cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Genomic characterization of rare molecular subclasses of hepatocellular carcinoma
Creators: name: Smith, M.A
name: Mose, L.E
name: Thennavan, A
name: Damrauer, J.S
name: Walter, V
name: Hoadley, K.A
name: Selitsky, S.R
Publisher: name: Nature Research
Year: 2021

description: Primary liver cancer, consisting of both cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC), is the second leading cause of cancer deaths worldwide. Our goal is to genomically characterize rare HCC subclasses to provide insight into disease biology. Leveraging The Cancer Genome Atlas (TCGA) to perform a combined analysis of CCA (n = 36) and HCC (n = 275), we integrated multiple genomic platforms, to assess transcriptional profiles, mutational signatures, and copy number patterns to uncover underlying etiology and linage specific patterns. We identified two molecular classes distinct from prototypical HCC tumors. The first, CCA-Like, although histologically indistinguishable from HCC, had enrichment of CCA mutations (IDH1, BAP1), mutational signatures, and transcriptional patterns (SOX9, KRT19). CCA-Like, however, retained a copy number landscape similar to HCC, suggesting a hepatocellular linage. The second, Blast-Like, is enriched in TP53 mutations, HBV infection, exposure related mutational signatures and transcriptionally similar to hepatoblasts. Although these subclasses are molecularly distinct, they both have a worse progression-free survival compared to classical HCC tumors, yet are clinically treated the same. The identification of and characterization of CCA-Like and Blast-Like subclasses advance our knowledge of HCC as well as represents an urgent need for the identification of class specific biomarkers and targeted therapy.
Unification Constraints in the Next-to-Minimal Supersymmetric Standard Model
Creators: name: Elliott, T.
name: King, S. F.
name: White, P. L.
Publisher: name: arXiv
Year: 1994
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We perform a renormalisation group analysis of the next-to-minimal supersymmetric standard model (NMSSM) based on the following constraints: two-loop gauge coupling unification at a variable scale $M_X$, running the gauge couplings through the low energy thresholds; universal soft supersymmetry breaking parameters; correct electroweak symmetry breaking. The phenomenological implications of our results include a standard model-like Higgs boson of mass in the range 70-140 GeV.
description: Uses revtex macros. This is the published version, Phys. Lett. B351 (1995) 213
K-shell decomposition reveals hierarchical cortical organization of the human brain
Creators: name: Lahav, Nir
name: Ksherim, Baruch
name: Ben-Simon, Eti
name: Maron-Katz, Adi
name: Cohen, Reuven
name: Havlin, Shlomo
Publisher: name: arXiv
Year: 2018
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: FOS: Biological sciences

description: In recent years numerous attempts to understand the human brain were undertaken from a network point of view. A network framework takes into account the relationships between the different parts of the system and enables to examine how global and complex functions might emerge from network topology. Previous work revealed that the human brain features 'small world' characteristics and that cortical hubs tend to interconnect among themselves. However, in order to fully understand the topological structure of hubs one needs to go beyond the properties of a specific hub and examine the various structural layers of the network. To address this topic further, we applied an analysis known in statistical physics and network theory as k-shell decomposition analysis. The analysis was applied on a human cortical network, derived from MRI\DSI data of six participants. Such analysis enables us to portray a detailed account of cortical connectivity focusing on different neighborhoods of interconnected layers across the cortex. Our findings reveal that the human cortex is highly connected and efficient, and unlike the internet network contains no isolated nodes. The cortical network is comprised of a nucleus alongside shells of increasing connectivity that formed one connected giant component. All these components were further categorized into three hierarchies in accordance with their connectivity profile, with each hierarchy reflecting different functional roles. Such a model may explain an efficient flow of information from the lowest hierarchy to the highest one, with each step enabling increased data integration. At the top, the highest hierarchy (the nucleus) serves as a global interconnected collective and demonstrates high correlation with consciousness related regions, suggesting that the nucleus might serve as a platform for consciousness to emerge.
description: New Journal of Physics, Volume 18, August 2016
Supplementary document for Active Remote Focus Stabilization in Oblique Plane Microscopy - 7390275.pdf
Creators: name: Nguyen, Duc Trung
name: Rahmani, Amir
name: Ponjavic, Aleks
name: Millett-Sikking, Alfred
name: Fiolka, Reto
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Biological Techniques

description: Supplementary Document
Additional file 1 of Highly potent multivalent VHH antibodies against Chikungunya isolated from an alpaca naïve phage display library
Creators: name: Li, Qianlin
name: Zhang, Fuqiang
name: Lu, Yi
name: Hu, Huan
name: Wang, Jin
name: Guo, Cheng
name: Deng, Qiang
name: Liao, Conghui
name: Wu, Qin
name: Hu, Tingsong
name: Chen, Zeliang
name: Lu, Jiahai
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: Additional file 1: Fig. S1. Expression of 20 candidate nanobodies using the E.coli system. Fig. S2. Reactivities of 18 to the E2 protein of CHIKV measured by indirect ELISA. Fig. S3. Representative flow cytometry plots and data analysis of mean fluorescence value. A representative experiment among 2 is shown.
Madrepora verrucaria Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Anthozoa
Scleractinia
Oculinidae
Madrepora
Madrepora verrucaria

