cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Measuring and theorizing regional governance
Creators: name: Osterkatz, S.C.
name: Harbers, I.
name: Marks, G.
name: Schakel, A.H.
name: Eaton, K.
name: Hooghe, L.
name: Shair-Rosenfield, S.
name: Niedzwiecki, S.
name: Faguet, J.-P.
Publisher: name: Routledge
Year: 2019

description: This symposium Regional Authority and the Postfunctionalist Theory of Governance engages two recent books on regional governance. The first sets out a measure of regional authority for 81 countries in North America, Europe, Latin America, Asia and the Pacific between 1950 and 2010. The second theorizes how regional governance is shaped by functional and communal pressures. These pressures are detected in many historical episodes of jurisdictional reform. These books seek to pin them down empirically. Community and efficiency appear to have tangible and contrasting effects that explain how jurisdictions are designed, why regional governance has become differentiated and how multilevel governance has deepened over the past several decades. The symposium consists of contributions by Kent Eaton, Jean-Paul Faguet and Imke Harbers followed by a response from the authors: Liesbet Hooghe, Gary Marks, Arjan H. Schakel, Sara Niedzwiecki, Sandra Chapman Osterkatz and Sarah Shair-Rosenfield, Measuring Regional Authority: A Postfunctionalist Theory of Governance, Vol. I. Oxford: Oxford University Press, 2016; and Liesbet Hooghe and Gary Marks, with Arjan H. Schakel, Sara Niedzwiecki, Sandra Chapman Osterkatz and Sarah Shair-Rosenfield, Community, Scale, and Regional Governance: A Postfunctionalist Theory of Governance, Vol. II. Oxford: Oxford University Press, 2016.
title: Book review : Taylor, C. (2012). Empathic Care for Children with Disorganised Attachments: A Model for Mentalizing, Attachment and Trauma-Informed Care
Creators: name: Kieran, Nicola
Publisher: name: Strathprints - University of Strathclyde
Year: 2015

description: If you work in residential childcare, it seems likely that you will be supporting young people who have experienced traumatic events in their childhood. It is known that such experiences have a significant impact on brain development and the quality of attachment with their care givers (Cairns, 2015, p.50). You might think that there is little you can do to help them recover from their experiences. You might think that your young people have come into residential childcare too late; that the potential for therapeutic working is long gone. Chris Taylor suggests otherwise: he suggests that with understanding and empathy, young people can heal.
This Isn't Disneyland
Creators: name: Skinner, Anthea
Publisher: name: University of Melbourne
Year: 2023
Subjects: classificationCode: 360304
subject: Music performance
classificationCode: 420318
subject: People with disability

description: A review of all-disabled girl band Sister's of Invention's first single This Isn't Disneyland. Originally published in Link Disability Magazine, Vol 24, No 1, 2015, p42.
iMagine D2.1 First Communication, Dissemination and Engagement plan
Creators: name: Fava, Ilaria
Publisher: name: Zenodo
Year: 2023
Subjects: Communication
Dissemination
Engagement
Events

description: This deliverable provides an overview on how project results, developments and branding will be communicated. Moreover, a plan for the engagement with the targeted audiences, a dissemination strategy, the description of promotion, outreach, training and co-design activities are presented in the document along with a dissemination plan.
description: Version submitted to the EC, not yet approved
Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer
Creators: name: Knijnenburg, T.A.
name: Zhou, W.
name: Kemal, A.
name: Cherniack, A.D.
name: Beroukhim, R.
name: Carrot-Zhang, J.
name: Hoadley, K.A.
name: Robertson, A.G.
name: Chambwe, N.
name: Zenklusen, J.C.
name: Damrauer, J.S.
name: Yau, C.
Publisher: name: Cell Press
Year: 2021

description: Cellular and molecular aberrations contribute to the disparity of human cancer incidence and etiology between ancestry groups. Multiomics profiling in The Cancer Genome Atlas (TCGA) allows for querying of the molecular underpinnings of ancestry-specific discrepancies in human cancer. Here, we provide a protocol for integrative associative analysis of ancestry with molecular correlates, including somatic mutations, DNA methylation, mRNA transcription, miRNA transcription, and pathway activity, using TCGA data. This protocol can be generalized to analyze other cancer cohorts and human diseases. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020).
SCISSOR: a framework for identifying structural changes in RNA transcripts
Creators: name: Zhao, X.
name: Love, M.I.
name: Holt, J.
name: Hayes, D.N.
name: Jo, H.
name: Newman, S.
name: Hayward, M.C.
name: Hoadley, K.A.
name: Choi, H.Y.
name: Marron, J.S.
Publisher: name: Nature Research
Year: 2021

