cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Understanding the patient journey to diagnosis of lung cancer
Creators: name: Yichen Zhang
name: Simoff, Michael J.
name: Ost, David
name: Wagner, Oliver J.
name: Lavin, James
name: Nauman, Beth
name: Mei-Chin Hsieh
name: Wu, Xiao-Cheng
name: Pettiford, Brian
name: Lizheng Shi
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1: Appendix 1. Master Code list.
Formation and evolution of binary black holes in $N$-body simulations of star clusters with up to two million stars
Creators: name: Barber, Jordan
name: Antonini, Fabio
Publisher: name: arXiv
Year: 2024
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Understanding binary black hole (BBH) dynamics in dense star clusters is key to interpreting the gravitational wave detections by LIGO and Virgo. Here, we perform $N$-body simulations of star clusters, focusing on BBH formation mechanisms, dynamical evolution and merging properties. We explore a wide parameter space of initial conditions, with cluster masses ranging from $10^{4}$ to $10^{6}~\mathrm{M_{\odot}}$, densities from $10^{3}$ to $10^{5}~\rm M_{\odot}pc^{-3}$, and up to $100\%$ of massive stars in binaries. We show that most BBH mergers originate from the primordial binary population rather than being dynamically assembled, and that the evolution towards merger for most of these binaries is not significantly altered by dynamical encounters. As a result, the overall number of BBH mergers from the $N$-body simulations is nearly identical to that obtained when the same stellar population is evolved in isolation. Contrary to theoretical expectations, nearly all dynamically formed BBH mergers occur when the binary is still bound to its host cluster, with $\simeq 90\%$ of all dynamical mergers occurring within the cluster core region. In about half of these mergers the binary is part of a stable black hole-triple system. In one model, stellar mergers lead to the formation of a $\simeq 200\,\mathrm{M_\odot}$ black hole, which then grows to $\simeq 300\,\mathrm{M_\odot}$ through black hole mergers. Our study highlights the importance of detailed $N$-body simulations in capturing the evolution of black hole populations in dense clusters and challenges conclusions based on semi-analytical and Monte Carlo methods.
description: Accepted for publication in Monthly Notices of the Royal Astronomical Society
Spatially heterogeneous dynamics and dynamic facilitation in a model of viscous silica
Creators: name: Vogel, Michael
name: Glotzer, Sharon C.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: Performing molecular dynamics simulations, we find that the structural relaxation dynamics of viscous silica, the prototype of a strong glass former, are spatially heterogeneous and cannot be understood as a statistical bond breaking process. Further, we show that high particle mobility predominantly propagates continuously through the melt, supporting the concept of dynamic facilitation emphasized in recent theoretical work.
description: 4 pages, 4 figures
Fluctuations of topological disclination lines in nematics: renormalization of the string model
Creators: name: Svensek, D.
name: Zumer, S.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: The fluctuation eigenmode problem of the nematic topological disclination line with strength $\pm 1/2$ is solved for the complete nematic tensor order parameter. The line tension concept of a defect line is assessed, the line tension is properly defined. Exact relaxation rates and thermal amplitudes of the fluctuations are determined. It is shown that within the simple string model of the defect line the amplitude of its thermal fluctuations is significantly underestimated due to the neglect of higher radial modes. The extent of universality of the results concerning other systems possessing line defects is discussed.
description: 6 pages, 3 figures
Electro-optic eigenfrequency tuning of potassium tantalate-niobate microresonators
Creators: name: Szabados, Jan
name: Werner, Christoph S.
name: Herr, Simon J.
name: Breunig, Ingo
name: Buse, Karsten
Publisher: name: arXiv
Year: 2019
Subjects: subject: Optics (physics.optics)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Eigenfrequency tuning in microresonators is useful for a range of applications including frequency-agile optical filters and tunable optical frequency converters. In most of these applications, eigenfrequency tuning is achieved by thermal or mechanical means, while a few non-centrosymmetric crystals such as lithium niobate allow for such tuning using the linear electro-optic effect. Potassium tantalate-niobate ($\mathrm{KTa}_{1-x}\mathrm{Nb}_{x}\mathrm{O}_{3}$ with $0\leq x \leq1$, KTN) is a particularly attractive material for electro-optic tuning purposes. It has both non-centrosymmetric and centrosymmetric phases offering outstandingly large linear as well as quadratic electro-optic coefficients near the phase transition temperature. We demonstrate whispering-gallery resonators (WGRs) made of KTN with quality factors of $Q>10^{7}$ and electro-optic eigenfrequency tuning of more than 100 GHz at $λ=1040\,$nm for moderate field strengths of $E=250\,$V/mm. The tuning behavior near the phase transition temperature is analyzed by introducing a simple theoretical model. These results pave the way for applications such as electro-optically tunable microresonator-based Kerr frequency combs.
description: Letter, 4 figures, 6 pages
Measuring the ISM Content of Nearby, Luminous, Type 1 and Type 2 QSOs through CO and [C II]
Creators: name: Luo, Yuanze
name: Petric, A. O.
name: Janssen, R. M. J.
name: Fadda, D.
name: Flagey, N.
name: Omont, A.
name: Jacob, A. M.
name: Rowlands, K.
name: Alatalo, K.
name: Billot, N.
name: Heckman, T.
name: Husemann, B.
name: Kakkad, D.
name: Lacy, M.
name: Marshall, J.
name: Minchin, R.
name: Minsley, R.
name: Nesvadba, N.
name: Otter, J. A.
name: Patil, P.
name: Urrutia, T.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present observations of CO(1--0) and CO(2--1) lines from the Institut de radioastronomie millimétrique (IRAM) 30m telescope toward 20 nearby, optically luminous type 2 quasars (QSO2s) and observations of [C II] 158$μ$m line from the Stratospheric Observatory For Infrared Astronomy (SOFIA) for 5 QSO2s in the CO sample and 5 type 1 quasars (QSO1s). In the traditional evolutionary scenario explaining different types of QSOs, obscured QSO2s emerge from gas-rich mergers observed as luminous infrared galaxies (LIRGs) and then turn into unobscured QSO1s as the black holes clear out the obscuring material in a blow-out phase. We test the validity of this theoretical prediction by comparing the gas fractions and star formation efficiencies among LIRGs and QSOs. We find that CO luminosity, CO-derived gas masses and gas fractions in QSO1s are consistent with those estimated for QSO2s, while LIRGs exhibit a closer resemblance to QSO2s in terms of CO-derived gas masses and gas fractions. Comparisons between [C II] luminosity and star formation tracers such as the CO and infrared luminosity imply additional sources of [C II] emission in QSO1s likely tracing neutral atomic or ionized gas with the caveat of a small sample size. All three types of galaxies have statistically indistinguishable distributions of star formation efficiency. Our results are consistent with part of the evolutionary scenario where nearby QSO2s could emerge from LIRGs, but they may not be the precursors of nearby QSO1s.
description: 33 pages, 10 figures, 7 tables; the complete set of Figure 1 is appended to the end of document. Accepted for publication by ApJ
MOESM2 of Cardiac function evaluation for a novel one-step detoxification product of Aconiti Lateralis Radix Praeparata
Creators: name: He, Ya-nan
name: Zhang, Ding-kun
name: Lin, Jun-zhi
name: Han, Xue
name: Zhang, Ya-ming
name: Zhang, Hai-zhu
name: Pei, Jin
name: Yang, Ming
name: Wang, Jia-bo
Publisher: name: figshare
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 2. The Content Determination of Eight Alkaloids in NAP and HSP by HPLC-MS/MS.
Saddles in the energy landscape: extensivity and thermodynamic formalism
Creators: name: Shell, M. S.
name: Debenedetti, P. G.
name: Panagiotopoulos, A. Z.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system size, as well as several approximations for the properties of low-order saddles (i.e., those with only a few unstable directions). We then cast the canonical partition function in a saddle-explicit form and develop, for the first time, a rigorous energy landscape approach capable of reproducing trends observed in simulations, in particular the temperature dependence of the energy and fractional order of sampled saddles.
description: 4 pages, 1 figure
Tigris: Architecture and Algorithms for 3D Perception in Point Clouds
Creators: name: Xu, Tiancheng
name: Tian, Boyuan
name: Zhu, Yuhao
Publisher: name: arXiv
Year: 2019
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Machine perception applications are increasingly moving toward manipulating and processing 3D point cloud. This paper focuses on point cloud registration, a key primitive of 3D data processing widely used in high-level tasks such as odometry, simultaneous localization and mapping, and 3D reconstruction. As these applications are routinely deployed in energy-constrained environments, real-time and energy-efficient point cloud registration is critical. We present Tigris, an algorithm-architecture co-designed system specialized for point cloud registration. Through an extensive exploration of the registration pipeline design space, we find that, while different design points make vastly different trade-offs between accuracy and performance, KD-tree search is a common performance bottleneck, and thus is an ideal candidate for architectural specialization. While KD-tree search is inherently sequential, we propose an acceleration-amenable data structure and search algorithm that exposes different forms of parallelism of KD-tree search in the context of point cloud registration. The co-designed accelerator systematically exploits the parallelism while incorporating a set of architectural techniques that further improve the accelerator efficiency. Overall, Tigris achieves 77.2$\times$ speedup and 7.4$\times$ power reduction in KD-tree search over an RTX 2080 Ti GPU, which translates to a 41.7% registration performance improvements and 3.0$\times$ power reduction.
description: Published at MICRO-52 (52nd IEEE/ACM International Symposium on Microarchitecture); Tiancheng Xu and Boyuan Tian are co-primary authors
Effect of whole soy and purified daidzein on androgenic hormones in chinese equol-producing post-menopausal women: a six-month randomised, double-blinded and Placebo-Controlled trial
Creators: name: Liu, Zhao-Min
name: Guoyi Li
name: Zhang, Di
name: Ho, Suzanne C.
name: Chen, Yu-Ming
name: Ma, Jing
name: Huang, Qi
name: Shuyi Li
name: Ling, Wen-Hua
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Computational Biology

