cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 6: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells
Creators: name: Mostafa, Mahmoud
name: Rider, Christopher
name: Suharsh Shah
name: Traves, Suzanne
name: Gordon, Paul
name: Miller-Larsson, Anna
name: Leigh, Richard
name: Newton, Robert
Publisher: name: figshare
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Hematology
subject: 60506 Virology

description: Validation of budesonide-induced genes grouped by fold ≥1.25 cut-off. Figure 3b defines 7 groups, representing overlaps and unique genes (≥ 1.25 fold cut-off) within the 410 genes that were induced ≥2 fold (P ≤ 0.05) by budesonide in the three cell variants. Overall gene expression data for each of these 7 groups was summarized by: a, zero-mean log2 intensity, and; b, the log2 fold change when compared to untreated control. Data are color-coded (Red = A549, yellow/orange = BEAS-2B, Blue = HBE). In panel a, open bars represent untreated and solid bars are budesonide-treated cells. The box defines the upper and lower quartiles, and the line inside represents the median. Whiskers represent the 5th and 95th percentiles. c. Following either no treatment or budesonide (300 nM for A549 and BEAS-2B, 100 nM for HBE) for 6 h, real-time PCR was performed for the indicated genes and GAPDH in A549 (N = 6), BEAS-2B (N = 6) and HBE (N = 6 donors). Data, representing log2 fold change for each gene/GAPDH, are presented as scatter plots (from different experimental replicates) along with their means ± SE. Following qPCR, 19 genes had their grouping changed. The revised designations are indicated in green (15 upgraded genes) or red (4 downgraded genes), where A = A549, B = BEAS-2B and H = HBE. d. Correlation between the log2 fold change produced by budesonide treatment as obtained by microarray analysis and that acquired by real-time qPCR analysis in each cell variant. The dashed line represents the line of unity and the solid line represents the best fit line. (PDF 1730 kb)
Saururaceae F. Voigt
Creators: name: Reveal, James L.
name: Chase, Mark W.
name: Iii, - Apg
name: Iii, Apg
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy

description: 10. Saururaceae F.Voigt in L.C.M. Richard, Anal Frucht.: 45, 67. 1811, nom. cons.
description: Published as part of Reveal, James L., Chase, Mark W., Iii, - Apg & Iii, Apg, 2011, APG III: Bibliographical Information and Synonymy of Magnoliidae Abstract Kew words Introduction, pp. 71-134 in Phytotaxa 19 (1) on page 73, DOI: 10.11646/phytotaxa.19.1.4, http://zenodo.org/record/10121353
Additional file 3: of Conserved regulation of RNA processing in somatic cell reprogramming
Creators: name: Kanitz, Alexander
name: Syed, Afzal
name: Kaji, Keisuke
name: Zavolan, Mihaela
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Figure S1. RNA-Seq library statistics. The following parameters were evaluated for all analyzed reprogramming endpoint RNA-Seq data sets and shown as bar-and-whisker plots, grouped by study: (A) number of reads, (B) read length, (C) percent mapped reads, (D) percent uniquely mapped reads. The Sequence Read Archive accessions for each study are indicated on the y axes. Medians are indicated as thick black horizontal lines. The lower and upper limits of boxes denote the first and third quartile, respectively, while whiskers indicate the 5th (bottom) and 95th (top) percentiles. Where applicable, outliers are indicated as circles. (PDF 17 kb)
The Decays of Glueballs to two light mesons
Creators: name: Jin, J. Y. Cui H. Y.
name: Wu, J. M.
Publisher: name: arXiv
Year: 1998
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We solve the B.S. equation of glueballs under instantaneous approximation. With the B.S wave function obtained we calculate the decay width of glueballs to two pseudoscalar mesons, $Γ(ππ)$, $Γ(kk)$ and $Γ(ηη)$. $Γ(ηη^\prime)$ from QCD anomaly is also estimated.
description: 11 pages, latex, 4 figures
MOESM4 of Metabolomics combined with network pharmacology exploration reveals the modulatory properties of Astragali Radix extract in the treatment of liver fibrosis
Creators: name: Wang, Dan
name: Li, Ruisheng
name: Wei, Shizhang
name: Gao, Sijia
name: Xu, Zhuo
name: Liu, Honghong
name: Wang, Ruilin
name: Li, Haotian
name: Cai, Huadan
name: Wang, Jian
name: Zhao, Yanling
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Additional file 4: Figure S3. The OPLS-DA score plots, S-plots and 100-permutation test generated in ESIâ mode.
Lattice vibrations and structural instability in Cesium near the cubic to tetragonal transition
Creators: name: Kong, Y.
name: Jepsen, O.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Under pressure cesium undergoes a transition from a high-pressure fcc phase (Cs-II) to a collapsed fcc phase (Cs-III) near 4.2GPa. At 4.4GPa there follows a transition to the tetragonal Cs-IV phase. In order to investigate the lattice vibrations in the fcc phase and seek a possible dynamical instability of the lattice, the phonon spectra of fcc-Cs at volumes near the III-IV transition are calculated using Savrasov's density functional linear-response LMTO method. Compared with quasiharmonic model calculations including non-central interatomic forces up to second neighbours, at the volume $V/V_0= 0.44$ ($V_0$ is the experimental volume of bcc-Cs with $a_0$=6.048Å), the linear-response calculations show soft intermediate wavelength $T_{[1\bar{1}0]}[ξξ0]$ phonons. Similar softening is also observed for short wavelength $L[ξξξ]$ and $L[00ξ]$ phonons and intermediate wavelength $L[ξξξ]$ phonons. The Born-von Kármán analysis of dispersion curves indicates that the interplanar force constants exhibit oscillating behaviours against plane spacing $n$ and the large softening of intermediate wavelength $T_{[1\bar{1}0]}[ξξ0]$ phonons results from a negative (110)-interplanar force-constant $Φ_{n=2}$. The frequencies of the $T_{[1\bar{1}0]}[ξξ0]$ phonons with $ξ$ around 1/3 become imaginary and the fcc structure becomes dynamically unstable for volumes below $0.41V_0$. It is suggested that superstructures corresponding to the $\mathbf{q}{\neq}0$ soft mode should be present as a precursor of tetragonal Cs-IV structure.
description: 12 pages, 5 figures
Spectral correlations in disordered mesoscopic metals and their relevance for persistent currents
Creators: name: Voelker, Axel
name: Kopietz, Peter
Publisher: name: arXiv
Year: 1996
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We use the Lanczos method to calculate the variance of the number of energy levels in an energy window of width E below the Fermi energy for non-interacting disordered electrons on a thin three-dimensional ring threaded by an Aharonov-Bohm flux . We find that for small E the flux-dependent part of the variance is well described by a well-known Feynman diagram involving two Cooperons. However, this result cannot be extrapolated to energies E where the energy-dependence of the average density of states becomes significant. We discuss consequences for persistent currents.
description: minor modifications in the text, accepted for publication in Mod. Phys. Lett. B
Constrained Hamiltonian analysis of a non relativistic Schrodinger field coupled with C-S gravity
Creators: name: Mukherjee, Pradip
name: Sattar, Abdus
Publisher: name: arXiv
Year: 2018
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We provide a constrained Hamiltonian analysis of a non relativistic Schrodinger field in 2+1 dimensions , coupled with Chern - Simons gravity. The coupling is achieved by the recently advanced Galilean gauge theory \cite{BMM1},\cite{ BMM2}, \cite{BM4}. The calculations are repeated with a truncated model to show that deviation from Galilean gauge theory makes the theory untenable. The issue of nonrelativistic spatial diffeomorphism is discussed in this context.
description: 19 pages, Latex. This version is to remedy a mess in v3 which is spurious. This version is a considerably revised form of v2. Ignore v3
Four-quark Operators Relevant to B Meson Lifetimes from QCD Sum Rules
Creators: name: Baek, M. S.
name: Lee, Jungil
name: Liu, Chun
name: Song, H. S.
Publisher: name: arXiv
Year: 1997
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: At the order of 1/m_b^3, the B meson lifetimes are controlled by the hadronic matrix elements of some four-quark operators. The nonfactorizable magnitudes of these four-quark operator matrix elements are analyzed by QCD sum rules in the framework of heavy quark effective theory. The vacuum saturation for color-singlet four-quark operators is justified at hadronic scale, and the nonfactorizable effect is at a few percent level. However for color-octet four-quark operators, the vacuum saturation is violated sizably that the nonfactorizable effect cannot be neglected for the B meson lifetimes. The implication to the extraction of some of the parameters from B decays is discussed. The B meson lifetime ratio is predicted as τ(B^-)/τ(B^0)=1.09\pm 0.02. However, the experimental result of the lifetime ratio τ(Λ_b)/τ(B^0) still cannot be explained.
description: 20 pages, latex, 6 figures, discussion on non-factorizable effect of the four-quark condensate added, to appear in Phys. Rev. D57 (1998)
Lactoridaceae Engl.
Creators: name: Reveal, James L.
name: Chase, Mark W.
name: Iii, - Apg
name: Iii, Apg
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy

description: 12. Lactoridaceae Engl. in H. G. A.Engler & K.A.E. Prantl, Nat. Pflanzenfam. III, 2: 19. 27 Jan 1888, nom. cons. 13. Hydnoraceae C.Agardh, Aphor. Bot.: 88. 21 Dec 1821, nom. cons.
description: Published as part of Reveal, James L., Chase, Mark W., Iii, - Apg & Iii, Apg, 2011, APG III: Bibliographical Information and Synonymy of Magnoliidae Abstract Kew words Introduction, pp. 71-134 in Phytotaxa 19 (1) on page 74, DOI: 10.11646/phytotaxa.19.1.4, http://zenodo.org/record/10121353
Exciton transport enhancement across quantum Su-Schrieffer-Heeger lattices with quartic nonlinearity
Creators: name: Mendoza-Arenas, J. J.
name: Rojas-Gamboa, D. F.
name: Plenio, M. B.
name: Prior, J.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In the present work we discuss the propagation of excitons across a one-dimensional Su-Schrieffer-Heeger lattice, which possesses both harmonic oscillations and weak quartic anharmonicities. When quantizing these vibrational degrees of freedom we identify several phonon-conserving nonlinearities, each one with a different impact on the excitonic transport. Our analysis identifies a dominant nonlinear correction to the phonon hopping which leads to a strong enhancement of exciton conduction compared to a purely linear vibrational dynamics. Thus quartic lattice nonlinearities can be exploited to induce transitions from localized to delocalized transport, even for very weak amplitudes.
description: 9 pages, 9 figures
title: Changing Your Outlook to Reinvent Your Librarian Role: Finding Balance Between Your Job Description and What You Like to Do
Creators: name: Borrego, Paulina
name: Will, Carol
Publisher: name: University of Massachusetts Amherst
Year: 2021
Subjects: subject: Professional/staff development
subject: work-life balance
subject: work-life strategies
subject: leadership
subject: motivation
subject: goal-setting
subject: career planning
subject: librarian self-reflection
subject: proactive librarian
subject: Library and Information Science

