cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Detection of Replication-Competent Human Immunodeficiency Virus Type 1 (HIV-1) in Cultures from Patients with Levels of HIV-1 RNA in Plasma Suppressed to Less Than 500 or 50 Copies Per Milliliter
Creators: name: Demeter, L. M.
name: Squires, K. M.
name: Fiscus, S.
name: Erice, A.
name: Fischl, M. A.
name: Bremer, J.
name: Coombs, R. W.
name: Jackson, J. B.
name: Hammer, S. M.
name: Bosch, R. J.
name: Johnson, V. A.
name: Hughes, M. D.
name: Spector, S. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: We determined the frequency with which human immunodeficiency virus (HIV) peripheral blood mononuclear cell cultures convert from positive to negative in subjects enrolled in a substudy of AIDS Clinical Trials Group (ACTG) 320, which compared the efficacy of treatment with a combination of indinavir, zidovudine, and lamivudine (indinavir arm) to that of a combination of zidovudine and lamivudine (dual-nucleoside arm). All subjects included for study had positive baseline HIV cultures. Cultures were performed in real time with 107 fresh patient peripheral blood mononuclear cells, using the ACTG consensus method. We found lower rates of positive HIV cultures in the indinavir treatment arm than in the dual-nucleoside treatment arm (64 versus 96% at week 24, P < 0.001). Within the indinavir arm of the study, we found that positive cultures were less likely to occur in samples with a plasma HIV type 1 (HIV-1) RNA level of P < 0.001). In addition, HIV cultures from samples with HIV-1 RNA levels of ≥500 copies/ml turned positive 8.5 days earlier, on average, than those from samples with levels of P < 0.001). However, 38% of samples with plasma RNA levels of
Geometric persistence and distributional trends in worldwide terrorism
Creators: name: James, Nick
name: Menzies, Max
name: Chok, James
name: Milner, Aaron
name: Milner, Cas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: This paper introduces new methods for studying the prevalence of terrorism around the world and over time. Our analysis treats spatial prevalence of terrorism, the changing profile of groups carrying out the acts of terrorism, and trends in how many attacks take place over time. First, we use a time-evolving cluster analysis to show that the geographic distribution of regions of high terrorist activity remains relatively consistent over time. Secondly, we use new metrics, inspired by geometry and probability, to track changes in the distributions of which groups are performing the terrorism. We identify times at which this distribution changes significantly and countries where the time-varying breakdown is most and least homogeneous. We observe startling geographic patterns, with the greatest heterogeneity from Africa. Finally, we use a new implementation of distances between distributions to group countries according to their incidence profiles over time. This analysis can aid in highlighting structural similarities in outbreaks of extreme behavior and the most and least significant public policies in minimizing a country's terrorism.
description: Accepted manuscript. New analysis and minor text edits since v1
The Objectives, Scope and Activities of a Possible GO TRAIN Implementation Network
Creators: name: Hodson, Simon
name: Shanahan, Hugh
name: Gelder, Celia van
name: Mons, Barend
name: Ashley, Kevin
name: Attwood, Teresa
name: Brewer, Steve
name: Demchenko, Yuri
name: Dillo, Ingrid
name: Gryce, Clare
name: Kuchma, Iryna
name: Molloy, Laura
name: Oster, Per
name: Reilly, Susan
name: Rodriguez, Eloy
name: Rans, Jonathan
Publisher: name: Zenodo
Year: 2018
Subjects: FAIR Data
Data Skills
Data Competencies
Data Roles
Data Training
GO FAIR
GO TRAIN
CODATA

description: This report is the outcome of a workshop hosted by CODATA at the International Council for Science in Paris on Friday 3 February 2017. The objective of the workshop was ‘to inform the activities and focus of a possible GO TRAIN Implementation Network (IN) as part of the wider GO FAIR initiative.’
title: Étampes « Ancien hôpital » (Essonne) Vue d'une partie du cimetière médiéval en cours de fouille (Étampes, Ancien hôpital).  © Laure Pecqueur, Inrap. DAP 40 20 octobre 2023 Ancien hôpital : Un quartier d’Étampes du XIe siècle au début du XIXe siècle (Île-de-France, Essonne, Étampes, rue du Rempart, rue Évezard, rue Baugin) :  Rapport de fouille 2012
title: Documents d’archéologie préventive ; 40
titleType: AlternativeTitle
Creators: name: Peixoto, Xavier
name: Celly, Paul
Publisher: name: Inrap
Year: 2023

description: En 2005, la fouille du site de l’Ancien Hôpital d’Étampes a porté sur 2850 m2, dans le noyau d’origine de la ville médiévale fortifiée. L’opération a permis d’étudier l’évolution d’un îlot urbain depuis sa création au XIe siècle jusqu’au début du XIXe siècle. Depuis, plusieurs autres diagnostics ont eu lieu, mais n’ont essentiellement porté que sur Étampes-les-Vieilles ou bourg Saint-Martin et sur le quartier de Saint-Gilles, c’est-à-dire hors des limites d’Étampes-le-Châtel. La seule opération d’importance dans le même contexte a été celle réalisée rue de la République dont les résultats ont été intégrés dans le rapport présenté ici, avec notamment la position du fossé d’enceinte du XIe siècle. La publication de la fouille de l’hôpital, malgré son ancienneté, reste donc pleinement d’actualité.
