cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Quantum synchronization of two Van der Pol oscillators
Creators: name: Walter, Stefan
name: Nunnenkamp, Andreas
name: Bruder, Christoph
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study synchronization of two dissipatively coupled Van der Pol oscillators in the quantum regime. Due to quantum noise strict frequency locking is absent and is replaced by a crossover from weak to strong frequency entrainment. We discuss the differences to the behavior of one quantum Van der Pol oscillator subject to an external drive. Moreover, we describe a possible experimental realization of two coupled quantum van der Pol oscillators in an optomechanical setting.
description: 8 pages, 5 figures, submitted to the topical issue "Quantum and Hybrid Mechanical Systems" in Annalen der Physik
Position-dependent and pair diffusivity profiles from steady-state solutions of color reaction-counterdiffusion problems
Creators: name: Carmer, James
name: van Swol, Frank
name: Truskett, Thomas M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We show how the steady-state solution of the Smoluchowski (Fokker-Planck) equation for a color reaction-counterdiffusion problem, together with equilibrium trajectory information (e.g., from molecular simulations or confocal microscopy experiments), can be used to determine position-dependent or pair diffusivity profiles for condensed phases directly without the need for Bayesian inference, likelihood maximization, or the analysis of time-dependent data.
description: 5 pages, 3 figures
An accurate numerical method for systems of differentio-integral equations associated with multiphase flow
Creators: name: Shu, Jian-Jun
name: Wilks, Graham
Publisher: name: arXiv
Year: 2014
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: A very simple and accurate numerical method which is applicable to systems of differentio-integral equations with quite general boundary conditions has been devised. Although the basic idea of this method stems from the Keller Box method, it solves the problem of systems of differential equations involving integral operators not previously considered by the Keller Box method. Two main preparatory stages are required: (i) a merging procedure for differential equations and conditions without integral operators and; (ii) a reduction procedure for differential equations and conditions with integral operators. The differencing processes are effectively simplified by means of the unit-step function. The nonlinear difference equations are solved by Newton method using an efficient block arrow-like matrix factorization technique. As an example of the application of this method, the systems of equations for combined gravity body force and forced convection in laminar film condensation can be solved for prescribed values of physical constants.
T2.1 - Design of Reference Architecture
Creators: name: Kranas, Pavlos
name: Pereira, Javier
name: Doval, Fernando García
name: Burgos, Diego
name: Ramiro, Alejandro
name: De Pablo, Raúl
name: Rodriguez, Rogelio
name: Nvara, Francisco
name: Pablos, Spencer
name: Remedios, Jose Correas
name: Petrou, Petros
name: Iatropoulou, Stavroula
name: Anastasiou, Theodora
name: Chrysakis, Ioannis
name: Orphanoudakis, Theofanis
name: Zalonis, Andreas
name: Myroulla Drakos
name: Pirillos, Christoforos
name: Doulkeridis, Christos
name: Santipantakis, Georgios M.
name: Koutroumanis, Nikolaos
name: Makridis, George
name: Vasilis Koukos,
name: Theodoropoulos, George S.
name: Theodoridis, Yannis
name: Kyriazis, Dimosthenis
name: Duarte, Mariana Machado Garcez
name: Sakr, Mahmoud
name: Zimanyi, Esteban
name: Sanchez, Carlos
name: D'Andria, Francesco
name: Nechifo, Septimiu
name: Grigoras, Cosmin
name: Juergen Neises
name: Messina, Domenico
name: Catelli, Rosario
name: Brimos, Petros
name: Nasias, Kostas
name: Teixeira, Tiago
name: Almeida, Bruno
name: Malo, Pedro
name: Mehandjiev, Nikolay
name: Khan, Nadia Masood
name: Falsetta, Matteo
name: Graser, Anita
name: Heistracher, Clemens
name: Torp, Kristian
name: Compagnucci, Marcelo Corrales
name: Karagiorgou, Sophia
Publisher: name: Zenodo
Year: 2023
Subjects: MobiSpaces
Reference Architecture
Mobility
Data Governance
AI Edge Analytics
Data Management

description: This is the first of the series of deliverables related to the activities of task T2.1 (“Design of Reference Architecture”). This deliverable specifies the system and software requirements of the MobiSpaces integrated solution, the analysis of the state-of-the-art approaches and the background technologies that the platform will be built upon, and the definition of the reference architecture of MobiSpaces, along with the detailed description of its software building blocks presented in a componentised manner.
