scholarly journals Advances in understanding the evolution of fungal genome architecture

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 776 ◽  
Author(s):  
Shelby J. Priest ◽  
Vikas Yadav ◽  
Joseph Heitman
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Rapid Evolution ◽  
Genomic Diversity ◽  
Fungal Genome ◽  
Small Scale ◽  
Genomic Changes ◽  
Wide Range ◽  
Domains Of Life ◽  
Fungal Genomes

Diversity within the fungal kingdom is evident from the wide range of morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in long-read sequencing, coupled with the increasing efficiency and decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity and genomic evolution. These studies revealed the presence of both small-scale and large-scale genomic changes. In fungi, research has recently focused on many small-scale changes, such as how hypermutation and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than others. High-throughput sequencing of a diverse set of fungal genomes has also illuminated the frequency, mechanisms, and impacts of large-scale changes, which include chromosome structural variation and changes in chromosome number, such as aneuploidy, polyploidy, and the presence of supernumerary chromosomes. The studies discussed herein have provided great insight into how the architecture of the fungal genome varies within species and across the kingdom and how modern fungi may have evolved from the last common fungal ancestor and might also pave the way for understanding how genomic diversity has evolved in all domains of life.

Coupled Thermo-Hydro-Geochemical Models of Engineered Barrier Systems: The Febex Project

2000 ◽  
Vol 663 ◽  
Author(s):  
J. Samper ◽  
R. Juncosa ◽  
V. Navarro ◽  
J. Delgado ◽  
L. Montenegro ◽  
...  
Keyword(s):  
Large Scale ◽  
Reference Model ◽  
Numerical Models ◽  
Full Scale ◽  
Small Scale ◽  
Model Parameters ◽  
In Situ Test ◽  
Wide Range ◽  
Engineered Barrier

ABSTRACTFEBEX (Full-scale Engineered Barrier EXperiment) is a demonstration and research project dealing with the bentonite engineered barrier designed for sealing and containment of waste in a high level radioactive waste repository (HLWR). It includes two main experiments: an situ full-scale test performed at Grimsel (GTS) and a mock-up test operating since February 1997 at CIEMAT facilities in Madrid (Spain) [1,2,3]. One of the objectives of FEBEX is the development and testing of conceptual and numerical models for the thermal, hydrodynamic, and geochemical (THG) processes expected to take place in engineered clay barriers. A significant improvement in coupled THG modeling of the clay barrier has been achieved both in terms of a better understanding of THG processes and more sophisticated THG computer codes. The ability of these models to reproduce the observed THG patterns in a wide range of THG conditions enhances the confidence in their prediction capabilities. Numerical THG models of heating and hydration experiments performed on small-scale lab cells provide excellent results for temperatures, water inflow and final water content in the cells [3]. Calculated concentrations at the end of the experiments reproduce most of the patterns of measured data. In general, the fit of concentrations of dissolved species is better than that of exchanged cations. These models were later used to simulate the evolution of the large-scale experiments (in situ and mock-up). Some thermo-hydrodynamic hypotheses and bentonite parameters were slightly revised during TH calibration of the mock-up test. The results of the reference model reproduce simultaneously the observed water inflows and bentonite temperatures and relative humidities. Although the model is highly sensitive to one-at-a-time variations in model parameters, the possibility of parameter combinations leading to similar fits cannot be precluded. The TH model of the “in situ” test is based on the same bentonite TH parameters and assumptions as for the “mock-up” test. Granite parameters were slightly modified during the calibration process in order to reproduce the observed thermal and hydrodynamic evolution. The reference model captures properly relative humidities and temperatures in the bentonite [3]. It also reproduces the observed spatial distribution of water pressures and temperatures in the granite. Once calibrated the TH aspects of the model, predictions of the THG evolution of both tests were performed. Data from the dismantling of the in situ test, which is planned for the summer of 2001, will provide a unique opportunity to test and validate current THG models of the EBS.

