cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 9: Figure S4. of Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis
Creators: name: Yildiz, Soner
name: Béryl Mazel-Sanchez
name: Matheswaran Kandasamy
name: Balaji Manicassamy
name: Schmolke, Mirco
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: (A) Rarefection plot: number of sequences is plotted against Chao1 estimator. Error bars indicate SE. (B) Alpha diversity depicted as shannon index for fecal microbiota of baseline (gray), mock-treated (black) or IAV-infected (red) mice. Individual values per mouse and median are depicted. (C) 2D PCoA plots of fecal microbiota mock-treated (blue) or IAV-infected mice (red) at indicated time points post infection. Each symbol represents one mouse. (D) Most abundant OTU on genus level. Median relative abundance (%) is depicted. (E) Relative abundance (%) of significantly changing OTUs of individual mice and median are depicted (mock red, IAV black). (F) Cultivatable bacterial cfu/fecal pellet of mock-treated (black) or IAV-infected (H5N1 red, H1N1 green) 7 dpi grown under aerobic or anaerobic conditions are depicted (n = 6 per group per time point, two independent experiments). (PDF 1343 kb)
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome VI, Cart. 190 (11 H 75), 316 folios, f. 0168v
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: 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, (XVe siècle), tome VI, Archives départementales de la Côte-d'Or, Cart. 190 (11 H 75), 316 folios, f. 0168v, 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 VI, Archives départementales de la Côte-d'Or, Cart. 190 (11 H 75), 316 folios, f. 0168v, 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
High voltage DC gun for high intensity polarized electron source
Creators: name: Wang, Erdong
name: Rahman, Omer
name: Skaritka, John
name: Liu, Wei
name: Biswas, Jyoti
name: Degen, Chrisopher
name: Inacker, Patrick
name: Lambiase, Robert
name: Paniccia, Matthew
Publisher: name: arXiv
Year: 2021
Subjects: subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: The high intensity polarized electron source is a critical component for future nuclear physics facilities. The Electron Ion Collider (EIC) requires a polarized electron gun with higher voltage and higher bunch charge compared to any existing polarized electron source. At Brookhaven National Laboratory, we have built an inverted high voltage direct current (HVDC) photoemission gun with a large cathode size. We report on the performances of GaAs photocathodes in a high gradient with up to a 16 nC bunch charge. The measurements were performed at a stable operating gap voltage of 300 kV - demonstrating outstanding lifetime, and robustness. We observed obvious lifetime enhancement by biasing the anode. The gun also integrated a cathode cooling system for potential application on high current electron sources. The various novel features implemented and demonstrated in this polarized HVDC gun open the door towards future high intensity-high average current electron accelerator facilities.
description: 9 pages, 10 figures
Metastability in the driven-dissipative Rabi model
Creators: name: Boité, Alexandre Le
name: Hwang, Myung-Joong
name: Plenio, Martin B.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We explore the long-time dynamics of Rabi model in a driven-dissipative setting and show that, as the atom-cavity coupling strength becomes larger than the cavity frequency, a new time scale emerges. This time scale, much larger than the natural relaxation time of the atom and the cavity, leads to long-lived metastable states susceptible to being observed experimentally. By applying a Floquet-Liouville approach to the time-dependent master equation, we systematically investigate the set of possible metastable states. We find that the properties of the metastable states can differ drastically from those of the steady state and relate these properties to the energy spectrum of the Rabi Hamiltonian.
description: 12 pages, 6 figures
Discovery of an effective anti-inflammatory agent for inhibiting the activation of NF-κB
Creators: name: Yan, Yaoyao
name: Lv, Qi
name: Zhou, Feilong
name: Jian, Yujie
name: Xinhua, Liu
name: Chen, Xing
name: Hu, Yong
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: In this study, based on the effect of compounds on the activation of NF-κB and NO release, compound 51 was discovered as the best one with NO release inhibition IC50 value was 3.1 ± 1.1 μM and NF-κB activity inhibition IC50 value was 172.2 ± 11.4 nM. Compound 51 could inhibit the activation of NF-κB through suppressing phosphorylation and nuclear translocation of NF-κB, and suppress LPS-induced inflammatory response in RAW264.7 cells, such as the over-expression of TNF-α and IL-6, which were target genes of NF-κB. This compound also showed preferable anti-inflammatory activity in vivo, including alleviating significantly gastric distention and splenomegaly caused by LPS stimulation, reducing the level of oxidative stress induced by LPS, and inhibiting the expression of IL-6 and TNF-α in serum. Thus, it’s reasonable to consider that this compound is a promising small molecule with anti-inflammatory effect for inhibiting the NF-κB signalling pathway.