description: Madrepora verrucaria [spec. nov.]
M. stella orbiculari solitaria planiuscula sessili: disco cylindris flosculoso, ambitu radiato.
Ginann. adriat. 10 t. 4. s. 10. Fungus marinus.
Habitat in M. Mediterraneo.
Corallium magnitudine pisi dimidiati, sessile, planum, album; dum perfectum Disco ex tubis aggregatis, uti flos compositus, Ambituque striis exaratis more floris radiati; Media itaque inter Milleporas & Madreporas.
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 793, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Semi-supervised Adversarial Learning to Generate Photorealistic Face Images of New Identities from 3D Morphable Model
Creators: name: Gecer, Baris
name: Bhattarai, Binod
name: Kittler, Josef
name: Kim, Tae-Kyun
Publisher: name: arXiv
Year: 2018
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: We propose a novel end-to-end semi-supervised adversarial framework to generate photorealistic face images of new identities with wide ranges of expressions, poses, and illuminations conditioned by a 3D morphable model. Previous adversarial style-transfer methods either supervise their networks with large volume of paired data or use unpaired data with a highly under-constrained two-way generative framework in an unsupervised fashion. We introduce pairwise adversarial supervision to constrain two-way domain adaptation by a small number of paired real and synthetic images for training along with the large volume of unpaired data. Extensive qualitative and quantitative experiments are performed to validate our idea. Generated face images of new identities contain pose, lighting and expression diversity and qualitative results show that they are highly constraint by the synthetic input image while adding photorealism and retaining identity information. We combine face images generated by the proposed method with the real data set to train face recognition algorithms. We evaluated the model on two challenging data sets: LFW and IJB-A. We observe that the generated images from our framework consistently improves over the performance of deep face recognition network trained with Oxford VGG Face dataset and achieves comparable results to the state-of-the-art.
Getting Human Papillomavirus Vaccination Back on Track: A National Survey
Creators: name: Gilkey M.B
name: Brewer N.T
name: Huang Q
name: Kahn B.Z
name: Thompson P
name: Alton Dailey S
Publisher: name: Elsevier Inc.
Year: 2023

description: Purpose: Adolescent human papillomavirus (HPV) vaccine uptake in the United States dropped during the COVID-19 pandemic due to a decrease in well visits. This study sought to identify opportunities for primary care professionals (PCPs) to get adolescent vaccination back on track. Methods: In early 2021, we recruited 1,047 PCPs (71% physicians) who provided adolescent vaccines in the United States from an existing panel. Participants completed an online survey about changes in adolescent HPV vaccine uptake and actions taken to promote vaccination during the pandemic, as well as intentions to engage in activities to increase adolescent vaccination in the next 3 months. Results: A substantial proportion of PCPs (43%) reported that HPV vaccine uptake decreased in the first year of the pandemic; few (7%) PCPs reported an increase in uptake. PCPs reporting increased uptake were more likely to have used nurse-only vaccination visits, held drop-in and drive-through vaccination clinics, and used telehealth visits to recommend vaccination (all p < .05). Nearly two-thirds (62%) of all PCPs planned to promote adolescent vaccine uptake in the next 3 months. Planning was more common among PCPs who believed HPV vaccine uptake at their clinics increased during the pandemic, who saw more than 10 adolescent patients per week, who had ever reviewed their clinic's vaccination rates, and were nurses (all p < .05). Discussion: Many PCPs saw HPV vaccination drop during the pandemic. Several interventions could help clinics get HPV vaccination back on track, including increasing the availability of nurse-only vaccination visits and vaccination-only clinics.
Additional file 1: of A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle
Creators: name: Martin, Scott
name: Abhilash Chiramel
name: Schmidt, Marie
name: Chen, Yu-Chi
name: Whitt, Nadia
name: Watt, Ari
name: Dunham, Eric
name: Shifflett, Kyle
name: Traeger, Shelby
name: Leske, Anne
name: Buehler, Eugen
name: Martellaro, Cynthia
name: Brandt, Janine
name: Wendt, Lisa
name: MĂźller, Andreas
name: Peitsch, Stephanie
name: Best, Sonja
name: JĂźrgen Stech
name: Finke, Stefan
name: RĂśmer-OberdĂśrfer, Angela
name: Groseth, Allison
name: Feldmann, Heinz
name: Hoenen, Thomas
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology

description: Supplementary figures and methods. (PDF 884 kb)
Leading the Way Educational Excellence at Huahin Wittiyalai School in Thailand by Ryan James Whitehouse
Creators: name: Whitehouse, Ryan James
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 390403
subject: Educational administration, management and leadership

