cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
COMPUTATIONAL AND THEORETICAL STUDIES OF THE CONFORMATIONAL PROPERTIES OF PEPTIDES IN THEIR DENATURED STATE
Creators: name: MELONI, ROBERTO
Publisher: name: Universit� degli Studi di Milano
Year: 2017

description: The experimental characterization of the denatured state of proteins is still an open question, despite the heavy effort made in the last four decades to investigate it. The biologically-relevant disordered phase, in water, is not experimentally accessible, and little is known about the molecular mechanism of chemical-induced denaturation, and to which extent the chemical-induced denatured state is similar to the metastable denatured state in water. In the first part of the thesis, we address this problem by means of a computational approach. Using bias-exchange metadynamics simulations, we investigate the conformational properties of two peptides (the alpha-helix and a beta-hairpin of protein G B1 domain) in urea and guanidine hydrochloride solutions and we compare them with the denatured state simulated in pure water. We find that the denaturation mechanisms seem to be different from the two-state picture commonly assumed : the content of secondary structure is rather heterogeneous in the denatured alpha-helix, whereas the denatured beta-hairpin shows basically only beta-content, with different weights in the different solvents. Moreover, urea displays a local effect, establishing a competition with water in forming hydrogen bonds with the residues, while the guanidine hydrochloride affects the whole secondary structure via a long-range, electrical interaction. To perform the simulations with the metadynamics algorithm, we had to choose the biasing collective variables. In the second part, we explore the properties of collective variables from a theoretical perspective, setting up a framework to evaluate how suitable any specific variable is to bias efficiently a metadynamics simulation. In particular, we investigate whether their time evolution can be described as the outcome of an effective, overdamped Langevin equation and we develop an algorithm to recover the drift and diffusion coefficients from short time series. We apply this investigation to two variables commonly used to describe the conformational properties of proteins, the dRMSD and the fraction of native contacts. We show that the dynamics in the projected space depends on the microscopic conformations, although the equilibrium properties are compatible with a monodimensional description of the system.
The mollusc community associated with maerl beds of Ustica Island (Tyrrhenian Sea)
Creators: name: CASTRIOTA, Luca
name: AGAMENNONE, Franco
name: SUNSERI, Giuseppe
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2005

description: Living molluscs associated with circalittoral maerl have been studied at Ustica Island (southern Tyrrhenian Sea).
 Five sediment samples from two sites were collected in November 1996 and July 1997 using a van Veen grab (0.1 m2), at
 50 m depth. Two-way crossed PERMANOVA revealed non-significant temporal and spatial differences in abundance. The
 molluscan community was composed of both hard bottom and soft bottom species typical of circalittoral coastal detritic
 and to coarse sands and fine gravels under bottom currents assemblages. Suspension feeders dominated these communities,
 followed by herbivores and carnivores in similar percentages. Haminoea hydatis, Gibberula jansseni and Modiolula pha-
 seolina were the most abundant species followed by Acantochitona fascicularis, Hiatella arctica and Limatula subauricu-
 lata. Ischnochiton usticensis may be an exclusive maerl associated species. The low richness and high evenness values
 recorded let us consider this community as well structured.
On the vacuum Einstein equations along curves with a discrete local rotational and reflection symmetry
Creators: name: Korzyński, Mikołaj
name: Hinder, Ian
name: Bentivegna, Eloisa
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We discuss the possibility of a dimensional reduction of the Einstein equations in S3 black-hole lattices. It was reported in previous literature that the evolution of spaces containing curves of local, discrete rotational and reflection Symmetry (LDRRS) can be carried out via a system of ODEs along these curves. However, 3+1 Numerical Relativity computations demonstrate that this is not the case, and we show analytically that this is due to the presence of a tensorial quantity which is not suppressed by the symmetry. We calculate the term analytically, and verify numerically for an 8-black-hole lattice that it fully accounts for the anomalous results, and thus quantify its magnitude in this specific case. The presence of this term prevents the exact evolution of these spaces via previously-reported methods which do not involve a full 3+1 integration of Einstein's equation.
description: 18 pages, 4 figures
Star Formation in Semi-Analytic Galaxy Formation Models with Multiphase Gas
Creators: name: Somerville, Rachel S.
