Insights from the IronTract challenge: optimal methods for mapping brain pathways from multi-shell diffusion MRI

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accuracy. Over a period of two years, we have engaged the dMRI community in the IronTract Challenge, which aims to answer this question by leveraging a unique dataset. Macaque brains that have received both tracer injections and ex vivo dMRI at high spatial and angular resolution allow a comprehensive, quantitative assessment of tractography accuracy on state-of-the-art dMRI acquisition schemes. We find that, when analysis methods are carefully optimized, the HCP scheme can achieve similar accuracy as a more time-consuming, Cartesian-grid scheme. Importantly, we show that simple pre- and post-processing strategies can improve the accuracy and robustness of many tractography methods. Finally, we find that fiber configurations that go beyond crossing (e.g., fanning, branching) are the most challenging for tractography. The IronTract Challenge remains open and we hope that it can serve as a valuable validation tool for both users and developers of dMRI analysis methods.

The hindcast of recent tsunamis in Northern Pacific

Three earthquakes occurred in the North Pacific in 2020, causing observable tsunamis. The tsunamis were not devastating. Numerical modelling of tsunami propagation was performed to reproduce operational forecasting (retrospective analysis) of waveforms at deep-water stations. Direct calculation of tsunami using USGS finite-fault source data on GPU was carried out. The leap-frog (Arakawa staggered grid) scheme calculation over the Pacific Ocean on a regular grid with a spatial step of 0.5 arc minutes of 1440 min (1 day) tsunami propagation was performed in approximately 90 min of computer time. With use of a hybrid cluster with several GPU accelerators and proper optimization of the simulation algorithm, this time can be reduced by tens of times. Consequently, the time for estimating the transfer function will be comparable to the travel time of a tsunami to the stations, where the forecasts data is. It will make possible to forecast the shape of a tsunami at any point with a lead time enough to decide for tsunami alert at sites where a tsunami poses a real danger. The calculation results are in good agreement with the real data of deep-ocean measurements. The quality of the forecast is comparable to the quality of calculations by other methods.

Exploration of grid scheme for Frisch-grid ionization chamber

A new Frisch-grid ionization chamber has been built to explore the appropriate choice of Frisch-grid. Detailed studies of the relationship between grid geometries and detector performance have been performed with an $$^{241}$$ 241 Am source. This paper describes and compares the energy resolution of ionization chambers with parallel-wire and mesh grids of different grid parameters. Some specific recommendations for grid selection are provided based on the data currently available. To obtain optimal energy resolution, the operating voltage of the chamber must satisfy the condition of minimum electron collection on the grid with distinct geometries and parameters, respectively. Since there is no established theory applicable to both types of grids, we have devised a careful simulation procedure incorporating the COMSOL and Garfield++ codes to search for the conditions of the minimum electron collection on the grid. The simulation results fit the experimental data well, suggesting that this simulation method successfully predicts the suitable voltage setting when using a mesh grid or parallel wires grid as the shielding electrode.

The Momentum Conserving Scheme Implementation for Simulating Dambreak Flow in a Channel with Various Contractions

Rapid flow downstream due to dambreak has a detrimental effect on the surrounding environment or, more dangerously, can be life-threatening. From a practical point of view, these flows are important to studies due to the limited dambreak real case data. This paper discusses the numerical modelling of the dambreak flow through a channel with three different contractions. Our goal here is to investigate the performance of a numerical model for solving the Saint-Venant equations using a momentum conserving staggered grid scheme (MCS). The scheme is the conservative formulation of the governing equations. Flows across channels of various widths and depths have been successfully simulated using a version of this scheme. In this work, we extend our previous work by simulating dambreak flow in a wave tank through several forms of contraction; trapezoidal and triangular. Our simulation results show good agreement with the experimental data in the literature. This assessment shows the merit of the scheme, which is suitable for dambreak flows in channels of varying width.

A grid-based database on vascular plant distribution in the Meshchersky National Park, Ryazan Oblast, Russia

Ryazan Oblast, situated in the central part of European Russia, has a long tradition of biodiversity research. Large distributional, ecological and phenological data on various taxonomic groups are available from this territory, mainly in the form of paper publications items, undigitised museum collections and archival sources. The purpose of this dataset is to deliver floristic materials, collected by the authors in the Meshchera Lowlands in the form of GBIF-mediated electronic data, to a wider audience. The dataset covers wild tracheophytes (native species, naturalised aliens and casuals) of the Meshchersky National Park. In 2020, it was used for the production of grid maps in "Flora of the Meschchersky National Park: checklist and atlas". The dataset contains 14,476 grid records of 817 taxa (806 species and hybrids, ten species aggregates and one genus). Most of the records (82.4%) were made in the field by A.V. Shcherbakov, M.V. Kazakova, N.V. Lyubeznova and A.D. Pastushenko in 2017 and 2018. The dataset includes only one occurrence per species per grid square. Georeferences are based on the WGS84 grid scheme with 55 squares measuring ca. 25 km2 (2.5' lat. × 5' long.). Each occurrence is linked to the corresponding grid square centroid; therefore, actual coordinates, habitat details and voucher information are unavailable. As of September 2021, the dataset on the flora of the Meshchersky National Park represents the second largest dataset on the biodiversity of Ryazan Oblast, Russia, published in GBIF.