description: Educational leadership plays a pivotal role in shaping the academic environment of schools, fostering a culture of learning, and preparing students for the challenges of the future. In Thailand, a country with a rich cultural heritage and a rapidly evolving educational landscape, schools like Huahin Wittiyalai School in Huahin stand out as beacons of educational excellence.
L Dwarfs Found in Sloan Digital Sky Survey Commissioning Imaging Data
Creators: name: SDSS Collaboration
name: Fan, Xiaohui
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: This paper describes the discovery of seven dwarf objects of spectral type `L' (objects cooler than the latest M dwarfs) in commissioning imaging data taken by the Sloan Digital Sky Survey (SDSS). Low-resolution spectroscopy shows that these objects have spectral types from L0 to L8. Comparison of the SDSS and 2MASS photometry for several of these objects indicates the presence of significant opacity at optical wavelengths, perhaps due to atmospheric dust. This comparison also demonstrates the high astrometric accuracy (better than 1'' for these faint sources) of both surveys. The L dwarfs are shown to occupy a distinctive region of color-color space as measured in the SDSS filters, which should enable their identification in a straightforward way. This should lead eventually to a complete sample of many hundreds of these low mass objects, or about one per 15 square degrees to i'~20, in the complete SDSS data set.
description: 22 Pages Latex with embedded figures, submitted to AJ. Also available at http://www.astro.princeton.edu/~strauss/sdss/ldwarf.ps (with high-resolution figures)
On The Lack of Circumbinary Planets Orbiting Isolated Binary Stars
Creators: name: Fleming, David P.
name: Barnes, Rory
name: Graham, David E.
name: Luger, Rodrigo
name: Quinn, Thomas R.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We outline a mechanism that explains the observed lack of circumbinary planets (CBPs) via coupled stellar-tidal evolution of isolated binary stars. Tidal forces between low-mass, short-period binary stars on the pre-main sequence slow the stellar rotations, transferring rotational angular momentum to the orbit as the stars approach the tidally locked state. This transfer increases the binary orbital period, expanding the region of dynamical instability around the binary, and destabilizing CBPs that tend to preferentially orbit just beyond the initial dynamical stability limit. After the stars tidally lock, we find that angular momentum loss due to magnetic braking can significantly shrink the binary orbit, and hence the region of dynamical stability, over time impacting where surviving CBPs are observed relative to the boundary. We perform simulations over a wide range of parameter space and find that the expansion of the instability region occurs for most plausible initial conditions and that in some cases, the stability semi-major axis doubles from its initial value. We examine the dynamical and observable consequences of a CBP falling within the dynamical instability limit by running N-body simulations of circumbinary planetary systems and find that typically, at least one planet is ejected from the system. We apply our theory to the shortest period {\it Kepler} binary that possesses a CBP, Kepler-47, and find that its existence is consistent with our model. Under conservative assumptions, we find that coupled stellar-tidal evolution of pre-main sequence binary stars removes at least one close-in CBP in $87\%$ of multi-planet circumbinary systems.
description: 26 pages, 16 figures, accepted, ApJ
Geographic Heterogeneity in Behavioral and Social Drivers of COVID-19 Vaccination
Creators: name: Lu P.-J
name: Boone K
name: Black C
name: Omari A
name: Brewer N.T
name: Carter R.J
name: Singleton J.A
name: Zhou T
name: Kriss J.L
name: Masters N.B
name: Weiss D
name: Meng L
Publisher: name: Elsevier Inc.
Year: 2022

description: Introduction: Little is known about how the drivers of COVID-19 vaccination vary across the U.S. To inform vaccination outreach efforts, this study explores geographic variation in correlates of COVID-19 nonvaccination among adults. Methods: Participants were a nationally representative sample of U.S. adults identified through random-digit dialing for the National Immunization Survey–Adult COVID Module. Analyses examined the geographic and temporal landscape of constructs in the Behavioral and Social Drivers of Vaccination Framework among unvaccinated respondents from May 2021 to December 2021 (n=531,798) and sociodemographic and geographic disparities and Behavioral and Social Drivers of Vaccination predictors of COVID-19 nonvaccination from October 2021 to December 2021 (n=187,756). Results: National coverage with at least 1 dose of COVID-19 vaccine was 79.3% by December 2021, with substantial geographic heterogeneity. Regions with the largest proportion of unvaccinated persons who would probably get a COVID-19 vaccine or were unsure resided in the Southeast and Midwest (Health and Human Services Regions 4 and 5). Both regions had similar temporal trends regarding concerns about COVID-19 and confidence in vaccine importance, although the Southeast had especially low confidence in vaccine safety in December 2021, lowest in Florida (5.5%) and highest in North Carolina (18.0%). The strongest Behavioral and Social Drivers of Vaccination correlate of not receiving a COVID-19 vaccination was lower confidence in COVID-19 vaccine importance (adjusted prevalence ratio=5.19, 95% CI=4.93, 5.47; strongest in the Northeast, Southwest, and Mountain West and weakest in the Southeast and Midwest). Other Behavioral and Social Drivers of Vaccination correlates also varied by region. Conclusions: Contributors to nonvaccination showed substantial geographic heterogeneity. Strategies to improve COVID-19 vaccination uptake may need to be tailored regionally.
Additional file 2: of Comparative transcriptome analysis of the interaction between Actinidia chinensis var. chinensis and Pseudomonas syringae pv. actinidiae in absence and presence of acibenzolar-S-methyl
Creators: name: Michelotti, Vania
name: Lamontanara, Antonella
name: Buriani, Giampaolo
name: OrrĂš, Luigi
name: Cellini, Antonio
name: Donati, Irene
name: Vanneste, Joel
name: Cattivelli, Luigi
name: Tacconi, Gianni
name: Spinelli, Francesco
Publisher: name: figshare
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Plant Biology

