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  • 1
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    Maligner: a fast ordered restriction map aligner (2016)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
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  • 2
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    The Fas-FADD death domain complex structure unravels signalling by receptor clustering (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-01-02
    Description: The death inducing signalling complex (DISC) formed by Fas receptor, FADD (Fas-associated death domain protein) and caspase 8 is a pivotal trigger of apoptosis. The Fas-FADD DISC represents a receptor platform, which once assembled initiates the induction of programmed cell death. A highly oligomeric network of homotypic protein interactions comprised of the death domains of Fas and FADD is at the centre of DISC formation. Thus, characterizing the mechanistic basis for the Fas-FADD interaction is crucial for understanding DISC signalling but has remained unclear largely because of a lack of structural data. We have successfully formed and isolated the human Fas-FADD death domain complex and report the 2.7 A crystal structure. The complex shows a tetrameric arrangement of four FADD death domains bound to four Fas death domains. We show that an opening of the Fas death domain exposes the FADD binding site and simultaneously generates a Fas-Fas bridge. The result is a regulatory Fas-FADD complex bridge governed by weak protein-protein interactions revealing a model where the complex itself functions as a mechanistic switch. This switch prevents accidental DISC assembly, yet allows for highly processive DISC formation and clustering upon a sufficient stimulus. In addition to depicting a previously unknown mode of death domain interactions, these results further uncover a mechanism for receptor signalling solely by oligomerization and clustering events.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661029/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661029/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, Fiona L -- Stec, Boguslaw -- Pop, Cristina -- Dobaczewska, Malgorzata K -- Lee, JeongEun J -- Monosov, Edward -- Robinson, Howard -- Salvesen, Guy S -- Schwarzenbacher, Robert -- Riedl, Stefan J -- P01 CA069381/CA/NCI NIH HHS/ -- P01 CA069381-130009/CA/NCI NIH HHS/ -- P01CA69381/CA/NCI NIH HHS/ -- P30 CA030199/CA/NCI NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01AA017238/AA/NIAAA NIH HHS/ -- England -- Nature. 2009 Feb 19;457(7232):1019-22. doi: 10.1038/nature07606. Epub 2008 Dec 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Apoptosis and Cell Death Research, The Burnham Institute for Medical Research, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19118384" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, CD95/*chemistry/*metabolism ; Crystallography, X-Ray ; Death Domain Receptor Signaling Adaptor Proteins/chemistry/metabolism ; Fas-Associated Death Domain Protein/*chemistry/*metabolism ; Humans ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism ; *Receptor Aggregation ; *Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Catalytic activity of the caspase-8-FLIP(L) complex inhibits RIPK3-dependent necrosis (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-03-04
    Description: Caspase-8 has two opposing biological functions--it promotes cell death by triggering the extrinsic pathway of apoptosis, but also has a survival activity, as it is required for embryonic development, T-lymphocyte activation, and resistance to necrosis induced by tumour necrosis factor-alpha (TNF-alpha) and related family ligands. Here we show that development of caspase-8-deficient mice is completely rescued by ablation of receptor interacting protein kinase-3 (RIPK3). Adult animals lacking both caspase-8 and RIPK3 display a progressive lymphoaccumulative disease resembling that seen with defects in CD95 or CD95-ligand (also known as FAS and FASLG, respectively), and resist the lethal effects of CD95 ligation in vivo. We have found that caspase-8 prevents RIPK3-dependent necrosis without inducing apoptosis by functioning in a proteolytically active complex with FLICE-like inhibitory protein long (FLIP(L), also known as CFLAR), and this complex is required for the protective function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077893/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077893/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oberst, Andrew -- Dillon, Christopher P -- Weinlich, Ricardo -- McCormick, Laura L -- Fitzgerald, Patrick -- Pop, Cristina -- Hakem, Razq -- Salvesen, Guy S -- Green, Douglas R -- P01 CA069381/CA/NCI NIH HHS/ -- P01 CA069381-14/CA/NCI NIH HHS/ -- England -- Nature. 2011 Mar 17;471(7338):363-7. doi: 10.1038/nature09852. Epub 2011 Mar 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dept. of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21368763" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD95/deficiency/metabolism ; Apoptosis ; *Biocatalysis ; CASP8 and FADD-Like Apoptosis Regulating Protein/*metabolism ; Caspase 8/genetics/*metabolism ; Caspase Inhibitors ; Cell Line ; Female ; Male ; Mice ; Multiprotein Complexes/chemistry/metabolism ; *Necrosis ; Phenotype ; Receptor-Interacting Protein Serine-Threonine Kinases/*antagonists & ; inhibitors/deficiency/genetics/*metabolism ; Serpins/pharmacology ; Tumor Necrosis Factor-alpha/antagonists & inhibitors/biosynthesis/pharmacology ; Viral Proteins/pharmacology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Dimensional synthesis of a leg mechanism (2016)
    Institute of Physics (IOP)
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    Publication Date: 2016-09-03