Leptogenesis Constraints on the Mass of Right-handed Gauge Bosons
Creators: name: Dev, P. S. Bhupal
name: Lee, Chang-Hun
name: Mohapatra, R. N.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We discuss leptogenesis constraints on the mass of the right-handed $W$-boson ($W_R$) in a TeV-scale Left-Right seesaw model (LRSM) for neutrino masses. For generic Dirac mass of the neutrinos, i.e. with all Yukawa couplings $\lesssim 10^{-5.5}$, it has been pointed out that successful leptogenesis requires a lower bound of 18 TeV on the $W_R$ mass, pushing it beyond the reach of LHC. Such TeV-scale LRSM must, however, be parity-asymmetric for type-I seesaw to give the observed neutrino masses. This class of models can accommodate larger Yukawa couplings, which give simultaneous fits to charged-lepton and neutrino masses, by invoking either cancellations or specific symmetry-textures for Dirac ($M_D$) and Majorana ($M_N$) masses in the seesaw formula. We show that in this case, the leptogenesis bound on $M_{W_R}$ can be substantially weaker, i.e. $M_{W_R}\gtrsim 3$ TeV for $M_N \lesssim M_{W_R}$. This happens due to considerable reduction of the dilution effects from $W_R$-mediated decays and scatterings, while the washout effects due to inverse decays are under control for certain parameter ranges of the Yukawa couplings. We also show that this model is consistent with all other low energy constraints, such as lepton flavor violation and neutrinoless double beta decay. Thus, a discovery of the right-handed gauge bosons alone at the LHC will not falsify leptogenesis as the mechanism behind the matter-antimatter asymmetry in our Universe.
description: 29 pages, 5 figures, 2 tables; some clarifications and references added; version accepted for publication in Phys. Rev. D
Identical phosphatase mechanisms achieved through distinct modes of binding phosphoprotein substrate
Creators: name: Motaleb, M. A.
name: Guarnieri, M. T.
name: Zhao, R.
name: Charon, N. W.
name: Silversmith, R. E.
name: Pazy, Y.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Two-component signal transduction systems are widespread in prokaryotes and control numerous cellular processes. Extensive investigation of sensor kinase and response regulator proteins from many two-component systems has established conserved sequence, structural, and mechanistic features within each family. In contrast, the phosphatases which catalyze hydrolysis of the response regulator phosphoryl group to terminate signal transduction are poorly understood. Here we present structural and functional characterization of a representative of the CheC/CheX/FliY phosphatase family. The X-ray crystal structure of Borrelia burgdorferi CheX complexed with its CheY3 substrate and the phosphoryl analogue reveals a binding orientation between a response regulator and an auxiliary protein different from that shared by every previously characterized example. The surface of CheY3 containing the phosphoryl group interacts directly with a long helix of CheX which bears the conserved (E - X2 - N) motif. Conserved CheX residues Glu96 and Asn99, separated by a single helical turn, insert into the CheY3 active site. Structural and functional data indicate that CheX Asn99 and CheY3 Thr81 orient a water molecule for hydrolytic attack. The catalytic residues of the CheX·CheY3 complex are virtually superimposable on those of the Escherichia coli CheZ phosphatase complexed with CheY, even though the active site helices of CheX and CheZ are oriented nearly perpendicular to one other. Thus, evolution has found two structural solutions to achieve the same catalytic mechanism through different helical spacing and side chain lengths of the conserved acid/amide residues in CheX and CheZ.
Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes
Creators: name: Wolfenden, R.
name: Lewis, C. A.
name: Yuan, Y.
name: Stockbridge, R. B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: All reactions are accelerated by an increase in temperature, but the magnitude of that effect on very slow reactions does not seem to have been fully appreciated. The hydrolysis of polysaccharides, for example, is accelerated 190,000-fold when the temperature is raised from 25 to 100 °C, while the rate of hydrolysis of phosphate monoester dianions increases 10,300,000-fold. Moreover, the slowest reactions tend to be the most heat-sensitive. These tendencies collapse, by as many as five orders of magnitude, the time that would have been required for early chemical evolution in a warm environment. We propose, further, that if the catalytic effect of a “proto-enzyme”—like that of modern enzymes—were mainly enthalpic, then the resulting rate enhancement would have increased automatically as the environment became cooler. Several powerful nonenzymatic catalysts of very slow biological reactions, notably pyridoxal phosphate and the ceric ion, are shown to meet that criterion. Taken together, these findings greatly reduce the time that would have been required for early chemical evolution, countering the view that not enough time has passed for life to have evolved to its present level of complexity.
Geisteswissenschaftliche Grundlagenforschung auf dem Weg zu Open Science
Creators: name: Schnöpf, Markus
Publisher: name: Zenodo
Year: 2023
Subjects: Open Access
Digital Humanities
Digital Editions
Longterm preservation

description: Das Poster zeigt am Beispiel einer vorwiegend geisteswissenschaftlich ausgerichteten Forschungsinstitution verschiedene Stationen auf, die bei der Ausrichtung auf Open Science hilfreich sind. Archiv, Bibliothek, Informationstechnologie, Digital Humanities und Forschungsdatenmanagement arbeiten bei der Umsetzung der FAIR-Prinzipien Hand in Hand. Dennoch ist Open Science kein Zustand, der erreicht werden kann, sondern bleibt ein Ziel, welches zu erreichen gilt. Auch wenn die Berlin Declaration on Open Access schon zwanzig Jahre her ist, so sind die Ziele der Erklärung noch nicht erreicht und es bedarf kontinuierliche Arbeit, um weiter zu kommen. Die Verabschiedung des Leitbilds Open Science der Berlin-Brandenburgischen Akademie der Wissenschaften 2019 sowie anderer Policies steckt den formalen Rahmen ab, in dem Open Science an der Akademie umgesetzt werden kann.
