cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Interaction networks for jet characterisation at the LHC
Creators: name: Pierini, Maurizio
name: Ngadiuba, Jennifer
name: Wozniak, Kinga Anna
name: Olmo Cerri
name: Nguyen, Thong
name: Duarte, Javier Mauricio
name: Spiropulu, Maria
name: Moreno, Eric
name: Jean-Roch Vlimant
Publisher: name: Zenodo
Year: 2019

description: We study the use of interaction networks to perform tasks related to jet reconstruction. In particular, we consider jet tagging for generic boosted-jet topologies, tagging of large-momentum H$\to$bb decays, and anomalous-jet detection. The achieved performance is compared to state-of-the-art deep learning approaches, based on Convolutional or Recurrent architectures. Unlike these approaches, Interaction Networks allow to reach state-of-the art performance without making assumptions on the underlying data (e.g., detector geometry or resolution, particle ordering criterion, etc.). Given their flexibility, Interaction Networks provide an interesting possibility for deployment-friendly deep learning algorithms for the LHC experiments.
Deep Brain Stimulation for the Treatment of Tremor and Ataxia Associated with Abetalipoproteinemia
Creators: Mammis, Antonios
Pourfar, Michael
Feigin, Andrew
Mogilner, Alon Y.
Publisher: name: Columbia University
Year: 2012
Subjects: subject: Neurosciences
subject: FOS: Clinical medicine

description: Background: Abetalipoproteinemia is a rare disorder of fat absorption, characterized by vitamin deficiency, acanthocytosis, and neurologic symptoms including ataxia and tremor. Case Report: A 41-year-old male with abetalipoproteinemia is presented. He underwent staged bilateral thalamic deep brain stimulation (DBS) for the treatment of his tremors. After DBS, the patient achieved significant improvements in his tremors, ataxia, and quality of life. Discussion: Thalamic DBS proved to be both safe and efficacious in the management of ataxia and tremors in a patient with abetalipoproteinemia. This is the first report of DBS in abetalipoproteinemia in the literature.
New-Physics agnostic searches for New Physics
Creators: name: Duarte, Javier Mauricio
name: Pierini, Maurizio
name: Wozniak, Kinga Anna
name: Ngadiuba, Jennifer
name: Moreno, Eric
name: Spiropulu, Maria
name: Jean-Roch Vlimant
name: Olmo Cerri
name: Nguyen, Thong
Publisher: name: Zenodo
Year: 2019

description: We propose a new search strategy, based on deep-learning (DL) anomaly detection, to search for new physics in all-jet final states without specific assumptions. The DL model identifies events with anomalous radiation pattern in the jets. This is done applying a threshold to the reconstruction loss. The threshold is tuned so that the rejected events provide an estimate of the QCD-background distribution of analysis-specific interesting quantities. The method can be generalized to many final states without re-training the model and allows to determine the presence of a new-physics signal without making specific assumptions on the signal shape.
Additional file 1 of The application of Chinese version of SARC-F and SARC-CalF in sarcopenia screening against five definitions: a diagnostic test accuracy study
Creators: name: Guo, Jia-Yu
name: Yu, Kang
name: Li, Chun-Wei
name: Bao, Yuan-Yuan
name: Zhang, Yu
name: Wang, Fang
name: Li, Rong-Rong
name: Xie, Hai-Yan
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology

description: Supplementary Material 1
title: 02_1233
Creators: name: Wesley Baldwin, John
name: Baldwin, John W.
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2018
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: L'ensemble de ces notes ont été crée par John Baldwin lors d'une de ses premières périodes de résidence à Paris. Ces documents comprennent tous les magistri qu’il avait pu rencontrer dans ses sources. Aux XIIème et XIIIème siècles, les universités n'existant pas encore, le titre de magister s'il évoque certainement une compétence n'est pas rattaché de façon systématique au passage par les écoles. De surcroît, les magistris sont le plus souvent désignés par leur seul prénom. La lecture de ces données est donc difficile et suppose un long travail pour tenter d'identifier un individu auquel on pourrait rattacher plusieurs mentions. John Baldwin avait donc renoncé à utiliser ces données pour donner un prolongement à sa magnifique étude sur les gradués d'université et leur emploi par les Capétiens et les Plantagenêts. Néanmoins, il a conservé ces données et elles sont potentiellement très utile dans le cadre de Studium, comme le sont toutes les mentions dans les volumes des Fasti Ecclesiae Gallicanae de chanoines portant ce titre de magister sans autres précisions. L'ampleur des dépouillements rend ces données très utiles et nous devons une grande reconnaissance à John Baldwin pour avoir pris la peine de faire photocopier ses fiches et de nous les avoir transmises amicalement.
Les données ainsi que les images des fiches sont accessibles sur le site Internet à l'adresse suivante : http://studium-baldwin.lamop.fr/.
Les transcriptions des fiches ont été effectuées par des étudiants de Paris 1 Panthéon - Sorbonne mais elles n'ont pas été corrigées par la suite.
description: Relation: https://lamop.hypotheses.org/
OPeNDAP Tutorial
Creators: name: Cornillon, Peter
name: Gallagher, James
name: Callahan, Jonathan
Publisher: name: Zenodo
Year: 2004

description: About the workshop:

OPeNDAP and NOAA/PMEL held a joint tutorial/workshop at the Stennis Space Center from 29-31 September 2004. The workshop covered OPeNDAP's software, the operation of some of the clients and installation of servers as well as some of the DAP-compliant software developed at PMEL.

