cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Galaxy for protected datasets
Creators: name: Mahmoud, Alexandru
name: Sargent, Luke
name: Chilton, John
name: Title, Rob
name: Dannon Baker
name: Overbeck, Charles
name: Nuwan Goonasekera
name: Mosher, Stephen
name: Schatz, Michael C
name: Afgan, Enis
Publisher: name: F1000 Research Limited
Year: 2021

description: Galaxy has traditionally been designed as a multi-tenant system focused on user activities such as accessibility and sharing as the core pillars designed to promote collaboration and transparency. Those same design characteristics were at odds when deploying Galaxy to operate on sensitive datasets, where confidentiality of the data is critical and requires adoption of infrastructure security practices that are broadly out of reach for individual researchers or labs. In the context of the AnVIL project (anvilproject.org), we have architected Galaxy deployments to support operation on protected datasets. To support this usage model, we have implemented the deployment of single-user Galaxy that can be scaled to hundreds of independent instances, operate simultaneously, and serve many users. Each Galaxy instance is largely autonomously managed with options for the user to administer the software. We have connected Galaxy to data workspaces to browse, import, and export data of interest. We have retained key Galaxy collaboration capabilities by enabling sharing and publishing of methods via integration with Dockstore (an online repository of tools and workflows; dockstore.org). The entire system is deployed on controlled infrastructure with FISMA Moderate certifications and available to anyone. In this talk, we will present the data protection requirements for controlled datasets, explain the architecture devised to support Galaxy’s operation on such data, and showcase an end-to-end usage example.
title: PAC-Australia (2023): Recording with DC4, word list n°1
title: 2019 - post PSS2
titleType: AlternativeTitle
Creators: name: Mas, Erwanne
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2023
Subjects: subject: Australian English
subject: eng

description: PAC word list n°1
description: Conforms to: Praat textgrid
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Evolution of the Cosmic Gas and the Relic Supernova Neutrino Background
Creators: name: Malaney, Robert A.
Publisher: name: arXiv
Year: 1996
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Using the redshift evolution of the cosmic gas, as inferred from QSO absorption line studies, we calculate the past supernova rate and the relic supernova neutrino background. Using this new technique we find the predicted relic neutrino flux at low energies to be at least an order of magnitude below previous estimates. We argue that the evolution of the cosmic gas is consistent with a large decrease in the number of early-type galaxies at redshifts $\sim 3$, and that this evolution is the source of the reduction in the predicted neutrino flux. Additional observational constraints from recent redshift surveys lead us to propose a modified model for the evolution of the cosmic gas in which significant infall at low redshift occurs. We discuss the possible relevance of our calculations to the X-ray emitting metal-enriched gas observed in the intergalactic medium.
description: minor clarifications added to text. 27 pages, latex, 6 figures, also available at ftp://ftp.cita.utoronto.ca/ftp/cita/malaney Accepted for publication in Astroparticle Physics
Supplemental Material_JCEM_Association of objectively measured physical activity with brown adipose tissue volume and activity in young adults
Creators: name: Manzano, Francisco Miguel Acosta
Publisher: name: figshare
Year: 2018
Subjects: subject: 110602 Exercise Physiology
subject: FOS: Health sciences
subject: 110306 Endocrinology
subject: FOS: Clinical medicine
subject: 110604 Sports Medicine

description: Supplemental Material_Association of objectively measured physical activity with brown adipose tissue volume and activity in young adults
Naturalness bounds on gauge mediated soft terms
Creators: name: Ciafaloni, Paolo
name: Strumia, Alessandro
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: After a general discussion about the quantitative meaning of the naturalness upper bounds on the masses of supersymmetric particles, we compute these bounds in models with gauge-mediated soft terms. We find interesting upper limits on the right-handed slepton masses that, unless the messenger fields are very light, disfavor minimal models with large messenger content. Deep unphysical minima, that however turn out to be not dangerous, are usually present in such models. The mu-problem can be solved by adding a light singlet only at the price of a large amount of fine tuning that gives also rise to heavy sparticles and large tanβ.
description: 10 pages, figures included. Published version, with inclusion of all one-loop corrections to the potential
The dp-rank of abelian groups
Creators: name: Halevi, Yatir
name: Palacín, Daniel
Publisher: name: arXiv
Year: 2017
Subjects: subject: Logic (math.LO)
subject: Group Theory (math.GR)
subject: FOS: Mathematics

