cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Quantitative High-Throughput Screening for Chemical Toxicity in a Population-Based In Vitro Model
Creators: name: Huang, Ruili
name: Tice, Raymond R.
name: Kosyk, Oksana
name: Zhou, Yi-Hui
name: Wright, Fred A.
name: Xia, Menghang
name: Abdo, Nour
name: Rusyn, Ivan
name: Austin, Christopher P.
name: Sedykh, Alexander
name: Tropsha, Alexander
name: O’Shea, Shannon H.
name: Lock, Eric F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: A shift in toxicity testing from in vivo to in vitro may efficiently prioritize compounds, reveal new mechanisms, and enable predictive modeling. Quantitative high-throughput screening (qHTS) is a major source of data for computational toxicology, and our goal in this study was to aid in the development of predictive in vitro models of chemical-induced toxicity, anchored on interindividual genetic variability. Eighty-one human lymphoblast cell lines from 27 Centre d’Etude du Polymorphisme Humain trios were exposed to 240 chemical substances (12 concentrations, 0.26nM–46.0μM) and evaluated for cytotoxicity and apoptosis. qHTS screening in the genetically defined population produced robust and reproducible results, which allowed for cross-compound, cross-assay, and cross-individual comparisons. Some compounds were cytotoxic to all cell types at similar concentrations, whereas others exhibited interindividual differences in cytotoxicity. Specifically, the qHTS in a population-based human in vitro model system has several unique aspects that are of utility for toxicity testing, chemical prioritization, and high-throughput risk assessment. First, standardized and high-quality concentration-response profiling, with reproducibility confirmed by comparison with previous experiments, enables prioritization of chemicals for variability in interindividual range in cytotoxicity. Second, genome-wide association analysis of cytotoxicity phenotypes allows exploration of the potential genetic determinants of interindividual variability in toxicity. Furthermore, highly significant associations identified through the analysis of population-level correlations between basal gene expression variability and chemical-induced toxicity suggest plausible mode of action hypotheses for follow-up analyses. We conclude that as the improved resolution of genetic profiling can now be matched with high-quality in vitro screening data, the evaluation of the toxicity pathways and the effects of genetic diversity are now feasible through the use of human lymphoblast cell lines.
Whole and Particle-Free Diesel Exhausts Differentially Affect Cardiac Electrophysiology, Blood Pressure, and Autonomic Balance in Heart Failure–Prone Rats
Creators: name: Carll, Alex P.
name: Costa, Daniel L.
name: King, Charly J.
name: Winsett, Darrell W.
name: Perez, Christina M.
name: Hazari, Mehdi S.
name: Krantz, Quentin Todd
name: Farraj, Aimen K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Epidemiological studies strongly link short-term exposures to vehicular traffic and particulate matter (PM) air pollution with adverse cardiovascular (CV) events, especially in those with preexisting CV disease. Diesel engine exhaust is a key contributor to urban ambient PM and gaseous pollutants. To determine the role of gaseous and particulate components in diesel exhaust (DE) cardiotoxicity, we examined the effects of a 4-h inhalation of whole DE (wDE) (target PM concentration: 500 µg/m3) or particle-free filtered DE (fDE) on CV physiology and a range of markers of cardiopulmonary injury in hypertensive heart failure–prone rats. Arterial blood pressure (BP), electrocardiography, and heart rate variability (HRV), an index of autonomic balance, were monitored. Both fDE and wDE decreased BP and prolonged PR interval during exposure, with more effects from fDE, which additionally increased HRV triangular index and decreased T-wave amplitude. fDE increased QTc interval immediately after exposure, increased atrioventricular (AV) block Mobitz II arrhythmias shortly thereafter, and increased serum high-density lipoprotein 1 day later. wDE increased BP and decreased HRV root mean square of successive differences immediately postexposure. fDE and wDE decreased heart rate during the 4th hour of postexposure. Thus, DE gases slowed AV conduction and ventricular repolarization, decreased BP, increased HRV, and subsequently provoked arrhythmias, collectively suggesting parasympathetic activation; conversely, brief BP and HRV changes after exposure to particle-containing DE indicated a transient sympathetic excitation. Our findings suggest that whole- and particle-free DE differentially alter CV and autonomic physiology and may potentially increase risk through divergent pathways.
Additional file 1 of Required sample size to detect mediation in 3-level implementation studies
Creators: name: Williams, Nathaniel J.
name: Preacher, Kristopher J.
name: Allison, Paul D.
name: Mandell, David S.
name: Marcus, Steven C.
Publisher: name: figshare
Year: 2022
Subjects: subject: Statistics
subject: FOS: Mathematics

description: Additional file 1. Mplus code for power analyses.