name: Popping, Gergö
name: Trager, Scott C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We implement physically motivated recipes for partitioning cold gas into different phases (atomic, molecular, and ionized) in galaxies within semi-analytic models of galaxy formation based on cosmological merger trees. We then model the conversion of molecular gas into stars using empirical recipes motivated by recent observations. We explore the impact of these new recipes on the evolution of fundamental galaxy properties such as stellar mass, star formation rate (SFR), and gas and stellar phase metallicity. We present predictions for stellar mass functions, stellar mass vs. SFR relations, and cold gas phase and stellar mass-metallicity relations for our fiducial models, from redshift $z\sim 6$ to the present day. In addition we present predictions for the global SFR, mass assembly history, and cosmic enrichment history. We find that the predicted stellar properties of galaxies (stellar mass, SFR, metallicity) are remarkably insensitive to the details of the recipes used for partitioning gas into HI and H$_2$. We see significant sensitivity to the recipes for H$_2$ formation only in very low mass halos, which host galaxies that are not detectable with current observational facilities except very nearby. The properties of low-mass galaxies are also quite insensitive to the details of the recipe used for converting H$_2$ into stars, while the formation epoch of massive galaxies does depend on this significantly. (Abridged)
description: 35 pages, 23 figures, submitted to MNRAS
Copidognathus fistulosus, a new Halacarid mite (Acari: Halacaridae) from Korea
Creators: name: CHATTERJEE, Tapas
name: CHANG2, Cheon Young
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2005

description: 3A new species of halacarid mite belonging to the genus Copidognathus viz. C. fistulosus is described on the
 basis of specimens collected from an algal bed in Jeju Island, South Korea. Copidognathus fistulosus sp. nov. is closely
 related to C. koreanus Chatterjee & Chang and C. laevisetosus Chatterjee, Lee & Chang. Morphological similarities and
 dissimilarities among them are discussed.
Wnt1/βcatenin injury response activates the epicardium and cardiac fibroblasts to promote cardiac repair: Wnt1/βcatenin injury response regulates cardiac repair
Creators: name: Willis, Monte
name: Liu, Dianxin
name: Majesky, Mark
name: Rojas, Mauricio
name: Srikantha, Luxman
name: Regan, Jenna N.
name: Rodgers, Laurel
name: Duan, Jinzhu
name: Deb, Arjun
name: Leask, Andrew
name: Hamlett, Eric
name: Gherghe, Costin
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Wnts are required for cardiogenesis but the role of specific Wnts in cardiac repair remains unknown. In this report, we show that a dynamic Wnt1/βcatenin injury response activates the epicardium and cardiac fibroblasts to promote cardiac repair. Acute ischaemic cardiac injury upregulates Wnt1 that is initially expressed in the epicardium and subsequently by cardiac fibroblasts in the region of injury. Following cardiac injury, the epicardium is activated organ-wide in a Wnt-dependent manner, expands, undergoes epithelial–mesenchymal transition (EMT) to generate cardiac fibroblasts, which localize in the subepicardial space. The injured regions in the heart are Wnt responsive as well and Wnt1 induces cardiac fibroblasts to proliferate and express pro-fibrotic genes. Disruption of downstream Wnt signalling in epicardial cells decreases epicardial expansion, EMT and leads to impaired cardiac function and ventricular dilatation after cardiac injury. Furthermore, disruption of Wnt/βcatenin signalling in cardiac fibroblasts impairs wound healing and decreases cardiac performance as well. These findings reveal that a pro-fibrotic Wnt1/βcatenin injury response is critically required for preserving cardiac function after acute ischaemic cardiac injury.
Stabilization of integrin-linked kinase by the Hsp90-CHIP axis impacts cellular force generation, migration and the fibrotic response
Creators: name: Wickström, Sara A.
name: Radovanac, Korana
name: Schulz, Jan Niklas
name: Patterson, Cam
name: Eckes, Beate
name: Blumbach, Katrin
name: Geiger, Tamar
name: Fässler, Reinhard
name: Mann, Matthias
name: Krieg, Thomas
name: Morgner, Jessica
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Integrin-linked kinase (ILK) is an adaptor protein required to establish and maintain the connection between integrins and the actin cytoskeleton. This linkage is essential for generating force between the extracellular matrix (ECM) and the cell during migration and matrix remodelling. The mechanisms by which ILK stability and turnover are regulated are unknown. Here we report that the E3 ligase CHIP–heat shock protein 90 (Hsp90) axis regulates ILK turnover in fibroblasts. The chaperone Hsp90 stabilizes ILK and facilitates the interaction of ILK with α-parvin. When Hsp90 activity is blocked, ILK is ubiquitinated by CHIP and degraded by the proteasome, resulting in impaired fibroblast migration and a dramatic reduction in the fibrotic response to bleomycin in mice. Together, our results uncover how Hsp90 regulates ILK stability and identify a potential therapeutic strategy to alleviate fibrotic diseases.
(4293) Kate Morton
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Supplementary Material from The mere physical presence of another person reduces human autonomic responses to aversive sounds.
