cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain.
Creators: name: Charlton, Sophy
name: Brace, Selina
name: Hajdinjak, Mateja
name: Kearney, Rebecca
name: Booth, Thomas
name: Reade, Hazel
name: Tripp, Jennifer A
name: Sayle, Kerry L
name: Grimm, Sonja B
name: Bello, Silvia M
name: Walker, Elizabeth A
name: Gilardet, Alexandre
name: East, Philip
name: Glocke, Isabelle
name: Larson, Greger
name: Higham, Tom
name: Stringer, Chris
name: Skoglund, Pontus
name: Barnes, Ian
name: Stevens, Rhiannon E
Publisher: name: The Francis Crick Institute
Year: 2022
Subjects: Tumour Biology
Genetics & Genomics
Genome Integrity & Repair
Chemical Biology & High Throughput
Infectious Disease
Ecology,Evolution & Ethology
Computational & Systems Biology

description: Genetic investigations of Upper Palaeolithic Europe have revealed a complex and transformative history of human population movements and ancestries, with evidence of several instances of genetic change across the European continent in the period following the Last Glacial Maximum (LGM). Concurrent with these genetic shifts, the post-LGM period is characterized by a series of significant climatic changes, population expansions and cultural diversification. Britain lies at the extreme northwest corner of post-LGM expansion and its earliest Late Glacial human occupation remains unclear. Here we present genetic data from Palaeolithic human individuals in the United Kingdom and the oldest human DNA thus far obtained from Britain or Ireland. We determine that a Late Upper Palaeolithic individual from Gough's Cave probably traced all its ancestry to Magdalenian-associated individuals closely related to those from sites such as El Mirón Cave, Spain, and Troisième Caverne in Goyet, Belgium. However, an individual from Kendrick's Cave shows no evidence of having ancestry related to the Gough's Cave individual. Instead, the Kendrick's Cave individual traces its ancestry to groups who expanded across Europe during the Late Glacial and are represented at sites such as Villabruna, Italy. Furthermore, the individuals differ not only in their genetic ancestry profiles but also in their mortuary practices and their diets and ecologies, as evidenced through stable isotope analyses. This finding mirrors patterns of dual genetic ancestry and admixture previously detected in Iberia but may suggest a more drastic genetic turnover in northwestern Europe than in the southwest.
EFSA ListeriaPredict Workshop Use of microbial risk assessment tools
Creators: name: Valero Antonio
Publisher: name: Zenodo
Year: 2023
Subjects: subject: Food safety
subject: Predictive microbiology
subject: Risk assessment
subject: http://id.agrisemantics.org/gacs/C1146

description: EFSA ListeriaPredict Workshop Use of microbial risk assessment tools - Presentations from the workshop, October 2022, University of Cordoba
description: Es;en;pdf;f.butler@ucd.ie
Multivalent interactions by the set8 histone methyltransferase with its nucleosome substrate
Creators: name: Tan, S.
name: Girish, T.S.
name: McGinty, R.K.
Publisher: name: Academic Press
Year: 2016

description: Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucleosome complex. Our studies indicate that Set8 employs its i-SET and c-SET domains to engage nucleosomal DNA 1 to 1.5 turns from the nucleosomal dyad and in doing so, it positions the SET domain for catalysis with H4 Lys20. Surprisingly, we find that a basic N-terminal extension to the SET domain plays an even more prominent role in nucleosome binding, possibly by making an arginine anchor interaction with the nucleosome H2A/H2B acidic patch. We further show that proliferating cell nuclear antigen and the nucleosome compete for binding to Set8 through this basic extension, suggesting a mechanism for how nucleosome binding protects Set8 from proliferating cell nuclear antigen-dependent degradation during the cell cycle.
The toggle group, homomesy, and the Razumov-Stroganov correspondence
Creators: name: Striker, Jessica
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: The Razumov-Stroganov correspondence, an important link between statistical physics and combinatorics proved in 2011 by L. Cantini and A. Sportiello, relates the ground state eigenvector of the O(1) dense loop model on a semi-infinite cylinder to a refined enumeration of fully-packed loops, which are in bijection with alternating sign matrices. This paper reformulates a key component of this proof in terms of posets, the toggle group, and homomesy, and proves two new homomesy results on general posets which we hope will have broader implications.
description: 14 pages, 10 figures, final version
The television policies of the British Labour Party 1951-2000
Creators: name: Freedman, Des
Publisher: name: University of Westminster
Year: 2000

