cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Constraints on Neutron Star Parameters from Burst Oscillation Light Curves of the Accreting Millisecond Pulsar XTE J1814-338
Creators: name: Bhattacharyya, Sudip
name: Strohmayer, Tod E.
name: Miller, M. Coleman
name: Markwardt, Craig B.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Detailed modeling of the millisecond brightness oscillations during thermonuclear bursts from low mass X-ray binaries can provide important information about neutron star structure. Until now the implementation of this idea has not been entirely successful, largely because of the negligible harmonic content in burst oscillation lightcurves. However, the recent discovery of non-sinusoidal burst oscillation lightcurves from the accreting millisecond pulsar XTE J1814-338 has changed this situation. We, therefore, for the first time, make use of this opportunity to constrain neutron star parameters. In our detailed study of the lightcurves of 22 bursts, we fit the burst oscillation lightcurves with fully general relativistic models that include light-bending and frame-dragging for lightcurve calculation, and compute numerically the structure of neutron stars using realistic equations of state. We find that for our model and parameter grid values, at the 90% confidence level, Rc^2/GM > 4.2 for the neutron star in XTE J1814-338. We also find that the photons from the thermonuclear flash come out through the layers of accreted matter under conditions consistent with Thomson scattering, and show that the secondary companion is a hydrogen burning main sequence star, with possible bloating (probably due to X-ray heating).
description: 32 pages, 14 figures, 4 tables, thorough revision, accepted for publication in ApJ
Supplementary document for Exploring the limits of metasurface polarization multiplexing capability based on deep learning - 6399304.pdf
Creators: name: zhang, xiaohu
name: Yang, Yang
name: liu, kaifeng
name: zhang, haimo
name: shi, lintong
name: he, mengyao
name: Guo, Yongcai
Publisher: name: Optica Publishing Group
Year: 2023
Subjects: Uncategorized

description: revised Supplement 1
MOESM1 of Assessing attitudes towards medical assisted dying in Canadian family medicine residents: a cross-sectional study
Creators: name: Wong, Aaron
name: Hsu, Amy
name: Tanuseputro, Peter
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. Questionnaire on MAID. Copy of the survey questions and the order that they were presented in.
The cosmological baryon density from the deuterium to hydrogen ratio towards QSO absorption systems: D/H towards Q1243+3047
Creators: name: Kirkman, David
name: Tytler, David
name: Suzuki, Nao
name: O'Meara, John M.
name: Lubin, Dan
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We report the detection of Deuterium absorption at redshift 2.525659 towards Q1243+3047. We describe improved methods to estimate the Deuterium to Hydrogen abundance ratio (D/H) in absorption systems, including improved modeling of the continuum level, the Ly-alpha forest and the velocity structure of the absorption. Together with improved relative flux calibration, these methods give D/H = 2.42^+0.35_-0.25 x 10^-5 cm^-2 from our Keck-I HIRES spectra of Q1243+3047, where the error is from the uncertainty in the shape of the continuum level and the amount of D absorption in a minor second component. The measured D/H is likely the primordial value because the [O/H] = -2.79 +/- 0.05. This absorption system has a neutral Hydrogen column density of 19.73 +/- 0.04 cm^-2, it shows five D lines and is mostly ionized. The best estimate of the primordial D/H is 2.78^+0.44_-0.38 x 10^-5, from the log D/H values towards five QSOs. The dispersion in the five values is larger than we expect from their individual measurement errors and we suspect this is because some of these errors were underestimated. We observe a trend in D/H with neutral H column density that we also suspect is spurious. The D/H corresponds to a baryon-to-photon ratio ETA = 5.9 +/- 0.5 x 10^-10 and a cosmological baryon density Omega_b h^2 = 0.0214 +/- 0.0020 (9.3%) that agrees with values from the pre-MAP measurements of the anisotropy of the Cosmic Microwave Background.
description: 62 pages, 32 figures, submitted to ApJS
On a Nadaraya-Watson Estimator with Two Bandwidths
Creators: name: Comte, Fabienne
name: Marie, Nicolas
Publisher: name: arXiv
Year: 2020
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics
subject: 62G08, 62G05

description: In a regression model, we write the Nadaraya-Watson estimator of the regression function as the quotient of two kernel estimators, and propose a bandwidth selection method for both the numerator and the denominator. We prove risk bounds for both data driven estimators and for the resulting ratio. The simulation study confirms that both estimators have good performances, compared to the ones obtained by cross-validation selection of the bandwidth. However, unexpectedly, the single-bandwidth cross-validation estimator is found to be much better than the ratio of the previous two good estimators, in the small noise context. However, the two methods have similar performances in models with large noise.
description: 43 pages
MOESM1 of An adjunctive human-animal interaction intervention for veterans with PTSD: study protocol for a randomized controlled trial
Creators: name: Grubaugh, Anouk
name: Myers, Ursula
name: Keller, Stephanie
name: Wangelin, Bethany
name: Lozano, Brian
name: Tuerk, Peter
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) 2013 Checklist.
