cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Origin of the Mid Cretaceous Heavy Oils from the Safaniya Sandstone Reservoir (Wasia Formation), Saudi Arabia
Creators: name: AlGeer, Ranya
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Geochemistry
subject: FOS: Earth and related environmental sciences
subject: Heavy Oil
subject: Water washing
subject: Biodegradation
subject: maturity
subject: Kerogen Type-IIS

description: Heavy oil, extra heavy oil and natural bitumen deposits dominate the world oil inventory. There are several mechanisms by which heavy oil and natural bitumen form. They could originate by an early expulsion of oil from low-maturity-organic rich carbonate source rocks (Type II-S), or by in-situ natural alteration processes of conventional oils during migration or in the reservoir. Understanding heavy oil and natural bitumen formation mechanisms, and the geological factors controlling their occurrences, is of importance for petroleum exploration and production. While biodegradation is the main mechanism producing most Albertan heavy oils, the origin of the Saudi heavy oils is much less clear. A geochemical characterization of reservoir rock extracts and produced oil across the Mid Cretaceous Safaniya (SFNY) reservoir (Wasia Fm) section in Saudi Arabia was conducted using bulk, molecular and isotopic composition analysis of these oils to assess their origin. The samples are reservoired at a very shallow depth (3373-3480 feet below surface) and are similar in their physical properties and bulk compositions. The results indicate that the occurrence of these heavy petroleums is controlled primarily by maturity. They were mostly generated at an early stage of maturation (vitrinite reflectance (RC) ≈ < 0.5%) from a high sulfur (7.8% S), carbonate source rock (marine algal Type II-S) deposited under a highly reducing environment. The data further suggests that the SFNY petroleum probably has experienced incipient biodegradation as mirrored in the unusual selective depletion in the long chain alkylbenzenes (C15+), while similar molecular weight n-alkanes and other paraffins remain intact. The deactivation of microbes in the shallow SFNY reservoir by deep burial in the Miocene and heating to temperatures up to 76°C prior to uplift was probably the reason for the preservation of the SFNY oils from severe biodegradation. Also, the data reveals a significant alteration in the low molecular weight (LMW) polycyclic aromatic hydrocarbons (C15-) of the petroleum towards the oil water contact zone (OWCZ), possibly caused by water washing. However, a broader study on the hydrology of the Arabian basin involving hydrogen and oxygen isotopes, and oil/water partition coefficient measurement under subsurface conditions is needed to better understand interactions between static water and different compound classes of petroleum, and hence to draw a firm conclusion on whether water washing was the main cause for the compositional gradients observed in the LMW aromatic hydrocarbons of the studied oils from the SFNY reservoir.
Additional file 17 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development
Creators: name: Zhao, Yunpo
name: Lindberg, Bo Gustav
name: Esfahani, Shiva Seyedoleslami
name: Tang, Xiongzhuo
name: Piazza, Stefano
name: Engström, Ylva
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 17. Original immunoblots Fig. 7.
Feature Engineering with Regularity Structures
Creators: name: Chevyrev, Ilya
name: Gerasimovics, Andris
name: Weber, Hendrik
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (stat.ML)
subject: Machine Learning (cs.LG)
subject: Probability (math.PR)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: We investigate the use of models from the theory of regularity structures as features in machine learning tasks. A model is a polynomial function of a space-time signal designed to well-approximate solutions to partial differential equations (PDEs), even in low regularity regimes. Models can be seen as natural multi-dimensional generalisations of signatures of paths; our work therefore aims to extend the recent use of signatures in data science beyond the context of time-ordered data. We provide a flexible definition of a model feature vector associated to a space-time signal, along with two algorithms which illustrate ways in which these features can be combined with linear regression. We apply these algorithms in several numerical experiments designed to learn solutions to PDEs with a given forcing and boundary data. Our experiments include semi-linear parabolic and wave equations with forcing, and Burgers' equation with no forcing. We find an advantage in favour of our algorithms when compared to several alternative methods. Additionally, in the experiment with Burgers' equation, we find non-trivial predictive power when noise is added to the observations.
description: 33 pages, 7 figures, 7 tables. Improved presentation of model feature vector (Section 2) and experiments (Section 3). Added new experiment in 2D spatial domain (Section 3.1.2). To appear in Journal of Scientific Computing
Effect of the frequency chirp on laser wakefield acceleration
Creators: name: Pathak, V. B.
name: Vieira, J.
name: Fonseca, R. A.
name: Silva, L. O.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: The role of laser frequency chirps in the laser wakefield accelerator is examined. We show that in the linear regime, the evolution of the laser pulse length is affected by the frequency chirp, and that positive (negative) chirp compresses (stretches) the laser pulse, thereby increasing (decreasing) the peak vector potential and wakefield amplitude. In the blowout regime, the frequency chirp can be used to fine tune the localized etching rates at the front of the laser. In our simulations, chirped laser pulses can lead to 15% higher self-trapped electrons, and 10% higher peak energies as compare to the transform-limited pulse. Chirps may be used to control the phase velocity of the wake, and to relax the self-guiding conditions at the front of the laser. Our predictions are confirmed by multi-dimensional particle-in-cell simulations with OSIRIS.