description: A randomised, double-blind and placebo-controlled trial was performed to examine the effects of whole soy and isoflavone daidzein on serum androgenic hormones in Chinese equol-producing post-menopausal women. A total of 270 eligible women aged 45–70 years were randomised to either one of the three iso-caloric supplements: 40 g soy flour (whole soy group), 40 g low-fat milk powder +63 mg daidzein (daidzein group) or 40 g low-fat milk powder (placebo group) daily for 6 months. Fasting venous samples were tested for serum androstenedione (AD), testosterone (T), prolactin, sex hormone binding globulin and dehydroepiandrosterone sulphate. Intention-to-treat analysis indicated that serum T (p = .022) and AD (p = .05) levels modestly but significantly decreased after 6-month daidzein treatment in comparison with placebo, with a mean difference of –0.057 nmol/L (95%CI: –0.185 to 0.070, p = .018) and –0.118 ng/mL (95%CI: –0.240–0.004, p = .045), respectively. This 6-month trial suggested that purified daidzein may exhibit less androgenic effect.Trial registration: The trial was registered in ClinicalTrials.gov with identifier of NCT01270737. (URL: http://clinicaltrials.gov/ct2/show/NCT01270737.) Trial registration: The trial was registered in ClinicalTrials.gov with identifier of NCT01270737. (URL: http://clinicaltrials.gov/ct2/show/NCT01270737.)
title: Testing the limits of the ‘hard man’ in film: masculinity and male health behaviour in Scotland’s public health films 1934-2000
Creators: name: Chandler, Alex Steven
Publisher: name: University of Glasgow
Year: 2021
Subjects: subject: Public health, public health film, Scottish masculinities, toxic masculinity, hegemonic masculinities, filmmaking, public health policy, gender stereotypes, gender performance, smoking, alcohol misuse, drug misuse, Sexual Health.