Additional file of A digital mental health intervention to reduce depressive symptoms among overseas Filipino workers: protocol for a pilot hybrid type 1 effectiveness-implementation randomized controlled trial
Creators: name: Liem, Andrian
name: Garabiles, Melissa R.
name: Karmia A. Pakingan
name: Chen, Wen
name: Lam, Agnes Iok Fong
name: Burchert, Sebastian
name: Hall, Brian J.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file of A digital mental health intervention to reduce depressive symptoms among overseas Filipino workers: protocol for a pilot hybrid type 1 effectiveness-implementation randomized controlled trial
Evidence that the a0(980) and f0(980) are not elementary particles
Creators: name: Baru, V.
name: Haidenbauer, J.
name: Hanhart, C.
name: Kalashnikova, Yu.
name: Kudryavtsev, A.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study the interesting problem of whether it is possible to distinguish composite from elementary particles. In particular we generalize a model-independent approach of S. Weinberg to the case of unstable particles. This allows us to apply our formalism to the case of the a0(980) and f0(980) resonances and to address the question whether these particles are predominantly genuine, confined quark states (of $\bar q q$ or $qq\bar q\bar q$ structure) or governed by mesonic components.
description: 15 pages, 4 Figures
Nonperturbative contributions to the quark form factor at high energy
Creators: name: Cherednikov, Igor O.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The analysis of nonperturbative effects in high energy asymptotics of the electomagnetic quark form factor is presented. It is shown that the nonperturbative effects determine the initial value for the perturbative evolution of the quark form factor and find their general structure with respect to the high energy asymptotics. Within the Wilson integral formalism which is natural for investigation of the soft, IR sensitive, part of the factorized form factor, the structure of the instanton induced effects in the evolution equation is discussed. It is demonstrated that the instanton contributions result in the finite renormalization of the subleading perturbative result and numerically are characterized by small factor reflecting the diluteness of the QCD vacuum within the instanton liquid model. The relevance of the IR renormalon induced effects in high energy asymptotic behaviour is discussed. The consequences of the various analytization procedures of the strong coupling constant in the IR domain are considered.
description: REVTeX, 12 pages, 1 figure. Important references and discussions added, misprints corrected, minor changes in text
Open quantum systems in thermal non-ergodic environments
Creators: name: Parra-Murillo, Carlos A.
name: Bramberger, Max
name: Hubig, Claudius
name: de Vega, Inés
Publisher: name: arXiv
Year: 2019
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The dynamics of an open system crucially depends on the correlation function of its environment, $C_B(t)$. We show that for thermal non-Harmonic environments $C_B(t)$ may not decay to zero but to an offset, $C_0>0$. The presence of such offset is determined by the environment eigenstate structure, and whether it fulfills or not the eigenstate thermalization hypothesis. Moreover, we show that a $C_0>0$ could render the weak coupling approximation inaccurate and prevent the open system to thermalize. Finally, for a realistic environment of dye molecules, we show the emergence of the offset by using matrix product states (MPS), and discuss its link to a 1/f noise spectrum that, in contrast to previous models, extends to zero frequencies. Thus, our results may be relevant in describing dissipation in quantum technological devices like superconducting qubits, which are known to be affected by such noise.
description: 4 pages, 1 figure, plus suplementary material
Modeling spectral lags in active galactic nucleus flares in the context of Lorentz invariance violation searches
Creators: name: Cédric, Perennes
name: Hélène, Sol
name: Julien, Bolmont
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: High-energy photons emitted by flaring active galactic nuclei (AGNs) have been used for many years to constrain modified dispersion relations in vacuum encountered in the context of quantum gravity phenomenology. In such studies, done in the GeV-TeV range, energy-dependent delays (spectral lags) are searched for, usually neglecting any source-intrinsic time delay. With the aim being to distinguish lorentz invariance violation (LIV) effects from lags generated at the sources themselves, a detailed investigation into intrinsic spectral lags in flaring AGNs above 100 GeV is presented in the frame of synchrotron-self-Compton (SSC) scenarios for their very-high-energy (VHE) emission. A simple model of VHE flares in blazars is proposed, allowing to explore the influence of the main physical parameters describing the emitting zones on intrinsic delays. For typical conditions expected in TeV blazars, significant intrinsic lags are obtained, which can dominate over LIV effects, especially at low redshifts, and should therefore be carefully disentangled from any extrinsic lags. Moreover, two main regimes are identified with characteristic spectral lags, corresponding to long-lasting and fast particle acceleration. Such intrinsic spectral lags should be detected with new-generation instruments at VHE such as the Cherenkov Telescope Array which begins operation in a few years. This will provide original constraints on AGN flare models and open a new era for LIV searches in the photon sector.
