cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Hydroxy Acid Activation in Fungal Non‐Ribosomal Peptide Synthesis Assessed by Site‐Directed Mutagenesis
Creators: name: Hoffmann, Sylvester
name: Damm, Maik
name: Roth, Leonard
name: Süssmuth, Roderich D.
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften
subject: adenylation domains
subject: biosynthesis
subject: fungal cyclodepsipeptides
subject: mutagenesis
subject: natural products
subject: NRPS

description: The fungal cyclodepsipeptides (CDPs) enniatin, beauvericin, bassianolide, and PF1022 consist of alternating N-methylated l-amino and d-hydroxy acids. They are synthesized by non-ribosomal peptide synthetases (NRPS). The amino acid and hydroxy acid substrates are activated by adenylation (A) domains. Although various A domains have been characterized thus giving insights into the mechanism of substrate conversion, little is known about the utilization of hydroxy acids in NRPSs. Therefore, we used homology modelling and molecular docking of the A1 domain of enniatin synthetase (EnSyn) to gain insights into the mechanism of hydroxy acid activation. We introduced point mutations into the active site and used a photometric assay to study the substrate activation. The results suggest that the hydroxy acid is selected by interaction with backbone carbonyls rather than by a specific side chain. These insights enhance the understanding of non-amino acid substrate activation and could contribute to the engineering of depsipeptide synthetases.
Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse
Creators: name: Beard, William A.
name: Pedersen, Lee G.
name: Shock, David D.
name: Freudenthal, Bret D.
name: Wilson, Samuel H.
name: Perera, Lalith
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: DNA polymerases use a general two-metal ion mechanism for DNA synthesis. Recent time-lapse crystallographic studies identified additional adjunct metal ions in the polymerase active site. One of these ions correlates with appearance of pyrophosphate and was proposed to be involved in pyrophosphorolysis (reverse reaction of DNA synthesis). Because DNA polymerases can use pyrophosphorolysis to remove chain-terminating nucleotides during chemotherapies, a better understanding of this reaction is warranted. Through site-directed mutagenesis, pyrophosphorolysis measurements, and computational analysis, we examine the role of metal ions in the reverse reaction. The results indicate that the product-associated metal ion facilitates pyrophosphorolysis during the early stages of the reaction but deters the reaction at later stages, suggesting dynamic metal behavior that can modulate the chemical equilibrium.
Coherent and dephasing spectroscopy for single-impurity probing of an ultracold bath
Creators: name: Adam, Daniel
name: Bouton, Quentin
name: Nettersheim, Jens
name: Burgardt, Sabrina
name: Widera, Artur
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We report Ramsey spectroscopy on the clock states of individual Cs impurities immersed in an ultracold Rb bath. We record both the interaction-driven phase evolution and the decay of fringe contrast of the Ramsey interference signal to obtain information about bath density or temperature nondestructively. The Ramsey fringe is modified by a differential shift of the collisional energy when the two Cs states superposed interact with the Rb bath. This differential shift is directly affected by the mean gas density and the details of the Rb-Cs interspecies scattering length, affecting the phase evolution and the contrast of the Ramsey signal. Additionally, we enhance the temperature dependence of the phase shift preparing the system close to a low-magnetic-field Feshbach resonance where the $s$-wave scattering length is significantly affected by the collisional (kinetic) energy. Analyzing coherent phase evolution and decay of the Ramsey fringe contrast, we probe the Rb cloud's density and temperature. Our results point at using individual impurity atoms as nondestructive quantum probes in complex quantum systems.
description: 9 pages, 11 figures
Temperature dependence of amino acid hydrophobicities
Creators: name: Lewis, Charles A.
name: Carter, Charles W.
name: Wolfenden, Richard
name: Yuan, Yang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Systematic relationships have long been recognized between the hydrophobicities of amino acids and (i) their tendencies to be located at the exposed surfaces of globular and membrane proteins and (ii) the composition of their triplets in the genetic code. Here, we show that the same coding relationships are compatible with the high temperatures at which life is widely believed to have originated. An accompanying paper reports that these two properties appear to be encoded separately by bases in the acceptor stem and the anticodon of tRNA.
The global structure of magnetic fields and gas in simulated Milky Way-analogue galaxies
Creators: name: Wibking, Benjamin D.
name: Krumholz, Mark R.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We simulate an isolated, magnetised Milky Way-like disc galaxy using a self-consistent model of unresolved star formation and feedback, evolving the system until it reaches statistical steady state. We show that the quasi-steady-state structure is distinctly layered in galactocentric height $z$, with an innermost region having comparable gas and magnetic pressures (plasma beta $β\sim 1$), an outermost region having dominant gas pressures ($β\gg 1$), and an intermediate region between $300$ pc $\lesssim |z| \lesssim 3$ kpc that is dynamically dominated by magnetic fields ($β\ll 1$). We find field strengths, gas surface densities, and star formation rates that agree well with those observed both in the Galactic centre and in the Solar neighbourhood. The most significant dynamical effect of magnetic fields on the global properties of the disc is a reduction of the star formation rate by a factor of 1.5-2 with respect to an unmagnetised control simulation. At fixed star formation rate, there is no significant difference in the mass outflow rates or profiles between the magnetised and non-magnetised simulations. Our results for the global structure of the magnetic field have significant implications for models of cosmic ray-driven winds and cosmic-ray propagation in the Galaxy, and can be tested against observations with the forthcoming Square Kilometre Array and other facilities. Finally, we report the discovery of a physical error in the implementation of neutral gas heating and cooling in the popular GIZMO code, which may lead to qualitatively incorrect phase structures if not corrected.