description: An equation to compute the dp-rank of any abelian group is given. It is also shown that its dp-rank, or more generally that of any one-based group, agrees with its Vapnik-Chervonenkis density. Furthermore, strong abelian groups are characterised to be precisely those abelian groups $A$ such that there is only finitely many primes $p$ such that the group $A/pA$ is infinite and for every prime $p$, there is only finitely many natural numbers $n$ such that $(p^nA)[p]/(p^{n+1}A)[p]$ is infinite. Finally, it is shown that an infinite stable field of finite dp-rank is algebraically closed.
An X-ray Flare Detected on the M8 Dwarf VB 10
Creators: name: Fleming, T. A.
name: Giampapa, M. S.
name: Schmitt, J. H. M. M.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We have detected an X-ray flare on the very low mass star VB 10 (GL 752 B; M8 V) using the ROSAT High Resolution Imager. VB 10 is the latest type (lowest mass) main sequence star known to exhibit coronal activity. X-rays were detected from the star during a single 1.1-ksec segment of an observation which lasted 22 ksec in total. The energy released by this flare is on the order of 10^27 ergs/sec. This is at least two orders of magnitude greater than the quiescent X-ray luminosity of VB 10, which has yet to be measured. This X-ray flare is very similar in nature to the far ultraviolet flare which was observed by Linsky et al. (1995) using the Goddard High Resolution Spectrograph onboard Hubble Space Telescope. We discuss reasons for the extreme difference between the flare and quiescent X-ray luminosities, including the possibility that VB 10 has no quiescent (10^6 K) coronal plasma at all.
description: 11 pages, 6 figures, Figs. 2 & 3 are embedded in text; Fig. 1a,b,&c are separate files
Association of infant feeding patterns with body fat mass and obesity in the first 2 years of life: a longitudinal twin birth cohort study
Creators: name: Jin, Huili
name: Shan, Tengfei
name: Li, Sisi
name: Fan, Xin
name: Zhao, Yan
name: Li, Jie
name: Tang, Xiqin
name: Saffery, Richard
name: Tong, Chao
name: Wen, Li
name: Qi, Hongbo
name: Kilby, Mark D.
name: Baker, Philip N.
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy
subject: Computational Biology

description: Childhood obesity is a major public health problem with no effective intervention. We explored the influence of feeding patterns on infants’ growth indices within the first 2 years in a twin birth cohort. Dietary intake at 12 months was recorded with a food frequency questionnaire, and dietary patterns were identified by principal component analysis. Milk feeding methods in first 6 months were categorised as breastfeeding or exclusive formula feeding. Correlations between feeding patterns and infants’ growth indices were examined via generalised estimating equations. Two dietary patterns were identified and neither of which was related to growth indices. Breastfed infants had a higher body fat mass (BFM) percentage at 12 months, a higher body mass index (BMI) increment from birth to 6 months and a lower BMI increment from 6 to 12 months. Breastfed infants were likely positively correlated with BFM at 12 months; as complementary food was added, the effect of breastfeeding on growth gradually decreased.
title: PAC-Australia (2023): Recording with DR2, word list n°2
title: 2019 - post PSS2
titleType: AlternativeTitle
Creators: name: Mas, Erwanne
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2023
Subjects: subject: Australian English
subject: eng

description: PAC word list n°2
description: Conforms to: Praat textgrid
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
X-ray emission and internal kinematics in early-type galaxies. I. Observations
Creators: name: Pellegrini, S.
name: Held, E. V.
name: Ciotti, L.
Publisher: name: arXiv
Year: 1996
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Long slit spectroscopic data for 7 early-type galaxies with X-ray emission have been analyzed to derive velocity dispersion and radial velocity profiles. Major axis rotation curves out to $R\sim R_e$ are presented. Adding these new data to those available in the literature, we have built a sample of early-type galaxies with detected X-ray emission and known kinematics (central velocity dispersion $σ_0$ and maximum rotational velocity $v_r$). Using this sample we investigate from an observational point of view the role of rotation and flattening on the X-ray emission, particularly with regard to the X-ray underluminosity of flat systems. The trend between the X-ray to optical ratio $L_X/L_B$, a measure of the hot gas content of the galaxies, and $v_r/σ_0$ is L-shaped, with the X-ray brightest objects confined at $v_r/σ_0 <0.4$, both for Es and S0s. Neither for low or intermediate, nor for high $L_X/L_B$, there is any clear correlation between X-ray emission and rotational properties. The trend between $L_X/L_B$ and the ellipticity $ε$ is also L-shaped: there are no high $L_X/L_B$ objects with high $ε$. The existence of a relation between $v_r/σ_0$ and $ε$ makes it difficult to assess whether rotation or flattening is at the basis of the trends found. Our observational findings are finally discussed in connection with the effects that rotation and flattening are predicted to have in the cooling flow and in the wind/outflow/inflow scenarios.
description: 10 pages, plain tex, plus 7 .ps figures and tex-macro mn.tex -- accepted by MNRAS (main journal)
Additional file 16 of Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya
Creators: name: Chen, Canbin
name: Xie, Fangfang
name: Hua, Qingzhu
name: Zur, Noemi Tel
name: Zhang, Lulu
name: Zhang, Zhike
name: Zhang, Rong
name: Zhao, Jietang
name: Hu, Guibing
name: Qin, Yonghua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 16: Table S9. Prediction of targets for differentially expression miRNAs in pitaya.
An Optimization Approach to Rough Terrain Locomotion
Creators: name: Zucker, Matt
name: J. Andrew  Bagnell
name: Atkeson, Christopher G.
name: Kuffner, James
Publisher: name: Carnegie Mellon University
Year: 2010
Subjects: subject: 80101 Adaptive Agents and Intelligent Robotics
subject: FOS: Computer and information sciences