An Autonomic Link Between Inhaled Diesel Exhaust and Impaired Cardiac Performance: Insight From Treadmill and Dobutamine Challenges in Heart Failure–Prone Rats
Creators: name: Perez, Christina M.
name: Costa, Daniel L.
name: Cascio, Wayne E.
name: King, Charly J.
name: Krantz, Q. Todd
name: Carll, Alex P.
name: Haykal-Coates, Najwa
name: Farraj, Aimen K.
name: Hazari, Mehdi S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Cardiac disease exacerbation is associated with short-term exposure to vehicular emissions. Diesel exhaust (DE) might impair cardiac performance in part through perturbing efferent sympathetic and parasympathetic autonomic nervous system (ANS) input to the heart. We hypothesized that acute changes in ANS balance mediate decreased cardiac performance upon DE inhalation. Young adult heart failure–prone rats were implanted with radiotelemeters to measure heart rate (HR), HR variability (HRV), blood pressure (BP), core body temperature, and pre-ejection period (PEP, a contractility index). Animals pretreated with sympathetic antagonist (atenolol), parasympathetic antagonist (atropine), or saline were exposed to DE (500 µg/m3 fine particulate matter, 4h) or filtered air and then treadmill exercise challenged. At 1 day postexposure, separate rats were catheterized for left ventricular pressure (LVP), contractility, and lusitropy and assessed for autonomic influence using the sympathoagonist dobutamine and surgical vagotomy. During DE exposure, atenolol inhibited increases in HR, BP, and contractility, but not body temperature, suggesting a role for sympathetic dominance. During treadmill recovery at 4h post-DE exposure, HR and HRV indicated parasympathetic dominance in saline- and atenolol-pretreated groups that atropine inhibited. Conversely, at treadmill recovery 21h post-DE exposure, HRV and PEP indicated sympathetic dominance and subsequently diminished contractility that only atenolol inhibited. LVP at 1 day postexposure indicated that DE impaired contractility and lusitropy while abolishing parasympathetic-regulated cardiac responses to dobutamine. This is the first evidence that air pollutant inhalation both causes time-dependent oscillations between sympathetic and parasympathetic dominance and decreases cardiac performance via aberrant sympathetic dominance.
Spontaneous Lorentz Violation: The Case of Infrared QED
Creators: name: Balachandran, A. P.
name: Kurkcuoglu, S.
name: de Queiroz, A. R.
name: Vaidya, S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: It is by now clear that infrared sector of QED has an intriguingly complex structure. Based on earlier pioneering works on this subject, two of us recently proposed a simple modification of QED by constructing a generalization of the $U(1)$ charge group of QED to the "Sky" group incorporating the known spontaneous Lorentz violation due to infrared photons, but still compatible in particular with locality. There it was shown that the "Sky" group is generated by the algebra of angle dependent charges and a study of its superselection sectors has revealed a manifest description of spontaneous breaking of Lorentz symmetry. We further elaborate this approach here and investigate in some detail the properties of charged particles dressed by the infrared photons. We find that Lorentz violation due to soft photons may be manifestly codified in an angle dependent fermion mass modifying therefore the fermion dispersion relations. The fact that the masses of the charged particles are not Lorentz invariant affects their spin content too.Time dilation formulae for decays should also get corrections. We speculate that these effects could be measured possibly in muon decay experiments.
description: 18+1 pages, revised version, expanded discussion in section 5,
Biomarkers of Exposure and Effect in Human Lymphoblastoid TK6 Cells Following [13C2]-Acetaldehyde Exposure
Creators: name: Moeller, Benjamin C.
name: Swenberg, James A.
name: Bodnar, Wanda M.
name: Sun, Wei
name: Green, Amanda
name: Wright, Fred A.
name: Recio, Leslie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The dose-response relationship for biomarkers of exposure (N2-ethylidene-dG adducts) and effect (cell survival and micronucleus formation) was determined across 4.5 orders of magnitude (50nM–2mM) using [13C2]-acetaldehyde exposures to human lymphoblastoid TK6 cells for 12h. There was a clear increase in exogenous N 2-ethylidene-dG formation at exposure concentrations ≥ 1µM, whereas the endogenous adducts remained nearly constant across all exposure concentrations, with an average of 3.0 adducts/107 dG. Exogenous adducts were lower than endogenous adducts at concentrations ≤ 10µM and were greater than endogenous adducts at concentrations ≥ 250µM. When the endogenous and exogenous adducts were summed together, statistically significant increases in total adduct formation over the endogenous background occurred at 50µM. Cell survival and micronucleus formation were monitored across the exposure range and statistically significant decreases in cell survival and increases in micronucleus formation occurred at ≥ 1000µM. This research supports the hypothesis that endogenously produced reactive species, including acetaldehyde, are always present and constitute the majority of the observed biological effects following very low exposures to exogenous acetaldehyde. These data can replace default assumptions of linear extrapolation to very low doses of exogenous acetaldehyde for risk prediction.