description: High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA variation through differential splicing/alternative exon usage, challenges in its analysis remain. Here, we propose a framework for unbiased and robust discovery of aberrant RNA transcript structures using short read sequencing data based on shape changes in an RNA-seq coverage profile. Shape changes in selecting sample outliers in RNA-seq, SCISSOR, is a series of procedures for transforming and normalizing base-level RNA sequencing coverage data in a transcript independent manner, followed by a statistical framework for its analysis (https://github.com/hyochoi/SCISSOR). The resulting high dimensional object is amenable to unsupervised screening of structural alterations across RNA-seq cohorts with nearly no assumption on the mutational mechanisms underlying abnormalities. This enables SCISSOR to independently recapture known variants such as splice site mutations in tumor suppressor genes as well as novel variants that are previously unrecognized or difficult to identify by any existing methods including recurrent alternate transcription start sites and recurrent complex deletions in 3′ UTRs.
Development of energy recovery linacs: Towards a European ERL roadmap
Creators: name: Klein, Max
Publisher: name: Zenodo
Year: 2021

description: A summary will be given of the current status and the prospects for energy recovery linac (ERL) technology and its possible application for future ep and e+e- colliders, as well as for low energy particle and nuclear physics. The talk will give an overview of ERL development facilities, current and future, describe key technology challenges and also cover the aspect of sustainability of ERLs. Energy recovery has been recognised as one of the major new, promising accelerator technologies of the future by the recent deliberation on the strategy for particle physics. The presentation is on behalf of an 18 person expert panel on ERL which develops a roadmap on ERL technology developments towards the end of 21, following a mandate by CERN Council and the group of directors of larger laboratories (LDG) associated to CERN.
2nd International Conference on Circular Economy, Renewable Energies, and Green Hydrogen in Africa
Creators: name: Narra, Satyanarayana
name: Narra, Mona-Maria
name: Jobe, Fatou Balleh
name: Gbiete, Djangbadjoa
name: Universität Rostock. Professur Abfall- Und Stoffstromwirtschaft
Publisher: name: University Rostock, Waste- and Resource Management, Professorship for Material and Energy Valorisation of Biogenous Residues
Year: 2024
Subjects: subject: 333.7 Natural resources, energy and environment

description: The rapid increase in energy costs due to the double effect of inflation and currency depreciation means that smart choices driven by research, development, demonstration, and sustainability should lead the way, especially as they affect the growth of developing countries. African countries, therefore, have the opportunity to leverage the current global economic situation for sustainable technology enhancement and growth, and also transition towards green and sustainable pathways while securing energy needs and ensuring modern energy fuels from alternative and nonconventional sources. These energy sources, therefore, can easily be made available to the population at affordable and competitive prices. This conference focuses on Africa and seeks to bring together various stakeholders such as academia and research scientists, industrialists, small and medium-scale enterprises, technocrats and political actors, NGOs, etc. to exchange knowledge on the following: 1. Establishing facilities. 2. Producing and marketing different green fuels and renewable energy options. 3. Creating an alternative sustainable future for Africa. 4. Advocating and considering the energy and fuel needs of rural, peri-urban, and urban communities. 5. Shaping the inclusive green pathways within the continent.
Stochastic equations for thermodynamics
Creators: name: Tsekov, R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The applicability of stochastic differential equations to thermodynamics is considered and a new form, different from the classical Ito and Stratonovich forms, is introduced. It is shown that the new presentation is more appropriate for the description of thermodynamic fluctuations. The range of validity of the Boltzmann-Einstein principle is also discussed and a generalized alternative is proposed. Both expressions coincide in the small fluctuation limit, providing a normal distribution density.
Protein-based immune profiles of basal-like vs. luminal breast cancers
Creators: name: Olsson, L.T.
name: Sherman, M.E.
name: Calhoun, B.C.
name: Troester, M.A.
name: Midkiff, B.R.
name: Xia, Y.
name: Walens, A.
name: Hamilton, A.M.
name: Hoadley, K.A
name: Nikolaishvili-Feinberg, N.
name: Gao, X.
name: Cohen, S.M.
name: Serody, J.S.
name: Kirk, E.L.
Publisher: name: Springer Nature
Year: 2021

description: Tumor-infiltrating lymphocytes play an important, but incompletely understood role in chemotherapy response and prognosis. In breast cancer, there appear to be distinct immune responses by subtype, but most studies have used limited numbers of protein markers or bulk sequencing of RNA to characterize immune response, in which spatial organization cannot be assessed. To identify immune phenotypes of Basal-like vs. Luminal breast cancer we used the GeoMx® (NanoString) platform to perform digital spatial profiling of immune-related proteins in tumor whole sections and tissue microarrays (TMA). Visualization of CD45, CD68, or pan-Cytokeratin by immunofluorescence was used to select regions of interest in formalin-fixed paraffin embedded tissue sections. Forty-four antibodies representing stromal markers and multiple immune cell types were applied to quantify the tumor microenvironment. In whole tumor slides, immune hot spots (CD45+) had increased expression of many immune markers, suggesting a diverse and robust immune response. In epithelium-enriched areas, immune signals were also detectable and varied by subtype, with regulatory T-cell (Treg) markers (CD4, CD25, and FOXP3) being higher in Basal-like vs. Luminal breast cancer. Extending these findings to TMAs with more patients (n = 75), we confirmed subtype-specific immune profiles, including enrichment of Treg markers in Basal-likes. This work demonstrated that immune responses can be detected in epithelium-rich tissue, and that TMAs are a viable approach for obtaining important immunoprofiling data. In addition, we found that immune marker expression is associated with breast cancer subtype, suggesting possible prognostic, or targetable differences.
title: A Theory for Event-Driven Specifications Using Focus and MontiArc on the Example of a Data Link Uplink Feed System
Creators: name: Kausch, Hendrik
name: Pfeiffer, Mathias
name: Raco, Deni
name: Rath, Amelie
name: Rumpe, Bernhard
name: Schweiger, Andreas
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: event-based components||automata||formal verification||model-driven development||underspecification||distributed systems||avionics

