cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 3: of Pharmacological characterisation of CR6086, a potent prostaglandin E2 receptor 4 antagonist, as a new potential disease-modifying anti-rheumatic drug
Creators: name: Caselli, Gianfranco
name: Bonazzi, Albino
name: Lanza, Marco
name: Ferrari, Flora
name: Maggioni, Daniele
name: Ferioli, Cristian
name: Giambelli, Roberto
name: Comi, Eleonora
name: Zerbi, Silvia
name: Perrella, Marco
name: Letari, Ornella
name: Luccio, Elena Di
name: Colovic, Milena
name: Persiani, Stefano
name: Zanelli, Tiziano
name: Mennuni, Laura
name: Piepoli, Tiziana
name: Rovati, Lucio
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Data table showing cytokine serum concentrations (pg/ml) of samples determined from 3-PLEX (MSD) in CIA mice. Arthritis was induced in mice by intradermal injection of bovine type II collagen. Upon onset, animals were recruited and randomised into experimental groups. Oral treatments with drugs were administered daily and lasted 10 days. At the end of the study, sera were isolated for determination of indicated cytokines by multiplex analysis on the MSD platform (Artialis, LiĂ¨ge, Belgium). Data represent mean Âą SEM of the number of animals per group: N = 8 (sham, vehicle, 30 mg/kg CR6086), 6 (60 mg/kg CR6086) and 7 (60 mg/kg naproxen). (DOCX 40 kb)
title: ADCO, Cartulaire de l'abbaye de Saint-Seine (XIIIe siècle), Cart. 165 (10 H 6, ms. 139), 354 pages, f. 0072
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2009
name: Petot, Frédéric
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire

description: Cartulaire de l'abbaye de Saint-Seine (XIIIe siècle), Archives départementales de la Côte-d'Or, Cart. 165 (10 H 6, ms. 139), 354 pages, f. 0072, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire de l'abbaye de Saint-Seine (XIIIe siècle), Archives départementales de la Côte-d'Or, Cart. 165 (10 H 6, ms. 139), 354 pages, f. 0072, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye de Saint-Seine
description: Provenance: http://www.wikidata.org/entity/Q2820709
The Impact of Damping in Second-Order Dynamical Systems with Applications to Power Grid Stability
Creators: name: Gholami, Amin
name: Sun, X. Andy
Publisher: name: arXiv
Year: 2020
Subjects: subject: Dynamical Systems (math.DS)
subject: Systems and Control (eess.SY)
subject: FOS: Mathematics
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: We consider a broad class of second-order dynamical systems and study the impact of damping as a system parameter on the stability, hyperbolicity, and bifurcation in such systems. We prove a monotonic effect of damping on the hyperbolicity of the equilibrium points of the corresponding first-order system. This provides a rigorous formulation and theoretical justification for the intuitive notion that damping increases stability. To establish this result, we prove a matrix perturbation result for complex symmetric matrices with positive semidefinite perturbations to their imaginary parts, which may be of independent interest. Furthermore, we establish necessary and sufficient conditions for the breakdown of hyperbolicity of the first-order system under damping variations in terms of observability of a pair of matrices relating damping, inertia, and Jacobian matrices, and propose sufficient conditions for Hopf bifurcation resulting from such hyperbolicity breakdown. The developed theory has significant applications in the stability of electric power systems, which are one of the most complex and important engineering systems. In particular, we characterize the impact of damping on the hyperbolicity of the swing equation model which is the fundamental dynamical model of power systems, and demonstrate Hopf bifurcations resulting from damping variations.
From atomistic model to the Peierls-Nabarro model with $γ$-surface for dislocations
Creators: name: Luo, Tao
name: Ming, Pingbing
name: Xiang, Yang
Publisher: name: arXiv
Year: 2017
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: The Peierls-Nabarro (PN) model for dislocations is a hybrid model that incorporates the atomistic information of the dislocation core structure into the continuum theory. In this paper, we study the convergence from a full atomistic model to the PN model with $γ$-surface for the dislocation in a bilayer system (e.g. bilayer graphene). We prove that the displacement field of and the total energy of the dislocation solution of the PN model are asymptotically close to those of the full atomistic model. Our work can be considered as a generalization of the analysis of the convergence from atomistic model to Cauchy-Born rule for crystals without defects in the literature.
