cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Holographic thermalization and gravitational collapse in the spacetime dominated by quintessence dark energy
Creators: name: Zeng, Xiao-Xiong
name: Chen, De-You
name: Li, Li-Fang
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper, the thermalization has been studied holographically. Explicitly in the gravity side, we consider the gravitational collapse of a thin shell of dust in a spacetime dominated by quintessence dark energy. With the thermalization probes such as the normalized geodesic length and minimal area surface, we study the effect of the state parameter for the quintessence dark energy on the thermalization. Our results show that the smaller the state parameter of quintessence is, the harder the plasma to thermalize. We also investigate the thermalization velocity and thermalization acceleration. We hope our results here can shed light on the nature of the quintessence dark energy.
description: minor modifications. arXiv admin note: text overlap with arXiv:1407.5262
The level of association between functional performance status measures and patient-reported outcomes in cancer patients: a systematic review
Creators: name: Atkinson, Thomas M.
name: Andreotti, Charissa F.
name: Saracino, Rebecca M.
name: Roberts, Kailey E.
name: Basch, Ethan
name: Hernandez, Marisol
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The process of assessing patient symptoms and functionality using patient-reported outcomes (PROs) and functional performance status (FPS) is an essential aspect of patient-centered oncology research and care. However, PRO and FPS measures are often employed separately or inconsistently combined. Thus, the purpose of this study was to conduct a systematic review of the level of association between PRO and FPS measures to determine their differential or combined utility.
$J/Ψ$, $Ψ(2S)$ Production in pp Collisions at E=510 GeV
Creators: name: Kisslinger, Leonard S.
name: Das, Debasish
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: This brief report is an extension of studies of $J/Ψ,Ψ(2S)$ production in pp collisions at the BNL with E=$\sqrt{s}$=200 GeV to E=510 GeV at PHENIX.
description: 3 pages, 1 figure
Bacterial-dependent up-regulation of intestinal bile acid binding protein and transport is FXR-mediated following ileo-cecal resection
Creators: name: Lund, P. Kay
name: Helmrath, Michael A.
name: Dekaney, Christopher M.
name: Rigby, Rachael J.
name: Henning, Susan J.
name: Garrison, Aaron P.
name: von Allmen, Douglas C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Bile acid reclamation following ileo-cecal resection (ICR) may prevent colonic mucosa from chronic injury. In this study, we hypothesized that in a murine model of ICR the remnant colon would upregulate the cellular machinery necessary for BA reclamation and would do so in an FXR- and bacteria-dependent manner.
Necdin–E2F4 interaction provides insulin-sensitizing effect after weight loss induced by gastric bypass surgery
Creators: name: Torquati, Alfonso
name: Chen, Jiegen
name: Spagnoli, Anna
name: Muehlbauer, Michael
name: Pamuklar, Zehra N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The insulin/ growth factor 1 (IGF-1) signaling pathway promotes adipocyte differentiation and therefore insulin sensitivity via suppression of Necdin expression, which represses PPAR γ promoter activity via interaction with E2F4 in mouse adipocytes.
Adipogenic differentiation of adipose tissue-derived human mesenchymal stem cells: effect of gastric bypass surgery
Creators: name: Chen, Jie-Gen
name: Spagnoli, Anna
name: Torquati, Alfonso
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Adipose tissue dysfunction is an important feature of obesity characterized by enlarged adipocytes and marked changes in secretion of cytokines. These changes result in insulin resistance, chronic vascular inflammation, oxidative stress, and activation of the renin–angiotensin system (RAS), eventually leading to type 2 diabetes, obesity-related hypertension, and cardiovascular disease (CVD). Several trials have shown that bariatric surgery significantly reduces these comorbidities. However, there is a gap in knowledge regarding the mechanisms whereby bariatric surgery reduces the burden of CVD in obese individuals.
Serum leptin levels are inversely correlated with omental gene expression of adiponectin and markedly decreased after gastric bypass surgery
Creators: name: Pamuklar, Zehra
name: Chen, Jiegen
name: Spagnoli, Anna
name: Torquati, Alfonso
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Adipose tissue is the most abundant endocrine tissue in the body, producing leptin, a hormone important in regulating hunger, and adiponectin, a hormone involved in insulin sensitivity and inflammation. The aim of this study was to assess the impact of gastric bypass surgery (GBS) on leptin levels and its relation to adipose tissue expression of adiponectin.
