cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Ultrafast Optical Spectroscopy of Micelle-Suspended Single-Walled Carbon Nanotubes
Creators: name: Kono, J.
name: Ostojic, G. N.
name: Zaric, S.
name: Strano, M. S.
name: Moore, V. C.
name: Shaver, J.
name: Hauge, R. H.
name: Smalley, R. E.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We present results of wavelength-dependent ultrafast pump-probe experiments on micelle-suspended single-walled carbon nanotubes. The linear absorption and photoluminescence spectra of the samples show a number of chirality-dependent peaks, and consequently, the pump-probe results sensitively depend on the wavelength. In the wavelength range corresponding to the second van Hove singularities (VHSs), we observe sub-picosecond decays, as has been seen in previous pump-probe studies. We ascribe these ultrafast decays to intraband carrier relaxation. On the other hand, in the wavelength range corresponding to the first VHSs, we observe two distinct regimes in ultrafast carrier relaxation: fast (0.3-1.2 ps) and slow (5-20 ps). The slow component, which has not been observed previously, is resonantly enhanced whenever the pump photon energy resonates with an interband absorption peak, and we attribute it to radiative carrier recombination. Finally, the slow component is dependent on the pH of the solution, which suggests an important role played by H$^+$ ions surrounding the nanotubes.
description: 6 pages, 8 figures, changed title, revised, to be published in Applied Physics A
Dynamic Relationships and Efficiency of Rice Byproduct Prices
Creators: name: Brorsen, B. Wade
name: Grant, Warren R.
name: Chavas, Jean-Paul
name: Brorsen, B. Wade
name: Grant, Warren R.
name: Chavas, Jean-Paul
Publisher: name: Unknown
Year: 1985
Subjects: subject: Crop Production/Industries
subject: Demand and Price Analysis
subject: Productivity Analysis
subject: Prices
subject: rice
subject: byproducts
subject: causality
subject: multipliers

description: This article analyzes the dynamic relationships among weekly prices of price byproducts, long gram rice, and corn, using causality tests and dynamic multipliers The authors use forecasts to evaluate the time series model rice byproducts prices may be influenced more by shifts 10 demand than 10 supply. Long gram rice prices are related to brewers and seconds prices, but not to bran or mill feed prices Mill feed and corn prices move together. Corn prices exhibited no consistent relationship With seconds, brewers, or long gram prices
SUMO conjugation regulates immune signalling
Creators: name: Sushmitha Hegde
name: X. Amarendranath Soory
name: Bhagyashree Kaduskar
name: Girish Ratnaparkhi
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Post-translational modifications (PTMs) are critical drivers and attenuators for proteins that regulate immune signalling cascades in host defence. In this review, we explore functional roles for one such PTM, the small ubiquitin like modifier (SUMO). Very few of the SUMO conjugation targets identified by proteomic studies have been validated in terms of their roles in host defence. Here, we compare and contrast potential SUMO substrate proteins in immune signalling for flies and mammals, with an emphasis on NFκB pathways. We discuss, using the few mechanistic studies that exist for validated targets, the effect of SUMO conjugation on signalling and also explore current molecular models that explain regulation by SUMO. We also discuss in detail roles of evolutionary conservation of mechanisms, SUMO interaction motifs, crosstalk of SUMO with other PTMs, emerging concepts such as group SUMOylation and finally, the potentially transforming roles for genome editing technologies in studying the effect of PTMs.
MOESM1 of In vitro activity of a G-quadruplex-stabilizing small molecule that synergizes with Navitoclax to induce cytotoxicity in acute myeloid leukemia cells
Creators: name: Montoya, Justin
name: Turnidge, Megan
name: Wai, Daniel
name: Apurvi Patel
name: Lee, David
name: Gokhale, Vijay
name: Hurley, Laurence
name: Arceci, Robert
name: Wetmore, Cynthia
name: Azorsa, David
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 1: Table S1. AUC values for Combination Drug Screen with GQC-05 in KG-1a Cells.
Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression
Creators: name: Ciuculete, Diana M.
name: Voisin, Sarah
name: Kular, Lara
name: Nipuni Welihinda
name: Jonsson, Jörgen
name: Jagodic, Maja
name: Mwinyi, Jessica
name: Schiöth, Helgi B.
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.
