cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Recognition and repair of the cyclobutane thymine dimer, a major cause of skin cancers, by the human excision nuclease
Creators: name: Reardon, J. T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The cyclobutane thymine dimer is the major DNA lesion induced in human skin by sunlight and is a primary cause of skin cancer, the most prevalent form of cancer in the Northern Hemisphere. In humans, the only known cellular repair mechanism for eliminating the dimer from DNA is nucleotide excision repair. Yet the mechanism by which the dimer is recognized and removed by this repair system is not known. Here we demonstrate that the six-factor human excision nuclease recognizes and removes the dimer at a rate consistent with the in vivo rate of removal of this lesion, even though none of the six factors alone is capable of efficiently discriminating the dimer from undamaged DNA. We propose a recognition mechanism by which the low-specificity recognition factors, RPA, XPA, and XPC, act in a cooperative manner to locate the lesion and, aided by the kinetic proofreading provided by TFIIH, form a high-specificity complex at the damage site that initiates removal of thymine dimers at a physiologically relevant rate and specificity.
Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27
Creators: name: Min, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The chromodomain of Drosophila Polycomb protein is essential for maintaining the silencing state of homeotic genes during development. Recent studies suggest that Polycomb mediates the assembly of repressive higher-order chromatin structures in conjunction with the methylation of Lys 27 of histone H3 by a Polycomb group repressor complex. A similar mechanism in heterochromatin assembly is mediated by HP1, a chromodomain protein that binds to histone H3 methylated at Lys 9. To understand the molecular mechanism of the methyl-Lys 27 histone code recognition, we have determined a 1.4-Å-resolution structure of the chromodomain of Polycomb in complex with a histone H3 peptide trimethylated at Lys 27. The structure reveals a conserved mode of methyl-lysine binding and identifies Polycomb-specific interactions with histone H3. The structure also reveals a dPC dimer in the crystal lattice that is mediated by residues specifically conserved in the Polycomb family of chromodomains. The dimerization of dPC can effectively account for the histone-binding specificity and provides new mechanistic insights into the function of Polycomb. We propose that self-association is functionally important for Polycomb.
Characterization-based approach for construction of goodness-of-fit test for Lévy distribution
Creators: name: Lukić, Žikica
name: Milošević, Bojana
Publisher: name: arXiv
Year: 2023
Subjects: subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences
subject: 62E10, 62G10, 62G20

description: The Lévy distribution, alongside the Normal and Cauchy distributions, is one of the only three stable distributions whose density can be obtained in a closed form. However, there are only a few specific goodness-of-fit tests for the Lévy distribution. In this paper, two novel classes of goodness-of-fit tests for the Lévy distribution are proposed. Both tests are based on V-empirical Laplace transforms. New tests are scale free under the null hypothesis, which makes them suitable for testing the composite hypothesis. The finite sample and limiting properties of test statistics are obtained. In addition, a generalization of the recent Bhati-Kattumannil goodness-of-fit test to the Lévy distribution is considered. For assessing the quality of novel and competitor tests, the local Bahadur efficiencies are computed, and a wide power study is conducted. Both criteria clearly demonstrate the quality of the new tests. The applicability of the novel tests is demonstrated with two real-data examples.
description: 28 pages, 4 figures
Detection of Potential Transit Signals in 17 Quarters of Kepler Mission Data
Creators: name: Seader, Shawn
name: Jenkins, Jon M.
name: Tenenbaum, Peter
name: Twicken, Joseph D.
name: Smith, Jeffrey C.
name: Morris, Rob
name: Catanzarite, Joseph
name: Clarke, Bruce D.
name: Li, Jie
name: Cote, Miles T.
name: Burke, Christopher J.
name: McCauliff, Sean
name: Girouard, Forrest R.
name: Campbell, Jennifer R.
name: Uddin, Akm Kamal
name: Zamudio, Khadeejah A.
name: Sabale, Anima
name: Henze, Christopher E.
name: Thompson, Susan E.
name: Klaus, Todd C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We present the results of a search for potential transit signals in the full 17-quarter data set collected during Kepler's primary mission that ended on May 11, 2013, due to the on-board failure of a second reaction wheel needed to maintain high precision, fixed, pointing. The search includes a total of 198,646 targets, of which 112,001 were observed in every quarter and 86,645 were observed in a subset of the 17 quarters. We find a total of 12,669 targets that contain at least one signal that meets our detection criteria: periodicity of the signal, a minimum of three transit events, an acceptable signal-to-noise ratio, and four consistency tests that suppress false positives. Each target containing at least one transit-like pulse sequence is searched repeatedly for other signals that meet the detection criteria, indicating a multiple planet system. This multiple planet search adds an additional 7,698 transit-like signatures for a total of 20,367. Comparison of this set of detected signals with a set of known and vetted transiting planet signatures in the Kepler field of view shows that the recovery rate of the search is 90.3%. We review ensemble properties of the detected signals and present various metrics useful in validating these potential planetary signals. We highlight previously undetected planetary candidates, including several small potential planets in the habitable zone of their host stars.
