cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Deciphering nucleotide modification-induced structure and stability changes
Creators: name: Hurst, Travis
name: Chen, Shi-Jie
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Nucleotide modification in RNA controls a bevy of biological processes, including RNA degradation, gene expression, and gene editing. In turn, misregulation of modified nucleotides is associated with a host of chronic diseases and disorders. However, the molecular mechanisms driving these processes remain poorly understood. To partially address this knowledge gap, we used alchemical and temperature replica exchange molecular dynamics (TREMD) simulations on an RNA duplex and an analogous hairpin to probe the structural effects of modified and/or mutant nucleotides. The simulations successfully predict the modification/mutation-induced relative free energy change for complementary duplex formation, and structural analyses highlight mechanisms driving stability changes. Furthermore, TREMD simulations for a hairpin-forming RNA with and without modification provide reliable estimations of the energy landscape. Illuminating the impact of methylated and/or mutated nucleotides on the structure-function relationship and the folding energy landscape, the simulations provide insights into modification-induced alterations to the folding mechanics of the hairpin. The results here may be biologically significant as hairpins are widespread structure motifs that play critical roles in gene expression and regulation. Specifically, the tetraloop of the probed hairpin is phylogenetically abundant, and the stem mirrors a miRNA seed region whose modification has been implicated in epilepsy pathogenesis.
Supplementary methods, figures and tables from Effects of body plan evolution on the hydrodynamic drag and energy requirements of swimming in ichthyosaurs
Creators: name: Gutarra, Susana
name: Moon, Benjamin C.
name: Rahman, Imran A.
name: Palmer, Colin
name: Lautenschlager, Stephan
name: Brimacombe, Alison J.
name: Benton, Michael J.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences
subject: 110601 Biomechanics
subject: FOS: Health sciences

description: Ichthyosaurs are an extinct group of fully marine tetrapods that were well adapted to aquatic locomotion. During their approximately 160-Myr existence, they evolved from elongate and serpentine forms into stockier, fish-like animals, convergent with sharks and dolphins. Here, we use computational fluid dynamics (CFD) to quantify the impact of this transition on the energy demands of ichthyosaur swimming for the first time. We run computational simulations of water flow using three-dimensional digital models of nine ichthyosaurs and an extant functional analogue, a bottlenose dolphin, providing the first comparison of ichthyosaur hydrodynamics across phylogeny. Our results show that morphology did not have a major effect on the drag coefficient or the energy cost of steady swimming through geological time. We show that even the early ichthyosaurs produced low levels of drag for a given volume, comparable to those of a modern dolphin, and that deep ‘torpedo-shaped’ bodies did not reduce the cost of locomotion. Our analysis also provides important insight into the choice of scaling parameters for CFD applied to swimming mechanics and underlines the great influence of body size evolution on ichthyosaur locomotion. A combination of large bodies and efficient swimming modes lowered the cost of steady swimming as ichthyosaurs became increasingly adapted to a pelagic existence.
Effect of in vitro simulated digestion on the anti-Helicobacter Pylori activity of different Propolis extracts
Creators: name: Governa, Paolo
name: Romagnoli, Giulia
name: Albanese, Paola
name: Rossi, Federico
name: Manetti, Fabrizio
name: Biagi, Marco
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Helicobacter pylori (HP) is among the most common pathogens causing infection in humans worldwide. Oxidative stress and gastric inflammation are involved in the progression of HP-related gastric diseases, and they can be targeted by integrating conventional antibiotic treatment with polyphenol-enriched natural products. In this work, we characterised three different propolis extracts and evaluated their stability under in vitro simulated gastric digestion, compared to their main constituents alone. The extract with the highest stability to digestion (namely, the dark propolis extract, DPE) showed a minimum bactericidal concentration (MBC) lower than 1 mg/mL on HP strains with different virulence factors. Finally, since urease is one of the virulence factors contributing to the establishment of a microenvironment that promotes HP infection, we evaluated the possible inhibition of this enzyme by using molecular docking simulations and in vitro colorimetric assay, showing that galangin and pinocembrin may be involved in this activity.
Deregulation, Misallocation, and Size: Evidence from India
Creators: name: Alfaro, Laura
name: Chari, Anusha
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: This paper examines the impact of the deregulation of compulsory industrial licensing in India on firm size dynamics and reallocation of resources within industries. Following deregulation, resource misallocation declines, and the left-hand tail of the firm size distribution thickens significantly, suggesting increased entry by small firms. However, the dominance and growth of large incumbents remains unchallenged. Quantile regressions reveal that the distributional effects of deregulation on firm size are significantly non-linear. The reallocation of market shares toward a small number of large firms and a large number of small firms is characterized as the "shrinking middle" in Indian manufacturing. Small- and medium-sized firms may continue to face constraints in their attempts to grow.