Additional file of Novel transposable elements from Anopheles gambiae
Creators: name: Fernández-Medina, Rita D
name: Struchiner, Cláudio J
name: Ribeiro, José MC
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file of Novel transposable elements from Anopheles gambiae
Improving the sensitivity of FM spectroscopy using nano-mechanical cantilevers
Creators: name: Chernobrod, Boris M.
name: Berman, Gennady P.
name: Milonni, Peter W.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: It is suggested that nano-mechanical cantilevers can be employed as high-Q filters to circumvent laser noise limitations on the sensitivity of frequency modulation spectroscopy. In this approach a cantilever is actuated by the radiation pressure of the amplitude modulated light that emerges from an absorber. Numerical estimates indicate that laser intensity noise will not prevent a cantilever from operating in the thermal noise limit, where the high Q's of cantilevers are most advantageous.
description: 5 pages, 1 figure
As Incubadoras Tecnologicas de Cooperativas Populares: Uma Primeira Tentativa de Construcao de Modelo
Creators: name: Gervais, Ana Maria Dubeux
name: Gervais, Ana Maria Dubeux
Publisher: name: Unknown
Year: 2006
Subjects: Research and Development/Tech Change/Emerging Technologies
Research Methods/ Statistical Methods

description: As incubadoras de empresas de base tecnológica existem desde os anos 50. No Brasil, elas surgem a partir dos anos 70 nos chamados ‘sciences parks’ ou parques tecnológicos. Tais incubadoras têm por objetivo principal hospedar pequenas empresas produtoras de inovação e de alta tecnologia para que, num certo período de tempo possam ser autônomas em sua gestão. Inspiradas deste modelo surgem no Brasil, em meados dos anos 90, as chamadas Incubadoras Tecnológicas de Cooperativas Populares (ITCP’s) voltadas para um público excluído de um ponto de vista sócioeconômico e de acesso aos mecanismos de exercício da cidadania. Desde esta época temos observado um crescimento significativo das ITCP’s, importante vertente da extensão universitária brasileira que vêm contribuindo para o apoio e fomento à grupos econômicos solidários urbanos e rurais na perspectiva mais ampla de construção da economia solidária. O presente trabalho, resultado de uma pesquisa de tese de doutorado, apresenta um estudo comparativo entre as incubadoras de empresas de base tecnológicas e as ITCP’s na perspectiva de estabelecer semelhanças e diferenças entre as mesmas na perspectiva de sistematizar uma modelização principalmente da experiência das ITCP’s. Analisar a natureza do trabalho das incubadoras e a natureza das empresas criadas foram os nossos objetivos principais. No que se refere à primeira categoria a comparação se dá a partir das instituições promotoras das incubadoras, de suas missões e objetivos, do tipo de projeto ao qual elas se dirigem, do tipo de serviçoofertado, do modelo de financiamento e do contexto (caracterizado pelo entorno onde a incubadora exerce suas atividades). Finalmente na segunda categoria de critérios temos como parâmetros comparativos a idade e o nível de escolaridade dos membros, o ramo de atividade, a estimativa do volume de negócios, o número de associados e o tempo de permanência das empresas na incubadora
Holomorphic anomaly equation for $(\mathbb{P}^2,E)$ and the Nekrasov-Shatashvili limit of local $\mathbb{P}^2$
Creators: name: Bousseau, Pierrick
name: Fan, Honglu
name: Guo, Shuai
name: Wu, Longting
Publisher: name: arXiv
Year: 2020
Subjects: subject: Algebraic Geometry (math.AG)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We prove a higher genus version of the genus $0$ local-relative correspondence of van Garrel-Graber-Ruddat: for $(X,D)$ a pair with $X$ a smooth projective variety and $D$ a nef smooth divisor, maximal contact Gromov-Witten theory of $(X,D)$ with $λ_g$-insertion is related to Gromov-Witten theory of the total space of $\mathcal{O}_X(-D)$ and local Gromov-Witten theory of $D$. Specializing to $(X,D)=(S,E)$ for $S$ a del Pezzo surface or a rational elliptic surface and $E$ a smooth anticanonical divisor, we show that maximal contact Gromov-Witten theory of $(S,E)$ is determined by the Gromov-Witten theory of the Calabi-Yau 3-fold $\mathcal{O}_S(-E)$ and the stationary Gromov-Witten theory of the elliptic curve $E$. Specializing further to $S=\mathbb{P}^2$, we prove that higher genus generating series of maximal contact Gromov-Witten invariants of $(\mathbb{P}^2,E)$ are quasimodular and satisfy a holomorphic anomaly equation. The proof combines the quasimodularity results and the holomorphic anomaly equations previously known for local $\mathbb{P}^2$ and the elliptic curve. Furthermore, using the connection between maximal contact Gromov-Witten invariants of $(\mathbb{P}^2,E)$ and Betti numbers of moduli spaces of semistable one-dimensional sheaves on $\mathbb{P}^2$, we obtain a proof of the quasimodularity and holomorphic anomaly equation predicted in the physics literature for the refined topological string free energy of local $\mathbb{P}^2$ in the Nekrasov-Shatashvili limit.
description: 66 pages, revised version, published in Forum of Mathematics, Pi
The Evolutionary Status of Early-type Galaxies in Abell 2390
Creators: name: Fritz, Alexander
name: Ziegler, Bodo L.