Antistars in the Galaxy
Creators: name: Dolgov, A. D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Possible existence of antimatter in our Galaxy, in particular of antistars is discussed and the mechanism of their creation is described.
description: 7 pages, invited talk at 20th Lomonosov Conference on Elementary Particle Physics, Moscow State University (Moscow, Russia) 19 - 25 August, 2021
Lattice Vibrational Modes and Raman Scattering Spectra of Strained Phosphorene
Creators: name: Fei, Ruixiang
name: Yang, Li
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Strain is prominent in fabricated samples of two-dimensional semiconductors and it also serves as an exploitable tool for engineering their properties. However, quantifying strain and characterizing its spatially inhomogeneous distribution across a material are challenging tasks. Here, we report the lattice vibrational modes and corresponding Raman spectra of strained monolayer black phosphorus (phosphorene) by first-principles simulations. We show that frequencies of vibrational modes of phosphorene and their Raman scattering peaks exhibit substantial and distinct shifts according to the types and size of strain. Therefore, combined with high spatial-resolution Raman scattering measurements, our calculated results can quantify strain distributions in phosphorene. This information is essential for understanding structures of future large-scale fabrication and strain engineering of phosphorene.
Protein binder purification in bacteria
Creators: name: Pascoa, Tomas
name: Bohstedt, Tina
name: Hansen, Jesper S.
name: Li, Huanyu
name: Raturi, Sagar
name: Scacioc, Andreea
name: Balakrishnan, Abilasha
name: Sauer, David B.
Publisher: name: Zenodo
Year: 2023
Subjects: Protocol

description: This protocol is used to purify the protein binders (nanobodies, sybodies, sFABs, etc) cloned into pBXNP_1xFLAG-His from periplasm of MC1061 bacteria.
Development and Validation of a PCR-Based Enzyme-Linked Immunosorbent Assay with Urine for Use in Clinical Research Settings To Detect Trichomonas vaginalis in Women
Creators: name: Cohen, M. S.
name: Sena, A. C.
name: Hobbs, M. M.
name: Swygard, H.
name: Kaydos, S. C.
name: Wise, S. L.
name: Miller, W. C.
name: Leone, P. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Trichomonas vaginalis infection is highly prevalent worldwide and is associated with poor birth outcomes and enhanced human immunodeficiency virus transmission. Traditional detection methods rely on microscopic examination of vaginal specimens (wet mount) and culture, which can be insensitive and time-consuming. More than 3,000 women attending two sexually transmitted disease clinics were enrolled in this cross-sectional study to evaluate urine-based PCR for detection of T. vaginalis using a combined reference standard of wet mount and culture from vaginal swab. The prevalence of trichomoniasis in the population was 16.7% (502 of 3,009 women) using the reference standard. PCR with urine combined with agarose gel-based detection was 66.9% sensitive and 98.3% specific compared to the reference standard. Detection of PCR products using an unlabeled enzyme-linked immunosorbent assay (ELISA) improved the sensitivity to 86.4%, but specificity fell to 86.1%. Using a digoxigenin-labeled ELISA for detection of amplified T. vaginalis DNA from urine, the sensitivity and specificity of the PCR improved to 90.8 and 93.4%, respectively, compared to wet mount or culture from vaginal swabs. For clinical research settings in which vaginal specimens are not available and culture conditions are not feasible, urine-based PCR-ELISA may be useful for the detection of trichomoniasis in women.
On the charge transfer between single-walled carbon nanotubes and graphene
Creators: name: Rao, Rahul
name: Pierce, Neal
name: Dasgupta, Archi
Publisher: name: arXiv
Year: 2014
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: It is important to understand the electronic interaction between single-walled carbon nanotubes (SWNTs) and graphene in order to use them efficiently in multifunctional hybrid devices. Here we deposited SWNT bundles on graphene-covered copper and SiO2 substrates by chemical vapor deposition and investigated the charge transfer between them by Raman spectroscopy. Our results revealed that, on both copper and SiO2 substrates, graphene donates electrons to the SWNTs, resulting in p-type doped graphene and n-type doped SWNTs.
description: 18 pages, 3 figures
Towards a Dark Sector Model from String Theory
Creators: name: Bernardo, Heliudson
name: Brandenberger, Robert
name: Fröhlich, Jürg
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: An embedding of a unified dark sector model into string theory with the following features is proposed: The model-independent axion descending from the Kalb-Ramond 2-form field is identified with the dark-matter field, and the real part of a Kähler modulus field -- the ``radius'' of one of the extra spatial dimensions -- accounts for dark energy. The expectation value of the dilaton field is stabilized by a gaugino condensation mechanism. A dark-energy potential corresponding to a realistic low energy scale results from some gentle tuning of the stabilized expectation value of the dilaton. The resulting potential reproduces the one in a previous dark-sector model proposed by two of us.