description: We present a novel approach to legged locomotion over rough terrain that is thoroughly rooted in optimization. This approach relies on a hierarchy of fast, anytime algorithms to plan a set of footholds, along with the dynamic body motions required to execute them. Components within the planning framework coordinate to exchange plans, cost-to-go estimates, and “certificates” that ensure the output of an abstract high-level planner can be realized by deeper layers of the hierarchy. The burden of careful engineering of cost functions to achieve desired performance is substantially mitigated by a simple inverse optimal control technique. Robustness is achieved by real-time re-planning of the full trajectory, augmented by reflexes and feedback control. We demonstrate the successful application of our approach in guiding the LittleDog quadruped robot over a variety of rough terrains.
title: PAC-Australia (2023): Recording with LP2, word list n°2
title: 2019 - post PSS2
titleType: AlternativeTitle
Creators: name: Mas, Erwanne
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2023
Subjects: subject: Australian English
subject: eng

description: PAC word list n°2
description: Conforms to: Praat textgrid
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Addressing the demand for secure and scalable on-demand Galaxy platforms
Creators: name: Afgan, Enis
name: Dannon Baker
name: Balnkenberg, Daniel
name: Chilton, John
name: Coraor, Nathan
name: Goecks, Jeremy
name: Nuwan Goonasekera
name: Aysam Guerler
name: Nekrutenko, Anton
name: Sauria, Michael
Publisher: name: F1000 Research Limited
Year: 2021

description: The Galaxy project has long strived to provide a highly accessible data analysis service with open and free access to hosted servers that span the world. These servers offer the benefit of instant access to Galaxy without any overhead of infrastructure and software management on the user's part. However, there are also inherent limitations on what such services can offer. In part, this is due to the availability of infrastructure, which necessitates the enforcement of usage quotas. Related, acceptable use policies have been devised to ensure fair access to anyone but in turn, restrict the type of data that may be uploaded to public services. Meanwhile, user adoption of Galaxy continues to grow, with a great example being the recent Smorgasbord training event that attracted over 1,200 trainees. Further, the number of jobs processed by usegalaxy.org has nearly doubled over the past year. To support the continued growth of the Galaxy ecosystem, we are introducing “Galaxy Pro Researcher” - a managed Galaxy service that opens Galaxy to users whose needs are not catered to. Galaxy Pro Researcher is a fee-based service with Service Level Agreement (SLA) guarantees and without usage quotas or queue wait times that anyone can subscribe to via a self-signup process. This is the first ever such Galaxy service, offering users an option to grow their adoption of Galaxy without having to manage their own Galaxy server. In this talk, we will present the motivation for this service, including findings from >100 interviews with potential Galaxy users from a variety of fields. We will showcase differences from public servers, including SLAs and security practices. Lastly, we will present the system architecture that enables this service.
Background subtraction method is not only much simpler, but also as applicable as covariant counterterm method
Creators: name: Guo, Wei
name: Guo, Xiyao
name: Lan, Xin
name: Zhang, Hongbao
name: Zhang, Wei
Publisher: name: arXiv
Year: 2025
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: As the criterion for the applicability of the background subtraction method, not only the finiteness condition of the resulting Hamiltonian but also the condition for the validity of the first law of black hole thermodynamics can be reduced to the form amenable to much simpler analysis at infinity by using the covariant phase space formalism. With this, we further establish that the background subtraction method is as applicable as the covariant counterterm method not only to Einstein's gravity, but also to its higher derivative corrections for black hole thermodynamics in both asymptotically flat and AdS spacetimes. In addition, our framework also provides us with the first derivation of the universal expression of the Gibbs free energy in terms of the Euclidean on-shell action beyond Einstein's gravity. Among others, our findings have a far reaching impact on the shift in methodology for the Euclidean approach to black hole thermodynamics, where the well justified background subtraction method by our wieldy criterion is supposed to be the favored choice compared to the covariant counterterm method.
description: version to appear in PRD
$ρ$ - nucleus bound states in Walecka model
Creators: name: Ghosh, Sanjay K.
name: Jennings, Byron
Publisher: name: arXiv
Year: 2000
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Possible formation of $ρ$ nucleus bound state is studied in the framework of Walecka model. The bound states are found in different nuclei ranging from $^3He$ to $^{208}Pb$. These bound states may have a direct bearing on the recent experiments on the photoproduction of $ρ$ meson in the nuclear medium.
description: RevTeX file
MPEC 2024-G125 : 2024 GD2
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2024
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2024 GD2

