cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
A multi-wavelength study of GRS 1716-249
Creators: name: Saikia, Payaswini
name: Russell, Dave
Publisher: name: Zenodo
Year: 2021
Subjects: X-ray binary
Black hole

description: We present a detailed study of the evolution of the galactic black hole transient GRS 1716-249 during its 2016-2017 outburst at optical, mid-Infrared, near-Infrared, UV, radio and X-ray wavelengths. From a detailed analysis using spectral energy distributions, multi-wavelength correlations and the color evolution of the source during the outburst, we show that the optical and UV emission of the source is broadly originating from a multi-temperature X-ray irradiated accretion disc with possibly some additional contribution from the viscous disc during the outburst fade, while the mid-infrared and radio detections are dominated by synchrotron emission from a compact jet. Our analysis suggests that GRS 1716-249 is either significantly optically fainter compared to other black hole X-ray binaries with similar accretion activity, or is at a much further distance (> 5 kpc) than what was previously assumed in the literature.
The importance of episodic accretion for low-mass star formation
Creators: name: Stamatellos, Dimitris
name: Whitworth, Anthony
name: Hubber, David
Publisher: name: arXiv
Year: 2011
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: A star acquires much of its mass by accreting material from a disc. Accretion is probably not continuous but episodic. We have developed a method to include the effects of episodic accretion in simulations of star formation. Episodic accretion results in bursts of radiative feedback, during which a protostar is very luminous, and its surrounding disc is heated and stabilised. These bursts typically last only a few hundred years. In contrast, the lulls between bursts may last a few thousand years; during these lulls the luminosity of the protostar is very low, and its disc cools and fragments. Thus, episodic accretion enables the formation of low-mass stars, brown dwarfs and planetary-mass objects by disc fragmentation. If episodic accretion is a common phenomenon among young protostars, then the frequency and duration of accretion bursts may be critical in determining the low-mass end of the stellar initial mass function.
description: To appear in the Astrophysical Journal. Press release available at: http://www.astro.cf.ac.uk/pub/Dimitrios.Stamatellos/News/News.html Full resolution paper available at http://stacks.iop.org/0004-637X/730/32
A self-learning algorithm for biased molecular dynamics
Creators: name: Tribello, Gareth A.
name: Ceriotti, Michele
name: Parrinello, Michele
Publisher: name: arXiv
Year: 2010
Subjects: subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences.
description: 6 pages, 5 figures + 9 pages of supplementary information
Exotic singularities and spatially curved Loop Quantum Cosmology
Creators: name: Singh, Parampreet
name: Vidotto, Francesca
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We investigate the occurrence of various exotic spacelike singularities in the past and the future evolution of $k = \pm 1$ Friedmann-Robertson-Walker model and loop quantum cosmology using a sufficiently general phenomenological model for the equation of state. We highlight the non-trivial role played by the intrinsic curvature for these singularities and the new physics which emerges at the Planck scale. We show that quantum gravity effects generically resolve all strong curvature singularities including big rip and big freeze singularities. The weak singularities, which include sudden and big brake singularities are ignored by quantum gravity when spatial curvature is negative, as was previously found for the spatially flat model. Interestingly, for the spatially closed model there exist cases where weak singularities may be resolved when they occur in the past evolution. The spatially closed model exhibits another novel feature. For a particular class of equation of state, this model also exhibits an additional physical branch in loop quantum cosmology, a baby universe separated from the parent branch. Our analysis generalizes previous results obtained on the resolution of strong curvature singularities in flat models to isotropic spacetimes with non-zero spatial curvature.
description: 12 pages, 9 figures
Survey on the Event Orderings Semantics Used for Distributed System
Creators: name: Gazali, Yaser Miaji Osman
name: Hassan, Suhaidi
Publisher: name: arXiv
Year: 2010
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Event ordering in distributed system (DS) is disputable and proactive subject in DS particularly with the emergence of multimedia synchronization. According to the literature, different type of event ordering is used for different DS mode such as asynchronous or synchronous. Recently, there are several novel implementation of these types introduced to fulfill the demand for establishing a certain order according to a specific criterion in DS with lighter complexity.
description: 9 pages
3D RMHD simulations of jet-wind interactions in High Mass X-ray Binaries
Creators: name: López-Miralles, Jose
name: Perucho, Manel
name: Martí, José María
name: Migliari, Simone
name: Bosch-Ramón, Valentí
Publisher: name: Zenodo
Year: 2021
Subjects: magnetohydrodynamics
X-ray Binaries
jet-wind interactions

