cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
(617) Henry Holmes
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Supplementary Figure 2 from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity.
Creators: name: Kauzlaric, Annamaria
name: Jang, Suk Min
name: Morchikh, Mehdi
name: Cassano, Marco
name: Evarist Planet
name: Monsef Benkirane
name: Trono, Didier
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Molecular Biology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Automatic retrieval of volcanic SO2 emission source from TROPOMI products
Creators: name: Markus, Balazs
name: Valade, Sébastien
name: Wöllhaf, Manuel
name: Hellwich, Olaf
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 550 Geowissenschaften
subject: clustering
subject: satellite remote sensing
subject: semantic segmentation
subject: SO2 volcanic plumes
subject: volcano monitoring

description: Volcanic sulfur dioxide (SO2) satellite observations are key for monitoring volcanic activity, and for mitigation of the associated risks on both human health and aviation safety. Automatic analysis of this data source, including robust source emission retrieval, is in turn essential for near real-time monitoring applications. We have developed fast and accurate SO2 plume classifier and segmentation algorithms using classic clustering, segmentation and image processing techniques. These algorithms, applied to measurements from the TROPOMI instrument onboard the Sentinel-5 Precursor platform, can help in the accurate source estimation of volcanic SO2 plumes originating from various volcanoes. In this paper, we demonstrate the ability of different pixel classification methodologies to retrieve SO2 source emission with a good accuracy. We compare the algorithms, their strengths and shortcomings, and present plume classification results for various active volcanoes throughout the year 2021, including examples from Etna (Italy), Sangay and Reventador (Ecuador), Sabancaya and Ubinas (Peru), Scheveluch and Klyuchevskoy (Russia), as well as Ibu and Dukono (Indonesia). The developed algorithms, shared as open-source code, contribute to improving analysis and monitoring of volcanic emissions from space.
title: Identification of Crohn’s disease immunopathotypes
Creators: name: Baer, Hannah Moana
Publisher: name: University of Glasgow
Year: 2023

description: Crohn’s disease (CD) describes an inflammatory condition characterised by chronic gastrointestinal (GI) inflammation. Currently, >1 in 150 people are estimated to be affected in the UK, with the incidence rising. The pathology of CD is linked to an aberrant immune response against the gut microbiota. CD is a heterogenous disease with different disease phenotypes (stricturing and fistulating disease) and locations; it can affect any part of the GI tract. A range of drugs is approved for CD treatment. However, response rates to these specific therapies are low, and 46% of patients still require bowel resective surgery. The high rates of surgical interventions and unpredictable disease relapse pose challenges for the clinical management of CD. Little is known about the molecular mechanisms underlying the different treatment responses, and cost-effective and feasible approaches to predict these responses are still a long way off. Disease relapse has been linked with decreased T cell immunoreceptor with Ig and ITIM (TIGIT) on CD38+ CD4+ T cells in the peripheral blood of paediatric patients. Other clinical markers of inflammation have been found to lack specificity in predicting disease progression. Several biomarkers predicting non-response to frontline therapeutics blocking the pro-inflammatory cytokine tumour necrosis factor (TNF) have been proposed, including the levels of luminal membrane-bound TNF and gene expression of the pro-inflammatory cytokines oncostatin-M (OSM) and TNF itself. None of these markers are currently used clinically, and there is still a need for reliable ways to predict disease progression and treatment responses. Based on these findings I hypothesised that distinct immunopathotypes in CD drive distinct disease phenotypes and underlie distinct treatment responses to biologic therapies, such as anti-TNF. My project aimed to elucidate distinct immunopathotypes in the blood and intestines of CD patients and link them to disease phenotype, state of inflammation and treatment response. Two distinct immunopathotypes were identified. One showed decreased circulating T cells and increased intestinal CD8+ and cytotoxic immune responses. The second immunopathotype was defined by IL-1β-driven inflammation and granuloma formation in the intestines of people and was linked to anti-TNF refractory disease.
Unbeamed tidal disruption events at hard X-rays
Creators: name: Hryniewicz, Krzysztof
name: Walter, Roland
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Owing to their thermal emission, tidal disruption events (TDEs) were regularly detected in the soft X-rays and sometimes in the optical. Only a few TDEs have been detected at hard X-rays: two are high redshift beamed events, one of which occurred at the core of a nearby galaxy, and the most recent one is of a different nature, involving a compact object in the Milky Way. The aims of this work are to obtain a first sample of hard X-ray-selected unbeamed TDEs, to determine their frequency and to probe whether TDEs usually or exceptionally emit at hard X-ray energies. We performed extensive searches for hard X-ray flares at positions in over 53000 galaxies, up to a distance of 100 Mpc in the Swift BAT archive. Light curves were extracted and parametrized. The quiescent hard X-ray emission was used to exclude persistently active galactic nuclei. Significant flares from non-active galaxies were derived and checked for possible contamination. We found a sample of nine TDE candidates, which translates into a rate of $2 \times 10^{-5}\,{\rm galaxy}^{-1}\,{\rm yr}^{-1}$ above the BAT detection limit. This rate is consistent with those observed by XMM-Newton at soft X-rays and in the optical from SDSS observations, and is as expected from simulations. We conclude that hard X-ray emission should be ubiquitous in un-beamed TDEs and that electrons should be accelerated in their accretion flow.
description: accepted for publication in A&A; 14 pages, 6 figures, 2 tables
title: Interplay of cell proliferation and tissue remodelling in colorectal cancer
Creators: name: Halim, Silvia
Publisher: name: University of Glasgow
Year: 2019
Subjects: subject: colorectal cancer, patient stratification, supervised clustering, cell proliferation, tissue remodelling, immune cell infiltration, myeloid cell, transcription factor, transcriptional activity, inference model, microRNA, KLF4, mir-22, IRF8, SPI1, PU.1.

