cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Ramucirumab in combination with dacarbazine in patients with progressive well-differentiated metastatic pancreatic neuroendocrine tumors (RamuNET) : study protocol for a multicenter single-arm trial
Creators: name: Krug, Sebastian
name: Kegel, Thomas
name: Gress, Thomas Mathias
name: Rinke, Anja
name: Apostolidis, Leonidas
name: Jann, Henning
name: König, Alexander
name: Hörsch, Dieter
name: Schrader, Jörg
name: Ettrich, Thomas J.
name: Richter, Michael
name: Steighardt, Jörg
name: Michl, Patrick
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2021
Subjects: subject: 610

description: Background: Cytotoxic chemotherapy combinations and targeted agents represent established treatment concepts in advanced pancreatic neuroendocrine tumors (PNETs). However, response rates, side effects and outcome data strongly vary among these therapeutic approaches. Head-to-head comparisons between chemo- and molecular therapies are missing and secondary resistances frequently occur. The RamuNET trial aims to identify the effectiveness of dual treatment with DTIC and ramucirumab in progressive advanced PNET patients. Methods: The RamuNET study is an investigator-initiated multicenter prospective single-arm trial to evaluate the efficacy of ramucirumab in combination with dacarbazine (DTIC) over a period of at least 6 months. Patients with progressive well-differentiated and metastatic pancreatic neuroendocrine tumors are eligible. The study aims to include 45 patients over a period of 24 months with a minimum follow-up of 24 months. The primary endpoint is disease control after 6 months. Secondary endpoints include progression-free survival, biochemical response, overall survival, quality of life and toxicity. Based on the hypothesis that 80% of the patients can achieve a disease control after 6 months, the sample size calculation follows an exact binomial single-stage design. H0: p =p1 = 80%, alpha = 0.05, beta = 0.1. Discussion: This study investigates a new therapeutic approach using the combination of cytotoxic and targeted antiangiogenic therapy in advanced PNET. If positive, this trial will be the basis for a randomized two-arm study to investigate the combination of ramucirumab and DTIC against other established therapies in PNET.
Motion of Wavefronts in Semiconductor Superlattices
Creators: name: Carpio, A.
name: Bonilla, L. L.
name: Dell'Acqua, G.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: An analysis of wavefront motion in weakly coupled doped semiconductor superlattices is presented. If a dimensionless doping is sufficiently large, the superlattice behaves as a discrete system presenting front propagation failure and the wavefronts can be described near the threshold currents $J_i$ ($i=1,2$) at which they depin and move. The wavefront velocity scales with current as $|J-J_i|^{1\over 2}$. If the dimensionless doping is low enough, the superlattice behaves as a continuum system and wavefronts are essentially shock waves whose velocity obeys an equal area rule.
description: 10 pages, 9 figures
Interplay between disorder and intersubband collective excitations in the two-dimensional electron gas
Creators: name: Luin, Stefano
name: Pellegrini, Vittorio
name: Beltram, Fabio
name: Marcadet, Xavier
name: Sirtori, Carlo
Publisher: name: arXiv
Year: 2001
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: Intersubband absorption in modulation-doped quantum wells is usually appropriately described as a collective excitation of the confined two-dimensional electron gas. At sufficiently low electron density and low temperatures, however, the in-plane disorder potential is able to damp the collective modes by mixing the intersubband charge-density excitation with single-particle localized modes. Here we show experimental evidence of this transition. The results are analyzed within the framework of the density functional theory and highlight the impact of the interplay between disorder and the collective response of the two-dimensional electron gas in semiconductor heterostructures.
description: 5 pages, 4 figures, RevTeX. Accepted for publication in Phys. Rev. B (Rapid. Comm.)
Additional file 1 of Broadening the phenotype and genotype spectrum of novel mutations in pontocerebellar hypoplasia with a comprehensive molecular literature review
Creators: name: Ghasemi, Mohammad-Reza
name: Tehrani Fateh, Sahand
name: Moeinafshar, Aysan
name: Sadeghi, Hossein
name: Karimzadeh, Parvaneh
name: Mirfakhraie, Reza
name: Rezaei, Mitra
name: Hashemi-Gorji, Farzad
name: Rezvani Kashani, Morteza
name: Fazeli Bavandpour, Fatemehsadat
name: Bagheri, Saman
name: Moghimi, Parinaz
name: Rostami, Masoumeh
name: Madannejad, Rasoul
name: Roudgari, Hassan
name: Miryounesi, Mohammad
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Figure 1. Flowchart of included cases in this study. Supplementary Figure 2. Variant filtering and pathogenicity evaluation algorithm. Supplementary Figure 3. Pedigree of included cases in this study. Pedigree a-k are cases 1-12, respectively. The proband is shown by an arrow in each pedigree. Circle and squares represent female and male, respectively. People with same color in each pedigree have same clinical manifestations. Supplementary Figure 4. The structure of protein [1] included in this study and the position of mutated amino acid. a) Structure of human nuclear RNA exosome (PDB: 6H25) [2]. EXOS3 is shown by an arrow and the position of Asp132 which is substituted with Ala in case 1 and 2 b) Structure human tRNA Splicing Endonuclease (TSEN) Complex (PDB: 7UXA) [3]. TSEN2 and TSEN54 are shown by arrows c) Structure of human holo SepSecS (PDB: 7L1T) [4] and the position of Cys70 and His425 which are substituted with Arg in case 4 and 5 d) Structure of AMP deaminase 2 (PDB: 8HUB)[5] and the position of Arg 620 which is substituted with Ser in case 8 e) Structure of CLP1(Swiss model: Q92989) [6] and the position of Leu262 which is substituted with Val in case 9 and Arg140 which is substituted with His in case 10 and 11 f) Structure of TBC1D23 N terminal domain (PDB: 6JL7) [7] and the position of Met 153 which is substituted with Thr in case 12.