description: Submitted in NJP, 4 figures
Characterization of Aerobic Methane Oxidizing Bacteria in Oil Sands Tailings Ponds
Creators: name: Saidi-Mehrabad, Alireza
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Methane Oxidizing Bacteria
subject: oil sands
subject: Tailings Ponds
subject: pyrotag sequencing
subject: Stable Isotope Probing
subject: Methylocaldum
subject: Methylobacter oleiharenae

description: The current study for the first time investigated the potential methane oxidation capacity of the surface layers of oil sands tailing ponds in Alberta, which are anthropogenic methane sources. This research by the aid of recently developed molecular analysis tools such as 16S rRNA gene pyrotag sequencing, Stable Isotope Probing, 16S rRNA and pmoA gene sequence analysis highlighted the presence of methanotrophic bacteria (mainly Gammaproteobacteria), in these tailings ponds, with potential methane oxidation activity ranging from 75.6 – 135.6 nmol CH4 ml-1 d-1. 16S rRNA pyrotag sequencing and construction of phylogenetic trees detected OTUs affiliated to the genus Methylocaldum present in all sampling sites and times (July/2011- December/2011). Later investigations resulted in the isolation of a novel strain dubbed “Methylobacter oleiharenae”, which is able to thrive at optimum pH of 8 and contains 729 specific genes not detected in closely related reference methanotroph strains.
A robust, scanning quantum system for nanoscale sensing and imaging
Creators: name: Maletinsky, P.
name: Hong, S.
name: Grinolds, M. S.
name: Hausmann, B.
name: Lukin, M. D.
name: Walsworth, R. -L.
name: Loncar, M.
name: Yacoby, A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Controllable atomic-scale quantum systems hold great potential as sensitive tools for nanoscale imaging and metrology. Possible applications range from nanoscale electric and magnetic field sensing to single photon microscopy, quantum information processing, and bioimaging. At the heart of such schemes is the ability to scan and accurately position a robust sensor within a few nanometers of a sample of interest, while preserving the sensor's quantum coherence and readout fidelity. These combined requirements remain a challenge for all existing approaches that rely on direct grafting of individual solid state quantum systems or single molecules onto scanning-probe tips. Here, we demonstrate the fabrication and room temperature operation of a robust and isolated atomic-scale quantum sensor for scanning probe microscopy. Specifically, we employ a high-purity, single-crystalline diamond nanopillar probe containing a single Nitrogen-Vacancy (NV) color center. We illustrate the versatility and performance of our scanning NV sensor by conducting quantitative nanoscale magnetic field imaging and near-field single-photon fluorescence quenching microscopy. In both cases, we obtain imaging resolution in the range of 20 nm and sensitivity unprecedented in scanning quantum probe microscopy.
Fergusobia Currie 1937 (Christie 1941
Creators: name: Davies, Kerrie A.
name: Ye, Weimin
name: Giblin-Davis, Robin M.
name: Taylor, Gary S.
name: Hodda, Mike
name: Thomas, W. Kelley
Publisher: name: Zenodo
Year: 2014
Subjects: Biodiversity
Taxonomy
Animalia
Nematoda
Secernentea
Tylenchida
Fergusobiidae
Fergusobia

description: Fergusobia Currie 1937 (Christie 1941)   Fergusobia Currie 1937: 158. Type species: Anguillulina (Fergusobia) tumifaciens Currie, 1937, by original designation (type lost).
description: Published as part of Davies, Kerrie A., Ye, Weimin, Giblin-Davis, Robin M., Taylor, Gary S., Hodda, Mike & Thomas, W. Kelley, 2014, Nematodes from galls on Myrtaceae. VII. Fergusobia from ' leafy' leaf bud galls in Australia, with re-description of Fergusobia tumifaciens (Currie 1937) Wachek 1955 and descriptions of Fergusobia planchonianae n. sp. and Fergusobia viminalisae n. sp., pp. 529-554 in Zootaxa 3856 (4) on page 533, DOI: 10.11646/zootaxa.3856.4.4, http://zenodo.org/record/225916
XIST/Xist-induced epigenetic events in somatic cells
Creators: name: Thorogood, Nancy P.
