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1.
Phys Chem Chem Phys ; 22(46): 27191-27205, 2020 Dec 07.
Article in English | MEDLINE | ID: mdl-33226053

ABSTRACT

Domain-based local pair natural orbital (DLPNO) coupled cluster single and double (CCSD) with triple perturbation (T) correction methods were performed to elucidate the relative stabilities of ten different intermediate structures of the CaMn4Ox cluster in the S0 state of the oxygen evolving complex (OEC) of photosystem II (PSII). Full geometry optimizations of all the S0 intermediates were performed by the UB3LYP-D3/Def2-TZVP methods, providing the assumed geometrical structures and starting natural orbitals (UNO) for DLPNO-CCSD(T)/Def2TZVP calculations. The effective exchange integrals (J) for the spin Hamiltonian models for the ten intermediates were obtained by the UB3LYP/Def2-TZVP calculations followed by the general spin projections. DLPNO-CCSD(T) calculations followed by the CBS extrapolation procedure elucidated that the (II, III, IV, IV) and (III, III, III, IV) valence states in the CaMn4O5 cluster of the OEC of the PS II were nearly degenerated in energy in the S0 state, indicating an important role of dynamical electron correlation effects for the valence and spin fluctuations in strongly correlated electron systems (SCESs) consisting of 3d transition metals.


Subject(s)
Calcium/chemistry , Manganese/chemistry , Oxygen/chemistry , Photosystem II Protein Complex/chemistry , Bacterial Proteins/chemistry , Density Functional Theory , Models, Chemical , Protein Domains , Protons , Thermodynamics , Thermosynechococcus/enzymology
2.
Earth Planets Space ; 72(1): 111, 2020.
Article in English | MEDLINE | ID: mdl-32831576

ABSTRACT

We investigate the longitudinal structure of the oxygen torus in the inner magnetosphere for a specific event found on 12 September 2017, using simultaneous observations from the Van Allen Probe B and Arase satellites. It is found that Probe B observed a clear enhancement in the average plasma mass (M) up to 3-4 amu at L = 3.3-3.6 and magnetic local time (MLT) = 9.0 h. In the afternoon sector at MLT ~ 16.0 h, both Probe B and Arase found no clear enhancements in M. This result suggests that the oxygen torus does not extend over all MLT but is skewed toward the dawn. Since a similar result has been reported for another event of the oxygen torus in a previous study, a crescent-shaped torus or a pinched torus centered around dawn may be a general feature of the O+ density enhancement in the inner magnetosphere. We newly find that an electromagnetic ion cyclotron (EMIC) wave in the H+ band appeared coincidently with the oxygen torus. From the lower cutoff frequency of the EMIC wave, the ion composition of the oxygen torus is estimated to be 80.6% H+, 3.4% He+, and 16.0% O+. According to the linearized dispersion relation for EMIC waves, both He+ and O+ ions inhibit EMIC wave growth and the stabilizing effect is stronger for He+ than O+. Therefore, when the H+ fraction or M is constant, the denser O+ ions are naturally accompanied by the more tenuous He+ ions, resulting in a weaker stabilizing effect (i.e., larger growth rate). From the Probe B observations, we find that the growth rate becomes larger in the oxygen torus than in the adjacent regions in the plasma trough and the plasmasphere.

3.
Public Health ; 188: 51-53, 2020 Nov.
Article in English | MEDLINE | ID: mdl-33120232

ABSTRACT

OBJECTIVES: The purpose of this study is to show that social distancing is a public good under the COVID-19 pandemic. STUDY DESIGN: We apply economic theory to analyse a cross-sectional survey. METHODS: Economic theory is complemented with empirical evidence. An online survey of those aged 30-49 years in Japan (n = 2177) was conducted between April 28 and May 7. Respondents were selected by quota sampling with regard to age group, gender and prefecture of residence. Our main figure shows the proportion of people who increased/did not change/decreased social distancing, relative to the level of altruism and sensitivity to public shaming. The results of OLS and logit models are shown in Supplementary Materials. RESULTS: Social distancing is a public good under the COVID-19 pandemic for which the free-rider problem is particularly severe. Altruism and social norms are crucial factors in overcoming this problem. Using an original survey, we show that people with higher altruistic concerns and sensitivity to shaming are more likely to follow social distancing measures. CONCLUSIONS: Altruism and social norms are important for reducing the economic cost of the pandemic.