Summary of the slide deck: 

This slide deck provides an introduction and overview to the multi-day tutorial/workshop about OPeNDAP. The tutorial was structured over several sessions:

OPeNDAP Overview

Covers the download of OPeNDAP Data Connector, a demo showing different interfaces like Matlab, GUI, and command-line client, and discusses the philosophical underpinnings and history of OPeNDAP.

Server Side 

Discusses OPeNDAP servers, their role, and the various types such as CODAR, netCDF, HDF4, etc.

Server Side/Client Side

Further delves into OPeNDAP servers, clients, aggregation servers, processing servers, and ancillary information services.

Ferret 

Focuses on Ferret, a visualization and analysis tool, and its integration with OPeNDAP.

FDS/LAS

Covers Ferret Data Server and Live Access Server, which are components of OPeNDAP.

Throughout the tutorial, various aspects of OPeNDAP were discussed, including its philosophy, data model, metadata, data types, server services, and interfaces. Practical demonstrations were provided for accessing data via web browsers and using the OPeNDAP Data Connector. Additionally, the tutorial emphasized the importance of interoperability and provided guidance on how to explore and access data sets using OPeNDAP tools like the OPeNDAP Data Connector and the OPeNDAP Data Client (ODC). Lastly, the tutorial offered resources for further learning and documentation on OPeNDAP.
A biologically inspired two-species exclusion model: effects of RNA polymerase motor traffic on simultaneous DNA replication
Creators: name: Ghosh, Soumendu
name: Mishra, Bhavya
name: Patra, Shubhadeep
name: Schadschneider, Andreas
name: Chowdhury, Debashish
Publisher: name: arXiv
Year: 2017
Subjects: subject: Subcellular Processes (q-bio.SC)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: We introduce a two-species exclusion model to describe the key features of the conflict between the RNA polymerase (RNAP) motor traffic, engaged in the transcription of a segment of DNA, concomitant with the progress of two DNA replication forks on the same DNA segment. One of the species of particles ($P$) represents RNAP motors while the other ($R$) represents replication forks. Motivated by the biological phenomena that this model is intended to capture, a maximum of only two $R$ particles are allowed to enter the lattice from two opposite ends whereas the unrestricted number of $P$ particles constitute a totally asymmetric simple exclusion process (TASEP) in a segment in the middle of the lattice. Consequently, the lattice consists of three segments; the encounters of the $P$ particles with the $R$ particles are confined within the middle segment (segment $2$) whereas only the $R$ particles can occupy the sites in the segments $1$ and $3$. The model captures three distinct pathways for resolving the co-directional as well as head-collision between the $P$ and $R$ particles. Using Monte Carlo simulations and heuristic analytical arguments that combine exact results for the TASEP with mean-field approximations, we predict the possible outcomes of the conflict between the traffic of RNAP motors ($P$ particles engaged in transcription) and the replication forks ($R$ particles). The outcomes, of course, depend on the dynamical phase of the TASEP of $P$ particles. In principle, the model can be adapted to the experimental conditions to account for the data quantitatively.
description: 10 pages, including 7 figures
MOESM5 of Bronze Age meat industry: ancient mitochondrial DNA analyses of pig bones from the prehistoric salt mines of Hallstatt (Austria)
Creators: name: Hammer, Sabine
name: Tautscher, Barbara
name: Pucher, Erich
name: Kowarik, Kerstin
name: Reschreiter, Hans
name: Kern, Anton
name: Haring, Elisabeth
Publisher: name: figshare
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 5. Detailed sequencing outcome for the 10 prehistoric porcine teeth specimens. For each specimen, DNA concentration and the number of obtained sequence reads for fragments A, B and C, are given.
Quasars Probing Quasars I: Optically Thick Absorbers Near Luminous Quasars
Creators: name: Hennawi, Joseph F.
name: Prochaska, Jason X.
name: Burles, Scott
name: Strauss, Michael A.
name: Richards, Gordon T.
name: Schlegel, David J.
name: Fan, Xiaohui
name: Schneider, Donald P.
name: Zakamska, Nadia L.
name: Oguri, Masamune
name: Gunn, James E.
name: Lupton, Robert H.
name: Brinkmann, Jon
name: Brunner, Robert J.