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Galaxy as a global platform for the analysis of SARS-CoV-2 sequence variants
Creators: name: Maier, Wolfgang
name: Nekrutenko, Anton
name: Pond, Sergei
name: Covid19.Galaxyproject.Org
name: Covid19.Datamonkey.Org
name: Viral Beacon
Publisher: name: F1000 Research Limited
Year: 2021

description: Under the umbrella of covid19.galaxyproject.org many members of the Galaxy community have been working together since February 2020 to provide workflows, data sources and best-practice recommendations for SARS-CoV-2-related data analysis. In particular, the subproject of sequencing data analysis has undergone substantial transformation since the early phase of the pandemic. What started out as a collection of workflows for the assembly of early WGS data into reference genomes, for phylogenetic analysis to put a date on the emergence of Covid-19 and for variant calling from relatively few WGS datasets, has developed into a complete system capable of supporting global genome surveillance efforts and involving collaborations and public infrastructure across many countries. Here, we will present the current status of our efforts and how it aims at bringing Galaxy's key features, reproducibility and accessibility, to public health systems.
Additional file 17 of Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya
Creators: name: Chen, Canbin
name: Xie, Fangfang
name: Hua, Qingzhu
name: Zur, Noemi Tel
name: Zhang, Lulu
name: Zhang, Zhike
name: Zhang, Rong
name: Zhao, Jietang
name: Hu, Guibing
name: Qin, Yonghua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 17: Table S10. cDNA sequences of 17 target genes.
An Invitation to Imitation
Creators: name: J. Andrew  Bagnell
Publisher: name: Carnegie Mellon University
Year: 2015
Subjects: subject: 80101 Adaptive Agents and Intelligent Robotics
subject: FOS: Computer and information sciences

description: Imitation learning is the study of algorithms that attempt to improve performance by mimicking a teacher’s decisions and behaviors. Such techniques promise to enable effective “programming by demonstration” to automate tasks, such as driving, that people can demonstrate but find difficult to hand program. This work represents a summary from a very personal perspective of research on computationally effective methods for learning to imitate behavior. I intend it to serve two audiences: to engage machine learning experts in the challenges of imitation learning and the interesting theoretical and practical distinctions with more familiar frameworks like statistical supervised learning theory; and equally, to make the frameworks and tools available for imitation learning more broadly appreciated by roboticists and experts in applied artificial intelligence.
PAC-Australia (2023): Recording with LP2, "A Christmas interview"
Creators: name: Mas, Erwanne
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2023
Subjects: subject: Australian English
subject: eng

description: PAC-LVTI Reading Task
description: Conforms to: Praat textgrid
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
title: ADCO, Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome I, Cart. 185 (11 H 70), f. 0146r
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris

description: Cartulaire général de Cîteaux, dit de Jean de Cirey, (XVe siècle), tome I, Archives départementales de la Côte-d'Or, Cart. 185 (11 H 70), f. 0146r, 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 I, Archives départementales de la Côte-d'Or, Cart. 185 (11 H 70), f. 0146r, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
Scattering of soft, cool pions
Creators: name: Pisarski, Robert D.
name: Tytgat, Michel
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Consider the effective lagrangian for pions in the chiral limit, computed to leading order in an expansion about zero temperature. To describe the scattering of pions with small momenta, it is necessary to include not just the usual shift in the pion decay constant, but also a new, nonlocal term, which is precisely analogous to the hard thermal loops of hot gauge theories.
description: 4 pages, 2 figures, revtex + epsfig
Structural Relations of Symmetry among Players in Strategic Games
Creators: name: Tohmé, Fernando
name: Viglizzo, Ignacio
Publisher: name: arXiv
Year: 2017
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 91A06, 05E18

description: The notions of symmetry and anonymity in strategic games have been formalized in different ways in the literature. We propose a combinatorial framework to analyze these notions, using group actions. Then, the same framework is used to define partial symmetries in payoff matrices. With this purpose, we introduce the notion of the role a player plays with respect to another one, and combinatorial relations between roles are studied. Building on them, we define relations directly between players, which provide yet another characterization of structural symmetries in the payoff matrices of strategic games.
On the Jeans Instability During the QCD Phase Transition
Creators: name: Nagasawa, Michiyasu
name: Yokoyama, Jun'ichi
Publisher: name: arXiv
Year: 1996
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The Jeans scale is estimated during the coexistence epoch of quark-gluon and hadron phases in the first-order QCD phase transition. It is shown that, contrary to the previous claims, reduction of the sound speed is so little that the phase transition does not affect evolution of cosmological density fluctuations appreciably.
description: 9 pages (LaTeX), no figure, revised version of Progress of Theoretical Physics 97 (Letters), 173 (1997)
title: PAC-Australia (2023): Recording with LS2, word list n°2
title: 2019 - post PSS2
titleType: AlternativeTitle
Creators: name: Mas, Erwanne
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2023
Subjects: subject: Australian English
subject: eng