D8.3 Report on the standardization landscape and applicable standards
Creators: name: Suo, Amanda
Publisher: name: Zenodo
Year: 2019

description: This deliverable D8.3 “Report on Standardization landscape and applicable standards” (M6) is the first deliverable for task T8.3 “Standardization activities” inside WP8 “Exploitation, Standardization, Dissemination and Communication”. The main objective of this task is to facilitate the acceptance and utilization by the market of the developed solutions. Other objectives are to provide starting information for other WPs, ensure compatibility and interoperability with what already exists in the market through standards, as well as to use the standardization system as a tool for dissemination of the project results and interaction with the market stakeholders. The standardization activities planned in this task to fulfil the above objectives will be considered under two specific activities, which are mutually linked: the identification and analysis of related existing standards and the contribution to the ongoing and future standardization developments from the results of the project. The participation of a Standardization Body, representing CEN and CENELEC, provides the relevance, knowledge and experience in the standardization system and its internal procedures. This first delivery provides, analysis of the available and applicable standardization landscape, starting from needs of other WPs about existing standards that can be related, as well as the related Standardization Committees and organizations involved, in order to ensure compatibility and interoperability of SHAREWORK and facilitate the acceptance and utilization by the market of the developed solutions. The Spanish Association for Standardization, UNE, (previous called AENOR), as National Standardization Body (NSB), member of CEN-CENELEC has been subcontracted by SHAREWORK (EURECAT – the coordinator) to provide support regarding the standardization tasks included in the project (WP8 - Exploitation, Standardization, Dissemination and Communication).
Autor*innenidentifikation mit ORCID an wissenschaftlichen Einrichtungen im Zusammenspiel mit der GND
Creators: name: Schrader, Antonia C.
name: Glagla-Dietz, Stephanie
name: Pampel, Heinz
Publisher: name: Forschungzentrum Jülich
Year: 2021

description: 109. Deutscher Bibliothekartag in Bremen 2021, Bremen, Germany
description: Im Rahmen des Publikationsmanagements an wissenschaftlichen Einrichtungen sind Bibliotheken mit vielfältigen Herausforderungen rund um die eindeutige Identifikation von wissenschaftlichen Autor*innen konfrontiert. Dabei gilt es über textuelle Veröffentlichungen hinaus, Publikationen von Forschungsdaten und Forschungssoftware zu organisieren. Die ORCID iD (orcid.org) schafft hierfür einen internationalen Standard, indem sie die eindeutige Identifikation der Forschenden und die persistente Verknüpfung zwischen ihnen und ihren Publikationen gewährleistet. Dabei wird durch das von der Deutschen Forschungsgemeinschaft geförderte Projekt ORCID DE das Zusammenspiel mit der Gemeinsamen Normdatei (GND) sichergestellt. Immer mehr GND-Personendatensätze und Personenfelder der Publikationsdatensätze im Katalog der Deutschen Nationalbibliothek (DNB) enthalten ORCID iDs und Wissenschaftler und Wissenschaftlerinnen verbinden mit Hilfe des Claiming-Services ihren ORCID-Record mit den Publikationen im DNB-Katalog. Häufig werden ORCID iDs von Verlagen direkt mit Netzpublikationen abgeliefert. So können maschinelle Prozesse GND- und Titeldatensätze verknüpfen und durch Abgleichsverfahren weitere ORCID iDs ermitteln und in die GND einspielen, wodurch die Qualität bibliothekarischer Metadaten deutlich verbessert wird. Bis Ende 2020 konnten bereits 100.000 GND-Personendatensätze mit ORCID-Records verknüpft werden. Im Vortrag wird dieses Zusammenspiel von ORCID und GND sowie die Vorteile für wissenschaftliche Einrichtungen beschrieben. Darüber hinaus wird zum Stand und den Perspektiven des ORCID DE Projektes berichtet.
A Brg1 mutation that uncouples ATPase activity from chromatin remodeling reveals an essential role for SWI/SNF-related complexes in  -globin expression and erythroid development
Creators: name: Bultman, S. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The Brg1 catalytic subunit of SWI/SNF-related complexes has been implicated in many developmental and physiological processes, but null homozygotes die as blastocysts prior to implantation. To circumvent this early embryonic lethality, we performed an ENU mutagenesis screen and generated a Brg1 hypomorph mutation in the ATPase domain. The mutant Brg1 protein is stable, assembles into SWI/SNF-related complexes, and exhibits normal ATPase activity but is unable to establish DNase I hypersensitivity sites characteristic of open chromatin. Mutant embryos develop normally until midgestation but then exhibit a distinct block in the development of the erythroid lineage, leading to anemia and death. The mutant Brg1 protein is recruited to the β-globin locus, but chromatin remodeling and transcription are perturbed. Histone acetylation and DNA methylation are also affected. To our knowledge, Brg1 is the first chromatin-modifying factor shown to be required for β-globin regulation and erythropoiesis in vivo. Not only does this mutation establish a role for Brg1 during organogenesis, it also demonstrates that ATPase activity can be uncoupled from chromatin remodeling.
