cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Molecular Targets in Campylobacter Infections
Creators: name: Heimesaat, Markus M.
name: Backert, Steffen
name: Alter, Thomas
name: Bereswill, Stefan
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2023
Subjects: subject: one health concept
subject: infection prevention strategies
subject: campylobacteriosis
subject: Campylobacter jejuni infection models
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Human campylobacteriosis results from foodborne infections with Campylobacter bacteria such as Campylobacter jejuni and Campylobacter coli, and represents a leading cause of bacterial gastroenteritis worldwide. After consumption of contaminated poultry meat, constituting the major source of pathogenic transfer to humans, infected patients develop abdominal pain and diarrhea. Post-infectious disorders following acute enteritis may occur and affect the nervous system, the joints or the intestines. Immunocompromising comorbidities in infected patients favor bacteremia, leading to vascular inflammation and septicemia. Prevention of human infection is achieved by hygiene measures focusing on the reduction of pathogenic food contamination. Molecular targets for the treatment and prevention of campylobacteriosis include bacterial pathogenicity and virulence factors involved in motility, adhesion, invasion, oxygen detoxification, acid resistance and biofilm formation. This repertoire of intervention measures has recently been completed by drugs dampening the pro-inflammatory immune responses induced by the Campylobacter endotoxin lipo-oligosaccharide. Novel pharmaceutical strategies will combine anti-pathogenic and anti-inflammatory effects to reduce the risk of both anti-microbial resistance and post-infectious sequelae of acute enteritis. Novel strategies and actual trends in the combat of Campylobacter infections are presented in this review, alongside molecular targets applied for prevention and treatment strategies.
Decomposing Textual Information For Style Transfer
Creators: name: Yamshchikov, Ivan P.
name: Shibaev, Viacheslav
name: Nagaev, Aleksander
name: Jost, Jürgen
name: Tikhonov, Alexey
Publisher: name: arXiv
Year: 2019
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: This paper focuses on latent representations that could effectively decompose different aspects of textual information. Using a framework of style transfer for texts, we propose several empirical methods to assess information decomposition quality. We validate these methods with several state-of-the-art textual style transfer methods. Higher quality of information decomposition corresponds to higher performance in terms of bilingual evaluation understudy (BLEU) between output and human-written reformulations.
description: arXiv admin note: substantial text overlap with arXiv:1908.06809
Quantifying metabolic activity of Ascaris suum L3 using resazurin reduction
Creators: name: Kundik, Arkadi
name: Musimbi, Zaneta D.
name: Krücken, Jürgen
name: Hildebrandt, Thomas
name: Kornilov, Oleg
name: Hartmann, Susanne
name: Ebner, Friederike
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: Drug screening assay
subject: Ascaris suum
subject: Larvae
subject: Viability assay
subject: Resazurin
subject: Metabolic activity
subject: Anthelmintics
subject: 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::630 Landwirtschaft und verwandte Bereiche

description: Background Helminth infections are an important public health problem in humans and have an even greater impact on domestic animal and livestock welfare. Current readouts for anthelmintic drug screening assays are stage development, migration, or motility that can be subjective, laborious, and low in throughput. The aim of this study was to apply and optimize a fluorometric technique using resazurin for evaluating changes in the metabolic activity of Ascaris suum third-stage larvae (L3), a parasite of high economic relevance in swine. Methods Ascaris suum L3 were mechanically hatched from 6- to 8-week embryonated and sucrose-gradient-enriched eggs. Resazurin dye and A. suum L3 were titrated in 96-well microtiter plates, and resazurin reduction activity was assessed by fluorometry after 24 h of incubation. Fluorescence microscopy was used to localize the resazurin reduction site within the larvae. Finally, we exposed A. suum L3 to various stress conditions including heat, methanol, and anthelmintics, and investigated their impact on larval metabolism through resazurin reduction activity. Results We show that the non-fluorescent dye resazurin is reduced inside vital A. suum L3 to fluorescent resorufin and released into the culture media. Optimal assay parameters are 100–1000 L3 per well, a resazurin concentration of 7.5 µg/ml, and incubation at 37 °C/5% CO2 for 24 h. An intact L2 sheath around the L3 of A. suum completely prevents the uptake of resazurin, while in unsheathed L3, the most intense fluorescence signal is observed along the larval midgut. L3 exposed to methanol or heat show a gradually decreased resazurin reduction activity. In addition, 24 h exposure to ivermectin at 0.625 µM, mebendazole at 5 µM, and thiabendazole from 10 to 100 µM significantly decreased larval metabolic activity by 55%, 73%, and 70% to 89%, respectively. Conclusions Together, our results show that both metabolic stressors and anthelmintic drugs significantly and reproducibly reduce the resazurin reduction activity of A. suum L3, making the proposed assay a sensitive and easy-to-use method to evaluate metabolic activity of A. suum L3 in vitro.
WAYS TO PROVIDE QUALITY COMMUNICATION SERVICES TO THE POPULATION OF THE REGION.
Creators: name: Ochilov, Laziz
Publisher: name: Zenodo
Year: 2023

description: The rapid development of information and communication technologies, the digitalization of the economy, the growth of consumer information culture, increase the presence of enterprises in the virtual space and radically change marketing methods. Virtual markets have been shown to provide new opportunities for merchants as telecommunications services evolve, combining traditional marketing tools with networked Internet communications and digital marketing techniques.