description: Human cancers can be classified based on gene expression signatures quantifying the degree of cell proliferation and a feature we term tissue remodelling. Yet, specific factors regulating the gene expression programs of cell proliferation and tissue remodelling are not well understood. In this work, I address this question using colorectal cancer as a case study. In an initial evaluation of clinical outcome prediction in the case study cohort, our classification based on cell proliferation and tissue remodelling signatures delivers a better patient stratification than a recently reported consensus molecular subtyping (CMS). Although the CMS scheme predicts a worse prognosis for patients with a mesenchymal signature (a feature that strongly overlaps with tissue remodelling), it cannot differentiate the remaining patients based on clinical outcome. I show that cell proliferation is the missing factor, which is associated with good prognosis. In the analyses of specific factors driving the tissue remodelling programme, I identify transcription factor KLF4 and microRNA mir-22 as putative regulators. Concordant with KLF4 role in immune cell regulation, KLF4 activity scores are significantly higher in colorectal tumours with predicted myeloid cells infiltration, suggesting its association with myeloid cell infiltration and poor prognosis in colorectal cancer. However, mir-22 is not associated with immune cell infiltration, suggesting it may be expressed in the tumour stroma as well. Lastly, I propose a network that may be regulated by IRF8, SPI1, KLF4 and mir-22 in monocyte differentiation and in colorectal cancer. The correlation analysis suggests a negative feedback loop, whereby mir-22 may repress Irf8 gene to control the rate of IRF8 transcription. Taken together, I have identified specific regulators driving remodelling processes and their association with immune cell infiltration. In the future, it will be beneficial to conduct further studies to understand the mechanisms driving myeloid cell infiltration in colorectal cancer, particularly to propose treatments for patients exhibiting poor prognosis.
Supplementary Figure 3 from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity.
Creators: name: Kauzlaric, Annamaria
name: Jang, Suk Min
name: Morchikh, Mehdi
name: Cassano, Marco
name: Evarist Planet
name: Monsef Benkirane
name: Trono, Didier
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Molecular Biology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
GOODS-$Herschel$: identification of the individual galaxies responsible for the 80-290$μ$m cosmic infrared background
Creators: name: Leiton, R.
name: Elbaz, D.
name: Okumura, K.
name: Hwang, H. S.
name: Magdis, G.
name: Magnelli, B.
name: Valtchanov, I.
name: Dickinson, M.
name: Béthermin, M.
name: Schreiber, C.
name: Charmandaris, V.
name: Dole, H.
name: Juneau, S.
name: Borgne, D. Le
name: Pannella, M.
name: Pope, A.
name: Popesso, P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We propose a new method of pushing $Herschel$ to its faintest detection limits using universal trends in the redshift evolution of the far infrared over 24$μ$m colours in the well-sampled GOODS-North field. An extension to other fields with less multi-wavelength information is presented. This method is applied here to raise the contribution of individually detected $Herschel$ sources to the cosmic infrared background (CIRB) by a factor 5 close to its peak at 250$μ$m and more than 3 in the 350$μ$m and 500$μ$m bands. We produce realistic mock $Herschel$ images of the deep PACS and SPIRE images of the GOODS-North field from the GOODS-$Herschel$ Key Program and use them to quantify the confusion noise at the position of individual sources, i.e., estimate a "local confusion noise". Two methods are used to identify sources with reliable photometric accuracy extracted using 24$μ$m prior positions. The clean index (CI), previously defined but validated here with simulations, which measures the presence of bright 24$μ$m neighbours and the photometric accuracy index (PAI) directly extracted from the mock $Herschel$ images. After correction for completeness, thanks to our mock $Herschel$ images, individually detected sources make up as much as 54% and 60% of the CIRB in the PACS bands down to 1.1 mJy at 100$μ$m and 2.2 mJy at 160$μ$m and 55, 33, and 13% of the CIRB in the SPIRE bands down to 2.5, 5, and 9 mJy at 250$μ$m, 350$μ$m, and 500$μ$m, respectively. The latter depths improve the detection limits of $Herschel$ by factors of 5 at 250$μ$m, and 3 at 350$μ$m and 500$μ$m as compared to the standard confusion limit. Interestingly, the dominant contributors to the CIRB in all $Herschel$ bands appear to be distant siblings of the Milky Way ($z$$\sim$0.96 for $λ$$
description: 22 pages, 16 figures. Accepted for publication by Astronomy and Astrophysics
(619) Elizabeth Richardson
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Barjols, abattoir, poursuite des opérations de refendage et de débitage du bœuf
Creators: name: Musée National Des Arts Et Traditions Populaires (Paris)
name: Centre D'ethnologie Française
Publisher: name: École des Hautes Études en Sciences Sociales; Institut  interdisciplinaire d'anthropologie du contemporain (Paris); Laboratoire d'anthropologie et d'histoire de l'institution de la culture (Paris)
Year: 2024