DDB1 functions as a linker to recruit receptor WD40 proteins to CUL4-ROC1 ubiquitin ligases
Creators: name: McCall, C. M.
name: Zeng, Y.
name: Hu, J.
name: He, Y. J.
name: Xiong, Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Cullins assemble the largest family of ubiquitin ligases by binding with ROC1 and various substrate receptors. CUL4 function is linked with many cellular processes, but its substrate-recruiting mechanism remains elusive. We identified a protein motif, the DWD box (DDB1-binding WD40 protein), and demonstrated the binding of 15 DWD proteins with DDB1–CUL4A. We provide evidence supporting the critical function of the DWD box and DDB1’s role as the linker mediating DWD protein association with CUL4A. A database search predicts that about one-third of WD40 proteins, 90 in humans, contain the DWD box, suggesting a potentially large number of DWD–DDB1–CUL4–ROC1 E3 ligases.
Computation Offloading with Multiple Agents in Edge-Computing-Supported IoT
Creators: name: Shen, Shihao
name: Han, Yiwen
name: Wang, Xiaofei
name: Wang, Yan
Publisher: name: arXiv
Year: 2023
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: With the development of the Internet of Things (IoT) and the birth of various new IoT devices, the capacity of massive IoT devices is facing challenges. Fortunately, edge computing can optimize problems such as delay and connectivity by offloading part of the computational tasks to edge nodes close to the data source. Using this feature, IoT devices can save more resources while still maintaining the quality of service. However, since computation offloading decisions concern joint and complex resource management, we use multiple Deep Reinforcement Learning (DRL) agents deployed on IoT devices to guide their own decisions. Besides, Federated Learning (FL) is utilized to train DRL agents in a distributed fashion, aiming to make the DRL-based decision making practical and further decrease the transmission cost between IoT devices and Edge Nodes. In this article, we first study the problem of computation offloading optimization and prove the problem is an NP-hard problem. Then, based on DRL and FL, we propose an offloading algorithm that is different from the traditional method. Finally, we studied the effects of various parameters on the performance of the algorithm and verified the effectiveness of both the DRL and FL in the IoT system.
description: 28 pages
Expression of the Bcl-3 proto-oncogene suppresses p53 activation
Creators: name: Kashatus, D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: While Bcl-3 expression in cancer was originally thought to be limited to B-cell lymphomas with a 14;19 chromosomal translocation, more recent evidence indicates that expression of this presumptive oncoprotein is significantly more widespread in cancer. However, an oncogenic role for Bcl-3 has not been clearly identified. Experiments presented here indicate that Bcl-3 is inducible by DNA damage and is required for the induction of Hdm2 gene expression and the suppression of persistent p53 activity. Furthermore, constitutive expression of Bcl-3 suppresses DNA damage-induced p53 activation and inhibits p53-induced apoptosis through a mechanism that is at least partly dependent on the up-regulation of Hdm2. The results provide insight into a mechanism whereby altered expression of Bcl-3 leads to tumorigenic potential. Since Bcl-3 is required for germinal center formation, these results suggest functional similarities with the unrelated Bcl-6 oncoprotein in suppressing potential p53-dependent cell cycle arrest and apoptosis in response to somatic hypermutation and class switch recombination.
A split SUSY model from SUSY GUT
Creators: name: Wang, Fei
name: Wang, Wenyu
name: Yang, Jin Min
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We propose to split the sparticle spectrum from the hierarchy between the GUT scale and the Planck scale. A split supersymmetric model, which gives non-universal gaugino masses, is built with proper high dimensional operators in the framework of SO(10) GUT. Based on a calculation of two-loop beta functions for gauge couplings (taking into account all weak scale threshold corrections), we check the gauge coupling unification and dark matter constraints (relic density and direct detections). We find that our scenario can achieve the gauge coupling unification and satisfy the dark matter constraints in some part of parameter space. We also examine the sensitivity of the future XENON1T experiment and find that the currently allowed parameter space in our scenario can be covered for a neutralino dark matter below about 1.0 TeV.
description: 16 pages, 3 figure; minor changes, references added
Photo-electrocatalytic activity of praseodymium oxide modified titania nanorods
Creators: name: Balachandran, Subramanian
name: Karthikeyan, Rajan
name: Selvakumar, Karuppaiah
name: Swaminathan, Meenakshisundaram
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Developmental Biology
subject: Plant Biology

description: Modification of semiconductor oxides leads to a major development in functional characteristics. Characterisation of Pr6O11-TiO2, fabricated by a cost-effective hydrothermal – decomposition method reveals the nanorod like structure of this catalyst. The XRD pattern definite the formation of face-centred cubic or cubic close-packed structure of Pr6O11 and the high crystallinity indicate the existence of anatase TiO2. XPS analysis indicates the presence of both Pr3+and Pr4+ ions in Pr6O11. Pr6O11-TiO2 is more photoactive under visible light than Pr6O11, prepared TiO2 and TiO2-P25 (80% Anatase and 20% Rutile mixture) in the degradation of toxic azo dyes. Pr6O11-TiO2 is stable and recyclable consecutively. Pr6O11-TiO2 catalyst shows higher electrocatalytic activity in methanol oxidation than pure TiO2. These results reveal new insights on the efficiency of catalysts in photo- and electrocatalytic applications.