Targeting Angiogenesis and the Tumor Microenvironment
Creators: name: Samples, Jennifer
name: Willis, Monte
name: Klauber-DeMore, Nancy
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The role of the microenvironment during the initiation and progression of malignancy is appreciated to be of critical importance for improved molecular diagnostics and therapeutics. The tumor microenvironment is the product of a crosstalk between different cells types. Critical elements in the microenvironment include tumor associated fibroblasts, which provide an essential communication network via secretion of growth factors and chemokines, inducing an altered extracellular matrix (ECM), thereby providing additional oncogenic signals that enhance cancer-cell proliferation and invasion. Active contribution of tumor-associated stromal cells to cancer progression has been recognized. Stromal elements consist of the ECM, fibroblasts of various phenotypes, and a scaffold composed of immune and inflammatory cells, blood and lymph vessels, and nerves. This review will focus on therapeutic targets in the microenvironment related to tumor endothelium, tumor associated fibroblasts and the extracellular matrix.
title: Лесные культуры и способы содействия лесозащите и лесовосстановлению
Creators: name: Бутин, Данил
Publisher: name: Новгородский государственный университет имени Ярослава Мудрого (НовГУ)
Year: 2022

description: Лесовосстановление в наше время является очень актуальной темой, потому что как в Новгородской области, так и в России постоянно идут вырубки леса. Так, до 2010 года в России был кризис убытия лесов, и лишь затем этот кризис закончился и площадь лесных насаждений увеличилась на 4,3 миллиона гектаров. На сегодняшний день площадь лесов России приблизительно равна 1187,6 миллиона гектаров. На данный момент люди исчерпали больше половины начальных лесных ресурсов планеты. Сейчас очень большие площади лесных массивов преобразованы для того, чтобы получать с них ресурсы в виде древесины, энергии и тому подобные. Необходимо лесовосстановление, для которого нужны: политическая поддержка, сотрудничество с заинтересованными в лесовосстановлении участниками лесных отношений, наличие официального органа
управления лесами, который будет контролировать длительный процесс лесовосстановления от начала и до конца.
The “Electronic Jihad” - How Social Media are Used for Disseminating Terrorist Propaganda
Creators: name: Radulescu, Bogdan-George
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 470101
subject: Communication studies
classificationCode: 440217
subject: Terrorism
classificationCode: 440811
subject: Political theory and political philosophy
classificationCode: 440804
subject: Defence studies

description: Communication technology and social media in particular have a decisive effect on expanding the global community of terrorist organizations. More than any other terrorist group in history, the Islamic State organization (also known as ISIS, ISIL or Daesh) has made the most of social networks to increase its efforts and achieve its violent goals. The Europol study shows that about 150 different social media platforms have been used by this terrorist organization as a means of recruiting and to spread propaganda using high quality videos and other media. The term “electronic jihad” was launched by Professor Martin Rudner, a researcher at Carleton University. The clear components of this electronic jihad are propaganda, misinformation, subversion, and the attempt to destroy the moral values of the Western world.
Targeted Therapies in Melanoma
Creators: name: Moschos, Stergios J.
name: Pinnamaneni, Ramya
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Advances in understanding the biology of melanoma have provided great insights about the mechanisms of chemoresistance and its genetic heterogeneity in parallel with advances in drug design culminating in recent major treatment breakthroughs using small molecules inhibitors in metastatic melanoma (MM). While clinical benefit of targeted therapies has been unquestionable, future advances can only be possible if we better understand the interplay between genetic aberrations and role of other crucial non-genetic changes yet to be identified by such projects as the Cancer Genome Atlas Project (TCGA) in Melanoma. Combination therapies, either among small molecule inhibitors themselves and/or with immunotherapies may be the optimal strategy to prevent development of drug resistance that is inherently linked with such targeted therapies.
Surface Reconstructions in Molecular Beam Epitaxy of SrTiO3
Creators: name: Kajdos, Adam P.
name: Stemmer, Susanne
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We show that reflection high-energy electron diffraction (RHEED) can be used as a highly sensitive tool to track surface and resulting film stoichiometry in adsorption-limited molecular beam epitaxy of (001) SrTiO3 thin films. Even under growth conditions that yield films with a lattice parameter that is identical to that of stoichiometric bulk crystals within the detection limit of high-resolution x-ray diffraction (XRD), changes in surface reconstruction occur from (1x1) to (2x1) to c(4x4) as the equivalent beam pressure of the Ti metalorganic source is increased. These surface reconstructions are correlated with a shift from mixed SrO/TiO2 termination to pure TiO2 termination. The crossover to TiO2 surface termination is also apparent in a phase shift in RHEED oscillations observed at the beginning of growth. Comparison with prior results for carrier mobilities of doped films shows that the best films are grown under conditions of a TiO2-saturated surface [c(4x4) reconstruction] within the XRD growth window.
description: Accepted for publication in Applied Physics Letters
GABAA receptor regulation of voluntary ethanol drinking requires PKCε
Creators: name: Hodge, Clyde W.