description: PAC word list n°2
description: Conforms to: Praat textgrid
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Comprehensive and streamlined quality control for single-cell RNA data with singleCellTK
Creators: name: Koga, Yusuke
name: Hong, Rui
name: Leshchyk, Anastasia
name: Shruthi Bandyadka
name: Wang, Zhe
name: Yichen Wang
name: Irzam Sarfraz
name: Yajima, Masanao
name: W. Evan Johnson
name: Campbell, Joshua D.
Publisher: name: F1000 Research Limited
Year: 2021

description: Single-cell RNA sequencing (scRNA-seq) can be used to gain insights into cellular heterogeneity within complex tissues. However, a variety of technical artifacts can be present in scRNA-seq data and need to be assessed before downstream analyses can be performed. While several algorithms and tools have been developed to perform individual quality control (QC) tasks, they are scattered in different packages across several programming environments. Comprehensive pipelines to streamline the process of generating and visualizing QC metrics are lacking. To address this need, we built the SCTK-QC pipeline within the singleCellTK R package (https://github.com/compbiomed/singleCellTK). Features in this pipeline include the ability to import data from 11 different preprocessing tools or file formats, perform empty droplet detection with 2 different algorithms, generate standard quality control metrics such as number of UMIs per cell or the percentage of mitochondrial counts, predict doublets using 6 different algorithms, and estimate ambient RNA. QC data can be exported to R and/or Python objects used in popular down-stream workflows. Results are visualized in an easy-to-read HTML report. This pipeline can also be used by non-computational users with an interactive graphical user interface developed with R/Shiny. Overall, the SCTK-QC pipeline will streamline and standardize QC analysis for scRNA-seq data across a variety of different single-cell transcriptomic platforms and preprocessing tools.
The role of the outer boundary condition in accretion disk models: theory and application
Creators: name: Yuan, Feng
name: Peng, Qiuhe
name: Lu, Ju-fu
name: Wang, Jianmin
Publisher: name: arXiv
Year: 2000
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The influence of the outer boundary condition (OBC) on the dynamics and radiation of optically thin accretion flow is investigated. Bremsstrahlung and synchrotron radiations amplified by Comptonization are taken into account and two-temperature plasma assumption is adopted. The three OBCs we adopted are the temperatures of the electrons and ions and the specific angular momentum of the accretion flow at a certain outer boundary. We find that when the general parameters such as the mass accretion rate and the viscous parameter are fixed, the peak flux at various bands such as radio, IR and X-ray, can differ by as large as several orders of magnitude under different OBCs in our example. Our results indicate that OBC is both dynamically and radiatively important therefore should be regarded as a new ``parameter'' in accretion disk models. We apply the above results to the compact radio source Sgr A* and find that the discrepancy between the mass accretion rate favored by ADAF models in the literature and that favored by the three dimensional hydrodynamical simulation can be naturally resolved by seriously considering the outer boundary condition of the accretion flow.
description: 23 pages, 9 figures,accepted by the Astrophysical Journal
An Intelligent Approach to Hysteresis Compensation while Sampling using a Fleet of Autonomous Watercraft
Creators: name: Abhinav  Valada
name: Tomaszewski, Christopher
name: Balajee  Kannan
name: Prasanna  Velagapudi
name: Kantor, George
name: Scerri, Paul
Publisher: name: Carnegie Mellon University
Year: 2012
Subjects: subject: 80101 Adaptive Agents and Intelligent Robotics
subject: FOS: Computer and information sciences

description: This paper addresses the problem of using a fleet of autonomous watercraft to create models of various water quality parameters in complex environments using intelligent sampling algorithms. Maps depicting the spatial variation of these parameters can help researchers understand how certain ecological processes work and in turn help reduce the negative impact of human activities on the environment. In our domain of interest, it is infeasible to exhaustively sample the field to obtain statistically significant results. This problem is pertinent to autonomous water sampling where hysteresis in sensors causes delay in obtaining accurate measurements across a large field. In this paper, we present several different approaches to sampling with cooperative vehicles to quickly build accurate models of the environment. In addition, we describe a novel filter and a specialized planner that uses the gradient of sensor measurements to compensate for hysteresis while ensuring a fast sampling process. We validate the algorithms using results from both simulation and field experiments with four autonomous airboats measuring temperature and dissolved oxygen in a lake.
Creep Characterization of Refractory Materials at High Temperatures Using the Integrated Digital Image Correlation Technique
Creators: name: BREDER TEIXEIRA Lucas
name: GILLIBERT Jean
name: BLOND Eric
name: SAYET Thomas
Publisher: name: Zenodo
Year: 2019
Subjects: Creep
refractory
high temperatures
i-DIC