Extensive post-transcriptional regulation of microRNAs and its implications for cancer
Creators: name: Thomson, J. M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: MicroRNAs (miRNAs) are short, noncoding RNAs that post-transcriptionally regulate gene expression. While hundreds of mammalian miRNA genes have been identified, little is known about the pathways that regulate the production of active miRNA species. Here we show that a large fraction of miRNA genes are regulated post-transcriptionally. During early mouse development, many miRNA primary transcripts, including the Let-7 family, are present at high levels but are not processed by the enzyme Drosha. An analysis of gene expression in primary tumors indicates that the widespread down-regulation of miRNAs observed in cancer is due to a failure at the Drosha processing step. These data uncover a novel regulatory step in miRNA function and provide a mechanism for miRNA down-regulation in cancer.
Raman scattering investigation of large positive magnetoresistance material WTe$_2$
Creators: name: Kong, W. -D.
name: Wu, S. -F.
name: Richard, P.
name: Lian, C. -S.
name: Wang, J. -T.
name: Yang, C. -L.
name: Shi, Y. -G.
name: Ding, H.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We have performed polarized Raman scattering measurements on WTe$_2$, for which an extremely large positive magnetoresistance has been reported recently. We observe 5 A$_1$ phonon modes and 2 A$_2$ phonon modes out of 33 Raman active modes, with frequencies in good accordance with first-principles calculations. The angular dependence of the intensity of the peaks observed is consistent with the Raman tensors of the $C_{2v}$ point group symmetry attributed to WTe$_2$. Although the phonon spectra suggest neither strong electron-phonon nor spin-phonon coupling, the intensity of the A$_1$ phonon mode at 160.6 cm$^{-1}$ shows an unconventional decrease with temperature decreasing, for which the origin remains unclear.
description: 4 pages, 3 figures, 2 tables. Resistivity scale in Fig. 1 normalized
Discovering Trustworthy Data Repositories with re3data – the Registry of Research Data Repositories
Creators: name: Weisweiler, Nina Leonie
Publisher: name: Forschungzentrum Jülich
Year: 2021
Subjects: Research Data Repositories
re3data
re3data COREF Project
FAIR Research Data

description: Meeting FORCE2021, , 7 Dec 2021 - 9 Dec 2021; doi:10.5281/ZENODO.5763836
description: The global registry for research data repositories - re3data - lists over 2700 digital repositories across all scientific disciplines (as of December 2021). The service provides an extensive description of repositories based on a detailed metadata schema, the updated version of which was recently published [1]. It promotes open science practices and the visibility of science-driven open infrastructures. A variety of funders, publishers, and scientific organizations around the world refer to re3data within their guidelines and policies, recommending it as a trusted service to researchers looking for appropriate repositories for storage and discovery of research data [2,3]. The re3data web interface and API enable end users and third-party providers to discover the largest index of research data repositories in the world. In January 2020, the project 're3data COREF' (Community Driven Open Reference for Research Data Repositories) [4] started, funded by the German Research Foundation (DFG) for three years, with the goal to further develop and improve the registry. The presentation introduces the re3data service and gives an overview of the ongoing project work, including a short introduction to the recently published “Conceptual Model for User Stories” [5], which is intended to help the project team recalibrate re3data according to current and future needs of the community. [1] Strecker, D. et al. (2021) ‘Metadata Schema for the Description of Research Data Repositories: Version 3.1’. https://doi.org/10.48440/re3.010 [2] Kindling, M. et al. (2017) ‘The Landscape of Research Data Repositories in 2015: a Re3data Analysis’, D-Lib Magazine, 23(3/4). https://doi.org/10.1045/march2017-kindling [3] Witt, M. et al. (2019) ‘Connecting Researchers to Data Repositories in the Earth, Space, and Environmental Sciences’, in Manghi, P., Candela, L., and Silvello, G. (eds) Digital Libraries: Supporting Open Science. Cham: Springer International Publishing, pp. 86–96. https://doi.org/10.1007/978-3-030-11226-4_7 [4] https://coref.project.re3data.org/project [5] Vierkant, P. et al. (2021): re3data Conceptual Model for User Stories’. https://doi.org/10.48440/re3.012
Fractal dimension and turbulence in Giant HII Regions
Creators: name: Caicedo-Ortiz, H. E.
name: Santiago-Cortés, E.
name: López-Bonilla, J.
name: Castañeda, H. O.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: We have measured the fractal dimensions of the Giant HII Regions Hubble X and Hubble V in NGC6822 using images obtained with the Hubble's Wide Field Planetary Camera 2 (WFPC2). These measures are associated with the turbulence observed in these regions, which is quantified through the velocity dispersion of emission lines in the visible. Our results suggest low turbulence behaviour.
description: 5 pages, 4 figures. Correction table includes data on fractal dimension values
D6.5 White paper Report on best practices for HRC integration into production
Creators: name: Vonsy, Aurélie
name: Morisseau, Tiffany
name: Canale, Francesca
name: Jaunet, Alexandra
Publisher: name: Zenodo
Year: 2022

description: This document reviews the best practices stemming from the Sharework project, contributing to a smooth cobot integration on the workplace from a human factors point of view. It was written based on four project’s use cases and focuses on a number of success factors that were identified for all the use cases. Cobots are a costly investment that aim to reduce ergonomics issue, mental load and increase productivity. How the final users perform with them is thus a key element of successful integration. Any robot integration should be carefully prepared to make sure that the social terrain is ready, and that the technology can adapt to how the operators work (and not the other way around). Three indicators were measured in collaboration with the operators themselves: trust, situational awareness, and cognitive load. We also identified six key points for a successful integration, which focus on the integrator’s location, the operators’ expertise in the task, their perception of technology, the feeling of safety around the robot, how operator’s feedback is addressed and the involvement of the management team.