SALT spectroscopic observations of galaxy clusters detected by ACT and a Type II quasar hosted by a brightest cluster galaxy
Creators: name: Kirk, Brian
name: Hilton, Matt
name: Cress, Catherine
name: Crawford, Steven M.
name: Hughes, John P.
name: Battaglia, Nicholas
name: Bond, J. Richard
name: Burke, Claire
name: Gralla, Megan B.
name: Hajian, Amir
name: Hasselfield, Matthew
name: Hincks, Adam D.
name: Infante, Leopoldo
name: Kosowsky, Arthur
name: Marriage, Tobias A.
name: Menanteau, Felipe
name: Moodley, Kavilan
name: Niemack, Michael D.
name: Sievers, Jonathan L.
name: Sifón, Cristóbal
name: Wilson, Susan
name: Wollack, Edward J.
name: Zunckel, Caroline
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present Southern African Large Telescope (SALT) follow-up observations of seven massive clusters detected by the Atacama Cosmology Telescope (ACT) on the celestial equator using the Sunyaev-Zel'dovich (SZ) effect. We conducted multi-object spectroscopic observations with the Robert Stobie Spectrograph in order to measure galaxy redshifts in each cluster field, determine the cluster line-of-sight velocity dispersions, and infer the cluster dynamical masses. We find that the clusters, which span the redshift range 0.3 < z < 0.55, range in mass from (5 -- 20) x 10$^{14}$ solar masses (M200c). Their masses, given their SZ signals, are similar to those of southern hemisphere ACT clusters previously observed using Gemini and the VLT. We note that the brightest cluster galaxy in one of the systems studied, ACT-CL J0320.4+0032 at z = 0.38, hosts a Type II quasar. Only a handful of such systems are currently known, and therefore ACT-CL J0320.4+0032 may be a rare example of a very massive halo in which quasar-mode feedback is actively taking place.
description: Accepted for publication in MNRAS, 18 pages, 9 figures
Diesel Exhaust Inhalation Increases Cardiac Output, Bradyarrhythmias, and Parasympathetic Tone in Aged Heart Failure–Prone Rats
Creators: name: Lust, Robert M.
name: Perez, Christina M.
name: Carll, Alex P.
name: Hazari, Mehdi S.
name: Krantz, Quentin Todd
name: Farraj, Aimen K.
name: King, Charly J.
name: Winsett, Darrell W.
name: Costa, Daniel L.
name: Cascio, Wayne E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Acute air pollutant inhalation is linked to adverse cardiac events and death, and hospitalizations for heart failure. Diesel engine exhaust (DE) is a major air pollutant suspected to exacerbate preexisting cardiac conditions, in part, through autonomic and electrophysiologic disturbance of normal cardiac function. To explore this putative mechanism, we examined cardiophysiologic responses to DE inhalation in a model of aged heart failure–prone rats without signs or symptoms of overt heart failure. We hypothesized that acute DE exposure would alter heart rhythm, cardiac electrophysiology, and ventricular performance and dimensions consistent with autonomic imbalance while increasing biochemical markers of toxicity. Spontaneously hypertensive heart failure rats (16 months) were exposed once to whole DE (4h, target PM2.5 concentration: 500 µg/m3) or filtered air. DE increased multiple heart rate variability (HRV) parameters during exposure. In the 4h after exposure, DE increased cardiac output, left ventricular volume (end diastolic and systolic), stroke volume, HRV, and atrioventricular block arrhythmias while increasing electrocardiographic measures of ventricular repolarization (i.e., ST and T amplitudes, ST area, T-peak to T-end duration). DE did not affect heart rate relative to air. Changes in HRV positively correlated with postexposure changes in bradyarrhythmia frequency, repolarization, and echocardiographic parameters. At 24h postexposure, DE-exposed rats had increased serum C-reactive protein and pulmonary eosinophils. This study demonstrates that cardiac effects of DE inhalation are likely to occur through changes in autonomic balance associated with modulation of cardiac electrophysiology and mechanical function and may offer insights into the adverse health effects of traffic-related air pollutants.
A parametric study of possible solutions to the high-redshift overproduction of stars in modeled dwarf galaxies
Creators: name: White, Catherine E.
name: Somerville, Rachel S.
name: Ferguson, Henry C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Both numerical hydrodynamic and semi-analytic cosmological models of galaxy formation struggle to match observed star formation histories of galaxies in low mass halos (M$_{\rm{H}} \lesssim 10^{11} M_\odot$), predicting more star formation at high redshift and less star formation at low redshift than observed. The fundamental problem is that galaxies' gas accretion and star formation rates are too closely coupled in the models: the accretion rate largely drives the star formation rate. Observations point to gas accretion rates that outpace star formation at high redshift, resulting in a buildup of gas and a delay in star formation until lower redshifts. We present three empirical adjustments of standard recipes in a semi-analytic model motivated by three physical scenarios that could cause this decoupling: 1) the mass-loading factors of outflows driven by stellar feedback may have a steeper dependence on halo mass at earlier times, 2) the efficiency of star formation may be lower in low mass halos at high redshift, and 3) gas may not be able to accrete efficiently onto the disk in low mass halos at high redshift. These new recipes, once tuned, better reproduce the evolution of $f_\star \equiv M_\star/M_{\rm{H}}$ as a function of halo mass as derived from abundance matching over redshifts $z=0$ to $3$, though they have different effects on cold gas fractions, star formation rates, and metallicities. Changes to gas accretion and stellar-driven winds are promising, while direct modification of the star formation timescale requires drastic measures that are not physically well-motivated.
