cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
ClinGen clinical actionability curation tools, web services and knowledge repository
Creators: name: Subramanian, Sai Lakshmi
name: Neethu Shah
name: Jackson, Andrew R.
name: Patel, Ronak Y.
name: Paithankar, Sameer
name: Gilmore, Marian J.
name: Hunter, Jessica Ezzell
name: Lee, Kristy
name: Mittendorf, Kathleen
name: Powell, Bradford
name: Wallace, Kathleen
name: Webber, Elizabeth M.
name: Whitebirch, William C.
name: Goddard, Katrina A.B.
name: Milosavljevic, Aleksandar
name: Clinical Genome Resource
Publisher: name: F1000 Research Limited
Year: 2019

description: The ClinGen Adult and Pediatric Actionability Working Groups (AWG) assess the clinical implications of human genes and genetic disorders using a standardized protocol. The AWG generates evidence-based summary reports regarding clinical actions that can be taken to avert or mitigate a poor outcome due to high genetic risk of disease. This curated evidence provides a resource to aid decision makers as they determine best practices regarding return of secondary findings from clinical whole-exome and whole-genome sequencing. To facilitate the curation and dissemination of clinical actionability knowledge in both human and machine readable formats, we have developed: the Actionability Curation Interface (ACI), which is a web-based curation portal, a knowledge repository of curation summaries and reports and REST-APIs to programmatically access machine-readable content. The ACI has been developed to streamline the curation of actionability knowledge and capture the curation workflow. The workflow begins with an early rule-out assessment to determine if a topic meets minimal criteria for actionability. If a topic meets this criteria, the ACI documents the workflow of evidence curation, including searching the literature for evidence, documenting the references, associating sets of gene-disease pairs with outcome-intervention pairs, applying semi-quantitative scores by experts and generating consensus scores, and abstracting data into a structured format.

The ACI application is implemented as a Redmine Ruby-on-Rails plugin and it includes role-based access control, a repository of version histories and a web interface for browsing, filtering, searching and export of curated knowledge. REST-APIs enable retrieval of reports and summaries of individual and consensus scores and structured representation of curated evidence in RDF-serializable JSON-LD format using the Scientific Evidence and Provenance Information Ontology (SEPIO) ontology framework.

Currently, 92 genetic disorders have been curated in the adult context and 22 in the pediatric context. The reports and scores are publicly accessible through https://actionability.clinicalgenome.org and are integrated with other curation efforts of ClinGen through https://clinicalgenome.org. Together, these efforts provide a centralized resource for recording and disseminating the AWG curation and scoring outcomes to the public.
Additional file 1 of Effects of chromosomal translocation characteristics on fertilization and blastocyst development — a retrospective cohort study
Creators: name: Wu, Shanshan
name: Zhang, Jianrui
name: Guan, Yichun
name: Ren, Bingnan
name: Zhang, Yuchao
name: Liu, Xinmi
name: Wang, Kexin
name: Zhang, Mingmei
name: Li, Zhen
Publisher: name: figshare
Year: 2023
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy

description: Supplementary Material 1
title: ADCO, Cartulaire de Cîteaux pour les possessions d'Aloxe (XVe siècle), Cart. 182 (11 H 233), 105 folios, f. 0014
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/2017
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: Cartulaire de Cîteaux pour les possessions d'Aloxe (XVe siècle), Archives départementales de la Côte-d'Or, Cart. 182 (11 H 233), 105 folios, f. 0014, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire de Cîteaux pour les possessions d'Aloxe (XVe siècle), Archives départementales de la Côte-d'Or, Cart. 182 (11 H 233), 105 folios, f. 0014, 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
Somatic variant calling benchmarking
Creators: name: Mijalkovic, Sanja
name: Domazet, Milan
name: Topalovic, Luka
name: Majic, Boris
Publisher: name: F1000 Research Limited
Year: 2019