description: The development of avionics message communication systems is expensive due to their complexity and the need to get them accepted by the certification authorities. We need to develop high-integrity software, but we also face cost pressure. For managing complex large systems, several time-synchronous modeling languages have been proposed. While these are appropriate for hardware specifications, when it comes to specifying distributed software systems, an event-based specification style is better suited. We present an event-based specification theory based on the framework Focus by giving the signatures and data types for specifications using event automata. For this, we capture message processing order as a further dimension of non-determinism by specifying a general timed merge component. These event automata can represent underspecification of behavior, and a refinement calculus can be applied to these for a stepwise reduction of non-determinism. Furthermore, we present the necessary concepts for enabling a user-friendly specification and simulation of event-based systems by using the architecture description language MontiArc. Finally, we evaluate our approach by performing a top-down architecture design of an avionics case study and demonstrating event-based specifications of requirements in MontiArc. The presented methodology improves the management of complexity, reduces costs, and increases the system quality.
title: Providing Evidence for Correct and Timely Functioning of Software Safety Mechanisms
Creators: name: Becker, Jan Steffen
name: Koopmann, Björn
name: Stierand, Ingo
name: Westhofen, Lukas
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Safety Assurance||Timing Analysis||Contract-based Design||Model Checking||Safety Mechanisms||ISO 262626||Traceability

description: In many application domains, the development of safety-critical systems must follow standards that define process steps and artifacts to establish a comprehensive safety argumentation. Commonly, this involves the identification of hazards and risks as well as the formulation of a safety concept to mitigate these risks. The concept is decomposed into safety requirements, which are finally implemented in hardware and software. All steps must be covered by analyses to ensure that the concept is effective and correctly implemented. This work focuses on timing aspects of the safety concept, i.e., on how it can be ensured that risk mitigation occurs in time. Based on an industrial use case, we show how consistent timing specifications can be derived, decomposed, and implemented in a complete and sound way. The approach extends previous work on contract-based design and investigates on explicating failure modes and fault detection in contract specifications. Finally, we show how model checking can support the verification of safety concepts and their implementation.
title: 5th Workshop on Avionics Systems and Software Engineering (AvioSE'23)
Creators: name: Annighoefer, Bjoern
name: Schweiger, Andreas
name: Poulaine, Stéphane
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: avionics||systems engineering||software engineering||formal method||model-based||requirement||qualification||certification||simulation||process||tool||platform||architecture||AI

description: Systems and software engineering in aerospace is subject to special challenges. For their resolution the AvioSE'23 workshop connects academia and industry with selected scientific presentations of high quality, motivating keynote talks, and an interactive panel discussion.
Interpretive Methods of the Second Temple Period
Creators: name: Williams, Jonathan
Publisher: name: Zenodo
Year: 2020
Subjects: Second Temple, Interpretation, Hermeneutics, Midrash, Pesher, Allegory, Literal, New Testament, Paul, Peter, Acts 2, Acts 23, Romans 10, Galatians 4

description: As partial requirement for my Ph.D. in Biblical Studies I created a short paper illustrating how NT authors in their writing of Scripture used Second Temple interpretive methods. They were men of their time. Richard Longenecker, Distinguished Professor of New Testament at McMaster University captured the import of this when he said, It is hardly surprising to find that the exegesis of the New Testament is heavily dependent on Jewish procedural precedents. Theoretically, one would expect a divine redemption that is worked out in the categories of a particular history – which is exactly what the Christian gospel claims to be – to express itself in all its various manifestations in terms of the concepts and methods of that particular people and day.”[1] I concur with his statement, and in the NT we discover the following Second Temple interpretive methods. [1] Richard N. Longenecker, Biblical Exegesis in the Apostolic Period, Eerdmans, Grand Rapids, MI, 1999, 187.
Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway
Creators: name: Beroukhim, R.
name: Carrot-Zhang, J.
name: Mungall, K.L.
name: Zhou, M.
name: Laird, P.W.
name: Yang, L.
name: Berger, A.
name: Zhang, H.
name: Wong, C.K.
name: TCGA Research Network
name: Damrauer, J.S.
name: Zhitomirsky, B.
name: Stuart, J.
name: Trieu, T.
name: Chang, J.C.
name: Berger, A.H.
name: Silva, T.C.
name: Govindan, R.
name: Shapira, O.
name: Castro, M.A.A.
name: Elemento, O.
name: Benz, C.C.,
name: Hinoue, T.
name: Bao, L.
name: Robine, N.
name: Yao, X.
name: Liu, Y.
name: Getz, G.
name: Rheinbay, E.
name: Devarakonda, S.
name: Meyerson, M.
name: Deshpande, A.
name: Gao, G.F.
name: Liang, W.-W.
name: Zody, M.C.
name: Choi, H.Y.
name: Hayes, D.N.
name: Lee, J.J.-K.
name: Felau, I.
name: Moorthi, S.
name: Imielinski, M.
name: Liu, E.M.
name: Kwiatkowski, D.J.
name: Berman, B.P.
name: Kumar, K.
name: Zenklusen, J.C.
name: Ding, L.
name: Yau, C.
name: Tsao, M.S.
name: Haan, D.
name: Cherniack, A.D.
name: Weinstein, J.N.
name: Hoadley, K.A.
name: Travis, W.D.
name: Robertson, A.G.
name: Khurana, E.
name: Collisson, E.A.
name: Campbell, J.D.
Publisher: name: Elsevier B.V.
Year: 2021