description: There have been several attempts to describe the propagation of jets in X-ray Binaries from a numerical point of view, specially on understanding how the ambient medium affects the flow dynamical evolution. However, previous numerical simulations ignore the effect of one fundamental ingredient: the existence of magnetic fields. In this work, we present the first 3D RMHD numerical simulations of microquasar jets performed with our new computational tool for Relativistic Astrophysics; the code LÓSTREGO v1.0. We explore the interaction of the jet with the wind of the companion star, focusing on how the presence of magnetic fields with different intensity may affect the jet propagation, collimation and long-term stability.
description: {"references": ["Perucho, M., Bosch-Ram\u00f3n, V., Khangulyan, D. 2010, A&A 512, L4.", "Yoon, D. & Heinz, S. 2015, ApJ, 801, 55.", "Mart\u00ed, J.M & Muller, E. 2015, Living Reviews in Computational Astrophysics, 1,3.", "Wagner, A.Y & Bicknell, G.V. 2011, APJ, 728, 29."]}
Large X-ray time lags from compact black hole coronae
Creators: name: Uttley, Phil
name: Malzac, Julien
Publisher: name: Zenodo
Year: 2021
Subjects: X-ray binaries
Black holes
X-ray variability

description: The positive (‘hard’) and negative (‘soft’) X-ray time lags in black hole X-ray binary hard states can shed light on the innermost geometry of their emitting regions. The observed lags can be surprisingly large. Explanations for the lags which include light-travel delays (e.g. scattering in the jet, or thermal reverberation of coronal emission by the disk) or propagation through a ‘hot flow’ corona with radial temperature dependence, are difficult to reconcile with the small disk radii inferred from observed disk variability time-scales and broad Fe K profiles. Here we show that these lags can be produced by compact single-temperature coronae, by accounting for the natural delay expected between seed photon variations and coronal heating, as accretion fluctuations propagate through the disk to the corona.
Effect of Ambipolar Diffusion on the Non-linear Evolution of Magnetorotational Instability in Weakly Ionized Disks
Creators: name: Bai, Xue-Ning
name: Stone, James M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We study the role of ambipolar diffusion (AD) on the non-linear evolution of the MRI in protoplanetary disks using the strong coupling limit, which applies when the electron recombination time is much shorter than the orbital time. The effect of AD in this limit is characterized by the dimensionless number Am, the frequency of which neutral particles collide with ions normalized to the orbital frequency. We perform three-dimensional unstratified shearing-box simulations of the MRI over a wide range of Am as well as different magnetic field strengths and geometries. The saturation level of the MRI turbulence depends on the magnetic geometry and increases with the net magnetic flux. There is an upper limit to the net flux for sustained turbulence, corresponding to the requirement that the most unstable vertical wavelength be less than the disk scale height. Correspondingly, at a given Am, there exists a maximum value of the turbulent stress alpha_max. For Am<1, the largest stress is associated with a field geometry that has both net vertical and toroidal flux. In this case, we confirm the results of linear analyses that show the fastest growing mode has a non-zero radial wave number with growth rate exceeding the pure vertical field case. We find there is a very tight correlation between the turbulent stress (alpha) and the plasma beta=P_gas/P_mag~1/(2alpha) at the saturated state of the MRI turbulence regardless of field geometry, and alpha_max rapidly decreases with decreasing Am. In particular, we quote alpha_max~0.007 for Am=1 and alpha_max~0.0006 for Am=0.1.
description: 20 pages, 16 figures, submitted to ApJ
Semantic models in biomedicine : building interoperating ontologies for biomedical data representation and processing in pharmacovigilance
Creators: name: Courtot, Melanie
Publisher: name: University of British Columbia
Year: 2014

description: It is increasingly challenging to analyze the data produced in biomedicine, even more so when relying on manual analysis methods. My hypothesis is that using a common representation of knowledge, implemented via standard tools, and logically formalized can make those datasets computationally amenable, help with data integration from multiple sources and allow to answer complex queries. The first part of this dissertation demonstrates that ontologies can be used as common knowledge models, and details several use cases where they have been applied to existing information in the domain of biomedical investigations, clinical data and vaccine representation. In a second part, I address current issues in developing and implementing ontologies, and proposes solutions to make ontologies and the datasets they are applied to available on the Semantic Web, increasing their visibility and reuse. The last part of my thesis then builds upon the first two, and applies their results to pharmacovigilance, and specifically to analysis of reports of adverse events following immunization. I encoded existing standard clinical guidelines from the Brighton Collaboration in Web Ontology Language (OWL) in the Adverse Events Reporting Ontology (AERO) I developed within the framework of the Open Biological and Biomedical Ontologies Foundry. I show that it is possible to automate the classification of adverse events using the AERO with very high specificity (97%). I also demonstrate that AERO can be used with other types of guidelines. Finally, my pipeline relies on open and widely used data standards (Resource Description Framework (RDF), OWL, SPARQL) for implementation, making the system easily transposable to other domains. This thesis validates the usefulness of ontologies as semantic models in biomedicine enabling automated, computational processing of large datasets. It also fulfills the goal of raising awareness of semantic technologies in the clinical community of users. Following my results the Brighton Collaboration is moving towards providing a logical representation of their guidelines.
Asymmetric magnetic dots: A way to control magnetic properties
Creators: name: Vargas, N. M.
name: Allende, S.
name: Leighton, B.
name: Escrig, J.
name: Mejía-López, J.
name: Altbir, D.
name: Schuller, Ivan K.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We have used Monte Carlo simulations to investigate the magnetic properties of asymmetric dots as a function of their geometry. The asymmetry of round dots is produced by cutting off a fraction of the dot and is characterized by an asymmetry parameter $α$. This shape asymmetry has interesting effects on the coercivity ($H_{c}$), remanence ($M_{r}$), and barrier for vortex and C- state formation. The dependences of $H_{c}$ and $M_{r}$ are non monotonic as a function of $α$ with a well defined minima in these parameters. The vortex enters the most asymmetric part and exits through the symmetric portion of the dot. With increasing $α$ the vortex formation starts with a C-state which persists for longer fields and the barrier for vortex exit diminishes with increasing asymmetry, thus providing control over the magnetic chirality. This implies interesting, naively-unexpected, magnetic behavior as a function of geometry and magnetic field.
description: 6 pages, 6 figures
Investigation of biomechanics of skull structures damages caused by dynamic loads
Creators: name: Ptak, Mariusz
name: Ratajczak, Monika
name: Kwiatkowski, Artur
name: Sawicki, Marek
name: Wilhelm, Johannes
name: Fernandes, Fábio A.O.
name: Druszcz, Adam
Publisher: name: Institute of Machine Design and Operation, Wrocław University of Technology, Wrocław
Year: 2018
Subjects: skull fracture, biomechanics, cranial sutures, vulnerable road user, finite element method

