cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Thermodynamics with continuous information flow
Creators: name: Horowitz, Jordan M.
name: Esposito, Massimiliano
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We provide a unified thermodynamic formalism describing information transfers in autonomous as well as nonautonomous systems described by stochastic thermodynamics. We demonstrate how information is continuously generated in an auxiliary system and then transferred to a relevant system that can utilize it to fuel otherwise impossible processes. Indeed, while the joint system satisfies the second law, the entropy balance for the relevant system is modified by an information term related to the mutual information rate between the two systems. We show that many important results previously derived for nonautonomous Maxwell demons can be recovered from our formalism and use a cycle decomposition to analyze the continuous information flow in autonomous systems operating at steady-state. A model system is used to illustrate our findings.
description: 11 pages, 5 figures
Phenomenology in Minimal Cascade Seesaw for Neutrino Mass
Creators: name: Ding, Ran
name: Han, Zhi-Long
name: Liao, Yi
name: Liu, Hong-Jun
name: Liu, Ji-Yuan
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We make a comprehensive analysis on the phenomenology in the minimal version of cascade seesaw for tiny neutrino mass. The seesaw induces at tree level a neutrino mass operator at dimension nine, by introducing a quadruple scalar $Φ$ of hypercharge unity and a quintuple fermion $Σ$ of hypercharge zero. We work in a framework that handles the complicated Yukawa couplings in a nice way without losing generality. All mixing matrices are essentially expressed in terms of the vacuum expectation value of the quadruple scalar v_Φ, a free complex parameter, and known neutrino parameters. We show that the low-energy lepton flavor violating transitions of the charged leptons set strong constraints on the free parameters. The constraints have a significant impact on collider physics, and are incorporated in our signal analysis at the LHC. We investigate the signatures of new particles by surveying all potentially important channels. We find that the 4j2\ell^\pm signal is most important for the detection of the scalars and the 2\ell^{\pm}2\ell^{\mp}2j, 3\ell^{\pm}\ell^{\mp}2j and 3\ell^{\pm}2\ell^{\mp}+\cancel{E_T} signals are quite promising for the fermions.
description: v1: 48 pages, including 18 figures and 10 tables; v2: version to appear in PRD, 50 pages, including 19 figures and 10 tables, changes are: (1) detailed discussion of LFV constraints on parameters together with a new figure (Fig. 3); (2) more refs; (3) typos and grammatical issues fixed
The study of reproduction of stress tolerance in tropical crops as a means to achieve zero hunger
Creators: name: Bolanos-Villegas, Pablo Alberto
Publisher: name: F1000 Research Limited
Year: 2018

description: Maize and papaya are important crops in Central America. We show results suggesting that in papaya AGO9 orthologs regulate the development of embryo sacs. We also show results that imply that in maize homozygous lines there are changes in root architecture after exposure to 5 and 15 Gy.
The Effects of Music Listening on Executive Functions: A Systematic Review.
Creators: name: Schittenhelm, Andrea
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Music
subject: Arts and Humanities
subject: Sports Sciences
subject: Cognitive Psychology
subject: Medicine and Health Sciences
subject: Psychology
subject: FOS: Psychology
subject: Social and Behavioral Sciences

description: The aim is to investigate, which effects music (characteristics) and the circumstances of music listening (e.g., pre-intervention music listening, or during) have on executive functions.
A No-Scale Inflationary Model to Fit Them All
Creators: name: Ellis, John
name: Garcia, Marcos A. G.
name: Nanopoulos, Dimitri V.
name: Olive, Keith A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The magnitude of B-mode polarization in the cosmic microwave background as measured by BICEP2 favours models of chaotic inflation with a quadratic $m^2 ϕ^2/2$ potential, whereas data from the Planck satellite favour a small value of the tensor-to-scalar perturbation ratio $r$ that is highly consistent with the Starobinsky $R + R^2$ model. Reality may lie somewhere between these two scenarios. In this paper we propose a minimal two-field no-scale supergravity model that interpolates between quadratic and Starobinsky-like inflation as limiting cases, while retaining the successful prediction $n_s \simeq 0.96$.
description: 25 pages, 12 figures
title: Analysis of Substrate Integrated Waveguides
Creators: name: Nag, Robin
Publisher: name: University of Kent
Year: 2022

