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  • 1
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    Recent segmental duplications in the human genome (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-08-10
    Description: Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bailey, Jeffrey A -- Gu, Zhiping -- Clark, Royden A -- Reinert, Knut -- Samonte, Rhea V -- Schwartz, Stuart -- Adams, Mark D -- Myers, Eugene W -- Li, Peter W -- Eichler, Evan E -- CA094816/CA/NCI NIH HHS/ -- GM58815/GM/NIGMS NIH HHS/ -- HG002318/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2002 Aug 9;297(5583):1003-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Center for Computational Genomics, and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12169732" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Base Sequence ; Biological Evolution ; Chromosomes, Human/genetics ; Computational Biology ; Databases, Nucleic Acid ; Exons ; Expressed Sequence Tags ; *Gene Duplication ; Gene Rearrangement ; *Genes, Duplicate ; Genetic Diseases, Inborn/genetics ; *Genome, Human ; Humans ; Models, Genetic ; Polymorphism, Single Nucleotide ; Proteome ; Recombination, Genetic ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Strand-specific postreplicative processing of mammalian telomeres (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-09-29
    Description: Telomeres are specialized nucleoprotein structures that stabilize the ends of linear eukaryotic chromosomes. In mammalian cells, abrogation of telomeric repeat binding factor TRF2 or DNA-dependent protein kinase (DNA-PK) activity causes end-to-end chromosomal fusion, thus establishing an essential role for these proteins in telomere function. Here we show that TRF2-mediated end-capping occurs after telomere replication. The postreplicative requirement for TRF2 and DNA-PKcs, the catalytic subunit of DNA-PK, is confined to only half of the telomeres, namely, those that were produced by leading-strand DNA synthesis. These results demonstrate a crucial difference in postreplicative processing of telomeres that is linked to their mode of replication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bailey, S M -- Cornforth, M N -- Kurimasa, A -- Chen, D J -- Goodwin, E H -- AG-917709/AG/NIA NIH HHS/ -- CA50519/CA/NCI NIH HHS/ -- CA76260/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2001 Sep 28;293(5539):2462-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11577237" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Division ; Cell Line ; Chromatids/physiology/ultrastructure ; Chromosomes/physiology/ultrastructure ; *DNA Replication ; DNA-Activated Protein Kinase ; DNA-Binding Proteins/genetics/*metabolism ; Humans ; In Situ Hybridization ; Mice ; Mitosis ; Mutation ; Nuclear Proteins ; Protein-Serine-Threonine Kinases/deficiency/metabolism ; Telomere/*metabolism ; Telomeric Repeat Binding Protein 2 ; Tumor Cells, Cultured
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Data Retrieval Algorithms for Validating the Optical Transient Detector and the Lightning Imaging Sensor (2000)
    In:  CASI
    Details
    Publication Date: 2013-08-31
    Description: A linear algebraic solution is provided for the problem of retrieving the location and time of occurrence of lightning ground strikes from an Advanced Lightning Direction Finder (ALDF) network. The ALDF network measures field strength, magnetic bearing, and arrival time of lightning radio emissions. Solutions for the plane (i.e., no earth curvature) are provided that implement all of these measurements. The accuracy of the retrieval method is tested using computer-simulated datasets, and the relative influence of bearing and arrival time data an the outcome of the final solution is formally demonstrated. The algorithm is sufficiently accurate to validate NASA:s Optical Transient Detector and Lightning Imaging Sensor. A quadratic planar solution that is useful when only three arrival time measurements are available is also introduced. The algebra of the quadratic root results are examined in detail to clarify what portions of the analysis region lead to fundamental ambiguities in sc)iirce location, Complex root results are shown to be associated with the presence of measurement errors when the lightning source lies near an outer sensor baseline of the ALDF network. For arbitrary noncollinear network geometries and in the absence of measurement errors, it is shown that the two quadratic roots are equivalent (no source location ambiguity) on the outer sensor baselines. The accuracy of the quadratic planar method is tested with computer-generated datasets, and the results are generally better than those obtained from the three-station linear planar method when bearing errors are about 2 deg.