Subject(s)
Altruism , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Psychological Distance , Adult , COVID-19 , Coronavirus Infections/epidemiology , Cross-Sectional Studies , Female , Humans , Japan/epidemiology , Male , Middle Aged , Pandemics/economics , Pneumonia, Viral/epidemiology , Social Norms , Surveys and Questionnaires , Young Adult
4.
Eur J Neurol ; 26(12): 1487-1493, 2019 12.
Article in English | MEDLINE | ID: mdl-31232495

ABSTRACT

BACKGROUND AND PURPOSE: A nationwide survey was conducted to understand the epidemiology of cerebral amyloid angiopathy-related intracerebral hemorrhage (CAA-related ICH) and cerebral amyloid angiopathy-related inflammation/vasculitis (CAA-ri) in Japan. METHODS: To estimate the total number and clinical features of patients with CAA-related ICH and CAA-ri between January 2012 and December 2014 and to analyze their clinical features, questionnaires were sent to randomly selected hospitals in Japan. RESULTS: In the first survey, 2348 of 4657 departments responded to the questionnaire (response rate 50.4%). The total numbers of reported patients with CAA-related ICH and CAA-ri were 1338 and 61, respectively, and their total numbers in Japan were estimated to be 5900 [95% confidence interval (CI) 4800-7100] and 170 (95% CI 110-220), respectively. The crude prevalence rates were 4.64 and 0.13 per 100 000 population, respectively. The clinical information of 474 patients with CAA-related ICH obtained in the second survey was as follows: (i) the average age of onset was 78.4 years; (ii) the prevalence increased with age; (iii) the disease was common in women; and (iv) hematoma most frequently occurred in the frontal lobe. Sixteen patients with CAA-ri for whom data were collected in the second survey had the following characteristics: (i) median age of onset was 75 years; (ii) cognitive impairment and headache were the most frequent initial manifestations; and (iii) focal neurological signs, such as motor paresis and visual disturbance, were frequently observed during the clinical course. CONCLUSIONS: The numbers of patients with CAA-related ICH and CAA-ri in Japan were estimated.


Subject(s)
Cerebral Amyloid Angiopathy/epidemiology , Cerebral Hemorrhage/epidemiology , Adult , Aged , Aged, 80 and over , Female , Health Surveys , Humans , Japan/epidemiology , Magnetic Resonance Imaging , Male , Middle Aged , Prevalence , Surveys and Questionnaires
5.
Biomarkers ; 21(2): 164-7, 2016.
Article in English | MEDLINE | ID: mdl-26635084

ABSTRACT

Diabetic nephropathy has dramatically increased worldwide. In this study, we measured urinary podocalyxin in 240 patients with diabetes. The relationship between urinary podocalyxin and clinical parameters and the effects of dipeptidyl peptidase-4 inhibitors (DPP4i) and alpha-glucosidase inhibitor (a-GI) on urinary podocalyxin levels were examined. Urinary podocalyxin levels were significantly higher in patients with microalbuminuria than in those with normoalbuminuria. Urinary podocalyxin levels were also significantly related to albumin-to-creatinine ratio. Neither DPP4i nor α-GI ameliorated the increase in urinary podocalyxin levels. Our results indicated that urinary podocalyxin will be not only an early marker but also a treatment target for DN.


Subject(s)
Albuminuria/urine , Biomarkers/urine , Diabetes Mellitus, Type 2/urine , Sialoglycoproteins/urine , Aged , Creatinine/urine , Diabetes Mellitus, Type 2/complications , Diabetes Mellitus, Type 2/diagnosis , Diabetic Nephropathies/complications , Diabetic Nephropathies/diagnosis , Diabetic Nephropathies/urine , Disease Progression , Early Diagnosis , Female , Humans , Linear Models , Male , Middle Aged , Multivariate Analysis
6.
Phys Chem Chem Phys ; 16(24): 11911-23, 2014 Jun 28.
Article in English | MEDLINE | ID: mdl-24632787