description: 27 pages, 29 figures
Infinite time singularities of the Kähler-Ricci flow
Creators: name: Tosatti, Valentino
name: Zhang, Yuguang
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 53C44, 53C55, 14J32, 32Q25, 58J35

description: We study the long-time behavior of the Kahler-Ricci flow on compact Kahler manifolds. We give an almost complete classification of the singularity type of the flow at infinity, depending only on the underlying complex structure. If the manifold is of intermediate Kodaira dimension and has semiample canonical bundle, so that it is fibered by Calabi-Yau varieties, we show that parabolic rescalings around any point on a smooth fiber converge smoothly to a unique limit, which is the product of a Ricci-flat metric on the fiber and of a flat metric on Euclidean space. An analogous result holds for collapsing limits of Ricci-flat Kahler metrics.
description: 22 pages
Search for the $b\bar{b}$ decay of the Standard Model Higgs boson in associated $(W/Z)H$ production 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: A search for the $b\bar{b}$ decay of the Standard Model Higgs boson is performed with the ATLAS experiment using the full dataset recorded at the LHC in Run 1. The integrated luminosities used from $pp$ collisions at $\sqrt{s}=7$ and 8 TeV are 4.7 and 20.3 fb$^{-1}$, respectively. The processes considered are associated $(W/Z)H$ production, where $W\to eν/μν$, $Z\to ee/μμ$ and $Z\toνν$. The observed (expected) deviation from the background-only hypothesis corresponds to a significance of 1.4 (2.6) standard deviations and the ratio of the measured signal yield to the Standard Model expectation is found to be $μ= 0.52 \pm 0.32 \mathrm{(stat.)} \pm 0.24 \mathrm{(syst.)}$ for a Higgs boson mass of 125.36 GeV. The analysis procedure is validated by a measurement of the yield of $(W/Z)Z$ production with $Z\to b\bar{b}$ in the same final states as for the Higgs boson search, from which the ratio of the observed signal yield to the Standard Model expectation is found to be $0.74 \pm 0.09 \mathrm{(stat.)} \pm 0.14 \mathrm{(syst.)}$.
description: 69 pages plus author list + cover pages (93 pages total), 25 figures, 11 tables, submitted to JHEP, All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HIGG-2013-23/
Additional file 1 of Impact of refractory and unexplained chronic cough on disease burden: a qualitative study
Creators: name: Ueda, Naoya
name: Yakushiji, Anzu
name: Schelfhout, Jonathan
name: Tokita, Shigeru
name: Kubo, Takekazu
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. Supplementary Figure 1 Clustering of patients from all transcripts. Supplementary Table 2 Semi-structured interview guide for individual interviews for the patients.
Additional file 1 of Stents versus bypass surgery: 3-year mortality risk of patients with coronary interventions aged 50+ in Germany
Creators: name: Nestler, Sophia
name: Kreft, Daniel
name: Donndorf, Peter
name: Ince, Hüseyin
name: Doblhammer, Gabriele
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1: Scheme of included and excluded person-times in the study using the example of five fictitious persons with different study entries and exits and health histories.
Delta r and the W-boson mass in the Singlet Extension of the Standard Model
Creators: name: Lopez-Val, D.
name: Robens, T.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The link between the electroweak gauge boson masses and the Fermi constant via the muon lifetime measurement is instrumental for constraining and eventually pinning down new physics. We consider the simplest extension of the Standard Model with an additional real scalar SU(2)_L x U(1)_Y singlet and compute the electroweak precision parameter Delta r, along with the corresponding theoretical prediction for the W-boson mass. When confronted with the experimental W-boson mass measurement, our predictions impose limits on the singlet model parameter space. We identify regions where these correspond to the most stringent experimental constraints that are currently available.
description: 21 pages, 6 figures; v2: 23 pages, slight modifications, references added. Corresponds to published journal version
Prototype: Digital twin for urban overheating management in Riga, Latvia
Creators: name: Rozenvalde, Anita Līvija
Publisher: name: Zenodo
Year: 2023
Subjects: prototype
digital twin
urban overheating
planning

description: This publication is a part of the MSc Geoinformatics for Urbanised Society (University of Tartu) thesis "Exploring the applicability of the digital twin technology for mitigating urban overheating: the case of Riga, Latvia". The publication shows a prototype for a digital twin for urban overheating management for a section of the Teika neighbourhood in Riga, Latvia. This prototype was built in Unreal Engine and contains the built infrastructure, high and medium vegetation, ground surface cover of the area, as well as a dynamic Sun and temperature data. It presents a potential initial base needed for a digital twin with functionalities needed to better plan urban form in a way that reduces urban heat trapping. This publication includes two versions of the prototype - an Unreal Engine developer project (Teika_twin_project.zip) and an exported version of the prototype as a user application (Teika_twin_exe_v2.zip).
