In contrast to artificial intelligence and machine learning approaches, KEGG (https://www.kegg.jp) has relied on human intelligence to develop “models” of biological systems, especially in the form ...of KEGG pathway maps that are manually created by capturing knowledge from published literature. The KEGG models can then be used in biological big data analysis, for example, for uncovering systemic functions of an organism hidden in its genome sequence through the simple procedure of KEGG mapping. Here we present an updated version of KEGG Mapper, a suite of KEGG mapping tools reported previously (Kanehisa and Sato, Protein Sci 2020; 29:28–35), together with the new versions of the KEGG pathway map viewer and the BRITE hierarchy viewer. Significant enhancements have been made for BRITE mapping, where the mapping result can be examined by manipulation of hierarchical trees, such as pruning and zooming. The tree manipulation feature has also been implemented in the taxonomy mapping tool for linking KO (KEGG Orthology) groups and modules to phenotypes.
KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database ...entry) is identified by the KEGG identifier (kid), which generally takes the form of a prefix followed by a five-digit number, and can be retrieved by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/kid, /brite/kid and /genome/kid, respectively, in the URL. Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree. Multiple taxonomy files are generated for classification of KEGG organisms and viruses, and the Brite hierarchy viewer is used for taxonomy mapping, a variant of Brite mapping in the new KEGG Mapper suite. The taxonomy mapping enables analysis of, for example, how functional links of genes in the pathway and physical links of genes on the chromosome are conserved among organism groups.
Abstract
Realistic mesoscale model simulations using the Weather Research and Forecasting (WRF) Model and idealized dry simulations were used to study the mechanisms responsible for the formation and ...evolution of wide cold-frontal rainbands (WCFRs) associated with a wintertime cyclone that moved onto the Washington coast. The WRF simulation reproduced observed characteristics of three successively formed WCFRs, including their spacing and movement as well as the timing of the formation of two WCFRs behind the first. Sensitivity experiments showed that melting-induced cooling in the stratiform precipitation area behind the surface cold front was essential for the formation of the first and second WCFRs, whereas the third WCFR was formed by the release of potential instability within an ascent forced by upper-level frontogenesis. Enhanced frontal updrafts responsible for the first and second WCFRs were created by a superposition of a broad updraft caused by frontal dynamics and upward-propagating gravity waves generated by the melting-induced cooling. The dry simulations forced by specified cooling revealed specific mechanisms for the wave generation and the evolution of the first and second WCFRs. The gravity waves were generated at the intersection of the low-level frontal zone and the melting layer, where strong vertical shear of the cross-front wind and upshear-sloped cooling by melting cooperatively enhanced the wave generation. The formation of the second WCFR behind the first and subsequent dissipation of these WCFRs was attributed to the evolution of a wave pattern associated with the evolution of cross-front flow above the frontal zone.
A central-moments-based lattice Boltzmann model for large-eddy simulation of neutrally-stratified turbulent flows is described. Through comparative simulations of the airflow within and above a ...homogeneous plant canopy, the performance of the model is evaluated with respect to a conventional large-eddy-simulation model based on the incompressible Navier–Stokes equations. Simulated turbulence statistics, such as the mean velocity, velocity variances, velocity skewness, and power spectra, are shown to be almost identical between the two models. The spatial structure of coherent eddies and their maintenance processes are also confirmed to be properly represented by the lattice Boltzmann method through analysis of the turbulence kinetic energy budget and spatial two-point correlation functions. Using the simulated results, the energetics of the streamwise-elongated streaky structures commonly observed over vegetation and urban canopies are examined. While the short-wavelength components of the shear-generated streamwise kinetic energy are redirected rapidly by pressure to the lateral and vertical velocity components, long-wavelength energy tends to remain in the streamwise velocity component, which is dissipated in relatively slower processes. Consequently, the streaky structures persist in the streamwise velocity component.
A double-distribution-function lattice Boltzmann model for large-eddy simulations of a passive scalar field in a neutrally stratified turbulent flow is described. In simulations of the scalar ...turbulence within and above a homogeneous plant canopy, the model’s performance is found to be comparable with that of a conventional large-eddy simulation model based on the Navier–Stokes equations and a scalar advection–diffusion equation in terms of the mean turbulence statistics, budgets of the second moments, power spectra, and spatial two-point correlation functions. For a top-down scalar, for which the plant canopy serves as a distributed sink, the variance and flux of the scalar near the canopy top are predominantly determined by sweep motions originating far above the canopy. These sweep motions, which have spatial scales much larger than the canopy height, penetrate deep inside the canopy and cause scalar sweep events near the canopy floor. By contrast, scalar ejection events near the canopy floor are induced by coherent eddies generated near the canopy top. The generation of such eddies is triggered by the downward approach of massive sweep motions to existing wide regions of weak ejective motions from inside to above the canopy. The non-local transport of scalars from above the canopy to the canopy floor, and vice versa, is driven by these eddies of different origins. Such non-local transport has significant implications for the scalar variance and flux budgets within and above the canopy, as well as the transport of scalars emitted from the underlying soils to the atmosphere.
