cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Bounds on the power of proofs and advice in general physical theories
Creators: name: Lee, Ciarán M.
name: Hoban, Matty J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum theory presents us with the tools for computational and communication advantages over classical theory. One approach to uncovering the source of these advantages is to determine how computation and communication power vary as quantum theory is replaced by other operationally-defined theories from a broad framework of such theories. Such investigations may reveal some of the key physical features required for powerful computation and communication. In this paper we investigate how simple physical principles bound the power of two different computational paradigms which combine computation and communication in a non-trivial fashion: computation with advice and interactive proof systems. We show that the existence of non-trivial dynamics in a theory implies a bound on the power of computation with advice. Moreover, we provide an explicit example of a theory with no non-trivial dynamics in which the power of computation with advice is unbounded. Finally we show that the power of simple interactive proof systems in theories where local measurements suffice for tomography is non-trivially bounded. This result provides a proof that QMA is contained in PP which does not make use of any uniquely quantum structure - such as the fact that observables correspond to self-adjoint operators - and thus may be of independent interest.
description: 19 pages, no figures. Title and presentation changed in response to referees' suggestions
Zika Virus: New Clinical Syndromes and Its Emergence in the Western Hemisphere
Creators: name: Diamond, Michael S.
name: Lazear, Helen M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Zika virus (ZIKV) had remained a relatively obscure flavivirus until a recent series of outbreaks accompanied by unexpectedly severe clinical complications brought this virus into the spotlight as causing an infection of global public health concern. In this review, we discuss the history and epidemiology of ZIKV infection, recent outbreaks in Oceania and the emergence of ZIKV in the Western Hemisphere, newly ascribed complications of ZIKV infection, including Guillain-Barré syndrome and microcephaly, potential interactions between ZIKV and dengue virus, and the prospects for the development of antiviral agents and vaccines.
Oedera virgata N. G. Bergh. 2018, comb. nov.
Creators: name: Bergh, Nicola G.
name: Bentley, Joanne
name: Verboom, George Anthony
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Asterales
Asteraceae
Oedera
Oedera virgata

description: 6. Oedera virgata (N.E.Br) N.G.Bergh, comb. nov.
 Basionym: Nestlera virgata Brown (1895: 25). Comborhiza virgata (N.E.Br.) Anderberg & Bremer (1991: 1070); Relhania tuberosa Bremer (1976a: 63).—Type: SOUTH AFRICA, on the Drakensberg, 6000–7000 ft, Evans 50 (K, holotype!; Z, isotype).
 Section V. Oedera sect. Calycinae N.G.Bergh, sect. nov.
 — Lapeirousia Thunberg (1800b: 163), nom. illeg., non Lapeyrousia Pourret (1788: 79). Peyrousea Candolle (1838b: 76), non Peyrousia Poirret (1826: 363).— Type species: Relhania calycina (Linnaeus f.) L’Héritier
 Type species: Oedera calycina (Linnaeus f.) N.G.Bergh (Relhania calycina (Linnaeus f.) L’Héritier)
 Diagnostic features: leaves acute to acuminate, frequently pungent, with involute margins, often with 3–9 abaxial veins; capitula solitary, (sub-) sessile, large; receptacle paleate.
 Description: sparsely branched, frequently resprouting shrublets, branches erect, closely leafy; leaves imbricate, erect, or erect to spreading, recurved in one species, alternate or decussate; leaves brittle, sometimes rigid, leaf margins involute; leaf adaxial surface concave, sparsely to densely white-woolly; leaf abaxial surface rounded, glabrous to deciduously tomentose, mid-ribbed or with 3–9 distinct raised nerves; leaf apices acute to acuminate, often pungent. Capitula solitary, sessile or very shortly pedunculate, terminal, often partly covered by upper leaves; large (involucre broad and long); receptacle paleate; rays 14–45; disc florets 25–250; cypselas hairy, more so on ray florets; pappus of short, lacerate free scales.
 Cytology: all examined species are diploids with 2n = 14 (Oe. decussata, Oe. pungens ssp. angustifolia, Oe. calycina ssp. calycina, Oe. calycina ssp. apiculata and Oe. speciosa; Bremer, 1976a).
description: Published as part of Bergh, Nicola G., Bentley, Joanne & Verboom, George Anthony, 2018, Classification of the Relhania generic group (Asteraceae, Gnaphalieae) revisited using molecular phylogenetic analysis, pp. 101-132 in Phytotaxa 344 (2) on page 119, DOI: 10.11646/phytotaxa.344.2.1, http://zenodo.org/record/13719571
Supplementary methods, figures, analyses, results, and discussion from Intertemporal choice reflects value comparison rather than self-control: insights from confidence judgements
Creators: name: Bulley, Adam
name: Lempert, Karolina M.
name: Conwell, Colin
name: Irish, Muireann
name: Schacter, Daniel L.
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology
subject: 60801 Animal Behaviour
subject: FOS: Biological sciences