description: 45 pages, 2 figures
Additional file 1: of Therapeutic and pharmaco-biological, dose-ranging multicentre trial to determine the optimal dose of TRAnexamic acid to reduce blood loss in haemorrhagic CESarean delivery (TRACES): study protocol for a randomised, double-blind, placebo-controlled trial
Creators: name: Anne-Sophie Bouthors
name: Hennart, Benjamin
name: Jeanpierre, Emmanuelle
name: Anne-Sophie Baptiste
name: Imen Saidi
name: Simon, Elodie
name: Lannoy, Damien
name: Duhamel, Alain
name: Allorge, Delphine
name: Susen, Sophie
Publisher: name: figshare
Year: 2018
Subjects: Medicine
Cell Biology
Pharmacology
Cancer
Science Policy

description: Trial publication spirit check list. (DOC 130 kb)
The Erdős-Gyárfás function with respect to Gallai-colorings
Creators: name: Li, Xihe
name: Broersma, Hajo
name: Wang, Ligong
Publisher: name: arXiv
Year: 2020
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C55, 05D10

description: For fixed $p$ and $q$, an edge-coloring of the complete graph $K_n$ is said to be a $(p, q)$-coloring if every $K_p$ receives at least $q$ distinct colors. The function $f(n, p, q)$ is the minimum number of colors needed for $K_n$ to have a $(p, q)$-coloring. This function was introduced about 45 years ago, but was studied systematically by Erdős and Gyárfás in 1997, and is now known as the Erdős-Gyárfás function. In this paper, we study $f(n, p, q)$ with respect to Gallai-colorings, where a Gallai-coloring is an edge-coloring of $K_n$ without rainbow triangles. Combining the two concepts, we consider the function $g(n, p, q)$ that is the minimum number of colors needed for a Gallai-$(p, q)$-coloring of $K_n$. Using the anti-Ramsey number for $K_3$, we have that $g(n, p, q)$ is nontrivial only for $2\leq q\leq p-1$. We give a general lower bound for this function and we study how this function falls off from being equal to $n-1$ when $q=p-1$ and $p\geq 4$ to being $Θ(\log n)$ when $q = 2$. In particular, for appropriate $p$ and $n$, we prove that $g=n-c$ when $q=p-c$ and $c\in \{1,2\}$, $g$ is at most a fractional power of $n$ when $q=\lfloor\sqrt{p-1}\rfloor$, and $g$ is logarithmic in $n$ when $2\leq q\leq \lfloor\log_2 (p-1)\rfloor+1$.
description: 25 pages
title: ADCO, Cart. 186 (11 H 71), f. 0411v
Creators: name: de la Côte d'Or, Archives départementales
name: Petot, Frédéric
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CBMA/CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, t. II (XVe siècle), tome II, Archives départementales de la Côte-d'Or, C
art. 186 (11 H 71). Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire général de Cîteaux, dit de Jean de Cirey, t. II (XVe siècle), tome II, Archives départementales de la
 Côte-d'Or, Cart. 186 (11 H 71), f. 0411v, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-
project.eu/
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
Dimensional Regularization of Renyi's Statistical Mechanics
Creators: name: Plastino, A.
name: Rocca, M. C.
name: Rocca, M. C.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We show that typical Renyi's statistical mechanics' quantifiers exhibit poles. We are referring to the partition function ${\cal Z}$ and the mean energy $$. Renyi's entropy is characterized by a real parameter $α$. The poles emerge in a numerable set of rational numbers belonging to the $α-$line. Physical effects of these poles are studied by appeal to dimensional regularization, as usual. Interesting effects are found, as for instance, gravitational ones.
