cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dynamics of entropy and information of time-dependent quantum systems: exact results
Creators: name: Andrzejewski, K.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Dynamical aspects of information-theoretic and entropic measures of quantum systems are studied. First, we show that for the time-dependent harmonic oscillator, as well as for the charged particle in certain time-varying electromagnetic fields, the increase of the entropy and dynamics of the Fisher information can be directly described and related. To illustrate these results we have considered several examples for which all the relations take the elementary form. Moreover, we show that the integrals of (geodesic) motion associated with some conformal Killing vectors lead to the Ermakov-Lewis invariants for the considered electromagnetic fields. Next, we explicitly work out the dynamics of the entanglement entropy of the oscillators coupled by a continuous time-dependent parameter as well as we analyse some aspects of quantum-classical transition (in particular decoherence). Finally, we study in some detail the behavior of quantum quenches (in the presence of the critical points) for the case of mutually non-interacting non-relativistic fermions in a harmonic trap.
description: 31 pages, matches the published version
Additional file 1: of Epidemiologic analysis of respiratory viral infections among Singapore military servicemen in 2016
Creators: name: Yuk-Fai Lau
name: Wee-Hong Koh
name: Kan, Clement
name: Poh-Choo Dua
name: Ai-Sim Lim
name: Chin-Wen Liaw
name: Qiu-Han Gao
name: Chng, Jeremiah
name: Lee, Vernon
name: Boon-Huan Tan
name: Jin-Phang Loh
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Detailed distribution pattern of the combinations found in 2016 as dual infections. (PDF 116Â kb)
Asymptotic behavior of solutions of linear multi-order fractional differential equation systems
Creators: name: Diethelm, Kai
name: Siegmund, Stefan
name: Tuan, H. T.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: 34A08, 34A12, 34A30, 34D05

description: In this paper, we investigate some aspects of the qualitative theory for multi-order fractional differential equation systems. First, we obtain a fundamental result on the existence and uniqueness for multi-order fractional differential equation systems. Next, a representation of solutions of homogeneous linear multi-order fractional differential equation systems in series form is provided. Finally, we give characteristics regarding the asymptotic behavior of solutions to some classes of linear multi-order fractional differential equation systems.
description: 24 pages
Non-unitary multiorbital superconductivity from competing interactions in Dirac materials
Creators: name: Wolf, Tobias M. R.
name: Holst, Maximilian F.
name: Sigrist, Manfred
name: Lado, Jose L.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Unconventional superconductors represent one of the most intriguing quantum states of matter. In particular, multiorbital systems have the potential to host exotic non-unitary superconducting states. While the microscopic origin of non-unitarity is not yet fully solved, competing interactions are suggested to play a crucial role in stabilizing such states. The interplay between charge order and superconductivity has been a recurring theme in unconventionally superconducting systems, ranging from cuprate-based superconductors to dichalcogenide systems and even to twisted van der Waals materials. Here, we demonstrate that the existence of competing interactions gives rise to a non-unitary superconducting state. We show that the non-unitarity stems from a competing charge-ordered state whose interplay with superconductivity promotes a non-trivial multiorbital order. We establish this mechanism both from a Ginzburg-Landau perspective, and also from a fully microscopic selfconsistent solution of a multiorbital Dirac material. Our results put forward competing interactions as a powerful mechanism for driving non-unitary multiorbital superconductivity.
description: Main: 4 pages, 3 figures. Supmat: 4 pages, 1 figure. Comments are welcome!
The Geometry of Genetics - The Codeware of Life
Creators: name: Førde, Dr Vincent
Publisher: name: Zenodo
Year: 2025
Subjects: Genetics, Quantum Mechanics, Consciousness, Codeware, Sound & Light.