description: Intertemporal decision-making has long been assumed to measure self-control, with prominent theories treating choices of smaller, sooner rewards as failed attempts to override immediate temptation. If this view is correct, people should be more confident in their intertemporal decisions when they ‘successfully’ delay gratification than when they do not. In two pre-registered experiments with built-in replication, adult participants (n = 117) made monetary intertemporal choices and rated their confidence in having made the right decisions. Contrary to assumptions of the self-control account, confidence was not higher when participants chose delayed rewards. Rather, participants were more confident in their decisions when possible rewards were further apart in time-discounted subjective value, closer to the present, and larger in magnitude. Demonstrating metacognitive insight, participants were more confident in decisions that better aligned with their separate valuation of possible rewards. Decisions made with less confidence were more prone to changes-of-mind and more susceptible to a patience-enhancing manipulation. Together, our results establish that confidence in intertemporal choice tracks uncertainty in estimating and comparing the value of possible rewards—just as it does in decisions unrelated to self-control. Our findings challenge self-control views and instead cast intertemporal choice as a form of value-based decision-making about future possibilities.This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Model derivation and additional results. from Our fragile future under the cumulative cultural evolution of two technologies
Creators: name: Efferson, Charles
name: Richerson, Peter J.
name: Weinberger, Vanessa
Publisher: name: The Royal Society
Year: 2023
Subjects: Ecology not elsewhere classified
Evolutionary Biology not elsewhere classified
Animal Behaviour

description: We derive and analyse a model with unusual features characterizing human activities over the long-run. First, human population dynamics draw heavily on consumer–resource modelling in ecology in that humans must consume biological resources to produce new humans. Second, the model also draws heavily from economic growth theory in that humans do not simply consume biological resources; they also produce the resources they consume. Finally, humans use two types of technology. Consumption technology affects the rate at which humans can extract resources. Production technology controls how effectively humans convert labour into new resources. The dynamics of both types of technology are subject to cumulative cultural evolutionary processes that allow both technological progress and regress. The resulting model exhibits a wide range of dynamical regimes. That said, the system is routinely sensitive to initial conditions, with wildly different outcomes given the same parameter values. Moreover, the system exhibits a basic fragility in the sense that human activities often lead to the endogenous extinction of the human species. This can happen gently, or it can follow periods of explosive human activity with super-exponential growth that ends in collapse.This article is part of the theme issue ‘Evolution and Sustainability: Gathering the strands for an Anthropocene synthesis’.
Additional file 1 of Clinical trial design in the era of precision medicine
Creators: name: Fountzilas, Elena
name: Tsimberidou, Apostolia M.
name: Vo, Henry Hiep
name: Kurzrock, Razelle
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Science Policy

description: Additional file 1. Selected first-generation precision medicine clinical trial designs (see also Tables 1 and 2). A basket trial is a tissue-agnostic study assessing one drug targeting a specific molecular alteration or pathway across multiple tumor type. An umbrella trial evaluates different treatments matched to molecular alterations in a single tumor type. Complete phase I trial enables comprehensive evaluation of a specific drug in different combination regimens. An octopus trial consists of multiple arms and investigates different combinations of a drug across multiple tumor types. Telescope trials allow seamless transition from phase I to phase II and/or phase III clinical trials, thus combining all phases, learning and confirmatory, into a single trial.
A Cytoplasmic RNA Virus Alters the Function of the Cell Splicing Protein SRSF2
Creators: name: Fritch, Ethan J.
name: Rivera-Serrano, Efraín E.
name: Scholl, Elizabeth H.
name: Sherry, Barbara
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: ABSTRACT To replicate efficiently, viruses must create favorable cell conditions and overcome cell antiviral responses. We previously reported that the reovirus protein μ2 from strain T1L, but not strain T3D, represses one antiviral response: alpha/beta interferon signaling. We report here that T1L, but not T3D, μ2 localizes to nuclear speckles, where it forms a complex with the mRNA splicing factor SRSF2 and alters its subnuclear localization. Reovirus replicates in cytoplasmic viral factories, and there is no evidence that reovirus genomic or messenger RNAs are spliced, suggesting that T1L μ2 might target splicing of cell RNAs. Indeed, RNA sequencing revealed that reovirus T1L, but not T3D, infection alters the splicing of transcripts for host genes involved in mRNA posttranscriptional modifications. Moreover, depletion of SRSF2 enhanced reovirus replication and cytopathic effect, suggesting that T1L μ2 modulation of splicing benefits the virus. This provides the first report of viral antagonism of the splicing factor SRSF2 and identifies the viral protein that determines strain-specific differences in cell RNA splicing. IMPORTANCE Efficient viral replication requires that the virus create favorable cell conditions. Many viruses accomplish this by repressing specific antiviral responses. We demonstrate here that some mammalian reoviruses, RNA viruses that replicate strictly in the cytoplasm, express a protein variant that localizes to nuclear speckles, where it targets a cell mRNA splicing factor. Infection with a reovirus strain that targets this splicing factor alters splicing of cell mRNAs involved in the maturation of many other cell mRNAs. Depletion of this cell splicing factor enhances reovirus replication and cytopathic effect. Our results provide the first evidence of viral antagonism of this splicing factor and suggest that downstream consequences to the cell are global and benefit the virus.
Features of Operation of the Ruris R-Power GE 1000 Generator Set
Creators: name: Popov, Stanislav
name: Levchenko, Yulia
name: Kharak, Ruslan
name: Basova, Yulia
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 400803
subject: Electrical energy generation (incl. renewables, excl. photovoltaics)

