cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
An Automotive Case Study on the Limits of Approximation for Object Detection
Creators: name: Caro, Martí
name: Tabani, Hamid
name: Abella, Jaume
name: Moll, Francesc
name: Morancho, Enric
name: Canal, Ramon
name: Altet, Josep
name: Calomarde, Antonio
name: Cazorla, Francisco J.
name: Rubio, Antonio
name: Fontova, Pau
name: Fornt, Jordi
Publisher: name: arXiv
Year: 2023
Subjects: subject: Hardware Architecture (cs.AR)
subject: FOS: Computer and information sciences

description: The accuracy of camera-based object detection (CBOD) built upon deep learning is often evaluated against the real objects in frames only. However, such simplistic evaluation ignores the fact that many unimportant objects are small, distant, or background, and hence, their misdetections have less impact than those for closer, larger, and foreground objects in domains such as autonomous driving. Moreover, sporadic misdetections are irrelevant since confidence on detections is typically averaged across consecutive frames, and detection devices (e.g. cameras, LiDARs) are often redundant, thus providing fault tolerance. This paper exploits such intrinsic fault tolerance of the CBOD process, and assesses in an automotive case study to what extent CBOD can tolerate approximation coming from multiple sources such as lower precision arithmetic, approximate arithmetic units, and even random faults due to, for instance, low voltage operation. We show that the accuracy impact of those sources of approximation is within 1% of the baseline even when considering the three approximate domains simultaneously, and hence, multiple sources of approximation can be exploited to build highly efficient accelerators for CBOD in cars.
Eine Sammlung oligozäner Petrefakten aus der La-Tène-Zeit
Creators: name: Zahn, Wilhelm
Publisher: name: Jahresschrift für mitteldeutsche Vorgeschichte
Year: 2019

description: -
description: Jahresschrift für mitteldeutsche Vorgeschichte, Bd. 3 (1904): Jahresschrift für die Vorgeschichte der sächsisch-thüringischen Länder
Single-electron current sources: towards a refined definition of ampere
Creators: name: Pekola, J. P.
name: Saira, O. -P.
name: Maisi, V. F.
name: Kemppinen, A.
name: Möttönen, M.
name: Pashkin, Yu. A.
name: Averin, D. V.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Controlling electrons at the level of elementary charge $e$ has been demonstrated experimentally already in the 1980's. Ever since, producing an electrical current $ef$, or its integer multiple, at a drive frequency $f$ has been in a focus of research for metrological purposes. In this review we first discuss the generic physical phenomena and technical constraints that influence charge transport. We then present the broad variety of proposed realizations. Some of them have already proven experimentally to nearly fulfill the demanding needs, in terms of transfer errors and transfer rate, of quantum metrology of electrical quantities, whereas some others are currently "just" wild ideas, still often potentially competitive if technical constraints can be lifted. We also discuss the important issues of read-out of single-electron events and potential error correction schemes based on them. Finally, we give an account of the status of single-electron current sources in the bigger framework of electric quantum standards and of the future international SI system of units, and briefly discuss the applications and uses of single-electron devices outside the metrological context.
description: 55 pages, 38 figures; (v2) fixed typos and misformatted references, reworded the section on AC pumps
The Abundance of Star-Forming Galaxies in the Redshift Range 8.5 to 12: New Results from the 2012 Hubble Ultra Deep Field Campaign
Creators: name: Ellis, Richard S
name: McLure, Ross J
name: Dunlop, James S
name: Robertson, Brant E
name: Ono, Yoshiaki
name: Schenker, Matthew A
name: Koekemoer, Anton
name: Bowler, Rebecca A A
name: Ouchi, Masami
name: Rogers, Alexander B
name: Curtis-Lake, Emma
name: Schneider, Evan
name: Charlot, Stephane
name: Stark, Daniel P
name: Furlanetto, Steven R
name: Cirasuolo, Michele
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present the results of the deepest search to date for star-forming galaxies beyond a redshift z~8.5 utilizing a new sequence of near-infrared Wide Field Camera 3 images of the Hubble Ultra Deep Field. This `UDF12' campaign completed in September 2012 doubles the earlier exposures with WFC3/IR in this field and quadruples the exposure in the key F105W filter used to locate such distant galaxies. Combined with additional imaging in the F140W filter, the fidelity of high redshift candidates is greatly improved. Using spectral energy distribution fitting techniques on objects selected from a deep multi-band near-infrared stack we find 7 promising z>8.5 candidates. As none of the previously claimed UDF candidates with 8.510 galaxies with JWST.
description: Submitted to Astrophys. J. Lett. on Nov. 7, 2012. Resubmitted after responding to referee report. UDF12 public webpage available at http://udf12.arizona.edu
Additional file 3 of Genomic landscape, immune characteristics and prognostic mutation signature of cervical cancer in China
Creators: name: Liu, Jing
name: Li, Zirong
name: Lu, Ting
name: Pan, Junping
name: Li, Li
name: Song, Yanwen
name: Hu, Dan
name: Zhuo, Yanhong
name: Chen, Ying
name: Xu, Qin
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Figure S1. Kaplan-Meier estimated A PFS and B OS by PD-L1 expression.
Übersicht über vorgeschichtliche Veröffentlichungen des letzten Jahres im Gebiet der sächsischen und thüringischen Länder
Creators: name: Höfer, Paul
Publisher: name: Jahresschrift für mitteldeutsche Vorgeschichte
Year: 2019