description: By using a transverse resonance technique, the frequency characteristics of slotted substrate integrated waveguides (SSIWs), slotted half mode substrate integrated waveguides (slotted HMSIWs) and slotted parallel plate SIWs loaded with capacitances and inductances are analyzed theoretically and related to those of conventional waveguides. In practice, the slotted SIWs and HMSIWs are distributed structures, so that they are loaded with ladders of capacitances and inductances across their slots. The cut-off frequencies of the slotted SIWs and HMSIWs loaded with specific capacitances and inductances are then calculated from our analytic technique. These numerical predictions are both compared with and also in some cases used to clarify the corresponding values of cut-off frequencies estimated by HFSS and also by CST Microwave Studio by means of using S-parameters. Field plots for some of these practical examples are used to provided further insights regarding the design and operation of these structures. A tuneable resonator and tuneable single port narrow band antenna are designed. A rudimentary design of a bandpass filter (in the form of a SIW loaded with both inductances and capacitances in series across the slot) is also outlined. Finally, a modal analysis technique for a general composite waveguide structure, essentially consisting of three sections of SIW, is developed from first principles. This method is used to establish matrices which are used to calculate the S-parameters of the full structure. Though the technique itself is not entirely original, its application is a novel one which can be applied to a whole range of hybrid waveguide structures. Some specific examples of the general case which have practical importance, namely rectangular SIW sections at either end of a slotted SIW region via means of a step with E-planes and H-planes respectively, are considered. The operational characteristics of these waveguide structures are analyzed by means of examining their S-parameters over a suitable range of frequencies. These predicitions are then compared with, and also in some cases, used to interpret the S-parameter estimates from HFSS. The calculated predictions from the modal analysis for these examples are useful for the determination of frequency characteristics of SSIWs, which are instrumental in the novel design of a plethora of microwave devices. In fact, the mode matching method is compared with CST Microwave Studio to estimate the cutoff frequency of a slot SIW antenna.
Flowchart for publication selection process from Could non-native species boost their chances of invasion success by socializing with natives?
Creators: name: Camacho-Cervantes, Morelia
name: Keller, Reuben P.
name: Vilà, Montserrat
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Flowchart for publication selection process of our literature review.
Vortex dynamics in spin-orbit coupled Bose-Einstein condensates
Creators: name: Fetter, Alexander L.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: I use a time-dependent Lagrangian formalism and a variational trial function to study the dynamics of a two-component vortex in a spin-orbit coupled Bose-Einstein condensate (BEC). For a single-component BEC, various experiments have validated this theoretical approach, for example a thermal quench that yields a quantized vortex in roughly 25% of trials. To be definite, I assume the specific spin-orbit form used in recent NIST experiments, which introduces a spatial asymmetry because of the external Raman laser beams. I here generalize this formalism to include a two-component order parameter that has quantized circulation in each component but not necessarily with the same circulation. For example a singly quantized vortex in just one component yields a BEC analog of the half-quantum vortex familiar in $^3$He-A and in $p$-wave chiral superconductors. This and other unusual two-component vortices have both periodic trajectories and unbounded trajectories that leave the condensate, depending on the initial conditions. The optimized phase of the order parameter induces a term in the particle current that cancels the contribution from the vector potential, leaving pure circulating current around the vortex.
description: 16 pages, three figures
M5-branes and Wilson Surfaces in AdS$_{7}$/CFT$_{6}$ Correspondence
Creators: name: Mori, Hironori
name: Yamaguchi, Satoshi
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study AdS$_{7}$/CFT$_{6}$ correspondence between M-theory on AdS$_{7} \times S^{4}$ and the 6D $\mathcal{N} = (2,0)$ superconformal field theory. In particular we focus on Wilson surfaces. We use the conjecture that the (2,0) theory compactified on $S^{1}$ is equivalent to the 5D maximal super Yang-Mills (MSYM) and Wilson surfaces wrapping this $S^1$ correspond to Wilson loops in 5D MSYM. The Wilson loops in 5D MSYM obtained by the localization technique result in the Chern-Simons matrix model. We calculate the expectation values of Wilson surfaces in large rank symmetric representations and anti-symmetric representations by using this result. In the gravity side, the expectation values for probe M5-branes wrapping submanifolds of the background are computed. Consequently we find new, non-trivial evidence for the AdS$_{7}$/CFT$_{6}$ correspondence that the results in the gravity side perfectly agree with those in the CFT side.
description: 22 pages, 1 figure; v2: references added; v3: discussions added, typos corrected, and published in Physical Review D
Phase structure of three and four flavor QCD
Creators: name: Fischer, Christian S.
name: Luecker, Jan
name: Welzbacher, Christian A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Lattice (hep-lat)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We investigate the phase structure of QCD at finite temperature and light-quark chemical potential. We improve upon earlier results for N_f=2+1 dynamical quark flavors and investigate the effects of charm quarks in an extension to N_f=2+1+1. We determine the quark condensate and the Polyakov loop potential using solutions of a coupled set of (truncated) Dyson-Schwinger equations for the quark and gluon propagators of Landau gauge QCD. At zero chemical potential we find excellent agreement with results from lattice-QCD. With input fixed from physical observables we find only a very small influence of the charm quark on the resulting phase diagram at finite chemical potential. We discuss the location of the emerging critical end-point and compare with expectations from lattice gauge theory.
description: 10 pages, 9 figures, v2: typos corrected, minor changes, version accepted by PRD
title: Slovakia Report. Sustainable Governance Indicators 2022
Creators: name: Kneuer, Marianne
name: Malová, Darina
name: Bönker, Frank
Publisher: name: Bertelsmann Stiftung
Year: 2022
Subjects: Governance
Democracy
Regierungshandeln
Demokratie