description: Acta of Bioengineering and Biomechanics; 04/2018; ISSN 1509-409X
Evaluation of the retention characteristics of various stud attachment systems for implant retained overdenture
Creators: name: Gonuldas, Fehmi
name: Tokar, Emre
name: Ozturk, Caner
Publisher: name: Institute of Machine Design and Operation, Wrocław University of Technology, Wrocław
Year: 2018
Subjects: overdenture, implant-supported dental prosthesis, denture precision attachment, retention

description: Acta of Bioengineering and Biomechanics; 04/2018; ISSN 1509-409X
Secret Sharing and Proactive Renewal of Shares in Hierarchical Groups
Creators: name: Naskar, Ruchira
name: Sengupta, Indranil
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Secret sharing in user hierarchy represents a challenging area for research. Although a lot of work has already been done in this direc- tion, this paper presents a novel approach to share a secret among a hierarchy of users while overcoming the limitations of the already exist- ing mechanisms. Our work is based on traditional (k +1; n)-threshold secret sharing, which is secure as long as an adversary can compromise not more than k secret shares. But in real life it is often feasible for an adversary to obtain more than k shares over a long period of time. So, in our work we also present a way to overcome this vulnerability, while implementing our hierarchical secret sharing scheme. The use of Elliptic Curve Cryptography makes the computations easier and faster in our work.
description: 20 Pages
Core properties of alpha Cen A using asteroseismology
Creators: name: de Meulenaer, P.
name: Carrier, F.
name: Miglio, A.
name: Bedding, T. R.
name: Campante, T. L.
name: Eggenberger, P.
name: Kjeldsen, H.
name: Montalban, J.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: A set of long and nearly continuous observations of alpha Centauri A should allow us to derive an accurate set of asteroseismic constraints to compare to models, and make inferences on the internal structure of our closest stellar neighbour. We intend to improve the knowledge of the interior of alpha Centauri A by determining the nature of its core. We combined the radial velocity time series obtained in May 2001 with three spectrographs in Chile and Australia: CORALIE, UVES, and UCLES. The resulting combined time series has a length of 12.45 days and contains over 10,000 data points and allows to greatly reduce the daily alias peaks in the power spectral window. We detected 44 frequencies that are in good overall agreement with previous studies, and found that 14 of these show possible rotational splittings. New values for the large and small separations have been derived. A comparison with stellar models indicates that the asteroseismic constraints determined in this study allows us to set an upper limit to the amount of convective-core overshooting needed to model stars of mass and metallicity similar to those of alpha Cen A.
description: 8 pages, 11 figures, A&A accepted
p-brane dynamics in (N+1)-dimensional FRW universes: a unified framework
Creators: name: Sousa, L.
name: Avelino, P. P.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We develop a velocity-dependent one-scale model describing p-brane dynamics in flat homogeneous and isotropic backgrounds in a unified framework. We find the corresponding scaling laws in frictionless and friction dominated regimes considering both expanding and collapsing phases.
description: 6 pages
Possible detection of two giant extrasolar planets orbiting the eclipsing polar UZ Fornacis
Creators: name: Potter, Stephen B.
name: Romero--Colmenero, Encarni
name: Ramsay, Gavin
name: Crawford, Steven
name: Gulbis, Amanda
name: Barway, Sudhanshu
name: Zietsman, Ewald
name: Kotze, Marissa
name: Buckley, David A. H.
name: O'Donoghue, Darragh
name: Siegmund, O. H. W.
name: McPhate, J.
name: Welsh, B. Y.
name: Vallerga, John
Publisher: name: arXiv
Year: 2011
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present new high-speed, multi-observatory, multi-instrument photometry of the eclipsing polar UZ For in order to measure precise mid-eclipse times with the aim of detecting any orbital period variations. When combined with published eclipse times and archival data spanning ~27 years, we detect departures from a linear and quadratic trend of ~60 s. The departures are strongly suggestive of two cyclic variations of 16(3) and 5.25(25) years. The two favoured mechanisms to drive the periodicities are either two giant extrasolar planets as companions to the binary (with minimum masses of 6.3(1.5)M(Jupiter) and 7.7(1.2)M(Jupiter)) or a magnetic cycle mechanism (e.g. Applegate's mechanism) of the secondary star. Applegate's mechanism would require the entire radiant energy output of the secondary and would therefore seem to be the least likely of the two, barring any further refinements in the effect of magnetic fieilds (e.g. those of Lanza et al.). The two planet model can provide realistic solutions but it does not quite capture all of the eclipse times measurements. A highly eccentric orbit for the outer planet would fit the data nicely, but we find that such a solution would be unstable. It is also possible that the periodicities are driven by some combination of both mechanisms. Further observations of this system are encouraged.
description: 10 pages, 4 figures, 2 tables
Does XTE J1550-564 Exhibit Limit-Cycle Behavior During Outburst Episodes?
Creators: name: Saraswati, Tiara Andamari
name: Vierdayanti, Kiki
Publisher: name: Zenodo
Year: 2021
Subjects: Accretion Disks
Disk Instability
Mini-Outburst
Outburst
X-ray Novae