description: -
description: Jahresschrift für mitteldeutsche Vorgeschichte, Bd. 3 (1904): Jahresschrift für die Vorgeschichte der sächsisch-thüringischen Länder
Hadron Physics and Lattice QCD
Creators: name: Alexandrou, Constantia
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: A review of recent lattice QCD hadron structure calculations is presented. Important hadronic properties such as the axial charge and spin content of the nucleon, as well as, the mass and axial charge of hyperons and charmed baryons are discussed.
description: Plenary talk at CIPANP 2012 - Eleventh Conference on the Intersections of Particle and Nuclear Physics, 28 May - 3 June 2012, St. Petersburg, FL, USA
Freund, Stephan / Köster, Gabriele (Hrsg.), Dome – Gräber – Grabungen. Winchester und Magdeburg. Zwei Kulturlandschaften des 10. Jahrhunderts im Vergleich
Creators: name: Blaich, Markus C.
Publisher: name: Nachrichten aus Niedersachsens Urgeschichte
Year: 2019

description: Rezension zu: Freund, Stephan / Köster, Gabriele (Hrsg.), Dome – Gräber – Grabungen. Winchester und Magdeburg. Zwei Kulturlandschaften des 10. Jahrhunderts im Vergleich, Schriftenreihe des Zentrums für Mittelalterausstellungen Magdeburg 2, Schnell & Steiner, Regensburg 2016, 207 Seiten, 88 Abbildungen, ISBN 978-3-7954-3067-2
description: Nachrichten aus Niedersachsens Urgeschichte, Bd. 85 (2016): Nachrichten aus Niedersachsens Urgeschichte
Rudolf Bergmann, Die Wüstungen des Hoch- und Ostsauerlandes. Studien zur Kulturlandschaftsentwicklung in Mittelalter und früher Neuzeit
Creators: name: Gärtner, Tobias
Publisher: name: Nachrichten aus Niedersachsens Urgeschichte
Year: 2019

description: Rezension zu: Rudolf Bergmann, Die Wüstungen des Hoch- und Ostsauerlandes. Studien zur Kulturlandschaftsentwicklung in Mittelalter und früher Neuzeit, Bodenaltertümer Westfalens 53, Zabern Verlag, Darmstadt 2015, 815 Seiten mit 287 Abbildungen und 7 Beilagen, ISBN 978-3-8053-4934-5
description: Nachrichten aus Niedersachsens Urgeschichte, Bd. 85 (2016): Nachrichten aus Niedersachsens Urgeschichte
title: Elevated body weight modulates subcortical volume change and associated clinical response following electroconvulsive therapy
Creators: name: Opel, Nils
name: Narr, Katherine L.
name: Abbott, Christopher
name: Argyelan, Miklos
name: Espinoza, Randall
name: Emsell, Louise
name: Bouckaert, Filip
name: Sienaert, Pascal
name: Vandenbulcke, Mathieu
name: Nordanskog, Pia
name: Repple, Jonathan
name: Kavakbasi, Erhan
name: Balslev Jørgensen, Martin
name: Paulson, Olaf B.
name: Hanson, Lars G.
name: Dols, Annemieke
name: Exel, Eric van
name: Oudega, Mardien L.
name: Takamiya, Akihiro
name: Kishimoto, Taishiro
name: Ousdal, Olga Therese
name: Haavik, Jan
name: Hammar, Åsa
name: Oedegaard, Ketil Joachim
name: Kessler, Ute
name: Bartsch, Hauke
name: Dale, Anders M.
name: Baune, Bernhard Th.
name: Dannlowski, Udo
name: Oltedal, Leif
name: Redlich, Ronny
Publisher: name: University of Muenster, Institutional Repository MIAMI
Year: 2022
Subjects: subject: 610 Medicine and health