name: Bower, Richard G.
name: Smail, Ian
name: Davies, Roger L.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We explore the evolution of the early-type galaxy population in the rich cluster Abell 2390 at z=0.23. For this purpose, we have obtained spectroscopic data of 51 elliptical and lenticular galaxies with MOSCA at the 3.5 m telescope on Calar Alto Observatory. As our investigation spans both a broad range in luminosity (-22.3
description: 6 pages, 4 figures, to appear in the proceedings of the JENAM 2002 Workshop WS-GE "Galaxy Evolution in Groups and Clusters", Eds. by C. Lobo, M. Serote Roos, A. Biviano, Ap&SS, Kluwer, in press; oral contribution, held in Porto, Portugal, September 2-7, 2002
Are China’s grain trade policies effective in the stabilization of domestic food prices? An investigation based on a structural break regime switching model
Creators: name: Lu, Jie
name: Zhu, Xinkai
name: Yu, Zhonghua
name: Lu, Jie
name: Zhu, Xinkai
name: Yu, Zhonghua
Publisher: name: Unknown
Year: 2013
Subjects: subject: Agricultural and Food Policy
subject: Food Price
subject: Stabilizing Point
subject: Structural Break Regime Switching

description: As the base price, grain prices have played considerably important role in China’s macro-economy and social price level. In this study we investigate the fluctuation characteristics of some main crops of China’s grain during the past two decades by using Structural Break Regime Switching Model. We find that China’s grain price growth has become more stable since 2004 with narrowing low-and high-growth regimes. The implementation of minimum grain purchase price policy, improvement of market structure and diversification of acquisitions which improve farmers’ overall earning expectation and stabilize food price, are the most important motivating factors.
On the Origin of Superconductivity at Nickel-Bismuth Interfaces
Creators: name: Vaughan, Matthew
name: Satchell, Nathan
name: Ali, Mannan
name: Kinane, Christy J.
name: Stenning, Gavin B. G.
name: Langridge, Sean
name: Burnell, Gavin
Publisher: name: arXiv
Year: 2019
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Unconventional superconductivity has been suggested to be present at the interface between bismuth and nickel in thin-film bilayers. In this work, we study the structural, magnetic and superconducting properties of sputter deposited Bi/Ni bilayers. As-grown, our films do not display a superconducting transition, however, when stored at room temperature, after about 14 days our bilayers develop a superconducting transition up to 3.8 K. To systematically study the effect of low temperature annealing on our bilayers, we perform structural characterization with X-ray diffraction and polarized neutron reflectometry, along with magnetometry and low temperature electrical transport measurements on samples annealed at $70\,^\circ$C. We show that the onset of superconductivity in our samples is coincident with the formation of ordered NiBi$_3$ intermetallic alloy, a known $s$-wave superconductor. We calculate that the annealing process has an activation energy of $(0.86\pm 0.06)$eV. As a consequence, gentle heating of the bilayers will cause formation of the superconducting NiBi$_3$ at the Ni/Bi interface, which poses a challenge to studying any distinct properties of Bi/Ni bilayers without degrading that interface.
description: 13 pages, 7 figures
τ\to μ\bar{ν_i} ν_i decay in the general two Higgs doublet model
Creators: name: Iltan, E.
name: Sundu, H.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study τ\to μ\bar{ν_i} ν_i, i=e,μ,τdecay in the model III version of the two Higgs doublet model. We calculated the BR at the order of the magnitude of 10^{-6}-10^{-4} for the intermediate values of the Yukawa couplings. Furthermore, we predict the upper limit of the coupling for the τ-h^0 (A^0)-τtransition as \sim 0.3 in the case that the BR is \sim 10^{-6}. We observe that the experimental result of the process under consideration can give comprehensive information about the physics beyond the standard model and the free parameters existing.
description: 9 pages, 5 figures
MOESM2 of Creating performance intelligence for primary health care strengthening in Europe
Creators: name: Barbazza, Erica
name: Kringos, Dionne
name: Kruse, Ioana
name: Klazinga, Niek
name: Tello, Juan
Publisher: name: figshare
Year: 2019
Subjects: subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 2. Tracer conditions
Evaluating liquid biopsies for methylomic profiling of prostate cancer
Creators: name: Silva, Romina
name: Moran, Bruce
name: Russell, Niamh M.
name: Fahey, Ciara
name: Vlajnic, Tatjana
name: Rustom P. Manecksha
name: Finn, Stephen P.
name: Brennan, Donal J.
name: Gallagher, William M.
name: Perry, Antoinette S.
