cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Schwinger effect impacting primordial magnetogenesis
Creators: name: Stahl, Clement
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We explore the enhancement of an electromagnetic field in an inflationary background with an anti-conductive plasma of scalar particles. The scalar particles are created by Schwinger effect in curved spacetime and backreact to the electromagnetic field. The possibility of a negative conductivity was recently put forward in the context of the renormalization of the Schwinger induced current in de Sitter spacetime. While a negative conductivity enhances the produced magnetic field, we find that it is too weak to seed the observed intergalactic magnetic field today. This results on pair creation in inflationary scenario is however important for primordial scenarios of magnetogenesis as the presence of a conductivity alters the spectral index of the magnetic field. This also shows on a specific example that backreaction can increase the electromagnetic field and not only suppress it.
description: 8 pages, 0 figure, matches published version
High-speed 3-D fluorescence imaging by oblique plane microscopy: multi-well plate-reader development, biological applications and image analysis
Creators: name: Maioli, Vincent Albert
Publisher: name: Imperial College London
Year: 2016

description: Light-sheet microscopy has enabled high-speed 3D fluorescence microscopy with lower levels of phototoxicity and photobleaching compared to more established fluorescence microscopy techniques. However, conventional light sheet configurations prevent the use of many common sample mounting techniques including multi-well plates. The oblique plane microscope (OPM) is a light-sheet microscope implemented on a standard microscope frame. This thesis presents the development of a high-speed OPM plate-reader and analysis of high speed 2D and 3D OPM data of isolated cardiomyocytes. First, the modifications made to the OPM system to achieve the plate-reading mode are presented. In particular, the electrical triggering system and the software developed for image acquisition control are discussed, as well as modifications including an immersion-fluid replenishing cap and to the microscope enclosure system. Finally, the algorithm and software used to reconstruct the OPM data are presented, together with a discussion of their influence on the final image. An experimental characterisation of the OPM system optical performance is then presented. Optical modelling of the different parts of the OPM is detailed together with experimental measurements of the transmission efficiency of light through the OPM system, the light sheet thickness, the aberrations introduced when refocusing away from the designed focal plane, and the influence of the refocusing distance and scanning speed on the size of the system point spread function. Image analysis of high speed 2D and 3D OPM data acquired of calcium dynamics in isolated cardiomyocytes is then presented. The software developed is presented and applied to study the relationships between cardiomyocyte transverse tubule structure and dynamic calcium spark and wave events. Finally, the applications of the OPM plate-reader to ratiometric imaging of FRET biosensors in 3D tissue cultures and a range of biological samples will be detailed. These results demonstrate the ability of the system to acquire data over an extended field of view, in particular to study cell invasion into collagen in multi-well plates. The OPM plate-reader is then applied to the imaging of spheroids, and in particular of spatio-temporal glucose dynamics with ratiometric imaging of a FRET biosensor, along with the image processing to quantity the FRET ratio as a function of the distance from the outside of the spheroid.
Singularities of meager composants and filament composants
Creators: name: Lipham, David Sumner
Publisher: name: arXiv
Year: 2018
Subjects: subject: General Topology (math.GN)
subject: FOS: Mathematics
subject: 54F15, 54D35, 54H15

description: Suppose $Y$ is a continuum, $x\in Y$, and $X$ is the union of all nowhere dense subcontinua of $Y$ containing $x$. Suppose further that there exists $y\in Y$ such that every connected subset of $X$ limiting to $y$ is dense in $X$. And, suppose $X$ is dense in $Y$. We prove $X$ is homeomorphic to a composant of an indecomposable continuum, even though $Y$ may be decomposable. An example establishing the latter was given by Christopher Mouron and Norberto Ordoñez in 2016. If $Y$ is chainable or, more generally, an inverse limit of identical topological graphs, then we show $Y$ is indecomposable and $X$ is a composant of $Y$. For homogeneous continua we explore similar problems which are related to a 2007 question of Janusz Prajs and Keith Whittington.
description: 12 pages, 3 figures
Small-scale structure from neutron dark decay
Creators: name: Karananas, Georgios K.
name: Kassiteridis, Alexis
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: It was recently proposed that the disagreement in the experimental measurements of the lifetime of the neutron might be eradicated if the neutron decays to particles responsible for the dark matter in the Universe. In this paper we construct a proto- type self-interacting dark matter model which, apart from reproducing the correct relic abundance, resolves all small-scale problems of the $Λ$CDM paradigm. The theory is compatible with all present cosmological observations and astrophysical bounds.
description: Journal version---discussion extended, typos corrected, references added
The Gravitational Demise of Cold Degenerate Stars
Creators: name: Adams, Fred C.
name: Laughlin, Greg
name: Mbonye, Manasse
name: Perry, Malcolm J.
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We consider the long term fate and evolution of cold degenerate stars under the action of gravity alone. Although such stars cannot emit radiation through the Hawking mechanism, the wave function of the star will contain a small admixture of black hole states. These black hole states will emit radiation and hence the star can lose its mass energy in the long term. We discuss the allowed range of possible degenerate stellar evolution within this framework.
description: LaTeX, 18 pages, one figure, accepted to Physical Review D
CMB Anisotropies in the Weak Coupling Limit
Creators: name: Hu, Wayne
name: White, Martin
Publisher: name: arXiv
Year: 1995
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present a new, more powerful and accurate, analytic treatment of cosmic microwave background (CMB) anisotropies in the weakly coupled regime. Three applications are presented: gravitational redshifts in a time dependent potential, the Doppler effect in reionized scenarios, and the Vishniac effect. The Vishniac effect can dominate primary anisotropies at small angles even in late and minimally reionized models in flat dark-matter dominated universes with Harrison-Zel'dovich initial conditions. The techniques developed here refine previous calculations yielding a larger coherence angle for the Vishniac effect and moreover can be applied to non-trivial ionization histories. These analytic expressions may be used to modify results for the standard cold dark matter model to its cosmological constant and reionized extensions without detailed and time consuming recalculation.
description: 8pg, uuencoded postscript, submitted to A&A
Divergence Free Polar Wavelets for the Analysis and Representation of Fluid Flows
Creators: name: Lessig, Christian
Publisher: name: arXiv
Year: 2018
Subjects: subject: Numerical Analysis (math.NA)
subject: Computational Engineering, Finance, and Science (cs.CE)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 42C15, 42C40, 76B99