description: This thesis provides an extended analysis of the television policies of the British Labour Party from 1951 up to the present day. It examines the evolution of Labour's television policy and focuses on the social, political and economic contexts in which policies were developed, the party forums in which policies were discussed and the consequences of these policies for British television as a whole. It evaluates the contrasting contributions to television policy made by the parliamentary leadership, the Labour left, the trade unions, and intellectuals sympathetic to the party. Although the Conservatives have been widely acknowledged to be responsible for the majority of innovations in British television, the thesis refutes the view that this is due to any lack of interest in television policy inside the Labour Party. Drawing on extensive archive material and interviews with key participants, it argues that the Labour Party has intervened in all the main debates concerning British broadcasting and has produced a wide range of proposals for the reform, modernisation and consolidation of television structures in the UK. The thesis examines the party's response to the development of commercial television in the 1950s and to the Pilkington Report in the early 1960s. It assesses the impact on television policy of the Labour governments in the 1960s and highlights the contribution of left-wing demands for television reform in the 1970s. The thesis then considers the government's response to the Annan Report at the end of the 1970s and analyses how the party responded to the Conservative government's reform of television in the following decade. The thesis concludes with an evaluation of the role of television in the emergence of New Labour and provides a critique of the current Labour government's record concerning television developments. The thesis suggests that divisions between rival interests in the Labour Party have undermined the possibility of a unified television policy. The result of these divisions has been that the leadership has marginalised innovative proposals for reform in favour of policies that have safeguarded the existing structures of and power relations in television.
Sampling for Inference in Probabilistic Models with Fast Bayesian Quadrature
Creators: name: Gunter, Tom
name: Osborne, Michael A.
name: Garnett, Roman
name: Hennig, Philipp
name: Roberts, Stephen J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: We propose a novel sampling framework for inference in probabilistic models: an active learning approach that converges more quickly (in wall-clock time) than Markov chain Monte Carlo (MCMC) benchmarks. The central challenge in probabilistic inference is numerical integration, to average over ensembles of models or unknown (hyper-)parameters (for example to compute the marginal likelihood or a partition function). MCMC has provided approaches to numerical integration that deliver state-of-the-art inference, but can suffer from sample inefficiency and poor convergence diagnostics. Bayesian quadrature techniques offer a model-based solution to such problems, but their uptake has been hindered by prohibitive computation costs. We introduce a warped model for probabilistic integrands (likelihoods) that are known to be non-negative, permitting a cheap active learning scheme to optimally select sample locations. Our algorithm is demonstrated to offer faster convergence (in seconds) relative to simple Monte Carlo and annealed importance sampling on both synthetic and real-world examples.
On the defect and stability of differential expansion
Creators: name: Kononov, Ya.
name: Morozov, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Geometric Topology (math.GT)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: Empirical analysis of many colored knot polynomials, made possible by recent computational advances in Chern-Simons theory, reveals their stability: for any given negative N and any given knot the set of coefficients of the polynomial in r-th symmetric representation does not change with r, if it is large enough. This fact reflects the non-trivial and previously unknown properties of the differential expansion, and it turns out that from this point of view there are universality classes of knots, characterized by a single integer, which we call defect, and which is in fact related to the power of Alexander polynomial.
description: 6 pages
R script for plot figure 2 & 3
Creators: name: Liu, Xiao-Ming
Publisher: name: figshare
Year: 2020
Subjects: subject: 40299 Geochemistry not elsewhere classified
subject: FOS: Earth and related environmental sciences

description: # R script for plot figures 2 and 3# of paper "A persistently low level of atmospheric oxygen in Earth's middle age"# by Xiaoming Liu et al., published on Nature communications
Additional file 1 of A methodological framework for evaluating transitions in acute care services in the Netherlands to achieve Triple Aim
Creators: name: Minderhout, Rosa Naomi
name: Numans, Mattijs E.
name: Vos, Hedwig M. M.
name: Bruijnzeels, Marc A.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1: Appendix A. Example of an integration meter questionnaire. This ‘Integration monitor care coordination’ was used in the Netherlands.
Webinar: How to conduct challenge test studies assessing growth potential or maximum growth rate
Creators: name: Iannetti, Luigi
Publisher: name: Zenodo
Year: 2023
Subjects: Listeria
challenge tests

