cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
[ITA] Aurosphere Ecological. How Science of Networks, Information Dynamics and Connectivism could help Politics to be more inclusive, transparent, equitable for people, incorporating different disciplines in the progressive stages of decision making.
Creators: name: Laquidara, Giuseppe
name: Boém, Marika Mazzi
name: Jovenal, J.
Publisher: name: figshare
Year: 2013
Subjects: subject: Applied Physics
subject: Philosophy
subject: FOS: Philosophy, ethics and religion
subject: Genetic Engineering
subject: History
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: Computational Physics
subject: Theoretical Computer Science
subject: Applied Computer Science
subject: Biological Engineering
subject: Sociology
subject: FOS: Sociology
subject: Economics
subject: Biophysics

description: Second draft, Italian submission — Superstring Machine Ecology
High doses of melatonin confer abiotic stress tolerance to phytopathogenic fungi grown in vitro
Creators: name: Madigan, Andrew
name: Harris, Christopher
name: Bedon, Frank
name: Franks, Ashley
name: Plummer, Kim
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 3004
subject: Crop and pasture production
classificationCode: 30
subject: Agricultural, veterinary and food sciences
classificationCode: 3108
subject: Plant biology
classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences

description: ABSTRACT: Melatonin is a secondary metabolite produced in all domains of life. Exogenous melatonin triggers defence mechanisms in plants that enhance abiotic stress tolerance. However, knowledge regarding the role of melatonin as a signal or an antioxidant in microbes is lacking. We investigated the in vitro growth responses of three phytopathogenic fungi, Sclerotinia sclerotiorum, Botrytis cinerea and Fusarium oxysporum f.sp. vasinfectum, to abiotic stress (2.5% ethanol with/without cold priming) under varying concentrations of melatonin. Melatonin at high concentrations (1000 – 2000 µM) partially restored fungal growth under stress, compared to controls, suggesting a role for melatonin in alleviating the impacts of stress exposure. Understanding how melatonin impacts fungal growth during stress conditions will be important for future applications using melatonin as a tool for crop protection.
title: #22 Staatliche Hilfe zu militärischen Operationen: Regeln und Grenzen
Creators: name: Tuchtfeld, Erik
name: Lischewski, Isabel
name: Eschenhagen, Philipp
name: Schuberth, Sophie
Publisher: name: Fachinformationsdienst für internationale und interdisziplinäre Rechtsforschung
Year: 2022
Subjects: subject: 341

description: Staaten leisten sich gegenseitig Hilfe zu militärischen Operationen, z.B. gehen sie Verteidigungsbündnisse ein, sie liefern Waffen an andere Staaten und vieles mehr. Aber was sagt das Völkerrecht eigentlich dazu, wenn Staaten anderen Staaten militärisch Hilfe leisten? Isabel Lischewski erklärt im Grundlagenteil, welche generellen völkerrechtlichen Regeln es zur staatlichen Beihilfe bei einer Verletzungen von völkerrechtlichen Normen durch andere Staaten gibt. Im Interview spricht Sophie Schuberth mit Benjamin Nußberger dann spezieller über den Fall von staatlichen Hilfeleistungen zu militärischer Gewaltanwendung. Gibt es dafür noch weitere Regeln und inwiefern unterscheiden sie sich? Welche Relevanz haben diese Fragen ganz aktuell im russischen Krieg gegen die Ukraine? Wir freuen uns über Lob, Anmerkungen und Kritik an podcast@voelkerrechtsblog.org. Abonniert unseren Podcast via RSS, über Spotify oder überall dort, wo es Podcasts gibt. Es gibt nun die Möglichkeit, auf diesen Plattformen den Völkerrechtspodcast zu bewerten, wir freuen uns sehr über 5 Sterne! Hintergrundinformationen: ICRC, Allies ‚Partners and Proxies: Managing Support Relationships in Armed Conflict to Reduce The Human Cost of War (Januar 2022) Marko Milanovic, The Complicity of Iran in Russia’s Aggression and War Crimes in Ukraine, Articles of War, 19. Oktober 2022 Deustche Welle, Russia Warns UN Against Probing Use of Iran Made Drones in Ukraine (20. Oktober 2022) Moderation: Philipp Eschenhagen & Sophie Schuberth Grundlagen: Dr. Isabel Lischewski Interview: Dr. Benjamin Nußberger & Sophie Schuberth Schnitt: Daniela Rau
description: Völkerrechtsblog
Compressed representation of brain genetic transcription
Creators: name: Ruffle, James K
name: Watkins, Henry
name: Gray, Robert J
name: Hyare, Harpreet
name: de Schotten, Michel Thiebaut
name: Nachev, Parashkev
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Genomics (q-bio.GN)
subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Computer and information sciences
subject: FOS: Biological sciences