description: Creep Characterization of Refractory Materials at High Temperatures Using the Integrated Digital Image Correlation Technique
Wavefunction corrections and off-forward gluon distributions in diffractive J/psi electroproduction
Creators: name: Hoodbhoy, Pervez
Publisher: name: arXiv
Year: 1996
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Diffractive production of J/Psi particles by virtual photons on a proton target is studied with a view towards understanding two important corrections to the leading order result. First, the effect of Fermi motion of the heavy quarks is studied by performing a systematic expansion in the relative velocity, and a simple correction factor is derived. This is considerably less than estimated previously. Second, since the kinematics necessarily requires that non-zero momentum be transferred to the proton, off-forward gluon distributions are probed by the scattering process. To estimate the importance of the off-forwardness, we compute, in leading order perturbation theory, the extent of deviation from the usual forward gluon distribution in a quark.
description: 14 pages, 3 figures (Latex)
Formal approaches to number in Slavic and beyond
Creators: name: Tomaszewicz-Özakın, Barbara
Publisher: name: Zenodo
Year: 2021
Subjects: quantifiers
semantics–cognition interface
eye
tracking
Polish

description: In a visual world eye-tracking study I find that Polish quantifiers niektóre ‘some’,
 większość ‘most of’, najwięcej ‘the most’ and wszystkie ‘all’ elicit distinctive patterns
 of looks, consistent with their semantics. Niektóre ‘some’ has a strong scalar impli-
 cature: the meaning ‘some-not-all’ is processed immediately as the quantifier is
 heard. The superlative najwięcej ‘the most’ quickly triggers comparisons between
 the target and the other sets. The proportional większość ‘most of’ elicits a
 pattern suggesting that its verification involves the estimation of the total set. With
 wszystkie ‘all’ the identification of the target set is the fastest.
Fundamental Limits of Communication Over State-Dependent Channels With Feedback
Creators: name: Kovačević, Mladen
name: Wang, Carol
name: Tan, Vincent Y. F.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences
subject: 94A24, 94A45, 68P30

description: The fundamental limits of communication over state-dependent discrete memoryless channels with noiseless feedback are studied, under the assumption that the communicating parties are allowed to use variable-length coding schemes. Various cases are analyzed, with the employed coding schemes having either bounded or unbounded codeword lengths, and with state information revealed to the encoder and/or decoder in a strictly causal, causal, or non-causal manner. In each of these settings, necessary and sufficient conditions for positivity of the zero-error capacity are obtained and it is shown that, whenever the zero-error capacity is positive, it equals the conventional vanishing-error capacity. Moreover, it is shown that the vanishing-error capacity of state-dependent channels is not increased by the use of feedback and variable-length coding. Both these kinds of capacities of state-dependent channels with feedback are thus fully characterized.
description: 10 pages. To appear in IEEE Transactions on Communications
An Integrated System for Autonomous Robotics Manipulation
Creators: name: J. Andrew  Bagnell
name: Cavalcanti, Felipe
name: Cui, Lei
name: Galluzzo, Thomas
name: Hebert, Martial
name: Moslem  Kazemi
name: Klingensmith, Matthew
name: Libby, Jacqueline
name: Liu, Tian Yu
name: Pollard, Nancy
name: Pivtoraiko, Mihail
name: Jean-Sebastien Valois
name: Ranqi  Zhu
Publisher: name: Carnegie Mellon University
Year: 2012
Subjects: subject: 80101 Adaptive Agents and Intelligent Robotics
subject: FOS: Computer and information sciences

description: We describe the software components of a robotics system designed to autonomously grasp objects and perform dexterous manipulation tasks with only high-level supervision. The system is centered on the tight integration of several core functionalities, including perception, planning and control, with the logical structuring of tasks driven by a Behavior Tree architecture. The advantage of the implementation is to reduce the execution time while integrating advanced algorithms for autonomous manipulation. We describe our approach to 3- D perception, real-time planning, force compliant motions, and audio processing. Performance results for object grasping and complex manipulation tasks of in-house tests and of an independent evaluation team are presented.
A New Parameter In Accretion Disk Model
Creators: name: Yuan, Feng
Publisher: name: arXiv
Year: 2000
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Taking optically thin accretion flows as an example, we investigate the dynamics and the emergent spectra of accretion flows with different outer boundary conditions (OBCs) and find that OBC plays an important role in accretion disk model. This is because the accretion equations describing the behavior of accretion flows are a set of {\em differential} equations, therefore, accretion is intrinsically an initial-value problem. We argue that optically thick accretion flow should also show OBC-dependent behavior. The result means that we should seriously consider the initial physical state of the accretion flow such as its angular momentum and its temperature. An application example to Sgr A$^*$ is presented.
description: 6 pages, 4 figures, to appear in the Proceeding of "Pacific Rim Conference on Stellar Astrophysics", Aug. 1999, HongKong, China
On the metric dimension of Cartesian powers of a graph
Creators: name: Jiang, Zilin
name: Polyanskii, Nikita
Publisher: name: arXiv
Year: 2017
Subjects: subject: Combinatorics (math.CO)
subject: Discrete Mathematics (cs.DM)
subject: Information Theory (cs.IT)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 05C12, 05C76, 06A07