description: The increased number of sequenced cancer genomes since the completion of the human genome project, and the importance of correctly identifying somatic mutations, which can influence treatment or prognosis, is driving forward the development of novel somatic variant calling tools (somatic callers). A lack of best practice algorithms for identifying somatic variants, however, requires constant testing, comparing, and benchmarking of these tools. The absence of a truth set further hinders the effort for the evaluation. By comparing widely used open source somatic callers, such as Strelka, VarDict, VarScan2, Seurat and LoFreq, through analysis of in-house generated synthetic data, we found complex dependencies of somatic caller parameters relative to coverage depth, allele frequency, variant type, and detection goals. Next, we normalized and filtered the output data such that it can be appropriately compared to the truth set. The acquired benchmarking results were automatically and efficiently structured and stored. All of the tools used for the analysis have been implemented in Common Workflow Language which makes them portable and reproducible.
Properties of the Intracluster Medium in an Ensemble of Nearby Galaxy Clusters
Creators: name: Mohr, Joe
name: Mathiesen, Ben
name: Evrard, Gus
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present a systematic analysis of the intracluster medium (ICM) in an X-ray flux limited sample of 45 galaxy clusters. Using archival ROSAT PSPC data and published ICM temperatures, we present best fit double and single beta model profiles and extract ICM central densities and radial distributions. We use numerical cluster simulations to estimate uncertainties for all measurements. We examine the ICM properties within the context of models of structure formation and galaxy feedback. We present best fit ICM mass-temperature MICM-TX relations for MICM calculated within R500 and 1Mpc. These relations exhibit small scatter (17%), providing evidence of regularity in large, X-ray flux limited cluster ensembles. The slope of the MICM-TX relation (at limiting radius R500) is steeper than the self-similar expectation by 4.3sigma. There is a mild dependence of ICM mass fraction fICM on TX; the clusters with ICM temperatures below 5keV have a lower mass fraction =0.160\pm0.008 than hotter clusters =0.212\pm0.006 (H0=50; 90% conf intervals). Our large, X-ray flux limited cluster sample provides no evidence for a more extended radial ICM distribution in low TX clusters down to the sample limit of 2.4keV. We find that density variations in simulated clusters cause MICM to be overestimated by 12%. We also use simulations to estimate an fICM depletion factor at R500. We use the bias corrected mean fICM within the hotter cluster subsample as a lower limit on the cluster baryon fraction. In combination with nucleosynthesis constraints this measure provides a firm upper limit on the density parameter for clustered matter Omega_M<0.36\pm0.01 (H0=50).
description: accepted on 12/15/98 for publication in ApJ, Latex, 26 pages, 9 figs, see also http://astro.uchicago.edu/home/web/mohr
ETONG ARMAND BRICE, CONSTITUTIONAL LAW AND NATIVES OF SABAH AND SARAWAK.pdf
Creators: name: Armand Brice, Etong
Publisher: name: figshare
Year: 2021
Subjects: subject: 180102 Access to Justice
subject: FOS: Law
subject: 180106 Comparative Law
subject: 180108 Constitutional Law
subject: 180114 Human Rights Law

description: Sovereign governments and states do have obligations, rights and responsibilities1 under international and national or municipal laws to protect and promote human rights, principles of equality, non-discrimination, fair and equal treatment before the law regardless of your race, belief, political status, including ethnic, and cultural as well as linguistic minority groups. Under Article 160A (6) of the Federal Constitution of Malaysia the term “native” means— 135 (a) in relation to Sarawak, a person who is a citizen and either belongs to one of the races specified in Clause (7) as indigenous to the State or is of mixed blood deriving exclusively from those races; and (b) in relation to Sabah, a person who is a citizen, is the child or grandchild of a person of a race indigenous to Sabah, and was born (whether on or after Malaysia Day or not) either in Sabah or to a father domiciled in Sabah at the time of the birth and under Article 160, the concept “Malay” means a person who professes the religion of Islam, habitually speaks the Malay language, conforms to Malay custom and—(a) was before Merdeka Day born in the Federation or in Singapore or born of parents one of whom was born in the Federation or in Singapore, or is on that day domiciled in the Federation or in Singapore; or (b) is the issue of such a person. Moreover, under Article160 (2) the term “Aborigine” means an aborigine of the Malay Peninsula” so, the ethnic label Orang Asli2 meaning “natural people” in Malay replaced the term “ aborigines” used by the British Colonial Administration. Orang Asli refers to the native peoples3 of peninsular Malaysia who are not Malay Muslims, Malaysia’s main ethnic group and conventionally are divided into eighteen ethno-linguistic subgroups4 . They appear to be the most vulnerable and disempowered groups of people since they have been either socially and politically excluded or marginalized historically5 speaking and as a result of that they do need a significant protection and contribution and support from the Government with regard to the recognition, protection and management of their native customary lands6 or rights as well as proprietary interests. Firstly, this paper will critically explore through a qualitative analysis some constitutional rights7 of aboriginal people of Malaysia as basis of their claims, rights and duties. Secondly, it will examine how some judicial decisions or case laws played a key role in shaping and changing the way native customary rights are perceived and understood today with respect to the right to land, property etc. Finally, it will highlight some challenges faced by the Orang Asli despite some improvements.
Additional file 1: of Photoluminescence Study of the Influence of Additive Ammonium Hydroxide in Hydrothermally Grown ZnO Nanowires
Creators: name: A. Dahiya
name: S. Boubenia
name: G. Franzo
name: G. Poulin-Vittrant
name: S. Mirabella
name: D. Alquier
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified

description: Figure S1. Raman spectroscopy acquired from ZnO NWs grown with different ammonium hydroxide concentrations. (DOCX 99 kb)
Equation of state of the intergalactic medium in the early Universe
Creators: name: Telikova, K. N.
name: Balashev, S. A.
name: Shternin, P. S.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Spectroscopy of the Ly$α$ forest in quasar spectra proved to be a useful tool for probing the intergalactic gas. We developed the automatic program for Voigt profile fitting of Ly$α$ forest lines. We run this code on 9 high resolution ($\sim 50000$) quasars spectra with a high signal-to-noise ratio ($\sim 50 -100$) from the Keck telescope archive and obtained the sample of single well-fitted Ly$α$ lines. Fitting the joint 2d distribution of column density and Doppler parameter from this sample by physically reasonable model we estimate a power law index $γ$ of the equation of state of the intergalactic medium in the redshift range $z\sim 2-3$. We found that our measurement is in an agreement with measurements by other groups obtained with Voigt profile fitting technique.
description: 6 pages, 3 figures, to appear in proceedings of the International Conference PhysicA.Spb, St. Petersburg, October 24-26, 2017
Phase Separation Dynamics in a Concentration Gradient
Creators: name: Lacasta, A. M.
name: Sancho, J. M.
name: Yeung, Chuck
Publisher: name: arXiv
Year: 1994
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: Phase separation dynamics with an initially non-uniform concentration are studied. Critical and off-critical behavior is observed simultaneously. A mechanism for an expanding phase separated region is demonstrated and the time dependence of the concentration is determined. The final equilibrium state consists of a planar interface separating one phase from the other. The evolution to this state is characterized by an experimentally observable flux, $j$, crossing this interface. We find that $j \sim t^{-2/3}$ if patterns are formed in the bulk and $j \sim t^{-1/2}$ if the bulk remains homogeneous. The results are explained in terms of scaling arguments which are confirmed numerically. (postScript figures appended to end of lateX file).
description: 11 pages, REVTEX.3.0, U
Papilio tages Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Papilionidae
Papilio
Papilio tages

description: Papilio tages [spec. nov.]
P. P. alis denticulatis divaricatis fuscis obsolete albopunctatis.
Habitat in Europa.
Similis P. Malvae sed magis fuscus.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 485, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
The Efficiency of Globular Cluster Formation
Creators: name: McLaughlin, Dean E.
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: (Abridged): The total populations of globular cluster systems (GCSs) are discussed in terms of their connection to the efficiency of globular cluster formation---the mass fraction of star-forming gas that was able to form bound stellar clusters rather than isolated stars or unbound associations---in galaxy halos. Observed variations in GCS specific frequencies (S_N=N_gc/L_gal), both as a function of galactocentric radius in individual systems and globally between entire galaxies, are reviewed in this light. It is argued that trends in S_N do not reflect any real variation in the underlying efficiency of cluster formation; rather, they result from ignoring the hot gas in many large ellipticals. This claim is checked and confirmed in each of M87, M49, and NGC 1399, for which existing data are combined to show that the volume density profile of globular clusters, rho_cl, is directly proportional to the sum of (rho_gas+rho_stars) at large radii. The constant of proportionality is the same in each case: epsilon=0.0026 +/- 0.0005 in the mean. This is identified with the globular cluster formation efficiency. The implication that epsilon might have had a universal value is supported by data on the GCSs of 97 early-type galaxies, on the GCS of the Milky Way, and on the ongoing formation of open clusters. These results have specific implications for some issues in GCS and galaxy formation, and they should serve as a strong constraint on more general theories of star and cluster formation.
description: 36 pages with 11 figures; accepted for publication in The Astronomical Journal
Additional file 1 of FAM171B stabilizes vimentin and enhances CCL2-mediated TAM infiltration to promote bladder cancer progression
Creators: name: Hu, Wei-Min
name: Li, Ming
name: Ning, Jin-Zhuo
name: Tang, Yu-Qi
name: Song, Tian-Bao
name: Li, Lin-Zhi
name: Zou, Fan
name: Cheng, Fan
name: Yu, Wei-Min
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Supplementary Material 1
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome VIII, Cart. 192 (11 H 77), 295 folios, f. 0199r
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
name: Petot, Frédéric
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: 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 VIII, Archives départementales de la Côte-d'Or, Cart. 192 (11 H 77), 295 folios, f. 0199r, 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 VIII, Archives départementales de la Côte-d'Or, Cart. 192 (11 H 77), 295 folios, f. 0199r, 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
Supplementary Document
Creators: name: Arvind, Shikhar
name: Fallica, Roberto
name: Bezard, Philippe
name: Petersen, John
name: de Gendt, Stefan
name: Larsen, Esben
Publisher: name: AIP Publishing
Year: 2025
Subjects: classificationCode: 34
subject: Chemical sciences
subject: FOS: Chemical sciences