Creators: name: Yanyan Qi
name: Herrmann, Martin J.
name: Bell, Luisa
name: Fackler, Anna
name: Shihui Han
name: Deckert, Jürgen
name: Hein, Grit
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Supplementary Methods and Results
The local stellar luminosity function and mass-to-light ratio in the NIR
Creators: name: Just, A.
name: Fuchs, B.
name: Jahreiss, H.
name: Flynn, C.
name: Dettbarn, C.
name: Rybizki, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: A new sample of stars, representative of the solar neighbourhood luminosity function, is constructed from the Hipparcos catalogue and the Fifth Catalogue of Nearby Stars. We have cross-matched to sources in the 2MASS catalogue so that for all stars individually determined Near Infrared photometry (NIR) is available on a homogeneous system (typically K_s). The spatial completeness of the sample has been carefully determined by statistical methods, and the NIR luminosity function of the stars has been derived by direct star counts. We find a local volume luminosity of 0.121 +/- 0.004 L_K_sun/(pc**3), corresponding to a volumetric mass-to-light ratio of M/L_K = 0.31 +/- 0.02 M_sun/L_K_sun, where giants contribute 80 per cent to the light but less than 2 per cent to the stellar mass. We derive the surface brightness of the solar cylinder with the help of a vertical disc model. We find a surface brightness of 99 L_K_sun/(pc**2) with an uncertainty of approximately 10 %. This corresponds to a mass-to-light ratio for the solar cylinder of M/L_K = 0.34 M_sun/L_K_sun. The mass-to-light ratio for the solar cylinder is only 10% larger than the local value despite the fact that the local population has a much larger contribution of young stars. It turns out that the effective scale heights of the lower main sequence carrying most of the mass is similar to that of the giants, which are dominating the NIR light. The corresponding colour for the solar cylinder is V-K=2.89 mag compared to the local value of V-K = 2.46 mag. An extrapolation of the local surface brightness to the whole Milky Way yields a total luminosity of M_K = -24.2 mag. The Milky Way falls in the range of K band Tully-Fisher (TF) relations from the literature.
description: 11 pages, 11 figures, accepted to MNRAS. Resolution of images reduced
Regulation of G6PD acetylation by SIRT2 and KAT9 modulates NADPH homeostasis and cell survival during oxidative stress
Creators: name: Zhou, Li Sha
name: Wang, Yi Ping
name: Yang, Yi
name: Ling, Zhi Qiang
name: Sun, Yi Ping
name: Chen, Lei Lei
name: Wang, Shi Wen
name: Guan, Kun Liang
name: Liu, Li Xia
name: Zhang, Jing Ye
name: Zhao, Yu Zheng
name: Yang, Chen
name: Xiong, Yue
name: Hu, Fu Jun
name: Ye, Dan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme in the pentose phosphate pathway (PPP) and plays an essential role in the oxidative stress response by producing NADPH, the main intracellular reductant. G6PD deficiency is the most common human enzyme defect, affecting more than 400 million people worldwide. Here, we show that G6PD is negatively regulated by acetylation on lysine 403 (K403), an evolutionarily conserved residue. The K403 acetylated G6PD is incapable of forming active dimers and displays a complete loss of activity. Knockdown of G6PD sensitizes cells to oxidative stress, and re-expression of wild-type G6PD, but not the K403 acetylation mimetic mutant, rescues cells from oxidative injury. Moreover, we show that cells sense extracellular oxidative stimuli to decrease G6PD acetylation in a SIRT2-dependent manner. The SIRT2-mediated deacetylation and activation of G6PD stimulates PPP to supply cytosolic NADPH to counteract oxidative damage and protect mouse erythrocytes. We also identified KAT9/ELP3 as a potential acetyltransferase of G6PD. Our study uncovers a previously unknown mechanism by which acetylation negatively regulates G6PD activity to maintain cellular NADPH homeostasis during oxidative stress.
Scanning X-ray diffraction microscopy of a 6 GHz surface acoustic wave
Creators: name: Hanke, M.
name: Ashurbekov, N.
name: Zatterin, E.
name: Msall, M. E.
name: Hellemann, J.
name: Santos, P. V.
name: Schulli, T. U.
name: Ludwig, S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Surface acoustic waves at frequencies beyond a few GHz are promising components for quantum technology applications. Applying scanning X-ray diffraction microcopy we directly map the locally resolved components of the three-dimensional strain field generated by a standing surface acoustic wave on GaAs with wavelength $λ\simeq500\,$nm corresponding to frequencies near 6 GHz. We find that the lattice distortions perpendicular to the surface are phase-shifted compared to those in propagation direction. Model calculations based on Rayleigh waves confirm our measurements. Our results represent a break through in providing a full characterization of a radio frequency surface acoustic wave beyond plain imaging.
description: 9 pages, 6 figures
Dysregulated miRNA biogenesis downstream of cellular stress and ALS-causing mutations: a new mechanism for ALS
Creators: name: Silvestroni, Aurelio
name: Möller, Thomas
name: Levin, Yishai
name: Sons, Robert
name: Ben-Dov, Iddo Z.
name: Reichenstein, Irit
name: Hammond, Scott M.
name: Hornstein, Eran
name: Liou, Lee Loung
name: Emde, Anna
name: Magen, Iddo
name: Oppenheim, Hagar
name: Alajajian, Betty
name: Rivkin, Natali
name: Eitan, Chen
name: Libby, Ryan T.
name: Aebischer, Julianne
name: Ravits, John M.
