cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Lightweight Syntactic API Usage Analysis with UCov
Creators: name: Monce, Gustave
name: Couturou, Thomas
name: Hamdaoui, Yasmine
name: Degueule, Thomas
name: Falleri, Jean-Rémy
Publisher: name: arXiv
Year: 2024
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: Designing an effective API is essential for library developers as it is the lens through which clients will judge its usability and benefits, as well as the main friction point when the library evolves. Despite its importance, defining the boundaries of an API is a challenging task, mainly due to the diverse mechanisms provided by programming languages that have non-trivial interplays. In this paper, we present a novel conceptual framework designed to assist library maintainers in understanding the interactions allowed by their APIs via the use of syntactic usage models. These customizable models enable library maintainers to improve their design ahead of release, reducing friction during evolution. The complementary syntactic usage footprints and coverage scores, inferred from client code using the API (e.g., documentation samples, tests, third-party clients), enable developers to understand in-the-wild uses of their APIs and to reflect on the adequacy of their tests and documentation. We implement these models for Java libraries in a new tool UCov and demonstrate its capabilities on three libraries exhibiting diverse styles of interaction: jsoup, commons-cli, and spark. Our exploratory case study shows that UCov provides valuable information regarding API design and fine-grained analysis of client code to identify under-tested and under-documented library code.
The Coptic Theme in Egyptian novels The case of Bayt al-Qibṭiyya (“The house of the Copt woman”) by ʼAšraf al-‘Ašmāwī
Creators: name: Waly, Naglaa
Publisher: name: Kervan. International Journal of African and Asian Studies
Year: 2021

description: This article discusses Bayt al-Qibṭiyya (“The Hhouse of the Copt woman”), a novel by ʼAšraf al-ʻAšmāwī; published in 2019, the novel is a recent iteration of the Coptic theme in Egyptian fiction. The Copts are an integral component of Egyptian society. They form part of Egypt’s social fabric and today constitute some 8% to 9% per cent of the population. Their presence has been evident in the Egyptian novel since its birth. In the second half of the nineteenth century and the first half of the twentieth century, they were at the forefront of the renaissance that led the country towards a cultural and economic resurgence. Discrimination against Copts in Egypt increased markedly in the second half of the twentieth century, notably since the Revolution of 1952 and in the context of the Islamic revival following the Arab-Israeli war of 1967. This trend gained strength during the Sadat era and erupted in numerous episodes of religious violence during the 1970s. The violence continued during the Mubarak era and escalated in the wake of the Arab Spring in 2011. This contentious issue is reflected in modern Egyptian literature. In his novel, al-ʻAšmāwī addresses the tensions between Muslims and Coptic Christians in Upper Egypt through the story of Huda Habīb, the Coptic heroine. In order to contextualize his treatment of the theme and afford a broader perspective on its development in Egyptian literature, this article also outlines its representation in other Egyptian novels at different points in history.
description: Kervan. International Journal of African and Asian Studies, V. 25 N. 1 (2021): Kervan
StandICT Webinar_Women in ICT Standardisation, third edition - Slides
Creators: name: Muscella, Silvana
name: Batta, Eszter
name: Belhassine-Cherif, Rim
name: Reiter, Barbara
name: De Michelis, Isabella
name: Paola, Amato
name: Marsal Llacuna, Lluïsa
name: Iyer, Sudha
name: Feliciano, Sandra
name: Bolpagni, Marzia
name: Llaneza, Paloma
Publisher: name: Zenodo
Year: 2024

description: The third edition of the Women in ICT Standardisation Webinar presented by StandICT.eu, in coordination with 5 other EU-funded projects dedicated to accelerating European standardisation activities, addressed the key priorities outlined in the 2024 publication of the European Commission’s Annual Union Work Programme for European Standardisation (AUWP). The online session brought together leading women voices in the field of European standardisation to reinforce the relationship between standards, technology, and policy, while highlighting the gender gaps in the field of ICT standardisation and 8 policy priorities identified under the AUWP.

The speakers were selected based on their contributions to the development of standards across a variety of ICT domains, in addition to being ambassadors of diversity and inclusion in the ICT standardisation space. 