description: 12 pages + appendix, 7 figures. Simulated with 100 percent renewable electricity
Simultaneous separation for the Neumann and Chaplygin systems
Creators: name: Tsiganov, A. V.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: The Neumann and Chaplygin systems on the sphere are simultaneously separable in variables obtained from the standard elliptic coordinates by the proper Backlund transformation. We also prove that after similar Backlund transformations other curvilinear coordinates on the sphere and on the plane become variables of separations for the system with quartic potential, for the Henon-Heiles system and for the Kowalevski top. It allows us to say about some analog of the hetero Backlund transformations relating different Hamilton-Jacobi equations.
description: 21 pages, LaTeX with Amsfonts. arXiv admin note: text overlap with arXiv:nlin/0307021 by other authors
Orthogonal translation with 5‐cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding
Creators: name: Von Freiherr Sass, Georg Johannes
name: Blain‐Hartung, Matthew
name: Baumann, Tobias
name: Forest, Katrina T.
name: Hildebrandt, Peter
name: Budisa, Nediljko
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften
subject: 5‐cyanotryptophan
subject: genetic code expansion
subject: infrared spectroscopy
subject: local electrostatics
subject: noninvasive probe
subject: photoreceptor protein
subject: vibrational stark effect

description: Orthogonal translation is an efficient tool that provides many valuable spectral probes capable of covering different parts of the electromagnetic spectrum and thus enabling parameterization of various structural and dynamic phenomena in proteins. In this context, nitrile-containing tryptophan analogs are very useful probes to study local electrostatics and hydrogen bonding in both rigid and dynamic environments. Here, we report a semi-rational approach to engineer a tyrosyl-tRNA synthetase (TyrRS) variant of Methanocaldococcus jannaschii capable of incorporating 5-cyanotryptophan (5CNW) via orthogonal translation. We combined one round of the well-established positive selection system with saturation mutagenesis at preselected TyrRS positions, resulting in a novel 5CNW-specific enzyme that also exhibits high substrate tolerance to other aromatic noncanonical amino acids. We demonstrated the utility of our orthogonal pair by inserting 5CNW into the cyanobacteriochrome Slr1393g3, a bilin-binding photosensor of the phytochrome superfamily. The nitrile (CN) group of the inserted 5CNW provides non-invasive labeling in the local structural context while yielding information on local electrostatics and hydrogen bonding by IR spectroscopy. 5CNW is a versatile probe that can be used for both static and dynamic measurements.
Thiopeptide antibiotics stimulate biofilm formation in Bacillus subtilis
Creators: name: Bleich, Rachel
name: Watrous, Jeramie D.
name: Shank, Elizabeth A.
name: Bowers, Albert A.
name: Dorrestein, Pieter C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Thiazolyl peptides are known antibiotics produced by diverse bacterial taxa. It has been believed that antibiotics are deployed by bacteria as weapons, providing them with an evolutionary advantage over other microbes. We show here that these weapons can also act as chemical tools that elicit biofilm production in the model bacterium Bacillus subtilis. Importantly, the biofilm-inducing (and therefore signaling) properties of these compounds are independent of their killing activity. We go on to use this biofilm-inducing activity to identify and confirm the presence of thiazolyl peptide gene clusters in other bacteria. These results indicate that thiazolyl peptides, and potentially other antibiotics, have the ability to alter bacterial behavior in ways important both to the environment and to human health.
Effect of Process Variables on Microstructure, Flow, and Tensile Properties of Nickel‐Based Superalloys with Designed Porous Structures Manufactured by Laser‐Based Powder Bed Fusion
Creators: name: Albert, Johannes
name: Purschke, Simon
name: Fleck, Claudia
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 600 Technik, Medizin, angewandte Wissenschaften::620 Ingenieurwissenschaften::620 Ingenieurwissenschaften und zugeordnete Tätigkeiten
subject: additive manufacturing
subject: designed materials
subject: functional properties
subject: hierarchical structures
subject: mechanical properties
subject: porous metals
subject: process parameter influences

description: The nickel-based superalloys Haynes 282 and Inconel 625 are processed using laser-based powder bed fusion of metals (PBF-LB/M) to manufacture designed materials (DMs) with configurable open-porous morphology. Such structures can be utilized in large gas turbines, for example, as high-frequency dampers, heat exchangers, and for transpiration cooling features. This research investigates the effects of the applied volume energy input and laser deflection angle (as calculated by position) on the macro- and microstructure and tensile and flow properties of DMs made from Haynes 282. Furthermore, a novel combination of DMs and cubic lattice structures made from Inconel 625 has been investigated regarding potential improvements. The substantial interface between the two features, DM and lattice structure, is visually analyzed using microcomputed tomography. The analysis of the hierarchical DMs reveals that the combination of lattice structures and DMs is manufacturable and has benefits in terms of mechanical strength while having less significant effects on flow properties.