description: Background: Obesity is a frequent somatic comorbidity of major depression, and it has been associated with worse clinical outcomes and brain structural abnormalities. Converging evidence suggests that electroconvulsive therapy (ECT) induces both clinical improvements and increased subcortical grey matter volume in patients with depression. However, it remains unknown whether increased body weight modulates the clinical response and structural neuroplasticity that occur with ECT. Methods: To address this question, we conducted a longitudinal investigation of structural MRI data from the Global ECT-MRI Research Collaboration (GEMRIC) in 223 patients who were experiencing a major depressive episode (10 scanning sites). Structural MRI data were acquired before and after ECT, and we assessed change in subcortical grey matter volume using FreeSurfer and Quarc. Results: Higher body mass index (BMI) was associated with a significantly lower increase in subcortical grey matter volume following ECT. We observed significant negative associations between BMI and change in subcortical grey matter volume, with pronounced effects in the thalamus and putamen, where obese participants showed increases in grey matter volume that were 43.3% and 49.6%, respectively, of the increases found in participants with normal weight. As well, BMI significantly moderated the association between subcortical grey matter volume change and clinical response to ECT. We observed no significant association between BMI and clinical response to ECT. Limitations: Because only baseline BMI values were available, we were unable to study BMI changes during ECT and their potential association with clinical and grey matter volume change. Conclusion: Future studies should take into account the relevance of body weight as a modulator of structural neuroplasticity during ECT treatment and aim to further explore the functional relevance of this novel finding.
description: Finanziert durch den Open-Access-Publikationsfonds der Westfälischen Wilhelms-Universität Münster (WWU Münster).
Equilibration and aging of dense soft-sphere glass-forming liquids
Creators: name: Sanchez-Diaz, Luis Enrique
name: Ramirez-Gonzalez, Pedro
name: Medina-Noyola, Magdaleno
Publisher: name: arXiv
Year: 2012
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: The recently-developed non-equilibrium extension of the self-consistent generalized Langevin equation theory of irreversible relaxation [Phys. Rev. E (2010) 82, 061503; ibid. 061504] is applied to the description of the irreversible process of equilibration and aging of a glass-forming soft-sphere liquid that follows a sudden temperature quench, within the constraint that the local mean particle density remains uniform and constant. For these particular conditions, this theory describes the non-equilibrium evolution of the static structure factor S(k;t) and of the dynamic properties, such as the self-intermediate scattering function F_S(k,τ;t), where tau is the correlation delay time and t is the evolution or waiting time after the quench. Specific predictions are presented, for the deepest quench (to zero temperature). The predicted evolution of the alpha-relaxation time τ_α(t) as a function of t allows us to define the equilibration time t^{eq}, as the time after which τ_αhas attained its equilibrium value τ_α^{eq}. It is predicted that both, t^{eq}(ϕ) and τ_α^{eq}, diverge as ϕ\to ϕ^{(a)}, where ϕ^{(a)} is the hard-sphere dynamic-arrest volume fraction ϕ^{(a)}\ (\approx 0.582), thus suggesting that the measurement of equilibrium properties at and above ϕ^{(a)} is experimentally impossible.
description: 41 pages, 23 figures
Patrizio Pensabene, II teatro Romano di Ferento. Architettura e decorazione scultorea
Creators: name: Hesberg, Henner Von
Publisher: name: Bonner Jahrbücher
Year: 2019

description: Rezension zu: Patrizio Pensabene, II teatro Romano di Ferento. Architettura e decorazione scultorea. Bibliotheca Archaeologica, Band 8. Giorgio Bretschneider Editore, Rom 1989. 211 Seiten, 117 Tafeln und 15 Tafeln mit Zeichnungen
description: Bonner Jahrbücher, Bd. 191.1991(1992): Bonner Jahrbücher
Jean Durliat, Les finances publiques de Dioclétien aux Carolingiens, 284-889
Creators: name: Noethlichs, Karl Leo
Publisher: name: Bonner Jahrbücher
Year: 2019

description: Rezension zu: Jean Durliat, Les finances publiques de Dioclétien aux Carolingiens, 284-889. Beihefte zur Francia, Band 21. Jan Thorbecke Verlag, Sigmaringen 1990. 370 Seiten, 1 Karte.
description: Bonner Jahrbücher, Bd. 192.1992(1993): Bonner Jahrbücher
Strain control of hybridization between dark and localized excitons in a 2D semiconductor
Creators: name: Hernández López, Pablo
name: Heeg, Sebastian
name: Schattauer, Christoph
name: Kovalchuk, Sviatoslav
name: Kumar, Abhijeet
name: Bock, Douglas J.
name: Kirchhof, Jan Niklas
name: Höfer, Bianca
name: Greben, Kyrylo
name: Yagodkin, Denis
name: Linhart, Lukas
name: Libisch, Florian
name: Bolotin, Kirill
Publisher: name: Humboldt-Universität zu Berlin
Year: 2022
Subjects: subject: Electronic properties and materials
subject: Two-dimensional materials
subject: 530 Physik