description: RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(−) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of STK11 (n = 7) or KEAP1 (n = 3), and promoter mutations associated with the increased expression of ILF2 (n = 6). We also identify complex structural variations associated with high-level copy number amplifications. Moreover, an enrichment of focal deletions is found in TP53 mutant cases. Our results indicate that RPA(−) cases demonstrate tumor suppressor deletions and genome instability, but lack unique or recurrent genetic lesions compensating for the lack of RPAs. Larger WGS studies of RPA(−) cases are required to understand this important LUAD subset. © 2021 The AuthorsCarrot-Zhang et al. perform whole-genome characterization of lung adenocarcinomas (LUADs) lacking RTK/RAS/RAF pathway alterations (RPAs) and identify mutations or structural variants in both coding and non-coding spaces that define a unique entity of RPA(−) LUADs and potentially explain the underlying biology of this disease.
Work Wise
Creators: name: Skinner, Anthea
Publisher: name: University of Melbourne
Year: 2023
Subjects: classificationCode: 420318
subject: People with disability
classificationCode: 350502
subject: Employment equity and diversity
classificationCode: 480707
subject: Welfare, insurance, disability and social security law

description: An article about proposed changes to the Disability Support Pension in Australia and a discussion of reasonable workplace adjustments. Originally published in Link Disability Magazine, Vol 20, No 4, 2011, pp28-9.
title: Model-Based and Automated Software Tool Qualification of Domain-Specific Modeling Tools as per RTCA DO-330
Creators: name: Frey, Constantin
name: Annighoefer, Bjoern
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Domain-specific modeling||software tool qualification||qualification artefacts||RTCA DO-330

description: The use of domain-specific modeling (DSM) in a software life cycle that includes the objectives and activities as per RTCA DO-178C offers a variety of opportunities. With the help of DSM tools, development artefacts can be generated from a system design model. DSM tools that are used in the software life cycle and whose output is not verified require a tool qualification according to RTCA DO-330. This tool qualification is associated with an extensively high effort. Therefore, this paper proposes a model-based and automated approach for tool qualification. Qualification templates should be developed, covering requirements and tests for DSM specific aspects. These template models are instantiated in a qualification model transformation. The result should be qualification artefacts. This approach should greatly reduce the qualification effort. The component in the DSM tool for tool qualification is the Tool Qualification Agent (TQA). First, the concept of the Tool Qualification Agent is presented. Afterwards, the results from a first implementation are analyzed. First requirement templates and a qualification model transformation were developed. Requirements were generated with the qualification model transformation. Although the Tool Qualification Agent so far only covers small parts of the tool qualification, it demonstrates that the concept is feasible.
Controlling hysteresis in superconducting constrictions with a resistive shunt
Creators: name: Kumar, Nikhil
name: Winkelmann, C. B.
name: Biswas, Sourav
name: Courtois, H.
name: Gupta, Anjan K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We demonstrate control of the thermal hysteresis in superconducting constrictions by adding a resistive shunt. In order to prevent thermal relaxation oscillations, the shunt resistor is placed in close vicinity of the constriction, making the inductive current-switching time smaller than the thermal equilibration time. We investigate the current-voltage characteristics of the same constriction with and without the shunt-resistor. The widening of the hysteresis-free temperature range is explained on the basis of a simple model.
description: 6 pages, 7 figures, including Supplementary Information
title: Adaption des Software-Qualitätsmanagements im Automotive-Bereich für eine Nutzung von Fremdkomponenten
Creators: name: Schlosser, Joachim
name: Mattausch, Alexander
name: Neukirchner, Moritz
name: Holve, Rainer
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Qualitätssicherung||Softwarequalität ASPICE||Open Source||Legacy Software||Lizenzierung||Entwicklungsrisiko