description: Supplementary document including details on the metrology techniques used and sputter times of different films during XPS depth profiling.
Additional file 1: of The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus
Creators: name: Morales-Hojas, Ramiro
name: Hinsley, Malcolm
name: Armean, Irina
name: Silk, Rhiannon
name: Harrup, Lara
name: Gonzalez-Uriarte, Asier
name: Veronesi, Eva
name: Lahcen Campbell
name: Nayduch, Dana
name: Saski, Christopher
name: Tabachnick, Walter
name: Kersey, Paul
name: Carpenter, Simon
name: Fife, Mark
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Supplementary Methods. DNA extraction. Protocol followed to extract DNA from C. sonorensis samples. Genome annotation and comparative analysis. Details about the genomes of species used in the gene annotation and in the comparative analyses. RNA extraction. Protocol used to extract RNA from C. sonorensis. RT-qPCR for the detection of BTV-1 infection. Description of the method used to detect the presence of BTV-1 in C. sonorensis females after the experimental infections. RT-qPCR protocol for the validation of differentially expressed genes. Description of the protocol used to verify the change in expression of Toll-like protein, glutathione-s-transferase, glutathione-s-transferase 1 and ski2 antiviral helicase genes observed in the transcriptomes of vector-competent and refractory samples. Alignment of gst-1 and ski2. The commands used to align the protein sequences of gst-1 and ski2. These alignments were then used to run the phylogenetic analyses. (ZIP 117 kb)
Localization of Charged Quantum Particles in a Static Random Magnetic Field
Creators: name: Aronov, A. G.
name: Mirlin, A. D.
name: Woelfle, P.
Publisher: name: arXiv
Year: 1994
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: We consider a charged quantum particle in a random magnetic field with Gaussian, delta-correlated statistics. We show that although the single particle properties are peculiar, two particle quantities such as the diffusion constant can be calculated in perturbation theory. We map the problem onto a non-linear sigma-model for Q-matrices of unitary symmetry with renormalized diffusion coefficient for which all states are known to be localized in $d=2$ dimensions. Our results compare well with recent numerical data.
description: REVTEX, 12 pages, 1 figure attached as a postscript file. To appear in Phys.Rev.B
Binary Neutron Star Mergers: Mass Ejection, Electromagnetic Counterparts and Nucleosynthesis
Creators: name: Radice, David
name: Perego, Albino
name: Hotokezaka, Kenta
name: Fromm, Steven A.
name: Bernuzzi, Sebastiano
name: Roberts, Luke F.
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present a systematic numerical relativity study of the mass ejection and the associated electromagnetic transients and nucleosynthesis from binary neutron star (NS) mergers. We find that a few $10^{-3}\, M_\odot$ of material are ejected dynamically during the mergers. The amount and the properties of these outflow depend on binary parameters and on the NS equation of state (EOS). A small fraction of these ejecta, typically ${\sim}10^{-6}\, M_\odot$, is accelerated by shocks formed shortly after merger to velocities larger than $0.6\, {\rm c}$ and produces bright radio flares on timescales of weeks, months, or years after merger. Their observation could constrain the strength with which the NSs bounce after merger and, consequently, the EOS of matter at extreme densities. The dynamical ejecta robustly produce second and third $r$-process peak nuclei with relative isotopic abundances close to solar. The production of light $r$-process elements is instead sensitive to the binary mass ratio and the neutrino radiation treatment. Accretion disks of up to ${\sim}0.2\, M_\odot$ are formed after merger, depending on the lifetime of the remnant. In most cases, neutrino- and viscously-driven winds from these disks dominate the overall outflow. Finally, we generate synthetic kilonova light curves and find that kilonovae depend on the merger outcome and could be used to constrain the NS EOS.
description: 33 pages, 32 figures, 3 tables. Dynamical ejecta data from the simulation is available at https://zenodo.org/record/3235675
The Parallax of the Red Hypergiant VX Sgr with Accurate Tropospheric Delay Calibration
Creators: name: Xu, Shuangjing
name: Zhang, Bo
name: Reid, Mark J.
name: Menten, Karl M.
name: Zheng, Xingwu
name: Wang, Guangli
Publisher: name: arXiv
Year: 2018
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We report astrometric results of VLBI phase-referencing observations of 22 GHz \hho\ masers emission toward the red hypergiant \vxsgr, one of most massive and luminous red hypergiant stars in our Galaxy, using the Very Long Baseline Array. A background source, \Jtwoze, projected 4\d4 from the target \vxsgr, was used as the phase reference. For the low declinations of these sources, such a large separation normally would seriously degrade the relative astrometry. We use a two-step method of tropospheric delay calibration, which combines the VLBI geodetic-block (or GPS) calibration with an image-optimization calibration, to obtain a trigonometric parallax of $0.64\pm0.04$ mas, corresponding to a distance of 1.56$^{+0.11}_{-0.10}$ kpc. The measured proper motion of \vxsgr\ is $0.36\pm0.76$ and $-2.92\pm0.78$ \masy\ in the eastward and northward directions. The parallax and proper motion confirms that \vxsgr\ belong to the Sgr OB1 association. Rescaling bolometric luminosities in the literature to our parallax distance, we find the luminosity of \vxsgr~is $(1.95 \pm 0.62) \times 10^5$ \Lsun, where the uncertainty is dominated by differing photometry measurements.
description: 16 pages, 10 figures, accepted by ApJ
Papilio (Barbarus) Linnaeus, 1758, subgen. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Papilionidae
Papilio