name: Savidor, Alon
name: Eilam, Raya
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Abstract Interest in RNA dysfunction in amyotrophic lateral sclerosis (ALS) recently aroused upon discovering causative mutations in RNA‐binding protein genes. Here, we show that extensive down‐regulation of miRNA levels is a common molecular denominator for multiple forms of human ALS. We further demonstrate that pathogenic ALS‐causing mutations are sufficient to inhibit miRNA biogenesis at the Dicing step. Abnormalities of the stress response are involved in the pathogenesis of neurodegeneration, including ALS. Accordingly, we describe a novel mechanism for modulating microRNA biogenesis under stress, involving stress granule formation and re‐organization of DICER and AGO2 protein interactions with their partners. In line with this observation, enhancing DICER activity by a small molecule, enoxacin, is beneficial for neuromuscular function in two independent ALS mouse models. Characterizing miRNA biogenesis downstream of the stress response ties seemingly disparate pathways in neurodegeneration and further suggests that DICER and miRNAs affect neuronal integrity and are possible therapeutic targets.
Muonic atom spectroscopy with microgram target material
Creators: name: Adamczak, A.
name: Antognini, A.
name: Berger, N.
name: Cocolios, T. E.
name: Deokar, N.
name: Düllmann, Ch. E.
name: Eggenberger, A.
name: Eichler, R.
name: Heines, M.
name: Hess, H.
name: Indelicato, P.
name: Kirch, K.
name: Knecht, A.
name: Krauth, J. J.
name: Nuber, J.
name: Ouf, A.
name: Papa, A.
name: Pohl, R.
name: Rapisarda, E.
name: Reiter, P.
name: Ritjoho, N.
name: Roccia, S.
name: Seidlitz, M.
name: Severijns, N.
name: von Schoeler, K.
name: Skawran, A.
name: Vogiatzi, S. M.
name: Warr, N.
name: Wauters, F.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Muonic atom spectroscopy -- the measurement of the x rays emitted during the formation process of a muonic atom -- has a long standing history in probing the shape and size of nuclei. In fact, almost all stable elements have been subject to muonic atom spectroscopy measurements and the absolute charge radii extracted from these measurements typically offer the highest accuracy available. However, so far only targets of at least a few hundred milligram could be used as it required to stop a muon beam directly in the target to form the muonic atom. We have developed a new method relying on repeated transfer reactions taking place inside a 100-bar hydrogen gas cell with an admixture of 0.25% deuterium that allows us to drastically reduce the amount of target material needed while still offering an adequate efficiency. Detailed simulations of the transfer reactions match the measured data, suggesting good understanding of the processes taking place inside the gas mixture. As a proof of principle we demonstrate the method with a measurement of the 2p-1s muonic x rays from a 5-μg gold target.
description: 16 pages, 14 figures
Two-Higgs-Doublet type-II and -III models and $t\to c h$ at the LHC
Creators: name: Arhrib, A.
name: Benbrik, R.
name: Chen, Chuan-Hung
name: Gomez-Bock, M.
name: Semlali, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the constraints of the generic two-Higgs-doublet model (2HDM) type-III and the impacts of the new Yukawa couplings. For comparisons, we revisit the analysis in the 2HDM type-II. To understand the influence of all involving free parameters and to realize their correlations, we employ $χ$-square fitting approach by including theoretical and experimental constraints, such as S, T, and U oblique parameters, the production of standard model Higgs and its decay to $γγ$, $WW^*/ZZ^*$, $τ^+τ^-$, etc. The errors of analysis are taken at $68\%$, $95.5\%$, and $99.7\%$ confidence levels. Due to the new Yukawa couplings being associated with $\cos(β-α)$ and $\sin(β-α)$, we find that the allowed regions for $\sinα$ and $\tanβ$ in the type-III model can be broader when the dictated parameter $χ_F$ is positive; however, for negative $χ_F$, the limits are stricter than those in the type-II model. By using the constrained parameters, we find that the deviation from the SM in the $h\to Zγ$ can be of ${\cal O}(10\%)$. Additionally, we also study the top-quark flavor-changing processes induced at the tree level in the type-III model and find that when all current experimental data are considered, we get $Br(t\to c(h, H) )< 10^{-3}$ for $m_h=125.36$ and $m_H=150$ GeV and $Br(t\to cA)$ slightly exceeds $10^{-3}$ for $m_A =130$ GeV.
description: 22 pages, 11 figures. v3: Slight change in the abstract, Figure.1 added and commented, the conclusion remains unchanged
EglN2 associates with the NRF1‐PGC1α complex and controls mitochondrial function in breast cancer
Creators: name: Pestell, Richard G.
name: Chen, Xi
name: Zhang, Jing
name: Zhang, Qing
name: Zheng, Xingnan
name: Aird, Katherine M.
name: Kaelin, William G.