description: Materialism is effectively dead. Quantum mechanics, super symmetry, genetic geometry, and the algorithmic, hyper-complex nature of functional, dynamic genetic configurations have revealed the true, computational nature of reality. The nature of the universe is subjective and causally complex. All is interconnected. Every expression of reality is a consequence of the preceding (and potentially, in some cases, succeeding) phenomena that led to, and followed such. Subsequently, these are features of the closed loop of repeatable coherence that is present throughout the universal system. The universe is fractally systemic, and through being so, every constituting aspect of such, is an indivisible component of an algorithmically coded, self-similar, repeating series of interconnected, geometrical, holographic matrixes. Consciousness is not an epiphenomenon; i.e., some indistinct and ineffectual consequence of random, meaningless physical and physiological processes, resultant ramifications, and related effects. Materialism is a lie, and like all untruths, such miscalculated paradigms must die, once the truth has been exposed and accepted. We are simply experiencing the slow death of old, outmoded scientific ideals and dogma, which bred divisionism, dehumanization, hegemonic elitism, and ultimately, an ontological disconnection from the perpetually generative simulacrum of reality, borne from the inevitability of causal source; the original quantum-holographic coder: God. Geometry is intricately embedded into the functional dynamics and inherent design features of reality and the universe, providing essential structure to facilitate both life-based and astrophysical computational processes, which would otherwise, be impossible. Consciousness imprints upon the quantum field. This quantum coding is manifested firstly through sound, and secondly, through light. Reality is a consciousness-quantum-sound-light-consciousness feedback loop; a communicative dance between intention and potential, all made possible by the geometrical quantum codeware that undergirds the nature of all things. Ultimately, the codeware of life is intrinsically bound to the geometry of genetics and consciousness.
Thomas Suddick - Malta Convoys
Creators: name: Project Team, Their Finest Hour
Publisher: name: University of Oxford
Year: 2024
Subjects: classificationCode: 430304
subject: British history
classificationCode: 430308
subject: European history (excl. British, classical Greek and Roman)
classificationCode: 430316
subject: International history

description: Fay Cunningham talking about her stepfather Thomas Suddick: "Thomas Suddick was born on the 17th of July, 1917 at Jarrow, died on 23rd of March 1994, at Lawe Road South Shields of lung cancer. His occupation was a caulker burner in the shipyards, and he worked in most of the Tyne shipyards. World War II served in the Royal Navy as a stoker, and took part in the Malta convoys from Gibraltar.""1941 Operation Pedestal was one of the largest convoys ever; carrying food, oil, airplanes to relieve Malta, which had more bombs fall on the island than London. I didn't know that, but it did. So the convoy, 14 merchant vessels, nine sunk 44 royal naval vessels, five sunk, two battleships and three aircraft carriers.""As a stoker, my stepfather was locked in the boiler room during battle, which makes your blood run cold. During one of the actions of the convoy, he was sunk. He was picked up from the water torpedoed and sunk again in another vessel and picked up again all in one day.""The relief of Malta was vital to the allies. If Malta had fallen, we would've lost access to the Suez Canal. The island of Malta received the George Cross.""The oil tanker, Ohio, which was fully laden, was bombed five times and was sinking, but they lashed her to two destroyers and a tug and got her into the Valetta harbour with the oil intact." "My stepfather never, ever, talked about his war experiences to the family. But after a few beers sitting in the sun in the garden at Lawe Road, when pressed, he told his story to our friend Jack Brown. After the war, he returned to Jarrow and to the shipyards. His fiancé died of TB and he suffered from nerves, not surprisingly, he married my mother a widow, Francis Annie Cunningham at St. Mark's Church, Jarrow on the 19th of May, 1952.""So Thomas Suddick, quiet, kind, gentle, brave man.""But he never ever talked about it. Just didn't at all."
Additional file 1: of Building the evidence base on the HIV programme in India: an integrated approach to document programmatic learnings
Creators: name: Ganju, Deepika
name: Bidhubhusan Mahapatra
name: Rajatashuvra Adhikary
name: Sangram Patel
name: Niranjan Saggurti
name: Dallabetta, Gina
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Papers on the HIV epidemic in India published under the programme. (DOCX 37 kb)
EXPLORING THE IMPACT OF SOCRATIC QUESTIONING ON THE DEVELOPMENT OF CRITICAL THINKING SKILLS IN HIGHER EDUCATION
Creators: name: Malikahon Rahimdjanova Lecturer, Uzbek State University of World Languages
Publisher: name: Zenodo
Year: 2024

description: This article investigates the influence of Socratic questioning, a pedagogical approach emphasizing inquiry-based dialogue, on the development of critical thinking skills in students within higher education settings. The theoretical underpinnings of Socratic questioning are explored, demonstrating its alignment with the core tenets of critical thinking.  A review of the existing empirical research is presented, highlighting the effectiveness of Socratic questioning in fostering critical thinking abilities as measured by standardized assessments and its capacity to cultivate deeper engagement with course material. However, the article acknowledges the challenges associated with implementing Socratic questioning effectively.  The importance of establishing a safe and supportive classroom environment is emphasized, along with the need for instructors to refine their questioning techniques.  Best practices for educators are outlined, including the utilization of diverse question types, the implementation of wait time to allow for thoughtful student responses, the demonstration of active listening skills, and the encouragement of collaborative learning to foster peer interaction and diverse perspectives.In conclusion, this article posits that Socratic questioning offers a valuable pedagogical tool for nurturing critical thinking skills in higher education.  By promoting student engagement in thoughtful inquiry and analysis, instructors can empower students to become independent learners and critical thinkers prepared for the complexities of the contemporary world.  The article concludes with a call for further research to explore the long-term impact of Socratic questioning and its effectiveness in a broader range of learning environments.