description: Papilio (Barbarus) [subgen. nov.]
* Barbari.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 485, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Additional file 1: of Antioxidant and anticancer activities of Trigonella foenum-graecum, Cassia acutifolia and Rhazya stricta
Creators: name: Al-Dabbagh, Bayan
name: Elhaty, Ismail
name: Ala’a Al Hrout
name: Sakkaf, Reem Al
name: El-Awady, Raafat
name: S. Salman Ashraf
name: Amin, Amr
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer

description: Figure S1. Assessment of the cytotoxic effects of Trigonella foenum-graecum (Helba), Cassia acutifolia (Holoul), and Rhazya stricta (Harmal) extracts on HCT116 in vitro. MTT assay results of 9cHCT116 cells viability after treatment with increasing concentrations of Helba (a) Holoul (b) and Harmal (c) for 24 h. *P
Interaction of a supersonic particle with a three-dimensional complex plasma
Creators: name: Zaehringer, E.
name: Schwabe, M.
name: Zhdanov, S.
name: Mohr, D. P.
name: Knapek, C. A.
name: Huber, P.
name: Semenov, I. L.
name: Thomas, H. M.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: The influence of a supersonic projectile on a three-dimensional complex plasma is studied. Micron sized particles in a low-temperature plasma formed a large undisturbed system in the new 'Zyflex' chamber during microgravity conditions. A supersonic probe particle excited a Mach cone with Mach number M $\approx$ 1.5 - 2 and double Mach cone structure in the large weakly damped particle cloud. The speed of sound is measured with different methods and particle charge estimations are compared to calculations from standard theories. The high image resolution enables the study of Mach cones in microgravity on the single particle level of a three-dimensional complex plasma and gives insight to the dynamics. A heating of the microparticles is discovered behind the supersonic projectile but not in the flanks of the Mach cone.
Learning Rate Adaptation for Federated and Differentially Private Learning
Creators: name: Koskela, Antti
name: Honkela, Antti
Publisher: name: arXiv
Year: 2018
Subjects: subject: Machine Learning (stat.ML)
subject: Cryptography and Security (cs.CR)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: We propose an algorithm for the adaptation of the learning rate for stochastic gradient descent (SGD) that avoids the need for validation set use. The idea for the adaptiveness comes from the technique of extrapolation: to get an estimate for the error against the gradient flow which underlies SGD, we compare the result obtained by one full step and two half-steps. The algorithm is applied in two separate frameworks: federated and differentially private learning. Using examples of deep neural networks we empirically show that the adaptive algorithm is competitive with manually tuned commonly used optimisation methods for differentially privately training. We also show that it works robustly in the case of federated learning unlike commonly used optimisation methods.
description: 17 pages, 9 figures
Origin of the transient unpulsed radio emission from the PSR B1259-63 binary system
Creators: name: Ball, Lewis
name: Melatos, Andrew
name: Johnston, Simon
name: Skjaeraasen, Olaf
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We discuss the interpretation of transient, unpulsed radio emission detected from the unique pulsar/Be-star binary system PSR B1259-63. Extensive monitoring of the 1994 and 1997 periastron passages has shown that the source flares over a 100-day interval around periastron, varying on time-scales as short as a day and peaking at 60 mJy (~100 times the apastron flux density) at 1.4 GHz. Interpreting the emission as synchrotron radiation, we show that (i) the observed variations in flux density are too large to be caused by the shock interaction between the pulsar wind and an isotropic, radiatively driven, Be-star wind, and (ii) the radio emitting electrons do not originate from the pulsar wind. We argue instead that the radio electrons originate from the circumstellar disk of the Be star and are accelerated at two epochs, one before and one after periastron, when the pulsar passes through the disk. A simple model incorporating two epochs of impulsive acceleration followed by synchrotron cooling reproduces the essential features of the radio light curve and spectrum and is consistent with the system geometry inferred from pulsed radio data.
description: To be published in Astrophysical Journal Letters 7 pages, 1 postscript figure
Periodic orbits in Large Eddy Simulation of Box Turbulence
Creators: name: van Veen, Lennaert
name: Martin, Alberto Vela
name: Kawahara, Genta
name: Yasuda, Tatsuya
Publisher: name: arXiv
Year: 2018
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences
subject: 76F05, 76F20