Fast-forward pipeline for cryo-EM structural analysis of native plant protein complexes
Creators: name: Muniyandi, Selvaraj
name: Pai, Hsuan
name: Madhuprakash, Jogi
name: Toghani, AmirAli
name: Webster, Michael
name: Kamoun, Sophien
name: Contreras, Mauricio P.
Publisher: name: Zenodo
Year: 2024
Subjects: subject: Structural biology
subject: molecular plant microbe interaction
subject: cryo-EM

description: *This is a poster for British Society of Plant Pathology (BSPP) conference - Plant Pathology 2024 (PPATH2024), Oxford

 

Fast-forward pipeline for cryo-EM structural analysis of native plant protein complexes

Selvaraj Muniyandi (1), Hsuan Pai (1), Jogi Madhuprakash (1), AmirAli Toghani (1), Michael Webster (2), Sophien Kamoun  (1), and Mauricio Contreras (1)

(1)  The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom

(2)  John Innes Centre, Norwich Research Park, Norwich, United Kingdom

Nucleotide-binding domain leucine-rich repeat (NLR) proteins play a vital role in plant innate immunity, forming oligomerized complexes called resistosomes upon activation. NLRs can operate individually or in higher-order configurations, such as pairs or networks, displaying functional connections between specialized sensor and helper proteins. Previous studies have utilized the hypersensitive response (HR) assay to screen functional NLRs and their target effectors, alongside blue native polyacrylamide gel electrophoresis (BN-PAGE) to visualize the oligomeric status of resistosomes upon effector perception. However, understanding the biological process of NLR activation requires bridging these macroscopic readouts with molecular and biochemical mechanisms, which remains challenging due to the difficulty in resolving NLR protein complex structures in their native state. Here, we showcase two fast-forward methods, immunoprecipitation – electron microscopy (IP-EM) and BN-PAGE EM (BN-EM), involving small-scale protein purification but capable of deciphering structures of large protein complexes using cryo-EM. Through IP-EM, we showed that the helper NLR required for cell death (NRC) exists as an inactive homodimer, transitioning to a hexameric state upon effector perception triggered by its cognate sensor NLR. These findings highlight the diversity of forms and modes of action in resistosome activation. Additionally, we determined the structure of the RuBisCO enzyme as a test case for cryo-EM of protein complexes electro-eluted from BN-PAGE. The BN-EM pipeline enabled the determination of the Nicotiana benthamiana and rice hexadecameric RuBisCO structures at 3.4Å resolution. Together, these methods represent versatile tools for fast-forward elucidation of a broad range of plant protein complexes.
Radial velocities and binarity of southern SIM grid stars
Creators: name: Makarov, Valeri V.
name: Unwin, Stephen C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present analysis of precision radial velocities (RV) of 1134 mostly red giant stars in the southern sky, selected as candidate astrometric grid objects for the Space Interferometry Mission (SIM). Only a few (typically, 2 or 3) spectroscopic observations per star have been collected, with the main goal of screening binary systems. The estimated rate of spectroscopic binarity in this sample of red giants is 32% at the 0.95 confidence level, and 46% at the 0.75 confidence. The true binarity rate is likely to be higher, because our method is not quite sensitive to very wide binaries and low-mass companions. The estimated lower and upper bounds of stellar RV jitter for the entire sample are 24 and 51 m/s, respectively; the adopted mean value is 37 m/s. A few objects of interest are identified with large variations of radial velocities, implying abnormally high mass ratios.
description: Accepted in MNRAS. The full table with data is available online
Semiparametric estimation of duration models when the parameters are subject to inequality constraints and the error distribution is unknown
Creators: name: Ranasinghe, Kulan
name: Silvapulle, Mervyn J.
Publisher: name: Monash University
Year: 2017
Subjects: Uncategorized

description: This paper proposes a semiparametric method for estimating duration models when there are inequality constraints on some parameters and the error distribution may be unknown. Thus, the setting considered here is particularly suitable for practical applications. The parameters in duration models are usually estimated by a quasi-MLE. Recent advances show that a semiparametrically efficient estimator[SPE] has better asymptotic optimality properties than the QMLE provided that the parameter space is unrestricted. However, in several important duration models, the parameter space is restricted, for example in the commonly used linear duration model some parameters are non-negative. In such cases, the SPE may turn out to be outside the allowed parameter space and hence are unsuitable for use. To overcome this difficulty, we propose a new constrained semiparametric estimator. In a simulation study involving duration models with inequality constraints on parameters, the new estimator proposed in this paper performed better than its competitors. An empirical example is provided to illustrate the application of the new constrained semiparametric estimator and to show how it overcomes difficulties encountered when the unconstrained estimator of nonnegative parameters turn out to be negative.
