cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Human cytomegalovirus pTRS1 stimulates cap-independent translation
Creators: name: Vincent, Heather A.
name: Ziehr, Benjamin
name: Moorman, Nathaniel J.
name: Lenarcic, Erik M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description: Human cytomegalovirus (HCMV) manipulates multiple cellular processes to facilitate virus replication, including the control of mRNA translation. We previously showed that the HCMV TRS1 protein (pTRS1) promotes cap-dependent mRNA translation independent of its ability to antagonize the antiviral protein PKR. Here we find that pTRS1 enhances internal ribosome entry site (IRES) activity using a novel circular RNA reporter that lacks an mRNA cap and poly(A) tail. Additionally, pTRS1 expression increases the activity of cellular IRESs that control the expression of proteins needed for efficient HCMV replication. We find that the ability of pTRS1 to enhance cap-independent translation is separable from its ability to antagonize PKR, but requires the pTRS1 RNA binding domain. Together these data show that pTRS1 stimulates cap-independent translation and suggest a role for pTRS1 in alternative translation initiation pathways during HCMV infection.
Complexity of Anticipated Rejection Algorithms and the Darling-Mandelbrot Distribution
Creators: name: Bacher, Axel
name: Sportiello, Andrea
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: Probability (math.PR)
subject: FOS: Mathematics

description: We study in limit law the complexity of some anticipated rejection random sampling algorithms. We express this complexity in terms of a probabilistic process, the threshold sum process. We show that, under the right conditions, the complexity is linear and admits as a limit law a so-called Darling-Mandelbrot distribution, studied by Darling (Trans Am Math Soc 73:95-107, 1952) and Lew (Constr Approx 10(1):15-30, 1994). We also give an explicit form to the density of the Darling-Mandelbrot distribution and derive some of its analytic properties.
description: 20 pages. Using Algorithmica LaTeX style
The Ex Vivo Treatment of Donor T Cells with Cosalane, an HIV Therapeutic and Small-Molecule Antagonist of CC-Chemokine Receptor 7, Separates Acute Graft-versus-Host Disease from Graft-versus-Leukemia Responses in Murine Hematopoietic Stem Cell Transplantation Models
Creators: name: Whitehurst, Christopher
name: Moorman, Nathaniel J.
name: Coghill, James M.
name: Li, Kelin
name: Bruce, Danny W.
name: Fowler, Kenneth A.
name: Aube, Jeffrey
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description: Despite recent advances in therapy, allogeneic hematopoietic stem cell transplantation (HSCT) remains the only curative option for a range of high-risk hematologic malignancies. However, acute graft-versus-host disease (aGVHD) continues to limit the long-term success of HSCT, and new therapies are still needed. We previously demonstrated that aGVHD depends on the ability of donor conventional T cells (Tcon s) to express the lymph node trafficking receptor, CC-Chemokine Receptor 7 (CCR7). Consequently, we examined the ability of cosalane, a recently identified CCR7 small-molecule antagonist, to attenuate aGVHD in mouse HSCT model systems. Here we show that the systemic administration of cosalane to transplant recipients after allogeneic HSCT did not prevent aGVHD. However, we were able to significantly reduce aGVHD by briefly incubating donor Tcons with cosalane ex vivo before transplantation. Cosalane did not result in Tcon toxicity and did not affect their activation or expansion. Instead, cosalane prevented donor Tcon trafficking into host secondary lymphoid tissues very early after transplantation and limited their subsequent accumulation within the liver and colon. Cosalane did not appear to impair the intrinsic ability of donor Tcon s to produce inflammatory cytokines. Furthermore, cosalane-treated Tcon s retained their graft-versus-leukemia (GVL) potential and rejected a murine P815 inoculum after transplantation. Collectively, our data indicate that a brief application of cosalane to donor Tcon s before HSCT significantly reduces aGVHD in relevant preclinical models while generally sparing beneficial GVL effects, and that cosalane might represent a viable new approach for aGVHD prophylaxis.
Additional file 5 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels
Creators: name: Hodel, Flavia
name: Naret, Olivier
name: Bonnet, Clara
name: Brenner, Nicole
name: Bender, Noemi
name: Waterboer, Tim
name: Marques-Vidal, Pedro
name: Vollenweider, Peter
name: Fellay, Jacques
Publisher: name: figshare
Year: 2022
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 5: Fig. S5. Polygenic risk score for hs-CRP (CRP-PRS) was significantly associated with hs-CRP levels. Scatter plots with linear regression line of polygenic risk scores predicting hs-CRP levels for individuals in the cohort. 95% confidence interval is showed in grey shade.
