mikheev, Evgeny
name: Stemmer, Susanne
name: Natelson, Douglas
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Transport measurements on thin films of NdNiO$_3$ reveal a crossover to a regime of pronounced nonlinear conduction below the well-known metal-insulator transition temperature. The evolution of the transport properties at temperatures well below this transition appears consistent with a gradual formation of a gap in the hole-like Fermi surface of this strongly correlated system. As $T$ is decreased below the nominal transition temperature, transport becomes increasily non-Ohmic, with a model of Landau-Zener breakdown becoming most suited for describing $I(V)$ characteristics as the temperature approaches 2~K.
description: 18 pages, 6 figures, accepted for publication in PRB
A note on boundary point principles for partial differential inequalities of elliptic type
Creators: name: Meyer, John Christopher
Publisher: name: arXiv
Year: 2019
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35B51, 35R45, 35B50, 35J15, 35J62

description: In this note we consider boundary point principles for partial differential inequalities of elliptic type. Firstly, we highlight the difference between conditions required to establish classical strong maximum principles and classical boundary point lemmas for second order linear elliptic partial differential inequalities. We highlight this difference by introducing a singular set in the domain where the coefficients of the partial differential inequality need not be defined, and in a neighborhood of which, can blow-up. Secondly, as a consequence, we establish a comparison-type boundary point lemma for classical elliptic solutions to quasi-linear partial differential inequalities. Thirdly, we consider tangency principles, for $C^1$ elliptic weak solutions to quasi-linear divergence structure partial differential inequalities. We highlight the necessity of certain hypotheses in the aforementioned results via simple examples.
description: 17 pages. No figures
Additional file 4 of Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP)
Creators: name: Mautner, Lena
name: Christin-Kirsty Baillie
name: Herold, Heike Marie
name: Volkwein, Wolfram
name: Guertler, Patrick
name: Eberle, Ute
name: Ackermann, Nikolaus
name: Sing, Andreas
name: Pavlovic, Melanie
name: Goerlich, Ottmar
name: Busch, Ulrich
name: Wassill, Lars
name: Huber, Ingrid
name: Baiker, Armin
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: 60506 Virology
subject: Computational Biology

description: Additional file 4: Figure S3. Specificity of the assay. SARS-CoV Frankfurt 1 RNA and nucleic acid extracts from 20 different samples from respiratory pathogens were tested with RT-LAMP targeting ORF8 (A) and N (B) to determine cross reactivity. For non-template control (NTC) PCR grade water was used.
High-Energy Neutrino Emission from Espresso-Reaccelerated Ions in Jets of Active Galactic Nuclei
Creators: name: Mbarek, Rostom
name: Caprioli, Damiano
name: Murase, Kohta
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present a bottom-up calculation of the flux of ultra-high energy cosmic rays (UHECRs) and high-energy neutrinos produced by powerful jets of active galactic nuclei (AGNs). By propagating test particles in 3D relativistic magnetohydrodynamic jet simulations, including a Monte Carlo treatment of sub-grid pitch-angle scattering and attenuation losses due to realistic photon fields, we study the spectrum and composition of the accelerated UHECRs and estimate the amount of neutrinos produced in such sources. We find that UHECRs may not be significantly affected by photodisintegration in AGN jets where the espresso mechanism efficiently accelerates particles, consistent with Auger's results that favor a heavy composition at the highest energies. Moreover, we present estimates and upper bounds for the flux of high-energy neutrinos expected from AGN jets. In particular, we find that: i) source neutrinos may account for a sizable fraction, or even dominate, the expected flux of cosmogenic neutrinos; ii) neutrinos from the beta-decay of secondary neutrons produced in nucleus photodisintegration end up in the TeV-PeV band observed by IceCube, but can hardly account for the observed flux; iii) UHECRs accelerated via the espresso mechanism lead to nearly isotropic neutrino emission, which suggests that nearby radio galaxies may be more promising as potential sources. We discuss our results in the light of multimessenger astronomy and current/future neutrino experiments.
description: 16 pages, 7 figures, ApJ, Figure 5 and 6 amended
Additional file 3 of Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP)
Creators: name: Mautner, Lena
name: Christin-Kirsty Baillie
name: Herold, Heike Marie
name: Volkwein, Wolfram
name: Guertler, Patrick
name: Eberle, Ute
name: Ackermann, Nikolaus
name: Sing, Andreas
name: Pavlovic, Melanie
name: Goerlich, Ottmar
name: Busch, Ulrich
name: Wassill, Lars
name: Huber, Ingrid
name: Baiker, Armin
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: 60506 Virology
subject: Computational Biology

description: Additional file 3: Figure S2. Determination of the sensitivity of the assay. Isolated RNA from SARS-CoV-2 infected Vero cell culture supernatant was quantified using RT-ddPCR and serially diluted to determine the LOD. 1000 copies/µL and 200 copies/µL dilutions were analysed in six replicates, while every lower dilution (1000–0.2 copies/µL) were analysed in 12 replicates. For both target genes ORF8 (A) and N (B) the LOD is 100 copies/µL as the last dilution where all 12 replicates are positive. For non-template control (NTC) PCR grade water substituted SARS-CoV-2 RNA.
Reducing symmetry in topology optimization of two-dimensional porous phononic crystals
Creators: name: Dong, Hao-Wen
name: Wang, Yue-Sheng
name: Wang, Yan-Feng
name: Zhang, Chuanzeng
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: In this paper we present a comprehensive study on the multi-objective optimization of two-dimensional porous phononic crystals (PnCs) in both square and triangular lattices with the reduced topology symmetry of the unit-cell. The fast non-dominated sorting-based genetic algorithm II is used to perform the optimization, and the Pareto-optimal solutions are obtained. The results demonstrate that the symmetry reduction significantly influences the optimized structures. The physical mechanism of the optimized structures is analyzed. Topology optimization combined with the symmetry reduction can discover new structures and offer new degrees of freedom to design PnC-based devices. Especially, the rotationally symmetrical structures presented here can be utilized to explore and design new chiral metamaterials.
description: 24 pages, 11 figures in AIP Advances 2015