description: X-ray nova (XRN), a black hole binary with transient nature, poses a serious challenge for standard disk theory. Outburst and quiescent phenomena observed from the source cannot be explained by steady-state accretion onto the compact object. Disk instability model (or limit-cycle instability model) was developed mainly to account for the outbursts seen in dwarf-novae, which later was found to work just as well in XRN but with a larger timescale and energy range. XRN XTE J1550-564 provides a better chance for the time-dependent study of the accretion disk around a black hole. This source has undergone multiple outbursts with different intensities and is known to be the only XRN to exhibit "X-ray mini-outbursts". We use RXTE data to analyze X-ray light curves and spectra, especially during its outbursts and mini-outbursts.
 The first main outburst has the longest duration (197 days), while the 4 mini-outbursts have an average duration of 42 days. The time spent in the quiescent period for this source was approximately 330 days between outburst episodes. This is much shorter than the typical quiescent timescale (or viscous diffusion timescale) for black hole binaries, indicating that the following mini-outbursts were practically "residual" of the main outburst and not separate ones. Decreasing peak intensity and the absence of disk components in the last three mini-outbursts provide an insight into the physical condition of the accretion disk. The disk has already receded to a large radius and the flux was dominated by a power-law component that might have originated from ADAF or jet.
 After those subsequent events of outbursts and mini-outbursts, the source has since gone quiet, likely undergoing a "real" quiescent phase to accumulate material to form an accretion disk. While the values of a few parameters obtained from the data may differ from the theory, the existence of limit-cycle instability in the accretion disk cannot be ruled out. The next outburst of XTE J1550-564 may shed some light on the complexity of this source.
description: {"references": ["Chen, et al. 1997, ApJ, 491, 312\u2013338 associated to arXiv:astro-ph/9707138", "Homan, et al. 2001, Astrophys. Journal. Sup. Series, 132, 377-402 associated to \tarXiv:astro-ph/0001163", "Remillard & McClintock. 2006, Annu. Rev. Astron. Astrophys., 44, 49-92 associated to arXiv:astro-ph/0606352", "Sobczak, et al. 2000, Astrophys. Journal, 544, 993\u20131015 associated to arXiv:astro-ph/0005599"]}
Genetic and Physiological Characterization of Fructose-1,6-Bisphosphate Aldolase and Glyceraldehyde-3-Phosphate Dehydrogenase in the Crabtree-Negative Yeast Kluyveromyces lactis
Creators: name: Rodicio, Rosaura
name: Schmitz, Hans-Peter
name: Heinisch, Jürgen J.
Publisher: name: Universität Osnabrück
Year: 2022
Subjects: subject: glycolysis
subject: pentose phosphate pathway
subject: oxidative stress
subject: moonlighting enzymes
subject: 570 - Biowissenschaften, Biologie