description: The architecture of the brain is too complex to be intuitively surveyable without the use of compressed representations that project its variation into a compact, navigable space. The task is especially challenging with high-dimensional data, such as gene expression, where the joint complexity of anatomical and transcriptional patterns demands maximum compression. Established practice is to use standard principal component analysis (PCA), whose computational felicity is offset by limited expressivity, especially at great compression ratios. Employing whole-brain, voxel-wise Allen Brain Atlas transcription data, here we systematically compare compressed representations based on the most widely supported linear and non-linear methods-PCA, kernel PCA, non-negative matrix factorization (NMF), t-stochastic neighbour embedding (t-SNE), uniform manifold approximation and projection (UMAP), and deep auto-encoding-quantifying reconstruction fidelity, anatomical coherence, and predictive utility with respect to signalling, microstructural, and metabolic targets. We show that deep auto-encoders yield superior representations across all metrics of performance and target domains, supporting their use as the reference standard for representing transcription patterns in the human brain.
description: 22 pages, 5 main figures, 1 supplementary figure
Reduced Insulin Resistance and Oxidative Stress in a Mouse Model of Metabolic Syndrome following Twelve Weeks of Citrus Bioflavonoid Hesperidin Supplementation: A Dose–Response Study
Creators: name: Jamal, Abdulsatar
name: Brettle, Holly
name: Jamil, Dina
name: Tran, Vivian
name: Diep, Henry
name: Bobik, Alexander
name: Van-Der-Poel, Christopher
name: Vinh, Antony
name: Drummond, Grant
name: Thomas, Colleen
name: Jelinic, Maria
name: Al-Aubaidy, Hayder
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 3102
subject: Bioinformatics and computational biology
classificationCode: 3101
subject: Biochemistry and cell biology
classificationCode: 3206
subject: Medical biotechnology
subject: FOS: Medical biotechnology

description: Metabolic syndrome (MetS) is a cluster of metabolic abnormalities affecting ~25% of adults and is linked to chronic diseases such as cardiovascular disease, cancer, and neurodegenerative diseases. Oxidative stress and inflammation are key drivers of MetS. Hesperidin, a citrus bioflavonoid, has demonstrated antioxidant and anti-inflammatory properties; however, its effects on MetS are not fully established. We aimed to determine the optimal dose of hesperidin required to improve oxidative stress, systemic inflammation, and glycemic control in a novel mouse model of MetS. Male 5-week-old C57BL/6 mice were fed a high-fat, high-salt, high-sugar diet (HFSS; 42% kcal fat content in food and drinking water with 0.9% saline and 10% high fructose corn syrup) for 16 weeks. After 6 weeks of HFSS, mice were randomly allocated to either the placebo group or low- (70 mg/kg/day), mid- (140 mg/kg/day), or high-dose (280 mg/kg/day) hesperidin supplementation for 12 weeks. The HFSS diet induced significant metabolic disturbances. HFSS + placebo mice gained almost twice the weight of control mice (p < 0.0001). Fasting blood glucose (FBG) increased by 40% (p < 0.0001), plasma insulin by 100% (p < 0.05), and HOMA-IR by 150% (p < 0.0004), indicating insulin resistance. Hesperidin supplementation reduced plasma insulin by 40% at 140 mg/kg/day (p < 0.0001) and 50% at 280 mg/kg/day (p < 0.005). HOMA-IR decreased by 45% at both doses (p < 0.0001). Plasma hesperidin levels significantly increased in all hesperidin groups (p < 0.0001). Oxidative stress, measured by 8-OHdG, was increased by 40% in HFSS diet mice (p < 0.001) and reduced by 20% with all hesperidin doses (p < 0.005). In conclusion, hesperidin supplementation reduced insulin resistance and oxidative stress in HFSS-fed mice, demonstrating its dose-dependent therapeutic potential in MetS.
Towards Semi-Automatic Deployment of Scientific and Engineering Applications
Creators: name: Jaroslaw Slawinski
name: Vaidy Sunderam
Publisher: name: figshare
Year: 2013
Subjects: Applied Computer Science

description: The progress in science and engineering greatly depends on new software advances, and computational models become everyday tools for experiments and explorations. However, such software is often developed in isolation, for internal use of a research group, and without deployment plans. As a result, other researchers who wish to test these software tools in their settings face challenges during software deployment and execution. Moreover, this is further complicated as typical execution environments for scientific software are HPC machines that may significantly differ from familiar, desktop workstations. The lack of simple and uniform software deployment dissuades the users from experimenting with new applications and hampers overall progress and collaboration. In this paper, we propose a software metadeployment toolkit, called ADAPT, based on adaptable deployment recipes that can preserve deployment knowledge related to a particular software component and automate dependency soft-conditioning. These recipes may be reused for different targets and in various contexts, e.g., recipes may deliver dependencies for software mesh-ups combining scientific codes from a variety of disciplines, thus promoting collaborations among groups. Finally, our proposal has the potential to increase productivity in HPC by providing systematic and automatic software conditioning.
rOpenSci - a collaborative effort to develop R-based tools for facilitating Open Science
Creators: name: Chamberlain, Scott
name: Hart, Edmund
name: Ram, Karthik
name: Boettiger, Carl
Publisher: name: figshare
Year: 2013
Subjects: subject: 80309 Software Engineering
subject: FOS: Computer and information sciences

description: This is a submission for the WSSSPE conference (http://wssspe.researchcomputing.org.uk/).
Para que eSTEMos más atentos: factores que afectan el ingreso de mujeres a carreras STEM
Creators: name: Gómez Arizaga, M. P.
name: Conejeros Solar, M. L.
Publisher: name: Zenodo
Year: 2022
Subjects: Women, Science, CBHE, EU, gender, STEM, W-STEM, Latin-America