tRNA acceptor stem and anticodon bases form independent codes related to protein folding
Creators: name: Carter, Charles W.
name: Wolfenden, Richard
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The universal genetic code is the earliest point to which we can trace biological inheritance. Earlier work hinted at a relationship between the codon bases and the physical properties of the 20 amino acids that dictate the 3D conformations of proteins in solution. Here, we show that acceptor stems and anticodons, which are at opposite ends of the tRNA molecule, code, respectively, for size and polarity. These two distinct properties of the amino acid side-chains jointly determine their preferred locations in folded proteins. The early appearance of an acceptor stem code based on size, β-branching, and carboxylate groups might have favored the appearance of antiparallel peptides that have been suggested to have a special affinity for RNA.
Efficient Algorithms for Quantitative Attack Tree Analysis
Creators: name: Budde, Carlos E.
name: Stoelinga, Mariëlle
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cryptography and Security (cs.CR)
subject: Data Structures and Algorithms (cs.DS)
subject: FOS: Computer and information sciences
subject: F.1.0; F.2.2; G.2.3

description: Numerous analysis methods for quantitative attack tree analysis have been proposed. These algorithms compute relevant security metrics, i.e. performance indicators that quantify how good the security of a system is, such as the most likely attack, the cheapest, or the most damaging one. This paper classifies attack trees in two dimensions: proper trees vs. directed acyclic graphs (i.e. with shared subtrees); and static vs. dynamic gates. For each class, we propose novel algorithms that work over a generic attribute domain, encompassing a large number of concrete security metrics defined on the attack tree semantics. We also analyse the computational complexity of our methods.
description: Public version of CSF'21 paper, including an appendix with all proofs of lemmas and theorems
Unconstrained muscle-tendon workloops indicate resonance tuning as a mechanism for elastic limb behavior during terrestrial locomotion
Creators: name: Sawicki, Gregory S.
name: Robertson, Benjamin D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The fields of terrestrial biomechanics and bio-inspired robotics have identified spring-like limb mechanics as critical to stable and efficient gait. In biological systems, distal muscle groups cycling large amounts of energy in series tendons are a primary source of compliance. To investigate the origins of this behavior, we coupled a biological muscle-tendon to a feedback controlled servomotor simulating the inertial/gravitational environment of terrestrial gait. We drove this bio-robotic system via direct nerve stimulation across a range of frequencies to explore the influence of neural control on muscle-tendon interactions. This study concluded that by matching stimulation frequency to that of the passive biomechanical system, muscle-tendon interactions resulting in spring-like behavior occur naturally and do not require closed-loop neural control.
NanoString dataset for study: Therapy-induced normal tissue damage promotes breast cancer metastasis
Creators: name: Perkins, Douglas
name: Steiner, Ivana
name: Haider, Syed
name: Robertson, David
name: Buus, Richard
name: O'Leary, Lynda
name: Isacke, Clare
Publisher: name: Zenodo
Year: 2023

description: Raw mRNA abundance datasets used in this study.
description: Disseminated tumor cells frequently exhibit a period of dormancy rendering them chemotherapy insensitive, conversely the systemic delivery of chemotherapies can result in normal tissue damage. Using multiple mouse and human breast cancer models, we demonstrate that prior chemotherapy administration enhances metastatic colonization and outgrowth. In vitro, chemotherapy-treated fibroblasts display a pro-tumoriegnic senescence associated secretory phenotype (SASP) and are effectively eliminated by targeting the anti-apoptotic protein BCL-xL. In vivo, chemotherapy treatment induces SASP expression in normal tissues, however the accumulation of senescent cells is limited and BCL-xL inhibitors are unable to reduce chemotherapy-enhanced metastasis. This likely reflects that chemotherapy-exposed stromal cells do not enter a BCL-xL-dependent phenotype or switch their dependency to other anti-apoptotic BCL-2 family members. This study highlights the role of the metastatic microenvironment in controlling outgrowth of disseminated tumor cells and the need to identify novel approaches to limit the pro-tumorigenic effects of therapy-induced normal tissue damage.