description: Mechanical strain is a powerful tuning knob for excitons, Coulomb-bound electron–hole complexes dominating optical properties of two-dimensional semiconductors. While the strain response of bright free excitons is broadly understood, the behaviour of dark free excitons (long-lived excitations that generally do not couple to light due to spin and momentum conservation) or localized excitons related to defects remains mostly unexplored. Here, we study the strain behaviour of these fragile many-body states on pristine suspended WSe2 kept at cryogenic temperatures. We find that under the application of strain, dark and localized excitons in monolayer WSe2—a prototypical 2D semiconductor—are brought into energetic resonance, forming a new hybrid state that inherits the properties of the constituent species. The characteristics of the hybridized state, including an order-of-magnitude enhanced light/matter coupling, avoided-crossing energy shifts, and strain tunability of many-body interactions, are all supported by first-principles calculations. The hybridized excitons reported here may play a critical role in the operation of single quantum emitters based on WSe2. Furthermore, the techniques we developed may be used to fingerprint unidentified excitonic states.
Divergences and Orientation in Spinfoams
Creators: name: Christodoulou, Marios
name: Långvik, Miklos
name: Riello, Aldo
name: Röken, Christian
name: Rovelli, Carlo
Publisher: name: arXiv
Year: 2012
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We suggest that large radiative corrections appearing in the spinfoam framework might be tied to the implicit sum over orientations. Specifically, we show that in a suitably simplified context the characteristic "spike" divergence of the Ponzano-Regge model disappears when restricting the theory to just one of the two orientations appearing in the asymptotic limit of the vertex amplitude.
description: 10 pages, 5 figures
Wave-particle duality in an environment with arbitrary white noise
Creators: name: Filgueiras, J. G.
name: Sarthour, R. S.
name: Souza, A. M. S.
name: Oliveira, I. S.
name: Serra, R. M.
name: Céleri, L. C.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The development of quantum technologies depends on investigating of the behavior of quantum systems in noisy environments, since complete isolation from its environment is impossible to achieve. In this paper we show that a wave-particle duality experiment performed in a system with an arbitrarily white noise level cannot be explained in classical terms, using hidden-variables models. In the light of our results, we analyze recent optical and NMR experiments and show that a loophole on non-locality is not fundamental.
description: 5 Pages. 1 Figure. Comments are welcome!
Existence of Wormholes in $f(\mathcal{G})$ Gravity using Symmetries
Creators: name: Naz, Tayyaba
name: Mustafa, G.
name: Shamir, M. Farasat
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The current study examines the geometry of static wormholes with anisotropic matter distribution in context of modified $f(\mathcal{G})$ gravity. We consider the well known Noether and conformal symmetries, which help in investigating wormholes in $f(\mathcal{G})$ gravity. For this purpose, we develop symmetry generators associated with conserved quantities by taking into consideration the $f(\mathcal{G})$ gravity model. Moreover, we use the conservation relationship gained from the classical Noether method and conformal Killing symmetries to develop the metric potential. These symmetries provide a strong mathematical background to investigate wormhole solutions by incorporating some suitable initial conditions. The obtained conserved quantity performs a significant role in defining the essential physical characteristics of the shape-function and energy conditions. Further, we also describe the stability of obtained wormholes solutions by employing the equilibrium condition in modified $f(\mathcal{G})$ gravity. It is observed from graphical representation of obtained wormhole solutions that Noether and conformal Killing symmetries provide the results with physically accepted patterns.
description: 10 pages, 7 figures
A High Resolution Study of the Atomic Hydrogen in CO-Rich Early-Type Galaxies
Creators: name: Lucero, Danielle M.
name: Young, Lisa M.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present an analysis of new and archival VLA HI observations of a sample of eleven early-type galaxies rich in CO, with detailed comparisons of CO and HI distributions and kinematics. The early-type sample consists of both lenticular and elliptical galaxies in a variety of environments. A range of morphologies and environments were selected in order to give a broader understanding of the origins, distribution, and fate of the cold gas in early-type galaxies. Six of the eleven galaxies in the sample are detected in both HI and CO. The H$_{2}$ to HI mass ratios for this sample range from 0.2-120. The HI morphologies of the sample are consistent with that of recent HI surveys of early-type galaxies which also find a mix of HI morphologies and masses, low HI peak surface densities, and a lack of HI in early-type galaxies which reside in high density environments. The HI-detected galaxies have a wide range of HI masses (1.4$\times10^{6}$ to 1.1$\times10^{10}$ M$_{\odot}$). There does not appear to be any correlation between the HI mass and morphology (E versus S0). When HI is detected, it is centrally peaked - there are no central kpc-scale central HI depressions like those observed for early-type spiral galaxies at similar spatial resolutions and scales. A kinematic comparison between the HI and CO indicates that both cold gas components share the same origin. The primary goal of this and a series of future papers is to better understand the relationship between the atomic and molecular gas in early-type galaxies, and to compare the observed relationships with those of spiral galaxies where this relationship has been studied in depth.
description: 35 pages, 26 figures, Accepted to AJ. I have used emulateapj to make the article resemble how it may appear in the actual Journal. The result is not perfect, but will take up less paper and will hopefully be easier for you all to read
Development of a GA4GH beacon for structured clinical data discovery using the OMOP common data model
Creators: name: S Aguiló-Castillo
name: A Labarga
name: M.A. Mayer
name: J.M.  Ramirez Anguita
name: J. Rambla
name: S. Capella-Gutierrez
Publisher: name: F1000 Research Limited
Year: 2023

description: The Global Alliance for Genomics and Health (GA4GH) has developed a framework for sharing genomic and health-related data in a secure and privacy-preserving manner. The GA4GH Beacon project is a key component of this framework, enabling the discovery of data sources that meet specific genomic or phenotypic criteria. However, the current implementation of the Beacon project is limited to genomic data sources, and there is a need for a similar mechanism for structured clinical-related data.

 We present here the development of a GA4GH Beacon for structured clinical data discovery based on the Observational Medical Outcomes Partnership (OMOP) common data model. OMOP is a widely used standardized model for organizing and harmonizing clinical information mostly coming from Electronic Health Records (EHRs) data, enabling large-scale data analysis across multiple data sources. Importantly, OMOP deals with structured data leaving to each data provider the effort of extracting, normalizing and harmonizing it before uptakes it in OMOP. This Beacon implementation uses the OMOP common data model to enable querying of clinical data sources for specific phenotypic criteria, such as diagnoses, treatments, and laboratory results.

