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  • Meteorology and Climatology  (55)
  • Cell Line
  • 2005-2009  (76)
  • 2000-2004
  • 1955-1959
  • 2007  (76)
  • 1
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    TLR3 deficiency in patients with herpes simplex encephalitis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-18
    Description: Some Toll and Toll-like receptors (TLRs) provide immunity to experimental infections in animal models, but their contribution to host defense in natural ecosystems is unknown. We report a dominant-negative TLR3 allele in otherwise healthy children with herpes simplex virus 1 (HSV-1) encephalitis. TLR3 is expressed in the central nervous system (CNS), where it is required to control HSV-1, which spreads from the epithelium to the CNS via cranial nerves. TLR3 is also expressed in epithelial and dendritic cells, which apparently use TLR3-independent pathways to prevent further dissemination of HSV-1 and to provide resistance to other pathogens in TLR3-deficient patients. Human TLR3 appears to be redundant in host defense to most microbes but is vital for natural immunity to HSV-1 in the CNS, which suggests that neurotropic viruses have contributed to the evolutionary maintenance of TLR3.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Shen-Ying -- Jouanguy, Emmanuelle -- Ugolini, Sophie -- Smahi, Asma -- Elain, Gaelle -- Romero, Pedro -- Segal, David -- Sancho-Shimizu, Vanessa -- Lorenzo, Lazaro -- Puel, Anne -- Picard, Capucine -- Chapgier, Ariane -- Plancoulaine, Sabine -- Titeux, Matthias -- Cognet, Celine -- von Bernuth, Horst -- Ku, Cheng-Lung -- Casrouge, Armanda -- Zhang, Xin-Xin -- Barreiro, Luis -- Leonard, Joshua -- Hamilton, Claire -- Lebon, Pierre -- Heron, Benedicte -- Vallee, Louis -- Quintana-Murci, Lluis -- Hovnanian, Alain -- Rozenberg, Flore -- Vivier, Eric -- Geissmann, Frederic -- Tardieu, Marc -- Abel, Laurent -- Casanova, Jean-Laurent -- G0900867/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1522-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Genetics of Infectious Diseases, Institut National de la Sante et de la Recherche Medicale (INSERM), U550, Faculty Necker, Paris 75015, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17872438" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; CD8-Positive T-Lymphocytes/immunology ; Cell Line ; Child, Preschool ; Dendritic Cells/immunology ; Encephalitis, Herpes Simplex/*genetics/*immunology ; Female ; Fibroblasts/immunology/metabolism/virology ; Genes, Dominant ; *Herpesvirus 1, Human/physiology ; Heterozygote ; Humans ; Immunity, Innate ; Infant ; Interferons/biosynthesis ; Keratinocytes/immunology ; Killer Cells, Natural/immunology ; Leukocytes, Mononuclear/immunology ; Mutation ; Poly I-C/pharmacology ; Toll-Like Receptor 3/chemistry/*deficiency/*genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Ethics. The ISSCR guidelines for human embryonic stem cell research (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Daley, George Q -- Ahrlund Richter, Lars -- Auerbach, Jonathan M -- Benvenisty, Nissim -- Charo, R Alta -- Chen, Grace -- Deng, Hong-Kui -- Goldstein, Lawrence S -- Hudson, Kathy L -- Hyun, Insoo -- Junn, Sung Chull -- Love, Jane -- Lee, Eng Hin -- McLaren, Anne -- Mummery, Christine L -- Nakatsuji, Norio -- Racowsky, Catherine -- Rooke, Heather -- Rossant, Janet -- Scholer, Hans R -- Solbakk, Jan Helge -- Taylor, Patrick -- Trounson, Alan O -- Weissman, Irving L -- Wilmut, Ian -- Yu, John -- Zoloth, Laurie -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):603-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Children's Hospital, Boston, Massachusetts, USA. george.daley@childrens.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272706" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Chimera ; *Embryo Research/ethics/legislation & jurisprudence ; Embryonic Development ; *Embryonic Stem Cells ; *Guidelines as Topic ; Humans ; Informed Consent ; International Cooperation ; Oocyte Donation/economics/ethics ; Pluripotent Stem Cells ; Societies, Scientific ; Tissue Donors/ethics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Validation of the Aura Microwave Limb Sounder Temperature and Geopotential Height Measurements (2007)
    In:  CASI
    Details
    Publication Date: 2018-06-06
    Description: This paper describes the retrievals algorithm used to determine temperature and height from radiance measurements by the Microwave Limb Sounder on EOS Aura. MLS is a "limbscanning" instrument, meaning that it views the atmosphere along paths that do not intersect the surface - it actually looks forwards from the Aura satellite. This means that the temperature retrievals are for a "profile" of the atmosphere somewhat ahead of the satellite. Because of the need to view a finite sample of the atmosphere, the sample spans a box about 1.5km deep and several tens of kilometers in width; the optical characteristics of the atmosphere mean that the sample is representative of a tube about 200-300km long in the direction of view. The retrievals use temperature analyses from NASA's Goddard Earth Observing System, Version 5 (GEOS-5) data assimilation system as a priori states. The temperature retrievals are somewhat deperrde~zt on these a priori states, especially in the lower stratosphere. An important part of the validation of any new dataset involves comparison with other, independent datasets. A large part of this study is concerned with such comparisons, using a number of independent space-based measurements obtained using different techniques, and with meteorological analyses. The MLS temperature data are shown to have biases that vary with height, but also depend on the validation dataset. MLS data are apparently biased slightly cold relative to correlative data in the upper troposphere and slightly warm in the middle stratosphere. A warm MLS bias in the upper stratosphere may be due to a cold bias in GEOS-5 temperatures.