description: We present a Parseval tight wavelet frame for the representation and analysis of velocity vector fields of incompressible fluids. Our wavelets have closed form expressions in the frequency and spatial domains, are divergence free in the ideal, analytic sense, have a multi-resolution structure and fast transforms, and an intuitive correspondence to common flow phenomena. Our construction also allows for well defined directional selectivity, e.g. to model the behavior of divergence free vector fields in the vicinity of boundaries or to represent highly directional features like in a von Kármán vortex street. We demonstrate the practicality and efficiency of our construction by analyzing the representation of different divergence free vector fields in our wavelets.
description: To appear in Journal of Mathematical Fluid Dynamics. Extensive supplementary material available at http://graphics.cs.uni-magdeburg.de/projects/psidiv/psidiv_supp.pdf
Castor Linnaeus, 1758, gen. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Mammalia
Rodentia
Castoridae
Castor

description: Castor [gen. nov.]
Dentes Primores Superiores truncati, angulo transverso excavati; inferiores apice transversi.
Cauda depressa.
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 58, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Transient superconductivity without superconductivity
Creators: name: Chiriacò, Giuliano
name: Millis, Andrew J.
name: Aleiner, Igor L.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Recent experiments on K$_3$C$_{60}$ and layered copper-oxide materials have reported substantial changes in the optical response following application of an intense THz pulse. These data have been interpreted as the stimulation of a transient superconducting state even at temperatures well above the equilibrium transition temperature. We propose an alternative phenomenology based on the assumption that the pulse creates a non-superconducting, though non-equilibrium situation in which the linear response conductivity is negative. The negative conductivity implies that the spatially uniform pre-pulse state is unstable and evolves to a new state with a spontaneous electric polarization. This state exhibits coupled oscillations of entropy and electric charge whose coupling to incident probe radiation modifies the reflectivity, leading to an apparently superconducting-like response that resembles the data. Dependencies of the reflectivity on polarization and angle of incidence of the probe are predicted and other experimental consequences are discussed.
description: 5 pages, 3 figures
Supplementary document for Rotating twisted templates for imprinting polarization gratings with sub- to dozens-micron period - 7002385.pdf
Creators: name: Jiang, Xiangyu
name: ye, xianglin
name: Xue, Kuangdi
name: Zhou, Yingjie
name: Fan, Fan
name: Wen, Shuangchun
Publisher: name: Optica Publishing Group
Year: 2024
Subjects: Uncategorized

description: Supplementary information for rotating twisted templates for imprinting polarization gratings with sub- to dozens-micron period
Large Eddy simulation of premixed and stratified turbulent combustion
Creators: name: Brauner, Timothy
Publisher: name: Imperial College London
Year: 2016