description: 22 pages, 3 figures. Text has changed. References added
Additional file 1: of High-Sensitivity and High-Resolution In Situ Hybridization of Coding and Long Non-coding RNAs in Vertebrate Ovaries and Testes
Creators: name: Takei, Natsumi
name: Nakamura, Takuma
name: Kawamura, Shohei
name: Takada, Yuki
name: Satoh, Yui
name: Kimura, Atsushi
name: Kotani, Tomoya
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: Developmental Biology
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: Table S1. Reagents used in this study. Table S2. RNA probes used for detection of target mRNAs. Table S3. Sequences of transcripts used for making RNA probes in this study. Figure S1. Single in situ hybridization of Pou5f1/Oct4 mRNA in mouse ovaries. (A-D) Sections hybridized with the sense (A and C) or antisense (B and D) Pou5f1/Oct4 RNA probe with amplification of signals using the TSA system (+TSA). Bars: 100 μm. Figure S2. Double fluorescence in situ hybridization of mos and cyclin B1 mRNAs in zebrafish ovaries. (A-C) A section hybridized with the sense probes for mos and cyclin B1 mRNAs in a fully grown oocyte. (D-F) A section hybridized with the antisense probes for mos and cyclin B1 mRNAs in a fully grown oocyte. Bars: 50 μm in A-C, 10 μm in D-F. Figure S3. Double fluorescence in situ hybridization of cyclin B1 and dazl mRNAs in zebrafish ovaries. (A-D) Sections hybridized with the sense probes for cyclin B1 and dazl mRNAs. Follicles consisting of stage Ia (A), stage Ib (B), stage II (C), and stage III (D) oocytes. (E-H) Sections hybridized with the antisense probes for cyclin B1 and dazl mRNAs. Follicles consisting of stage Ia (E), stage Ib (F), stage II (G), and stage III (H) oocytes. Bars: 20 μm in A, B, E and F, 50 μm in C, D, G and H. Figure S4. Double fluorescence in situ hybridization of Cyclin B1 and Dazl mRNAs in mouse ovaries. (A) A section hybridized with the sense probes for Cyclin B1 and Dazl mRNAs. (B and C) Sections hybridized with the antisense probes for Cyclin B1 and Dazl mRNAs. Bars: 20 μm. Figure S5. Fluorescence in situ hybridization of lncRNA-HSVIII in mouse testes. (A-B) Transverse sections of seminiferous tubules hybridized with the fluorescein-labeled sense (A) and antisense (B) probes. (C-F) Transverse sections of seminiferous tubules hybridized with the DIG-labeled sense (C and E) and antisense (D and F) probes. Bars: 50 μm. (PDF 16.6 mb)
Additional file 6 of Splicing factor SRSF1 promotes breast cancer progression via oncogenic splice switching of PTPMT1
Creators: name: Du, Jun-Xian
name: Luo, Yi-Hong
name: Zhang, Si-Jia
name: Wang, Biao
name: Chen, Cong
name: Zhu, Gui-Qi
name: Zhu, Ping
name: Cai, Cheng-Zhe
name: Wan, Jing-Lei
name: Cai, Jia-Liang
name: Chen, Shi-Ping
name: Dai, Zhi
name: Zhu, Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 6: Supplementary Table 2
ATCN: Resource-Efficient Processing of Time Series on Edge
Creators: name: Baharani, Mohammadreza
name: Tabkhi, Hamed
Publisher: name: arXiv
Year: 2020
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: This paper presents a scalable deep learning model called Agile Temporal Convolutional Network (ATCN) for high-accurate fast classification and time series prediction in resource-constrained embedded systems. ATCN is a family of compact networks with formalized hyperparameters that enable application-specific adjustments to be made to the model architecture. It is primarily designed for embedded edge devices with very limited performance and memory, such as wearable biomedical devices and real-time reliability monitoring systems. ATCN makes fundamental improvements over the mainstream temporal convolutional neural networks, including residual connections to increase the network depth and accuracy, and the incorporation of separable depth-wise convolution to reduce the computational complexity of the model. As part of the present work, two ATCN families, namely T0, and T1 are also presented and evaluated on different ranges of embedded processors - Cortex-M7 and Cortex-A57 processor. An evaluation of the ATCN models against the best-in-class InceptionTime and MiniRocket shows that ATCN almost maintains accuracy while improving the execution time on a broad range of embedded and cyber-physical applications with demand for real-time processing on the embedded edge. At the same time, in contrast to existing solutions, ATCN is the first time-series classifier based on deep learning that can be run bare-metal on embedded microcontrollers (Cortex-M7) with limited computational performance and memory capacity while delivering state-of-the-art accuracy.
description: Published in ACM Trans. Embed. Comput. Syst. (March 2022)
Additional file 1: of “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system
Creators: name: A. Naas
name: L. Solden
name: A. Norbeck
name: H. Brewer
name: L. Hagen
name: I. Heggenes
name: A. McHardy
name: R. Mackie
name: L. Paša-Tolić
name: M. Arntzen
name: V. Eijsink
name: N. Koropatkin
name: M. Hess
name: K. Wrighton
name: P. Pope
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Figure S1. Two-way average nucleotide identity (blue) and average amino acid identity (red) values calculated for reference Bacteroidetes genomes and the AGa genome. (DOCX 386 kb)
title: ADCO, Cart. 186 (11 H 71), f. 0101v
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: Petot, Frédéric
name: CBMA/CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire
subject: LaMOP

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, t. II (XVe siècle), tome II, Archives départementales de la Côte-d'Or, C
art. 186 (11 H 71). Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire général de Cîteaux, dit de Jean de Cirey, t. II (XVe siècle), tome II, Archives départementales de la
 Côte-d'Or, Cart. 186 (11 H 71), f. 0101v, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-
project.eu/
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
description: Provenance: http://www.wikidata.org/entity/Q843261
description: Provenance: abbaye de Cîteaux
Theory of superconductivity with non-Hermitian and parity-time reversal symmetric cooper pairing symmetry
Creators: name: Ghatak, Ananya
name: Das, Tanmoy
Publisher: name: arXiv
Year: 2017
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Recently developed parity (P) and time-reversal (T) symmetric non-Hermitian systems govern a rich variety of new and characteristically distinct physical properties, which may or may not have a direct analog in their Hermitian counterparts. We study here a non-Hermitian, PT-symmetric superconducting Hamiltonian that possesses real quasiparticle spectrum in the PT-region of the Brillouin zone. Within a single-band mean-field theory, we find that real quasiparticle energies are possible when the superconducting order parameter itself is either Hermitian or anti-Hermitian. Within the corresponding Bardeen-Cooper-Schrieffer (BCS) theory, we find that several properties are characteristically distinct and novel in the non-Hermitian pairing case than its Hermitian counterpart. One of our significant findings is that while a Hermitian superconductor gives a second order phase transition, the non-Hermitian one produces a robust first order phase transition. The corresponding thermodynamic properties, and the Meissner effect are also modified accordingly. Finally, we discuss how such a PT-symmetric pairings can emerge from an anti-symmetric potential, such as the Dzyloshinskii-Moria interaction, but with an external external bath, or complex potential, among others.