description: The murder of investigative journalist Ján Kuciak and his fiancée Martina Kušnírová in February 2018 continued to impact political developments in 2020 and 2021. The investigations and the trials that eventually started in 2020 revealed the unimaginable size of the corrupt network built by businessman Marián Kočner and the involvement of several high-profile state representatives, including the long-serving Prime Minister Robert Fico, in this network.
Theory of Charge and Heat Polarizations with the Keldysh Formalism
Creators: name: Shitade, Atsuo
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate the heat polarization, a heat analog of the charge polarization, by using the gauge-covariant Keldysh formalism. In contrast to the charge-heat analogy naively expected, we find that the heat polarization does not appear spontaneously, since it consists not only of the heat-transfer contribution but of the heat-generation contribution, leading to the Mott rule. Nonetheless, it can be induced by a torsional magnetic field in $(3+1)$-D topological insulators and superconductors, which is described by the temporal part of the Nieh-Yan action.
description: 5 pages, no figures
Monte Carlo validation of optimal material discrimination using spectral x-ray imaging
Creators: name: Nik, Syen J.
name: Thing, Rune S.
name: Watts, Richard
name: Dale, Tony
name: Currie, Bryn
name: Meyer, Juergen
Publisher: name: arXiv
Year: 2014
Subjects: subject: Medical Physics (physics.med-ph)
subject: FOS: Physical sciences

description: The validation of a previous work on the optimization of material discrimination in spectral x-ray imaging is reported. Using Monte Carlo simulations based on the BEAMnrc package, material decomposition was performed on the projection images of phantoms containing up to three materials. The simulated projection data was first decomposed into material basis images by minimizing the z-score between expected and simulated counts. Statistical analysis was performed for the pixels within the region-of-interest consisting of contrast material(s) in the BEAMnrc simulations. With the consideration of scattered radiation and a realistic scanning geometry, the theoretical optima of energy bin borders provided by the algorithm were shown to have an accuracy of $\pm$2 keV for the decomposition of 2 and 3 materials. Finally, the signal-to-noise ratio predicted by the theoretical model was also validated. The counts per pixel needed for achieving a specific imaging aim can therefore be estimated using the validated model.
Recursive structure in the definitions of gauge-invariant variables for any order perturbations
Creators: name: Nakamura, Kouji
Publisher: name: arXiv
Year: 2014
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The construction of gauge-invariant variables for any order perturbations is discussed. Explicit constructions of the gauge-invariant variables for perturbations to 4th order are shown. From these explicit construction, the recursive structure in the definitions of gauge-invariant variables for any order perturbations is found. Through this recursive structure, the correspondence with the fully non-linear exact perturbations is briefly discussed.
description: 21 pages, no figure: (v2) one section and additional explanations are added. Accepted for publication to Classical and Quantum Gravity
On a multi-dimensional transport equation with nonlocal velocity
Creators: name: Dong, Hongjie
Publisher: name: arXiv
Year: 2014
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35R11, 35Q35, 82C70

description: We study a multi-dimensional nonlocal active scalar equation of the form $u_t+v\cdot \nabla u=0$ in $\mathbb R^+\times \mathbb R^d$, where $v=Λ^{-2+α}\nabla u$ with $Λ=(-Δ)^{1/2}$. We show that when $α\in (0,2]$ certain radial solutions develop gradient blowup in finite time. In the case when $α=0$, the equations are globally well-posed with arbitrary initial data in suitable Sobolev spaces.
description: 13 pages, minor revision, to appear in Adv. Math
The Effect of Dexamethasone, Adrenergic and Cholinergic Receptor Agonists on Phospholipid Metabolism in Human Osteoarthritic Synoviocytes
Creators: name: Sluzalska, Katarzyna D.
name: Liebisch, Gerhard
name: Ishaque, Bernd
name: Schmitz, Gerd
Publisher: name: Universität Regensburg
Year: 2019
Subjects: subject: dexamethasone; fibroblast-like synoviocytes; synoviocytes; osteoarthritis; phospholipids; sphingolipids; epinephrine; terbutaline; carbachol; pilocarpine
subject: 610 Medizin