description: The work presented in this thesis focuses on the modelling of turbulent fully premixed and stratified flames, where stratification refers to the equivalence ratio of the unburned mixture varying in space. The modelling approach is based on a transported probability density function formulation in the context of Large Eddy Simulation, in conjunction with the fully Eulerian stochastic fields solution method. This method provides detailed statistical information about the flow field and reactive scalars without making assumptions about the combustion regime, maintaining generality. In the probability density function formulation the chemical reaction rate term appears in closed form and a reduced yet still detailed reaction mechanism is employed to model the methane-air combustion over a range of stratification ratios. Amendments to the formulation and implementation are proposed. These account properly for the limit case of no sub-grid viscosity, which is important in modelling flames in well resolved and low Reynolds number flow regions as found in the vicinity of flame holders used in many premixed burner configurations. Two laboratory scale burner configurations are investigated numerically, under various operating conditions and mixture stratification ratios, and results are compared against existing detailed experimental measurements. Theses configurations are a low Reynolds number slot burner that uses a rod to stabilise a V-shaped flame and a moderate Reynolds number co-annular burner with a central bluff-body to stabilise swirling and non-swirling flames. The equivalence ratio of the mixtures fed in by the slots or annuli were varied to produce different stratification ratios. Improvements in ability to model low Reynolds number flames and capture stratified flame behaviour are demonstrated. The methods is able to predict the flow field as well as the mean and rms values of the reactive scalars to a good degree of accuracy.
Hybrid 2D/3D Photonic Integration for Non-Planar Circuit Topologies
Creators: name: Nesic, Aleksander
name: Blaicher, Matthias
name: Hoose, Tobias
name: Lauermann, Matthias
name: Kutuvantavida, Yasar
name: Freude, Wolfgang
name: Koos, Christian
Publisher: name: VDE Verlag
Year: 2016

description: We present a concept for realizing crossing-free photonic integrated circuits (PIC) using 3D freeform waveguides. We prove the viability of the approach using a silicon photonic 4 x 4 switch-andselect device. The method is applicable to a wide range of PIC technologies.
Terminating contamination – Large-scale search identifies >2,000,000 contaminated entries in GenBank
Creators: name: Steinegger, Martin
name: Salzberg, Steven L.
Publisher: name: F1000 Research Limited
Year: 2019