description: Often adapted from long standing hegemonies of masculine bravery and strength, and visible in a wide range of Scottish popular art, literature, and film, not to mention certain Hollywood adaptations, the Scottish hard-man character has infiltrated many aspects of the country’s history and culture1. Most recently, a particular form of this character – a stubborn, strong-willed version, wary of official health intervention and reckless with his own health behaviours – has emerged within both popular and academic attempts to explain some of Scotland’s public health problems and their often-disproportionate effects on Scottish men2. But who is the Scottish hard man, what does he look like, what does he say, how does he behave and what is his relationship to the country’s public health problems? In order to answer some of these questions, this thesis turns to the texts in which the visual images of the hard-man are most closely linked to his health behaviours – public health film. Three years of archive research has uncovered a wealth of film and accompanying public health materials that variously attempt to challenge or control men’s public health behaviours. From state sponsored public health films to locally organised campaigns, these texts are filled with visual representations of Scottish masculinity as well as the bodies, the medicines, the tools, the doctors, the patients and the spaces of 20th century public health language. Tracing the steps of the Sottish hard-man character through these texts, I aim to discover how this figure has been constructed and utilised in public health film and what this can tell us about the cultural connections between gender, the media and health in the 20th century and beyond.
Calf Muscle Strain Injuries in Sport
Creators: name: Green, Brady
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 420702
subject: Exercise physiology
classificationCode: 420799
subject: Sports science and exercise not elsewhere classified
classificationCode: 420106
subject: Physiotherapy

description: Submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy to the La Trobe Sport and Exercise Medicine Research Centre, Department of Physiotherapy, Podiatry, Prosthetics and Orthotics, School of Allied Health, Human Services and Sport, College of Science, Health and Engineering, La Trobe University, Victoria, Australia.
Uncertainty Propagation in a Multiscale CALPHAD-Reinforced Elastochemical Phase-field Model
Creators: name: Attari, Vahid
name: Honarmandi, Pejman
name: Duong, Thien
name: Sauceda, Daniel J
name: Allaire, Douglas
name: Arroyave, Raymundo
Publisher: name: arXiv
Year: 2019
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: ICME approaches provide decision support for materials design by establishing quantitative process-structure-property relations. Confidence in the decision support, however, must be achieved by establishing uncertainty bounds in ICME model chains. The quantification and propagation of uncertainty in computational materials science, however, remains a rather unexplored aspect of computational materials science approaches. Moreover, traditional uncertainty propagation frameworks tend to be limited in cases with computationally expensive simulations. A rather common and important model chain is that of CALPHAD-based thermodynamic models of phase stability coupled to phase field models for microstructure evolution. Propagation of uncertainty in these cases is challenging not only due to the sheer computational cost of the simulations but also because of the high dimensionality of the input space. In this work, we present a framework for the quantification and propagation of uncertainty in a CALPHAD-based elasto-chemical phase field model. We motivate our work by investigating the microstructure evolution in Mg$_2$(Si$_x$Sn$_{1-x}$) thermoelectric materials. We first carry out a Markov Chain Monte Carlo-based inference of the CALPHAD model parameters for this pseudobinary system and then use advanced sampling schemes to propagate uncertainties across a high-dimensional simulation input space. Through high-throughput phase field simulations we generate 200,000 time series of synthetic microstructures and use machine learning approaches to understand the effects of propagated uncertainties on the microstructure landscape of the system under study. The microstructure dataset has been curated in the Open Phase-field Microstructure Database (OPMD), available at \href{http://microstructures.net}{http://microstructures.net}.
Supplemental data from A newly identified trigeminal brain pathway in a night-migratory bird could be dedicated to transmitting magnetic map information
Creators: name: Kobylkov, Dmitry
name: Schwarze, Susanne
name: Michalik, Bianca
name: Winklhofer, Michael
name: Mouritsen, Henrik
name: Heyers, Dominik
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Neuroscience
subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology
subject: 60801 Animal Behaviour
subject: FOS: Biological sciences