This webinar was not only an opportunity for women to demonstrate expertise in their specific discipline.  It provided a platform to share personal experiences about being a woman working in science, technology, engineering and mathematics (STEM), and captured insights and best practices to empower inclusion and promote equity in this male-dominated field.
De la variation au changement phonologique : une étude en synchronie dynamique du système consonantique de l’arabe parlé en Jordanie
Creators: name: Al Zboun, Bassel
name: Abu Hanak, Nisreen
Publisher: name: Kervan. International Journal of African and Asian Studies
Year: 2020

description: Varieties of Jordanian spoken Arabic are interesting not only because they violate the standard Arabic phonological system, but also because they exhibit innovative internal mechanisms of articulations, best be described as evolution of languages (or dialects). While research highlights the social aspects of the emergence of varieties of languages in general and Jordanian spoken Arabic in particular, the present study focuses on the internal processes of evolution of those sounds. In this, the study steps from extrinsic to intrinsic factors of language evolution in the given context. For this purpose, the study draws its discussions and arguments from a quantitative and qualitative analyses of data obtained from an audio corpus of spoken Arabic language from 90 speakers in their natural settings. The study thus aims to contribute to the field of varieties of language through surpassing the traditional tendencies (i.e. extrinsic or conscious factors) of this filed into more precise descriptions of the unconscious articulation of language sounds.
description: Kervan. International Journal of African and Asian Studies, V. 25 N. 1 (2021): Kervan
Multiscale simulation of transport phenomena in semi-solid flow batteries
Creators: name: Burrows, Stephen Anthony
Publisher: name: Imperial College London
Year: 2017

description: Semi-solid electrodes are suspensions of high energy density anode and cathode materials in ionic electrolytes. The addition of conductive carbon black particles creates a multi scale system with complex rheology. Here it is investigated how two important simulation methods—molecular dynamics and lattice Boltzmann—can be applied to this technology. Firstly we review some commonly used force fields for molecular simulation of the pure solvents, observing highly variable results. We select TraPPE as the most consistent model, and develop a series of optimizations to the intramolecular terms in the potential in order to improve the prediction of the relative permittivity of alkyl ethers such as 1,2-Dimethoxyethane (DMEt). The new dihedral potentials, generated by fitting two dimensional potential energy surfaces from dispersion-corrected density functional theory, were successful in reproducing the experimentally observed conformer populations of DMEt, and its relative permittivity. We then generate an atomistic model of carbon black (CB) particles using reactive force fields and a quenching simulation. Fictitious repulsive particles are used to generate a specified porosity. The resulting structure is converted into a molecular connectivity format compatible with the GROMACS software, allowing two CB nanoparticles to be simulated using a classical force field, again based on TraPPE. A potential of mean force was calculated for their interaction in an explicit solvent. Finally the development of an OpenCL lattice Boltzmann code is discussed, which makes simultaneous use of CPU and GPU compute hardware. It can simulate spherical particles suspended in a variety of non-Newtonian fluids. It is used to investigate how the dependence of viscosity on the suspension volume fraction differs between Newtonian and non-Newtonian fluids.
Discovery of a Low-Mass Brown Dwarf Companion of the Young Nearby Star G196-3
Creators: name: Rebolo, R.
name: Osorio, M. R. Zapatero
name: Madruga, S.
name: Bejar, V. J. S.
name: Arribas, S.
name: Licandro, J.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: A substellar-mass object in orbit at about 300 astronomical units (AU) from the young low-mass star G196-3 was detected by direct imaging. Optical and infrared photometry and low- and intermediate-resolution spectroscopy of the faint companion, hereafter referred to as G196-3B, confirms its cool atmosphere and allows its mass to be estimated at 25^{+15}_{-10} Jupiter masses. The separation between both objects and their mass ratio suggest the fragmentation of a collapsing cloud as the most likely origin for G196-3B, but alternatively it could have originated from a proto-planetary disc which has been dissipated. Whatever the formation process was, the young age of the primary star (about 100 Myr) demonstrates that substellar companions can form in short time scales.
description: Published in Science (13 Nov). One color figure
Towards a Less Subjective Model of Singability Analysis: Investigating the Persian Translation of Dubbed Songs in Animated Movies
Creators: name: Golchinnezhad, Maryam
name: Afrouz, Mahmoud
Publisher: name: Kervan. International Journal of African and Asian Studies
Year: 2020

description: Song Translation as a relevant area to Translation Studies, has been receiving attention over the past decade. As Song Translation grows, so does the urge to develop a resourceful model to assist researchers in this domain, to study and understand translated songs and hopefully propose solutions to tackle some issues regarding translating a song that would be performable and singable. The two most common models to analyze the singability of translated songs were proposed by Low (2003; 2008) and Franzon (2008). These two models are compatible; therefore, in the current study, they have been merged and adjusted to analyze Persian translations of dubbed songs. In doing so, attempts have been made to fabricate a less subjective model by developing a marking system. The recommended model was verified by applying it to twenty-five songs selected from five animated movies; namely Trolls (2016), Sing (2016), Moana (2016), Coco (2017), and Smallfoot (2018).
description: Kervan. International Journal of African and Asian Studies, V. 25 N. 1 (2021): Kervan
Localized Mode and Nonergodicity of a Harmonic Oscillator Chain
Creators: name: Ishikawa, Fumihiro
name: Todo, Synge
Publisher: name: arXiv
Year: 2018
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We present a simple and microscopic physical model that breaks the ergodicity. Our model consists of coupled classical harmonic oscillators, and the motion of the tagged particle obeys the generalized Langevin equation satisfying the second fluctuation dissipation theorem. It is found that although the nonergodicity strength, which is expected to detect the ergodicity breaking, for this model vanishes, the velocity auto correlation function of the tagged particle asymptotically oscillates. We analyze the model by using the molecular dynamics and the exact diagonalization as well as the rigorous mapping to the generalized Langevin equation. Our analysis reveals that the asymptotic oscillation is caused by a localized mode with an isolated frequency from the continuous phonon spectrum.
Alauda alpestris Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Passeriformes
Alaudidae
Alauda
Alauda alpestris