name: Mole, Beth
name: Lepoutre, Veronique
name: Besheer, Joyce
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Protein kinase C (PKC) regulates a variety of neural functions, including ion channel activity, neurotransmitter release, receptor desensitization and differentiation. We have shown previously that mice lacking the ε-isoform of PKC (PKCε) self-administer 75% less ethanol and exhibit supersensitivity to acute ethanol and allosteric positive modulators of GABAA receptors when compared with wild-type controls. The purpose of the present study was to examine involvement of PKCε in GABAA receptor regulation of voluntary ethanol drinking. To address this question, PKCε null-mutant and wild-type control mice were allowed to drink ethanol (10% v/v) vs. water on a two-bottle continuous access protocol. The effects of diazepam (nonselective GABAA BZ positive modulator), zolpidem (GABAA α1 agonist), L-655,708 (BZ-sensitive GABAA α5 inverse agonist), and flumazenil (BZ antagonist) were then tested on ethanol drinking. Ethanol intake (grams/kg/day) by wild-type mice decreased significantly after diazepam or zolpidem but increased after L-655,708 administration. Flumazenil antagonized diazepam-induced reductions in ethanol drinking in wild-type mice. However, ethanol intake by PKCε null mice was not altered by any of the GABAergic compounds even though effects were seen on water drinking in these mice. Increased acute sensitivity to ethanol and diazepam, which was previously reported, was confirmed in PKCε null mice. Thus, results of the present study show that PKCε null mice do not respond to doses of GABAA BZ receptor ligands that regulate ethanol drinking by wild-type control mice. This suggests that PKCε may be required for GABAA receptor regulation of chronic ethanol drinking.
Spin Hanle effect in mesoscopic superconductors
Creators: name: Silaev, M.
name: Virtanen, P.
name: Heikkilä, T. T.
name: Bergeret, F. S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We present a theoretical study of spin transport in a superconducting mesoscopic spin valve under the action of a magnetic field misaligned with respect to the injected spin. We demonstrate that superconductivity can either strongly enhance or suppress the coherent spin rotation depending on the type of spin relaxation mechanism being dominated either by spin-orbit coupling or spin-flip scattering at impurities. We also predict a hitherto unknown subgap contribution to the nonlocal conductance in multiterminal superconducting hybrid structures which completely eliminates the effect of spin rotation at sufficiently low temperatures.
Supplementary document for A comparative study of photoluminescence dynamics of CdSe quantum dots on glass and ITO - 7192183.pdf
Creators: name: Xiang, Guohong
name: zhang, xinhai
name: Wang, Kai
name: Kwok, Hoi-Sing
name: Sun, Xiao Wei
Publisher: name: Optica Publishing Group
Year: 2024
Subjects: Uncategorized

description: fitted parameters
Pre-Town Meeting on Spin Physics at an Electron-Ion Collider
Creators: name: Aschenauer, Elke-Caroline
name: Balitsky, Ian
name: Bland, Leslie
name: Brodsky, Stanley J.
name: Burkardt, Matthias
name: Burkert, Volker
name: Chen, Jian-Ping
name: Deshpande, Abhay
name: Diehl, Markus
name: Gamberg, Leonard
name: Perdekamp, Matthias Grosse
name: Huang, Jin
name: Hyde, Charles
name: Ji, Xiangdong
name: Jiang, Xiaodong
name: Kang, Zhong-Bo
name: Kubarovsky, Valery
name: Lajoie, John
name: Liu, Keh-Fei
name: Liu, Ming
name: Liuti, Simonetta
name: Melnitchouk, Wally
name: Mulders, Piet
name: Prokudin, Alexei
name: Tarasov, Andrey
name: Qiu, Jian-Wei
name: Radyushkin, Anatoly
name: Richards, David
name: Sichtermann, Ernst
name: Stratmann, Marco
name: Vogelsang, Werner
name: Yuan, Feng
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: A polarized $ep/eA$ collider (Electron--Ion Collider, or EIC), with polarized proton and light-ion beams and unpolarized heavy-ion beams with a variable center--of--mass energy $\sqrt{s} \sim 20$ to $\sim100$~GeV (upgradable to $\sim 150$ GeV) and a luminosity up to $\sim 10^{34} \, \textrm{cm}^{-2} \textrm{s}^{-1}$, would be uniquely suited to address several outstanding questions of Quantum Chromodynamics, and thereby lead to new qualitative and quantitative information on the microscopic structure of hadrons and nuclei. During this meeting at Jefferson Lab we addressed recent theoretical and experimental developments in the spin and the three--dimensional structure of the nucleon (sea quark and gluon spatial distributions, orbital motion, polarization, and their correlations). This mini--review contains a short update on progress in these areas since the EIC White paper~\cite{Accardi:2012qut}.
description: 7 pages, 4 figures; Summary of the Informal Pre-Town Meeting held at Jefferson Lab, Newport News, VA, from August 13 - 15, 2014
Distinct patterns of ΔFosB induction in brain by drugs of abuse
Creators: name: Perrotti, L.I.
name: Bachtell, R.K.
name: Knapp, D.J.
name: Maze, I.