description: 14 pages, 13 figures, 1 appendix. Accepted by A&A
Electric/Magnetic Deformations of S^3 and AdS_3, and Geometric Cosets
Creators: name: Israel, Dan
name: Kounnas, Costas
name: Orlando, Domenico
name: Petropoulos, P. Marios
Publisher: name: arXiv
Year: 2004
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We analyze asymmetric marginal deformations of SU(2)_k and SL(2,R)_k WZW models. These appear in heterotic string backgrounds with non-vanishing Neveu--Schwarz three-forms plus electric or magnetic fields, depending on whether the deformation is elliptic, hyperbolic or parabolic. Asymmetric deformations create new families of exact string vacua. The geometries which are generated in this way, deformed S^3 or AdS_3, include in particular geometric cosets such as S^2, AdS_2 or H_2. Hence, the latter are consistent, exact conformal sigma models, with electric or magnetic backgrounds. We discuss various geometric and symmetry properties of the deformations at hand as well as their spectra and partition functions, with special attention to the supersymmetric AdS_2 x S^2 background. We also comment on potential holographic applications.
description: 38 pages, Added References. Aesthetic retouchings
Additional file 1 of A digital mental health intervention to reduce depressive symptoms among overseas Filipino workers: protocol for a pilot hybrid type 1 effectiveness-implementation randomized controlled trial
Creators: name: Liem, Andrian
name: Garabiles, Melissa R.
name: Karmia A. Pakingan
name: Chen, Wen
name: Lam, Agnes Iok Fong
name: Burchert, Sebastian
name: Hall, Brian J.
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1.
Spatiotemporal dynamics of frictional systems: The interplay of interfacial friction and bulk elasticity
Creators: name: Bar-Sinai, Yohai
name: Aldam, Michael
name: Spatschek, Robert
name: Brener, Efim A.
name: Bouchbinder, Eran
Publisher: name: arXiv
Year: 2019
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: Frictional interfaces are abundant in natural and engineering systems, and predicting their behavior still poses challenges of prime scientific and technological importance. At the heart of these challenges lies the inherent coupling between the interfacial constitutive relation -- the macroscopic friction law -- and the bulk elasticity of the bodies that form the frictional interface. In this feature paper, we discuss the generic properties of the macroscopic friction law and the many ways in which its coupling to bulk elasticity gives rise to rich spatiotemporal frictional dynamics. We first present the widely used rate-and-state friction constitutive framework, discuss its power and limitations, and propose extensions that are supported by experimental data. We then discuss how bulk elasticity couples different parts of the interface, and how the range and nature of this interaction are affected by the system's geometry. Finally, in light of the coupling between interfacial and bulk physics, we discuss basic phenomena in spatially-extended frictional systems, including the stability of homogeneous sliding, the onset of sliding motion and a wide variety of propagating frictional modes (e.g. rupture fronts, healing fronts and slip pulses). Overall, the results presented and discussed in this feature paper highlight the inseparable roles played by interfacial and bulk physics in spatially-extended frictional systems.
description: An invited feature paper (24 pages including Appendices, 8 figures)
MOESM2 of The effect of childhood trauma, ApoE genotype and HIV-1 viral protein R variants on change in cognitive performance
Creators: name: Womersley, Jacqueline
name: Clauss, Lara
name: Varathan, Olivette
name: Engelbrecht, Susan
name: Hemmings, Sian
name: Seedat, Soraya
name: Spies, Georgina
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Neuroscience
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 2: Table S2. Predictive value of interactions on one-year global cognitive scores.
A novel transgenic zebrafish line allows for in vivo quantification of autophagic activity in neurons
Creators: name: Sataree Khuansuwan
name: Barnhill, Lisa M.
name: Sizhu Cheng
name: Bronstein, Jeff M.
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: The pathophysiology of most neurodegenerative diseases includes aberrant accumulation of protein aggregates. Recent evidence highlights the role of protein degradation pathways in neurodegeneration. Concurrently, genetic tools have been generated to enable zebrafish, Danio rerio, to be used as an animal model to study neurodegenerative processes. In addition to optical clarity and fast ex utero development, the zebrafish brain is relatively small and has conserved structures with its mammalian counterparts. To take advantage of this model organism and to aid further studies on autophagy and neurodegeneration, we created a stable transgenic zebrafish line that expresses eGFP-Map1lc3b specifically in post-mitotic neurons under the elavl3 promoter. This line is useful for indirectly monitoring autophagic activity in neurons in vivo and screening for macroautophagy/autophagy-modulating compounds. We determined the applicability of this transgenic line by modulating and quantifying the number of autophagosomes via treatment with a known autophagy inducer (rapamycin) and inhibitors (3-methyladenine, protease inhibitors). Additionally, we proposed an in vivo method for quantifying rates of autophagosome accumulation, which can be used to infer occurrence of autophagic flux. Last, we tested two FDA-approved drugs currently undergoing clinical studies for Parkinson disease, isradipine and nilotinib, and found that isradipine did not modulate autophagy, whereas nilotinib induced both autophagosome number and autophagic flux. It is hoped that others will find this line useful as an in vivo vertebrate model to find or validate autophagy modulators that might be used to halt the progression of neurodegenerative diseases. Abbreviations: 3MA: 3-methyladenine; BafA: bafilomycin A1; dd: dorsal diencephalon; dpf: days post fertilization; e: eye; eGFP: enhanced green fluorescent protein; Elavl3: ELAV like neuron-specific RNA binding protein 3; FDA: Food and Drug Administration; hb: habenula; hpt, hours post treatment; Map1lc3b: microtubule-associated protein 1 light chain 3 beta; nt: neural tube; ot, optic tectum; P/E: pepstatin A and E64d; PD: Parkinson disease; PMTs: photomultiplier tubes; PTU: 1-phenyl-2-thiourea; Ta: annealing temperature; Tel, telencephalon
The dark burst 010214 with BeppoSAX: possible variable absorption and jet X-ray emission
Creators: name: Guidorzi, C.