description: Figure S1. (A-D) Highly replicable retrograde tracing patterns from NFT into PrVv between 4 different individual Eurasian blackcaps (Sylvia atricapilla). (E) Closely matching retrograde tracing pattern in the distantly related, non-migratory, chicken (GG, Gallus gallus). (F) Retrograde tracer transport from NFT into the contralateral posterior pallial amygdala (PoA) [30]. (G) Anterograde tracer transport from NFT to the ipsilateral caudolateral nidopallium (NCL) [31]. (H) Bidirectional connectivities between NFT and the ventral part of the frontal mesopallium (MFV) [32]. (I) PrVd neuron labelled with HuC/HuD closely matches in size and morphology of (J) PrVd neuron retrogradely labelled from NB. (K) PrVv neuron labelled with HuC/HuD closely matches in size and morphology of (L) PrVv neuron retrogradely labelled from NFT. Note the obvious morphological and size differences between PrVd (I/J) and PrVv (K/L) neurons. Abbreviations: BC, Eurasian blackcap (Sylvia atricapilla); CtB, Cholera toxin B subunit; GG, domestic chicken (Gallus gallus); PrVd, Dorsal part of the principal sensory trigeminal nucleus; PrVv, Ventral part of the principal sensory trigeminal nucleus. Scale bars: D (for A-D): 100 µm; E, F, G, H: 200 µm; J (for I and J): 10 µm; L (for K and L): 10 µm.
Unitarity at the LHC energies
Creators: name: Troshin, S. M.
name: Tyurin, N. E.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Phenomena related to the non-perturbative aspects of strong interactions at the LHC are discussed with emphasis on elastic and inelastic soft and hard diffraction processes. Predictions for the global characteristics and angular distributions in proton-proton collisions with elastic and multiparticle final states are given. Potential for discovery of the novel effects related to the increasing role of the elastic scattering at the LHC energies and its physical implications in diffractive and multiparticle production processes are reviewed.
description: 25 pages, 7 figures
The Effect of Peanut and Walnut Shells powders on Tensile and Microstructure of the PMMA for prosthetic Denture
Creators: name: Oleiwi, Jawad K.
Publisher: name: figshare
Year: 2021
Subjects: subject: 90301 Biomaterials
subject: FOS: Medical engineering
subject: 91202 Composite and Hybrid Materials
subject: FOS: Materials engineering
subject: 91299 Materials Engineering not elsewhere classified

description: In the current research, the heat-cured matrix material powder of PMMA was reinforced with Peanut and Walnut Shells (natural powders) which are chemically treated with 5% (w/v) (NaOH) to improve the matrix bonding (PMMA) before being used as a reinforcing powder and adding to exactly similar averages particle sizes ≤ (53μm), with different weight fractions of (4, 8, and 12 wt.%). The results indicated that the Elastic modulus values reached their maximum value at (8 wt.%.) when reinforced with Peanut Shells powders (1.053Gpa), while, the values of tensile strength, elongation percentage at the break, decrease as the weight fraction of Peanut and Walnut Shells powders increase and the lowest values are obtained by reinforcing with Peanut Shells powders to reach their minimum values at (12 wt.%) where the lowest values of them are (29 MPa, 2.758%) respectively. The fracture surface morphology of pure PMMA seemed to be homogenous morphology in (SEM) test, whereas the fracture surface morphology of PMMA composite reinforced by (Peanut and Walnut Shells) powders and shows a smoothness fracture surface morphology this refers to brittle to semi ductile or ductile transformation.
Multiplicity fluctuations in the Glauber Monte Carlo approach
Creators: name: Deliyergiyev, Maksym
name: Rybczynski, Maciej
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We discuss multiplicity fluctuations of charged particles produced in nuclear collisions measured event-by-event by the NA49 experiment at CERN SPS within the Glauber Monte Carlo approach. We use the concepts of wounded nucleons and wounded quarks in the mechanism of multiparticle production to characterize multiplicity fluctuations expressed by the scaled variance of multiplicity distribution. Although Wounded Nucleon Model correctly reproduce the centrality dependence of the average multiplicity in Pb+Pb collisions, it completely fails in description of corresponding centrality dependence of scaled variance of multiplicity distribution. Using subnucleonic degrees of freedom, i.e. wounded quarks within Wounded Quark Model, it is possible to describe quite well the multiplicity distribution of charged particles produced in proton+proton interactions. However, the Wounded Quark Model with parameters describing multiplicity distribution of particles produced in proton+proton interactions substantially exceeds the average multiplicity of charged particles produced in Pb+Pb collisions. To obtain values of average multiplicities close to those experimentally measured in Pb+Pb collisions, the concept of shadowed quark sources is implemented. Wounded Quark Model with implemented shadowing source scenario reproduces the centrality dependence of scaled variance of multiplicity distribution of charged particles produced in Pb+Pb collisions in the range from the most central to mid-peripheral interactions.
description: 18 pages, 8 figures
UK ORCID Consortium Update May 2021
Creators: name: Duke, Monica
Publisher: name: Zenodo
Year: 2021
Subjects: ORCID
UK
Consortium
Jisc
UKRI
Peer review