description: The milk yeast Kluyveromyces lactis degrades glucose through glycolysis and the pentose phosphate pathway and follows a mainly respiratory metabolism. Here, we investigated the role of two reactions which are required for the final steps of glucose degradation from both pathways, as well as for gluconeogenesis, namely fructose-1,6-bisphosphate aldolase (FBA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). In silico analyses identified one gene encoding the former (KlFBA1), and three genes encoding isoforms of the latter (KlTDH1, KlTDH2, KlGDP1). Phenotypic analyses were performed by deleting the genes from the haploid K. lactis genome. While Klfba1 deletions lacked detectable FBA activity, they still grew poorly on glucose. To investigate the in vivo importance of the GAPDH isoforms, different mutant combinations were analyzed for their growth behavior and enzymatic activity. KlTdh2 represented the major glycolytic GAPDH isoform, as its lack caused a slower growth on glucose. Cells lacking both KlTdh1 and KlTdh2 failed to grow on glucose but were still able to use ethanol as sole carbon sources, indicating that KlGdp1 is sufficient to promote gluconeogenesis. Life-cell fluorescence microscopy revealed that KlTdh2 accumulated in the nucleus upon exposure to oxidative stress, suggesting a moonlighting function of this isoform in the regulation of gene expression. Heterologous complementation of the Klfba1 deletion by the human ALDOA gene renders K. lactis a promising host for heterologous expression of human disease alleles and/or a screening system for specific drugs.
Genbit Compress Tool(GBC): A Java-Based Tool to Compress DNA Sequences and Compute Compression Ratio(bits/base) of Genomes
Creators: name: Rajeswari, P. Raja
name: Apparo, Allam
name: Kumar, V. K.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mathematical Software (cs.MS)
subject: FOS: Computer and information sciences

description: We present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better compression results show that GenBit compress algorithm is the best among the remaining Genome compression algorithms for non-repetitive DNA sequences in Genomes. The standard Compression algorithms such as gzip or compress cannot compress DNA sequences but only expand them in size. In this paper we consider the problem of DNA compression. It is well known that one of the main features of DNA Sequences is that they contain substrings which are duplicated except for a few random Mutations. For this reason most DNA compressors work by searching and encoding approximate repeats. We depart from this strategy by searching and encoding only exact repeats. our proposed algorithm achieves the best compression ratio for DNA sequences for larger genome. As long as 8 lakh characters can be given as input While achieving the best compression ratios for DNA sequences, our new GenBit Compress program significantly improves the running time of all previous DNA compressors. Assigning binary bits for fragments of DNA sequence is also a unique concept introduced in this program for the first time in DNA compression.
description: 11 pages
Additional file 1 of Cytokines secreted from adipose tissues mediate tumor proliferation and metastasis in triple negative breast cancer
Creators: name: Zhang, Kai
name: Chen, Lin
name: Zheng, Hongbo
name: Zeng, Yi
Publisher: name: figshare
Year: 2022
Subjects: subject: Space Science
subject: Medicine
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 1: Figure S1. Insulin-resistant model of 3T3-L1 adipocytes.
The Effects of X-Ray Feedback from AGN on Host Galaxy Evolution
Creators: name: Hambrick, D. Clay
name: Ostriker, Jeremiah P.
name: Naab, Thorsten
name: Johansson, Peter H.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Hydrodynamic simulations of galaxies with active galactic nuclei (AGN) have typically employed feedback that is purely local: i.e., an injection of energy to the immediate neighborhood of the black hole. We perform GADGET-2 simulations of massive elliptical galaxies with an additional feedback component: an observationally calibrated X-ray radiation field which emanates from the black hole and heats gas out to large radii from the galaxy center. We find that including the heating and radiation pressure associated with this X-ray flux in our simulations enhances the effects which are commonly reported from AGN feedback. This new feedback model is twice as effective as traditional feedback at suppressing star formation, produces 3 times less star formation in the last 6 Gyr, and modestly lowers the final BH mass (30%). It is also significantly more effective than an X-ray background in reducing the number of satellite galaxies.
description: 9 emulateapj pages, 8 figures; accepted to ApJ
Social reality without language
Creators: name: Velasco, Pablo Fernández
Publisher: name: Journal of Social Ontology
Year: 2023

description: According to a popular view, the creation of social reality requires language: social institutions emerge when we successfully declare them into existence. Making language central to institutions deprives the non-human of any claim to a social reality. This is particularly problematic in the light of mounting research showing many animals have social institutions even in the absence of language. In this paper, I will offer an alternative view. I will employ a concept –enacted representation– from the distributed cognition framework of cognitive science to develop a social ontology that does not take language as a requirement to create social institutions.
description: Journal of Social Ontology, Vol. 9 No. 1 (2023)
Novel mechanisms of fibrinolysis in health and disease
Creators: name: De Asis, Kathleen Gayle
Publisher: name: University of British Columbia
Year: 2014