Abstract
Higher Hamming weights for locally recoverable codes on algebraic curves
Creators: name: Ballico, Edoardo
name: Marcolla, Chiara
Publisher: name: arXiv
Year: 2015
Subjects: subject: Commutative Algebra (math.AC)
subject: Information Theory (cs.IT)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: We study the locally recoverable codes on algebraic curves. In the first part of this article, we provide a bound of generalized Hamming weight of these codes. Whereas in the second part, we propose a new family of algebraic geometric LRC codes, that are LRC codes from Norm-Trace curve. Finally, using some properties of Hermitian codes, we improve the bounds of distance proposed in [1] for some Hermitian LRC codes. [1] A. Barg, I. Tamo, and S. Vlladut. Locally recoverable codes on algebraic curves. arXiv preprint arXiv:1501.04904, 2015.
Developing Climate-Smart Agriculture Indicators for SDG 1 and Environmental Implications in Northern Thailand
Creators: name: Thatchakorn Khamkhunmuang
name: Kittiyut Punchay
name: Panomsak Promburom
name: Prasit Wangpakapattanawong
Publisher: name: Thai Society of Higher Education Institutes on Environment
Year: 2022
Subjects: Climate change
Adaptation
Mitigation
Highland agriculture
Smallholder farming

description: EnvironmentAsia, 15, 3, 1-13
Identification of thimet oligopeptidase substrates in Arabidopsis thaliana
Creators: name: Rogers, Holden
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2021
Subjects: Analytical chemistry