description: Webinar presented on 25 May 2023 as part of the EFSA funded ListeriaPredict project entitled: How to conduct challenge test studies assessing growth potential or maximum growth rate
description: IT; en; pdf; f.butler@ucd.ie
Quantum Szilard engines with arbitrary spin
Creators: name: Zhuang, Zekun
name: Liang, Shi-Dong
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The quantum Szilard engine (QSZE) is a conceptual quantum engine for understanding the fundamental physics of quantum thermodynamics and information physics. We generalize the QSZE to an arbitrary spin case, i.e., a spin QSZE (SQSZE), and we systematically study the basic physical properties of both fermion and boson SQSZEs in a low-temperature approximation. We give the analytic formulation of the total work. For the fermion SQSZE, the work might be absorbed from the environment, and the change rate of the work with temperature exhibits periodicity and even-odd oscillation, which is a generalization of a spinless QSZE. It is interesting that the average absorbed work oscillates regularly and periodically in a large-number limit, which implies that the average absorbed work in a fermion SQSZE is neither an intensive quantity nor an extensive quantity. The phase diagrams of both fermion and boson SQSZEs give the SQSZE doing positive or negative work in the parameter space of the temperature and the particle number of the system, but they have different behaviors because the spin degrees of the fermion and the boson play different roles in their configuration states and corresponding statistical properties. The critical temperature of phase transition depends sensitively on the particle number. By using Landauer's erasure principle, we give the erasure work in a thermodynamic cycle, and we define an efficiency (we refer to it as information-work efficiency) to measure the engine's ability of utilizing information to extract work. We also give the conditions under which the maximum extracted work and highest information-work efficiencies for fermion and boson SQSZEs can be achieved.
description: 24 pages, 11 figures
A First Look at the X-ray Population of the Young Massive Cluster VVV CL077
Creators: name: Bodaghee, Arash
name: Tomsick, John A.
name: Fornasini, Francesca
name: Rahoui, Farid
name: Bauer, Franz E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Multi-wavelength analysis of the young massive cluster VVV CL077 is presented for the first time. Our Chandra survey of this region enabled the detection of three X-ray emitting stellar members of the cluster, as well as a possible diffuse X-ray component that extends a few arcseconds from the cluster core with an intrinsic flux of (9+/-3)x10^-14 erg cm^-2 s^-1 in the 0.5-10 keV band. Infrared spectra we obtained for two of these X-ray point sources show absorption lines typical of the atmospheres of massive O stars. The X-ray spectrum from the visible extent of VVV CL077 i.e., a 15"-radius around the cluster, can be modeled with an absorbed power law with nH = (6+/-4)x10^22 cm^-2 and gamma = 2+/-1. In addition, the X-ray core of VVV CL077 coincides with diffuse emission seen in the infrared band and with a local maximum in the radio continuum map. A possible association with a neighboring H II region would place VVV CL077 at a distance of around 11 kpc; on the far side of the Norma Arm. At this distance, the cluster is 0.8 pc wide with a mass density of (1-4)x10^3 Msol pc^-3.
description: accepted for publication in The Astrophysical Journal: 9 pages, 5 figures
FAIR Implementation Workshop: Support for Research Performing Organisations slide deck
Creators: name: Davidson, Joy
name: Meneses, Rita
Publisher: name: Zenodo
Year: 2023
Subjects: FAIR Implementation Workshop
FAIR-IMPACT
FAIR-enabling Research Performing Organisations Support Programme

description: These slides were presented during the FAIR Implementation Workshop to introduce the Support Programme for Research Performing Organsiations which took place on 28 August 2023. The results of the menti poll referenced in the slide deck have been uploaded as part of this submission as well. The event page is available at https://fair-impact.eu/events/fair-impact-events/fair-implementation-workshop-support-research-performing-organisations. Event description: Researchers play a key role in making their outputs findable, accessible, interoperable and reusable (FAIR) but equally the organisations who employ them, the funding bodies that financially support and influence the way they work, and the range of infrastructures that are used by researchers to create, share and curate their outputs also play critical roles. To help foster a FAIR ecosystem, FAIR-IMPACT will support representatives from research performing organisations to begin or progress their FAIR-enabling journeys. This support programme is geared toward those RPOs who are getting started on their FAIR-enabling journeys. FAIR-IMPACT will provide dedicated guidance and one-to-one support to successful applicants to self-assess their current capabilities and to develop FAIR implementation action plans. For more information on this support programme, see Route 1 on our open call webpage. FAIR-IMPACT delivered an hour long, virtual workshops to introduce the support programme for research performing organisations on August 28th. The session outlined the support that will be provided for research performing organisations, explained what is expected of participants, and provided an overview of the application process. There was time set aside for participants to have a chance to ask any practical questions about the support programmes. Registration for this webinar was free and open to all.
Association between alcoholic (poly)phenol-rich beverage consumption and cognitive status in older adults living in a Mediterranean area
Creators: name: Micek, Agnieszka
name: Alshatwi, Ali A.
name: Paladino, Nadia
name: Guerrera, Ida
name: Grosso, Giuseppe
name: Castellano, Sabrina
name: Godos, Justyna
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Neuroscience
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Mental Health

description: The prevalence of cognitive disorders is growing and evidence suggests the putative role of plant-based foods and beverages containing (poly)phenols. The aim of this study was to explore the association between the consumption of (poly)phenol-rich beverages, including wine and beer, resveratrol intake, and cognitive status in a cohort of older adults. The dietary intakes were assessed using a validated food frequency questionnaire, and cognitive status using the Short Portable Mental Status Questionnaire. Multivariate logistic regression analyses showed that individuals in the second and third tertile of red wine consumption were less likely to have cognitive impairment than those in the first tertile. In contrast, only individuals in the highest tertile of white wine intake were having lower odds of cognitive impairment. No significant results were found for beer intake. Individuals with higher resveratrol intake were less likely to have cognitive impairment. In conclusion, consumption of (poly)phenol-rich beverages may potentially affect cognition among older adults.
Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome
Creators: name: Tan, S.
name: Henrici, R.C.
name: McGinty, R.K.
Publisher: name: Nature Publishing Group
Year: 2014