Halo-independent tests of dark matter direct detection signals: local DM density, LHC, and thermal freeze-out
Creators: name: Blennow, Mattias
name: Herrero-Garcia, Juan
name: Schwetz, Thomas
name: Vogl, Stefan
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: From an assumed signal in a Dark Matter (DM) direct detection experiment a lower bound on the product of the DM--nucleon scattering cross section and the local DM density is derived, which is independent of the local DM velocity distribution. This can be combined with astrophysical determinations of the local DM density. Within a given particle physics model the bound also allows a robust comparison of a direct detection signal with limits from the LHC. Furthermore, the bound can be used to formulate a condition which has to be fulfilled if the particle responsible for the direct detection signal is a thermal relic, regardless of whether it constitutes all DM or only part of it. We illustrate the arguments by adopting a simplified DM model with a Z' mediator and assuming a signal in a future xenon direct detection experiment.
description: 23 pages, 6 figures
title: Bat Mortality at Ontario Wind Farms Quantified and Compared using Four Candidate Estimator Equations
Creators: name: Thurber, Bethany
name: Jardine, Catherine
name: Zimmerling, J. Ryan
Publisher: name: Utah State University
Year: 2022

description: Wind farm development is expanding globally. While wind energy is a low cost option for new electricity supply, the impacts to wildlife populations, including bats (Chiroptera), are of ecological concern. To quantify these impacts, scientists have developed estimator equations to estimate bat mortality, which vary in assumptions related to correction factors. We compared the results of 4 estimators applied to post-construction monitoring data from Ontario, Canada wind farms to evaluate the effects of field methods and correction factors on estimator consistency. To conduct our study, we obtained data from 21 wind farms between 2011 and 2017 for a total of 26 wind farm survey years, because some wind farms supplied fatality monitoring data in more than one year, to estimate mortality. The Ontario Ministry of Natural Resources and Forestry estimator (OMNRF) tended to be highest, while the Huso, Schoenfeld-Erickson, and GenEst estimators produced similar results. Huso and Schoenfeld-Erickson estimates tended to fall within 95% confidence intervals for GenEst, while OMNRF estimates tended to be higher than the upper confidence interval for GenEst. The results from the OMNRF estimator were consistent with the other candidates when carcass persistence times were >6.5 days, but inconsistent when carcass persistence times were shorter. Our results demonstrated the degree to which mortality estimates can vary among estimators and highlight the need for a consistent estimator in comparative studies. We recommend GenEst for such studies, as this estimator can incorporate more inputs with flexibility to reflect site-specific field conditions and produces highly consistent results. Conversely, the OMNRF estimator produced consistently higher estimates than the other candidate estimators and assumptions related to carcass persistence were regularly violated. We recommend that these limitations be acknowledged when interpreting results from this estimator, and that its use be reconsidered when assumptions related to carcass persistence are not met.
title: Aesthetics and Geometry in Proclus, Spinoza, Leibniz, Kant and Bergson
Creators: name: Rawes, Margaret S. H.
Publisher: name: Goldsmiths, University of London
Year: 2004

description: The thesis proposes a series of 'forgotten' aesthetic geometries that are retrieved from metaphysical philosophy. Organised into five chapters, the discussion identifies geometric methods and figures in a series of selected texts from Neoplatonic, post-Cartesian and Kantian thinking. Chapter 1 situates the argument in an examination of Kant's Critical philosophy and identifies two kinds of aesthetic and geometric procedure that are constructed in the first and third Critiques. In the Critique of Pure Reason (1781/1787) Kant constructs geometry as both pure 'cognition' (i. e. as intuition) and sense-perception (i. e. space). In the Critique ofJudgment (1790), however, geometry is a procedure that is generated by the imagination and the reflective subject as a form of aesthetic judgment. Geometric procedure becomes, therefore, an aesthetic act of construction that reflects the irreducible unity of the thinking subject and is reconfigured in relation to intuition, limit and unlimit, the soul, imagination and space and time. This discussion provides the context through which the aesthetic geometric methods and figures in the writings of Proclus, Spinoza, Leibniz and Bergson are explored. Chapter 2 reveals the synthetic figure of the fold from Proclus' (410-485AD) procedure of 'unfolding' a divine geometry from Euclid's Elements. Chapter 3 proposes an aesthetic 'comportment' that generates a 'passage' through Spinoza's geometric text, the Ethics (1677). Chapter 4 examines the analytic and aesthetic geometric figure of the 'plenum', which is constructed from an intensive corporeal and incorporeal magnitude in Leibniz's 'Monadology' (1714). Chapter 5 proposes that Bergson's text, Matter and Memory (1896), reinstates intuition as a 'natural geometry' or 'life' in the figure of the 'envelope'. The thesis explores, therefore, a geometric tradition in which Kantian aesthetics looks both backwards and forwards, and each method and figure represents a different 'recollection' of its potential.
Ichthyosaur body sizes from Effects of body plan evolution on the hydrodynamic drag and energy requirements of swimming in ichthyosaurs.