Keywords: Socratic questioning, critical thinking skills, higher education, student engagement, quasi-experimental design, pre-test post-test control group, thematic analysis, challenges, best practices
title: 02_1657
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/
Transport properties across the many-body localization transition in quasiperiodic and random systems
Creators: name: Setiawan, F.
name: Deng, Dong-Ling
name: Pixley, J. H.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We theoretically study transport properties in one-dimensional interacting quasiperiodic systems at infinite temperature. We compare and contrast the dynamical transport properties across the many-body localization (MBL) transition in quasiperiodic and random models. Using exact diagonalization we compute the optical conductivity $σ(ω)$ and the return probability $R(τ)$ and study their average low-frequency and long-time power-law behavior, respectively. We show that the low-energy transport dynamics is markedly distinct in both the thermal and MBL phases in quasiperiodic and random models and find that the diffusive and MBL regimes of the quasiperiodic model are more robust than those in the random system. Using the distribution of the DC conductivity, we quantify the contribution of sample-to-sample and state-to-state fluctuations of $σ(ω)$ across the MBL transition. We find that the activated dynamical scaling ansatz works poorly in the quasiperiodic model but holds in the random model with an estimated activation exponent $ψ\approx 0.9$. We argue that near the MBL transition in quasiperiodic systems, critical eigenstates give rise to a subdiffusive crossover regime on finite-size systems.
description: 15 pages, 15 figures. Published version
Semi-supervised Network Embedding with Differentiable Deep Quantisation
Creators: name: He, Tao
name: Gao, Lianli
name: Song, Jingkuan
name: Li, Yuan-Fang
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Social and Information Networks (cs.SI)
subject: FOS: Computer and information sciences