description: Proteostasis is essential for proper cellular function, including the production of peptides with biological functions via the degradation of proteins/peptides through controlled proteolysis. Proteostasis contributes to the maintenance of cellular functions and plant-environment interactions under physiological conditions. Plant stress continues to reduce agricultural yields resulting in significant economic losses; thus, it is crucial to understand how plants perceive stress signals to elicit responses for survival. As previously shown in Arabidopsis thaliana, thimet oligopeptidases (TOPs) are essential components in plant response to oxidative stress triggered by pathogens. However, further characterization of TOPs, and their peptide substrates is required to understand their contributions to stress perception and defense signaling. Label-free peptidomics via liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to differentially quantify 1111 peptides, originating from 369 proteins, between the Arabidopsis Col-0 wild type and top1top2 knock-out mutant. This revealed 350 peptides as significantly more abundant in the mutant, representing accumulation of these potential TOP substrates. Ten direct substrates were validated using in vitro enzyme assays and electrospray ionization mass spectrometry (ESI-MS) with recombinant TOPs and synthetic candidate peptides. The TOP substrates discovered are derived from proteins involved in photosynthesis, biogenesis, glycolysis, protein folding, and antioxidant defense, implicating TOP involvement in processes beyond defense signaling. Identification of these substrates provides a framework for TOP signaling networks, through which the interplay between proteolytic pathways and defense signaling can be further characterized.
Supplementary Figure 4 from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity.
Creators: name: Kauzlaric, Annamaria
name: Jang, Suk Min
name: Morchikh, Mehdi
name: Cassano, Marco
name: Evarist Planet
name: Monsef Benkirane
name: Trono, Didier
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Molecular Biology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Emancipation from Slavery and Serfdom, and Land Rights. The Americas and Eastern Europe Compared
Creators: name: Dal Lago, Enrico
Publisher: name: Moving the Social
Year: 2017

description: A comparative study of the complex processes of emancipation in the Americas and Eastern Europe shows that, in both cases, the established governments were the main agents that decreed the end of unfree labour, with the single exception represented by the case of the Haitian Revolution. As a result, in most cases, the governments’ provisions were conservative in conception and practice and tended to safeguard the interests of slaveholders and serfowners, rather than those of slaves and serfs, by providing the former with some type of compensation for their loss in capital and by keeping the latter in some transitional form of coerced labour before the achievement of their full free status. Here,the exception was the 1863 United States Emancipation Proclamation, which declared African American slaves immediately free and with no compensation for slaveholders, with some similarities with Brazil’s 1888 Golden Law. In the case of the ex-slaves’ and the ex-serfs’ rights to own land, however, all the governments enacting emancipation acted in remarkably similar ways, by providing no avenues for the liberated labourers’ immediate acquisition of landed property, and thus effectively preventing the formation of landed peasantries out of the newly freed populations of the Americas and Eastern Europe for many decades.
description: Moving the Social, Vol 56 (2016): Essays on Social History and the History of Social Movements
Supplementary Figure 2 from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity
Creators: name: Kauzlaric, Annamaria
name: Jang, Suk Min
name: Morchikh, Mehdi
name: Cassano, Marco
name: Evarist Planet
name: Monsef Benkirane
name: Trono, Didier
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Molecular Biology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Two-Dimensional Core-Collapse Supernova Simulations with the Isotropic Diffusion Source Approximation for Neutrino Transport
Creators: name: Pan, Kuo-Chuan
name: Liebendörfer, Matthias
name: Hempel, Matthias
name: Thielemann, Friedrich-Karl
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The neutrino mechanism of core-collapse supernova is investigated via non-relativistic, two-dimensional (2D), neutrino radiation-hydrodynamic simulations. For the transport of electron flavor neutrinos, we use the interaction rates defined by Bruenn (1985) and the isotropic diffusion source approximation (IDSA) scheme, which decomposes the transported particles into trapped particle and streaming particle components. Heavy neutrinos are described by a leakage scheme. Unlike the "ray-by-ray" approach in some other multi-dimensional supernova models, we use cylindrical coordinates and solve the trapped particle component in multiple dimensions, improving the proto-neutron star resolution and the neutrino transport in angular and temporal directions. We provide an IDSA verification by performing 1D and 2D simulations with 15 and 20 $M_\odot$ progenitors from Woosley et al.~(2007) and discuss the difference of our IDSA results with those existing in the literature. Additionally, we perform Newtonian 1D and 2D simulations from prebounce core collapse to several hundred milliseconds postbounce with 11, 15, 21, and 27 $M_\odot$ progenitors from Woosley et al.~(2002) with the HS(DD2) equation of state. General relativistic effects are neglected. We obtain robust explosions with diagnostic energies $E_{\rm dig} \gtrsim 0.1- 0.5$~B for all considered 2D models within approximately $100-300$ milliseconds after bounce and find that explosions are mostly dominated by the neutrino-driven convection, although standing accretion shock instabilities are observed as well. We also find that the level of electron deleptonization during collapse dramatically affect the postbounce evolution, e.g.~the ignorance of neutrino-electron scattering during collapse will lead to a stronger explosion.
description: 23 pages. Accepted for publication in ApJ
Optimal Stateless Model Checking based on View-equivalence (Artifact)
Creators: name: Singh, Sanjana
name: Sharma, Subodh
Publisher: name: Zenodo
Year: 2023
Subjects: concurrency, stateless model checking, coarse equivalence, view-equivalence