name: Frontera, F.
name: Montanari, E.
name: Amati, L.
name: Antonelli, L. A.
name: Zand, J. J. M. in 't
name: Costa, E.
name: Farinelli, R.
name: Feroci, M.
name: Heise, J.
name: Masetti, N.
name: Nicastro, L.
name: Orlandini, M.
name: Palazzi, E.
name: Piro, L.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: We report on the prompt and afterglow emission observations of the dark burst GRB010214 with BeppoSAX. The prompt emission shows possible evidence of variable absorption from N_H = 3.0^{+5.1}_{-2.0} x 10^23 cm-2 in the first 6 s of the event to a value consistent with the Galactic column density (N_H^(G) = 2.66 x 10^20 cm-2) in the GRB direction. An X-ray afterglow emission in the 2-10 keV energy band was detected with BeppoSAX, but an analogue search at lower wavelengths (optical, IR and radio) was unsuccessful. The X-ray afterglow spectrum is consistent with a power-law with Galactic absorption. The light curve shows a complex decay, if the tail of the prompt emission is assumed as the onset of the afterglow: if the origin of the afterglow is coincident with the GRB onset, a bump before ~ 3 x 10^4 s is inferred, while if the afterglow is assumed to start later, a steepening of the power-law light curve at t ~ 3 x 10^4 s is deduced. We discuss these results in the light of the current models of afterglows and the possible origin of the GRB darkness. Finally, we tentatively derive an estimate of the burst redshift.
description: 8 pages, 8 figures. Accepted for publication in Astronomy & Astrophysics
Evidence for anisotropy in the distribution of short-lived gamma-ray bursts
Creators: name: Magliocchetti, M.
name: Ghirlanda, G.
name: Celotti, A.
Publisher: name: arXiv
Year: 2003
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Measurements of the two-point angular correlation function w(θ) for 407 short gamma-ray bursts collected in the Current BATSE Catalogue reveal a ~2 σdeviation from isotropy on angular scales θ~ 2-4 degrees. Such an anisotropy is not observed in the distribution of long gamma-ray bursts and hints to the presence of repeated bursts for up to ~13% of the sources under exam. However, the available data cannot exclude the signal as due to the presence of large-scale structure. Under this assumption, the amplitude of the observed w(θ) is compatible with those derived for different populations of galaxies up to redshifts ~0.5, result that suggests short gamma-ray bursts to be relatively local sources.
description: 5 pages, 4 figures, submitted to MNRAS
Additional file 1 of Metabolic syndrome among children and adolescents in low and middle income countries: a systematic review and meta-analysis
Creators: name: Bitew, Zebenay Workneh
name: Ayinalem Alemu
name: Ermias Getaneh Ayele
name: Zelalem Tenaw
name: Anmut Alebel
name: Teshager Worku
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. Extraction checklist.
MOESM2 of The effect of daily consumption of different doses of fortified Lavash bread versus plain bread on serum vitamin-D status, body composition, metabolic and inflammatory biomarkers, and gut microbiota in apparently healthy adult: study protocol of a randomized clinical trial
Creators: name: Hadith Tangestani
name: Kurosh Djafarian
name: Shab-Bidar, Sakineh
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Cancer

description: Additional file 2. Consent form.
Semiflexible polymers in a random environment
Creators: name: Dua, Arti
name: Vilgis, Thomas A.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We present using simple scaling arguments and one step replica symmetry breaking a theory for the localization of semiflexible polymers in a quenched random environment. In contrast to completely flexible polymers, localization of semiflexible polymers depends not only on the details of the disorder but also on the ease with which polymers can bend. The interplay of these two effects can lead to the delocalization of a localized polymer with an increase in either the disorder density or the stiffness. Our theory provides a general criterion for the delocalization of polymers with varying degrees of flexibility and allows us to propose a phase diagram for the highly folded (localized) states of semiflexible polymers as a function of the disorder strength and chain rigidity.
description: 10 pages, 3 figures, Revtex4
The Practice of Religious Leaders in Confronting the Corporal Punishment of Children
Creators: name: Peimanpak, Faezeh
Publisher: name: figshare
Year: 2022
Subjects: subject: 170111 Psychology of Religion
subject: FOS: Psychology

description: Reviewing the practice of the religious leaders, including the prophet of Islam (PBUH) and the infallible Imams, show that their system of child rearing is taken from a divine system targets the absolute perfection. Therefore, the maturity and development of an individual is addressed, always focusing on prevention prior to cure.
