Super High Resolution Research Articles

8-2 高品質大画面画像コンテンツの感性評価(第8部門ヒューマンインフォメーション)

8-2 高品質大画面画像コンテンツの感性評価(第8部門ヒューマンインフォメーション)

Distinguishing Individual DNA Bases in a Network by Non-Resonant Tip-Enhanced Raman Scattering.

The importance of identifying DNA bases at the single-molecule level is well recognized for many biological applications. Although such identification can be achieved by electrical measurements using special setups, it is still not possible to identify single bases in real space by optical means owing to the diffraction limit. Herein, we demonstrate the outstanding ability of scanning tunneling microscope (STM)-controlled non-resonant tip-enhanced Raman scattering (TERS) to unambiguously distinguish two individual complementary DNA bases (adenine and thymine) with a spatial resolution down to 0.9 nm. The distinct Raman fingerprints identified for the two molecules allow to differentiate in real space individual DNA bases in coupled base pairs. The demonstrated ability of non-resonant Raman scattering with super-high spatial resolution will significantly extend the applicability of TERS, opening up new routes for single-molecule DNA sequencing.

Use of remotely sensed data in mapping underwater landscapes of Srednyaya Bay (Peter the Great Gulf, Sea of Japan)

We examine the selection criteria for satellite images and methods of processing them in the process of mapping underwater landscapes using remotely sensed data, discuss the interpretation principles and algorithms as well as some issues related to the support of observations with field material. It is shown that a detailed landscape mapping of shallow marine waters by methods of visual and automated interpretation requires multispectral superhigh spatial resolution images. Results of investigations made on underwater profiles by using lightweight diving outfits were employed to describe seven types of underwater landscapes, and echo sounder measurements were used in constructing the digital elevation model for the bottom of Srednyaya Bay. It is established that the regions for which it was possible to carry out a reliable interpretation of data from the IKONOS-2 spacecraft are in the range of depths between 0 and 10 m and make up about three-fourths of the area of the bay bottom. Ten facies were identified and put on the map, for each of which we determined the area, the range of depths and the mean depth of propagation. Remotely sensed data were used to assess the contribution (in the spatial structure of the geosystem) of algal vegetation on the littoral; the eelgrass fields were ranked according to the degree of projective cover. As a result of a clustering according to the similarity of spectral attributes, we identified ten groups of pixels of the image analyzed. An analysis is made of the agreement between the distribution of facies identified by expert interpretation and results of an automated classification of pixels, and the contours of landscape units were updated. The conclusion is drawn regarding integration of the computer-aided and visual approaches to interpretation of remotely sensed data for shallow marine waters leading to a “hybrid” express method of mapping landscapes of shallow marine waters.

Expression of Rho GTPases family in melanoma cells and its influence on cytoskeleton and migration.

Rho GTPases family members influenced the filopodia, lamellipodia, stress fiber and adhesion plaque of melanoma cells through regulating cytoskeleton recombination. The role of Rho GTPases family in the migration and invasion of melanoma and its molecular mechanism were explored. The morphological difference between three types of melanoma cells (M14, A375 and MV3) and human melanocyte (MC) was observed by the Hoffman microscope. Cells were stained by phalloidin labeled by rhodamine. The differences between 4 types of cells in filopodia, lamellipodia, stress fiber and adhesion plaque (microfilament is the main constituent) were observed under the super-high resolution microscope. The migration ability of 4 types of cells was detected by Transwell migration assay. QPCR was used to detect the mRNA transcription level of Rho GTPases family. WB was adopted to detect the expression of RhoD and DIAPH2 proteins. There were significant differences in filopodia, lamellipodia, stress fiber and adhesion plaque between MC and 3 types of melanoma cells (M14, A375 and MV3). MC did not have stress fiber or adhesion plaque, while M14, A375 and MV3 had stress fiber and adhesion plaque. All 4 types of cells had thin and short filopodia. MV3 had fewer but thicker stress fibers than the latter two. Transwell migration test indicated the followings: M14 and A375 had a similar high migration rate; the migration rate of MV3 was slightly low; MC did not have the ability of transmembrane migration. QPCR results of Rho GTPases family in 4 types of cells showed the change corresponding to immunofluorescence. WB results showed that RhoD was barely expressed in M14, A375 or MV3. DIAPH2, the downstream effector molecule of RhoD, had the corresponding change. Rho GTPases influences the migration and invasion of melanoma cells through regulating filopodia, lamellipodia, stress fiber and adhesion plaque (microfilament is the main constituent).