Federated Analytics: A survey
Creators: name: Elkordy, Ahmed Roushdy
name: Ezzeldin, Yahya H.
name: Han, Shanshan
name: Sharma, Shantanu
name: He, Chaoyang
name: Mehrotra, Sharad
name: Avestimehr, Salman
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Federated analytics (FA) is a privacy-preserving framework for computing data analytics over multiple remote parties (e.g., mobile devices) or silo-ed institutional entities (e.g., hospitals, banks) without sharing the data among parties. Motivated by the practical use cases of federated analytics, we follow a systematic discussion on federated analytics in this article. In particular, we discuss the unique characteristics of federated analytics and how it differs from federated learning. We also explore a wide range of FA queries and discuss various existing solutions and potential use case applications for different FA queries.
description: To appear in APSIPA Transactions on Signal and Information Processing, Volume 12, Issue 1
GSK2801, a BAZ2/BRD9 bromodomain inhibitor, synergizes with BET inhibitors to induce apoptosis in triple-negative breast cancer
Creators: name: Moorman, Nathaniel J.
name: Beltran, Adriana
name: Santos, Charlene M.
name: Hale, Andrew
name: Angus, Steven P.
name: Olivares-Quintero, Jose F.
name: Johnson, Gary L.
name: Zawistowski, Jon S.
name: Stuhlmiller, Timothy
name: Rashid, Naim U.
name: Golitz, Brian T.
name: Sciaky, Noah
name: Singh, Darshan
name: Bevill, Samantha M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description: Screening of an inhibitor library targeting kinases and epigenetic regulators identified several molecules having antiproliferative synergy with extraterminal domain (BET) bromodomain (BD) inhibitors (JQ1, OTX015) in triplenegative breast cancer (TNBC). GSK2801, an inhibitor of BAZ2A/B BDs, of the imitation switch chromatin remodeling complexes, and BRD9, of the SWI/SNF complex, demonstrated synergy independent of BRD4 control of P-TEFb- mediated pause-release of RNA polymerase II. GSK2801 or RNAi knockdown of BAZ2A/B with JQ1 selectively displaced BRD2 at promoters/enhancers of ETS-regulated genes. Additional displacement of BRD2 from rDNA in the nucleolus coincided with decreased 45S rRNA, revealing a function of BRD2 in regulating RNA polymerase I transcription. In 2D cultures, enhanced displacement of BRD2 from chromatin by combination drug treatment induced senescence. In spheroid cultures, combination treatment induced cleaved caspase-3 and cleaved PARP characteristic of apoptosis in tumor cells. Thus, GSK2801 blocks BRD2-driven transcription in combination with BET inhibitor and induces apoptosis of TNBC.
Distinguishing Neutrino Mass Hierarchies using Dark Matter Annihilation Signals at IceCube
Creators: name: Allahverdi, Rouzbeh
name: Dutta, Bhaskar
name: Ghosh, Dilip Kumar
name: Knockel, Bradley
name: Saha, Ipsita
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We explore the possibility of distinguishing neutrino mass hierarchies through the neutrino signal from dark matter annihilation at neutrino telescopes. We consider a simple extension of the standard model where the neutrino masses and mixing angles are obtained via the type-II seesaw mechanism as an explicit example. We show that future extensions of IceCube neutrino telescope may detect the neutrino signal from DM annihilation at the Galactic Center and inside the Sun, and differentiate between the normal and inverted mass hierarchies, in this model.
description: 19 pages, 7 captioned figures, minor changes in text, typos are fixed, version accepted in JCAP
Local energy balance, specific heats and the Oberbeck-Boussinesq approximation
Creators: name: Barletta, A.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: A thermodynamic argument is proposed in order to discuss the most appropriate form of the local energy balance equation within the Oberbeck-Boussinesq approximation. The study is devoted to establish the correct thermodynamic property to be used in order to express the relationship between the change of internal energy and the temperature change. It is noted that, if the fluid is a perfect gas, this property must be identified with the specific heat at constant volume. If the fluid is a liquid, a definitely reliable approximation identifies this thermodynamic property with the specific heat at constant pressure. No explicit pressure work term must be present in the energy balance. The reasoning is extended to the case of fluid saturated porous media.
description: 14 pages, 2 figures, 1 table, submitted for publication
Mitochondrial Protease ClpP is a Target for the Anticancer Compounds ONC201 and Related Analogues
Creators: name: Gilbert, Thomas S. K.
name: Lockett, Matthew R.
name: Fennell, Emily M. J.
name: Hale, Andrew E.
name: Ashamalla, Hani
name: East, Michael P.
name: Herring, Laura E.
name: Graves, Paul R.
name: Moorman, Nathaniel J.
name: Iwanowicz, Edwin J.
name: Holmuhamedov, Ekhson
name: McDonald, Ian M.
name: Karanewsky, Donald S.
name: Graves, Adam C.
name: Dicheva, Nedyalka
name: Graves, Lee M.