Ab Initio Multi-Reference In-Medium Similarity Renormalization Group Calculations of Even Calcium and Nickel Isotopes
Creators: name: Hergert, H.
name: Bogner, S. K.
name: Morris, T. D.
name: Binder, S.
name: Calci, A.
name: Langhammer, J.
name: Roth, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: We use the newly developed Multi-Reference In-Medium Similarity Renormalization Group to study all even isotopes of the calcium and nickel isotopic chains, based on two- plus three-nucleon interactions derived from chiral effective field theory. We present results for ground-state and two-neutron separation energies and quantify their theoretical uncertainties. At shell closures, we find excellent agreement with Coupled Cluster results obtained with the same Hamiltonians. Our results highlight the importance of the chiral 3N interaction to obtain a correct reproduction of experimental energy trends, and their subtle impact on the location of the neutron drip lines in the Ca and Ni chains. At the same time, we uncover and discuss deficiencies of the input Hamiltonians which need to be addressed by the next generation of chiral interactions.
description: 7 pages, 5 figures
Discovery of the Lanthipeptide Curvocidin and Structural Insights into its Trifunctional Synthetase CuvL
Creators: name: Sigurdsson, Arnar
name: Martins, Berta M.
name: Düttmann, Simon A.
name: Jasyk, Martin
name: Dimos‐Röhl, Benjamin
name: Schöpf, Felix
name: Gemander, Manuel
name: Knittel, Caroline H.
name: Schnegotzki, Romina
name: Schmid, Bianca
name: Kosol, Simone
name: Pommerening, Lea
name: Gonzáles‐Viegaz, María
name: Seidel, Maria
name: Hügelland, Manuela
name: Leimkühler, Silke
name: Dobbek, Holger
name: Mainz, Andi
name: Süssmuth, Roderich D.
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::572 Biochemie
subject: enzymes
subject: lanthipeptide synthetase
subject: lanthipeptides
subject: protein structures
subject: RIPPs

description: Lanthipeptides are ribosomally-synthesized natural products from bacteria featuring stable thioether-crosslinks and various bioactivities. Herein, we report on a new clade of tricyclic class-IV lanthipeptides with curvocidin from Thermomonospora curvata as its first representative. We obtained crystal structures of the corresponding lanthipeptide synthetase CuvL that showed a circular arrangement of its kinase, lyase and cyclase domains, forming a central reaction chamber for the iterative substrate processing involving nine catalytic steps. The combination of experimental data and artificial intelligence-based structural models identified the N-terminal subdomain of the kinase domain as the primary site of substrate recruitment. The ribosomal precursor peptide of curvocidin employs an amphipathic α-helix in its leader region as an anchor to CuvL, while its substrate core shuttles within the central reaction chamber. Our study thus reveals general principles of domain organization and substrate recruitment of class-IV and class-III lanthipeptide synthetases.
Does publicity in the science press drive citations? A vindication of peer review
Creators: name: Antonoyiannakis, Manolis
Publisher: name: arXiv
Year: 2021
Subjects: subject: Digital Libraries (cs.DL)
subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: We study how publicity, in the form of highlighting in the science press, affects the citations of research papers. After a brief review of prior work, we analyze papers published in Physical Review Letters (PRL) that are highlighted across eight different platforms. Using multiple linear regression we identify how each platform contributes to citations. We also analyze how frequently the highlighted papers end up in the top 1% cited papers in their field. We find that the strongest predictors of medium-term citation impact -- up to 7 years post-publication -- are Viewpoints in Physics, followed by Research Highlights in Nature, Editors' Suggestions in PRL, and Research Highlights in Nature Physics. Our key conclusions are that (a) highlighting for importance identifies a citation advantage, which (b) is stratified according to the degree of vetting during peer review (internal and external to the journal). This implies that we can view highlighting platforms as predictors of citation accrual, with varying degrees of strength that mirror each platform's vetting level.
description: Preprint of a chapter in the book "Predicting the Dynamics of Research Impact", edited by T. Vergoulis and Y. Manolopoulos (Springer, to appear); 18 pages, 6 Figures, 4 Tables
Visible photoelectrochemical water splitting into H 2 and O 2 in a dye-sensitized photoelectrosynthesis cell
Creators: name: Norris, Michael R.
name: Sherman, Benjamin D.
name: Alibabaei, Leila
name: Brennaman, M. Kyle
name: Meyer, Thomas J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Mesoporous SnO2/TiO2 core/shell nanostructured electrodes derivatized with a surface-bound Ru(II) polypyridyl-based chromophore–catalyst assembly are used for water splitting into H2 and O2 with visible light in a dye-sensitized photoelectrosynthesis cell. Photocurrents with a small applied bias are among the highest reported. Stabilization of the assembly on the surface of the TiO2 shell by using atomic layer deposition to deposit overlayers of Al2O3 or TiO2 results in long-term water splitting even in a phosphate buffer at pH 7.