description: https://doi.org/10.7275/31gx-7j97
description: In every job, there is a balance between what you like to do and what you must do. Learning how to strike a balance between the two can help lead to a more fulfilling and harmonious career. Using storytelling and attendee prompts, we will discuss words of advice and encouragement based on our experiences of how we have each taken our roles and transformed them to suit our talents, strengths, and passions.
MOESM5 of Metabolomics combined with network pharmacology exploration reveals the modulatory properties of Astragali Radix extract in the treatment of liver fibrosis
Creators: name: Wang, Dan
name: Li, Ruisheng
name: Wei, Shizhang
name: Gao, Sijia
name: Xu, Zhuo
name: Liu, Honghong
name: Wang, Ruilin
name: Li, Haotian
name: Cai, Huadan
name: Wang, Jian
name: Zhao, Yanling
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 5: Figure S5. The interrelation between metabolic differences.
Interaction of Magnetic Monopoles and Domain Walls
Creators: name: Pogosian, Levon
name: Vachaspati, Tanmay
Publisher: name: arXiv
Year: 1999
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Astrophysics (astro-ph)
subject: Condensed Matter (cond-mat)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study the interaction of magnetic monopoles and domain walls in a model with SU(5)\times Z_2 symmetry by numerically evolving the field equations. We find that the monopoles unwind and dissipate their magnetic energy on collision with domain walls within which the full SU(5) symmetry is restored.
description: 4 pages; included additional degree of freedom in ansatz (eq. 4), discussed time and distance scales; version to be published in PRD
Transfer entropy computation using the Perron-Frobenius operator
Creators: name: Diego, David
name: Haaga, Kristian Agasøster
name: Hannisdal, Bjarte
Publisher: name: arXiv
Year: 2018
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences
subject: 37M25 (approximation of invariant measures and entropy), 37M10 (time series analysis)

description: We propose a method for computing the transfer entropy between time series using Ulam's approximation of the Perron-Frobenius (transfer) operator associated with the map generating the dynamics. Our method differs from standard transfer entropy estimators in that the invariant measure is estimated not directly from the data points but from the invariant distribution of the transfer operator approximated from the data points. For sparse time series and low embedding dimension, the transfer operator is approximated using a triangulation of the attractor, whereas for data-rich time series or higher embedding dimension we use a faster grid approach. We compare the performance of our methods with existing estimators such as the k nearest neighbors method and kernel density estimation method, using coupled instances of well known chaotic systems: coupled logistic maps and a coupled Rössler-Lorenz system. We find that our estimators are robust against moderate levels of noise. For sparse time series with less than a hundred observations and low embedding dimension, our triangulation estimator shows improved ability to detect coupling directionality, relative to standard transfer entropy estimators.
description: 21 pages, 25 figures, 6 appendices
QCD Corrections to the Masses of the neutral CP-even Higgs Bosons in the MSSM
Creators: name: Heinemeyer, S.
name: Hollik, W.
name: Weiglein, G.
Publisher: name: arXiv
Year: 1998
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We perform a diagrammatic calculation of the leading two-loop QCD corrections to the masses of the neutral CP-even Higgs bosons in the Minimal Supersymmetric Standard Model (MSSM). The results are valid for arbitrary values of the parameters of the Higgs and scalar top sector of the MSSM. The two-loop corrections are found to reduce the mass of the lightest Higgs boson considerably compared to its one-loop value. The numerical results are analyzed in the GUT favored regions of small and large \tan β. Their impact on a precise prediction for the mass of the lightest Higgs boson is briefly discussed.
description: 9 pages, 4 figures, more detailed discussion about comparison with other approaches, minor further changes, version to appear in Phys. Rev. D Rapid Comm
Aristolochiaceae Juss., Gen. Pl.
Creators: name: Reveal, James L.
name: Chase, Mark W.
name: Iii, - Apg
name: Iii, Apg
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy

description: 14. Aristolochiaceae Juss., Gen. Pl.: 72. 4 Aug 1789, nom. cons.
 Asaraceae Vent., Tabl. Règne Vég. 2: 226. 5 Mai 1799
description: Published as part of Reveal, James L., Chase, Mark W., Iii, - Apg & Iii, Apg, 2011, APG III: Bibliographical Information and Synonymy of Magnoliidae Abstract Kew words Introduction, pp. 71-134 in Phytotaxa 19 (1) on page 74, DOI: 10.11646/phytotaxa.19.1.4, http://zenodo.org/record/10121353
Sensitivity of a micromechanical displacement detector based on the radio-frequency single-electron transistor
Creators: name: Blencowe, Miles P.
name: Wybourne, Martin N.
Publisher: name: arXiv
Year: 2000
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate the tunneling shot noise limits on the sensitivity of a micromechanical displacement detector based on a metal junction, radio-frequency single-electron transistor (rf-SET). In contrast with the charge sensitivity of the rf-SET electrometer, the displacement sensitivity improves with increasing gate voltage bias and, with a suitably optimized rf-SET, displacement sensitivities of $10^{-6} {\rmÅ}/\sqrt{\rm Hz}$ may be possible.
description: 12 pages, 3 figures
title: Rapport activité chercheuse invitée İpek Çelik 2013
Creators: name: Celik, Ipek
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2019

description: Rapport d'activités d'İpek Çelik, chercheure invitée au sein du laboratoire TELEMME (UMR 7303), avec le soutien du LabexMed.
Code of manuscript: Using imperfect data in predictive mapping of vectors: a regional example of Ixodes ricinus distribution.
Creators: name: Ribeiro, Rita
Publisher: name: Zenodo
Year: 2019
Subjects: Bayesian model
INLA
Zero inflated Poisson
raster data

description: This file is the R script with the code to conduct the analyses (models, maps and plots) of the manuscript "Using imperfect data in predictive mapping of vectors: a regional example of Ixodes ricinus distribution". List of authors:  Rita Ribeiro1, 2*, Jude I. Eze1, 5, Lucy Gilbert3, G.R. William Wint4, George Gunn1, Alastair Macrae2, Jolyon M. Medlock6, Harriet Auty1. 1Department of Veterinary and Animal Science, Northern Faculty, Scotland’s Rural College, An Lòchran, 10 Inverness Campus, Inverness, IV2 5NA, UK 2The Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK 3Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK 4Environmental Research Group Oxford, c/o Department of Zoology, South Parks Road, Oxford, OX1 3PS, UK 5Biomathematics and Statistics Scotland, JCMB, The King's Buildings, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK 6Medical Entomology & Zoonoses Ecology, Emergency Response Department - Science & Technology, Public Health England (PHE), Porton Down, Salisbury, SP4 0JG, UK
Additional file 14: of Conserved regulation of RNA processing in somatic cell reprogramming
Creators: name: Kanitz, Alexander
name: Syed, Afzal
name: Kaji, Keisuke
name: Zavolan, Mihaela
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology

description: Figure S10. Impact of Esrp1/2 overexpression on selected splicing events. TNG-MKOS-MEFs transduced with retroviruses harboring expression cassettes for either Esrp1 (green), Esrp2 (purple) or Luciferase (red), or not transduced (blue) were treated with doxycycline to induce reprogramming. RNA-Seq libraries (n = 1) were generated from samples taken at day 0 through 5 and day 15 (representing fully reprogrammed iPSCs). (A) Percent spliced in (PSI) values are plotted for each day for those of the mouse events in Additional file 3 that correspond to genes that have been associated with the network of splicing changes in Fig. 5c or have previously been identified as Esrp1/2 targets [15, 39]. (B) Total gene expression of Esrp1 (top) and Esrp2 (bottom) along the reprogramming time course. (C and D) The fractions of total Grhl1 gene expression (C) and abundances (D) of the Grhl1 isoforms 201 and 202 are indicated for each time point. (PDF 53 kb)
Scanning Tunneling Microscopy of a Luttinger Liquid
Creators: name: Eggert, Sebastian
Publisher: name: arXiv
Year: 1999
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Explicit predictions for Scanning Tunneling Microscopy (STM) on interacting one-dimensional electron systems are made using the Luttinger liquid formalism. The STM current changes with distance from an impurity or boundary in a characteristic way, which reveals the spin-charge separation and the interaction strength in the system. The current exhibits Friedel-like oscillations, but also carries additional modulated behavior as a function of voltage and distance, which shows the spin-charge separation in real space. Moreover, very close to the boundary the current is strongly reduced, which is an indication of the interaction strength in the system.
description: Final published version. 4 pages in revtex format including 2 epsfig-embedded figures. The latest version in PDF format is available from http://fy.chalmers.se/~eggert/papers/stm.pdf
MOESM1 of Evaluating the role of RAD52 and its interactors as novel potential molecular targets for hepatocellular carcinoma
Creators: name: Li, Ping
name: Xu, YanZhen
name: Zhang, Qinle
name: Li, Yu
name: Jia, Wenxian
name: Wang, Xiao
name: Xie, Zhibin
name: Liu, Jiayi
name: Zhao, Dong
name: Shao, Mengnan
name: Chen, Suixia
name: Mo, Nanfang
name: Jiang, Zhiwen
name: Li, Liuyan
name: Liu, Run
name: Huang, Wanying
name: Chang, Li
name: Chen, Siyu
name: Li, Hongtao
name: Zuo, Wenpu
name: Li, Jiaquan
name: Zhang, Ruoheng
name: Yang, Xiaoli
Publisher: name: figshare
Year: 2019
Subjects: Physical Sciences not elsewhere classified
Molecular Biology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer
Computational Biology