Avalanche induced co-existing localised and thermal regions in disordered chains
Creators: name: Crowley, Philip J. D.
name: Chandran, Anushya
Publisher: name: arXiv
Year: 2019
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We investigate the stability of an Anderson localized chain to the inclusion of a single finite interacting thermal seed. This system models the effects of rare low-disorder regions on many-body localized chains. Above a threshold value of the mean localization length, the seed causes runaway thermalization in which a finite fraction of the orbitals are absorbed into a thermal bubble. This `partially avalanched' regime provides a simple example of a delocalized, non-ergodic dynamical phase. We derive the hierarchy of length scales necessary for typical samples to exhibit the avalanche instability, and show that the required seed size diverges at the avalanche threshold. We introduce a new dimensionless statistic that measures the effective size of the thermal bubble, and use it to numerically confirm the predictions of avalanche theory in the Anderson chain at infinite temperature.
description: 26 pages, 18 figures
Phonon-number-resolving Detection of Multiple Local Phonon Modes in Trapped Ions
Creators: name: Ohira, Ryutaro
name: Mukaiyama, Takashi
name: Toyoda, Kenji
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We propose and demonstrate phonon-number-resolving detection of the multiple local phonon modes in a trapped-ion chain. To mitigate the effect of phonon hopping during the detection process, the probability amplitude of each local phonon mode is mapped to the auxiliary long-lived motional ground states. Sequential state-dependent fluorescence detection is then performed. In the experiment, we have successfully observed the time evolution of two local phonon modes in two ions, including the phonon-number correlation between the two modes.
description: 5 pages, 3 figures
Why has Safety Improved at Rail-Highway Grade Crossings?
Creators: name: Mok, Shannon
name: Savage, Ian
name: Mok, Shannon
name: Savage, Ian
Publisher: name: Unknown
Year: 2004
Subjects: Research and Development/Tech Change/Emerging Technologies
Research Methods/ Statistical Methods

description: The number of collisions and fatalities at rail-highway intersections has declined significantly over the past thirty years, despite considerable increases in the volume of both rail and highway traffic. This paper disaggregates the improvement into its constituent causes. Negative binomial regressions are conducted on a pooled data set for 49 states from 1975 to 2001. The analysis concludes that about two-fifths of the decrease is due to factors such as reduced drunk driving and improved emergency medical response that have improved safety on all parts of the highway network. The installation of gates and/or flashing lights accounts for about a fifth of the reduction. The development of the “Operation Lifesaver” campaign, that seeks to inform the public on appropriate conduct at crossings, in the 1970s and early 1980s; and the installation of “ditch lights” on locomotives in the mid 1990s, each led to about a seventh of the reduction. Finally, about a tenth is due to closure of crossings resulting from line abandonments or consolidation of little-used crossings.
Revisiting the Fertility Transition in England and Wales: The Role of Social Class and Migration
Creators: name: Jaadla, Hannaliis
name: Reid, Alice
name: Garrett, Eilidh
name: Schürer, Kevin
name: Day, Joseph
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Article
Fertility transition
Nineteenth century
Census microdata
Migration
England and Wales

description: Funder: University of Cambridge
description: Abstract: We use individual-level census data for England and Wales for the period 1851–1911 to investigate the interplay between social class and geographical context determining patterns of childbearing during the fertility transition. We also consider the effect of spatial mobility or lifetime migration on individual fertility behavior in the early phases of demographic modernization. Prior research on the fertility transition in England and Wales has demonstrated substantial variation in fertility levels and declines by different social groups; however, these findings were generally reported at a broad geographical level, disguising local variation and complicated by residential segregation along social class and occupational lines. Our findings confirm a clear pattern of widening social class differences in recent net fertility, providing strong support for the argument that belonging to a certain social group was an important determinant of early adoption of new reproductive behavior in marriage in England and Wales. However, a relatively constant effect of lower net fertility among long-distance migrants both before the transition and in the early phases of declining fertility indicates that life course migration patterns were most likely factor in explaining the differences in fertility operating through postponement of marriage and childbearing.