description: Metagenomics enables us to investigate organisms sampled from their native environments by sequencing their DNA directly, for example by quantifying their abundance and unraveling their taxonomic composition. However, these types of analyses are sensitive to contamination in public databases caused by incorrectly labeled reference sequences.
We propose Conterminator, an efficient method to detect and removes incorrect sequences across kingdoms by an exhaustive all-against-all sequence comparison. Our analysis reports contaminations in 114,035 sequences in the NCBI Reference Sequence Database (RefSeq) and 2,161,746 sequences in the GenBank. The median length of 519 nucleotide residues in the reported sequences suggests that a stricter length cut-off would improve the quality of reference databases. Conterminator uncovers contamination in sequences spanning the whole range from draft genomes to complete model organism. Our method scales linearly with input size and was able to process 1.5 terabytes of genomic sequence data in five days on a single 32-core compute node. We believe that Conterminator will become an important tool to ensure the quality of our reference databases and will improve the reliability of downstream metagenomic analyses. Source code (GPLv3):https://github.com/martin-steinegger/conterminator
Asymptotic Iteration and Variational Methods for Gaussian Potential
Creators: name: Mutuk, Halil
Publisher: name: arXiv
Year: 2018
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In this paper we studied approximate solutions of the radial Schrödinger equation with the attractive Gaussian potential. We used asymptotic iteration method and variational method in order to obtain energy eigenvalues for any $n$ and $l$ quantum numbers. Our results are in good agreement with the other studies.
description: 8 pages, 2 tables, Accepted publication in Pramana Journal of Physics
An asymmetric arcsecond radio jet from Circinus X-1
Creators: name: Fender, Robert
name: Spencer, Ralph
name: Tzioumis, Tasso
name: Wu, Kinwah
name: van der Klis, Michiel
name: van Paradijs, Jan
name: Johnston, Helen
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: In observations with the Australia Telescope Compact Array we have resolved the radio counterpart of the unusual X-ray binary Cir X-1 into an asymmetric extended structure on arcsecond scales. In order to quantify the asymmetry we have redetermined as accurately as possible both the optical and radio coordinates of the source. The extended emission can be understood as a compact, absorbed core at the location of the X-ray binary, and extended emission up to 2 arcsec to the southeast of the core. The arcsec-scale extended emission aligns with the larger, more symmetric arcmin-scale collimated structures in the surrounding synchrotron nebula. This suggests that the transport of mass and/or energy from the X-ray binary to the synchroton nebula is occurring via the arcsec-scale structures. The ratio of extended flux from the southeast to that from the northwest of the core is at least 2:1. Interpreted as relativistic aberration of an intrinsically symmetric jet from the source, this implies a minimum outflow velocity of 0.1 c. Alternatively, the emission may be intrinsically asymmetric, perhaps as a result of the high space velocity of the system.
description: Accepted for publication in ApJ Letters. Three figures
Stability in Distribution of Neutral Stochastic Functional Differential Equations with Infinite Delay
Creators: name: Asker, Hussein K.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: In this paper, we investigate stability in distribution of neutral stochastic functional differential equations with infinite delay (NSFDEwID) at the state space \begin{equation*} C_{r}=\{{φ\in C((-\infty,0];R^{d}):\|φ\|_{r}=\sup_{-\infty 0 \}. \end{equation*} We drive a sufficient strong monotone condition for the existence and uniqueness of the global solutions of NSFDEwID in the state space $ C_{r} $. We also address the stability of the solution map $ x_{t} $ and illustrate the theory with an example.
description: arXiv admin note: text overlap with arXiv:1805.10674
Quantum limited superresolution of an incoherent source pair in three dimensions
Creators: name: Yu, Zhixian
name: Prasad, Sudhakar
Publisher: name: arXiv
Year: 2018
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The error in estimating the separation of a pair of incoherent sources from radiation emitted by them and subsequently captured by an imager is fundamentally bounded below by the inverse of the corresponding quantum Fisher information (QFI) matrix. We calculate the QFI for estimating the full three-dimensional (3D) pair separation vector, extending previous work on pair separation in one and two dimensions. We also show that the pair-separation QFI is, in fact, identical to source localization QFI, which underscores the fundamental importance of photon-state localization in determining the ultimate estimation-theoretic bound for both problems. We also propose general coherent-projection bases that can attain the QFI in two special cases. We present simulations of an approximate experimental realization of such quantum limited pair superresolution using the Zernike basis, confirming the achievability of the QFI bounds.
description: Supplemental material follows the main paper. The paper has been submitted to Physical Review Letters
$z=2$ Quantum Critical Dynamics in a Spin Ladder
Creators: name: Blosser, D.
name: Bhartiya, V. K.
name: Voneshen, D. J.
name: Zheludev, A.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: By means of inelastic neutron scattering we investigate finite temperature dynamics in the quantum spin ladder compound (C$_5$H$_{12}$N)$_2$CuBr$_4$ (BPCB) near the magnetic field induced quantum critical point with dynamical exponent $z=2$. We observe universal finite-temperature scaling of the transverse local dynamic structure factor in spectacular quantitative agreement with long-standing theoretical predictions. At the same time, already at rather low temperatures, we observe strong non-universal longitudinal fluctuations. To separate the two, we make use of an intrinsic leg-exchange symmetry of the spin ladder. Complementary measurements of specific heat also reveal striking scaling behavior near the quantum critical point.
description: Minor corrections, extension of supplemental material
Higgs relaxation after inflation
Creators: name: Fonseca, Nayara
name: Morgante, Enrico
name: Servant, Geraldine
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We show that the mechanism of cosmological relaxation of the electroweak scale can take place independently of the inflation mechanism, thus relieving burdens from the original relaxion proposal. What eventually stops the (fast-rolling) relaxion field during its cosmological evolution is the production of particles whose mass is controlled by the Higgs vacuum expectation value. We first show that Higgs particle production does not work for that purpose as the Higgs field does not track the minimum of its potential in the regime where Higgs particles get efficiently produced through their coupling to the relaxion. We then focus on gauge boson production. We provide a detailed analysis of the scanning and stopping mechanism and determine the parameter space for which the relaxion mechanism can take place after inflation, while being compatible with cosmological constraints, such as the relaxion dark matter overabundance and Big Bang Nucleosynthesis. We find that the cutoff scale can be as high as two hundreds of TeV. In this approach, the relaxion sector is responsible for reheating the visible sector. The stopping barriers of the periodic potential are large and Higgs-independent, facilitating model-building. The allowed relaxion mass ranges from 200 MeV up to the weak scale. In this scenario, the relaxion field excursion is subplanckian, and is thus many orders of magnitude smaller than in the original relaxion proposal.
description: 51 pages, 16 figures. v3: Minor revisions, version published in JHEP
Detection of pitting in gears using a deep sparse autoencoder
Creators: name: Qu, Y
name: He, M
name: Deutsch, J
name: He, David
Publisher: name: University of Illinois at Chicago
Year: 2021
Subjects: Uncategorized

description: In this paper a new method for gear pitting fault detection is presented. The presented method is developed based on a deep sparse autoencoder. The method integrates dictionary learning in sparse coding into a stacked autoencoder network. Sparse coding with dictionary learning is viewed as an adaptive feature extraction method for machinery fault diagnosis. An autoencoder is an unsupervised machine learning technique. A stacked autoencoder network with multiple hidden layers is considered to be a deep learn ing network. The presented method uses a stacked autoencoder network to perform the dictionary learning in sparse coding and extract features from raw vibration data automatically. These features are then used to perform gear pitting fault detection. The presented method is validated with vibration data collected from gear tests with pitting faults in a gearbox test rig and compared with an existing deep learning-based approach.
ROLES FOR FARMERS' KNOWLEDGE IN AFRICA
Creators: name: Riches, C
name: Shaxson, L
name: Logan, J
name: Munthali, D
name: Batterbury, Simon
name: Riches, C
name: Shaxson, L
name: Logan, J
name: Munthali, D
name: Batterbury, Simon
Publisher: name: Unknown
Year: 1993
Subjects: Environmental Economics and Policy
Farm Management