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Marine Biology
subject: Cancer

description: Background: Liquid biopsies offer significant potential for informing on cancer progression and therapeutic resistance via minimally invasive serial monitoring of genetic alterations. Although the cancer epigenome is a central driving force in most neoplasia, the accuracy of monitoring the tumor methylome using liquid biopsies remains relatively unknown. Objectives: to investigate how well two types of liquid biopsy (urine and blood) capture the prostate cancer methylome, and may thus serve as a non-invasive surrogate for studying the tumor epigenome. Methods: A cohort of four metastatic treatment naïve prostate cancer (PCa) patients was selected. Matched biopsy cores (tumor and histologically matched-normal), post-DRE, pre-biopsy urine, and peripheral blood plasma were available for each subject. DNA methylation was profiled utilizing the Infinium® MethylationEPIC BeadChip (Illumina) and analysed using the RnBeads software. Significantly (FDR adjusted P < 0.05) differentially methylated probes (DMPs) between tumor and MN were identified and examined in the liquids (done at a grouped and individual subject level). Results: DNA methylation analysis of urine and blood in men with metastatic PCa showed highly correlated patterns between the different liquid types (ρ = 0.93, P < 0.0001), with large contributions from non-tumor sources. DNA methylation profiles of liquids were more similar between subjects, than intra-individual liquid-tumor correlations. Overall, both urine and plasma are viable surrogates for tumor tissue biopsies, capturing up to 39.40% and 64.14% of tumor-specific methylation alterations, respectively. Conclusion: We conclude that both urine and blood plasma are easily accessible and sensitive biofluids for the study of PCa epigenomic alterations.
A geometric phase gate without dynamical phases
Creators: name: Unanyan, R. G.
name: Fleischhauer, M.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A general scheme for an adiabatic geometric phase gate is proposed which is maximally robust against parameter fluctuations. While in systems with SU(2) symmetry geometric phases are usually accompanied by dynamical phases and are thus not robust, we show that in the more general case of a SU(2) x SU(2) symmetry it is possible to obtain a non-vanishing geometric phase without dynamical contributions. The scheme is illustrated for a phase gate using two systems with dipole-dipole interactions in external laser fields which form an effective four-level system.
description: 4 pages, 5 figures
Two-Branch Fiber Link for International Clock Networks
Creators: name: Xu, Dan
name: Cantin, Etienne
name: Frank, Florian
name: Quintin, Nicolas
name: Meynadier, Frédéric
name: Tuckey, Philip
name: Amy-Klein, Anne
name: Lopez, Olivier
name: Pottie, Paul-Eric
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: We present our work on realizing two-branch fiber links enabling multiple-partner clock comparisons in Europe. We report in detail on the setup connecting two long haul links, and report for the relative frequency stability and accuracy. We report on a combined uptime of 90% for our dual-branch link during almost one month. We finally discuss the combined uncertainty contribution of the ensemble of the link architecture to a clock comparison. We show that the frequency transfer uncertainty is 2 x 10 --19 .
Assessing the impact of crop specialization on farms’ performance in vegetables farming in Benin: a non-neutral stochastic frontier approach
Creators: name: Singbo, Alphonse G.
name: Emvalomatis, Grigorios
name: Alfons, Oude Lansink
name: Singbo, Alphonse G.
name: Emvalomatis, Grigorios
name: Alfons, Oude Lansink
Publisher: name: Unknown
Year: 2013
Subjects: subject: Agricultural and Food Policy
subject: Crop Production/Industries
subject: Farm Management
subject: Food Security and Poverty
subject: Production Economics
subject: Productivity Analysis
subject: Farm performance
subject: Specialization
subject: Impact
subject: Input distance function
subject: Non-neutral stochastic frontier
subject: Benin

description: A non-neutral stochastic distance function model is used to examine whether output specialization has an impact on the economic performance of vegetable producers in Benin. Specialization is assumed to have an effect on the production frontier and on the distance to the production frontier (technical inefficiency). The technology is found to exhibit diseconomies of scope, indicating that vegetable producers have an incentive for specialization. At the same time, the degree of specialization has a positive effect on technical efficiency. From a policy perspective, the findings imply that current government policies to encourage diversification may lead to a lower performance.