P019 Collection of major HLA allele sequences in japanese population towards precise NGS based HLA DNA typing at the field 4 level

Aim We previously reported on the use of the Ion PGM next generation sequencing (NGS) platform to genotype HLA class I and class II genes by a super-high resolution, single-molecule, sequence-based typing (SS-SBT) method. However, HLA alleles could not be assigned at the field 4 level at some HLA loci such as DQA1, DPA1 and DPB1 because the SNP and indel densities were too low to identify and separate both of the phases. In this regard, we have now added the single molecule, real-time (SMRT®) DNA sequencer PacBio RS II method to our analysis in order to test whether it might determine the HLA allele sequences in some of the loci with which we previously had difficulties. Here, we report on sequence-based genotyping from the promoter-enhancer region to 3 ′ UTR of the major HLA genes in the Japanese using the PacBio RS II and Ion PGM NGS systems. Method Forty-six DNA samples were obtained from a reference set used previously to establish the HLA allele frequency data in the Japanese population. The reference samples represented more than 99.5% of the HLA alleles at each of the nine HLA loci. The genomic DNA samples were amplified by long ranged PCR using eleven HLA loci specific primer pairs (A, B, C, DRB1, DRB3/4/5, DQA1, DQB1, DPA1 and DPB1). After NGS, consensus sequences were obtained via Long Amplicon analysis such as overlapping, clustering of filtered sub-reads, phasing and removing PCR artifacts. The HLA allele sequences for generating a library of consensus sequences were determined by mapping of sequence reads obtained from Ion PGM sequencer. Results A total of 219 HLA allele sequences (20 A, 40 B, 23 C, 31 DRB1, 36 DQA1, 14 DQB1, 15 DPA1 and 40 DPB1) that covered the promoter-enhancer region to 3’UTR were determined for the 46 samples. The classification of the newly identified SNPs and/or indels revealed at least three non-synonymous substitutions for one B and two DPA1 alleles, although most of the substitutions were observed in intron regions. Conclusion We determined at least 219 Japanese major HLA alleles at the field 4 level by NGS and we expect that this HLA genotyping method of entire HLA gene regions by NGS will help to precisely detect rare, novel and null alleles in population genetic and disease studies.

Tip-enhanced Raman spectroscopy: From concepts to practical applications

Tip-enhanced Raman spectroscopy (TERS) is a powerful technique that integrates the vibrational fingerprinting of Raman spectroscopy and the sub-nanometer resolution of scanning probe microscopy (SPM). As a result, TERS is capable of obtaining chemical maps of analyzed specimens with exceptional lateral resolution. This is extremely valuable for the study of interactions between molecules and substrates, in addition to structural characterization of biological objects, such as viruses and amyloid fibrils, 2D polymeric materials, and monitoring electrochemical and photo-catalytic processes. In this mini-review, we discuss the most significant advances of TERS, including: super high resolution chemical imaging, monitoring of catalytic processes, incorporation of pulsed-excitation techniques, single-site electrochemistry, biosensing, and art conservation. We begin with a short overview of TERS, comparing it with other surface analytical techniques, followed by an overview of recent developments and future applications in TERS.

Novel Method of Contrast Improvement Applied to Lithium Ion Battery Electrode Materials Enabling Multi Modal and Super-High Resolution 3D Imaging and Advanced Quantification

The authors present for the first time a new methodology of contrast enhancement for multi modal 3D imaging including novel advanced quantification for a commercial Lithium Iron Phosphate (LFP) LiFePO4 cathode. The research aim of this work is to improve the 3D imaging of challenging battery materials by developing methods to increase the contrast between otherwise previously poorly differentiated phases. This is necessary to enable the capture of the real geometry of electrode microstructures, which allows measurement of a wide range of microstructural properties such as pore/particle size distributions, surface area, tortuosity and porosity. Those properties play vital roles in determining the performance of battery electrodes. In this study we present a novel method of sample preparation which is introduced here for the first time for this purpose and found suitable for multi modal imaging, for both FIB-SEM tomography and X-ray tomography. This novel method improves image contrast, which enables higher FIB-SEM resolution (3D image) the highest yet reported for carbon containing electrode materials (e.g. composite LFP cathodes) using FIB-SEM. It means that all the particles are well defined and the size distribution of each phase can be analysed very accurately from the complex 3D electrode microstructure using an advanced novel quantification algorithm.