name: Fan, Cheng
name: Liu, Yong
name: Takada, Mamoru
name: Wen, Haitao
name: Liu, Xiaole Shirley
name: Wang, Chenguang
name: Wang, Chengyang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Abstract The EglN2/PHD1 prolyl hydroxylase is an important oxygen sensor contributing to breast tumorigenesis. Emerging studies suggest that there is functional cross talk between oxygen sensing and mitochondrial function, both of which play an essential role for sustained tumor growth. However, the potential link between EglN2 and mitochondrial function remains largely undefined. Here, we show that EglN2 depletion decreases mitochondrial respiration in breast cancer under normoxia and hypoxia, which correlates with decreased mitochondrial DNA in a HIF1/2α‐independent manner. Integrative analyses of gene expression profile and genomewide binding of EglN2 under hypoxic conditions reveal nuclear respiratory factor 1 (NRF1) motif enrichment in EglN2‐activated genes, suggesting NRF1 as an EglN2 binding partner. Mechanistically, by forming an activator complex with PGC1α and NRF1 on chromatin, EglN2 promotes the transcription of ferridoxin reductase (FDXR) and maintains mitochondrial function. In addition, FDXR, as one of effectors for EglN2, contributes to breast tumorigenesis in vitro and in vivo. Our findings suggest that EglN2 regulates mitochondrial function in ERα‐positive breast cancer.
Polychaete assemblages on shallow-water benthic habitats along the Sinop Peninsula (Black Sea, Turkey)
Creators: name: ÇINAR, Melih Ertan
name: GÖNLÜGÜR-DEMIRCI, Gamze
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2005

description: The present study describes polychaete assemblages on three shallow-water benthic habitats, Ulva rigida,
 Cytoseira barbata and Mytilus galloprovincialis, in relation to space and time from the Sinop Peninsula (Turkish Black Sea
 coast). A total of 55 polychaete species and 21493 individuals belonging to 16 families were identified. Among the species,
 eight are reported for the first time from the Black Sea and 29 species from the Turkish Black Sea coasts. The polychaete
 density in the area ranged from 500 ind.m-2 to 46775 ind.m-2 (both on M. galloprovincialis), the polychaete biomass from
 3.97 g.m-2 (on U. rigida) to 72.01 g.m-2 (on M. galloprovincialis). The highest diversity index values were calculated on
 M. galloprovincialis. Among the biotopes, C. barbata had the highest mean polychaete density in all seasons, whereas M.
 galloprovincialis possessed the highest mean biomass value in all seasons except in spring. Analysis of similarity revealed
 that polychaete community structure significantly differed among biotopes, sites and seasons.
Supplementary Material from The mere physical presence of another person reduces human autonomic responses to aversive sounds
Creators: name: Yanyan Qi
name: Herrmann, Martin J.
name: Bell, Luisa
name: Fackler, Anna
name: Shihui Han
name: Deckert, Jürgen
name: Hein, Grit
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Supplementary Methods and Results
Distinguishing cusp effects and near-threshold-pole effects
Creators: name: Zhou, Zhi-Yong
name: Xiao, Zhiguang
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We make use of a unitarized coupled-channel model to analyze the mass distribution data of final states in production processes of $X(4260)$. By analyzing the analytical structures of the decay amplitudes, we find that the line shape of $Z_c(3900)$ signal is related to the combined effect of a pair of near-threshold "shadow" poles and the $(D\bar{D}^*)^\pm$ thresholds, in which the third-sheet pole might provide a dominant contribution. As all the coupled channels effects are tuning off, the trajectories of these two poles suggest that the $Z_c(3900)$ might originate from the attractive interaction of $(D^*\bar{D}^*)^\pm$ through a long-distance interaction, $e.g.$ $π$-exchange interaction, as a "deuteron-like" state. There is no nearby pole structure corresponding to the $Z_c(4025)$ signal in the $(D^*\bar{D}^*)^\pm$ mass distribution.
description: 10 pages, 3 figures
SIRT3-dependent GOT2 acetylation status affects the malate-aspartate NADH shuttle activity and pancreatic tumor growth
Creators: name: Yang, Hui
name: Shi, Qian
name: Lin, Huaipeng
name: Xiong, Yue
name: Zhao, Shimin
name: Yang, Yi
name: Guan, Kun Liang
name: Zhao, Yuzheng
name: Zhang, Mengli
name: Zhou, Lisha
name: Ye, Dan
name: Ling, Zhi Qiang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The malate–aspartate shuttle is indispensable for the net transfer of cytosolic NADH into mitochondria to maintain a high rate of glycolysis and to support rapid tumor cell growth. The malate–aspartate shuttle is operated by two pairs of enzymes that localize to the mitochondria and cytoplasm, glutamate oxaloacetate transaminases (GOT), and malate dehydrogenases (MDH). Here, we show that mitochondrial GOT2 is acetylated and that deacetylation depends on mitochondrial SIRT3. We have identified that acetylation occurs at three lysine residues, K159, K185, and K404 (3K), and enhances the association between GOT2 and MDH2. The GOT2 acetylation at these three residues promotes the net transfer of cytosolic NADH into mitochondria and changes the mitochondrial NADH/NAD+ redox state to support ATP production. Additionally, GOT2 3K acetylation stimulates NADPH production to suppress ROS and to protect cells from oxidative damage. Moreover, GOT2 3K acetylation promotes pancreatic cell proliferation and tumor growth in vivo. Finally, we show that GOT2 K159 acetylation is increased in human pancreatic tumors, which correlates with reduced SIRT3 expression. Our study uncovers a previously unknown mechanism by which GOT2 acetylation stimulates the malate–aspartate NADH shuttle activity and oxidative protection.