Molecular Mechanisms of Fibrosis-Associated Promotion of Liver Carcinogenesis
Creators: name: Pogribny, Igor P.
name: Rusyn, Ivan
name: Kutanzi, Kristi
name: Kosyk, Oksana
name: Ainslie, Garrett R.
name: Muskhelishvili, Levan
name: Bataller, Ramon
name: Bradford, Blair U.
name: Boorman, Gary A.
name: Izawa, Takeshi
name: Uehara, Takeki
name: Yamate, Jyoji
name: Shymonyak, Svitlana
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Hepatocellular carcinoma (HCC) mostly develops in patients with advanced fibrosis; however, the mechanisms of interaction between a genotoxic insult and fibrogenesis are not well understood. This study tested a hypothesis that fibrosis promotes HCC via a mechanism that involves activation of liver stem cells. First, B6C3F1 mice were administered diethylnitrosamine (DEN; single ip injection of 1mg/kg at 14 days of age). Second, carbon tetrachloride (CCl4; 0.2ml/kg, 2/week ip starting at 8 weeks of age) was administered for 9 or 14 weeks to develop advanced liver fibrosis. In animals treated with DEN as neonates, presence of liver fibrosis led to more than doubling (to 100%) of the liver tumor incidence as early as 5 months of age. This effect was associated with activation of cells with progenitor features in noncancerous liver tissue, including markers of replicative senescence (p16), oncofetal transformation (Afp, H19, and Bex1), and increased “stemness” (Prom1 and Epcam). In contrast, the dose of DEN used did not modify the extent of liver inflammation, fibrogenesis, oxidative stress, proliferation, or apoptosis induced by subchronic CCl4 administration. This study demonstrates the potential role of liver stem-like cells in the mechanisms of chemical-induced, fibrosis-promoted HCC. We posit that the combination of genotoxic and fibrogenic insults is a sensible approach to model liver carcinogenesis in experimental animals. These results may contribute to identification of cirrhotic patients predisposed to HCC by analyzing the expression of hepatic progenitor cell markers in the noncancerous liver tissue.
Non-minimally Coupled Tachyon Field in Teleparallel Gravity
Creators: name: Fazlpour, Behnaz
name: Banijamali, Ali
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We perform a full investigation on dynamics of a new dark energy model in which the four-derivative of a non-canonical scalar field (tachyon) is non-minimally coupled to the vector torsion. Our analysis is done in the framework of teleparallel equivalent of general relativity which is based on torsion instead of curvature. We show that in our model there exists a late-time scaling attractor (point $P_{4}$), corresponding to an accelerating universe with the property that dark energy and dark matter densities are of the same order. Such a point can help to alleviate the cosmological coincidence problem. Existence of this point is the most significant difference between our model and another model in which a canonical scalar field (quintessence) is used instead of tachyon field.
description: 15 pages, 6 figures
Rethinking access to aggregated cultural heritage data. User-centered restructuring at Deutsche Digitale Bibliothek
Creators: name: Breuer, Martin
name: Hennewig, Lena
Publisher: name: Zenodo
Year: 2023

description: Platforms such as the Deutsche Digitale Bibliothek (henceforth: DDB) aggregate large-scale and cross-disciplinary digitized cultural heritage data. Conceived as a one-size-fits-all solution for the general public and specific target groups alike, cultural heritage platforms (CHPs) face a variety of fundamental problems to effectively structure, present, and offer access to the aggregated data. One central aspect is usability: Who uses the platforms for what purposes? This raises the question of how CHPs may actively design their data, search environments, and offered activities to become more user-friendly for a vastly heterogeneous user pool. The DDB has addressed these questions in the large-scale project "User-oriented restructuring of the DDB" (2020-2023), whose outcomes we critically analyse in our contribution. The project has endowed us with a unique data set of surveys and customer interactions that we exploit to derive key insights for user-centric design of CHPs. Our paper highlights the usability of our data for academic research. We inquire into how the DDB, and CHPs more broadly, may become more relevant and sustainable partners for (digital) humanities researchers. In this, our paper focuses on four key points. First, we will give a brief introduction to the structure of the DDB and the data made available on it. Second, we report on the aims, activities, and achievements of DDB’s user-oriented restructuring. The project’s principal objective is to simultaneously improve the usability of both the web interface and the aggregated data for different user groups (researchers, cultural heritage professionals, teachers, general public). This implies re-designing the website and its search functionalities, creating specific content and theme-focused information for particular user groups, and fostering collaborations with partner institutions from education and research. Third, we present our user-facing activities to enhance the usability of the DDB and its data for academic researchers. Here, we address and discuss the prospects and limits which we consider crucial for improving aggregating platforms like the DDB for the field of (digital) humanities research: the creation of specialized sub-portals, the gathering of interoperable, cross-sector datasets, and the development of customized outreach activities. Fourth, we take a step back to ask which role CHPs can play in providing and adapting cultural heritage data for research in the humanities. In the fast-growing and changing field of digital humanities, cultural heritage data has to be FAIR. Here, we argue that CHPs can serve as a critical and sustainable interface between research projects and cultural institutions worldwide, opening new ways for inclusive collaboration.