description: Table S2. Summary of annotations of the Actinidia chinensis var. chinensis transcriptome. (DOC 66 kb)
Navigating the Post-COVID Landscape Challenges and Solutions in the Private Educational Industry in New Zealand and Thailand (by Ryan James Whitehouse)
Creators: name: Whitehouse, Ryan James
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 520102
subject: Educational psychology

description: The COVID-19 pandemic has significantly impacted various sectors worldwide, and the private educational industry is no exception. In this article, we will explore the challenges faced by the private educational sector in New Zealand and Thailand using the PESTLE analysis framework. PESTLE stands for Political, Economic, Social, Technological, Legal, and Environmental factors, providing a comprehensive view of the external macro-environmental influences. Additionally, I shall endeavor to discuss potential solutions to these challenges.
The Asteroseismology Metacomputer
Creators: name: Metcalfe, T. S.
name: Nather, R. E.
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We have developed a specialized computational instrument for fitting models of pulsating white dwarfs to observations made with the Whole Earth Telescope. This metacomputer makes use of inexpensive PC hardware and free software, including a parallel genetic algorithm which performs a global search for the best-fit set of parameters.
description: Submitted to Baltic Astronomy, 5 pages, plain TeX, uses balticw.tex
Can microplastic mediate soil properties, plant growth and carbon/nitrogen turnover in the terrestrial ecosystem?
Creators: name: Yao, Yao
name: Lili, Wang
name: Shufen, Pan
name: Gang, Li
name: Hongmei, Liu
name: Weiming, Xiu
name: Lingxuan, Gong
name: Jianning, Zhao
name: Guilong, Zhang
name: Dianlin, Yang
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Plant Biology
subject: Virology
subject: Computational Biology