Creators: name: Gutarra, Susana
name: Moon, Benjamin C.
name: Rahman, Imran A.
name: Palmer, Colin
name: Lautenschlager, Stephan
name: Brimacombe, Alison J.
name: Benton, Michael J.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences
subject: 110601 Biomechanics
subject: FOS: Health sciences

description: Ichthyosaurs are an extinct group of fully marine tetrapods that were well adapted to aquatic locomotion. During their approximately 160 Myr existence, they evolved from elongate and serpentine forms into stockier, fish-like animals, convergent with sharks and dolphins. Here, we use computational fluid dynamics (CFD) to quantify the impact of this transition on the energy demands of ichthyosaur swimming, to our knowledge for the first time. We run computational simulations of water flow using three-dimensional digital models of nine ichthyosaurs and an extant functional analogue, a bottlenose dolphin, providing, to our knowledge, the first quantitative evaluation of ichthyosaur hydrodynamics across phylogeny. Our results show that morphology did not have a major effect on the drag coefficient or the energy cost of steady swimming through geological time. We show that even the early ichthyosaurs produced low levels of drag for a given volume, comparable to those of a modern dolphin, and that deep ‘torpedo-shaped’ bodies did not reduce the cost of locomotion. Our analysis also provides important insight into the choice of scaling parameters for CFD applied to swimming mechanics, and underlines the great influence of body size evolution on ichthyosaur locomotion. A combination of large bodies and efficient swimming modes lowered the cost of steady swimming as ichthyosaurs became increasingly adapted to a pelagic existence.
Inanspruchnahme gynäkologischer und allgemeinärztlicher Leistungen durch Frauen ab 50 Jahren
Creators: name: Krause, Laura
name: Prütz, Franziska
Publisher: name: Robert Koch-Institut
Year: 2020
Subjects: subject: INANSPRUCHNAHME
subject: GYNÄKOLOGIE
subject: ALLGEMEINMEDIZIN
subject: FRAUEN
subject: DEUTSCHLAND
subject: DEGS1
subject: 610 Medizin und Gesundheit

description: In Deutschland gibt es relativ wenige repräsentative Daten zur Nutzung ärztlicher Leistungen und deren Einflussfaktoren. Auf Datenbasis der Studie zur Gesundheit Erwachsener in Deutschland (DEGS1, 2008–2011) wird die gynäkologische und allgemeinärztliche Inanspruchnahme von Frauen mit Fokus auf die Altersgruppe 50 Jahre und älter untersucht, mit Daten des Bundes-Gesundheitssurveys 1998 (BGS98) verglichen und auf Basis dieser sowie weiterer Daten die mögliche aktuelle Entwicklung diskutiert. Während die allgemeinärztliche Inanspruchnahme im Altersverlauf mit stets über 80% konstant hoch liegt, sinkt die gynäkologische Inanspruchnahme mit zunehmendem Alter. Rund 60% der Frauen ab 50 Jahren besuchen mindestens einmal im Jahr eine gynäkologische Praxis. Sozioökonomischer Status und Wohnort stellen sich als wichtige Determinanten der Inanspruchnahme bei Frauen im mittleren und höheren Lebensalter heraus. Etwa die Hälfte der Frauen ab 50 Jahren hat mindestens einmal im Jahr sowohl Ärztinnen und Ärzte für Gynäkologie als auch für Allgemeinmedizin in Anspruch genommen. Unter 10% haben nur Gynäkologinnen und Gynäkologen aufgesucht, etwa ein Drittel hat von den beiden Facharztgruppen nur Ärztinnen und Ärzte für Allgemeinmedizin konsultiert. Im Vergleich zum BGS98 haben in DEGS1 die allgemeinärztliche und die gynäkologische Inanspruchnahme deutlich zugenommen, allerdings lässt sich aus Krankenkassendaten kein Anstieg der gynäkologischen Inanspruchnahme zwischen 2008 und 2018 ablesen. Die Ergebnisse legen nahe, Allgemeinärztinnen und -ärzte stärker für gynäkologische Beratungs- und Behandlungsbedarfe von mittelalten und älteren Frauen zu sensibilisieren.
The Smelly Eight: An Empirical Study on the Prevalence of Code Smells in Quantum Computing - Artifact
Creators: name: Qihong Chen
name: Rúben Câmara
name: Campos, José
name: Souto, André
name: Iftekhar Ahmed
Publisher: name: Zenodo
Year: 2023

description: This artifact contains all scripts, data, and instructions required to repeat and reproduce the study 'The Smelly Eight: An Empirical Study on the Prevalence of Code Smells in Quantum Computing' published at the 45th International Conference on Software Engineering (ICSE), 2023. Please find more information, including an overview of the artifact's documentation, in the top-level README.md file of the artifact.