MOESM1 of Low seroprevalence of Zika virus infection among adults in Southern Taiwan
Creators: name: Chien, Yu-Wen
name: Tzu-Chuan Ho
name: Huang, Pei-Wen
name: Nai-Ying Ko
name: Wen-Chien Ko
name: Guey Perng
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Ecology
subject: FOS: Biological sciences
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1.Â Questions used in the original survey.
Wavefront depinning transition in discrete one-dimensional reaction-diffusion systems
Creators: name: Carpio, A.
name: Bonilla, L. L.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Pinning and depinning of wavefronts are ubiquitous features of spatially discrete systems describing a host of phenomena in physics, biology, etc. A large class of discrete systems is described by overdamped chains of nonlinear oscillators with nearest-neighbor coupling and controlled by constant external forces. A theory of the depinning transition for these systems, including scaling laws and asymptotics of wavefronts, is presented and confirmed by numerical calculations.
description: 4 pages, 4 figures
Lithium niobate waveguides with high-index contrast and preserved nonlinearity fabricated by High Vacuum Vapor-phase Proton Exchange
Creators: name: Rambu, Alicia Petronela
name: Apetrei, Alin Marian
name: Doutre, Florent
name: Tronche, Herve
name: Tiron, Vasile
name: De Micheli, Marc
name: Tascu, Sorin
Publisher: name: arXiv
Year: 2019
Subjects: subject: Applied Physics (physics.app-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Highly confining waveguides without degraded nonlinear coefficient and low propagation losses have been fabricated in lithium niobate by a new process that we called High Vacuum Vapor-phase Proton Exchange (HiVac-VPE). Index contrast, index profile, nonlinearity and crystallographic phases are carefully investigated. Original analysis of index profiles indicates that the waveguides contains sub-layers whose depths are depending on the exchange durations. Propagation behavior, propagation losses and Second Harmonic Generation (SHG) response of HiVac-VPE channel waveguides are investigated at telecom wavelength. The results recommend HiVac-VPE as very promising technique for fabricating efficient nonlinear photonic integrated circuits in LN crystals.
On pressure boundary conditions for thermoconvective problems
Creators: name: Herrero, H.
name: Mancho, A. M.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 76M22(Primary) 76R05(Secondary)

description: Solving numerically hydrodynamical problems of incompressible fluids raises the question of handling first order derivatives (those of pressure) in a closed container and determining its boundary conditions. We research several pressure boundary conditions for the primitive variables formulation of thermoconvective problems. In particular we study the Marangoni instability of an infinite fluid layer and we show that the numerical results with a Chebyshev collocation method are highly correspondent to the exact ones. These ideas have been applied to linear stability analysis of the Bénard-Marangoni (BM) problem in cylindrical geometry and the results obtained have been very accurate.
description: 16 pages, Latex, 1 figure. Some typos corrected. To appear in Int. J. for Numerical Methods in Fluids
Mortoniella catarinensis
Creators: name: Blahnik, Roger J.
name: Holzenthal, Ralph W.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Mortoniella
Mortoniella catarinensis

description: Mortoniella catarinensis (Flint, 1974)
Fig. 24
 Mexitrichia catarinensis Flint, 1974: 12.
 Mortoniella catarinensis (Flint); Blahnik & Holzenthal 2008: 70 [M. ormina species group].
This species can be diagnosed be the wide lateral expansions of its dorsal phallic spine and by its paramere appendages, which apparently consist of 3 pairs of spine-like structures.
Adult. Length of forewing: male 2.0 mm. Venation difficult to discern; forewing (probably) with forks I, II, and III present, hind wing with fork II only. Spur formula 0:3:4. Specimen in alcohol and totally cleared, color not evident.
Male genitalia: Ventral process of segment VI posteriorly projecting, elongate, narrow, length more than 2 times width at base; apex dorsoventrally compressed, acute as viewed laterally (Fig. 24E), rounded as viewed ventrally. Segment IX rounded anterolaterally, length greatest in ventral 1/2, posterolateral margin nearly linear; segment deeply excised dorsomesally and ventromesally, forming lateral lobes, lobes separated dorsomesally by about 1/2 width of segment. Tergum X elongate, simple in structure, with V-shaped mesal excision extending about 1/2 length of segment; apical lobes acute. Inferior appendages inconspicuous, subtriangular as viewed laterally, each with acute apicoventral projection and short dorsal lobe; posteromesal margin convex. Mesal pockets of fused inferior appendages with apical processes elongate, narrow, sinuous, posteriorly directed, extending beyond inferior appendages. Paramere appendages (apparently) composed of 3 pairs of elongate, acute processes (lateral 2 possibly from base of phallicata). Dorsal phallic spine of distinctive structure, laterally with wing-like, depressed, lateral projections, basal margin of each wing rounded, apical margins acute; apical 1/3rd of dorsal phallic spine sharply upturned, apex acute. Phallicata lightly sclerotized, without obvious spines. Endophallic membrane bulbous, with lightly sclerotized, paired apicodorsal projections (probably phallotremal spines).