description: En el contexto del proyecto W-STEM ERASMUS + Capacity-building in Higher Education European Project (Ref. 598923-EPP-1-2018-1-ES-EPPKA2-CBHE-JP) se ha celebrado la Conferencia Internacional W-STEM Chile los días 19 y 20 de abril de 2022 de forma presencial en Valparaíso (Chile), auspiciada por la Pontificia Universidad Católica de Valparaíso y por la Universidad Técnica Federico Santa María, tras más de dos años trabajando virtualmente por la pandemia mundial de COVID-19. La Dra. María Paz Gómez Arizaga y la Dra. María Leonor Conejeros Solar impartieron la conferencia titulada “Para que eSTEMos más atentos: factores que afectan el ingreso de mujeres a carreras STEM”. En ella presentan las expectativas de los padres con respecto de las carreras STEM que sus hijos e hijas estudiarían, las expectativas del profesorado preuniversitario con respecto a las niñas, cuando los estudios dicen que no hay diferencias intrínsecas entre hombres y mujeres. También presentan su proyecto FONDECYT N°1181770 en el que analizan el proceso de elección de carreras de mujeres con alta capacidad y con actitudes positivas hacia la ciencia y la matemática, considerando factores intrapersonales y contextuales.

description: The European Commission support for the production of this publication does not constitute an endorsement of the contents which reflects the views only of the authors, and the Commission cannot be held responsible for any use which may be made of the information contained therein.
Quantum-Acoustical Drude Peak Shift
Creators: name: Keski-Rahkonen, J.
name: Ouyang, X. -Y.
name: Yuan, S.
name: Graf, A. M.
name: Aydin, A.
name: Heller, E. J.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum acoustics -- a recently developed framework parallel to quantum optics -- establishesa nonperturbative and coherent treatment of the electron-phonon interaction in real space. The quantum-acoustical representation reveals a displaced Drude peak hid ing in plain sight within the venerable Fröhlich model: the optical conductivity exhibits a finite frequency maximum in the far-infrared range and the d.c. conductivity is suppressed. Our results elucidate the origin of the high-temperature absorption peaks in strange or bad metals, revealing that dynamical lattice disorder steers the system towards a non-Drude behavior
Niche Modeling: Ecological Metaphors for Sustainable Software in Science
Creators: name: Weber, Nicholas
name: Thomer, Andrea
name: Twidale, Michael
Publisher: name: figshare
Year: 2013
Subjects: Applied Computer Science

description: Position paper submitted to: Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE) SC13, Sunday, 17 November 2013, Denver, CO, USA
Reduced Insulin Resistance and Oxidative Stress in a Mouse Model of Metabolic Syndrome following Twelve Weeks of Citrus Bioflavonoid Hesperidin Supplementation: A Dose–Response Study
Creators: name: Jamal, Abdulsatar
name: Brettle, Holly
name: Jamil, Dina
name: Tran, Vivian
name: Diep, Henry
name: Bobik, Alexander
name: van der Poel, Chris
name: Vinh, Antony
name: Drummond, Grant
name: Thomas, Colleen
name: Jelinic, Maria
name: Al-Aubaidy, Hayder
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 3102
subject: Bioinformatics and computational biology
classificationCode: 3101
subject: Biochemistry and cell biology
classificationCode: 3206
subject: Medical biotechnology
subject: FOS: Medical biotechnology

description: Metabolic syndrome (MetS) is a cluster of metabolic abnormalities affecting ~25% of adults and is linked to chronic diseases such as cardiovascular disease, cancer, and neurodegenerative diseases. Oxidative stress and inflammation are key drivers of MetS. Hesperidin, a citrus bioflavonoid, has demonstrated antioxidant and anti-inflammatory properties; however, its effects on MetS are not fully established. We aimed to determine the optimal dose of hesperidin required to improve oxidative stress, systemic inflammation, and glycemic control in a novel mouse model of MetS. Male 5-week-old C57BL/6 mice were fed a high-fat, high-salt, high-sugar diet (HFSS; 42% kcal fat content in food and drinking water with 0.9% saline and 10% high fructose corn syrup) for 16 weeks. After 6 weeks of HFSS, mice were randomly allocated to either the placebo group or low- (70 mg/kg/day), mid- (140 mg/kg/day), or high-dose (280 mg/kg/day) hesperidin supplementation for 12 weeks. The HFSS diet induced significant metabolic disturbances. HFSS + placebo mice gained almost twice the weight of control mice (p < 0.0001). Fasting blood glucose (FBG) increased by 40% (p < 0.0001), plasma insulin by 100% (p < 0.05), and HOMA-IR by 150% (p < 0.0004), indicating insulin resistance. Hesperidin supplementation reduced plasma insulin by 40% at 140 mg/kg/day (p < 0.0001) and 50% at 280 mg/kg/day (p < 0.005). HOMA-IR decreased by 45% at both doses (p < 0.0001). Plasma hesperidin levels significantly increased in all hesperidin groups (p < 0.0001). Oxidative stress, measured by 8-OHdG, was increased by 40% in HFSS diet mice (p < 0.001) and reduced by 20% with all hesperidin doses (p < 0.005). In conclusion, hesperidin supplementation reduced insulin resistance and oxidative stress in HFSS-fed mice, demonstrating its dose-dependent therapeutic potential in MetS.
Quantum-embeddable stochastic matrices
Creators: name: Shahbeigi, Fereshte
name: Chubb, Christopher T.
name: Kukulski, Ryszard
name: Pawela, Łukasz
name: Korzekwa, Kamil
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The classical embeddability problem asks whether a given stochastic matrix $T$, describing transition probabilities of a $d$-level system, can arise from the underlying homogeneous continuous-time Markov process. Here, we investigate the quantum version of this problem, asking of the existence of a Markovian quantum channel generating state transitions described by a given $T$. More precisely, we aim at characterising the set of quantum-embeddable stochastic matrices that arise from memoryless continuous-time quantum evolution. To this end, we derive both upper and lower bounds on that set, providing new families of stochastic matrices that are quantum-embeddable but not classically-embeddable, as well as families of stochastic matrices that are not quantum-embeddable. As a result, we demonstrate that a larger set of transition matrices can be explained by memoryless models if the dynamics is allowed to be quantum, but we also identify a non-zero measure set of random processes that cannot be explained by either classical or quantum memoryless dynamics. Finally, we fully characterise extreme stochastic matrices (with entries given only by zeros and ones) that are quantum-embeddable.
description: Accepted version
Walking the talk: adopting and adapting sustainable scientiﬁc software development processes in a small biology lab
Creators: name: Crusoe, Michael R.
name: Brown, C. Titus
Publisher: name: figshare
Year: 2013
Subjects: subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences

description: Submission to the First Workshop on Sustainable Software for Science: Practice and Experiences by the Genetics, Evolution, Development lab at Michigan State University. Submission was accepted. v 0.2: fixed omission of URLs in bibliography
v 0.3: added funding metadata; changed Figshare file type from 'Fileset' to 'Paper'; added link to the workshop webpage
False Data Injection Attacks in Smart Grids: State of the Art and Way Forward
Creators: name: Irfan, Muhammad
name: Sadighian, Alireza
name: Tanveer, Adeen
name: Al-Naimi, Shaikha J.
name: Oligeri, Gabriele
Publisher: name: arXiv
Year: 2023
Subjects: subject: Cryptography and Security (cs.CR)
subject: Signal Processing (eess.SP)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: In the recent years cyberattacks to smart grids are becoming more frequent Among the many malicious activities that can be launched against smart grids False Data Injection FDI attacks have raised significant concerns from both academia and industry FDI attacks can affect the internal state estimation processcritical for smart grid monitoring and controlthus being able to bypass conventional Bad Data Detection BDD methods Hence prompt detection and precise localization of FDI attacks is becomming of paramount importance to ensure smart grids security and safety Several papers recently started to study and analyze this topic from different perspectives and address existing challenges Datadriven techniques and mathematical modelings are the major ingredients of the proposed approaches The primary objective of this work is to provide a systematic review and insights into FDI attacks joint detection and localization approaches considering that other surveys mainly concentrated on the detection aspects without detailed coverage of localization aspects For this purpose we select and inspect more than forty major research contributions while conducting a detailed analysis of their methodology and objectives in relation to the FDI attacks detection and localization We provide our key findings of the identified papers according to different criteria such as employed FDI attacks localization techniques utilized evaluation scenarios investigated FDI attack types application scenarios adopted methodologies and the use of additional data Finally we discuss open issues and future research directions
MINRES-QLP Pack and Reliable Reproducible Research via Staunch Scientific Software
Creators: name: Sou-Cheng (Terrya) Choi
Publisher: name: figshare
Year: 2013
Subjects: subject: 10301 Numerical Analysis
subject: FOS: Mathematics
subject: Education
subject: Applied Computer Science

description: MINRES-QLP Pack is a suite of (extended) Krylov subspace methods for solving large linear systems and linear least-squares problems possibly with singular or ill-conditioned matrices or linear operators with special symmetries. Our purpose is to create and develop robust open-source implementations of the associated algorithms in MATLAB, Fortran, and PETSc that are faithful to the theory, following the philosophy of reproducible research and practicing development principles of staunch scienti fic software (SSS) that promote reliable reproducible research (RRR).
In this paper, we review the key features in the ongoing theoretical and software development of our algorithms in MINRES-QLP Pack. We highlight the most eff ective software engineering tools known to us, that are potentially useful to other scienti c research areas. We contend that the principles of RRR and SSS should be propagated to computational science students in advanced courses of scienti fic computing. To this end, we have started an experimental seminar course, "Reliable Mathematical Software" (IIT MATH-573) in our institution. We will share our research practice and pedagogic experiences in the Workshop on Sustainable Software for Science.
Art Therapy and Spiritual Care
Creators: name: Byrne, Libby
name: Levey, Libby
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 420306
subject: Health care administration

description: Libby Byrne & Libby Levey (2018). Art Therapy and Spiritual Care. In: Carey, L.B. & Mathisen, B.A. Spiritual Care for Allied Health Practice: A Person-Centered Approach (Chapter 7: pp: 137-161). London: Jessica Kingsley Publishers [ISBN 9781785922206]. DOI10.4225/22/5ae17f7aed798
Summary: This chapter considers the evidence base for the efficacy of art therapy and addressing psychological and spiritual health before going on to explore how an art making practice can support spiritual health and wellbeing. Consideration is given to how art can offer an experience of being known to oneself, and of being known in relation to what philosophers since Georg Hegel (1770–1831) have described as “the Other.” This leads on to an exploration of how the various nuances of an aesthetic experience can support and extend the possibilities for spiritual care.
Art Therapy and Spiritual Care
Creators: name: Byrne, Libby
name: Levey, Libby
Publisher: name: La Trobe
Year: 2018
Subjects: Health Care

