cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Gain-of-function RHOA mutations promote focal adhesion kinase activation and dependency in diffuse gastric cancer
Creators: name: Bass, A.J.
name: Zhou, J.
name: Blake, D.R.
name: Derks, S.
name: Pierobon, M.
name: Hodge, R.G.
name: Church, G.
name: Akarca, F.G.
name: Papageorge, A.G.
name: Stachler, M.D.
name: de Klerk, L.K.
name: Petricoin, E.F.
name: Wang, T.C.
name: Wong, K.-K.
name: Diehl, J.N.
name: Cox, A.D.
name: Der, C.J.
name: Wang, Y.
name: Lowy, D.R.
name: Zhang, H.
name: Liao, J.
name: Wu, Z.
name: Schaefer, A.
name: Hoadley, K.A.
Publisher: name: American Association for Cancer Research Inc.
Year: 2020

description: Diffuse gastric cancer (DGC) is a lethal malignancy lacking effective systemic therapy. Among the most provocative recent results in DGC has been that of highly recurrent missense mutations in the GTPase RHOA. The function of these mutations has remained unresolved. We demonstrate that RHOAY42C, the most common RHOA mutation in DGC, is a gain-of-function oncogenic mutant, and that expression of RHOAY42C with inactivation of the canonical tumor suppressor Cdh1 induces metastatic DGC in a mouse model. Biochemically, RHOAY42C exhibits impaired Y42C GTP hydrolysis and enhances interaction with its effector ROCK. RHOA mutation and Cdh1 loss induce actin/cytoskeletal rearrangements and activity of focal adhesion kinase (FAK), which activates YAP–TAZ, PI3K–AKT, and β-catenin. RHOAY42C murine models were sensitive to FAK inhibition and to combined YAP and PI3K pathway blockade. These results, coupled with sensitivity to FAK inhibition in patient-derived DGC cell lines, nominate FAK as a novel target for these cancers. SIGNIFICANCE: The functional significance of recurrent RHOA mutations in DGC has remained unresolved. Through biochemical studies and mouse modeling of the hotspot RHOAY42C mutation, we establish that these mutations are activating, detail their effects upon cell signaling, and define how RHOA-mediated FAK activation imparts sensitivity to pharmacologic FAK inhibitors.
Territorial anchorage in the French dairy ewe sector: Historical analysis of the construction of interdependent localized agrifood systems
Creators: name: Millet, Morgane
name: Casabianca, François
name: Millet, Morgane
name: Casabianca, François
Publisher: name: Unknown
Year: 2014
Subjects: subject: Agribusiness
subject: Agricultural and Food Policy
subject: SYAL
subject: territorial anchorage
subject: trajectory
subject: interdependence
subject: Pyrénées-Atlantiques
subject: Corsica Island
subject: Roquefort

description: In the eighties, the dairy ewe producers of Pyrenées Atlantiques (PA) and Corsica (CS) faced a crisis: most of the Roquefort (RF) industrial cheesemakers that had collected their milk for nearly a century withdrew from both areas. A new dynamic had to be created: the rebirth of on-farm processing (involving local technical and cultural memory) and the emergence of new processing firms. Local stake-holders created PDO (Protected Designation of Ori-gin) products: “Ossau Iraty” in PA and “Brocciu” in CS. These PDOs are still having some difficulty in building consensus within their local stakeholder systems. The shared history of producing milk for RF cheesemakers (the Roquefort Era) and the period that followed their withdrawal conditioned the situation for both the PA and the CS systems: the last 40 years have been a period of re-appropriation of the production system by local stakeholders (with varying degrees of success and completeness). To analyze this period and the current situation of the PA and CS systems, we have adopted the concept of “territorial anchorage”. This concept implies two things: (i) A geographical area and a system of stake-holders can interact in a dynamic way. A long-term analysis provides an overview of how a local system has changed over time. Such an analysis may make the current situation more understandable and shed some light on how it could evolve; (ii) For activities to be linked to an area, there must be a set of links of different intensities and past durations (social cohesion, economic value-added, a recognized terroir). As these links have been recently reactivated or re-created, some elements (e.g. certified cheeses) are becoming territorial resources. These mechanisms are also subject to external forces (co-existence of different processing methods, use of the territory’s image). With the territorial anchorage concept we can com-pare two territories, the study of each being enriched by examining the other’s trajectory and pattern of links with its area. It may help us to understand the constraints faced in building coherence and autonomy in a cheese production system at different institutional levels (local economy, social and economic organization, policy).
Additional file 1 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 1: Methods on size measurement and scoring of CCV/CCP in soma/dendrites.
title: Updates at Runtime for Cyber Physical Systems. A Game Theoretic Approach
Creators: name: Kröger, Janis
name: Fränzle, Martin
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Game Theory||Software Updates||Update Process||Operating Modes