description: Learning accurate low-dimensional embeddings for a network is a crucial task as it facilitates many downstream network analytics tasks. For large networks, the trained embeddings often require a significant amount of space to store, making storage and processing a challenge. Building on our previous work on semi-supervised network embedding, we develop d-SNEQ, a differentiable DNN-based quantisation method for network embedding. d-SNEQ incorporates a rank loss to equip the learned quantisation codes with rich high-order information and is able to substantially compress the size of trained embeddings, thus reducing storage footprint and accelerating retrieval speed. We also propose a new evaluation metric, path prediction, to fairly and more directly evaluate model performance on the preservation of high-order information. Our evaluation on four real-world networks of diverse characteristics shows that d-SNEQ outperforms a number of state-of-the-art embedding methods in link prediction, path prediction, node classification, and node recommendation while being far more space- and time-efficient.
Additional file 2 of Effects of iron on the growth, biofilm formation and virulence of Klebsiella pneumoniae causing liver abscess
Creators: name: Chen, Tao
name: Dong, Guofeng
name: Zhang, Siqin
name: Zhang, Xiucai
name: Zhao, Yajie
name: Cao, Jianming
name: Zhou, Tieli
name: Wu, Qing
Publisher: name: figshare
Year: 2020
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 2: Table S2. Primers used for qRT-PCR of siderophore genes
Stress Topology Analysis for Porous Infill Optimization
Creators: name: Wang, Junpeng
name: Wu, Jun
name: Westermann, Rüdiger
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computational Engineering, Finance, and Science (cs.CE)
subject: Numerical Analysis (math.NA)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: The optimization of porous infill structures via local volume constraints has become a popular approach in topology optimization. In some design settings, however, the iterative optimization process converges only slowly, or not at all even after several hundreds or thousands of iterations. This leads to regions in which a distinct binary design is difficult to achieve. Interpreting intermediate density values by applying a threshold results in large solid or void regions, leading to sub-optimal structures. We find that this convergence issue relates to the topology of the stress tensor field that is simulated when applying the same external forces on the solid design domain. In particular, low convergence is observed in regions around so-called trisector degenerate points. Based on this observation, we propose an automatic initialization process that prescribes the topological skeleton of the stress field into the material field as solid simulation elements. These elements guide the material deposition around the degenerate points, but can also be remodelled or removed during the optimization. We demonstrate significantly improved convergence rates in a number of use cases with complex stress topologies. The improved convergence is demonstrated for infill optimization under homogeneous as well as spatially varying local volume constraints.
description: 10 pages, submitted to Structural and Multidisciplinary Optimization. The submission id is: SAMO-D-21-00727
Some aspects of an induced electric dipole moment in rotating and nonrotating frames
Creators: name: Oliveira, Abinael B.
name: Bakke, Knut
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum effects on a neutral particle (atom or molecule) with an induced electric dipole moment are investigated when it is subject to the Kratzer potential and a scalar potential proportional to the radial distance. In addition, this neutral is placed in a region with electric and magnetic fields. This system is analysed in both nonrotating and rotating reference frames. Then, it is shown that bound state solutions to the Schrödinger equation can be achieved and, in the search for polynomial solutions to the radial wave function, a restriction on the values of the cyclotron frequency is analysed in both references frames.
description: 14 pages
Application of superconducting-superfluid magnetohydrodynamics to nuclear "pasta" in neutron stars
Creators: name: Kobyakov, D. N.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: A mixture of superconducting and superfluid nuclear liquids of protons coupled to the ultrarelativistic electron gas, and neutrons is considered. In the magnetohydrodynamic (MHD) approximation, the energy-momentum (stress) tensor is derived, and the entrainment contribution is found in the explicit form. It is shown that this contribution generates a force density, when a superfluid velocity lag and the magnetic field are simultaneously present. This force may be important in the nuclear "pasta" phase in neutron stars, if the proton and neutron Cooper pairing in the pasta phase is taken into account. It is found that if the liquid-crystalline matter of the pasta phase is superfluid and superconducting, then magnitude of the forces acting upon element of matter at typical magnetic field and the superfluid velocity lag, under certain conditions may become large enough to induce a critical stress in the neutron star crust. As an application, the necessary conditions for triggering of a starquake are found in the pasta phase of neutron stars, assuming that the nuclei are flat slabs in parallel magnetic field. The present model includes two independent local parameters: the superfluid velocity lag and the magnetic field. Possible links between the entrainment force and the magnetar starquake triggering mechanism, and some open problems are discussed.
description: Accepted version for Physical Review C. 8 pages, no figures
Additional file 1: of Ancylostoma ceylanicum, novel etiological agent for travelerâ s diarrheaâ report of four Japanese patients who returned from Southeast Asia and Papua New Guinea
Creators: name: Yoshikawa, Masahide
name: Yukiteru Ouji
name: Hirai, Nobuyasu
name: Nakamura-Uchiyama, Fukumi
name: Yamada, Minoru
name: Arizono, Naoki
name: Naoaki Akamatsu
name: Yoh, Takaharu
name: Kaya, Daisuke
name: Nakatani, Toshiya
name: Eiryo Kikuchi
name: Katanami, Yuichi
name: Kimitoshi Satoh
name: Maki, Ryosuke
name: Miyazato, Yusuke
name: Oba, Yuichiro
name: Kasahara, Kei
name: Mikasa, Keiichi
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Table S1. List of gene-specific primers used for PCR. (PDF 60Â kb)
Evaluating machine learning classifiers for glaucoma referral decision support in primary care settings
Creators: name: Grace, Landon
name: Fleischman, David
name: Kaskar, Omkar G.
name: Wells-Gray, Elaine
Publisher: name: Springer Nature
Year: 2022

description:
Several artificial intelligence algorithms have been proposed to help diagnose glaucoma by analyzing the functional and/or structural changes in the eye. These algorithms require carefully curated datasets with access to ocular images. In the current study, we have modeled and evaluated classifiers to predict self-reported glaucoma using a single, easily obtained ocular feature (intraocular pressure (IOP)) and non-ocular features (age, gender, race, body mass index, systolic and diastolic blood pressure, and comorbidities). The classifiers were trained on publicly available data of 3015 subjects without a glaucoma diagnosis at the time of enrollment. 337 subjects subsequently self-reported a glaucoma diagnosis in a span of 1–12 years after enrollment. The classifiers were evaluated on the ability to identify these subjects by only using their features recorded at the time of enrollment. Support vector machine, logistic regression, and adaptive boosting performed similarly on the dataset with F1 scores of 0.31, 0.30, and 0.28, respectively. Logistic regression had the highest sensitivity at 60% with a specificity of 69%. Predictive classifiers using primarily non-ocular features have the potential to be used for identifying suspected glaucoma in non-eye care settings, including primary care. Further research into finding additional features that improve the performance of predictive classifiers is warranted.
Complementarity Relations Between Quantum Steering Criteria
Creators: name: Mondal, Debasis
name: Kaszlikowski, Dagomir
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Recently, a connection between quantum coherence and quantum steering was established and criteria for quantum steering or in other words, nonlocal advantage of quantum coherence (NAQC) were derived for two-qubit states. Here, we derive a set of complementarity relations between the steering or NAQC inequalities achieved by various criteria. We also extend the idea in the multi-partite scenario, specifically, in the three-qubit scenario, which can easily be generalized to the multi-partite scenario.
description: 6 pages, 3 figures
Pathway Instability analysis for "Genomic events stratifying prognosis of early gastric cancer" - Molinari et al. (2024)
Creators: name: Prascevic, Dusan
name: Ewald, Jan
name: Molinari, Chiara
Publisher: name: Zenodo
Year: 2024