description: Presentation on the highlights and plans of the UK ORCID Consortium since the last meeting (August 2020) and looking forward Outline: The team What we do Current shape of the consortium Highlights 2020-2021 5 year anniversary celebration UKRI and peer review News: pricing 2022-24 2021-22 priorities and plans
Tachiuo
Creators: name: Lab of Systems and Network Biology
name: Hsu, Po-Cheng
name: Chuang, Wei-Hsuan
name: Hsieh, Ping-Heng
name: Chen, Shu-Hwa
name: Chao-lun Allen, Chao-lun Allen
name: Lin, Chung-Yen
Publisher: name: Zenodo
Year: 2025

description: This repository contains the structural, functional and topological annotation of Trichiurus japonicus.For fasta files, the nuclear genome itself is available in NCBI. Here we deposited only mitochondria genome, and structural annotation result.

 

Class

File name

Tools

Database

Sequence assembly
T_jap_mito.fasta
 –
 –

Repeat annotation
T_jap_repeat.gffT_jap_repeat_table
Tetools 1.89.2
partition 0, 2 and 6 of Dfam 3.8Repbase (2018/10/26)

Structural annotation

T_jap_merged_fix.gff.gz

T_jap_merged_fix.gtf.gz

braker3:v3.0.7.6mitos (v2.1.9)INFERNAL 1.1.5 (cmscan)tRNAscan‑SE 2.0.12

custom python script for merging gff from braker/mitos/infernal/trnascan-se

AGAT (v1.4.1) gff to gtf

Odbv12/UniProtKB_7898/ncbi_1489894RefSeq 89 MetazoaRfam 15.0

 

T_jap_combined_gene.faT_jap_combined_trans.faT_jap_combined_CDS.faT_jap_combined_pep.fa

parse with custom script, using bedtools (v2.31.1) to mask intron and extract sequence

extract CDS with gffread (v0.12.7)

combined braker3:v3.0.7.6 and mitos (v2.1.9) result and modify .t -> .p and removed * (stop codon)

-

Functional annotation
T_jap_diamond.tsv
diamond (v2.1.10.164)
nr.000–125

 
T_jap_interproscan_result.tsv
InterProScan‑5.73‑104.0
AntiFam-8.0CDD-3.21Coils-2.2.1FunFam-4.3.0Gene3D-4.3.0Hamap-2023_05MobiDBLite-4.0NCBIfam-17.0PANTHER-19.0Pfam-37.2PIRSF-3.10PIRSR-2023_05PRINTS-42.0ProSitePatterns-2023_05ProSiteProfiles-2023_05SFLD-4SMART-9.0SUPERFAMILY-1.75

 
T_jap_kaas_ghostz.tar.gz
KEGG Automatic Annotation Server 2.1ghostz + BBH method
Fishes

Topological annotation
T_jap_deeptmhmm.tsv
DeepTMHMM 1.0.24
 –
Periodic solutions for completely resonant nonlinear wave equations
Creators: name: Gentile, Guido
name: Mastropietro, Vieri
name: Procesi, Michela
Publisher: name: arXiv
Year: 2004
Subjects: subject: Dynamical Systems (math.DS)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: We consider the nonlinear string equation with Dirichlet boundary conditions $u_{xx}-u_{tt}=ϕ(u)$, with $ϕ(u)=Φu^{3} + O(u^{5})$ odd and analytic, $Φ\neq0$, and we construct small amplitude periodic solutions with frequency $ø$ for a large Lebesgue measure set of $ø$ close to 1. This extends previous results where only a zero-measure set of frequencies could be treated (the ones for which no small divisors appear). The proof is based on combining the Lyapunov-Schmidt decomposition, which leads to two separate sets of equations dealing with the resonant and nonresonant Fourier components, respectively the Q and the P equations, with resummation techniques of divergent powers series, allowing us to control the small divisors problem. The main difficulty with respect the nonlinear wave equations $u_{xx}-u_{tt}+ M u = ϕ(u)$, $M\neq0$, is that not only the P equation but also the Q equation is infinite-dimensional
Subtraction terms at NNLO
Creators: name: Weinzierl, Stefan
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Perturbative calculations at next-to-next-to-leading order for multi-particle final states require a method to cancel infrared singularities. I discuss the subtraction method at NNLO. As a concrete example I consider the leading-colour contributions to e+ e- --> 2 jets. This is the simplest example which exhibits all essential features. For this example, explicit subtraction terms are given, which approximate the four-parton and three-parton final states in all double and single unresolved limits, such that the subtracted matrix elements can be integrated numerically.
description: 41 pages
Heavy Flavour Jet Substructure
Creators: name: Dhani, Prasanna K.
name: Fedkevych, Oleh
name: Ghira, Andrea
name: Marzani, Simone
name: Soyez, Gregory
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present a comprehensive study of energy correlation functions and jet angularities for heavy-flavour QCD jets. In particular, we discuss the possibility of using these observables to expose the dead cone effect, i.e. the suppression of collinear QCD radiation around massive quarks, and to investigate the sensitivity of different observable definitions to the presence of quark masses. Our calculations are presented as all-order resummed predictions at next-to-leading-logarithmic accuracy, matched to (partial) fixed-order results to obtain a better description of the transition around the dead cone threshold. We also compare our analytic results with Pythia, Herwig and Sherpa Monte Carlo predictions to estimate the impact of non-perturbative contributions such as hadronisation, underlying events and $B$-hadron decays.
description: 41 pages, 8 figures, version accepted by JHEP
Leveraging spurious Omori-Utsu relation in the nearest-neighbor declustering method
Creators: name: Puy, Andreu
name: Baró, Jordi
name: Davidsen, Jörn
name: Pastor-Satorras, Romualdo
Publisher: name: arXiv
Year: 2024
Subjects: subject: Geophysics (physics.geo-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Static and dynamic stress changes in the Earth's crust induced by an earthquake typically trigger other earthquakes. Identifying such aftershocks is an important step in seismic hazard assessment but has remained challenging, especially in cases involving natural fluid migration or anthropogenic fluid injections, which can occur with varying time scales and/or episodically, leading to strong temporal variations in earthquake occurrences. Here, we demonstrate analytically and numerically that earthquake catalogs without triggering can lead to spurious Omori-Utsu and productivity relations for the commonly used nearest-neighbor declustering method. However, we show that the robustness of the Omori-Utsu exponent on newly introduced parameters of the method allows one to determine whether indeed aftershocks are present. For a natural swarm catalog, which lacks a clear distinction between triggered and background events, we find that the catalog is dominated by aftershocks.
description: Main paper (11 pages) + Supplementary Material (11 pages)
Bounding the generalization error of convex combinations of classifiers: balancing the dimensionality and the margins
Creators: name: Koltchinskii, Vladimir
name: Panchenko, Dmitry
name: Lozano, Fernando
Publisher: name: arXiv
Year: 2004
Subjects: subject: Probability (math.PR)
subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62G05