description: The Polycomb group of epigenetic enzymes represses expression of developmentally regulated genes in many eukaryotes. This group includes the Polycomb repressive complex 1 (PRC1), which ubiquitylates nucleosomal histone H2A Lys 119 using its E3 ubiquitin ligase subunits, Ring1B and Bmi1, together with an E2 ubiquitin-conjugating enzyme, UbcH5c. However, the molecular mechanism of nucleosome substrate recognition by PRC1 or other chromatin enzymes is unclear. Here we present the crystal structure of the human Ring1B-Bmi1-UbcH5c E3-E2 complex (the PRC1 ubiquitylation module) bound to its nucleosome core particle substrate. The structure shows how a chromatin enzyme achieves substrate specificity by interacting with several nucleosome surfaces spatially distinct from the site of catalysis. Our structure further reveals an unexpected role for the ubiquitin E2 enzyme in substrate recognition, and provides insight into how the related histone H2A E3 ligase, BRCA1, interacts with and ubiquitylates the nucleosome.
Additional file 1 of EQ-5D-5L measurement properties are superior to EQ-5D-3L across the continuum of health using US value sets
Creators: name: Jiang, Ruixuan
name: Rand, Kim
name: Kuharic, Maja
name: Pickard, A. Simon
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Additional file 1. Triangular weighting function explanation.
Testing the Dark Matter Scenario for PeV Neutrinos Observed in IceCube
Creators: name: Murase, Kohta
name: Laha, Ranjan
name: Ando, Shin'ichiro
name: Ahlers, Markus
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Late time decay of very heavy dark matter is considered as one of the possible explanations for diffuse PeV neutrinos observed in IceCube. We consider implications of multimessenger constraints, and show that proposed models are marginally consistent with the diffuse gamma-ray background data. Critical tests are possible by a detailed analysis and identification of the sub-TeV isotropic diffuse gamma-ray data observed by Fermi and future observations of sub-PeV gamma rays by observatories like HAWC or Tibet AS+MD. In addition, with several-year observations by next-generation telescopes such as IceCube-Gen2, muon neutrino searches for nearby dark matter halos such as the Virgo cluster should allow us to rule out or support the dark matter models, independently of gamma-ray and anisotropy tests.
description: 6 pages, 4 figures, minor revision, published in PRL
Non Binary Local Gradient Contours for Face Recognition
Creators: name: Gubbi, Abdullah
name: Azeem, Mohammad Fazle
name: Kumari, M Sharmila
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: As the features from the traditional Local Binary Patterns (LBP) and Local Directional Patterns (LDP) are found to be ineffective for face recognition, we have proposed a new approach derived on the basis of Information sets whereby the loss of information that occurs during the binarization is eliminated. The information sets expand the scope of fuzzy sets by connecting the attribute and the corresponding membership function value as a product. Since face is having smooth texture in a limited area, the extracted features must be highly discernible. To limit the number of features, we consider only the non overlapping windows. By the application of the information set theory we can reduce the number of feature of an image. The derived features are shown to work fairly well over eigenface, fisherface and LBP methods.
description: 12 pages
Gut microbiota fermentation profiles of pre-digested mycoprotein (Quorn) using faecal batch cultures in vitro: a preliminary study
Creators: name: Cherta-Murillo, Anna
name: Danckert, Nathan P.
name: Valdivia-Garcia, Maria
name: Chambers, Edward S.
name: Roberts, Lauren
name: Miguens-Blanco, Jesus
name: McDonald, Julie A. K
name: Marchesi, Julien R.
name: Frost, Gary S.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Space Science
subject: Genetics
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: High-fibre diets are beneficial for many health outcomes via a wide range of mechanisms including gut microbiota fermentation-derived short-chain fatty acid (SCFAs) production. Mycoprotein (marketed as Quorn) is a food high in fibre (>6 g/100 g wet weight (ww)) and protein (13 g/100 g ww) which has been shown to have positive effects on glycemic control and appetite in humans. Nevertheless, the mechanisms underpinning this are poorly understood. Here, we investigate the changes in gut microbiota α- and β-diversity, pH and SCFAs production in faecal batch cultures supplemented with pre-digested mycoprotein (Quorn), soy, chicken and control (unsupplemented) using eight fresh stools from healthy donors. The results showed that pre-digested mycoprotein did not alter pH (p = .896), α- or β-diversity of the gut microbiota when compared to the control, soy, and chicken. Nevertheless, chicken led to a significant increase in total SCFAs post-24 h vs. control (+57.07 mmol/L, p = .01). In particular, propionate increased when compared to soy (+19.59 mmol/L, p = .03) and the control (+23.19 mmol/L, p < .01). No other differences in SCFAs were detected. In conclusion, pre-digested mycoprotein was not fermented in vitro by healthy gut microbiota in the settings of this experiment.
Super Fair Dominating Set in the Cartesian Product of Graphs
Creators: name: Gemina, Glenna T.
name: Enriquez, Enrico L.
Publisher: name: figshare
Year: 2020
Subjects: subject: 80204 Mathematical Software
subject: FOS: Computer and information sciences