 We have developed a proof-of-concept implementation of the Beacon for clinical data, leveraging existing tools and resources from the OMOP community. Our implementation provides a user-friendly interface for querying clinical data sources, and we demonstrate its feasibility through querying of several OMOP-formatted EHR datasets. We also discuss the challenges and opportunities for implementing a GA4GH Beacon for clinical data discovery, including data privacy and security considerations, and the potential impact of such a tool for clinical research and healthcare delivery.

 We expect this reference implementation will become an important element for the ELIXIR Beacon Network future developments to extend its reach facilitating the work with structured clinical data.
Fault-Tolerance of "Bad" Quantum Low-Density Parity Check Codes
Creators: name: Kovalev, Alexey A.
name: Pryadko, Leonid P.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We discuss error-correction properties for families of quantum low-density parity check (LDPC) codes with relative distance that tends to zero in the limit of large blocklength. In particular, we show that any family of LDPC codes, quantum or classical, where distance scales as a positive power of the block length, $d \propto n^α$, $α>0$, can correct all errors with certainty if the error rate per (qu)bit is sufficiently small. We specifically analyze the case of LDPC version of the quantum hypergraph-product codes recently suggested by Tillich and Zémor. These codes are a finite-rate generalization of the toric codes, and, for sufficiently large quantum computers, offer an advantage over the toric codes.
description: 4.5 pages, 1 figure
Deliverable D1.3: Report on Innovation and Quality  management
Creators: name: Korniszewska, Dorata
Publisher: name: Zenodo
Year: 2022

description: This Innovation and Quality Management Plan highlights a structured set of procedures and guidelines through which all tasks of the RADOV project will undergo a quality and innovation check while the project is being implemented. These procedures have been established with the objective to meet the quality standards set by RADOV for the resulting project outputs deliverables.
A note on binary completely regular codes with large minimum distance
Creators: name: Gillespie, Neil I.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Combinatorics (math.CO)
subject: Information Theory (cs.IT)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 94B05, 94C30

description: We classify all binary error correcting completely regular codes of length $n$ with minimum distance $δ>n/2$.
description: 4 pages
FAIR workflows to chart and characterize the conformational landscape of native proteins.
Creators: name: Hospital, Adam
name: 3D-BioInfo Community
Publisher: name: F1000 Research Limited
Year: 2023

description: Proteins are dynamic systems that adopt multiple conformational states, a property essential for many biological processes (e.g. binding other proteins, nucleic acids, small molecule ligands, or switching between functionally active and inactive states). Characterizing the different conformational states of proteins and the transitions between them is therefore critical for gaining insight into their biological function and can help explain the effects of genetic variants in health and disease and the action of drugs.
 The ELIXIR 3D-BioInfo structural community gathers together experts in the field of structural bioinformatics providing methods and tools to analyse, predict, archive and validate the three-dimensional (3D) structure data of biomacromolecules such as proteins, RNA or DNA.
 The 3D-BioInfo Implementation Study Building on PDBe-KB to chart and characterize the conformational landscape of native proteins aims to create an infrastructure to chart the experimentally sampled conformational diversity of native proteins by exploiting data from the PDB and state-of-the-art computational tools. The project was designed from scratch to generate FAIR workflows with the integration of these tools.
 The BioExcel Centre of Excellence for Computational Biomolecular Research has designed and developed a software library for interoperable and reproducible biomolecular simulation workflows (BioExcel Building Blocks, BioBB). The combination of the BioBB library and the ELIXIR 3D-BioInfo Implementation Study tools is producing a set of FAIR workflows for the generation of conformational ensembles and its flexibility analysis.
Communicating Actor Automata -- Modelling Erlang Processes as Communicating Machines
Creators: name: Orchard, Dominic
name: Munteanu, Mihail
name: Torrens, Paulo
Publisher: name: arXiv
Year: 2023
Subjects: subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: Brand and Zafiropulo's notion of Communicating Finite-State Machines (CFSMs) provides a succinct and powerful model of message-passing concurrency, based around channels. However, a major variant of message-passing concurrency is not readily captured by CFSMs: the actor model. In this work, we define a variant of CFSMs, called Communicating Actor Automata, to capture the actor model of concurrency as provided by Erlang: with mailboxes, from which messages are received according to repeated application of pattern matching. Furthermore, this variant of CFSMs supports dynamic process topologies, capturing common programming idioms in the context of actor-based message-passing concurrency. This gives a new basis for modelling, specifying, and verifying Erlang programs. We also consider a class of CAAs that give rise to freedom from race conditions.
description: In Proceedings PLACES 2023, arXiv:2304.05439
Uplifting trimAl for handling thousands of sequences
Creators: name: Roussel, Nicolás Díaz
name: Capella-Gutierrez, Salvador
Publisher: name: F1000 Research Limited
Year: 2023

description: Motivation: Multiple sequence alignments are the basis of many downstream analysis such as phylogenetic trees reconstruction. The appearance of NGS has fueled many large-scale studies that imply the generation of an incredible number of alignments, making the use of automated filtering methods a requirement.