description: 15 pages including appendices (2 columns), (v2): Hermitian pairing solution of the DM interaction is added; and conditions for obtaining non-Hermitian pairings are further delineated
Wayback Machine: A tool to capture the evolutionary behaviour of the bug reports and their triage process in open-source software systems
Creators: name: Jahanshahi, Hadi
name: Cevik, Mucahit
name: Navas-Sú, José
name: Başar, Ayşe
name: González-Torres, Antonio
Publisher: name: arXiv
Year: 2020
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: The issue tracking system (ITS) is a rich data source for data-driven decision-making. Different characteristics of bugs, such as severity, priority, and time to fix, provide a clear picture of an ITS. Nevertheless, such information may be misleading. For example, the exact time and the effort spent on a bug might be significantly different from the actual reporting time and the fixing time. Similarly, these values may be subjective, e.g., severity and priority values are assigned based on the intuition of a user or a developer rather than a structured and well-defined procedure. Hence, we explore the evolution of the bug dependency graph together with priority and severity levels to explore the actual triage process. Inspired by the idea of the "Wayback Machine" for the World Wide Web, we aim to reconstruct the historical decisions made in the ITS. Therefore, any bug prioritization or bug triage algorithms/scenarios can be applied in the same environment using our proposed ITS Wayback Machine. More importantly, we track the evolutionary metrics in the ITS when a custom triage/prioritization strategy is employed. We test the efficiency of the proposed algorithm using data extracted from three open-source projects. Our empirical study sheds light on the overlooked evolutionary metrics--e.g., overdue bugs and developers' loads--which are facilitated via our proposed past-event re-generator.
description: 43 Pages - Accepted for the Journal of Systems & Software
A Derivation of AdS/CFT for Vector Models
Creators: name: Aharony, Ofer
name: Chester, Shai M.
name: Urbach, Erez Y.
Publisher: name: arXiv
Year: 2020
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We explicitly rewrite the path integral for the free or critical $O(N)$ (or $U(N)$) bosonic vector models in $d$ space-time dimensions as a path integral over fields (including massless high-spin fields) living on ($d+1$)-dimensional anti-de Sitter space. Inspired by de Mello Koch, Jevicki, Suzuki and Yoon and earlier work, we first rewrite the vector models in terms of bi-local fields, then expand these fields in eigenmodes of the conformal group, and finally map these eigenmodes to those of fields on anti-de Sitter space. Our results provide an explicit (non-local) action for a high-spin theory on anti-de Sitter space, which is presumably equivalent in the large $N$ limit to Vasiliev's classical high-spin gravity theory (with some specific gauge-fixing to a fixed background), but which can be used also for loop computations. Our mapping is explicit within the $1/N$ expansion, but in principle can be extended also to finite $N$ theories, where extra constraints on products of bulk fields need to be taken into account.