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: With close pairs of quasars at different redshifts, a background quasar sightline can be used to study a foreground quasar's environment in absorption. We search 149 moderate resolution background quasar spectra, from Gemini, Keck, the MMT, and the SDSS to survey Lyman Limit Systems (LLSs) and Damped Ly-alpha systems (DLAs) in the vicinity of 1.8 < z < 4.0 luminous foreground quasars. A sample of 27 new quasar-absorber pairs is uncovered with column densities, 17.2 < log (N_HI/cm^2) < 20.9, and transverse (proper) distances of 22 kpc/h < R < 1.7 Mpc/h, from the foreground quasars. If they emit isotropically, the implied ionizing photon fluxes are a factor of ~ 5-8000 times larger than the ambient extragalactic UV background over this range of distances. The observed probability of intercepting an absorber is very high for small separations: six out of eight projected sightlines with transverse separations R < 150 kpc/h have an absorber coincident with the foreground quasar, of which four have log N_HI > 10^19. The covering factor of log N_HI > 10^19 absorbers is thus ~ 50 % (4/8) on these small scales, whereas < 2% would have been expected at random. There are many cosmological applications of these new sightlines: they provide laboratories for studying fluorescent Ly-alpha recombination radiation from LLSs, constrain the environments, emission geometry, and radiative histories of quasars, and shed light on the physical nature of LLSs and DLAs.
description: 27 pages (10 pages of figures), 5 tables, submitted to ApJ
MOESM1 of Assessment of the Bacteria community structure across life stages of the Chinese Citrus Fly, Bactrocera minax (Diptera: Tephritidae)
Creators: name: Andongma, Awawing
name: Wan, Lun
name: Dong, Yong-Cheng
name: Wang, Yu-Lei
name: He, Jin
name: Niu, Chang-Ying
Publisher: name: figshare
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Additional file 1. Relative abundance of taxa in the 16S rRNA libraries from different developmental stages of Bactrocera minax: BME- B. minax egg, BM1L- B. minax first instar larva, BM2L- B. minax second instar BM3L- B. minax third instar larva, BMP- B. minax pupa, BMF- B. minax female, BMM- B. minax male. Classification results were obtained from sequence alignment against RDP training set version 9 [34] and can be displayed for different taxonomic levels (Phylum; Class; Order; Family; Genus; Operational taxonomic units created at 97% sequence similarity)
Dynamics of Clusters in Two-dimensional Potts Model
Creators: name: Gunduc, Yigit
name: Aydin, Meral
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Dynamical behavior of the clusters during relaxation is studied in two-dimensional Potts model using cluster algorithm. Average cluster size and cluster formation velocity are calculated on two different lattice sizes for different number of states during initial stages of the Monte Carlo simulation. Dependence of these quantities on the order of the transition provides an efficient method to study nature of the phase transitions occuring in similar models.
description: 16 pages,latex,4 figures(postscript),Accepted for publication in Physica A
Additional file 4: of Three-dimensional printed PLA scaffold and human gingival stem cell-derived extracellular vesicles: a new tool for bone defect repair
Creators: name: Diomede, Francesca
name: Gugliandolo, Agnese
name: Cardelli, Paolo
name: Merciaro, Ilaria
name: Ettorre, Valeria
name: Traini, Tonino
name: Bedini, Rossella
name: Scionti, Domenico
name: Bramanti, Alessia
name: Nanci, Antonio
name: Caputi, Sergio
name: Fontana, Antonella
name: Mazzon, Emanuela
name: Trubiani, Oriana
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Table S1. The differential gene expression between 3D-PLA+ EVs + hGMSCs and 3D-PLA+ PEI-EVs + hGMSCs compared with hGMSCs is given as expression value and fold change expressed in logarithm with base 2 (FC Log2). Gene ontology (GO) processes indicate the gene classification in the “regulation of ossification” and “ossification”. Instead, the statistical significance is indicated by the false discovery rate (FDR), q values ≤ 0.05 were considered statistically significant. Table S2. The differential gene expression between 3D-PLA+ EVs + hGMSCs and 3D-PLA+ PEI-EVs + hGMSCs compared with hGMSCs is given as expression value and fold change expressed in logarithm with base 2 (FC Log2). Gene ontology (GO) processes indicate the gene classification in the “regulation of osteoblast differentiation” and “osteoblast differentiation”. Instead, the statistical significance is indicated by the false discovery rate (FDR), q values ≤ 0.05 were considered statistically significant. Table S3. The differential gene expression between 3D-PLA+ EVs + hGMSCs and 3D-PLA+ PEI-EVs + hGMSCs compared with hGMSCs is given as expression value and fold change expressed in logarithm with base 2 (FC Log2). The statistical significance is indicated by the false discovery rate (FDR), q values ≤ 0.05 were considered statistically significant. Table S4. The differential gene expression in 3D-PLA+ PEI-EVs + hGMSCs compared with hGMSCs is given in fold change expressed in logarithm with base 2 (FC Log2). The statistical significance is indicated by the false discovery rate (FDR), q values ≤ 0.05 were considered statistically significant. (DOCX 59 kb)
Particle Reconstruction with Graph Networks for irregular detector geometries
Creators: name: Verzetti, Mauro
name: Pierini, Maurizio
name: Kieseler, Jan
name: Swapneel Sundeep Mehta
name: Shah Rukh Qasim
name: Yutaro Iiyama
Publisher: name: Zenodo
Year: 2019