Supplementary Information from Modelling of dysregulated glucagon secretion in type 2 diabetes by considering mitochondrial alterations in pancreatic α-cells.
Creators: name: Grubelnik, Vladimir
name: Markovič, Rene
name: Saška Lipovšek
name: Leitinger, Gerd
name: Gosak, Marko
name: Dolenšek, Jurij
name: Valladolid-Acebes, Ismael
name: Per-Olof Berggren
name: Andraž Stožer
name: Matjaž Perc
name: Marhl, Marko
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Biophysics
subject: 80201 Analysis of Algorithms and Complexity
subject: FOS: Computer and information sciences

description: Type 2 diabetes mellitus (T2DM) has been associated with insulin resistance and the failure of β-cells to produce and secrete enough insulin as the disease progresses. However, clinical treatments based solely on insulin secretion and action have had limited success. The focus is therefore shifting towards α-cells, in particular to the dysregulated secretion of glucagon. Our qualitative electron-microscopy-based observations gave an indication that mitochondria in α-cells are altered in Western-diet-induced T2DM. In particular, α-cells extracted from mouse pancreatic tissue showed a lower density of mitochondria, a less expressed matrix and a lower number of cristae. These deformities in mitochondrial ultrastructure imply a decreased efficiency in mitochondrial ATP production, which prompted us to theoretically explore and clarify one of the most challenging problems associated with T2DM, namely the lack of glucagon secretion in hypoglycaemia and its oversecretion at high blood glucose concentrations. To this purpose, we constructed a novel computational model that links α-cell metabolism with their electrical activity and glucagon secretion. Our results show that defective mitochondrial metabolism in α-cells can account for dysregulated glucagon secretion in T2DM, thus improving our understanding of T2DM pathophysiology and indicating possibilities for new clinical treatments.
First record of Trunculariopsis trunculus (Linnaeus, 1758) (Mollusca: Gastropoda) from the basin of Arcachon (Gironde): the second exotic muricid on the French Atlantic coast
Creators: name: MERLE, Didier
name: FILIPPOZZI, Daniel
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2005

description: The species Trunculariopsis trunculus (Linnaeus, 1758) is first recorded in the basin of Arcachon (Gironde,
 France). Eight living specimens, of which three are illustrated here, were collected in 1996/1997, 2002, 2003 and 2004, at
 3 to 5 meters deep in the Courbey channel, close to the city of Lège-Cap-Ferret. They reach a large size (84-105 mm in
 height) and correspond to adult individuals. Thus, this record shows the occurrence of a second exotic muricid on the
 French Atlantic coast, the first one being Ocinebrellus inornatus (Recluz, 1851). The geological history of Trunculariopsis
 (Cossmann, 1921) shows that T. trunculus disappeared from the French Atlantic coast from the Late Pliocene to the
 Quaternary, but still persists in the Mediterranean Sea and in the Algarve. The T. trunculus from the basin of Arcachon,
 which is a place of commercial exchanges of molluscs, probably come from these areas.
Discrete exterior calculus discretization of incompressible Navier-Stokes equations over surface simplicial meshes
Creators: name: Mohamed, Mamdouh S.
name: Hirani, Anil N.
name: Samtaney, Ravi
Publisher: name: arXiv
Year: 2015
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Differential Geometry (math.DG)
subject: Numerical Analysis (math.NA)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: A conservative discretization of incompressible Navier-Stokes equations is developed based on discrete exterior calculus (DEC). A distinguishing feature of our method is the use of an algebraic discretization of the interior product operator and a combinatorial discretization of the wedge product. The governing equations are first rewritten using the exterior calculus notation, replacing vector calculus differential operators by the exterior derivative, Hodge star and wedge product operators. The discretization is then carried out by substituting with the corresponding discrete operators based on the DEC framework. Numerical experiments for flows over surfaces reveal a second order accuracy for the developed scheme when using structured-triangular meshes, and first order accuracy for otherwise unstructured meshes. By construction, the method is conservative in that both mass and vorticity are conserved up to machine precision. The relative error in kinetic energy for inviscid flow test cases converges in a second order fashion with both the mesh size and the time step.