Buoyancy effects on large-scale motions in convective atmospheric boundary layers: implications for modulation of near-wall processes

2018 ◽  
Vol 856 ◽  
pp. 135-168 ◽  
Author(s):  
S. T. Salesky ◽  
W. Anderson
Keyword(s):  
Boundary Layer ◽  
Velocity Field ◽  
Boundary Layers ◽  
Vertical Velocity ◽  
Amplitude Modulation ◽  
Large Scale ◽  
Streamwise Velocity ◽  
Small Scale ◽  
Convective Conditions ◽  
Wide Range

A number of recent studies have demonstrated the existence of so-called large- and very-large-scale motions (LSM, VLSM) that occur in the logarithmic region of inertia-dominated wall-bounded turbulent flows. These regions exhibit significant streamwise coherence, and have been shown to modulate the amplitude and frequency of small-scale inner-layer fluctuations in smooth-wall turbulent boundary layers. In contrast, the extent to which analogous modulation occurs in inertia-dominated flows subjected to convective thermal stratification (low Richardson number) and Coriolis forcing (low Rossby number), has not been considered. And yet, these parameter values encompass a wide range of important environmental flows. In this article, we present evidence of amplitude modulation (AM) phenomena in the unstably stratified (i.e. convective) atmospheric boundary layer, and link changes in AM to changes in the topology of coherent structures with increasing instability. We perform a suite of large eddy simulations spanning weakly ($-z_{i}/L=3.1$) to highly convective ($-z_{i}/L=1082$) conditions (where$-z_{i}/L$is the bulk stability parameter formed from the boundary-layer depth$z_{i}$and the Obukhov length $L$) to investigate how AM is affected by buoyancy. Results demonstrate that as unstable stratification increases, the inclination angle of surface layer structures (as determined from the two-point correlation of streamwise velocity) increases from$\unicode[STIX]{x1D6FE}\approx 15^{\circ }$for weakly convective conditions to nearly vertical for highly convective conditions. As$-z_{i}/L$increases, LSMs in the streamwise velocity field transition from long, linear updrafts (or horizontal convective rolls) to open cellular patterns, analogous to turbulent Rayleigh–Bénard convection. These changes in the instantaneous velocity field are accompanied by a shift in the outer peak in the streamwise and vertical velocity spectra to smaller dimensionless wavelengths until the energy is concentrated at a single peak. The decoupling procedure proposed by Mathiset al.(J. Fluid Mech., vol. 628, 2009a, pp. 311–337) is used to investigate the extent to which amplitude modulation of small-scale turbulence occurs due to large-scale streamwise and vertical velocity fluctuations. As the spatial attributes of flow structures change from streamwise to vertically dominated, modulation by the large-scale streamwise velocity decreases monotonically. However, the modulating influence of the large-scale vertical velocity remains significant across the stability range considered. We report, finally, that amplitude modulation correlations are insensitive to the computational mesh resolution for flows forced by shear, buoyancy and Coriolis accelerations.

scholarly journals Self-Supervised Pre-Training of Transformers for Satellite Image Time Series Classification

2020 ◽  
Author(s):  
Yuan Yuan ◽  
Lei Lin
Keyword(s):  
Time Series ◽  
Deep Learning ◽  
Large Scale ◽  
Temporal Structure ◽  
Satellite Image ◽  
Fine Tuning ◽  
Small Scale ◽  
Model Parameters ◽  
Learning Approaches ◽  
Wide Range

Satellite image time series (SITS) classification is a major research topic in remote sensing and is relevant for a wide range of applications. Deep learning approaches have been commonly employed for SITS classification and have provided state-of-the-art performance. However, deep learning methods suffer from overfitting when labeled data is scarce. To address this problem, we propose a novel self-supervised pre-training scheme to initialize a Transformer-based network by utilizing large-scale unlabeled data. In detail, the model is asked to predict randomly contaminated observations given an entire time series of a pixel. The main idea of our proposal is to leverage the inherent temporal structure of satellite time series to learn general-purpose spectral-temporal representations related to land cover semantics. Once pre-training is completed, the pre-trained network can be further adapted to various SITS classification tasks by fine-tuning all the model parameters on small-scale task-related labeled data. In this way, the general knowledge and representations about SITS can be transferred to a label-scarce task, thereby improving the generalization performance of the model as well as reducing the risk of overfitting. Comprehensive experiments have been carried out on three benchmark datasets over large study areas. Experimental results demonstrate the effectiveness of the proposed method, leading to a classification accuracy increment up to 1.91% to 6.69%. <div><b>This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible.</b></div>

scholarly journals Physical Transport Processes that Affect the Distribution of Oil in the Gulf of Mexico: Observations and Modeling