Epicatechin Supplementation on Muscular Atrophy - Systematic Review..pdf
Creators: name: German, Iris
name: Tadashi Cosin Shindo, João Vitor
name: Shinohara, André Luis
name: Pomini, Karina Torres
name: Matsumoto, Mariza Akemi
name: Andreo, Jesus Carlos
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Anatomy

description: Polyphenol epicatechin has been investigated by the biological effects on the reduction of the catabolic process in skeletal musculature-related diseases. Due to the potential benefits described in the literature and clinical relevance, the purpose of this systematic review was to conduct an analysis of epicatechin effects on muscular atrophy in humans and animals. A search was conducted in PubMed/MEDLINE, Embase, Web of Science and Cochraine Library databases, with no restriction concerning the year of publication, by combining the following keywords: “Catechin AND muscular atrophy”, “Epicatechin AND muscle regeneration”, “Epicatechin AND muscle AND damage”. A total of 241 articles were initially identified, being that 14 studies were selected once they complied with the eligibility criteria. The qualitative analysis showed a prevalence of the inhibitory action of epicatechin in myostatin expression and atrogenes FOXO, MAFbx and MuRF1. Epicatechin showed positive effects on increased follistatin and on the activation of the myogenic regulatory factors (Myf5, MyoD and myogenin). In addition, the studies evidenced the impact of epicatechin on the mitochondrias' biosynthesis in muscle fibers, activation of the signaling pathway of AKT/mTOR protein synthesis and improvement of the skeletal musculature performance, particularly when associated to physical training. In conclusion, epicatechin showed a promising clinical applicability through beneficial results under conditions which negatively affect the skeletal musculature. However, there's no standardization of protocol allowing to draw more specific conclusions on its therapeutic use.
Endogenous chloride channels of insect sf9 cells. Evidence for coordinated activity of small elementary channel units
Creators: name: Hviid Larsen, E.
name: Gabriel, S. E.
name: Stutts, M. J.
name: Price, E. M.
name: Boucher, R. C.
name: Fullton, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1996

description: The endogenous Cl- conductance of Spodoptera frugiperda (Sf9) cells was studied 20-35 h after plating out of either uninfected cells or cells infected by a baculovirus vector carrying the cloned beta-galactosidase gene (beta-Gal cells). With the cation Tris+ in the pipette and Na+ in the bath, the reversal potential of whole-cell currents was governed by the prevailing Cl- equilibrium potential and could be fitted by the Goldman-Hodgkin-Katz equation with similar permeabilities for uninfected and beta-Gal cells. In the frequency range 0.12 < f < 300 Hz, the power density spectrum of whole-cell Cl- currents could be fitted by three Lorentzians. Independent of membrane potential, >50% of the total variance of whole-cell current fluctuations was accounted for by the low frequency Lorentzian (fc = 0.40 +/- 0.03 Hz, n = 6). Single-Cl- channels showed complex gating kinetics with long lasting (seconds) openings interrupted by similar long closures. In the open state, channels exhibited fast burst-like closures. Since the patches normally contained more than a single channel, it was not possible to measure open and closed dwell-time distributions for comparing single-Cl- channel activity with the kinetic features of whole-cell currents. However, the power density spectrum of Cl- currents of cell-attached and excised outside-out patches contained both high and low frequency Lorentzian components, with the corner frequency of the slow component (fc = 0.40 +/- 0.02 Hz, n = 4) similar to that of whole-cell current fluctuations. Chloride channels exhibited multiple conductance states with similar Goldman-Hodgkin-Katz-type rectification. Single-channel permeabilities covered the range from approximately 0.6.10(-14) cm5/s to approximately 6.10(-14) cm3/s, corresponding to a limiting conductance (gamma 150/150) of approximately 3.5 pS and approximately 35 pS, respectively. All states reversed near the same membrane potential, and they exhibited similar halide ion selectivity, P1 > PCl approximately PBr. Accordingly, Cl- current amplitudes larger than current flow through the smallest channel unit resolved seem to result from simultaneous open/shut events of two or more channel units.
Magnetic hard-axis ordering near ferromagnetic quantum criticality
Creators: name: Krüger, F.
name: Pedder, C. J.
name: Green, A. G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We investigate the interplay of quantum fluctuations and magnetic anisotropies in metallic ferromagnets. Our central result is that fluctuations close to a quantum critical point can drive the moments to point along a magnetic hard axis. As a proof of concept, we show this behavior explicitly for a generic two-band model with local Coulomb and Hund's interactions, and a spin-orbit-induced easy plane anisotropy. The phase diagram is calculated within the fermionic quantum order-by-disorder approach, which is based on a self-consistent free energy expansion around a magnetically ordered state with unspecified orientation. Quantum fluctuations render the transition of the easy-plane ferromagnet first-order below a tricritical point. At even lower temperatures, directionally dependent transverse fluctuations dominate the magnetic anisotropy and the moments flip to lie along the magnetic hard axis. We discuss our findings in the context of recent experiments that show this unusual ordering along the magnetic hard direction.
