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  • 1
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    Ground-Motion Observations at Hotel Montana during the M 7.0 2010 Haiti Earthquake: Topography or Soil Amplification? (2013)
    Seismological Society of America (SSA)
    Details
    Publication Date: 2013-10-01
    Description: Unusually severe structural damage was reported during the 2010 M  7.0 Haiti earthquake in the vicinity of Hotel Montana, located on top of a ridge in the district of Pétionville. Prompted by the observations, U.S. Geological Survey seismic stations were deployed, and aftershock recordings indicated ground-motion amplification on the top of the hill compared to adjacent stations on reference site conditions. The presence of topographic relief has been shown to significantly aggravate the consequences of strong ground motion during past events, and topographic effects were brought forward to explain the observations. In this paper, we test the hypothesis of topographic amplification as the dominant factor that contributed to the damage concentration in the vicinity of Hotel Montana. We initially conduct numerical simulations of the ridge seismic response assuming elastic homogeneous site conditions, and show that numerical predictions of topographic amplification disagree with the field data both in amplitude and in frequency. Conversely, while 1D ground-response analyses for the site conditions at the hilltop predict amplification in the same frequency range as the field data, they significantly underestimate the recorded amplitude. We then conduct numerical simulations of the foothill ridge response to seismic motion while accounting for soil layering, and qualitatively demonstrate that the recorded amplification is most likely attributed to coupled site–topographic amplification effects, namely to seismic waves trapped in the soft soil layers of the near surface, amplified as a consequence of reverberations, and further modified due to diffraction and scattering upon incidence on the irregular ground surface. Parametric investigations of the topography–soil amplification coupling effects are then conducted, and our results show that when accounting for a hypothetical soil–bedrock interface at 100 m depth, predictions are in excellent agreement with the observed motion.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
    Published by Seismological Society of America (SSA)
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  • 2
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    hiHMM: Bayesian non-parametric joint inference of chromatin state maps (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-27
    Description: Motivation: Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications. Results: Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets. Conclusion: The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chromatin landscape analysis. Availability and implementation: Source codes are available at https://github.com/kasohn/hiHMM . Chromatin data are available at http://encode-x.med.harvard.edu/data_sets/chromatin/ . Contact: peter_park@harvard.edu or juhan@snu.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Inhibition of stemness factors for differentiation [Biochemistry] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-02-05
    Description: The potential for pluripotent cells to differentiate into diverse specialized cell types has given much hope to the field of regenerative medicine. Nevertheless, the low efficiency of cell commitment has been a major bottleneck in this field. Here we provide a strategy to enhance the efficiency of early differentiation of...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    SUMO1-dependent modulation of SERCA2a in heart failure (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-09-09
    Description: The calcium-transporting ATPase ATP2A2, also known as SERCA2a, is a critical ATPase responsible for Ca(2+) re-uptake during excitation-contraction coupling. Impaired Ca(2+) uptake resulting from decreased expression and reduced activity of SERCA2a is a hallmark of heart failure. Accordingly, restoration of SERCA2a expression by gene transfer has proved to be effective in improving cardiac function in heart-failure patients, as well as in animal models. The small ubiquitin-related modifier (SUMO) can be conjugated to lysine residues of target proteins, and is involved in many cellular processes. Here we show that SERCA2a is SUMOylated at lysines 480 and 585 and that this SUMOylation is essential for preserving SERCA2a ATPase activity and stability in mouse and human cells. The levels of SUMO1 and the SUMOylation of SERCA2a itself were greatly reduced in failing hearts. SUMO1 restitution by adeno-associated-virus-mediated gene delivery maintained the protein abundance