Search results for "ATL"

NESSie.jl – Efficient and intuitive finite element and boundary element methods for nonlocal protein electrostatics in the Julia language

2018

Abstract The development of scientific software can be generally characterized by an initial phase of rapid prototyping and the subsequent transition to computationally efficient production code. Unfortunately, most programming languages are not well-suited for both tasks at the same time, commonly resulting in a considerable extension of the development time. The cross-platform and open-source Julia language aims at closing the gap between prototype and production code by providing a usability comparable to Python or MATLAB alongside high-performance capabilities known from C and C++ in a single programming language. In this paper, we present efficient protein electrostatics computations a…

Clustering of low-correlated spatial gene expression patterns in the mouse brain in the Allen Brain Atlas

2018

In this paper, clustering techniques are applied to spatial gene expression patterns with a low genomic correlation between the sagittal and coronal projections. The data analysed here are hosted on an available public DB named ABA (Allen Brain Atlas). The results are compared to those obtained by Bohland et al. on the complementary dataset (high correlation values). We prove that, by analysing a reduced dataset,hence reducing the computational burden, we get the same accuracy in highlighting different neuroanatomical region.

Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions

2016

AbstractGenome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalizatio…

2017

Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits. By combining population genomic analyses based on 12K single nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show…

Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

2017

Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and nonmigratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the >100 000-year-old trans-Atlantic separation of Atlantic cod. The long…

Operative Anatomy of the Skull Base: 3D Exploration with a Highly Detailed Interactive Atlas.

2020

Abstract Objective We evaluated the usefulness of a three-dimensional (3D) interactive atlas to illustrate and teach surgical skull base anatomy in a clinical setting. Study Design A highly detailed atlas of the adult human skull base was created from multiple high-resolution magnetic resonance imaging (MRI) and computed tomography (CT) scans of a healthy Caucasian male. It includes the parcellated and labeled bony skull base, intra- and extracranial vasculature, cranial nerves, cerebrum, cerebellum, and brainstem. We are reporting retrospectively on our experiences with employing the atlas for the simulation and teaching of neurosurgical approaches and concepts in a clinical setting. Setti…

Carbon isotope stratigraphy, magnetostratigraphy, and 40Ar/39Ar age of the Cretaceous South Atlantic coast, Namibe Basin, Angola

2014

This publication results from Projecto PaleoAngola, an international cooperative research effort among the contributing authors and their institutions, funded by the National Geographic Society, the Petroleum Research Fund of the American Chemical Society, Sonangol E.P., Esso Angola, Fundacao Vida of Angola, LS Films, Maersk, Damco, Safmarine, ISEM at SMU, The Royal Dutch Embassy in Luanda, TAP Airlines, Royal Dutch Airlines, The Saurus Institute, and the Perot Museum of Nature and Science. JS was additionally funded by Yale University and the Alfred Kordelin Foundation. We dedicate this contribution to the late Kalunga Lima, our friend and colleague in Projecto PaleoAngola. We thank Margar…

Photochemical mineralization of terrigenous DOC to dissolved inorganic carbon in ocean

2018

When terrigenous dissolved organic carbon (tDOC) rich in chromophoric dissolved organic matter (tCDOM) enters the ocean, solar radiation mineralizes it partially into dissolved inorganic carbon (DIC). This study addresses the amount and the rates of DIC photoproduction from tDOC and the area of ocean required to photomineralize tDOC. We collected water samples from 10 major rivers, mixed them with artificial seawater, and irradiated them with simulated solar radiation to measure DIC photoproduction and the photobleaching of tCDOM. The linear relationship between DIC photoproduction and tCDOM photobleaching was used to estimate the amount of photoproduced DIC from the tCDOM fluxes of the stu…

Evidence for the production of three massive vector bosons with the ATLAS detector

2019

A search for the production of three massive vector bosons in proton–proton collisions is performed using data at TeV recorded with the ATLAS detector at the Large Hadron Collider in the years 2015–2017, corresponding to an integrated luminosity of 79.8 fb−1. Events with two same-sign leptons ℓ (electrons or muons) and at least two reconstructed jets are selected to search for . Events with three leptons without any same-flavour opposite-sign lepton pairs are used to search for , while events with three leptons and at least one same-flavour opposite-sign lepton pair and one or more reconstructed jets are used to search for . Finally, events with four leptons are analysed to search for and .…

Constraints on off-shell Higgs boson production and the Higgs boson total width in ZZ → 4ℓ and ZZ → 2ℓ2ν final states with the ATLAS detector

2018

A measurement of off-shell Higgs boson production in the and decay channels, where ℓ stands for either an electron or a muon, is performed using data from proton–proton collisions at a centre-of-mass energy of TeV. The data were collected by the ATLAS experiment in 2015 and 2016 at the Large Hadron Collider, and they correspond to an integrated luminosity of . An observed (expected) upper limit on the off-shell Higgs signal strength, defined as the event yield normalised to the Standard Model prediction, of 3.8 (3.4) is obtained at 95% confidence level (CL). Assuming the ratio of the Higgs boson couplings to the Standard Model predictions is independent of the momentum transfer of the Higgs…