Design, synthesis, conformational analysis, and biological activity of Cα1-to-Cα6 1,4- and 4,1-disubstituted 1H-[1,2,3]triazol-1-yl-bridged oxytocin analogues
Creators: name: Nuti, Francesca
name: Larregola, Maud
name: Staśkiewicz, Agnieszka
name: Retzl, Bernhard
name: Tomašević, Nataša
name: Macchia, Lorenzo
name: Street, Maria E.
name: Jewgiński, Michał
name: Lequin, Olivier
name: Latajka, Rafal
name: Rovero, Paolo
name: Gruber, Christian W.
name: Chorev, Michael
name: Papini, Anna Maria
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified

description: Oxytocin (OT) is a neurohypophyseal peptide hormone containing a disulphide-bridged pseudocyclic conformation. The biomedical use of OT peptides is limited amongst others by disadvantageous pharmacokinetic parameters. To increase the stability of OT by replacing the disulphide bridge with the stable and more rigid [1,2,3]triazol-1-yl moiety, we employed the Cu2+-catalysed side chain-to-side chain azide-alkyne 1,3-cycloaddition. Here we report the design, synthesis, conformational analysis, and in vitro pharmacological activity of a homologous series of Cα1-to-Cα6 side chain-to-side chain [1,2,3]triazol-1-yl-containing OT analogues differing in the length of the bridge, location, and orientation of the linking moiety. Exploiting this macrocyclisation approach, it was possible to generate a systematic series of compounds providing interesting insight into the structure-conformation-function relationship of OT. Most analogues were able to adopt similar conformation to endogenous OT in water, namely, a type I β-turn. This approach may in the future generate stabilised pharmacological peptide tools to advance understanding of OT physiology.
The Potential Role of Cellular Senescence in Non-Alcoholic Fatty Liver Disease
Creators: name: Engelmann, Cornelius
name: Tacke, Frank
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2022
Subjects: subject: NAFLD
subject: NASH
subject: SASP
subject: senescence associated secretory phenotype
subject: mitochondrial dysfunction
subject: fibrosis
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Non-alcoholic fatty liver disease (NAFLD) represents an increasing global health burden. Cellular senescence develops in response to cellular injury, leading not only to cell cycle arrest but also to alterations of the cellular phenotype and metabolic functions. In this review, we critically discuss the currently existing evidence for the involvement of cellular senescence in NAFLD in order to identify areas requiring further exploration. Hepatocyte senescence can be a central pathomechanism as it may foster intracellular fat accumulation, fibrosis and inflammation, also due to secretion of senescence-associated inflammatory mediators. However, in some non-parenchymal liver cell types, such as hepatic stellate cells, senescence may be beneficial by reducing the extracellular matrix deposition and thereby reducing fibrosis. Deciphering the detailed interaction between NAFLD and cellular senescence will be essential to discover novel therapeutic targets halting disease progression.
(1444) Hannah Porritt
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Sequence determines degree of knottedness in a coarse-grained protein model
Creators: name: Wüst, Thomas
name: Reith, Daniel
name: Virnau, Peter
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar (HP) lattice protein model. By employing large scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that, even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just one additional degree of freedom per monomer (in our case sequence) facilitates evolution towards a protein universe in which knots are rare.
Extended Trochanteric Osteotomy with Intermediate Resection Arthroplasty Is Safe for Use in Two-Stage Revision Total Hip Arthroplasty for Infection
Creators: name: Hardt, Sebastian
name: Leopold, Vincent Justus
name: Khakzad, Thilo
name: Pumberger, Matthias
name: Perka, Carsten
name: Hipfl, Christian
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2021
Subjects: subject: extended trochanteric osteotomy
subject: revision total hip arthroplasty
subject: periprosthetic infection
subject: two-stage revision
subject: resection arthroplasty
subject: reinfection
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Background: This study sought to compare the results of two-stage revision total hip arthroplasty (THA) for periprosthetic infection (PJI) in patients with and without the use of an extended trochanteric osteotomy (ETO) for removal of a well-fixed femoral stem or cement. Methods: Thirty-two patients who had undergone an ETO as part of a two-stage revision without spacer placement were matched 1:2 with a cohort of sixty-four patients of the same sex and age who had stem removal without any osteotomy. Clinical outcomes including interim revision, reinfection and aseptic failure rates were evaluated. Modified Harris hip scores (mHHS) were calculated. Minimum follow-up was two years. Results: Patients undergoing ETO had a significantly lower rate of interim re-debridement compared to non-ETO patients (0% vs. 14.1%, p = 0.026). Reinfection following reimplantation was similar in both groups (12.5% in ETO patients vs. 9.4% in non-ETO patients, p = 0.365). Revision for aseptic reason was necessary in 12.5% in the ETO group and 14.1% in the non-ETO group (p = 0.833). Periprosthetic femoral fractures were seen in three patients (3.1%), of which all occurred in non-ETO patients. Dislocation was the most common complication, which was equally distributed in both groups (12.5%). The mean mHHS was 37.7 in the ETO group and 37.3 in the non-ETO group, and these scores improved significantly in both groups following reimplantation (p < 0.01). Conclusion: ETO without the use of spacer is a safe and effective method to manage patients with well-fixed femoral stems and for thorough cement removal in two-stage revision THA for PJI. While it might reduce the rate of repeated debridement in the interim period, the use of ETO appears to lead to similar reinfection rates following reimplantation.