description: Phospholipids (PLs) possess the unique ability to contribute to synovial joint lubrication. The aim of our study was to determine for the first time the effect of dexamethasone and some adrenergic and cholinergic agonists on the biosynthesis and release of PLs from human fibroblast-like synoviocytes (FLS). Osteoarthritic human knee FLS were treated with dexamethasone, terbutaline, epinephrine, carbachol, and pilocarpine, or the glucocorticoid receptor antagonist RU 486. Simultaneously PL biosynthesis was determined through the incorporation of stable isotope-labeled precursors into PLs. Radioactive isotope-labeled precursors were used to radiolabel PLs for the subsequent quantification of their release into nutrient media. Lipids were extracted and quantified using electrospray ionization tandem mass spectrometry or liquid scintillation counting. Dexamethasone significantly decreased the biosynthesis of phosphatidylcholine, phosphatidylethanolamine (PE), PE-based plasmalogen, and sphingomyelin. The addition of RU 486 abolished these effects. A release of PLs from FLS into nutrient media was not recognized by any of the tested agents. None of the adrenergic or cholinergic receptor agonists modulated the PL biosynthesis. We demonstrate for the first time an inhibitory effect of dexamethasone on the PL biosynthesis of FLS from human knees. Moreover, our study indicates that the PL metabolism of synovial joints and lungs are differently regulated.
Combined Gastric and Colorectal Cancer Screening—A New Strategy
Creators: name: Selgrad, Michael
name: Bornschein, J.
name: Kandulski, Arne
Publisher: name: Universität Regensburg
Year: 2018
Subjects: subject: gastric cancer; Helicobacter pylori; screening; pepsinogen; screening colonoscopy
subject: 610 Medizin

description: Background: Our aim was to evaluate the feasibility of a serological assessment of gastric cancer risk in patients undergoing colonoscopy in countries with low-to-moderate incidence rates. Methods: Serum samples were prospectively collected from 453 patients (>50 years old) undergoing colonoscopies. Of these, 279 (61.6%) also underwent gastroscopy to correlate the results for serum pepsinogen I and II (sPG-I and sPG-II), sPG-I/II ratio, and anti-H. pylori antibodies with gastric histopathology findings (graded according to the updated Sydney classification and the Operative Link of Gastritis Assessment (OLGA) and the Operative Link for Gastric Intestinal Metaplasia assessment (OLGIM) systems). Results: H. pylori was found in 85 patients (30.5%). Chronic atrophic gastritis was diagnosed in 89 (31.9%) patients. High-risk OLGA (III–IV) stages were present in 24 patients, and high-risk OLGIM stages were present in 14 patients. There was an inverse correlation of sPG-I with the degree of atrophy and intestinal metaplasia (IM), as well as with the respective OLGA (r = −0.425; p < 0.001) and OLGIM (r = −0.303; p < 0.001) stages. A pathological sPG-I result was associated with a relative risk (RR) of 12.2 (95% confidence interval: 6.29–23.54; p < 0.001) for gastric preneoplastic changes. Conclusions: The assessment of serum pepsinogen allows the identification of patients at increased risk of gastric cancer. A prevention strategy of combining a screening colonoscopy with a serological screening for preneoplastic gastric changes should be considered in the general population.
Harnessing Nature's Bounty: The Promise of Bio-fortification in Battling Global Malnutrition
Creators: name: Bhumika Singh Lodhi1*, Arzoo Dhakad2, Deepika Parte1, Pramod Kumar3
Publisher: name: The Science world a Monthly e magazine
Year: 2023

description: Malnutrition poses significant health and economic challenges globally, with regions like Asia and Africa experiencing up to 11% losses in annual GDP. Bio-fortification emerges as a strategic solution, enhancing the nutritional value of staple foods at their source, either through conventional breeding, agronomic practices, or biotechnology. This article delves into the nuances of bio-fortification methods, highlighting successes in crops like pearl millet, wheat, and rice, especially in the Indian context. While the potential of bio-fortification is evident, it's not without challenges, including technical hurdles in breeding and societal concerns over GMOs. As India envisages a future rich in bio-fortified crops, the synergy of research, public-private partnerships, community engagement, and supportive policies will be pivotal. In addressing global malnutrition, bio-fortification stands as a promising, sustainable approach, warranting increased investment and advocacy.
mRNA-Expression of KRT5 and KRT20 Defines Distinct Prognostic Subgroups of Muscle-Invasive Urothelial Bladder Cancer Correlating with Histological Variants
Creators: name: Eckstein, M.
name: Wirtz, R. M.
name: Gross-Weege, M.
name: Breyer, Johannes
name: Burger, Maximilian
Publisher: name: Universität Regensburg
Year: 2018
Subjects: subject: Bladder cancer; muscle-invasive bladder cancer; molecular diagnostics; molecular subtyping; KRT5; KRT20
subject: 610 Medizin