description: Alauda alpestris [spec. nov.]
A. rectricibus dimidio inferiore albis, gula flava, fascia suboculari pectoralique nigra.
Alauda gutture flavo. Catesb. car. 1. p. {?X}. t. 32.
Habitat in America septentrionali, & visa a Kleinio Gedani.
Corpus supra fuscum. Guttur ad pectus usque flavum. Abdomen album. Pectorale transversum nigrum. Fascia nigra, obtusa, pone sinum otis.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 166, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Can BERT Dig It? - Named Entity Recognition for Information Retrieval in the Archaeology Domain
Creators: name: Brandsen, Alex
name: Verberne, Suzan
Publisher: name: Zenodo
Year: 2021
Subjects: BERT, Named Entity Recognition, Archaeology

description: Poster presented at CLIN31.

 Abstract: ArcheoBERTje outperforms both the multilingual and Dutch BERT models on NER in the archaeology domain, reaching an average F1 score of 0.735
Numerical simulations of Josephson Traveling Wave Parametric Amplifiers (JTWPAs): comparative study of open-source tools
Creators: name: Levochkina, A. Yu.
name: Ahmad, H. G.
name: Mastrovito, P.
name: Chatterjee, I.
name: Massarotti, D.
name: Montemurro, D.
name: Tafuri, F.
name: Pepe, G. P.
name: Esposito, M.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Josephson Traveling Wave Parametric Amplifiers (JTWPAs) are largely exploited in quantum technologies for their broadband and low noise performance in the microwave regime. When one or more microwave tones are applied at the input, such devices show a complex wave-mixing response due to their intrinsic nonlinear nature. Numerical simulations of the JTWPAs nonlinear behaviour provide useful insights not only for the design of such devices, but also for the interpretation and validation of the experimental results. Here we present and discuss a comparative analysis of different open-source tools which can be used for JTWPAs numerical simulations. We focus on two tools for transient simulations, WRSPICE and PSCAN2, and on one tool for direct simulation of the frequency domain behaviour, JosephsonCircuit.jl. We describe the working principle of these three tools and test them considering as a benchmark a JTWPA based on SNAILs (Superconducting Nonlinear Asymmetric Inductive eLement) with realistic experimental parameters. Our results can serve as a guide for numerical simulations of JTWPAs with open-source tools, highlighting advantages and disadvantages depending on the simulation tasks.
description: version accepted for publication
Spectroelectrochemical studies of oxidation reactions on hematite photoelectrodes
Creators: name: Mesa Zamora, Camilo Arturo
Publisher: name: Imperial College London
Year: 2018