 Material examined. BRAZIL: Santa Catarina: i.1963, F Plaumann — 1 male (holotype, in alcohol, USNM type 72739) (NMNH).
Distribution. Brazil
description: Published as part of Blahnik, Roger J. & Holzenthal, Ralph W., 2011, Revision of the austral South American species of Mortoniella (Trichoptera: Glossosomatidae: Protoptilinae) 2851, pp. 1-75 in Zootaxa 2851 (1) on page 49, DOI: 10.11646/zootaxa.2851.1.1, http://zenodo.org/record/5286934
A deep learning approach for staging embryonic tissue isolates with small data
Creators: name: Pond, Adam Joseph Ronald
name: Hwang, Seongwon
name: Verd, Berta
name: Steventon, Benjamin
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: subject: Research Article
subject: Research and analysis methods
subject: Biology and life sciences
subject: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Physical sciences
subject: FOS: Physical sciences

description: Machine learning approaches are becoming increasingly widespread and are now present in most areas of research. Their recent surge can be explained in part due to our ability to generate and store enormous amounts of data with which to train these models. The requirement for large training sets is also responsible for limiting further potential applications of machine learning, particularly in fields where data tend to be scarce such as developmental biology. However, recent research seems to indicate that machine learning and Big Data can sometimes be decoupled to train models with modest amounts of data. In this work we set out to train a CNN-based classifier to stage zebrafish tail buds at four different stages of development using small information-rich data sets. Our results show that two and three dimensional convolutional neural networks can be trained to stage developing zebrafish tail buds based on both morphological and gene expression confocal microscopy images, achieving in each case up to 100% test accuracy scores. Importantly, we show that high accuracy can be achieved with data set sizes of under 100 images, much smaller than the typical training set size for a convolutional neural net. Furthermore, our classifier shows that it is possible to stage isolated embryonic structures without the need to refer to classic developmental landmarks in the whole embryo, which will be particularly useful to stage 3D culture in vitro systems such as organoids. We hope that this work will provide a proof of principle that will help dispel the myth that large data set sizes are always required to train CNNs, and encourage researchers in fields where data are scarce to also apply ML approaches.
Birth and stabilization of phase clusters by multiplexing of adaptive networks
Creators: name: Berner, Rico
name: Sawicki, Jakub
name: Schöll, Eckehard
Publisher: name: arXiv
Year: 2019
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: We propose a concept to generate and stabilize diverse partial synchronization patterns (phase clusters) in adaptive networks which are widespread in neuro- and social sciences, as well as biology, engineering, and other disciplines. We show by theoretical analysis and computer simulations that multiplexing in a multi-layer network with symmetry can induce various stable phase cluster states in a situation where they are not stable or do not even exist in the single layer. Further, we develop a method for the analysis of Laplacian matrices of multiplex networks which allows for insight into the spectral structure of these networks enabling a reduction to the stability problem of single layers. We employ the multiplex decomposition to provide analytic results for the stability of the multilayer patterns. As local dynamics we use the paradigmatic Kuramoto phase oscillator, which is a simple generic model and has been successfully applied in the modeling of synchronization phenomena in a wide range of natural and technological systems.
Additional file 1 of Recommendations for optimal interdisciplinary management and healthcare settings for patients with rare neurological diseases
Creators: name: Graessner, Holm
name: Reinhard, Carola
name: Bäumer, Tobias
name: Baumgärtner, Annette
name: Brockmann, Knut
name: Brüggemann, Norbert
name: Bültmann, Eva
name: Erdmann, Jeanette
name: Heise, Kirstin
name: Höglinger, Günter
name: Hüning, Irina
name: Kaiser, Frank J.
name: Klein, Christine
name: Klopstock, Thomas
name: Krägeloh-Mann, Ingeborg
name: Kraemer, Markus
name: Luedtke, Kerstin
name: Mücke, Martin
name: Musacchio, Thomas
name: Nadke, Andreas
name: Osmanovic, Alma
name: Ritter, Gabriele
name: Röse, Katharina
name: Schippers, Christopher
name: Schöls, Ludger
name: Schüle, Rebecca
name: Schulz, Jörg B.
name: Sproß, Joachim
name: Stasch, Eveline
name: Wunderlich, Gilbert
name: Münchau, Alexander
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Full formulation of recommendations for optimal interdisciplinary management and healthcare settings for patients with rare neurological diseases.
Mortoniella ormina
Creators: name: Blahnik, Roger J.
name: Holzenthal, Ralph W.
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Magnoliopsida
Gentianales
Apocynaceae
Mortoniella
Mortoniella ormina

description: Mortoniella ormina (Mosely, 1939)
Fig. 26
 Mexitrichia ormina Mosely, 1939: 222.
 Mortoniella ormina (Mosely); Blahnik & Holzenthal 2008; 70 [M. ormina species group].