Publisher: name: University of British Columbia
Year: 2010

description: Mammalian dosage compensation of X-linked genes is achieved between XX females and XY males by silencing one of the two X chromosomes. It is the expression of a functional non-coding RNA transcript, XIST that is responsible for the initiation of silencing during X-chromosome inactivation. XIST expression and subsequent in cis localization to the future inactive X chromosome initiates a cascade of epigenetic events that leads to the formation of facultative heterochromatin. The exact role the XIST RNA plays in establishing and maintaining the inactive state is uncertain. It is hypothesized that the XIST RNA sets up a repressive nuclear compartment and transcriptionally silences through the recruitment of factors required for setting up the heterochromatic state of the inactive X. In this thesis I address XIST/Xist’s recruitment of factors with two separate approaches: 1) I ask whether Xist, in the absence of silencing is able to recruit epigenetic marks in a somatic cell hybrid system, 2) I evaluate a system whereby the XIST RNA is tagged and can be isolated to identify novel RNA-protein interactions. To assess epigenetic features that may be directly recruited by the expression of the XIST/Xist RNA, I have analyzed mouse/human somatic cell hybrids where XIST/Xist expression and silencing are disconnected. Loss of active chromatin marks, H3 acetylation and H3 lysine 4 methylation, was not observed with XIST/Xist expression; nor was there a gain of DNA methylation or the silencing of the Cot-1 fraction. Therefore, these marks of heterochromatin are not solely dependent upon XIST/Xist expression in a somatic cell. The isolation of the XIST RNA with its interacting partners would allow us to better understand the mechanism by which XIST acts to silence the inactive X. I have developed a MS2 stem loop-tagged XIST RNA and integrated it into an inducible XIST system. The MS2 tagging system is a valid system for pulling out the XIST RNA and identifying interacting proteins since the tagged RNA was able to interact with whatever factor(s) are required to silence the Cot-1 fraction and form a localized RNA signal.
Additional file 1 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development
Creators: name: Zhao, Yunpo
name: Lindberg, Bo Gustav
name: Esfahani, Shiva Seyedoleslami
name: Tang, Xiongzhuo
name: Piazza, Stefano
name: Engström, Ylva
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. The dfr/vvl is a single exon gene with no signs of RNA editing. a No alternative splicing was observed in the dfr gene around the first stop codon. Gel electrophoresis of an RT-PCR product of dfr mRNA around the first in-frame stop codon. Only a single band was detected. b Sequencing results show no indication of RNA editing around the first stop codon. Upper panel, sequenced with forward primer; lower panel, with reverse primer. Stop codon sequences are boxed.
Dispersion of orbital excitations in 2D quantum antiferromagnets
Creators: name: Wohlfeld, Krzysztof
name: Daghofer, Maria
name: Khaliullin, Giniyat
name: Brink, Jeroen van den
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We map the problem of the orbital excitation (orbiton) in a 2D antiferromagnetic and ferroorbital ground state onto a problem of a hole in 2D antiferromagnet. The orbiton turns out to be coupled to magnons and can only be mobile on a strongly renormalized scale by dressing with magnetic excitations. We show that this leads to a dispersion relation reflecting the two-site unit cell of the antiferromagnetic background, in contrast to the predictions based on a mean-field approximation and linear orbital-wave theory.
description: 4 pages, 2 figures, submitted to SCES 2011 conference proceedings
The role of synovial progenitor cells in cartilage repair
Creators: name: Mak, Joyce
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Biology--Cell
subject: Biology--Molecular
subject: mesenchymal stem cells
subject: synovium
subject: synovial membrane
subject: Cartilage
subject: repair
subject: magnetic resonance imaging (MRI)
subject: Sca-1
subject: stem cell tracking
subject: in vivo imaging

description: In this study, we have isolated a Sca-1 positive population of mouse synovial cells that contains progenitors capable of chondrogenesis. Intra-articular injection of Sca-1+-GFP+ synovial cells preserved proteoglycan content in the cartilage following cartilage injury but GFP expression could not be detected in the injury sites. Histological analysis suggests that in vivo mechanical stimulation of the injected cells due to joint loading results in the secretion of GAGs by the exogenous cells and thereby protects the joints from further degradation. Furthermore, progressive changes in cell morphology were observed in Sca-1+ synovial cells in response to injury, changing from a flatten, fibroblast-like appearance to a spherical and detached morphology 48 hours after injury. The presented study provides insight as to how endogenous synovial cells might act in response to injury as well as a mechanism by which the cells could protect the joint from degradation.
Application of Visual Clustering Properties of Self Organizing Map in Machine-part Cell Formation
Creators: name: Chattopadhyay, Manojit
name: Dan, Pranab K.
name: Majumdar, Sitanath
Publisher: name: arXiv
Year: 2012
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: Cellular manufacturing (CM) is an approach that includes both flexibility of job shops and high production rate of flow lines. Although CM provides many benefits in reducing throughput times, setup times, work-in-process inventories but the design of CM is complex and NP complete problem. The cell formation problem based on operation sequence (ordinal data) is rarely reported in the literature. The objective of the present paper is to propose a visual clustering approach for machine-part cell formation using Self Organizing Map (SOM) algorithm an unsupervised neural network to achieve better group technology efficiency measure of cell formation as well as measure of SOM quality. The work also has established the criteria of choosing an optimum SOM map size based on results of quantization error, topography error, and average distortion measure during SOM training which have generated the best clustering and preservation of topology. To evaluate the performance of the proposed algorithm, we tested the several benchmark problems available in the literature. The results show that the proposed approach not only generates the best and accurate solution as any of the results reported, so far, in literature but also, in some instances the results produced are even better than the previously reported results. The effectiveness of the proposed approach is also statistically verified.