Analysis of Awarded Australian Grants by Gender
Creators: name: Kingsley, Isabelle
name: Williams, Lisa
name: Slavich, Eve
name: Gomes, Clara
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Australia
subject: funding
subject: gender
subject: grants

description: Examining temporal trends in the award of research grants in Australia by the Australian Research Council (ARC) and the National Health and Medical Research Council (NHMRC) according to awardee gender.
Explaining Recurring Maser Flares in the ISM Through Large-scale Entangled Quantum Mechanical States
Creators: name: Rajabi, Fereshteh
name: Houde, Martin
Publisher: name: arXiv
Year: 2017
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We apply Dicke's theory of superradiance introduced in 1954 to the methanol 6.7 GHz and water 22 GHz spectral lines, often detected in molecular clouds as signposts for the early stages of the star formation process. We suggest that superradiance, characterized by burst-like features taking place over a wide range of time-scales, may provide a natural explanation for the recent observations of periodic and seemingly alternating methanol and water maser flares in G107.298+5.639. Although these observations would be very difficult to explain within the context of maser theory, we show that these flares may result from simultaneously initiated 6.7-GHz methanol and 22-GHz water superradiant bursts operating on different time-scales, thus providing a natural mechanism for their observed durations and time ordering. The evidence of superradiance in this source further suggests the existence of entangled quantum mechanical states, involving a very large number of molecules, over distances up to a few kilometres in the interstellar medium.
description: 14 pages, 3 figures
University of York Open Research Survey 2023/24
Creators: name: Muraina, Luqman
name: Kays, Melissa
name: Hansford, Kirralise
name: Catt, Ben
Publisher: name: OSF
Year: 2024
Subjects: Open Research
Open Science
Reproducibility
UK Network of Open Science Working Groups
York Open Research

description: This report details a survey into open research at the University of York in the 2023/24 academic year
Additional file 16: Table S10. of Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice
Creators: name: Kaifa Wei
name: Huiqin Chen
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: List of predicted miRNA-OsCYP pairs with target regions and assessing results. (PDF 137 kb)
Additional file 1: of The combination of nonthyroidal illness syndrome and renal dysfunction further increases mortality risk in patients with acute myocardial infarction: a prospective cohort study
Creators: name: Wang, Jun-Wei
name: Ren, Ying
name: Lu, Zhi-Gang
name: Gao, Jing
name: Zhao, Cui-Chun
name: Li, Lian-Xi
name: Wei, Meng
Publisher: name: figshare
Year: 2019
Subjects: Space Science
Medicine
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Developmental Biology
Science Policy
Computational Biology

description: Table S1. Comparison of Odds Ratio of in-hospital mortality when eGFR was calculated with CKD-EPI formula. (DOC 32 kb)
Additional file 2: of The combination of nonthyroidal illness syndrome and renal dysfunction further increases mortality risk in patients with acute myocardial infarction: a prospective cohort study
Creators: name: Wang, Jun-Wei
name: Ren, Ying
name: Lu, Zhi-Gang
name: Gao, Jing
name: Zhao, Cui-Chun
name: Li, Lian-Xi
name: Wei, Meng
Publisher: name: figshare
Year: 2019
Subjects: Space Science
Medicine
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Developmental Biology
Computational Biology

description: Table S2. Comparison of Hazard Ratio of all-cause and cardiovascular mortality when eGFR was calculated with CKD-EPI formula. (DOCX 20 kb)
Additional file 15: Table S9. of Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice
Creators: name: Kaifa Wei
name: Huiqin Chen
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: List of the number of potential cis-acting elements in 326 OsCYP promoter regions. (PDF 94 kb)
Additional file 1: of Ablation of tau causes an olfactory deficit in a murine model of Parkinson’s disease
Creators: name: Beauchamp, Leah
name: Chan, Jacky
name: Hung, Lin
name: Padman, Benjamin
name: Vella, Laura
name: Liu, Xiang
name: Coleman, Bradley
name: Bush, Ashley
name: Lazarou, Michael
name: Hill, Andrew
name: Jacobson, Laura
name: Barnham, Kevin
Publisher: name: figshare
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Chemical Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology
subject: Cardiology