Oceanography ◽  
2021 ◽  
Vol 34 (1) ◽  
pp. 58-75
Author(s):  
Michel Boufadel ◽  
◽  
Annalisa Bracco ◽  
Eric Chassignet ◽  
Shuyi Chen ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Physical Environment ◽  
Large Scale ◽  
Transport Processes ◽  
Small Scale ◽  
Surface Mixed Layer ◽  
Physical Processes ◽  
Mixing Processes ◽  
Near Surface ◽  
Wide Range

Physical transport processes such as the circulation and mixing of waters largely determine the spatial distribution of materials in the ocean. They also establish the physical environment within which biogeochemical and other processes transform materials, including naturally occurring nutrients and human-made contaminants that may sustain or harm the region’s living resources. Thus, understanding and modeling the transport and distribution of materials provides a crucial substrate for determining the effects of biological, geological, and chemical processes. The wide range of scales in which these physical processes operate includes microscale droplets and bubbles; small-scale turbulence in buoyant plumes and the near-surface “mixed” layer; submesoscale fronts, convergent and divergent flows, and small eddies; larger mesoscale quasi-geostrophic eddies; and the overall large-scale circulation of the Gulf of Mexico and its interaction with the Atlantic Ocean and the Caribbean Sea; along with air-sea interaction on longer timescales. The circulation and mixing processes that operate near the Gulf of Mexico coasts, where most human activities occur, are strongly affected by wind- and river-induced currents and are further modified by the area’s complex topography. Gulf of Mexico physical processes are also characterized by strong linkages between coastal/shelf and deeper offshore waters that determine connectivity to the basin’s interior. This physical connectivity influences the transport of materials among different coastal areas within the Gulf of Mexico and can extend to adjacent basins. Major advances enabled by the Gulf of Mexico Research Initiative in the observation, understanding, and modeling of all of these aspects of the Gulf’s physical environment are summarized in this article, and key priorities for future work are also identified.

scholarly journals Dependence of Model Energy Spectra on Vertical Resolution

2016 ◽  
Vol 144 (4) ◽  
pp. 1407-1421 ◽  
Author(s):  
Michael L. Waite
Keyword(s):  
High Resolution ◽  
Large Scale ◽  
Vertical Mixing ◽  
Energy Spectra ◽  
Small Scale ◽  
Rossby Number ◽  
Vertical Resolution ◽  
Wide Range ◽  
Qualitative Shape ◽  
Vertical Grid

Abstract Many high-resolution atmospheric models can reproduce the qualitative shape of the atmospheric kinetic energy spectrum, which has a power-law slope of −3 at large horizontal scales that shallows to approximately −5/3 in the mesoscale. This paper investigates the possible dependence of model energy spectra on the vertical grid resolution. Idealized simulations forced by relaxation to a baroclinically unstable jet are performed for a wide range of vertical grid spacings Δz. Energy spectra are converged for Δz 200 m but are very sensitive to resolution with 500 m ≤ Δz ≤ 2 km. The nature of this sensitivity depends on the vertical mixing scheme. With no vertical mixing or with weak, stability-dependent mixing, the mesoscale spectra are artificially amplified by low resolution: they are shallower and extend to larger scales than in the converged simulations. By contrast, vertical hyperviscosity with fixed grid-scale damping rate has the opposite effect: underresolved spectra are spuriously steepened. High-resolution spectra are converged except for the stability-dependent mixing case, which are damped by excessive mixing due to enhanced shear over a wide range of horizontal scales. It is shown that converged spectra require resolution of all vertical scales associated with the resolved horizontal structures: these include quasigeostrophic scales for large-scale motions with small Rossby number and the buoyancy scale for small-scale motions at large Rossby number. It is speculated that some model energy spectra may be contaminated by low vertical resolution, and it is recommended that vertical-resolution sensitivity tests always be performed.

