Characterization of 3D coastal mesoscale structures and transports from multiplatform observations and a data reconstruction method

2021 ◽  
Author(s):  
Ivan Manso ◽  
Anna Rubio ◽  
Gabriel Jordà ◽  
Jeffrey Carpenter ◽  
Lucas Merckelbach ◽  
...  
Keyword(s):  
Particle Density ◽  
3D Structure ◽  
Hf Radar ◽  
Water Volume ◽  
Coastal Processes ◽  
Data Reconstruction ◽  
Reconstruction Method ◽  
Mode Water ◽  
Mesoscale Structures

<p>The role of coastal mesoscale variability in the modulation of surface along-shelf and cross-shelf exchanges in the SE Bay of Biscay has been demonstrated by several works, from land-based and satellite observations, including high resolution current fields from high-frequency (HF) radars. However, the characterization of physical processes and associated transports at subsurface levels from observations remains a challenge since observations are often too scarce to offer the required spatio-temporal resolution and coverage. In addition to the numerical modelling, the use of methods to reconstruct three-dimensional (3D) current fields from the combination of multiplatform data offers an alternative approach for the study of 3D properties of mesoscale coastal processes, and an improved background to explore bio-physical interactions. Studying the physical properties of coastal mesoscale structures at subsurface levels, where primary production and plankton concentration peak, is key to understand the coupling between physical and biological processes. In this work, we use a previously validated data-reconstruction method and different CMEMS products (coastal simulations, observations from HF radar, satellite, mooring) and glider data, to better characterize the 3D structure of a coastal mode-water eddy and its associated water volume transport. Different Lagrangian properties (maps of particle density, residence times, Lagrangian eddy kinetic energy) obtained at surface and subsurface levels provide a new insight into the water volume transports associated with the main coastal processes in the area.</p>

scholarly journals Three-Dimensional Characterization of a Coastal Mode-Water Eddy from Multiplatform Observations and a Data Reconstruction Method

2021 ◽  
Vol 13 (4) ◽  
pp. 674
Author(s):  
Ivan Manso-Narvarte ◽  
Anna Rubio ◽  
Gabriel Jordà ◽  
Jeffrey Carpenter ◽  
Lucas Merckelbach ◽  
...  
Keyword(s):  
Water Column ◽  
High Frequency ◽  
Three Dimensional ◽  
Joint Analysis ◽  
Water Volume ◽  
Data Reconstruction ◽  
Reconstruction Method ◽  
Mode Water ◽  
Near Surface ◽  
High Frequency Radar

Coastal mesoscale eddies are important oceanic structures partially responsible for regulating ocean-shelf exchanges. However, their description and characterization are challenging; observations are often too scarce for studying their physical properties and environmental impacts at the required spatio-temporal resolution. Therefore, models and data extrapolation methods are key tools for this purpose. Observations from high-frequency radar, one satellite and two gliders, are used here to better characterize the three-dimensional structure of a coastal mode-water eddy from a multiplatform approach in the southeastern Bay of Biscay in spring 2018. After the joint analysis of the observations, a three-dimensional data reconstruction method is applied to reconstruct the eddy current velocity field and estimate the associated water volume transport. The target eddy is detected by surface observations (high-frequency radar and satellite) for two weeks and presents similar dimensions and lifetimes as other eddies studied previously in the same location. However, this is the first time that the water column properties are also observed for this region, which depicts a mode-water eddy behavior, i.e., an uplift of the isopycnals in the near-surface and a downlift deeper in the water column. The reconstructed upper water column (1–100 m) eddy dynamics agree with the geostrophic dynamics observed by one of the gliders and result in cross-shelf inshore (offshore) volume transports between 0.04 (−0.01) and 0.15 (−0.11) Sv. The multiplatform data approach and the data reconstruction method are here highlighted as useful tools to characterize and three-dimensionally reconstruct coastal mesoscale processes in coastal areas.