Genomic instability due to V(D)J recombination-associated transposition
Creators: name: Reddy, Y. V.R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The first step in assembling immunoglobulin and T-cell receptors by V(D)J recombination has similarities to transposon excision. The excised transposon-like element then integrates into DNA targets at random in vitro, but whether this activity significantly threatens the genomic integrity of its host has been unclear. Here, we recover examples where the putative transposon associated with V(D)J recombination integrated into the genome of a pre-B-cell line. Transposition accounted for a surprisingly high proportion (one-third) of integrations, while most of the remaining events had parallels to other aberrant V(D)J recombination pathways linked to oncogenic translocation. In total, transposition occurred approximately once every 50,000 V(D)J recombinations. Transposition may thus contribute significantly to genomic instability.
EcoDM Werkstattbericht - Erkenntnisse aus den Interviews
Creators: name: Bruch, Christoph
name: Burkart, Christine
name: Endres, Kirsten
name: Neuroth, Heike
name: Schneidenbach, Esther
name: Senst, Henriette
name: Spiecker, Claus
Publisher: name: Forschungzentrum Jülich
Year: 2021
Subjects: FAIR Data
Research Data
Forschungsdatenmanagement
FAIR
Open Data

description: doi:10.5281/ZENODO.5550395
description: Das Verbundprojekt EcoDM „Ökosystem Datenmanagement: Analysen – Empfehlungen – FAIRification“ untersucht, wie die stetig wachsenden digitalen Datenmengen aus unterschiedlichen Bereichen systematisch und entsprechend der FAIR-Prinzipien (Findable, Accessible, Interoperable, and Reusable) nachhaltig genutzt werden können. Die Projektergebnisse sollen einen Überblick über bestehende Bedarfe und Herausforderungen sowie konkrete Handlungsempfehlungen für ein FAIRes Datenmanagement enthalten. Damit soll ein Beitrag zur Entwicklung von Strategien für einen bereichsübergreifenden Datenaustausch geleistet werden. Die an EcoDM beteiligten Projektpartner sind das Deutsche Archäologische Institut, das am Helmholtz-Zentrum Potsdam – Deutsches GeoForschungsZentrum GFZ angesiedelte Helmholtz Open Science Office und die Fachhochschule Potsdam. Das Poster gibt als Werkstattbericht einen Überblick zu ersten Erkenntnissen aus der Auswertung der Expert*innen-Interviews. In den Bereichen Wissenschaft und Public Sector wurde der Bedarf an Ausbildungsangeboten sowie eine ungenügende Verankerung des Themas Datenmanagement in der Lehre deutlich. Diese Identifizierung als Problemfelder wurde durch Erkenntnisse aus dem Bereich Qualifizierung gestützt. Im Hinblick darauf, dass in den Bereichen Wissenschaft, Public Sector und Wirtschaft ein wachsender Bedarf an Datenmanagement-Expert*innen zu verzeichnen ist, wurde im Bereich Qualifizierung deutlich, dass sich die Bedarfe von Weiterbildungsangeboten und der thematischen Einbindung in Ausbildungs- und Studiengänge bis hin zur gezielten Ausbildung von Data Scientists, Data Stewards und neuen Berufen erstrecken. Die Notwendigkeit für einen Kulturwandel im Umgang mit Daten bzw. für ein stärkeres Bewusstsein für die Relevanz des Themas Datenmanagement war im Public Sector zu erkennen. Im Bereich Wissenschaft hingegen werden als Bedarfe eine Verstetigung des Datenmanagements und die Bereitstellung von Ressourcen geäußert. In den Interviews aus dem Bereich Wirtschaft hingegen wurde deutlich, dass das Teilen von Daten für Firmen mit einem Mehrwert verbunden sein muss. Hier wurde besonders der Bedarf nach rechtlichen Rahmenbedingungen hervorgehoben.
On the Effects of Regional Spelling Conventions in Retrieval Models
Creators: name: Chari, Andreas
name: MacAvaney, Sean
name: Ounis, Iadh
Publisher: name: arXiv
Year: 2023
Subjects: subject: Information Retrieval (cs.IR)
subject: FOS: Computer and information sciences

description: One advantage of neural ranking models is that they are meant to generalise well in situations of synonymity i.e. where two words have similar or identical meanings. In this paper, we investigate and quantify how well various ranking models perform in a clear-cut case of synonymity: when words are simply expressed in different surface forms due to regional differences in spelling conventions (e.g., color vs colour). We first explore the prevalence of American and British English spelling conventions in datasets used for the pre-training, training and evaluation of neural retrieval methods, and find that American spelling conventions are far more prevalent. Despite these biases in the training data, we find that retrieval models often generalise well in this case of synonymity. We explore the effect of document spelling normalisation in retrieval and observe that all models are affected by normalising the document's spelling. While they all experience a drop in performance when normalised to a different spelling convention than that of the query, we observe varied behaviour when the document is normalised to share the query spelling convention: lexical models show improvements, dense retrievers remain unaffected, and re-rankers exhibit contradictory behaviour.