description: In this thesis, the key factors governing the solar fuels catalytic process, i.e. photoelectrochemical water splitting, are studied by means of different spectroelectrochemical techniques. Photo-induced absorption spectroscopy together with transient photocurrent measurements are employed to study the catalytic function of different metal oxide photoanodes, focusing particularly on hematite, by the construction of rate law analyses. An introduction to the field is given in Chapter 1 followed by a description of the methods used herein in Chapter 2. Chapter 3, the first results chapter, focuses on the kinetics of water oxidation on hematite photoanodes at conditions of suppressed surface recombination. This chapter provides evidence of 2 different water oxidation mechanisms, with different activation energies, upon increasing the irradiation intensity. These mechanisms show faster kinetics upon surface deprotonation of the photoanode and a secondary kinetic isotope effect. In this chapter, a detailed water oxidation mechanism at a molecular level for hematite photoanodes is proposed and compared with biological systems such photosystem II. Further comparisons with other metal oxides such titania, bismuth vanadate and tungsten oxide indicate similar mechanisms whose kinetics are sensitive to the valence band edge of the materials. Chapter 4 explores the use of methanol oxidation on hematite, as a model organic substrate reaction, to improve the hydrogen production rate. This is proposed to be done concomitant with either, the degradation of organic pollutants or the synthesis of high value-added products when these reactions are selective. This chapter shows the selective oxidation of methanol to formaldehyde with kinetics faster than those for water oxidation and sensitive to the valence band edge when the reaction was performed on titania. The data collected allow the proposal of a detailed mechanism of reaction for the selective oxidation of methanol to formaldehyde. Finally, Chapter 5 focuses on the decay kinetics of the photogenerated holes in state-of-the-art thin, flat hematite films. This chapter discusses the recombination, accumulation and reaction dynamics of photogenerated holes upon laser excitation. Upon hole accumulation at the photoanode surface, this chapter provides evidence of a kinetic competition between surface recombination and trapping and hole extraction by the electrolyte.
Spin freezing and the Sachdev-Ye model
Creators: name: Werner, Philipp
name: Kim, Aaram
name: Hoshino, Shintaro
Publisher: name: arXiv
Year: 2018
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Spin-freezing is the origin of bad-metal physics and non-Fermi liquid (non-FL) properties in a broad range of correlated compounds. In a multi-orbital lattice system with Hund coupling, doping of the half-filled Mott insulator results in a highly incoherent metal with frozen magnetic moments. These moments fluctuate and collapse in a crossover region that is characterized by unusual non-Fermi liquid properties such as a self-energy whose imaginary part varies $\propto \sqrtω$ over a wide energy range. At low enough temperature, the local moment fluctuations induce electron pairing and this mechanism may be the unifying principle of unconventional superconductivity. While this physics has been discovered in numerical studies of multi-orbital Hubbard systems, it exhibits a striking similarity to the analytically solvable Sachdev-Ye (SY) model, and its recent fermionic extensions. Here, we clarify the relation between spin-freezing and SY physics, and thus shed light on fundamental properties of Hund metals.
Modelling and analysing of neural network dynamics
Creators: name: Pernelle, Guillaume
Publisher: name: Imperial College London
Year: 2017

description: Neurons are often considered as the basic functional units of the brain. Our brain contains about 100 billions of neurons, of many different types and connected among themselves in a multitude of different ways. Yet, from this overwhelming complexity, order can emerge in the form of neural dynamics, when cohorts of neurons show synchronous activity. For example, oscillations of neural activity can be observed in many brain regions and are thought to be associated with cognitive processes such as information transfer or memory consolidation. However, too much oscillation can be detrimental, as during epilepsy crisis. Therefore, there must be mechanisms regulating the dynamics of neural networks. Our aim in this thesis is to further our understanding of neural networks dynamics. First, we modelled a network of cortical neurons known to exhibit oscillations. In this network, GABAergic interneurons are connected via chemical and electrical synapses (also called gap junctions), which promote synchronisation of neural assemblies. We implemented a novel model of gap junction plasticity, based on recent experimental evidence that they alter their strength in an activity-dependent manner. We hypothesised that gap junction plasticity can regulate network-wide neural dynamics and we investigated functional implications on information transmission in cortex. We then considered a brain region rich in neuronal gap junctions, the thalamic reticular nucleus (TRN). The TRN is thought to be the source of patterns of waxing-and-waning oscillations called spindles. We hypothesised that gap junction plasticity could lead to spindles and we simulated their pharmacological manipulation. Finally, we analysed and modelled the relationship between neural activity and hemodynamic response from in vivo recordings. We hypothesised that this relationship can be modelled with a transfer function. We then investigated the transfer function dependency of location and brain states. At last, we studied the prediction of neural activity from hemodynamic response.
Helical spin texture in a thin film of superfluid ${}^3$He
Creators: name: Brauner, Tomas
name: Moroz, Sergej
Publisher: name: arXiv
Year: 2018
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We consider a thin film of superfluid ${}^3$He under conditions that stabilize the A-phase. We show that in the presence of a uniform superflow and an external magnetic field perpendicular to the film, the spin degrees of freedom develop a nonuniform, helical texture. Our prediction is robust and relies solely on Galilei invariance and other symmetries of ${}^3$He, which induce a coupling of the orbital and spin degrees of freedom. The length scale of the helical order can be tuned by varying the velocity of the superflow and the magnetic field, and may be in reach of near-future experiments.
description: 9 pages, 1 figure; v2: matches text to appear in PRB
Grids of white dwarf evolutionary models with masses from M= 0.1 to 1.2 Ms
Creators: name: Benvenuto, O. G.
name: Althaus, L. G.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present detailed evolutionary calculations for carbon - oxygen - and helium - core white dwarf (WD) models with masses ranging from M= 0.1 to M= 1.2 solar masses and for metallicities Z= 0.001 and Z= 0. The sequences cover a wide range of hydrogen envelopes as well. We employed a detailed WD evolutionary code. In particular, the energy transport by convectcion is treated within the formalism of the full spectrum turbulence theory. The set of models presented here is very detailed and should be valuable for the interpretation of the observational data on low - mass WDs recently discovered in numerous binary configurations and also for the general problem of determining the theoretical luminosity function for WDs. In this context, we compare our cooling sequences with the observed WD luminosity function recently improved by Leggett, Ruiz and Bergeron (1998) and we obtain an age for the Galactic disc of approximately 8 Gyr. Finally, we applied the results of this paper to derive stellar masses of a sample of low - mass white dwarfs.
description: 9 pages, 8 figures; accepted for publication in MNRAS; replaced with minor corrections to text
Alauda magna Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Passeriformes
Alaudidae
Alauda
Alauda magna