description: 33 pages, 7 figures, 7 tables
Calibration of the MaGIXS experiment II: Flight Instrument Calibration
Creators: name: Athiray, P. S.
name: Winebarger, Amy R.
name: Champey, Patrick
name: Kobayashi, Ken
name: Savage, Sabrina
name: Beabout, Brent
name: Beabout, Dyana
name: Broadway, David
name: Bruccoleri, Alexander R.
name: Cheimets, Peter
name: Golub, Leon
name: Gullikson, Eric
name: Haight, Harlan
name: Heilmann, Ralf K.
name: Hertz, Edward
name: Hogue, William
name: Johnson, Steven
name: Kegley, Jeffrey
name: Kolodziejczak, Jeffery
name: Madsen, Chad
name: Schattenburg, Mark L.
name: Siler, Richard
name: Vigil, Genevieve D.
name: Wright, Ernest
Publisher: name: arXiv
Year: 2021
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The Marshall Grazing Incidence X-ray Spectrometer (MaGIXS) is a sounding rocket experiment that observes the soft X-ray spectrum of the Sun from 6.0 - 24 Angstrom (0.5 - 2.0 keV), successfully launched on 30 July 2021. End-to-end alignment of the flight instrument and calibration experiments are carried out using the X-ray and Cryogenic Facility (XRCF) at NASA Marshall Space Flight Center. In this paper, we present the calibration experiments of MaGIXS, which include wavelength calibration, measurement of line spread function, and determination of effective area. Finally, we use the measured instrument response function to predict the expected count rates for MaGIXS flight observation looking at a typical solar active region
description: 20 pages, 16 figures, Accepted for publication in the Astrophysical Journal
A simple scheme for quantum networks based on orbital angular momentum states of photons
Creators: name: Su, Zhi-Kun
name: Wang, Fa-Qiang
name: Jin, Rui-Bo
name: Liang, Rui-Sheng
name: Liu, Song-Hao
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We propose a new quantum network scheme using orbital angular momentum states of photons to route the network and spin angular momentum states to encode the information. A four-user experimental scheme based on this efficient quantum network is analyzed in detail, which is particularly appealing for the free space quantum key distribution. Users can freely exchange quantum keys with each other.
description: 9 pages, published in Optics Communications, 281, 5063-5066
Quantitative reconstruction of defects in multi-layered bonded composites using fully convolutional network-based ultrasonic inversion
Creators: name: Rao, Jing
name: Yang, Fangshu
name: Mo, Huadong
name: Kollmannsberger, Stefan
name: Rank, Ernst
Publisher: name: arXiv
Year: 2021
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Machine Learning (cs.LG)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Ultrasonic methods have great potential applications to detect and characterize defects in multi-layered bonded composites. However, it remains challenging to quantitatively reconstruct defects, such as disbonds and kissing bonds, that influence the integrity of adhesive bonds and seriously reduce the strength of assemblies. In this work, an ultrasonic method based on the supervised fully convolutional network (FCN) is proposed to quantitatively reconstruct defects hidden in multi-layered bonded composites. In the training process of this method, an FCN establishes a non-linear mapping from measured ultrasonic data to the corresponding velocity models of multi-layered bonded composites. In the predicting process, the trained network obtained from the training process is used to directly reconstruct the velocity models from the new measured ultrasonic data of adhesively bonded composites. The presented FCN-based inversion method can automatically extract useful features in multi-layered composites. Although this method is computationally expensive in the training process, the prediction itself in the online phase takes only seconds. The numerical results show that the FCN-based ultrasonic inversion method is capable to accurately reconstruct ultrasonic velocity models of the high contrast defects, which has great potential for online detection of adhesively bonded composites.
Symmetry-broken Chern insulators in twisted double bilayer graphene
Creators: name: He, Minhao
name: Cai, Jiaqi
name: Zhang, Ya-Hui
name: Liu, Yang
name: Li, Yuhao
name: Taniguchi, Takashi
name: Watanabe, Kenji
name: Cobden, David H.