description: We describe and compare two time-periodic flows embedded in Large Eddy Simulation (LES) of turbulence in a three-dimensional, periodic domain subject to constant external forcing. One of these flows models the regeneration of large-scale structures that was observed in this geometry by Yasuda et al. ({\sl Fluid Dyn. Res.} {\bf 46}, 061413, 2014), who used a smaller LES filter length and thus obtained a greater separation of scales of coherent motion. We speculate on the feasibility of modelling the regenerative dynamics with time-periodic solutions in such a flow, which may require novel techniques to deal with the extreme ill-conditioning of the associated boundary value problems.
Relics of cosmological quark-hadron phase transition
Creators: name: Kim, Hee Il
name: Lee, Bum-Hoon
name: Lee, Chul H.
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We propose that the amplified density fluctuations by the vanishing sound velocity effect during the cosmological quark-hadron phase transition lead to quark-gluon plasma lumps decoupled from the expansion of the universe, which may evolve to quark nuggets (QNs). Assuming power-law spectrum of density fluctuations, we investigate the parameter ranges for the QNs to play the role of baryonic dark matter and give inhomogeneities which could affect big-bang nucleosynthesis within the observational bounds of CMBR anisotropy. The QNs can give the strongest constraint ever found on the spectral index.
description: REVTEX, 4 pages, 2 eps figures
Papilio tiphus Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Lepidoptera
Papilionidae
Papilio
Papilio tiphus

description: Papilio tiphus [spec. nov.]
P. B. alis subcaudatis supra nigris: primoribus maculis duabus; posticis disco margine rubro albis. 3.
Habitat in Indiis.
Alae praeterea punctis albis versus margines & primoribus subtus venis rubris.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 485, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Thermodynamics and Excitation Spectrum of a Quasi-One-Dimensional Superconductor in a High Magnetic Field
Creators: name: Dupuis, N.
Publisher: name: arXiv
Year: 1994
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: At high magnetic field, the semiclassical approximation which underlies the Ginzburg-Landau theory of the mixed state of type II superconductors breaks down. In a quasi-1D superconductor with an {\it open Fermi surface}, a high magnetic field stabilizes a cascade of superconducting phases which ends in a strong reentrance of the superconducting phase. From a microscopic mean-field model, we determine the thermodynamics and the excitation spectrum of these quantum superconducting phases.
description: 4 pages (twocolumn) + 3 figures (upon request), RevTex, ORSAY-LPS-04
A Super-Alfvenic Model of Dark Clouds
Creators: name: Padoan, Paolo
name: Nordlund, AAke
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Supersonic random motions are observed in dark clouds and are traditionally interpreted as Alfven waves, but the possibility that these motions are super-Alfvenic has not been ruled out. In this work we report the results of numerical experiments in two opposite regimes; M_a ~ 1 and M_a >> 1, where M_a is the initial Alfvenic Mach number --the ratio of the rms velocity to the Alfven speed. Our results show that models with M_a >> 1 are consistent with the observed properties of molecular clouds that we have tested --statistics of extinction measurements, Zeeman splitting measurements of magnetic field strength, line width versus integrated antenna temperature of molecular emission line spectra, statistical B-n relation, and scatter in that relation-- while models with M_a ~ 1 have properties that are in conflict with the observations. We find that both the density and the magnetic field in molecular clouds may be very intermittent. The statistical distributions of magnetic field and gas density are related by a power law, with an index that decreases with time in experiments with decaying turbulence. After about one dynamical time it stabilizes at B ~ n^{0.4}. Magnetically dominated cores form early in the evolution, while later on the intermittency in the density field wins out, and also cores with weak field can be generated, by mass accretion along magnetic field lines.
description: 10 figures, 2 tables included
STRATEGIES FOR AFLATOXIN RISK REDUCTION IN ARABICA COFFEE: EXPERIMENTAL TRIALS ON ADDITIVE APPROACHES TO INHIBIT FUNGAL GROWTH
Creators: name: Al-Mansour, Fatima Ahmed
name: Mohammed Abdullah, Al-Harbi
Publisher: name: Zenodo
Year: 2024
Subjects: Aspergillus, Aflatoxins, Coffee beans, Contamination, Food safety

description: Aspergillus, a filamentous fungus, poses a significant threat to food and feed safety due to its ability to produce mycotoxins, particularly aflatoxins. These secondary metabolites, derived from polyketides, exhibit profound toxicity, mutagenicity, teratogenicity, and carcinogenicity in higher vertebrates and animals. Aflatoxins are primarily synthesized by several Aspergillus species, including Aspergillus flavus, Aspergillus parasiticus, Aspergillus nomius, Aspergillus toxicarius, and Aspergillus parvisclerotigens, commonly contaminating crops such as corn, peanuts, cotton seeds, and coffee beans.