description: Supplementary data Table S1. Animal numbers (genotype and sex). Table S2. ODT ANOVA factors. Normality test: Shapiro-Wilk. Table S3. ODT one sample t test, hypothetical mean = 50% (chance). Figure S1. ODT (A) and motor evaluation (B) of 12-month-old tau−/− (n = 12) and WT (n = 12). ODT analysed by two-way repeated measures ANOVA (one factor repetition) with Fisher LSD post-hoc comparisons. # represents significant main effect of genotype, ## p < 0.01. Motor tests analysed by unpaired two-sided t test. Ns = not significant. Figure S2. Western blot confirmation of tau ablation in 7- and 15-month old tissue. A) Tau antibody (Dako, catalogue number: A0024, dilution 1:10,000) confirmed tau ablation B) Protein loading in all wells confirmed by GAPDH (Cell Signaling Technology, catalogue number 2118, dilution 1:10,000). Figure S3. Full Western Blots of 7 mo WT (+) and Tau−/− (−) cell lysate. A, B, C: immunoblot of p62 from OB, CPU and SN respectively. D, E, F: immunoblot of LCB3 from OB, CPU and SN respectively. G, H, I: immunoblot of α-synuclein from OB, CPU and SN respectively. Red box indicates the section represented in Figures. Figure S4. Full Western Blots of 15 mo WT (+) and Tau−/− (−) cell lysate. A, B, C: immunoblot of p62 from OB, CPU and SN respectively. D, E, F: immunoblot of LCB3 from OB, CPU and SN respectively. G, H, I: immunoblot of α-synuclein from OB, CPU and SN respectively. Red box indicates the section represented in Figures. Figure S5. A) Full Western Blots of PCN for LC3B from WT (+) and Tau−/− (−) cell lysate. B) Full Western Blot of PCN-derived exosomes for α-synuclein from WT (+) and Tau−/− (−) cells. C) Exosome verification using exosome negative markers (GM130 & bcl-2), exosome positive marker (Tsg101) and microvesicle marker (Flotillin) in primary cortical neuron cell lysate and exosomes. (PDF 1104 kb)
Hydrogeophysical characterization of transport processes in fractured rock by combining push-pull tracer tests and single-hole ground penetrating radar
Creators: name: Shakas, A.
name: Linde, N.
name: Baron, L.
name: Bochet, O.
name: T.
name: Bour, O.
name: Borgne, Le
Publisher: name: arXiv
Year: 2017
Subjects: subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: The in situ characterization of transport processes in fractured media is particularly challenging due to the considerable spatial uncertainty on tracer pathways and dominant controlling processes, such as dispersion, channeling, trapping, matrix diffusion, ambient and density driven flows. We attempted to reduce this uncertainty by coupling push-pull tracer experiments with single-hole ground penetrating radar (GPR) time-lapse imaging. The experiments involved different injection fractures, chaser volumes and resting times, and were performed at the fractured rock research site of Ploemeur in France (H+ network, hplus.ore.fr/en). For the GPR acquisitions, we used both fixed and moving antenna setups in a borehole that was isolated with a flexible liner. During the fixed-antenna experiment, time-varying GPR reflections allowed us to track the spatial and temporal dynamics of the tracer during the push-pull experiment. During the moving antenna experiments, we clearly imaged the dominant fractures in which tracer transport took place, fractures in which the tracer was trapped for longer time periods, and the spatial extent of the tracer distribution (up to 8 m) at different times. This demonstrated the existence of strongly channelized flow in the first few meters and radial flow at greater distances. By varying the resting time of a given experiment, we identified regions affected by density-driven and ambient flow. These experiments open up new perspectives for coupled hydrogeophysical inversion aimed at understanding transport phenomena in fractured rock formations.
Edge spin transport in the disordered two-dimensional topological insulator WTe$_2$
Creators: name: Copenhaver, Justin
name: Väyrynen, Jukka I.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: The spin conductance of two-dimensional topological insulators (2D TIs) is not expected to be quantized in the presence of perturbations that break the spin-rotational symmetry. However, the deviation from the pristine-limit quantization has yet to be studied in detail. In this paper, we define the spin current operator for the helical edge modes of a 2D TI and introduce a four-terminal setup to measure spin conductances. Using the developed formalism, we consider the effects of disorder terms that break spin-rotational symmetry or give rise to edge-to-edge coupling. We identify a key role played by spin torque in an out-of-equilibrium edge. We then utilize a tight-binding model of topological monolayer WTe$_2$ and scattering matrix formalism to numerically study spin transport in a four-terminal 2D TI device. In particular, we calculate the spin conductances and characteristic spin decay length in the presence of magnetic disorder. In addition, we study the effects of inter-edge scattering in a quantum point contact geometry. We find that the spin Hall conductance is surprisingly robust to spin symmetry-breaking perturbations, as long as time-reversal symmetry is preserved and inter-edge scattering is weak.