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
Creators: name: Cheng, C. K.
name: Hoegger, P. J.
name: Kilaru, S.
name: Goldberg, J.
name: Birren, B. W.
name: Hooker, J. B.
name: James, T. Y.
name: Huggins, A.
name: Borodovsky, M.
name: Stajich, J. E.
name: Kues, U.
name: Lomsadze, A.
name: Lilly, W. W.
name: Ahren, D.
name: Mackey, A. J.
name: Fargo, D. C.
name: Burns, C.
name: Farman, M. L.
name: Kwan, H. S.
name: Li, W.
name: Ma, L.-J.
name: Kodira, C.
name: Wilke, S. K.
name: Gathman, A. C.
name: Guigo, R.
name: Canback, B.
name: Kamada, T.
name: Dietrich, F. S.
name: Casselton, L. A.
name: Au, C. H.
name: Deng, J.
name: Kupfer, D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 108 synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
Verifying Component and Connector Models against Crosscutting Structural Views
Creators: name: Maoz, Shahar
name: Ringert, Jan Oliver
name: Rumpe, Bernhard
Publisher: name: arXiv
Year: 2014
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: The structure of component and connector (C&C) models, which are used in many application domains of software engineering, consists of components at different containment levels, their typed input and output ports, and the connectors between them. C&C views, presented in [24], can be used to specify structural properties of C&C models in an expressive and intuitive way. In this work we address the verification of a C&C model against a C&C view and present efficient (polynomial) algorithms to decide satisfaction. A unique feature of our work, not present in existing approaches to checking structural properties of C&C models, is the generation of witnesses for satisfaction/non-satisfaction and of short naturallanguage texts, which serve to explain and formally justify the verification results and point the engineer to its causes. A prototype tool and an evaluation over four example systems with multiple views, performance and scalability experiments, as well as a user study of the usefulness of the witnesses for engineers, demonstrate the contribution of our work to the state-of-the-art in component and connector modeling and analysis.
description: 11 pages, 8 figures
Hamiltonian Adaptive Importance Sampling
Creators: name: Mousavi, Ali
name: Monsefi, Reza
name: Elvira, Víctor
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Importance sampling (IS) is a powerful Monte Carlo (MC) methodology for approximating integrals, for instance in the context of Bayesian inference. In IS, the samples are simulated from the so-called proposal distribution, and the choice of this proposal is key for achieving a high performance. In adaptive IS (AIS) methods, a set of proposals is iteratively improved. AIS is a relevant and timely methodology although many limitations remain yet to be overcome, e.g., the curse of dimensionality in high-dimensional and multi-modal problems. Moreover, the Hamiltonian Monte Carlo (HMC) algorithm has become increasingly popular in machine learning and statistics. HMC has several appealing features such as its exploratory behavior, especially in high-dimensional targets, when other methods suffer. In this paper, we introduce the novel Hamiltonian adaptive importance sampling (HAIS) method. HAIS implements a two-step adaptive process with parallel HMC chains that cooperate at each iteration. The proposed HAIS efficiently adapts a population of proposals, extracting the advantages of HMC. HAIS can be understood as a particular instance of the generic layered AIS family with an additional resampling step. HAIS achieves a significant performance improvement in high-dimensional problems w.r.t. state-of-the-art algorithms. We discuss the statistical properties of HAIS and show its high performance in two challenging examples.
Characteristics of a hydraulic jump in Bingham fluid
Creators: name: Shu, Jian-Jun
name: Zhou, Jian Guo
Publisher: name: arXiv
Year: 2014
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: In this paper, we seek an adequate macroscopic model for a hydraulic jump in Bingham fluid. The formulas for conjugate depths, sequent bottom shear stress and critical depth are established. Since no exact analytical solution in closed form is available for conjugate depths, an approximate formula is developed. This formula can provide good results with an error less than 4%. The analytical results have revealed that the critical depth and the ratio of conjugate depths increase until bottom shear stress exceeds a certain value and then decrease afterwards. The bottom shear stress downstream of the jump is smaller than that upstream. The results are verified by experimental data and observations available in the literature.
A Dataset of Alt Texts from HCI Publications: Analyses and Uses Towards Producing More Descriptive Alt Texts of Data Visualizations in Scientific Papers
Creators: name: Chintalapati, Sanjana
name: Bragg, Jonathan
name: Wang, Lucy Lu
Publisher: name: arXiv
Year: 2022
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Figures in scientific publications contain important information and results, and alt text is needed for blind and low vision readers to engage with their content. We conduct a study to characterize the semantic content of alt text in HCI publications based on a framework introduced by Lundgard and Satyanarayan. Our study focuses on alt text for graphs, charts, and plots extracted from HCI and accessibility publications; we focus on these communities due to the lack of alt text in papers published outside of these disciplines. We find that the capacity of author-written alt text to fulfill blind and low vision user needs is mixed; for example, only 50% of alt texts in our sample contain information about extrema or outliers, and only 31% contain information about major trends or comparisons conveyed by the graph. We release our collected dataset of author-written alt text, and outline possible ways that it can be used to develop tools and models to assist future authors in writing better alt text. Based on our findings, we also discuss recommendations that can be acted upon by publishers and authors to encourage inclusion of more types of semantic content in alt text.