ABSTRACT

Full geometry optimizations followed by the vibrational analysis were performed for eight spin configurations of the CaMn4O4X(H2O)3Y (X = O, OH; Y = H2O, OH) cluster in the S1 and S3 states of the oxygen evolution complex (OEC) of photosystem II (PSII). The energy gaps among these configurations obtained by vertical, adiabatic and adiabatic plus zero-point-energy (ZPE) correction procedures have been used for computation of the effective exchange integrals (J) in the spin Hamiltonian model. The J values are calculated by the (1) analytical method and the (2) generalized approximate spin projection (AP) method that eliminates the spin contamination errors of UB3LYP solutions. Using J values derived from these methods, exact diagonalization of the spin Hamiltonian matrix was carried out, yielding excitation energies and spin densities of the ground and lower-excited states of the cluster. The obtained results for the right (R)- and left (L)-opened structures in the S1 and S3 states are found to be consistent with available optical and magnetic experimental results. Implications of the computational results are discussed in relation to (a) the necessity of the exact diagonalization for computations of reliable energy levels, (b) magneto-structural correlations in the CaMn4O5 cluster of the OEC of PSII, (c) structural symmetry breaking in the S1 and S3 states, and (d) the right- and left-handed scenarios for the O-O bond formation for water oxidation.


Subject(s)
Calcium/chemistry , Manganese Compounds/chemistry , Oxides/chemistry , Oxygen/chemistry , Photosystem II Protein Complex/chemistry , Electron Spin Resonance Spectroscopy
7.
Nat Commun ; 14(1): 955, 2023 Feb 21.
Article in English | MEDLINE | ID: mdl-36804939

ABSTRACT

Proton-boron (p11B) fusion is an attractive potential energy source but technically challenging to implement. Developing techniques to realize its potential requires first developing the experimental capability to produce p11B fusion in the magnetically-confined, thermonuclear plasma environment. Here we report clear experimental measurements supported by simulation of p11B fusion with high-energy neutral beams and boron powder injection in a high-temperature fusion plasma (the Large Helical Device) that have resulted in diagnostically significant levels of alpha particle emission. The injection of boron powder into the plasma edge results in boron accumulation in the core. Three 2 MW, 160 kV hydrogen neutral beam injectors create a large population of well-confined, high -energy protons to react with the boron plasma. The fusion products, MeV alpha particles, are measured with a custom designed particle detector which gives a fusion rate in very good relative agreement with calculations of the global rate. This is the first such realization of p11B fusion in a magnetically confined plasma.

8.
Eur J Neurol ; 19(8): 1070-8, 2012 Aug.
Article in English | MEDLINE | ID: mdl-22353375

ABSTRACT

BACKGROUND: A variety of hereditary spinocerebellar ataxia (SCA) develops a broad spectrum of both ataxia and non-ataxia symptoms. Cognitive and affective changes are one such non-ataxia symptoms, but have been described only in hereditary SCAs with exonic CAG gene expansion. METHODS: We newly found intronic hexanucleotide GGCCTG gene expansion in NOP56 gene as the causative mutation (=SCA36) in nine unrelated Japanese familial SCA originating from Asida river area in the western part of Japan, thus nicknamed Asidan for this mutation. These patients show unique clinical balance of cerebellar ataxia and motor neuron disease (MND), locating on the crossroad of these two diseases. In the nine families, 14 patients were clinically examined and genetically confirmed to Asidan. In the present study, we examined cognitive and affective analyses on 12 patients (seven men and five women) who agreed to join the examination with average age at onset of 53.1 ± 3.2 years, average duration of 12.1 ± 5.2 years, and current average age at 65.1 ± 6.2 years. RESULTS: The 12 Asidan patients demonstrated a significant decrease in their frontal executive functions measured by frontal assessment battery (FAB) and Montreal cognitive assessment (MoCA) compared with age- and gender-matched controls, whilst mini-mental state examination (MMSE) and Hasegawa dementia score-revised (HDS-R) were within normal range. The decline of frontal executive function was related to their disease duration and scale for the assessment and rating of ataxias (SARA). They also demonstrated mild depression and apathy. Single-photon emission tomography (SPECT) analysis showed that these Asidan patients showed decline of regional cerebral blood flow (rCBF) in a particular areas of cerebral cortices such as Brodmann areas 24 and 44-46. CONCLUSION: These data suggest that the patients with Asidan mutation show unique cognitive and affective characteristics different from other hereditary SCAs with exonal CAG expansion or MND.