description: Alauda magna [spec. nov.]
A. subtus flava, fascia pectorali curva nigra: rectricibus tribus lateralibus albis.
Alauda magna. Catesb. car. 1. p. 33. t. 33.
Habitat in America, Africa.
Corpus scolopacinum, magnitudine Turdi, totum subtus flavissimum. Pectus macula magna nigricante lunari. Remiges fuscae: secundariae testaceo maculatae. Cauda rotundata: Rectrices 3 laterales maximam partem albae. Unguis posticus pedum major, sed magis curvus quam in reliquis. Rostrum rectum: Maxilla superior teretiuscula, basi nuda.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 167, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Additional file 1: of Frequency and phenotype consequence of APOC3 rare variants in patients with very low triglyceride levels
Creators: name: Crawford, Dana
name: Restrepo, Nicole
name: Diggins, Kirsten
name: Farber-Eger, Eric
name: Wells, Quinn
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Table S1. Genetic variants previously associated with risk of coronary artery disease in European Americans. (DOCX 27 kb)
Conformal gradient vector fields on Riemannian manifolds with boundary
Creators: name: Evangelista, Israel
name: Viana, Emanuel
Publisher: name: arXiv
Year: 2018
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C20, 53A30

description: Let $(M^n,g)$ be an $n$-dimensional compact connected Riemannian manifold with smooth boundary. We show that the presence of a nontrivial conformal gradient vector field on $M$, with an appropriate control on the Ricci curvature makes $M$ to be isometric to a hemisphere of $\mathbb{S}^{n}$. We also prove that if an Einstein manifold admits nonzero conformal gradient vector field, then its scalar curvature is positive and it is isometric to a hemisphere of $\mathbb{S}^{n}$. Furthermore, we prove that if $ M $ admits a nontrivial conformal vector field and has constant scalar curvature, then the scalar curvature is positive. Finally, a suitable control on the energy of a conformal vector field implies that $M$ is isometric to a hemisphere $\mathbb{S}^n_+$.
description: To appear in Colloquium Mathematicum
A vertically and temporally diverse bacterial community in a shallow lake-water sediment site of a eutrophic lake
Creators: name: Moschos, Stefanos
name: Piperagkas, Odysseas
name: Karayanni, Hera
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Aquatic sediment accumulates organic matter and provides microenvironments for the growth of a diverse microbial community with key roles in the biogeochemical nutrient cycling of the lacustrine ecosystem. We investigated vertical and temporal variations of the sedimentary bacterial community composition in a shallow coastal site of eutrophic Lake Pamvotis (northwestern Greece) across 3 horizons between the surface and 5 cm below lake floor (cmblf) during transition to the cold period of the year (Oct–Dec). For this analysis we used Illumina sequencing of the V3–V4 hypervariable regions of the 16S rRNA gene. Bacterial community composition was dominated by Proteobacteria, Bacteroidetes, and Chloroflexi. Rare operational taxonomic units (OTUs) represented 96.09% (standard deviation 0.61%) of richness per sample, contributing significantly to diversity, and only a few became abundant during the study. Abundant OTUs represented <0.005% of richness but accounted for 20–33% of reads in different samples, mainly associated with anaerobic/microaerobic taxa common in polluted aquatic systems, sludge digesters, or wastewater (e.g., Thiolamprovum pedioforme, Candidatus Competibacter, Petrimonas). About 50% of OTUs found at the surface persisted with depth while shared OTUs between any 2 months were always >70% of richness. Overall, sediment bacterial community composition was diverse but remained largely homogeneous in the sediment of this human-impacted ecosystem at the temporal and vertical scale studied here. The study revealed the potential of specific bacterial taxa (e.g., Anaerolineae, Bellilinea) to serve as monitors of specific pollutants (e.g., polycyclic aromatic hydrocarbons) as well as the need to investigate the role of the rare biosphere in ecosystem functioning.
Computation of Mass Outflow Rate from Relativistic Quasi-Spherical Accretion onto Black Holes
Creators: name: Das, Tapas K.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We compute mass outflow rate $R_{\dot m}$ from relativistic matter accreting quasi-spherically onto Schwarzschild black holes. Taking the pair-plasma pressure mediated shock surface as the {\it effective} boundary layer (of the black hole) from where bulk of the outflow is assumed to be generated, computation of this rate is done using combinations of exact transonic inflow and outflow solutions. We find that $R_{\dot m}$ depends on the initial parameters of the flow, the polytropic index of matter, the degree of compression of matter near the shock surface and on the location of the shock surface itself. We thus not only study the variation of the mass outflow rate as a function of various physical parameters governing the problem but also provide a sufficiently plausible estimation of this rate.
description: 6 twocoloumn pages with 5 figures. mn.sty used. Accepted for publication in MNRAS
B cells, Bach2 and Immune deficiency
Creators: name: O'Brien, Charlotte Rose
Publisher: name: Imperial College London
Year: 2017