MOESM3 of Creating performance intelligence for primary health care strengthening in Europe
Creators: name: Barbazza, Erica
name: Kringos, Dionne
name: Kruse, Ioana
name: Klazinga, Niek
name: Tello, Juan
Publisher: name: figshare
Year: 2019
Subjects: subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy

description: Additional file 3. Indicator passports
A multispectral analysis of the northeastern shell of IC 443
Creators: name: Alarie, Alexandre
name: Drissen, Laurent
Publisher: name: arXiv
Year: 2019
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We have carried out optical observations of the north-eastern part of the supernova remnant IC 443 using the CFHT imaging spectrograph SITELLE. The observations consist of three multispectral cubes covering an 11$^{\prime}$ $\times$11$^{\prime}$ area allowing the investigation of both the spatial and spectral variation of 9 emission lines : [OII] $λλ$3726+3729, [OIII] $λλ$4959,5007, H$β$, H$α$, [NII] $λλ$6548,6583 and [SII] $λλ$6716,6731. Extinction measurement from the H$α$ / H$β$ ratio shows significant variation across the observed region with E(B-V) = 0.8-1.1. Electron density measurements using [SII] lines indicate densities ranging from 100 up to 2500 cm$^{-3}$. Models computed with the shock modelling code MAPPINGS are presented and compared with the observations. A combination of complete shock model and truncated ones are required in order to explain the observed spectrum. The shock velocities found in IC 443 are between 20 and 150 km/s with 75 km/s being the most prominent velocity. The pre-shock number density varies from 20 to 60 cm$^{-3}$. A single set of abundances close to solar values combined with varying shock parameters (shock velocity, pre-shock density and shock age) are sufficient to explain to great variation of lines intensities observed in IC 443. Despite the relatively modest spectral resolution of the data (R$\sim 1500$ at H$α$), we clearly separate the red and blue velocity components of the expanding nebula, which show significant morphological differences.
description: 13 pages, 30 figures; submitted to MNRAS (revised version)
Additional file 1 of Novel transposable elements from Anopheles gambiae
Creators: name: Fernández-Medina, Rita D
name: Struchiner, Cláudio J
name: Ribeiro, José MC
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1:AnoTExcel database in standalone format. It includes the links that need to be extracted to the user's computer http://exon.niaid.nih.gov/transcriptome/TE/A_gambiae/AnoTExcel-SA.zip . (DOC 24 KB)
A regulatory role for CHD2 in myelopoiesis
Creators: name: Varnoosfaderani, Farzaneh Shahin
name: Palau, Anna
name: Wenbo Dong
name: Persson, Jenna
name: Durand-Dubief, Mickaël
name: J Peter Svensson
name: Lennartsson, Andreas
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology

description: The transcriptional program that dictates haematopoietic cell fate and differentiation requires an epigenetic regulatory and memory function, provided by a network of epigenetic factors that regulate DNA methylation, post-translational histone modifications and chromatin structure. Disturbed epigenetic regulation causes perturbations in the blood cell differentiation program that results in various types of haematopoietic disorders. Thus, accurate epigenetic regulation is essential for functional haematopoiesis. In this study, we used a CRISPR-Cas9 screening approach to identify new epigenetic regulators in myeloid differentiation. We designed a Chromatin-UMI CRISPR guide library targeting 1092 epigenetic regulators. Phorbol 12-myristate 13-acetate (PMA) treatment of the chronic myeloid leukaemia cell line K-562 was used as a megakaryocytic myeloid differentiation model. Both previously described developmental epigenetic regulators and novel factors were identified in our screen. In this study, we validated and characterized a role for the chromatin remodeller CHD2 in myeloid proliferation and megakaryocytic differentiation.
From the Outside Looking in: What can Milky Way Analogues Tell us About the Star Formation Rate of Our Own Galaxy?
Creators: name: Fraser-McKelvie, Amelia
name: Merrifield, Michael
name: Aragón-Salamanca, Alfonso
Publisher: name: arXiv
Year: 2019
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The Milky Way has been described as an anaemic spiral, but is its star formation rate (SFR) unusually low when compared to its peers? To answer this question, we define a sample of Milky Way Analogues (MWAs) based on stringent cuts on the best literature estimates of non-transient structural features for the Milky Way. This selection yields only 176 galaxies from the whole of the SDSS DR7 spectroscopic sample which have morphological classifications in GZ2, from which we infer SFRs from two separate indicators. The mean SFRs found are $\log(\rm{SFR}_{SED}/\rm{M}_{\odot}~\rm{yr}^{-1})=0.53$ with a standard deviation of 0.23 dex from SED fits, and $\log(\rm{SFR}_{W4}/\rm{M}_{\odot}~\rm{yr}^{-1})=0.68$ with a standard deviation of 0.41 dex from a mid-infrared calibration. The most recent estimate for the Milky Way's star formation rate of $\log(\rm{SFR}_{MW}/\rm{M}_{\odot}~\rm{yr}^{-1})=0.22$ fits well within 2$σ$ of these values, where $σ$ is the standard deviation of each of the SFR indicator distributions. We infer that the Milky Way, while being a galaxy with a somewhat low SFR, is not unusual when compared to similar galaxies.
description: 10 pages, 5 figures, accepted for publication in MNRAS
Additional file 1 of Circular RNA mmu_circ_0005019 inhibits fibrosis of cardiac fibroblasts and reverses electrical remodeling of cardiomyocytes
Creators: name: Wu, Na
name: Li, Chengying
name: Xu, Bin
name: Xiang, Ying
name: Jia, Xiaoyue
name: Yuan, Zhiquan
name: Wu, Long
name: Zhong, Li
name: Li, Yafei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Biological Sciences not elsewhere classified

description: Additional file 1. Supplementary Information.