In child rearing, Islam adopts an approach which puts affection, love and advice together with tolerance and caution at the center. Therefore, punishment is not a priority but as an instrument which may be used when kindness and affection fail to develop appropriate habits.
In Islamic cultivation, going to extremes is not favored and only this way can we cultivate balanced individuals with all their potentials and capacities being full-fledged and their body, soul, intellect functioning in harmony.
Although, in Islamic law and jurisprudence, the corporal punishment of children is allowed on the condition that their body does not turn red, black or bruised and it is only for the purpose of disciplining children. However, the violence of parents against children is disapproved and it is considered to be detrimental to their proper cultivation and guidance. Parents are persuaded to treat their children kindly, tenderly and caressingly.
Alborixin clears amyloid-β by inducing autophagy through PTEN-mediated inhibition of the AKT pathway
Creators: name: Abubakar Wani
name: Mehak Gupta
name: Masroor Ahmad
name: Aabid M. Shah
name: Aitizaz Ul Ahsan
name: Parvaiz H Qazi
name: Fayaz Malik
name: Singh, Gurdarshan
name: Parduman R. Sharma
name: Kaddoumi, Amal
name: Sandip B. Bharate
name: Vishwakarma, Ram A.
name: Kumar, Ajay
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Marine Biology
subject: Cancer
subject: Plant Biology

description: Imbalance in production and clearance of amyloid beta (Aβ) is the primary reason for its deposition in Alzheimer disease. Macroautophagy/autophagy is one of the important mechanisms for clearance of both intracellular and extracellular Aβ. Here, through screening, we identified alborixin, an ionophore, as a potent inducer of autophagy. We found that autophagy induced by alborixin substantially cleared Aβ in microglia and primary neuronal cells. Induction of autophagy was accompanied by up regulation of autophagy proteins BECN1/Beclin 1, ATG5, ATG7 and increased lysosomal activities. Autophagy induced by alborixin was associated with inhibition of the phosphoinositide 3-kinase (PI3K)-AKT pathway. A knock down of PTEN and consistent, constitutive activation of AKT inhibited alborixin-induced autophagy and consequent clearance of Aβ. Furthermore, clearance of Aβ by alborixin led to significant reduction of Aβ-mediated cytotoxicity in primary neurons and differentiated N2a cells. Thus, our findings put forward alborixin as a potential anti-Alzheimer therapeutic lead. Aβ: amyloid beta; ALB: alborixin; ATG: autophagy-related; BECN1: beclin 1; DAPI: 4, 6-diamidino-2-phenylindole; DCFH-DA: 2,7-dichlorodihydrofluorescein diacetate; fAβ: fibrillary form of amyloid beta; GFAP: glial fibrillary acidic protein; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MAP2: microtubule-associated protein 2; MTOR: mechanistic target of rapamycin kinase; PTEN: phosphatase and tensin homolog; ROS: reactive oxygen species; SQSTM1: sequestosome 1; TMRE: tetramethylrhodamine, ethyl ester
MOESM1 of The effect of childhood trauma, ApoE genotype and HIV-1 viral protein R variants on change in cognitive performance
Creators: name: Womersley, Jacqueline
name: Clauss, Lara
name: Varathan, Olivette
name: Engelbrecht, Susan
name: Hemmings, Sian
name: Seedat, Soraya
name: Spies, Georgina
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: 60506 Virology

description: Additional file 1: Table S1. Predictive value of variables on one-year global cognitive scores.
The transcription factor Spt4-Spt5 complex regulates the expression of ATG8 and ATG41
Creators: name: Wen, Xin
name: Gatica, Damián
name: Zhangyuan Yin
name: Zehan Hu
name: Dengjel, Jörn
name: Klionsky, Daniel J.