 Results: We show how the use of machine-learning techniques allows us to generate new automated filtering algorithms based on the most relevant MSAs features. This work is complemented by additional investigations on how to extend the benchmark to measure the impact of trimming on (very) large alignments in terms of global accuracy. Finally, we demonstrate the technical capabilities of the newest trimAl version when there are no limitations in terms of computational resources.
Creating bio-inspired hierarchical 3D-2D photonic stacks via planar lithography on self-assembled inverse opals
Creators: name: Burgess, Ian B.
name: Aizenberg, Joanna
name: Loncar, Marko
Publisher: name: arXiv
Year: 2012
Subjects: subject: Optics (physics.optics)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Structural hierarchy and complex 3D architecture are characteristics of biological photonic designs that are challenging to reproduce in synthetic materials. Top-down lithography allows for designer patterning of arbitrary shapes, but is largely restricted to planar 2D structures. Self-assembly techniques facilitate easy fabrication of 3D photonic crystals, but controllable defect-integration is difficult. In this paper we combine the advantages of top-down and bottom-up fabrication, developing two techniques to deposit 2D-lithographically-patterned planar layers on top of or in between inverse-opal 3D photonic crystals and creating hierarchical structures that resemble the architecture of the bright green wing scales of the butterfly, Parides sesostris. These fabrication procedures, combining advantages of both top-down and bottom-up fabrication, may prove useful in the development of omnidirectional coloration elements and 3D-2D photonic crystal devices.
description: 7 pages, 4 figures
Kind Inference for the FreeST Programming Language
Creators: name: Almeida, Bernardo
name: Mordido, Andreia
name: Vasconcelos, Vasco T.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Programming Languages (cs.PL)
subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: We present a kind inference algorithm for the FREEST programming language. The input to the algorithm is FREEST source code with (possibly part of) kind annotations replaced by kind variables. The algorithm infers concrete kinds for all kind variables. We ran the algorithm on the FREEST test suite by first replacing kind annotation on all type variables by fresh kind variables, and concluded that the algorithm correctly infers all kinds. Non surprisingly, we found out that programmers do not choose the most general kind in 20% of the cases.
description: In Proceedings PLACES 2023, arXiv:2304.05439
Simulation of heavy ion collision using a time-dependent density functional theory including nuclear superfluidity
Creators: name: Ebata, Shuichiro
Publisher: name: arXiv
Year: 2012
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We carried out a simulation of heavy ion collision using a time-dependent density functional theory. We call it the canonical-basis time-dependent Hartree-Fock-Bogoliubov theory (Cb-TDHFB) which can describe nuclear dynamics in three-dimensional coordinate space, treating nuclear pairing correlation. We simulate 20O+20O collision using the Cb-TDHFB with a contact-type pairing functional, and show the behavior of gap energy which is decreasing and vibrating while colliding.
description: 4 pages, 2 figures, Conference on Computational Physics 2012 (CCP2012) proceedings
title: Mid-teen maxillary myxoma: A rare odontogenic neoplasm
Creators: name: Donaldson, Joe
Publisher: name: EURORAD
Year: 2023
Subjects: subject: Head & neck imaging
subject: Head and neck
subject: Conventional radiography
subject: CT
subject: Cysts
subject: Clinical Case

description: Clinical History: A 16-year-old female presented to the maxillofacial department with a two-month history of increasing swelling to the left midface with associated left nasal obstruction and left epiphora. On examination, the swelling corresponded to a retained deciduous molar (ULE). ULE was promptly extracted, and the extensive underlying fibrous lesion was biopsied.

description: 16 years, female
A Declarative Validator for GSOS Languages
Creators: name: Cimini, Matteo
Publisher: name: arXiv
Year: 2023
Subjects: subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: Rule formats can quickly establish meta-theoretic properties of process algebras. It is then desirable to identify domain-specific languages (DSLs) that can easily express rule formats. In prior work, we have developed Lang-n-Change, a DSL that includes convenient features for browsing language definitions and retrieving information from them. In this paper, we use Lang-n-Change to write a validator for the GSOS rule format, and we augment Lang-n-Change with suitable macros on our way to do so. Our GSOS validator is concise, and amounts to a few lines of code. We have used it to validate several concurrency operators as adhering to the GSOS format. Moreover, our code expresses the restrictions of the format declaratively.
description: In Proceedings PLACES 2023, arXiv:2304.05439
A Logical Account of Subtyping for Session Types
Creators: name: Horne, Ross
name: Padovani, Luca
Publisher: name: arXiv
Year: 2023
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: We study the notion of subtyping for session types in a logical setting, where session types are propositions of multiplicative/additive linear logic extended with least and greatest fixed points. The resulting subtyping relation admits a simple characterization that can be roughly spelled out as the following lapalissade: every session type is larger than the smallest session type and smaller than the largest session type. At the same time, we observe that this subtyping, unlike traditional ones, preserves termination in addition to the usual safety properties of sessions. We present a calculus of sessions that adopts this subtyping relation and we show that subtyping, while useful in practice, is superfluous in the theory: every use of subtyping can be "compiled away" via a coercion semantics.
description: In Proceedings PLACES 2023, arXiv:2304.05439
The fractional Schrödinger equation and the infinite potential well - numerical results using the Riesz derivative
Creators: name: Herrmann, Richard
Publisher: name: arXiv
Year: 2012
Subjects: subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Based on the Riesz definition of the fractional derivative the fractional Schrödinger equation with an infinite well potential is investigated. First it is shown analytically, that the solutions of the free fractional Schrödinger equation are not eigenfunctions, but good approximations for large k and in the vicinity of α=2. The first lowest eigenfunctions are then calculated numerically and an approximate analytic formula for the level spectrum is derived.
description: revised version: eqs. (2.15)ff corrected, figures actualized, arbitrary size of potential well
Graph4Med: a web application and a graph database for visualizing and analyzing medical databases
Creators: name: Schäfer, Jero
name: Tang, Ming
name: Luu, Danny
name: Bergmann, Anke Katharina
name: Wiese, Lena
Publisher: name: London : BioMed Central
Year: 2022
Subjects: subject: Data exploration
subject: Graph database
subject: Medical database
subject: Visualization
subject: Web application
subject: 004
subject: 570
subject: 610