scholarly journals Gyrotactic swimmers in turbulence: shape effects and role of the large-scale flow

2018 ◽  
Vol 856 ◽  
Author(s):  
M. Borgnino ◽  
G. Boffetta ◽  
F. De Lillo ◽  
M. Cencini
Keyword(s):  
Large Scale ◽  
Stokes Equations ◽  
Navier Stokes ◽  
Small Scale ◽  
Navier Stokes Equations ◽  
Preferential Sampling ◽  
Wide Range ◽  
Shape Effects ◽  
Dilute Suspensions ◽  
Large Scale Flow

We study the dynamics and the statistics of dilute suspensions of gyrotactic swimmers, a model for many aquatic motile microorganisms. By means of extensive numerical simulations of the Navier–Stokes equations at different Reynolds numbers, we investigate preferential sampling and small-scale clustering as a function of the swimming (stability and speed) and shape parameters, considering in particular the limits of spherical and rod-like particles. While spherical swimmers preferentially sample local downwelling flow, for elongated swimmers we observe a transition from downwelling to upwelling regions at sufficiently high swimming speed. The spatial distribution of both spherical and elongated swimmers is found to be fractal at small scales in a wide range of swimming parameters. The direct comparison between the different shapes shows that spherical swimmers are more clusterized at small stability and speed numbers, while for large values of the parameters elongated cells concentrate more. The relevance of our results for phytoplankton swimming in the ocean is briefly discussed.

Host defense mechanisms induce genome instability leading to rapid evolution in an opportunistic fungal pathogen

2021 ◽  
Author(s):  
Amanda Smith ◽  
Levi Morran ◽  
Meleah A. Hickman
Keyword(s):  
Fungal Pathogen ◽  
Defense Mechanisms ◽  
Large Scale ◽  
Genome Instability ◽  
Rapid Evolution ◽  
Genomic Changes ◽  
Opportunistic Fungal Pathogen ◽  
Immunocompromised Hosts ◽  
Stressful Environments

The ability to generate genetic variation facilitates rapid adaptation in stressful environments. The opportunistic fungal pathogen Candida albicans frequently undergoes large-scale genomic changes, including aneuploidy and loss-of heterozygosity (LOH), following exposure to host environments. However, the specific host factors inducing C. albicans genome instability remain largely unknown. Here, we leveraged the genetic tractability of nematode hosts to investigate whether innate immune components, including antimicrobial peptides (AMPs) and reactive oxygen species (ROS), induced host-associated C. albicans genome instability. C. albicans associated with immunocompetent hosts carried multiple large-scale genomic changes including LOH, whole chromosome, and segmental aneuploidies. In contrast, C. albicans associated with immunocompromised hosts deficient in AMPs or ROS production had reduced LOH frequencies and fewer, if any, additional genomic changes. To evaluate if extensive host-induced genomic changes had long-term consequences for C. albicans adaptation, we experimentally evolved C. albicans in either immunocompetent or immunocompromised hosts and selected for increased virulence. C. albicans evolved in immunocompetent hosts rapidly increased virulence, but not in immunocompromised hosts. Taken together, this work suggests that host-produced ROS and AMPs induces genotypic plasticity in C. albicans which facilitates rapid evolution.

scholarly journals Surface toughening – An industrial approach to increase the robustness of pure adhesive joints with film adhesives

2020 ◽  
Vol 234 (13) ◽  
pp. 1980-1987
Author(s):  
MJ Schollerer ◽  
J Kosmann ◽  
D Holzhüter ◽  
C Bello-Larroche ◽  
C Hühne
Keyword(s):  
Large Scale ◽  
Adhesive Bonding ◽  
Bolted Joints ◽  
Small Scale ◽  
Bonded Joints ◽  
Fiber Reinforced ◽  
Load Path ◽  
Stress Concentrations ◽  
Manufacturing Defects ◽  
Wide Range