name: Self, D.W.
name: Elmore, R.G.
name: Renthal, W.
name: Nestler, E.J.
name: Yazdani, S.
name: Robison, B.
name: Selley, D.E.
name: Martin, B.R.
name: Sim-Selley, L.
name: Weaver, R.R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The transcription factor ΔFosB accumulates and persists in brain in response to chronic stimulation. This accumulation after chronic exposure to drugs of abuse has been demonstrated previously by Western blot most dramatically in striatal regions, including dorsal striatum (caudate/putamen) and nucleus accumbens. In the present study, we used immunohistochemistry to define with greater anatomical precision the induction of ΔFosB throughout the rodent brain after chronic drug treatment. We also extended previous research involving cocaine, morphine, and nicotine to two additional drugs of abuse, ethanol and Δ9-tetrahydrocannabinol (Δ9-THC, the active ingredient in marijuana). We show here that chronic, but not acute, administration of each of four drugs of abuse, cocaine, morphine, ethanol, and Δ9-THC, robustly induces ΔFosB in nucleus accumbens, although different patterns in the core vs. shell subregions of this nucleus were apparent for the different drugs. The drugs also differed in their degree of ΔFosB induction in dorsal striatum. In addition, all four drugs induced ΔFosB in prefrontal cortex, with the greatest effects observed with cocaine and ethanol, and all of the drugs induced ΔFosB to a small extent in amygdala. Furthermore, all drugs induced ΔFosB in the hippocampus, and, with the exception of ethanol, most of this induction was seen in the dentate. Lower levels of ΔFosB induction were seen in other brain areas in response to a particular drug treatment. These findings provide further evidence that induction of ΔFosB in nucleus accumbens is a common action of virtually all drugs of abuse and that, beyond nucleus accumbens, each drug induces ΔFosB in a region-specific manner in brain.
In vivo measurement of somatodendritic release of dopamine in the ventral tegmental area
Creators: name: Parker, Lauren E.
name: Kita, Justin M.
name: Wightman, R. Mark
name: Kile, Brian M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The ventral tegmental area (VTA), the locus of mesolimbic dopamine cell bodies, contains dopamine. Experiments in brain slices have demonstrated that VTA dopamine can be released by local electrical stimulation. Measurements with both push-pull cannula and microdialysis in intact animals have also obtained evidence for releasable dopamine. Here we demonstrate that dopamine release in the VTA can be evoked by remote stimulations of the medial forebrain bundle (MFB) in the anesthetized rat. In initial experiments, the MFB was electrically stimulated while a carbon-fiber electrode was lowered to the VTA, with recording by fast-scan cyclic voltammetry. While release was not observed with the carbon fiber 4 to 6 mm below dura, a voltammetric response was observed a t 6-8 mm below dura, but the voltammogram was poorly defined. At lower depths, in the VTA, dopamine release was evoked. Immunohistochemistry experiments with antibodies for tyrosine hydroxylase (TH) confirmed that dopamine processes were primarily found below 8 mm. Similarly, tissue content determined by liquid chromatography revealed serotonin but not dopamine dorsal to 8 mm with both dopamine and serotonin at lower depths. Evaluation of the VTA signal by pharmacological means showed that it increased with inhibitors of dopamine uptake, but release was not altered by D2 agents. Dopamine release in the VTA was frequency dependent and could be exhausted by stimulations longer than 5 s. Thus, VTA dopamine release can be evoked in vivo by remote stimulations and it resembles release in terminal regions, possessing a similar uptake mechanism and a finite releasable storage pool.
A Scalable Protocol for the Regioselective Alkylation of 2-Methylcyclohexane-1,3-dione with Unactivated sp3 Electrophiles
Creators: name: Sharpe, Robert
name: Portillo, Maribel
name: Johnson, Jeffrey
name: Vélez, Robert
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: A method for the C-selective alkylation of 2-methylcyclohexane-1,3-dione with unactivated sp3 electrophiles is accomplished via alkylation and subsequent deprotection of the derived ketodimethyl hydrazones. The present method provides a high-yielding entry to dialkyl cycloalkanones that cannot be accessed via direct alkylation of 2-methylcyclohexane-1,3-dione. The title reaction may be useful in the scalable preparation of terpene and steroidal building blocks in the arena of natural product synthesis.