description: Pathway Instability analysis in early gastric cancer (scripts and supplementary table)/ Molinari et al. 2024Repository contains scripts for reproducing the pathway instability analysis for "Genomic events stratifying prognosis of early gastric cancer" by  Molinari et al 2024 (currently in peer review) [1].  Additionally, Supplementary Table S4 which shows significantly disrupted pathways per identifed cluster is also included, due to space limitations in the manuscript.

We investigate the pathway instability on the basis of mutational burden on a selection of REACTOME (https://reactome.org) pathways which were significantly enriched in an Italian cohort of Early Gastric Cancer patients (EGC). The original implementation of pathway instability (PI) scores by Zolotovskaia et al [2] is expanded on by including CNA data whenever available.

In addition to the original EGC cohort, early gastric cancer patients from the TCGA-STAD [3] cohort were included in the analysis.

Performing the analysis

The analysis scripts are found within the .zip archive. 

conda/mamba environment

Create a virtual environment with required dependencies found in *environment.yml*.

conda env create -f environment.yml

Activate the environment and run the analysis notebook - *PIscore_AnalysisNotebook.ipynb* (e.g. using JupyterLab (https://jupyter.org/) or Jupyter extension in VSCode).

Disclaimer: Clinical and variants data from the internal EGC cohort is not available!

References:

[1]: TBA[2]: Zolotovskaia, Marianna A., Maxim I. Sorokin, Sergey A. Roumiantsev, Nikolay M. Borisov, and Anton A. Buzdin. “Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers.” Frontiers in Oncology 8 (2019). https://www.frontiersin.org/articles/10.3389/fonc.2018.00658.[3]: https://www.cancer.gov/ccg/research/genome-sequencing/tcga; accessed via https://www.cbioportal.org/