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Macroautophagy/autophagy, a highly conserved dynamic process, is one of the major degradative pathways in cells. So far, over 40 autophagy-related (ATG) genes have been identified in Saccharomyces cerevisiae, most of which have homologs in more complex eukaryotes. Autophagy plays a crucial role in cell survival and maintenance, and its dysfunction is related to various diseases, indicating that the proper regulation of autophagy is important. Although the overall process of autophagy has been extensively studied, in particular with regard to the function of the Atg proteins, relatively little is known about the regulatory mechanisms that control autophagy activity. Spt5 is one of the transcriptional factors that is universally conserved across all domains. This protein can form a complex with Spt4, together playing a central role in transcription. In complex eukaryotic cells, the Spt4-Spt5 complex plays a dual role in gene regulation, acting both to delay transcription through promoter-proximal pausing, and to facilitate transcriptional elongation. In contrast, in S. cerevisiae, only the positive function of the Spt4-Spt5 complex has been identified. Here, we show for the first time that the Spt4-Spt5 transcription factor complex negatively regulates ATG genes in S. cerevisiae, inhibiting autophagy activity during active growth. Under autophagy-inducing conditions, the repression is released by Spt5 phosphorylation, allowing an upregulation of autophagy activity. AID: auxin-inducible degron; ATG: autophagy-related; ChIP: chromatin immunoprecipitation;Cvt: cytoplasm-to-vacuole targeting; DSIF: DRB sensitivity-inducible factor; NELF: negativeelongation factor; ORF: open reading frame; PA: protein A; PE: phosphatidylethanolamine;prApe1: precursor aminopeptidase I; RT-qPCR: real-time quantitative PCR; RNAP II: RNApolymerase II; TSS: transcription start site; WT: wild-type
BIRC5/Survivin is a novel ATG12–ATG5 conjugate interactor and an autophagy-induced DNA damage suppressor in human cancer and mouse embryonic fibroblast cells
Creators: name: Tzu-Yu Lin
name: Hsiu-Han Chan
name: Shang-Hung Chen
name: Sailu Sarvagalla
name: Pai-Sheng Chen
name: Mohane Selvaraj Coumar
name: Siao Muk Cheng
name: Yung-Chieh Chang
name: Lin, Chun-Hui
name: Leung, Euphemia
name: Cheung, Chun Hei Antonio
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biophysics
subject: Biochemistry
subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Developmental Biology
subject: Cancer

description: BIRC5/Survivin is known as a dual cellular functions protein that directly regulates both apoptosis and mitosis in embryonic cells during embryogenesis and in cancer cells during tumorigenesis and tumor metastasis. However, BIRC5 has seldom been demonstrated as a direct macroautophagy/autophagy regulator in cells. ATG7 expression and ATG12–ATG5-ATG16L1 complex formation are crucial for the phagophore elongation during autophagy in mammalian cells. In this study, we observed that the protein expression levels of BIRC5 and ATG7 were inversely correlated, whereas the expression levels of BIRC5 and SQSTM1/p62 were positively correlated in normal breast tissues and tumor tissues. Mechanistically, we found that BIRC5 negatively modulates the protein stability of ATG7 and physically binds to the ATG12–ATG5 conjugate, preventing the formation of the ATG12–ATG5-ATG16L1 protein complex in human cancer (MDA-MB-231, MCF7, and A549) and mouse embryonic fibroblast (MEF) cells. We also observed a concurrent physical dissociation between BIRC5 and ATG12–ATG5 (but not CASP3/caspase-3) and upregulation of autophagy in MDA-MB-231 and A549 cells under serum-deprived conditions. Importantly, despite the fact that upregulation of autophagy is widely thought to promote DNA repair in cells under genotoxic stress, we found that BIRC5 maintains DNA integrity through autophagy negative-modulations in both human cancer and MEF cells under non-stressed conditions. In conclusion, our study reveals a novel role of BIRC5 in cancer cells as a direct regulator of autophagy. BIRC5 may act as a “bridging molecule”, which regulates the interplay between mitosis, apoptosis, and autophagy in embryonic and cancer cells. ACTA1: actin; ATG: autophagy related; BIRC: baculoviral inhibitor of apoptosis repeat-containing; BAF: bafilomycin A1; CQ: chloroquine; CASP3: caspase 3; HSPB1/Hsp27: heat shock protein family B (small) member 1/heat shock protein 27; IAPs: inhibitors of apoptosis proteins; IP: immunoprecipitation; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PLA: proximity ligation assay; SQSTM1/p62: sequestosome 1; siRNA: small interfering RNA
Additional file 3 of Metabolic syndrome among children and adolescents in low and middle income countries: a systematic review and meta-analysis
Creators: name: Bitew, Zebenay Workneh
name: Ayinalem Alemu
name: Ermias Getaneh Ayele
name: Zelalem Tenaw
name: Anmut Alebel
name: Teshager Worku
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 3. List of excluded studies.
The Price of Disclosure in the Thoroughbred Yearling Market
Creators: name: Plant, Emily J.
name: Stowe, C. Jill
name: Plant, Emily J.
name: Stowe, C. Jill
Publisher: name: Unknown
Year: 2013
Subjects: subject: Livestock Production/Industries
subject: Marketing
subject: FOS: Economics and business
subject: asymmetric information
subject: mandatory disclosure
subject: voluntary disclosure
subject: Thoroughbred industry
subject: auction
subject: disclosure

description: In this article, we examine disclosure as a tool to mitigate the effects of asymmetric information in a Thoroughbred yearling market. If disclosures influence market price, information contained therein must be valuable to buyers and hence diminish asymmetric information. Using public auction data, we find that disclosures do not influence price in a segment of the auction in which an implicit quality certification is available. However, in the other segment, we find evidence that some disclosures may provide valuable information to buyers.