description: Recently, muscle-invasive bladder cancer (MIBC) has been subclassified by gene expression profiling, with a substantial impact on therapy response and patient outcome. We tested whether these complex molecular subtypes of MIBC can be determined by mRNA detection of keratin 5 (KRT5) and keratin 20 (KRT20). Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) was applied to quantify gene expression of KRT5 and KRT20 using TaqMan®-based assays in 122 curatively treated MIBC patients (median age 68.0 years). Furthermore, in silico analysis of the MD Anderson Cancer Center (MDACC) cohort (GSE48277 + GSE47993) was performed. High expression of KRT5 and low expression of KRT20 were associated with significantly improved recurrence-free survival (RFS) and disease-specific survival disease specific survival (DSS: 5-year DSS for KRT5 high: 58%; 5-year DSS for KRT20 high: 29%). KRT5 and KRT20 were associated with rates of lymphovascular invasion and lymphonodal metastasis. The combination of KRT5 and KRT20 allowed identification of patients with a very poor prognosis (KRT20+/KRT5−, 5-year DSS 0%, p < 0.0001). In silico analysis of the independent MDACC cohorts revealed congruent results (5-year DSS for KRT20 low vs. high: 84% vs. 40%, p = 0.042). High KRT20-expressing tumors as well as KRT20+/KRT− tumors were significantly enriched with aggressive urothelial carcinoma variants (micropapillary, plasmacytoid, nested).
Comparison of EM-seq and PBAT methylome library methods for low-input DNA
Creators: name: Han, Yanan
name: Zheleznyakova, Galina Yurevna
name: Marincevic-Zuniga, Yanara
name: Kakhki, Majid Pahlevan
name: Raine, Amanda
name: Needhamsen, Maria
name: Jagodic, Maja
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Science Policy
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: Plant Biology

description: DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1–10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples.
Norepinephrine Inhibits Synovial Adipose Stem Cell Chondrogenesis via α2a-Adrenoceptor-Mediated ERK1/2 Activation
Creators: name: El Bagdadi, K.
name: Zaucke, F.
name: Meurer, Andrea
name: Straub, Rainer H.
name: Jenei-Lanzl, Z.
Publisher: name: Universität Regensburg
Year: 2019
Subjects: subject: synovial adipose stem cells; sympathicus; norepinephrine; adrenoceptors; chondrogenesis; osteoarthritis; physioxia
subject: 610 Medizin

description: In recent years, first evidences emerged that sympathetic neurotransmitters influence osteoarthritis (OA) manifestation. Joint-resident stem cells might contribute to cartilage repair, however, their chondrogenic function is reduced. The neurotransmitter norepinephrine (NE) was detected in the synovial fluid of trauma and OA patients. Therefore, the aim of this study was to analyse how NE influences the chondrogenesis of synovial adipose tissue-derived stem cells (sASCs). sASCs were isolated from knee-OA patients synovia. After adrenoceptor (AR) expression analysis, proliferation and chondrogenic differentiation in presence of NE and/or α- and β-AR antagonist were investigated. Cell count, viability, chondrogenic and hypertophic gene expression, sulfated glycosaminoglycan (sGAG) and type II collagen content were determined. Key AR-dependent signaling (ERK1/2, PKA) was analyzed via western blot. sASC expressed α1A-, α1B-, α2A-, α2B-, α2C-, and β2-AR in monolayer and pellet culture. NE did not affect proliferation and viability, but 10−7 and 10−6 M NE significantly reduced sGAG and type II collagen content as well as ERK1/2 phosphorylation. These effects were fully reversed by yohimbine (α2-AR antagonist). Our study confirms the important role of NE in sASC chondrogenic function and provides new insights in OA pathophysiology. Future studies might help to develop novel therapeutic options targeting neuroendocrine pathways for OA treatment
Comparison of EM-seq and PBAT methylome library methods for low-input DNA
Creators: name: Han, Yanan
name: Zheleznyakova, Galina Yurevna
name: Marincevic-Zuniga, Yanara
name: Kakhki, Majid Pahlevan
name: Raine, Amanda
name: Needhamsen, Maria
name: Jagodic, Maja
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Science Policy
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: Plant Biology