description: Libby Byrne & Libby Levey (2018). Art Therapy and Spiritual Care. In: Carey, L.B. & Mathisen, B.A. Spiritual Care for Allied Health Practice: A Person-Centered Approach (Chapter 7: pp: 137-161). London: Jessica Kingsley Publishers [ISBN 9781785922206]. DOI10.4225/22/5ae17f7aed798
Summary: This chapter considers the evidence base for the efficacy of art therapy and addressing psychological and spiritual health before going on to explore how an art making practice can support spiritual health and wellbeing. Consideration is given to how art can offer an experience of being known to oneself, and of being known in relation to what philosophers since Georg Hegel (1770–1831) have described as “the Other.” This leads on to an exploration of how the various nuances of an aesthetic experience can support and extend the possibilities for spiritual care.
Finite element modelling of nuclear fuel performance in advanced gas-cooled reactors
Creators: name: Haynes, Thomas Anthony
Publisher: name: Imperial College London
Year: 2018

description: This thesis presents a two dimensional (r-θ) finite element model (PELICAN) for pellet-clad interaction in advanced gas-cooled reactors; it can also be applied to light water reactor designs. The model consists of a number of user-defined subroutines, together with a set of finite element models built using the commercial finite element software Abaqus. PELICAN can model cracked fuel pellets; slivers of fuel bonded to the cladding; a cross-pin temperature tilt, due to carbon deposition; and clad bore cracks. Pellet bore closure during power ramps was predicted by this model. Closure of the pellet bore reduces the increase in pellet outer radius during ramps and therefore the intensity of pellet-clad interaction. It was found that radial cracks through the pellet act as significant stress raisers in the cladding. This stress concentration is increased further in the presence of fuel-clad bonding. The stress concentration was however reduced to close to that observed in un-bonded fuel when microscopic ‘ladder cracks’ in the adherent sliver of fuel were modelled as being open. The cracks were modelled by reducing the elastic modulus of the sliver when the hoop stress was tensile. This was achieved by using a non-local approach, which has not previously been applied to nuclear fuel. The same broad trends were seen in the inelastic cladding strains in the models with both cracked and un-cracked fuel pellets. In the upper fuel elements (which have hotter cladding and lower linear rating), the creep strain is highest and the instantaneous plastic strain negligible. In the lower (colder cladding and higher linear rating) fuel elements, instantaneous plastic strains were of more importance. In addition, whilst instantaneous plastic strains were due mostly to increases in power, creep strains were due mostly to continuous full power operation. The impact of a cross-pin temperature tilt was investigated. Despite some stress concentration due to greater pellet fragment motion, the maximum hoop stress and inelastic strains were bounded by models with uniformly deposited and un-deposited thermal boundary conditions.
Epigenomic and genomic dissection of oestrogen receptor-positive breast cancer
Creators: name: Corleone, Giacomo
Publisher: name: Imperial College London
Year: 2019

description: Genetic and Epigenetic mechanisms underlie the natural complexity of phenotypical and morphological aspects of cancer. Extensive phenotypical intra and inter-patient heterogeneity of cancer specimens is a relevant limiting factor in cancer studies. Besides, loss of cell identity and frequent phenotypic switches occurring during cancer progression are elusive and intrinsically challenging to study. Historically, significant efforts have been devoted to identifying the genetic alterations occurring within DNA coding regions of cancer cells. More recently, new studies point the attention on the strong interplay between the epigenetic layout of cells and non-coding regulatory network of DNA. Mutations and alterations of the epigenetic asset among these regions are frequent in cancer; however relevant questions about the different key players involved are still unsolved. This dissertation aims to provide novel insights into the complex regulatory network of oestrogen receptor-positive breast cancer progression by mining the epigenetic and genetic landscape of patient tissues. We depict the epigenomic landscape ERα-positive BC focusing on active promoters and enhancers. We describe a novel computational workflow which led to the identification of YY1 and SLC9A3R1 proteins. We show data supporting the concept of a phenotypical evolution of epigenetic traits during cancer progression and experimentally validate the findings. Also, we introduce a new approach aiming to prioritise the investigation of sites prone to be critical players in breast cancer by coupling the systematic tracking of regulatory regions modulation during cancer progression with single nucleotide variants (SNV) discovery at high depth. This approach resulted with the identification of a recurrent mutation occurring in the core of a CTCF site lying at a border of a silent TAD in q25.1 of the chromosome 17. Finally, we provide evidence of an epigenetic induced reprogramming occurring in a distinct subpopulation of cancer cell lines exhibiting high plasticity. These cells become quiescent upon oestrogen deprivation and resume proliferation after a deterministic epigenetic modulation of NOTCH target regions.
Data Management Lifecycle and Software Lifecycle Management in the Context of Conducting Science
Creators: name: Lenhardt, W. Christopher
name: Ahalt, Stanley
name: Blanton, Brian
name: Christopherson, Laura
name: Idaszak, Ray
Publisher: name: figshare
Year: 2013
Subjects: subject: 80309 Software Engineering
subject: FOS: Computer and information sciences
subject: Environmental Science

description: This paper presents an overview of the data management lifecycle and software development lifecycles to look for ways to improve sustainable science software.
A Majority Rule Philosophy for Instant Runoff Voting
Creators: name: Hyman, Ross
name: Otis, Deb
name: Allen, Seamus
name: Dennis, Greg
Publisher: name: arXiv
Year: 2023
Subjects: subject: Theoretical Economics (econ.TH)
subject: FOS: Economics and business