description: In this paper, we characterize the super fair dominating set in the Cartesian product of two graphs and give some important results.
The n-SET Domain of Set1 Regulates H2B Ubiquitylation-Dependent H3K4 Methylation
Creators: name: Kim, J.-A.
name: Muir, T.W.
name: Kim, J.
name: Nguyen, U.T.T.
name: McGinty, R.K.
name: Roeder, R.G.
name: Allis, C.D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Past studies have documented a crosstalk between H2B ubiquitylation (H2Bub) and H3K4 methylation, but little (if any) direct evidence exists explaining the mechanism underlying H2Bub-dependent H3K4 methylation on chromatin templates. Here, we took advantage of an in vitro histone methyltransferase assay employing a reconstituted yeast Set1 complex (ySet1C) and a recombinant chromatin template containing fully ubiquitylated H2B to gain valuable insights. Combined with genetic analyses, we demonstrate that the n-SET domain within Set1, but not Swd2, is essential for H2Bub-dependent H3K4 methylation. Spp1, a homolog of human CFP1, is conditionally involved in this crosstalk. Our findings extend to the human Set1 complex, underscoring the conserved nature of this disease-relevant crosstalk pathway. As not all members of the H3K4 methyltransferase family contain n-SET domains, our studies draw attention to the n-SET domain as a predictor of an H2B ubiquitylation-sensing mechanism that leads to downstream H3K4 methylation.
Additional file 1 of Is primary health care ready for artificial intelligence? What do primary health care stakeholders say?
Creators: name: Terry, Amanda L.
name: Kueper, Jacqueline K.
name: Beleno, Ron
name: Brown, Judith Belle
name: Cejic, Sonny
name: Dang, Janet
name: Leger, Daniel
name: McKay, Scott
name: Meredith, Leslie
name: Pinto, Andrew D.
name: Ryan, Bridget L.
name: Stewart, Moira
name: Zwarenstein, Merrick
name: Lizotte, Daniel J.
Publisher: name: figshare
Year: 2022
Subjects: subject: Biotechnology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. Supplement: Additional Quotes by Theme.
Habitual adherence to a traditional Mediterranean diet and risk of SARS-CoV-2 infection and Coronavirus disease 2019 (COVID-19): a longitudinal analysis
Creators: name: Sharma, Sukshma
name: Di Castelnuovo, Augusto
name: Costanzo, Simona
name: Persichillo, Mariarosaria
name: Panzera, Teresa
name: Ruggiero, Emilia
name: De Curtis, Amalia
name: Storto, Marianna
name: Cavallo, Pierpaolo
name: Gianfagna, Francesco
name: Donati, Maria Benedetta
name: de Gaetano, Giovanni
name: Cerletti, Chiara
name: Iacoviello, Licia
name: Bonaccio, Marialaura
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Evidence on habitual Mediterranean diet (MD) and risk of SARS-CoV-2 infection, and COVID-19 is limited. 1,520 participants from the Moli-sani Study (2017-2020) were tested during January-September 2021 and adherence to MD was ascertained through the Mediterranean Diet Score (MDS). SARS-CoV-2 infection cases were determined through serology, and previous clinical diagnosis of COVID-19 disease was self-reported. Results were presented as odd ratios (OR) with 95% confidence intervals (CI). The MDS was not associated with the likelihood of SARS-CoV-2 infection (OR= 0.94; 95% CI: 0.83–1.06) and COVID-19 (OR= 0.82; 95% CI: 0.62–1.10) diagnosis. High consumption of cereals was associated with lower odds of SARS-CoV-2 infection (OR = 0.91; 95% CI: 0.83–1.00; for each 25 g/d increase). Likelihood of having being diagnosed with COVID-19 disease decreased in association with increasing olive oil intake (OR= 0.10; 95% CI: 0.01–0.79; for each additional 10 g/d), moderate alcohol consumption (OR= 0.18; 95% CI: 0.04–0.82) and higher intakes of fruits and nuts (OR = 0.89; 95% CI: 0.79–0.99). Our findings emphasise the adoption and maintenance of a balanced MD as a key strategy to reduce the risk of future SARS-CoV-2 infections and COVID-19.
Using radio jets of PKS J0334-3900 to probe the intra-cluster medium in A3135
Creators: name: Pratley, L.
name: Johnston-Hollitt, M.
name: Dehghan, S.
name: Sun, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present a multi-wavelength study of the radio galaxy PKS J0334-3900, which resides at the centre of Abell 3135. Using Australia Telescope Compact Array (ATCA) observations at 1.4, 2.5, 4.6 & 8.6 GHz, we performed a detailed analysis of PKS J0334-3900. The morphology and spectral indices give physical parameters that constrain the dynamical history of the galaxy, which we use to produce a simulation of PKS J0334-3900. This simulation shows that the morphology can be generated by a wind in the intracluster medium (ICM), orbital motion caused by a companion galaxy, and precession of the black hole (BH).
description: To appear in the Proceedings of the IAU Symposium No. 313: Extragalactic jets from every angle, Galapagos, Ecuador, 15-19 September 2014, F. Massaro, C. C. Cheung, E. Lopez, and A. Siemiginowska (Eds.), Cambridge University Press
Baryon Number Violation via Majorana Neutrinos in the Early Universe, at the LHC, and Deep Underground
Creators: name: Davoudiasl, Hooman
name: Zhang, Yue
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We propose and investigate a novel, minimal, and experimentally testable framework for baryogenesis, dubbed dexiogenesis, using baryon number violating effective interactions of right-handed Majorana neutrinos responsible for the seesaw mechanism. The distinct LHC signature of our framework is same-sign top quark final states, possibly originating from displaced vertices. The region of parameters relevant for LHC phenomenology can also yield concomitant signals in nucleon decay experiments. We provide a simple ultraviolet origin for our effective operators, by adding a color-triplet scalar, which could ultimately arise from a grand unified theory.
description: 5 pages, 3 figures. references and discussions added
A positive feedback loop mediates crosstalk between calcium, cyclic nucleotide and lipid signalling in calcium-induced Toxoplasma gondii egress.
Creators: name: Nofal, Stephanie D
name: Dominicus, Caia
name: Broncel, Malgorzata
name: Katris, Nicholas J
name: Flynn, Helen R
name: Arrizabalaga, Gustavo
name: Botté, Cyrille Y
name: Invergo, Brandon M
name: Treeck, Moritz
Publisher: name: The Francis Crick Institute
Year: 2022
Subjects: subject: Biochemistry & Proteomics
subject: Cell Biology
subject: Chemical Biology & High Throughput
subject: Infectious Disease
subject: Immunology
subject: FOS: Clinical medicine
subject: Computational & Systems Biology