name: Aponte-Collazo, Lucas J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2019

description: ONC201 is a first-in-class imipridone molecule currently in clinical trials for the treatment of multiple cancers. Despite enormous clinical potential, the mechanism of action is controversial. To investigate the mechanism of ONC201 and identify compounds with improved potency, we tested a series of novel ONC201 analogues (TR compounds) for effects on cell viability and stress responses in breast and other cancer models. The TR compounds were found to be ∼50-100 times more potent at inhibiting cell proliferation and inducing the integrated stress response protein ATF4 than ONC201. Using immobilized TR compounds, we identified the human mitochondrial caseinolytic protease P (ClpP) as a specific binding protein by mass spectrometry. Affinity chromatography/drug competition assays showed that the TR compounds bound ClpP with ∼10-fold higher affinity compared to ONC201. Importantly, we found that the peptidase activity of recombinant ClpP was strongly activated by ONC201 and the TR compounds in a dose- and time-dependent manner with the TR compounds displaying a ∼10-100 fold increase in potency over ONC201. Finally, siRNA knockdown of ClpP in SUM159 cells reduced the response to ONC201 and the TR compounds, including induction of CHOP, loss of the mitochondrial proteins (TFAM, TUFM), and the cytostatic effects of these compounds. Thus, we report that ClpP directly binds ONC201 and the related TR compounds and is an important biological target for this class of molecules. Moreover, these studies provide, for the first time, a biochemical basis for the difference in efficacy between ONC201 and the TR compounds.
Additional file 6 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels
Creators: name: Hodel, Flavia
name: Naret, Olivier
name: Bonnet, Clara
name: Brenner, Nicole
name: Bender, Noemi
name: Waterboer, Tim
name: Marques-Vidal, Pedro
name: Vollenweider, Peter
name: Fellay, Jacques
Publisher: name: figshare
Year: 2022
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 6: Fig. S6. Seroprevalence of tested antigens in the CoLaus|PsyCoLaus. List of the 27 antigens available from the CoLaus|PsyCoLaus study that are shared with the UK Biobank. The percentages indicate the seroprevalence of antibodies against infectious disease antigens tested using Multiplex Serology platform. The grey boxes indicate the pathogen on which the antigen protein is found, and the family to which the pathogen belongs.
Exact dipolar moments of a localized electric current distribution
Creators: name: Fernandez-Corbaton, Ivan
name: Nanz, Stefan
name: Alaee, Rasoul
name: Rockstuhl, Carsten
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: The multipolar decomposition of current distributions is used in many branches of physics. Here, we obtain new exact expressions for the dipolar moments of a localized electric current distribution. The typical integrals for the dipole moments of electromagnetically small sources are recovered as the lowest order terms of the new expressions in a series expansion with respect to the size of the source. All the higher order terms can be easily obtained. We also provide exact and approximated expressions for dipoles that radiate a definite polarization handedness (helicity). Formally, the new exact expressions are only marginally more complex than their lowest order approximations.
T-duality, Non-geometry and Lie Algebroids in Heterotic Double Field Theory
Creators: name: Blumenhagen, Ralph
name: Sun, Rui
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: A number of issues in heterotic double field theory are studied. This includes the analysis of the T-dual configurations of a flat constant gauge flux background, which turn out to be non-geometric. Performing a field redefinition to a non-geometric frame, these T-duals take a very simple form reminiscent of the constant Q- and R-flux backgrounds. In addition, it is shown how the analysis of arXiv:1304.2784 generalizes to heterotic generalized geometry. For every field redefinition specified by an O(D,D+n) transformation, the structure of the resulting supergravity action is governed by the differential geometry of a corresponding Lie algebroid.
description: 27 pages, 1 figure, v2: refs added
The Flux-Scaling Scenario: De Sitter Uplift and Axion Inflation
Creators: name: Blumenhagen, Ralph
name: Damian, Cesar
name: Font, Anamaria
name: Herschmann, Daniela
name: Sun, Rui
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Non-geometric flux-scaling vacua provide promising starting points to realize axion monodromy inflation via the F-term scalar potential. We show that these vacua can be uplifted to Minkowski and de Sitter by adding an anti D3-brane or a D-term containing geometric and non-geometric fluxes. These uplifted non-supersymmetric models are analyzed with respect to their potential to realize axion monodromy inflation self-consistently. Admitting rational values of the fluxes, we construct examples with the required hierarchy of mass scales.
description: 30 pages, 7 figures, v2: refs added
MTORC2 activity disrupts lysosome acidification in systemic lupus erythematosus by impairing caspase-1 cleavage of Rab39a
Creators: name: Moorman, Nathaniel J.
name: Claiborne, Tauris M.
name: Vincent, Heather A.
name: Vilen, Barbara J.
name: Jacobson, Ken
name: Kang, SunAh
name: Li, Patrick
name: Monteith, Andrew J.