description: 16 pages, 11 figures; updated to version published in Phys. Rev. B
Additional file 1: of Architectures and accuracy of artificial neural network for disease classification from omics data
Creators: name: Yu, Hui
name: Samuels, David
name: Zhao, Ying-yong
name: Guo, Yan
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Biotechnology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: Supplementary text, table, and figures. Here we included explanation to Cohenâ s Kappa, Table S1, Table S2, and Figures S1 & Figure S2 cited in the manuscript. (PDF 807 kb)
Additional file 1: of Current status of nylon teeth myth in Tanzania: a cross sectional study
Creators: name: Mugonzibwa, Emeria Abella
name: Febronia Kahabuka
name: Mwalutambi, Samwel
name: Kikwilu, Emil
Publisher: name: figshare
Year: 2018
Subjects: Medicine
Biotechnology
Cancer
Science Policy

description: Nylon teeth myth and associated practices questionnaire (NB: part of the information collected through this questionnaire was published in Tanzania Journal of Health Research Doi: https://doi.org/10.4314/thrb.v17i2.7 Volume 17, Number 2, April 2015 1). (DOC 36Â kb)
Additional file 10: of The neoepitope landscape of breast cancer: implications for immunotherapy
Creators: name: Narang, Pooja
name: Chen, Meixuan
name: Sharma, Amit
name: Anderson, Karen
name: Wilson, Melissa
Publisher: name: figshare
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Table S3. Number of neoepitopes predicted for HLA class I alleles in all the breast cancer samples as well as for the three subtypes. For each allele, we also list the proportion of neoepitopes for each subtype (PDF 54 kb)
Solar mass black holes from neutron stars and bosonic dark matter
Creators: name: Garani, Raghuveer
name: Levkov, Dmitry
name: Tinyakov, Peter
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Black holes with masses $\approx 1\, M_{\odot}$ cannot be produced via stellar evolution. A popular scenario of their formation involves transmutation of neutron stars - by accumulation of dark matter triggering gravitational collapse in the star centers. We show that this scenario can be realized in the models of bosonic dark matter despite the apparently contradicting requirements on the interactions of dark matter particles: on the one hand, they should couple to neutrons strongly enough to be captured inside the neutron stars, on the other, their loop-induced self-interactions impede collapse. Observing that these conflicting conditions are imposed at different scales, we demonstrate that models with efficient accumulation of dark matter can be deformed at large fields to make unavoidable its subsequent collapse into a black hole. Workable examples include weakly coupled models with bended infinite valleys.
description: 14 pages, 2 figures; journal version
Adaptive Density-Matrix Renormalization-Group study of the disordered antiferromagnetic spin-1/2 Heisenberg chain
Creators: name: Wada, Alexander H. O.
name: Hoyos, José A.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Using the recently introduced adaptive density-matrix renormalization-group method, we study the many spin-spin correlations of the spin-$1/2$ antiferromagnetic Heisenberg chain with random coupling constants, namely, the mean value of the bulk and of the end-to-end correlations, the typical value of the bulk correlations, and the distribution of the bulk correlations. Our results are in striking agreement with the predictions of the strong-disorder renormalization group method. We do not find any hint of logarithmic corrections neither in the bulk average correlations, which were recently reported by Shu et al. [Phys. Rev. B 94,174442 (2016)], nor in the end-to-end average correlations. We report computed the existence of logarithmic correction on the end-to-end correlations of the clean chain. Finally, we have determined that the distribution of the bulk correlations, when properly rescaled by an associated Lyapunov exponent, is a narrow and universal (disorder-independent) probability function.
description: (v1) 8 pages, 8 figures; (v2) extended introduction and discussion, 9 pages, 9 figures, published version
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome IV, Cart. 188 (11 H 73), f. 0174r
Creators: name: de la Côte d'Or, Archives départementales
name: Projet CBMA
name: CG21/F.PETOT/2012
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
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: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome IV, Archives départementales de la Côte-d'Or, Cart. 188 (11 H 73), f. 0174r, 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 IV, Archives départementales de la Côte-d'Or, Cart. 188 (11 H 73), f. 0174r, 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
Phonon transport in $\mathrm{Na_2He}$ at high pressure from a first-principles study
Creators: name: Guo, San-Dong
name: Zhang, Ai-Xia
Publisher: name: arXiv
Year: 2017
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Phonon transport of recently-fabricated $\mathrm{Na_2He}$ at high pressure is investigated from a combination of first-principles calculations and the linearized phonon Boltzmann equation within the single-mode relaxation time approximation (RTA). The calculated room-temperature lattice thermal conductivity is 149.19 $\mathrm{W m^{-1} K^{-1}}$, which is very close to one of Si. It is found that low-frequency optical modes comprise 16\% of the lattice thermal conductivity, while high-frequency optical modes have negligible contribution. The high lattice thermal conductivity is due to large group velocities, small Gr$\mathrm{\ddot{u}}$neisen parameters, and long phonon lifetimes. The size effects on lattice thermal conductivity are considered by cumulative thermal conductivity with respect to phonon mean free path(MFP). To significantly reduce the lattice thermal conductivity, the characteristic length smaller than 100 nm is required, and can reach a decrease of 36\%. These results may be useful to understand thermal transport processes that occur inside giant planets.