of SERCA2a and markedly improved cardiac function in mice with heart failure. This effect was comparable to SERCA2A gene delivery. Moreover, SUMO1 overexpression in isolated cardiomyocytes augmented contractility and accelerated Ca(2+) decay. Transgene-mediated SUMO1 overexpression rescued cardiac dysfunction induced by pressure overload concomitantly with increased SERCA2a function. By contrast, downregulation of SUMO1 using small hairpin RNA (shRNA) accelerated pressure-overload-induced deterioration of cardiac function and was accompanied by decreased SERCA2a function. However, knockdown of SERCA2a resulted in severe contractile dysfunction both in vitro and in vivo, which was not rescued by overexpression of SUMO1. Taken together, our data show that SUMOylation is a critical post-translational modification that regulates SERCA2a function, and provide a platform for the design of novel therapeutic strategies for heart failure.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443490/" 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/PMC3443490/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kho, Changwon -- Lee, Ahyoung -- Jeong, Dongtak -- Oh, Jae Gyun -- Chaanine, Antoine H -- Kizana, Eddy -- Park, Woo Jin -- Hajjar, Roger J -- HL080498/HL/NHLBI NIH HHS/ -- HL093183/HL/NHLBI NIH HHS/ -- P20 HL100396/HL/NHLBI NIH HHS/ -- P20 HL100396-02/HL/NHLBI NIH HHS/ -- P20HL100396/HL/NHLBI NIH HHS/ -- R01 HL078731/HL/NHLBI NIH HHS/ -- R01 HL078731-04/HL/NHLBI NIH HHS/ -- R01 HL080498/HL/NHLBI NIH HHS/ -- R01 HL080498-05/HL/NHLBI NIH HHS/ -- R01 HL083156/HL/NHLBI NIH HHS/ -- R01 HL083156-05/HL/NHLBI NIH HHS/ -- R01 HL088434/HL/NHLBI NIH HHS/ -- R01 HL088434-02/HL/NHLBI NIH HHS/ -- England -- Nature. 2011 Sep 7;477(7366):601-5. doi: 10.1038/nature10407.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cardiovascular Research Center, Mount Sinai School of Medicine, 1 Gustave L. Levy Place, Box 1030, New York, New York 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21900893" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; HEK293 Cells ; Heart Failure/*metabolism/physiopathology ; Humans ; Lysine/metabolism ; Mice ; Rats ; Rats, Sprague-Dawley ; SUMO-1 Protein/genetics/*metabolism ; Sarcoplasmic Reticulum Calcium-Transporting ATPases/*metabolism ; *Sumoylation ; Sus scrofa
    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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  • 5
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    Inhibition of miR-25 improves cardiac contractility in the failing heart (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-03-29
    Description: Heart failure is characterized by a debilitating decline in cardiac function, and recent clinical trial results indicate that improving the contractility of heart muscle cells by boosting intracellular calcium handling might be an effective therapy. MicroRNAs (miRNAs) are dysregulated in heart failure but whether they control contractility or constitute therapeutic targets remains speculative. Using high-throughput functional screening of the human microRNAome, here we identify miRNAs that suppress intracellular calcium handling in heart muscle by interacting with messenger RNA encoding the sarcoplasmic reticulum calcium uptake pump SERCA2a (also known as ATP2A2). Of 875 miRNAs tested, miR-25 potently delayed calcium uptake kinetics in cardiomyocytes in vitro and was upregulated in heart failure, both in mice and humans. Whereas adeno-associated virus 9 (AAV9)-mediated overexpression of miR-25 in vivo resulted in a significant loss of contractile function, injection of an antisense oligonucleotide (antagomiR) against miR-25 markedly halted established heart failure in a mouse model, improving cardiac function and survival relative to a control antagomiR oligonucleotide. These data reveal that increased expression of endogenous miR-25 contributes to declining cardiac function during heart failure and suggest that it might be targeted therapeutically to restore function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131725/" 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/PMC4131725/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wahlquist, Christine -- Jeong, Dongtak -- Rojas-Munoz, Agustin -- Kho, Changwon -- Lee, Ahyoung -- Mitsuyama, Shinichi -- van Mil, Alain -- Park, Woo Jin -- Sluijter, Joost P G -- Doevendans, Pieter A F -- Hajjar, Roger J -- Mercola, Mark -- HHSN268201000045C/HL/NHLBI NIH HHS/ -- HHSN26820100045C/PHS HHS/ -- P01 HL098053/HL/NHLBI NIH HHS/ -- P01HL098053/HL/NHLBI NIH HHS/ -- P20 HL100396/HL/NHLBI NIH HHS/ -- P20HL100396/HL/NHLBI NIH HHS/ -- P30 AR061303/AR/NIAMS NIH HHS/ -- P30 CA030199/CA/NCI NIH HHS/ -- P30AR061303/AR/NIAMS NIH HHS/ -- P30CA030199/CA/NCI NIH HHS/ -- P50 HL112324/HL/NHLBI NIH HHS/ -- P50HL112324/HL/NHLBI NIH HHS/ -- R01 HL088434/HL/NHLBI NIH HHS/ -- R01 HL093183/HL/NHLBI NIH HHS/ -- R01 HL108176/HL/NHLBI NIH HHS/ -- R01 HL113601/HL/NHLBI NIH HHS/ -- R01HL088434/HL/NHLBI NIH HHS/ -- R01HL093183/HL/NHLBI NIH HHS/ -- R01HL108176/HL/NHLBI NIH HHS/ -- R01HL113601/HL/NHLBI NIH HHS/ -- S10 RR021084/RR/NCRR NIH HHS/ -- England -- Nature. 