description: OEMs verlangen für alle zugekaufte Software die Einhaltung von Standards wie ASPICE und oft auch ihrer eigenen. In High Performance Controllern wird jedoch bereits in großem Umfang nicht-konforme Software eingesetzt. Softwarelieferungen werden eher aufgrund von Erfahrungswerten als aufgrund einer systematischen Risikobewertung akzeptiert. Viele der vorhandenen Open-Source-Software-Komponenten haben sich als zuverlässig erwiesen und läuft sogar auf kritischen Teilen der Internet-Infrastruktur. Keine dieser Komponenten ist nach automobilen Entwicklungsprinzipien entwickelt worden, dennoch handelt es sich um insgesamt robuste und qualitativ hochwertige Implementierungen. Wie kann das Qualitätsmanagement von diesen Softwareprojekten lernen und dadurch die Entwicklungseffizienz steigern, ohne dass die Codequalität darunter leidet?
title: A Seamless and End-to-End Approach for Early and Continuous Validation of Next-Generation Avionics Platforms
Creators: name: Abdo, Kamiran
name: Broehan, Jasmin
name: Thielecke, Frank
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: AvioNET||early validation||continuous validation||virtual product||hybrid platform

description: Emerging technologies, such as multi-core avionics, mixed-critical systems on shared resources and the adaption of artificial intelligence (AI) in the field of avionics, drive a growth of complexity, as well as a higher uncertainty during early design phases for avionic platforms. This results in an error-prone and time-consuming development process, as these technologies have not yet been fully evaluated for avionics. Consequently, it is important to continuously validate design choices to detect potential design flaws as early as possible. This shall avoid unnecessary iterations during the development process, reduce related costs and ultimately, time to market. This work proposes a seamless and model-based concept for early and continuous validation of next generation avionics platforms through all their phases – design, implementation, testing and ultimately, integration.
title: Professionalisation in ERP Selection Revisited III
Creators: name: Humpl, Stefan
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: ERP selection||professionalisation||requirements

description: The implementation of new ERP systems or the adaptation of existing ERP systems is a central challenge for modern companies, which is also reflected in the development of relevant job advertisements. A specific analysis of relevant job advertisements in Austria shows a professionalisation in ERP selection, but also a shift towards employing such experts in the own company versus outsourcing this expertise. Job titles and job specific requirements (competences) mentioned in job advertisements in 2017 and 2022 show a respective development. But it also becomes visible that the labour market for relevant experts is marked by a growing demand and insufficient supply, which implies that the more recent job advertisements are broader, more detailed in asking for competences, and therefore showing a hope for somehow fitting candidates. The COVID-19 crisis led to an increased in-house recruiting, which is turning back to a mixed in-house and external recruiting approach after COVID-19 in 2022.
Hepatocyte growth factor pathway expression in breast cancer by race and subtype
Creators: name: Fleming, J.M.
name: Jones, G.S.
name: Tipaldos, H.J.
name: Hamilton, A.M.
name: Olshan, A.F.
name: Kirk, E.L.
name: Love, M.I.
name: Olsson, L.T.
name: Nichols, H.B.
name: Bhattacharya, A.
name: Troester, M.A.
name: Hoadley, K.A.
Publisher: name: BioMed Central Ltd
Year: 2021

description: Background: African American women have the highest risk of breast cancer mortality compared to other racial groups. Differences in tumor characteristics have been implicated as a possible cause; however, the tumor microenvironment may also contribute to this disparity in mortality. Hepatocyte growth factor (HGF) is a stroma-derived marker of the tumor microenvironment that may affect tumor progression differentially by race. Objective: To examine whether an HGF gene expression signature is differentially expressed by race and tumor characteristics. Methods: Invasive breast tumors from 1957 patients were assessed for a 38-gene RNA-based HGF gene expression signature. Participants were black (n = 1033) and non-black (n = 924) women from the population-based Carolina Breast Cancer Study (1993–2013). Generalized linear models were used to estimate the relative frequency differences (RFD) in HGF status by race, clinical, and demographic factors. Results: Thirty-two percent of tumors were positive for the HGF signature. Black women were more likely [42% vs. 21%; RFD = + 19.93% (95% CI 16.00, 23.87)] to have HGF-positive tumors compared to non-black women. Triple-negative patients had a higher frequency of HGF positivity [82% vs. 13% in non-triple-negative; RFD = + 65.85% (95% CI 61.71, 69.98)], and HGF positivity was a defining feature of basal-like subtype [92% vs. 8% in non-basal; RFD = + 81.84% (95% CI 78.84, 84.83)]. HGF positivity was associated with younger age, stage, higher grade, and high genomic risk of recurrence (ROR-PT) score. Conclusion: HGF expression is a defining feature of basal-like tumors, and its association with black race and young women suggests it may be a candidate pathway for understanding breast cancer disparities.
Hand Me the Beet Nuts
Creators: name: Skinner, Anthea
Publisher: name: University of Melbourne
Year: 2023
Subjects: classificationCode: 420318
subject: People with disability
classificationCode: 360505
subject: Screen media
classificationCode: 470214
subject: Screen and media culture
classificationCode: 470107
subject: Media studies