description: We use Graph Networks to learn representations of irregular detector geometries and perform on it typical tasks such as cluster segmentation or pattern recognition. Thanks to the flexibility and generality of the graph architecture, this kind of network can be applied to detector of arbitrarly geometry, representing the detector elements through a unique detector identification (e.g., physical position) and the readout value and embedding as vertices in a graph. We apply this idea to tasks related to calorimetry and tracking in LHC-like conditions, investigating original graph architectures to optimise performance and memory footprint.
The BCS critical temperature in a weak homogeneous magnetic field
Creators: name: Frank, Rupert L.
name: Hainzl, Christian
name: Langmann, Edwin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Mathematical Physics (math-ph)
subject: Superconductivity (cond-mat.supr-con)
subject: Spectral Theory (math.SP)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We show that, within a linear approximation of BCS theory, a weak homogeneous magnetic field lowers the critical temperature by an explicit constant times the field strength, up to higher order terms. This provides a rigorous derivation and generalization of results obtained in the physics literature from WHH theory of the upper critical magnetic field. A new ingredient in our proof is a rigorous phase approximation to control the effects of the magnetic field.
description: 46 pages
Quark deconfinement in neutron star cores: The effects of spin-down
Creators: name: Staff, Jan
name: Ouyed, Rachid
name: Jaikumar, Prashanth
Publisher: name: arXiv
Year: 2006
Subjects: subject: Astrophysics (astro-ph)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We study the role of spin-down in driving quark deconfinement in the high density core of isolated neutron stars. Assuming spin-down to be solely due to magnetic braking, we obtain typical timescales to quark deconfinement for neutron stars that are born with Keplerian frequencies. Employing different equations of state (EOS), we determine the minimum and maximum neutron star masses that will allow for deconfinement via spin-down only. We find that the time to reach deconfinement is strongly dependent on the magnetic field and that this time is least for EOS that support the largest minimum mass at zero spin, unless rotational effects on stellar structure are large. For a fiducial critical density of $5ρ_0$ for the transition to the quark phase ($ρ_0=2.5\times10^{14}$g/cm$^3$ is the saturation density of nuclear matter), we find that neutron stars lighter than $1.5M_{\odot}$ cannot reach a deconfined phase. Depending on the EOS, neutron stars of more than $1.5M_{\odot}$ can enter a quark phase only if they are spinning faster than about 3 milliseconds as observed now, whereas larger spin periods imply that they are either already quark stars or will never become one.
description: 4 pages, 4 figures, submitted to ApJL
Additional file 2 of CRISPR-Cas system positively regulates virulence of Salmonella enterica serovar Typhimurium
Creators: name: Sharma, Nandita
name: Das, Ankita
name: Nair, Abhilash Vijay
name: Sethi, Palash
name: Negi, Vidya Devi
name: Chakravortty, Dipshikha
name: Marathe, Sandhya Amol
Publisher: name: figshare
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Environmental Sciences not elsewhere classified
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Supplementary Material 2
Fuel Minimisation for a Vehicle Equipped with a Flywheel and Battery on a Three-Dimensional Track
Creators: name: Masouleh, Mehdi Imani
name: Limebeer, David J. N.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: An optimal control based methodology is proposed for minimising the combustible fuel consumption of a hybrid vehicle equipped with an internal combustion engine, a high-speed flywheel and a battery. The three-dimensionality of the road is recognised by the optimal control calculations. Fuel efficiency is achieved by optimally exploiting the primary and secondary energy sources and controlling the vehicle so that the fuel consumption is minimised for a given, but arbitrary three-dimensional route. A time-of-arrival constraint rather than a driving cycle is used. The benefits of using multiple auxiliary storage systems are demonstrated and a lower-bound estimate of the fuel consumption is presented.
Entanglement on linked boundaries in Chern-Simons theory with generic gauge groups
Creators: name: Dwivedi, Siddharth
name: Singh, Vivek Kumar
name: Dhara, Saswati
name: Ramadevi, P.
name: Zhou, Yang
name: Joshi, Lata Kh
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the entanglement for a state on linked torus boundaries in $3d$ Chern-Simons theory with a generic gauge group and present the asymptotic bounds of Rényi entropy at two different limits: (i) large Chern-Simons coupling $k$, and (ii) large rank $r$ of the gauge group. These results show that the Rényi entropies cannot diverge faster than $\ln k$ and $\ln r$, respectively. We focus on torus links $T(2,2n)$ with topological linking number $n$. The Rényi entropy for these links shows a periodic structure in $n$ and vanishes whenever $n = 0 \text{ (mod } \textsf{p})$, where the integer $\textsf{p}$ is a function of coupling $k$ and rank $r$. We highlight that the refined Chern-Simons link invariants can remove such a periodic structure in $n$.
description: 31 pages, 5 figures
Effective Dynamics for Boson Stars
Creators: name: Froehlich, Juerg
name: Jonsson, B. Lars G.
name: Lenzmann, Enno
Publisher: name: arXiv
Year: 2006
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 35Q55; 37K40; 81Q05