The effects of variations in low-level ambient vertical shear and horizontal shear on the alongfront variability of narrow cold frontal rainbands (NCFRs) that propagate into neutral and slightly ...unstable environments are investigated through a series of idealized cloud-resolving simulations. In cases initialized with slightly unstable sounding and weak ambient cross-frontal vertical shears, core-gap structures of precipitation along NCFRs occur that are associated with wavelike disturbances that derive their kinetic energy mainly from the mean local vertical shear and buoyancy. However, over a wide range of environmental conditions, core-gap structures of precipitation occur because of the development of a horizontal shear instability (HSI) wave along the NCFRs. The growth rate and amplitude of the HSI wave decrease significantly as the vertical shear of the ambient cross-front wind is reduced. These decreases are a consequence of the enhancement of the low-level local vertical shear immediately behind the leading edge. The strong local vertical shear acts to damp the vorticity edge wave on the cold air side of the shear zone, thereby suppressing the growth of the HSI wave through the interaction of the two vorticity edge waves. It is also noted that the initial wavelength of the HSI wave increases markedly with increasing horizontal shear. The local vertical shear around the leading edge is shown to damp long HSI waves more strongly than short waves, and the horizontal shear dependency of the wavelength is explained by the decrease in the magnitude of the vertical shear relative to that of the horizontal shear.
Abstract
Prominent cirrus cloud banding occurred episodically within a northern cirrus canopy of Typhoon Talim (2017) during its recurvature. The generation mechanisms of the cirrus bands and low ...static-stability layers that support the bands are investigated using a numerical simulation with the Advanced Research Weather Research and Forecasting Model. Inspection of model output reveals that thin layers of near-neutral to weakly unstable static stability are persistently present in the upper and lower parts of the upper-level outflow, and shallow convection aligned along the vertical shear vector is prevalent in these layers. The cirrus banding occurs as the lowered outflow from the weakening storm ascends slantwise over a midlatitude baroclinic zone, and updrafts of the preexisting shallow convection in the upper part of the outflow layer become saturated. It is shown that the strong outflow resulting from violation of gradient-wind balance in the core region, by itself, creates the low static-stability layers. Analyses of potential temperature and static stability budgets show that the low static-stability layers are created mainly by the differential radial advection of radial thermal gradients on the vertical edges of the outflow. The radial thermal gradients occur in response to the outward air parcel acceleration in the core region and deceleration in the outer region, which, by inducing compensating vertical mass transport into and out of the outflow, act to tilt the isentropes within the shear layers. The effects of environmental flow and cloud radiative forcing on the cirrus banding are also addressed.
Topology of mixed hypersurfaces of cyclic type INABA, Kazumasa; KAWASHIMA, Masayuki; OKA, Mutsuo
Journal of the Mathematical Society of Japan,
1/2018, Volume:
70, Issue:
1
Journal Article
Abstract
Sea-effect snowstorms generated over the Sea of Japan produce consistent and often heavy snowfall throughout the winter season, impacting downstream communities in northern and central ...Japan. Here, we use observations and Weather Research and Forecasting (WRF) Model simulations to examine the precipitation distribution produced by transverse-mode sea-effect snowbands that interacted with the mountainous terrain circumscribing Ishikari Bay, Hokkaido Island, Japan, on 12 January 2014. The bands observed here were horizontal convective rolls aligned normal to the mean flow and were ~10 km wide and up to ~100 km long. The bands approached Ishikari Bay at intervals of ~10–16 min, intensifying as they progressed through a quasi-stationary, elongated enhancement region that paralleled the Shakotan Peninsula and extended into the Ishikari plain. Hydrometeor advection, through an ascent region over the northeast slope of the Shakotan Peninsula, and along clockwise-turning trajectories steered by the boundary layer directional shear, contributed to sustained precipitation enhancement along a curve in the elongated enhancement region near the entrance to Ishikari Bay. Downstream, orographic flow deflection by the coastal mountains, likely accentuated by thermal and roughness gradients along the Shakotan Peninsula’s shoreline, produced convergence and ascent along the elongated enhancement region. This study demonstrates the impact of downstream topography on sea-effect snowstorms and has implications for improving the prediction of snowfall in this and other lake- and sea-effect regions.
Bipolar segmental clavicle fractures are simultaneous clavicle fractures of both proximal and distal ends. Few case reports describing these fractures have been published, and the management of these ...injuries have remained controversial. Non-operative treatment is likely to result in poor shoulder function due to the instability of the fracture in patients with high physical demands. In contrast, surgical treatment with fixation of both proximal and distal ends of the clavicle possibly may cause life-threatening complications. We present a 74-year old female farmer who had injured her left shoulder and was diagnosed with a bipolar segmental clavicle fracture. Taking the fracture mechanism into consideration, we surgically treated only the distal end of the clavicle fracture with a locking plate. The proximal end of the clavicle fracture was treated without surgical intervention. Both fracture sites achieved bony union after four months and she returned to her activities as a farmer. Quick DASH score was 5.0 with excellent results at three years after operation.
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