description: DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1-10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole genome methylation quantification of low input samples.
Ferromagnetism and Borromean binding in three-fermion clusters
Creators: name: Kornilovitch, Pavel
Publisher: name: arXiv
Year: 2013
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: A three-particle spin-1/2 fermion problem with on-site repulsion and nearest-neighbor attraction is solved on the two-dimensional square lattice by discretizing a Schroedinger equation in momentum space. Energies of bound complexes (trions) and their binding conditions are obtained. For total spin S = 1/2, a wide region of trion instability toward decaying into a stable singlet pair plus a free fermion is identified. The instability is attributed to the formation of a wave function node upon addition of the third fermion. In the S = 3/2 sector, trions are found to form before triplet pairs indicating Borromean binding. In the strong repulsion, strong attraction limit the system transitions from an S = 1/2 ground state to a ferromagnetic S = 3/2 ground state in agreement with the Nagaoka theorem for a four-site plaquette.
description: Published version. 4 pages, 4 figures, 11 pages of supplemental material
Cosmological perturbations in \bar{QCD}- inflation. Estimates confronting the observations, including BICEP2
Creators: name: Zhitnitsky, Ariel R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We discuss a new scenario for early cosmology, when inflationary de Sitter phase dynamically emergent. This genuine quantum effect occurs as a result of dynamics of the topologically nontrivial sectors in a (conjectured) strongly coupled QCD- like gauge theory with scale ${Λ_{\overline{\mathrm{QCD}}}} \sim 10^{17} $ GeV in expanding universe. Inflaton in this ${\overline{\mathrm{QCD}}}$- inflation framework is an auxiliary non-propagating field, similar to an effective field known to emerge in topologically ordered condensed matter systems. Number of e-folds in the ${\overline{\mathrm{QCD}}}$-inflation framework is determined by the gauge coupling constant at the moment of inflation, and estimated as $N_{\rm inf}\sim α^{-2}(H_0)\sim 10^2$. We analyze the equation of state in this framework at the end of inflation in terms of the gauge dynamics and confront our estimates with observations. We make predictions for the tensor tilt, $n_t \simeq -0.02$, the running of the tensor tilt $α_t= {\partial n_t}/{\partial \ln k}\sim α^4(H_0)\sim 10^{-4}$ and the running for the spectral index $α_s= {\partial n_s}/{\partial \ln k}\sim α^4(H_0)\sim 10^{-4}$ in terms of the same gauge coupling constant $α(H_0)$, which is fixed in our framework by recent BICEP2 measurements of the tensor fraction $r\simeq 0.2$.
description: New refs, including some lattice studies, supporting the linear dependence on Hubble constant "H". Few new comments emphasizing the importance of a non-trivial holonomy. Final version to appear in Phys Rev. D
Infinitary Term Rewriting for Weakly Orthogonal Systems: Properties and Counterexamples
Creators: name: Endrullis, Joerg
name: Grabmayer, Clemens
name: Hendriks, Dimitri
name: Klop, Jan Willem
name: van Oostrom, Vincent
Publisher: name: arXiv
Year: 2014
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: We present some contributions to the theory of infinitary rewriting for weakly orthogonal term rewrite systems, in which critical pairs may occur provided they are trivial. We show that the infinitary unique normal form property fails by an example of a weakly orthogonal TRS with two collapsing rules. By translating this example, we show that this property also fails for the infinitary lambda-beta-eta-calculus. As positive results we obtain the following: Infinitary confluence, and hence the infinitary unique normal forms property, holds for weakly orthogonal TRSs that do not contain collapsing rules. To this end we refine the compression lemma. Furthermore, we establish the triangle and diamond properties for infinitary multi-steps (complete developments) in weakly orthogonal TRSs, by refining an earlier cluster-analysis for the finite case.
Integral Euler characteristic of Out F_{11}
Creators: name: Morita, Shigeyuki
name: Sakasai, Takuya
name: Suzuki, Masaaki
Publisher: name: arXiv
Year: 2014
Subjects: subject: Algebraic Topology (math.AT)
subject: Geometric Topology (math.GT)
subject: Quantum Algebra (math.QA)
subject: FOS: Mathematics
subject: Primary 20F28, Secondary 20J06, 20F65