description: The materials consider the issue of the first start-up and running-in of an electric generator set.
Oedera decussata N. G. Bergh 2018, comb. nov.
Creators: name: Bergh, Nicola G.
name: Bentley, Joanne
name: Verboom, George Anthony
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Asterales
Asteraceae
Oedera
Oedera decussata

description: 7. Oedera decussata (L’Héritier) N.G.Bergh, comb. nov.
 Basionym: Relhania decussata L’Héritier (1789: 14).—Type: SOUTH AFRICA, “Promont. b. Spei”, Masson s.n. (BM, lectotype! [designated by Bremer 1976a]).
description: Published as part of Bergh, Nicola G., Bentley, Joanne & Verboom, George Anthony, 2018, Classification of the Relhania generic group (Asteraceae, Gnaphalieae) revisited using molecular phylogenetic analysis, pp. 101-132 in Phytotaxa 344 (2) on page 119, DOI: 10.11646/phytotaxa.344.2.1, http://zenodo.org/record/13719571
Transmission coefficient and two-fold degenerate discrete spectrum of spin-1 bosons in a double-step potential
Creators: name: de Oliveira, L. P.
name: de Castro, A. S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The scattering of spin-1 bosons in a nonminimal vector double-step potential is described in terms of eigenstates of the helicity operator and it is shown that the transmission coefficient is insensitive to the choice of the polarization of the incident beam. Poles of the transmission amplitude reveal the existence of a two-fold degenerate spectrum. The results are interpreted in terms of solutions of two coupled effective Schrödinger equations for a finite square well with additional $δ$-functions situated at the borders.
description: arXiv admin note: substantial text overlap with arXiv:1203.1195
Additional file 2 of Clinical trial design in the era of precision medicine
Creators: name: Fountzilas, Elena
name: Tsimberidou, Apostolia M.
name: Vo, Henry Hiep
name: Kurzrock, Razelle
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Science Policy

description: Additional file 2. Selected next-generation precision medicine clinical trial designs (see also Tables 1 and 2). An N-of-1 trial assesses different drugs evaluated in the same patient. N-of-1 trials are patient centered and every patient receives a different drug regimen. The strategy (algorithm) of drug assignment, rather than the drugs themselves, is evaluated. Home-based trials enable access to drugs for patients who are unable to travel and participate in traditional site-based clinical trials. In patient-reported outcome measures, patients directly reports data, often via digital devices, regarding their symptoms, treatment toxicities, or health-related quality of life. Registry trial provides a rich source of structured data including cancer incidence, patient demographics, treatment patterns, molecular profiling, and clinical outcomes. Real-world data enables collection of data in parallel and the assessment of efficacy and toxicity of treatment agents.
Characterizing HIV-1 Splicing by Using Next-Generation Sequencing
Creators: name: Zhou, Shuntai
name: Emery, Ann
name: Swanstrom, Ronald
name: Pollom, Elizabeth
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: ABSTRACT Full-length human immunodeficiency virus type 1 (HIV-1) RNA serves as the genome or as an mRNA, or this RNA undergoes splicing using four donors and 10 acceptors to create over 50 physiologically relevant transcripts in two size classes (1.8 kb and 4 kb). We developed an assay using Primer ID-tagged deep sequencing to quantify HIV-1 splicing. Using the lab strain NL4-3, we found that A5 ( env / nef ) is the most commonly used acceptor (about 50%) and A3 ( tat ) the least used (about 3%). Two small exons are made when a splice to acceptor A1 or A2 is followed by activation of donor D2 or D3, and the high-level use of D2 and D3 dramatically reduces the amount of vif and vpr transcripts. We observed distinct patterns of temperature sensitivity of splicing to acceptors A1 and A2. In addition, disruption of a conserved structure proximal to A1 caused a 10-fold reduction in all transcripts that utilized A1. Analysis of a panel of subtype B transmitted/founder viruses showed that splicing patterns are conserved, but with surprising variability of usage. A subtype C isolate was similar, while a simian immunodeficiency virus (SIV) isolate showed significant differences. We also observed transsplicing from a downstream donor on one transcript to an upstream acceptor on a different transcript, which we detected in 0.3% of 1.8-kb RNA reads. There were several examples of splicing suppression when the env intron was retained in the 4-kb size class. These results demonstrate the utility of this assay and identify new examples of HIV-1 splicing regulation. IMPORTANCE During HIV-1 replication, over 50 conserved spliced RNA variants are generated. The splicing assay described here uses new developments in deep-sequencing technology combined with Primer ID-tagged cDNA primers to efficiently quantify HIV-1 splicing at a depth that allows even low-frequency splice variants to be monitored. We have used this assay to examine several features of HIV-1 splicing and to identify new examples of different mechanisms of regulation of these splicing patterns. This splicing assay can be used to explore in detail how HIV-1 splicing is regulated and, with moderate throughput, could be used to screen for structural elements, small molecules, and host factors that alter these relatively conserved splicing patterns.
Improvement on Asymptotic Density of Packing Families Derived from Multiplicative Lattices
Creators: name: Cheng, Shantian
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: Information Theory (cs.IT)
subject: Algebraic Geometry (math.AG)
subject: Metric Geometry (math.MG)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 52C17, 11R58, 94B65, 14H05