Black Silicon Solar Thin-film Microcells Integrating Top Nanocone Structures for Broadband and Omnidirectional Light-Trapping
Creators: name: Xu, Zhida
name: Yao, Yuan
name: Brueckner, Eric P.
name: Li, Lanfang
name: Jiang, Jing
name: Nuzzo, Ralph G.
name: Liu, Gang L.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Recently developed classes of monocrystalline silicon solar microcells (u-cell) can be assembled into modules with characteristics (i.e., mechanically flexible forms, compact concentrator designs, and high-voltage outputs) that would be impossible to achieve using conventional, wafer-based approaches. In this paper, we describe a highly dense, uniform and non-periodic nanocone forest structure of black silicon (bSi) created on optically-thin (30 um) u-cells for broadband and omnidirectional light-trapping with a lithography-free and high-throughput plasma texturizing process. With optimized plasma etching conditions and a silicon nitride passivation layer, black silicon u-cells, when embedded in a polymer waveguiding layer, display dramatic increases of as much as 65.7% in short circuit current, as compared to a bare silicon device. The conversion efficiency increases from 8% to 11.5% with a small drop in open circuit voltage and fill factor.
description: 24page, 5 figures, Nanotechnology 25 305301
Identification of the Catalytic Residues in the Cyclase Domain of the Class IV Lanthipeptide Synthetase SgbL
Creators: name: Hegemann, Julian D.
name: Süssmuth, Roderich D.
Publisher: name: Technische Universität Berlin
Year: 2021
Subjects: subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften
subject: biocatalysis
subject: biosynthesis
subject: lanthipeptides
subject: natural products
subject: RiPPs

description: Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs) and are subdivided into different classes based on their processing enzymes. The three-domain class IV lanthipeptide synthetases (LanL enzymes) consist of N-terminal lyase, central kinase, and C-terminal cyclase domains. While the catalytic residues of the kinase domains (mediating ATP-dependent Ser/Thr phosphorylations) and the lyase domains (carrying out subsequent phosphoserine/phosphothreonine (pSer/pThr) eliminations to yield dehydroalanine/dehydrobutyrine (Dha/Dhb) residues) have been characterized previously, such studies are missing for LanL cyclase domains. To close this gap of knowledge, this study reports on the identification and validation of the catalytic residues in the cyclase domain of the class IV lanthipeptide synthetase SgbL, which facilitate the nucleophilic attacks by Cys thiols on Dha/Dhb residues for the formation of β-thioether crosslinks.
Measurement of flow harmonics with multi-particle cumulants in Pb+Pb collisions at $\sqrt{s_{NN}}=2.76$ TeV with the ATLAS detector
Creators: name: ATLAS Collaboration
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: ATLAS measurements of the azimuthal anisotropy in lead-lead collisions at $\sqrt{s_{NN}}=2.76$ TeV are shown using a dataset of approximately 7 $μ$b$^{-1}$ collected at the LHC in 2010. The measurements are performed for charged particles with transverse momenta $0.5
description: 17 pages plus author list + cover pages (31 pages total), 14 figures, 2 tables, submitted to EPJC, All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2012-04/
The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age
Creators: name: Vision, Todd J.
name: Lundberg, John G.
name: Lapp, Hilmar
name: Haendel, Melissa A.
name: Westerfield, Monte
name: Balhoff, James P.
name: Midford, Peter E.
name: Dahdul, Wasila M.
name: Mabee, Paula M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.
NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata
Creators: name: Lapp, Hilmar
name: Sukumaran, Jeet
name: Caravas, Jason A.
name: Maddison, Wayne P.
name: Stoltzfus, Arlin
name: Xia, Xuhua
name: Balhoff, James P.
name: Midford, Peter E.
name: Priyam, Anurag
name: Holder, Mark T.
name: Vos, Rutger A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richly annotated data. The challenges of conveying reusable data are particularly acute in regard to evolutionary comparative analysis, which comprises an ever-expanding list of data types, methods, research aims, and subdisciplines. To facilitate interoperability in evolutionary comparative analysis, we present NeXML, an XML standard (inspired by the current standard, NEXUS) that supports exchange of richly annotated comparative data. NeXML defines syntax for operational taxonomic units, character-state matrices, and phylogenetic trees and networks. Documents can be validated unambiguously. Importantly, any data element can be annotated, to an arbitrary degree of richness, using a system that is both flexible and rigorous. We describe how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats. By relying on XML Schema Definition, the design of NeXML facilitates the development and deployment of software for processing, transforming, and querying documents. The adoption of NeXML for practical use is facilitated by the availability of (1) an online manual with code samples and a reference to all defined elements and attributes, (2) programming toolkits in most of the languages used commonly in evolutionary informatics, and (3) input–output support in several widely used software applications. An active, open, community-based development process enables future revision and expansion of NeXML.