description: This is a two-part thesis, focusing first on a clinical and then on a biochemical aspect of fibrinolysis, the process that dissolves blood clots. Hyperfibrinolysis: An explanation for reduced cardiovascular disease in hemophilia patients Hemophilia is a coagulation disorder where factor (F) VIII or FIX deficiency results in prolonged bleeding. Therapeutic FVIII or FIX replacement has lengthened hemophilia patient life expectancy. Interestingly, retrospective studies have demonstrated a lower standard mortality risk from cardiovascular disease (CVD) compared to the normal population and enhanced fibrinolytic capability has been proposed as an explanation for this relative protection from CVD. Through the analysis of tissue-type plasminogen activator (tPA), the initiator of fibrinolysis and two inhibitors of fibrinolysis: plasminogen activator inhibitor-1 (PAI-1) and thrombin activatable fibrinolysis inhibitor (TAFI), the current study showed that some hemophilia patients have reduced inhibition of the fibrinolytic pathway compared to age and cardiovascular risk matched controls. A trend of hyperfibrinolysis was also seen in hemophilia patients through accelerated plasma clot lysis with 50% of the patients having at least a 2-fold enhancement, and 22% with at least a 10-fold enhancement. Regulation of Clotting Factor Xa Auxiliary Cofactor Function in Fibrinolysis through β-Peptide Excision We have shown that clotting factor Xa (FXa) cleaved by the fibrinolysis protease, plasmin (Pn), produces consecutive fragments, called FXaβ and Xa33/13. These both have newly exposed C-terminal lysines (Lys) that accelerate tPA in purified clot lysis assays. However, in plasma Xa33/13 rapidly loses this fibrinolytic function due to degradation. It is therefore important to define the role of four possible basic amino acid residues in generating FXaβ; Lys(K)427, Arg(R)429, K433 and K435. Using site directed mutagenesis, K435 was defined as the preferred cleavage site, while R429 was unfavourable. K433 and K435 were found to be important for RVV-X activation and β-peptide cleavage facilitates the production of Xa33/13. Interestingly, when all four basic residues were mutated to Gln (Q), preventing production of FXaβ, an unexpected distal cleavage site was demonstrated to also enhance Pn generation. Replacing the R429 with lysine generated a hyperfibrinolytic species suggesting a potential novel therapeutic approach.
On Multibrane Solutions in Open String Field Theory
Creators: name: Murata, Masaki
name: Schnabl, Martin
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Existence of open string field theory solutions describing configurations of multiple space-filling D-branes has been a subject of numerous speculations for quite some time. In this talk we present some new results giving further support to these ideas.
description: 8 pages. Contribution to the proceedings of the 3rd International Conference on String Field Theory and Related Aspects (SFT 2010), Kyoto, Japan, 18-22 Oct 2010
Modelling overflow metabolism in Escherichia coli by acetate cycling
Creators: name: Anane, Emmanuel
name: López Cárdenas, Diana Carolina
name: Neubauer, Peter
name: Cruz-Bournazou, Mariano Nicolas
Publisher: name: Technische Universität Berlin
Year: 2017
Subjects: subject: 660 Chemische Verfahrenstechnik
subject: 570 Biowissenschaften; Biologie
subject: Escherichia coli
subject: overflow metabolism
subject: acetate
subject: modelling
subject: fed-batch

description: A new set of mathematical equations describing overflow metabolism and acetate accumulation in E. coli cultivation is presented. The model is a significant improvement of already existing models in the literature, with modifications based on the more recent concept of acetate cycling in E. coli, as revealed by proteomic studies of overflow routes. This concept opens up new questions regarding the speed of response of the acetate production and its consumption mechanisms in E. coli. The model is formulated as a set of continuous differentiable equations, which significantly improves model tractability and facilitates the computation of dynamic sensitivities in all relevant stages of fermentation (batch, fed-batch, starvation). The model is fitted to data from a simple 2 L fed-batch cultivation of E. coli W3110 M, where twelve (12) out of the sixteen (16) parameters were exclusively identified with relative standard deviation less than 10%. The framework presented gives valuable insight into the acetate dilemma in industrial fermentation processes, and serves as a tool for the development, optimization and control of E. coli fermentation processes.
Interface ferromagnetism and orbital reconstruction in BiFeO3- La0.7Sr0.3MnO3 heterostructures
Creators: name: Yu, P.
name: Lee, J. -S.
name: Okamoto, S.
name: Rossell, M. D.
name: Huijben, M.
name: Yang, C. -H.
name: He, Q.
name: Zhang, J. -X.
name: Yang, S. Y.
name: Lee, M. J.
name: Ramasse, Q. M.
name: Erni, R.
name: Chu, Y. -H.
name: Arena, D. A.
name: Kao, C. -C.
name: Martin, L. W.
name: Ramesh, R.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We report the formation of a novel ferromagnetic state in the antiferromagnet BiFeO3 at the interface with La0.7Sr0.3MnO3. Using x-ray magnetic circular dichroism at Mn and Fe L2,3-edges, we discovered that the development of this ferromagnetic spin structure is strongly associated with the onset of a significant exchange bias. Our results demonstrate that the magnetic state is directly related with an electronic orbital reconstruction at the interface, which is supported by the linearly polarized x-ray absorption measurement at oxygen K-edge.
description: 17 pages, 4 figures, PRL in press
Canberra Planning for Gender Kinds
Creators: name: Fletcher, Jade
Publisher: name: Journal of Social Ontology
Year: 2023