---

This work is licensed under a Creative Commons Attribution 4.0 International License.
Measuring social spam and the effect of bots on information diffusion in social media
Creators: name: Ferrara, Emilio
Publisher: name: arXiv
Year: 2017
Subjects: subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: Bots have been playing a crucial role in online platform ecosystems, as efficient and automatic tools to generate content and diffuse information to the social media human population. In this chapter, we will discuss the role of social bots in content spreading dynamics in social media. In particular, we will first investigate some differences between diffusion dynamics of content generated by bots, as opposed to humans, in the context of political communication, then study the characteristics of bots behind the diffusion dynamics of social media spam campaigns.
description: Chapter of the book "Spreading Dynamics in Social Systems" edited by Y.Y. Ahn and Sune Lehmann
Approximate Petz recovery from the geometry of density operators
Creators: name: Cree, Sam
name: Sorce, Jonathan
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We derive a new bound on the effectiveness of the Petz map as a universal recovery channel in approximate quantum error correction using the second sandwiched Rényi relative entropy $\tilde{D}_{2}$. For large Hilbert spaces, our bound implies that the Petz map performs quantum error correction with order-$ε$ accuracy whenever the data processing inequality for $\tilde{D}_{2}$ is saturated up to terms of order $ε^2$ times the inverse Hilbert space dimension. Conceptually, our result is obtained by extending arXiv:2011.03473, in which we studied exact saturation of the data processing inequality using differential geometry, to the case of approximate saturation. Important roles are played by (i) the fact that the exponential of the second sandwiched Rényi relative entropy is quadratic in its first argument, and (ii) the observation that the second sandwiched Rényi relative entropy satisfies the data processing inequality even when its first argument is a non-positive Hermitian operator.
description: 10 pages; most recent version published in Commun. Math. Phys. (2022)
Isospin effect on baryon and charge fluctuations from the pNJL model
Creators: name: Liu, He
name: Xu, Jun
Publisher: name: arXiv
Year: 2017
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: We have studied the possible isospin corrections on the skewness and kurtosis of net-baryon and net-charge fluctuations in the isospin asymmetric matter formed in relativistic heavy-ion collisions at RHIC-BES energies, based on a 3-flavor polyakov-looped Nambu-Jona-Lasinio model. With typical scalar-isovector and vector-isovector couplings leading to the splitting of $u$ and $d$ quark chiral phase transition boundaries and critical points, we have observed dramatic isospin effects on the susceptibilities, especially those of net-charge fluctuations. Reliable experimental measurements at even lower collision energies are encouraged to confirm the observed isospin effects.
description: 7 pages, 4 figures
Additional file 3 of Midgut microbiota diversity of potato tuber moth associated with potato tissue consumed
Creators: name: Zheng, Yaqiang
name: Xiao, Guanli
name: Zhou, Wenwu
name: Gao, Yulin
name: Li, Zhengyue
name: Du, Guangzu
name: Chen, Bin
Publisher: name: figshare
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 3: Figure S3. Comparison of endophytic bacteria in leaves and tubers in two potato varieties.
Additional file 5: of Spherical Body Protein 2 truncated copy 11 as a specific Babesia bovis attenuation marker
Creators: name: Gallego-Lopez, Gina
name: Lau, Audrey
name: Brown, Wendy
name: Johnson, Wendell
name: Massaro Ueti
name: Suarez, Carlos
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Figure S4. Comprehensive amino acid sequence alignment of the SBP2 family members (n = 13). Members of the SBP2 proteins are highly conserved at the Nâ terminus and more variable at the Câ terminus. Exact identity values are shown in Additional file 1: Table S4. Red boxes indicate the PEXEL-like motif (PLM) and number of amino acids of each protein. Abbreviations: T, truncated; SBP, spherical body protein. (PDF 682 kb)
Robust Tube-based Model Predictive Control with Koopman Operators--Extended Version
Creators: name: Zhang, Xinglong
name: Pan, Wei
name: Scattolini, Riccardo
name: Yu, Shuyou
name: Xu, Xin
Publisher: name: arXiv
Year: 2021
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Koopman operators are of infinite dimension and capture the characteristics of nonlinear dynamics in a lifted global linear manner. The finite data-driven approximation of Koopman operators results in a class of linear predictors, useful for formulating linear model predictive control (MPC) of nonlinear dynamical systems with reduced computational complexity. However, the robustness of the closed-loop Koopman MPC under modeling approximation errors and possible exogenous disturbances is still a crucial issue to be resolved. Aiming at the above problem, this paper presents a robust tube-based MPC solution with Koopman operators, i.e., r-KMPC, for nonlinear discrete-time dynamical systems with additive disturbances. The proposed controller is composed of a nominal MPC using a lifted Koopman model and an off-line nonlinear feedback policy. The proposed approach does not assume the convergence of the approximated Koopman operator, which allows using a Koopman model with a limited order for controller design. Fundamental properties, e.g., stabilizability, observability, of the Koopman model are derived under standard assumptions with which, the closed-loop robustness and nominal point-wise convergence are proven. Simulated examples are illustrated to verify the effectiveness of the proposed approach.
description: 18 pages, 9 figures
Frame-dependence of higher-order inflationary observables in scalar-tensor theories
Creators: name: Karam, Alexandros
name: Pappas, Thomas
name: Tamvakis, Kyriakos
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In the context of scalar-tensor theories of gravity we compute the third-order corrected spectral indices in the slow-roll approximation. The calculation is carried out by employing the Green's function method for scalar and tensor perturbations in both the Einstein and Jordan frames. Then, using the interrelations between the Hubble slow-roll parameters in the two frames we find that the frames are equivalent up to third order. Since the Hubble slow-roll parameters are related to the potential slow-roll parameters, we express the observables in terms of the latter which are manifestly invariant. Nevertheless, the same inflaton excursion leads to different predictions in the two frames since the definition of the number of e-folds differs. To illustrate this effect we consider a nonminimal inflationary model and find that the difference in the predictions grows with the nonminimal coupling and it can actually be larger than the difference between the first and third order results for the observables. Finally, we demonstrate the effect of various end-of-inflation conditions on the observables. These effects will become important for the analyses of inflationary models in view of the improved sensitivity of future experiments.
description: Title changed per journal request, typos fixed, a few comments and references added, to appear in PRD
Hitting distribution of a correlated planar Brownian motion in a disk
Creators: name: Marchione, Manfred Marvin
name: Orsingher, Enzo
Publisher: name: arXiv
Year: 2021
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: In this paper we study the hitting probability of a circumference $C_R$ for a correlated Brownian motion $\underline{B}(t)=\left(B_1(t), B_2(t)\right)$, $ρ$ being the correlation coefficient. The analysis starts by first mapping the circle $C_R$ into an ellipse $E$ with semiaxes depending on $ρ$ and transforming the differential operator governing the hitting distribution into the classical Laplace operator. By means of two different approaches (one obtained by applying elliptic coordinates) we obtain the desired distribution as a series of Poisson kernels.
Additional file 1: of Emotional labor, workplace violence, and depressive symptoms in female Bank employees: a questionnaire survey using the K-ELS and K-WVS
Creators: name: Kim, Guang
name: Lee, Hee
name: Jung, Sung
name: Lee, Jae
name: Lee, June
name: Lee, Kyung
name: Kim, Joo
Publisher: name: figshare
Year: 2018
Subjects: subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Korean Emotional Labor Scale and Korean Workplace Violence Scale ( K-ELS & K-WVS). (DOCX 19 kb)
Study of $D_{s}^{+} \rightarrow K^{+} K^{-} π^{+}$ decay
Creators: name: Wang, Zhong-Yu
name: Yi, Jing-Yu
name: Sun, Zhi-Feng
name: Xiao, C. W.
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We investigate the $D_{s}^{+} \rightarrow K^{+} K^{-} π^{+}$ decay theoretically with the final state interactions, which is based on the chiral unitary approach and takes into account the external and internal $W$-emission mechanisms at the quark level. Only considering three resonances contributions, the $f_0(980)$ in $S$-wave, the $\bar {K}^{*}(892)^{0}$ and $ϕ(1020)$ in $P$-wave, one can make a good description of the recent experimental data from BESIII Collaboration, where the contribution from $S$-wave is found to be small. Besides, we also make a calculation of the corresponding branching fractions, which are consistent with the results of BESIII Collaboration and Particle Data Group.
description: More discussions were made. Welcome for comments
A systematic study of the class imbalance problem in convolutional neural networks
Creators: name: Buda, Mateusz
name: Maki, Atsuto
name: Mazurowski, Maciej A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: Neural and Evolutionary Computing (cs.NE)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: In this study, we systematically investigate the impact of class imbalance on classification performance of convolutional neural networks (CNNs) and compare frequently used methods to address the issue. Class imbalance is a common problem that has been comprehensively studied in classical machine learning, yet very limited systematic research is available in the context of deep learning. In our study, we use three benchmark datasets of increasing complexity, MNIST, CIFAR-10 and ImageNet, to investigate the effects of imbalance on classification and perform an extensive comparison of several methods to address the issue: oversampling, undersampling, two-phase training, and thresholding that compensates for prior class probabilities. Our main evaluation metric is area under the receiver operating characteristic curve (ROC AUC) adjusted to multi-class tasks since overall accuracy metric is associated with notable difficulties in the context of imbalanced data. Based on results from our experiments we conclude that (i) the effect of class imbalance on classification performance is detrimental; (ii) the method of addressing class imbalance that emerged as dominant in almost all analyzed scenarios was oversampling; (iii) oversampling should be applied to the level that completely eliminates the imbalance, whereas the optimal undersampling ratio depends on the extent of imbalance; (iv) as opposed to some classical machine learning models, oversampling does not cause overfitting of CNNs; (v) thresholding should be applied to compensate for prior class probabilities when overall number of properly classified cases is of interest.
Additional file 4: of Spherical Body Protein 2 truncated copy 11 as a specific Babesia bovis attenuation marker
Creators: name: Gallego-Lopez, Gina
name: Lau, Audrey
name: Brown, Wendy
name: Johnson, Wendell
name: Massaro Ueti
name: Suarez, Carlos
Publisher: name: figshare
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology

description: Figure S3. Nucleotide alignment of sbp2t11 gene in Australian and Texas B. bovis. (PDF 193 kb)
On the stability of projection methods for the incompressible Navier-Stokes equations based on high-order discontinuous Galerkin discretizations
Creators: name: Fehn, Niklas
name: Wall, Wolfgang A.
name: Kronbichler, Martin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Numerical Analysis (math.NA)
subject: Computational Physics (physics.comp-ph)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: The present paper deals with the numerical solution of the incompressible Navier-Stokes equations using high-order discontinuous Galerkin (DG) methods for discretization in space. For DG methods applied to the dual splitting projection method, instabilities have recently been reported that occur for coarse spatial resolutions and small time step sizes. By means of numerical investigation we give evidence that these instabilities are related to the discontinuous Galerkin formulation of the velocity divergence term and the pressure gradient term that couple velocity and pressure. Integration by parts of these terms with a suitable definition of boundary conditions is required in order to obtain a stable and robust method. Since the intermediate velocity field does not fulfill the boundary conditions prescribed for the velocity, a consistent boundary condition is derived from the convective step of the dual splitting scheme to ensure high-order accuracy with respect to the temporal discretization. This new formulation is stable in the limit of small time steps for both equal-order and mixed-order polynomial approximations. Although the dual splitting scheme itself includes inf-sup stabilizing contributions, we demonstrate that spurious pressure oscillations appear for equal-order polynomials and small time steps highlighting the necessity to consider inf-sup stability explicitly.
description: 31 pages
Retrieving cosmological information from small-scale CMB foregrounds I. The thermal Sunyaev Zel'dovich effect
Creators: name: Douspis, Marian
name: Salvati, Laura
name: Gorce, Adélie
name: Aghanim, Nabila
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We propose a new analysis of small scale CMB data by introducing the cosmological dependency of the foreground signals, focusing first on the thermal Sunyaev-Zel'dovich (tSZ) power spectrum, derived from the halo model. We analyse the latest observations by the South Pole Telescope (SPT) of the high-$\ell$ power (cross) spectra at 90, 150 and 220 GHz, as the sum of CMB and tSZ signals, both depending on cosmological parameters, and remaining contaminants. In order to perform faster analyses, we propose a new tSZ modelling based on machine learning algorithms (namely Random Forest). We show that the additional information contained in the tSZ power spectrum tightens constraints on cosmological and tSZ scaling relation parameters. We combine for the first time the Planck tSZ data with SPT high-$\ell$ to derive even stronger constraints. Finally, we show how the amplitude of the remaining kSZ power spectrum varies depending on the assumptions made on both tSZ and cosmological parameters.
description: Accepted in A&A, Random Forest code for tSZ spectra computation is available on IAS SZ portal SZDB: https://szdb.osups.universite-paris-saclay.fr/
Additional file 2: of Fatty fish intake and cognitive function: FINS-KIDS, a randomized controlled trial in preschool children
Creators: name: Jannike ĂYen
name: Kvestad, Ingrid
name: MidtbĂ¸, Lisa
name: Graff, Ingvild
name: Hysing, Mari
name: Stormark, Kjell
name: Markhus, Maria
name: Baste, Valborg
name: Livar FrĂ¸Yland
name: Koletzko, Berthold
name: Demmelmair, Hans
name: Dahl, Lisbeth
name: ĂYvind Lie
name: Kjellevold, Marian
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Computational Biology