description: This artifact is associated with the work, titled “Optimal Stateless Model Checking based on View-equivalence”.
A new approach to modeling positive random variables with repeated measures
Creators: name: de Freitas, João Victor B.
name: Nobre, Juvêncio S.
name: Bourguignon, Marcelo
name: Santos-Neto, Manoel
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences

description: In many situations, it is common to have more than one observation per experimental unit, thus generating the experiments with repeated measures. In the modeling of such experiments, it is necessary to consider and model the intra-unit dependency structure. In the literature, there are several proposals to model positive continuous data with repeated measures. In this paper, we propose one more with the generalization of the beta prime regression model. We consider the possibility of dependence between observations of the same unit. Residuals and diagnostic tools also are discussed. To evaluate the finite-sample performance of the estimators, using different correlation matrices and distributions, we conducted a Monte Carlo simulation study. The methodology proposed is illustrated with an analysis of a real data set. Finally, we create an R package for easy access to publicly available the methodology described in this paper.
Supplementary materials and methods, and captions for Supplementary Figures and Table from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity.
Creators: name: Kauzlaric, Annamaria
name: Jang, Suk Min
name: Morchikh, Mehdi
name: Cassano, Marco
name: Evarist Planet
name: Monsef Benkirane
name: Trono, Didier
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Molecular Biology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
title: inSIDE Fair Dialogues: Assessing and Maintaining Fairness in Human-Computer-Interaction
Creators: name: Janzen, Sabine
name: Bleymehl, Ralf
name: Alam, Aftab
name: Xu, Sascha
name: Stein, Hannah
Publisher: name: Gesellschaft für Informatik e.V.
Year: 2018
Subjects: subject: Fairness
subject: dialogues
subject: robot
subject: retailing
subject: HCI

description: For simulating human-like intelligence in dialogue systems, individual and partially conflicting motives of interlocutors have to be processed in dialogue planning. Little attention has been given to this topic in dialogue planning in contrast to dialogues that are fully aligned with anticipated user motives. When considering dialogues with congruent and incongruent interlocutor motives like sales dialogues, dialogue systems need to find a balance between competition and cooperation. As a means for balancing such mixed motives in dialogues, we introduce the concept of fairness defined as combination of fair-ness state and fairness maintenance process. Focusing on a dialogue between human and robot in a retailing scenario, we show the application of the SatIsficing Dialogue Engine (inSIDE) - a platform for assessing and maintaining fairness in dialogues with mixed motives.
Merging of vortices and antivortices in polariton superfluids
Creators: name: Cancellieri, Emiliano
name: Boulier, Thomas
name: Hivet, Romain
name: Ballarini, Dario
name: Sanvitto, Daniele
name: Szymanska, Marzena
name: Ciuti, Cristiano
name: Giacobino, Elisabeth
name: Bramati, Albeerto
Publisher: name: arXiv
Year: 2015
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: Quantised vortices are remarkable manifestations on a macroscopic scale of the coherent nature of quantum fluids, and the study of their properties is of fundamental importance for the understanding of this peculiar state of matter. Cavity-polaritons, due to their double light-matter nature, offer a unique controllable environment to investigate these properties. In this work we theoretically investigate the possibility to deterministically achieve the annihilation of a vortex with an antivortex through the increase of the polariton density in the region surrounding the vortices. Moreover we demonstrate that by means of this mechanism an array of vortex-antivortex pairs can be completely washed out.
Loud Cypriot Women: Reimagining Cypriot Identity Through a Feminist Lens
Creators: name: Efthymiou, Andreamarie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2021