description: Background: Medical databases normally contain large amounts of data in a variety of forms. Although they grant significant insights into diagnosis and treatment, implementing data exploration into current medical databases is challenging since these are often based on a relational schema and cannot be used to easily extract information for cohort analysis and visualization. As a consequence, valuable information regarding cohort distribution or patient similarity may be missed. With the rapid advancement of biomedical technologies, new forms of data from methods such as Next Generation Sequencing (NGS) or chromosome microarray (array CGH) are constantly being generated; hence it can be expected that the amount and complexity of medical data will rise and bring relational database systems to a limit. Description: We present Graph4Med, a web application that relies on a graph database obtained by transforming a relational database. Graph4Med provides a straightforward visualization and analysis of a selected patient cohort. Our use case is a database of pediatric Acute Lymphoblastic Leukemia (ALL). Along routine patients’ health records it also contains results of latest technologies such as NGS data. We developed a suitable graph data schema to convert the relational data into a graph data structure and store it in Neo4j. We used NeoDash to build a dashboard for querying and displaying patients’ cohort analysis. This way our tool (1) quickly displays the overview of patients’ cohort information such as distributions of gender, age, mutations (fusions), diagnosis; (2) provides mutation (fusion) based similarity search and display in a maneuverable graph; (3) generates an interactive graph of any selected patient and facilitates the identification of interesting patterns among patients. Conclusion: We demonstrate the feasibility and advantages of a graph database for storing and querying medical databases. Our dashboard allows a fast and interactive analysis and visualization of complex medical data. It is especially useful for patients similarity search based on mutations (fusions), of which vast amounts of data have been generated by NGS in recent years. It can discover relationships and patterns in patients cohorts that are normally hard to grasp. Expanding Graph4Med to more medical databases will bring novel insights into diagnostic and research.
Choreographic Programming of Isolated Transactions
Creators: name: Smeele, Ton
name: Jongmans, Sung-Shik
Publisher: name: arXiv
Year: 2023
Subjects: subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: Implementing distributed systems is hard; choreographic programming aims to make it easier. In this paper, we present the design of a new choreographic programming language that supports isolated transactions among overlapping sets of processes. The first idea is to track for every variable which processes are permitted to use it. The second idea is to use model checking to prove isolation.
description: In Proceedings PLACES 2023, arXiv:2304.05439
Phase diagram, ferromagnetic martensitic transformation and magnetoresponsive properties of Fe-doped MnCoGe alloys
Creators: name: Li, G. J.
name: Liu, E. K.
name: Zhang, H. G.
name: Zhang, Y. J.
name: Chen, J. L.
name: Wang, W. H.
name: Zhang, H. W.
name: Wu, G. H.
name: Yu, S. Y.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The crystal structure and magnetoresponsive properties of Fe-doped MnCoGe alloys have been investigated using x-ray diffraction (XRD) and magnetic measurements. By alloying the Fe-containing isostructure compounds into MnCoGe, a magnetostructural transition from paramagnetic austenite to ferromagnetic martensite with large magnetization difference can be realized in a temperature window between the Curie temperatures of the austenite and martensite, resulting in magnetic-field-induced martensitic transformations and large magnetic-entropy changes. A structural and magnetic phase diagram of Fe-doped MnCoGe alloys has been proposed.
description: 13 pages, 5 figures, submitted to JMMM
Balanced electric-magnetic dihole in Kaluza-Klein theory
Creators: name: Chen, Yu
name: Teo, Edward
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We present a four-dimensional double-black-hole (or dihole) solution in Kaluza-Klein theory, describing a superposition of an electrically charged and a magnetically charged black hole. This system can be balanced for appropriately chosen parameters, and the resulting space-time is completely regular on and outside the event horizons. This solution was constructed using the inverse-scattering method in five-dimensional vacuum gravity, in which it describes a rotating black ring surrounding a static black hole on a Taub-NUT background space. Various properties of this solution are studied, from both a four- and five-dimensional perspective.
description: 33 pages, 6 figures; v2: expanded discussion of phase space, published version
Medium Baseline Reactor Neutrino Experiments with 2 Identical Detectors
Creators: name: Ciuffoli, Emilio
name: Evslin, Jarah
name: Wang, Zhimin
name: Yang, Changgen
name: Zhang, Xinmin
name: Zhong, Weili
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: In the next 10 years medium baseline reactor neutrino experiments will attempt to determine the neutrino mass hierarchy and to precisely measure θ_12. Both of these determinations will be more reliable if data from identical detectors at distinct baselines are combined. While interference effects can be eliminated by choosing detector sites orthogonal to the reactor arrays, one of the greatest challenges facing a determination of the mass hierarchy is the detector's unknown energy response. By comparing peaks at similar energies at two identical detectors at distinct baselines, one eliminates any correlated dependence upon a monotonic energy response. In addition, a second detector leads to new hierarchy-dependent observables, such as the ratio of the locations of the maxima of the Fourier cosine transforms. Simultaneously, one may determine the hierarchy by comparing the χ^2 best fits of ΔM^2_32 at the two detectors using the spectra associated to both hierarchies. A second detector at a distinct baseline also breaks the degeneracy between θ_12 and the background neutrino flux from, for example, distant reactors and increases the effective target mass, which is limited by current designs to about 20 kton/detector.
description: 17 pages, 7 jpg figures
On a reconstruction theorem for holonomic systems
Creators: name: D'Agnolo, Andrea
name: Kashiwara, Masaki
Publisher: name: arXiv
Year: 2012
Subjects: subject: Algebraic Geometry (math.AG)
subject: Complex Variables (math.CV)
subject: FOS: Mathematics
subject: 32C38, 35A20, 32S60, 34M40