2014 Apr 24;508(7497):531-5. doi: 10.1038/nature13073. Epub 2014 Mar 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Bioengineering, University of California, San Diego, and the Muscle Development and Regeneration Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA [2]. ; 1] The Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2]. ; Department of Bioengineering, University of California, San Diego, and the Muscle Development and Regeneration Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA. ; The Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA. ; 1] Department of Bioengineering, University of California, San Diego, and the Muscle Development and Regeneration Program, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA [2] Department of Cardiology, University Medical Center Utrecht and ICIN Netherlands Heart Institute, Heidelberglaan 100, room G02.523, 3584 CX Utrecht, The Netherlands. ; Global Research Laboratory, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 500-712, South Korea. ; Department of Cardiology, University Medical Center Utrecht and ICIN Netherlands Heart Institute, Heidelberglaan 100, room G02.523, 3584 CX Utrecht, The Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24670661" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcium/metabolism ; Dependovirus/genetics ; Disease Models, Animal ; HEK293 Cells ; Heart/drug effects/physiology/physiopathology ; Heart Failure/*genetics/*therapy ; Humans ; Kinetics ; Male ; Mice ; MicroRNAs/analysis/*antagonists & inhibitors/genetics/metabolism ; Myocardial Contraction/*drug effects ; Myocardium/metabolism ; Myocytes, Cardiac/metabolism ; Oligonucleotides, Antisense/genetics/metabolism/pharmacology ; RNA, Messenger/genetics/metabolism ; Sarcoplasmic Reticulum/metabolism ; Sarcoplasmic Reticulum Calcium-Transporting ATPases/genetics/metabolism ; Survival Analysis ; Up-Regulation/genetics
    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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  • 6
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    Increasing N abundance in the northwestern Pacific Ocean due to atmospheric nitrogen deposition (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-24
    Description: The relative abundance of nitrate (N) over phosphorus (P) has increased over the period since 1980 in the marginal seas bordering the northwestern Pacific Ocean, located downstream of the populated and industrialized Asian continent. The increase in N availability within the study area was mainly driven by increasing N concentrations and was most likely due to deposition of pollutant nitrogen from atmospheric sources. Atmospheric nitrogen deposition had a high temporal correlation with N availability in the study area (r = 0.74 to 0.88), except in selected areas wherein riverine nitrogen load may be of equal importance. The increase in N availability caused by atmospheric deposition and riverine input has switched extensive parts of the study area from being N-limited to P-limited.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Tae-Wook -- Lee, Kitack -- Najjar, Raymond G -- Jeong, Hee-Dong -- Jeong, Hae Jin -- New York, N.Y. -- Science. 2011 Oct 28;334(6055):505-9. doi: 10.1126/science.1206583. Epub 2011 Sep 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, 790-784, Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21940860" target="_blank"〉PubMed〈/a〉
    Keywords: *Air Pollutants ; Atmosphere/*chemistry ; Ecosystem ; Nitrates/*analysis ; Nitrogen/*analysis ; Pacific Ocean ; Phosphorus/analysis ; Seawater/*chemistry
    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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  • 7
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    Low-Salinity Liquid-Rich Or Vapor-Like Fluids In A Porphyry-Type Mo Deposit, South Korea (2017)
    Mineralogical Association of Canada
    Details
    Publication Date: 2017-04-06