FPGA implementation of a HEVC deblocking filter for fast processing of super high resolution applications

FPGA implementation of a HEVC deblocking filter for fast processing of super high resolution applications

Assessment of climate change impact on river flow regimes in The Red River Delta, Vietnam – A case study of the Nhue-Day River Basin

Global warming has caused dramatic changes in regional climate variability, particularly regarding fluctuations in temperature and rainfall. Thus, it is predicted that river flow regimes will be altered accordingly. The purpose of this paper is to present the results of modeling such changes by simulating discharge using the HEC-HMS model. The precipitation was projected using super-high resolution multiple climate models (20 km resolution) with newly updated emission scenarios as the input for the HEC-HMS model for flow analysis at the Red River Basin in the northern area of Vietnam. The findings showed that climate change impact on the river flow regimes tend towards a decrease in the dry season and a longer duration of flood flow. A slight runoff reduction is simulated for November while a considerable runoff increase is modeled for July and August amounting to 30% and 25%, respectively. The discharge scenarios serve as a basis for water managers to develop suitable adaptation methods and responses on the river basin scale.

Summer Convective Afternoon Rainfall Simulation and Projection Using WRF Driven by Global Climate Model. Part I: Over Taiwan

This paper is the first of a two-part study that investigates summer convective afternoon rainfall (CAR) activity over the East Asian continent through simulation and projection. We focus on the CAR activity over Taiwan in Part I. In Part II, the changes in CAR activity over South China and Luzon are examined. Using the WRF (Weather Research and Forecasting) model driven by two super-high resolution global climate models: HiRAM (High Resolution Atmospheric Model) and MRI (Meteorological Research Institute Atmospheric General Circulation Model), this study evaluates the performance of models (HiRAM, MRI, and WRF) used to simulate the summer CAR activity over Taiwan. The evaluations focus on the spatial-temporal variations in CAR activity during two time periods: the present-day (1979 - 2003, historical run) and the future (2075 - 2099, RCP8.5 scenario). For the present-day simulations, analyses indicate that both HiRAM and MRI cannot accurately simulate the temporal evolution of diurnal rainfall. This timing shift problem can be fixed after dynamical downscaling using WRF. The WRF dynamical downscaling approach also helps generate a more realistic CAR amount simulation over western Taiwan, where most residents live. In future projections all models predict that a significant decrease in CAR amount will occur over southwest Taiwan. This decrease in CAR amount is suggested due to the decrease in CAR frequency, not a change in the CAR rate. All models suggest that the cause of decrease in CAR frequency over southwest Taiwan is weaker local afternoon surface wind convergence and thermal instability to suppress CAR genesis.

Remote analysis of changes in the number of small thermokarst lakes and their distribution with respect to their sizes in the cryolithozone of Western Siberia, 2015

Regularities of changes in the number of thermokarst lakes in the cryolithozone of Western Siberia have been studied using multitemporal satellite images. The studies were conducted on 33 test sites selected in different landscape zones of the study area with the use of 134 cloud-free Landsat images obtained during warm months in the period from 1973 to 2013. It is shown that the total number of new lakes is significantly (almost 20 times) higher than the number of disappeared lakes. The area of newly formed thermokarst lakes is, on average, 22 times smaller than the size of disappearing lakes. Therefore, one can assume that the rapid growth in the number of small thermokarst lakes that is observed under the conditions of global warming will lead to an increase in methane emissions into the atmosphere in permafrost zones in the Arctic territories. Results of remote sensing of statistical distribution of small thermokarst lakes with respect to their sizes are given. The studies were performed on eight test sites selected in different permafrost zones of Western Siberia. The size of small lakes was determined according to QuickBird super-high resolution satellite images. It is shown that histograms of distribution of lakes with respect to their sizes allow their approximation by power and exponential functions, which can be used for modeling and predicting the dynamics of thermokarst methane emission in permafrost zones.