description: Updates are becoming increasingly important in the field of cyber physical systems in order to increase the lifetime of these systems and to save resources and costs. One way to achieve this is to update the system at runtime. This paper describes our vision of a game-theoretic approach to determine when an update is possible at runtime, taking into account the system behavior. This ensures that the system behaves safely at all points in time. For this purpose we use so-called timed games and synthesize a strategy under which the update can be performed. We sketch the approach and illustrate its application on an automotive example of an autopilot.
Additional file 7 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 7: Number of clathrin-labeled CCVs and CCPs measured at 1 μm depth of cytoplasm from PM / μm PM under control and depolarizing conditions.
Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer
Creators: name: Damrauer, J.S.
name: Sayaman, R.W.
name: Benz, C.
name: Knijnenburg, T.A.
name: Chambwe, N.
name: Tarnuzzer, R.
name: Alfoldi, J.
name: Beroukhim, R.
name: Aguet, F.
name: Demchok, J.A.
name: Shen, H.
name: Demichelis, F.
name: Carrot-Zhang, J.
name: Mensah, M.K.A.
name: Wong, C.K.
name: Cherniack, A.D.
name: Ziv, E.
name: Robertson, A.G.
name: Stuart, J.M.
name: Berger, A.C.
name: Laird, P.W.
name: Karczewski, K.J.
name: Le, X.
name: Caesar-Johnson, S.
name: Cancer Genome Atlas Analysis Network
name: Wang, Z.
name: Newberg, J.Y.
name: Lazar, A.J.
name: Huang, K.-L.
name: Kemal, A.
name: Hoadley, K.A.
name: Han, S.
name: Oak, N.
name: MacArthur, D.G.,
name: Yang, L.
name: Zenklusen, J.C.
name: Zhou, W.
name: Meyerson, M.
name: Frampton, G.M.
name: Yau, C.
name: Mashl, R.J.
name: Felau, I.
name: Romanel, A.
name: Ding, L.
Publisher: name: Cell Press
Year: 2020

description: We evaluated ancestry effects on mutation rates, DNA methylation, and mRNA and miRNA expression among 10,678 patients across 33 cancer types from The Cancer Genome Atlas. We demonstrated that cancer subtypes and ancestry-related technical artifacts are important confounders that have been insufficiently accounted for. Once accounted for, ancestry-associated differences spanned all molecular features and hundreds of genes. Biologically significant differences were usually tissue specific but not specific to cancer. However, admixture and pathway analyses suggested some of these differences are causally related to cancer. Specific findings included increased FBXW7 mutations in patients of African origin, decreased VHL and PBRM1 mutations in renal cancer patients of African origin, and decreased immune activity in bladder cancer patients of East Asian origin.
title: Tool Qualification Aspects in ML-Based Airborne Systems Development
Creators: name: Dmitriev, Konstantin
name: Kaakai, Fateh
name: Ibrahim, Mohamad
name: Durak, Umut
name: Potter, Bill
name: Holzapfel, Florian
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Machine Learning||Certification||Design Assurance||Tool Qualification

description: Machine Learning (ML) technology can provide the best results in many highly complex tasks such as computer vision and natural language processing and quickly evolving further. These unique ML capabilities and apparent potential can enable the next epoch of automation in airborne systems including single pilot or even autonomous operation of large commercial aircraft. The main problems to be solved towards ML deployment in commercial aviation are safety and certification, because there are several major incompatibilities between ML development aspects and traditional design assurance practices, in particular traceability and coverage verification issues. In this paper, we study the qualification aspects of tools used for development and verification of ML-based systems (ML tools) and propose mitigation measures for some known ML verification gaps through ML tools qualification. In particular, we review the DO-330 and DO-200B tool classification approach with respect to ML-specific workflows and propose to extend the tool qualification criteria for ML data management and ML model training tools.
QUALITY OF LIFE IN THE KING’S PROPERTIES: A CASE STUDY OF POLICES’ WORK TOWARDS THAIS’ HAPPINESS THROUGH CRIME PREVENTION
Creators: name: Khemtida PETCHTAM
Publisher: name: International Journal of Crime, Law and Social Issues
Year: 2022
Subjects: Quality of Life
King’s Properties
Police Work
Crime Prevention

description: International Journal of Crime, Law and Social Issues, 9, 2, 23-33
title: A Domain-Specific Language for Requirements Engineering in Safety-Critical Automotive Software Development
Creators: name: Schlichthaerle, Stefan
name: Wullstein-Kammler, Philipp
name: Schanda, Florian
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Requirements engineering||Agile software development||Domain-specific language

description: Requirements engineering is a crucial part of every software development project. Deficits in this discipline have tremendous impact on the overall project's success. In this paper, we present our approach that treats requirements like source code and therefore benefits from modern software development workflows and paradigms, to bridge the gap between requirements engineering and large-scale agile software development. We derive the requirements for our approach and discuss the underlying tooling as well as the corresponding impact on processes. We show examples, including validation of requirements and the traceability towards source code.
title: Cyber Security and Software Update management system for connected vehicles in compliance with UNECE WP.29, R155 and R156
Creators: name: Bohara, Rohit
name: Ross, Mirko
name: Rahlfs, Sven
name: Ghatta, Sara
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Software supply chain security||Software Bill of Material||Over the Air software updates||Regulatory compliance||Software vulnerability management