description: Let $ω=(-1+\sqrt{-3})/2$. For any lattice $P\subseteq \mathbb{Z}^n$, $\mathcal{P}=P+ωP$ is a subgroup of $\mathcal{O}_K^n$, where $\mathcal{O}_K=\mathbb{Z}[ω]\subseteq \mathbb{C}$. As $\mathbb{C}$ is naturally isomorphic to $\mathbb{R}^2$, $\mathcal{P}$ can be regarded as a lattice in $\mathbb{R}^{2n}$. Let $P$ be a multiplicative lattice (principal lattice or congruence lattice) introduced by Rosenbloom and Tsfasman. We concatenate a family of special codes with $t_{\mathfrak{P}}^\ell\cdot(P+ωP)$, where $t_{\mathfrak{P}}$ is the generator of a prime ideal $\mathfrak{P}$ of $\mathcal{O}_K$. Applying this concatenation to a family of principal lattices, we obtain a new family with asymptotic density exponent $λ\geqslant-1.26532182283$, which is better than $-1.87$ given by Rosenbloom and Tsfasman considering only principal lattice families. For a new family based on congruence lattices, the result is $λ\geqslant -1.26532181404$, which is better than $-1.39$ by considering only congruence lattice families.
What even is a Research Infrastructure, anyway? How RIs like DARIAH enable and lift up researchers
Creators: name: Gray, Edward
Publisher: name: Zenodo
Year: 2023
Subjects: research infrastructure
DARIAH-EU
Slovakia

description: Researchers are busy people, torn between various professional duties (administration, teaching, research, work travel). They are by necessity ruthlessly efficient in time management, having to make judgements on what helps them reach the various impending deadlines which they face on a weekly basis. In this charged atmosphere, which is only exacerbated by the cycle of chasing after grant money and limited-term project funding, research infrastructures (RIs) can pass by unseen and underutilized, due to lack of familiarity. Indeed, like any infrastructure, it is often only seen when it is not working. This talk will propose an introduction to why researchers should dedicate their precious time to understand what RIs have to offer, using concrete examples of how DARIAH-EU helps lift up SSH researchers, providing a Europe-wide platform for cutting-edge tools, knowledge-exchange, and networking that enable ground-breaking research.
Oedera pungens N. G. Bergh 2018, comb. nov.
Creators: name: Bergh, Nicola G.
name: Bentley, Joanne
name: Verboom, George Anthony
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Asterales
Asteraceae
Oedera
Oedera pungens

description: 8. Oedera pungens (L’Héritier) N.G.Bergh, comb. nov.
 Basionym: Relhania pungens L’Héritier (1789: 14).—Type: SOUTH AFRICA, “Promont. b. Spei”, Masson s.n. (BM, lectotype! [designated by Bremer 1976a]).
description: Published as part of Bergh, Nicola G., Bentley, Joanne & Verboom, George Anthony, 2018, Classification of the Relhania generic group (Asteraceae, Gnaphalieae) revisited using molecular phylogenetic analysis, pp. 101-132 in Phytotaxa 344 (2) on page 120, DOI: 10.11646/phytotaxa.344.2.1, http://zenodo.org/record/13719571
Lebesgue measure of escaping sets of entire functions of completely regular growth
Creators: name: Bergweiler, Walter
name: Chyzhykov, Igor
Publisher: name: arXiv
Year: 2015
Subjects: subject: Complex Variables (math.CV)
subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics
subject: 37F10, 30D05, 30D15