description: 71 pages + appendices (2 figures); v2: minor changes and added references; v3: minor changes; v4: corrected the discussion of the mass deformation when $d \neq 3$
Additional file 2: of Pharmacological characterisation of CR6086, a potent prostaglandin E2 receptor 4 antagonist, as a new potential disease-modifying anti-rheumatic drug
Creators: name: Caselli, Gianfranco
name: Bonazzi, Albino
name: Lanza, Marco
name: Ferrari, Flora
name: Maggioni, Daniele
name: Ferioli, Cristian
name: Giambelli, Roberto
name: Comi, Eleonora
name: Zerbi, Silvia
name: Perrella, Marco
name: Letari, Ornella
name: Luccio, Elena Di
name: Colovic, Milena
name: Persiani, Stefano
name: Zanelli, Tiziano
name: Mennuni, Laura
name: Piepoli, Tiziana
name: Rovati, Lucio
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Inorganic Chemistry
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Data tables showing the cross-reactivity data for CR6086: 10 eicosanoid receptors, 2 cyclooxygenase isoforms and 76 receptors/transporters/channels. (DOCX 58 kb)
Onsager's variational principle in active soft matter
Creators: name: Wang, Haiqin
name: Qian, Tiezheng
name: Xu, Xinpeng
Publisher: name: arXiv
Year: 2020
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Onsager's variational principle (OVP) was originally proposed by Lars Onsager in 1931 [L. Onsager, $Phys. Rev.$, 1931, $37$, 405]. This fundamental principle provides a very powerful tool for formulating thermodynamically consistent models. It can also be employed to find approximate solutions, especially in the study of soft matter dynamics. In this work, OVP is extended and applied to the dynamic modeling of active soft matter such as suspensions of bacteria and aggregates of animal cells. We first extend the general formulation of OVP to active matter dynamics where active forces are included as external non-conservative forces. We then use OVP to analyze the directional motion of individual active units: a molecular motor walking on a stiff biofilament and a toy two-sphere microswimmer. Next, we use OVP to formulate a diffuse-interface model for an active polar droplet on a solid substrate. In addition to the generalized hydrodynamic equations for active polar fluids in the bulk region, we have also derived thermodynamically consistent boundary conditions. Finally, we consider the dynamics of a thin active polar droplet under the lubrication approximation. We use OVP to derive a generalized thin film equation and then employ OVP as an approximation tool to find the spreading laws for the thin active polar droplet. By incorporating the activity of biological systems into OVP, we develop a general approach to construct thermodynamically consistent models for better understanding the emergent behaviors of individual animal cells and cell aggregates or tissues.
Relativistic Gas Drag on Dust Grains and Implications
Creators: name: Hoang, Thiem
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We study the drag force on dust grains moving at relativistic velocities through interstellar gas and explore its application. First, we derive a new analytical formula of the drag force at high energies and find that it is significantly reduced compared to the classical model. Second, we apply the obtained drag force to calculate the terminal velocities of interstellar grains by strong radiation sources such as supernovae and active galactic nuclei (AGNs). We find that grains can be accelerated to relativistic velocities by very luminous AGNs. We then quantify the deceleration of relativistic spacecraft proposed by the Breakthrough Starshot initiative due to gas drag on a relativistic lightsail. We find that the spacecraft's slowing down is negligible because of the suppression of gas drag at relativistic velocities, suggesting that the lightsail may be open for communication during its journey to $α$ Centauri without causing a considerable delay. Finally, we show that the damage to relativistic thin lightsails by interstellar dust is a minor effect.
description: ApJ, in press; 7 pages, 5 figures
Continuum elastic models for force transmissions in biopolymer gels
Creators: name: Wang, Haiqin
name: Xu, Xinpeng
Publisher: name: arXiv
Year: 2020
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We review continuum elastic models for the transmission of both external forces and internal active cellular forces in biopolymer gels, and relate them to recent experiments. Rather than being exhaustive, we focus on continuum elastic models for small affine deformations and intend to provide a systematic continuum method and some analytical perspectives to the study of force transmissions in biopolymer gels. We start from a very brief review of the nonlinear mechanics of individual biopolymers and a summary of constitutive models for the nonlinear elasticity of biopolymer gels. We next show that the simple 3-chain model can give predictions that well fit the shear experiments of some biopolymer gels, including the effects of strain-stiffening and negative normal stress. We then review continuum models for the transmission of internal active forces that are induced by a spherically contracting cell embedded in a three-dimensional biopolymer gel. Various scaling regimes for the decay of cell-induced displacements are identified for linear isotropic and anisotropic materials, and for biopolymer gels with nonlinear compressive-softening and strain-stiffening elasticity, respectively. After that, we present (using an energetic approach) the generic and unified continuum theory proposed in [Ben-Yaakov, Soft Matter, 2015, 11, 1412] about how the transmission of forces in the biogel matrix can mediate long-range interactions between cells with mechanical homeostasis. We show the predictions of the theory in a special hexagonal multicellular array, and relate them to recent experiments. Finally, we conclude this paper with comments on the limitations and outlook of continuum modeling, and highlight the needs of complementary theoretical approaches such as discrete network simulations to force transmissions in biopolymer gels and phenomenological active gel theories for multicellular systems.