Simulasi Numerik Persamaan Gelombang Air Dangkal untuk Kasus Bendungan Bobol

Technological failure and natural disasters that caused the dam-break resulted in huge losses, both material loss and loss of life. The mathematical model for the dam-break can use the shallow water equation. In this paper, modeling the dam-break in two dimensions is solved by using the finite volume method with a stagerred-grid scheme. The staggered-grid scheme produces more accurate and robust when compared to the Lax-Friedrics scheme. The stability of the water waves on the part of the damaged dam wall is also well preserved using a staggered-grid scheme. Modeling a dam-break with real bathymetric data will be a challenge for further research, because it involves a more complex geometry.

Computational Modeling of Flow Characteristics in Three Products Hydrocyclone Screen

Three products hydrocyclone screen (TPHS) can be considered as the combination of a conventional hydrocyclone and a cylindrical screen. In this device, particles are separated based on size under the centrifugal classification coupling screening effect. The objective of this work is to explore the characteristics of fluid flow in TPHS using the computational fluid dynamics (CFD) simulation. The 2 million grid scheme, volume fraction model, and linear pressure–strain Reynolds stress model were utilized to generate the economical grid-independence solution. The pressure profile reveals that the distribution of static pressure was axisymmetric, and its value was reduced with the increasing axial depth. The maximum and minimum were located near the tangential inflection point of the feed inlet and the outlets, respectively. However, local asymmetry was created by the left tangential inlet and the right screen underflow outlet. Furthermore, at the same axial height, the static pressure gradually decreased along the wall to the center. Near the cylindrical screen, the pressure difference between the inside and the outside cylindrical screen dropped from positive to negative as the axial depth increased from −35 to −185 mm. Besides, TPHS shows similar distributions of turbulence intensity I, turbulence kinetic energy k, and turbulence dissipation rate ε; i.e., the values fell with the decrease in axial height. Meanwhile, from high to low, the pressure values are distributed in the feed chamber, the cylindrical screen, and conical vessel; the value inside the screen was higher than the outer value.

Flora of Vladimir Oblast, Russia: an updated grid dataset (1867–2020)

The dataset covers wild tracheophytes (native species, naturalised aliens and casuals) of Vladimir Oblast, Russia. It includes only one occurrence per species per grid square, thereby recently confirmed earlier records are not duplicated. Georeferences are based on the WGS84 grid scheme with 342 squares with areas ranging from 94.7 km2 in the northernmost part to 98.2 km2 on the southern boundary (5′ lat. × 10′ long.). Each occurrence is linked to the corresponding grid square centroid, therefore actual coordinates, habitat details and voucher information are unavailable. In late 2011, the earlier version of the dataset was used for the production of grid maps in the standard "Flora of Vladimir Oblast: checklist and atlas". Additional records, obtained during field excursions of 2012 and 2013, were fully included in the "Flora of Vladimir Oblast: grid data analysis". The stable version of the dataset with 123,054 grid records (as of 1867–2013) was published in GBIF in 2017. Data obtained in the field during 2014–2020, as well as those extracted from recently published sources, were digitised, structured and finally published in GBIF in April 2021. The last update added 7,000 new grid records. Currently, "Flora of Vladimir Oblast, Russia: an updated grid dataset (1867–2020)" contains 130,054 unique occurrences of 1,465 vascular plant taxa (species, hybrids, species aggregates) from Vladimir Oblast and tiny parts of the adjacent areas. The average number of grid records has grown over the seven years from 363 to 380 species. The grid occurrences are largely based on the field studies by the author, performed during 1999–2020 (121,737 records), as well as on data extracted from the relevant literature, unpublished sources, herbarium collections and citizen science projects (8,317 records). The taxonomic backbone of the occurrence grid dataset follows the accompanying checklist dataset to ensure correct cross-linking of the names. As of April 2021, the dataset on the Vladimir Oblast flora represents the fourth largest dataset on vascular plants of Russia published in GBIF.