description: An interview with blind film maker gough about his production company Beer Nuts Productions. Originally published in Link Disability Magazine, Vol 26, No 3, 2017, pp52-3.
In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators
Creators: name: Brown, N.G.
name: Suzuki, A.
name: Tiedemann, R.L.
name: Emanuele, M.J.
name: Rothbart, S.B.
name: Enrico, T.P.
name: Martinez-Chacin, R.C.
name: Franks, J.L.
name: Yan, F.
name: Mouery, R.D.
name: Choudhury, R.
name: Damrauer, J.S.
name: Bonacci, T.,
name: Bolhuis, D.L.
name: Major, M.B.
name: Hoadley, K.A.
name: Wang, X.
name: Harrison, J.S.
Publisher: name: Public Library of Science
Year: 2020

description: The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase and critical regulator of cell cycle progression. Despite its vital role, it has remained challenging to globally map APC/C substrates. By combining orthogonal features of known substrates, we predicted APC/C substrates in silico. This analysis identified many known substrates and suggested numerous candidates. Unexpectedly, chromatin regulatory proteins are enriched among putative substrates, and we show experimentally that several chromatin proteins bind APC/C, oscillate during the cell cycle, and are degraded following APC/C activation, consistent with being direct APC/C substrates. Additional analysis revealed detailed mechanisms of ubiquitylation for UHRF1, a key chromatin regulator involved in histone ubiquitylation and DNA methylation maintenance. Disrupting UHRF1 degradation at mitotic exit accelerates G1-phase cell cycle progression and perturbs global DNA methylation patterning in the genome. We conclude that APC/C coordinates crosstalk between cell cycle and chromatin regulatory proteins. This has potential consequences in normal cell physiology, where the chromatin environment changes depending on proliferative state, as well as in disease.
Additional file 2 of Stimulation-induced differential redistributions of clathrin and clathrin-coated vesicles in axons compared to soma/dendrites
Creators: name: Tao-Cheng, Jung-Hwa
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences

description: Additional file 2: Measurement for density and distance of label for clathrin at presynaptic terminals.
title: Brake or Drive: On the Relation Between Morality and Traffic Rules when Driving Autonomously
Creators: name: Rakow, Astrid
name: Schwammberger, Maike
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: autonomous traffic agents||traffic rules||moral reasoning||conflicts||ethics

description: For a safe and successful future with autonomous traffic agents (ATAs), these ATAs need to be enabled to understand and abide by traffic rules. However, purely formalising and analysing traffic rules is not enough to solve this task. In this paper, we discuss the role of moral for ATAs that follow traffic rules. In particular, moral values may enable an ATA to prioritise traffic rules, in case of conflicts. We outline an approach that uses formal verification to identify situations where traffic rules are in conflict with each other, with moral values or with specific goals of an ATA. We sketch how moral values and reasoning can help an ATA to resolve such conflicts autonomously.
Reply To Kenneth B. Yatai, Mark J. Dunning, Dennis Wang. Consensus Genomic Subtypes of Muscle-invasive Bladder Cancer: A Step in the Right Direction but Still a Long Way To Go. Eur Urol 2020;77:434–5
Creators: name: Groeneveld, C.S.
name: Liedberg, F.
name: Bellmunt, J.
name: Radvanyi, F.
name: Dyrskjøt, L.
name: Allory, Y.
name: Hoadley, K.A.,
name: Aine, M.
name: Taber, A.
name: Bernard-Pierrot, I.
name: Al-Ahmadie, H.
name: Sjödahl, G.
name: Kardos, J.
name: Hartmann, A.
name: Real, F.X.
name: Siefker-Radtke, A.A.
name: Mo, Q.
name: Höglund, M.
name: Castro, M.A.A.
name: Lebret, T.
name: Czerniak, B.
name: Black, P.C.
name: Malats, N.
name: Eriksson, P.
name: Zlotta, A.
name: Weinstein, J.N.
name: McConkey, D.J.
name: Kamoun, A.
name: Powles, T.
name: Dinney, C.P.
name: Seiler, R.
name: de Reyniès, A.
name: Gibb, E.A.
name: Sirab, N.
name: Choi, W.
name: Kim, J.
name: Chan, K.S.
name: Lerner, S.P.
name: Robertson, A.G.
name: Fontugne, J
name: Kim, W.Y.
name: Kwiatkowski, D.J.
Publisher: name: Elsevier B.V.
Year: 2020

description: In our study the Bladder Cancer Molecular Taxonomy Group collaborated to extend a first consensus report, addressing the need for a consensus molecular classification for muscle-invasive bladder cancer (MIBC) that would support basic research and clinical trials. We provide such a consensus classification and offer a single-sample classifier (http://cit.ligue-cancer.net:3838/apps/consensusMIBC_web).
Children's Wellbeing Continuum
Creators: name: Darling, Simone
name: OBERKLAID, FRANK
Publisher: name: Murdoch Childrens Research Institute
Year: 2022
Subjects: Health Sciences