On the Initialization of Long Short-Term Memory Networks
Creators: name: Ghazi, Mostafa Mehdipour
name: Nielsen, Mads
name: Pai, Akshay
name: Modat, Marc
name: Cardoso, M. Jorge
name: Ourselin, Sebastien
name: Sorensen, Lauge
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (cs.LG)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: Weight initialization is important for faster convergence and stability of deep neural networks training. In this paper, a robust initialization method is developed to address the training instability in long short-term memory (LSTM) networks. It is based on a normalized random initialization of the network weights that aims at preserving the variance of the network input and output in the same range. The method is applied to standard LSTMs for univariate time series regression and to LSTMs robust to missing values for multivariate disease progression modeling. The results show that in all cases, the proposed initialization method outperforms the state-of-the-art initialization techniques in terms of training convergence and generalization performance of the obtained solution.
Exact solution of the totally asymmetric Oslo model
Creators: name: Pruessner, Gunnar
Publisher: name: arXiv
Year: 2004
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Recently it has been found [G. Pruessner and H. J. Jensen, Phys. Rev. Lett. 91, 244303 (2003)] that a totally asymmetric variant of the Oslo model [K. Christensen et al., Phys. Rev. Lett. 77, 107 (1996)] represents the entire universality class of the Oslo model with anisotropy. The totally asymmetric model can be solved without scaling assumptions by finding recursively the eigenvectors of the Markov matrix, which can be suitably modified to produce the moment generating function of the relevant observable. This method should be applicable to many other stochastic processes.
description: 19 pages, 3 figures, JPA style
Replica symmetry breaking in the `small world' spin glass
Creators: name: Wemmenhove, B
name: Nikoletopoulos, T
name: Hatchett, J P L
Publisher: name: arXiv
Year: 2004
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We apply the cavity method to a spin glass model on a `small world' lattice, a random bond graph super-imposed upon a 1-dimensional ferromagnetic ring. We show the correspondence with a replicated transfer matrix approach, up to the level of one step replica symmetry breaking (1RSB). Using the scheme developed by Mézard & Parisi for the Bethe lattice, we evaluate observables for a model with fixed connectivity and $\pm J$ long range bonds. Our results agree with numerical simulations significantly better than the replica symmetric (RS) theory.
description: 21 pages, 3 figures
MOESM5 of Rearrangement analysis of multiple bacterial genomes
Creators: name: Mehwish Noureen
name: Ipputa Tada
name: Kawashima, Takeshi
name: Arita, Masanori
Publisher: name: figshare
Year: 2019
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology

description: Additional file 5: Figure S4. Complex rearrangement
MOESM1 of The effect of daily consumption of different doses of fortified Lavash bread versus plain bread on serum vitamin-D status, body composition, metabolic and inflammatory biomarkers, and gut microbiota in apparently healthy adult: study protocol of a randomized clinical trial
Creators: name: Hadith Tangestani
name: Kurosh Djafarian
name: Shab-Bidar, Sakineh
Publisher: name: figshare
Year: 2019
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Ecology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: Additional file 1. SPIRIT Checklist.
ESTIMATIVA DO CONSUMO DE FERTILIZANTES PELA LARANJA EM SÃO PAULO AO LONGO DAS ÚLTIMAS DÉCADAS
Creators: name: Figueiredo, Margarida Garcia De
name: Barros, Alexandre Lahóz Mendonça De
name: Figueiredo, Margarida Garcia De
name: Barros, Alexandre Lahóz Mendonça De
Publisher: name: Unknown
Year: 2006
Subjects: subject: Crop Production/Industries
subject: Productivity Analysis
subject: Laranja
subject: Fertilizantes
subject: Produtividade
subject: São Paulo
subject: Modelo Econométrico

description: O Brasil, além de representar sozinho cerca de 75% do total de suco de laranja concentrado e congelado comercializado no mercado internacional, juntamente com os EUA responde por cerca de 50% da produção mundial de laranja. O Estado de São Paulo, por sua vez, responde por cerca de 80% da produção nacional de laranja e 98% das exportações brasileiras de suco concentrado. A relevância econômica dessa atividade tem estimulado inúmeras pesquisas no sentido de analisar diversos aspectos relacionados ao sistema de produção da cultura. Dentre os diversos fatores de produção, o fertilizante é um insumo de grande importância para a cadeia citrícola, especialmente na composição dos custos. Desta forma, o presente estudo procurou estimar o consumo de fertilizantes pela cultura da laranja em São Paulo ao longo das três últimas décadas. Os resultados encontrados foram satisfatórios, seguindo tendência condizente com a realidade do Estado. Além disso, foram desenvolvidos modelos teóricos para estimar o consumo dos nutrientes N, K2O e P2O5, em função da produtividade dos pomares, bem como a produtividade em função da idade do pomar. Os modelos ficaram bem ajustados, atendendo a todos os requisitos exigidos do ponto de vista econométrico.