The natural occurrence of toxigenic Aspergillus species and aflatoxin production in coffee beans has been extensively documented by researchers. Studies by Levi (1980), Daivasikamani and Kannan (1986), Abdel-Hafez and Elmaghraby (1992), Nakajima et al. (1997), and Batista et al. (2003) have provided compelling evidence of aflatoxin contamination in coffee beans. However, despite these findings, the prevalence and extent of aflatoxin contamination in coffee beans remain a concern for food safety and public health.

This paper aims to provide a comprehensive overview of the occurrence and implications of aflatoxin contamination in coffee beans. Drawing upon insights from existing literature and empirical studies, the paper examines the factors contributing to Aspergillus growth and aflatoxin production in coffee beans, including environmental conditions, post-harvest handling practices, and storage conditions. Furthermore, the paper discusses the potential health risks associated with aflatoxin consumption, emphasizing the need for stringent regulatory measures and quality control protocols to mitigate contamination risks and ensure consumer safety.
Additional file 1: of Post-infectious sequelae after Campylobacter enteric infection: a pilot study in Maricopa County, Arizona, USA
Creators: name: Barrett, Erika
name: Dametreea Carr
name: Bell, Melanie
name: Pogreba-Brown, Kristen
Publisher: name: figshare
Year: 2018
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Protocol, Recruitment Script, and CQ. (DOCX 27 kb)
Probabilistic nilpotence in infinite groups
Creators: name: Martino, Armando
name: Tointon, Matthew
name: Valiunas, Motiejus
name: Ventura, Enric
Publisher: name: arXiv
Year: 2018
Subjects: subject: Group Theory (math.GR)
subject: Combinatorics (math.CO)
subject: Probability (math.PR)
subject: FOS: Mathematics