Simulated Galactic methanol maser distribution to constrain Milky Way parameters
Creators: name: Quiroga-Nuñez, L. H.
name: van Langevelde, H. J.
name: Reid, M. J.
name: Green, J. A.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Using trigonometric parallaxes and proper motions of masers associated with massive young stars, the Bar and Spiral Structure Legacy (BeSSeL) survey has reported the most accurate values of the Galactic parameters so far. The determination of these parameters with high accuracy has a widespread impact on Galactic and extragalactic measurements. This research is aimed at establishing the confidence with which such parameters can be determined. This is relevant for the data published in the context of the BeSSeL survey collaboration, but also for future observations, in particular from the Southern Hemisphere. In addition, some astrophysical properties of the masers can be constrained, notably the luminosity function. We have simulated the population of maser-bearing young stars associated with Galactic spiral structure, generating several samples and comparing them with the observed samples used in the BeSSeL survey. Consequently, we checked the determination of Galactic parameters for observational biases introduced by the sample selection. Galactic parameters obtained by the BeSSeL survey do not seem to be biased by the sample selection used. In fact, the published error estimates appear to be conservative for most of the parameters. We show that future BeSSeL data and future observations with Southern arrays will improve the Galactic parameters estimates and smoothly reduce their mutual correlation. Moreover, by modeling future parallax data with larger distance and, thus, greater relative uncertainties for a larger numbers of sources, we found that parallax-distance biasing is an important issue. Hence, using fractional parallax uncertainty in the weighting of the motion data is imperative. Finally, the luminosity function for 6.7 GHz methanol masers was determined, allowing us to estimate the number of Galactic methanol masers.
description: Accepted for publication in A&A. Language edition included
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome V, Cart. 189 (11 H 74), 316 folios, f. 0248v
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome V, Archives départementales de la Côte-d'Or, Cart. 189 (11 H 74), 316 folios, f. 0248v, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome V, Archives départementales de la Côte-d'Or, Cart. 189 (11 H 74), 316 folios, f. 0248v, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
Additional file 7 of Splicing factor SRSF1 promotes breast cancer progression via oncogenic splice switching of PTPMT1
Creators: name: Du, Jun-Xian
name: Luo, Yi-Hong
name: Zhang, Si-Jia
name: Wang, Biao
name: Chen, Cong
name: Zhu, Gui-Qi
name: Zhu, Ping
name: Cai, Cheng-Zhe
name: Wan, Jing-Lei
name: Cai, Jia-Liang
name: Chen, Shi-Ping
name: Dai, Zhi
name: Zhu, Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 7: Supplementary Table 3
การพัฒนารูปแบบระบบส่งต่อผู้ป่วยโรคเรื้อนและการเพิ่มคุณภาพงานควบคุมโรคเรื้อน ภายใต้สภาวการณ์ความชุกต่ำ จังหวัดสุรินทร์
Creators: name: สุชัญญา มานิตย์ศิริกุล
Publisher: name: สำนักจัดการความรู้ กรมควบคุมโรค กระทรวงสาธารณสุข
Year: 2558
Subjects: การพัฒนารูปแบบ
โรคเรื้อน

description: วารสารควบคุมโรค, 41, 3, 170-178
Additional file 18: of “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system
Creators: name: A. Naas
name: L. Solden
name: A. Norbeck
name: H. Brewer
name: L. Hagen
name: I. Heggenes
name: A. McHardy
name: R. Mackie
name: L. Paša-Tolić
name: M. Arntzen
name: V. Eijsink
name: N. Koropatkin
name: M. Hess
name: K. Wrighton
name: P. Pope
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
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

description: Table S7. Expression constructs used in this study. (DOCX 13 kb)
Active elastocapillarity in soft solids with negative surface tension
Creators: name: Binysh, Jack
name: Wilks, Thomas R.
name: Souslov, Anton
Publisher: name: arXiv
Year: 2021
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: Active solids consume energy to allow for actuation, shape change, and wave propagation not possible in equilibrium. Whereas active interfaces have been realized across many experimental systems, control of three-dimensional (3D) bulk materials remains a challenge. Here, we develop continuum theory and microscopic simulations that describe a 3D soft solid whose boundary experiences active surface stresses. The competition between active boundary and elastic bulk yields a broad range of previously unexplored phenomena, which are demonstrations of so-called active elastocapillarity. In contrast to thin shells and vesicles, we discover that bulk 3D elasticity controls snap-through transitions between different anisotropic shapes. These transitions meet at a critical point, allowing a universal classification via Landau theory. The active surface modifies elastic wave propagation to allow zero, or even negative, group velocities. These phenomena offer robust principles for programming shape change and functionality into active solids, from robotic metamaterials down to shape-shifting nanoparticles.
