scholarly journals Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution

2006 ◽  
Vol 16 (10) ◽  
pp. 1270-1275 ◽  
Author(s):  
S. W. Roy ◽  
D. Penny
Keyword(s):  
Large Scale ◽  
Intron Loss ◽  
Order Of Magnitude ◽  
Magnitude Variation ◽  
Intron Conservation

scholarly journals Nebula: ultra-efficient mapping-free structural variant genotyper

2021 ◽  
Author(s):  
Parsoa Khorsand ◽  
Fereydoun Hormozdiari
Keyword(s):  
Large Scale ◽  
Structural Variants ◽  
Sequencing Technologies ◽  
Generic Framework ◽  
Common Genetic Variants ◽  
Order Of Magnitude ◽  
Complex Events ◽  
Comparable Accuracy ◽  
Using Data ◽  
Computational Resources

Abstract Large scale catalogs of common genetic variants (including indels and structural variants) are being created using data from second and third generation whole-genome sequencing technologies. However, the genotyping of these variants in newly sequenced samples is a nontrivial task that requires extensive computational resources. Furthermore, current approaches are mostly limited to only specific types of variants and are generally prone to various errors and ambiguities when genotyping complex events. We are proposing an ultra-efficient approach for genotyping any type of structural variation that is not limited by the shortcomings and complexities of current mapping-based approaches. Our method Nebula utilizes the changes in the count of k-mers to predict the genotype of structural variants. We have shown that not only Nebula is an order of magnitude faster than mapping based approaches for genotyping structural variants, but also has comparable accuracy to state-of-the-art approaches. Furthermore, Nebula is a generic framework not limited to any specific type of event. Nebula is publicly available at https://github.com/Parsoa/Nebula.

scholarly journals Mineralogical, numerical and analytical studies of the coupled oxidation of pyrite and coal

2003 ◽  
Vol 67 (2) ◽  
pp. 381-398 ◽  
Author(s):  
K. A. Evans ◽  
C. J. Gandy ◽  
S. A. Banwart
Keyword(s):  
Reactive Transport ◽  
Transport Model ◽  
Pyrite Oxidation ◽  
Spoil Heap ◽  
Reaction Fronts ◽  
Order Of Magnitude ◽  
Magnitude Variation ◽  
Discharge Chemistry ◽  
Analytical Expressions

Mineralogical, bulk and field leachate compositions are used to identify important processes governing the evolution of discharges from a coal spoil heap in County Durham. These processes are incorporated into a numerical one-dimensional advective-kinetic reactive transport model which reproduces field results, including gas compositions, to within an order of magnitude. Variation of input parameters allows the effects of incorrect initial assumptions on elemental profiles and discharge chemistry to be assessed. Analytical expressions for widths and speeds of kinetic reaction fronts are developed and used to predict long-term development of mineralogical distribution within the heap. Results are consistent with observations from the field site. Pyrite oxidation is expected to dominate O2 consumption in spoil heaps on the decadal timescale, although C oxidation may stabilize contaminants in effluents on the centennial scale.

Efficient and High-Quality Seeded Graph Matching: Employing Higher-order Structural Information

2021 ◽  
Vol 15 (3) ◽  
pp. 1-31
Author(s):  
Haida Zhang ◽  
Zengfeng Huang ◽  
Xuemin Lin ◽  
Zhe Lin ◽  
Wenjie Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Graph Matching ◽  
Structural Information ◽  
Experimental Studies ◽  
Higher Order ◽  
Personalized Pagerank ◽  
Matching Accuracy ◽  
Approximation Techniques ◽  
Order Of Magnitude ◽  
Matching Score