description: 5 pages, 3 figures
Hodgkin Lymphoma Cell Lines and Tissues Express mGluR5: A Potential Link to Ophelia Syndrome and Paraneoplastic Neurological Disease
Creators: name: Schnell, Sofia
name: Knierim, Ellen
name: Bittigau, Petra
name: Kreye, Jakob
name: Hauptmann, Kathrin
name: Hundsdoerfer, Patrick
name: Morales-Gonzalez, Susanne
name: Schuelke, Markus
name: Nikolaus, Marc
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2023
Subjects: subject: metabotropic glutamate 5 receptor
subject: anti-mGluR5 encephalitis
subject: neuroimmunology
subject: pediatric neurology
subject: pediatric oncology
subject: transcriptome analysis
subject: Hodgkin lymphoma
subject: Ophelia syndrome
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Ophelia syndrome is characterized by the coincidence of severe neuropsychiatric symptoms, classical Hodgkin lymphoma, and the presence of antibodies to the metabotropic glutamate 5 receptor (mGluR5). Little is known about the pathogenetic link between these symptoms and the role that anti-mGluR5-antibodies play. We investigated lymphoma tissue from patients with Ophelia syndrome and with isolated classical Hodgkin lymphoma by quantitative immunocytochemistry for mGluR5-expression. Further, we studied the L-1236, L-428, L-540, SUP-HD1, KM-H2, and HDLM-2 classical Hodgkin lymphoma cell lines by FACS and Western blot for mGluR5-expression, and by transcriptome analysis. mGluR5 surface expression differed significantly in terms of receptor density, distribution pattern, and percentage of positive cells. The highest expression levels were found in the L-1236 line. RNA-sequencing revealed more than 800 genes that were higher expressed in the L-1236 line in comparison to the other classical Hodgkin lymphoma cell lines. High mGluR5-expression was associated with upregulation of PI3K/AKT and MAPK pathways and of downstream targets (e.g., EGR1) known to be involved in classical Hodgkin lymphoma progression. Finally, mGluR5 expression was increased in the classical Hodgkin lymphoma-tissue of our Ophelia syndrome patient in contrast to five classical Hodgkin lymphoma-patients without autoimmune encephalitis. Given the association of encephalitis and classical Hodgkin lymphoma in Ophelia syndrome, it is possible that mGluR5-expression in classical Hodgkin lymphoma cells not only drives tumor progression but also triggers anti-mGluR5 encephalitis even before classical Hodgkin lymphoma becomes manifest.
title: Modellierung und Berechnung der Strömungsvorgänge im Luftspalt einer permanentmagneterregten Synchronmaschine
Creators: name: Meier, Vinzent
Publisher: name: UNSPECIFIED
Year: 2023

description: Batterieelektrische Fahrzeuge stellen hohe Anforderungen an Effizienz, Leistungsdichte und Dauerleistung der elektrischen Maschine, wozu auch das verwendete Kühlkonzept einen erheblichen Beitrag leistet. Die Kühlmethoden und das thermische Verhalten möglichst früh im Entwicklungsprozess zu bewerten ist ein Ziel der digitalen Entwicklung. Dabei kommen auch numerische Berechnungen der Temperaturverteilung elektrischer Maschinen zum Einsatz. Eine bestehende Herausforderung für die thermische Berechnung permanentmagneterregter Synchronmaschinen sind die Strömungsvorgänge im Luftspalt zwischen Rotor und Stator. Wird neben Luft noch eine Kühlflüssigkeit in den Innenraum der elektrischen Maschine eingebracht, kann diese in den Luftspalt zwischen Rotor und Stator gelangen. Infolgedessen entsteht eine komplexe zweiphasige Strömung, die sich sowohl auf die Schleppverluste als auch den Wärmetransport über den Spalt auswirkt. Bisherige Untersuchungen zu Schleppverlusten und Wärmeübergang beschränken sich auf einphasige Spaltströmungen, weshalb in der vorliegenden Arbeit ein Modellaufbau zur Berechnung der zweiphasigen Strömungsformen entwickelt und mit Experimenten verglichen wird. Die Randbedingungen des Luftspalts, wie bspw. die geringe Luftspalthöhe und hohe Geschwindigkeitsgradienten führen zur Notwendigkeit einer feinen, räumlichen und zeitlichen Diskretisierung in der Berechnung. Aufgrund periodischer Strömungsformen kann das Rechengebiet soweit reduziert werden, dass trotz der hohen Anforderungen eine Berechnung der Strömungsvorgänge im Luftspalt möglich wird. Für die Abbildung der zweiphasigen Strömungsformen haben sich Large Eddy Simulationen in Kombination mit der Volume of Fluid Methode als geeignet erwiesen. Die vorgestellten Berechnungsmodelle werden für die detaillierte Analyse der Strömung im Luftspalt angewendet. In Abhängigkeit des Ölanteils im Luftspaltmodell ergeben sich drei Bereiche, die sich durch unterschiedliche Ölstrukturen voneinander abgrenzen. Es tritt eine geschichtete Spaltströmung bei geringen Ölanteilen, eine alternierend geschichtete und chaotische Spaltströmung bei mittleren Ölanteilen und eine chaotische Spaltströmung bei hohen Ölanteilen auf. Drehzahl, Temperatur und Luftspaltgeometrie wirken sich auf diese Strömungsformen und damit auf die Verlustleistung im Luftspalt aus. Abgeleitet von der detaillierten Analyse wird ein Ansatz zur Bestimmung des Ölanteils im Luftspalt für quasistationäre Betriebspunkte vorgestellt und durch Experimente bestätigt. Schlussendlich ermöglichen die präsentierten Modelle die Berechnung des Wärmeübergangs und der Verlustleistung im Luftspalt und damit auch aller Bauteiltemperaturen im Gesamtmodell der elektrischen Maschine.