description: Fundamental processes that govern the lytic cycle of the intracellular parasite Toxoplasma gondii are regulated by several signalling pathways. However, how these pathways are connected remains largely unknown. Here, we compare the phospho-signalling networks during Toxoplasma egress from its host cell by artificially raising cGMP or calcium levels. We show that both egress inducers trigger indistinguishable signalling responses and provide evidence for a positive feedback loop linking calcium and cyclic nucleotide signalling. Using WT and conditional knockout parasites of the non-essential calcium-dependent protein kinase 3 (CDPK3), which display a delay in calcium inonophore-mediated egress, we explore changes in phosphorylation and lipid signalling in sub-minute timecourses after inducing Ca2+ release. These studies indicate that cAMP and lipid metabolism are central to the feedback loop, which is partly dependent on CDPK3 and allows the parasite to respond faster to inducers of egress. Biochemical analysis of 4 phosphodiesterases (PDEs) identified in our phosphoproteomes establishes PDE2 as a cAMP-specific PDE which regulates Ca2+ induced egress in a CDPK3-independent manner. The other PDEs display dual hydrolytic activity and play no role in Ca2+ induced egress. In summary, we uncover a positive feedback loop that enhances signalling during egress, thereby linking several signalling pathways.
SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53
Creators: name: Roeder, R.G.
name: Tang, Z.
name: Kim, J.
name: Muir, T.W.
name: Sun, X.-J.
name: Shimada, M.
name: Chen, W.-Y.
name: Fernandez, J.P.
name: McGinty, R.K.
name: Sengoku, T.
name: Nguyen, U.T.T.
Publisher: name: Elsevier B.V.
Year: 2013

description: The H3K4me3 mark in chromatin is closely correlated with actively transcribed genes, although the mechanisms involved in its generation and function are not fully understood. In vitro studies with recombinant chromatin and purified human factors demonstrate a robust SET1 complex (SET1C)-mediated H3K4 trimethylation that is dependent upon p53- and p300-mediated H3 acetylation, a corresponding SET1C-mediated enhancement of p53- and p300-dependent transcription that reflects a primary effect of SET1C through H3K4 trimethylation, and direct SET1C-p53 and SET1C-p300 interactions indicative of a targeted recruitment mechanism. Complementary cell-based assays demonstrate a DNA-damage-induced p53-SET1C interaction, a corresponding enrichment of SET1C and H3K4me3 on a p53 target gene (p21/WAF1), and a corresponding codependency of H3K4 trimethylation and transcription upon p300 and SET1C. These results establish a mechanism in which SET1C and p300 act cooperatively, through direct interactions and coupled histone modifications, to facilitate the function of p53.
Diseño y planificación de la enseñanza online
Creators: name: López Torres, Ana María
name: Sein-Echaluce Lacleta, María Luisa
Publisher: name: Zenodo
Year: 2020
Subjects: Enseñanza online
Enseñanza virtual
e-learning