    Keywords: Meteorology and Climatology
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  • 4
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    Reactive Nitrogen Distribution and Partitioning in the North American Troposphere and Lowermost Stratosphere (2007)
    In:  CASI
    Details
    Publication Date: 2019-07-12
    Description: A comprehensive group of reactive nitrogen species (NO, NO2, HNO3, HO2NO2, PANs, alkyl nitrates, and aerosol-NO3) were measured in the troposphere and lowermost stratosphere over North America and the Atlantic during July/August 2004 (INTEX-A) from the NASA DC-8 platform (0.1-12 km). Less reactive nitrogen species (HCN and CH3CN), that are also unique tracers of biomass combustion, were also measured along with a host of other gaseous (CO, VOC, OVOC, halocarbon) and aerosol tracers. Clean background air as well as air with influences from biogenic emissions, anthropogenic pollution, biomass combustion, and stratosphere was sampled both over continental U. S., Atlantic and Pacific. The North American upper troposphere was found to be greatly influenced by both lightning NO(x) and surface pollution lofted via convection and contained elevated concentrations of PAN, ozone, hydrocarbons, and NO(x). Under polluted conditions PAN was a dominant carrier of reactive nitrogen in the upper troposphere while nitric acid dominated in the lower troposphere. Peroxynitric acid (HO2NO2) was present in sizable concentrations always peaking at around 8 km. Aerosol nitrate appeared to be mostly contained in large soil based particles in the lower troposphere. Plumes from Alaskan fires contained large amounts of PAN and very little enhancement in ozone. Observational data suggest that lightning was a far greater contributor to NO(x) in the upper troposphere than previously believed. NO(x) and NO(y) reservoir appeared to be in steady state only in the middle troposphere where NO(x)/NO(y) was independent of air mass age. A first comparison of observed data with simulations from four 3-D models shows significant differences between observations and models as well as among models. These uncertainties likely propagate themselves in satellites derived NOx data. Observed data are interpreted to suggest that soil sinks of HCN/CH3CN are at best very small. We investigate the partitioning and interplay of the reactive nitrogen species within characteristic air masses and further examine their role in ozone formation.
    Keywords: Meteorology and Climatology
    Type: Submitted to the Journal of Geophysical Research to be published in volume 112, pp. 1-15, April 2007
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  • 5
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    Evaluating Model Performance of an Ensemble-based Chemical Data Assimilation System During INTEX-B Field Mission (2007)
    In:  Other Sources
    Details
    Publication Date: 2019-07-13
    Description: We present a global chemical data assimilation system using a global atmosphere model, the Community Atmosphere Model (CAM3) with simplified chemistry and the Data Assimilation Research Testbed (DART) assimilation package. DART is a community software facility for assimilation studies using the ensemble Kalman filter approach. Here, we apply the assimilation system to constrain global tropospheric carbon monoxide (CO) by assimilating meteorological observations of temperature and horizontal wind velocity and satellite CO retrievals from the Measurement of Pollution in the Troposphere (MOPITT) satellite instrument. We verify the system performance using independent CO observations taken on board the NSFINCAR C-130 and NASA DC-8 aircrafts during the April 2006 part of the Intercontinental Chemical Transport Experiment (INTEX-B). Our evaluations show that MOPITT data assimilation provides significant improvements in terms of capturing the observed CO variability relative to no MOPITT assimilation (i.e. the correlation improves from 0.62 to 0.71, significant at 99% confidence). The assimilation provides evidence of median CO loading of about 150 ppbv at 700 hPa over the NE Pacific during April 2006. This is marginally higher than the modeled CO with no MOPITT assimilation (-140 ppbv). Our ensemble-based estimates of model uncertainty also show model overprediction over the source region (i.e. China) and underprediction over the NE Pacific, suggesting model errors that cannot be readily explained by emissions alone. These results have important implications for improving regional chemical forecasts and for inverse modeling of CO sources and further demonstrate the utility of the assimilation system in comparing non-coincident measurements, e.g. comparing satellite retrievals of CO with in-situ aircraft measurements. The work described above also brought to light several short-comings of the data assimilation approach for CO profiles. Because of the limited vertical resolution of the measurement, the retrievals at different altitudes are correlated which can lead to problems with numerical error and overall efficiency. This has resulted in a manuscript that is about to be submitted to JGR:
    Keywords: Meteorology and Climatology
    Type: Journal of Atmospheric Chemistry and Physics; 7; 5695-5710
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  • 6
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    The genomic landscapes of human breast and colorectal cancers (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-13
    Description: Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalog the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene "mountains" and a much larger number of gene "hills" that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wood, Laura D -- Parsons, D Williams -- Jones, Sian -- Lin, Jimmy -- Sjoblom, Tobias -- Leary, Rebecca J -- Shen, Dong -- Boca, Simina M -- Barber, Thomas -- Ptak, Janine -- Silliman, Natalie -- Szabo, Steve -- Dezso, Zoltan -- Ustyanksky, Vadim -- Nikolskaya, Tatiana -- Nikolsky, Yuri -- Karchin, Rachel -- Wilson, Paul A -- Kaminker, Joshua S -- Zhang, Zemin -- Croshaw, Randal -- Willis, Joseph -- Dawson, Dawn -- Shipitsin, Michail -- Willson, James K V -- Sukumar, Saraswati -- Polyak, Kornelia -- Park, Ben Ho -- Pethiyagoda, Charit L -- Pant, P V Krishna -- Ballinger, Dennis G -- Sparks, Andrew B -- Hartigan, James -- Smith, Douglas R -- Suh, Erick -- Papadopoulos, Nickolas -- Buckhaults, Phillip -- Markowitz, Sanford D -- Parmigiani, Giovanni -- Kinzler, Kenneth W -- Velculescu, Victor E -- Vogelstein, Bert -- CA 43460/CA/NCI NIH HHS/ -- CA 57345/CA/NCI NIH HHS/ -- CA109274/CA/NCI NIH HHS/ -- CA112828/CA/NCI NIH HHS/ -- CA121113/CA/NCI NIH HHS/ -- CA62924/CA/NCI NIH HHS/ -- GM070219/GM/NIGMS NIH HHS/ -- GM07309/GM/NIGMS NIH HHS/ -- P30-CA43703/CA/NCI NIH HHS/ -- RR017698/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 16;318(5853):1108-13. Epub 2007 Oct 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932254" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breast Neoplasms/*genetics/metabolism ; Cell Line ; Chromosome Mapping ; Colorectal Neoplasms/*genetics/metabolism ; Computational Biology ; DNA, Neoplasm ; Databases, Genetic ; Genes, Neoplasm ; Genome, Human ; Humans ; Metabolic Networks and Pathways/genetics ; Mice ; Mutation ; Neoplasm Proteins/genetics/metabolism ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Immunization by avian H5 influenza hemagglutinin mutants with altered receptor binding specificity (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-11
    Description: Influenza virus entry is mediated by the receptor binding domain (RBD) of its spike, the hemagglutinin (HA). Adaptation of avian viruses to humans is associated with HA specificity for alpha2,6- rather than alpha2,3-linked sialic acid (SA) receptors. Here, we define mutations in influenza A subtype H5N1 (avian) HA that alter its specificity for SA either by decreasing alpha2,3- or increasing alpha2,6-SA recognition. RBD mutants were used to develop vaccines and monoclonal antibodies that neutralized new variants. Structure-based modification of HA specificity can guide the development of preemptive vaccines and therapeutic monoclonal antibodies that can be evaluated before the emergence of human-adapted H5N1 strains.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367145/" 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/PMC2367145/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Zhi-Yong -- Wei, Chih-Jen -- Kong, Wing-Pui -- Wu, Lan -- Xu, Ling -- Smith, David F -- Nabel, Gary J -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 10;317(5839):825-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, Building 40, Room 4502, Mailstop Code MSC-3005, 40 Convent Drive, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690300" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Monoclonal/immunology ; Antibodies, Viral/immunology ; Carbohydrate Conformation ; Cell Line ; Female ; Genes, Viral ; Hemagglutination Inhibition Tests ; Hemagglutinin Glycoproteins, Influenza Virus/*genetics/*immunology/metabolism ; Humans ; Influenza A Virus, H5N1 Subtype/*genetics/*immunology/metabolism ; Influenza Vaccines/immunology ; Mice ; Mice, Inbred BALB C ; Molecular Sequence Data ; *Mutation ; Neutralization Tests ; Receptors, Virus/*metabolism ; Sialic Acids/*metabolism ; Vaccination
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    An X chromosome gene, WTX, is commonly inactivated in Wilms tumor (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-01-06