description: 21 pages; construction slightly refined, references added
PHANGS-JWST First Results: Variations in PAH Fraction as a Function of ISM Phase and Metallicity
Creators: name: Chastenet, Jérémy
name: Sutter, Jessica
name: Sandstrom, Karin
name: Belfiore, Francesco
name: Egorov, Oleg V.
name: Larson, Kirsten L.
name: Leroy, Adam K.
name: Liu, Daizhong
name: Rosolowsky, Erik
name: Thilker, David A.
name: Watkins, Elizabeth J.
name: Williams, Thomas G.
name: Barnes, Ashley T.
name: Bigiel, Frank
name: Boquien, Médéric
name: Chevance, Mélanie
name: Chiang, I-Da
name: Dale, Daniel A.
name: Kruijssen, J. M. Diederik
name: Emsellem, Eric
name: Grasha, Kathryn
name: Groves, Brent
name: Hassani, Hamid
name: Hughes, Annie
name: Kreckel, Kathryn
name: Meidt, Sharon E.
name: Vaught, Ryan J. Rickards
name: Sardone, Amy
name: Schinnerer, Eva
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present maps tracing the fraction of dust in the form of polycyclic aromatic hydrocarbons (PAHs) in IC 5332, NGC 628, NGC 1365, and NGC 7496 from JWST/MIRI observations. We trace the PAH fraction by combining the F770W ($7.7~μ$m) and F1130W ($11.3~μ$m) filters to track ionized and neutral PAH emission, respectively, and comparing the PAH emission to F2100W which traces small, hot dust grains. We find average $R{\rm_{PAH} = (F770W+F1130W)/F2100W}$ values of 3.3, 4.7, 5.1, and 3.6 in IC 5332, NGC 628, NGC 1365, and NGC 7496, respectively. We find that H II regions traced by MUSE H$α$ show a systematically low PAH fraction. The PAH fraction remains relatively constant across other galactic environments, with slight variations. We use CO + H I + H$α$ to trace the interstellar gas phase and find that the PAH fraction decreases above a value of I$_{Hα}/Σ_{H~I+H_2}$ $\sim~10^{37.5}$ erg s$^{-1}$ kpc$^{-2}$ (M$_\odot$ pc$^{-2}$)$^{-1}$, in all four galaxies. Radial profiles also show a decreasing PAH fraction with increasing radius, correlated with lower metallicity, in line with previous results showing a strong metallicity dependence to the PAH fraction. Our results suggest that the process of PAH destruction in ionized gas operates similarly across the four targets.
description: 13 pages, 4 figures. Accepted as part of a PHANGS-JWST Focus Issue to appear in ApJ
Mapping SYK to the Sky
Creators: name: Pasterski, Sabrina
name: Verlinde, Herman
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The infrared behavior of gravity in 4D asymptotically flat spacetime exhibits a rich set of symmetries. This has led to a proposed holographic duality between the gravitational $\mathcal{S}$-matrix and a dual field theory living on the celestial sphere. Most of our current understanding of the dictionary relies on knowledge of the 4D bulk. As such, identifying intrinsic 2D models that capture the correct symmetries and soft dynamics of 4D gravity is an active area of interest. Here we propose that a 2D generalization of SYK provides an instructive toy model for the soft limit of the gravitational sector in 4D asymptotically flat spacetime. We find that the symmetries and soft dynamics of the 2D SYK model capture the salient features of the celestial theory: exhibiting chaotic dynamics, conformal invariance, and a $w_{1+\infty}$ symmetry. The holographic map from 2D SYK operators to the 4D bulk employs the Penrose twistor transform.
description: 16 pages
Are Bio-Based Plastics The Future For Toy Applications?
Creators: name: Foschi, Eleonora
name: Paletta, Angelo
name: Mersico, Luigi
name: Aureli, Selena
name: Alimehmeti, Genc
Publisher: name: Alma Mater Studiorum - Università di Bologna
Year: 2023
Subjects: SECS-P/07 Economia aziendale
SH3_1 Environment, resources and sustainability
SH3_4 Social and industrial ecology

description: This report summarises the findings of a multi-stakeholder dialogue conducted by the University of Bologna on November 11th 2022 at Ecomondo1, and presented on March22nd, 2023 at the bio!TOY20232 conference. The initiative is part of BIO-PLASTICS EUROPE project and aims to investigate the potential of bio-based plastics to increase the sustainability of the toy industry. In the form of focus group, the discussion was joined by experts and stakeholders from public and private organisations representing the whole toy value chain. With the use of system thinking and multi-dimensional analysis, the findings reveal that bio-based plastics have high potential to contribute to the sustainability of the toy industry if: 1. Eco-design for recycling criteria are defined 2. Strict methodology to assess environmental benefits is established 3. Robust communication about product sustainability is introduced 4. Clear information about the bio-based content is provided 5. Rigorous assessment of recyclability and biodegradability properties in range environments is performed. It follows that bio-based plastics are not conceived as a stand-alone solution but as one alternative in a more comprehensive sustainability roadmap. These elements reveal the necessity for a systemic joint policy intervention in the sector oriented to build up new business ecosystems, going beyond the boundaries of a single business to embrace collective actions.