description: In this paper I argue that the Canberra Plan is ill-equipped to offer a satisfactory theory of gender. Insofar as the Canberra Plan aims to provide a general and unified approach to philosophical theorising, this is a significant problem. I argue that this deficit in their method stems from the robust role assigned to pre-theoretical beliefs in constructing philosophical analyses. I utilise a critical conception of ideology to explain why our pre-theoretic beliefs about certain social kinds are likely to deliver politically dubious metaphysics of the social world. The first half of the paper is dedicated to exercising this theoretical shortcoming. In the second half, I suggest a way in which the Canberra Plan can address and rectify this problem, with a view to maintaining the theoretical viability of the Canberra Plan with respect to politically important concepts.
description: Journal of Social Ontology, Vol. 9 No. 1 (2023)
Transport in Coherent Quantum Hall Bilayers
Creators: name: Pesin, D. A.
name: MacDonald, A. H.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We discuss two phenomenological descriptions of low-current transport in bilayer quantum Hall system with exciton condensates, one based on a Landauer-Buttiker description of Andreev scattering at contacts to coherent bilayers and one based on a simplified single-parameter {\em p-ology} description of the weak to strong interlayer coupling crossover. The Andreev scattering phenomenology in intended to apply when the condensate is well developed and is used to predict current-voltage relationships for a variety of two contact geometries. We also apply this formalism to circumstances in which the tunnel current exceeds its critical value and the condensate is time-dependent. The {\em p-ology} approach is used to establish the universal development of large longitudinal drags, even in homogenous coherent samples, as the condensate weakens and the Hall drag is reduced.
description: 13 pages, 3 figures
Common Ground Between Social Ontology, Conceptual Engineering, and Conceptual Ethics
Creators: name: Oliphint, Jared
Publisher: name: Journal of Social Ontology
Year: 2023

description: Social objects have become common subjects of interest to both social ontologists and conceptual engineers, but up to this point much of the philosophical work from these two fields has surprisingly been done in isolation from each field. I show how these prolific research fields—social ontology, conceptual engineering, and conceptual ethics—can mutually benefit each other through a unifying model I propose called the 2D-CE model that shows the dependence relations between a given concept, its instantiation conditions, and whatever language represents such devices. This model combines a model from social ontology with insights from conceptual engineering and conceptual ethics into a powerful metaphilosophical tool that highlights the role of social agents for metaphysical and metalinguistic explanation. A major benefit of the model is its utility for not only social philosophy, but for other areas of research beyond the social world.
description: Journal of Social Ontology, Vol. 9 No. 1 (2023)
Orkestra Rumpilezz : musical constructions of Afro-Bahian identities
Creators: name: Diaz Meneses, Juan Diego
Publisher: name: University of British Columbia
Year: 2014

description: This dissertation examines the relationship between music and politics of black identities in Salvador, Bahia (Brazil), an epicenter of Afro-Brazilian culture. It focuses on discourses of blackness and on the role of grooves, instruments, symbolism, and perceptions of carnival music, candomblé, and jazz in the contruction of black identities in Bahia. I propose a model that integrates discourses of black primitivism and empowerment with seven notions commonly associated with black and African music: rhythmicity, percussiveness, spirituality, communalism, embodiment, traditionalism, and closeness to nature. My contribution uses a Foucauldian interpretation of these notions to explain how they work together to form discourses of blackness, not on the notions themselves for they are all widely known. The model accommodates a wide range of interpretations of these themes offering more flexible views of blackness. A Bahian big band called Rumpilezz that blends jazz with various forms of Afro- Bahian music (such as candomblé and samba-reggae), serves as my laboratory for applying this model. Aspects of public self-representation, performance practice, music structure, and musical reception are analyzed. Taking a constructivist approach, this study aims to respond to the following questions: 1) How do the most influential preconceived ideas about “African” music and culture impact musical activity in Bahia?; 2) What opportunities emerge when musical forms perceived as Afro-Brazilian encounter others seen as foreign?; and 3) How does music in Bahia express discourses of blackness? This work, based on ethnographic research, historical, cultural, and musical analysis, demonstrates that, in promoting black empowerment, Rumpilezz emphasizes the themes of rhythmicity, percussiveness and spirituality, and downplays the notions of closeness to nature and embodiment. In doing so, the orchestra reinforces the place of Bahia, and particularly of Bahian candomblé, as diasporic centers of black tradition. Finally, Rumpilezz is located in a broader tradition of jazz bands in the diaspora that appropriates African-diasporic music to promote black pride.
Dissipative dynamics of a solid-state qubit coupled to surface plasmons: from non-Markov to Markov regimes
Creators: name: Gonzalez-Tudela, Alejandro
name: Rodriguez, Ferney J.
name: Quiroga, Luis
name: Tejedor, Carlos
Publisher: name: arXiv
Year: 2010
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We theoretically study the dissipative dynamics of a quantum emitter placed near the planar surface of a metal supporting surface plasmon excitations. The emitter-metal coupling regime can be tuned by varying some control parameters such as the qubit-surface separation and/or the detuning between characteristic frequencies. By using a Green's function approach jointly with a time-convolutionless master equation, we analyze the non-Markovian dissipative features on the qubit time evolution in two cases of interest: i) an undriven qubit initially prepared in its excited state and ii) the evolution towards a steady-state for a system driven by a laser field. For weak to moderate qubit-metal coupling strength, and on timescales large compared to the surface plasmon oscillation time, a Markovian approximation for the master equation results to be adequate to describe the qubit main optical properties: surface enhancements of rate emission, optical spectra and time-dependent photon-photon correlation functions. The qubit decay shows a crossover passing from being purely dissipative for small qubit-surface distances to plasmon emission for larger separations.
description: 10 pages, 10 figures
Structural Parameters Obtained by Pixel-by-Pixel Processing of DXA Images: Poster Presentation at the 2016 Annual Meeting of the American Society of Biomechanics
Creators: name: Baker, Alexander
name: Beaupre, Gary
Publisher: name: Zenodo
Year: 2016
Subjects: BMD
DXA
Moment of Inertia
Biomechanics
Osteoporosis
Bone Strength Index