Spin waves along the edge states
Creators: name: Lara, A.
name: Metlushko, V.
name: Garcia-Hernandez, M.
name: Aliev, F. G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Spin waves have been studied experimentally and by simulations in 1000 nm side equilateral triangular Permalloy dots in the Buckle state (B, with in-plane field along the triangle base) and the Y state (Y, with in-plane field perpendicular to the base). The excess of exchange energy at the triangles edges creates channels that allow effective spin wave propagation along the edges inthe B state. These quasi one-dimensional spin waves emitted by the vertex magnetic charges gradually transform from propagating to standing due to interference and(as pointed out by simulations) areweakly affected by smallvariations of the aspect ratio(from equilateral to isosceles dots) or by interdot dipolar interaction present in our dot arrays. Spin waves excited in the Y state have mainly a two-dimensional character.Propagation of the spin waves along the edge states in triangular dots opens possibilities for creation of new and versatile spintronic devices.
description: 9 pages with 7 figures
α-Synuclein, a chemoattractant, directs microglial migration via H 2 O 2 -dependent Lyn phosphorylation
Creators: name: Guo, Mingri
name: Chu, Chun-Hsien
name: Wilson, Belinda
name: Wang, Shijun
name: Zhang, Jing
name: Wang, Yifei
name: Ginghina, Carmen
name: Stewart, Tessandra
name: Nie, Hui
name: Hong, Jau-Shyong
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: α-Synuclein (α-syn) aggregates released from neurons activate microglia, leading to chronic neuroinflammation that causes damage to neurons in brains with synucleinopathies, such as Parkinson’s disease (PD). However, little is known about the mechanism by which α-syn affects microglial activity, especially motility, and why microglia migrate toward the injured neurons and preferentially accumulate along with α-syn aggregates in the affected areas, e.g., in the substantia nigra of PD brains. Here we show that neuron-derived α-syn aggregates are chemoattractants that direct microglial migration by acting on NADPH oxidase and several specific downstream proteins. Blocking the targets involved in α-syn–mediated microglial directional migration may represent a therapeutic strategy to protect against progressive neuronal loss in PD and related synucleinopathies.
Fluctuations of the order parameter of a mesoscopic Floquet condensate
Creators: name: Gertjerenken, Bettina
name: Holthaus, Martin
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We suggest that nonequilibrium Bose-Einstein condensates may occur in time-periodically driven interacting Bose gases. Employing the model of a periodically forced bosonic Josephson junction, we demonstrate that resonance-induced ground state-like many-particle Floquet states possess an almost perfect degree of coherence, as corresponding to a mesoscopically occupied, explicitly time-dependent single-particle orbital. In marked contrast to the customary time-independent Bose-Einstein condensates, the order parameter of such systems is destroyed by violent fluctuations when the particle number becomes too large, signaling the non-existence of a proper mean field limit.
description: 5 pages, 4 figures
Linker Exchange as Facile Method for Post‐Synthetic Modification of β‐Ketoenamine‐linked Covalent Organic Frameworks
Creators: name: Dippold, Veit
name: Vogl, Sarah
name: Grüneberg, Julia
name: Thomas, Arne
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften
subject: β‐ketoenamine linkages
subject: building block exchanges
subject: covalent organic frameworks
subject: linker exchanges
subject: post‐synthetic modifications

description: Post-synthetic linker exchange performed on covalent organic frameworks (COFs) has become an important method to introduce functional building blocks into their backbone and thus to tune their chemical and physical properties. However, the linker exchange method has so far only been described for COFs with relatively weak linkages like imines. Herein, it is shown that this method can be also used for a post-synthetic linker exchange reaction on a β-ketoenamine linked COF. The time needed to achieve considerable linker exchange is much prolonged compared to other COFs with less stable linkages, however, this enables to achieve very good control on the ratio of the respective building blocks within the framework.
Chromatic and spatial analysis of one-pixel attacks against an image classifier
Creators: name: Alatalo, Janne
name: Korpihalkola, Joni
name: Sipola, Tuomo
name: Kokkonen, Tero
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: One-pixel attack is a curious way of deceiving neural network classifier by changing only one pixel in the input image. The full potential and boundaries of this attack method are not yet fully understood. In this research, the successful and unsuccessful attacks are studied in more detail to illustrate the working mechanisms of a one-pixel attack created using differential evolution. The data comes from our earlier studies where we applied the attack against medical imaging. We used a real breast cancer tissue dataset and a real classifier as the attack target. This research presents ways to analyze chromatic and spatial distributions of one-pixel attacks. In addition, we present one-pixel attack confidence maps to illustrate the behavior of the target classifier. We show that the more effective attacks change the color of the pixel more, and that the successful attacks are situated at the center of the images. This kind of analysis is not only useful for understanding the behavior of the attack but also the qualities of the classifying neural network.