Proton and electron temperatures in the solar wind and their correlations with the solar wind speed
Creators: name: Shi, Chen
name: Velli, Marco
name: Lionello, Roberto
name: Sioulas, Nikos
name: Huang, Zesen
name: Halekas, Jasper S.
name: Tenerani, Anna
name: Réville, Victor
name: Dakeyo, Jean-Baptiste
name: Maksimović, Milan
name: Bale, Stuart D.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Plasma Physics (physics.plasm-ph)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: The heating and acceleration of the solar wind remains one of the fundamental unsolved problems in heliophysics. It is usually observed that the proton temperature $T_i$ is highly correlated with the solar wind speed $V_{SW}$, while the electron temperature $T_e$ shows anti-correlation or no clear correlation with the solar wind speed. Here we inspect both Parker Solar Probe (PSP) and WIND data and compare the observations with simulation results. PSP observations below 30 solar radii clearly show a positive correlation between proton temperature and wind speed and a negative correlation between electron temperature and wind speed. One year (2019) of WIND data confirm that proton temperature is positively correlated with solar wind speed, but the electron temperature increases with the solar wind speed for slow wind while it decreases with the solar wind speed for fast wind. Using a one-dimensional Alfvén-wave-driven solar wind model with different proton and electron temperatures, we for the first time find that if most of the dissipated Alfvén wave energy heats the ions instead of electrons, a positive $T_i-V_{SW}$ correlation and a negative $T_e-V_{SW}$ correlation arise naturally. If the electrons gain a small but finite portion of the dissipated wave energy, the $T_e-V_{SW}$ correlation evolves with radial distance to the Sun such that the negative correlation gradually turns positive. The model results show that Alfvén waves are one of the possible explanations of the observed evolution of proton and electron temperatures in the solar wind.
Dimensionality Invariant Similarity Measure
Creators: name: Hassanat, Ahmad Basheer
Publisher: name: arXiv
Year: 2014
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: This paper presents a new similarity measure to be used for general tasks including supervised learning, which is represented by the K-nearest neighbor classifier (KNN). The proposed similarity measure is invariant to large differences in some dimensions in the feature space. The proposed metric is proved mathematically to be a metric. To test its viability for different applications, the KNN used the proposed metric for classifying test examples chosen from a number of real datasets. Compared to some other well known metrics, the experimental results show that the proposed metric is a promising distance measure for the KNN classifier with strong potential for a wide range of applications.
description: (ISSN: 1545-1003). http://www.jofamericanscience.org
Development of a Rapid Immunodiagnostic Test for Haemophilus ducreyi
Creators: name: Norn, D.
name: Olsen, B.
name: Tam, M.
name: Thomas, C.
name: Patterson, K.
name: Elkins, C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Haemophilus ducreyi is the etiologic agent of chancroid, a sexually transmitted disease that increases the rate of transmission of human immunodeficiency virus. Chancroid ulcerations are difficult to distinguish from those produced by syphilis and herpes. Diagnosis based solely on clinical grounds is inaccurate, and culture is insensitive. Highly sensitive PCR has largely superseded culture as the preferred method of laboratory diagnosis; however, neither culture nor PCR is feasible where chancroid is endemic. We developed a rapid (15-min) diagnostic test based on monoclonal antibodies (MAbs) to the hemoglobin receptor of H. ducreyi, HgbA. This outer membrane protein is conserved in all strains of H. ducreyi tested and is required for the establishment of experimental human infection. MAbs to HgbA were generated and tested for cross-reactivity against a panel of geographically diverse strains. Three MAbs were found to be unique and noncompetitive and bound to all strains of H. ducreyi tested. Using an immunochromatography format, we evaluated the sensitivity and specificity of the test using geographically diverse strains of H. ducreyi, other Haemophilus strains, and other bacteria known to superinfect genital ulcers. All H. ducreyi strains were positive, and all other bacteria were negative, resulting in a specificity of 100%. The minimum number of CFU of H. ducreyi detected was 2 × 106 CFU, and the minimum amount of purified HgbA protein detected was 8.5 ng. Although this level of sensitivity may not be sufficient to detect H. ducreyi in all clinical specimens, further work to increase the sensitivity could potentially make this a valuable bedside tool in areas where chancroid is endemic.
New Options for SUSY-kind Dark Matter
Creators: name: Arbuzova, E. V.
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In the conventional cosmology masses of the stable supersymmetric relics, candidates for the dark matter (DM) particles, should be typically below 1 TeV. This is in conflict with the LHC bounds on the low energy SUSY. However, in $R^2$-gravity the masses of the stable particles with the interaction strength typical for SUSY could be much higher depending upon the dominant decay mode of the scalaron. We discuss the bounds on the masses of DM particles for the following dominant decay modes: to minimally coupled massless scalars, to massive fermions, and to gauge bosons.