description: As a woman growing up in a Greek Cypriot household in the United States, I am privy to Cypriot women’s narratives that the general American public has not heard and that Cypriots living in Cyprus may not realize are valuable. Cypriot collective memory, specifically spanning the years from the 1950’s to the 1980’s, has a gap where unfiltered Cypriot women’s lived experiences should be. These narratives have been stricken from the public narrative or altered before making up part of the Cypriot collective memory. As these were the years most salient to the formation of Cyprus’ national identity, the exclusion of women’s voices resulted in an identity that is dictated by and representative of men alone. Neither the causes nor the effects of this are isolated. A complicated colonial history yokes the Cypriot identity to politics. This colonial past continues to influence a Cypriot identity formation reliant on the acceptance of certain dichotomies like “Greek vs. Turk” and “Subject vs. Colonizer” that women’s experiences have the possibility to weaken. The result has been the systemic silencing of women’s experiences outside of the nationalist project, and the promotion of the stereotype of the opinionated and loud Cypriot woman who loudly expresses male-controlled narratives of nationalism and colonialism. The effects of this practice range in scale but not in importance. Cypriot women do not have an authentic voice within their own society; they are excluded from participation in Cypriot politics. Furthermore, Cypriot identity, as a result of being based on an incomplete history, has become monolithic and culturally and politically stagnant. By exploring these themes in literature produced by Cypriots, I will pinpoint what female narratives exist but are hidden from the public portrayal of Cypriot women and society, and how the inclusion and recognition of these narratives changes what it means to be Cypriot. The lived experiences of Cypriot women in Cypriot literature challenge the existing conception of Cypriot identity and all the political decisions portrayed as the rational steps towards the protecting this identity.
Supplementary Figure 3 from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity
Creators: name: Kauzlaric, Annamaria
name: Jang, Suk Min
name: Morchikh, Mehdi
name: Cassano, Marco
name: Evarist Planet
name: Monsef Benkirane
name: Trono, Didier
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Molecular Biology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Confidence sets for dynamic poverty indexes
Creators: name: D'Amico, Guglielmo
name: De Blasis, Riccardo
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Science Policy

description: In this study, we consider different poverty indexes in a dynamic framework where individuals change their rate of income randomly in time. The primary objective of this paper is to assess the accuracy of the approximation of the indexes that can be obtained by applying the strong law of large numbers to an economic system composed of an infinite number of agents. The main result is a multivariate central limit theorem for dynamic poverty measures, which is obtained applying the theory of U-statistics. We also show how to get the confidence sets for the considered dynamic indexes, which show the appropriateness of the model. An application to the Italian income data from 1998 to 2012 confirms the effectiveness of the considered approach and the possibility to determine the evolution of poverty and inequality in real economies.
Synchronization and phase redistribution in self-replicating populations of coupled oscillators and excitable elements
Creators: name: Yu, Wen
name: Wood, Kevin B.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: We study the dynamics of phase synchronization in growing populations of discrete phase oscillatory systems when the division process is coupled to the distribution of oscillator phases. Using mean field theory, linear stability analysis, and numerical simulations, we demonstrate that coupling between population growth and synchrony can lead to a wide range of dynamical behavior, including extinction of synchronized oscillations, the emergence of asynchronous states with unequal state (phase) distributions, bistability between oscillatory and asynchronous states or between two asynchronous states, a switch between continuous (supercritical) and discontinuous (subcritical) transitions, and modulation of the frequency of bulk oscillations.
description: 15 pages, 13 figures
The Effects of HIV-1 Transactivator of Transcription (Tat) and MJN110 on Motivated Behavior
Creators: name: Kolagani, Ramya
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2021