Improvement in Precision, Accuracy, and Efficiency in Standardizing the Characterization of Granular Materials

2013 ◽  
Author(s):  
J. R. Tucker ◽  
L. J. Shadle ◽  
S. Benyahia ◽  
J. Mei ◽  
C. Guenther ◽  
...  
Keyword(s):  
Particle Size ◽  
Distribution Density ◽  
Particle Density ◽  
Solid Particles ◽  
Minimum Fluidization Velocity ◽  
Void Fractions ◽  
Multiphase Systems ◽  
Precision And Accuracy ◽  
Accuracy And Repeatability

Useful prediction of the kinematics, dynamics, and chemistry of a system relies on precision and accuracy in the quantification of component properties, operating mechanisms, and collected data. In an attempt to emphasize, rather than gloss over, the benefit of proper characterization to fundamental investigations of multiphase systems incorporating solid particles, a set of procedures were developed and implemented for the purpose of providing a revised methodology having the desirable attributes of reduced uncertainty, expanded relevance and detail, and higher throughput. Better, faster, cheaper characterization of multiphase systems result. Methodologies are presented to characterize particle size, shape, size distribution, density (particle, skeletal and bulk), minimum fluidization velocity, void fraction, particle porosity, and assignment within the Geldart Classification. A novel form of the Ergun equation was used to determine the bulk void fractions and particle density. Accuracy of properties-characterization methodology was validated on materials of known properties prior to testing materials of unknown properties. Several of the standard present-day techniques were scrutinized and improved upon where appropriate. Validity, accuracy, and repeatability were assessed for the procedures presented and deemed higher than present-day techniques. A database of over seventy materials has been developed to assist in model validation efforts and future designs.

scholarly journals Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control

2014 ◽  
Vol 207 (4) ◽  
pp. 463-480 ◽  
Author(s):  
Jonathan Bizarro ◽  
Christophe Charron ◽  
Séverine Boulon ◽  
Belinda Westman ◽  
Bérengère Pradet-Balade ◽  
...  
Keyword(s):  
Isotope Labeling ◽  
Core Protein ◽  
3D Structure ◽  
Assembly Mechanism ◽  
Core Proteins ◽  
Assembly Factors ◽  
Assembly Factor

In vitro, assembly of box C/D small nucleolar ribonucleoproteins (snoRNPs) involves the sequential recruitment of core proteins to snoRNAs. In vivo, however, assembly factors are required (NUFIP, BCD1, and the HSP90–R2TP complex), and it is unknown whether a similar sequential scheme applies. In this paper, we describe systematic quantitative stable isotope labeling by amino acids in cell culture proteomic experiments and the crystal structure of the core protein Snu13p/15.5K bound to a fragment of the assembly factor Rsa1p/NUFIP. This revealed several unexpected features: (a) the existence of a protein-only pre-snoRNP complex containing five assembly factors and two core proteins, 15.5K and Nop58; (b) the characterization of ZNHIT3, which is present in the protein-only complex but gets released upon binding to C/D snoRNAs; (c) the dynamics of the R2TP complex, which appears to load/unload RuvBL AAA+ adenosine triphosphatase from pre-snoRNPs; and (d) a potential mechanism for preventing premature activation of snoRNP catalytic activity. These data provide a framework for understanding the assembly of box C/D snoRNPs.

scholarly journals Characterization of a porin channel in the endosymbiont of the trypanosomatid protozoan Crithidia deanei

Microbiology ◽  
2011 ◽  
Vol 157 (10) ◽  
pp. 2818-2830 ◽  
Author(s):  
Iamara da Silva Andrade ◽  
João Lídio Vianez-Júnior ◽  
Carolina Lage Goulart ◽  
Fabrice Homblé ◽  
Jean-Marie Ruysschaert ◽  
...  
Keyword(s):  
3D Structure ◽  
Symbiotic Bacterium ◽  
Gram Negative Bacteria ◽  
Genome Database ◽  
Gram Negative ◽  
Secondary Structure Analysis ◽  
Electrophysiological Measurements ◽  
Mutualistic Relationship ◽  
Obligate Intracellular Bacteria