description: 5 pages, 1 table. Talk presented at 20th Lomonosov Conference on Elementary Particle Physics, Moscow, MSU, 19-25 August, 2021
Mechanizing Matching Logic In Coq
Creators: name: Bereczky, Péter
name: Chen, Xiaohong
name: Horpácsi, Dániel
name: Peña, Lucas
name: Tušil, Jan
Publisher: name: arXiv
Year: 2022
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: Matching logic is a formalism for specifying, and reasoning about, mathematical structures, using patterns and pattern matching. Growing in popularity, it has been used to define many logical systems such as separation logic with recursive definitions and linear temporal logic. In addition, it serves as the logical foundation of the K semantic framework, which was used to build practical verifiers for a number of real-world languages. Despite being a fundamental formal system accommodating substantial theories, matching logic lacks a general-purpose, machine-checked formalization. Hence, we formalize matching logic using the Coq proof assistant. Specifically, we create a new representation of matching logic that uses a locally nameless encoding, and we formalize the syntax, semantics, and proof system of this representation in the Coq proof assistant. Crucially, we prove the soundness of the formalized proof system and provide a means to carry out interactive matching logic reasoning in Coq. We believe this work provides a previously unexplored avenue for reasoning about matching logic, its models, and the proof system.
description: In Proceedings FROM 2022, arXiv:2209.09208
Muon g-2 and other observables in models with extended Higgs and matter sectors
Creators: name: Dermisek, Radovan
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: I review possible explanations of the muon g-2 anomaly in models with extended Higgs and matter sectors, focusing on extensions of the standard model and the two Higgs doublet model with vectorlike leptons. Predictions of these models, namely the modifications of muon Yukawa and gauge couplings, that can be searched for at the LHC and future colliders, are summarized. I also discuss striking predictions for di-Higgs and tri-Higgs signals at a muon collider that can be tested even at very low energies. Furthermore, I briefly comment on other interesting features and signatures of models with extended Higgs sector and vectorlike matter.
description: 5 pages, 6 figures, contribution to the proceedings of the 20th Lomonosov conference, Moscow, August 2021
Molecular Typing of Papillomatous Digital Dermatitis-Associated Treponema Isolates Based on Analysis of 16S-23S Ribosomal DNA Intergenic Spacer Regions
Creators: name: Walker, R. L.
name: Stamm, L. V.
name: Bergen, H. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Papillomatous digital dermatitis (PDD), an emerging infectious disease of cattle, is characterized by painful, ulcerative foot lesions. The detection of high numbers of invasive spirochetes in PDD lesions suggests an important role for these organisms in the pathogenesis of PDD. PDD-associated spirochetes have phenotypic characteristics consistent with members of the genus Treponema. Partial 16S ribosomal DNA (rDNA) sequence analysis of clonal isolates from California cattle showed that they comprise three phylotypes which cluster closely with human-associated Treponema spp. of the oral cavity (T. denticola and T. medium/T. vincentii) or genital area (T. phagedenis). The goal of our study was to apply 16S-23S rDNA intergenic spacer region (ISR) sequence analysis to the molecular typing of U.S. PDD-associated Treponema isolates. This methodology has potentially greater discriminatory power for differentiation of closely related bacteria than 16S rDNA analysis. We PCR amplified, cloned, and sequenced the ISRs from six California PDD-associated Treponema isolates and, for comparative purposes, one strain each of T. denticola, T. medium, T. vincentii, and T. phagedenis. Two ISRs that varied in length and composition were present in all the PDD-associated Treponema isolates and in T. denticola, T. medium, and T. phagedenis. ISR1 contained a tRNAAla gene, while ISR2 contained a tRNAIle gene. Only a single ISR (ISR1) was identified in T. vincentii. Comparative analyses of the ISR1 and ISR2 sequences indicated that the California PDD-associated Treponema isolates comprised three phylotypes, in agreement with the results of 16S rDNA analysis. PCR amplification of the 16S-tRNAIle region of ISR2 permitted rapid phylotyping of California and Iowa PDD-associated Treponema isolates based on product length polymorphisms.
Numerical approaches for investigating quasiconvexity in the context of Morrey's conjecture
Creators: name: Voss, Jendrik
name: Martin, Robert J.
name: Sander, Oliver
name: Kumar, Siddhant
name: Kochmann, Dennis M.
name: Neff, Patrizio
Publisher: name: arXiv
Year: 2022
Subjects: subject: Analysis of PDEs (math.AP)
subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics
subject: 74B20, 74A10, 26B25

description: Deciding whether a given function is quasiconvex is generally a difficult task. Here, we discuss a number of numerical approaches that can be used in the search for a counterexample to the quasiconvexity of a given function $W$. We will demonstrate these methods using the planar isotropic rank-one convex function \[ W_{\rm magic}^+(F)=\frac{λ_{\rm max}}{λ_{\rm min}}-\log\frac{λ_{\rm max}}{λ_{\rm min}}+\log\det F=\frac{λ_{\rm max}}{λ_{\rm min}}+2\logλ_{\rm min}\,, \] where $λ_{\rm max}\geqλ_{\rm min}$ are the singular values of $F$, as our main example. In a previous contribution, we have shown that quasiconvexity of this function would imply quasiconvexity for all rank-one convex isotropic planar energies $W:\operatorname{GL}^+(2)\rightarrow\mathbb{R}$ with an additive volumetric-isochoric split of the form \[ W(F)=W_{\rm iso}(F)+W_{\rm vol}(\det F)=\widetilde W_{\rm iso}\bigg(\frac{F}{\sqrt{\det F}}\bigg)+W_{\rm vol}(\det F) \] with a concave volumetric part. This example is therefore of particular interest with regard to Morrey's open question whether or not rank-one convexity implies quasiconvexity in the planar case.