name: Yankowitz, Matthew
name: Xu, Xiaodong
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Twisted double bilayer graphene (tDBG) has emerged as an especially rich platform for studying strongly correlated and topological states of matter. The material features moiré bands that can be continuously deformed by both perpendicular displacement field and twist angle. Here, we construct a phase diagram representing of the correlated and topological states as a function of these parameters, based on measurements on over a dozen tDBG devices encompassing the two distinct stacking configurations in which the constituent Bernal bilayer graphene sheets are rotated either slightly away from 0° or 60°. We find a hierarchy of symmetry-broken states that emerge sequentially as the twist angle approaches an apparent optimal value of $θ\approx$ 1.34°. Among them, we discover a sequence of symmetry-broken Chern insulator (SBCI) states that arise only within a narrow range of twist angles ($\approx$ 1.33° to 1.39°). We observe an associated anomalous Hall effect at zero field in all samples supporting SBCI states, indicating spontaneous time-reversal symmetry breaking and possible moiré unit cell enlargement at zero magnetic field.
description: 42 pages
Shortest billiard trajectories
Creators: name: Bezdek, Daniel
name: Bezdek, Karoly
Publisher: name: arXiv
Year: 2011
Subjects: subject: Metric Geometry (math.MG)
subject: FOS: Mathematics

description: In this paper we prove that any convex body of the d-dimensional Euclidean space (d>1) possesses at least one shortest generalized billiard trajectory moreover, any of its shortest generalized billiard trajectories is of period at most d+1. Actually, in the Euclidean plane we improve this theorem as follows. A disk-polygon with parameter r>0 is simply the intersection of finitely many (closed) circular disks of radii r, called generating disks, having some interior point in common in the Euclidean plane. Also, we say that a disk-polygon with parameter r>0 is a fat disk-polygon if the pairwise distances between the centers of its generating disks are at most r. We prove that any of the shortest generalized billiard trajectories of an arbitrary fat disk-polygon is a 2-periodic one. Also, we give a proof of the analogue result for ε-rounded disk-polygons obtained from fat disk-polygons by rounding them off using circular disks of radii ε>0. Our theorems give partial answers to the very recent question raised by S. Zelditch on characterizing convex bodies whose shortest periodic billiard trajectories are of period 2.
description: 14 pages, 3 figures
Overdensities of 24um Sources in the Vicinities of High-Redshift Radio Galaxies
Creators: name: Mayo, Jack H.
name: Vernet, Joel
name: De Breuck, Carlos
name: Galametz, Audrey
name: Seymour, Nick
name: Stern, Daniel
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present a statistical study of the environments of 63 high-redshift radio galaxies (HzRGs) between redshifts 1
description: 10 pages, 7 figures, 2 tables, accepted for publication in A&A
Duration-of-load and creep effects in thick MPB strand based wood composite
Creators: name: Wang, Bing
Publisher: name: University of British Columbia
Year: 2010

description: British Columbia (BC) is in the midst of the largest outbreak of the Mountain Pine Beetle (MPB) ever recorded in western Canada. Technologies capable of converting stained lumber into market acceptable products are urgently required to reduce the impact of the growing volume of MPB killed lumber on the profitability of forestry in BC. New, thick MPB strand-based structural composite products can be produced and help absorb a large volume of MPB wood. With appropriate mechanical properties, such products can be used as beams, headers, and columns in the low-rise commercial, multi-family residential and single family residential markets. This work was focused on the duration-load and creep behaviour of thick MPB strand-based wood composite. The beam specimens were made in the Timber Engineering and Applied Mechanics Laboratory at UBC. A series of tests were conducted on the matched groups to investigate the creep-rupture behaviour. These investigations comprised of ramp load tests at three loading rates, long-term constant load tests at two stress levels and cyclic bending tests at six stress levels. A damage accumulation model was developed to study the creep-rupture behaviour. This model stipulates that the rate of damage growth is given in terms of the current strain rate and the previously accumulated damage, and a 5-parameter rheological model is applied to describe the viscoelastic constitutive relationship to represent the time-dependent strain, while the damage accumulation law acts as the failure criterion. The results of the long-term constant load tests were then interpreted by means of the creep-rupture model which had been shown to be able to represent the time-dependent deflection and time-to-failure data for different stress levels. The predictions of the model were verified using results from ramp load tests at different loading rates and results from cyclic loading tests at different stress levels. The creep-rupture model incorporates the short term strength of the material, the load history and predicts the deflection history as well as the time-to-failure. As it is a probabilistic model, it allows its incorporation into a time-reliability study of wood composites’ applications.
Microcanonical Origin of the Maximum Entropy Principle for Open Systems
Creators: name: Lee, Julian
Publisher: name: arXiv
Year: 2012
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The canonical ensemble describes an open system in equilibrium with a heat bath of fixed temperature. The probability distribution of such a system, the Boltzmann distribution, is derived from the uniform probability distribution of the closed universe consisting of the open system and the heat bath, by taking the limit where the heat bath is much larger than the system of interest. Alternatively, the Boltzmann distribution can be derived from the Maximum Entropy Principle, where the Gibbs-Shannon entropy is maximized under the constraint that the mean energy of the open system is fixed. To make the connection between these two apparently distinct methods for deriving the Boltzmann distribution, it is first shown that the uniform distribution for a microcanonical distribution is obtained from the Maximum Entropy Principle applied to a closed system. Then I show that the target function in the Maximum Entropy Principle for the open system, is obtained by partial maximization of Gibbs-Shannon entropy of the closed universe over the microstate probability distributions of the heat bath. Thus, microcanonical origin of the Entropy Maximization procedure for an open system, is established in a rigorous manner, showing the equivalence between apparently two distinct approaches for deriving the Boltzmann distribution. By extending the mathematical formalism to dynamical paths, the result may also provide an alternative justification for the principle of path entropy maximization as well.