    Description: Small porphyry-type molybdenum (Mo) mineralization, the Geumeum deposit in the Gyeongsang Basin, South Korea, is associated with the crystallization of a Cretaceous granodiorite, exsolution of magmatic hydrothermal fluids, and related hydrofracturing. Quartz and molybdenite occur with minor amounts of uneconomic chalcopyrite, pyrite, sphalerite, and galena that precipitated from exsolved magmatic fluids and formed hydrothermal fissure-filling vein ores. Three distinct fluid inclusion assemblages responsible for the precipitation of molybdenite are present in the vein quartz. The earliest fluid is represented by low-salinity liquid-rich Type I fluid inclusions, which displayed homogenization temperatures ranging from 298 to 352 °C, and salinities from ~0 to 9 wt. % NaCl equiv. The Type I inclusions were trapped in a liquid-stable, vapor-absent, one-phase field. The intermediate fluid is represented by CO 2 -bearing vapor-rich Type IV inclusions, generally showing no visible CO 2 liquid phase. These CO 2 -bearing inclusions totally homogenized by vapor disappearance at 327~340 °C or vapor bubble expansion at 327~369 °C, exhibiting near-critical behaviors. The textural relationships and phase equilibria constraints indicate that the Type IV inclusions were derived from a single population, which formed as pressure and temperature fluctuated at near-critical conditions. The latest fluid can be represented by vapor-rich Type II fluid inclusions. No microthermometric data were obtained for these latest assemblages as no visible amounts of liquid phases are evident in small inclusions. Type III inclusions, which commonly refer to halite-bearing inclusions, are absent in the quartz veins studied. The oxygen and hydrogen isotopic fluid compositions of the vein quartz ( 18 O SMOW = 4.3 to 6.9 and D SMOW = –65 to –84 at 400 °C) is consistent with a magmatic origin with a possible slight influence from meteoric water. Molybdenum mineralization at Geumeum is a product of hypogene hydrothermal processes that were strongly fracture-controlled, highlighting the importance of low-salinity liquid-rich to vapor-like supercritical fluids for the mineralization. It seems likely that the magmas responsible for the formation of the deposit at Geumeum were emplaced at greater depths than those reported for economic porphyry copper deposits in the world. The deposit could thus have survived long periods of erosion, and represent the weakly mineralized "base" of porphyry systems in the Gyeongsang Basin, South Korea.
    Print ISSN: 0008-4476
    Topics: Geosciences
    Published by Mineralogical Association of Canada
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  • 8
    Electronic Resource
    Electronic Resource
    Microwave spectroscopy and magnetization measurements of flux trapping and hysteresis in YBa2Cu3O7−δ (1988)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 64 (1988), S. 1312-1317 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Microwave spectroscopic measurements at 9.2 GHz on a superconducting sample of YBa2Cu3O7−δ have established the occurrence of flux trapping and hysteresis associated with a low-field signal. The position of the signal peak is related to the field at which an abrupt change in the slope of the magnetization curve is observed. The data are consistent with a superconducting glass model.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.341852
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  • 9
    Electronic Resource
    Electronic Resource
    Phase transitional behavior and piezoelectric properties of the orthorhombic phase of Pb(Mg1/3Nb2/3)O3–PbTiO3 single crystals (2001)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 78 (2001), S. 3109-3111 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We report on the observation of an orthorhombic ferroelectric phase in 0.67Pb(Mg1/3Nb2/3)O3–0.33PbTiO3 single crystals, whose polarization is along 〈011〉 direction and stability can be altered by poling conditions. We studied the piezoelectric properties on poled 〈011〉 crystals, in both monodomain and polydomain states, and found that the piezoelectric d32 coefficient, which is the piezoelectric response in perpendicular to the poling direction, is positive in both cases. Based on the phenomenological theory, we show that this is possible in a crystal with the electrostrictive coefficients Q11〉Q44–Q12. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1372360
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  • 10
    Electronic Resource
    Electronic Resource
    Phase stabilities of "morphotropic" phases in Pb(Zn1/3Nb2/3)O3–PbTiO3 single crystals (2002)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 80 (2002), S. 1918-1920 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Based on the optic and dielectric data acquired under different mechanical and electric conditions and temperature, we show that an orthorhombic phase exists near the morphotropic phase boundary (MPB) (on both the rhombohedral and tetragonal sides of MPB). Because of the proximity of the free energy of this phase to the two other morphotropic phases, i.e., the rhombohedral and tetragonal phases, the experimentally observed phases and phase diagrams near MPB depend crucially on the mechanical and electric conditions as well as the sample history. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1461902
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