Circle detection using electro-magnetism optimization
Creators: name: Cuevas, Erik
name: Oliva, Diego
name: Zaldivar, Daniel
name: Perez-Cisneros, Marco
name: Sossa, Humberto
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: This paper describes a circle detection method based on Electromagnetism-Like Optimization (EMO). Circle detection has received considerable attention over the last years thanks to its relevance for many computer vision tasks. EMO is a heuristic method for solving complex optimization problems inspired in electromagnetism principles. This algorithm searches a solution based in the attraction and repulsion among prototype candidates. In this paper the detection process is considered to be similar to an optimization problem, the algorithm uses the combination of three edge points (x, y, r) as parameters to determine circles candidates in the scene. An objective function determines if such circle candidates are actually present in the image. The EMO algorithm is used to find the circle candidate that is better related with the real circle present in the image according to the objective function. The final algorithm is a fast circle detector that locates circles with sub-pixel accuracy even considering complicated conditions and noisy images.
description: arXiv admin note: substantial text overlap with arXiv:1405.7362
Evolution of ordered nanoporous phases during h-BN growth: Controlling the route from gas-phase precursor to 2D material by $\textit{in-situ}$ monitoring
Creators: name: Ruckhofer, Adrian
name: Sacchi, Marco
name: Payne, Anthony
name: Jardine, Andrew P.
name: Ernst, Wolfgang E.
name: Avidor, Nadav
name: Tamtögl, Anton
Publisher: name: arXiv
Year: 2022
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Large-area single-crystal monolayers of two-dimensional (2D) materials such as graphene and hexagonal boron nitride (h-BN) can be grown by chemical vapour deposition (CVD). However, the high temperatures and fast timescales at which the conversion from a gas-phase precursor to the 2D material appear, make it extremely challenging to simultaneously follow the atomic arrangements. We utilise helium atom scattering to discover and control the growth of novel 2D h-BN nanoporous phases during the CVD process. We find that prior to the formation of h-BN from the gas-phase precursor, a metastable $(3\times3)$ structure is formed, and that excess deposition on the resulting 2D h-BN leads to the emergence of a $(3\times4)$ structure. We illustrate that these nanoporous structures are produced by partial dehydrogenation and polymerisation of the borazine precursor upon adsorption. These steps are largely unexplored during the synthesis of 2D materials and we unveil the rich phases during CVD growth. Our results provide significant foundations for 2D materials engineering in CVD, by adjusting or carefully controlling the growth conditions and thus exploiting these intermediate structures for the synthesis of covalent self-assembled 2D networks.
PHANGS-JWST First Results: Mapping the 3.3 micron Polycyclic Aromatic Hydrocarbon Vibrational Band in Nearby Galaxies with NIRCam Medium Bands
Creators: name: Sandstrom, Karin
name: Chastenet, Jérémy
name: Sutter, Jessica
name: Leroy, Adam K.
name: Egorov, Oleg V.
name: Williams, Thomas G.
name: Bolatto, Alberto D.
name: Boquien, Médéric
name: Cao, Yixian
name: Dale, Daniel A.
name: Lee, Janice C.
name: Rosolowsky, Erik
name: Schinnerer, Eva
name: Barnes, Ashley. T.
name: Belfiore, Francesco
name: Bigiel, F.
name: Chevance, Mélanie
name: Grasha, Kathryn
name: Groves, Brent
name: Hassani, Hamid
name: Hughes, Annie
name: Klessen, Ralf S.
name: Kruijssen, J. M. Diederik
name: Larson, Kirsten L.
name: Liu, Daizhong
name: Lopez, Laura A.
name: Meidt, Sharon E.
name: Murphy, Eric J.
name: Sormani, Mattia C.
name: Thilker, David A.
name: Watkins, Elizabeth J.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present maps of the 3.3 micron polycyclic aromatic hydrocarbon (PAH) emission feature in NGC 628, NGC 1365, and NGC 7496 as observed with the Near-Infrared Camera (NIRCam) imager on JWST from the PHANGS-JWST Cycle 1 Treasury project. We create maps that isolate the 3.3 micron PAH feature in the F335M filter (F335M$_{\rm PAH}$) using combinations of the F300M and F360M filters for removal of starlight continuum. This continuum removal is complicated by contamination of the F360M by PAH emission and variations in the stellar spectral energy distribution slopes between 3.0 and 3.6 micron. We modify the empirical prescription from Lai et al. (2020) to remove the starlight continuum in our highly resolved galaxies, which have a range of starlight- and PAH-dominated lines-of-sight. Analyzing radially binned profiles of the F335M$_{\rm PAH}$ emission, we find that between 5-65% of the F335M intensity comes from the 3.3 micron feature within the inner 0.5 $r_{25}$ of our targets. This percentage systematically varies from galaxy to galaxy, and shows radial trends within the galaxies related to each galaxy's distribution of stellar mass, interstellar medium, and star formation. The 3.3 micron emission is well correlated with the 11.3 micron PAH feature traced with the MIRI F1130W filter, as is expected, since both features arise from C-H vibrational modes. The average F335M$_{\rm PAH}$/F1130W ratio agrees with the predictions of recent models by Draine et al. (2021) for PAHs with size and charge distributions shifted towards larger grains with normal or higher ionization.