description: A set of vertices $S$ resolves a graph if every vertex is uniquely determined by its vector of distances to the vertices in $S$. The metric dimension of a graph is the minimum cardinality of a resolving set of the graph. Fix a connected graph $G$ on $q \ge 2$ vertices, and let $M$ be the distance matrix of $G$. We prove that if there exists $w \in \mathbb{Z}^q$ such that $\sum_i w_i = 0$ and the vector $Mw$, after sorting its coordinates, is an arithmetic progression with nonzero common difference, then the metric dimension of the Cartesian product of $n$ copies of $G$ is $(2+o(1))n/\log_q n$. In the special case that $G$ is a complete graph, our results close the gap between the lower bound attributed to Erdős and Rényi and the upper bounds developed subsequently by Lindström, Chvátal, Kabatianski, Lebedev and Thorpe.
description: 12 pages, 1 figure, 1 table, accepted to J. Comb. Theory A, corrections suggested by the referees have been incorporated
Additional file 1 of Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya
Creators: name: Chen, Canbin
name: Xie, Fangfang
name: Hua, Qingzhu
name: Zur, Noemi Tel
name: Zhang, Lulu
name: Zhang, Zhike
name: Zhang, Rong
name: Zhao, Jietang
name: Hu, Guibing
name: Qin, Yonghua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. The length distributions of miRNA fragments in pitaya (unique).
Assessing Key Delay Factors in Construction Projects in Palestine: Cause-Effect Relationships Utilizing Construction Experts' Insights
Creators: name: FATHI S. A. ALRAWAGH
name: Mochamad S.
name: Senja R.H
Publisher: name: gjrpublication
Year: 2024

description: The performance of construction projects is crucial, yet many faces significant delays, failing to meet scheduled targets. These delays have severe economic and operational impacts, making it essential to identify and understand the underlying causes. This research aims to comprehend the causal relationships among key delay factors, using insights from construction experts, to ensure timely project completion. An extensive literature review on construction delays in Palestine and other similar developing countries identified 26 causes to prioritize key delay factors in Palestine. A process involving questionnaires distributed to 13 experts was used to Prioritize 11 key delay factors for Decision Making Trial and Evaluation Laboratory (DEMATEL) analysis. The DEMATEL analysis, involving 12 experts, revealed the influence weights of these factors. Occupation and political obstacles (F7) were identified as the most significant factor (10.770%), followed by lack of sufficient financing (F3) at 10.649%, and delay in payments (F4) at 10.619%. The analysis emphasizes the need for better financial management and improved internal processes to mitigate delays. The findings in this study can provide structural visualization of complex causal relationships among key delay factors and also allow construction experts to prioritize the resource allocation to achieve project objectives.
PAC-Australia (2023): Recording with LS2, "A Christmas interview"
Creators: name: Mas, Erwanne
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2023
Subjects: subject: Australian English
subject: eng

description: PAC-LVTI Reading Task
description: Conforms to: Praat textgrid
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Freeze-out in hydrodynamical models in relativistic heavy ion collisions
Creators: name: Magas, V. K.
name: Anderlik, Cs.
name: Csernai, L. P.
name: Grassi, F.
name: Greiner, W.
name: Hama, Y.
name: Kodama, T.
name: Lazar, Zs. I.
name: Stöcker, H.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Freeze-out of particles across 3-dimensional space-time hypersurface with space-like normal is discussed in a simple kinetic model. The final momentum distribution of emitted particles shows a non-exponential transverse momentum spectrum, which is in quantitative agreement with recently measured SPS pion and $h^-$ spectra.
description: 4 pages, 1 figure. Quark Matter'99 Proceedings
Lettre de Esprit-Claude-François Calvet à Jean-François Séguier, 1769-10-30
Creators: name: Calvet, Esprit-Claude-François
name: Esprit-Claude-François Calvet
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2021
Subjects: Antiquités (général)
Botanique
Epigraphie
Numismatique
Sciences naturelles (général)

description: [transcription] Monsieur et cher ami

J'aireçu votre lettre depuis à peu près huit jours, le paquet adressé à M. de Vérone l'avait précédée, mais on ne me rendit qu'hier celuidu père Pézenas. J'aifait rendre à ce père les suites et vos remerciements. La dissertation de M. de Vérone luia été envoyée depuis plusieurs jours.

J'airemis votre lettre à M. Pamard qui se fera un vraiplaisir de s'acquitter de vos commissions.M. l'abbé Chauffard son onclen'est point ici, il y arrivera vers la Toussaint, dès le moment de son retour ils seront très empressés l'un et l'autre de vous faire parvenir ce que vous souhaitez.
Quoique nous ayons ici un jardin botanique qui appartient à la faculté, je ne crois pas pouvoir vous fournir de ce côté-là des plantes étrangères, notre jardin est mal en ordre et le jardinier peu instruit. Cependant je ne désespère pas de vous avoir de ces plantes par un autre canal, il y aura seulement l'inconvénient de ne les avoir qu'en graines. Ce sera à l'entrée du printemps prochain.