Crithidia deanei is a trypanosomatid protozoan that harbours a symbiotic bacterium. The partners maintain a mutualistic relationship, thus constituting an excellent model for studying metabolic exchanges between the host and the symbiont, the origin of organelles and cellular evolution. According to molecular analysis, symbionts of different trypanosomatid species share high identity and descend from a common ancestor, a β-proteobacterium of the genus Bordetella. The endosymbiont is surrounded by two membranes, like Gram-negative bacteria, but its envelope presents special features, since phosphatidylcholine is a major membrane component and the peptidoglycan layer is highly reduced, as described in other obligate intracellular bacteria. Like the process that generated mitochondria and plastids, the endosymbiosis in trypanosomatids depends on pathways that facilitate the intensive metabolic exchanges between the bacterium and the host protozoan. A search of the annotated symbiont genome database identified one sequence with identity to porin-encoding genes of the genus Bordetella. Considering that the symbiont outer membrane has a great accessibility to cytoplasm host factors, it was important to characterize this single porin-like protein using biochemical, molecular, computational and ultrastructural approaches. Antiserum against the recombinant porin-like molecule revealed that it is mainly located in the symbiont envelope. Secondary structure analysis and comparative modelling predicted the protein 3D structure as an 18-domain β-barrel, which is consistent with porin channels. Electrophysiological measurements showed that the porin displays a slight preference for cations over anions. Taken together, the data presented herein suggest that the C. deanei endosymbiont porin is phylogenetically and structurally similar to those described in Gram-negative bacteria, representing a diffusion channel that might contribute to the exchange of nutrients and metabolic precursors between the symbiont and its host cell.

scholarly journals Identification and Characterization of a Novel Thermostable and Salt-Tolerant β-1,3 Xylanase from Flammeovirga pacifica Strain WPAGA1

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1287
Author(s):  
Zhiwei Yi ◽  
Zhengwen Cai ◽  
Bo Zeng ◽  
Runying Zeng ◽  
Guangya Zhang
Keyword(s):  
Thermal Stability ◽  
Salt Tolerance ◽  
3D Structure ◽  
Catalytic Efficiency ◽  
Dynamics Simulation ◽  
Carbohydrate Binding ◽  
Salt Tolerant ◽  
Excellent Thermal Stability ◽  
Moderately Thermophilic

β-1,3 xylanase is an important enzyme in the biorefinery process for some algae. The discovery and characterization of new β-1,3 xylanase is a hot research topic. In this paper, a novel β-1,3 xylanase (Xyl88) is revealed from the annotated genome of Flammeovirga pacifica strain WPAGA1. Bioinformatic analysis shows that Xyl88 belongs to the glycoside hydrolase 26 (GH26) with a suspected CBM (carbohydrate-binding module) sequence. The activity of rXyl88 is 75% of the highest enzyme activity (1.5 mol/L NaCl) in 3 mol/L NaCl buffer, which suggests good salt tolerance of rXy188. The optimum reaction temperature in the buffer without NaCl and with 1.5 mol/L NaCl is 45 °C and 55 °C, respectively. Notably, the catalytic efficiency of rXyl88 (kcat/Km) is approximately 20 higher than that of the thermophilic β-1,3 xylanase that has the highest catalytic efficiency. Xyl88 in this study becomes the most efficient enzyme ever found, and it is also the first reported moderately thermophilic and salt-tolerant β-1,3 xylanase. Results of molecular dynamics simulation further prove the excellent thermal stability of Xyl88. Moreover, according to the predicted 3D structure of the Xyl88, the surface of the enzyme is distributed with more negative charges, which is related to its salt tolerance, and significantly more hydrogen bonds and Van der Waals force between the intramolecular residues, which is related to its thermal stability.

scholarly journals Preparation and Characterization of Perforated SERS Active Array for Particle Trapping and Sensitive Molecular Analysis

Biosensors ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 93 ◽  
Author(s):  
István Rigó ◽  
Miklós Veres ◽  
Tamás Váczi ◽  
Eszter Holczer ◽  
Orsolya Hakkel ◽  
...  
Keyword(s):  
Molecular Analysis ◽  
Silicon Surface ◽  
3D Structure ◽  
Raman Spectroscopic ◽  
Cell Trapping ◽  
Highly Sensitive ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Flow Through

A gold-coated array of flow-through inverse pyramids applicable as substrate for entrapment and immobilization of micro-objects and for surface enhanced Raman spectroscopic measurements was fabricated using bulk micromachining techniques from silicon. Surface morphology, optical reflectance, immobilization properties, and surface enhanced Raman amplification of the array were modelled and characterized. It was found that the special perforated periodic 3D structure can be used for parallel particle and cell trapping and highly sensitive molecular analysis of the immobilized objects.