description: Human immunodeficiency virus (HIV)-1 is an inflammatory disease that disrupts central nervous system (CNS) function as viral proteins, such as transactivator of transcription (Tat), induce inflammatory responses leading to neuronal damage. This neurodegeneration translates to behavioral dysregulation such as motivational deficits which are commonly seen in HIV-1 infected individuals. With the emergence of the endocannabinoid (eCB) system as an area for therapeutics combatting neurodegenerative disorders, MJN110, a monoacylglycerol lipase (MAGL) inhibitor is evaluated in this study. In the present study, the effects of Tat and MJN110 treatment on motivated behavior were assessed in the doxycycline(DOX)-inducible Tat transgenic mouse model. An operant conditioning task was employed wherein mice learned to associate a nosepoke with a sucrose reward. To characterize motivation, breakpoints amongst other proxies for motivated behavior were analyzed. Although there were no significant differences or interactions between Genotype and Treatment on motivated behavior, we found that, on average, Tat(+) subjects appear more motivated than Tat(-) subjects. Additionally, MJN110 rescued neuronal damage in Tat(+) subjects but trended towards decreasing dendritic ultrastructural integrity in Tat(-) subjects. Interestingly, in MJN110-treated animals, lower levels of inflammation are associated with higher measures of motivated behavior and Tat(-) subjects display a correlation between lower levels of inflammation and higher measures of motivated behavior dependent on treatment duration. These contrasting trends suggest intrinsic differences between genotypes conversely modulating inflammatory response to MJN110 treatment. Future studies assessing immune tolerance due to chronic Tat exposure, over- enhancement of the eCB tone, and levels of differential pro-inflammatory protein expression in genotypes could elucidate these behavioral responses.
Three-dimensional foam flow resolved by fast X-ray tomographic microscopy
Creators: name: Raufaste, Christophe
name: Dollet, Benjamin
name: Mader, Kevin
name: Santucci, Stéphane
name: Mokso, Rajmund
Publisher: name: arXiv
Year: 2015
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Thanks to ultra fast and high resolution X-ray tomography, we managed to capture the evolution of the local structure of the bubble network of a 3D foam flowing around a sphere. As for the 2D foam flow around a circular obstacle, we observed an axisymmetric velocity field with a recirculation zone, and indications of a negative wake downstream the obstacle. The bubble deformations, quantified by a shape tensor, are smaller than in 2D, due to a purely 3D feature: the azimuthal bubble shape variation. Moreover, we were able to detect plastic rearrangements, characterized by the neighbor-swapping of four bubbles. Their spatial structure suggest that rearrangements are triggered when films faces get smaller than a characteristic area.
description: 5 pages, 5 figures
Toward a World Without Inhumanity: The United States, the International Criminal Court, and Promoting the Rule of Law
Creators: name: Fright, Lauryl
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2021
Subjects: International Criminal Court
international tribunal
Rule of law

description: In 2002, the United States un-signed the Rome Statute – which established the International Criminal Court (ICC), the world’s first standing international war crimes tribunal that investigates and tries alleged perpetrators of genocide, war crimes, crimes against humanity, and crimes of aggression. President Bush’s Under Secretary for Political Affairs, Marc Grossman, gave a speech that first outlined the reasons the U.S. unsigned. The speech then explained that although the U.S. agreed with the ICC’s objectives, it would rather promote the rule of law to achieve them. Grossman argued that rule of law systems are the best prevention mechanisms for genocide, war crimes, crimes against humanity, and crimes of aggression. 

This thesis decides whether the U.S. should reconsider joining the ICC by exploring whether the U.S.’ rule of law promotion approach is a viable alternative to joining the ICC. Should this approach demonstrate efficacy, there would be less impetus for the U.S. to reconsider joining the ICC than if this approach did not.