description: Let X be a complex manifold. The classical Riemann-Hilbert correspondence associates to a regular holonomic system M the C-constructible complex of its holomorphic solutions. Denote by t the affine coordinate in the complex projective line. If M is not necessarily regular, we associate to it the ind-R-constructible complex G of tempered holomorphic solutions to the exterior product of M with the D-module associated with the exponential e^t. We conjecture that this provides a Riemann-Hilbert correspondence for holonomic systems. We discuss the functoriality of this correspondence, we prove that M can be reconstructed from G if X has dimension 1, and we show how the Stokes data are encoded in G.
description: solved a problem with TeX macros, minor corrections, 10 pages
Experimental investigation of Bayesian bounds in multiparameter estimation
Creators: name: D'Aurelio, Simone E.
name: Valeri, Mauro
name: Polino, Emanuele
name: Cimini, Valeria
name: Gianani, Ilaria
name: Barbieri, Marco
name: Corrielli, Giacomo
name: Crespi, Andrea
name: Osellame, Roberto
name: Sciarrino, Fabio
name: Spagnolo, Nicolò
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum parameter estimation offers solid conceptual grounds for the design of sensors enjoying quantum advantage. This is realised not only by means of hardware supporting and exploiting quantum properties, but data analysis has its impact and relevance, too. In this respect, Bayesian methods have emerged as an effective and elegant solution, with the perk of incorporating naturally the availability of a priori information. In this article we present an evaluation of Bayesian methods for multiple phase estimation, assessed based on bounds that work beyond the usual limit of large samples assumed in parameter estimation. Importantly, such methods are applied to experimental data generated from the output statistics of a three-arm interferometer seeded by single photons. Our studies provide a blueprint for a more comprehensive data analysis in quantum metrology.
description: 8 pages, 6 figures
Rattling and Superconducting Properties of the Cage Compound GaxV2Al20
Creators: name: Hiroi, Zenji
name: Onosaka, Atsushi
name: Okamoto, Yoshihiko
name: Yamaura, Jun-ichi
name: Harima, Hisatomo
Publisher: name: arXiv
Year: 2012
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Low-energy rattling modes and their effects on superconductivity are studied in the cage compound GaxV2Al20. A series of polycrystalline samples of 0 < x =< 0.6 are examined through resistivity, magnetic susceptibility, and heat capacity measurements. A weak-coupling BCS superconductivity is observed below Tc = 1.4-1.7 K for all the samples. For small Ga contents below 0.20, approximately 30% of the cages are occupied by rattling Al atoms having an Einstein temperature TE of 23 K, probably with most Ga atoms substituting for the cage-forming Al atoms. For higher Ga contents, approximately 0.05 Ga and 0.25-0.35 Al atoms coexist statistically inside the cages and behave as rattlers with TE ~ 8 and 23 K, respectively. A significant effect of Ga rattling on the superconductivity is clearly evidenced by the observation of a sharp rise in Tc by 8% at x = 0.20 when 0.05 Ga atoms are introduced into the case. Probably, the electron-phonon interaction is significantly enhanced by an additional contribution to the phonon density of states from the extremely low energy rattling modes of Ga atoms. In addition, a large softening of the acoustic modes is observed for x => 0.20, suggesting that the cage itself becomes anomalously soft in the presence of low-energy Ga rattling modes.
description: 13 pages, 16 figures, 1 table; J. Phys. Soc. Jpn, in press