description: We give conditions ensuring that the Julia set and the escaping set of an entire function of completely regular growth have positive Lebesgue measure. The essential hypotheses are that the indicator is positive except perhaps at isolated points and that most zeros are located in neighborhoods of finitely many rays. We apply the result to solutions of linear differential equations.
description: 27 pages; Theorem 1.5 and its proof revised; some overall revision
Thermal evolution of the Schwinger model with Matrix Product Operators
Creators: name: Bañuls, M. C.
name: Cichy, K.
name: Cirac, J. I.
name: Jansen, K.
name: Saito, H.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We demonstrate the suitability of tensor network techniques for describing the thermal evolution of lattice gauge theories. As a benchmark case, we have studied the temperature dependence of the chiral condensate in the Schwinger model, using matrix product operators to approximate the thermal equilibrium states for finite system sizes with non-zero lattice spacings. We show how these techniques allow for reliable extrapolations in bond dimension, step width, system size and lattice spacing, and for a systematic estimation and control of all error sources involved in the calculation. The reached values of the lattice spacing are small enough to capture the most challenging region of high temperatures and the final results are consistent with the analytical prediction by Sachs and Wipf over a broad temperature range.
description: 6 pages, 11 figures
Cytomegalovirus Late Protein pUL31 Alters Pre-rRNA Expression and Nuclear Organization during Infection
Creators: name: Moorman, Nathaniel J.
name: Westdorp, Kristen N.
name: Sand, Andrea
name: Terhune, Scott S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: ABSTRACT The replication cycle of human cytomegalovirus (CMV) leads to drastic reorganization of domains in the host cell nucleus. However, the mechanisms involved and how these domains contribute to infection are not well understood. Our recent studies defining the CMV-induced nuclear proteome identified several viral proteins of unknown functions, including a protein encoded by the UL31 gene. We set out to define the role of UL31 in CMV replication. UL31 is predicted to encode a 74-kDa protein, referred to as pUL31, containing a bipartite nuclear localization signal, an intrinsically disordered region overlapping arginine-rich motifs, and a C-terminal dUTPase-like structure. We observed that pUL31 is expressed with true late kinetics and is localized to nucleolin-containing nuclear domains. However, pUL31 is excluded from the viral nuclear replication center. Nucleolin is a marker of nucleoli, which are membrane-less regions involved in regulating ribosome biosynthesis and cellular stress responses. Other CMV proteins associate with nucleoli, and we demonstrate that pUL31 specifically interacts with the viral protein, pUL76. Coexpression of both proteins altered pUL31 localization and nucleolar organization. During infection, pUL31 colocalizes with nucleolin but not the transcriptional activator, UBF. In the absence of pUL31, CMV fails to reorganize nucleolin and UBF and exhibits a replication defect at a low multiplicity of infection. Finally, we observed that pUL31 is necessary and sufficient to reduce pre-rRNA levels, and this was dependent on the dUTPase-like motif in pUL31. Our studies demonstrate that CMV pUL31 functions in regulating nucleolar biology and contributes to the reorganization of nucleoli during infection. IMPORTANCE Nucleolar biology is important during CMV infection with the nucleolar protein, with nucleolin playing a role in maintaining the architecture of the viral nuclear replication center. However, the extent of CMV-mediated regulation of nucleolar biology is not well established. Proteins within nucleoli regulate ribosome biosynthesis and p53-dependent cellular stress responses that are capable of inducing cell cycle arrest and/or apoptosis, and they are proposed targets for cancer therapies. This study establishes that CMV protein pUL31 is necessary and sufficient to regulate nucleolar biology involving the reorganization of nucleolar proteins. Understanding these processes will help define approaches to stimulate cellular intrinsic stress responses that are capable of inhibiting CMV infection.
CINECA First recommendations for implementation in IT Framework (Incl. a Data Management Plan) D7.3
Creators: name: Goisauf, Melanie
name: Feriol, Lisa
name: Rial-Sebbag, Emmanuelle
Publisher: name: Zenodo
Year: 2022
Subjects: ELSI
Ethical
Legal
Privacy
Data sharing
GDPR

description: Health data collected in cohort studies are valuable sources for knowledge generation and the advance of biomedical research. However, the use of these data for research projects beyond the initial purpose raises several ethical, legal, technical, and societal questions. This deliverable addresses these challenges regarding reuse of health/genomic data in CINECA from the ethical, legal, and societal issues (ELSI) perspective and in the light of Open Science and FAIR principles. In responding to the requirements for an appropriate IT and governance framework for CINECA and beyond, the research presented in this document builds on a review of GDPR provisions and their institutional sources of interpretation as well as national laws, the corresponding legal, ethical, and social science literature, as well as stakeholder engagement workshops with patient representatives, African researchers, and co-creative exercises with CINECA technical experts. The core of this deliverable are the ethical and legal recommendations that take societal implications into account for data access to European, Canadian, and African cohorts. The recommendations address four key areas: (1) Engagement and benefit sharing as prerequisites for data sharing, (2) Informed consent and reuse of data, (3) Safeguards and respect for privacy, and (4) Further uses and data-access. The deliverable concludes with an outlook on relevant projects such as the European Health Data Space (EHDS) and upcoming ELSI developments regarding data reuse and artificial intelligence (AI).
title: New Pier (NWS-2021-486-WRD, Seattle Parks and Rec)
titleType: AlternativeTitle
title: Endangered Species Act Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for Seattle Parks and Recreation’s Leschi South Marina Wave Attenuator and Public Access Facility Improvements Project, King County, Washington (USACE No. NWS-2021-486-WRD, HUC: 171100120400 – Lake Washington)
Creators: name: United States. National Marine Fisheries Service. West Coast Region
Publisher: name: United States. National Marine Fisheries Service. West Coast Region
Year: 2023