description: 35 pages, 8 figures
Kernel Normalized Convolutional Networks for Privacy-Preserving Machine Learning
Creators: name: Nasirigerdeh, Reza
name: Torkzadehmahani, Javad
name: Rueckert, Daniel
name: Kaissis, Georgios
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Normalization is an important but understudied challenge in privacy-related application domains such as federated learning (FL), differential privacy (DP), and differentially private federated learning (DP-FL). While the unsuitability of batch normalization for these domains has already been shown, the impact of other normalization methods on the performance of federated or differentially private models is not well-known. To address this, we draw a performance comparison among layer normalization (LayerNorm), group normalization (GroupNorm), and the recently proposed kernel normalization (KernelNorm) in FL, DP, and DP-FL settings. Our results indicate LayerNorm and GroupNorm provide no performance gain compared to the baseline (i.e. no normalization) for shallow models in FL and DP. They, on the other hand, considerably enhance the performance of shallow models in DP-FL and deeper models in FL and DP. KernelNorm, moreover, significantly outperforms its competitors in terms of accuracy and convergence rate (or communication efficiency) for both shallow and deeper models in all considered learning environments. Given these key observations, we propose a kernel normalized ResNet architecture called KNResNet-13 for differentially private learning. Using the proposed architecture, we provide new state-of-the-art accuracy values on the CIFAR-10 and Imagenette datasets, when trained from scratch.
description: To appear in the IEEE Conference on Secure and Trustworthy Machine Learning (SaTML), February 2023
L'ENCÉPHALE DE SCYLIORHINUS CANICULA (LINNÉ, 1758) (CHONDRICHTHYES, SELACHII, SCYLIORHINIDAE). RECHERCHE D'UNE GRANDEUR DE RÉFÉRENCE POUR DES ÉTUDES QUANTITATIVES
Creators: name: RIDET, Jean-Marc
name: BAUCHOT, Roland
name: DELFINI, Christian
name: PLATEL, Roland
name: THIREAU, Michel
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 1973

Abstract
Supplementary Information from Modelling of dysregulated glucagon secretion in type 2 diabetes by considering mitochondrial alterations in pancreatic α-cells
Creators: name: Grubelnik, Vladimir
name: Markovič, Rene
name: Saška Lipovšek
name: Leitinger, Gerd
name: Gosak, Marko
name: Dolenšek, Jurij
name: Valladolid-Acebes, Ismael
name: Per-Olof Berggren
name: Andraž Stožer
name: Matjaž Perc
name: Marhl, Marko
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Biophysics
subject: 80201 Analysis of Algorithms and Complexity
subject: FOS: Computer and information sciences

description: Type 2 diabetes mellitus (T2DM) has been associated with insulin resistance and the failure of β-cells to produce and secrete enough insulin as the disease progresses. However, clinical treatments based solely on insulin secretion and action have had limited success. The focus is therefore shifting towards α-cells, in particular to the dysregulated secretion of glucagon. Our qualitative electron-microscopy-based observations gave an indication that mitochondria in α-cells are altered in Western-diet-induced T2DM. In particular, α-cells extracted from mouse pancreatic tissue showed a lower density of mitochondria, a less expressed matrix and a lower number of cristae. These deformities in mitochondrial ultrastructure imply a decreased efficiency in mitochondrial ATP production, which prompted us to theoretically explore and clarify one of the most challenging problems associated with T2DM, namely the lack of glucagon secretion in hypoglycaemia and its oversecretion at high blood glucose concentrations. To this purpose, we constructed a novel computational model that links α-cell metabolism with their electrical activity and glucagon secretion. Our results show that defective mitochondrial metabolism in α-cells can account for dysregulated glucagon secretion in T2DM, thus improving our understanding of T2DM pathophysiology and indicating possibilities for new clinical treatments.
Morphometric analysis of treatment effects of bone-anchored maxillary protraction in growing Class III patients
Creators: name: Cevidanes, L. H.
name: Baccetti, Tiziano
name: Franchi, L.
name: De Clerck, H. J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The aim of the present morphometric investigation was to evaluate the effects of bone-anchored maxillary protraction (BAMP) in the treatment of growing patients with Class III malocclusion. The shape and size changes in the craniofacial configuration of a sample of 26 children with Class III malocclusions consecutively treated with the BAMP protocol were compared with a matched sample of 15 children with untreated Class III malocclusions. All subjects in the two groups were at a prepubertal stage of skeletal development at time of first observation. Average duration of treatment was 14 months. Significant treatment-induced modifications involved both the maxilla and the mandible. The most evident deformation consisted of marked forward displacement of the maxillary complex with more moderate favourable effects in the mandible. Deformations in the vertical dimension were not detected. The significant deformations were associated with significant differences in size in the group treated with the BAMP protocol.
(401755) Thomas High
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
(4290) William Henry Forde
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Fundamental limits of pulsed quantum light spectroscopy: Dipole moment estimation
Creators: name: Albarelli, Francesco
name: Bisketzi, Evangelia
name: Khan, Aiman
name: Datta, Animesh
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the fundamental limits of the precision of estimating parameters of a quantum matter system when it is probed by a travelling pulse of quantum light. In particular, we focus on the estimation of the interaction strength between the pulse and a two-level atom, equivalent to the estimation of the dipole moment. Our analysis of single-photon pulses highlights the interplay between the information gained from the absorption of the photon by the atom as measured in absorption spectroscopy, and the perturbation to the temporal mode of the photon due to spontaneous emission. Beyond the single-photon regime, we introduce an approximate model to study more general states of light in the limit of short pulses, where spontaneous emission can be neglected. We also show that for a vast class of entangled biphoton states, quantum entanglement between the signal mode interacting with the atom and the idler mode provides no fundamental advantage and the same precision can be obtained with a separable state. We conclude by studying the estimation of the electric dipole moment of a sodium atom using quantum light. Our work initiates a quantum information theoretic methodology for developing the theory and practice of quantum light spectroscopy.