description: B cell defects in HIV-1 infection are characterised by increased frequency of immature cell subsets, loss of memory cells, and hypergammaglobulinemia. There is increasing evidence that the capacity of B cells to secrete cytokines (IL-10) or express proteins (Bach2), may inhibit the T cell inflammatory response, which is believed to contribute to progressive immune deficiency in HIV-1. The aims were to determine if HIV-1 affects the capacity of B cells to express IL-10, TNF-α, and Bach2, and if alterations in cytokines and Bach2 expression were linked to T cell activation. An increase in immature B cell subsets and plasmablasts was found in HIV-1+ individuals, and was reversed by anti-retroviral therapy (ART). B cell proliferation and activation markers were increased in ART naïve individuals. However, TLR, T cell independent and dependent stimulation failed to increase expression of the co-stimulatory molecules, CD80 and CD86, or immunoglobulin synthesis, compared to healthy controls and HIV-1 patients on ART. No difference in the capacity of B cells to secrete IL-10 and TNF-α was noted in the study groups, and there was no association with markers of T cell activation. The results of flow cytometric Bach2 staining were unreliable. Analysis of B cell phenotype and function was undertaken in a patient with a history of chest infections and diarrhoea, and a heterozygous mutation in Bach2, c.T71C, was detected using whole exome sequencing. The patient did not have class-switched memory B cells, and decreased synthesis of immunoglobulins and cytokines. The immune findings supported the clinical phenotype of common variable immunodeficiency (CVID), which was confirmed by genetic correction experiments conducted by collaborators in the USA. In conclusion, HIV-1+ ART naïve patients retain the capacity to secrete cytokines despite a reduction in immunoglobulin synthesis. Mutation in Bach2 affects B cell maturation and function, and is implicated in the development of CVID.
Intense variability of dissolved oxygen and temperature in the internal swash zone of Hamilton Harbour, Lake Ontario
Creators: name: Flood, Bryan
name: Wells, Mathew
name: Midwood, Jonathan D.
name: Brooks, Jill
name: Kuai, Yulong
name: Li, Jingzhi
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Cancer
subject: Inorganic Chemistry

description: The thermocline of large, stratified lakes is constantly sloshing along the sloping bed, creating a spatially variable internal swash zone. Temperature and dissolved oxygen vary rapidly here, potentially impacting fish habitat on timescales of hours. Large spatial differences in the time-dependent variance of temperature around Hamilton Harbour, Lake Ontario, Canada, were partly controlled by basin shape and bathymetry. The temporal variability was nearly twice as large at sites along the mildly sloping, narrow, upwind end of the basin relative to those at a similar depth at the steeper, broad, downwind end. Because the thermocline and oxycline were coincident, the same physical mechanisms resulted in a dissolved oxygen variance also twice as great at the mild slope compared to the steeper slope. Frequent hypoxic events occurred throughout the internal swash zone, drastically reducing the availability of fish habitat for anoxia-intolerant species. In the dynamic littoral zone, weekly measurements would overlook the acute temporal variability of temperature and dissolved oxygen. Here, we demonstrate that field observations and 3-dimensional (3D) hydrodynamic modelling can predict how basin morphometry affects internal seiche dynamics and spatial variability of internal swash zones.
The input-to-state stability framework for multistable systems on manifolds
Creators: name: Forni, Paolo
Publisher: name: Imperial College London
Year: 2017