Sphere packing bounds in the Grassmann and Stiefel manifolds
Creators: name: Henkel, Oliver
Publisher: name: arXiv
Year: 2003
Subjects: subject: Metric Geometry (math.MG)
subject: Information Theory (cs.IT)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: Applying the Riemann geometric machinery of volume estimates in terms of curvature, bounds for the minimal distance of packings/codes in the Grassmann and Stiefel manifolds will be derived and analyzed. In the context of space-time block codes this leads to a monotonically increasing minimal distance lower bound as a function of the block length. This advocates large block lengths for the code design.
description: Replaced with final version, 11 pages
Additional file of Metabolic syndrome among children and adolescents in low and middle income countries: a systematic review and meta-analysis
Creators: name: Bitew, Zebenay Workneh
name: Ayinalem Alemu
name: Ermias Getaneh Ayele
name: Zelalem Tenaw
name: Anmut Alebel
name: Teshager Worku
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file of Metabolic syndrome among children and adolescents in low and middle income countries: a systematic review and meta-analysis
Velocity Modification of Power Spectrum from Absorbing Medium
Creators: name: Lazarian, A.
name: Pogosyan, D.
Publisher: name: arXiv
Year: 2004
Subjects: subject: Astrophysics (astro-ph)
subject: FOS: Physical sciences

description: Quantitative description of the statistics of intensity fluctuations within spectral line data cubes introduced in our earlier work is extended to the absorbing media. A possibility of extracting 3D velocity and density statistics from both integrated line intensity as well as from the individual channel maps is analyzed. We find that absorption enables the velocity effects to be seen even if the spectral line is integrated over frequencies. This regime that is frequently employed in observations is characterized by a non-trivial relation between the spectral index of velocities and the spectral index of intensity fluctuations. For instance when density is dominated by fluctuations at large scales, i.e. when correlations scale as r^{-γ}, γ<0, the intensity fluctuations exhibit a universal spectrum of fluctuations ~K^{-3} over a range of scales. When small scale fluctuations of density contain most of the energy, i.e. when correlations scale as r^{-γ}, γ>0, the resulting spectrum of the integrated lines depends on the scaling of the underlying density and scales as K^{-3+γ}. We show that if we take the spectral line slices that are sufficiently thin we recover our earlier results for thin slice data without absorption. As the result we extend the Velocity Channel Analysis (VCA) technique to optically thick lines enabling studies of turbulence in molecular clouds. In addition, the developed mathematical machinery enables a quantitative approach to solving other problems that involved statistical description of turbulence within emitting and absorbing gas.
description: 51 page, 3 figures. Accepted to Astrophysical Journal
Scaling laws in axisymmetric magnetohydrodynamic duct flows
Creators: name: Poyé, A.
name: Agullo, O.
name: Plihon, N.
name: Bos, W. J. T.
name: Desangles, V.
name: Bousselin, G.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: We report on a numerical study of axisymmetric flow of liquid metal in a circular duct with rectangular cross-section. The flow is forced through the combination of an axial magnetic field and a radial current. Sweeping a wide range of forcing parameters, we identify the different regimes which characterize the flows and explicit the associate scaling laws. Experimental results are interpreted in the light of our numerical simulations.
Extending partial suborders and implication classes
Creators: name: Fekete, Sándor P.
name: Köhler, Ekkehard
name: Teich, Jürgen
Publisher: name: Technische Universität Berlin
Year: 2000
Subjects: subject: 510 Mathematik
subject: scheduling
subject: precedence constraints
subject: transitive orientation
subject: interval graphs
subject: partial orders

description: We consider the following problem called transitive ordering with precedence constraints (TOP): Given a partial order P=(V,&;) and an (undirected) graph G=(V,E) such that all relations in P are represented by edges in G. Is there a transitive orientation D=(V,A) of G, such that P is contained in D?
Kaluza-Klein/$Z'$ Differentiation at the LHC and Linear Collider
Creators: name: Rizzo, Thomas. G.
Publisher: name: arXiv
Year: 2003
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We explore the capabilities of the LHC and the Linear Collider(LC) to distinguish the production of Kaluza-Klein(KK) excitations from an ordinary $Z'$ within the context of theories with TeV scale extra dimensions. At the LHC, these states are directly produced in the Drell-Yan channel while at the LC the effects of their exchanges are indirectly felt as new contact interactions in processes such as $e^+e^-\to f\bar f$. While we demonstrate that the LC is somewhat more capable at KK/$Z'$ differentiation than is the LHC, the simplest LC analysis relies upon the LHC data for the resonance mass as an important necessary input.
description: 19 pages, 7 Figs, LaTex, minor corrections/additions to text