 This species most closely resembles M. alicula, n. sp., particularly in the structure of its dorsal phallic spine, which has it apex distinctively narrowed, upturned and posteriorly curved. However, among other differences, in M. ormina, the phallic spine is not nearly so widely explanate preapically and the paramere appendages are much shorter.
Adult. Length of forewing: male 1.8-2.0 mm, female 2.1-2.5. Forewing with forks I, II, and III present, hind wing with fork II only. Spur formula 0:3:4. Overall color (in alcohol) pale yellowish-brown, appendages pale, without pigmentation. Wing bar at anastamosis evident in some specimens.
Male genitalia: Ventral process of segment VI posteriorly projecting, elongate, narrow, length more than 2 times width at base, apex acute (Fig. 26D). Segment IX rounded anterolaterally, length greatest in ventral 1/2, posterolateral margin weakly, convexly rounded in dorsal 1/2, narrowing ventrally; segment deeply excised dorsomesally and ventromesally, forming lateral lobes, lobes separated dorsomesally by 1/2 or more width of segment. Tergum X moderately elongate, simple in structure, with very deep, narrow, V-shaped mesal excision; apical lobes rounded, as viewed both laterally and dorsally. Inferior appendages very small, inconspicuous, with acute posterior projection. Mesal pockets of fused inferior appendages with apical processes short, posterodorsally curved, extending beyond inferior appendages. Paramere appendages moderate in length, extending about as far as dorsal phallic spine, uniformly narrow in width, acute apically. Dorsal phallic spine of distinctive structure, somewhat widened at middle, strongly dorsally curved in apical 1/4th, apex abruptly narrowed and posteriorly recurved. Phallicata bulbous, lightly sclerotized, dorsally with mesal, posteriorly-directed, spine-like process. Endophallic membrane short, simple in structure, with lightly sclerotized, rounded to subquadrate lateral processes; ventral spine and phallotremal spines absent.
 Material examined. BRAZIL: Santa Catarina: Nova Teutonia, 27°03'S, 052°24'W, i.1964, F Plaumann — 12 males, 35 females (alcohol) (NMNH, UMSP).
Distribution. Brazil.
description: Published as part of Blahnik, Roger J. & Holzenthal, Ralph W., 2011, Revision of the austral South American species of Mortoniella (Trichoptera: Glossosomatidae: Protoptilinae) 2851, pp. 1-75 in Zootaxa 2851 (1) on page 53, DOI: 10.11646/zootaxa.2851.1.1, http://zenodo.org/record/5286934
Domain formation in noninstantaneous symmetry breaking phase transitions
Creators: name: Alfinito, E.
name: Vitiello, G.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Condensed Matter (cond-mat)
subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In the framework of the Ginzburg-Landau harmonic potential approximation, we present a possible modeling of the time-dependence of the frequency of the order parameter mode suitable to account for the formation of correlated domains in non-instantaneous symmetry breaking phase transitions. An interesting spectrum of possibilities for the size and the life-time of these domains emerges, which appears to be consistent with the conclusions of other, differently grounded analysis.
description: Revised version, accepted for publications on PRB
Implementation of annihilation and junction reactions in vector density-based continuum dislocation dynamics
Creators: name: Lin, Peng
name: El-Azab, Anter
Publisher: name: arXiv
Year: 2019
Subjects: subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: In a continuum dislocation dynamics formulation by Xia and El-Azab, dislocations are represented by a set of vector density fields, one per crystallographic slip systems. The space-time evolution of these densities is obtained by solving a set of dislocation transport equations coupled with crystal mechanics. Here, we present an approach for incorporating dislocation annihilation and junction reactions into the dislocation transport equations. These reactions consume dislocations and result in nothing as in the annihilation reactions, or produce new dislocations of different types as in the case of junction reactions. Collinear annihilation, glissile junctions, and sessile junctions are particularly emphasized here. A generalized energy-based criterion for junction reactions is established in terms of the dislocation density and Burgers vectors of the reacting species, and the reaction rate terms for junction reactions are formulated in terms of the dislocation densities. In order to illustrate how the dislocation network changes as a result of junction formation and annihilation in a continuum dislocation dynamics setting, we present some numerical examples focusing on the reactions processes themselves. The results show that our modeling approach is able to capture the respective dislocation network changes associated with dislocation reactions in FCC crystals: dislocations of opposite line directions encountering each other on collinear slip systems annihilate to connect the dislocations on the two slip systems, glissile junctions form on new slip system behave like Frank-Read sources, and sessile junctions form and expand along the intersection of the slip planes of the reacting dislocation species. A collective-dynamics test showing the frequency of occurrence of junctions of different types relative to each other is also presented.