Subject(s)
Cognition Disorders/genetics , Motor Neuron Disease/complications , Motor Neuron Disease/genetics , Mutation , Nuclear Proteins/genetics , Spinocerebellar Ataxias/complications , Spinocerebellar Ataxias/genetics , Age of Onset , Aged , Female , Humans , Japan , Male , Middle Aged , Neuropsychological Tests , Tomography, Emission-Computed, Single-Photon
9.
Nat Commun ; 13(1): 6259, 2022 Oct 28.
Article in English | MEDLINE | ID: mdl-36307443

ABSTRACT

Electromagnetic whistler-mode waves in space plasmas play critical roles in collisionless energy transfer between the electrons and the electromagnetic field. Although resonant interactions have been considered as the likely generation process of the waves, observational identification has been extremely difficult due to the short time scale of resonant electron dynamics. Here we show strong nongyrotropy, which rotate with the wave, of cyclotron resonant electrons as direct evidence for the locally ongoing secular energy transfer from the resonant electrons to the whistler-mode waves using ultra-high temporal resolution data obtained by NASA's Magnetospheric Multiscale (MMS) mission in the magnetosheath. The nongyrotropic electrons carry a resonant current, which is the energy source of the wave as predicted by the nonlinear wave growth theory. This result proves the nonlinear wave growth theory, and furthermore demonstrates that the degree of nongyrotropy, which cannot be predicted even by that nonlinear theory, can be studied by observations.

10.
Space Sci Rev ; 218(5): 38, 2022.
Article in English | MEDLINE | ID: mdl-35757012

ABSTRACT

This paper presents the highlights of joint observations of the inner magnetosphere by the Arase spacecraft, the Van Allen Probes spacecraft, and ground-based experiments integrated into spacecraft programs. The concurrent operation of the two missions in 2017-2019 facilitated the separation of the spatial and temporal structures of dynamic phenomena occurring in the inner magnetosphere. Because the orbital inclination angle of Arase is larger than that of Van Allen Probes, Arase collected observations at higher L -shells up to L ∼ 10 . After March 2017, similar variations in plasma and waves were detected by Van Allen Probes and Arase. We describe plasma wave observations at longitudinally separated locations in space and geomagnetically-conjugate locations in space and on the ground. The results of instrument intercalibrations between the two missions are also presented. Arase continued its normal operation after the scientific operation of Van Allen Probes completed in October 2019. The combined Van Allen Probes (2012-2019) and Arase (2017-present) observations will cover a full solar cycle. This will be the first comprehensive long-term observation of the inner magnetosphere and radiation belts.

11.
Rev Sci Instrum ; 92(6): 063516, 2021 Jun 01.
Article in English | MEDLINE | ID: mdl-34243592

ABSTRACT

A new multi-tracer technique in the Tracer-Encapsulated Solid Pellet (TESPEL) method has been developed in order to acquire simultaneously the information about the behaviors of various impurities, i.e., to study concurrently the behaviors of low- and mid/high-Z impurities in magnetically confined high-temperature plasmas. In this new technique, an inorganic compound (for example, lithium titanate, Li2TiO3) is proposed to be used as a tracer embedded in the core of the TESPEL, instead of pure elements. The results of the proof-of-principle experiment clearly demonstrate the applicability of the new multi-tracer technique in the TESPEL method for the simultaneous study of behaviors of low- and mid/high-Z impurities in high-temperature plasmas.

12.
Sci Rep ; 11(1): 13724, 2021 Jul 13.
Article in English | MEDLINE | ID: mdl-34257336

ABSTRACT

Pulsating aurorae (PsA) are caused by the intermittent precipitations of magnetospheric electrons (energies of a few keV to a few tens of keV) through wave-particle interactions, thereby depositing most of their energy at altitudes ~ 100 km. However, the maximum energy of precipitated electrons and its impacts on the atmosphere are unknown. Herein, we report unique observations by the European Incoherent Scatter (EISCAT) radar showing electron precipitations ranging from a few hundred keV to a few MeV during a PsA associated with a weak geomagnetic storm. Simultaneously, the Arase spacecraft has observed intense whistler-mode chorus waves at the conjugate location along magnetic field lines. A computer simulation based on the EISCAT observations shows immediate catalytic ozone depletion at the mesospheric altitudes. Since PsA occurs frequently, often in daily basis, and extends its impact over large MLT areas, we anticipate that the PsA possesses a significant forcing to the mesospheric ozone chemistry in high latitudes through high energy electron precipitations. Therefore, the generation of PsA results in the depletion of mesospheric ozone through high-energy electron precipitations caused by whistler-mode chorus waves, which are similar to the well-known effect due to solar energetic protons triggered by solar flares.