Driven by many real applications, we study the problem of seeded graph matching. Given two graphs and , and a small set of pre-matched node pairs where and , the problem is to identify a matching between and growing from , such that each pair in the matching corresponds to the same underlying entity. Recent studies on efficient and effective seeded graph matching have drawn a great deal of attention and many popular methods are largely based on exploring the similarity between local structures to identify matching pairs. While these recent techniques work provably well on random graphs, their accuracy is low over many real networks. In this work, we propose to utilize higher-order neighboring information to improve the matching accuracy and efficiency. As a result, a new framework of seeded graph matching is proposed, which employs Personalized PageRank (PPR) to quantify the matching score of each node pair. To further boost the matching accuracy, we propose a novel postponing strategy, which postpones the selection of pairs that have competitors with similar matching scores. We show that the postpone strategy indeed significantly improves the matching accuracy. To improve the scalability of matching large graphs, we also propose efficient approximation techniques based on algorithms for computing PPR heavy hitters. Our comprehensive experimental studies on large-scale real datasets demonstrate that, compared with state-of-the-art approaches, our framework not only increases the precision and recall both by a significant margin but also achieves speed-up up to more than one order of magnitude.

Approximate Solution of Nonclassically Damped Systems

1991 ◽  
Author(s):  
F. Ma ◽  
J. H. Hwang
Keyword(s):  
Approximate Solution ◽  
Large Scale ◽  
Computational Effort ◽  
Frequency Separation ◽  
Common Procedure ◽  
Damping Matrix ◽  
Complex Modes ◽  
Modal Coupling ◽  
Order Of Magnitude ◽  
Damped Systems

Abstract In analyzing a nonclassically damped linear system, one common procedure is to neglect those damping terms which are nonclassical, and retain the classical ones. This approach is termed the method of approximate decoupling. For large-scale systems, the computational effort at adopting approximate decoupling is at least an order of magnitude smaller than the method of complex modes. In this paper, the error introduced by approximate decoupling is evaluated. A tight error bound, which can be computed with relative ease, is given for this method of approximate solution. The role that modal coupling plays in the control of error is clarified. If the normalized damping matrix is strongly diagonally dominant, it is shown that adequate frequency separation is not necessary to ensure small errors.

scholarly journals Psychometric properties of the Adelaide Diagnostic Learning Inventory - Brief (ADLIB)

2019 ◽  
Author(s):  
Harry Minas
Keyword(s):  
Academic Performance ◽  
Learning Styles ◽  
University Students ◽  
Psychometric Properties ◽  
Factor Structure ◽  
Life Stress ◽  
Large Scale ◽  
Well Being ◽  
Factor Congruence ◽  
Order Of Magnitude

Abstract Objective: There has been increased attention in recent years to mental health, quality of life, stress and academic performance among university students, and the possible influence of learning styles. Brief reliable questionnaires are useful in large-scale multivariate research designs, such as the largely survey-based research on well-being and academic performance of university students. The objective of this study was to examine the psychometric properties of a briefer version of the 39-item Adelaide Diagnostic Learning Inventory. Results: In two survey samples - medical and physiotherapy students - a 21-item version Adelaide Diagnostic Learning Inventory - Brief (ADLIB) was shown to have the same factor structure as the parent instrument, and the factor structure of the brief instrument was found to generalise across students of medicine and physiotherapy. Sub-scale reliability estimations were in the order of magnitude of the parent instrument. Sub-scale inter-correlations, inter-factor congruence coefficients, and correlations between ADLIB sub-scale scores and several external measures provide support support for the construct and criterion validity of the instrument.

scholarly journals Best-first Enumeration Based on Bounding Conflicts, and its Application to Large-scale Hybrid Estimation (Extended Abstract)

2020 ◽  
Author(s):  
Eric Timmons ◽  
Brian C. Williams
Keyword(s):  
Large Scale ◽  
Search Space ◽  
Estimation Methods ◽  
Directed Search ◽  
Hybrid Estimation ◽  
Continuous State ◽  
Order Of Magnitude ◽  
State Models ◽  
The Cost ◽  
Belief States

State estimation methods based on hybrid discrete and continuous state models have emerged as a method of precisely computing belief states for real world systems, however they have difficulty scaling to systems with more than a handful of components. Classical, consistency based diagnosis methods scale to this level by combining best-first enumeration and conflict-directed search. While best-first methods have been developed for hybrid estimation, conflict-directed methods have thus far been elusive as conflicts summarize constraint violations, but probabilistic hybrid estimation is relatively unconstrained. In this paper we present an approach (A*BC) that unifies best-first enumeration and conflict-directed search in relatively unconstrained problems through the concept of "bounding" conflicts, an extension of conflicts that represent tighter bounds on the cost of regions of the search space. Experiments show that an A*BC powered state estimator produces estimates up to an order of magnitude faster than the current state of the art, particularly on large systems.