A Bayesian analysis of the association between Leukotriene A4 Hydrolase genotype and survival in tuberculous meningitis
Creators: name: Whitworth, Laura
name: Coxon, Jacob
name: Van Laarhoven, Arjan
name: Thuong, Nguyen Thuy Thuong
name: Dian, Sofiati
name: Alisjahbana, Bachti
name: Ganiem, Ahmad Rizal
name: Van Crevel, Reinout
name: Thwaites, Guy E
name: Troll, Mark
name: Edelstein, Paul H
name: Sewell, Roger
name: Ramakrishnan, Lalita
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Research Article
Genetics and Genomics
Microbiology and Infectious Disease
TB meningitis
leukotriene A4 hydrolase
pharmacogenomics
dexamethasone
Bayesian inference
Human

description: Tuberculous meningitis has high mortality, linked to excessive inflammation. However, adjunctive anti-inflammatory corticosteroids reduce mortality by only 30%, suggesting that inflammatory pathophysiology causes only a subset of deaths. In Vietnam, the survival benefit of anti-inflammatory corticosteroids was most pronounced in patients with a C/T promoter variant in the leukotriene A4 hydrolase (LTA4H) gene encoding an enzyme that regulates inflammatory eicosanoids. LTA4H TT patients with increased expression had increased survival, consistent with corticosteroids benefiting individuals with hyper-inflammatory responses. However, an Indonesia study did not find an LTA4H TT genotype survival benefit. Here using Bayesian methods to analyse both studies, we find that LTA4H TT genotype confers survival benefit that begins early and continues long-term in both populations. This benefit is nullified in the most severe cases with high early mortality. LTA4H genotyping together with disease severity assessment may target glucocorticoid therapy to patients most likely to benefit from it.
Teenagers, screens and social media: a narrative review of reviews and key studies
Creators: name: Orben, Amy
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Invited Reviews
Digital technology use
Social media
Screen time
Well-being
Adolescents
Review

description: Abstract: Introduction: In light of growing concerns about an increasingly digital adolescence, the academic field investigating how digital technologies affect adolescents’ psychological well-being is growing rapidly. In the last years, much research has amassed, and this has been summarised in over 80 systematic reviews and meta-analyses. Materials and Methods: Systematic reviews, meta-analyses and key studies are reviewed to provide insights into the state of current research linking digital technology and social media use to well-being; possible future directions and improvements are discussed. Results: When examining the reviews, it becomes evident that the research field is dominated by cross-sectional work that is generally of a low quality standard. While research has highlighted the importance of differentiating between different types of digital technology use many studies do not consider such necessary nuances. These limitations aside, the association between digital technology use, or social media use in particular, and psychological well-being is—on average—negative but very small. Furthermore, the direction of the link between digital technology use and well-being is still unclear: effects have been found to exist in both directions and there has been little work done to rule out potential confounders. Conclusions: Reviewing the last decade of reviews in the area, it is evident that the research field needs to refocus on improving transparency, interpreting effect sizes and changing measurement. It also needs to show a greater appreciation for the individual differences that will inherently shape each adolescent’s reaction to digital technologies.
Multiple plasmon resonances in naturally-occurring multiwall nanotubes: infrared spectra of chrysotile asbestos
Creators: name: Balan, Etienne
name: Mauri, Francesco
name: Lemaire, Celine
name: Brouder, Christian
name: Guyot, Francois
name: Saitta, A. Marco
name: Devouard, Bertrand
Publisher: name: arXiv
Year: 2002
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Chrysotile asbestos is formed by densely packed bundles of multiwall hollow nanotubes. Each wall in the nanotubes is a cylindrically wrapped layer of $Mg_3 Si_2 O_5 (OH)_4$. We show by experiment and theory that the infrared spectrum of chrysotile presents multiple plasmon resonances in the Si-O stretching bands. These collective charge excitations are universal features of the nanotubes that are obtained by cylindrically wrapping an anisotropic material. The multiple plasmons can be observed if the width of the resonances is sufficiently small as in chrysotile.
description: 4 pages, 5 figures. Revtex4 compuscript. Misprint in Eq.(6) corrected
Metastability in a continuous mean-field model at low temperature and strong interaction
Creators: name: Bashiri, Kaveh
name: Menz, Georg
Publisher: name: arXiv
Year: 2019
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: We consider a system of $ N \in \mathbb{N} $ mean-field interacting stochastic differential equations that are driven by a single-site potential of double-well form and by Brownian noise. The strength of the noise is measured by a small parameter $ \varepsilon >0$ (which we interpret as the \emph{temperature}), and we suppose that the strength of the interaction is given by $ J>0 $. Choosing the \emph{empirical mean} ($ P:\mathbb{R}^N \rightarrow \mathbb{R} $, $ Px =1/N \sum_i x_i $) as the macroscopic order parameter for the system, we show that the resulting macroscopic Hamiltonian has two global minima, one at $ -m^\star_\varepsilon <0 $ and one at $ m^\star_\varepsilon>0 $. Following this observation, we are interested in the average transition time of the system to $ P^{-1}(m^\star_\varepsilon) $, when the initial configuration is drawn according to a probability measure (the so-called \emph{last-exit distribution}), which is supported around the hyperplane $ P^{-1}(-m^\star_\varepsilon) $. Under the assumption of strong interaction, $ J>1 $, the main result is a formula for this transition time, which is reminiscent of the celebrated Eyring-Kramers formula up to a multiplicative error term that tends to $ 1 $ as $ N \rightarrow \infty $ and $ \varepsilon \rightarrow 0 $. The proof is based on the \emph{potential-theoretic approach to metastability.} In the last chapter we add some estimates on the metastable transition time in the high temperature regime, where $ \varepsilon =1 $, and for a large class of single-site potentials.