description: We study solutions close to solitary waves of the pseudo-relativistic Hartree equation describing boson stars under the influence of an external gravitational field. In particular, we analyze the long-time effective dynamics of such solutions. In essence, we establish a (long-time) stability result for solutions describing boson stars that move under the influence of an external gravitational field.
description: 57 pages, 4 figures
The NOTED software tool-set enables improved exploitation of WAN bandwidth for Rucio data transfers via FTS
Creators: name: Martelli, Edoardo
name: Manzi, Andrea
name: Lassnig, Mario
name: Keeble, Oliver
name: Cass, Tony
name: Busse-Grawitz, Coralie
Publisher: name: Zenodo
Year: 2019

description: We describe the software tool-set being implemented in the contest of the NOTED [1] project to better exploit WAN bandwidth for Rucio and FTS data transfers, how it has been developed and the results obtained. The first component is a generic data-transfer broker that interfaces with Rucio and FTS. It identifies data transfers for which network reconfiguration is both possible and beneficial, translates the Rucio and FTS information into parameters that can be used by network controllers and makes these available via a public interface. The second component is a network controller that, based on the parameters provided by the transfer broker, decides which actions to apply to improve the path for a given transfer. Unlike the transfer-broker, the network controller described here is tailored to the CERN network as it has to choose the appropriate action given the network configuration and protocols used at CERN. However, this network controller can easily be used as a model for site-specific implementations elsewhere. The paper describes the design and the implementation of the two tools, the tests performed and the results obtained. It also analyses how the tool-set could be used for WLCG in the contest of the DOMA [2] activity. [1] Network Optimisation for Transport of Experimental Data - CERN project [2] Data Organisation, Management and Access - WLCG activity
A Discrete Choice Framework for Modeling and Forecasting The Adoption and Diffusion of New Transportation Services
Creators: name: Zarwi, Feras El
name: Vij, Akshay
name: Walker, Joan
Publisher: name: arXiv
Year: 2017
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences
subject: 62P20, 62P25, 62P30

description: Current travel demand models are unable to predict long-range trends in travel behavior as they do not entail a mechanism that projects membership and market share of new modes of transport (Uber, Lyft, etc). We propose integrating discrete choice and technology adoption models to address the aforementioned issue. In order to do so, we build on the formulation of discrete mixture models and specifically Latent Class Choice Models (LCCMs), which were integrated with a network effect model. The network effect model quantifies the impact of the spatial/network effect of the new technology on the utility of adoption. We adopted a confirmatory approach to estimating our dynamic LCCM based on findings from the technology diffusion literature that focus on defining two distinct types of adopters: innovator/early adopters and imitators. LCCMs allow for heterogeneity in the utility of adoption for the various market segments i.e. innovators/early adopters, imitators and non-adopters. We make use of revealed preference (RP) time series data from a one-way carsharing system in a major city in the United States to estimate model parameters. The data entails a complete set of member enrollment for the carsharing service for a time period of 2.5 years after being launched. Consistent with the technology diffusion literature, our model identifies three latent classes whose utility of adoption have a well-defined set of preferences that are significant and behaviorally consistent. The technology adoption model predicts the probability that a certain individual will adopt the service at a certain time period, and is explained by social influences, network effect, socio-demographics and level-of-service attributes. Finally, the model was calibrated and then used to forecast adoption of the carsharing system for potential investment strategy scenarios.
MOESM2 of Monitoring of patients treated with lithium for bipolar disorder: an international survey
Creators: name: M. Nederlof
name: E. Heerdink
name: A. Egberts
name: I. Wilting
name: L. Stoker
name: R. Hoekstra
name: R. Kupka
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 2: Appendix S2. List of Dutch lithium experts who contributed to the pilot study.
Encephalopathy, Hypoglycemia, and Flailing Extremities: A Case of Bilateral Chorea““Ballism Associated with Diabetic Ketoacidosis
Creators: Guerrero, Waldo R.
Okun, Michael S.
McFarland, Nikolaus R.
Publisher: name: Columbia University
Year: 2012
Subjects: subject: Neurosciences
subject: FOS: Clinical medicine