Determinants of Household Food Insecurity in Mexico
Creators: name: Magana-Lemus, David
name: Ishdorj, Ariun
name: Rosson, C. Parr
name: Magana-Lemus, David
name: Ishdorj, Ariun
name: Rosson, C. Parr
Publisher: name: Unknown
Year: 2013
Subjects: Consumer/Household Economics
Food Consumption/Nutrition/Food Safety
International Relations/Trade

description: Food security is defined as the situation when all people, at all times, have physical and economic access to sufficient safe and nutritious food to meet their dietary needs and food preferences for a healthy and active life (FAO 1996). According to official figures, 24.8% of Mexican population experienced moderate or severe food insecurity in 2010. This represents an increase of 3.1 percentage points with respect to 21.7% in 2008. In other words, this represents an increase of 4.1 million individuals, from 23.9 to 28 million, living under these conditions in two years, from 2008 to 2010 (CONEVAL 2011). CONEVAL validated the Mexican Food Security Scale (EMSA, for its acronym in Spanish) as a reliable instrument to measure food security using Rasch model at the national and state level in Mexico (Carrasco, Peinador, and Aparicio 2010). Despite the validity that the food security scale is proved to have, to the best of our knowledge, there is no available study that has intended to find association between demographic factors and food insecurity at a national level in Mexico. This study will bridge the gap in the literature regarding the identification of factors that determine food insecurity in Mexico. The data used in this study come from The Socioeconomic Conditions Module (MCS 2010, for its acronym in Spanish) of the National Household Income and Expenditure Survey (ENIGH, for its name in Spanish) in the third quarter of 2010. In this study we use an ordered probit model, along with nationally representative data and a newly developed food security scale for Mexico. The analysis was conducted for the general (total) population first and then for a subpopulation group of rural lower-income households. We found that households with younger, less-educated household heads were more likely to suffer food insecurity. Other groups that were found to be vulnerable in terms of food insecurity include: households headed by a single, widow or divorced mother, households with disabled family members, households with strong indigenous background, rural households, low income families, non-agricultural households and households with kids.
Near-Infrared Spectroscopy of McNeil's Nebula Object
Creators: name: Vacca, W. D.
name: Cushing, M. C.
name: Simon, T.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We present 0.8-5.2 micron spectroscopy of the compact source at the base of a variable nebula (McNeil's Nebula Object) in the Lynds 1630 dark cloud that went into outburst in late 2003. The spectrum of this object reveals an extremely red continuum, CO bands at 2.3-2.5 microns in emission, a deep 3.0 micron ice absorption feature, and a solid state CO absorption feature at 4.7 microns. In addition, emission lines of H, Ca II, Mg I, and Na I are present. The Paschen lines exhibit P Cygni profiles, as do two lines of He I, although the emission features are very weak in the latter. The Brackett lines, however, are seen to be purely in emission. The P Cygni profiles clearly indicate that mass outflow is occurring in a wind with a velocity of ~400 km/s. The H line ratios do not yield consistent estimates of the reddening, nor do they agree with the extinction estimated from the ice feature (A_V ~ 11). We propose that these lines are optically thick and are produced in a dense, ionized wind. The near-infrared spectrum does not appear similar to any known FUor or EXor object. However, all evidence suggests that McNeil's Nebula Object is a heavily-embedded low-mass Class I protostar, surrounded by a disk, whose brightening is due to a recent accretion event.
description: 11 pages, 2 ps figures, accepted for publication in ApJ Letters
Deep generative model-driven multimodal prostate segmentation in radiotherapy
Creators: name: Girum, Kibrom Berihu
name: Créhange, Gilles
name: Hussain, Raabid
name: Walker, Paul Michael
name: Lalande, Alain
Publisher: name: arXiv
Year: 2019
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Deep learning has shown unprecedented success in a variety of applications, such as computer vision and medical image analysis. However, there is still potential to improve segmentation in multimodal images by embedding prior knowledge via learning-based shape modeling and registration to learn the modality invariant anatomical structure of organs. For example, in radiotherapy automatic prostate segmentation is essential in prostate cancer diagnosis, therapy, and post-therapy assessment from T2-weighted MR or CT images. In this paper, we present a fully automatic deep generative model-driven multimodal prostate segmentation method using convolutional neural network (DGMNet). The novelty of our method comes with its embedded generative neural network for learning-based shape modeling and its ability to adapt for different imaging modalities via learning-based registration. The proposed method includes a multi-task learning framework that combines a convolutional feature extraction and an embedded regression and classification based shape modeling. This enables the network to predict the deformable shape of an organ. We show that generative neural networkbased shape modeling trained on a reliable contrast imaging modality (such as MRI) can be directly applied to low contrast imaging modality (such as CT) to achieve accurate prostate segmentation. The method was evaluated on MRI and CT datasets acquired from different clinical centers with large variations in contrast and scanning protocols. Experimental results reveal that our method can be used to automatically and accurately segment the prostate gland in different imaging modalities.