description: 12 pages, no figure
Denial-of-Service Attack Detection via Differential Analysis of Generalized Entropy Progressions
Creators: name: Subasi, Omer
name: Manzano, Joseph
name: Barker, Kevin
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cryptography and Security (cs.CR)
subject: FOS: Computer and information sciences

description: Denial-of-Service (DoS) attacks are one of the most common and consequential cyber attacks in computer networks. While existing research offers a plethora of detection methods, the issue of achieving both scalability and high detection accuracy remains open. In this work, we address this problem by developing a differential method based on generalized entropy progression. In this method, we continuously fit the line of best fit to the entropy progression and check if the derivative, that is, the slope of this line is less than the negative of the dynamically computed standard deviation of the derivatives. As a result, we omit the usage of the thresholds and the results with five real-world network traffic datasets confirm that our method outperforms threshold-based DoS attack detection by two orders of magnitude on average. Our method achieves false positive rates that are up to 7% where the arithmetic mean is 3% with Tsallis entropy and only 5% sampling of the total network flow. Moreover, since the main computation cost of our method is the entropy computation, which is linear in the volume of the unit-time network flow and it uses integer only operations and a small fraction of the total flow, it is therefore lightweight and scalable.
Additional file 2 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development
Creators: name: Zhao, Yunpo
name: Lindberg, Bo Gustav
name: Esfahani, Shiva Seyedoleslami
name: Tang, Xiongzhuo
name: Piazza, Stefano
name: Engström, Ylva
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2. MS analysis of Dfr-6xMyc following immunoprecipitation. a-b nLC-MS/MS and MASCOT analysis. a Two peaks in the MS spectrum (red boxes) were found to span the Dfr ORF1-ORF2 junction, with the same molecular weight but different charge. b MS/MS fragmentation of precursor m/z 757.36 [M + 3]+, with the amino acid sequence AAHXQSEIQESNSAAAASTPASL. Assigned β- and γ-ions are indicated in the figure. c MASCOT analysis against a Drosophila protein reference database (Swiss prot_2020, Drosophila (fruit flies) 5922 sequences) identified m/z 757.36[M + 3]+ among 15 other peptides as unique for Dfr (protein score = 154). The identified peptides (of identical sequence), spanning ORF1-ORF2 are highlighted (red box). A second MASCOT analysis was performed using the Dfr-Myc sequence as reference (score significance threshold > 45). Mr (expt), experimental m/z transformed to a relative molecular mass; Mr (calc), relative molecular mass calculated from the matched peptide sequence; ppm, difference (error) between the experimental and calculated masses in parts per million: M, number of missed cleavage sites; Ions score, if there are duplicate matches to the same peptide, then the lower scoring matches are shown in brackets; Expect, expectation value for the peptide match.; R, rank of the peptide match, (1 to 10, where 1 is the best match); U, indicates that the peptide sequence is unique to one protein family member.
The Emerging Discourse of Transdisciplinary Neurorehabilitation: Building Healthcare and Health Capacity on the Moral High Ground
Creators: name: Baird, Donna
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Public Health
subject: Transdisciplinary Teams
subject: Heathcare Reform
subject: Chronic Illness
subject: Rehabilitation

description: This 2-year comprehensive case study is the first of its kind to uncover the mechanisms through which a transdisciplinary neurorehabilitation team operationalizes the population health goal of increasing personal and family capacity. Data collection strategies included audio-taped interviews and focus groups, field observations and document analysis. A lengthy analysis was required to identify and unravel the emerging discourse of transdisciplinary practice from the traditional discourse of medicine. A transdisciplinary meta-narrative was constructed using interview and focus group data follow by interpretative repertoire analysis. The analytic approach allowed for a nuanced description of transdisciplinary practice to emerge. The interpretative repertoires coalesced around six discursive topics: the traditional model, creation of the clinic, transdisciplinary leadership, team membership, therapeutic interventions and physician practices. Result of this study demonstrate how this rare transdisciplinary healthcare team integrates a population health lens, salutogenic theory and transdisciplinary philosophy to maximize the capacity of individuals and families to take control of their health and health circumstances. The team also works collaboratively with family members to help clients reintegrate into their home, workforce and community and reduce reliance on family and the healthcare system. Finally, the study demonstrates how transdisciplinary practice, longevity, a shared ethos and an organization-wide orientation to salutogenesis are resources for organizational efficiency and employee health. The transdisciplinary team studied for this project is an example of a theoretically grounded and radical alternative to the existing health services paradigm. A transdisciplinary approach may be the nascent solution needed to curb the soaring cost of chronic illness in Canada.