description: We present the core support criterion, a voting criterion satisfied by Instant Runoff Voting (IRV) that is analogous to the Condorcet criterion but reflective of a different majority rule philosophy. Condorcet methods can be thought of as conducting elections between each pair of candidates, counting all ballots to determine the winner of each pair-election. IRV can also be thought of as conducting elections between all pairs of candidates but for each pair-election only counting ballots from voters who do not prefer another major candidate (as determined self-consistently from the IRV social ranking) to the two candidates in contention. The appropriateness of including all ballots or a subset of ballots for a pair-election, depends on whether the society deems the entire or a selected ballot set in compliance with freedom of association (which implies freedom of non-association) for a given pair election. Arguments based on freedom of association rely on more information about an electorate than can be learned from ranked ballots alone. We present a freedom-of-association based argument to explain why IRV may be preferable to Condorcet in some circumstances, including the 2022 Alaska special congressional election, based on the political context of that election.
description: 10 pages, Const Polit Econ (2024)
Assessing the invasiveness of Calotropis procera (Aiton) W.T. Aiton in northern Australia
Creators: name: Menge, Enock Ondeyo
Publisher: name: Charles Darwin University
Year: 2017

description: Rubber bush (Calotropis procera) was recognised during industry and expert weed prioritisation processes as an important economic and environmental weed in northern Australia. It establishes at high densities hindering pastoral management and reducing range productivity. It is estimated to infest 1.8-3. 7 million hectares of northern Australia, however, the drivers of its spread are not well known. This thesis documents various aspects of its reproductive biology and ecology, seed ecology, competitiveness and distribution in Australia; and how these attributes contribute to its invasiveness. A combination of greenhouse, field, laboratory, observational and computer simulation studies, covering the competitive ability, reproductive biology and ecology, seed ecology and species habitat modeling were performed at multiple locations in the Northern Territory and Queensland over three and a half years. This work addressed the question whether rubber bush invasions are a symptom of rangeland management practices or a consequence of natural biological interactions with native species. The results demonstrated that rubber bush is not a strong competitor of native grasses and its invasion is dependent on anthropogenic disturbance. The spread of rubber bush is facilitated by a self-compatible breeding system and an ability to recruit new pollinators during range expansion. Additionally, it exerts considerable propagule pressure through prolific wind-dispersed and highly germinable seeds in Australia compared to native environments. The seeds are quiescent under unfavourable temperature conditions but germinate rapidly when conditions improve. Species habitat modeling showed that it has not saturated the current suitable area, and its suitable area will expand under future climate scenarios. These abilities combine with ruderality to make rubber bush a high risk weed in northern Australia. Nevertheless, because feasibility of control is low, targeted control and protection of priority areas is recommended. Given the important role of disturbance in the spread of rubber bush, careful management of disturbance regimes on rangelands is necessary to limit the spread of rubber bush across northern Australia. For greater effectiveness, it is recommended that policy frameworks regarding the management of rubber bush be harmonised across affected Australian States and Territories.
Yang-Lee Zeros of Certain Antiferromagnetic Models
Creators: name: Sedik, Muhammad
name: Bhat, Junaid Majeed
name: Dhar, Abhishek
name: Shastry, B Sriram
Publisher: name: arXiv
Year: 2023
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We revisit the somewhat less studied problem of Yang-Lee zeros of the Ising antiferromagnet. For this purpose, we study two models, the nearest-neighbor model on a square lattice, and the more tractable mean-field model corresponding to infinite-ranged coupling between all sites. In the high-temperature limit, we show that the logarithm of the Yang-Lee zeros can be written as a series in half odd integer powers of the inverse temperature, $k$, with the leading term $\sim k^{1/2}$. This result is true in any dimension and for arbitrary lattices. We also show that the coefficients of the expansion satisfy simple identities (akin to sum rules) for the nearest-neighbor case. These new identities are verified numerically by computing the exact partition function for a 2D square lattice of size $16\times16$. For the mean-field model, we write down the partition function (termed the mean-field polynomials) for the ferromagnetic (FM) and antiferromagnetic (AFM) cases, and derive from them the mean-field equations. We analytically show that at high temperatures the zeros of the AFM mean-field polynomial scale as $\sim k^{1/2}$ as well. Using a simple numerical method, we find the roots lie on certain curves (the root curves), in the thermodynamic limit for the mean-field polynomials for the AFM case as well as for the FM one. Our results show a new root curve, that was not found earlier. Our results also clearly illustrate the phase transition expected for the FM and AFM cases, in the language of Yang-Lee zeros. Moreover, for the AFM case, we observe that the root curves separate two distinct phases of zero and non-zero complex staggered magnetization, and thus depict a complex phase boundary.
Software Engineering as Instrumentation for the Long Tail of Scientific Software
Creators: name: Daisie Huang
name: Lapp, Hilmar
Publisher: name: figshare
Year: 2013
Subjects: subject: 80309 Software Engineering
subject: FOS: Computer and information sciences
subject: 60102 Bioinformatics