description: Microplastic (MP) (particle size < 5mm) pollution is an emerging global environmental problem due to its abundant sources wide varieties and persistent existence. This has been studied in marine and freshwater environments, but our understanding of MP effect on terrestrial ecosystems, especially on terrestrial carbon (C) and nitrogen (N) turnover remains poor. This review summarizes the sources and distribution characteristics of MP in terrestrial ecosystems and explores the effects of MP on soil properties, plant growth, and C/N turnover. Once entering the terrestrial ecosystem, MP can involve in sequestrating carbon and nitrogen by changing soil properties (e.g. soil aggregate stability, pH and soil porosity). MP could exert direct influence on plants or indirectly alter the soil environment and microbial metabolic environment to affect plant growth, thus acting on the quantity and quality of soil carbon and nitrogen inputs by plant litter and roots. The changes of the dominant bacteria phyla, related functional genes and enzymes caused by MP could affect C/N turnover. Additionally, properties of MP (e.g. elemental composition, functional groups) or additives released by MP could also directly influence C/N turnover. Meanwhile, the types, size, even shapes of MP could affect the C/N turnover. Future researches should unify the standard system of MP separation, detection, and reveal the ecological effects of MP, especially their impacts on carbon and nitrogen cycles in terrestrial ecosystems in the context of climate changes.
Role of intra-band transitions in photo-carrier generation
Creators: name: Sato, Shunsuke A.
name: Lucchini, Matteo
name: Volkov, Mikhail
name: Schlaepfer, Fabian
name: Gallmann, Lukas
name: Keller, Ursula
name: Rubio, Angel
Publisher: name: arXiv
Year: 2018
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We theoretically investigate the role of intra-band transitions in laser-induced carrier-generation for different photon energy regimes: (i) strongly off-resonant, (ii) multi-photon resonant, and (iii) resonant conditions. Based on the analysis for the strongly off-resonant and multi-photon resonant cases, we find that intra-band transitions strongly enhance photo-carrier generation in both multi-photon absorption and tunneling excitation regimes, and thus, they are indispensable for describing the nonlinear photo-carrier generation processes. Furthermore, we find that intra-band transitions enhance photo-carrier generation even in the resonant condition, opening additional multi-photon excitation channels once the laser irradiation becomes sufficiently strong. The above findings suggest a potential for efficient control of photo-carrier generation via multi-color laser pulses through optimization of the contributions from intra-band transitions.
Emergence of spiral dark solitons in the merging of rotating Bose-Einstein condensates
Creators: name: Kanai, Toshiaki
name: Guo, Wei
name: Tsubota, Makoto
Publisher: name: arXiv
Year: 2018
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: Merging of isolated Bose-Einstein condensates (BECs) is an important topic due to its relevance to matter-wave interferometry and the Kibble-Zurek mechanism. Many past research focused on merging of BECs with uniform initial phases. In our recent numerical study (Phys. Rev. A 97, 013612 (2018)), we revealed that upon merging of rotating BECs with non-uniform initial phases, spiral-shaped dark solitons can emerge. These solitons facilitate angular momentum transfer and allow the merged condensate to rotate even in the absence of quantized vortices. More strikingly, the sharp endpoints of these spiral solitons can induce rotational motion in the BECs like vortices but with effectively a fraction of a quantized circulation. This paper reports our systematic study on the merging dynamics of rotating BECs. We discuss how the potential barrier that initially separates the BECs can affect the profile of the spiral solitons. We also show that the number of spiral solitons created in the BECs matches the relative winding number of the rotating BECs. The underlying mechanism of the observed soliton dynamics is explained.
description: 9 pages, 9 figures
A Novel Kind of Neutrino Oscillation Experiment
Creators: name: Segura, J.
name: Bernabéu, J.
name: Botella, F. J.
name: Peñarrocha, J. A.
Publisher: name: arXiv
Year: 1994
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A novel method to look for neutrino oscillations is proposed based on the elastic scattering process $\barν_{i} e^{-}\rightarrow \barν_{i} e^{-}$, taking advantage of the dynamical zero present in the differential cross section for $\barν_{e} e^{-}\rightarrow \barν_{e} e^{-}$. An effective tunable experiment between the "appearance" and "disappearance" limits is made possible. Prospects to exclude the allowed region for atmospheric neutrino oscillations are given.
description: 11 pages (+3 figures, available upon request),Standard Latex, FTUV/94-34
Three-dimensional dust mapping in the Orion Complex, combining Gaia-TGAS, 2MASS, and WISE
Creators: name: Kh., S. Rezaei
name: Bailer-Jones, C. A. L.
name: Schlafly, E. F.
name: Fouesneau, M.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present a map of the three-dimensional (3D) distribution of dust in the Orion complex. Orion is the closest site of high-mass star formation, making it an excellent laboratory for studying the interstellar medium and star formation. We use data from the Gaia-TGAS catalogue combined with photometry from 2MASS and WISE to get the distances and extinctions of individual stars in the vicinity of the Orion complex. We adopt the non-parametric method of Rezaei Kh. et al. (2017) to infer the probability distribution function of the dust densities at arbitrary points throughout the region. We map the dust distribution towards different parts of the Orion complex and find the distance and depth of the cloud compatible with other recent works which show the ability of the method to be applicable on the local molecular clouds to map their 3D dust distribution. We also demonstrate the danger of only using colours of stars to derive their extinctions without considering further physical constraints like the colour-magnitude diagram (CMD).
description: Accepted for publication in A&A
MOESM1 of High efficiency transformation of Brassica oleracea var. botrytis plants by Rhizobium rhizogenes
Creators: name: Kowalczyk, Tomasz
name: Gerszberg, Aneta
name: Durańska, Paulina
name: Róża Biłas
name: Hnatuszko-Konka, Katarzyna
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Cancer
subject: Plant Biology
subject: Computational Biology

description: Additional file 1: Fig. S1. A circular plasmid map of the modified pCAMBIA 1305.2 vector. Fig. S2. The regeneration from the Pionier cauliflower hypocotyls after R. radiobacter-mediated transformation approach: left side (a, c, e, g) after EHA 105 treatment, right side (b, d, f, h) after LBA 4404 treatment. a, b – growth of the hypocotyls on the selection medium I°; c, d – 10-day growth of the hypocotyls on the selection medium II° (shoot induction); e, f – 2-month shoot regeneration on the selection medium II° (all the regenerated shoots are gathered on one Petri dish per given strain); g, h – the effects of the GUS assay on the Pionier cauliflower hypocotyls after R. radiobacter-mediated transformation approach (EHA 105 and LBA 4404 strain respectively) .Table S1. The characteristic of the in vitro response of the Pionier hypocotyl explants to different variants of regeneration media. Table S2. The characteristics of the in vitro response of the Pionier cotyledon explants to different variants of regeneration media.
Counting trees in a graph
Creators: name: Petrunin, Anton
Publisher: name: arXiv
Year: 2018
Subjects: subject: History and Overview (math.HO)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 97K30