Additional file 4 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development
Creators: name: Zhao, Yunpo
name: Lindberg, Bo Gustav
name: Esfahani, Shiva Seyedoleslami
name: Tang, Xiongzhuo
name: Piazza, Stefano
name: Engström, Ylva
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4. Dfr-L is present in several larval and adult tissues. a-h Confocal images of Drosophila tissues stained with anti-Dfr-L (red) and DAPI (blue), and a merged image placed above the anti-Dfr-L image of adult brain (a); crop (b); adult salivary gland (c) with an arrow pointing at the tip cells with prominent Dfr-L staining; female oviduct (d) and germarium (e); late stage embryo (f) and boxed region in magnified view (f’), with arrow pointing at the embryonic ring gland; L3 wing imaginal disc (g) and gonad of female white prepupa (h). Scale bars 50 μm. i Summary of anti-Dfr-S/L and anti-Dfr-L staining in control (w1118) and dfr14 mutant larval and adult tissues. The fluorescence intensity is represented by -, -/+, +, ++, and +++, from barely detectable to strong.
The Epistemic Significance of Values in Science
Creators: name: Holter, Brandon
Publisher: name: Arts
Year: 2014
Subjects: subject: Philosophy
subject: FOS: Philosophy, ethics and religion
subject: Philosophy
subject: Science
subject: Epistemology

description: The proper role of values in science has been a hotly debated topic for many decades now. The traditional view of epistemic justification holds that scientific objectivity requires suppression of value judgments; theories are only justified by an impartial analysis of the evidence (Haack 1998; Pinnick, Koertge, and Almedar 2003). Traditionalists worry that values bias scientists, leading them to believe what they would like to be true regardless of the evidence. Proponents of value-laden science argue that the justification of scientific theories cannot be isolated from moral and practical judgments (Kuhn 1962; Longino 2002a). The arguments they advance purport to show that values are not merely biases, values can play a positive role in justifying beliefs. Underdetermination arguments claim that evidence alone cannot determine theory choice (Laudan 1990; Longino 1979; Quine 1951).These arguments do not motivate an epistemic role for values in science, however, because values may influence scientists' theoretical beliefs without justifying those beliefs. As a result, philosophers have advanced a number of new arguments for the epistemic necessity of values judgments. This dissertation examines several of these arguments with an eye toward their deficiencies in order to develop an account of values in scientific reasoning that does not legitimate bias or delusion, as the traditionalists fear. Drawing on both old and new arguments, I argue that values help determine when a theory is sufficiently justified by the evidence (Douglas 2000; Kitcher 2011a; Rudner 1953). While evidence alone provides justifying reasons for belief, scientists must decide how much evidence is needed to justify scientific claims. Different scientific inquiries require different epistemic standards and, I argue, traditional value-free epistemologies cannot account for this variation. Philosophers cannot explain why scientists in different contexts adopt different epistemic standards without appealing to value judgments. On the view I adopt, the evidence justifies a claim when we have good reasons to believe we can act on that claim; a theory is sufficiently justified in the epistemic sense when it is sufficiently justified for practical purposes. Allowing values to guide these decisions, I argue, does not allow values to displace rigorous attention to the evidence.
Identifying the Charge Carriers of the Quark-Gluon Plasma
Creators: name: Pratt, Scott
Publisher: name: arXiv
Year: 2012
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Charge correlations in lattice gauge calculations suggest that up, down and strange charges move independently in the QGP (quark-gluon plasma), and that the density of such charges is similar to what is expected from simple thermal arguments. Here, we show how specific elements of the charge-charge correlation matrix in the QGP survive hadronization and become manifest in final-state charge-charge correlation measurements.
description: 4 pages, 4 figures
Additional file 3 of Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development
Creators: name: Zhao, Yunpo
name: Lindberg, Bo Gustav
name: Esfahani, Shiva Seyedoleslami
name: Tang, Xiongzhuo
name: Piazza, Stefano
name: Engström, Ylva
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3. Disorder analysis of Dipteran Dfr/Vvl-L proteins. a-d The intrinsic disorder of Dfr/Vvl-L was calculated by the VSL2 algorithm ( http://www.pondr.com/ ). Schematic representation of ORF1 (red), ORF2 (Yellow) and the DNA-binding domains (DBD, blue) are shown above the disorder graph. The horizontal bold line indicates 0.5 disordered score, above which the amino acid sequence is disordered. Dpse, Drosophila pseudoobscura pseudoobscura; Gmor, Glossina morsitans; Aaeg; Aedes aegyptii; Cqui, Culex quinquefasciatus; DBD, DNA-binding domain.