scholarly journals Strength Tests on Newly Fallen Snow

1969 ◽  
Vol 8 (54) ◽  
pp. 427-440 ◽  
Author(s):  
R. Perla
Keyword(s):  
Cone Penetrometer ◽  
Light Weight ◽  
Large Drop ◽  
Torque Wrench ◽  
Strength Tests ◽  
Order Of Magnitude ◽  
Magnitude Variation ◽  
A New Technique ◽  
Shear Frame

AbstractModified versions ofin situstrength tests previously applied to metamorphosed snow were developed to measure the mechanical properties of newly fallen snow during storm periods. A large drop-cone penetrometer, protected from the wind by an aluminum shell, was used to determine snow “hardness”. A lightweight model of the Haefeli ram penetrometer measured “ram numbers”. Shear strengths were obtained from large, light-weight frames. Some preliminary tests were made with a shear vane driven by a torque wrench. A new technique was devised for measuring tensile strength whereby a cantilever beam of snow is undercut until it fails under its own weight. Comparisons between the cantilever test and the shear-frame test show high ratios for tensile to shear strength. Cantilever strength plotted against density shows an order of magnitude variation in strength at all densities.

scholarly journals MESSENGER observations of planetary ion enhancements at Mercury’s northern magnetospheric cusp during Flux Transfer Event Showers

2021 ◽  
Author(s):  
Weijie Sun ◽  
James Slavin ◽  
Anna Milillo ◽  
Ryan Dewey ◽  
Stefano Orsini ◽  
...  
Keyword(s):  
Solar Wind ◽  
Large Scale ◽  
Transfer Event ◽  
Order Of Magnitude ◽  
In Situ Observations ◽  
Flux Transfer ◽  
Magnetospheric Cusp ◽  
Upward Moving ◽  
Entry Layer

Abstract At Mercury, several processes can release ions and neutrals out of the planet’s surface. Here we present enhancements of dayside planetary ions in the solar wind entry layer during flux transfer event (FTE) “showers” near Mercury’s northern magnetospheric cusp. In this entry layer, solar wind ions are accelerated and move downward (i.e. planetward) toward the cusps, which sputter upward-moving planetary ions within 1 minute. The precipitation rate is enhanced by an order of magnitude during FTE showers and the neutral density of the exosphere can vary by >10% due to this FTE-driven sputtering. These in situ observations of enhanced planetary ions in the entry layer likely correspond to an escape channel of Mercury’s planetary ions, and the large-scale variations of the exosphere observed on minute-timescales by ground-based telescopes. Comprehensive, future multi-point measurements made by BepiColombo will greatly enhance our understanding of the processes contributing to Mercury’s dynamic exosphere and magnetosphere.

Probabilistic assessment of tephra fall hazards in Japan using a tephra fall distribution database

2020 ◽  
Author(s):  
Shimpei Uesawa ◽  
Kiyoshi Toshida ◽  
Shingo Takeuchi ◽  
Daisuke Miura
Keyword(s):  
Large Scale ◽  
Critical Infrastructure ◽  
Interpolation Method ◽  
Computational Techniques ◽  
Borehole Data ◽  
Regional Variability ◽  
Tephra Fall ◽  
Distribution Maps ◽  
Order Of Magnitude ◽  
Hazard Curves