description: A problem of bounding the generalization error of a classifier f in H, where H is a "base" class of functions (classifiers), is considered. This problem frequently occurs in computer learning, where efficient algorithms of combining simple classifiers into a complex one (such as boosting and bagging) have attracted a lot of attention. Using Talagrand's concentration inequalities for empirical processes, we obtain new sharper bounds on the generalization error of combined classifiers that take into account both the empirical distribution of "classification margins'' and an "approximate dimension" of the classifiers and study the performance of these bounds in several experiments with learning algorithms.
description: 35 pages, 7 figures
Evaluation of Centralized and Distributed Microgrid Topologies Considering Power Quality Constraints
Creators: name: Dunham, Hallie
name: Cutler, Dylan
name: Mishra, Sakshi
name: Li, Xiangkun
Publisher: name: arXiv
Year: 2019
Subjects: subject: Systems and Control (eess.SY)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Integration of renewable generation and energy storage technologies with conventional generation supports increased resilience, lower-costs, and clean energy goals. Traditionally, energy supply needs of rural off-grid communities have been addressed with diesel-generation. But with rapidly falling renewable generation costs, mini-grids are transforming into hybrid systems with a mix of renewables, energy storage, and diesel-generation. Optimal design of hybrid mini-grid requires an understanding of both the economic and power quality impacts of different designs. Existing approaches to modeling distributed energy resources address the economic viability and power quality impacts via separate/loosely coupled models. Here, we extend REopt - a techno-economic optimization model developed at National Renewable Energy Laboratory - to consider both within a single model. REopt formulates the design problem as a mixed-integer linear program that solves a deterministic optimization problem for a site's optimal technology mix, sizing, and operation to minimize life cycle cost. REopt has traditionally not constrained the power injection based on power quality. In the work presented here, we expand the REopt platform to consider multiple connected nodes. In order to do this, we model power flow using a fixed-point linear approximation method. Resulting system sizes and voltage magnitudes are validated against the base REopt model, and solutions of established power flow models respectively. We then use the model to explore design considerations of mini-grids in Sub-Saharan Africa. Specifically, we evaluate under what combinations of line length and line capacity it is economically beneficial (or technically required based on voltage limits) to build isolated mini-grids versus an interconnected system that benefits from the economies of scale associated with a single, centralized generation system.
description: under review
title: "FourVirx, IP Strategy"
Creators: name: Leibowitch, Jacques (1942-2020)
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020

description: Document sur la start-up créée en 2010.
Density of states of a binary Lennard-Jones Glass
Creators: name: Faller, Roland
name: de Pablo, Juan J.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We calculate the density of states of a binary Lennard-Jones glass using a recently proposed Monte Carlo algorithm. Unlike traditional molecular simulation approaches, the algorithm samples distinct configurations according to self-consistent estimates of the density of states, thereby giving rise to uniform internal-energy histograms. The method is applied to simulate the equilibrium, low-temperature thermodynamic properties of a widely studied glass former consisting of a binary mixture of Lennard-Jones particles. We show how a density-of-states algorithm can be combined with particle identity swaps and configurational bias techniques to study that system. Results are presented for the energy and entropy below the mode coupling temperature.
description: 6 pages, 3 figures, accepted by J Chem Phys
Concrete Billiard Arrays of Polynomial Type and Leonard Systems
Creators: name: Vineyard, Jimmy
Publisher: name: arXiv
Year: 2024
Subjects: subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: 05E30, 17B37, 15A21