description: El curso "Diseño y planificación de la enseñanza online" se ha impartido del 14 al 20 de septiembre de 2020, en modalidad online, dentro del Programa de Formación del Profesorado 2020-2021 de la Universidad de Zaragoza. El objetivo de este curso es que los participantes sean capaces de crear y desarrollar actividades formativas en entornos virtuales acordes con el escenario de enseñanza online, donde las interacciones y herramientas presentan claras diferencias con las correspondientes a la enseñanza presencial. Este diseño debe ir más allá de la adaptación de las actividades presenciales mediante el uso de herramientas tecnológicas.
Histone monoubiquitylation position determines specificity and direction of enzymatic cross-talk with histone methyltransferases Dot1L and PRC2
Creators: name: Whitcomb, S.J.
name: McGinty, R.K.
name: Holt, M.
name: Fierzs, B.
name: Muir, T.W.
name: Allis, C.D.
name: Ito, T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: It is well established that chromatin is a destination for signal transduction, affecting many DNA-templated processes. Histone proteins in particular are extensively post-translationally modified. We are interested in how the complex repertoire of histone modifications is coordinately regulated to generate meaningful combinations of "marks" at physiologically relevant genomic locations. One important mechanism is "cross-talk" between pre-existing histone post-translational modifications and enzymes that subsequently add or remove modifications on chromatin. Here, we use chemically defined "designer" nucleosomes to investigate novel enzymatic cross-talk relationships between the most abundant histone ubiquitylation sites, H2AK119ub and H2BK120ub, and two important histone methyltransferases, Dot1L and PRC2. Although the presence of H2Bub in nucleosomes greatly stimulated Dot1L methylation of H3K79, we found that H2Aub did not influence Dot1L activity. In contrast, we show that H2Aub inhibited PRC2 methylation of H3K27, but H2Bub did not influence PRC2 activity. Taken together, these results highlight how the position of nucleosome monoubiquitylation affects the specificity and direction of cross-talk with enzymatic activities on chromatin.
Faith, fatherland and the politics of exile: the Irish press in mid-Victorian Britain
Creators: name: Mcnicholas, Anthony
Publisher: name: University of Westminster
Year: 2000

description: The subject of this study is the attempt to establish a press amid the Irish immigrants in mid-Victorian England. There had long been a notable Irish contribution to English journalism, and the first Irish papers to be printed in England had been founded soon after the Act of Union. The press of the 1860s was to be different, however. Earlier papers had been aimed at a small, political elite but the massive immigration following the Famine meant that there was now, potentially, a large reading public. It was a public which was defined to a great extent by two ideas, nationality and religion-in the parlance of the time, faith and fatherland. These two elements crucially shaped the responses of both the migrants and of the wider English society to each other. Where Irish life in England was organised, it was Catholic and the secular, nationalist journalists of this study, wrote for a community and within a social organisation which was confessional. They were also operating at this time, against a political background of increasing turbulence-which led as the decade progressed, to rebellion and repression and which saw both the last public execution in Britain and the deaths of civilians on the streets of London. The central question for the press of the migrants was how to produce and sustain newspapers in a hostile political environment, which were at the same time secular but operated within a system of distribution particularly sensitive to clerical control.
Meat or meatless meals at lunch and dinner – exploring the associated factors and transition between meals
Creators: name: Carvalho, Catarina
name: Severo, Milton
name: Correia, Daniela
name: Lopes, Carla
name: Torres, Duarte
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: This study aimed to explore the factors associated with the consumption of meat vs. meatless meals and to assess the applicability of a multi-state model to describe transitions between lunch and dinner. Fifteen thousand four hundred and eight main meals (lunch and dinner) from a sample of adults (18–84 years, n = 3852) from the Portuguese Food, Nutrition and Physical Activity Survey (IAN-AF 2015–2016) were categorised as meat, fish, ovolactovegetarian or snack. Adjusted generalised-mixed-effects models were used to explore the associations and a time-homogeneous Markov-multi-state model was applied to study the transitions. Women, older and higher educated individuals presented higher odds of consuming meatless meals and lower hazard of transitioning to meat in the following main meal. Strategies for replacing meat with more sustainable foods should be specific towards different population groups. Studying transitions across main meals, using multi-state models, can support the development of feasible, realistic and group-specific strategies to replace meat and promote dietary variety.
Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction
Creators: name: Bar-Dagan, M.
name: Chatterjee, C.
name: Fierz, B.
name: Muir, T.W.
name: McGinty, R.K.
name: Raleigh, D.P.
Publisher: name: Nature Publishing Group
Year: 2011