OpenFOAM course for beginners: Hands-on training
Creators: name: Jibran Haider
Publisher: name: Zenodo
Year: 2018
Subjects: OpenFOAM
Training
Course
Tutorial

description: This course material is intended for beginners with no previous experience of using OpenFOAM. Existing users can also benefit by broadening their knowledge and learning new techniques. We familiarise ourselves with the OpenFOAM environment and understand the basic working of the software including meshing, solving and post-processing. The learning process is enhanced through a series of hands-on tutorials.
Experimental Measures of Amino Acid Hydrophobicity and the Topology of Transmembrane and Globular Proteins
Creators: name: Wolfenden, Richard
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Roles of Solvent Water in the Positions of Biological Equilibria The noncovalent binding interactions of biological molecules involve the stripping away of solvent water from regions of contact between the binding partners. Accordingly, the net strength of their interactions with other molecules can be considered to include the cost of removing the interacting molecules (at least those parts that make contact with each other) from the sol- vent to which they were previously exposed. Free ener- gies of solvation of biological molecules also play a major role in determining the positions of their chemi- cal equilibria. For example, the products of hydrolysis of ATP are so much more strongly solvated than the re- actants that changing solvation fully accounts for the favorable equilibrium of hydrolysis of ATP to ADP and inorganic phosphate (Williams and Wolfenden, 1985). It has long been suspected that solvent water plays a major role in the equilibrium structure of globular pro- teins in solution, which typically present the aspect of "an oil drop with a polar coat" (Kauzmann, 1959). Com- pared with the average environment experienced by an amino acid residue in the interior of a globular protein, an amino acid side chain's environment in the interior of a biological membrane is probably relatively isomor- phous. The penetrating experiments of von Heijne and his associates (Hessa et al., 2005) have furnished quan- titative information about the relative tendencies of the various amino acids to be found in deeply immersed re- gions of membrane proteins, and an opportunity to compare these tendencies with solvation properties of the amino acids. Those latter properties are the subject of this commentary. Amino acids: The Choice of a Representative Solute
Genes contributing to prion pathogenesis
Creators: name: Yehiely, Fruma
name: Carlson, George A.
name: Korth, Carsten
name: Dwek, Raymond A.
name: Yang, Xiaoping
name: Cruz, Tracey Dawson
name: Wille, Holger
name: Boucheix, Claude
name: Kuziel, William A.
name: Glidden, David V.
name: Groth, Darlene F.
name: Epstein, Charles J.
name: Lessard, Pierre
name: Weisgraber, Karl H.
name: Moskovitz, Jackob
name: Tesseur, Ina
name: Mucke, Lennart
name: Stanley, Pamela
name: Mahley, Robert W.
name: Moore, Richard C.
name: Prusiner, Stanley B.
name: Giles, Kurt
name: Tatzelt, Jörg
name: Sap, Jan
name: Rubinstein, Eric
name: Ashe, Karen Hsiao
name: Wyss-Coray, Tony
name: Rudd, Pauline M.
name: Lisanti, Michael P.
name: Maeda, Nobuyo
name: Tamgüney, Gültekin
name: Tremblay, Patrick
name: Cohen, Fred E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Prion diseases are caused by conversion of a normally folded, nonpathogenic isoform of the prion protein (PrPC) to a misfolded, pathogenic isoform (PrPSc). Prion inoculation experiments in mice expressing homologous PrPC molecules on different genetic backgrounds displayed different incubation times, indicating that the conversion reaction may be influenced by other gene products. To identify genes that contribute to prion pathogenesis, we analyzed prion incubation times in mice in which the gene product was inactivated, knocked out or overexpressed. We tested 20 gene candidates, because their products either colocalize with PrP, are associated with Alzheimer’s disease, are elevated during prion disease, or function in PrP-mediated signaling, PrP glycosylation, or protein maintenance. Whereas some of the candidates tested may have a role in the normal function of PrPC, our data show that many genes previously implicated in prion replication have no discernable effect on the pathogenesis of prion disease. While most genes tested did not significantly affect survival times, ablation of amyloid beta (A4) precursor protein (App) or interleukin 1 receptor, type I (Il1r1), and transgenic overexpression of human superoxide dismutase 1 (SOD1) prolonged incubation times by 13%, 16%, and 19%, respectively.
How the Phase Slips in a Current-Biased Narrow Superconducting Stripe?