name: Rajfur, Zenon
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2018

description: Lysosomes maintain immune homeostasis through the degradation of phagocytosed apoptotic debris; however, the signaling events regulating lysosomal maturation remain undefined. In this study, we show that lysosome acidification, key to the maturation process, relies on mTOR complex 2 (mTORC2), activation of caspase-1, and cleavage of Rab39a. Mechanistically, the localization of cofilin to the phagosome recruits caspase-11, which results in the localized activation of caspase-1. Caspase-1 subsequently cleaves Rab39a on the phagosomal membrane, promoting lysosome acidification. Although caspase-1 is critical for lysosome acidification, its activation is independent of inflammasomes and cell death mediated by apoptosis-associated speck-like protein containing a caspase recruitment domain, revealing a role beyond pyroptosis. In lupus-prone murine macrophages, chronic mTORC2 activity decouples the signaling pathway, leaving Rab39a intact. As a result, the lysosome does not acidify, and degradation is impaired, thereby heightening the burden of immune complexes that activate FcgRI and sustain mTORC2 activity. This feedforward loop promotes chronic immune activation, leading to multiple lupus-associated pathologies. In summary, these findings identify the key molecules in a previously unappreciated signaling pathway that promote lysosome acidification. It also shows that this pathway is disrupted in systemic lupus erythematosus.
Nonperturbative comparison of clover and HISQ quarks in lattice QCD and the properties of the phi meson
Creators: name: Chakraborty, Bipasha
name: Davies, C. T. H.
name: Donald, G. C.
name: Koponen, J.
name: Lepage, G. P.
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We compare correlators for pseudoscalar and vector mesons made from valence strange quarks using the clover quark and highly improved staggered quark (HISQ) formalisms in full lattice QCD. We use fully nonperturbative methods to normalise vector and axial vector current operators made from HISQ quarks, clover quarks and from combining HISQ and clover fields. This allows us to test expectations for the renormalisation factors based on perturbative QCD, with implications for the error budget of lattice QCD calculations of the matrix elements of clover-staggered $b$-light weak currents, as well as further HISQ calculations of the hadronic vacuum polarisation. We also compare the approach to the (same) continuum limit in clover and HISQ formalisms for the mass and decay constant of the $ϕ$ meson. Our final results for these parameters, using single-meson correlators and neglecting quark-line disconnected diagrams are: $m_ϕ =$ 1.023(6) GeV and $f_ϕ = $ 0.238(3) GeV in good agreement with experiment. The results come from calculations in the HISQ formalism using gluon fields that include the effect of $u$, $d$, $s$ and $c$ quarks in the sea with three lattice spacing values and $m_{u/d}$ values going down to the physical point.
description: 21 pages, 11 figures. Version published by Phys.Rev.D. Minor changes to text. HISQ Z_V value derived in Appendix B for a=0.06fm lattices changed slightly
Quantum entanglement of dark matter
Creators: name: Lee, Jae-Weon
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We suggest that the dark matter in the universe has quantum entanglement if the dark matter is a Bose-Einstein condensation of ultra-light scalar particles. In this theory, any two regions of a galaxy are quantum entangled due to the quantum nature of the condensate. We calculate the entanglement entropy of a typical galactic halo, which turns out to be at least $O(ln(M/m))$, where $M$ is the mass of the halo and $m$ is the mass of a dark matter particle. The entanglement can be inferred from the rotation curves of the galaxy or the interference patterns of the dark matter density.
Multilinear compressive sensing and an application to convolutional linear networks
Creators: name: Malgouyres, François
name: Landsberg, Joseph
Publisher: name: arXiv
Year: 2017
Subjects: subject: Optimization and Control (math.OC)
subject: Artificial Intelligence (cs.AI)
subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: We study a deep linear network endowed with a structure. It takes the form of a matrix $X$ obtained by multiplying $K$ matrices (called factors and corresponding to the action of the layers). The action of each layer (i.e. a factor) is obtained by applying a fixed linear operator to a vector of parameters satisfying a constraint. The number of layers is not limited. Assuming that $X$ is given and factors have been estimated, the error between the product of the estimated factors and $X$ (i.e. the reconstruction error) is either the statistical or the empirical risk. In this paper, we provide necessary and sufficient conditions on the network topology under which a stability property holds. The stability property requires that the error on the parameters defining the factors (i.e. the stability of the recovered parameters) scales linearly with the reconstruction error (i.e. the risk). Therefore, under these conditions on the network topology, any successful learning task leads to stably defined features and therefore interpretable layers/network.In order to do so, we first evaluate how the Segre embedding and its inverse distort distances. Then, we show that any deep structured linear network can be cast as a generic multilinear problem (that uses the Segre embedding). This is the {\em tensorial lifting}. Using the tensorial lifting, we provide necessary and sufficient conditions for the identifiability of the factors (up to a scale rearrangement). We finally provide the necessary and sufficient condition called \NSPlong~(because of the analogy with the usual Null Space Property in the compressed sensing framework) which guarantees that the stability property holds. We illustrate the theory with a practical example where the deep structured linear network is a convolutional linear network. As expected, the conditions are rather strong but not empty. A simple test on the network topology can be implemented to test if the condition holds.