description: 4 pages, 6 figures
Additional file 7: Figure S3. of Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis
Creators: name: Yildiz, Soner
name: Béryl Mazel-Sanchez
name: Matheswaran Kandasamy
name: Balaji Manicassamy
name: Schmolke, Mirco
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
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: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: (A) rarefection plot: number of sequences is plotted against Chao1 estimator. Error bars indicate SE. (B) 2D PCoA of SI microbiota mock-treated (blue symbols) or IAV-infected mice (red symbols) at indicated time points post infection. (C) Mean UNIFRAC distances for the comparison of indicated experimental groups. Statistical significance was determined by two-tailed student’s T test. (D) 2D PCoA of SI microbiota mock-treated (blue symbols) or IAV-infected mice (red symbols) at indicated time points post infection. Each symbol represents one mouse. Each symbol type refers to an individual cage. (E) Shannon index, relative abundances of indicated bacterial classes determined by 16S rRNA gene NGS, and relative 16S/18S levels of animals 7 dpi are shown. Each symbol represents one animal. Each symbol type refers to an individual cage. (F) Relative abundance of total bacteria based on qPCR (16S/18S) normalized to median of mock samples is shown for individual mice and indicated time points treated with mock (black symbols) or indicated viruses (red symbols) for for H1N1 7 dpi (n = 8 per group) pH1N1 6 dpi (n = 5 per group). (G) Most abundant OTU on genus level. Median relative abundance (%) is depicted. (PDF 1956 kb)
Additional file 11: of The neoepitope landscape of breast cancer: implications for immunotherapy
Creators: name: Narang, Pooja
name: Chen, Meixuan
name: Sharma, Amit
name: Anderson, Karen
name: Wilson, Melissa
Publisher: name: figshare
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Figure S8. Distribution of neoepitopes binding to HLA class I alleles in the three subtypes of breast cancer. HLA-A and HLA-C binding alleles are seen in higher proportion in ER/PR(+)HER-2(â ) subtype, while HLA-B binding alleles are in higher proportion in HER-2(+) and TNBC subtype. (PDF 240 kb)
Periodic approximation of Oseledets subspaces for semi-invertible cocycles
Creators: name: Backes, Lucas
Publisher: name: arXiv
Year: 2017
Subjects: subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: We prove that, for semi-invertible linear cocycles, Oseledets subspaces associated to ergodic measures may be approximated by Oseledets subspaces associated to periodic points.
description: arXiv admin note: text overlap with arXiv:1511.08423
One Sketch for All: One-Shot Personalized Sketch Segmentation
Creators: name: Qi, Anran
name: Gryaditskaya, Yulia
name: Xiang, Tao
name: Song, Yi-Zhe
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: We present the first one-shot personalized sketch segmentation method. We aim to segment all sketches belonging to the same category provisioned with a single sketch with a given part annotation while (i) preserving the parts semantics embedded in the exemplar, and (ii) being robust to input style and abstraction. We refer to this scenario as personalized. With that, we importantly enable a much-desired personalization capability for downstream fine-grained sketch analysis tasks. To train a robust segmentation module, we deform the exemplar sketch to each of the available sketches of the same category. Our method generalizes to sketches not observed during training. Our central contribution is a sketch-specific hierarchical deformation network. Given a multi-level sketch-strokes encoding obtained via a graph convolutional network, our method estimates rigid-body transformation from the target to the exemplar, on the upper level. Finer deformation from the exemplar to the globally warped target sketch is further obtained through stroke-wise deformations, on the lower level. Both levels of deformation are guided by mean squared distances between the keypoints learned without supervision, ensuring that the stroke semantics are preserved. We evaluate our method against the state-of-the-art segmentation and perceptual grouping baselines re-purposed for the one-shot setting and against two few-shot 3D shape segmentation methods. We show that our method outperforms all the alternatives by more than $10\%$ on average. Ablation studies further demonstrate that our method is robust to personalization: changes in input part semantics and style differences.