description: Code is the new fuel of a modern car. Almost every aspect of a car is controlled and managed by software running in electronic control units (ECU). This has led to enormous complexity in automotive software. To put this in perspective, automotive software has grown from few 100 lines of code to 100 million in a span of 40 years. Additionally, inherent convolution in the automotive software supply chain introduces its own set of problems for cyber security and safety of a car. The research paper proposes a pioneered approach for cyber security and software update management to transform the automotive software engineering principles. It aims to strengthen the security of automotive software, bring transparency in the software supply chain and establishes regulatory compliance management processes by design.
title: Anforderungen an ein Vorgehensmodell zur Auswahl von Unternehmens-Software
Creators: name: Weiss, Christoph
name: Keckeis, Johannes
name: Weiss, Elisabeth
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Anforderungen||Auswahl||Inhaltsanalyse||Software||Unternehmens-Software||Vorgehensmodell

description: Im vorliegenden Paper wird, anhand eines Literaturreviews, der Frage nachgegangen, welchen Anforderungen Vorgehensmodelle bei deren Erstellung unterliegen. Aufgrund der zum großen Teil fragmentarischen Darstellung der Genese von Vorgehensmodellen konnten lediglich vier Anforderungen, welche in mehreren Quellen Niederschlag gefunden hatten, identifiziert werden. Diese Erkenntnis führt zu weiteren Fragen, welche einer wissenschaftlichen Untersuchung zugeführt werden sollten.
The immune microenvironment in hormone receptor-positive breast cancer before and after preoperative chemotherapy
Creators: name: Wu, Y.
name: Wesolowski, R.
name: Osmani, W.
name: Brauer, H.A.
name: Sullivan, A.s
name: Hartl, C.
name: Mittendorf, E.A.
name: Brock, J.
name: Lipschitz, M.
name: Waks, A.G.
name: Goldberg, M.
name: Li, Z.
name: Gjini, E.
name: Winer, E.P.
name: Yang, F.
name: Lo, W.
name: Dillon, D.
name: Stover, D.G.
name: Danaher, P.
name: Savoie, J.
name: Perou, C.M.
name: Krop, I.E.
name: Philips, A.V.
name: Hoadley, K.A.
name: Damicis, A.
name: Rodig, S.
name: Guerriero, J.L.
name: Barry, W.T.
name: Tolaney, S.M.
Publisher: name: American Association for Cancer Research Inc.
Year: 2019

description: Purpose: Hormone receptor-positive/HER2-negative (HR+/HER2_) breast cancer is associated with low levels of stromal tumor-infiltrating lymphocytes (sTIL) and PD-L1, and demonstrates poor responses to checkpoint inhibitor therapy. Evaluating the effect of standard chemotherapy on the immune microenvironment may suggest new opportunities for immunotherapy-based approaches to treating HR+/HER2_ breast tumors. Experimental Design: HR+/HER2_ breast tumors were analyzed before and after neoadjuvant chemotherapy. sTIL were assessed histologically; CD8+ cells, CD68+ cells, and PD-L1 staining were assessed immunohistochemically; whole transcriptome sequencing and panel RNA expression analysis (NanoString) were performed. Results: Ninety-six patients were analyzed from two cohorts (n = 55, Dana-Farber cohort; n = 41, MD Anderson cohort). sTIL, CD8, and PD-L1 on tumor cells were higher in tumors with basal PAM50 intrinsic subtype. Higher levels of tissuebased lymphocyte (sTIL, CD8, PD-L1) and macrophage (CD68) markers, as well as gene expression markers of lymphocyte or macrophage phenotypes (NanoString or CIBERSORT), correlated with favorable response to neoadjuvant chemotherapy, but not with improved distant metastasis-free survival in these cohorts or a large gene expression dataset (N = 302). In paired pre-/postchemotherapy samples, sTIL and CD8+ cells were significantly decreased after treatment, whereas expression analyses (NanoString) demonstrated significant increase of multiple myeloid signatures. Single gene expression implicated increased expression of immunosuppressive (M2-like) macrophage-specific genes after chemotherapy. Conclusions: The immune microenvironment of HR+/ HER2_ tumors differs according to tumor biology. This cohort of paired pre-/postchemotherapy samples suggests a critical role for immunosuppressive macrophage expansion in residual disease. The role of macrophages in chemoresistance should be explored, and further evaluation of macrophagetargeting therapy is warranted.
FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer
Creators: name: Emanuele, M.J.
name: Stewart, K.
name: Damrauer, J.S.
name: Arceci, A.
name: Hoadley, K.A.
name: Bonacci, T.
name: Wang, X.
Publisher: name: Elsevier B.V.
Year: 2019