description: The vast majority of the long tail of scientific software, the myriads of tools that implement the many analysis and visualization methods for different scientific fields, is highly specialized, purpose-built for a research project, and has to rely on community uptake and reuse for its continued development and maintenance. Although uptake cannot be controlled over even guaranteed, some of the key factors that influence whether new users or developers decide to adopt an existing tool or start a new one are about how easy or difficult it is to use or enhance a tool for a purpose for which it was not originally designed. The science of software engineering has produced techniques and practices that would reduce or remove a variety of barriers to community uptake of software, but for a variety of reasons employing trained software engineers as part of the development of long tail scientific software has proven to be challenging. As a consequence, community uptake of long tail tools is often far more difficult than it would need to be, even though opportunities for reuse abound. We discuss likely reasons why employing software engineering in the long tail is challenging, and propose that many of those obstacles could be addressed in the form of a cross-cutting non-profit center of excellence that makes software engineering broadly accessible as a shared service, conceptually and in its effect similar to shared instrumentation. This is a submission to the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE).
Ultrafast Raman thermometry in driven YBa$_2$Cu$_3$O$_{6.48}$
Creators: name: Chou, T. -H.
name: Först, M.
name: Fechner, M.
name: Henstridge, M.
name: Roy, S.
name: Buzzi, M.
name: Nicoletti, D.
name: Liu, Y.
name: Nakata, S.
name: Keimer, B.
name: Cavalleri, A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Signatures of photo-induced superconductivity have been reported in cuprate materials subjected to a coherent phonon drive. A 'cold' superfluid was extracted from the transient Terahertz conductivity and was seen to coexist with 'hot' uncondensed quasi-particles, a hallmark of a driven-dissipative system of which the interplay between coherent and incoherent responses are not well understood. Here, time resolved spontaneous Raman scattering was used to probe the lattice temperature in the photo-induced superconducting state of YBa2Cu3O6.48. An increase in lattice temperature of approximately 80 K was observed by measuring the time dependent Raman scattering intensity of an undriven 'spectator' phonon mode. This is to be compared with an estimated increase in quasi-particle temperatures of nearly 200 K. These temperature changes provide quantitative information on the nature of the driven state and its decay, and may provide a strategy to optimize this effect.
description: 14 pages, 4 figures
Occupational Ergonomics and Spiritual Care
Creators: name: Stuckey, Margaret
name: Brown, Jarrod W.
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 420306
subject: Health care administration

description: Rwth Stuckey & Jarrod W. Brown (2018). Occupational Ergonomics and Spiritual Care. In: Carey, L.B. & Mathisen, B.A. Spiritual Care for Allied Health Practice: A Person-Centered Approach (Chapter 9: pp: 183-206). London: Jessica Kingsley Publishers [ISBN 9781785922206]. DOI10.4225/22/5ae1823b432ea
Summary: This chapter, from an occupational ergonomics perspective, explores
 the relationship between meaningful work and health, wellbeing and job performance, and how spirituality in its varied expressions may be used to enrich the experience of contemporary workplaces. It addresses the questions of, “What is spirituality in the workplace?”; Why is consideration of spirituality important to workplace design and culture?”; and “How can ergonomists integrate spirituality into contemporary workplace practices?”
ENGLISH LANGUAGE TEACHING ELT
Creators: name: Shakhrisabz State Pedagogical Institute 3 th stage student : Jabborova Sabina
Publisher: name: Zenodo
Year: 2024

description: English Language Teaching (ELT) has become an essential field, catering to the increasing global demand for English proficiency in education, business, and cross-cultural communication. This paper reviews the evolution of ELT methodologies, from traditional Grammar Translation and the Direct Method to communicative approaches such as Communicative Language Teaching (CLT) and Task-Based Language Teaching (TBLT). Central principles, including communicative competence, learner-centered approaches, and formative assessment, are examined for their roles in shaping effective instruction. Additionally, the integration of technology in ELT—through digital platforms, Learning Management Systems (LMS), and Artificial Intelligence (AI)—is discussed, highlighting how these tools provide personalized learning experiences and greater accessibility. Current trends, such as blended learning, gamification, and culturally responsive teaching, reflect the dynamic, adaptive nature of ELT in meeting diverse learner needs. Challenges in the field, including resource accessibility, teacher training, and accurate assessment, are also explored. The review concludes by examining future directions for ELT, emphasizing the importance of inclusivity, technological integration, and personalized learning to enhance English language proficiency worldwide
A Framework for Discussing e-Research Infrastructure Sustainability
Creators: name: Katz, Daniel S.
name: Proctor, David
Publisher: name: figshare
Year: 2013
Subjects: Science Policy

description: Accepted by Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE), extended version published by Journal of Open Research Software as http://dx.doi.org/10.5334/jors.av
Co-production in action: Improving the relevance of a Cochrane Review on person-centred care
Creators: name: Merner, Bronwen
name: Hill, Sophie
name: Colombo, Cinzia
name: Xafis, Vicki
name: Gaulden, Carolyn M
name: Graham-Wisener, Lisa
name: Lowe, Dianne
name: Walsh, Louisa
Publisher: name: La Trobe
Year: 2018
Subjects: Health Care

description: Presentation at 2018 Cochrane Colloquium about co-producing a Cochrane Review on person-centred care with a stakeholder panel.
Occupational Ergonomics and Spiritual Care
Creators: name: Rwth Stuckey
name: Brown, Jarrod W.
Publisher: name: La Trobe
Year: 2018
Subjects: Health Care