description: WCRO-2021-01428
Dynamical coupled-channels model of $K^- p$ reactions (II): Extraction of $Λ^*$ and $Σ^*$ hyperon resonances
Creators: name: Kamano, H.
name: Nakamura, S. X.
name: Lee, T. -S. H.
name: Sato, T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Nuclear Theory (nucl-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: Resonance parameters (pole masses and residues) associated with the excited states of hyperons, Lambda^* and Sigma^*, are extracted within a dynamical coupled-channels model developed recently by us [Phys. Rev. C 90, 065204 (2014)] through a comprehensive partial-wave analysis of the K^- p --> barK N, pi Sigma, pi Lambda, eta Lambda, K Xi data up to invariant mass W = 2.1 GeV. We confirm the existence of resonances corresponding to most, if not all, of the four-star resonances rated by the Particle Data Group. We also find several new resonances, and in particular propose a possible existence of a new narrow J^P=3/2^+ Lambda resonance that couples strongly to the eta Lambda channel. The J^P=1/2^- Lambda resonances located below the barK N threshold are also discussed. Comparing our extracted pole masses with the ones from a recent analysis by the Kent State University group, some significant differences in the extracted resonance parameters are found, suggesting the need of more extensive and accurate data of K^- p reactions including polarization observables to eliminate such an analysis dependence of the resonance parameters. In addition, the determined large branching ratios of the decays of high-mass resonances to the pi Sigma^* and barK^* N channels also suggest the importance of the data of 2 --> 3 reactions such as K^- p --> pi pi Lambda and K^- p --> pi barK N. Experiments on measuring cross sections and polarization observables of these fundamental reactions are highly desirable at hadron beam facilities such as J-PARC for establishing the Lambda^* and Sigma^* spectrum.
description: 25 pages, 8 figures. Version to appear in Physical Review C
title: BOEM Research Project: Frying Pan Shoals NC, Ecosystem Dynamics
titleType: AlternativeTitle
title: National Marine Fisheries Service Endangered Species Act Section 7 Biological And Conference Opinion Biological Opinion and Conference on the Bureau of Ocean Energy Management’s Proposal to Fund a Study on Shoal Ecosystem Dynamics at Frying Pan Shoals, North Carolina
Creators: name: United States. National Marine Fisheries Service. Office of Protected Resources
Publisher: name: United States. National Marine Fisheries Service. Office of Protected Resources
Year: 2023

description: OPR-2023-00400
Hyperscaling violating black holes in scalar-torsion theories
Creators: name: Kofinas, Georgios
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study a gravity theory where a scalar field with potential, beyond its minimal coupling, is also coupled through a non-minimal derivative coupling with the torsion scalar which is the teleparallel equivalent of Einstein gravity. This theory provides second order equations of motion and we find large-distance non-perturbative static spherically symmetric four-dimensional solutions. Among them a general class of black hole solutions is found for some range of the parameters/integration constants with asymptotics of the form of hyperscaling violating Lifshitz spacetime with spherical horizon topology. Although the scalar field diverges at the horizon, its energy density and pressures are finite there. From the astrophysical point of view, this solution provides extra deflection of light compared to the Newtonian deflection.
description: Version to appear in Phys. Rev. D
Local Interactions and the Emergence of a Twitter Small-World Network
Creators: name: Ch'ng, Eugene
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The small-world phenomenon is found in many self-organising systems. Systems configured in small-world networks spread information more easily than in random or regular lattice-type networks. Whilst it is a known fact that small-world networks have short average path length and high clustering coefficient in self-organising systems, the ego centralities that maintain the cohesiveness of small-world network have not been formally defined. Here we show that instantaneous events such as the release of news items via Twitter, coupled with active community arguments related to the news item form a particular type of small-world network. Analysis of the centralities in the network reveals that community arguments maintain the small-world network whilst actively maintaining the cohesiveness and boundary of the group. The results demonstrate how an active Twitter community unconsciously forms a small-world network whilst interacting locally with a bordering community. Over time, such local interactions brought about the global emergence of the small-world network, connecting media channels with human activities. Understanding the small-world phenomenon in relation to online social or civic movement is important, as evident in the spate of online activists that tipped the power of governments for the better or worst in recent times. The support, or removal of high centrality nodes in such networks has important ramifications in the self-expression of society and civic discourses. The presentation in this article anticipates further exploration of man-made self-organising systems where a larger cluster of ad-hoc and active community maintains the overall cohesiveness of the network.
description: Ch'ng E. (2015) Local Interactions and the Emergence and Maintenance of a Twitter Small-World Network, Social Networking 4(2), p.33-40
title: NPDES Permit for Dworshak Dam
titleType: AlternativeTitle
title: Endangered Species Act Section 7(a)(2) Biological Opinion and Magnuson–Stevens Fishery Conservation and Management Act Essential Fish Habitat Response for the National Pollutant Discharge Elimination System permit for Dworshak Dam, U.S. Army Corps of Engineers, Permit No. ID0028568
Creators: name: United States. National Marine Fisheries Service. West Coast Region
Publisher: name: United States. National Marine Fisheries Service. West Coast Region
Year: 2023