description: The 10th International Conference on Networked Systems (NETYS 2022)
Renyi entropy, stationarity, and entanglement of the conformal scalar
Creators: name: Lee, Jeongseog
name: Lewkowycz, Aitor
name: Perlmutter, Eric
name: Safdi, Benjamin R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We extend previous work on the perturbative expansion of the Renyi entropy, $S_q$, around $q=1$ for a spherical entangling surface in a general CFT. Applied to conformal scalar fields in various spacetime dimensions, the results appear to conflict with the known conformal scalar Renyi entropies. On the other hand, the perturbative results agree with known Renyi entropies in a variety of other theories, including theories of free fermions and vector fields and theories with Einstein gravity duals. We propose a resolution stemming from a careful consideration of boundary conditions near the entangling surface. This is equivalent to a proper treatment of total-derivative terms in the definition of the modular Hamiltonian. As a corollary, we are able to resolve an outstanding puzzle in the literature regarding the Renyi entropy of ${\cal N}=4$ super-Yang-Mills near $q=1$. A related puzzle regards the question of stationarity of the renormalized entanglement entropy (REE) across a circle for a (2+1)-dimensional massive scalar field. We point out that the boundary contributions to the modular Hamiltonian shed light on the previously-observed non-stationarity. Moreover, IR divergences appear in perturbation theory about the massless fixed point that inhibit our ability to reliably calculate the REE at small non-zero mass.
description: 37 pages
Atroposelective Silylation of 1,1′‐Biaryl‐2,6‐diols by a Chiral Counteranion Directed Desymmetrization Enhanced by a Subsequent Kinetic Resolution
Creators: name: Zhu, Min
name: Jiang, Hua‐Jie
name: Sharanov, Illia
name: Irran, Elisabeth
name: Oestreich, Martin
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften
subject: atropisomerism
subject: desymmetrization
subject: kinetic resolution
subject: organocatalysis
subject: silylium Ions

description: A desymmetrizing silylation of aromatic diols is reported. The previously unknown asymmetric silyl ether formation of phenol derivatives is achieved by applying List's counteranion directed silylation technique. A silylium-ion-like silicon electrophile generated from an allylic silane paired with an imidodiphosphorimidate (IDPi) enables enantioselective discrimination of achiral 1,1′-biaryl-2,6-diols. The enantioselectivity of that desymmetrization is further improved by a downstream kinetic resolution, converting the monosilylated minor enantiomer into the corresponding, again achiral bissilylated diol.
A Study about the Knowledge and Use of Requirements Engineering Standards in Industry
Creators: name: Franch, Xavier
name: Glinz, Martin
name: Mendez, Daniel
name: Seyff, Norbert
Publisher: name: arXiv
Year: 2021
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: Context: The use of standards is considered a vital part of any engineering discipline. So one could expect that standards play an important role in Requirements Engineering (RE) as well. However, little is known about the actual knowledge and use of RE-related standards in industry. Objective: In this article, we investigate to which extent standards and related artifacts such as templates or guidelines are known and used by RE practitioners. Method: To this end, we have conducted a questionnaire-based online survey. We could analyze the replies from 90 RE practitioners using a combination of closed and open-text questions. Results: Our results indicate that the knowledge and use of standards and related artifacts in RE is less widespread than one might expect from an engineering perspective. For example, about 47% of the respondents working as requirements engineers or business analysts do not know the core standard in RE, ISO/IEC/IEEE 29148. Participants in our study mostly use standards by personal decision rather than being imposed by their respective company, customer, or regulator. Beyond insufficient knowledge, we also found cultural and organizational factors impeding the widespread adoption of standards in RE. Conclusions: Overall, our results provide empirically informed insights into the actual use of standards and related artifacts in RE practice and - indirectly - about the value that the current standards create for RE practitioners.
description: Preprint accepted for publication at IEEE Transactions on Software Engineering and presented as Journal First at the International Requirements Engineering conference 2021. Latest update: Several smaller corrections along the creation of the final version of the manuscript
EuroVoc and thesauri from EU institutions and agencies Interoperability and perspectives for collaborative thesaurus  management
Creators: name: Laaboudi, Christine
Publisher: name: ISKO UK
Year: 2013
Subjects: Eurovoc
thesaurus development
Thesaurus management
Multi-lingual vocabularies
Multilingual thesauri

description: The EuroVoc thesaurus maintained by the EU Publications Office is available in 24 languages and is focused on the main areas of activity of the EU. Like EuroVoc, a number of multilingual specialised thesauri or controlled vocabularies are also maintained and disseminated independently with their own thesaurus management systems, inside the EU institutions and agencies.  Thesaurus Alignment carried out in the Publications Office has shown that a number of concepts and terms are shared and duplicated amongst the EU thesauri. 
With the objective of enhanced collaboration between EU multilingual thesauri, the Publications Office proposes to offer a collaborative environment for thesaurus maintenance, dissemination and alignment for EU institutions and agencies. The collaboration will enable mutual enrichment of our thesauri in terms of coverage, languages and the generation of Linked Data. Additionally, the project will help with reducing the efforts and costs of thesaurus maintenance, translation, hosting and development.