description: As central topics in systems and control theory, the study of stability, robustness, and sensitivity to disturbances for nonlinear systems has gained with the Input-to-State Stability (ISS) paradigm one of its most powerful tools. Standard formulations of ISS and several related notions characterize stability properties in a global setting with respect to a single equilibrium in the origin and for systems defined in Euclidean space. This classical requirements make the basic theory not applicable for a global analysis of many dynamical behaviours of interest for applications, such as: multistability, periodic oscillations, and different class of attractors. The aim of this work is to extend and further characterize the variety of notions available in standard ISS literature to multistable systems evolving on Riemannian manifolds. The definition of global multistability in consideration is based on the existence of a finite number of compact, globally attractive, invariant sets satisfying a specific condition of acyclicity. Such definition allows for Lyapunov characterizations in hybrid systems and is used to generalize ISS, integral ISS, and Output-to-State Stability (OSS) to multistable systems on manifolds. In different modalities, the novel properties of ISS and integral ISS - respectively denoted as Input-to-State Multistability (ISM) and integral ISM - are shown to be preserved in cascade interconnection and with input shifts. In particular, under suitable conditions, we can establish semi-global practical ISM in perturbed flows and in singular perturbation models.
Additional file 1. of Nivolumab induced encephalopathy in a man with metastatic renal cell cancer: a case report
Creators: name: Jindřich Kopecký
name: Ondřej Kubeček
name: Tomáš Geryk
name: Birgita Slováčková
name: Hoffmann, Petr
name: Žiaran, Miroslav
name: Priester, Peter
Publisher: name: figshare
Year: 2018
Subjects: subject: Space Science
subject: Cell Biology
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Marine Biology
subject: Cancer

description: Timeline of the case report. (PDF 177 kb)
Sturnus Linnaeus, 1758, gen. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Aves
Passeriformes
Sturnidae
Sturnus

description: Sturnus [gen. nov.]
Rostrum subulatum, angulato-de- pressum, obtusiusculum: Mandibula superiore integerrima, marginibus patentiusculis.
Nares supra marginatae.
Lingua emarginata, acuta.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 167, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
title: ADCO, Premier cartulaire de Saint-Étienne de Dijon (XIIe siècle), Cart. 21 (G 125), 71 folios, f. 00127
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Projet CBMA
name: CG21/F.PETOT/2015
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge
subject: cartulaire

description: Premier cartulaire de Saint-Étienne de Dijon (XIIe siècle), Archives départementales de la Côte-d'Or, Cart. 21 (G 125), 71 folios, f. 00127, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Premier cartulaire de Saint-Étienne de Dijon (XIIe siècle), Archives départementales de la Côte-d'Or, Cart. 21 (G 125), 71 folios, f. 00127, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https://manuscrits.cbma-project.eu/
description: Provenance: abbaye Saint-Étienne de Dijon
description: Provenance: http://www.wikidata.org/entity/Q15945019
Solitons in a chain of charge-parity-symmetric dimers
Creators: name: Kirikchi, O. B.
name: Malomed, B. A.
name: Karjanto, N.
name: Kusdiantara, R.
name: Susanto, H.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: Optics (physics.optics)
subject: FOS: Physical sciences
subject: 35Q55, 35C08, 37K40

description: We consider an array of dual-core waveguides, which represent an optical realization of a chain of dimers, with an active (gain-loss) coupling between the cores, opposite signs of discrete diffraction in the parallel arrays, and a phase-velocity mismatch between them (which is necessary for the stability of the system). The array provides an optical emulation of the charge-parity ($\mathcal{CP}$) symmetry. The addition of the intracore cubic nonlinearity gives rise to several species of fundamental discrete solitons, which exist in continuous families, although the system is non-Hermitian. The existence and stability of the soliton families are explored by means of analytical and numerical methods. An asymptotic analysis is presented for the case of weak intersite coupling (i.e., near the anticontinuum limit), as well as weak coupling between cores in each dimer. Several families of fundamental discrete solitons are found in the semi-infinite gap of the system's spectrum, that have no counterparts in the continuum limit, as well as a branch which belongs to the finite band gap and carries over into a family of stable gap solitons in that limit. One branch develops an oscillatory instability above a critical strength of the intersite coupling, others being stable in their entire existence regions. Unlike solitons in conservative lattices, which are controlled solely by the strength of the intersite coupling, here fundamental-soliton families have several control parameters, one of which, viz., the coefficient of the intercore coupling in the active host medium, may be readily adjusted in the experiment by varying the gain applied to the medium.
description: 11 pages, 8 figures
Current and future threats for ecological quality management of South American freshwater ecosystems
Creators: name: Torremorell, Ana
name: Hegoburu, Cecilia
name: Brandimarte, Ana Lucia
name: Rodrigues, Eduardo Henrique Costa
name: Pompêo, Marcelo
name: da Silva, Sheila Cardoso
name: Moschini-Carlos, Viviane
name: Caputo, Luciano
name: Fierro, Pablo
name: Mojica, José Iván
name: Matta, Ángela Lucia Pantoja
name: Donato, Jhon Charles
name: Jiménez-Pardo, Pedro
name: Molinero, Jon
name: Ríos-Touma, Blanca
name: Goyenola, Guillermo
name: Iglesias, Carlos
name: López-Rodríguez, Anahí
name: Meerhoff, Mariana
name: Pacheco, Juan Pablo
name: de Mello, Franco Teixeira
name: Rodríguez-Olarte, Douglas
name: Gómez, Margenny Barrios
name: Montoya, José Vicente
name: López-Doval, Julio Cesar
name: Navarro, Enrique
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Global change drivers including eutrophication, hydrological disturbance, climate change, chemical pollution, overexploitation, invasive species, and land-use change are affecting the function and structure of freshwater ecosystems. South American freshwater ecosystems are especially threatened by the combination of rising human pressures on natural resources (i.e., water use, intensive agriculture, mining, deforestation, and afforestation) and the lack of adequate legislation and economic resources for environmental protection and restoration. We assess the state of freshwater ecosystems in Argentina, Brazil, Chile, Colombia, Ecuador, Uruguay, and Venezuela, focusing on broad categories of human-induced threats grouped into 5 categories: climate change, watershed stressors, hydrological alteration, channel modification, and biological stressors. For most countries, the most severe threats are related to land uses such as mining, agriculture, and urban expansion. Other threats relate to the abstraction or wasteful use of water and the intense regulation of flows, including the effects of large hydraulic infrastructure. There is also an increasing need to empower public organisations that focus on environmental protection, to update or develop an adequate regulatory and legal framework, to provide adequate funding for the implementation of environmental legislation, and not least to implement ecological rehabilitation. Implementation of these steps would reduce the threats to South American aquatic ecosystems and allow progress toward the sustainable development of this region in future decades.
Astrophysics on the GRAPE Family of Special Purpose Computers
Creators: name: Hut, Piet
name: Makino, Jun
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The GRAPE-4, the world's fastest computer in 1995-1997, has produced some major scientific results, through a wide diversity of large-scale simulations in astrophysics. Applications have ranged from planetary formation, through the evolution of star clusters and galactic nuclei, to the formation of galaxies and clusters of galaxies.
description: 15 pages, to apper in Science
Asymptomatic carotid stenosis and risk stratification
Creators: name: Giannopoulos, Argyrios
Publisher: name: Imperial College London
Year: 2019