description: While bone mineral density (BMD) from DXA has traditionally been used to quantify fracture risk, recent studies have shown it is possible to improve bone strength prediction by including additional engineering metrics, such as section modulus and cross sectional moment of inertia. These engineering metrics are almost exclusively calculated by peripheral QCT (pQCT) scanners. However, unlike DXA scanners, pQCT scanners are rarely found in clinical settings. In a 2017 study, Baker et al. (1) developed and validated a pixel-by-pixel method to calculate engineering properties at the distal femur using a Hologic QDR-1000 W DXA scanner and compared them against similar parameters measured using a Stratec XCT-3000 pQCT scanner. Baker et al. found excellent agreement between standard DXA and pixel-by-pixel measured BMD (r2 = 0.996). Cross-sectional moment of inertia about the anteroposterior axis measured using DXA and pQCT also correlated very strongly (r2 = 0.99). Finally, cross-sectional moment of inertia (CSMI) about the anteroposterior axis measured using DXA also correlated strongly with pQCT measured bone strength index (r2 = 0.99). These correlations indicate that DXA scans are able to measure equivalent pQCT parameters.

In the experimental study described in this poster, we performed mechanical testing of cadaver femora in three-point bending to failure and showed significant and strong correlations between CSMI (derived from pixel-by-pixel DXA measurements) and failure moment, and strong correlations between Section Modulus and failure moment. This indicates that DXA has the potential to be used clinically to provide an estimate of fracture-risk at the knee in fracture-prone populations such as those with spinal cord injuries.

To check out our software for processing DXA scans from a Hologic QDR1000/W pencil-beam scanner visit: https://simtk.org/projects/va-dxamoi

	Baker AM, Wagner DW, Kiratli BJ, Beaupre GS. Pixel-Based DXA-Derived Structural Properties Strongly Correlate with pQCT Measures at the One-Third Distal Femur Site. Ann Biomed Eng. 2017 May;45(5):1247-1254. doi:10.1007/s10439-017-1796-6. Epub 2017 Jan 19. PubMed PMID: 28105580.
The Impact of COVID-19-triggered Changes to Instruction and Assessment on University Students’ Self-Reported Motivation, Engagement, and Perceptions
Creators: Daniels, Lia M.
Goegan, Lauren, D.
Parker, Patti C.
Publisher: name: University of Alberta Library
Year: 2022

In March 2020, university students had to adjust to remote learning in response to the COVID-19 pandemic. This abrupt change likely impacted students’ motivation, engagement, and perceptions of success and cheating. We used a single survey to collect retrospective self-report data from a convenience sample of Canadian undergraduate students (n = 98) about their motivation, engagement, and perceptions of success and cheating before COVID-19 and then in remote learning. Students' achievement goals, engagement, and perceptions of success all significantly decreased, while their perceptions of cheating increased. Moreover, we used regression analyses to examine associations amongst achievement goals and engagement, perceptions of success, and cheating concerns. The most consistent association was that mastery-approach goals were positively associated with more engagement and higher perceptions of success. An interesting effect for performance-avoidance goals and perceptions of success also emerged. Achievement goals were unrelated to cheating. Students in large classes and who were originally concerned about cheating became more concerned about cheating in remote learning conditions. Our study provides information to researchers and instructors about how achievement goals relate to student outcomes across learning conditions. By extension, we provide timely recommendations for instructors as they continue to wrestle with how to deliver their courses during the COVID-19 pandemic.
Conformal hydrodynamics in Minkowski and de Sitter spacetimes
Creators: name: Gubser, Steven S.
name: Yarom, Amos
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We show how to generate non-trivial solutions to the conformally invariant, relativistic fluid dynamic equations by appealing to the Weyl covariance of the stress tensor. We use this technique to show that a recently studied solution of the relativistic conformally invariant Navier-Stokes equations in four-dimensional Minkowski space can be recast as a static flow in three-dimensional de Sitter space times a line. The simplicity of the de Sitter form of the flow enables us to consider several generalizations of it, including flows in other spacetime dimensions, second order viscous corrections, and linearized perturbations. We also construct the anti-de Sitter dual of the original four-dimensional flow. Finally, we discuss possible applications to nuclear physics.
description: 60 pages, 10 figures