    Description: An eight bar leg mechanism dimensional synthesis is presented. The mathematical model regarding the synthesis is described and the results obtained after computation are verified with help of 2D mechanism simulation in Matlab. This mechanism, inspired from proposed solution of Theo Jansen, is integrated into the structure of a 2 DOF quadruped robot. With help of the kinematic synthesis method described, it is tried to determine new dimensions for the mechanism, based on a set of initial conditions. These are established by taking into account the movement of the end point of the leg mechanism, which enters in contact with the ground, during walking. An optimization process based on the results obtained can be conducted further in order to find a better solution for the leg mechanism.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 5
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    Detection of low-level periodic signals through enhanced self-correlation method. The case of ER Vulpeculae (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-27
    Description: The self-correlation (SC) method proposed three decades ago by Percy, Jakate and Matthews is a complementary time series analysis method which provides a characterization of a variability phenomenon and an estimation of the involved time-scale. It can be applied to periodic, quasi-periodic and irregular phenomena, for either evenly or unevenly sampled data. An important deficiency of this method – mentioned by Percy himself – is the fact that the statistical properties of the SC are unknown so that the statistical significance of an ‘observed’ (quasi-)periodicity cannot be estimated. In this paper, we investigate analytically and numerically the properties of the SC of a harmonic periodic signal by taking into account the influence of the finite length of the data set, the non-equidistant sampling, and the presence of an additive Gaussian white noise. This method is used to investigate the already inferred periodic modulation of the orbital period of the eclipsing binary system ER Vul. In addition, we propose an improvement of the SC method by applying the ‘stacking method’ already used in seismology, which we call the enhanced SC (ESC) method. A statistical test relying on the ESC method together with Monte Carlo simulations allow us to claim the presence of a deterministic component at a significantly higher confidence level than that obtained through a Fourier based method. The evaluation of the detectability of the ER Vul periodic phenomenon through the ESC method provides similar results as those previously obtained using the Fourier based method.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Applications of energy harvesting for ultralow power technology (2015)
    Institute of Physics (IOP)
    Details
    Publication Date: 2015-06-19
    Description: Ultra-low-power (ULP) technology is enabling a wide range of new applications that harvest ambient energy in very small amounts and need little or no maintenance ? self-sustaining devices that are capable of perpetual or nearly perpetual operation. These new systems, which are now appearing in industrial and consumer electronics, also promise great changes in medicine and health. Until recently, the idea of micro-scale energy harvesting, and collecting miniscule amounts of ambient energy to power electronic systems, was still limited to research proposals and laboratory experiments.Today an increasing number of systems are appearing that take advantage of light, vibrations and other forms of previously wasted environmental energy for applications where providing line power or maintaining batteries is inconvenient. In the industrial world, where sensors gather information from remote equipment and hazardous processes; in consumer electronics, where mobility and convenience are ser...
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 7
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    RF waves - Measuring their energy (dBm) in three points into Baia Mare, Romania (2016)
    Institute of Physics (IOP)
    Details
    Publication Date: 2016-02-02
    Description: For the general public - and even for people with a science education - knowing to be subject to Radio Frequency (RF) radiation may arouse a feeling of uneasiness or even fear. Those feelings are instigated by the fact that you cannot see, hear, smell or feel RF radiation. Furthermore, the term „radiation” in itself has become very sensitive from the moment that the hazardous health effects of excessive radioactive decay (ionizing radiation) have become apparent. Media announcements of mostly unconfirmed scientific studies add to the feeling of uneasiness. So, naturally, whenever a new Global System of Mobile communications (GSM) base station is installed in an urban environment, the people living in the neighborhood may get worried. The same applies when we propose to use RF radiation for powering wireless sensors in office and home spaces using harvesting energy sistem (HE).In this paper we determine if the electromagnetic field intensity values, measured at certain points, res...
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 8
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    On the heavy elements content of sediments and rocks from two semiclosed ecosystems: Proglacial Lake Balea (Fagara Mountains) and Crater Lake St. Ana (Harghita Mountains) (2013)
    Springer
    Details
    Publication Date: 2013-09-01
    Print ISSN: 1547-4771
    Electronic ISSN: 1531-8567
    Topics: Physics
    Published by Springer
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  • 9
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    Determination of elastic mechanical characteristics of surface coatings from analysis of signals obtained by impulse excitation (2018)
    Institute of Physics
    Details
    Publication Date: 2018-01-01
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics
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  • 10
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    Determination of the critical bending speeds of a multy-rotor shaft from the vibration signal analysis (2018)
    Institute of Physics
    Details
    Publication Date: 2018-01-01
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics
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