One-Dimensional Traps, Two-Body Interactions, Few-Body Symmetries: II. $N$ Particles
Creators: name: Harshman, N. L.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: This is the second in a pair of articles that classify the configuration space and kinematic symmetry groups for $N$ identical particles in one-dimensional traps experiencing Galilean-invariant two-body interactions. These symmetries explain degeneracies in the few-body spectrum and demonstrate how tuning the trap shape and the particle interactions can manipulate these degeneracies. The additional symmetries that emerge in the non-interacting limit and in the unitary limit of an infinitely strong contact interaction are sufficient to algebraically solve for the spectrum and degeneracy in terms of the one-particle observables. Symmetry also determines the degree to which the algebraic expressions for energy level shifts by weak interactions or nearly-unitary interactions are universal, i.e.\ independent of trap shape and details of the interaction. Identical fermions and bosons with and without spin are considered. This article analyzes the symmetries of $N$ particles in asymmetric, symmetric, and harmonic traps; the prequel article treats the one, two and three particle cases.
description: v2 46 pages, 2 figures, 2 tables. Revised notation, added commentary and references, and made corrections. Some of this materially originally appeared in version 1 of arXiv:1501.00215, but that article has been split into two pieces, and this is the second piece
Discarded surrogates, modified traditions, welcome complements
Creators: name: Moss, Timothy
Publisher: name: Humboldt-Universität zu Berlin
Year: 2016
Subjects: subject: Berlin
subject: Germany
subject: infrastructure
subject: socio-technical transitions
subject: technology
subject: 333.7 Natürliche Resourcen, Energie und Umwelt
subject: 301 Soziologie, Anthropologie

description: This article takes an historical perspective on current attempts to ‘open up’ established, centralized systems of urban infrastructure to alternative technologies designed to minimize resource use and environmental pollution. The process of introducing alternative technologies into, or alongside, centralized urban infrastructures is not a novel phenomenon, as is often assumed. The physical and institutional entrenchment of large technical systems for urban energy, water or sanitation services in industrialized countries in the late 19th and early 20th centuries did not close the door completely on alternatives. I investigate a number of alternative technologies used in Berlin in the interwar period (1920–1939), in order to reveal the rationales developed around each technology and the ways in which each emerged, disappeared and re-emerged or survived across highly diverse political regimes. The selection of cases is guided by the desire to illustrate three different phenomena of alternative technology diffusion (and exclusion) experienced in Berlin: (1) technologies promoted by early pioneers and discarded by their successors (waste-to-energy), (2) technologies modifying traditional practices that were at odds with modernized systems (wastewater reuse for agriculture) and (3) technologies co-existing alongside the dominant centralized system throughout the 20th century (cogeneration). The empirical findings are interpreted with reference to their contribution to scholarship on urban socio-technical transitions.
The Smelly Eight: An Empirical Study on the Prevalence of Code Smells in Quantum Computing - Artifact
Creators: name: Qihong Chen
name: Rúben Câmara
name: Campos, José
name: Souto, André
name: Iftekhar Ahmed
Publisher: name: Zenodo
Year: 2023

description: This artifact contains all scripts, data, and instructions required to repeat and reproduce the study 'The Smelly Eight: An Empirical Study on the Prevalence of Code Smells in Quantum Computing' published at the 45th International Conference on Software Engineering (ICSE), 2023. Please find more information, including an overview of the artifact's documentation, in the top-level README.md file of the artifact.
description: This version adds support to docker.
Ichthyosaur body sizes from Effects of body plan evolution on the hydrodynamic drag and energy requirements of swimming in ichthyosaurs
Creators: name: Gutarra, Susana
name: Moon, Benjamin C.
name: Rahman, Imran A.
name: Palmer, Colin
name: Lautenschlager, Stephan
name: Brimacombe, Alison J.
name: Benton, Michael J.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences
subject: 110601 Biomechanics
subject: FOS: Health sciences

description: Ichthyosaurs are an extinct group of fully marine tetrapods that were well adapted to aquatic locomotion. During their approximately 160-Myr existence, they evolved from elongate and serpentine forms into stockier, fish-like animals, convergent with sharks and dolphins. Here, we use computational fluid dynamics (CFD) to quantify the impact of this transition on the energy demands of ichthyosaur swimming for the first time. We run computational simulations of water flow using three-dimensional digital models of nine ichthyosaurs and an extant functional analogue, a bottlenose dolphin, providing the first comparison of ichthyosaur hydrodynamics across phylogeny. Our results show that morphology did not have a major effect on the drag coefficient or the energy cost of steady swimming through geological time. We show that even the early ichthyosaurs produced low levels of drag for a given volume, comparable to those of a modern dolphin, and that deep ‘torpedo-shaped’ bodies did not reduce the cost of locomotion. Our analysis also provides important insight into the choice of scaling parameters for CFD applied to swimming mechanics and underlines the great influence of body size evolution on ichthyosaur locomotion. A combination of large bodies and efficient swimming modes lowered the cost of steady swimming as ichthyosaurs became increasingly adapted to a pelagic existence.