description: Additional file 1. Molecular docking total energy values for RAD52 and its interactors with hot spot analyses.
Complete Result for Positronium Energy Levels at Order alpha^6 m
Creators: name: Pachucki, Krzysztof
name: Karshenboim, Savely G.
Publisher: name: arXiv
Year: 1997
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We have completed theoretical predictions for positronium energy levels through order alpha^6 m by the calculation of the spin independent, radiative recoil correction. This contribution is significant and amounts to 10.64 MHz for the 1S state. We further perform detailed comparison of theoretical predictions to experimental results for 1S-2S and 2S-2P transitions.
description: 9 pages, 2 tables. Email: sgk@onti.vniim.spb.su
Flat $\mathfrak{so}(p,q)$-Connections for Manifolds of Non-Euclidean Signature
Creators: name: Ranjbar, Arash
name: Zanelli, Jorge
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: Differential Geometry (math.DG)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: The well-known fact that $S^1$, $S^3$ and $S^7$ are parallelizable manifolds admitting flat connections is revisited. The role of torsion in the construction of those flat connections is made explicit, and the possibilities allowed by different metric signatures are examined. A necessary condition for parallelizability in an open region is that the torsion tensor must be covariantly constant. This property can be used to obtain a relation between a torsion-free and flat connections. Our treatment covers Riemannian and pseudo-Riemannian (non-Euclidean signature) hyperbolic manifolds of dimensions three and seven. Apart from the spherical cases mentioned above, the explicit flat $\mathfrak{so}(p,q)$ connections with $p+q=3,7$ are constructed for the coset manifolds $SO(p,q+1)/SO(p,q)$ or $SO(p+1,q)/SO(p,q)$.
description: 25 pages, 2 figures, v2: minor changes made
Magnoliales Bercht. & J. Presl, P
Creators: name: Reveal, James L.
name: Chase, Mark W.
name: Iii, - Apg
name: Iii, Apg
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy

description: 6. Magnoliales Juss. ex Bercht. & J.Presl, P  ř ir . Rostlin: 223. Jan–Apr 1820
 Annonales Juss. ex Bercht. & J.Presl,  P ř ir . Rostlin: 223. Jan–Apr 1820
 Degeneriales C.Y.Wu et al., Acta Phytotax. Sin. 40: 291. 2002
 Eupomatiales Takht. ex Reveal, Novon 2: 238. 13 Oct 1992
 Himantandrales Doweld & Shevyryova, Ann. Bot. (London) 81: 345. Feb 1998
 Myristicales R.Br. ex Bercht. & J.Presl,  P ř ir . Rostlin: 235. Jan–Apr 1820
description: Published as part of Reveal, James L., Chase, Mark W., Iii, - Apg & Iii, Apg, 2011, APG III: Bibliographical Information and Synonymy of Magnoliidae Abstract Kew words Introduction, pp. 71-134 in Phytotaxa 19 (1) on page 74, DOI: 10.11646/phytotaxa.19.1.4, http://zenodo.org/record/10121353
A mass-dependent slope of the galaxy size-mass relation out to z~3: further evidence for a direct relation between median galaxy size and median halo mass
Creators: name: Mowla, Lamiya
name: van der Wel, Arjen
name: van Dokkum, Pieter
name: Miller, Tim
Publisher: name: arXiv
Year: 2019
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We reassess the galaxy size-mass relation out to z~3 using a new definition of size and a sample of >29,000 galaxies from the 3D-HST, CANDELS, and COSMOS-DASH surveys. Instead of the half-light radius r_50 we use r_80, the radius containing 80% of the stellar light. We find that the r_80 -- M_star relation has the form of a broken power law, with a clear change of slope at a pivot mass M_p. Below the pivot mass the relation is shallow (r_80 \propto M_star^0.15) and above it it is steep (r_80\propto M_star^0.6). The pivot mass increases with redshift, from log(M_p/M_sun)~ 10.2 at z=0.4 to log(M_p/M_sun)~ 10.9 at z=1.7-3. We compare these r_80-M_star relations to the M_halo-M_star relations derived from galaxy-galaxy lensing, clustering analyses, and abundance matching techniques. Remarkably, the pivot stellar masses of both relations are consistent with each other at all redshifts, and the slopes are very similar both above and below the pivot when assuming M_halo \propto r_80^3. The implied scaling factor to relate galaxy size to halo size is r_80 / R_vir = 0.047, independent of stellar mass and redshift.From redshift 0 to 1.5, the pivot mass also coincides with the mass where the fraction of star-forming galaxies is 50%, suggesting that the pivot mass reflects a transition from dissipational to dissipationless galaxy growth. Finally, our results imply that the scatter in the stellar-to-halo mass ratio is relatively small for massive halos (~0.2 dex for M_halo>10^12.5 M_sun).
description: Accepted in ApJL. Please also see complementary paper Miller et al. 2019
Ordering temperatures and critical exponents in Ising spin glasses
Creators: name: Bernardi, L. W.
name: Prakash, S.
name: Campbell, I. A.
Publisher: name: arXiv
Year: 1996
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: We propose a numerical criterion which can be used to obtain accurate and reliable values of the ordering temperatures and critical exponents of spin glasses. Using this method we find an value of the ordering temperature for the $\pm J$ Ising spin glass in three dimensions which is definitely non-zero and in good agreement with previous estimates. We show that the critical exponents of three dimensional Ising spin glasses do not appear to obey the usual universality rules.
description: use epsfig package, 10 pages, 2 figures included, to be published in PRL
Myristicaceae R. Br., Prodr.
Creators: name: Reveal, James L.
name: Chase, Mark W.
name: Iii, - Apg
name: Iii, Apg
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy

description: 15. Myristicaceae R.Br., Prodr.: 399. 27 Mar 1810, nom. cons.
description: Published as part of Reveal, James L., Chase, Mark W., Iii, - Apg & Iii, Apg, 2011, APG III: Bibliographical Information and Synonymy of Magnoliidae Abstract Kew words Introduction, pp. 71-134 in Phytotaxa 19 (1) on page 74, DOI: 10.11646/phytotaxa.19.1.4, http://zenodo.org/record/10121353
Towards Real-time Eyeblink Detection in The Wild:Dataset,Theory and Practices
Creators: name: Hu, Guilei
name: Xiao, Yang
name: Cao, Zhiguo
name: Meng, Lubin
name: Fang, Zhiwen
name: Zhou, Joey Tianyi
name: Yuan, Junsong
Publisher: name: arXiv
Year: 2019
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Effective and real-time eyeblink detection is of wide-range applications, such as deception detection, drive fatigue detection, face anti-spoofing, etc. Although numerous of efforts have already been paid, most of them focus on addressing the eyeblink detection problem under the constrained indoor conditions with the relative consistent subject and environment setup. Nevertheless, towards the practical applications eyeblink detection in the wild is more required, and of greater challenges. However, to our knowledge this has not been well studied before. In this paper, we shed the light to this research topic. A labelled eyeblink in the wild dataset (i.e., HUST-LEBW) of 673 eyeblink video samples (i.e., 381 positives, and 292 negatives) is first established by us. These samples are captured from the unconstrained movies, with the dramatic variation on human attribute, human pose, illumination condition, imaging configuration, etc. Then, we formulate eyeblink detection task as a spatial-temporal pattern recognition problem. After locating and tracking human eye using SeetaFace engine and KCF tracker respectively, a modified LSTM model able to capture the multi-scale temporal information is proposed to execute eyeblink verification. A feature extraction approach that reveals appearance and motion characteristics simultaneously is also proposed. The experiments on HUST-LEBW reveal the superiority and efficiency of our approach. It also verifies that, the existing eyeblink detection methods cannot achieve satisfactory performance in the wild.
Atmospheric Neutrino Oscillation and a Phenomenological Lepton Mass Matrix
Creators: name: Fukugita, M.
name: Tanimoto, M.
name: Yanagida, T.
Publisher: name: arXiv
Year: 1997
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We propose simple phenomenological lepton mass matrices which describe the three neutrinos almost degenerate in mass, leading to a very large mixing angle between $ν_μ$ and $ν_τ$, as consistent with a recent report on atmospheric neutrino oscillation from the Superkamiokande collaboration. Our matrix model also gives $ν_e-ν_μ$ mixing in agreement with the value required for neutrino oscillation to explain the solar neutrino problem.
description: 10 pages, Latex file, small corrections in text and references, to appear in PRD
Phase Behavior of a Simple Model for Membrane Proteins
Creators: name: Noro, Massimo G.
name: Frenkel, Daan
Publisher: name: arXiv
Year: 2000
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Quantitative Biology (q-bio)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: We report a numerical simulation of the phase diagram of a simple model for membrane proteins constrained to move in a plane. In analogy with the corresponding three dimensional models, the liquid-gas transition becomes metastable as the range of attraction decreases. Spontaneous crystallization happens much more readily in the two dimensional models rather than in their three dimensional counterparts.
description: Revtex, 9 pages, 7 figures
Spin-polarized transport and Andreev reflection in semiconductor/superconductor hybrid structures
Creators: name: Zutic, Igor
name: Sarma, S. Das
Publisher: name: arXiv
Year: 1999
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We show that spin-polarized electron transmission across semiconductor/superconductor (Sm/S) hybrid structures depends sensitively on the degree of spin polarization as well as the strengths of potential and spin-flip scattering at the interface. We demonstrate that increasing the Fermi velocity mismatch in the Sm and S regions can lead to enhanced junction transparency in the presence of spin polarization. We find that the Andreev reflection amplitude at the superconducting gap energy is a robust measure of the spin polarization magnitude, being independent of the strengths of potential and spin-flip scattering and the Fermi velocity of the superconductor.
description: 4 pages, 2 figures
Additional file 2: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells
Creators: name: Mostafa, Mahmoud
name: Rider, Christopher
name: Suharsh Shah
name: Traves, Suzanne
name: Gordon, Paul
name: Miller-Larsson, Anna
name: Leigh, Richard
name: Newton, Robert
Publisher: name: figshare
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Marine Biology
subject: Cancer
subject: Hematology
subject: Plant Biology
subject: 60506 Virology