description: submitted to AAS journals and revised according to referee comments, part of a PHANGS-JWST Focus Issue to appear in ApJ
Efficient Gating of Magnons by Proximity Superconductors
Creators: name: Yu, Tao
name: Bauer, Gerrit E. W.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Electrostatic gating confines and controls the transport of electrons in integrated circuits. Magnons, the quanta of spin waves of the magnetic order, are promising alternative information carriers, but difficult to gate. Here we report that superconducting strips on top of thin magnetic films can totally reflect magnons by its diamagnetic response to the magnon stray fields. The induced large frequency shifts unidirectionally blocks the magnons propagating normal to the magnetization. Two superconducting gates parallel to the magnetization create a magnonic cavity. The option to gate coherent magnons adds functionalities to magnonic devices, such as reprogrammable logical devices and increased couplings to other degrees of freedom.
description: 6 pages, 4 figures
Element-Specific Depth Profile of Magnetism and Stoichiometry at the La0.67Sr0.33MnO3/BiFeO3 Interface
Creators: name: Bertinshaw, J.
name: Brück, S.
name: Lott, D.
name: Fritzsche, H.
name: Khaydukov, Y.
name: Soltwedel, O.
name: Keller, T.
name: Goering, E.
name: Audehm, P.
name: Cortie, D. L.
name: Hutchison, W. D.
name: Ramasse, Q. M.
name: Arredondo, M.
name: Maran, R.
name: Nagarajan, V.
name: Klose, F.
name: Ulrich, C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Depth-sensitive magnetic, structural and chemical characterization is important in the understanding and optimization of novel physical phenomena emerging at interfaces of transition metal oxide heterostructures. In a simultaneous approach we have used polarized neutron and resonant X-ray reflectometry to determine the magnetic profile across atomically sharp interfaces of ferromagnetic La0.67Sr0.33MnO3 / multiferroic BiFeO3 bi-layers with sub-nanometer resolution. In particular, the X-ray resonant magnetic reflectivity measurements at the Fe and Mn resonance edges allowed us to determine the element specific depth profile of the ferromagnetic moments in both the La0.67Sr0.33MnO3 and BiFeO3 layers. Our measurements indicate a magnetically diluted interface layer within the La0.67Sr0.33MnO3 layer, in contrast to previous observations on inversely deposited layers. Additional resonant X-ray reflection measurements indicate a region of an altered Mn- and O-content at the interface, with a thickness matching that of the magnetic diluted layer, as origin of the reduction of the magnetic moment.
description: 13 pages, 4 figures, supplemental material included
AGN spiral galaxies in groups: effects of bars
Creators: name: Alonso, Sol
name: Coldwell, Georgina
name: Lambas, Diego García
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We explore properties of barred active spiral galaxies in groups selected from the SDSS-DR7, with the aim of assessing the effects of bars on AGN and the role of the high density environment. We identified barred active galaxies that reside in groups from SDSS-DR7 group catalog. To provide a suitable quantification of the effects of bars, a reliable control sample of unbarred active galaxies in high density environments with similar redshift, magnitude, morphology, and bulge size distributions was constructed. We found that the fraction of barred AGN galaxies in groups (~ 38 %) is higher than those in the total barred AGN sample ( ~ 28 %), indicating that AGN spiral galaxies in groups are more likely to be barred than those in the field. We also found that barred AGN galaxies are more concentrated towards the group centers than the other unbarred AGN group members. In addition, barred AGN host galaxies show an excess of population dominated by red colors suggesting that bars produce an importanteffect on galaxy colors of AGN hosts. The host groups of the barred AGN exhibit a larger fraction of red colors than the host groups of the corresponding unbarred active galaxies. Color-magnitude relations of both host groups of AGN differ significantly: the host group colors of barred active galaxies display distributions spreading toward red populations, with respect to the host groups of the unbarred AGN objects. Barred active galaxies show an excess of nuclear activity compared to galaxies without bars. We found that barred active galaxies located farther from the group-center have stronger Lum[OIII]. Our findings suggest that the efficiency of bars to transport material towards the more central regions of the AGN galaxies in high density environments reveals an important dependence on the localization of objects within the group and on the host group colors.
description: 10 pages, 10 figures. Accepted for Astronomy & Astrophysics
title: What is a pain coach?