description: Let $d$ denote a nonnegative integer and let $\mathbb{F}$ denote a field. Let $V$ denote a $d+1$ dimensional vector space over $\mathbb{F}$. Given an ordering $\{θ_i\}_{i=0}^d$ of the eigenvalues of a multiplicity-free linear map $A: V \to V$, we construct a Concrete Billiard Array $\mathcal{L}$ with the property that for $0 \leq i \leq d$, the $i^{\rm th}$ vector on its bottom border is in the $θ_i$-eigenspace of $A$. The Concrete Billiard Array $\mathcal{L}$ is said to have polynomial type. We also show the following. Assume that there exists a Leonard system $Φ=(A;\{E_i\}_{i=0}^d;A^*;\{E_i^*\}_{i=0}^d)$ where $E_i$ is the primitive idempotent of $A$ corresponding to $θ_i$ for $0 \leq i \leq d$. Then, we show that after a suitable normalization, the left (resp. right) boundary of $\mathcal{L}$ corresponds to the $Φ$-split (resp. $Φ^{\Downarrow}$-split) decomposition of $V$.
description: 14 pages
Random Metric Spaces and Universality
Creators: name: Vershik, A. M.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Representation Theory (math.RT)
subject: Geometric Topology (math.GT)
subject: Metric Geometry (math.MG)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 28-XX,60-XX,51-XX

description: WWe define the notion of a random metric space and prove that with probability one such a space is isometricto the Urysohn universal metric space. The main technique is the study of universal and random distance matrices; we relate the properties of metric (in particulary universal) space to the properties of distance matrices. We show the link between those questions and classification of the Polish spaces with measure (Gromov or metric triples) and with the problem about S_{\infty}-invariant measures in the space of symmetric matrices. One of the new effects -exsitence in Urysohn space so called anarchical uniformly distributed sequences. We give examples of other categories in which the randomness and universality coincide (graph, etc.).
description: 38 PAGES
Supplementary data to Barriers on establishing passive strategies in office spaces: a case study in a historic university building
Creators: name: Saraiva, Nuno Baía
name: Pereira, Luisa Dias
name: Gaspar, Adélio Rodrigues
name: Da Costa, José Joaquim
Publisher: name: Zenodo
Year: 2021
Subjects: Data article
Heritage building
Thermal comfort
Office buildings
Field survey
Free cooling
PMV-PPD indices
TSV

description: The data presented in the article are related to the research article entitled "Barriers on establishing passive strategies in office spaces: a case study in a historic university building", submitted to the SI "Advances in Historic Buildings Conservation and Energy Efficiency" (energies) (https://bit.ly/32jclpv), currently under review.
Implications of partially degenerate neutrinos at a high scale in the light of KamLAND and WMAP
Creators: name: Joshipura, Anjan S.
name: Mohanty, Subhendra
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Electroweak radiative corrections can generate the neutrino (mass)$^2$ difference required for the large mixing angle solution (LMA) to the solar neutrino problem if two of the neutrinos are assumed degenerate at high energy. We test this possibility with the existing experimental knowledge of the low energy neutrino mass and mixing parameters. We derive restrictions on ranges of the high scale mixing matrix elements and obtain predictions for the low energy parameters required in order to get the LMA solution of the solar neutrino problem picked out by KamLAND. We find that in the case of standard model this is achieved only when the (degenerate) neutrino masses lie in the range $(0.7-2) \eV$ which is at odds with the cosmological limit $m_ν<0.23 \eV$ (at $95 % C.L$) established recently using WMAP results. Thus SM radiative corrections cannot easily generate the LMA solution in this scenario. However, the LMA solution is possible in case of the MSSM electroweak corrections with (almost) degenerate spectrum or with inverted mass hierarchy for limited ranges in the high scale parameters.
description: 15 pages, LATEX includes five postscript figures
The Intermediate Phase in Ternary GexAsxSe1-2x Glasses
Creators: name: Qu, Tao
name: Georgiev, D. G.
name: Boolchand, P.
name: Micoulaut, M.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: Melt-quenched AsxGexSe1-2x glasses over the composition range, 0 < x < 0.26, are examined in Raman scattering, T-modulated Differential Scanning Calorimetry (MDSC), and 119Sn Mossbauer spectroscopy measurements. The non-reversing enthalpy near Tg, DHnr(x), accessed from MDSC shows a global minimum (~ 0) in the xc(1) = 0.09 < x < xc(2) = 0.16 range, and increases by an order of magnitude both at x < xc(1) and at x > xc(2). Raman mode frequency of corner-sharing Ge(Se1/2)4 tetrahedra studied as a function of x, also shows three distinct regimes (or power-laws, p) that coincide with DHnr(x) trends. These regimes are identified with mechanically floppy (x < xc(1)), intermediate (xc(1) < x < xc(2)), and stressed-rigid (x > xc(2)) phases. The Raman elasticity power-law in the intermediate phase, p1 = 1.04(3), and in the stressed rigid phase, p2= 1.52(5), suggest effective dimensionalities of d = 2 and 3 respectively.
Plethystic formulas for permutation enumeration
Creators: name: Gessel, Ira M.
name: Zhuang, Yan
Publisher: name: arXiv
Year: 2020
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05A05, 05A15, 05E05