13.
Eur J Neurol ; 17(6): 823-9, 2010 Jun 01.
Article in English | MEDLINE | ID: mdl-20158508

ABSTRACT

BACKGROUND AND PURPOSE: The present study aims to clarify the clinical features of non-hypertensive cerebral amyloid angiopathy-related lobar intracerebral hemorrhage (CAA-L-ICH). METHODS: We investigated clinical, laboratory, and neuroimaging findings in 41 patients (30, women; 11, men) with pathologically supported CAA-L-ICH from 303 non-hypertensive Japanese patients aged >OR=55, identified via a nationwide survey as symptomatic CAA-L-ICH. RESULTS: The mean age of patients at onset of CAA-L-ICH was 73.2 +/- 7.4 years; the number of patients increased with age. The corrected female-to-male ratio for the population was 2.2, with significant female predominance. At onset, 7.3% of patients received anti-platelet therapy. In brain imaging studies, the actual frequency of CAA-L-ICHs was higher in the frontal and parietal lobes; however, after correcting for the estimated cortical volume, the parietal lobe was found to be the most frequently affected. CAA-L-ICH recurred in 31.7% of patients during the average 35.3-month follow-up period. The mean interval between intracerebral hemorrhages (ICHs) was 11.3 months. The case fatality rate was 12.2% at 1 month and 19.5% at 12 months after initial ICH. In 97.1% of patients, neurosurgical procedures were performed without uncontrollable intraoperative or post-operative hemorrhage. CONCLUSIONS: Our study revealed the clinical features of non-hypertensive CAA-L-ICH, including its parietal predilection, which will require further study with a larger number of patients with different ethnic backgrounds.


Subject(s)
Cerebral Amyloid Angiopathy/pathology , Cerebral Hemorrhage/pathology , Age Distribution , Age of Onset , Aged , Aged, 80 and over , Cerebral Amyloid Angiopathy/complications , Cerebral Hemorrhage/etiology , Female , Humans , Male , Middle Aged
14.
Science ; 201(4358): 826-8, 1978 Sep 01.
Article in English | MEDLINE | ID: mdl-210503

ABSTRACT

A decrease in the activity of the enzyme cytidine 3',5'-monophosphate (cyclic CMP) phosphodiesterase was noted in the regenerating liver of young rats as early as 8 hours after partial hepatectomy, with a maximum decrease occurring 12 hours after the surgery. In comparison, in old rats which showed a slower liver growth, the maximum decrease in the activity of cyclic CMP phosphodiesterase was smaller and occurred at a much later time (2 days after surgery). A similar decrease in the enzyme activity was observed in the fetal liver of guinea pigs. These findings suggest that regulation of tissue concentration of cyclic CMP may be crucial for the regeneration and development of the liver.


Subject(s)
Liver Regeneration , Liver/growth & development , Phosphoric Diester Hydrolases/metabolism , 3',5'-Cyclic-AMP Phosphodiesterases/metabolism , 3',5'-Cyclic-GMP Phosphodiesterases/metabolism , Aging , Animals , Cytidine Monophosphate/analogs & derivatives , Liver/enzymology , Male , Rats
15.
Science ; 258(5079): 126-9, 1992 Oct 02.
Article in English | MEDLINE | ID: mdl-1439760

ABSTRACT

The 4-kilodalton (39 to 43 amino acids) amyloid beta protein (beta AP), which is deposited as amyloid in the brains of patients with Alzheimer's diseases, is derived from a large protein, the amyloid beta protein precursor (beta APP). Human mononuclear leukemic (K562) cells expressing a beta AP-bearing, carboxyl-terminal beta APP derivative released significant amounts of a soluble 4-kilodalton beta APP derivative essentially identical to the beta AP deposited in Alzheimer's disease. Human neuroblastoma (M17) cells transfected with constructs expressing full-length beta APP and M17 cells expressing only endogenous beta APP also released soluble 4-kilodalton beta AP, and a similar, if not identical, fragment was readily detected in cerebrospinal fluid from individuals with Alzheimer's disease and normal individuals. Thus cells normally produce and release soluble 4-kilodalton beta AP that is essentially identical to the 4-kilodalton beta AP deposited as insoluble amyloid fibrils in Alzheimer's disease.