description: Researchers worked with a group of farmers in Southern Malawi to find out what farmers know about witchweed (Striga asiatica), the sweet potato weevil (Cylas puncticollis) and the beanfly (Ophiomyia spp.) and how this affects the ways in which a control programme could be implemented. Although some relationships between pest problems and other factors such as soil fertility were generally well recognised by the farming community, the farmers contacted by this project lacked some of the detailed biological and ecological knowledge that is necessary for an understanding of why,certain control practices are necessary. These gaps in their understanding have a direct bearing on farmers' current approaches to control. The authors conclude that providing farmers with this information is essential if the control technologies being developed are to be sustainable.
GESTIÓN DE LA INFORMACIÓN DE LOS DATOS DE PACIENTES UTILIZANDO HERRAMIENTAS TECNOLÓGICAS PARA EL LABORATORIO CLÍNICO KENNEDY
Creators: name: Ligia Cepeda
name: Madelyn Gil
name: Adriana Mosquera
name: Diego Fernandez
Publisher: name: Zenodo
Year: 2025

description: SISTEMA WEB PARA EL LABORATORIO CLINICO KENNEDY
On broad iron K-alpha lines in Seyfert 1 galaxies
Creators: name: Fabian, A. C.
name: Nandra, K.
name: Reynolds, C. S.
name: Brandt, W. N.
name: Otani, C.
name: Tanaka, Y.
name: Inoue, H.
name: Iwasawa, K.
Publisher: name: arXiv
Year: 1995
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The X-ray spectrum obtained by Tanaka et al from a long observation of the active galaxy MCG$-6-30-15$ shows a broad iron K$α$ line skewed to low energies. The simplest interpretation of the shape of the line is that it is due to doppler and gravitational redshifts from the inner parts of a disk about a massive black hole. Similarly broad lines are evident in shorter observations of several other active galaxies. In this paper we investigate other line broadening and skewing mechanisms such as Comptonization in cold gas and doppler shifts from outflows. We have also fitted complex spectral models to the data of MCG$-6-30-15$ to see whether the broad skewed line can be mimicked well by other absorption or emission features. No satisfactory mechanism or spectral model is found, thus strengthening the relativistic disk line model.
description: uuencoded compressed postscript. The preprint is also available at http://www.ast.cam.ac.uk/preprint/PrePrint.html
Learning Analytics Dashboard with Peer Comparison for Student Feedback in Conceptual Modeling Education: Online appendices
Creators: name: Tiukhova, Elena
name: Verbruggen, Charlotte
name: De Laet, Tinne
name: Baesens, Bart
name: Snoeck, Monique
Publisher: name: Zenodo
Year: 2025

description: Online appendices for the paper:

Tiukhova, E., Verbruggen, C., De Laet, T., Baesens, B., Snoeck, M. (2025). Learning Analytics Dashboard with Peer Comparison for Student Feedback in Conceptual Modeling Education. EMMSAD 2025
BIASED PREDICTORS, RATIONALITY AND THE EVALUATION OF FORECASTS
Creators: name: Zelliner, Arnold
name: Zelliner, Arnold
Publisher: name: Unknown
Year: 1986
Subjects: Risk and Uncertainty

description: Optimal, rational forecasts are often biased and thus the empirical finding that actual forecasts are biased is not necessarily evidence of irrational behavior. Using an asymmetric loss function and a regression forecasting problem, these points are explicitly demonstrated.
Additional file 1: of The adaptation strategies of Herpetospermum pedunculosum (Ser.) Baill at altitude gradient of the Tibetan plateau by physiological and metabolomic methods
Creators: name: Zhao, Yong
name: Xu, Fuling
name: Liu, Jia
name: Guan, Fachun
name: Quan, Hong
name: Meng, Fanjuan
Publisher: name: figshare
Year: 2019
Subjects: subject: Biophysics
subject: Space Science
subject: Medicine
subject: Molecular Biology
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Marine Biology
subject: Plant Biology

description: Figure S1. Effects of altitude gradient on the Seed length (A), Stomatal length (B), Seed width (C), Stomatal density (D), Seed thickness (E) and Trichomes density (D) of Herpetospermum pedunculosum (Ser.) Baill. (DOC 1830 kb)
Additional file 4: of The gut of the finch: uniqueness of the gut microbiome of the GalĂĄpagos vampire finch
Creators: name: Michel, Alice
name: Ward, Lewis
name: Goffredi, Shana
name: Dawson, Katherine
name: Baldassarre, Daniel
name: Brenner, Alec
name: Gotanda, Kiyoko
name: McCormack, John
name: Mullin, Sean
name: OâNeill, Ariel
name: Tender, Gabrielle
name: J. Uy
name: Yu, Kristie
name: Orphan, Victoria
name: Chaves, Jaime
Publisher: name: figshare
Year: 2018
Subjects: subject: Evolutionary Biology
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