    Description: Wilms tumor is a pediatric kidney cancer associated with inactivation of the WT1 tumor-suppressor gene in 5 to 10% of cases. Using a high-resolution screen for DNA copy-number alterations in Wilms tumor, we identified somatic deletions targeting a previously uncharacterized gene on the X chromosome. This gene, which we call WTX, is inactivated in approximately one-third of Wilms tumors (15 of 51 tumors). Tumors with mutations in WTX lack WT1 mutations, and both genes share a restricted temporal and spatial expression pattern in normal renal precursors. In contrast to biallelic inactivation of autosomal tumor-suppressor genes, WTX is inactivated by a monoallelic "single-hit" event targeting the single X chromosome in tumors from males and the active X chromosome in tumors from females.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rivera, Miguel N -- Kim, Woo Jae -- Wells, Julie -- Driscoll, David R -- Brannigan, Brian W -- Han, Moonjoo -- Kim, James C -- Feinberg, Andrew P -- Gerald, William L -- Vargas, Sara O -- Chin, Lynda -- Iafrate, A John -- Bell, Daphne W -- Haber, Daniel A -- P01-CA101942/CA/NCI NIH HHS/ -- R37 CA054358/CA/NCI NIH HHS/ -- R37 CA054358-17/CA/NCI NIH HHS/ -- R37-CA058596/CA/NCI NIH HHS/ -- T32-CA009216/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):642-5. Epub 2007 Jan 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Massachusetts General Hospital Cancer Center, Harvard Medical Center, Boston, MA 02114, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17204608" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Alleles ; Amino Acid Sequence ; Animals ; Cell Line ; Chromosome Deletion ; Chromosomes, Human, X/*genetics ; Female ; Gene Expression ; *Gene Silencing ; *Genes, Wilms Tumor ; Heterozygote ; Humans ; In Situ Hybridization, Fluorescence ; Kidney/embryology/metabolism ; Kidney Neoplasms/*genetics ; Male ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Mutation ; Point Mutation ; Tumor Suppressor Proteins/chemistry/*genetics/physiology ; Wilms Tumor/*genetics ; beta Catenin/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Observed and Modeled HOCl Profiles in the Midlatitude Stratosphere: Implication for Ozone Loss (2007)
    In:  Other Sources
    Details
    Publication Date: 2018-06-11
    Description: Vertical profiles of stratospheric HOCl calculated with a diurnal steady-state photochemical model that uses currently recommended reaction rates and photolysis cross sections underestimate observed profiles of HOCl obtained by two balloon-borne instruments, FIRS-2 (a far-infrared emission spectrometer) and MkIV (a mid-infrared, solar absorption spectrometer). Considerable uncertainty (a factor of two) persists in laboratory measurements of the rate constant (k(sub 1)) for the reaction ClO + HO2 yields HOCl + O2. Agreement between modeled and measured HOCl can be attained using a value of k(sub 1) from Stimpfle et al. (1979) that is about a factor-of-two faster than the currently recommended rate constant. Comparison of modeled and measured HOCl suggests that models using the currently recommended value for k(sub 1) may underestimate the role of the HOCl catalytic cycle for ozone depletion, important in the midlatitude lower stratosphere.
    Keywords: Meteorology and Climatology
    Type: Geophysical Research Letters (ISSN 0094-8276); Volume 34
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  • 10
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    Solar Occultation Satellite Data and Derived Meteorological Products: Sampling Issues and Comparisons with Aura MLS (2007)
    In:  CASI
    Details
    Publication Date: 2018-06-06
    Description: Derived Meteorological Products (DMPs, including potential temperature (theta), potential vorticity, equivalent latitude (EqL), horizontal winds and tropopause locations) have been produced for the locations and times of measurements by several solar occultation (SO) instruments and the Aura Microwave Limb Sounder (MLS). DMPs are calculated from several meteorological analyses for the Atmospheric Chemistry Experiment-Fourier Transform Spectrometer, Stratospheric Aerosol and Gas Experiment II and III, Halogen Occultation Experiment, and Polar Ozone and Aerosol Measurement II and III SO instruments and MLS. Time-series comparisons of MLS version 1.5 and SO data using DMPs show good qualitative agreement in time evolution of O3, N2O, H20, CO, HNO3, HCl and temperature; quantitative agreement is good in most cases. EqL-coordinate comparisons of MLS version 2.2 and SO data show good quantitative agreement throughout the stratosphere for most of these species, with significant biases for a few species in localized regions. Comparisons in EqL coordinates of MLS and SO data, and of SO data with geographically coincident MLS data provide insight into where and how sampling effects are important in interpretation of the sparse SO data, thus assisting in fully utilizing the SO data in scientific studies and comparisons with other sparse datasets. The DMPs are valuable for scientific studies and to facilitate validation of non-coincident measurements.
    Keywords: Meteorology and Climatology
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