Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. ...Genome skimming (or low‐coverage genome sequencing) is a promising method to not only extract high‐copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements UCEs and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome‐skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target‐capture baitsets, we bioinformatically obtained UCEs and exons from the genome‐skimming data and incorporated them with data from previously published target‐capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low‐cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.
Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming is a viable and low‐cost option for phylogenetic studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 loci for hexacorals; phylogenetic relationships were well resolved within each class. We also obtained loci from historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886.
Environmental DNA (eDNA) quantification and sequencing are emerging techniques for assessing biodiversity in marine ecosystems. Environmental DNA can be transported by ocean currents and may remain ...at detectable concentrations far from its source depending on how long it persist. Thus, predicting the persistence time of eDNA is crucial to defining the spatial context of the information derived from it. To investigate the physicochemical controls of eDNA persistence, we performed degradation experiments at temperature, pH, and oxygen conditions relevant to the open ocean and the deep sea. The eDNA degradation process was best explained by a model with two phases with different decay rate constants. During the initial phase, eDNA degraded rapidly, and the rate was independent of physicochemical factors. During the second phase, eDNA degraded slowly, and the rate was strongly controlled by temperature, weakly controlled by pH, and not controlled by dissolved oxygen concentration. We demonstrate that marine eDNA can persist at quantifiable concentrations for over 2 weeks at low temperatures (≤10 °C) but for a week or less at ≥20 °C. The relationship between temperature and eDNA persistence is independent of the source species. We propose a general temperature-dependent model to predict the maximum persistence time of eDNA detectable through single-species eDNA quantification methods.
Lamé's formulas for the eigenvalues and eigenfunctions of the Laplacian with Dirichlet boundary conditions on an equilateral triangle are derived using direct elementary mathematical techniques. They ...are shown to form a complete orthonormal system. Various properties of the spectrum and nodal lines are explored. Implications for related geometries are considered.
Lame's formulas for the eigenvalues and eigenfunctions of the Laplacian with Neumann boundary conditions on an equilateral triangle are derived using direct elementary mathematical techniques. They ...are shown to form a complete orthonormal system. Various properties of the spectrum and nodal lines are explored. Implications for related geometries are considered.
CMS computing operations during run 1 Adelman, J; Alderweireldt, S; Artieda, J ...
Journal of physics. Conference series,
01/2014, Letnik:
513, Številka:
3
Journal Article
Recenzirano
Odprti dostop
During the first run, CMS collected and processed more than 10B data events and simulated more than 15B events. Up to 100k processor cores were used simultaneously and 100PB of storage was managed. ...Each month petabytes of data were moved and hundreds of users accessed data samples. In this document we discuss the operational experience from this first run. We present the workflows and data flows that were executed, and we discuss the tools and services developed, and the operations and shift models used to sustain the system. Many techniques were followed from the original computing planning, but some were reactions to difficulties and opportunities. We also address the lessons learned from an operational perspective, and how this is shaping our thoughts for 2015.
The method of angled derivatives McCartin, Brian J.
Applied mathematics and computation,
11/2005, Letnik:
170, Številka:
1
Journal Article
Recenzirano
A hybrid numerical method is presented for a linear, first order, hyperbolic partial differential equation (PDE): the nonhomogeneous one-way advection equation. The unifying thread is the reduction ...of the PDE to an ordinary differential equation (ODE) along a characteristic emanating backward in time from each mesh point. These ODEs are then integrated numerically to advance in time. Such integration requires an interpolation procedure dependent upon the slope of the local characteristic. If the local Courant number is less than one then the interpolation is afforded by the angled derivative method while if greater than one then a reflected angled derivative approximation is introduced. Otherwise, if the Courant number is transitioning through one then the box scheme is employed. At the boundary, parabolic tracing of the characteristics provides a comparable level of accuracy. The net result is a compact, nondissipative, three-level explicit method which is second-order accurate and unconditionally stable. The efficacy of this method of angled derivatives (MAD) scheme for both constant and variable coefficient problems, with or without inhomogeneities, is demonstrated numerically.
From respiratory physiology to laser-based optical devices, the so-called delayed recruitment/renewal equation
(1)
ε
dc(t)
dt
=−c(t)+f(c(t−1)),
provides the mathematical model in a diverse spectrum ...of practical applications. Here,
ε is inversely proportional to the product of the time-delay inherent in the physical system and its rate of decay. When this time-lag is large relative to the reciprocal of the decay rate,
ε is small and this delay differential equation (DDE) is singularly perturbed. When this situation obtains,
c(
t) can exhibit initial layers and chaotic oscillations. In order to accurately capture such solution features numerically, one must use an approximation technique tailored to singular perturbation problems. In this work, we develop such a family of exponentially fitted schemes for the numerical approximation of this fundamental DDE. Application of this new technique is then made to a variety of interesting and important problems, not the least of which is the subject of dynamical diseases.
Identifying effective treatment combinations for MS patients failing standard therapy is an important goal. We report the results of a phase II open label baseline-to-treatment trial of a humanized ...monoclonal antibody against CD25 (daclizumab) in 10 multiple sclerosis patients with incomplete response to IFN-β therapy and high brain inflammatory and clinical disease activity. Daclizumab was very well tolerated and led to a 78% reduction in new contrast-enhancing lesions and to a significant improvement in several clinical outcome measures.
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