description: Table S2. Dietary intake (background diet) presented as number of meals per week at pre- and post- intervention and mean change. Figure S1. Percentages of the participants (n = 197) who comply with the different recommendations in the diet score at baseline. Figure S2. Overview of the percentage of participants (n = 197) with diet score sums from zero to eight points at baseline. (PDF 452 kb)
Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
Creators: name: Cang, Zixuan
name: Mu, Lin
name: Wei, Guowei
Publisher: name: arXiv
Year: 2017
Subjects: subject: Quantitative Methods (q-bio.QM)
subject: Biomolecules (q-bio.BM)
subject: FOS: Biological sciences

description: This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the representation, characterization, and description of small molecules and biomolecular complexes. Multicomponent persistent homology retains critical chemical and biological information during the topological simplification of biomolecular geometric complexity. Multi-level persistent homology enables a tailored topological description of inter- and/or intra-molecular interactions of interest. Electrostatic persistence incorporates partial charge information into topological invariants. These topological methods are paired with Wasserstein distance to characterize similarities between molecules and are further integrated with a variety of machine learning algorithms, including k-nearest neighbors, ensemble of trees, and deep convolutional neural networks, to manifest their descriptive and predictive powers for chemical and biological problems. Extensive numerical experiments involving more than 4,000 protein-ligand complexes from the PDBBind database and near 100,000 ligands and decoys in the DUD database are performed to test respectively the scoring power and the virtual screening power of the proposed topological approaches. It is demonstrated that the present approaches outperform the modern machine learning based methods in protein-ligand binding affinity predictions and ligand-decoy discrimination.