Enforced symmetry breaking by invertible topological order
Creators: name: Ning, Shang-Qiang
name: Qi, Yang
name: Gu, Zheng-Cheng
name: Wang, Chenjie
Publisher: name: arXiv
Year: 2021
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Superconductivity (cond-mat.supr-con)
subject: High Energy Physics - Theory (hep-th)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: It is well known that two-dimensional fermionic systems with a nonzero Chern number must break the time reversal symmetry, manifested by the appearance of chiral edge modes on an open boundary. Such an incompatibility between topology and symmetry can occur more generally. We will refer to this phenomenon as enforced symmetry breaking by topological orders. In this work, we systematically study enforced breaking of a general finite group $G_f$ by a class of topological orders, namely 0D, 1D and 2D fermionic invertible topological orders. Mathematically, the symmetry group $G_f$ is a central extension of a bosonic group $G$ by the fermion parity group $Z_2^f$, characterized by a 2-cocycle $λ$ $\in H^2(G,Z_2)$. With some minor assumptions and for given $G$ and $λ$, we are able to obtain a series of criteria on the existence or non-existence of enforced symmetry breaking by the fermionic invertible topological orders. Using these criteria, we discover many examples that are not known previously. For 2D systems, we define the physical quantities to describe symmetry-enriched invertible topological orders and derive some obstruction functions using both fermionic and bosonic languages. In the latter case which is done via gauging the fermion parity, we find that some obstruction functions are consequences of conditional anomalies of the bosonic symmetry-enriched topological states, with the conditions inherited from the original fermionic system. We also study enforced breaking of the continuous group $SU_f(N)$ by 2D invertible topological orders through a different argument.
description: 29 pages, 4 figures, 6 tables, comment and suggestion are welcome
Automatic Network Reconstruction using ASP
Creators: name: Ostrowski, Max
name: Schaub, Torsten
name: Durzinsky, Markus
name: Marwan, Wolfgang
name: Wagler, Annegret
Publisher: name: arXiv
Year: 2011
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Building biological models by inferring functional dependencies from experimental data is an im- portant issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available ap- proaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuris- tic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by ap- peal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several ben- efits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems.
Burstiness and Uncertainty Aware Service Level Planning for Enterprise Clouds
Creators: name: Youssef, Anas
Publisher: name: Graduate Studies
Year: 2014
Subjects: subject: Computer Science
subject: Engineering--Operations Research
subject: Cloud Resource Management
subject: Cloud Service Level Planning
subject: Workload Burstiness
subject: Heuristic Optimization

description: As enterprises begin to increasingly adopt the cloud paradigm, Cloud Service Providers (SPs) need tools to help them plan their infrastructure capacity and decide on Service Level Agreements (SLAs) with customers prior to deploying their customers' applications. Service Level Objectives (SLOs) are specified for customers' applications as part of customers' SLAs with cloud SPs. A cloud SP need Service Level Planning (SLP) tools that consider the workloads of the applications deployed on the cloud to determine the adequate capacity required to satisfy the applications' SLOs. Existing SLP approaches have not considered important challenges such as workload burstiness, workload uncertainty, and scalability to large number of applications. This thesis presents an SLP framework that addresses the above challenges simultaneously. The framework implements a novel Resource Allocation Planning (RAP) method to identify a time varying allocation of resources to applications to satisfy their bursts. RAP is a heuristic optimization technique that in conjunction with a trace-driven performance prediction technique estimates the near minimal degree of service level violations that the cloud SP can incur with a given cloud resource capacity. RAP works in consort with a Monte Carlo simulation technique, which allows cloud SPs to systematically consider the impact of workload uncertainty in SLP. Finally, a new burstiness-aware workload clustering algorithm is proposed to increase the scalability of the SLP framework while preserving workload burstiness. Detailed simulation results are presented to characterize the behaviour of the proposed SLP framework. The results show that the proposed RAP variants can identify optimal or near optimal resource allocation plans without exhaustively generating all possible plans. Secondly, the results show that RAP can permit cloud SPs to more accurately determine the capacity required for delivering specified SLOs compared to other competing techniques especially for bursty workloads. Thirdly, the results demonstrate that the proposed Monte Carlo simulation technique enables cloud SPs to accurately estimate the impact of workload uncertainty in their SLP exercises without exhaustively traversing all combinations of application workload scenarios. Finally, the results show that the proposed workload clustering algorithm reduces the number of computations needed to support SLP exercises without significantly impacting accuracy.
Constructing a Large Variety of Dirac-Cone Materials in the Bi${}_{1-x}$Sb${}_{x}$ Thin Film System
Creators: name: Tang, Shuang
name: Dresselhaus, Mildred S.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We theoretically predict that a large variety of Dirac-cone materials can be constructed in Bi${}_{1-x}$Sb${}_{x}$ thin films, and we here show how to construct single-, bi- and tri- Dirac-cone materials with various amounts of wave vector anisotropy. These different types of Dirac cones can be of special interest to electronic devices design, quantum electrodynamics and other fields.