description: 11 pages, 4 figures, 4 tables, published at ASSETS 2022
Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus
Creators: name: Ireland, R. M.
name: Porcella, S. F.
name: Kobayashi, S. D.
name: Parnell, M. J.
name: Musser, J. M.
name: Wright, F. A.
name: Sturdevant, D. E.
name: Gardner, D. J.
name: Barry, W. T.
name: Babar, I.
name: Virtaneva, K.
name: Carmody, A.
name: Shea, P. R.
name: Johnson, C. A.
name: Ricklefs, S. M.
name: Kupko, J. J.
name: Bailey, J. R.
name: DeLeo, F. R.
name: Graham, M. R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Relatively little is understood about the dynamics of global host–pathogen transcriptome changes that occur during bacterial infection of mucosal surfaces. To test the hypothesis that group A Streptococcus (GAS) infection of the oropharynx provokes a distinct host transcriptome response, we performed genome-wide transcriptome analysis using a nonhuman primate model of experimental pharyngitis. We also identified host and pathogen biological processes and individual host and pathogen gene pairs with correlated patterns of expression, suggesting interaction. For this study, 509 host genes and seven biological pathways were differentially expressed throughout the entire 32-day infection cycle. GAS infection produced an initial widespread significant decrease in expression of many host genes, including those involved in cytokine production, vesicle formation, metabolism, and signal transduction. This repression lasted until day 4, at which time a large increase in expression of host genes was observed, including those involved in protein translation, antigen presentation, and GTP-mediated signaling. The interactome analysis identified 73 host and pathogen gene pairs with correlated expression levels. We discovered significant correlations between transcripts of GAS genes involved in hyaluronic capsule production and host endocytic vesicle formation, GAS GTPases and host fibrinolytic genes, and GAS response to interaction with neutrophils. We also identified a strong signal, suggesting interaction between host γδ T cells and genes in the GAS mevalonic acid synthesis pathway responsible for production of isopentenyl-pyrophosphate, a short-chain phospholipid that stimulates these T cells. Taken together, our results are unique in providing a comprehensive understanding of the host–pathogen interactome during mucosal infection by a bacterial pathogen.
CN type system formalisation for "CN: Verifying Systems C Code with Separation-Logic Refinement Types"
Creators: name: Pulte, Christopher
name: Makwana, Dhruv C.
name: Sewell, Thomas
name: Memarian, Kayvan
name: Sewell, Peter
name: Krishnaswami, Neel
Publisher: name: Zenodo
Year: 2022

description: This repository contains the formalisation of the CN type system: definitions (defns.pdf) and the soundness proof of type checking (soundness.pdf). The formalisation is by Dhruv Makwana.
Lack of both bradykinin B1 and B2 receptors enhances nephropathy, neuropathy, and bone mineral loss in Akita diabetic mice
Creators: name: Gasim, A. M. H.
name: Jennette, J. C.
name: Grant, R.
name: Feldman, E. L.
name: Nossov, S. B.
name: Smithies, O.
name: Backus, C.
name: Tomita, H.
name: Kim, H.-S.
name: Kakoki, M.
name: Hua, K.
name: Hayes, J. M.
name: Sullivan, K. A.
name: Oh, S. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: An insertion polymorphism of the angiotensin-I converting enzyme gene (ACE) is common in humans and the higher expressing allele is associated with an increased risk of diabetic complications. The ACE polymorphism does not significantly affect blood pressure or angiotensin II levels, suggesting that the kallikrein-kinin system partly mediates the effects of the polymorphism. We have therefore explored the influence of lack of both bradykinin receptors (B1R and B2R) on diabetic nephropathy, neuropathy, and osteopathy in male mice heterozygous for the Akita diabetogenic mutation in the insulin 2 gene (Ins2). We find that all of the detrimental phenotypes observed in Akita diabetes are enhanced by lack of both B1R and B2R, including urinary albumin excretion, glomerulosclerosis, glomerular basement membrane thickening, mitochondrial DNA deletions, reduction of nerve conduction velocities and of heat sensation, and bone mineral loss. Absence of the bradykinin receptors also enhances the diabetes-associated increases in plasma thiobarbituric acid-reactive substances, mitochondrial DNA deletions, and renal expression of fibrogenic genes, including transforming growth factor beta1, connective tissue growth factor, and endothelin-1. Thus, lack of B1R and B2R exacerbates diabetic complications. The enhanced renal injury in diabetic mice caused by lack of B1R and B2R may be mediated by a combination of increases in oxidative stress, mitochondrial DNA damage and over expression of fibrogenic genes.