Multiple NSAID-Induced Hits Injure the Small Intestine: Underlying Mechanisms and Novel Strategies
Creators: name: Saitta, Kyle S.
name: Redinbo, Matthew R.
name: Boelsterli, Urs A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Nonsteroidal anti-inflammatory drugs (NSAIDs) can cause serious gastrointestinal (GI) injury including jejunal/ileal mucosal ulceration, bleeding, and even perforation in susceptible patients. The underlying mechanisms are largely unknown, but they are distinct from those related to gastric injury. Based on recent insights from experimental models, including genetics and pharmacology in rodents typically exposed to diclofenac, indomethacin, or naproxen, we propose a multiple-hit pathogenesis of NSAID enteropathy. The multiple hits start with an initial pharmacokinetic determinant caused by vectorial hepatobiliary excretion and delivery of glucuronidated NSAID or oxidative metabolite conjugates to the distal small intestinal lumen, where bacterial β-glucuronidase produces critical aglycones. The released aglycones are then taken up by enterocytes and further metabolized by intestinal cytochrome P450s to potentially reactive intermediates. The “first hit” is caused by the NSAID and/or oxidative metabolites that induce severe endoplasmic reticulum stress or mitochondrial stress and lead to cell death. The “second hit” is created by the significant subsequent inflammatory response that would follow such a first-hit injury. Based on these putative mechanisms, strategies have been developed to protect the enterocytes from being exposed to the parent NSAID and/or oxidative metabolites. Among these, a novel strategy already demonstrated in a murine model is the selective disruption of bacteria-specific β-glucuronidases with a novel small molecule inhibitor that does not harm the bacteria and that alleviates NSAID-induced enteropathy. Such mechanism-based strategies require further investigation but provide potential avenues for the alleviation of the GI toxicity caused by multiple NSAID hits.
Additional file 2 of Stents versus bypass surgery: 3-year mortality risk of patients with coronary interventions aged 50+ in Germany
Creators: name: Nestler, Sophia
name: Kreft, Daniel
name: Donndorf, Peter
name: Ince, Hüseyin
name: Doblhammer, Gabriele
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 2: Table S1. Number of coronary interventions per patient 2005–2012 and deaths 2005–2015. Table S2. Kaplan-Meier survival estimates by coronary intervention, survival in % after 1, 2 and 3 years, 2005–2015. Table S3. Sensitivity analysis: multivariable analysis: Cox model adjusted for risk factors effecting mortality in CAD patients with coronary interventions, 2005–2015a.
Properties of an Aloha-like stability region
Creators: name: Xie, Nan
name: Walsh, John MacLaren
name: Weber, Steven
Publisher: name: arXiv
Year: 2014
Subjects: subject: Information Theory (cs.IT)
subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: A well-known inner bound on the stability region of the finite-user slotted Aloha protocol is the set of all arrival rates for which there exists some choice of the contention probabilities such that the associated worst-case service rate for each user exceeds the user's arrival rate, denoted $Λ$. Although testing membership in $Λ$ of a given arrival rate can be posed as a convex program, it is nonetheless of interest to understand the properties of this set. In this paper we develop new results of this nature, including $i)$ an equivalence between membership in $Λ$ and the existence of a positive root of a given polynomial, $ii)$ a method to construct a vector of contention probabilities to stabilize any stabilizable arrival rate vector, $iii)$ the volume of $Λ$, $iv)$ explicit polyhedral, spherical, and ellipsoid inner and outer bounds on $Λ$, and $v)$ characterization of the generalized convexity properties of a natural ``excess rate'' function associated with $Λ$, including the convexity of the set of contention probabilities that stabilize a given arrival rate vector.
description: 28 pages, 9 figures. Submitted August 15, 2014, revised September 21, 2015 and August 31, 2016, and accepted November 06, 2016 for publication in IEEE Transactions on Information Theory. Preliminary results presented at ISIT 2010, ITA 2010, and ITA 2011. DOI: 10.1109/TIT.2016.2640302. Copyright transferred to IEEE. This is last version uploaded by the authors prior to IEEE proofing process
A Systems Biology Approach Utilizing a Mouse Diversity Panel Identifies Genetic Differences Influencing Isoniazid-Induced Microvesicular Steatosis
Creators: name: Sumner, Susan J.
name: Pletcher, Mathew T.
name: Adkins, Karissa
name: Kurtz, Catherine L.
name: Church, Rachel J.
name: Mosedale, Merrie
name: Watkins, Paul B.
name: Harrill, Alison H.
name: Batheja, Ameesha
name: Singer, Monica
name: Wu, Hong
name: Pathmasiri, Wimal
name: Eaddy, John S.
name: Pandher, Karamjeet
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Isoniazid (INH), the mainstay therapeutic for tuberculosis infection, has been associated with rare but serious hepatotoxicity in the clinic. However, the mechanisms underlying inter-individual variability in the response to this drug have remained elusive. A genetically diverse mouse population model in combination with a systems biology approach was utilized to identify transcriptional changes, INH-responsive metabolites, and gene variants that contribute to the liver response in genetically sensitive individuals. Sensitive mouse strains developed severe microvesicular steatosis compared with corresponding vehicle control mice following 3 days of oral treatment with INH. Genes involved in mitochondrial dysfunction were enriched among liver transcripts altered with INH treatment. Those associated with INH treatment and susceptibility to INH-induced steatosis in the liver included apolipoprotein A-IV, lysosomal-associated membrane protein 1, and choline phosphotransferase 1. These alterations were accompanied by metabolomic changes including reduced levels of glutathione and the choline metabolites betaine and phosphocholine, suggesting that oxidative stress and reduced lipid export may additionally contribute to INH-induced steatosis. Finally, genome-wide association mapping revealed that polymorphisms in perilipin 2 were linked to increased triglyceride levels following INH treatment, implicating a role for inter-individual differences in lipid packaging in the susceptibility to INH-induced steatosis. Taken together, our data suggest that INH-induced steatosis is caused by not one, but multiple events involving lipid retention in the livers of genetically sensitive individuals. This work also highlights the value of using a mouse diversity panel to investigate drug-induced responses across a diverse population.