description: 8 pages, camera ready paper, accepted for Artificial Intelligence in Radiation Therapy (AIRT), in conjunction with MICCAI 2019
Dynamic shifts in chromatin states differentially mark the proliferative basal cells and terminally differentiated cells of the developing epidermis
Creators: name: Shue, Yan Ting
name: Lee, Kang Ting
name: Walters, Benjamin William
name: Ong, Hui Binn
name: Shaktheeshwari Silvaraju
name: Lam, Wei Jun
name: Lim, Chin Yan
Publisher: name: Taylor & Francis
Year: 2020
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Post-translational modifications on nucleosomal histones represent a key epigenetic regulatory mechanism to mediate the complex gene expression, DNA replication, and cell cycle changes that occur in embryonic cells undergoing lineage specification, maturation, and differentiation during development. Here, we investigated the dynamics of 13 key histone marks in epidermal cells at three distinct stages of embryonic skin development and identified significant changes that corresponded with the maturation of the proliferative basal epidermal cells and terminally differentiated cells in the stratified layers. In particular, H3K4me3 and H3K27ac were accumulated and became more prominent in the basal cells at later stages of epidermal development, while H3K27me3 was found to be low in the basal cells but highly enriched in the differentiated suprabasal cell types. Constitutive heterochromatin marked by H4K20me3 was also significantly elevated in differentiated epidermal cells at late gestation stages, which exhibited a concomitant loss of H4K16 acetylation. These differential chromatin profiles were established in the embryonic skin by gestation day 15 and further amplified at E18 and in postnatal skin. Our results reveal the dynamic chromatin states that occur as epidermal progenitor cells commit to the lineage and differentiate into the different cells of the stratified epidermis and provide insight to the underlying epigenetic pathways that support normal epidermal development and homoeostasis.
Nonlinear force-free configurations in cylindrical geometry
Creators: name: Lyutikov, Maxim
Publisher: name: arXiv
Year: 2019
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: We find a new family of solutions for force-free magnetic structures in cylindrical geometry. These solutions have radial power-law dependance and are periodic but non-harmonic in azimuthal direction; they generalize the vacuum $z$-independent potential fields to current-carrying configurations.
MOESM1 of Creating performance intelligence for primary health care strengthening in Europe
Creators: name: Barbazza, Erica
name: Kringos, Dionne
name: Kruse, Ioana
name: Klazinga, Niek
name: Tello, Juan
Publisher: name: figshare
Year: 2019
Subjects: subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: Science Policy

description: Additional file 1. Literature reviewed
Institutional Change on First Nations: Examining factors influencing First Nations Adoption of the Framework Agreement on First Nation Land Management
Creators: name: Doidge, Mary
name: Deaton, B. James
name: Woods, Bethany
name: Doidge, Mary
name: Deaton, B. James
name: Woods, Bethany
Publisher: name: Unknown
Year: 2013
Subjects: subject: International Relations/Trade
subject: Land Economics/Use
subject: Research and Development/Tech Change/Emerging Technologies
subject: First Nations Land Management
subject: Institutions
subject: Land
subject: Probit

description: In 1999 the Canadian Federal government passed the First Nations Land Management Act, ratifying the Framework Agreement on First Nation Land Management signed by the government and 14 original signatory First Nations in 1996. This Agreement allows First Nations to opt out of the 34 land code provisions of the Indian Act and develop individual land codes, and has been promoted as a means of increasing First Nation autonomy and facilitating economic growth and development on reserve lands. This paper is the first to empirically examine factors that may influence a First Nation’s decision to become signatory to the Framework Agreement. There are currently 77 First Nation signatories to the Agreement, 39 with operational independent land codes. A unique dataset characterizing each First Nation by socioeconomic and demographic characteristics is used with a probit model to determine the effects of these characteristics on the probability of First Nation adoption of the Agreement. The results of this study indicate that proximity to an urban centre positively affects the probability that a First Nation will adopt. This finding is consistent with the idea that urban proximity is associated with increased economic opportunities, and that First Nations close to urban centres may adopt the Framework Agreement to gain greater control over their reserve land in an attempt to capture these opportunities.
Ogyges adamsi Schuster y Reyes-Castillo 1990
Creators: name: Cano, Enio B.
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Passalidae
Ogyges
Ogyges adamsi

description: Ogyges adamsi Schuster y Reyes-Castillo, 1990   Holotipo, Fig. 2
 Ogyges adamsi Schuster y Reyes-Castillo 1990: 10–12, 15; Schuster y Cano 2005: 258–259, 2006: 67; Schuster 2006: 383, 386; Schuster y Schuster 1997: 264–265; Cano 2014: 456, 473, 479, 482.