Abstract Tephra falls can disrupt critical infrastructure, including transportation and electricity networks. Probabilistic assessments of tephra fall hazards have been performed using computational techniques, but it is also important to integrate long-term, regional geological records. To assess tephra fall load hazards in Japan, we re-digitized an existing database of 551 tephra distribution maps. We used the re-digitized datasets to produce hazard curves for a range of tephra loads for various localities. We calculated annual exceedance probabilities (AEPs) and constructed hazard curves from the most complete part of the geological record. We used records of tephra fall events with a Volcanic Explosivity Index (VEI) of 4–7 (based on survivor functions) that occurred over the last 150 ka, as the database contains a very high percentage (around 90%) of VEI 4–7 events for this period. We fitted the data for this period using a Poisson distribution function. Hazard curves were constructed for the tephra fall load at 47 prefectural offices throughout Japan, and four broad regions were defined (NE–W, NE–E, W, and SW Japan). AEPs were relatively high, exceeding 1 × 10 −4 for loads greater than 0 kg/m 2 on the eastern (down-wind) side of the volcanic front in the NE–E region. In much of the W and SW regions, maximum loads were heavier, but AEPs were lower (<10 −4 ). Tephras from large (VEI ≥ 6) events are the predominant hazard in every region. A parametric analysis was applied to investigate regional variability using AEP diagrams and slope shape parameters via curve fitting with exponential and double-exponential decay functions. Two major differences were recognized between the hazard curves from borehole data and those from the digitized tephra database. The first is a significant underestimation of AEP for frequent events using the tephra database, by one to two orders of magnitude. This is explained in terms of the lack of records for smaller tephra fall events in the database. The second is an overestimation of the heaviest tephra load events, which differ by a factor of two to three. This difference might be due to the tephra fall distribution contour interpolation methodology used to generate the original database. The hazard curve for Tokyo developed in this study differs from those that have been generated previously using computational techniques. For the Tokyo region, the probabilities and tephra loads produced by computational methods are at least one order of magnitude greater than those generated during the present study. These discrepancies are inferred to have been caused by initial parameter settings in the computational simulations, including their incorporation of large-scale eruptions of up to VEI = 7 for all large stratovolcanoes, regardless of their eruptive histories. To improve the precision of the digital database, we plan to incorporate recent (since 2003) tephra distributions, revise questionable isopach maps, and develop an improved interpolation method for digitizing tephra fall distributions.

scholarly journals Global torques and stochasticity as the drivers of massive black hole pairing in the young Universe

2020 ◽  
Vol 498 (3) ◽  
pp. 3601-3615 ◽  
Author(s):  
Elisa Bortolas ◽  
Pedro R Capelo ◽  
Tommaso Zana ◽  
Lucio Mayer ◽  
Matteo Bonetti ◽  
...  
Keyword(s):  
Black Hole ◽  
Large Scale ◽  
High Redshift ◽  
Dynamical Evolution ◽  
Dynamical Friction ◽  
Massive Black Hole ◽  
Orbital Decay ◽  
Orbital Phase ◽  
Order Of Magnitude ◽  
Statistical Sample

ABSTRACT The forthcoming Laser Interferometer Space Antenna (LISA) will probe the population of coalescing massive black hole (MBH) binaries up to the onset of structure formation. Here, we simulate the galactic-scale pairing of ∼106 M⊙ MBHs in a typical, non-clumpy main-sequence galaxy embedded in a cosmological environment at z = 7–6. In order to increase our statistical sample, we adopt a strategy that allows us to follow the evolution of six secondary MBHs concomitantly. We find that the magnitude of the dynamical-friction-induced torques is significantly smaller than that of the large-scale, stochastic gravitational torques arising from the perturbed and morphologically evolving galactic disc, suggesting that the standard dynamical friction treatment is inadequate for realistic galaxies at high redshift. The dynamical evolution of MBHs is very stochastic, and a variation in the initial orbital phase can lead to a drastically different time-scale for the inspiral. Most remarkably, the development of a galactic bar in the host system either significantly accelerates the inspiral by dragging a secondary MBH into the centre, or ultimately hinders the orbital decay by scattering the MBH in the galaxy outskirts. The latter occurs more rarely, suggesting that galactic bars overall promote MBH inspiral and binary coalescence. The orbital decay time can be an order of magnitude shorter than what would be predicted relying on dynamical friction alone. The stochasticity and the important role of global torques have crucial implications for the rates of MBH coalescences in the early Universe: both have to be accounted for when making predictions for the upcoming LISA observatory.

Sign in / Sign up

Export Citation Format

Share Document