Air Pollution Upregulates Endothelial Cell Procoagulant Activity via Ultrafine Particle-Induced Oxidant Signaling and Tissue Factor Expression
Creators: name: Snow, S. J.
name: Carraway, M. S.
name: Cheng, W.
name: Wolberg, A. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Air pollution exposure is associated with cardiovascular events triggered by clot formation. Endothelial activation and initiation of coagulation are pathophysiological mechanisms that could link inhaled air pollutants to vascular events. Here we investigated the underlying mechanisms of increased endothelial cell procoagulant activity following exposure to soluble components of ultrafine particles (soluble UF). Human coronary artery endothelial cells (HCAEC) were exposed to soluble UF and assessed for their ability to trigger procoagulant activity in platelet-free plasma. Exposed HCAEC triggered earlier thrombin generation and faster fibrin clot formation, which was abolished by an anti-tissue factor (TF) antibody, indicating TF-dependent effects. Soluble UF exposure increased TF mRNA expression without compensatory increases in key anticoagulant proteins. To identify early events that regulate TF expression, we measured endothelial H2O2 production following soluble UF exposure and identified the enzymatic source. Soluble UF exposure increased endothelial H2O2 production, and antioxidants attenuated UF-induced upregulation of TF, linking the procoagulant responses to reactive oxygen species (ROS) formation. Chemical inhibitors and RNA silencing showed that NOX-4, an important endothelial source of H2O2, was involved in UF-induced upregulation of TF mRNA. These data indicate that soluble UF exposure induces endothelial cell procoagulant activity, which involves de novo TF synthesis, ROS production, and the NOX-4 enzyme. These findings provide mechanistic insight into the adverse cardiovascular effects associated with air pollution exposure.
Linearized fluid/gravity correspondence: from shear viscosity to all order hydrodynamics
Creators: name: Bu, Yanyan
name: Lublinsky, Michael
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: In ref. \cite{1406.7222}, we reported a construction of all order linearized fluid dynamics with strongly coupled $\mathcal{N}=4$ super-Yang-Mills theory as underlying microscopic description. The linearized fluid/gravity correspondence makes it possible to resum all order derivative terms in the fluid stress tensor. Dissipative effects are fully encoded by the shear term and a new one, emerging starting from third order in hydrodynamic derivative expansion. In this work, we provide all computational details omitted in \cite{1406.7222} and present additional results. We derive closed-form linear holographic RG flow-type equations for momenta-dependent transport coefficient functions. Generalized Navier-Stokes equations are shown to emerge from the constraint components of the bulk Einstein equations. We perturbatively solve the RG equations for the viscosity functions, up to third order in derivative expansion, and up to this order compute spectrum of small fluctuations. Finally, we solve the RG equations numerically, thus accounting for all order derivative terms in the boundary stress tensor.
description: v1: 33 pages, 4 multi-figures; v2: added 6 refs, made a couple of clarifications, to appear in JHEP; v3: corrected sound wave dispersion relation in equation (2.44)
Large tensor-to-scalar ratio and running of the scalar spectral index with Instep Inflation
Creators: name: Ballesteros, Guillermo
name: Casas, J. Alberto
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: If a sizeable tensor-to-scalar ratio ~0.1 turns out to be detected and a negative running of the scalar spectral index ~0.01 is significantly required by the data, the vast majority of single field models of inflation will be ruled out. We show that a flat tree-level effective potential, lifted by radiative corrections and by the imprints of a high energy scale (in the form of non-renormalizable operators) can explain those features and produce enough inflation in the slow-roll regime.
description: 16 pages, 2 figures, to appear in Physical Review D
Cumulative Risk: Toxicity and Interactions of Physical and Chemical Stressors
Creators: name: Simmons, Jane Ellen
name: Selgrade, MaryJane K.
name: Rider, Cynthia V.
name: Sexton, Kenneth
name: Catlin, Natasha
name: Morata, Thais
name: Gordon, Christopher J.
name: Boekelheide, Kim
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Recent efforts to update cumulative risk assessment procedures to incorporate nonchemical stressors ranging from physical to psychosocial reflect increased interest in consideration of the totality of variables affecting human health and the growing desire to develop community-based risk assessment methods. A key roadblock is the uncertainty as to how nonchemical stressors behave in relationship to chemical stressors. Physical stressors offer a reasonable starting place for measuring the effects of nonchemical stressors and their modulation of chemical effects (and vice versa), as they clearly differ from chemical stressors; and “doses” of many physical stressors are more easily quantifiable than those of psychosocial stressors. There is a commonly held belief that virtually nothing is known about the impact of nonchemical stressors on chemically mediated toxicity or the joint impact of coexposure to chemical and nonchemical stressors. Although this is generally true, there are several instances where a substantial body of evidence exists. A workshop titled “Cumulative Risk: Toxicity and Interactions of Physical and Chemical Stressors” held at the 2013 Society of Toxicology Annual Meeting provided a forum for discussion of research addressing the toxicity of physical stressors and what is known about their interactions with chemical stressors, both in terms of exposure and effects. Physical stressors including sunlight, heat, radiation, infectious disease, and noise were discussed in reference to identifying pathways of interaction with chemical stressors, data gaps, and suggestions for future incorporation into cumulative risk assessments.