description: We discuss a recursive formula for number of spanning trees in a graph. The paper is written primary for school students.
description: (Russian)
Sparse Dowker Nerves
Creators: name: Blaser, Nello
name: Brun, Morten
Publisher: name: arXiv
Year: 2018
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics
subject: 55U10

description: We propose sparse versions of filtered simplicial complexes used to compte persistent homology of point clouds and of networks. In particular we extend a slight variation of the Sparse Čech Complex of Cavanna, Jahanseir and Sheehy from point clouds in Cartesian space to point clouds in arbitrary metric spaces. Along the way we formulate interleaving in terms of strict $2$-categories, and we introduce the concept of Dowker dissimilarities that can be considered as a common generalization of metric spaces and networks.
description: 25 pages
French Word Recognition through a Quick Survey on Recurrent Neural Networks Using Long-Short Term Memory RNN-LSTM
Creators: name: Sarraf, Saman
Publisher: name: arXiv
Year: 2018
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Optical character recognition (OCR) is a fundamental problem in computer vision. Research studies have shown significant progress in classifying printed characters using deep learning-based methods and topologies. Among current algorithms, recurrent neural networks with long-short term memory blocks called RNN-LSTM have provided the highest performance in terms of accuracy rate. Using the top 5,000 French words collected from the internet including all signs and accents, RNN-LSTM models were trained and tested for several cases. Six fonts were used to generate OCR samples and an additional dataset that included all samples from these six fonts was prepared for training and testing purposes. The trained RNN-LSTM models were tested and achieved the accuracy rates of 99.98798% and 99.91889% for edit distance and sequence error, respectively. An accurate preprocessing followed by height normalization (standardization methods in deep learning) enabled the RNN-LSTM model to be trained in the most efficient way. This machine learning work also revealed the robustness of RNN-LSTM topology to recognize printed characters.
Supplementary document for Fast Blood Flow Index Reconstruction of Diffuse Correlation Spectroscopy Using a Back-Propagation-Free Data-Driven Algorithm - 7387452.pdf
Creators: name: Zang, Zhenya
name: Pan, Mingliang
name: Zhang, Yuanzhe
name: Li, David
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Uncategorized

description: Figures S1 and S2
Testing linear-theory predictions of galaxy formation
Creators: name: Sugerman, Ben
name: Summers, F. J.
name: Kamionkowski, Marc
Publisher: name: arXiv
Year: 1999
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: The angular momentum of galaxies is routinely ascribed to a process of tidal torques acting during the early stages of gravitational collapse, and is predicted from the initial mass distribution using second-order perturbation theory and the Zel'dovich approximation. We have tested this theory for a flat hierarchical cosmogony using a large N-body simulation with sufficient dynamic range to include tidal fields, allow resolution of individual galaxies, and thereby expand on previous studies. We find relatively good correlation between the predictions of linear theory and actual galaxy evolution. While structure formation from early times is a complex history of hierarchical merging, salient features are well described by the simple spherical-collapse model. Most notably, we test several methods for determining the turnaround epoch, and find that turnaround is succesfully described by the spherical collapse model. The angular momentum of collapsing structures grows linearly until turnaround, as predicted, and continues quasi-linearly until shell crossing. The predicted angular momentum for well-resolved galaxies at turnaround overestimates the true turnaround and final values by a factor of ~3 with a scatter of ~70 percent, and only marginally yields the correct direction of the angular momentum vector. We recover the prediction that final angular momentum scales as mass to the 5/3 power. We find that mass and angular momentum also vary proportionally with peak height.
description: 20 pages, 16 figures, Accepted for publication in MNRAS
Madrepora turbinata Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Anthozoa
Scleractinia
Oculinidae
Madrepora
Madrepora turbinata