description: Additional information regarding the observations of finch feeding behavior, core microbiome results, and microbiome differences between vampire finches on Darwin and Wolf islands. (DOCX 20 kb)
Microlensing and the Search for Extraterrestrial Life
Creators: name: Di Stefano, Rosanne
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Are microlensing searches likely to discover planets that harbor life? Given our present state of knowledge, this is a difficult question to answer. We therefore begin by asking a more narrowly focused question: are conditions on planets discovered via microlensing likely to be similar to those we experience on Earth? In this paper I link the microlensing observations to the well-known "Goldilocks Problem" (conditions on the Earth-like planets need to be "just right"), to find that Earth-like planets discovered via microlensing are likely to be orbiting stars more luminous than the sun. This means that light from the planetary system's central star may contribute a significant fraction of the baseline flux relative to the star that is lensed. Such blending of light from the lens with light from the lensed source can, in principle, limit our ability to detect these events. This turns out not to be a significant problem, however. A second consequence of blending is the opportunity to determine the spectral type of the lensed spectral type of the lensed star. This circumstance, plus the possibility that finite-source-size effects are important, implies that some meaningful follow-up observations are likely to be possible for a subset Earth-like planets discovered via microlensing. In addition, calculations indicate that reasonable requirements on the planet's density and surface gravity imply that the mass of Earth-like planets is likely to be within a factor of $\sim 15$ of an Earth mass.
description: 15 pages, 2 figures. To be published in the Astrophysical Journal
On the use of Peer Comparison in Conceptual Modeling Education: Online appendices
Creators: name: Tiukhova, Elena
name: Verbruggen, Charlotte
name: De Laet, Tinne
name: Baesens, Bart
name: Snoeck, Monique
Publisher: name: Zenodo
Year: 2025

description: Online appendices for the paper:

Tiukhova, E., Verbruggen, C., De Laet, T., Baesens, B., Snoeck, M. (2025). On the use of Peer Comparison in Conceptual Modeling Education. Submitted to EMMSAD 2025
Molecular Realization of a Quantum NAND Tree
Creators: name: Jensen, Phillip W. K.
name: Jin, Chengjun
name: Dallaire-Demers, Pierre-Luc
name: Aspuru-Guzik, Alán
name: Solomon, Gemma C.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Quantum Physics (quant-ph)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The negative-AND (NAND) gate is universal for classical computation making it an important target for development. A seminal quantum computing algorithm by Farhi, Goldstone and Gutmann has demonstrated its realization by means of quantum scattering yielding a quantum algorithm that evaluates the output faster than any classical algorithm. Here, we derive the NAND outputs analytically from scattering theory using a tight-binding (TB) model and show the restrictions on the TB parameters in order to still maintain the NAND gate function. We map the quantum NAND tree onto a conjugated molecular system, and compare the NAND output with non-equilibrium Green's function (NEGF) transport calculations using density functional theory (DFT) and TB Hamiltonians for the electronic structure. Further, we extend our molecular platform to show other classical gates that can be realized for quantum computing by scattering on graphs.
description: 17 pages, 6 figures, 1 table
Circulating tumour cells and EpCAM as tools for diagnostic and mechanistic studies of lung cancer
Creators: name: Tay, Andee
Publisher: name: Imperial College London
Year: 2015