Performance of super high resolution numerical weather prediction model in forecasting terrain‐disrupted airflow at the Hong Kong International Airport: case studies

ABSTRACTHong Kong International Airport (HKIA) is situated in an area of complex terrain. Mountains near the airport can lead to terrain‐disrupted airflow disturbances, which may bring about hazardous weather phenomena for aviation, such as low‐level windshear and turbulence. Timely forecasting of such airflow disturbances would be useful in providing early warnings to the pilots. The Hong Kong Observatory has been running a super high resolution numerical weather prediction model suite, the aviation model (AVM), since late 2013, with spatial resolution up to 200 m immediately around HKIA. After testing and tuning over the past year, the performance of the AVM in forecasting terrain‐disrupted airflow at the airport area is investigated in this study. Two typical cases of such complex airflow are considered, Foehn wind and mountain wave. The AVM is found to capture successfully some salient features of the airflow as observed around HKIA through comparison with light detection and ranging (LIDAR) and weather buoy observations. The model also helps in shedding new light on the airflow from the vertical cross sections of the winds across the mountains. Limitations of the AVM are also discussed.

VirtualMicroscopy: ultra-fast interactive microscopy of gigapixel/terapixel images over internet.

As digital imaging technology advances, gigapixel or terapixel super resolution microscopic images become available. We have built a real time virtual microscopy technique for interactive analysis of super high resolution microscopic images over internet on standard desktops, laptops or mobile devices. The presented virtual microscopy technique is demonstrated to perform as fast as using a microscopy locally without any delay to assess gigapixel ultra high resolution image data through wired or wireless internet by a Tablet or a standard PC. More importantly, the presented technology enables analysis of super high resolution microscopic image across sites and time and allows multi-person analysis at the same time, which greatly speed up data analysis process and reduces miscommunication among scientists and doctors. A web site has been created for illustration purposes. (http://www-o.ntust.edu.tw/~cweiwang/VirtualMicroscopy).

Climate change effects on the worst-case storm surge: a case study of Typhoon Haiyan

Effects of climate change on the worst case scenario of a storm surge induced by a super typhoon in the present climate are investigated through the case study of Typhoon Haiyan. We present the results of our investigation on super-typhoon Haiyan by using a super high resolution (1 km grid) regional model that explicitly handles cloud microphysical processes. As the parent model, we adopted the operational weekly ensemble experiments (60 km grid) of the Japan Meteorological Agency, and compared experiments using sea surface temperatures and atmospheric environmental parameters from before the beginning of anthropogenic climate change (150 years ago) with those using observed values throughout the typhoon. We were able not only to represent the typhoon’s intensity but also to evaluate the influences of climate change on worst case storm surges in the Gulf of Leyte due to a typhoon with high robustness. In 15 of 16 ensemble experiments, the intensity of the simulated worst case storm in the actual conditions was stronger than that in a hypothetical natural condition without historical anthropogenic forcing during the past 150 years. The intensity of the typhoon is translated to a disaster metric by simulating the storm surge height by using a shallow-water long-wave model. The result indicates that the worst case scenario of a storm surge in the Gulf of Leyte may be worse by 20%, though changes in frequency of such events are not accounted for here.

Miniaturized Precision Stages with Piezo‐based Inertia Drives

AbstractThere are a number of areas in automation technology where precise positioning is necessary. This particularly applies to laser technology. High‐precision beam steering and focusing is just as indispensable in ophthalmology as in super‐high resolution microscopy, interferometry or photonics where the objective is to align fibers precisely. At the same time, laser beam steering and focusing also requires the drive systems used to be dynamic, reliable, and compactly dimensioned, so that they can be easily integrated into applications. Now, small positioning systems based on piezo inertia drives offer possible new solutions. In miniaturized design, they offer a high resolution at theoretically unlimited travel ranges, are self‐locking and on top of that, they are also inexpensive.

Super-resolution spinning-disk confocal microscopy using optical photon reassignment.