Colour matters: the effects of lensing on the positional offsets between optical and submillimetre galaxies in Herschel-ATLAS
Creators: name: Bourne, N.
name: Maddox, S. J.
name: Dunne, L.
name: Dye, S.
name: Eales, S.
name: Hoyos, C.
name: Gonzalez-Nuevo, J.
name: Smith, D. J. B.
name: Valiante, E.
name: de Zotti, G.
name: Ivison, R. J.
name: Rowlands, K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We report an unexpected variation in the positional offset distributions between Herschel-ATLAS sub-millimetre (submm) sources and their optical associations, depending on both 250-μm signal-to-noise ratio and 250/350-μm colour. We show that redder and brighter submm sources have optical associations with a broader distribution of positional offsets than would be expected if these offsets were due to random positional errors in the source extraction. The observation can be explained by two possible effects: either red submm sources trace a more clustered population than blue ones, and their positional errors are increased by confusion; or red submm sources are generally at high redshifts and are frequently associated with low-redshift lensing structures which are identified as false counterparts. We perform various analyses of the data, including the multiplicity of optical associations, the redshift and magnitude distributions in H-ATLAS in comparison to HerMES, and simulations of weak lensing, and we conclude that the effects are most likely to be explained by widespread weak lensing of Herschel-SPIRE sources by foreground structures. This has important consequences for counterpart identification and derived redshift distributions and luminosity functions of submm surveys.
description: 10 pages, 6 figures. Accepted for publication in MNRAS
Triaenonychoidea Sorensen 1886
Creators: name: Derkarabetian, Shahan
name: Baker, Caitlin M.
name: Hedin, Marshal
name: Prieto, Carlos E.
name: Giribet, Gonzalo
Publisher: name: Zenodo
Year: 2021
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Opiliones

description: Superfamily TRIAENONYCHOIDEA SØrensen 1886 Included families: Triaenonychidae Sørensen 1886, Synthetonychiidae Forster 1954, Lomanellidae Mendes & Derkarabetian, fam. nov., Buemarinoidae Karaman 2019, stat. nov.
description: Published as part of Derkarabetian, Shahan, Baker, Caitlin M., Hedin, Marshal, Prieto, Carlos E. & Giribet, Gonzalo, 2021, Phylogenomic re-evaluation of Triaenonychoidea (Opiliones: Laniatores), and systematics of Triaenonychidae, including new families, genera and species, pp. 277-288 in Invertebrate Systematics 167 (1) on page 140, DOI: 10.1071/is20047, http://zenodo.org/record/4531309
description: {"references": ["Forster, R. R. (1954). The New Zealand harvestmen (sub-order Laniatores). Canterbury Museum Bulletin 2, 1 - 329.", "Karaman, I. (2019). A redescription and family placement of Buemarinoa patrizii Roewer, 1956 (Opiliones, Laniatores, Triaenonychidae). Biologia Serbica 41, 67 - 77. doi: 10.5281 / zenodo. 3373487"]}
Mutual information on the fuzzy sphere
Creators: name: Sabella-Garnier, Philippe
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We numerically calculate entanglement entropy and mutual information for a massive free scalar field on commutative (ordinary) and noncommutative (fuzzy) spheres. We regularize the theory on the commutative geometry by discretizing the polar coordinate, whereas the theory on the noncommutative geometry naturally posseses a finite and adjustable number of degrees of freedom. Our results show that the UV-divergent part of the entanglement entropy on a fuzzy sphere does not follow an area law, while the entanglement entropy on a commutative sphere does. Nonetheless, we find that mutual information (which is UV-finite) is the same in both theories. This suggests that nonlocality at short distances does not affect quantum correlations over large distances in a free field theory.
description: 16 pages, 10 figures. Fixed minor typos, references updated, discussion slightly expanded
A Semantic Model for Species Description Applied to the Ensign Wasps (Hymenoptera: Evaniidae) of New Caledonia
Creators: name: Balhoff, James P.
name: Mullins, Patricia L.
name: Deans, Andrew R.
name: Mikó, István
name: Yoder, Matthew J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Taxonomic descriptions are unparalleled sources of knowledge of life's phenotypic diversity. As natural language prose, these data sets are largely refractory to computation and integration with other sources of phenotypic data. By formalizing taxonomic descriptions using ontology-based semantic representation, we aim to increase the reusability and computability of taxonomists' primary data. Here, we present a revision of the ensign wasp (Hymenoptera: Evaniidae) fauna of New Caledonia using this new model for species description. Descriptive matrices, specimen data, and taxonomic nomenclature are gathered in a unified Web-based application, mx, then exported as both traditional taxonomic treatments and semantic statements using the OWL Web Ontology Language. Character:character-state combinations are then annotated following the entity–quality phenotype model, originally developed to represent mutant model organism phenotype data; concepts of anatomy are drawn from the Hymenoptera Anatomy Ontology and linked to phenotype descriptors from the Phenotypic Quality Ontology. The resulting set of semantic statements is provided in Resource Description Framework format. Applying the model to real data, that is, specimens, taxonomic names, diagnoses, descriptions, and redescriptions, provides us with a foundation to discuss limitations and potential benefits such as automated data integration and reasoner-driven queries. Four species of ensign wasp are now known to occur in New Caledonia: Szepligetella levipetiolata, Szepligetella deercreeki Deans and Mikó sp. nov., Szepligetella irwini Deans and Mikó sp. nov., and the nearly cosmopolitan Evania appendigaster. A fifth species, Szepligetella sericea, including Szepligetella impressa, syn. nov., has not yet been collected in New Caledonia but can be found on islands throughout the Pacific and so is included in the diagnostic key. [Biodiversity informatics; Evaniidae; New Caledonia; new species; ontology; semantic phenotypes; semantic species description; taxonomy.]