description: Carotid endarterectomy in patients with asymptomatic carotid stenosis (ACS) is controversial. Researchers focus on identification of the vulnerable carotid plaque to improve patients’ selection for surgery. However, there is no consensus on a specific algorithm. Also, most studies analyse static plaque measurements, despite carotid plaques being dynamic structures. The aims of this thesis were to determine the association of clinical parameters and ultrasonic plaque characteristics with stroke and mortality risk; also, stroke risk in terms of time. The final endpoint was to provide new methods of stroke and mortality stratification and assess new features of plaque instability, in patients with ACS. In a natural history study of 1121 patients with ACS, a high-risk subgroup with annual stroke risk of 7.2%, based on clinical parameters, was identified. Independent stroke predictors were creatinine, severity of stenosis, history of contralateral neurological events and progression of stenosis. A model based on six computer-extracted plaque texture features, predicting cerebrovascular events in the first two years, was developed. Finally, a subgroup of patients with 100% 5-year cardiovascular mortality was identified. Independent predictors of cardiovascular mortality were male gender, age, diabetes, stenosis >80%, not taking aspirin, cardiac failure and left ventricular hypertrophy. In the final part of the thesis, quantification of discordant plaque motion and its relationship to symptoms was evaluated. In a cross-sectional study, involving 116 patients (58 symptomatic and 58 asymptomatic), discordant motion was associated with a high prevalence of symptomatic carotid plaques. A method of objective computerised measurements for identification and quantification of discordant plaque motion was developed. The optimal predictor and a cut-off point for discordant motion were found. Plaque motion analysis is a potential tool in stroke risk stratification. It should be tested, in combination with other plaque features, in prospective studies of patients with ACS.
Quantum interference in universal linear optical devices for quantum computation and simulation
Creators: name: Sparrow, Christopher
Publisher: name: Imperial College London
Year: 2017

description: It is believed that the exotic properties of quantum systems can be harnessed to perform certain computational tasks more efficiently than classical theories allow. The production, manipulation and detection of single photons constitutes a potential platform for performing such non-classical information processing. The development of integrated quantum photonics has provided a miniaturised, monolithic architecture that is promising for the realisation of near-term analog quantum devices as well as full-scale universal quantum computers. In this thesis we investigate the viability of these photonic quantum computational approaches from an experimental and theoretical perspective. We implement the first universally reconfigurable linear optical network; a key capability for the rapid prototyping of photonic quantum protocols. We propose and demonstrate the use of these devices as a new platform for the programmable quantum simulation of molecular vibrational dynamics. We then tackle an important outstanding problem in linear optical quantum computing; quantifying how partial-distinguishability amongst photons aff ects logical error rates. Finally, we propose a series of schemes aimed at counteracting these distinguishability errors in order to achieve practical quantum technologies with imperfect photonic components.