description: The cell cycle transcription factor FOXM1 is activated in basal-like breast cancer (BLBC) and associated with therapeutic resistance and poor patient outcomes. Arceci et al. show USP21 antagonizes FOXM1 degradation, thereby promoting proliferation and paclitaxel resistance. USP21 is catalytically active and recurrently overexpressed in BLBC, representing a potential therapeutic target. © 2019 The Author(s)The transcription factor FOXM1 contributes to cell cycle progression and is significantly upregulated in basal-like breast cancer (BLBC). Despite its importance in normal and cancer cell cycles, we lack a complete understanding of mechanisms that regulate FOXM1. We identified USP21 in an RNAi-based screen for deubiquitinases that control FOXM1 abundance. USP21 increases the stability of FOXM1, and USP21 binds and deubiquitinates FOXM1 in vivo and in vitro, indicating a direct enzyme-substrate relationship. Depleting USP21 downregulates the FOXM1 transcriptional network and causes a significant delay in cell cycle progression. Significantly, USP21 depletion sensitized BLBC cell lines and mouse xenograft tumors to paclitaxel, an anti-mitotic, frontline therapy in BLBC treatment. USP21 is the most frequently amplified deubiquitinase in BLBC patient tumors, and its amplification co-occurs with the upregulation of FOXM1 protein. Altogether, these data suggest a role for USP21 in the proliferation and potentially treatment of FOXM1-high, USP21-high BLBC.
Operational Region of D2D Communications for Enhancing Cellular Network Performance
Creators: name: Stefanatos, Stelios
name: Gotsis, Antonis G.
name: Alexiou, Angeliki
Publisher: name: arXiv
Year: 2015
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: An important enabler towards the successful deployment of any new element/feature to the cellular network is the investigation and characterization of the operational conditions where its introduction will enhance performance. Even though there has been significant research activity on the potential of device-to-device (D2D) communications, there are currently no clear indications of whether D2D communications are actually able to provide benefits for a wide range of operational conditions, thus justifying their introduction to the system. This paper attempts to fill this gap by taking a stochastic geometry approach on characterizing the set (region) of operational conditions for which D2D communications enhance performance in terms of average user rate. For the practically interesting case of a heavy loaded network, the operational region is provided in closed form as a function of a variety of parameters such as maximum D2D link distances and user densities, reflecting a wide range of operational conditions (points). It is shown that under the appropriate deployment scheme, D2D communications can indeed be beneficial not only for the usually considered regime of "proximal communications" but to a wide range of operational conditions that include D2D link distances comparable to the distance to the cellular access point and considerably large user densities.
description: to appear in IEEE Transactions on Wireless Communications
THE SUITABILITY LEVEL OF CSI FACTORS AND PROBLEMATIC CONDITIONS IN CRIME SCENE INVESTIGATION OF INQUIRY OFFICERS UNDER THAILAND'S PROVINCIAL POLICE REGION 7
Creators: name: Supachai SUPALAKNARI
Publisher: name: International Journal of Crime, Law and Social Issues
Year: 2022
Subjects: Crime Scene Investigation
Problematic Conditions
Inquiry Officers

description: International Journal of Crime, Law and Social Issues, 9, 2, 34-44
Additional file 8 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 8: Number of CCPs per neuronal soma under control and depolarizing conditions.
title: A study of interactive projected demonstration techniques for school science in Oman
Creators: name: Al-Shuaili, Ali Huwaishel Ali
Publisher: name: University of Glasgow
Year: 2000
Subjects: subject: Science education.

description: Laboratory based practical work has been considered as one of the "Sacred Cows" of chemistry teaching for many years. However, attempts to measure the benefits of the laboratory experience to which learners are subjected, with regard to how much learning actually occurs, revealed what can be described as a "pessimistic picture". Whilst practical work is generally popular with learners and can, to varying degrees of proficiency, engage hand-skills, its ability to generate much active thought or teach theory appears at best questionable. It is my contention (and that of many others) that, for many experiments, the learner's Working Space is bombarded with information from a variety of different sources which swamps it, leading to an unstable overload state which precludes systematic, intelligent working and causes the learner to seek some more stable (and comfortable) state by a number of devices leading to poor learning. Consequently, it is common to find observers of laboratory classes, who have their own anecdotes of learners whose behaviour suggests a lack of appreciation or understanding of what is happening. What may be clearly organised and understood by the teacher (expert) may not be so for the learner (novice), in that information received by the latter may have no apparent structure since adequate previous knowledge is required to make sense of the incoming information. As the important can not be distinguished from the irrelevant, the point of the lesson is lost to the learner. The very common response to this is that the learner follows instructions line by line (blind recipe following) or gives one section of the experiment an inordinate amount of time and attention, whether it warrants it or not and so never finishes the experiment. He may copy nearby learners' actions or even volunteer to act as the recorder of information for group experiments. All the above actions are attempts by the student to lessen the load and their facts. Also the strain on school resources by the increased number entering schools, could increase the reluctance to change to demonstration. However, the weak points of demonstration are the issues of visibility and the fact that the learners are not engaged in such an activity. A new technique which considers these points, is required and demanded. Therefore, Tested Overhead Projections (TOPs) might be the remedy for the problems mentioned above. In addition to that, in TOPs the teacher has the control to reduce the "noise", enhance the "signal", and engage learners both in hands and minds and, as a bonus, brings benefits of safety, cost, speed, durability, visibility, student-friendliness and easy disposal of smaller quantities of chemicals. It is the researcher's hope to convince the reader (and people in-charge of Education in Oman) that the benefits of this new technique far outweigh the effort which would be required in adopting this new system.
World Music
Creators: name: Skinner, Anthea
Publisher: name: University of Melbourne
Year: 2023
Subjects: classificationCode: 360306
subject: Musicology and ethnomusicology
classificationCode: 420318
subject: People with disability