Seminolipid and its precursor/degradative product, galactosylalkylacylglycerol, in the testis of saposin A- and prosaposin-deficient mice
Creators: name: Ishizuka, Ineo
name: Tadano-Aritomi, Keiko
name: Matsuda, Junko
name: Fujimoto, Hirokazu
name: Suzuki, Kunihiko
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Sphingolipid activator proteins (saposins A, B, C, and D) are derived from a common precursor protein (prosaposin) and specifically activate in vivo degradation of glycolipids with short carbohydrate chains. A mouse model of prosaposin deficiency (prosaposin
Promising inhibition of diabetes-related enzymes and antioxidant properties of Ptilostemon casabonae leaves extract
Creators: name: Sanna, Cinzia
name: Fais, Antonella
name: Era, Benedetta
name: Delogu, Giovanna L.
name: Sanna, Enrico
name: Dazzi, Laura
name: Rosa, Antonella
name: Marengo, Arianna
name: Rubiolo, Patrizia
name: De Agostini, Antonio
name: Floris, Sonia
name: Pintus, Francesca
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Pharmacology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified

description: Type 2 diabetes (T2D) is a progressive metabolic disorder of glucose metabolism. One of the therapeutic approaches for the treatment of T2D is reducing postprandial hyperglycaemia through inhibition of the digestive enzymes α-glucosidase and α-amylase. In this context, aimed at identifying natural products endowed with anti-T2D potential, we focused on Ptilostemon casabonae (L.) Greuter, a species belonging to Asteraceae family. Enzymatic inhibition, antioxidant activity, phenolic composition and cellular assays were performed. This study revealed that the P. casabonae hydroalcoholic extract exerts a potent inhibitory activity against α-glucosidase. This activity is supported by an antioxidant effect, preventing ROS formation in a stressed cellular system. HPLC-PDA-MS/MS analysis, revealed a complex polyphenolic fraction. Among the tested pure compounds, 1,5-dicaffeoylquinic acid, apigenin and rutin displayed good α-glucosidase inhibitory activity. Our study suggested new potential of P. casabonae encouraging us to further testing the possible therapeutic potential of this extract.
Phosphatidylcholine deficiency upregulates enzymes of triacylglycerol metabolism in CHO cells
Creators: name: Coleman, Rosalind A.
name: De Gómez Dumm, I. Nelva T.
name: Caviglia, J. Matias
name: Igal, R. Ariel
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: We studied the regulation of triacylglycerol (TAG) metabolism by phosphatidylcholine (PC) in CHO MT58 cells, which are deficient in PC synthesis because of a temperature-sensitive CTP:phosphocholine cytidylyltransferase. At the permissive growth temperature (34 degrees C), these cells contained 49% less TAG and 30% less PC than wild-type CHO K1 cells. Treatment with dipalmitoylphosphatidylcholine normalized both the PC and TAG levels. Despite low TAG levels, the incorporation of [14C]oleate into TAG was increased in CHO MT58 cells. The in vitro de novo synthesis of TAG and the activity of diacylglycerol acyltransferase were 90% and 34% higher, respectively. Two other key enzyme activities in TAG synthesis, acyl-CoA synthetase and mitochondrial glycerol-3-phosphate acyltransferase (GPAT), increased by 48% and 2-fold, respectively, and mitochondrial GPAT mRNA increased by approximately 4-fold. Additionally, TAG hydrolysis was accelerated in CHO MT58 cells, and in vitro lipolytic activity increased by 68%. These studies suggest that a homeostatic mechanism increases TAG synthesis and recycling in response to PC deficiency. TAG recycling produces diacylglycerol and fatty acids that can be substrates for de novo PC synthesis and for lysophosphatidylcholine (lysoPC) acylation. In CHO MT58 cells, in which de novo PC synthesis is blocked, lysoPC acylation with fatty acid originating from TAG may represent the main pathway for generating PC.
Revised nomenclature for the mammalian long-chain acyl-CoA synthetase gene family: TABLE 1.