description: Concentration-dependent induction of gene expression by budesonide in primary human bronchial epithelial (HBE) cells. Primary HBE cells were either not treated or treated with the indicated concentrations of budesonide. After 6 h, cells were harvested for RNA and qPCR was performed for the indicated genes and GAPDH. Data (N = 3 individuals), normalized to GAPDH, were expressed as fold relative to untreated control and are plotted as mean ± SE. (PDF 21 kb)
Additional file 5 of Urinary peptidomics reveals proteases involved in idiopathic membranous nephropathy
Creators: name: Lin, Baoxu
name: Liu, Jianhua
name: Zhang, Yue
name: Wu, Yabin
name: Chen, Shixiao
name: Bai, Yibo
name: Liu, Qiuying
name: Qin, Xiaosong
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Computational Biology

description: Additional file 5
A screening mechanism for extra W and Z gauge bosons
Creators: name: Matias, Joaquim
name: Vicini, Alessandro
Publisher: name: arXiv
Year: 1998
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We generalize a previous construction of a fermiophobic model to the case of more than one extra $W$ and $Z$ gauge bosons. We focus in particular on the existence of screening configurations and their implication on the gauge boson mass spectrum. One of these configurations allows for the existence of a set of relatively light new gauge bosons, without violation of the quite restrictive bounds coming from the $ρ_{\rm NC}$ parameter. The links with Bess and degenerate Bess models are also discussed. Also the signal given here by this more traditional gauge extension of the SM could help to disentangle it from the towers of Kaluza-Klein states over $W$ and $Z$ gauge bosons in extra dimensions.
description: 23 pages, 1 figure, extended discussion on precision tests. To appear in International Journal of Modern Physics A
MOESM2 of Evaluating the role of RAD52 and its interactors as novel potential molecular targets for hepatocellular carcinoma
Creators: name: Li, Ping
name: Xu, YanZhen
name: Zhang, Qinle
name: Li, Yu
name: Jia, Wenxian
name: Wang, Xiao
name: Xie, Zhibin
name: Liu, Jiayi
name: Zhao, Dong
name: Shao, Mengnan
name: Chen, Suixia
name: Mo, Nanfang
name: Jiang, Zhiwen
name: Li, Liuyan
name: Liu, Run
name: Huang, Wanying
name: Chang, Li
name: Chen, Siyu
name: Li, Hongtao
name: Zuo, Wenpu
name: Li, Jiaquan
name: Zhang, Ruoheng
name: Yang, Xiaoli
Publisher: name: figshare
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified

description: Additional file 2. Gene ontology (GO) analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of RAD52 and its node genes.
title: ADCO, Cartulaire de l'abbaye de Cîteaux dit Cartulare Antiquum t.1 (début XIIIe siècle), Cart. 166 (11 H 64), 136 folios, f. 0064v
Creators: name: de la Côte d'Or, Archives départementales
name: Archives Départementales De La Côte-D'Or
name: Petot, Frédérique
name: Petot, Frédéric
name: Projet CBMA
name: CG21/F.PETOT/2012
Publisher: name: NAKALA - https://nakala.fr (Huma-Num - CNRS)
publisherIdentifier: https://ror.org/04ces3204
publisherIdentifierScheme: ROR
Year: 2020
Subjects: subject: cartulaire
subject: LaMOP
subject: Laboratoire de Médiévistique Occidentale de Paris
subject: Corpus Burgundiae Medii Aevi
subject: Chartes de la Bourgogne du Moyen Âge

description: Cartulaire de l'abbaye de Cîteaux dit Cartulare Antiquum t.1 (début XIIIe siècle), Archives départementales de la Côte-d'Or, Cart. 166 (11 H 64), 136 folios, f. 0064v, Numérisation en mode image.
description: Relation: http://www.cbma-project.eu/
description: Bibliographic citation: Cartulaire de l'abbaye de Cîteaux dit Cartulare Antiquum t.1 (début XIIIe siècle), Archives départementales de la Côte-d'Or, Cart. 166 (11 H 64), 136 folios, f. 0064v, in Projet CBMA - Corpus Burgundiae Medii Aevi [Ressource en ligne], https:// manuscrits.cbma-project.eu/
description: Provenance: https://www.geonames.org/3024876
description: Provenance: http://www.idref.fr/030974844/id
description: Provenance: https://catalogue.bnf.fr/ark:/12148/cb12228351v
description: Provenance: abbaye de Cîteaux
description: Provenance: http://www.wikidata.org/entity/Q843261
Theory of the Breakdown of the Quantum Hall Effect
Creators: name: Tsemekhman, V.
name: Tsemekhman, K.
name: Wexler, C.
name: Han, J. H.
name: Thouless, D. J.
Publisher: name: arXiv
Year: 1996
Subjects: subject: Condensed Matter (cond-mat)
subject: FOS: Physical sciences