description: A description of the disability-related content at the 43rd World Conference of the International Council on Traditional Music (ICTM), now the International Council of Traditions in Music and Dance (ICTMD), in Kazakhstan in 2015. Originally published in Link Disability Magazine, Vol 24, No 5, 2015, p46.
title: On the Design and Model-Based Validation of Flight Control System Automation for an Unmanned Coaxial Helicopter
Creators: name: Hofsäß, Hannes
name: Hosseini, Barzin
name: Rhein, Julian
name: Holzapfel, Florian
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2023
Subjects: subject: Aircraft Automation||Contingency Procedures||System Operation||Large Scale Drones||UAS||Model-Based Development

description: An existing coaxial helicopter with a maximum takeoff weight of 600 kg has been transformed into a unmanned aerial system. To enable unmanned experimental validation of novel flight control-laws in flight tests, the helicopter's flight control system has been extended by digital components. As the loss of the helicopter platform due to a failure in the experimental digital flight control system has been identified a risk for the project, contingency procedures have been considered in the system design. In this paper, we suggest a model-based and lean development approach for system automation development, which to the best of the authors knowledge, is new. Within the process we suggest to introduce Operational Sequence Diagrams that only represent procedural system behavior to describe the Design Reference Scenarios of the Concept of Operations. Thereby we enable the total exploitation of a System Architecture Behavioral model within the design process, considering the definition of procedures, the validation of architecture design and automated code generation. To validate the suggested approach, we present its application to the design of the system automation for the flight control system of the unmanned helicopter. The system has been successfully integrated and tested in caged flight tests in November 2022.
Tumor mutational burden is a determinant of immune-mediated survival in breast cancer
Creators: name: Miller, L.D.
name: Routh, E.D.
name: Wang, E.
name: Su, J.
name: Jones, W.D.
name: Black, M.A.
name: Hoadley, K.A.
name: Triozzi, P.
name: Print, C.
name: Pullikuth, A.
name: Bedognetti, D.
name: Thomas, A.
name: Chou, J.W.
name: Jin, G.
name: Gatza, M.L.
name: Demaria, S.
name: Perou, C.M.
name: Mehta, G.A.
name: Knowlton, N
name: Page, D.B.
Publisher: name: Taylor and Francis Inc.
Year: 2018

description: Mounting evidence supports a role for the immune system in breast cancer outcomes. The ability to distinguish highly immunogenic tumors susceptible to anti-tumor immunity from weakly immunogenic or inherently immune-resistant tumors would guide development of therapeutic strategies in breast cancer. Genomic, transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) breast cancer cohorts were used to examine statistical associations between tumor mutational burden (TMB) and the survival of patients whose tumors were assigned to previously-described prognostic immune subclasses reflecting favorable, weak or poor immune-infiltrate dispositions (FID, WID or PID, respectively). Tumor immune subclasses were associated with survival in patients with high TMB (TMB-Hi, P < 0.001) but not in those with low TMB (TMB-Lo, P = 0.44). This statistical relationship was confirmed in the METABRIC cohort (TMB-Hi, P = 0.047; TMB-Lo, P = 0.39), and also found to hold true in the more-indolent Luminal A tumor subtype (TMB-Hi, P = 0.011; TMB-Lo, P = 0.91). In TMB-Hi tumors, the FID subclass was associated with prolonged survival independent of tumor stage, molecular subtype, age and treatment. Copy number analysis revealed the reproducible, preferential amplification of chromosome 1q immune-regulatory genes in the PID immune subclass. These findings demonstrate a previously unappreciated role for TMB as a determinant of immune-mediated survival of breast cancer patients and identify candidate immune-regulatory mechanisms associated with immunologically cold tumors. Immune subtyping of breast cancers may offer opportunities for therapeutic stratification.
Robustness of cosmological axion mass limits
Creators: name: Di Valentino, Eleonora
name: Gariazzo, Stefano
name: Giusarma, Elena
name: Mena, Olga
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present cosmological bounds on the thermal axion mass in an extended cosmological scenario in which the primordial power spectrum of scalar perturbations differs from the usual power-law shape predicted by the simplest inflationary models. The power spectrum is instead modeled by means of a "piecewise cubic Hermite interpolating polynomial" (PCHIP). When using Cosmic Microwave Background measurements combined with other cosmological data sets, the thermal axion mass constraints are degraded only slightly. The addition of the measurements of $σ_8$ and $Ω_m$ from the 2013 Planck cluster catalogue on galaxy number counts relaxes the bounds on the thermal axion mass, mildly favouring a $\sim 1$~eV axion mass, regardless of the model adopted for the primordial power spectrum.However, in general, such a preference disappears if the sum of the three active neutrino masses is also considered as a free parameter in our numerical analyses, due to the strong correlation between the masses of these two hot thermal relics.
description: 13 pages, 8 figures Replaced article: Added references, Added plots, Added a table, Corrected typos, Revised sections
Assistance dogs for military veterans with PTSD: a systematic review, meta-analysis, and meta-synthesis
Creators: name: Leighton, Sarah
Publisher: name: Purdue University Graduate School
Year: 2022
Subjects: Other psychology not elsewhere classified
Health psychology
Veterinary sciences not elsewhere classified
Animal welfare
Animal behaviour
Traditional, complementary and integrative medicine not elsewhere classified
Rehabilitation