description: Rwth Stuckey & Jarrod W. Brown (2018). Occupational Ergonomics and Spiritual Care. In: Carey, L.B. & Mathisen, B.A. Spiritual Care for Allied Health Practice: A Person-Centered Approach (Chapter 9: pp: 183-206). London: Jessica Kingsley Publishers [ISBN 9781785922206]. DOI10.4225/22/5ae1823b432ea
Summary: This chapter, from an occupational ergonomics perspective, explores the relationship between meaningful work and health, wellbeing and job performance, and how spirituality in its varied expressions may be used to enrich the experience of contemporary workplaces. It addresses the questions of, “What is spirituality in the workplace?”; Why is consideration of spirituality important to workplace design and culture?”; and “How can ergonomists integrate spirituality into contemporary workplace practices?”
L'application des radiations pour l'obtention de vignes résistantes au Plasmopara
Creators: name: Coutinho, M. P.
Publisher: name: VITIS - Journal of Grapevine Research
Year: 2017

description: L'amélioration génétique de la vigne, en ce qui concerne la résistance au Plasmopara viticola, est un problème d'un très grand intérêt au Portugal, parce que le mildiou est encore la maladie cryptogamique la plus importante de la vigne dans ce pays. Le caractère polyfactoriel de cette résistance traduit par des taches limitées d'infection sur les feuilles, le manque de «sources de résistance» de Vitis vinifera et de corrélations entre les gènes de résistance et quelques autres gènes responsables de mauvaises qualités des raisins, justifient l'intérêt de la mutagenèse expérimentale. En conséquence, nous avons indu dans notre programme d'amélioration, initié depuis longtemps avec des méthodes classiques (sélection clonale, hybridation et semis en masse), l'application des rayons X et des neutrons sur des semences et des greffes. Dans cette communication on présente les résultats obtenus jusqu'à présent en ce qui concerne le pourcentage de la germination des pépins et des plants de semis chlorotiques et en ce qui concerne la sélection des plantes résistantes au mildiou. Anwendung der Strahlungstechnik zur Erzielung plasmopararesistenter Reben Die Züchtung von Reben mit dem Ziel der Resistenz gegen Piasmopara viticoia ist für Portugal von sehr großer Bedeutung, denn in diesem Land ist der Mehltau noch die häufigste Pilzkrankheit der Rebe. Der polyfaktorielle Charakter dieser Resistenz, der sich in Form begrenzter Infektionsflecken auf den Blättern äußert, fehlende „Resistenzquellen" in Vitis vinifera und Korrelationen zwischen den Resistenzgenen und einigen anderen Genen, die eine mindere Traubenqualität verursachten, rechtfertigen das Interesse an der experimentellen Mutagenese. Wir haben daher in unser Züchtungsprogramm, das wir seit langem mit klassischen Methoden durchführen (Klonenzüchtung, Kreuzung und Massenaussaat), die Behandlung von Sämlingen und Edelreisern mit X- und Neutronen-Strahlen einbezogen. In diesem Referat werden die bisher in bezug auf den Prozentsatz der Samenkeimung und der chlorotischen Sämlinge sowie auf die Züchtung mehltauresistenter Pflanzen erzielten Resultate dargelegt.
description: VITIS - Journal of Grapevine Research, Vol. 13 No. 4 (1974): Vitis
Murray-Darling Basin Environmental Water Knowledge and Research Project: Fish Theme Research Appendix
Creators: name: Price, Amina
name: Balcombe, Stephen
name: Humphries, Paul
name: King, Alison
name: Zampatti, Brenton
name: Gawne, Ben
name: Nogueira, Lorena
Publisher: name: La Trobe
Year: 2020
Subjects: subject: 60801 Animal Behaviour
subject: FOS: Biological sciences
subject: 60201 Behavioural Ecology
subject: 60202 Community Ecology (excl. Invasive Species Ecology)
subject: 60204 Freshwater Ecology
subject: 60207 Population Ecology
subject: Ecology
subject: 50102 Ecosystem Function
subject: FOS: Earth and related environmental sciences
subject: 50205 Environmental Management
subject: Environmental Science
subject: 50211 Wildlife and Habitat Management

description: Appendix A1.1 The influence of flow and non-flow related stressors on the drivers of fish recruitment
Appendix A1.2 Prioritising fish research for flow management in the Murray-Darling Basin
Appendix A1.3 Riverscape recruitment: a conceptual synthesis of drivers of fish recruitment in rivers
Appendix A1.4 Examination of the relationship between food density, temperature and early-life stage growth and survival
Appendix A1.5 Understanding the feeding requirements of larval fish in the northern Murray–Darling Basin
Appendix A1.6 Comparison of the thermal and nutritional regimes among main channel and floodplain habitat patches
Appendix A1.7 The relationship between discharge, reach hydraulic complexity, zooplankton production and retention in a lowland river system
Appendix A1.8 Investigating the relationship between flow, structural habitat, hydrodynamics and patterns of larval settlement and retention
Appendix A1.9 Water infrastructure and challenges for fish conservation: A trait-based analysis to foresee fish recruitment in regulated rivers
Appendix A1.10 Basin-scale population dynamics of Golden Perch and Murray Cod: relating flow to provenance, movement and recruitment in the Murray–Darling Basin
Appendix 2: Theme Data Inventory
Appendix 3: Theme Outputs
Appendix 4: Theme Engagement and Communications Activities