A Spin-Orbit Alignment for the Hot Jupiter HATS-3b
Creators: name: Addison, B. C.
name: Tinney, C. G.
name: Wright, D. J.
name: Bayliss, D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We have measured the alignment between the orbit of HATS-3b (a recently discovered, slightly inflated Hot Jupiter) and the spin-axis of its host star. Data were obtained using the CYCLOPS2 optical-fiber bundle and its simultaneous calibration system feeding the UCLES spectrograph on the Anglo-Australian Telescope. The sky-projected spin-orbit angle of $λ= 3\pm25^{\circ}$ was determined from spectroscopic measurements of Rossiter-McLaughlin effect. This is the first exoplanet discovered through the HATSouth transit survey to have its spin-orbit angle measured. Our results indicate that the orbital plane of HATS-3b is consistent with being aligned to the spin axis of its host star. The low obliquity of the HATS-3 system, which has a relatively hot mid F-type host star, agrees with the general trend observed for Hot Jupiter host stars with effective temperatures $>6250$K to have randomly distributed spin-orbit angles.
description: 13 pages. Accepted for publication in the Astrophysical Journal
Albedo variegation on Comet 67P/Churyumov-Gerasimenko
Creators: name: Davidsson, Björn J. R.
name: Buratti, Bonnie J.
name: Hicks, Michael. D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We here study the level of albedo variegation on the nucleus of Comet 67P/Churyumov-Gerasimenko. This is done by fitting the parameters of a standard photometric phase function model to disk-average radiance factor data in images acquired by the Rosetta/OSIRIS Narrow Angle Camera in the orange filter. Local discrepancies between the observed radiance factor and the disk-average solution are interpreted as a proxy W of the local single-scattering albedo. We find a wide range 0.02
description: 19 pages, 40 figures. This is a pre-copyedited, author-produced PDF of an article accepted for publication in MNRAS following peer review
Maternal dietary choline deficiency alters angiogenesis in fetal mouse hippocampus
Creators: name: Zeisel, S. H.
name: Mehedint, M. G.
name: Craciunescu, C. N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: We examined whether maternal dietary choline modulates angiogenesis in fetal brain. Pregnant C57BL/6 mice were fed either a choline-deficient (CD), control (CT), or choline-supplemented diet (CS) from days 12 to 17 (E12-17) of pregnancy and then fetal brains were studied. In CD fetal hippocampus, proliferation of endothelial cells (EC) was decreased by 32% (p < 0.01 vs. CT or CS) while differentiated EC clusters (expressing factor VIII related antigen (RA)) increased by 25% (p < 0.01 vs. CT or CS). These changes were associated with > 25% decrease in the number of blood vessels in CD fetal hippocampus (p < 0.01 vs. CT and CS), with no change in total cross-sectional area of these blood vessels. Expression of genes for the angiogenic signals derived from both endothelial and neuronal progenitor cells (NPC) was increased in CD fetal hippocampus VEGF C (Vegfc), 2.0-fold, p < 0.01 vs. CT and angiopoietin 2 (Angpt2), 2.1-fold, (p < 0.01 vs. CT)). Similar increased expression was observed in NPC isolated from E14 fetal mouse brains and exposed to low (5 μM), CT (70 μM), or high choline (280 μM) media for 72 h (low choline caused a 9.7-fold increase in relative gene expression of Vegfc (p < 0.001 vs. CT and high) and a 3.4-fold increase in expression of Angpt2, (p < 0.05 vs. CT and high). ANGPT2 protein was increased 42.2% (p < 0.01). Cytosine-phosphate-guanine dinucleotide islands in the proximity of the promoter areas of Vegfc and Angpt2 were hypomethylated in low choline NPC compared to CT NPC (p < 0.01). We conclude that maternal dietary choline intake alters angiogenesis in the developing fetal hippocampus.
Non-Adiabatic Quantum Dynamics of Grover's Adiabatic Search Algorithm
Creators: name: Oh, Sangchul
name: Kais, Sabre
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study quantum dynamics of Grover's adiabatic search algorithm with the equivalent two-level system. Its adiabatic and non-adiabatic evolutions are visualized as trajectories of Bloch vectors on a Bloch sphere. We find the change in the non-adiabatic transition probability from exponential decay for short running time to inverse-square decay for long running time. The size dependence of the critical running time is expressed in terms of Lambert $W$ function. The transitionless driving Hamiltonian is obtained to make a quantum state follow the adiabatic path. We demonstrate that a constant Hamiltonian, approximate to the exact time-dependent driving Hamiltonian, can alter the non-adiabatic transition probability from the inverse square decay to the inverse fourth power decay with running time. This may open up a new way of reducing errors in adiabatic quantum computation.
description: 7 figures, submitted
Enabling the maximal re-use of data while ensuring IPR compliance.
Creators: name: Koltsida, Panagiota
name: Toli, Eleni
name: Giuffrida, Maria
name: Willems, Marieke
Publisher: name: Zenodo
Year: 2022
Subjects: tool
licence
clearance
repository
RDM
, research data management
EOSCinPractice

description: This EOSC in practice story is mainly addressed at researchers or research organisations who want to make their work available to the community, while protecting it with a compatible license. The Licence Clearance Tool (LCT) here described automates the licence clearance of derivative works and the selection of the most suitable licence for the users’ resources. The tool provides a guided approach for establishing the proper open-source license required for the creation of a new (or synthetic) dataset, media, software etc. or for the re-use of existing unlicensed content. The service described is available on NI4OS-Europe service catalogue The full list of EOSC in practice stories is available here
Metal templated design of protein interfaces
Creators: name: Ambroggio, X. I.