Optomechanical Rydberg-atom excitation via dynamic Casimir-Polder coupling
Creators: name: Antezza, Mauro
name: Braggio, Caterina
name: Carugno, Giovanni
name: Noto, Antonio
name: Passante, Roberto
name: Rizzuto, Lucia
name: Ruoso, Giuseppe
name: Spagnolo, Salvatore
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the optomechanical coupling of a oscillating effective mirror with a Rydberg atomic gas, mediated by the dynamical atom-mirror Casimir-Polder force. This coupling may produce a near-field resonant atomic excitation whose probability scales as $\propto (d^2\;a\;n^4\;t)^2/z_0^8$, where $z_0$ is the average atom-surface distance, $d$ the atomic dipole moment, $a$ the mirror's effective oscillation amplitude, $n$ the initial principal quantum number, and $t$ the time. We propose an experimental configuration to realize this system with a cold atom gas trapped at a distance $\sim 2\cdot10 \, μ$m from a semiconductor substrate, whose dielectric constant is periodically driven by an external laser pulse, hence realizing en effective mechanical mirror motion due to the periodic change of the substrate from transparent to reflecting. For a parabolic gas shape, this effect is predicted to excite about $\sim 10^2$ atoms of a dilute gas of $10^3$ trapped Rydberg atoms with $n=75$ after about $0.5 \,μ\mbox{s}$, hence high enough to be detected in typical Rydberg gas experimental conditions.
description: 6 pages, 1 figure
A unified thermodynamic picture of Hořava-Lifshitz black hole in arbitrary space time
Creators: name: Suresh, Jishnu
name: R, Tharanath
name: Kuriakose, V C
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this paper, we analyze the complete thermodynamic and phase transition phenomena of a black hole solution in Hořava-Lifshitz gravity in arbitrary space time. Nature of phase transition is studied using geometrothermodynamic and Ehrenfest's scheme of standard thermodynamics. We analytically check the Ehrenfest's equations near the critical point, which is the point of divergence in the heat capacity. Our analysis revels that this black hole exhibits a second order phase transition.
description: 15 pages, 9 figures, To appear in JHEP
Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies
Creators: name: Balhoff, James P.
name: Mabee, Paula M.
name: Lapp, Hilmar
name: Dececchi, T. Alexander
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB; kb.phenoscape.org), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 639 variable characters scored for 1051 taxa, resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, that is, cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin-to-limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype-to-genome relationships.
A novel LC–ESI-MS method for the simultaneous determination of etravirine, darunavir and ritonavir in human blood plasma
Creators: name: Kashuba, Angela D.M.
name: Rezk, Naser L.
name: White, Nicole R.
name: Jennings, Steven H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The new potent combination of antiretrovirals etravirine, darunavir, and ritonavir requires a new bioanalytical method for clinical pharmacology investigations and potential therapeutic drug monitoring. The development and validation of a novel LC–MS method for the simultaneous quantification of the most recently FDA-approved protease inhibitor and non-nucleoside reverse transcriptase inhibitor is described. This novel method was developed and validated using a sub-2 μm particle column, and provides excellent chromatographic separation and peak shape for all three analytes and internal standard. The method was validated over the range of 0.002–2.0 μg/mL. Intra- and inter-day accuracy of all analytes ranged from 88 to 106%, and intra- and inter-day precision was <7%. Dilution of samples 2-, 5-, and 10-fold maintained accuracy and precision, using a sample volume as low as 10 μL. Finally, the applicability of the method was investigated with clinical samples and external quality assurance proficiency testing samples.
Emerging molecular classification in RCC: implications for drug development
Creators: name: Rathmell, W. Kimryn
name: Hacker, Kathryn E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: In the past decade, progress has been made in the development of targeted therapies for advanced renal cell carcinoma. However, as multiple therapeutic choices become available for clinicians, we currently lack effective indicators to allow physicians to choose the best treatment option for specific patients. For approved targeted therapies, potential molecules that could indicate drug effectiveness in a specific tumor follow naturally from both the therapeutic mechanism and the previously elucidated tumor biology. However, in advanced RCC, the use of these molecules as biomarkers for treatment selection has shown equivocal results and requires further investigation. In addition to looking at specific molecular targets, subclassification of tumors based on their molecular characteristics may also allow stratification of patients based on therapeutic benefits, providing information for treatment selection. Furthermore, the continued development of such tumor classification schemes will hopefully uncover other molecular targets that warrant development as future RCC therapies. The use of molecular classification of patients’ tumors for treatment selection will provide the opportunity to increase the effectiveness of currently available therapies for advanced RCC and to judiciously pursue promising options for future RCC therapies.