Creators: name: Kuypers, Frans A.
name: Bornfeldt, Karin E.
name: Maltais, Lois J.
name: DiRusso, Concerta C.
name: Black, Paul
name: Schaffer, Jean E.
name: Coleman, Rosalind A.
name: Vasiliou, Vasilis
name: Mashek, Douglas G.
name: Yamamoto, Tokuo T.
name: Renieri, Alessandra
name: Bernlohr, David A.
name: Nebert, Daniel W.
name: Khodiyar, Varsha
name: Guo, Wen
name: Watkins, Paul A.
name: Farber, Steven A.
name: Hashimoto, Naohiro
name: Stahl, Andreas
name: Berger, Johannes
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: By consensus, the acyl-CoA synthetase (ACS) community, with the advice of the human and mouse genome nomenclature committees, has revised the nomenclature for the mammalian long-chain acyl-CoA synthetases. ACS is the family root name, and the human and mouse genes for the long-chain ACSs are termed
Versatile approach to access the low temperature thermodynamics of lattice polymers and proteins
Creators: name: Wüst, Thomas
name: Landau, David P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and the interacting self-avoiding walk (ISAW) model for homopolymers. We obtained accurate estimates of thermodynamic quantities for HP sequences with $>100$ monomers and for ISAWs up to $>500$ monomers. Our procedure possesses an intrinsic simplicity and overcomes the limitations inherent in more tailored approaches making it interesting for a broad range of protein and polymer models.
SI Tables; Reduced matrix; Figure of rates including Xenarthra branch; Topological constraint from Rapid morphological evolution in placental mammals post-dates the origin of the crown group.
Creators: name: Halliday, Thomas J. D.
name: Reis, Mario Dos
name: Tamuri, Asif U.
name: Ferguson-Gow, Henry
name: Ziheng Yang
name: Goswami, Anjali
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences
subject: 60408 Genomics

description: Tables containing the raw values depicted in Figure 1; An exemplar matrix of morphological and molecular data with which a basic version of the results can be replicated; Morphological:molecular rates like that of Figure 2A but including the aberrant xenarthran ratios.; Constraint file for RAxML analysis
title: Complexity-Adjusted Learning Curves for Robotic and Laparoscopic Liver Resection
title: A Word of Caution
titleType: Subtitle
Creators: name: Krenzien, Felix
name: Benzing, Christian
name: Feldbrügge, Linda
name: Ortiz Galindo, Santiago Andres
name: Hillebrandt, Karl
name: Raschzok, Nathanael
name: Nevermann, Nora
name: Haber, Philipp
name: Malinka, Thomas
name: Schöning, Wenzel
name: Pratschke, Johann
name: Schmelzle, Moritz
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2022
Subjects: subject: Minimally invasive liver surgery (MILS)
subject: learning curves
subject: laparoscopic liver resection (LLR)
subject: robotic liver resection (RLR)
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Background: Minimally invasive liver surgery (MILS) has a high variance in the type of resection and complexity, which has been underestimated in learning curve studies in the past. The aim of this work was to evaluate complexity-adjusted learning curves over time for laparoscopic liver resection (LLR) and robotic liver resection (RLR). Methods: Cumulative sum analysis (CUSUM) and complexity adjustment were performed using the Iwate score for LLR and RLR (n = 647). Lowest point of smoothed data was used to capture the cutoff of the increase in complexity. Data were collected retrospectively at the Department of Surgery of the Charité-Universitätsmedizin Berlin. Results: A total of 132 RLR and 514 LLR were performed. According to the complexity-adjusted CUSUM analysis, the initial learning phase was reached after 117 for LLR and 93 procedures for RLR, respectively. With increasing experience, the rate of (extended) right hemihepatectomy multiplied from 8.4% to 18.9% for LLR (P = 0.031) and from 21.6% to 58.3% for RLR (P < 0.001). Complication rates remained comparable between both episodes for LLR and RLR (T1 vs T2, P > 0.05). The complexity-adjusted CUSUM analysis demonstrated for blood transfusion, conversion, and operative time an increase during the learning phase (T1), while a steady state was reached in the following (T2). Conclusions: The learning phase for MILS after adjusting for complexity is about 4 times longer than assumed in previous studies, which should urge caution.
Coupling of COX-1 to mPGES1 for prostaglandin E 2 biosynthesis in the murine mammary gland
Creators: name: Clark, Patsy
name: Foley, Nicholas A.
name: Chandrasekharan, Subhashini
name: Koller, Beverly H.