description: Psychiatric assistance dogs for military veterans with posttraumatic stress disorder (PTSD) currently make up over 19% of assistance dog partnerships globally. We conducted a systematic review of the literature relating to these partnerships, with specific aims to (1) summarize their characteristics, (2) evaluate the quality of existing evidence, and (3) summarize outcomes. A total of 432 records were independently screened (Cohen’s kappa=0.90). Of these, 41 articles (29 peer-reviewed publications and 12 unpublished dissertations) met inclusion criteria. Data extraction was conducted to address the research aims, including a meta-analysis (quantitative outcomes) and meta-synthesis (qualitative outcomes). All peer-reviewed publications on the topic of psychiatric assistance dogs for veterans with PTSD were published within the last five years. The majority of included articles were quantitative (53%), 41% were qualitative, and 6% employed mixed methods. Mean methodological rigor scores were 80% for peer reviewed articles and 71% for dissertations, where higher scores represent more rigorous methodology. Quantitative articles reported significant improvements in the domains of PTSD severity, mental health, and social health. Impacts on physical health and global quality of life appear inconclusive. Meta-analysis (9 articles) revealed that partnership with an assistance dog had a clinically meaningful, significant, and large effect on PTSD severity scores (g=−1.129; p<0.0001). Qualitative meta-synthesis identified two third order constructs: (1) Impact on the individual: mental & physical health and (2) Impact beyond the individual: building relationships & connection. This synthesis of increasingly prevalent research on assistance dogs for veterans with PTSD provides support for the impact of this complementary and integrative health intervention on PTSD symptom severity, and signs of meaningful improvements in adjacent domains including mental and social health. Gaps between quantitative and qualitative findings, along with the need to report greater demographic detail, highlight key opportunities for future research.
Differences in race, molecular and tumor characteristics among women diagnosed with invasive ductal and lobular breast carcinomas
Creators: name: Perou, C.M.
name: Williams, L.A.
name: Geradts, J.
name: Olshan, A.F.
name: Hoadley, K.A.
name: Troester, M.A.
name: Love, M.I.
name: Nichols, H.B.
Publisher: name: Springer International Publishing
Year: 2019

description: Background: The dominant invasive breast cancer histologic subtype, ductal carcinoma, shows intrinsic subtype diversity. However, lobular breast cancers are predominantly Luminal A. Both histologic subtypes show distinct relationships with patient and tumor characteristics, but it is unclear if these associations remain after accounting for intrinsic subtype. Methods: Generalized linear models were used to estimate relative frequency differences (RFDs) and 95% confidence intervals (95% CIs) for the associations between age, race, tumor characteristics, immunohistochemistry (IHC) and RNA-based intrinsic subtype, TP53 status, and histologic subtype in the Carolina Breast Cancer Study (CBCS, n = 3,182) and The Cancer Genome Atlas (TCGA, n = 808). Results: Relative to ductal tumors, lobular tumors were significantly more likely to be Luminal A [CBCS RNA RFD: 44.9%, 95% CI (39.6, 50.1); TCGA: RFD: 50.5%, 95% CI (43.9, 57.1)], were less frequent among young (≤ 50 years) and black women, were larger in size, low grade, less frequently had TP53 pathway defects, and were diagnosed at later stages. These associations persisted among Luminal A tumors (n = 242). Conclusions: While histology is strongly associated with molecular characteristics, histologic associations with age, race, size, grade, and stage persisted after restricting to Luminal A subtype. Histology may continue to be clinically relevant among Luminal A breast cancers.
title: Inclusion of looked after children in education
Creators: name: Leslie, Claire
name: Mohammed, Azra
Publisher: name: Strathprints - University of Strathclyde
Year: 2015

description: This paper will describe a piece of research carried out in a Scottish local education authority on the inclusion of looked after children. Key themes pertinent to this vulnerable group were identified through data gathered from looked after children; foster carers; education and social work professionals. Key questions will be addressed, such as what inclusion means; what barriers to inclusion can exist; and what factors promote the inclusion of looked after children in schools. This paper concludes with the important messages that we can learn from in order to promote the inclusion of every looked after child and young person in education.
Supplementary materials from A mobile application to protect groundwater during unconventional oil and gas extraction
Creators: name: Worthmann, Charissa
name: Esterhuyse, Surina
Publisher: name: The Royal Society
Year: 2022
Subjects: Hydrology