description: Breakdown of the Quantum Hall Effect at high values of injected current is explained as a consequence of an abrupt formation of a metallic ``river'' percolating from one edge of the sample to the other. Such river is formed when lakes of compressible liquid, where the long-range disorder potential is screened, get connected with each other due to the strong electric field. Our theory predicts critical currents consistent with experiment values and explains various features of the breakdown.
description: Presented at the 12th conference on High Magnetic Fields in Semiconductor Physics, Wuerzburg, Germany, July/1996
From coherent collective excitation to Rydberg blockade on an atom chip
Creators: name: de Hond, Julius
name: van Bijnen, Rick
name: Kokkelmans, S. J. J. M. F.
name: Spreeuw, R. J. C.
name: Heuvell, H. B. van Linden van den
name: van Druten, N. J.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Using time-resolved measurements, we demonstrate coherent collective Rydberg excitation crossing over into Rydberg blockade in a dense and ultracold gas trapped at a distance of 100 $μ$m from a room-temperature atom chip. We perform Ramsey-type measurements to characterize the coherence. The experimental data are in good agreement with numerical results from a master equation using a mean-field approximation, and with results from a super-atom-based Hamiltonian. These results represent significant progress in exploring a strongly interacting driven Rydberg gas on an atom chip.
description: 6 pages, 3 figures
Mirror Symmetry for hyperkaehler manifolds
Creators: name: Verbitsky, Misha
Publisher: name: arXiv
Year: 1995
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Algebraic Geometry (math.AG)
subject: FOS: Physical sciences
subject: FOS: Mathematics

description: We prove the Mirror Conjecture for Calabi-Yau manifolds equipped with a holomorphic symplectic form. Such manifolda are also known as complex manifolds of hyperkaehler type. We obtain that a complex manifold of hyperkaehler type is Mirror dual to itself. The Mirror Conjecture is stated (following Kontsevich, ICM talk) as the equivalence of certain algebraic structures related to variations of Hodge structures. We compute the canonical flat coordinates on the moduli space of Calabi-Yau manifolds of hyperkaehler type, introduced to Mirror Symmetry by Bershadsky, Cecotti, Ooguri and Vafa.
description: 62 pages, LaTeX 2e, minor corrections (grammar and typos) added since then
Additional file 12: of Conserved regulation of RNA processing in somatic cell reprogramming
Creators: name: Kanitz, Alexander
name: Syed, Afzal
name: Kaji, Keisuke
name: Zavolan, Mihaela
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 60506 Virology
subject: Computational Biology

description: Figure S9. Splicing events in human and mouse reprogramming. The heatmaps depict ‘percent spliced in’ (PSI) values across the indicated comparisons (column labels) for the top 100 alternative splicing (AS) events (row labels), ranked by absolute mean z-scores across comparisons, in human (A) and mouse (B). Row labels represent shorthand event identifiers derived from gene symbols or, if unavailable, Ensembl gene identifiers. See Additional file 3 for the corresponding SUPPA event identifiers. AS event classes are indicated by colored boxes with the following abbreviations: A3, alternative 3’ splice site; A5, alternative 5’ splice site; AF, alternative first exons; AL, alternative last exon; MX, mutually exclusive exons; RI, retained intron; SE, skipping exon. Filtering of events by expression as in Fig. 5a. Dendrograms/clustering as in Fig. 1d/e. (PDF 62 kb)
Quantum inverse iteration algorithm for programmable quantum simulators
Creators: name: Kyriienko, Oleksandr
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We propose a quantum inverse iteration algorithm which can be used to estimate the ground state properties of a programmable quantum device. The method relies on the inverse power iteration technique, where the sequential application of the Hamiltonian inverse to an initial state prepares an approximate groundstate. To apply the inverse Hamiltonian operation, we write it as a sum of unitary evolution operators using the Fourier approximation approach. This allows to reformulate the protocol as separate measurements for the overlap of initial and propagated wavefunction. The algorithm thus crucially depends on the ability to run Hamiltonian dynamics with an available quantum device. We benchmark the performance using paradigmatic examples of quantum chemistry, corresponding to molecular hydrogen and beryllium hydride. Finally, we show its use for studying the ground state properties of relevant material science models which can be simulated with existing devices, considering an example of the Bose-Hubbard atomic simulator.
description: revised version, Bose-Hubbard simulation added
Additional file 1: of Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells
Creators: name: Mostafa, Mahmoud
name: Rider, Christopher
name: Suharsh Shah
name: Traves, Suzanne
name: Gordon, Paul
name: Miller-Larsson, Anna
name: Leigh, Richard
name: Newton, Robert
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Pharmacology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Oligonucleotides used for qPCR. Forward and reverse primer sequences (5â ˛- 3â ˛) are shown. For genes with more than one splice variant, primers were designed to detect all variants. All primers were designed using Primer BLAST (NCBI) and were synthesized by the DNA synthesis lab at the University of Calgary. (DOCX 19 kb)
Magnoliaceae Juss., Gen. Pl.
Creators: name: Reveal, James L.
name: Chase, Mark W.
name: Iii, - Apg
name: Iii, Apg
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy

description: 16. Magnoliaceae Juss., Gen. Pl.: 280. 4 Aug 1789, nom. cons.
 Liriodendraceae F.A.Barkley, Phytologia 32: 304. 29 Oct 1975
description: Published as part of Reveal, James L., Chase, Mark W., Iii, - Apg & Iii, Apg, 2011, APG III: Bibliographical Information and Synonymy of Magnoliidae Abstract Kew words Introduction, pp. 71-134 in Phytotaxa 19 (1) on page 74, DOI: 10.11646/phytotaxa.19.1.4, http://zenodo.org/record/10121353