Subject(s)
Alzheimer Disease/cerebrospinal fluid , Amyloid beta-Peptides/biosynthesis , Leukemia, Myeloid/metabolism , Neuroblastoma/metabolism , Amino Acid Sequence , Amyloid beta-Protein Precursor/metabolism , Animals , Base Sequence , Cell Line , Immunoblotting , Molecular Sequence Data , Transfection
16.
J Phys Chem A ; 113(52): 15281-97, 2009 Dec 31.
Article in English | MEDLINE | ID: mdl-19908878

ABSTRACT

Symmetry and broken symmetry in the molecular orbital description of spin frustration systems have been investigated in relation to the resonating valence bond (RVB) theory of the spin liquid state and non-BCS superconductivity. Broken symmetry (BS) and resonating BS (RBS) molecular orbital (MO) methods have been employed to obtain resonating valence bond (RVB)-type explanations of spin frustrated systems. RBS MO solutions are expanded using the localized molecular orbitals (LMO) to elucidate a universal MO-VB description. The BS and RBS MO descriptions of triangular spin frustrated systems corresponding to transition structures for exchange-forbidden radical insertions were investigated in comparison with the RVB-type explanations of such systems. The BS and RBS calculations by the use of three different axial (SDW) solutions or three noncollinear GSO (helical SDW) solutions of a triangular hydrogen cluster were performed to obtain potential curves with and without resonance (quantum) effects. The resonating GSO (noncollinear) state responsible for short-range correlation was found to be the most stable for the system. The reliability of the approximate spin projection (AP) procedure to eliminate the high-spin component was also elucidated, comparing with the AP BS and RBS potential curves. The BS GSO (GHF) computations of several triangular systems, N(CH(2))(3), (CH(2))(3), and Mn(II)(3)O(4), were performed to obtain total energies and total spin angular momentums and effective exchange integrals (J) between local spins, which are crucial for construction of effective spin Hamiltonian models. The exact diagonalization of the Heisenberg models was also performed to depict the energy levels and magnetic susceptibility curves for triangular and kagome lattices to elucidate spin frustration effects and related quantum spin behaviors. Implications of the computational results have been discussed in relation to magnetic properties of several triangular and kagome systems synthesized recently and the superconductivity of triangular systems discovered recently.


Subject(s)
Quantum Theory , Amines/chemistry , Benzene/chemistry , Hydrogen/chemistry , Models, Molecular , Molecular Conformation , Transition Elements/chemistry
17.
Space Sci Rev ; 215(1): 9, 2019.
Article in English | MEDLINE | ID: mdl-30880847

ABSTRACT

With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have "crib-sheets," user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer's Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its "modes of use" with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11214-018-0576-4) contains supplementary material, which is available to authorized users.

18.
Eur J Clin Invest ; 38(3): 166-73, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18257779

ABSTRACT

BACKGROUND: Interleukin-6 (IL-6) and metalloproteinases (MMPs) are involved in the instability of vulnerable plaque associated with the induction of acute myocardial infarction (AMI). We examined the regional changes of cytokines, MMPs and adhesion molecules in patients with AMI to elucidate how these factors are involved in the onset of AMI. MATERIALS AND METHODS: One hundred and twenty-two patients with AMI were included. Blood was aspirated from the culprit coronary artery with a thrombectomy catheter, and was also sampled from peripheral veins during the coronary intervention. Control samples were obtained from the peripheral blood of age-matched patients. RESULTS: The serum levels of IL-6 (P < 0.05), tumour necrosis factor-alpha (P < 0.005), MMP-1 (P < 0.001), MMP-13 (P < 0.001), soluble intercellular adhesion molecule-1 (P < 0.005), and soluble vascular cellular adhesion molecule-1 (P < 0.05) in peripheral blood were significantly higher in the AMI group than in the controls. Aspirated serum contained significantly higher levels of IL-6 (P < 0.001), MMP-1 (P < 0.001), and MMP-13 (P < 0.05) compared to the peripheral blood of AMI. Serum IL-6 levels were significantly higher in the aspirated than in the peripheral blood in the patients hospitalized within 6 h and 6-12 h, but were similar in the aspirated and peripheral blood of the patients hospitalized 12-24 h after the onset of AMI. There were no differences between the aspirated serum and peripheral blood in the levels of interleukin-1beta and MMP-2. CONCLUSIONS: The levels of MMP-1, MMP-13 and IL-6 were higher in the culprit coronary artery than in the peripheral blood. These factors appear to be involved in the early stage of AMI.


