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  • 1
    Publication Date: 2014-11-28
    Description: Resolving the deep relationships of ancient animal lineages has proven difficult using standard Sanger-sequencing approaches with a handful of markers. We thus reassess the relatively well-studied phylogeny of the phylum Nemertea (ribbon worms)—for which the targeted gene approaches had resolved many clades but had left key phylogenetic gaps—by using a phylogenomic approach using Illumina-based de novo assembled transcriptomes and automatic orthology prediction methods. The analysis of a concatenated data set of 2,779 genes (411,138 amino acids) with about 78% gene occupancy and a reduced version with 95% gene occupancy, under evolutionary models accounting or not for site-specific amino acid replacement patterns results in a well-supported phylogeny that recovers all major accepted nemertean clades with the monophyly of Heteronemertea, Hoplonemertea, Monostilifera, being well supported. Significantly, all the ambiguous patterns inferred from Sanger-based approaches were resolved, namely the monophyly of Palaeonemertea and Pilidiophora. By testing for possible conflict in the analyzed supermatrix, we observed that concatenation was the best solution, and the results of the analyses should settle prior debates on nemertean phylogeny. The study highlights the importance, feasibility, and completeness of Illumina-based phylogenomic data matrices.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 2
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    Addison-Wesley Publ. Comp.
    In:  Amsterdam, Addison-Wesley Publ. Comp., vol. 18, no. Publ. No. 12, pp. 9, (ISBN 0-521-35367-X, ISBN 0-521-79836-1 paper)
    Publication Date: 1987
    Keywords: Handbook of informatics
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  • 3
    Publication Date: 2016-06-28
    Description: The use of telemonitoring is a promising approach to optimizing outcomes in the treatment of heart failure (HF) for patients living in the community. HF telemonitoring interventions, however, have not been tes...
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
    Published by BioMed Central
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  • 4
    Publication Date: 2013-10-01
    Description: Author(s): L. M. Schwartz, D. L. Johnson, J. Mitchell, T. C. Chandrasekera, and E. J. Fordham We present numerical simulations of a two-dimensional (2D) nuclear magnetic resonance process, T 2 -storage- T 2 , on a simple mixed porosity system, the micrograin consolidation ( μ GC) model. The results of these calculations are compared with predictions based on the analytic two-site exchange model, fo... [Phys. Rev. E 88, 032813] Published Mon Sep 30, 2013
    Keywords: Networks and Interdisciplinary Physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
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  • 5
    Publication Date: 2015-05-09
    Description: We calculate geometrical and transport properties (electrical conductivity, permeability, specific surface area, and surface conductivity) of a family of model granular porous media from an image based representation of its microstructure. The models are based on the packing described by Finney and cover a wide range of porosities. Finite difference methods are applied to solve for electrical conductivity and hydraulic permeability. Two image processing methods are used to identify the pore-grain interface and to test correlations linking permeability to electrical conductivity. A three phase conductivity model is developed to compute surface conductivity associated with the grain-pore interface. Our results compare well against empirical models over the entire porosity range studied. We conclude by examining the influence of image resolution on our calculations.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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  • 6
    Publication Date: 2015-05-09
    Description: Mutations in the ABCA4 gene are a common cause of autosomal recessive retinal degeneration. All mouse models to date are based on knockouts of Abca4 , even though the disease is often caused by missense mutations such as the complex allele L541P;A1038V (PV). We now show that the PV mutation causes severe human disease whereas the V mutation alone causes mild disease. Mutant ABCA4 proteins expressed heterologously in mammalian cells retained normal cellular localization. However, basal and all- trans -retinal-stimulated ATPase activities were reduced substantially for P and PV but only mildly for V. Electron microscopy revealed marked structural changes and misfolding for the P and PV mutants but few changes for the V mutant, consistent with the disease severity difference in patients. We generated Abca4 PV/PV knock-in mice homozygous for the complex PV allele to investigate the effects of this misfolding mutation in vivo . Mutant ABCA4 RNA levels approximated WT ABCA4 RNA levels but, surprisingly, only trace amounts of mutant ABCA4 protein were noted in the retina. RNA sequencing of WT, Abca4 –/– and Abca4 PV/PV mice revealed mild gene expression alterations in the retina and RPE. Similar to Abca4 –/– mice, Abca4 PV/PV mice showed substantial A2E and lipofuscin accumulation in their RPE cells but no retinal degeneration up to 12 months of age. Thus, rapid degradation of this large misfolded mutant protein in mouse retina caused little detectable photoreceptor degeneration. These findings suggest likely differences in the unfolded protein response between murine and human photoreceptors and support development of therapies directed at increasing this capability in patients.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2016-03-26