Gravity anomaly reconstruction based on nonequispaced Fourier transform

Geophysics ◽  
2019 ◽  
Vol 84 (6) ◽  
pp. G83-G92
Author(s):  
Ya Xu ◽  
Fangzhou Nan ◽  
Weiping Cao ◽  
Song Huang ◽  
Tianyao Hao
Keyword(s):  
Fourier Transform ◽  
Compressed Sensing ◽  
Gravity Data ◽  
Signal Reconstruction ◽  
Gaussian Function ◽  
Reconstruction Algorithm ◽  
Data Reconstruction ◽  
Reconstruction Method ◽  
Grid Data ◽  
2D Data

Irregular sampled gravity data are often interpolated into regular grid data for convenience of data processing and interpretation. The compressed sensing theory provides a signal reconstruction method that can recover a sparse signal from far fewer samples. We have introduced a gravity data reconstruction method based on the nonequispaced Fourier transform (NFT) in the framework of compressed sensing theory. We have developed a sparsity analysis and a reconstruction algorithm with an iterative cooling thresholding method and applied to the gravity data of the Bishop model. For 2D data reconstruction, we use two methods to build the weighting factors: the Gaussian function and the Voronoi method. Both have good reconstruction results from the 2D data tests. The 2D reconstruction tests from different sampling rates and comparison with the minimum curvature and the kriging methods indicate that the reconstruction method based on the NFT has a good reconstruction result even with few sampling data.

scholarly journals Multi-Perspective Ultrasound Imaging Technology of the Breast with Cylindrical Motion of Linear Arrays

2019 ◽  
Vol 9 (3) ◽  
pp. 419 ◽  
Author(s):  
Chang Liu ◽  
Binzhen Zhang ◽  
Chenyang Xue ◽  
Wendong Zhang ◽  
Guojun Zhang ◽  
...  
Keyword(s):  
Chest Wall ◽  
Ultrasound Imaging ◽  
Ultrasonic Transducer ◽  
Absolute Error ◽  
Data Reconstruction ◽  
Reconstruction Method ◽  
Water Tank ◽  
Volume Data ◽  
Imaging Technology ◽  
Linear Arrays

In this paper, we propose a multi-perspective ultrasound imaging technology with the cylindrical motion of four piezoelectric micromachined ultrasonic transducer (PMUT) rotatable linear arrays. The transducer is configured in a cross shape vertically on the circle with the length of the arrays parallel to the z axis, roughly perpendicular to the chest wall. The transducers surrounded the breast, which achieves non-invasive detection. The electric rotary table drives the PMUT to perform cylindrical scanning. A breast model with a 2 cm mass in the center and six 1-cm superficial masses were used for the experimental analysis. The detection was carried out in a water tank and the working temperature was constant at 32 °C. The breast volume data were acquired by rotating the probe 90° with a 2° interval, which were 256 × 180 A-scan lines. The optimized segmented dynamic focusing technology was used to improve the image quality and data reconstruction was performed. A total of 256 A-scan lines at a constant angle were recombined and 180 A-scan lines were recombined according to the nth element as a dataset, respectively. Combined with ultrasound imaging algorithms, multi-perspective ultrasound imaging was realized including vertical slices, horizontal slices and 3D imaging. The seven masses were detected and the absolute error of the size was approximately 1 mm where even the image of the injection pinhole could be seen. Furthermore, the breast boundary could be seen clearly from the chest wall to the nipple, so the location of the masses was easier to confirm. Therefore, the validity and feasibility of the data reconstruction method and imaging algorithm were verified. It will be beneficial for doctors to be able to comprehensively observe the pathological tissue.

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