Subject(s)
Biomarkers/blood , Coronary Vessels/metabolism , Myocardial Infarction/blood , Acute Disease , Coronary Circulation , Female , Humans , Intercellular Adhesion Molecule-1/blood , Interleukin-6/blood , Male , Matrix Metalloproteinases/blood , Middle Aged , Tumor Necrosis Factor-alpha/blood
19.
Oral Microbiol Immunol ; 23(5): 413-8, 2008 Oct.
Article in English | MEDLINE | ID: mdl-18793365

ABSTRACT

INTRODUCTION: Porphyromonas gingivalis, an oral anaerobic bacterium, is considered a major pathogen for chronic periodontitis. Pathogenic bacteria usually upregulate or downregulate gene expression to combat the protective responses of their hosts. METHODS: To determine what protein is regulated when P. gingivalis cells invade host tissues, we analyzed the proteome of P. gingivalis cells that were placed in a mouse subcutaneous chamber by two-dimensional gel electrophoresis and mass spectrometry. RESULTS: Fourteen proteins were upregulated, while four proteins were downregulated. We focused on three upregulated proteins, PG1089 (DNA-binding response regulator RprY), PG1385 (TPR domain protein), and PG2102 (immunoreactive 61-kDa antigen), and constructed mutant strains that were defective in these proteins. Mouse abscess model experiments revealed that the mutant strain defective in PG1385 was clearly less virulent than the wild-type parent strain. CONCLUSION: These results indicate that the PG1385 protein is involved in P. gingivalis virulence and that the method used here is useful when investigating the P. gingivalis proteins responsible for virulence.


Subject(s)
Bacterial Proteins/analysis , Porphyromonas gingivalis/chemistry , Proteome/analysis , Subcutaneous Tissue/microbiology , Abscess/microbiology , Animals , Antigens, Bacterial/analysis , Bacteroidaceae Infections/microbiology , Disease Models, Animal , Down-Regulation , Electrophoresis, Gel, Two-Dimensional , Female , Mass Spectrometry , Mice , Mice, Inbred BALB C , Mutation/genetics , Porphyromonas gingivalis/genetics , Porphyromonas gingivalis/pathogenicity , Signal Transduction , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Transcription Factors/analysis , Up-Regulation , Virulence/genetics , Virulence/physiology
20.
Mol Oral Microbiol ; 33(1): 68-80, 2018 02.
Article in English | MEDLINE | ID: mdl-28972686

ABSTRACT

Porphyromonas gingivalis can synthesize both A-LPS and O-LPS lipopolysaccharides, which contain anionic O-polysaccharides and conventional O-polysaccharides, respectively. A-LPS can anchor virulence proteins to the cell surface, so elucidating the mechanism of A-LPS synthesis is important for understanding the pathogenicity of this bacterium. To identify the genes involved in LPS synthesis, we focused on uncharacterized genes encoding the glycosyltransferases, PGN_0361, PGN_1239, PGN_1240 and PGN_1668, which were tentatively named gtfC, gtfD, gtfE and gtfF, respectively, and characterized their mutants. We found that disruption of gtfC and gtfF resulted in A-LPS deficiency. In addition, a gtfD mutant had abnormal A-LPS synthesis, and a gtfE mutant exhibited a rough-type LPS that possesses a short oligosaccharide with lipid A-core. We then constructed a gtfC and gtfD double mutant, because their amino acid sequences were very similar, and this mutant similarly possessed a rough-type LPS. Cross-complementation analysis revealed that the GtfD protein is a functional homologue of the Escherichia coli WbbL protein, which is a rhamnosyltransferase. These results suggested that the GtfE protein is essential for the synthesis of both O-LPS and A-LPS, and that GtfC and GtfD proteins may work together to synthesize the two kinds of LPS. In addition, the GtfF protein was essential for A-LPS synthesis, although this may be achieved in a strain-specific manner.


Subject(s)
Bacterial Proteins/genetics , Genes, Bacterial/genetics , Glycosyltransferases/genetics , Lipopolysaccharides/biosynthesis , Porphyromonas gingivalis/enzymology , Porphyromonas gingivalis/genetics , Amino Acid Sequence , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Glucosyltransferases/genetics , Glycosyltransferases/metabolism , Hexosyltransferases/genetics , Lipopolysaccharides/analysis , Mutation , Pigmentation , Porphyromonas gingivalis/metabolism , Virulence/genetics
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