    Keywords: Optics
    Type: Journal of Atmospheric and Oceanic Technology; Volume 17; 279-297
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  • 4
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    Scanning Tunneling Optical Resonance Microscopy Developed (2004)
    In:  CASI
    Details
    Publication Date: 2018-06-05
    Description: The ability to determine the in situ optoelectronic properties of semiconductor materials has become especially important as the size of device architectures has decreased and the development of complex microsystems has increased. Scanning Tunneling Optical Resonance Microscopy, or STORM, can interrogate the optical bandgap as a function of its position within a semiconductor micro-structure. This technique uses a tunable solidstate titanium-sapphire laser whose output is "chopped" using a spatial light modulator and is coupled by a fiber-optic connector to a scanning tunneling microscope in order to illuminate the tip-sample junction. The photoenhanced portion of the tunneling current is spectroscopically measured using a lock-in technique. The capabilities of this technique were verified using semiconductor microstructure calibration standards that were grown by organometallic vapor-phase epitaxy. Bandgaps characterized by STORM measurements were found to be in good agreement with the bulk values determined by transmission spectroscopy and photoluminescence and with the theoretical values that were based on x-ray diffraction results.
    Keywords: Optics
    Type: Research and Technology 2003; NASA/TM-2004-212729
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  • 5
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    Algorithm Updates for the Fourth SeaWiFS Data Reprocessing (2003)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: The efforts to improve the data quality for the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) data products have continued, following the third reprocessing of the global data set in May 2000. Analyses have been ongoing to address all aspects of the processing algorithms, particularly the calibration methodologies, atmospheric correction, and data flagging and masking. All proposed changes were subjected to rigorous testing, evaluation and validation. The results of these activities culminated in the fourth reprocessing, which was completed in July 2002. The algorithm changes, which were implemented for this reprocessing, are described in the chapters of this volume. Chapter 1 presents an overview of the activities leading up to the fourth reprocessing, and summarizes the effects of the changes. Chapter 2 describes the modifications to the on-orbit calibration, specifically the focal plane temperature correction and the temporal dependence. Chapter 3 describes the changes to the vicarious calibration, including the stray light correction to the Marine Optical Buoy (MOBY) data and improved data screening procedures. Chapter 4 describes improvements to the near-infrared (NIR) band correction algorithm. Chapter 5 describes changes to the atmospheric correction and the oceanic property retrieval algorithms, including out-of-band corrections, NIR noise reduction, and handling of unusual conditions. Chapter 6 describes various changes to the flags and masks, to increase the number of valid retrievals, improve the detection of the flag conditions, and add new flags. Chapter 7 describes modifications to the level-la and level-3 algorithms, to improve the navigation accuracy, correct certain types of spacecraft time anomalies, and correct a binning logic error. Chapter 8 describes the algorithm used to generate the SeaWiFS photosynthetically available radiation (PAR) product. Chapter 9 describes a coupled ocean-atmosphere model, which is used in one of the changes described in Chapter 4. Finally, Chapter 10 describes a comparison of results from the third and fourth reprocessings along the US. Northeast coast.
    Keywords: Optics
    Type: NASA/TM-2003-206892/VOL22 , Rept-2003-01915-0/VOL22 , NAS 1.15:206892/VOL22 , (ISSN 1522-8789)
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  • 6
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    Physics of Colloids in Space: Flight Hardware Operations on ISS (2002)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: The Physics of Colloids in Space (PCS) experiment was launched on Space Shuttle STS-100 in April 2001 and integrated into EXpedite the PRocess of Experiments to Space Station Rack 2 on the International Space Station (ISS). This microgravity fluid physics investigation is being conducted in the ISS U.S. Lab 'Destiny' Module over a period of approximately thirteen months during the ISS assembly period from flight 6A through flight 9A. PCS is gathering data on the basic physical properties of simple colloidal suspensions by studying the structures that form. A colloid is a micron or submicron particle, be it solid, liquid, or gas. A colloidal suspension consists of these fine particles suspended in another medium. Common colloidal suspensions include paints, milk, salad dressings, cosmetics, and aerosols. Though these products are routinely produced and used, we still have much to learn about their behavior as well as the underlying properties of colloids in general. The long-term goal of the PCS investigation is to learn how to steer the growth of colloidal structures to create new materials. This experiment is the first part of a two-stage investigation conceived by Professor David Weitz of Harvard University (the Principal Investigator) along with Professor Peter Pusey of the University of Edinburgh (the Co-Investigator). This paper describes the flight hardware, experiment operations, and initial science findings of the first fluid physics payload to be conducted on ISS: The Physics of Colloids in Space.
    Keywords: Optics
    Type: NASA/TM-2002-211371 , E-13194 , NAS 1.15:211371 , AIAA Paper 2002-0762 , 40th Aerospace Sciences Meeting and Exhibit; Jan 14, 2002 - Jan 17, 2002; Reno, NV; United States
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