description: Increasingly, lung cancer treatment depends on the molecular characteristics of the lung tumour and studying the mechanisms of potential lung cancer molecular markers is important in order to identify new, targeted treatment options. The cell surface protein, EpCAM is one potential therapeutic target. Traditionally considered an adhesion protein, recent studies in breast and colon cancer have shown that EpCAM also undergoes proteolytic cleavage. Its c-terminal tail is released, acting as nuclear signalling factor that may contribute to cancer progression. Lung Cancer is the leading cause of global cancer-related mortality, largely due to a tendency for late-stage diagnosis. Screening with CT scans suffers from high false positives and requires additional confirmatory diagnosis, using more invasive techniques. Less-invasive detection methods could potentially improve the ease of screening and detection, increasing the chances for early diagnosis. EpCAM is widely used as a target for isolating circulating tumour cells (CTCs) from the blood of cancer patients. This is problematic as EpCAM-positive CTCs only represent a sub- population of total CTCs. This thesis evaluates the clinical utility of EpCAM- independent CTCs detection for diagnosis, as well as the mechanisms of EpCAM cleavage, in the context of lung cancer. Two different EpCAM-independent CTC isolation systems were assessed. Both isolate CTCs from peripheral blood using a size- and deformability-exclusion strategy. The Clearbridge system comprises a microfluidic chip with permeable traps and the ScreenCell system utilizes a permeable membrane subjected to a vacuum pressure gradient. A combination of primary, matched normal and tumour lung tissue and lung cancer cell lines were used to investigate EpCAM cleavage activity in lung cancer. The ScreenCell system was both easier to use and produced better results than the Clearbridge system. EpCAM cleavage experiments showed that while it does occur in lung cancer, it differed from previously reported EpCAM cleavage behaviour in breast and colon cancer cell lines. The most interesting difference was the discovery of N-terminal cleavage in lung cancer, which has not been described in published literature. While both CTC-isolation systems have the potential to be used as a diagnostic blood test for lung cancer, low sensitivity and specificity values prohibit their use in the clinical setting presently. The discovery of EpCAM cleavage in lung cancer, especially N-terminal cleavage, is particularly relevant in the context of treatment strategies targeting extracellular domains of EpCAM, and EpCAM cleavage mechanisms and their effect on lung cancer progression warrants further exploration.
Combined measurement of differential and total cross sections in the $H \rightarrow γγ$ and the $H \rightarrow ZZ^* \rightarrow 4\ell$ decay channels at $\sqrt{s} = 13$ TeV with the ATLAS detector
Creators: name: ATLAS Collaboration
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: A combined measurement of differential and inclusive total cross sections of Higgs boson production is performed using 36.1 fb$^{-1}$ of 13 TeV proton-proton collision data produced by the LHC and recorded by the ATLAS detector in 2015 and 2016. Cross sections are obtained from measured $H \rightarrow γγ$ and $H \rightarrow ZZ^* \rightarrow 4\ell$ event yields, which are combined taking into account detector efficiencies, resolution, acceptances and branching fractions. The total Higgs boson production cross section is measured to be 57.0$^{+6.0}_{-5.9}$ (stat.) $^{+4.0}_{-3.3}$ (syst.) pb, in agreement with the Standard Model prediction. Differential cross-section measurements are presented for the Higgs boson transverse momentum distribution, Higgs boson rapidity, number of jets produced together with the Higgs boson, and the transverse momentum of the leading jet. The results from the two decay channels are found to be compatible, and their combination agrees with the Standard Model predictions.
description: 33 pages in total, author list starting page 17, 2 figures, 3 tables, submitted to PLB. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HIGG-2017-11
Reconstruction of electric fields and source distributions in EEG brain imaging
Creators: name: Koulouri, Alexandra
Publisher: name: Imperial College London
Year: 2014

description: In this thesis, three different approaches are developed for the estimation of focal brain activity using EEG measurements. The proposed approaches have been tested and found feasible using simulated data. First, we develop a robust solver for the recovery of focal dipole sources. The solver uses a weighted dipole strength penalty term (also called weighted L1,2 norm) as prior information in order to ensure that the sources are sparse and focal, and that both the source orientation and depth bias are reduced. The solver is based on the truncated Newton interior point method combined with a logarithmic barrier method for the approximation of the penalty term. In addition, we use a Bayesian framework to derive the depth weights in the prior that are used to reduce the tendency of the solver to favor superficial sources. In the second approach, vector field tomography (VFT) is used for the estimation of underlying electric fields inside the brain from external EEG measurements. The electric field is reconstructed using a set of line integrals. This is the first time that VFT has been used for the recovery of fields when the dipole source lies inside the domain of reconstruction. The benefit of this approach is that we do not need a mathematical model for the sources. The test cases indicated that the approach can accurately localize the source activity. In the last part of the thesis, we show that, by using the Bayesian approximation error approach (AEA), precise knowledge of the tissue conductivities and head geometry are not always needed. We deliberately use a coarse head model and we take the typical variations in the head geometry and tissue conductivities into account statistically in the inverse model. We demonstrate that the AEA results are comparable to those obtained with an accurate head model.
Sparse multivariate models for pattern detection in high-dimensional biological data
Creators: name: Wang, Zi
Publisher: name: Imperial College London
Year: 2015