Je n'aiplus pensé depuis longtemps à mon ouvrage sur Orsippe,[fol. 126v] il faut pour cela un loisir suivi et constant, il viendra peut-être. D'ailleurs les livres me manquent, imaginez-vous que le père Béraud n'a pas pu trouver encore dans tout Lyon l'Anthologie in-fol. de Francfort, il est vraiqu'il ne va pas à la bibliothèque du collège.

J'aivuM. d'Ennery dont le projet est je crois d'aller acheter les médailles des jésuites de Rome et de ceux de Florence. Quel médailler sera-ce alors que le sien! Nous avons beaucoup parlé médailles, il s'en va fort content.

M. de Vérone vient de m'envoyer deux inscriptions, l'une de Vaison sur l'autel où on lit simplement AVGVSTO, l'autre d'Orange sur une belle pierre qui parait avoir orné le frontispice de quelque édifice public, on y lit:

T [Dessin] LICINVS

MAXVMVS

AEDIL

D P S F

Conservez-vous, Monsieur, et comptez toujours sur l'attachement inviolable avec lequel je suis

Votre très humble et très obéissant serviteur

Calvet

Avignon ce 30 octobre 1769
description: [description ill.] fol. 126v, dans l'inscription latine: Dessin d'une feuille ressemblant à un coeur
description: [personnes citées] Abraham Joseph Michelet d' Ennery, Denis Moreau de Vérone, Esprit Pézenas, Laurent Béraud, M. Chauffard, M. Pamard
description: [reférence bibliographique citée] Planude Maxime, Anthologie de Planude, Francfort, Wechel, 1600
description: Source: [lieu de Conservation] Nîmes, Bibliothèque Carré d'Art [cote]ms. 140, fol. 126-126v
description: Source: ark:/12148/btv1b10015185m
An Integrated System for Autonomous Off-Road Navigation
Creators: name: Langer, Dirk
name: Rosenblatt, Julio K
name: Hebert, Martial
Publisher: name: Carnegie Mellon University
Year: 1994
Subjects: subject: 80101 Adaptive Agents and Intelligent Robotics
subject: FOS: Computer and information sciences

description: In this paper, we report on experiments with a core system for autonomous navigation in outdoor natural terrain. The system consists of three parts: a perception module which processes range images to identify untraversable regions of the terrain, a local map management module which maintains a representation of the environment in the vicinity of the vehicle, and a planning module which issues commands to the vehicle controller. Our approach uses reactive planning for generating commands to drive the vehicle along with “early traversability evaluation,” in which the perception module decides which parts of the terrain are traversable as soon as a new image is taken. We argue that our approach leads to a robust and efficient navigation system. We illustrate our approach by an experiment in which a vehicle travelled autonomously for one kilometer through unmapped cross-country terrain
title: PAC-Australia (2023): Recording with LS2, word list n°1
title: 2019 - post PSS2
titleType: AlternativeTitle
Creators: name: Mas, Erwanne
Publisher: name: COCOON - https://cocoon.huma-num.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2023
Subjects: subject: Australian English
subject: eng

description: PAC word list n°1
description: Conforms to: Praat textgrid
description: Conforms to: doi:10.34847/cocoon.49aefa90-8c1f-3ba8-a099-0ebefc6a2aa7
Group-denoting vs. counting: Against the scalar explanation of children's interpretation of `some'
Creators: name: Kiss, Katalin É.
name: Pintér, Lilla
name: Zétényi, Tamás
Publisher: name: Zenodo
Year: 2021
Subjects: scalar implicature
`some'
counting quantifier
partitive
Hungarian
language acquisition

description: The computation of scalar implicatures based on the scale 〈some, all〉 represents
 a problem for children. This paper argues that the source of children’s difficulties
 with interpreting ‘some’ is that it is ambiguous; it has a non-partitive
 interpretation, corresponding to ‘a few’, which forms a scale with non-partitive ‘many’, and
 a partitive reading, corresponding to ‘a subset of’, which forms a scale with ‘all’.
 The two readings have different distributions; they are selected by different
 predicates, and in Hungarian, they occur in different structural positions. We tested and
 confirmed the hypothesis that young children are not sensitive to the partitivity
 feature of ‘some’-phrases; they first acquire the non-partitive reading, which they
 overgeneralize for a while. Experiment 1, a forced choice task, showed that the
 default reading of ‘some’ NPs for six-year olds is the ‘a few’ interpretation. Exper-
 iment 2, a truth value judgement task, demonstrated that children also accept the
 ‘not all’ interpretation of ‘some’, and the acceptance rates of the ‘a few’ and the
 ‘not all’ readings are similar irrespective of the partitivity feature of the given NP.
Additional file 2 of Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya
Creators: name: Chen, Canbin
name: Xie, Fangfang
name: Hua, Qingzhu
name: Zur, Noemi Tel
name: Zhang, Lulu
name: Zhang, Zhike
name: Zhang, Rong
name: Zhao, Jietang
name: Hu, Guibing
name: Qin, Yonghua
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Figure S2. The length distributions of assembled transcripts and genes. A, The length distributions of transcripts; B, The length distributions of genes.