description: 10 pages, 3 tables, short paper published in SIGIR '23
title: ACOE Blue Ocean Mariculture Operation and Installation of New Net Pens
titleType: AlternativeTitle
title: Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion Authorization to Install New Net Pens and Ongoing, Revised Mariculture Operations by Blue Ocean Mariculture, LLC
Creators: name: United States. National Marine Fisheries Service. Pacific Islands Region
Publisher: name: United States. National Marine Fisheries Service. Pacific Islands Region
Year: 2022

description: PIRO-2018-00437
Evolution of field line helicity during magnetic reconnection
Creators: name: Russell, Alexander J. B.
name: Yeates, Anthony R.
name: Hornig, Gunnar
name: Wilmot-Smith, Antonia L.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We investigate the evolution of field line helicity for magnetic fields that connect two boundaries without null points, with emphasis on localized finite-B magnetic reconnection. Total (relative) magnetic helicity is already recognized as an important topological constraint on magnetohydrodynamic processes. Field line helicity offers further advantages because it preserves all topological information and can distinguish between different magnetic fields with the same total helicity. Magnetic reconnection changes field connectivity and field line helicity reflects these changes; the goal of this paper is to characterize that evolution. We start by deriving the evolution equation for field line helicity and examining its terms, also obtaining a simplified form for cases where dynamics are localized within the domain. The main result, which we support using kinematic examples, is that during localized reconnection in a complex magnetic field, the evolution of field line helicity is dominated by a work-like term that is evaluated at the field line endpoints, namely the scalar product of the generalized field line velocity and the vector potential. Furthermore, the flux integral of this term over certain areas is very small compared to the integral of the unsigned quantity, which indicates that changes of field line helicity happen in a well-organized pairwise manner. It follows that reconnection is very efficient at redistributing helicity in complex magnetic fields despite having little effect on the total helicity.
description: 11 pages, 8 figures. Accepted for publication in Physics of Plasmas
Gute wissenschaftliche Praxis und Open Science: Zur Rolle der Bibliotheken im DFG-Kodex
Creators: name: Ferguson, Lea Maria
name: Weisweiler, Nina Leonie
name: Pampel, Heinz
name: Bertelmann, Roland
name: Schrader, Antonia
Publisher: name: Forschungzentrum Jülich
Year: 2021

description: 109. Deutscher Bibliothekartag in Bremen 2021, Bremen
description: Seit August 2019 ist der Kodex „Leitlinien zur Sicherung guter wissenschaftlicher Praxis" [1] der Deutschen Forschungsgemeinschaft (DFG) gültig. Hochschulen und außeruniversitäre Einrichtungen müssen nun ihre institutionellen Leitlinien anpassen. Für viele der im Kodex enthaltenen Leitlinien sind Open-Science-Aspekte relevant. So beinhaltet der Kodex Anforderungen an den Umgang mit textuellen Publikationen, Forschungsdaten sowie Forschungssoftware und wirkt somit direkt auf die Dienstleistungen wissenschaftlicher Bibliotheken. Der Vortrag beschreibt praxisnah anhand ausgewählter Empfehlungen des Kodexes die Relevanz von Open Science bei der Förderung der guten wissenschaftlichen Praxis an Forschungseinrichtungen und vertieft hiermit die Empfehlungen aus dem Helmholtz Open Science Briefing "Gute (digitale) wissenschaftliche Praxis und Open Science” [2]. Es werden praktische Impulse zur Verankerung von Open Science in der guten (digitalen) wissenschaftlichen Praxis, insb. im Bibliotheks-Kontext besprochen. Zudem wird ein Diskussionsforum für interessierte Personen aus Bibliotheken, Forschung und verwandten Infrastrukturen angeboten, um einen weiteren Austausch zu diesem Thema zu ermöglichen.[1] Deutschen Forschungsgemeinschaft (2019). Leitlinien zur Sicherung guter wissenschaftlicher Praxis. Kodex. Online unter: https://www.dfg.de/download/pdf/foerderung/rechtliche_rahmenbedingungen/gute_wissenschaftliche_praxis/kodex_gwp.pdf [Zugriff am: 01.02.2020][2] Ferguson, L. M., Pampel, H., Bruch, C., Bertelmann, R., Weisweiler, N. L., Schrader, A. C., Messerschmidt, R., Faensen, K. (2020). Gute (digitale) wissenschaftliche Praxis und Open Science: Support und Best Practices zur Umsetzung des DFG-Kodex „Leitlinien zur Sicherung guter wissenschaftlicher Praxis". Online unter: https://doi.org/10.2312/os.helmholtz.012 [Zugriff am: 01.01.2020]
Materials Databases Integration using the Materials Design Ontology
Creators: name: Huanyu Li
Publisher: name: Zenodo
Year: 2023
Subjects: ontology
standard
data management
global workshop
ontology commons ecosystem
FAIR

description: In the materials design domain, much of the data from materials calculations is stored in different heterogeneous databases with different data and access models. Therefore, integrating data from different sources is challenging. As ontology-based access and integration alleviate such issues, we developed the Materials Design Ontology (MDO) for increasing interoperability among computational materials databases. Then, the team introduced a generic framework (OBG-gen) for using GraphQL in which a global domain ontology informs the generation of a GraphQL server that answers requests by querying heterogeneous data sources. By using MDO in this framework, it is possible to generate a GraphQL server for data integration among heterogeneous computational materials databases. Additionally, the team introduced a method (ToPMine-FTCA) for ontology extension and applied it in the materials science domain.