Creators: name: Ovchinnikov, Yu. N.
name: Varlamov, A. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The theory of current transport in a narrow superconducting channel accounting for thermal fluctuations is revisited. The value of voltage appearing in the sample is found as the function of temperature (close to transition temperature $T-T_{\mathrm{c}}$ $\ll T_{\mathrm{c}}$) and bias current $J
description: 6 pages, 2 figures
Impaired Intestinal Permeability of Tricellular Tight Junctions in Patients with Irritable Bowel Syndrome with Mixed Bowel Habits (IBS-M)
Creators: name: Awad, Karem
name: Barmeyer, Christian
name: Bojarski, Christian
name: Nagel, Oliver
name: Lee, In-Fah M.
name: Schweiger, Michal R.
name: Schulzke, Jörg-Dieter
name: Bücker, Roland
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2023
Subjects: subject: irritable bowel syndrome
subject: intestinal barrier function
subject: tight junctions
subject: tricellulin
subject: occludin
subject: leaky gut
subject: RNA-seq
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Background: The underlying pathophysiology of irritable bowel syndrome (IBS) is still unclear. Our aim was to investigate the pathophysiological mechanisms of diarrhea, constipation, and antigen uptake in mixed-type IBS (IBS-M). Methods: Colonoscopic biopsies were obtained from IBS-M patients. Epithelial transport and barrier function of colonic mucosae were characterized in Ussing chambers using impedance spectroscopy. Mucosal permeability to macromolecules was measured. Western blotting for tight junction (TJ) proteins was performed and their subcellular localization was visualized by confocal microscopy. RNA-sequencing was performed for gene expression and signaling pathway analysis. Results: In IBS-M, epithelial resistance and ENaC-dependent sodium absorption were unchanged, while short-circuit current reflecting chloride secretion was reduced. Concomitantly, epithelial permeability for fluorescein and FITC-dextran-4000 increased. TJ protein expression of occludin decreased, whereas claudins were unaltered. Confocal microscopy revealed the de-localization of tricellulin from tricellular TJs. Involved pathways were detected as proinflammatory cytokine pathways, LPS, PGE2, NGF, and vitamin D. Conclusions: Decreased anion secretion explains constipation in IBS-M, while ion permeability and sodium absorption were unaltered. Reduced occludin expression resulted in the delocalization of tricellulin from the tricellular TJ, leading to increased macromolecular permeability that contributes to antigen influx into the mucosa and perpetuates a low-grade inflammatory process.
Cosmological Parameters From Supernovae Associated With Gamma-ray Bursts
Creators: name: Li, Xue
name: Hjorth, Jens
name: Wojtak, Radosław
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We report estimates of the cosmological parameters $Ω_m$ and $Ω_Λ$ obtained using supernovae (SNe) associated with gamma-ray bursts (GRBs) at redshifts up to 0.606. Eight high-fidelity GRB-SNe with well-sampled light curves across the peak are used. We correct their peak magnitudes for a luminosity-decline rate relation to turn them into accurate standard candles with dispersion $σ= 0.18$ mag. We also estimate the peculiar velocity of the low-redshift host galaxy of SN 1998bw, using constrained cosmological simulations. In a flat universe, the resulting Hubble diagram leads to best-fit cosmological parameters of $(Ω_m, Ω_Λ) = (0.58^{+0.22}_{-0.25},0.42 ^{+0.25}_{-0.22})$. This exploratory study suggests that GRB-SNe can potentially be used as standardizable candles to high redshifts to measure distances in the universe and constrain cosmological parameters.
description: 7 pages, 3 figures, Accepted for publication in ApJL
Universal Adversarial Perturbations for CNN Classifiers in EEG-Based BCIs
Creators: name: Liu, Zihan
name: Meng, Lubin
name: Zhang, Xiao
name: Fang, Weili
name: Wu, Dongrui
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (cs.LG)
subject: Human-Computer Interaction (cs.HC)
subject: Signal Processing (eess.SP)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Multiple convolutional neural network (CNN) classifiers have been proposed for electroencephalogram (EEG) based brain-computer interfaces (BCIs). However, CNN models have been found vulnerable to universal adversarial perturbations (UAPs), which are small and example-independent, yet powerful enough to degrade the performance of a CNN model, when added to a benign example. This paper proposes a novel total loss minimization (TLM) approach to generate UAPs for EEG-based BCIs. Experimental results demonstrated the effectiveness of TLM on three popular CNN classifiers for both target and non-target attacks. We also verified the transferability of UAPs in EEG-based BCI systems. To our knowledge, this is the first study on UAPs of CNN classifiers in EEG-based BCIs. UAPs are easy to construct, and can attack BCIs in real-time, exposing a potentially critical security concern of BCIs.
Nonlinear evolution of dark matter subhalos and applications to warm dark matter
Creators: name: Pullen, Anthony R.
name: Benson, Andrew J.
name: Moustakas, Leonidas A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We describe the methodology to include nonlinear evolution, including tidal effects, in the computation of subhalo distribution properties in both cold (CDM) and warm (WDM) dark matter universes. Using semi-analytic modeling, we include effects from dynamical friction, tidal stripping, and tidal heating, allowing us to dynamically evolve the subhalo distribution. We calibrate our nonlinear evolution scheme to the CDM subhalo mass function in the Aquarius N-body simulation, producing a subhalo mass function within the range of simulations. We find tidal effects to be the dominant mechanism of nonlinear evolution in the subhalo population. Finally, we compute the subhalo mass function for $m_χ=1.5$ keV WDM including the effects of nonlinear evolution, and compare radial number densities and mass density profiles of subhalos in CDM and WDM models. We show that all three signatures differ between the two dark matter models, suggesting that probes of substructure may be able to differentiate between them.