description: Regulation of chromatin structure involves histone posttranslational modifications that can modulate intrinsic properties of the chromatin fiber to change the chromatin state. We used chemically defined nucleosome arrays to demonstrate that H2B ubiquitylation (uH2B), a modification associated with transcription, interferes with chromatin compaction and leads to an open and biochemically accessible fiber conformation. Notably, these effects were specific for ubiquitin, as compaction of chromatin modified with a similar ubiquitin-sized protein, Hub1, was only weakly affected. Applying a fluorescence-based method, we found that uH2B acts through a mechanism distinct from H4 tail acetylation, a modification known to disrupt chromatin folding. Finally, incorporation of both uH2B and acetylated H4 resulted in synergistic inhibition of higher-order chromatin structure formation, possibly a result of their distinct modes of action.
Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions
Creators: name: McGinty, R.K.
name: Dou, Y.
name: Ueberheide, B.
name: Ruthenburg, A.J.
name: Yuen, M.
name: Milne, T.A.
name: Li, H.
name: Allis, C.D.
name: Muir, T.W.
name: Patel, D.J.
name: Dewell, S.
Publisher: name: Elsevier B.V.
Year: 2011

description: Little is known about how combinations of histone marks are interpreted at the level of nucleosomes. The second PHD finger of human BPTF is known to specifically recognize histone H3 when methylated on lysine 4 (H3K4me2/3). Here, we examine how additional heterotypic modifications influence BPTF binding. Using peptide surrogates, three acetyllysine ligands are indentified for a PHD-adjacent bromodomain in BPTF via systematic screening and biophysical characterization. Although the bromodomain displays limited discrimination among the three possible acetyllysines at the peptide level, marked selectivity is observed for only one of these sites, H4K16ac, in combination with H3K4me3 at the mononucleosome level. In support, these two histone marks constitute a unique trans-histone modification pattern that unambiguously resides within a single nucleosomal unit in human cells, and this module colocalizes with these marks in the genome. Together, our data call attention to nucleosomal patterning of covalent marks in dictating critical chromatin associations.
Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB
Creators: name: McGinty, R.K.
name: Fraterman, S.
name: De Ayala Alonso, A.G.
name: Müller, J.
name: Oktaba, K.
name: Ly-Hartig, N.
name: Muir, T.W.
name: Wilm, M.
name: Scheuermann, J.C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Polycomb group (PcG) proteins are transcriptional repressors that control processes ranging from the maintenance of cell fate decisions and stem cell pluripotency in animals to the control of flowering time in plants 1-6. In Drosophila, genetic studies identified more than 15 different PcG proteins that are required to repress homeotic (HOX) and other developmental regulator genes in cells where they must stay inactive 1,7,8. Biochemical analyses established that these PcG proteins exist in distinct multiprotein complexes that bind to and modify chromatin of target genes. Among those, Polycomb repressive complex 1 (PRC1) and the related dRing-associated factors (dRAF) complex contain an E3 ligase activity for monoubiquitination of histone H2A (refs 1-4). Here we show that the uncharacterized Drosophila PcG gene calypso encodes the ubiquitin carboxy-terminal hydrolase BAP1. Biochemically purified Calypso exists in a complex with the PcG protein ASX, and this complex, named Polycomb repressive deubiquitinase (PR-DUB), is bound at PcG target genes in Drosophila. Reconstituted recombinant Drosophila and human PR-DUB complexes remove monoubiquitin from H2A but not from H2B in nucleosomes. Drosophila mutants lacking PR-DUB show a strong increase in the levels of monoubiquitinated H2A. A mutation that disrupts the catalytic activity of Calypso, or absence of the ASX subunit abolishes H2A deubiquitination in vitro and HOX gene repression in vivo. Polycomb gene silencing may thus entail a dynamic balance between H2A ubiquitination by PRC1 and dRAF, and H2A deubiquitination by PR-DUB.
Additional file 1 of A community approach for pathogens and their arthropod vectors (ticks and fleas) in cats of sub-Saharan Africa
Creators: name: Madder, Maxime
name: Day, Michael
name: Schunack, Bettina
name: Fourie, Josephus
name: Labuschange, Michel
name: van der Westhuizen, Wouter
name: Johnson, Sherry
name: Githigia, Samuel Maina
name: Akande, Foluke Adedayo
name: Nzalawahe, Jahashi Saidi
name: Tayebwa, Dickson Stuart
name: Aschenborn, Ortwin
name: Marcondes, Mary
name: Heylen, Dieter
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1: Figure S1. Overview of the moments of sampling within the average seasonal variation in precipitation and temperature. Table S1. Different multiplex assays for the detection of tick- and flea-borne pathogens. Table S2. Accession numbers for tick and flea species identified. Table S3. Distribution of PCR signals allocated to an ectoparasite taxon (identification at genus level and more precise) in the infested cats of urban and rural areas. Table S4. Distribution of co-infested cats within the subpopulation of tick-infested cats. Table S5. Co-infestations by different flea species (identification at genus level and lower). Table S6. Co-infections in cat blood. Table S7. Co-infections in cat ticks. Table S8. Co-infections in cat fleas.