El holotipo proviene de un bosque nuboso en la Montaña Santa Bárbara, Santa Bárbara, Honduras (aproximadamente 14.899032, –88.13669, 2000 mnsm), colectado por P. Adams el 9 de Julio de 1968 (1968-12), y está depositado en IEXA. Las medidas son 39.95 (longitud total), 21.31 (longitud elitral), 13.35 (ancho humeral), 11.10 (largo del pronoto) y 14.29 (ancho del pronoto).
description: Published as part of Cano, Enio B., 2017, Redescripción del género Ogyges Kaup (Coleoptera: Passalidae) con una lista comentada de los tipos primarios, pp. 1-38 in Insecta Mundi 2017 (598) on page 5, DOI: 10.5281/zenodo.5169736
Evaluation of Multi-Slice Inputs to Convolutional Neural Networks for Medical Image Segmentation
Creators: name: Vu, Minh H.
name: Grimbergen, Guus
name: Nyholm, Tufve
name: Löfstedt, Tommy
Publisher: name: arXiv
Year: 2019
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: When using Convolutional Neural Networks (CNNs) for segmentation of organs and lesions in medical images, the conventional approach is to work with inputs and outputs either as single slice (2D) or whole volumes (3D). One common alternative, in this study denoted as pseudo-3D, is to use a stack of adjacent slices as input and produce a prediction for at least the central slice. This approach gives the network the possibility to capture 3D spatial information, with only a minor additional computational cost. In this study, we systematically evaluate the segmentation performance and computational costs of this pseudo-3D approach as a function of the number of input slices, and compare the results to conventional end-to-end 2D and 3D CNNs. The standard pseudo-3D method regards the neighboring slices as multiple input image channels. We additionally evaluate a simple approach where the input stack is a volumetric input that is repeatably convolved in 3D to obtain a 2D feature map. This 2D map is in turn fed into a standard 2D network. We conducted experiments using two different CNN backbone architectures and on five diverse data sets covering different anatomical regions, imaging modalities, and segmentation tasks. We found that while both pseudo-3D methods can process a large number of slices at once and still be computationally much more efficient than fully 3D CNNs, a significant improvement over a regular 2D CNN was only observed for one of the five data sets. An analysis of the structural properties of the segmentation masks revealed no relations to the segmentation performance with respect to the number of input slices. The conclusion is therefore that in the general case, multi-slice inputs appear to not significantly improve segmentation results over using 2D or 3D CNNs.
Chinese Producer Behavior: Aquaculture Farmers in Southern China
Creators: name: Ortega, David L.
name: Wang, H. Holly
name: Widmar, Nicole J. Olynk
name: Wu, Laping
name: Ortega, David L.
name: Wang, H. Holly
name: Widmar, Nicole J. Olynk
name: Wu, Laping
Publisher: name: Unknown
Year: 2013
Subjects: Agricultural and Food Policy
Farm Management
Institutional and Behavioral Economics
International Relations/Trade

description: The increasing share of imported food in developed countries, such as the US and European Union countries, poses new challenges for food safety and quality regulators. China as the world’s biggest food producer has the fastest growing share of fish and shellfish exports to these countries. While there have been an increasing number of studies conducted on consumer demand for various food product attributes, little research has been focused on producer behavior, and studies on Chinese food producers are especially absent in the literature. The objective of this study is to assess Chinese aquaculture producers’ willingness-to-change (WTC) and adopt certain production practices related to food safety. Producer preferences for enhanced food safety measures, and sustainable/eco-friendly production practices are assessed using a choice experiment. Primary data was collected in the leading aquaculture producing provinces of southern China. The average net income per farmer of our sample was 81,286 RMB/year of which approximately 72% originated from their aquaculture operation. Derived WTC estimates from a random parameters logit model suggest that the representative Chinese producer would require a 2.49 % premium per jin of fish to adopt enhanced food safety practices such as those required for China GAP, and No Public Harm voluntary certifications and they would accept a 3.22% discount before being indifferent between having an antibiotic-free facility and using antibiotics. WTC estimates of sustainable eco-friendly practices and verification by various entities were also assessed. A latent class model (LCM) is used to segregate producers into group with similar underlying characteristics to develop policies to improve producer practices and ultimately product safety and quality.
Additional file 2 of Novel transposable elements from Anopheles gambiae
Creators: name: Fernández-Medina, Rita D
name: Struchiner, Cláudio J
name: Ribeiro, José MC
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2:Web-based links of AnoTExcel. http://exon.niaid.nih.gov/transcriptome/TE/A_gambiae/AnoTExcel-WEB.zip . (DOC 24 KB)