CuNi Nanoalloys with Tunable Composition and Oxygen Defects for the Enhancement of the Oxygen Evolution Reaction**
Creators: name: Gioria, Esteban
name: Li, Shuang
name: Mazheika, Aliaksei
name: Naumann D'Alnoncourt, Raoul
name: Thomas, Arne
name: Rosowski, Frank
Publisher: name: Technische Universität Berlin
Year: 2023
Subjects: subject: 500 Naturwissenschaften und Mathematik::540 Chemie::546 Anorganische Chemie
subject: CuNi
subject: nanoalloy
subject: oxygen evolution reaction
subject: oxygen vacancies
subject: synergistic effects

description: Colloidal synthesis is an excellent tool for the study of cooperative effects in nanoalloys. In this work, bimetallic CuNi nanoparticles of defined size and composition are fully characterized and tested for the oxygen evolution reaction. Copper addition to nickel leads to modifications in the structural and electronic properties, showing a higher concentration of surface oxygen defects and formation of active Ni3+ sites under reaction conditions. The ratio OV/OL between oxygen vacancies and lattice oxygen shows a clear correlation with the overpotential, being an excellent descriptor of the electrocatalytic activity. This is attributed to modifications in the crystalline structure, leading to lattice strain and grain size effects. Bimetallic Cu50Ni50NP showed the lowest overpotential (318 mV vs RHE), low Tafel slope (63.9 mV dec−1), and excellent stability. This work unravels the relative concentration between oxygen defects and lattice oxygen (OV/OL) as an excellent descriptor of the catalytic activity of bimetallic precatalysts.
Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour
Creators: name: Wang, Dafang
name: Niederer, Steven A.
name: Trayanova, Natalia
name: Nash, Martyn P.
name: Blake, Robert
name: Castro, Sebastian
name: Seemann, Gunnar
name: Bradley, Chris
name: Rossi, Simone
name: Augustin, Christoph M.
name: Griffith, Boyce E.
name: Land, Sander
name: Sundnes, Joakim
name: Pezzuto, Simone
name: Ruprecht, Daniel
name: Krause, Rolf
name: Fritz, Thomas
name: Rice, J. Jeremy
name: Baron, Lukas
name: Favino, Marco
name: Arens, Sander
name: Hurtado, Daniel E.
name: Smith, Nicolas P.
name: Jenny Wang, Zhinuo
name: Gizzi, Alessio
name: Crozier, Andrew
name: Gao, Hao
name: Luo, Xiaoyu
name: Gurev, Viatcheslav
name: Plank, Gernot
name: Fastl, Thomas E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Models of cardiac mechanics are increasingly used to investigate cardiac physiology. These models are characterized by a high level of complexity, including the particular anisotropic material properties of biological tissue and the actively contracting material. A large number of independent simulation codes have been developed, but a consistent way of verifying the accuracy and replicability of simulations is lacking. To aid in the verification of current and future cardiac mechanics solvers, this study provides three benchmark problems for cardiac mechanics. These benchmark problems test the ability to accurately simulate pressure-type forces that depend on the deformed objects geometry, anisotropic and spatially varying material properties similar to those seen in the left ventricle and active contractile forces. The benchmark was solved by 11 different groups to generate consensus solutions, with typical differences in higher-resolution solutions at approximately 0.5%, and consistent results between linear, quadratic and cubic finite elements as well as different approaches to simulating incompressible materials. Online tools and solutions are made available to allow these tests to be effectively used in verification of future cardiac mechanics software.
Characterising Conical Refraction Optical Tweezers
Creators: name: McDonald, Craig
name: McDougall, Craig
name: Rafailov, Edik
name: McGloin, David
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Conical refraction occurs when a beam of light travels through an appropriately cut biaxial crystal. By focussing the conically refracted beam through a high numerical aperture microscope objective, conical refraction optical tweezers can be created, allowing for particle manipulation in both Raman spots and in the Lloyd/Poggendorff rings. We present a thorough quantification of the trapping properties of such a beam, focussing on the trap stiffness and how this varies with trap power and trapped particle location. We show that the lower Raman spot can be thought of as a single-beam optical gradient force trap, while radiation pressure dominates in the upper Raman spot, leading to optical levitation rather than trapping. Particles in the Lloyd/Poggendorff rings experience a lower trap stiffness than particles in the lower Raman spot but benefit from rotational control.
Family- and sex-specific vocal traditions in a cooperatively breeding songbird
Creators: name: Jordan Price, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Although songbirds provide well-known examples of cultural transmission of vocalizations, little is known about this process in species that live in stable social groups. Here I describe complex vocal traditions in a cooperatively breeding songbird, the stripe-backed wren (Campylorhynchus nuchalis). Repertoires of stereotyped calls were recorded from individually marked males and females in cooperative family groups. Males in the same patriline, whether in the same group or in different groups, had call repertoires that were nearly identical. Females in the same matriline also had identical call repertoires; however, female calls never matched the calls of males in the same group or in any nearby groups. Unrelated birds almost never shared calls. Call repertoires are apparently learned preferentially from same-sex relatives within family groups, so that call traditions separately follow patrilines and matrilines. This unique pattern of transmission results in vocal cues that reflect both sex and kinship.