EdgeMatrix: A Resource-Redefined Scheduling Framework for SLA-Guaranteed Multi-Tier Edge-Cloud Computing Systems
Creators: name: Shen, Shihao
name: Ren, Yuanming
name: Ju, Yanli
name: Wang, Xiaofei
name: Wang, Wenyu
name: Leung, Victor C. M.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: With the development of networking technology, the computing system has evolved towards the multi-tier paradigm gradually. However, challenges, such as multi-resource heterogeneity of devices, resource competition of services, and networked system dynamics, make it difficult to guarantee service-level agreement (SLA) for the applications. In this paper, we propose a multi-tier edge-cloud computing framework, EdgeMatrix, to maximize the throughput of the system while guaranteeing different SLA priorities. First, in order to reduce the impact of physical resource heterogeneity, EdgeMatrix introduces the Networked Multi-agent Actor-Critic (NMAC) algorithm to re-define physical resources with the same quality of service as logically isolated resource units and combinations, i.e., cells and channels. In addition, a multi-task mechanism is designed in EdgeMatrix to solve the problem of Joint Service Orchestration and Request Dispatch (JSORD) for matching the requests and services, which can significantly reduce the optimization runtime. For integrating above two algorithms, EdgeMatrix is designed with two time-scales, i.e., coordinating services and resources at the larger time-scale, and dispatching requests at the smaller time-scale. Realistic trace-based experiments proves that the overall throughput of EdgeMatrix is 36.7% better than that of the closest baseline, while the SLA priorities are guaranteed still.
description: JSAC. arXiv admin note: substantial text overlap with arXiv:2203.10470
Maternal BRG1 regulates zygotic genome activation in the mouse
Creators: name: Bultman, S. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Zygotic genome activation (ZGA) is a nuclear reprogramming event that transforms the genome from transcriptional quiescence at fertilization to robust transcriptional activity shortly thereafter. The ensuing gene expression profile in the cleavage-stage embryo establishes totipotency and is required for further development. Although little is known about the molecular basis of ZGA, oocyte-derived mRNAs and proteins that alter chromatin structure are likely crucial. To test this hypothesis, we generated a maternal-effect mutation of Brg1, which encodes a catalytic subunit of SWI/SNF-related complexes, utilizing Cre-loxP gene targeting. In conditional-mutant females, BRG1-depleted oocytes completed meiosis and were fertilized. However, embryos conceived from BRG1-depleted eggs exhibited a ZGA phenotype including two-cell arrest and reduced transcription for ∼30% of expressed genes. Genes involved in transcription, RNA processing, and cell cycle regulation were particularly affected. The early embryonic arrest is not a consequence of a defective oocyte because depleting maternal BRG1 after oocyte development is complete by RNA interference (RNAi) also resulted in two-cell arrest. To our knowledge, Brg1 is the first gene required for ZGA in mammals. Depletion of maternal BRG1 did not affect global levels of histone acetylation, whereas dimethyl-H3K4 levels were reduced. These data provide a framework for understanding the mechanism of ZGA.
String field theory vertex from integrability
Creators: name: Bajnok, Zoltan
name: Janik, Romuald A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We propose a framework for computing the (light cone) string field theory vertex in the case when the string worldsheet QFT is a generic integrable theory. The prime example and ultimate goal would be the $AdS_5 \times S^5$ superstring theory cubic string vertex and the chief application will be to use this framework as a formulation for ${ \cal N}=4$ SYM theory OPE coefficients valid at any coupling up to wrapping corrections. In this paper we propose integrability axioms for the vertex, illustrate them on the example of the pp-wave string field theory and also uncover similar structures in weak coupling computations of OPE coefficients.
description: pdflatex, 52 pages, 20 figures,v2: references added, typos corrected
SOX2 is a dose-dependent regulator of retinal neural progenitor competence
Creators: name: Taranova, O. V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Approximately 10% of humans with anophthalmia (absent eye) or severe microphthalmia (small eye) show haploid insufficiency due to mutations in SOX2, a SOXB1-HMG box transcription factor. However, at present, the molecular or cellular mechanisms responsible for these conditions are poorly understood. Here, we directly assessed the requirement for SOX2 during eye development by generating a gene-dosage allelic series of Sox2 mutations in the mouse. The Sox2 mutant mice display a range of eye phenotypes consistent with human syndromes and the severity of these phenotypes directly relates to the levels of SOX2 expression found in progenitor cells of the neural retina. Retinal progenitor cells with conditionally ablated Sox2 lose competence to both proliferate and terminally differentiate. In contrast, in Sox2 hypomorphic/null mice, a reduction of SOX2 expression to <40% of normal causes variable microphthalmia as a result of aberrant neural progenitor differentiation. Furthermore, we provide genetic and molecular evidence that SOX2 activity, in a concentration-dependent manner, plays a key role in the regulation of the NOTCH1 signaling pathway in retinal progenitor cells. Collectively, these results show that precise regulation of SOX2 dosage is critical for temporal and spatial regulation of retinal progenitor cell differentiation and provide a cellular and molecular model for understanding how hypomorphic levels of SOX2 cause retinal defects in humans.