description: Added a couple of references
Upregulation of special AT-rich-binding protein 1 by Epstein-Barr virus latent membrane protein 1 in human nasopharyngeal cells and nasopharyngeal cancer
Creators: name: Endo, K.
name: Pagano, J. S.
name: Yoshizaki, T.
name: Shackelford, J.
name: Aga, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: A global regulator of chromatin remodelling and gene expression, special AT-rich-binding protein 1 (SATB1) has been implicated in promotion of growth and metastasis of a number of cancers. Here, we demonstrate that the principal oncogene of Epstein–Barr virus (EBV), latent membrane protein 1 (LMP1) upregulates SATB1 RNA and protein expression in human nasopharyngeal cell lines. Silencing of endogenously expressed SATB1 with specific short hairpin RNA decreases cell proliferation and resistance to apoptosis induced by growth factor withdrawal. Additionally, we provide evidence that LMP1-mediated expression of Survivin, a multifunctional protein involved in promoting cell growth and survival, is mediated at least in part by SATB1 in human nasopharyngeal cells. Finally, we show that SATB1 protein levels are elevated in tissue samples from patients with nasopharyngeal carcinoma (NPC), and are directly correlated with the expression of LMP1. Taken together, our results suggest that SATB1 functions as a pro-metastatic effector of LMP1 signalling in EBV-positive NPC.
The Economic Impact of AIDS Treatment: Labor Supply in Western Kenya
Creators: name: Zivin, Joshua Graff
name: Thirumurthy, Harsha
name: Goldstein, Markus
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Using longitudinal survey data collected in collaboration with a treatment program, this paper estimates the economic impacts of antiretroviral treatment. The responses in two outcomes are studied: (1) labor supply of treated adult AIDS patients; and (2) labor supply of individuals in patients’ households. Within six months after treatment initiation, there is a 20 percent increase in the likelihood of the patient participating in the labor force and a 35 percent increase in weekly hours worked. Young boys in treated patients’ households work significantly less after treatment initiation, while girls and adult household members do not change their labor supply.
On the behavior of the DFA and DCCA in trend-stationary processes
Creators: name: Prass, Taiane Schaedler
name: Pumi, Guilherme
Publisher: name: arXiv
Year: 2019
Subjects: subject: Statistics Theory (math.ST)
subject: Methodology (stat.ME)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: In this work, we develop the asymptotic theory of the Detrended Fluctuation Analysis (DFA) and Detrended Cross-Correlation Analysis (DCCA) for trend-stationary stochastic processes without any assumption on the specific form of the underlying distribution. All results are presented and derived under the general framework of potentially overlapping boxes for the polynomial fit. We prove the stationarity of the DFA and DCCA, viewed as stochastic processes, obtain closed forms for moments up to second order, including the covariance structure for DFA and DCCA and a miscellany of law of large number related results. Our results generalize and improve several results presented in the literature. To verify the behavior of our theoretical results in small samples, we present a Monte Carlo simulation study and an empirical application to econometric time series.
Substrate quality of drained organic soils—Implications for carbon dioxide fluxes
Creators: name: Säurich, Annelie
name: Tiemeyer, Bärbel
name: Dettmann, Ullrich
name: Fiedler, Sabine
name: Don, Axel
Publisher: name: Weinheim : Wiley-VCH
Year: 2021
Subjects: subject: bog
subject: fen
subject: fibre analysis
subject: mineralisation
subject: NMR
subject: peat
subject: radiocarbon age
subject: Dewey Decimal Classification::500 | Naturwissenschaften::570 | Biowissenschaften, Biologie
subject: Dewey Decimal Classification::600 | Technik::630 | Landwirtschaft, Veterinärmedizin
subject: Dewey Decimal Classification::600 | Technik::640 | Hauswirtschaft und Familienleben

description: Background: Peatlands only cover a minor fraction of the global terrestrial surface, but due to drainage, they are major contributors to carbon dioxide (CO2) emissions from soils. Previous studies have shown that hydrological conditions, nutrient availability and anthropogenic disturbance play an important role in the mineralisation of organic matter. Furthermore, microbial turnover depends on peat quality, which is determined by its botanical origin and degree of transformation under natural conditions. Aims: The objective of this study was to shed light on the interdependence between mineralisation rates, secondary transformation of peat and chemical composition by examining the differences between bog and fen peat and between strongly degraded topsoil and well-preserved subsoil. Methods: Bog and fen peat from ten different peatlands under grassland use in Germany were analysed for their chemical composition using standard 13C nuclear magnetic resonance (NMR) spectroscopy and wet chemical extractions for fibre analysis. The radiocarbon age was determined as well. The results were combined with CO2 fluxes from a previous incubation study. Results: Topsoils had higher shares of proteins and lipids, and lower shares of carbohydrates and aromatics than subsoils. Bog peat subsoils were characterised by higher shares of carbohydrates and lower shares of aromatics than fen peat subsoils. Topsoils were more similar to each other in their chemical composition than the subsoils. Considering all samples, aromatics and phenolics were negatively correlated with CO2 fluxes. Measured CO2 fluxes from topsoils were significantly higher than from subsoils. However, no influences of chemical composition on CO2 fluxes were detected when examining topsoils and subsoils separately. Even though aromatics and phenolics showed positive relationships with radiocarbon age, differences in age alone were unable to explain the higher amounts of these compounds in the subsoil. Conclusions: The results imply that chemical composition of topsoil peat is not the reason for higher mineralisation rates compared to subsoil peat, but rather a consequence of decomposition and transformation. Thus, peat mineralisation of drained organic soils under agriculture might not slow down over time due to gradually decreasing peat quality but could increase further.