Creators: name: Parsons, Joseph
name: Dr Rebecca Hunter
Publisher: name: OSF Registries
Year: 2023
Subjects: subject: Public Health
subject: Other Medicine and Health Sciences
subject: Medicine and Health Sciences
subject: Adenomyosis
subject: Ankylosing Spondylitis
subject: CFS
subject: CRPS
subject: Chronic Fatigue
subject: Chronic pain
subject: Coaching
subject: Ehlers-Danlos Syndrome
subject: Endometriosis
subject: Fibromyalgia
subject: Healthcare
subject: ME
subject: Pain
subject: Pancreatitis
subject: Self-management
subject: Support

description: This project aims to understand what both patients and clinicians think the role of a pain coach should be. Conventionally, coaches provide more accessible support than clinicians and so it is important that these coaches are providing the service which provides best for patients but also aligns with the current healthcare systems in place.
PCR-Based Diagnosis of Acute and Chronic Cutaneous Leishmaniasis Caused by Leishmania (Viannia)
Creators: name: Lozano, C.
name: Labrada, L. A.
name: Santrich, C.
name: Barker, D. C.
name: Weigle, K. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: We evaluated PCR methods for diagnosis of acute and chronic cutaneous leishmaniasis (CL) in an area of Colombia where Leishmania (Viannia) is endemic. The PCR method specifically amplified whole linearized minicircle kinetoplast DNA (kDNA) of the Leishmania subgenus Viannia from biopsy lysates. PCR products were detected in agarose gels. For 255 acute cases, this PCR method had greater sensitivity (75.7%) than each conventional method, i.e., microscopic examination of Giemsa-stained lesion scraping (46.7%), biopsy culture (55.3%), aspirate culture (46.3%), and the conventional methods combined (70.2%). Among 44 cases of chronic CL, amplification of biopsy DNA was more sensitive (45.5%) than the individual (4.5 to 27.7%) and combined (27.3%) conventional methods. The detection of kDNA in biopsies from chronic lesions was enhanced by a chemiluminescent dot blot hybridization, which produced a sensitivity of 65.8% when alone and 90.9% when in combination with DNA extraction of biopsy lysates (P < 0.001). Three biopsies from 84 skin lesions of other etiologies were falsely positive by PCR (specificity, 96.4%). PCR detected kDNA more frequently in biopsies (detection level, 83.9%) than in aspirates (74.7%) from 103 cases of acute CL. Among aspirates from 53 chronic cases of CL, the alternative methods, DNA extraction and hybridization, increased sensitivity from 41.5 to 56.6% (P > 0.05). This enhanced PCR method in chronic biopsies was so much more sensitive than conventional methods that it should be considered the preferred diagnostic method for chronic CL. These findings support the appropriate incorporation of PCR into diagnostic strategies for cutaneous leishmaniasis.
Discerning between different 'Oumuamua models by optical and infrared observations
Creators: name: Flekkøy, Eirik Grude
name: Brodin, Joachim
Publisher: name: arXiv
Year: 2022
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: The first interstellar object to be observed in our solar system 1I/2017 U1 'Oumuamua combines the lack of observable cometary activity with an extra-gravitational acceleration. This has given rise to several mutually exclusive explanations based on different assumptions in the material composition of 'Oumuamua. We show how a combination of observations in the infrared and optical spectra may serve to distinguish between these explanations once another object with 'Omuamua-like properties comes close enough to earth. This possibility is linked to the widely different thermal properties of the different material models that have been proposed. Developing a model for the thermal conduction and infrared signal from a fractal model we compare predictions of the infrared signal with that from standard thermal models that assume 'Oumuamua to be either a solid piece of rock/ice or a thin sheet.
Status of the NEXT experiment for neutrinoless double beta decay searches
Creators: name: Romo-Luque, Carmen
Publisher: name: arXiv
Year: 2022
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: NEXT (Neutrino Experiment with a Xenon TPC) is a neutrinoless double beta decay experiment located at the Laboratorio Subterráneo de Canfranc (LSC, Spain). Its aim is to demonstrate that the neutrino is a Majorana particle by detecting the neutrinoless double beta decay process in xenon gas enriched in the $^{136}$Xe isotope. The detector technology used in NEXT is that of radiopure high pressure time projection chambers with electroluminescence amplification, which provide excellent energy resolution better than 1$\%$ FWHM in the energy region of interest, topological reconstruction that allows rejecting single-electron background events and a strong potential for "in situ" tagging of the barium daughter ion. The experiment has been developing in phases. The NEXT-White detector has recently finished operation at the LSC and contained approximately an active Xe mass of 5 kg. Its purpose was to demonstrate the excellent energy resolution, to validate the reconstruction algorithms and the background model, and to make a measurement of the two-neutrino double beta decay of $^{136}$Xe. The 100 kg NEXT-100 detector is under construction and is scheduled to be installed and assembled by the first half of 2022. The predicted 90$\%$ CL sensitivity to the neutrinoless double beta decay half-life will reach $10^{26}$ years for an exposure of about 400 kg $\cdot$ year. A vigorous program towards the development of ton-scale detectors is also under way, including extensive R$\&$D towards the realization of in-situ Ba$^{2+}$ tagging as means to achieve virtually zero-background detection. A first module with a mass of at least 500 kg may be operating as early as 2026 at the LSC. In this manuscript, recent results obtained with the NEXT-White detector will be presented, as well as the NEXT-100 construction status and on the prospects of future NEXT detectors.
description: Conference NuFact2021