The evolution of mate choice and the potential for conflict between species and mate-quality recognition
Creators: name: Pfennig, K. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Understanding how individuals select mates becomes complex when high-quality conspecifics resemble heterospecifics. Individuals facing such a situation may be unable to effectively identify both conspecifics (species recognition) and high-quality mates that can confer fitness benefits to the choosy individual or its offspring (mate-quality recognition). Here I suggest when a conflict may occur between species and mate-quality recognition, discuss the evolutionary consequences stemming from this conflict, and present a model of mate-preference evolution in response to heterospecifics. Determining how species and mate-quality recognition interact to shape mate-choice decisions is important for understanding the diversification of sexually selected traits among closely related taxonomic groups, the use of complex sensory systems for detecting mates, and seemingly inappropriate mate-choice decisions.
Cannibalistic tadpoles that pose the greatest threat to kin are most likely to discriminate kin
Creators: name: Pfennig, D. W.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1999

description: Inclusive fitness theory predicts that altruism should often be directed towards reproductive relatives, but it is unclear whether individuals that are most likely to help or harm relatives are also most likely to identify kin in the first place. Here I show that species and sibships of spadefoot toad tadpoles (Spea bombifrons and S. multiplicata) that were most likely to produce an environmentally induced cannibalistic morph were also most likely to avoid eating kin. Moreover, tadpoles avoided eating kin when they expressed the cannibal phenotype, but not when these same individuals reverted to the non-cannibalistic morph. Thus, individual tadpoles facultatively adjust their level of discrimination according to how likely they are to harm kin. In general, sensory systems and/or decision rules enabling recognition may be especially likely to evolve among those individuals that are most often faced with the problem of discrimination.
CircuitQ: An open-source toolbox for superconducting circuits
Creators: name: Aumann, Philipp
name: Menke, Tim
name: Oliver, William D.
name: Lechner, Wolfgang
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We introduce CircuitQ, an open-source toolbox for the analysis of superconducting circuits implemented in Python. It features the automated construction of a symbolic Hamiltonian of the input circuit and a dynamic numerical representation of the Hamiltonian with a variable basis choice. Additional features include the estimation of the T1 lifetimes of the circuit states under various noise mechanisms. We review previously established circuit quantization methods and formulate them in a way that facilitates the software implementation. The toolbox is then showcased by applying it to practically relevant qubit circuits and comparing it to specialized circuit solvers. Our circuit quantization is applicable to circuit inputs from a large design space, and the software is open-sourced. We thereby add an important resource for the design of new quantum circuits for quantum information processing applications.
Infrared Spectrum of the Adamantane +–Water Cation: Hydration‐Induced C−H Bond Activation and Free Internal Water Rotation
Creators: name: George, Martin Andreas Robert
name: Förstel, Marko
name: Dopfer, Otto
Publisher: name: Technische Universität Berlin
Year: 2020
Subjects: subject: 500 Naturwissenschaften und Mathematik::530 Physik::535 Licht, Infrarot- und Ultraviolettphänomene
subject: adamantane cation
subject: C−H activation
subject: hydration
subject: IR spectroscopy
subject: structure elucidation

description: Diamondoid cations are reactive intermediates in their functionalization reactions in polar solution. Hydration is predicted to strongly activate their C−H bonds in initial proton abstraction reactions. To study the effects of microhydration on the properties of diamondoid cations, we characterize herein the prototypical monohydrated adamantane cation (C10H16+–H2O, Ad+–W) in its ground electronic state by infrared photodissociation spectroscopy in the CH and OH stretch ranges and dispersion-corrected density functional theory (DFT) calculations. The water (W) ligand binds to the acidic CH group of Jahn–Teller distorted Ad+ via a strong CH⋅⋅⋅O ionic H-bond supported by charge–dipole forces. Although W further enhances the acidity of this CH group along with a proton shift toward the solvent, the proton remains with Ad+ in the monohydrate. We infer essentially free internal W rotation from rotational fine structure of the ν3 band of W, resulting from weak angular anisotropy of the Ad+–W potential.
Les rôles de l'accès à l'information et des facteurs géographiques dans l'adhésion à l'assurance santé en milieu rural sénégalais
Creators: name: Bousmah, Marwân-al-Qays
name: Boyer, Sylvie
name: Lalou, Richard
name: Ventelou, Bruno
Publisher: name: Zenodo
Year: 2022

description: Au Sénégal, comme ailleurs, l’accès à l’information semble déterminer l’intérêt porté par les individus aux systèmes d’assurance maladie, influençant ainsi leur comportement d’adhésion. En nous appuyant sur des données collectées en 2019-2020 dans la zone rurale de Niakhar au Sénégal, cette étude apporte un nouvel éclairage sur le rôle de l’accès à l’information et des facteurs géographiques comme déterminants clés d’une adhésion effective aux Mutuelles de Santé Communautaires par les habitants des zones rurales. Dans l’ensemble, nos résultats visent à aider les décideurs publics à mieux définir la feuille de route de la couverture de santé universelle, afin qu’ils adaptent leurs politiques de sensibilisation à l’assurance maladie et améliorent l’accès aux mutuelles ainsi qu’aux structures sanitaires qui leurs sont affiliées.