description: 16 pages including Methods, 6 figures. See https://youtu.be/04bqs0VKFCc for Supplementary Movie
Zero resistance from one atmosphere to the pressure of earth's outer core in a superconducting high entropy alloy
Creators: name: Guo, Jing
name: Wang, Honghong
name: von Rohr, Fabian
name: Wang, Zhe
name: Cai, Shu
name: Zhou, Yazhou
name: Yang, Ke
name: Li, Aiguo
name: Jiang, Sheng
name: Wu, Qi
name: Cava, Robert J
name: Sun, Liling
Publisher: name: arXiv
Year: 2017
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We report the observation of extraordinarily robust zero-resistance superconductivity in the pressurized (TaNb)0.67(HfZrTi)0.33 high entropy alloy - a new kind of material with a body-centered cubic crystal structure made from five randomly distributed transition metal elements. The transition to superconductivity (TC) increases from an initial temperature of 7.7 K at ambient pressure to 10 K at ~ 60 GPa, and then slowly decreases to 9 K by 190.6 GPa, a pressure that falls within that of the outer core of the earth. We infer that the continuous existence of the zero-resistance superconductivity from one atmosphere up to such a high pressure requires a special combination of electronic and mechanical characteristics. This high entropy alloy superconductor thus may have a bright future for applications under extreme conditions, and also poses a challenge for understanding the underlying quantum physics.
description: 15 pages and 4 figures
Deterministic parallel analysis: An improved method for selecting factors and principal components
Creators: name: Dobriban, Edgar
name: Owen, Art B.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: Factor analysis and principal component analysis (PCA) are used in many application areas. The first step, choosing the number of components, remains a serious challenge. Our work proposes improved methods for this important problem. One of the most popular state-of-the-art methods is Parallel Analysis (PA), which compares the observed factor strengths to simulated ones under a noise-only model. This paper proposes improvements to PA. We first de-randomize it, proposing Deterministic Parallel Analysis (DPA), which is faster and more reproducible than PA. Both PA and DPA are prone to a shadowing phenomenon in which a strong factor makes it hard to detect smaller but more interesting factors. We propose deflation to counter shadowing. We also propose to raise the decision threshold to improve estimation accuracy. We prove several consistency results for our methods, and test them in simulations. We also illustrate our methods on data from the Human Genome Diversity Project, where they significantly improve the accuracy.
description: Made title consistent with published version
Differentially Private SGD with Non-Smooth Losses
Creators: name: Wang, Puyu
name: Lei, Yunwen
name: Ying, Yiming
name: Zhang, Hai
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (stat.ML)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences
subject: 62P99

description: In this paper, we are concerned with differentially private {stochastic gradient descent (SGD)} algorithms in the setting of stochastic convex optimization (SCO). Most of the existing work requires the loss to be Lipschitz continuous and strongly smooth, and the model parameter to be uniformly bounded. However, these assumptions are restrictive as many popular losses violate these conditions including the hinge loss for SVM, the absolute loss in robust regression, and even the least square loss in an unbounded domain. We significantly relax these restrictive assumptions and establish privacy and generalization (utility) guarantees for private SGD algorithms using output and gradient perturbations associated with non-smooth convex losses. Specifically, the loss function is relaxed to have an $α$-Hölder continuous gradient (referred to as $α$-Hölder smoothness) which instantiates the Lipschitz continuity ($α=0$) and the strong smoothness ($α=1$). We prove that noisy SGD with $α$-Hölder smooth losses using gradient perturbation can guarantee $(ε,δ)$-differential privacy (DP) and attain optimal excess population risk $\mathcal{O}\Big(\frac{\sqrt{d\log(1/δ)}}{nε}+\frac{1}{\sqrt{n}}\Big)$, up to logarithmic terms, with the gradient complexity $ \mathcal{O}( n^{2-α\over 1+α}+ n).$ This shows an important trade-off between $α$-Hölder smoothness of the loss and the computational complexity for private SGD with statistically optimal performance. In particular, our results indicate that $α$-Hölder smoothness with $α\ge {1/2}$ is sufficient to guarantee $(ε,δ)$-DP of noisy SGD algorithms while achieving optimal excess risk with the linear gradient complexity $\mathcal{O}(n).$
description: 29 pages, 1 table, 1 figure
Additional file 1: of Pharmacological characterisation of CR6086, a potent prostaglandin E2 receptor 4 antagonist, as a new potential disease-modifying anti-rheumatic drug
Creators: name: Caselli, Gianfranco
name: Bonazzi, Albino