description: The Children's Wellbeing Continuum is an evidence-based tool designed to support conversations about children’s wellbeing. The four anchor points of the Children’s Wellbeing Continuum range from Good through to Coping, Struggling and Overwhelmed. The Continuum is not a screening or diagnostic tool. By enabling parents, teachers and children to more easily discuss and reflect on wellbeing, the Continuum can support health literacy, and early identification and action when children are struggling. The Continuum was developed by the Centre for Community Child Health, a department of The Royal Children’s Hospital and a research group of the Murdoch Children's Research Institute.
Improving fish health management and production protocols in marine finfish aquaculture in Indonesia and Australia
Creators: name: Rimmer, Michael A.
name: Whittington, Richard
name: Becker, Joy
name: Dhand, Navneet
name: Hick, Paul
name: Mahardika, Ketut
name: Sembiring, Sari B.M.
name: Ismi, Suko
name: Zafran
name: Haryanti
name: Roza, Des
name: Kusumawati, Daniar
name: Asih, Yasmina Nirmala
name: Sudewi
name: Mastuti, Indah
name: Wardana, Ida Komang
name: Murwantoko
name: Fusianto, Cahya Kurnia
name: Fachry, Mardiana E.
Publisher: name: Australian Centre for International Agricultural Research (ACIAR)
Year: 2019

description: Final report of "Improving fish health management and production protocols in marine finfish aquaculture in Indonesia and Australia" (Project number: FIS/2010/101, Final report number: FR2019-47).
Additional file 5 of Stimulation-induced differential redistributions of clathrin and clathrin-coated vesicles in axons compared to soma/dendrites
Creators: name: Tao-Cheng, Jung-Hwa
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences

description: Additional file 5: Number of CCVs and CCPs per 100 presynaptic profiles in perfusion-fixed brains (5A) and dissociated cultures (5B).
mAkE Sharing and Embedding Strategy
Creators: name: Wiedow, Kirstin
Publisher: name: Zenodo
Year: 2023

description: This document describes the sharing and embedding of resources and information for the mAkE project and the communities of makers and hubs in Africa and Europe. Access to technology has brought a new era of global connectedness where the concept of borders is virtually removed. Gaining access to open source and shared information, resources and like-minded individuals championing change across the globe is the pathway driving innovation and change today. The term ‘mAkErverse’ is a mAkE project umbrella term uniting different maker ecosystems in Africa, Europe and beyond. The mAkErverse is our ‘global village’ of connected makers, innovators, and their broader orbiting communities according to the seven circles within the spectrum outlined in the Community Activation and Engagement Strategy. Alongside the concept of the ‘global village’ or mAkErverse, is the concept of glocal; globally connected and locally rooted. These two concepts delineate the mAkE sharing and embedding strategy as sharing will be done across global networks and embed accessibility to key resources that give rise to the opportunity to realise local production of demand-driven global goods and services. The mAkE project aims to reach at least five hundred (500) businesses engaged in mAkE activities (makerspaces, founders, early-stage investors, corporates, NGOs etc), develop one hundred (100) open resources and provide access to seven hundred (700) additional open resources for DIHs across the project including blueprints, toolkits, and open-source business models. Through building communities and providing resources in a central repository shared across consortium member platforms, mAkE will catalyse a spill-over or ripple effect to the wider community because of borderless accessibility. The identified strategy to be implemented is that of the Ripple Effect. A ‘ripple effect’ can be defined as activities where information can be disseminated and passed from community to community to broaden its impact ultimately, amplifying and multiplying all efforts. As an abstract metaphor, it describes how our actions reverberate throughout the physical and social world and the impact that every person has within the ‘global village’. The embedding and sharing of community activities, information, knowledge and open access to resources in cohesiveness with the REF will impact the growth of the maker community and be an integral proponent for the rise of more local, supported, recognised, self-sustaining and educated maker communities that are globally interconnected and visible across the greater network of community networks or mAkErverse.
title: 20th Workshop on Automotive Software Engineering (ASE'23)
Creators: name: Kugele, Stefan
name: Grunske, Lars
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Automotive||Software Engineering||Workshop

description: Software-based systems play an increasingly important role and enable most innovations in modern cars. This workshop will address various topics related to automotive software development. The participants will discuss appropriate methods, techniques, and tools needed to address the most current challenges for researchers and practitioners.
title: RPA in the post-implementation phase of ERP systems
Creators: name: Ploder, Christian
name: Obermair, Philipp
name: Bernsteiner, Reinhard
name: Dilger, Thomas
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Robotic Process Automation||ERP Implementation||Post-Implementation Phase