Spinning-disk confocal microscopy is a proven technology for investigating 3D structures of biological specimens. Here we report a super-resolution method based on spinning-disk confocal microscopy that optically improves lateral resolution by a factor of 1.37 with a single exposure. Moreover, deconvolution yields twofold improvement over the diffraction limit. With the help of newly modified Nipkow disk which comprises pinholes and micro-lenses on the front and back respectively, emitted photons from specimen can be optically reassigned to the most probable locations they originate from. Consequently, the improvement in resolution is achieved preserving inherent sectioning capabilities of confocal microscopy. This extremely simple implementation will enable reliable observations at super high resolution in biomedical routine research.

Monoclinic ferroelectric NaNbO3 at room temperature: Crystal structure solved by using super high resolution neutron powder diffraction

The crystal structure of NaNbO3 at ambient temperature was solved using time-off-flight neutron data obtained from Super High Resolution Neutron Powder Diffractometer in J-PARC. The solved structure was a novel monoclinic type with the space group Pm and lattice parameters of a=5.50453(1), b=15.52975(3), c=5.56779(1)Å, and β=90.0645(2)°. Bond valence calculation indicates that the solved structure is chemically valid. This solved structure corresponds with the observed ferroelectric behaviors (Ps=11–25μC/cm2, S=0.03–0.04%). The calculated Ps (~21μC/cm2) using the refined atomic parameters for one-quarter unit cell conform well to the observed value. Cooperative NbO6 octahedral tilting accompanied by the phase transition from the parent structure Pcmb to the Pm mainly contributes to the spontaneous polarization.

Visualization of fibrinogen αC regions and their arrangement during fibrin network formation by high‐resolution AFM

Fibrinogen has been intensively studied with transmission electron microscopy and x-ray diffraction. But until now, a complete 3D structure of the molecule has not yet been available because the two highly flexible αC regions could not be resolved in fibrinogen crystals. This study was aimed at determining whether the αC regions can be visualized by high-resolution atomic force microscopy. Atomic force microscopy with super high resolution was used to image single molecules of fibrinogen and fibrin associates. The key approach was to use a graphite surface modified with the monolayer of amphiphilic carbohydrate-glycine molecules and unique supersharp cantilevers with 1nm tip diameter. Fibrinogen αC regions were visualized along with the complete domain structure of the protein. In almost all molecules at pH 7.4 the D domain regions had one or two protrusions of average height 0.4± 0.1nm and length 21±6nm. The complex, formed between thrombin and fibrinogen, was also visualized. Images of growing fibrin fibers with clearly visible αCregions have been obtained. Fibrin αC regions were visible in protofibrils and large fibers; αC regions intertwined near a branchpoint and looked like a zipper. These results support the idea that αC regions are involved in the thickening of fibrin fibers. In addition, new details were revealed about the behavior of individual fibrin molecules during formation of the fibrin network. Under the diluted condition, the positioning of the αC regions could suggest their involvement in long-range interactions between fibrin but not fibrinogen molecules.

Surface and interfacial engineering of iron oxide nanoplates for highly efficient magnetic resonance angiography.

Magnetic resonance angiography using gadolinium-based molecular contrast agents suffers from short diagnostic window, relatively low resolution and risk of toxicity. Taking into account the chemical exchange between metal centers and surrounding protons, magnetic nanoparticles with suitable surface and interfacial features may serve as alternative T1 contrast agents. Herein, we report the engineering on surface structure of iron oxide nanoplates to boost T1 contrast ability through synergistic effects between exposed metal-rich Fe3O4(100) facets and embedded Gd2O3 clusters. The nanoplates show prominent T1 contrast in a wide range of magnetic fields with an ultrahigh r1 value up to 61.5 mM(-1) s(-1). Moreover, engineering on nanobio interface through zwitterionic molecules adjusts the in vivo behaviors of nanoplates for highly efficient magnetic resonance angiography with steady-state acquisition window, superhigh resolution in vascular details, and low toxicity. This study provides a powerful tool for sophisticated design of MRI contrast agents for diverse use in bioimaging applications.

スーパーコンピュータ「京」とNHMを用いた伊豆大島の豪雨の高解像度実験

スーパーコンピュータ「京」とNHMを用いた伊豆大島の豪雨の高解像度実験