description: Background: Hypo/hyperglycemia is a known cause of chorea and hemiballism. The temporallobes, hippocampus, basal ganglia, and substantia nigra are most susceptible to hypoglycemic changes. Methods: We present a caseof bilateral chorea and bi-ballism accompanied by encephalopathyin the setting of severe hypoglycemia and diabetic ketoacidosis. The patient had brain MRI changes involving both caudate nuclei, temporal lobes, and hippocampi. Discussion: This case demonstrates the basal ganglia's vulnerability to hypoglycemia and the need for cautious evaluation of involuntary movements when they occur in the setting of encephalopathy.
Superstatistical generalised Langevin equation: non-Gaussian viscoelastic anomalous diffusion
Creators: name: Ślęzak, Jakub
name: Metzler, Ralf
name: Magdziarz, Marcin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Recent advances in single particle tracking and supercomputing techniques demonstrate the emergence of normal or anomalous, viscoelastic diffusion in conjunction with non-Gaussian distributions in soft, biological, and active matter systems. We here formulate a stochastic model based on a generalised Langevin equation in which non-Gaussian shapes of the probability density function and normal or anomalous diffusion have a common origin, namely a random parametrisation of the stochastic force. We perform a detailed analytical analysis demonstrating how various types of parameter distributions for the memory kernel result in the exponential, power law, or power-log law tails of the memory functions. The studied system is also shown to exhibit a further unusual property: the velocity has a Gaussian one point probability density but non-Gaussian joint distributions. This behaviour is reflected in relaxation from Gaussian to non-Gaussian distribution observed for the position variable. We show that our theoretical results are in excellent agreement with Monte Carlo simulations.
description: 40 pages, 7 figures
Chern-Simons Diffusion Rate near the Electroweak Phase Transition for $m_H \approx m_W$
Creators: name: Smit, Jan
name: Tang, Wai Hung
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The rate of $B$-violation in the standard model at finite temperature is closely related to the diffusion rate $Γ$ of Chern-Simons number. We compute this rate for $m_H \approx m_W$ in the classical approximation in an effective SU(2)-Higgs model, using Krasnitz's algorithm. The parameters in the effective hamiltonian are determined by comparison with dimensional reduction. In the high temperature phase we find $Γ/V (α_W T)^4 \approx 1$, neglecting a finite renormalization. In the low temperature phase near the transition we find the rate to be much larger than might be expected from previous analytic calculations based on the sphaleron.
description: 23 pages, 8 Postscript figures, uses epsf.sty
Evolution of the ROOT Tree I/O
Creators: name: Blomer, Jakob
name: Canal, Philippe
name: Naumann, Axel
name: Piparo, Danilo
Publisher: name: Zenodo
Year: 2019

description: The ROOT TTree data format encodes hundreds of petabytes of High Energy and Nuclear Physics events. Its columnar layout drives rapid analyses, as only those parts (branches) that are really used in a given analysis need to be read from storage. Its unique feature is the seamless C++ integration, which allows users to directly store their event classes without explicitly defining data schemas. In this contribution, we present the status and plans of the future ROOT 7 event I/O. Along with the ROOT 7 interface modernization, we aim for robust, where possible compile-time safe C++ interfaces to read and write event data. On the performance side, we show first benchmarks using ROOT's new experimental I/O subsystem that combines the best of TTrees with recent advances in columnar data formats. A core ingredient is a strong separation of the high-level logical data layout (C++ classes) from the low-level physical data layout (storage backed nested vectors of simple types). On the high level, we present new asynchronous and thread-friendly interfaces to support parallel reading and writing. On the low-level, we show how an optimized physical data layout speeds up serialization and deserialization and facilitates fast vectorized and bulk operations. This lets ROOT I/O run optimally on the upcoming ultra-fast NVRAM storage devices, as well as file-less storage systems such as object stores.
Discover Your Competition in LTE: Client-Based Passive Data Rate Prediction by Machine Learning
Creators: name: Falkenberg, Robert
name: Heimann, Karsten
name: Wietfeld, Christian
Publisher: name: arXiv
Year: 2017
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: To receive the highest possible data rate or/and the most reliable connection, the User Equipment (UE) may want to choose between different networks. However, current LTE and LTE-Advanced mobile networks do not supply the UE with an explicit indicator about the currently achievable data rate. For this reason, the mobile device will only see what it obtains from the network once it actively sends data. A passive estimation in advance is therefore not doable without further effort. Although the device can identify its current radio conditions based on the received signal strength and quality, it has no information about the cell's traffic load caused by other users. To close this gap we present an Enhanced Client-based Control-Channel Analysis for Connectivity Estimation (EC3ACE), which uncovers the cell load broken down by each single user. Based on this information and in conjunction with existing indicators like Reference Signal Received Power (RSRP) and Reference Signal Received Quality (RSRQ), a neural network is trained to perform a data rate prediction for the current LTE link. Compared to an earlier work, our approach reduces the average prediction error below one third. Applied in public networks, the predicted data rate differs by less than 1.5 Mbit/s in 93% of cases.
Enabling HEP software development for the 2020s - a coherent vision for training
Creators: name: Malik, Sudhir
name: Elmer, Peter
name: Lange, David
name: Cosden, Ian
Publisher: name: Zenodo
Year: 2019