description: Published version
Effects of disorder on the wave front depinning transition in spatially discrete systems
Creators: name: Carpio, A.
name: Bonilla, L. L.
name: Luzon, A.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Pinning and depinning of wave fronts are ubiquitous features of spatially discrete systems describing a host of phenomena in physics, biology, etc. A large class of discrete systems is described by overdamped chains of nonlinear oscillators with nearest-neighbor coupling and subject to random external forces. The presence of weak randomness shrinks the pinning interval and it changes the critical exponent of the wave front depinning transition from 1/2 to 3/2. This effect is derived by means of a recent asymptotic theory of the depinning transition, extended to discrete drift-diffusion models of transport in semiconductor superlattices and confirmed by numerical calculations.
description: 4 pages, 3 figures, to appear as a Rapid Commun. in Phys. Rev. E
Ice Rule and Emergent Frustration in Particle Ice and Beyond
Creators: name: Ortiz-Ambriz, Antonio
name: Nisoli, Cristiano
name: Reichhardt, Charles
name: Reichhardt, Cynthia J. O.
name: Tierno, Pietro
Publisher: name: arXiv
Year: 2019
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: Geometric frustration and the ice rule are two concepts that are intimately connected and widespread across condensed matter. The first refers to the inability of a system to satisfy competing interactions in the presence of spatial constraints. The second, in its more general sense, represents a prescription for the minimization of the topological charges in a constrained system. Both can lead to manifolds of high susceptibility and non-trivial, constrained disorder where exotic behaviors can appear and even be designed deliberately. In this Colloquium, we describe the emergence of geometric frustration and the ice rule in soft condensed matter. This Review excludes the extensive developments of mathematical physics within the field of geometric frustration, but rather focuses on systems of confined micro- or mesoscopic particles that emerge as a novel paradigm exhibiting spin degrees of freedom. In such systems, geometric frustration can be engineered artificially by controlling the spatial topology and geometry of the lattice, the position of the individual particle units, or their relative filling fraction. These capabilities enable the creation of novel and exotic phases of matter, and also potentially lead towards technological applications related to memory and logic devices that are based on the motion of topological defects. We review the rapid progress in theory and experiments and discuss the intimate physical connections with other frustrated systems at different length scales.
MOESM2 of Genetic counselling and personalised risk assessment in the Australian pancreatic cancer screening program
Creators: name: Dwarte, Tanya
name: McKay, Skye
name: Johns, Amber
name: Tucker, Katherine
name: Spigelman, Allan
name: Williams, David
name: Stoita, Alina
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: Additional file 2. Genetic counselling guidelines. (DOCX 31 kb)
Ion detector for Accelerator Mass Spectrometry based on low-pressure TPC with THGEM readout
Creators: name: Bondar, A.
name: Buzulutskov, A.
name: Frolov, E.
name: Parkhomchuk, V.
name: Petrozhitskiy, A.
name: Shakirova, T.
name: Sokolov, A.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: A new technique for ion identification in Accelerator Mass Spectrometry (AMS) has been proposed by measuring the ion track ranges using a low-pressure TPC. As a proof of principle, a low-pressure TPC with charge readout using a THGEM multiplier was developed. The tracks of alpha particles from various radioactive sources were successfully recorded in the TPC. The track ranges were measured with a high accuracy, reaching the 2% resolution level. Using these results and the SRIM code simulation, it is shown that the isobaric boron and beryllium ions can be effectively separated at ten sigma level. It is expected that this technique will be applied in the AMS facility in Novosibirsk for dating geological objects, in particular for the geochronology of Cenozoic Era.
description: 8 pages, 13 figures, 2 tables. Short paper version will be published in Nucl. Instr. Meth. A
Full genomic characterization of a porcine rotavirus strain detected in an asymptomatic piglet in Accra, Ghana
Creators: name: Stubbs, Samuel C. B.
name: Quaye, Osbourne
name: Acquah, Maame Ekua
name: Adadey, Samuel Mawuli
name: Kean, Iain R. L.