description: IEEE Transactions on Image Processing, 2022
Effective modeling of ground penetrating radar in fractured media using analytic solutions for propagation, thin-bed interaction and dipolar scattering
Creators: name: Shakas, A.
name: Linde, N.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: We propose a new approach to model ground penetrating radar signals that propagate through a homogeneous and isotropic medium, and are scattered at thin planar fractures of arbitrary dip, azimuth, thickness and material filling. We use analytical expressions for the Maxwell equations in a homogeneous space to describe the propagation of the signal in the rock matrix, and account for frequency-dependent dispersion and attenuation through the empirical Jonscher formulation. We discretize fractures into elements that are linearly polarized by the incoming electric field that arrives from the source to each element, locally, as a plane wave. To model the effective source wavelet we use a generalized Gamma distribution to define the antenna dipole moment. We combine microscopic and macroscopic Maxwell's equations to derive an analytic expression for the response of each element, which describes the full electric dipole radiation patterns along with effective reflection coefficients of thin layers. Our results compare favorably with finite-difference time-domain modeling in the case of constant electrical parameters of the rock-matrix and fracture filling. Compared with traditional finite-difference time-domain modeling, the proposed approach is faster and more flexible in terms of fracture orientations. A comparison with published laboratory results suggests that the modeling approach can reproduce the main characteristics of the reflected wavelet.
title: ADCO, Neuvième cartulaire de Saint-Étienne de Dijon (1661 - 1684), Cart. 32 (G 136), 745 folios, f. 0337
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: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Neuvième cartulaire de Saint-Étienne de Dijon (1661 - 1684), Archives départementales de la Côte-d'Or, Cart. 32 (G 136), 745 folios, f. 0337, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Neuvième cartulaire de Saint-Étienne de Dijon (1661 - 1684), Archives départementales de la Côte-d'Or, Cart. 32 (G 136), 745 folios, f. 0337, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: abbaye Saint-Étienne de Dijon
description: Provenance: http://www.wikidata.org/entity/Q15945019
Conduction at the onset of chaos
Creators: name: Baldovin, Fulvio
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: After a general discussion of the thermodynamics of conductive processes, we introduce specific observables enabling the connection of the diffusive transport properties with the microscopic dynamics. We solve the case of Brownian particles, both analytically and numerically, and address then whether aspects of the classic Onsager's picture generalize to the non-local non-reversible dynamics described by logistic map iterates. While in the chaotic case numerical evidence of a monotonic relaxation is found, at the onset of chaos complex relaxation patterns emerge.
description: 8 pages, 4 figures
The intrinsic ferromagnetism of two-dimensional (2D) MnO$_2$ revisited: A many-body Quantum Monte Carlo and DFT+U study
Creators: name: Wines, Daniel
name: Saritas, Kayahan
name: Ataca, Can
Publisher: name: arXiv
Year: 2021
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Monolayer MnO$_2$ is one of the few predicted two-dimensional (2D) ferromagnets that has been experimentally synthesized and is commercially available. The Mermin-Wagner theorem states that magnetic order in a 2D material cannot persist unless magnetic anisotropy (MA) is present and perpendicular to the plane, which permits a finite critical temperature. Previous computational studies have predicted the magnetic ordering and Curie temperature of 2D MnO$_2$ with DFT+U (Density Funtional Theory + Hubbard U correction), with the results having a strong dependence on the Hubbard U parameter. Diffusion Monte Carlo (DMC) is a correlated electronic structure method that has had demonstrated success for the electronic and magnetic properties of a variety of 2D and bulk systems since it has a weaker dependence on the starting Hubbard parameter and density functional. In this study, we used DMC and DFT+U to calculate the magnetic properties of monolayer MnO$_2$. We found that the ferromagnetic ordering is more favorable than antiferromagnetic and determined a statistical bound on the magnetic exchange parameter ($J$). In addition, we performed spin-orbit MA energy calculations using DFT+U and using our DMC and DFT+U parameters along with the analytical model of Torelli and Olsen, we estimated an upper bound of 28.8 K for the critical temperature of MnO$_2$. These QMC results intend to serve as an accurate theoretical benchmark, necessary for the realization and development of future 2D magnetic devices. These results also demonstrate the need for accurate methodologies to predict magnetic properties of correlated 2D materials.