name: Jania, Leigh
name: Audoly, Laurent P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The mammary gland, like most tissues, produces measurable amounts of prostaglandin E
Prevalence, predictors and types of unpleasant and adverse effects of meditation in regular meditators: international cross-sectional study
Creators: name: Pauly, Luca
name: Bergmann, Niklas
name: Hahne, Inge
name: Pux, Sarah
name: Hahn, Eric
name: Ta, Thi Minh Tam
name: Rapp, Michael
name: Böge, Kerem
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2021
Subjects: subject: Mindfulness
subject: meditation
subject: third wave of cognitive–behavioural therapy
subject: unpleasant events
subject: adverse events
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Background: Meditation is commonly implemented in psychological therapies since the ‘third wave’ of cognitive–behavioural therapy has increased the focus on mindfulness-based interventions. Although extensive research literature demonstrates its benefits, little is known about potential adverse effects. Aims: The aim of this study is to report the prevalence, type and severity of particularly unpleasant meditation-related experiences in the largest cross-sectional study on this topic to date, with 1370 regular meditators. Method: The participants were asked whether they ever encountered particularly unpleasant experiences as a result of their meditation experience. For the first time, the type and severity of those experiences were assessed and the association with several predictors, such as pre-existing mental disorders, were explored via logistic and linear regression. Results: Similar to previous studies, 22% of participants (95% CI 20–24) reported having encountered unpleasant meditation-related experiences, and 13% of participants (95% CI 3–5) reported experiences that were categorised as adverse. Those were mostly of affective, somatic and cognitive nature. Unpleasant meditation-related experiences were more likely to occur in participants with pre-existing mental illnesses (P = 0.000, 95% CI 1.25–2.12). Conclusions: This study demonstrates that unpleasant meditation-related experiences are prevalent among meditators and, to a relevant extent, severe enough to warrant further scientific inquiry. Longitudinal studies are needed to examine whether the unpleasant meditation-related experiences are merely negative and thus should be avoided, or are an inherent part of the contemplative path.
Genes used for molecular alignment from Rapid morphological evolution in placental mammals post-dates the origin of the crown group.
Creators: name: Halliday, Thomas J. D.
name: Reis, Mario Dos
name: Tamuri, Asif U.
name: Ferguson-Gow, Henry
name: Ziheng Yang
name: Goswami, Anjali
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences
subject: 60408 Genomics

description: Details of all genomic data used in this analysis
(1439) Mary Elizabeth Denton Cardew
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Kerr coefficients of plasma resonances in Josephson junction chains
Creators: name: Weißl, Thomas
name: Küng, Bruno
name: Dumur, Étienne
name: Feofanov, Alexey K.
name: Matei, Iulian
name: Naud, Cécile
name: Buisson, Olivier
name: Hekking, Frank W. J.
name: Guichard, Wiebke
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We present an experimental and theoretical analysis of the self- and cross-Kerr effect of extended plasma resonances in Josephson junction chains. We calculate the Kerr coefficients by deriving and diagonalizing the Hamiltonian of a linear circuit model for the chain and then adding the Josephson non-linearity as a perturbation. The calculated Kerr-coefficients are compared with the measurement data of a chain of 200 junctions. The Kerr effect manifests itself as a frequency shift that depends linearly on the number of photons in a resonant mode. By changing the input power on a low signal level, we are able to measure this shift. The photon number is calibrated using the self-Kerr shift calculated from the sample parameters. We then compare the measured cross-Kerr shift with the theoretical prediction, using the calibrated photon number.
description: 10 pages, 9 figures
Role of CYP27A in cholesterol and bile acid metabolism
Creators: name: Suchy, Frederick J.
name: Bollineni, Jaya
name: Hyogo, Hideyuki
name: Krauss, Ronald M.
name: Salen, Gerald
name: Lear, Steven R.
name: Ananthanarayanan, Meena
name: Dubrac, Sandrine
name: Shefer, Sarah
name: Balasubramaniyan, Natarajan
name: Cohen, David E.
name: Batta, Ashok K.
name: Maeda, Nobuyo
name: Blanche, Patricia J.
name: Erickson, Sandra K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The CYP27A gene encodes a mitochondrial cytochrome P450 enzyme, sterol 27-hydroxylase, that is expressed in many different tissues and plays an important role in cholesterol and bile acid metabolism. In humans, CYP27A deficiency leads to cerebrotendinous xanthomatosis. To gain insight into the roles of CYP27A in the regulation of cholesterol and bile acid metabolism, cyp27A gene knockout heterozygous, homozygous, and wild-type littermate mice were studied. In contrast to homozygotes, heterozygotes had increased body weight and were mildly hypercholesterolemic, with increased numbers of lipoprotein particles in the low density lipoprotein size range. Cyp7A expression was not increased in heterozygotes but was in homozygotes, suggesting that parts of the homozygous phenotype are secondary to increased cyp7A expression and activity. Homozygotes exhibited pronounced hepatomegaly and dysregulation in hepatic cholesterol, bile acid, and fatty acid metabolism. Hepatic cholesterol synthesis and synthesis of bile acid intermediates were increased; however, side chain cleavage was impaired, leading to decreased bile salt concentrations in gallbladder bile. Expression of Na-taurocholate cotransporting polypeptide, the major sinusoidal bile salt transporter, was increased, and that of bile salt export pump, the major canalicular bile salt transporter, was decreased. Gender played a modifying role in the homozygous response to cyp27A deficiency, with females being gene