description: Recent advances in technology have made it possible and affordable to collect biological data of unprecedented size and complexity. While analysing such data, traditional statistical methods and machine learning algorithms suffer from the curse of dimensionality. Parsimonious models, which may refer to parsimony in model structure and/or model parameters, have been shown to improve both biological interpretability of the model and the generalisability to new data. In this thesis we are concerned with model selection in both supervised and unsupervised learning tasks. For supervised learnings, we propose a new penalty called graphguided group lasso (GGGL) and employ this penalty in penalised linear regressions. GGGL is able to integrate prior structured information with data mining, where variables sharing similar biological functions are collected into groups and the pairwise relatedness between groups are organised into a network. Such prior information will guide the selection of variables that are predictive to a univariate response, so that the model selects variable groups that are close in the network and important variables within the selected groups. We then generalise the idea of incorporating network-structured prior knowledge to association studies consisting of multivariate predictors and multivariate responses and propose the network-driven sparse reduced-rank regression (NsRRR). In NsRRR, pairwise relatedness between predictors and between responses are represented by two networks, and the model identifies associations between a subnetwork of predictors and a subnetwork of responses such that both subnetworks tend to be connected. For unsupervised learning, we are concerned with a multi-view learning task in which we compare the variance of high-dimensional biological features collected from multiple sources which are referred as “views”. We propose the sparse multi-view matrix factorisation (sMVMF) which is parsimonious in both model structure and model parameters. sMVMF can identify latent factors that regulate variability shared across all views and the variability which is characteristic to a specific view, respectively. For each novel method, we also present simulation studies and an application on real biological data to illustrate variable selection and model interpretability perspectives.
The Age Dependent Luminosities of the Red Giant Branch Bump, Asymptotic Giant Branch Bump, and Horizontal Branch Red Clump
Creators: name: Alves, David R.
name: Sarajedini, Ata
Publisher: name: arXiv
Year: 1998
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Color-magnitude diagrams of globular clusters often exhibit a prominent horizontal branch (HB) and may also show features such as the red giant branch (RGB) bump and the asymptotic giant branch (AGB) bump. Stellar evolution theory predicts that the luminosities of these features will depend on the metallicity and age of the cluster. We calculate theoretical lines of 2 to 12 Gyr constant age RGB-bumps and AGB-bumps in the V(HB-Bump)--[Fe/H] diagram, which shows the brightness difference between the bump and the HB as a function of metallicity. In order to test the predictions, we identify giant branch bumps in new Hubble Space Telescope color-magnitude diagrams for 8 SMC clusters. First, we conclude that the SMC cluster bumps are RGB-bumps. The data for clusters younger than ~6 Gyr are in fair agreement the relative age dependent luminosities of the HB and RGB-bump. The V(HB-Bump)--[Fe/H] data for clusters older then ~6 Gyr demonstrate a less satisfactory agreement with our calculations. We conclude that ~6 Gyr is a lower bound to the age of clusters for which the Galactic globular cluster, age independent V(HB-Bump)--[Fe/H] calibration is valid. Application of the V(HB-bump)--[Fe/H] diagram to stellar population studies is discussed.
description: Accepted for publication in the Astrophysical Journal, 30 pages, Latex aaspp4.sty, including 7 postscript figures
Additional file 1: of Is sperm morphology functionally related to sperm swimming ability? A case study in a wild passerine bird with male hierarchies
Creators: name: Mora, Alfonso Rojas
name: Meniri, Magali
name: Ciprietti, Sabrina
name: Helfenstein, Fabrice
Publisher: name: figshare
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Figure S1. Relation between sperm morphological design and male body mass centered by social ranks. Lines represent a linear regression, whereas colors indicate dominant (D) and subordinate- 1 to 3 (S1â 3) males. Figure S2. Relation between the decay in sperm velocity (VCL) through time and sperm total length across social ranks before manipulating the social environment. The surfaces were obtained from predicted values extracted from linear mixed models. Values are centered by social rank. Figure S3. Relation between the decay in sperm velocity (VCL) through time and sperm total length across social ranks after manipulating the social environment. The surfaces were obtained from predicted values extracted from linear mixed models. Values are centered by social rank. (DOCX 2323 kb)
Backreaction of fermionic perturbations in the Hamiltonian of hybrid loop quantum cosmology
Creators: name: Navascués, Beatriz Elizaga
name: Marugán, Guillermo A. Mena
name: Loy, Santiago Prado
Publisher: name: arXiv
Year: 2018
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We discuss the freedom available in hybrid loop quantum cosmology to define canonical variables for the matter content and investigate whether this can be used to derive a quantum field theory with good properties for the matter sector. We study a primordial, inflationary, cosmological spacetime with inhomogeneous perturbations at lowest nontrivial order, and focus our attention on the contribution of minimally coupled fermionic perturbations of Dirac type. Within the framework of the hybrid quantization, we analyze the different possible separations of the homogeneous background and the inhomogeneous perturbations, by means of canonical transformations that mix the two separated sectors. These possibilities provide a family of sets of annihilation and creationlike fermionic variables, each of them with a different associated contribution to the total Hamiltonian. In all cases, imposing the quantum constraints and introducing a Born-Oppenheimer approximation, one can derive a Schrödinger equation for the fermionic part of the wave functions. The resulting evolution turns out to be generated, for each of the allowed choices of variables, by a version of the fermionic contribution to the Hamiltonian which is obtained by evaluating all the dependence on the homogeneous geometry at quantum expectation values. This equation contains a term that encodes the backreaction of the fermionic perturbations on the quantum dynamics of the homogeneous sector. We analyze this backreaction by solving the associated Heisenberg evolution of the fermionic annihilation and creation operators. Then, we identify the conditions that the choice of those operators must satisfy in order to lead to a finite backreaction. Finally, we discuss further restrictions on this choice so that the fermionic Hamiltonian that dictates the Schrödinger dynamics is densely defined in Fock space.
description: 20 pages, matches published version