name: Gupta, Srishti
name: Blacklaws, Barbara A.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Research Article
Virology
Rotavirus A
Full genome sequence constellation
Pig
Porcine
Ghana

description: Abstract: Background: The introduction of rotavirus A vaccination across the developing world has not proved to be as efficacious as first hoped. One cause of vaccine failure may be infection by zoonotic rotaviruses that are very variable antigenically from the vaccine strain. However, there is a lack of genomic information about the circulating rotavirus A strains in farm animals in the developing world that may be a source of infection for humans. We therefore screened farms close to Accra, Ghana for animals sub-clinically infected with rotavirus A and then sequenced the virus found in one of these samples. Results: 6.1% of clinically normal cows and pigs tested were found to be Rotavirus A virus antigen positive in the faeces. A subset of these (33.3%) were also positive for virus RNA. The most consistently positive pig sample was taken forward for metagenomic sequencing. This gave full sequence for all open reading frames except segment 5 (NSP1), which is missing a single base at the 5′ end. The virus infecting this pig had genome constellation G5-P[7]-I5-R1-C1-M1-A8-N1-T7-E1-H1, a known porcine genotype constellation. Conclusions: Farm animals carry rotavirus A infection sub-clinically at low frequency. Although the rotavirus A genotype discovered here has a pig-like genome constellation, a number of the segments most closely resembled those isolated from humans in suspected cases of zoonotic transmission. Therefore, such viruses may be a source of variable gene segments for re-assortment with other viruses to cause vaccine breakdown. It is recommended that further human and pig strains are characterized in West Africa, to better understand this dynamic.
MOESM1 of Genetic counselling and personalised risk assessment in the Australian pancreatic cancer screening program
Creators: name: Dwarte, Tanya
name: McKay, Skye
name: Johns, Amber
name: Tucker, Katherine
name: Spigelman, Allan
name: Williams, David
name: Stoita, Alina
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: Additional file 1. Inclusion and exclusion criteria. (DOCX 17 kb)
Learning Lenient Parsing & Typing via Indirect Supervision
Creators: name: Ahmed, Toufique
name: Devanbu, Premkumar
name: Hellendoorn, Vincent
Publisher: name: arXiv
Year: 2019
Subjects: subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences

description: Both professional coders and teachers frequently deal with imperfect (fragmentary, incomplete, ill-formed) code. Such fragments are common in STACKOVERFLOW; students also frequently produce ill-formed code, for which instructors, TAs (or students themselves) must find repairs. In either case, the developer experience could be greatly improved if such code could somehow be parsed & typed; this makes such code more amenable to use within IDEs and allows early detection and repair of potential errors. We introduce a lenient parser, which can parse & type fragments, even ones with simple errors. Training a machine learner to leniently parse and type imperfect code requires a large training set including many pairs of imperfect code and its repair; such training sets are limited by human effort and curation. In this paper, we present a novel, indirectly supervised, approach to train a lenient parser, without access to such human-curated training data. We leverage the huge corpus of mostly correct code available on Github, and the massive, efficient learning capacity of Transformer-based NN architectures. Using GitHub data, we first create a large dataset of fragments of code and corresponding tree fragments and type annotations; we then randomly corrupt the input fragments by seeding errors that mimic corruptions found in STACKOVERFLOW and student data. Using this data, we train high-capacity transformer models to overcome both fragmentation and corruption. With this novel approach, we can achieve reasonable performance on parsing & typing STACKOVERFLOW fragments; we also demonstrate that our approach performs well on shorter student error program and achieves best-in-class performance on longer programs that have more than 400 tokens. We also show that by blending Deepfix and our tool, we could achieve 77% accuracy, which outperforms all previously reported student error correction tools.
description: Accepted at EMSE (Empirical Software Engineering Journal)
RACH Optimization with Decision Tree Based Supervised Learning for Conditional Handover in 5G Beamformed Systems
Creators: name: Karabulut, Umur
name: Awada, Ahmad
name: Viering, Ingo
name: Barreto, Andre Noll
name: Fettweis, Gerhard P.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: Higher frequencies that are introduced in 5G networks cause rapid signal degradation and challenge user mobility. In recent studies, a conditional handover procedure has been adopted for 5G networks to enhance user mobility robustness. In this paper, mobility performance of the conditional handover is analysed for 5G mm-Wave systems with beamforming. In addition, a resource efficient random access procedure is proposed that increases the chance of contention-free random access during handover, which reduces signaling and interruption time. Moreover, simple, yet, effective decision tree based supervised learning method is proposed to minimize the handover failures that are caused by beam preparation phase of random access procedure. Results reveal the trade-off between contention free random access and handover failures. It is also shown that the optimum operation point of random access is achievable with proposed learning algorithm for conditional handover.
description: 8 pages, 7 figures, submitted to IEEE Access
Hydrodynamic response of a surfactant-laden interface to a radial flow
Creators: name: Bickel, T.
name: Loudet, J. -C.
name: Koleski, G.
name: Pouligny, B.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: We study the features of a radial Stokes flow due to a submerged jet directed toward a liquid-air interface. The presence of surface-active impurities confers to the interface an in-plane elasticity that resists the incident flow. Both analytical and numerical calculations show that a minute amount of surfactants is enough to profoundly alter the morphology of the flow. The hydrodynamic response of the interface is affected as well, shifting from slip to no-slip boundary condition as the surface compressibility decreases. We argue that the competition between the divergent outward flow and the elastic response of the interface may actually be used as a practical way to detect and quantify a small amount of impurities.