This thesis is organized similarly to Grossman’s speech in that Chapter 1 introduces the ICC and investigates and analyzes the reasons the U.S. un-signed the Rome Statute in order to determine whether these reasons are valid. Chapter 2 discusses types of rule of law systems and explores why the U.S. would believe that promoting the rule of law would be a viable method of combatting circumstances that may lead to genocide, war crimes, crimes against humanity, and crimes of aggression. Finally, Chapter 3 features a data analysis which helps to determine whether there is empirical evidence that rule of law systems offer better protection of and respect for human rights – and presumably do not participate in acts of genocide, war crimes, crimes against humanity, and crimes of aggression. Chapter 3 also issues recommendations for improving this area of research and a policy recommendation for the U.S. government. 

Until further research is conducted, this thesis recommends that the U.S. continue to promote the rule of law despite the fact that its reasons for un-signing the Rome Statute are unconvincing and the efficacy of U.S. rule of law promotion programs has yet to be determined. Based on Chapter 3’s data analysis, the U.S. has reason to believe that promoting the rule of law can aid, in at least some capacity, in the prevention of genocide, war crimes, crimes against humanity, and crimes of aggression.
An endemic–epidemic beta model for time series of infectious disease proportions
Creators: name: Lu, Junyi
name: Meyer, Sebastian
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Time series of proportions of infected patients or positive specimens are frequently encountered in disease control and prevention. Since proportions are bounded and often asymmetrically distributed, conventional Gaussian time series models only apply to suitably transformed proportions. Here we borrow both from beta regression and from the well-established HHH model for infectious disease counts to propose an endemic–epidemic beta model for proportion time series. It accommodates the asymmetric shape and heteroskedasticity of proportion distributions and is consistent for complementary proportions. Coefficients can be interpreted in terms of odds ratios. A multivariate formulation with spatial power-law weights enables the joint estimation of model parameters from multiple regions. In our application to a flu activity index in the USA, we find that the endemic–epidemic beta model provides a better fit than a seasonal ARIMA model for the logit-transformed proportions. Furthermore, a multivariate approach can improve regional forecasts and reduce model complexity in comparison to univariate beta models stratified by region.
Nonlocality with ultracold atoms in a lattice
Creators: name: Pelisson, S.
name: Pezzé, L.
name: Smerzi, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We sudy the creation of nonlocal states with ultracold atoms trapped in an optical lattice. We show that these states violate Bell inequality by measuring one- and two-body correlations. Our scheme only requires beam splitting operations and global phase shifts, and can be realized within the current technology, employing single-site addressing. This proposal paves the way to study multipartite nonlocality and entanglement in ultracold atomic systems.
description: 5 pages, 3 figures
Variation and Change of Hydro-Climatological Parameters in Iraq for the Period 1980-2019
Creators: name: Majeed, Husam T.
name: Mahmood, Dalia A.
name: Zahraa S. Mahdi
Publisher: name: Thai Society of Higher Education Institutes on Environment
Year: 2022
Subjects: Precipitation
Evaporation
Potential evaporation
Water storage
Aridity Index
Iraq

description: EnvironmentAsia, 15, 3, 14-24
Supplementary Figure 4 from KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity
Creators: name: Kauzlaric, Annamaria
name: Jang, Suk Min
name: Morchikh, Mehdi
name: Cassano, Marco
name: Evarist Planet
name: Monsef Benkirane
name: Trono, Didier
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Molecular Biology
subject: 60408 Genomics
subject: FOS: Biological sciences

description: KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.
Accumulation of Microplastics in the Freshwater Shrimp, Macrobrachium lanchesteri, from Khwae Noi Watershed in Western Thailand
Creators: name: Sampan Tongnunui
name: Treerat Sooksawat
name: Kohkaew, Ramil
name: Jiraporn Teampanpong
name: Amnuay Wattanakornsiri
Publisher: name: Thai Society of Higher Education Institutes on Environment
Year: 2022
Subjects: Freshwater shrimp
Ecosystem
Environmental pollutant
FT-IR
Plastic debris

description: EnvironmentAsia, 15, 3, 25-37