Tiny noise, big mistakes: Adversarial perturbations induce errors in Brain-Computer Interface spellers
Creators: name: Zhang, Xiao
name: Wu, Dongrui
name: Ding, Lieyun
name: Luo, Hanbin
name: Lin, Chin-Teng
name: Jung, Tzyy-Ping
name: Chavarriaga, Ricardo
Publisher: name: arXiv
Year: 2020
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: Machine Learning (cs.LG)
subject: Signal Processing (eess.SP)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: An electroencephalogram (EEG) based brain-computer interface (BCI) speller allows a user to input text to a computer by thought. It is particularly useful to severely disabled individuals, e.g., amyotrophic lateral sclerosis patients, who have no other effective means of communication with another person or a computer. Most studies so far focused on making EEG-based BCI spellers faster and more reliable; however, few have considered their security. This study, for the first time, shows that P300 and steady-state visual evoked potential BCI spellers are very vulnerable, i.e., they can be severely attacked by adversarial perturbations, which are too tiny to be noticed when added to EEG signals, but can mislead the spellers to spell anything the attacker wants. The consequence could range from merely user frustration to severe misdiagnosis in clinical applications. We hope our research can attract more attention to the security of EEG-based BCI spellers, and more broadly, EEG-based BCIs, which has received little attention before.
Transcriptional network analysis identifies key elements governing the recombinant protein production provoked reprogramming of carbon and energy metabolism in Escherichia coli BL21 (DE3)
Creators: name: Li, Zhaopeng
name: Geffers, Robert
name: Jain, Garima
name: Klawonn, Frank
name: Kökpinar, Öznur
name: Nimtz, Manfred
name: Schmidt‐Heck, Wolfgang
name: Rinas, Ursula
Publisher: name: Hoboken, NJ : Wiley
Year: 2021
Subjects: subject: Escherichia coli
subject: metabolic burden
subject: recombinant protein production
subject: regulatory network analysis
subject: Dewey Decimal Classification::600 | Technik
subject: Dewey Decimal Classification::600 | Technik::620 | Ingenieurwissenschaften und Maschinenbau

description: The impact of recombinant protein production on carbon and energy metabolism in Escherichia coli BL21 (DE3) was studied through transcriptome and proteome analysis of cells induced in carbon-limited fed-batch cultures during either fast or slow growth. Production of human basic fibroblast growth factor (pET expression system, T7 promoter) during fast growth leads to a macroscopically observable response classifiable into two consecutive steps: i. apparently unperturbed growth and respiration with concomitant formation of pyruvate and acetate followed by ii. inhibition of growth, respiratory activity and glucose uptake. Down-regulation of genes involved in sugar and acetate uptake, tricarboxylic acid (TCA) cycle, and respiratory energy generation started already during apparently unperturbed growth with the exceptions of up-regulated genes encoding the less energy efficient NADH dehydrogenase and terminal oxidases. A transcription factor target gene network analysis revealed that observed changes are mainly attributable to the vanishing influence of the transcription factor CRP-cAMP but also to a strong down-regulation of AcrA-P repressed genes. Moreover, down-regulation of MalT activated and up-regulation of PdhR repressed genes contribute among others to the reorganization of the transcriptome. The main drivers were identified as accumulating metabolites, for example, pyruvate, which affect transcription factor activity. The resulting restructured proteome leads to reduced glucose uptake, TCA cycle, and respiratory capacities this way decreasing catabolic carbon breakdown and metabolite accumulation. At slow growth, the production provoked transcriptome rearrangements are more subtle not leading to a macroscopically evident response. In summary, the transcriptomic response towards recombinant gene expression mimics a carbon or nutrient up-shift response aiming to match catabolic carbon processing with compromised anabolic capacities of induced cells. It is not the reason for growth inhibition and the metabolic burden but the cellular attempt to attenuate the “toxic effect” of recombinant gene expression by reducing carbon catabolism.
First detection and characterization of symbiotic stars in M31
Creators: name: Mikolajewska, Joanna
name: Caldwell, Nelson
name: Shara, Michael M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Symbiotic binaries are putative progenitors of type Ia supernovae. The census of Galactic symbiotic binaries is so incomplete that we cannot reliably estimate the total population of these stars, and use it to check whether that number is consistent with the observed type Ia supernova rate in spiral galaxies. We have thus begun a survey of the nearest counterpart of our own Galaxy, namely M31, where a relatively complete census of symbiotic stars is achievable. We report the first detections and spectrographic characterizations of 35 symbiotic binaries in M31, and compare these stars with the symbiotic population in the Milky Way. These newly detected M31 symbiotic binaries are remarkably similar to galactic symbiotics, though we are clearly only sampling (in this feasibility study) the most luminous symbiotics in M31. We have also found, in M31, the symbiotic star (M31SyS J004233.17+412720.7) with the highest ionization level known amongst all symbiotics. An optical outburst of the M31 symbiotic star M31SyS J004322.50+413940.9 was probably a nova-like outburst, the first symbiotic outburst detected outside the Milky Way and Magellanic Clouds.
description: 19 pages, 16 figures, MNRAS in press
SCALABLE - D7.1 Initial Communication Plan
Creators: name: Germetz, Emilie
name: Lefevre, Corentin
name: Weisz, Johanna
Publisher: name: Zenodo
Year: 2021

description: This deliverable defines the dissemination objectives for the SCALABLE project, the dissemination activities to be done during the SCALABLE project, the different target audiences and its dissemination tools. The key activities in this dissemination plan include: the development of a website that communicates the progress and results of the project; production of a collection of attractive dissemination material; publication of papers in journals; presentations delivered at conferences; attendance and representation at exhibitions. International and European collaboration via events and meetings is a pillar in this plan.