description: We show that the integral Euler characteristic of the outer automorphism group of the free group of rank 11 is -1202.
description: 7 pages, final version, to appear in Exp. Math
Epigenome-wide association study of global cortical volumes in generation Scotland: Scottish family health study
Creators: name: Barbu, Miruna Carmen
name: Harris, Mat
name: Shen, Xueyi
name: Aleks, Stolicyn
name: Green, Claire
name: Amador, Carmen
name: Walker, Rosie
name: Morris, Stewart
name: Adams, Mark
name: Sandu, Anca
name: McNeil, Christopher
name: Waiter, Gordon
name: Evans, Kathryn
name: Campbell, Archie
name: Wardlaw, Joanna
name: Steele, Douglas
name: Murray, Alison
name: Porteous, David
name: McIntosh, Andrew
name: Whalley, Heather
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: A complex interplay of genetic and environmental risk factors influence global brain structural alterations associated with brain health and disease. Epigenome-wide association studies (EWAS) of global brain imaging phenotypes have the potential to reveal the mechanisms of brain health and disease and can lead to better predictive analytics through the development of risk scores. We perform an EWAS of global brain volumes in Generation Scotland using peripherally measured whole blood DNA methylation (DNAm) from two assessments, (i) at baseline recruitment, ~6 years prior to MRI assessment (N = 672) and (ii) concurrent with MRI assessment (N=565). Four CpGs at baseline were associated with global cerebral white matter, total grey matter, and whole-brain volume (Bonferroni p≤7.41×10−8, βrange = −1.46x10−6 to 9.59 × 10−7). These CpGs were annotated to genes implicated in brain-related traits, including psychiatric disorders, development, and ageing. We did not find significant associations in the meta-analysis of the EWAS of the two sets concurrent with imaging at the corrected level. These findings reveal global brain structural changes associated with DNAm measured ~6 years previously, indicating a potential role of early DNAm modifications in brain structure. Although concurrent DNAm was not associated with global brain structure, the nominally significant findings identified here present a rationale for future investigation of associations between DNA methylation and structural brain phenotypes in larger population-based samples.
Dark Matter Induced Nucleon Decay: Model and Signatures
Creators: name: Huang, Junwu
name: Zhao, Yue
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: If dark matter (DM) carries anti-baryon number, a DM particle may annihilate with a nucleon by flipping to anti-DM. Inspired by Hylogenesis models, we introduce a single component DM model where DM is asymmetric and carries B and L as -1/2. It can annihilate with a nucleon to an anti-lepton and an anti-DM at leading order or with an additional meson at sub-leading order. Such signals may be observed in proton decay experiments. If DM is captured in the Sun, the DM induced nucleon decay can generate a large flux of anti-neutrinos, which could be observed in neutrino experiments. Furthermore, the anti-DM particle in the final state obtains a relatively large momentum (few hundred MeV), and escapes the Sun. These fast-moving anti-DM particles could also induce interesting signals in various underground experiments.
description: Discussion about (g-2) is added. References are updated. Introduction is expanded. Accepted by JHEP
Dirac electron in graphene under supersymmetry generated magnetic fields
Creators: name: Midya, Bikashkali
name: Fernández, David J
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We use supersymmetry transformations to obtain new one parameter family of inhomogeneous magnetic fields $\mathbf{B} = \widetilde{\mathcal{B}}(x,λ) \hat{e}_z$ for which the massless Dirac electron possesses exact solution. The inhomogeneity appearing in $\widetilde{\mathcal{B}}(x,λ)$ can be controlled by the parameter $λ$. The obtained magnetic fields are interpreted as deformed variants of some physically attainable well known magnetic fields. A particular example, when a constant magnetic field is deformed, is considered to show that equidistant Landau levels exist even in the presence of an infinite number of specially designed inhomogeneous magnetic fields.
Epigenome-wide association study of global cortical volumes in Generation Scotland: Scottish Family Health Study
Creators: name: Barbu, Miruna Carmen
name: Harris, Mat
name: Shen, Xueyi
name: Aleks, Stolicyn
name: Green, Claire
name: Amador, Carmen
name: Walker, Rosie
name: Morris, Stewart
name: Adams, Mark
name: Sandu, Anca
name: McNeil, Christopher
name: Waiter, Gordon
name: Evans, Kathryn
name: Campbell, Archie
name: Wardlaw, Joanna
name: Steele, Douglas
name: Murray, Alison
name: Porteous, David
name: McIntosh, Andrew
name: Whalley, Heather
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: A complex interplay of genetic and environmental risk factors influence global brain structural alterations associated with brain health and disease. Epigenome-wide association studies (EWAS) of global brain imaging phenotypes have the potential to reveal the mechanisms of brain health and disease and can lead to better predictive analytics through the development of risk scores. We perform an EWAS of global brain volumes in Generation Scotland using peripherally measured whole blood DNA methylation (DNAm) from two assessments, (i) at baseline recruitment, ~6 years prior to MRI assessment (N=672) and (ii) concurrent with MRI assessment (N=565). Four CpGs at baseline were associated with global cerebral white matter, total grey matter, and whole-brain volume (Bonferroni p≤7.41×10−8, βrange= -1.46x10-6 to 9.59x10-7). These CpGs were annotated to genes implicated in brain-related traits, including psychiatric disorders, development, and ageing. We did not find significant associations in the meta-analysis of the EWAS of the two sets concurrent with imaging at the corrected level. These findings reveal global brain structural changes associated with DNAm measured ~6 years previously, indicating a potential role of early DNAm modifications in brain structure. Although concurrent DNAm was not associated with global brain structure, the nominally significant findings identified here present a rationale for future investigation of associations between DNA methylation and structural brain phenotypes in larger population-based samples.
Comprehensive Assessment of GPR68 Expression in Normal and Neoplastic Human Tissues Using a Novel Rabbit Monoclonal Antibody
Creators: name: Herzig, M.
name: Dasgupta, P.
name: Kaemmerer, D.
name: Evert, Katja
Publisher: name: Universität Regensburg
Year: 2019
Subjects: subject: GPR68; OGR1; antibody; immunohistochemistry; neuroendocrine; tumours
subject: 610 Medizin