name: Tezcan, F. A.
name: Lewis, R. A.
name: Salgado, E. N.
name: Brodin, J. D.
name: Kuhlman, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Metal coordination is a key structural and functional component of a large fraction of proteins. Given this dual role we considered the possibility that metal coordination may have played a templating role in the early evolution of protein folds and complexes. We describe here a rational design approach, Metal Templated Interface Redesign (MeTIR), that mimics the time course of a hypothetical evolutionary pathway for the formation of stable protein assemblies through an initial metal coordination event. Using a folded monomeric protein, cytochrome cb562, as a building block we show that its non-self-associating surface can be made self-associating through a minimal number of mutations that enable Zn coordination. The protein interfaces in the resulting Zn-directed, D2-symmetrical tetramer are subsequently redesigned, yielding unique protein architectures that self-assemble in the presence or absence of metals. Aside from its evolutionary implications, MeTIR provides a route to engineer de novo protein interfaces and metal coordination environments that can be tuned through the extensive noncovalent bonding interactions in these interfaces.
Spatial patterns of dissipative polariton solitons in semiconductor microcavities
Creators: name: Chana, J. K.
name: Sich, M.
name: Fras, F.
name: Gorbach, A. V.
name: Skryabin, D. V.
name: Cancellieri, E.
name: Cerda-Méndez, E. A.
name: Biermann, K.
name: Hey, R.
name: Santos, P. V.
name: Skolnick, M. S.
name: Krizhanovskii, D. N.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Pattern Formation and Solitons (nlin.PS)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Semiconductor microcavities operating in the polaritonic regime are highly non-linear, high speed systems due to the unique half-light, half-matter nature of polaritons. Here, we report for the first time the observation of propagating multi-soliton polariton patterns consisting of multi-peak structures either along (x) or perpendicular to (y) the direction of propagation. Soliton arrays of up to 5 solitons are observed, with the number of solitons controlled by the size or power of the triggering laser pulse. The break-up along the x direction occurs due to interplay of bistability, negative effective mass and polariton-polariton scattering, while in the y direction the break-up results from nonlinear phase-dependent interactions of propagating fronts. We show the experimental results are in good agreement with numerical modelling. Our observations are a step towards ultrafast all-optical signal processing using sequences of solitons as bits of information.
Molecular basis for peptidoglycan recognition by a bactericidal lectin
Creators: name: Gardner, Kevin H.
name: Lehotzky, Rebecca E.
name: Mukherjee, Sohini
name: Hooper, Lora V.
name: Goldman, William E.
name: Partch, Carrie L.
name: Cash, Heather L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: RegIII proteins are secreted C-type lectins that kill Gram-positive bacteria and play a vital role in antimicrobial protection of the mammalian gut. RegIII proteins bind their bacterial targets via interactions with cell wall peptidoglycan but lack the canonical sequences that support calcium-dependent carbohydrate binding in other C-type lectins. Here, we use NMR spectroscopy to determine the molecular basis for peptidoglycan recognition by HIP/PAP, a human RegIII lectin. We show that HIP/PAP recognizes the peptidoglycan carbohydrate backbone in a calcium-independent manner via a conserved “EPN” motif that is critical for bacterial killing. While EPN sequences govern calcium-dependent carbohydrate recognition in other C-type lectins, the unusual location and calcium-independent functionality of the HIP/PAP EPN motif suggest that this sequence is a versatile functional module that can support both calcium-dependent and calcium-independent carbohydrate binding. Further, we show HIP/PAP binding affinity for carbohydrate ligands depends on carbohydrate chain length, supporting a binding model in which HIP/PAP molecules “bind and jump” along the extended polysaccharide chains of peptidoglycan, reducing dissociation rates and increasing binding affinity. We propose that dynamic recognition of highly clustered carbohydrate epitopes in native peptidoglycan is an essential mechanism governing high-affinity interactions between HIP/PAP and the bacterial cell wall.
VNP46A4 - VIIRS/NPP Lunar BRDF-Adjusted Nighttime Lights Yearly L3 Global 15 arc second Linear Lat Lon Grid
Creators: name: NASA Goddard Space Flight Center
Publisher: name: GEO Knowledge Hub
Year: 2023

description: VNP46A4 - VIIRS/NPP Lunar BRDF-Adjusted Nighttime Lights Yearly L3 Global 15 arc second Linear Lat Lon Grid, also referred to as VNP46A4, is a NASA data product generated from data collected by the Visible Infrared Imaging Radiometer Suite (VIIRS) Day-Night Band (DNB) sensor. VNP46A4 provides annual composites produced from daily atmospherically- and lunar-BRDF-corrected NTL radiance data. The VNP46A4 data product includes 28 layers. Variables captured in this product include number of observations, quality, snow cover, and coordinates. Validation of the data set was conducted through the Group on Earth Observations (GEO) Human Planet Initiatives's Nighttime Product Validation (NPV) task. The VNP46A4 data product is a part of NASA's Black Marble product suite, which supports the use of nightlight data for scientific use.