description: Madrepora turbinata [spec. nov.]
M. simplicissima turbinata laevis, stella concava. Amoen. acad. 1. p. 87. t. 84. f. I, II, III, IV, VII.
Brom. lith. t. 36, 38, 33, 32. Lang, figurat. 52. t. 12. Fungitis major orbicularis gotlandicus.
Helw. lith. t. 5. f. 9, 10, 11, 13, 15, 17. Wolff. hass. t. 10. f. 3, 4. Columellus turbinatus.
Habitat in M. Balthico.
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 793, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Charge Transfer Effects in Naturally Occurring van der Waals Heterostructures (PbSe)1.16(TiSe2)m (m=1, 2)
Creators: name: Yao, Q.
name: Shen, D. W.
name: Wen, C. H. P.
name: Hua, C. Q.
name: Zhang, L. Q.
name: Wang, N. Z.
name: Niu, X. H.
name: Chen, Q. Y.
name: Dudin, P.
name: Lu, Y. H.
name: Zheng, Y.
name: Chen, X. H.
name: Wan, X. G.
name: Feng, D. L.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Van der Waals heterostructures (VDWHs) exhibit rich properties and thus has potential for applications, and charge transfer between different layers in a heterostructure often dominates its properties and device performance. It is thus critical to reveal and understand the charge transfer effects in VDWHs, for which electronic structure measurements have proven to be effective. Using angle-resolved photoemission spectroscopy, we studied the electronic structures of (PbSe)1.16(TiSe2)m(m=1, 2), which are naturally occurring VDWHs, and discovered several striking charge transfer effects. When the thickness of the TiSe2 layers is halved from m=2 to m=1, the amount of charge transferred increases unexpectedly by more than 250%. This is accompanied by a dramatic drop in the electron-phonon interaction strength far beyond the prediction by first-principles calculations and, consequently, superconductivity only exists in the m=2 compound with strong electron-phonon interaction, albeit with lower carrier density. Furthermore, we found that the amount of charge transferred in both compounds is nearly halved when warmed from below 10 K to room temperature, due to the different thermal expansion coefficients of the constituent layers of these misfit compounds. These unprecedentedly large charge transfer effects might widely exist in VDWHs composed of metal-semiconductor contacts; thus, our results provide important insights for further understanding and applications of VDWHs.
description: 6 Pages, 4 figures
Short gamma-ray burst central engines
Creators: name: Ciolfi, Riccardo
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Growing evidence connects the progenitor systems of the short-hard subclass of gamma-ray bursts (GRBs) to the merger of compact object binaries composed by two neutron stars (NSs) or by a NS and a black hole (BH). The recent observation of the binary NS (BNS) merger event GW170817 associated with GRB 170817A brought a great deal of additional information and provided further support to the above connection, even though the identification of this burst as a canonical short GRB (SGRB) remains uncertain. Decades of observational constraints and theoretical models consolidated the idea of a jet origin for the GRB prompt emission, which can also explain the multiwavelength afterglow radiation observed in most of the events. However, the mechanisms through which a BNS or NS-BH merger remnant would power a collimated outflow are much less constrained. Understanding the properties of the remnant systems and whether they can provide the right conditions for jet production has been a main driver of the great effort devoted to study BNS and NS-BH mergers, and still represents a real challenge from both the physical and the computational point of view. One fundamental open question concerns the nature of the central engine itself. While the leading candidate system is a BH surrounded by a massive accretion disk, the recent observation of plateau-shaped X-ray afterglows in some SGRBs would suggest a longer-lived engine, i.e. a metastable (or even stable) massive NS, which would also exclude NS-BH progenitors. Here we elaborate on this key aspect, considering three different scenarios to explain the SGRB phenomenology based on different hypotheses on the nature of the merger remnant. Then, we discuss the basic properties of GRB 170817A and how this event would fit within the different frameworks of the above scenarios, under the assumption that it was or was not a canonical SGRB.
description: Submitted to IJMPD, Invited contribution for the Special Issue "Gamma-Ray Bursts in the Multi-Messenger Era"
Global landscape and genetic regulation of RNA editing in cortical samples from individuals with schizophrenia
Creators: name: Hoffman G.E
name: Wang J
name: Charney A
name: Haroutunian V
name: Francoeur N
name: Gil S.E
name: Lehner T
name: Lipska B.K
name: Devillers O
name: Marenco S
name: Dobbyn A
name: Brown L
name: Breen M.S
name: Bendl J
name: Gur R
name: Lauria M
name: Crawford G
name: Flatow E
name: Domenici E
name: Wiseman J
name: Rosenbluh C
name: Sullivan P
name: Devlin B
name: Li Q
name: Filosi M
name: Shah H.R
name: Browne A
name: Li J.B
name: Wang Y.-C
name: Girdhar K
name: Kassim B
name: Sloofman L
name: Xia E
name: Mangravite L.M
name: Zharovsky E.
name: Song L
name: Roussos P
name: Stahl E
name: Gulyás-Kovács A
name: Zhang W.
name: Hahn C.-G
name: Kramer R
name: Akbarian S
name: Couto L
name: Peters M.A
name: Hauberg M.E
name: Fullard J.F
name: Sklar P
name: Senthil G
name: Perumal T.M
name: Montgomery K
name: Huckins L
name: Chess A
name: Jiang Y
name: Brennand K
name: Sieberts S.K
name: Jacobov R
name: Johnson J.S
name: Lewis D.A
name: Ruderfer D.M
name: Visintainer R
name: Kim Y
name: Buxbaum J.D
name: Klei L
name: Park R
Publisher: name: Nature Publishing Group
Year: 2019