description: The 'degree of k-step nilpotence' of a finite group G is the proportion of the tuples (x_1,...,x_{k+1}) in G^{k+1} for which the simple commutator [x_1,...,x_{k+1}] is equal to the identity. In this paper we study versions of this for an infinite group G, with the degree of nilpotence defined by sampling G in various natural ways, such as with a random walk, or with a Folner sequence if G is amenable. In our first main result we show that if G is finitely generated then the degree of k-step nilpotence is positive if and only if G is virtually k-step nilpotent. This generalises both an earlier result of the second author treating the case k=1 and a result of Shalev for finite groups, and uses techniques from both of these earlier results. We also show, using the notion of polynomial mappings of groups developed by Leibman and others, that to a large extent the degree of nilpotence does not depend on the method of sampling. As part of our argument we generalise a result of Leibman by showing that if f is a polynomial mapping into a torsion-free nilpotent group then the set of roots of f is sparse in a certain sense. In our second main result we consider the case where G is residually finite but not necessarily finitely generated. Here we show that if the degree of k-step nilpotence of the finite quotients of G is uniformly bounded from below then G is virtually k-step nilpotent, answering a question of Shalev. As part of our proof we show that degree of nilpotence of finite groups is sub-multiplicative with respect to quotients, generalising a result of Gallagher.
description: 32 pages. Minor proofreading corrections. Final version
Theoretical Study of Friction: A Case of One-Dimensional Clean Surfaces
Creators: name: Matsukawa, Hiroshi
name: Fukuyama, Hidetoshi
Publisher: name: arXiv
Year: 1994
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: A new method has been proposed to evaluate the frictional force in the stationary state. This method is applied to the 1-dimensional model of clean surfaces. The kinetic frictional force is seen to depend on velocity in general, but the dependence becomes weaker as the maximum static frictional force increases and in the limiting case the kinetic friction gets only weakly dependent on velocity as described by one of the laws of friction. It is also shown that there is a phase transition between state with vanishing maximum static frictional force and that with finite one. The role of randomness at the interface and the relation to the impurity pinning of the sliding Charge-Density-Wave are discussed. to appear in Phys.Rev.B. abstract only. Full text is available upon request. E-mail: hiro@ena.wani.osaka-u.ac.jp.
description: 2 pages, Plain TEX, OUCMT-94-4
Fractal correlations in the CfA2-South redshift survey
Creators: name: Joyce, M.
name: Montuori, M.
name: Labini, F. Sylos
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We report our analysis of the properties of galaxy clustering for a new redshift sample of galaxies, the CfA2-South catalog, using statistical methods which do not rely on the assumption of homogeneity. We find that, up to ~ 20 Mpc/h, which is the largest scale to which correlation properties can be reliably inferred, the galaxy clustering is scale-invariant and characterized by a fractal dimension D=1.9 \pm 0.1. Further there is no statistical evidence for homogeneity at any of the larger scales (up to ~150 Mpc/h) probed more weakly by the catalog. These results means that characteristic ``correlation lengths'' for the clustering of galaxies derived using standards methods of analysis are not meaningful. Further the results are very consistent with those obtained from many other catalogs using the methods adopted here, which show the D =2 fractal continuing to beyond 100 Mpc/h. The incompleteness of the relevant data conjectured by various authors to give rise to such behaviour is therefore proved to have no significant effect (up to 20 Mpc/h) on the measured correlations.
description: 18 pages, latex, 1 postscript figure, also available at http://www.phys.uniroma1.it/DOCS/PIL/pil.html Accepted for publication in Astrophysical Journal Letters
Long-Distance Universality of Laughlin State and Calogero-Sutherland Model
Creators: name: Iso, Satoshi
Publisher: name: arXiv
Year: 1994
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: We study the universal long-distance behaviour of the Laughlin state for the fractional quantum Hall effect and the ground state of the Calogero-Sutherland model (one dimensional $1/r^2$ interaction model). In particular, it is shown that these two wave functions coincide exactly when Laughlin state is confined in a narrow cylinder geometry. The seeming difference of dimensionality is merely a difference of representation of wave functions. We also give a recipe to interpret operators acting on states in the lowest Landau level in terms of the usual one dimensional Fermion operators, which is important for extracting the Tomonaga-Luttinger liquid behaviour of the edge states.
description: 20, UT-676
Nanodiamonds-induced effects on neuronal firing of mouse hippocampal microcircuits
Creators: name: Guarina, L.
name: Calorio, C.
name: Gavello, D.
name: Moreva, E.
name: Traina, P.
name: Battiato, A.
name: Tchernij, S. Ditalia
name: Forneris, J.
name: Gai, M.
name: Picollo, F.
name: Olivero, P.
name: Genovese, M.
name: Carbone, E.
name: Marcantoni, A.
name: Carabelli, V.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Fluorescent nanodiamonds (FND) are carbon-based nanomaterials that can efficiently incorporate optically active photoluminescent centers such as the nitrogen-vacancy complex, thus making them promising candidates as optical biolabels and drug-delivery agents. FNDs exhibit bright fluorescence without photobleaching combined with high uptake rate and low cytotoxicity. Focusing on FNDs interference with neuronal function, here we examined their effect on cultured hippocampal neurons, monitoring the whole network development as well as the electrophysiological properties of single neurons. We observed that FNDs drastically decreased the frequency of inhibitory (from 1.81 Hz to 0.86 Hz) and excitatory (from 1.61 Hz to 0.68 Hz) miniature postsynaptic currents, and consistently reduced action potential (AP) firing frequency (by 36%), as measured by microelectrode arrays. On the contrary, bursts synchronization was preserved, as well as the amplitude of spontaneous inhibitory and excitatory events. Current-clamp recordings revealed that the ratio of neurons responding with AP trains of high-frequency (fast-spiking) versus neurons responding with trains of low-frequency (slow-spiking) was unaltered, suggesting that FNDs exerted a comparable action on neuronal subpopulations. At the single cell level, rapid onset of the somatic AP ("kink") was drastically reduced in FND-treated neurons, suggesting a reduced contribution of axonal and dendritic components while preserving neuronal excitability.
description: 34 pages, 9 figures
Period - luminosity - color - radius relationships of Cepheids as a function of metallicity: evolutionary effects
Creators: name: Alibert, Y.
name: Baraffe, I.
name: Hauschildt, P.
name: Allard, F.
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Based on consistent evolutionary and pulsation calculations, we analyse the effect of metallicity and of different convection treatments in the stellar models on period - magnitude, - color and - radius relationships. In order to perform an accurate comparison with observations, we have computed grids of atmosphere models and synthetic spectra for different metallicities, covering the range of effective temperatures and gravities relevant for Cepheids. The models are compared to recent observations of galactic and Magellanic Clouds Cepheids. Unprecedented level of agreement is found between models and observations. We show that within the range of metallicity for the Galaxy and the Magellanic Clouds, a change of slope in the period - luminosity (PL) relationship is predicted at low periods, due to the reduction of the blue loop during core He burning. The minimum mass undergoing a blue loop and consequently the critical period at which this change of slope occurs depend on the metallicity Z and on the convection treatment in the stellar models. However, besides this change of slope, we do not find any significant effect of metallicity on period - magnitude relationships from V to K bands, and on period - color relationships in IR colors. We only find a detectable effect of $Z$ on $(B-V)$ colors. These results are not affected by uncertainties inherent to current stellar models, mainly due to convection treatment.
description: 29 pages, Latex file, uses aa.cls, accepted for publication in Astronomy and Astrophysics