description: We prove several general formulas for the distributions of various permutation statistics over any set of permutations whose quasisymmetric generating function is a symmetric function. Our formulas involve certain kinds of plethystic substitutions on quasisymmetric generating functions, and the permutation statistics we consider include the descent number, peak number, left peak number, and the number of up-down runs. We apply these results to cyclic permutations, involutions, and derangements, and more generally, to derive formulas for counting all permutations by the above statistics jointly with the number of fixed points and jointly with cycle type. A number of known formulas are recovered as special cases of our results, including formulas of Désarménien-Foata, Gessel-Reutenauer, Stembridge, Fulman, Petersen, Diaconis-Fulman-Holmes, Zhuang, and Athanasiadis.
description: 50 pages
BOWIE-ALIGN: JWST reveals hints of planetesimal accretion and complex sulphur chemistry in the atmosphere of the misaligned hot Jupiter WASP-15b
Creators: name: Kirk, James
name: Ahrer, Eva-Maria
name: Claringbold, Alastair B.
name: Zamyatina, Maria
name: Fisher, Chloe
name: McCormack, Mason
name: Panwar, Vatsal
name: Powell, Diana
name: Taylor, Jake
name: Thorngren, Daniel P.
name: Christie, Duncan A.
name: Esparza-Borges, Emma
name: Tsai, Shang-Min
name: Alderson, Lili
name: Booth, Richard A.
name: Fairman, Charlotte
name: López-Morales, Mercedes
name: Mayne, N. J.
name: Meech, Annabella
name: Molliere, Paul
name: Owen, James E.
name: Penzlin, Anna B. T.
name: Sergeev, Denis E.
name: Valentine, Daniel
name: Wakeford, Hannah R.
name: Wheatley, Peter J.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present a transmission spectrum of the misaligned hot Jupiter WASP-15b from 2.8-5.2 microns observed with JWST's NIRSpec/G395H grating. Our high signal to noise data, which has negligible red noise, reveals significant absorption by H$_2$O ($4.2σ$) and CO$_2$ ($8.9σ$). From independent data reduction and atmospheric retrieval approaches, we infer that WASP-15b's atmospheric metallicity is super-solar ($\gtrsim 15\times$ solar) and its carbon-to-oxygen ratio is consistent with solar, that together imply planetesimal accretion. Our general circulation model simulations for WASP-15b suggest that the carbon-to-oxygen we measure at the limb is likely representative of the entire photosphere due to the mostly uniform spatial distribution of H$_2$O, CO$_2$ and CO. We additionally see evidence for absorption by SO$_2$ and absorption at 4.9$μ$m, for which the current leading candidate is OCS, albeit with several caveats. If confirmed, this would be the first detection of OCS in an exoplanet atmosphere and point towards complex photochemistry of sulphur-bearing species in the upper atmosphere. These are the first observations from the BOWIE-ALIGN survey which is using JWST's NIRSpec/G395H instrument to compare the atmospheric compositions of aligned/low-obliquity and misaligned/high-obliquity hot Jupiters around F stars above the Kraft break. The goal of our survey is to determine whether the atmospheric composition differs across two populations of planets that have likely undergone different migration histories (disc versus disc-free) as evidenced by their obliquities (aligned versus misaligned).
description: 27 pages, 25 figures, 6 tables. Accepted to MNRAS on 30th January 2025
Fractional Reaction-Diffusion Equation
Creators: name: Seki, Kazuhiko
name: Wojcik, Mariusz
name: Tachiya, M.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: A fractional reaction-diffusion equation is derived from a continuous time random walk model when the transport is dispersive. The exit from the encounter distance, which is described by the algebraic waiting time distribution of jump motion, interferes with the reaction at the encounter distance. Therefore, the reaction term has a memory effect. The derived equation is applied to the geminate recombination problem. The recombination is shown to depend on the intrinsic reaction rate, in contrast with the results of Sung et al. [J. Chem. Phys. {\bf 116}, 2338 (2002)], which were obtained from the fractional reaction-diffusion equation where the diffusion term has a memory effect but the reaction term does not. The reactivity dependence of the recombination probability is confirmed by numerical simulations.
description: to appear in Journal of Chemical Physics
Non-Hermitian spectral changes in the scattering of partially coherent radiation by periodic structures
Creators: name: Brandão, Paulo A.
name: Cavalcanti, S. B.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The physical aspects of partially coherent radiation interacting with deterministic non-Hermitian periodic materials remain largely unexplored in the statistical optics literature. Here, we consider the scattering of partially coherent radiation by a deterministic periodic medium, symmetric under the simultaneous transformations of parity inversion and time reversal, that is, a parity-time (PT)-symmetric periodic medium. Taking into account light fluctuations, one is able to describe the spectrum changes on propagation and the influence of the coherence-driven angular divergence effect. The far-field spectral density profile is found to depend crucially on the loss/gain properties of the material, giving rise to unexpected and contrasting spectral diffraction profiles when compared to the Hermitian ones.