description: Robotic Process Automation (RPA) can automate processes of various systems using their user interfaces. Back-office processes are particularly suitable for automation with the help of digital workers. Many back-office processes are carried out in Enterprise Resource Planning (ERP) systems. Companies worldwide use ERP systems, meaning they are in the post-implementation phase and interact with these systems daily. Changes to the system are expected during the post-implementation phase. In this paper, recommendations for action that help introduce this technology in the post-implementation phase of ERP systems are made, and decision factors that speak for using this technology are elaborated. For this purpose, twelve interviews are conducted with experts who have already gained experience with Robotic Process Automation in the context of ERP systems, and the results of the interviews will be compared and supplemented with the existing literature. A central result of the work is that the involvement of employees working in the processes to be automated in their daily work is an essential component in all phases of the implementation process. Decision-making factors contributing significantly to companies or organizations deciding to implement RPA can generally be divided into technical and organizational. In general, it can be said that Robotic Process Automation can be used to add value to ERP systems.
Energy-momentum tensor on the lattice: non-perturbative renormalization in Yang--Mills theory
Creators: name: Giusti, Leonardo
name: Pepe, Michele
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We construct an energy-momentum tensor on the lattice which satisfies the appropriate Ward Identities (WIs) and has the right trace anomaly in the continuum limit. It is defined by imposing suitable WIs associated to the Poincare` invariance of the continuum theory. These relations come forth when the length of the box in the temporal direction is finite, and they take a particularly simple form if the coordinate and the periodicity axes are not aligned. We implement the method for the SU(3) Yang--Mills theory discretized with the standard Wilson action in presence of shifted boundary conditions in the (short) temporal direction. By carrying out extensive numerical simulations, the renormalization constants of the traceless components of the tensor are determined with a precision of roughly half a percent for values of the bare coupling constant in the range 0<= g^2_0<=1.
description: 22 pages, 6 figures. Minor typos corrected. Version accepted for publication on PRD
DFG-KI event; ARENA - Abstract Representations in Neural Architectures
Creators: name: Toneva, Mariya
name: Fiebach, Christian
name: Roig, Gemma
name: Dadvar, Maral
Publisher: name: Zenodo
Year: 2024

description: This presentation was prepared for the DFG-KI event on 29-30 August 2024 to present the ARENA Research Unit while highlighting its AI related research topics and activities.  This presentation was presented by one of the ARENA PIs, Professor Mariya Toneva, Max Planck Institute for Software Systems.
Additional file 3 of Stimulation-induced differential redistributions of clathrin and clathrin-coated vesicles in axons compared to soma/dendrites
Creators: name: Tao-Cheng, Jung-Hwa
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences

description: Additional file 3: Serial sections (# 1-5) of a neuronal soma labeled for clathrin.
title: Towards Enabling Level 3A AI in Avionic Platforms
Creators: name: Zaeske, Wanja
name: Brust, Clemens-Alexander
name: Lund, Andreas
name: Durak, Umut
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Avionics||Resilience||ARINC 653||DO-178C||Fault-Tolerance

description: The role of AI evolves from human assistance over human/machine collaboration towards fully autonomous systems. As the push towards more autonomy subsequently removes the reliance on a human overseeing the system, means of self supervision must be provided to enable safe operations. This work explores dynamic reconfiguration to provide resilience to unforeseen environmental conditions that exceed the systems capabilities, but also against normal faults. We focus on providing the means for this in an ARINC 653 compliant environment, since we target avionics platforms. Scheduling and communication are two major aspects of dynamic reconfiguration. Hence, we discuss multiple respective implementation approaches. The third pillar of reconfiguration, the process of deciding when to reconfigure is also investigated. Combining these yields the building blocks for a self-supervising system.
A Pan-Cancer and Polygenic Bayesian Hierarchical Model for the Effect of Somatic Mutations on Survival
Creators: name: Hoadley, K.A.,
name: Lock, E.F.
name: Samorodnitsky, S.
Publisher: name: SAGE Publications Ltd
Year: 2020

description: We built a novel Bayesian hierarchical survival model based on the somatic mutation profile of patients across 50 genes and 27 cancer types. The pan-cancer quality allows for the model to “borrow” information across cancer types, motivated by the assumption that similar mutation profiles may have similar (but not necessarily identical) effects on survival across different tissues of origin or tumor types. The effect of a mutation at each gene was allowed to vary by cancer type, whereas the mean effect of each gene was shared across cancers. Within this framework, we considered 4 parametric survival models (normal, log-normal, exponential, and Weibull), and we compared their performance via a cross-validation approach in which we fit each model on training data and estimate the log-posterior predictive likelihood on test data. The log-normal model gave the best fit, and we investigated the partial effect of each gene on survival via a forward selection procedure. Through this we determined that mutations at TP53 and FAT4 were together the most useful for predicting patient survival. We validated the model via simulation to ensure that our algorithm for posterior computation gave nominal coverage rates. The code used for this analysis can be found at https://github.com/sarahsamorodnitsky/Pan-Cancer-Survival-Modeling.git, and the results are summarized at http://ericfrazerlock.com/surv_figs/SurvivalDisplay.html.
Additional file 4 of Stimulation-induced differential redistributions of clathrin and clathrin-coated vesicles in axons compared to soma/dendrites
Creators: name: Tao-Cheng, Jung-Hwa
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences

description: Additional file 4: Multivesicular body in astrocytes (a, b) and neuron (c).