Nonlinear inverse synthesis for high spectral efficiency transmission in optical fibers
Creators: name: Le, Son Thai
name: Prilepsky, Jaroslaw E.
name: Turitsyn, Sergei K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: In linear communication channels, spectral components (modes) defined by the Fourier transform of the signal propagate without interactions with each other. In certain nonlinear channels, such as the one modelled by the classical nonlinear Schrödinger equation, there are nonlinear modes (nonlinear signal spectrum) that also propagate without interacting with each other and without corresponding nonlinear cross talk; effectively, in a linear manner. Here, we describe in a constructive way how to introduce such nonlinear modes for a given input signal. We investigate the performance of the nonlinear inverse synthesis (NIS) method, in which the information is encoded directly onto the continuous part of the nonlinear signal spectrum. This transmission technique, combined with the appropriate distributed Raman amplification, can provide an effective eigenvalue division multiplexing with high spectral efficiency, thanks to highly suppressed channel cross talk. The proposed NIS approach can be integrated with any modulation formats. Here, we demonstrate numerically the feasibility of merging the NIS technique in a burst mode with high spectral efficiency methods, such as orthogonal frequency division multiplexing and Nyquist pulse shaping with advanced modulation formats (e.g., QPSK, 16QAM, and 64QAM), showing a performance improvement up to 4.5 dB, which is comparable to results achievable with multi-step per span digital back propagation.
description: 21 pages, 10 figures, accepted to Optics Express (Oct. 2014)
Modelling relativistic solitary wave interactions in over-dense plasmas: a perturbed nonlinear Schröndinger equation framework
Creators: name: Siminos, E.
name: Sánchez-Arriaga, G.
name: Saxena, V.
name: Kourakis, I.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: We investigate the dynamics of localized solutions of the relativistic cold fluid plasma model in the small but finite amplitude limit, for slightly overcritical plasma density. Adopting a multiple scale analysis, we derive a perturbed nonlinear Schröndinger equation that describes the evolution of the envelope of circularly polarized electromagnetic field. Retaining terms up to fifth order in the small perturbation parameter, we derive a self-consistent framework for the description of the plasma response in the presence of localized electromagnetic field. The formalism is applied to standing electromagnetic solitary wave interactions and the results are validated by simulations of the full cold-fluid model. To lowest order, a cubic nonlinear Schröndinger equation with a focusing nonlinearity is recovered. Classical quasiparticle theory is used to obtain analytical estimates for the collision time and minimum distance of approach between solitary waves. For larger solitary wave amplitudes the inclusion of the fifth order terms is essential for a qualitatively correct description of solitary wave interactions. The defocusing quintic nonlinearity leads to inelastic solitary wave collisions, while bound states of solitary waves appear unstable with respect to perturbations in the initial phase or amplitude.
description: 17 pages, 12 figures, added new material
Enriched cell-free and cell-based native membrane derived vesicles (nMV) enabling rapid in-vitro electrophysiological analysis of the voltage-gated sodium channel 1.5
Creators: name: Pandey, Yogesh
name: Dondapati, Srujan Kumar
name: Kubick, Stefan
Publisher: name: Freie Universität Berlin
Year: 2023
Subjects: subject: Cell-free protein synthesis
subject: Electrophysiology
subject: Membrane proteins
subject: Micro-transplantation
subject: Protein expression
subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::570 Biowissenschaften; Biologie

description: Here, we demonstrate the utility of native membrane derived vesicles (nMVs) as tools for expeditious electrophysiological analysis of membrane proteins. We used a cell-free (CF) and a cell-based (CB) approach for preparing protein-enriched nMVs. We utilized the Chinese Hamster Ovary (CHO) lysate-based cell-free protein synthesis (CFPS) system to enrich ER-derived microsomes in the lysate with the primary human cardiac voltage-gated sodium channel 1.5 (hNaV1.5; SCN5A) in 3 h. Subsequently, CB-nMVs were isolated from fractions of nitrogen-cavitated CHO cells overexpressing the hNaV1.5. In an integrative approach, nMVs were micro-transplanted into Xenopus laevis oocytes. CB-nMVs expressed native lidocaine-sensitive hNaV1.5 currents within 24 h; CF-nMVs did not elicit any response. Both the CB- and CF-nMV preparations evoked single-channel activity on the planar lipid bilayer while retaining sensitivity to lidocaine application. Our findings suggest a high usability of the quick-synthesis CF-nMVs and maintenance-free CB-nMVs as ready-to-use tools for in-vitro analysis of electrogenic membrane proteins and large, voltage-gated ion channels.