Coexistence of magnetism and superconductivity in separate layers of the iron-based superconductor Li_{1-x}Fe_{x}(OH)Fe_{1-y}Se
Creators: name: Topping, C. V.
name: Kirschner, F. K. K.
name: Blundell, S. J.
name: Baker, P. J.
name: Woodruff, D. N.
name: Schild, F.
name: Sun, H.
name: Clarke, S. J.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The magnetic properties attributed to the hydroxide layer of Li1-xFex(OH)Fe1-ySe have been elucidated by the study of superconducting and nonsuperconducting members of this family. Both ac magnetometry and muon spin relaxation measurements of nonsuperconductors find a magnetic state existing below approximately 10 K which exhibits slow relaxation of magnetization. This magnetic state is accompanied by a low-temperature heat capacity anomaly present in both superconducting and nonsuperconducting variants suggesting that the magnetism persists into the superconducting state. The estimated value of magnetic moment present within the hydroxide layer supports a picture of a glassy magnetic state, probably comprising clusters of iron ions of varying cluster sizes distributed within the lithium hydroxide layer.
description: 10 pages, 8 figures, Phys. Rev. B in press
Additional file 12: of The neoepitope landscape of breast cancer: implications for immunotherapy
Creators: name: Narang, Pooja
name: Chen, Meixuan
name: Sharma, Amit
name: Anderson, Karen
name: Wilson, Melissa
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Science Policy

description: Figure S9. Kaplan-Meier estimates for high and low mutation burden. KM survival curves are shown for (A) disease-free survival and (B) overall survival between cases with high and low mutation (MB) burden, the upper and lower quartiles, in each subtype of breast cancer. Here we defined the top quartile of mutation burden as high and the bottom quartile as low (PDF 903 kb)
Compressibility and the Equation of State of an Optical Quantum Gas in a Box
Creators: name: Busley, Erik
name: Miranda, Leon Espert
name: Redmann, Andreas
name: Kurtscheid, Christian
name: Umesh, Kirankumar Karkihalli
name: Vewinger, Frank
name: Weitz, Martin
name: Schmitt, Julian
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The compressibility of a medium, quantifying its response to mechanical perturbations, is a fundamental property determined by the equation of state. For gases of material particles, studies of the mechanical response are well established, in fields from classical thermodynamics to cold atomic quantum gases. Here we demonstrate a measurement of the compressibility of a two-dimensional quantum gas of light in a box potential and obtain the equation of state for the optical medium. The experiment is carried out in a nanostructured dye-filled optical microcavity. We observe signatures of Bose-Einstein condensation at high phase-space densities in the finite-size system. Strikingly, upon entering the quantum degenerate regime, the measured density response to an external force sharply increases, hinting at the peculiar prediction of an infinite compressibility of the deeply degenerate Bose gas.
description: 9 + 9 pages, 4 + 6 figures
Exploring the dietary intake of young adult Living and Eating for Health Segments
Creators: name: Sjodin, Ella
name: Saw, Wei Yee
name: Jenkins, Eva
name: Abdulgalimov, Dinislam
name: Olivier, Patrick
name: Foster, Emma
name: McCaffrey, Tracy
Publisher: name: Monash University
Year: 2024
Subjects: classificationCode: 321005
subject: Public health nutrition
classificationCode: 321099
subject: Nutrition and dietetics not elsewhere classified

description: Objective: To explore the dietary intake of young adults segmented by their knowledge,attitudes and behaviours towards health and healthy eating.Design: Cross-sectional nutrient intake data from Intake24, online 24-hour recall and lifestyle and demographic data from an online questionnaire.Setting: Online delivery to Australian young adults.Participants: Australian young adults aged 18-30 years (n=47).Results: All analyses were completed using SPSS, including descriptive statistics, Mann-Whitney U Tests, and Spearman's Rho. The findings indicated that young adults tended to study full-time, work casually, live with other adults, and earn low incomes. Overall, young adults did not meet the recommended serves for any major food groups. Lifestyle Mavens (LM)/Health Conscious (HC) were more likely to report energy intakes within the acceptable macronutrient distribution range (AMDR) compared to Aspirational Healthy Eaters (AHE)/Balanced All Rounders (BAR), placing the latter at an increased risk of chronic disease. Compared to the AHE/BAR, LM/HC appeared to have better healthy eating knowledge (p=0.048), better meal planning, preparation and food literacy skills (p=0.042), more engagement with food-related content on social media (p=0.032), more satisfaction with the healthiness of their diet (p=0.029), and more self-regulating attitude towards their food choices (p=0.020).Conclusions: Healthy eating campaigns that provide education on how to plan, purchase and prepare healthy meals with limited time and money are needed to improve the diets of Australian young adults and prevent chronic disease.