IGCT Seminar Series: Running Bayesian Clinical Trials:Practical Examples for Future Trialists
Creators: name: Fuller, Clifton D.
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 490501
subject: Applied statistics
classificationCode: 320222
subject: Radiology and organ imaging
classificationCode: 320299
subject: Clinical sciences not elsewhere classified
classificationCode: 320226
subject: Surgery
classificationCode: 321105
subject: Chemotherapy
classificationCode: 321104
subject: Cancer therapy (excl. chemotherapy and radiation therapy)
classificationCode: 321102
subject: Cancer diagnosis
classificationCode: 321109
subject: Predictive and prognostic markers
classificationCode: 321110
subject: Radiation therapy
classificationCode: 321111
subject: Solid tumours
classificationCode: 321199
subject: Oncology and carcinogenesis not elsewhere classified
classificationCode: 321108
subject: Molecular targets
classificationCode: 329999
subject: Other biomedical and clinical sciences not elsewhere classified
classificationCode: 420202
subject: Disease surveillance
classificationCode: 420309
subject: Health management
classificationCode: 420312
subject: Implementation science and evaluation
classificationCode: 490502
subject: Biostatistics
classificationCode: 490504
subject: Forensic evaluation, inference and statistics
classificationCode: 490508
subject: Statistical data science
classificationCode: 490509
subject: Statistical theory
classificationCode: 490599
subject: Statistics not elsewhere classified

description: The Image Guided Cancer Therapy (IGCT) Research Program together with the CCSG Image-Driven Biology-Informed Therapy (IDBT) Program Workshop Series presents: “Bayesian Clinical Trial Design Workshop”.
Slide presentation by Dr. Fuller on the topic "Running Bayesian Clinical Trials:Practical Examples for Future Trialists", delivered live via Zoom on 2024-09-16T1100-1145.Precis:"This presentation is an introductory discourse detailing the basics of practical features of Bayesian trials for clinician investigators. Non-technical exemplar approaches to Bayesian techniques as well as Phase I-III illustrative trials will be used to provide a general framework in for potential and developing clinical trialists without or with limited prior background, with a focus on adaptive methods."
Epigenetic Events Determine Tissue-Specific Toxicity of Inhalational Exposure to the Genotoxic Chemical 1,3-Butadiene in Male C57BL/6J Mice
Creators: name: Bodnar, Wanda
name: Kobets, Tetyana
name: Sangaraju, Dewakar
name: Rusyn, Ivan
name: Kosyk, Oksana
name: Tretyakova, Natalia
name: Chappell, Grace
name: O’Brien, Bridget
name: Sexton, Kenneth G.
name: Pogribny, Igor P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: 1,3-Butadiene (BD), a widely used industrial chemical and a ubiquitous environmental pollutant, is a known human carcinogen. Although genotoxicity is an established mechanism of the tumorigenicity of BD, epigenetic effects have also been observed in livers of mice exposed to the chemical. To better characterize the diverse molecular mechanisms of BD tumorigenicity, we evaluated genotoxic and epigenotoxic effects of BD exposure in mouse tissues that are target (lung and liver) and non-target (kidney) for BD-induced tumors. We hypothesized that epigenetic alterations may explain, at least in part, the tissue-specific differences in BD tumorigenicity in mice. We evaluated the level of N-7-(2,3,4-trihydroxybut-1-yl)guanine adducts and 1,4-bis-(guan-7-yl)-2,3-butanediol crosslinks, DNA methylation, and histone modifications in male C57BL/6 mice exposed to filtered air or 425 ppm of BD by inhalation (6 h/day, 5 days/week) for 2 weeks. Although DNA damage was observed in all three tissues of BD-exposed mice, variation in epigenetic effects clearly existed between the kidneys, liver, and lungs. Epigenetic alterations indicative of genomic instability, including demethylation of repetitive DNA sequences and alterations in histone-lysine acetylation, were evident in the liver and lung tissues of BD-exposed mice. Changes in DNA methylation were insignificant in the kidneys of treated mice, whereas marks of condensed heterochromatin and transcriptional silencing (histone-lysine trimethylation) were increased. These modifications may represent a potential mechanistic explanation for the lack of tumorigenesis in the kidney. Our results indicate that differential tissue susceptibility to chemical-induced tumorigenesis may be attributed to tissue-specific epigenetic alterations.
Additional file 3 of Stents versus bypass surgery: 3-year mortality risk of patients with coronary interventions aged 50+ in Germany
Creators: name: Nestler, Sophia
name: Kreft, Daniel
name: Donndorf, Peter
name: Ince, Hüseyin
name: Doblhammer, Gabriele
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 3: Fig. S2. Age-specific and age-standardized 3-year mortality rates of CAD-patients by sex and coronary interventions from 2005 to 2015: BMS (A), DES (B), CABG (C), mixed (D) or none (E).