description: GPR68 (OGR1) belongs to the proton-sensing G protein-coupled receptors that are involved in cellular adaptations to pH changes during tumour development. Although expression of GPR68 has been described in many tumour cell lines, little is known about its presence in human tumour entities. We characterised the novel rabbit monoclonal anti-human GPR68 antibody 16H23L16 using various cell lines and tissue specimens. The antibody was then applied to a large series of formalin-fixed, paraffin-embedded normal and neoplastic human tissue samples. Antibody specificity was demonstrated in a Western blot analysis of GPR68-expressing cells using specific siRNAs. Immunocytochemical experiments revealed pH-dependent changes in subcellular localisation of the receptor and internalisation after stimulation with lorazepam. In normal tissue, GPR68 was present in glucagon-producing islet cells, neuroendocrine cells of the intestinal tract, gastric glands, granulocytes, macrophages, muscle layers of arteries and arterioles, and capillaries. GPR68 was also expressed in neuroendocrine tumours, where it may be a positive prognostic factor, in pheochromocytomas, cervical adenocarcinomas, and endometrial cancer, as well as in paragangliomas, medullary thyroid carcinomas, gastrointestinal stromal tumours, and pancreatic adenocarcinomas. Often, tumour capillaries were also strongly GPR68-positive. The novel antibody 16H23L16 will be a valuable tool for basic research and for identifying GPR68-expressing tumours during histopathological examinations.
Resonant scattering due to adatoms in graphene: Top, bridge, and hollow positions
Creators: name: Irmer, Susanne
name: Kochan, Denis
name: Lee, Jeongsu
name: Fabian, Jaroslav
Publisher: name: Universität Regensburg
Year: 2018
Subjects: subject: 530 Physik

description: We present a theoretical study of resonance characteristics in graphene from adatoms with s or pz character binding in top, bridge, and hollow positions. The adatoms are described by two tight-binding parameters: on-site energy and hybridization strength. We explore a wide range of different magnitudes of these parameters by employing T-matrix calculations in the single adatom limit and by tight-binding supercell calculations for dilute adatom coverage. We calculate the density of states and the momentum relaxation rate and extract the resonance level and resonance width. The top position with a large hybridization strength or, equivalently, small on-site energy, induces resonances close to zero energy. The bridge position, compared to top, is more sensitive to variation in the orbital tight-binding parameters. Resonances within the experimentally relevant energy window are found mainly for bridge adatoms with negative on-site energies. The effect of resonances from the top and bridge positions on the density of states and momentum relaxation rate is comparable and both positions give rise to a power-law decay of the resonant state in graphene. The hollow position with s orbital character is affected from destructive interference, which is seen from the very narrow resonance peaks in the density of states and momentum relaxation rate. The resonant state shows no clear tendency to a power-law decay around the impurity and its magnitude decreases strongly with lowering the adatom content in the supercell calculations. This is in contrast to the top and bridge positions. We conclude our study with a comparison to models of pointlike vacancies and strong midgap scatterers. The latter model gives rise to significantly higher momentum relaxation rates than caused by single adatoms.
Experimental Realization of a Quantum Breathing Pyrochlore Antiferromagnet
Creators: name: Kimura, K.
name: Nakatsuji, S.
name: Kimura, T.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The synthesis and characterization of a new Yb-based material Ba3Yb2Zn5O11 are reported. This material is identified as the first model system of a pseudospin-1/2 quantum antiferromagnet on "breathing" pyrochlore lattice characterized by an alternating array of small and large Yb tetrahedra. Despite dominant antiferromagnetic interactions J ~ 7 K, a large amount of magnetic entropy (25%) remains at 0.38 K, indicating that each small Yb tetrahedron forms a unique doubly degenerate singlet state. These results are well described by the Heisenberg pseudospin-1/2 single tetrahedron model.
description: 11 pages, 4 figures, submitted to PRL; rejected and transferred to PRB