Muon g-2 in Focus Point SUSY
Creators: name: Harigaya, Keisuke
name: Yanagida, Tsutomu T.
name: Yokozaki, Norimi
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We point out that the anomaly of the muon $g-2$ can be easily explained in a focus point supersymmetry scenario, which realizes the semi-natural supersymmetry. Among known focus point supersymmetry scenarios, we find that a model based on Higgs-gaugino mediation works with a mild fine-tuning $Δ=40$-$80$. We propose two new focus point supersymmetry scenarios where the anomaly of the muon $g-2$ is also explained. These scenarios are variants of the widely known focus point supersymmetry based on gravity mediation with universal scalar masses.
description: 24 pages, 5 figures
Additional file 7 of The combined impact of persistent infections and human genetic variation on C-reactive protein levels
Creators: name: Hodel, Flavia
name: Naret, Olivier
name: Bonnet, Clara
name: Brenner, Nicole
name: Bender, Noemi
name: Waterboer, Tim
name: Marques-Vidal, Pedro
name: Vollenweider, Peter
name: Fellay, Jacques
Publisher: name: figshare
Year: 2022
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 7: Fig. S7. Seroprevalence of tested antigens in the UK Biobank. List of the 27 antigens available from the UK Biobank that are shared with the CoLaus|PsyCoLaus study. The percentages indicate the seroprevalence of antibodies against infectious disease antigens tested using Multiplex Serology platform. The grey boxes indicate the pathogen on which the antigen protein is found, and the family to which the pathogen belongs.
Bäcklund transformations for the Camassa-Holm equation
Creators: name: Rasin, Alexander G.
name: Schiff, Jeremy
Publisher: name: arXiv
Year: 2015
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The Bäcklund transformation (BT) for the Camassa-Holm (CH) equation is presented and discussed. Unlike the vast majority of BTs studied in the past, for CH the transformation acts on both the dependent and (one of) the independent variables. Superposition principles are given for the action of double BTs on the variables of the CH and the potential CH equations. Applications of the BT and its superposition principles are presented, specifically the construction of travelling wave solutions, a new method to construct multi-soliton, multi-cuspon and soliton-cuspon solutions, and a derivation of generating functions for the local symmetries and conservation laws of the CH hierarchy.
title: Enriching, Empowering, and Future-proofing: The benefits of Linked (Open) Data for archives
Creators: name: Hawkins, Ashleigh
Publisher: name: University of Liverpool Repository
Year: 2024

description: Since the early 2000s, there has been an explosion in the amount of archives and archival data available digitally. From online collections of digitised archives to exponentially increasing volumes of born-digital records, and digital data describing archives in catalogues, archival metadata aggregators, and other finding aids, the amount of digital data relating to archives increases daily. While archival processes have been revolutionised in response to technological developments, methods for the provision of access to such digital archives and archival data has failed to keep pace with these changes. Recent scholarship has shown the potential of Linked (Open) Data (L(O)D) to overcome some of the challenges associated with the increasing digitisation and datafication of archives. Existing research into the publication of archival L(O)D has predominately focused on individual projects detailing technological aspects of the process of producing and publishing L(O)D; the benefits that L(O)D can bring to the archives sector remain little understood. This thesis fills that gap in archival studies scholarship by exploring how archive services and their users can benefit from increased engagement with archival L(O)D. Taking a Constructivist Grounded Theory approach, this thesis articulates a comprehensive, coherent, and evidence-based understanding of the benefits of L(O)D. It provides a chronological account of archival L(O)D activity and identifies three core areas of benefit: enriching archival data, empowering users, and future-proofing the archives sector. Through analysis of L(O)D against the backdrop of current approaches to archival digitisation and datafication, and the growing FAIR movement, it problematises these benefits by interrogating the extent to which current archival practices are inhibiting wide-spread adoption of L(O)D. This analysis suggests the necessity for increased collaboration with Digital Humanities scholars and the Wikimedia Movement, essential to scaling up the production of archival L(O)D and ensuring that published L(O)D datasets meet the needs of users. Finally, this thesis concludes by exploring the role of Artificial Intelligence and predicts an emergence in the use of archival L(O)D as part of the growing trend in using archives in the promotion of social justice. Multiple areas of future research are identified, demonstrating the breadth of investigation necessary to enable the widespread implementation of L(O)D in the archives sector.