description: WCRO-2022-03050
Mispricing chasing, market competition and hedge fund performance
Creators: name: Ma, Tianyi
Publisher: name: Loughborough University
Year: 2020
Subjects: Other commerce, management, tourism and services not elsewhere classified

description: This thesis investigates the impact of market competition on hedge fund performance over hedge funds’ lifecycle and their market mispricing chasing behaviour. There has been a rapid growth in hedge funds in recent decades. Hedge Fund Research, Inc. estimates that the total capital in the hedge fund industry amounted to almost $3.235 trillion globally in 2018, with over 10,000 active hedge funds. In comparison there were only 1,200 hedge funds managing $200 billion in 1997. As the hedge fund market becomes more competitive, there has been growing interest from both academia and investors in how hedge funds deliver a superior performance under increasing market competition. In this thesis, we first examine the effect of market competition on the hedge fund lifecycle performance from several different perspectives, including (a) timeseries market competition effect on hedge funds’ inception and failure; and (b) crosssectional market competition, to assess individual hedge fund performance. Furthermore, to investigate the hedge fund managers’ mispricing chasing behaviour under market competition, we employ the mispricing timing skills models to measure the hedge fund manager’s market mispricing timing skills in the equity market and fixed income market. In addition, we introduce a fund classification model to classify individual funds into different types in terms of their mispricing timing skills. The empirical findings of this thesis show that market competition in the timesseries analysis induces more hedge fund inception and hedge fund failure. In addition, market competition subsequently leads to superior hedge fund overall performance in the early stages of the hedge fund lifecycle. However, a cross-sectional market competition will decrease the individual hedge funds’ overall performance, together with several other factors, including hedge fund age, hedge funds’ risk-taking preference and hedge fund market co-movement. Finally, we also find that hedge fund managers can time the stock market mispricing and bond market mispricing opportunities by adjusting their market exposure during the underpriced and undervalued market periods.
Oedera pungens subsp. trinervis Bremer 1976
Creators: name: Bergh, Nicola G.
name: Bentley, Joanne
name: Verboom, George Anthony
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Asterales
Asteraceae
Oedera
Oedera pungens
Oedera pungens (l'Héritier) n.g.bergh subsp. trinervis (thunberg) bremer (1976a: 70)

description: 8b. Oedera pungens (L’Héritier) N.G.Bergh subsp. trinervis (Thunberg) Bremer (1976a: 70)
 Basionym: Relhania trinervis Thunberg (1800b: 146).—Type: Thunberg, Herb. No. 20104 (UPS–THUNB lectotype [designated by Bremer 1976a]).
description: Published as part of Bergh, Nicola G., Bentley, Joanne & Verboom, George Anthony, 2018, Classification of the Relhania generic group (Asteraceae, Gnaphalieae) revisited using molecular phylogenetic analysis, pp. 101-132 in Phytotaxa 344 (2) on page 120, DOI: 10.11646/phytotaxa.344.2.1, http://zenodo.org/record/13719571
Bi-layer Kinetic Inductance Detectors for space observations between 80-120 GHz
Creators: name: Catalano, A.
name: Goupy, J.
name: Sueur, H. le
name: Benoit, A.
name: Bourrion, O.
name: Calvo, M.
name: Dumoulin, L.
name: Levy-Bertrand, F.
name: Macìas-Pérez, J.
name: Marnieros, S.
name: Ponthieu, N.
name: Monfardini, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences
subject: 85

description: We have developed Lumped Element Kinetic Inductance Detectors (LEKID) sensitive in the frequency band from 80 to 120~GHz. In this work, we take advantage of the so-called proximity effect to reduce the superconducting gap of Aluminium, otherwise strongly suppressing the LEKID response for frequencies smaller than 100~GHz. We have designed, produced and optically tested various fully multiplexed arrays based on multi-layers combinations of Aluminium (Al) and Titanium (Ti). Their sensitivities have been measured using a dedicated closed-circle 100 mK dilution cryostat and a sky simulator allowing to reproduce realistic observation conditions. The spectral response has been characterised with a Martin-Puplett interferometer up to THz frequencies, and with a resolution of 3~GHz. We demonstrate that Ti-Al LEKID can reach an optical sensitivity of about $1.4$ $10^{-17}$~$W/Hz^{0.5}$ (best pixel), or $2.2$ $10^{-17}$~$W/Hz^{0.5}$ when averaged over the whole array. The optical background was set to roughly 0.4~pW per pixel, typical for future space observatories in this particular band. The performance is close to a sensitivity of twice the CMB photon noise limit at 100~GHz which drove the design of the Planck HFI instrument. This figure remains the baseline for the next generation of millimetre-wave space satellites.
description: 7 pages, 9 figures, submitted to A&A
Additional file 1 of Distance is “a big problem”: a geographic analysis of reported and modelled proximity to maternal health services in Ghana
Creators: name: Dotse-Gborgbortsi, Winfred
name: Nilsen, Kristine
name: Ofosu, Anthony
name: Matthews, Zoë
name: Tejedor-Garavito, Natalia
name: Wright, Jim
name: Tatem, Andrew J.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy

description: Additional file 1.
One- and Two-Point Codes over Kummer Extensions
Creators: name: Masuda, Ariane M.
name: Quoos, Luciane
name: Sepúlveda, Alonso
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics

description: We compute the Weierstrass semigroup at one totally ramified place for Kummer extensions defined by $y^m=f(x)^λ$ where $f(x)$ is a separable polynomial over $\mathbb{F}_q$. In addition, we compute the Weierstrass semigroup at two certain totally ramified places. We then apply our results to construct one- and two-point algebraic geometric codes with good parameters.
description: Some corrections were made. Final version to appear in the IEEE Transactions on Information Theory
Expression of the Antisense-to-Latency Transcript Long Noncoding RNA in Kaposi's Sarcoma-Associated Herpesvirus
Creators: name: Dittmer, Dirk P.
name: Kelkar, Hemant
name: Schifano, Jason M.
name: Corcoran, Kathleen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: ABSTRACT The regulation of latency is central to herpesvirus biology. Recent transcriptome-wide surveys have uncovered evidence for promiscuous transcription across the entirety of the Kaposi's sarcoma-associated herpesvirus (KSHV) genome and postulated the existence of multiple viral long noncoding RNAs (lncRNAs). Next-generation sequencing studies are highly dependent on the specific experimental approach and particular algorithms of analysis and therefore benefit from independent confirmation of the results. The antisense-to-latency transcript (ALT) lncRNA was discovered by genome-tiling microarray (Chandriani et al., J Virol 86:7934–7942, 2010, https://doi.org/10.1128/JVI.00645-10 ). To characterize ALT in detail, we physically isolated this lncRNA by a strand-specific hybrid capture assay and then employed transcriptome sequencing and novel reverse transcription-PCR (RT-PCR) assays to distinguish all RNA species in the KSHV latency region. These methods confirm that ALT initiates at positions 120739/121012 and encodes a single splice site, which is shared with the 3′-coterminal K14-vGPCR/ORF74 mRNA, terminating at 130873 (GenBank accession number GQ994935 ), resulting in an ∼10,000-nucleotide transcript. No shorter ALT isoforms were identified. This study also identified a novel intron within the LANA 5′ untranslated region using a splice acceptor at 127888. In summary, ALT joins PAN/nut1/T1.1 as a bona fide lncRNA of KSHV with potentially important roles in viral gene regulation and pathogenesis. IMPORTANCE Increasing data support the importance of noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and lncRNAs, which have been shown to exert critical regulatory functions without coding for recognizable proteins. Defining the sequences of these ncRNAs is essential for future studies aiming to functionally characterize a specific ncRNA. Most lncRNA studies are highly dependent on high-throughput sequencing and bioinformatic analyses, few studies follow up on the initial predictions, and analyses are at times discordant. The manuscript characterizes one key viral lncRNA, ALT, by physically isolating ALT and by a sequencing-independent assay. It provides for a simple assay to monitor lncRNA expression in experimental and clinical samples. ALT is expressed antisense to the major viral latency transcripts encoding LANA as well as the viral miRNAs and thus has the potential to regulate this key part of the viral life cycle.
Oedera pungens subsp. angustifolia Bremer 1976
Creators: name: Bergh, Nicola G.
name: Bentley, Joanne
name: Verboom, George Anthony
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Asterales
Asteraceae
Oedera
Oedera pungens
Oedera pungens (l'Héritier) n.g.bergh subsp. angustifolia (candolle) bremer (1976a: 70)

description: 8c. Oedera pungens (L’Héritier) N.G.Bergh subsp. angustifolia (Candolle) Bremer (1976a: 70)
 Basionym: Eclopes parallelinervis Lessing var. angustifolia Candolle (1838a: 289).— Type: SOUTH AFRICA, Eastern Cape, between Omsamcaba and Omsamwubo, 1835. Drège 4993 (G-DC, holotype!; P!, W, isotypes).
description: Published as part of Bergh, Nicola G., Bentley, Joanne & Verboom, George Anthony, 2018, Classification of the Relhania generic group (Asteraceae, Gnaphalieae) revisited using molecular phylogenetic analysis, pp. 101-132 in Phytotaxa 344 (2) on page 120, DOI: 10.11646/phytotaxa.344.2.1, http://zenodo.org/record/13719571
A Fast and Accurate Universal Kepler Solver without Stumpff Series
Creators: name: Wisdom, Jack
name: Hernandez, David M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We derive and present a fast and accurate solution of the initial value problem for Keplerian motion in universal variables that does not use the Stumpff series. We find that it performs better than methods based on the Stumpff series.
description: 10 pages, 7 figures. Accepted by MNRAS, resubmitted because of a typo in the title, added author affiliations