Stroboscopic versus non-stroboscopic dynamics in the Floquet realization of the Harper-Hofstadter Hamiltonian
Creators: name: Bukov, Marin
name: Polkovnikov, Anatoli
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We study the stroboscopic and non-stroboscopic dynamics in the Floquet realization of the Harper-Hofstadter Hamiltonian. We show that the former produces the evolution expected in the high-frequency limit only for observables which commute with the operator to which the driving protocol couples. On the contrary, non-stroboscopic dynamics is capable of capturing the evolution governed by the Floquet Hamiltonian of any observable associated with the effective high-frequency model. We provide exact numerical simulations for the dynamics of the density operator following a quantum cyclotron orbit on a $2\times 2$ plaquette, as well as the chiral current operator flowing along the legs of a $2\times 20$ ladder. The exact evolution is compared with its stroboscopic and non-stroboscopic counterparts, including finite-frequency corrections.
description: 9 pages, 8 figures
Pain perception is altered by a nucleotide polymorphism in SCN9A
Creators: name: Cox, J. J.
name: Wheeler, J.
name: Belfer, I.
name: te Morsche, R. H. M.
name: Drenth, J. P. H.
name: Mannikko, M.
name: Max, M. B.
name: Woods, C. G.
name: Wood, L.
name: Kelempisioti, A.
name: Wu, T.-X.
name: Gribble, F. M.
name: McHale, D. P.
name: Karppinen, J.
name: Maixner, W.
name: Gibson, D.
name: Zaykin, D. V.
name: Poddar, M.
name: Nikolajsen, L.
name: Dai, F.
name: Kiselycznyk, C.
name: Smith, S.
name: Reimann, F.
name: Diatchenko, L.
name: Sanders, F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: The gene SCN9A is responsible for three human pain disorders. Nonsense mutations cause a complete absence of pain, whereas activating mutations cause severe episodic pain in paroxysmal extreme pain disorder and primary erythermalgia. This led us to investigate whether single nucleotide polymorphisms (SNPs) in SCN9A were associated with differing pain perception in the general population. We first genotyped 27 SCN9A SNPs in 578 individuals with a radiographic diagnosis of osteoarthritis and a pain score assessment. A significant association was found between pain score and SNP rs6746030; the rarer A allele was associated with increased pain scores compared to the commoner G allele (P = 0.016). This SNP was then further genotyped in 195 pain-assessed people with sciatica, 100 amputees with phantom pain, 179 individuals after lumbar discectomy, and 205 individuals with pancreatitis. The combined P value for increased A allele pain was 0.0001 in the five cohorts tested (1277 people in total). The two alleles of the SNP rs6746030 alter the coding sequence of the sodium channel Nav1.7. Each was separately transfected into HEK293 cells and electrophysiologically assessed by patch-clamping. The two alleles showed a difference in the voltage-dependent slow inactivation (P = 0.042) where the A allele would be predicted to increase Nav1.7 activity. Finally, we genotyped 186 healthy females characterized by their responses to a diverse set of noxious stimuli. The A allele of rs6746030 was associated with an altered pain threshold and the effect mediated through C-fiber activation. We conclude that individuals experience differing amounts of pain, per nociceptive stimulus, on the basis of their SCN9A rs6746030 genotype.
A method to explore flavor symmetries of the 3HDM and their implications on lepton masses and mixing
Creators: name: Dziewit, Bartosz
name: Zralek, Marek
name: Vergeest, Joris
name: Chaber, Piotr
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We present a method to identify symmetry groups of the Yukawa sector of the three-Higgs-doublet model and to determine the implication that the symmetry has on the lepton masses and mixing. The method can accommodate different hypotheses about the group representation assignments, and thus support the exploration of candidate symmetry groups. For one particular representation selection scheme we apply the computer-implemented method to scan all discrete groups of order less than 1035. It can be proven that none of these groups defines a flavor symmetry that implies masses and neutrino mixing angles consistent with the experimental lepton data, although several cases are found that are partially or approximately consistent.
description: arXiv admin note: text overlap with arXiv:2203.03514
LHC searches for the CP-odd Higgs by the jet substructure analysis
Creators: name: Chen, Ning
name: Li, Jinmian
name: Liu, Yandong
name: Liu, Zuowei
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The LHC searches for the CP-odd Higgs boson is studied (with masses from 300 GeV to 1 TeV) in the context of the general two-Higgs-doublet model. With the discovery of the 125 GeV Higgs boson at the LHC, we highlight one promising discovery channel of the hZ. This channel can become significant after the global signal fitting to the 125 GeV Higgs boson in the general two-Higgs-doublet model. It is particularly important in the scenario where two CP-even Higgs bosons in the two-Higgs-doublet model have the common mass of 125 GeV. Since the final states involve a Standard-Model-like Higgs boson, we apply the jet substructure analysis of the fat Higgs jet in order to eliminate the Standard Model background sufficiently. After performing the kinematic cuts, we present the LHC search sensitivities for the CP-odd Higgs boson with mass up to 1 TeV via this channel.
description: 26 pages, 12 figures, submitted to Phys. Rev. D