Consistent crust-core interpolation and its effect on non-radial neutron star oscillations
Creators: name: Canullan-Pascual, Martin O.
name: Mariani, Mauro
name: Ranea-Sandoval, Ignacio F.
name: Orsaria, Milva G.
name: Weber, Fridolin
Publisher: name: arXiv
Year: 2025
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: To model the structure of neutron stars (NSs) theoretically,it is common to consider layers with different density regimes. Matching the equation of state (EoS) for the crust and core and obtaining a suitable description of these extreme conditions are crucial for understanding the properties of these compact objects. In this work, we construct ten different NS EoSs incorporating three distinct crust models, which are connected to the core using a thermodynamically and causally consistent formalism. For cold NSs, we propose a linear relationship between pressure and energy density in a narrow region between the crust and core, effectively establishing an interpolation function in the pressure-baryonic chemical potential plane. We then compare this EoS matching method with the classical approach, which neglects causal and thermodynamic consistency. We solve the Tolman-Oppenheimer-Volkoff equation to obtain the mass-radius relationship and compare our results with observational constraints on NSs. Furthermore, we investigate the influence of the new matching formalism on non-radial oscillation frequencies and damping times. Our findings suggest that the method used to glue the crust and core EoS impacts NS observables, such as the radius, oscillation frequencies, and damping times of non-radial modes, which may be crucial for interpreting future gravitational wave observations from neutron star mergers or isolated pulsars. The effects are particularly noticeable for low-mass NSs, regardless of the specific EoS model chosen. In particular, we find that the $p_1$ oscillation mode exhibits significant differences in frequencies among alternative matching methods, whereas the fundamental $f$-mode remains unaffected by changes in crust models or interpolation schemes.
description: 9 pages, 5 figures, IWARA2024 proceedings published in Astronomische Nachrichten
The optical torque: Electromagnetic spin and orbital angular momenta conservation laws and their significance
Creators: name: Nieto-Vesperinas, Manuel
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The physics involved in the fundamental conservation equations of the spin and orbital angular momenta leads to new laws and phenomena that I disclose. To this end, I analyse the scattering of an electromagnetic wavefield by the canonical system constituted by a small particle, which I assume dipolar in the wide sense. Specifically, under quite general conditions these laws lead to understanding how is the contribution and weight of each of those angular momenta to the electromagnetic torque exerted by the field on the object, which is shown to consist of an extinction and a scattering, or recoil, part. This leads to an interpretation of its effect different to that taken up till now by many theoretical and experimental works, and implies that a part of the recoil torque cancels the usually called intrinsic torque which was often considered responsible of the particle spinning. In addition, I obtain the contribution of the spatial structure of the wave to this torque, unknown to this date, showing its effect in the orbiting of the object, and demonstrating that it often leads to a negative torque on a single particle, i.e. opposite to the incident helicity, producing an orbital motion contrary to its spinning. Furthermore, I establish a decomposition of the electromagnetic torque into conservative and non-conservative components in which the helicity and its flow play a role analogous to the energy and its flux for electromagnetic forces. I illustrate these phenomena with examples of beams, also showing the difficulties of some paraxial formulations whose fields do not hold the transversality condition.
Brzozowski Goes Concurrent - A Kleene Theorem for Pomset Languages
Creators: name: Kappé, Tobias
name: Brunet, Paul
name: Luttik, Bas
name: Silva, Alexandra
name: Zanasi, Fabio
Publisher: name: arXiv
Year: 2017
Subjects: subject: Formal Languages and Automata Theory (cs.FL)
subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: Concurrent Kleene Algebra (CKA) is a mathematical formalism to study programs that exhibit concurrent behaviour. As with previous extensions of Kleene Algebra, characterizing the free model is crucial in order to develop the foundations of the theory and potential applications. For CKA, this has been an open question for a few years and this paper makes an important step towards an answer. We present a new automaton model and a Kleene-like theorem that relates a relaxed version of CKA to series-parallel pomset languages, which are a natural candidate for the free model. There are two substantial differences with previous work: from expressions to automata, we use Brzozowski derivatives, which enable a direct construction of the automaton; from automata to expressions, we provide a syntactic characterization of the automata that denote valid CKA behaviours.
description: Version 2 incorporates changes prompted by comments of the anonymous referees at CONCUR. Besides minor corrections, this includes additions to the introduction and the discussion section, as well as a proof of Lemma 2.5. Version 3 corrects the accent on the first author's surname in the metadata
The 5' untranslated region of the major immediate early mRNA is necessary for efficient human cytomegalovirus replication
Creators: name: Lenarcic, Erik M.
name: Moorman, Nathaniel J.