description: RNA editing critically regulates neurodevelopment and normal neuronal function. The global landscape of RNA editing was surveyed across 364 schizophrenia cases and 383 control postmortem brain samples from the CommonMind Consortium, comprising two regions: dorsolateral prefrontal cortex and anterior cingulate cortex. In schizophrenia, RNA editing sites in genes encoding AMPA-type glutamate receptors and postsynaptic density proteins were less edited, whereas those encoding translation initiation machinery were edited more. These sites replicate between brain regions, map to 3′-untranslated regions and intronic regions, share common sequence motifs and overlap with binding sites for RNA-binding proteins crucial for neurodevelopment. These findings cross-validate in hundreds of non-overlapping dorsolateral prefrontal cortex samples. Furthermore, ~30% of RNA editing sites associate with cis-regulatory variants (editing quantitative trait loci or edQTLs). Fine-mapping edQTLs with schizophrenia risk loci revealed co-localization of eleven edQTLs with six loci. The findings demonstrate widespread altered RNA editing in schizophrenia and its genetic regulation, and suggest a causal and mechanistic role of RNA editing in schizophrenia neuropathology.
Open or Closed? Information Flow Decided by Transfer Operators and Forecastability Quality Metric
Creators: name: Bollt, Erik M.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: A basic systems question concerns the concept of closure, meaning autonomomy (closed) in the sense of describing the (sub)system as fully consistent within itself. Alternatively, the system may be nonautonomous (open) meaning it receives influence from an outside coupling subsystem. Information flow, and related causation inference, are tenant on this simple concept. We take the perspective of Weiner-Granger causality, descriptive of a subsystem forecast quality dependence on considering states of another subsystem. Here we develop a new direct analytic discussion, rather than a data oriented approach. That is, we refer to the underlying Frobenius-Perron transfer operator that moderates evolution of densities of ensembles of orbits, and two alternative forms of the restricted Frobenius-Perron (FP) operator, interpreted as if either closed (determinstic FP) or not closed (the unaccounted outside influence seems stochastic and correspondingly the stochastic FP operator). From this follows contrasting the kernels of the variants of the operators, as if densities in their own rights. However, the corresponding differential entropy to compare by Kulback-Leibler divergence, as one would when leading to transfer entropy, becomes ill-defined. Instead we build our Forecastability Quality Metric (FQM) upon the "symmetrized" variant known as Jensen-Shanon divergence, and also we are able to point out several useful resulting properties that result. We illustrate the FQM by a simple coupled chaotic system. For now, this analysis is a new theoretical direction, but we describe data oriented directions for the future.
description: 16 pages 2 figures
What do we talk about when we speak of cosmological redshift?
Creators: name: Bengochea, Gabriel R.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: From the first observations made by Slipher, our understanding and interpretation of the cosmological redshift was evolving until reaching the current consensus, through the expanding universe and the emergence of modern physical cosmology within the framework of General Relativity. The redshift is one of the most basic concepts of astronomy, and is one of the few observational parameters that can be measured directly. To refer to the temporal evolution of objects or cosmic structures in the universe, we often do so indistinctly through cosmic time or cosmological redshift. But repeatedly this connection ends up generating confusion not only among popular science communicators but also within the professional astronomical community. In this article, we will make a pedagogical approach to the link between cosmic time and cosmological redshift, and we will also clarify several common misunderstandings around this relation.
description: 7 pages, 6 figures. Some changes, comments and references added
Madrepora fungites Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Anthozoa
Scleractinia
Oculinidae
Madrepora
Madrepora fungites

description: Madrepora fungites [spec. nov.]
M. simplex acaulis convexa, lamellis simplicibus.
Hort. cliff. 481. Madrepora simplex acaulis orbiculata convexa, lamellis denticulatis.
Bonan. kirch. 268. t. 267. f. 17. Fungus petrificatus.
Rumph. amb. 6. p. 247. t. 88. f. 1, 4. Fungus saxeus.
Bauh. hist. 3. p. 801. f. 1, 2. Fungus lapideus.
Olear. mus. 74. t. 34. f. 2. Fungites IV.
Besl. mus. t. 26. f. 3. Fungus marinus lapideus.
Clus. exot. 125. f. 1. Fungus lapidosus.
Boerh. lugdb. 1. p. 2. Fungus coralloides pileatus lamellatus.
Shaw. afr. 6. Fungus coralloides lamellatus maris rubri.
Habitat in Mari rubro.
Stella simplex centro concavo. Lamellae acutae, inaequales, basin versus isthmis connexae.
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 pages 793-794, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Jensen-type geometric shapes
Creators: name: Pasteczka, Paweł
Publisher: name: arXiv
Year: 2018
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: We present both necessary and sufficient conditions to the convex closed shape $X$ such that the inequality $$ \frac{1}{|X|} \int_X f(x)\:dx \le \frac{1}{|\partial X|} \int_{\partial X} f(x)\:dx$$ is valid for every convex function $f \colon X \to \mathbb{R}$ ($\partial X$ stands for the boundary of $X$). It is proved that this inequality holds if $X$ is (i) an $n$-dimensional parallelotope, (ii) an $n$-dimensional ball, (iii) a convex polytope having an inscribed sphere (tangent to all its facets) with center in the center of mass of $\partial X$.