Drosera pilosa Exell & J. R. Laundon
Creators: name: Rjosk, A.
name: Neinhuis, C.
name: Monizi, M.
name: Lautenschläger, T.
Publisher: name: Zenodo
Year: 2022
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Caryophyllales
Droseraceae
Drosera
Drosera pilosa

description: 9. Drosera pilosa Exell & J.R.Laundon — Fig. 11 Drosera pilosa Exell & J.R.Laundon (1956) 213;J.R. Laundon (1959) 4; (1970) 26; Troupin (1978) 305; A.S.Rob. et al. (2017) 1452. — Type: A. Stolz s.n. (holo BM), Tanzania, Tanganyika territory, Kyimbila District, North of Lake Nyasa, 1885. Acaulescent, perennial herb (Fig. 11b). Leaves in a basal rosette; stipules c. 3 mm long, connate at the base, apex lacer- ated; lamina elliptic, ovate or obovate, 4–13 by 2–8 mm, the adaxial surface and margins bearing tentacles, abaxially pilose (Fig.11a); petiole 3–15 by up to 2 mm, gradually broadening into the lamina, abaxially pilose. Inflorescences cymose, with 2 – 6 flowers; peduncles 1 or 2 together, 2–16 cm long, arising laterally from the rosette, ascending, canaliculate, pilose; bracts elliptic, 2–3 mm long; pedicels 1–7 mm long, pilose. Sepals 5, ± elliptic, 3–6 by 1.5–2.5 mm, apex acute, pilose. Petals 5, c. 6 mm long, red to purple. Stamens 5; filaments c. 4 mm long. Pollen in tetrads, tetrads c. 40–45 µm diam, single grains 30–35 µm diam, echinate (to baculate; Fig. 11e), echini broadly conical, 1–2 mm long, in high density with short clavate sculptural elements between them. Pistil: ovary subglobose, c. 1.5 by 2 mm; styles 3, c. 2 mm long, bipartite to the base. Seeds ovoid, 0.3–0.5 by c. 0.2 mm, black, testa smooth (Fig. 11f). Distribution — Angola, Burundi, Cameroun, DRC, Guinea, Kenya, Malawi, Ruanda, Sierra Leone, Tanzania (Fig. 11c). Habitat & Ecology — Montane species. Additional specimens (see Fig. 11d for province map). ANGOLA, Cuando Cubango, Cuito-Cuanavale, Longa, vale do Cuiriri, alt. 1360 m, 19 Mar. 1960, E.J. Mendes 3212 (COI). – DRC, Sud-Kivu, Environs de Kitwabaluzi, S2°53' E28°35', Dec.1942, Coutreaux 999 (BR); Kabare,alt. 2200 m, 9 Dec. 1956, Christiaensen 1953 (BR); Unknown province, Luemba, Sept. 1946, Kunet 32 (BR). Note — Very similar to D. burkeana but with pilose peduncle, pedicels and sepals.
description: Published as part of Rjosk, A., Neinhuis, C., Monizi, M. & Lautenschläger, T., 2022, Synopsis of the genus Drosera (Droseraceae) in Angola and the Democratic Republic of the Congo, pp. 1-14 in Blumea - Biodiversity, Evolution and Biogeography of Plants 67 (1) on page 12, DOI: 10.3767/blumea.2022.67.01.03, http://zenodo.org/record/7679465
description: {"references": ["Laundon JR. 1959. Droseraceae. In: Hubbard CE, Milne-Redhead E (eds), Flora of Tropical East Africa. Crown Agents for Oversea Governments and Administrations, London.", "Troupin G. 1978. Flore du Rwanda. Musee Royal de l'Afrique Centrale, Tervuren."]}
X-ray ejecta kinematics of the Galactic core-collapse supernova remnant G292.0+1.8
Creators: name: Bhalerao, Jayant
name: Park, Sangwook
name: Dewey, Daniel
name: Hughes, John P.
name: Mori, Koji
name: Lee, Jae-Joon
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We report on the results from the analysis of our 114 ks Chandra HETGS observation of the Galactic core-collapse supernova remnant G292.0+1.8. To probe the 3D structure of the clumpy X-ray emitting ejecta material in this remnant, we measured Doppler shifts in emission lines from metal-rich ejecta knots projected at different radial distances from the expansion center. We estimate radial velocities of ejecta knots in the range of -2300
description: 5 figures, accepted by ApJ
A computerized intervention to promote colorectal cancer screening for underserved populations: Theoretical background and algorithm development
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The aim of this exploratory study was to assess factors deemed by patients as “important” as they planned and considered undergoing colorectal cancer (CRC) screening, and to use this data to design a computer-delivered intervention to promote screening.