name: Arend, Kyle C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2018

description: The human cytomegalovirus (HCMV) immediate early 1 (IE1) and IE2 proteins are critical regulators of virus replication. Both proteins are needed to efficiently establish lytic infection, and nascent expression of IE1 and IE2 is critical for reactivation from latency. The regulation of IE1 and IE2 protein expression is thus a central event in the outcome of HCMV infection. Transcription of the primary transcript encoding both IE1 and IE2 is well studied, but relatively little is known about the posttranscriptional mechanisms that control IE1 and IE2 protein synthesis. The mRNA 5' untranslated region (5' UTR) plays an important role in regulating mRNA translation. Therefore, to better understand the control of IE1 and IE2 mRNA translation, we examined the role of the shared 5' UTR of the IE1 and IE2 mRNAs (MIE 5' UTR) in regulating translation. In a cell-free system, the MIE 5' UTR repressed translation, as predicted based on its length and sequence composition. However, in transfected cells we found that the MIE 5' UTR increased the expression of a reporter gene and enhanced its association with polysomes, demonstrating that the MIE 5' UTR has a positive role in translation control. We also found that the MIE 5' UTR was necessary for efficient IE1 and IE2 translation during infection. Replacing the MIE 5' UTR with an unstructured sequence of the same length decreased IE1 and IE2 protein expression despite similar levels of IE1 and IE2 mRNA and reduced the association of the IE1 and IE2 mRNAs with polysomes. The wild-type MIE 5'-UTR sequence was also necessary for efficient HCMV replication. Together these data identify the shared 5' UTR of the IE1 and IE2 mRNAs as an important regulator of HCMV lytic replication.
On the stable recovery of deep structured linear networks under sparsity constraints
Creators: name: Malgouyres, Francois
Publisher: name: arXiv
Year: 2017
Subjects: subject: Optimization and Control (math.OC)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: We consider a deep structured linear network under sparsity constraints. We study sharp conditions guaranteeing the stability of the optimal parameters defining the network. More precisely, we provide sharp conditions on the network architecture and the sample under which the error on the parameters defining the network scales linearly with the reconstruction error (i.e. the risk). Therefore, under these conditions, the weights obtained with a successful algorithms are well defined and only depend on the architecture of the network and the sample. The features in the latent spaces are stably defined. The stability property is required in order to interpret the features defined in the latent spaces. It can also lead to a guarantee on the statistical risk. This is what motivates this study. The analysis is based on the recently proposed Tensorial Lifting. The particularity of this paper is to consider a sparsity prior. This leads to a better stability constant. As an illustration, we detail the analysis and provide sharp stability guarantees for convolutional linear network under sparsity prior. In this analysis, we distinguish the role of the network architecture and the sample input. This highlights the requirements on the data in connection to parameter stability.
description: arXiv admin note: text overlap with arXiv:1703.08044
Additional file 1 of How symptoms of prolonged grief disorder, posttraumatic stress disorder, and depression relate to each other for grieving ICU families during the first two years of bereavement
Creators: name: Wen, Fur-Hsing
name: Prigerson, Holly G.
name: Chou, Wen-Chi
name: Huang, Chung-Chi
name: Hu, Tsung-Hui
name: Chiang, Ming Chu
name: Chuang, Li-Pang
name: Tang, Siew Tzuh
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. Table S1: Comparisons of family characteristics across participation status during bereavement follow-ups (N = 303).
A Component-oriented Framework for Autonomous Agents
Creators: name: Kappé, Tobias
name: Arbab, Farhad
name: Talcott, Carolyn
Publisher: name: arXiv
Year: 2017
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: The design of a complex system warrants a compositional methodology, i.e., composing simple components to obtain a larger system that exhibits their collective behavior in a meaningful way. We propose an automaton-based paradigm for compositional design of such systems where an action is accompanied by one or more preferences. At run-time, these preferences provide a natural fallback mechanism for the component, while at design-time they can be used to reason about the behavior of the component in an uncertain physical world. Using structures that tell us how to compose preferences and actions, we can compose formal representations of individual components or agents to obtain a representation of the composed system. We extend Linear Temporal Logic with two unary connectives that reflect the compositional structure of the actions, and show how it can be used to diagnose undesired behavior by tracing the falsification of a specification back to one or more culpable components.
Ginkgo biloba Transcriptome or Gene expression
Creators: name: BGI
Publisher: name: CNGB
Year: 2014
Subjects: transcriptome
Multiisolate

description: We sequenced mRNA from mature ovules and fully expanded leaves of female G. biloba to generate a comprehensive gene expression profile. These results provide valuable gene expression information, which will contribute to facilitate our understanding of various biological mechanisms between ovules and leaves and uncover a more important molecular insight toward ovule evolution in early seed plants.
Inducing circular RNA formation using the CRISPR endoribonuclease Csy4
Creators: name: Moorman, Nathaniel J.
name: Marzluff, William F.
name: Ball, Christopher B.
name: Ramos, Silvia B. V.
name: Asokan, Aravind
name: Meganck, Rita M.
name: Borchardt, Erin K.
name: Vincent, Heather A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Circular RNAs (circRNAs) are highly stable, covalently closed RNAs that are regulated in a spatiotemporal manner and whose functions are largely unknown. These molecules have the potential to be incorporated into engineered systems with broad technological implications. Here we describe a switch for inducing back-splicing of an engineered circRNA that relies on the CRISPR endoribonuclease, Csy4, as an activator of circularization. The endoribonuclease activity and 3' end-stabilizing properties of Csy4 are particularly suited for this task. Coexpression of Csy4 and the circRNA switch allows for the removal of downstream competitive splice sites and stabilization of the 5' cleavage product. This subsequently results in back-splicing of the 5' cleavage product into a circRNA that can translate a reporter protein from an internal ribosomal entry site (IRES). Our platform outlines a straightforward approach toward regulating splicing and could find potential applications in synthetic biology as well as in studying the properties of different circRNAs.