name: Lanza, Marco
name: Ferrari, Flora
name: Maggioni, Daniele
name: Ferioli, Cristian
name: Giambelli, Roberto
name: Comi, Eleonora
name: Zerbi, Silvia
name: Perrella, Marco
name: Letari, Ornella
name: Luccio, Elena Di
name: Colovic, Milena
name: Persiani, Stefano
name: Zanelli, Tiziano
name: Mennuni, Laura
name: Piepoli, Tiziana
name: Rovati, Lucio
Publisher: name: figshare
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Science Policy

description: Chemical structure of CR6086. (DOCX 41 kb)
Additional file 8 of Splicing factor SRSF1 promotes breast cancer progression via oncogenic splice switching of PTPMT1
Creators: name: Du, Jun-Xian
name: Luo, Yi-Hong
name: Zhang, Si-Jia
name: Wang, Biao
name: Chen, Cong
name: Zhu, Gui-Qi
name: Zhu, Ping
name: Cai, Cheng-Zhe
name: Wan, Jing-Lei
name: Cai, Jia-Liang
name: Chen, Shi-Ping
name: Dai, Zhi
name: Zhu, Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Additional file 8: Supplementary Table 4
Dynamic susceptibilities in dense soft athermal spheres under a finite-rate shear
Creators: name: Oyama, Norihiro
name: Kawasaki, Takeshi
name: Saitoh, Kuniyasu
Publisher: name: arXiv
Year: 2021
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: The mechanical responses of dense packings of soft athermal spheres under a finite-rate shear are studied by means of molecular dynamics simulations. We investigate the volume fraction and shear rate dependence of the fluctuations in the shear stress and the interparticle contact number. In particular, we quantify them by defining the susceptibility as the ratio of the global to local fluctuations. The obtained susceptibilities form ridges on the volume fraction-shear rate plane, which are reminiscent of the Widom lines around the critical point in an equilibrium phase transition.
description: 10 pages, 9 figures
Approximate analytic solution of the potential flow around a rectangle
Creators: name: Kim, Eunice J.
name: Kim, Ildoo
Publisher: name: arXiv
Year: 2017
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Applications (stat.AP)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: In undergraduate classes, the potential flow that goes around a circular cylinder is designed for complemental understanding of mathematical technique to handle the Laplace equation with Neumann boundary conditions and the physical concept of the multipolar expansion. The simplicity of the standard problem is suited for the introductory level, however, it has a drawback. The discussion of higher order multipoles is often missed because the exact analytic solution contains only the dipole term. In this article, we present a modified problem of the potential flow around a rectangle as an advanced problem. Although the exact solution of this case is intractable, the approximate solution can be obtained by the discretization and the optimization using multiple linear regression. The suggested problem is expected to deepen the students' insight on the concept of multipoles and also provides an opportunity to discuss the formalism of the regression analysis, which in many physics curricula is lacking even though it has a significant importance in experimental physics.
description: v2 (year 2019, 12 pages, 2 figures) v1 (year 2015, 13 pages, 5 figures)
Armstrong's Axioms and Navigation Strategies
Creators: name: Deuser, Kaya
name: Naumov, Pavel
Publisher: name: arXiv
Year: 2017
Subjects: subject: Artificial Intelligence (cs.AI)
subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: The paper investigates navigability with imperfect information. It shows that the properties of navigability with perfect recall are exactly those captured by Armstrong's axioms from the database theory. If the assumption of perfect recall is omitted, then Armstrong's transitivity axiom is not valid, but it can be replaced by two new weaker principles. The main technical results are soundness and completeness theorems for the logical systems describing properties of navigability with and without perfect recall.
Additional file 5: of A hypomorphic inherited pathogenic variant in DDX3X causes male intellectual disability with additional neurodevelopmental and neurodegenerative features
Creators: name: Kellaris, Georgios
name: Khan, Kamal
name: Baig, Shahid
name: I-Chun Tsai
name: Zamora, Francisca
name: Ruggieri, Paul
name: Natowicz, Marvin
name: Katsanis, Nicholas
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology

description: Figure S2. Dose-response effect of WNT3A and overexpression of DDX3X variants does not produce alterations in Wnt signaling. (A) Injection of WNT3A produces dose-dependent changes in ventralization. Embryos were scored at 48Â h post fertilization for degree of ventralization. (B) Zebrafish embryos were injected with 100Â pg of DDX3X mRNA containing either the wild-type sequence or the non-synonymous variants found in the affected individuals. At 36Â h, post-fertilization (hpf) the embryos were phenotyped; no abnormalities could be appreciated. (PDF 1438 kb)