Detection of quinolones in milk and groundwater samples using an indirect immunofluorescent magneto assay
Creators: name: Kergaravat, Silvina V.
name: Nagel, Orlando G.
name: Althaus, Rafael L.
name: Hernández, Silvia R.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Space Science
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: A simple magneto immunofluorescence assay for quinolone family detection in 96-well microplate was developed and applied to milk and groundwater samples. Norfloxacin (NOR) conjugated to albumin (BSA) was immobilised on magnetic beads (MBs) in a first step. The strategy was based on an indirect competitive assay between free and immobilised quinolone for anti-quinolone IgG antibody. Then, a peroxidase tracer was added as developer reagent. The fluorescence responses at 440 and 540 nm - excitation and emission wavelengths, respectively – were obtained by adding o-phenylenediamine and peroxide hydrogen as peroxidase substrates. The fluorescence response was indirectly proportional to the concentration of quinolone in the sample. Ciprofloxacin was selected as model quinolone with cut-off and limit of detection (LOD) of 4 and 8 μg L−1, respectively. Bovine milk and groundwater blank samples were spiked with ciprofloxacin at 5, 25 and 50 µg L−1 obtaining good recoveries (90–100%) with coefficient variation lower than 20% in all cases, in concordance with the results obtained by applying a reference method. Therefore, the method developed would be applicable for the detection of quinolones in bovine milk from dairy farms and in groundwater from sites with intensive livestock activities.
D1.7 Key Performance Indicators (KPIs) for assessment - II
Creators: name: Landini, Alberto
Publisher: name: Zenodo
Year: 2020

description: This document concludes the activities performed during WP1 regarding the collection of industrial requirements and the consequent definition of the most relevant metrics to be used for the assessment of the ShareWork system performances in industrial manufacturing environment. In this document, specific metrics are provided to allow the validation of the ShareWork system in each of the four use cases considered in the project. In addition to the metrics for the industrial impact evaluation, all technological modules of the ShareWork are here addressed, presenting the methodology, the baseline and the targets to validate the software modules performances with respect to the current state of the art. The information collected in this deliverable will be essential in WP7, when the system validation campaign and performance assessment will be performed.
Sox2 is required for development of taste bud sensory cells
Creators: name: Hogan, B. L.M.
name: Pevny, L. H.
name: Okubo, T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Sox2 is expressed in basal epithelial cells of the tongue, with high levels in taste bud placodes, fungiform papillae, and mature taste cells, and low levels in filiform papillae. High Sox2 expression appears to lie downstream from canonical Wnt signaling. In hypomorphic Sox2EGFP/LP embryos, placodes form but no mature taste buds develop. In contrast, transgenic overexpression of Sox2 in the basal cells inhibits differentiation of filiform keratinocytes. Together, our loss-of-function and gain-of-function studies suggest that Sox2 functions in a dose-dependent manner to regulate the differentiation of endodermal progenitor cells of the tongue into taste bud sensory cells versus keratinocytes.
Exciton band structure of monolayer MoS2
Creators: name: Wu, Fengcheng
name: Qu, Fanyao
name: MacDonald, A. H.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We address the properties of excitons in monolayer MoS$_2$ from a theoretical point of view, showing that low-energy excitonic states occur both at the Brillouin zone center and at the Brillouin-zone corners, that binding energies at the Brillouin-zone center deviate strongly from the $(n-1/2)^{-2}$ pattern of the two-dimensional hydrogenic model, and that the valley-degenerate exciton doublet at the Brillouin-zone center splits at finite momentum into an upper mode with non-analytic linear dispersion and a lower mode with quadratic dispersion. Although monolayer MoS$_2$ is a direct-gap semiconductor when classified by its quasiparticle band structure, it may well be an indirect gap material when classified by its excitation spectra.
description: 9 pages, 6 figures
pRB family proteins are required for H3K27 trimethylation and Polycomb repression complexes binding to and silencing p16INK4a tumor suppressor gene
Creators: name: Viatour, P.
name: Cao, R.
name: Zhang, Y.
name: Xiong, Y.
name: Sage, J.
name: Kotake, Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Genetic studies have demonstrated that Bmi1 promotes cell proliferation and stem cell self-renewal with a correlative decrease of p16INK4a expression. Here, we demonstrate that Polycomb genes EZH2 and BMI1 repress p16 expression in human and mouse primary cells, but not in cells deficient for pRB protein function. The p16 locus is H3K27-methylated and bound by BMI1, RING2, and SUZ12. Inactivation of pRB family proteins abolishes H3K27 methylation and disrupts BMI1, RING2, and SUZ12 binding to the p16 locus. These results suggest a model in which pRB proteins recruit PRC2 to trimethylate p16, priming the BMI1-containing PRC1L ubiquitin ligase complex to silence p16.