Fire Hose instability driven by alpha particle temperature anisotropy
Creators: name: Matteini, Lorenzo
name: Hellinger, Petr
name: Schwartz, Steven
name: Landi, Simone
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Plasma Physics (physics.plasm-ph)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: We investigate properties of a solar wind-like plasma including a secondary alpha particle population exhibiting a parallel temperature anisotropy with respect to the background magnetic field, using linear and quasi-linear predictions and by means of one-dimensional hybrid simulations. We show that anisotropic alpha particles can drive a parallel fire hose instability analogous to that generated by protons, but that, remarkably, the instability can be triggered also when the parallel plasma beta of alpha particles is below unity. The wave activity generated by the alpha anisotropy affects the evolution of the more abundant protons, leading to their anisotropic heating. When both ion species have sufficient parallel anisotropies both of them can drive the instability, and we observe generation of two distinct peaks in the spectra of the fluctuations, with longer wavelengths associated to alphas and shorter ones to protons. If a non-zero relative drift is present, the unstable modes propagate preferentially in the direction of the drift associated with the unstable species. The generated waves scatter particles and reduce their temperature anisotropy to marginally stable state, and, moreover, they significantly reduce the relative drift between the two ion populations. The coexistence of modes excited by both species leads to saturation of the plasma in distinct regions of the beta/anisotropy parameter space for protons and alpha particles, in good agreement with in situ solar wind observations. Our results confirm that fire hose instabilities are likely at work in the solar wind and limit the anisotropy of different ion species in the plasma.
description: 10 pages, 9 figures, Accepted for publication in The Astrophysical Journal
Concurrent Kleene Algebra: Free Model and Completeness
Creators: name: Kappé, Tobias
name: Brunet, Paul
name: Silva, Alexandra
name: Zanasi, Fabio
Publisher: name: arXiv
Year: 2017
Subjects: subject: Formal Languages and Automata Theory (cs.FL)
subject: FOS: Computer and information sciences

description: Concurrent Kleene Algebra (CKA) was introduced by Hoare, Moeller, Struth and Wehrman in 2009 as a framework to reason about concurrent programs. We prove that the axioms for CKA with bounded parallelism are complete for the semantics proposed in the original paper; consequently, these semantics are the free model for this fragment. This result settles a conjecture of Hoare and collaborators. Moreover, the techniques developed along the way are reusable; in particular, they allow us to establish pomset automata as an operational model for CKA.
description: Version 2 includes an overview section that outlines the completeness proof, as well as some extra discussion of the interpolation lemma. It also includes better typography and a number of minor fixes. Version 3 incorporates the changes by comments from the anonymous referees at ESOP. Among other things, these include a worked example of computing the syntactic closure by hand
A Direct Method for Photoacoustic Tomography with Inhomogeneous Sound Speed
Creators: name: Belhachmi, Zakaria
name: Glatz, Thomas
name: Scherzer, Otmar
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: The standard approach for photoacoustic imaging with variable speed of sound is time reversal, which consists in solving a well-posed final-boundary value problem for the wave equation backwards in time. This paper investigates the iterative Landweber regularization algorithm, where convergence is guaranteed by standard regularization theory, notably also in cases of trapping sound speed or for short measurement times. We formulate and solve the direct and inverse problem on the whole Euclidean space, what is common in standard photoacoustic imaging, but not for time-reversal algorithms, where the problems are considered on a domain enclosed by the measurement devices. We formulate both the direct and adjoint photoacoustic operator as the solution of an interior and an exterior differential equation which are coupled by transmission conditions. The prior is solved numerically using a Galerkin scheme in space and finite difference discretization in time, while the latter consists in solving a boundary integral equation. We therefore use a BEM-FEM approach for numerical solution of the forward operators. We analyze this method, prove convergence, and provide numerical tests. Moreover, we compare the approach to time reversal.
description: Revised Preprint
Additional file 2 of How symptoms of prolonged grief disorder, posttraumatic stress disorder, and depression relate to each other for grieving ICU families during the first two years of bereavement
Creators: name: Wen, Fur-Hsing
name: Prigerson, Holly G.
name: Chou, Wen-Chi
name: Huang, Chung-Chi
name: Hu, Tsung-Hui
name: Chiang, Ming Chu
name: Chuang, Li-Pang
name: Tang, Siew Tzuh
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 2. Table S2: Comparisons of psychological distress across participation status during bereavement follow-ups (N =293).