description: Unconventional oil and gas (UOG) is an important energy source for many countries, but requires large quantities of water for its development, and may pollute water resources. Regulations are one of the main tools to achieve government policy on natural resource protection. South Africa, which is energy-constrained, but also water-scarce, is currently considering UOG extraction as an additional energy resource. UOG development could commence as soon as regulations to protect natural resources such as water have been published. Such regulations are, however, often not effectively enforced, which negatively affects the protection of water resources during UOG extraction. This study addresses these enforcement challenges in South Africa. It focuses on the science–society–policy interface by proposing a civic informatics platform to assist with on-the-ground enforcement of regulations via a mobile application. This mobile application aims to address both groundwater monitoring and management as well as UOG extraction operations in a single platform, to enable regulators to protect groundwater resources more effectively during UOG extraction, while simultaneously enhancing transparency in the UOG industry.
TP53 protein levels, RNA-based pathway assessment, and race among invasive breast cancer cases
Creators: name: Cohen, S.M.
name: Williams, L.A.
name: Troester, M.A.
name: Perou, C.M.
name: Sun, X.
name: Butler, E.N.
name: Geradts, J.
name: Hoadley, K.A.
name: Fuller, A.M.
name: Allott, E.H.
name: Olshan, A.F.
Publisher: name: Nature Publishing Group
Year: 2018

description: Mutations in tumor suppressor TP53 have been inconsistently linked to breast cancer risk factors and survival. Immunohistochemistry (IHC) staining, a primary clinical means of TP53 mutation determination, only detects mutations that facilitate protein accumulation (e.g., missense mutations). RNA-based pathway methods capture functional status and may aid in understanding the role of TP53 function in racial disparities of breast cancer. TP53 status was assessed among invasive breast cancer cases from the Carolina Breast Cancer Study (CBCS) (2008–2013) using IHC and an established RNA-based TP53 signature (CBCS and The Cancer Genome Atlas (TCGA)). Frequency of TP53 status (IHC, RNA-based) was estimated in association with tumor characteristics, PAM50 intrinsic subtype, age, and race using relative frequency differences (RFDs) and 95% confidence intervals (95% CI) as the measure of association. Approximately 60% of basal-like tumors were TP53 protein positive (IHC), while nearly 100% were TP53 mutant-like (RNA). Luminal A tumors had low frequency of TP53 positivity (IHC: 7.9%) and mutant-like status (RNA: 1.7%). Mutant-like TP53 (RNA) was strongly associated with age ≤50 years, high tumor grade, advanced stage of disease, large tumor size, and basal-like and HER2 intrinsic subtypes. Black race was strongly associated with TP53 mutant-like status (RNA) (RFD: 24.8%, 95% CI: 20.5, 29.0) even after adjusting for age, grade, stage (RFD: 11.3%; 95% CI: 7.6, 15.0). Associations were attenuated and non-significant when measured by IHC. IHC-based TP53 status is an insensitive measurement of TP53 functional status. RNA-based methods suggest a role for TP53 in tumor prognostic features and racial disparities.
Jamboxx: Hands-Free Music Making
Creators: name: Skinner, Anthea
Publisher: name: University of Melbourne
Year: 2023
Subjects: classificationCode: 360304
subject: Music performance
classificationCode: 360303
subject: Music education
classificationCode: 360306
subject: Musicology and ethnomusicology
classificationCode: 420103
subject: Music therapy
classificationCode: 360305
subject: Music technology and recording
classificationCode: 420318
subject: People with disability
classificationCode: 390411
subject: Special education and disability

description: An interview with Dave Whelan, co-founder and player of Jamboxx, a midi instrument designed for people with disability that does not require use of the hands. Originally published in Link Disability Magazine, Vol 28, No 3, 2019, pp28-9.
Electronic Supplementary Material from Sex-specific endocrine regulation of seasonal aggression in Siberian hamsters
Creators: name: Munley, Kathleen M.
name: Trinidad, Jonathan C.
name: Demas, Gregory E.
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: File containing additional Methods, Tables, and Figures to supplement the manuscript.
Additional file 6 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 6: Density and median distance of label for clathrin at presynaptic terminals under control and depolarizing conditions.
Carboplatin in BRCA1/2-mutated and triple-negative breast cancer BRCAness subgroups: The TNT Trial
Creators: name: Pinder, S.E.
name: Kernaghan, S.
name: Wilson, G.
name: Wardley, A.M.
name: Flanagan, J.M.
name: Hatton, M.Q.
name: Gazinska, P.
name: Brown, R.
name: Timms, K.M.
name: Ellis, P.
name: Perou, C.M.
name: Roylance, R.
name: Cheang, M.C.U.
name: Harper-Wynne, C.
name: Parker, P.
name: Barrett-Lee, P.
name: Smith, I.E.
name: Dowsett, M.
name: Gillett, C.
name: Chan, S.
name: Bliss, J.M.
name: Parikh, J.
name: Kilburn, L.
name: Ashworth, A.
name: Owen, J.
name: Harries, M.
name: Rahman, N.
name: Abraham, J.
name: Barrett, S.
name: Hoadley, K.A.
name: Shaw, A.
name: Tovey, H.
name: Gutin, A.
name: Shah, V.
name: Tutt, A.
name: Grigoriadis, A.
name: Fox, L.
name: Lanchbury, J.S.
Publisher: name: Nature Publishing Group
Year: 2018