Additional file 14: Figure S6. of Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice
Creators: name: Kaifa Wei
name: Huiqin Chen
Publisher: name: figshare
Year: 2018
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Scatter plot of dN/dS ratio of 230 homologous gene pairs. The letters N, S, T on the right legend signify No duplication, Segmental duplication and Tandem duplication of the pairs, respectively. The different colors stand for different clans. (PDF 403 kb)
Determining the energetics of vicinal perovskite oxide surfaces
Creators: name: Wessels, Werner A.
name: Bollmann, Tjeerd R. J.
name: Koster, Gertjan
name: Zandvliet, Harold J. W.
name: Rijnders, Guus
Publisher: name: arXiv
Year: 2016
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The energetics of vicinal SrTiO$_3$(001) and DyScO$_3$(110), prototypical perovskite vicinal surfaces, has been studied using topographic atomic force microscopy imaging. The kink formation and strain relaxation energies are extracted from a statistical analysis of the step meandering. Both perovskite surfaces have very similar kink formation energies and exhibit a similar triangular step undulation. Our experiments suggest that the energetics of perovskite oxide surfaces is mainly governed by the local oxygen coordination.
description: 16 pages, 4 figures
Plasma proteomics for detection of early stage colorectal cancer biosignatures
Creators: name: Mahboob, Sadia
Publisher: name: Macquarie University
Year: 2022
Subjects: Other education not elsewhere classified

description: Colorectal cancer (CRC) is one of the top three most common cancers worldwide. In Australia, CRC alone accounted for around 13% of all new cancer cases and 10% of all cancer deaths. Early CRC detection is critical for improved survival rates and more effective treatment. Blood is an easily accessible circulating fluid that reflects the current physiological and health state of an individual. For this reason, it is thought to be one of the best sources of protein or peptide biomarkers that reflect the health or clinical status of an individual. This PhD initially addresses the possible challenges for developing a robust reproducible Tri-Tricine SDS PAGE-based technique for capturing and identifying the endogenous intact LMW protein/peptide plasma "peptidome". It compares this attempt with other conventional methods (i.e., extraction using membrane filtration with 30 KDa cut off, differential solubilization and SPE C18 chromatography) that have been practiced for the isolation of intact LMW propteins/peptides from complex biospecimens. Following that, the thesis examines the suitability of spray-dried EDTA-treated plasma samples for proteomic biomarker discovery investigations against recently developed proprietary tubes containing a cocktail of protease inhibitors (PIs). A range of proteomic analyses have been conducted on CRC plasma samples (age, sex matched with stringent exclusion/inclusion criteria) obtained from the Victoria Biobank. These investigations included immune-based multiplex assays using two different approaches: Proseek® Multiplex Oncology kit I (Proseek assay) based on novel Proximity Extension Assay (PEA) technology with real time PCR (Olink Biosciences) and Bio-Plex Pro™ human cytokine27-plex kit. The high throughput multiplex assay has identified three potential candidate biomarkers (CEA, IL-8 and prolactin) that were expressed among Dukes’ stages as well as healthy, benign and malignant groups. Finally, an extensive investigation to explore the available techniques for deep depletion of the complex plasma proteome is conducted, in the hope of allowing identification of lower abundance clinical stage specific novel diagnostic plasma biomarkers for CRC. A follow up study was designed to immunodeplete pooled CRC plasmas using commercially available Agilent MARS 14 as well as our in house patented immune based depletion methods. The depleted samples were analyzed through a data independent acquisition (DIA) method (SWATH-MS), and demonstrated that cystatin C,paraoxonase-1 and ADAM DEC1 were potential candidate biomarkers for stage specific CRC (i.e., significantly overexpressed in CRC patients). The findings reported in this thesis hold great promise for future identification of low abundance plasma proteomic biomarkers for CRC.
Additional file 13: of The neoepitope landscape of breast cancer: implications for immunotherapy
Creators: name: Narang, Pooja
name: Chen, Meixuan
name: Sharma, Amit
name: Anderson, Karen
name: Wilson, Melissa
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Molecular Biology
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Plant Biology
subject: FOS: Biological sciences

description: Figure S10. Kaplan-Meier estimates by neoepitope load. KM curves of (A) disease-free survival and (B) overall survival between cases with high and low neoepitope load (NEL) in each subtype of breast cancer. High and low are defined as the upper and bottom quartile, respectively, for each breast cancer subtype (PDF 885 kb)