description: v2: 30 pages, 10 figures, Fig. 7 fixes an error in Fig. 8 of v1, appendix E replaces appendix B of v1
Extracellular purines are biomarkers of neutrophilic airway inflammation
Creators: name: Moore, C. G.
name: Clas, M. L.
name: Pedrosa Ribeiro, C. M.
name: Lazarowski, E. R.
name: Davis, S. D.
name: Boucher, R. C.
name: Alexis, N. E.
name: Donaldson, S. H.
name: Esther Jr., C. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Purinergic signalling regulates airway defence mechanisms, suggesting that extracellular purines could serve as airway inflammation biomarkers in cystic fibrosis (CF).
Figures S1 - S3 from Structure–behaviour correlations between two genetically closely related snail species.
Creators: name: H. LE FERRAND
name: Y. Morii
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 90301 Biomaterials
subject: FOS: Medical engineering

description: Figure S1: Angle of the snail shell with respect to the snail body (angle swing) as a function of the time t and for 7 consecutive swings, for K. gainesi.; Figure S2: Schematics for the determination of the shell's moment when the snail is at rest on a horizontal surface (A) and when the snail is swinging its shell (B).; Figure S3: Energy dispersive X-Ray spectra up to 5 keV obtained for K. editha (A) and K. gainesi (B), respectively.
Orbital effect on the in-plane critical field in free-standing superconducting nanofilms
Creators: name: Wójcik, P.
name: Zegrodnik, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The superconductor to normal metal phase transition induced by the in-plane magnetic field is studied in free-standing Pb(111) nanofilms. In the considered structures the energy quantization induced by the confinement leads to the thickness-dependent oscillations of the critical field (the so-called 'shape resonances'). In this paper we examine the influence of the orbital effect on the in-plane critical magnetic field in nanofilms. We demonstrate that the orbital term suppresses the critical field and reduces the amplitude of the thickness-dependent critical field oscillations. Moreover, due to the orbital effect, the slope $H_{c,||}-T_c$ at $T_c(0)$ becomes finite and decreases with increasing film thickness in agreement with recent experiments. The temperature $t^*$ at which the superconductor to normal metal phase transition becomes of the first order is also analyzed.
description: 8 pages, 7 figures
MISURE DI PREVENZIONE PERSONALI E GIUSTO PROCESSO. UN EQUILIBRIO POSSIBILE IN UN SISTEMA AI CONFINI DELLA GIURISDIZIONE PENALE.
Creators: name: ALBANESE, DARIO
Publisher: name: Universit� degli Studi di Milano
Year: 2020

description: La tesi, intitolata ?Misure di prevenzione personali e giusto processo?, ha ad oggetto i profili processuali del sistema di prevenzione personale disciplinato dal d.lgs. 159/2011. L?elaborato si articola in quattro capitoli. Il primo capitolo � dedicato all?evoluzione storica del procedimento di prevenzione. In particolare, viene messo in luce come, dalla fine del XIX secolo a oggi, si sia lentamente passati da un procedimento avente natura amministrativa ? quello delle misure di polizia ? a un processo cui � pacificamente riconosciuta natura giurisdizionale. Il secondo e il terzo capitolo sono dedicati alla ricostruzione della disciplina vigente. In particolare, nel secondo capitolo vengono analizzati i profili ?statici? della materia e vengono messe in luce le interferenze tra il processo di prevenzione e il processo penale, mentre nel terzo capitolo viene illustrata la disciplina del procedimento, alla luce dell?elaborazione giurisprudenziale. Il quarto capitolo, infine, � dedicato ad alcuni spunti di riflessione per la costruzione di un ?giusto processo di prevenzione personale?. In un?ottica de jure condendo, si propone di seguire tre diverse linee evolutive. Per prima cosa, viene auspicata una ?riscoperta? del principio di proporzionalit� in materia preventiva, in modo da consentire l?applicazione delle sole misure ritenute idonee a fronteggiare le diverse forme di pericolosit� prese in considerazione dal legislatore. In secondo luogo, l?autore indica quali passi in avanti potrebbero essere ancora compiuti sul piano delle garanzie difensive, al fine di attuare i principi del giusto processo sanciti dalla Costituzione e dalla Convenzione europea dei diritti dell?uomo. Infine, l?autore osserva che per porre rimedio alle interferenze tra processo penale e processo di prevenzione occorrerebbe un mutamento delle fattispecie preventive, individuando delle condotte sintomatiche di pericolosit� che non si identificano con fatti penalmente rilevanti.
(4287) Marion Kincaid Turnbull
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.