description: Germline mutations in BRCA1/2 predispose individuals to breast cancer (termed germline-mutated BRCA1/2 breast cancer, gBRCA-BC) by impairing homologous recombination (HR) and causing genomic instability. HR also repairs DNA lesions caused by platinum agents and PARP inhibitors. Triple-negative breast cancers (TNBCs) harbor subpopulations with BRCA1/2 mutations, hypothesized to be especially platinum-sensitive. Cancers in putative 'BRCAness' subgroups - tumors with BRCA1 methylation; low levels of BRCA1 mRNA (BRCA1 mRNA-low); or mutational signatures for HR deficiency and those with basal phenotypes - may also be sensitive to platinum. We assessed the efficacy of carboplatin and another mechanistically distinct therapy, docetaxel, in a phase 3 trial in subjects with unselected advanced TNBC. A prespecified protocol enabled biomarker-treatment interaction analyses in gBRCA-BC and BRCAness subgroups. The primary endpoint was objective response rate (ORR). In the unselected population (376 subjects; 188 carboplatin, 188 docetaxel), carboplatin was not more active than docetaxel (ORR, 31.4% versus 34.0%, respectively; P = 0.66). In contrast, in subjects with gBRCA-BC, carboplatin had double the ORR of docetaxel (68% versus 33%, respectively; biomarker, treatment interaction P = 0.01). Such benefit was not observed for subjects with BRCA1 methylation, BRCA1 mRNA-low tumors or a high score in a Myriad HRD assay. Significant interaction between treatment and the basal-like subtype was driven by high docetaxel response in the nonbasal subgroup. We conclude that patients with advanced TNBC benefit from characterization of BRCA1/2 mutations, but not BRCA1 methylation or Myriad HRD analyses, to inform choices on platinum-based chemotherapy. Additionally, gene expression analysis of basal-like cancers may also influence treatment selection.
Additional file 9 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 9: Number of peri-PSD CCP under resting and depolarizing conditions.
title: Spontaneous CP violation in the Next-to-Minimal Supersymmetric Standard Model
Creators: name: Usai, Alessandro
Publisher: name: University of Glasgow
Year: 2000
Subjects: subject: Theoretical physics.

description: In this thesis we will investigate CP violation within the Next-to-Minimal Supersymmetric Standard Model (NMSSM). The study of the violation of the CP symmetry is relevant for several reasons. The origin of CP symmetry violation observed experimentally in the kaon system and nowhere else, is still uncertain and under active investigation. Also, and perhaps more intriguing, CP violation is a necessary ingredient of explanations of baryogenesis: supersymmetric theories allow for several sources of CP violation, whether explicit or not, therefore guaranteeing the necessary amount of CP violation. In fact, there are potentially so many CP violating phases, that it is an issue whether supersymmetry is compatible with the tight experimental constraints on the electron and neutron electric dipole moments. In particular we will concentrate on the study of Spontaneous CP Violation (SCPV), where the vacuum is CP non conserving. In the Standard Model, although the Electroweak symmetry is spontaneously broken, SCPV cannot occur, as at least two Higgs doublets are needed. Also, within the simplest extension of the Standard Model, the Minimal Supersymmetric Standard Model, SCPV, although possible in principle, is ruled out experimentally. Here we will show a detailed analysis of possible SCPV under general assumptions within the NMSSM. The implications of this are also addressed both for experiments at high energy colliders and also at low energy for the neutron and electron electric dipole moments when the CP violating phases are large. We have considered these phases as arbitrary parameters, and have studied the consequences as a function of the amount of CP violation present. In chapter 1 and 2 we briefly review the MSSM and the NMSSM. In chapter 3 we review the literature on SCPV, in both models, as a comparison. We also discuss the assumptions and formalism which will be used extensively in the following analysis. In chapter 4 we discuss weak SCPV 1 and its possible experimental consequences. The study of this scenario will effectively constitute the main aim of this work. In chapter 5 we present a thorough numerical analysis of SCPV both weak and not, over a vast area of the parameter space. The chapter also includes a discussion of the Higgs sector when CP is not violated, and when it is violated explicitly. In chapter 6 we address the issue of whether SCPV within the NMSSM is experimentally testable with emphasis on the weak SCPV case. In chapter 7 we then discuss the constraints coming from the neutron and electron electric dipole moments, which are relevant when SCPV is not weak. We then summarise our overall conclusions.