    Description: Motivation : The Optical Mapping System discovers structural variants and potentiates sequence assembly of genomes via scaffolding and comparisons that globally validate or correct sequence assemblies. Despite its utility, there are few publicly available tools for aligning optical mapping datasets. Results : Here we present software, named ‘Maligner’, for the alignment of both single molecule restriction maps (Rmaps) and in silico restriction maps of sequence contigs to a reference. Maligner provides two modes of alignment: an efficient, sensitive dynamic programming implementation that scales to large eukaryotic genomes, and a faster indexed based implementation for finding alignments with unmatched sites in the reference but not the query. We compare our software to other publicly available tools on Rmap datasets and show that Maligner finds more correct alignments in comparable runtime. Lastly, we introduce the M-Score statistic for normalizing alignment scores across restriction maps and demonstrate its utility for selecting high quality alignments. Availability and implementation : The Maligner software is written in C ++ and is available at https://github.com/LeeMendelowitz/maligner under the GNU General Public License. Contact : mpop@umiacs.umd.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2019
    Description: Weeds have been historically, and are still today, the primary and most economically important pest in agriculture. Several selection pressures associated with weed management, such as an overreliance on herbicides, have promoted the rapid evolution of herbicide-resistant weeds. Integrated Weed Management (IWM) is promoted as an ecological systems approach, through the combination of biological, chemical, cultural, ecological, and mechanical control methods. The concept of a systems approach is defined as managing weeds by combining practice and knowledge with the goals of increasing yield and minimizing economic loss, minimizing risks to human health and the environment, and reducing energy requirements and off-target impacts. The reliance on herbicides in modern cropping systems has shifted the management focus from requiring intimate knowledge of biology, ecology, and ecological systems to herbicide chemistry, mixes, and rotations, application technology, and herbicide-tolerant crop traits. Here, an ecological systems approach is considered, examining new trends and technologies in relation to IWM and weed ecology. Prevention of spread, seedbank management, crop rotations, tillage, cover crops, competitive cultivars, biological weed control, and future solutions in concept-only are presented, and knowledge gaps are identified where research advancements may be possible. An ecological systems approach will provide improved stewardship of new herbicide technologies and reduce herbicide resistance evolution through diversification of selection pressures. Agroecological interactions should be studied in light of new, developing weed control technologies. The science of weed management needs to refocus on the foundations of weed biology and ecology to enable an ecological systems approach and promote agricultural sustainability.
    Electronic ISSN: 2077-0472
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by MDPI
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  • 9
    Publication Date: 2018
    Description: 〈p〉Slow slip events have been suggested to trigger subduction earthquakes. However, examples to date have been poorly recorded, occurring offshore, where data are sparse. Better understanding of slow slip events and their influence on subsequent earthquakes is critical for hazard forecasts. We analyze a well-recorded event beginning 6 months before the 2012 〈i〉M〈/i〉〈sub〉w〈/sub〉 (moment magnitude) 7.6 earthquake in Costa Rica. The event migrates to the eventual megathrust rupture. Peak slip rate reached a maximum of 5 mm/day, 43 days before the earthquake, remaining high until the earthquake. However, changes in Mohr-Coulomb failure stress at the hypocenter were small (0.1 bar). Our data contradict models of earthquake nucleation that involve power law acceleration of slip and foreshocks. Slow slip events may prove useful for short-term earthquake forecasts.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 10
    Publication Date: 2015-05-20
    Description: Mucolipidosis II (MLII) and III alpha/beta are autosomal-recessive diseases of childhood caused by mutations in GNPTAB encoding the α/β-subunit precursor protein of the GlcNAc-1-phosphotransferase complex. This enzyme modifies lysosomal hydrolases with mannose 6-phosphate targeting signals. Upon arrival in the Golgi apparatus, the newly synthesized α/β-subunit precursor is catalytically activated by site-1 protease (S1P). Here we performed comprehensive expression studies of GNPTAB mutations, including two novel mutations T644M and T1223del, identified in Brazilian MLII/MLIII alpha/beta patients. We show that the frameshift E757K fs X1 and the non-sense R587X mutations result in the retention of enzymatically inactive truncated precursor proteins in the endoplasmic reticulum (ER) due to loss of cytosolic ER exit motifs consistent with a severe clinical phenotype in homozygosity. The luminal missense mutations, C505Y, G575R and T644M, partially impaired ER exit and proteolytic activation in accordance with less severe MLIII alpha/beta disease symptoms. Analogous to the previously characterized S399F mutant, we found that the missense mutation I403T led to retention in the ER and loss of catalytic activity. Substitution of further conserved residues in stealth domain 2 (I346 and W357) revealed similar biochemical properties and allowed us to define a putative binding site for accessory proteins required for ER exit of α/β-subunit precursors. Interestingly, the analysis of the Y937_M972del mutant revealed partial Golgi localization and formation of abnormal inactive β-subunits generated by S1P which correlate with a clinical MLII phenotype. Expression analyses of mutations identified in patients underline genotype–phenotype correlations in MLII/MLIII alpha/beta and provide novel insights into structural requirements of proper GlcNAc-1-phosphotransferase activity.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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