description: Developing, maintaining, and evolving the algorithms and software implementations for HEP experiments will continue for many decades. In particular, the HL-LHC will start collecting data 8 or 9 years from now, and then acquire data for at least another decade. Building the necessary software requires a workforce with a mix of HEP domain knowledge, advanced software skills, and strong connections to other related disciplines. The investments to grow this workforce must begin today. Several new efforts are working towards this goal, like the IRIS-HEP software institute, the FIRST-HEP project and the HEP Software Foundation. Past software training practices have largely been set of individual and disconnected activities. The HEP community planning process has established a coherent vision for software training as part of a larger framework where researchers progress from acquiring basic skills training through user training in existing software to training in skills needed to development new research software. This presentation will articulate this vision and describe recent efforts to enhance the sustainability, re-usability and impact of the software training activities as well as related education and outreach programs.
MOESM4 of Bronze Age meat industry: ancient mitochondrial DNA analyses of pig bones from the prehistoric salt mines of Hallstatt (Austria)
Creators: name: Hammer, Sabine
name: Tautscher, Barbara
name: Pucher, Erich
name: Kowarik, Kerstin
name: Reschreiter, Hans
name: Kern, Anton
name: Haring, Elisabeth
Publisher: name: figshare
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 4. PCR strategy for the 721-bp-long section of the mitochondrial Control Region (CR). Primers used to amplify three sections (A, B, C) of the mitochondrial control region.
Automatic Differentiation in ROOT
Creators: name: Vasilev, Vasil Georgiev
name: Shadura, Oksana
name: Efremov, Aleksandr
Publisher: name: Zenodo
Year: 2019

description: In mathematics and computer algebra, automatic differentiation (AD) is a set of techniques to evaluate the derivative of a function specified by a computer program. AD exploits the fact that every computer program, no matter how complicated, executes a sequence of elementary arithmetic operations (addition, subtraction, multiplication, division, etc.) and elementary functions (exp, log, sin, cos, etc.) including control flow statements. AD takes source code of a function as input and produces source code of the derived function. By applying the chain rule repeatedly to these operations, derivatives of arbitrary order can be computed automatically, accurately to working precision, and using at most a small constant factor more arithmetic operations than the original program. AD is an alternative technique to symbolic and numerical differentiation. These classical methods run into problems: symbolic differentiation leads to inefficient code (unless done carefully) and faces the difficulty of converting a computer program into a single expression, while numerical differentiation can introduce round-off errors in the discretization process and cancellation. Both classical methods have problems with calculating higher derivatives, where the complexity and errors increase. Finally, both classical methods are slow at computing the partial derivatives of a function with respect to many inputs, as is needed for gradient-based optimization algorithms. AD solves all of these problems, at the expense of introducing more software dependencies. Our talk presents AD techniques available in ROOT, supported by Cling, to produce derivatives of arbitrary C/C++ functions through implementing source code transformation and employing the chain rule of differential calculus in both forward mode and reverse mode. We explain it's current integration for gradient computation in TFormula. We demonstrate the correctness and performance improvements in ROOT's fitting algorithms.
Pion production within the hybrid relativistic plane wave impulse approximation model at MiniBooNE and MINERvA kinematics
Creators: name: González-Jiménez, R.
name: Niewczas, K.
name: Jachowicz, N.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The hybrid model for electroweak single-pion production (SPP) off the nucleon, presented in [González-Jiménez et al., Phys. Rev. D 95, 113007 (2017)], is extended here to the case of incoherent pion-production on the nucleus. Combining a low-energy model with a Regge approach, this model provides valid predictions in the entire energy region of interest for current and future accelerator-based neutrino-oscillation experiments. The Relativistic Mean-Field model is used for the description of the bound nucleons while the outgoing hadrons are considered as plane waves. This approach, known as Relativistic Plane-Wave Impulse Approximation (RPWIA), is a first step towards the development of more sophisticated models, it is also a test of our current understanding of the elementary reaction. We focus on the charged-current $ν$($\barν$)-nucleus interaction at MiniBooNE and MINERvA kinematics. The effect on the cross sections of the final-state interactions, which affect the outgoing hadrons on their way out of the nucleus, is judged by comparing our results with those from the NuWro Monte Carlo event generator. We find that the hybrid-RPWIA predictions largely underestimate the MiniBooNE data. In the case of MINERvA, our results fall below the $ν$-induced 1$π^0$ production data, while a better agreement is found for $ν$-induced 1$π^+$ and $\barν$-induced 1$π^0$ production.
description: 13 pages, 10 figures
Neuroimaging of Essential Tremor: What is the Evidence for Cerebellar Involvement?
Creators: Passamonti, Luca
Cerasa, Antonio
Quattrone, Aldo
Publisher: name: Columbia University
Year: 2012
Subjects: subject: Neurosciences
subject: FOS: Clinical medicine

description: Background: Clinical observations and electrophysiological studies have provided initial evidence for the involvement of the cerebellum in essential tremor (ET), the most frequent hyperkinetic disorder. Recently, this hypothesis has been reinvigorated by post-mortem studies that demonstrated a number of pathological changes in the cerebellum of ET patients compared with age-matched healthy controls. Advanced neuroimaging techniques have also made it possible to detect in vivo which cerebellar abnormalities are present in ET patients and to reveal the core mechanisms implicated in the development of motor and cognitive symptoms in ET. Objective: We discuss the neuroimaging research investigating the brain structure and function of ET patients relative to healthy controls. In particular, we review 1) structural neuroimaging experiments assessing the density/volume of cortical/subcortical regions and the integrity of the white-matter fibers connecting them; 2) functional studies exploring brain responses during motor/cognitive tasks and the function of specific neurotransmitters/metabolites within cortical–cerebellar circuits. Methods: A search in PubMed was conducted to identify the relevant literature. Discussion: Current neuroimaging research provides converging evidence for the role of the cerebellum in the pathophysiology of ET, although some inconsistencies exist, particularly in structural studies. These discrepancies may depend on the high clinical heterogeneity of ET and on differences among the experimental methods used across studies. Further investigations are needed to disentangle the relationships between specific ET phenotypes and the underlying patterns of neural abnormalities.
Additional file 2 of ATPIF1 maintains normal mitochondrial structure which is impaired by CCM3 deficiency in endothelial cells
Creators: name: Wang, Kang
name: Chen, Haixuan
name: Zhou, Zhongyang
name: Zhang, Haifeng
name: Zhou, Huanjiao Jenny
name: Min, Wang
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 2: Fig. S2. OXPHOS and glycolysis related genes in siRNA or lentivirus treatment endothelial cells. a glycolysis related gene in HUVECs after siCCM3 treatment. B, c OXPHOS related genes in selected CRISPR-CCM3 (b) and s-oeATPIF1 (c) EPCs. d, e glycolysis related genes in selected CRISPR-CCM3 (d) and s-oeATPIF1 (e) EPCs.
Cognitive Features of Essential Tremor: A Review of the Clinical Aspects and Possible Mechanistic Underpinnings
Creators: Bermejo-Pareja, Felix
Puertas-Martin, Veronica
Publisher: name: Columbia University
Year: 2012
Subjects: subject: Neurosciences
subject: FOS: Clinical medicine

description: The classical concept of essential tremor (ET) as a monosymptomatic tremorogenic disorder has been questioned in the last decade as new evidence has been described. Clinical, neuroimaging, and pathological studies have described a probable structural basis (mainly in cerebellum) and evidence that ET is associated with subtle clinical cerebellar deficits and several non-motor clinical manifestations, such as cognitive and mood disorders. We performed literature searches in Medline, ISI Web of Knowledge, and PsycInfo databases. The aim of this review is to describe cognitive deficits associated with ET. First, we present a brief history of ET cognitive disorders presented. Second, we describe several clinical cross-sectional series demonstrating that ET is associated with mild cognitive deficits of attention, executive functions, several types of memory (working memory, immediate, short term, delayed, and possibly others) and, mood disorders (depression). Recent neuroimaging studies favor a cerebellar basis for these cognitive deficits. Population-based surveys confirm that mild cognitive dysfunction is not limited to severe ET cases, the entire ET group, including mild and undiagnosed cases, can be affected. Cohort studies indicated that ET cognitive deficits could be progressive and that ET patients had an increased risk of dementia. The mood and cognitive deficits in ET are in agreement with cognitive affective cerebellar syndrome described in patients with cerebellar disorders. New evidence, mainly from functional (neuroimaging) and prospective clinical studies would further bolster recent descriptions of ET clinical manifestations.
C++ Modules in ROOT and Beyond
Creators: name: Vasilev, Vasil Georgiev
name: Shadura, Oksana
name: Takahashi, Yuka
name: Lange, David
name: Muzaffar, Malik Shahzad
name: Rodozov, Mircho Nikolaev
Publisher: name: Zenodo
Year: 2019

description: C++ Modules come in C++20 to fix the long-standing build scalability problems in the language. They provide an io-efficient, on-disk representation capable to reduce build times and peak memory usage. ROOT employs the C++ modules technology further in the ROOT dictionary system to improve its performance and reduce the memory footprint. ROOT with C++ Modules was released as a technology preview in fall 2018, after intensive development during the last few years. The current state is ready for production, however, there is still room for performance optimizations. In this talk, we show the roadmap for making the technology default in ROOT. We demonstrate a global module indexing optimization which allows reducing the memory footprint dramatically for many workflows. We will report user feedback on the migration to ROOT with C++ Modules.