Bonding is known for its wide range of advantages over bolted joints when joining different materials together. However, the advantages e.g. of homogeneous load distribution can quickly be lost in case of overload. For this reason, the load occurring in the adhesive is reduced by constructive measures far below the yield stress of the adhesive, which leads to a conservative joint design. And to be on the safe side, a few “chicken rivets” are then placed again. This problem is particularly well known in aviation. Highly loaded components are structurally bonded by a combination of rivets and adhesive in order to underline the advantages of structural adhesive bonding with the safety of the well-known bolted joints. Known as fail-safe design, this concept is damage tolerant and more robust against manufacturing defects through a secured double load path.  Especially when joining fiber-reinforced composites, bolts weaken the adherends of the joint and only contribute to load transfer when the brittle adhesive fails. With the help of Surface Toughening, a boltless technique for reducing stress concentrations and arresting cracks in adhesive bonded joints is available. This work describes the industrial application of this technique. Starting with coupon tests and a small scale demonstrator to ensure the compatibility with industrial manufacturing processes, such as infusion and prepreg manufacturing, a large scale demonstrator of a 2 m carbon fiber reinforced plastic (CFRP) - HTP leading edge with hybrid laminar flow control is manufactured by the industrial partner AERnnova. Verifying a simple and cost-effective application of the technology, Surface Toughening enables robust bonded joints with a minimum impact on today's process of adhesive bonding.

A new model of shoaling and breaking waves. Part 2. Run-up and two-dimensional waves

2019 ◽  
Vol 867 ◽  
pp. 146-194 ◽  
Author(s):  
G. L. Richard ◽  
A. Duran ◽  
B. Fabrèges
Keyword(s):  
Large Scale ◽  
Turbulent Viscosity ◽  
Breaking Waves ◽  
Small Scale ◽  
Two Dimensional ◽  
Numerical Resolution ◽  
Wide Range ◽  
Scale Turbulence ◽  
Run Up ◽  
Averaged Model

We derive a two-dimensional depth-averaged model for coastal waves with both dispersive and dissipative effects. A tensor quantity called enstrophy models the subdepth large-scale turbulence, including its anisotropic character, and is a source of vorticity of the average flow. The small-scale turbulence is modelled through a turbulent-viscosity hypothesis. This fully nonlinear model has equivalent dispersive properties to the Green–Naghdi equations and is treated, both for the optimization of these properties and for the numerical resolution, with the same techniques which are used for the Green–Naghdi system. The model equations are solved with a discontinuous Galerkin discretization based on a decoupling between the hyperbolic and non-hydrostatic parts of the system. The predictions of the model are compared to experimental data in a wide range of physical conditions. Simulations were run in one-dimensional and two-dimensional cases, including run-up and run-down on beaches, non-trivial topographies, wave trains over a bar or propagation around an island or a reef. A very good agreement is reached in every cases, validating the predictive empirical laws for the parameters of the model. These comparisons confirm the efficiency of the present strategy, highlighting the enstrophy as a robust and reliable tool to describe wave breaking even in a two-dimensional context. Compared with existing depth-averaged models, this approach is numerically robust and adds more physical effects without significant increase in numerical complexity.

Development of Efficient Small Scale Axial Turbine for Solar Driven Organic Rankine Cycle

2016 ◽  
Author(s):  
Ayad Al Jubori ◽  
Raya K. Al-Dadah ◽  
Saad Mahmoud ◽  
Khalil M. Khalil ◽  
A. S. Bahr Ennil
Keyword(s):  
Large Scale ◽  
Renewable Energy Sources ◽  
Cycle Performance ◽  
Working Fluid ◽  
Small Scale ◽  
Cfd Simulations ◽  
Axial Turbine ◽  
Working Fluids ◽  
Wide Range ◽  
Inlet Conditions

Recently, the increase in fossil fuel consumption and associated adverse impact on the environment led to significant interest in renewable energy sources like solar. This paper presents a new methodology that integrates the ORC cycle analysis with modeling of an efficient small scale subsonic axial turbine at low temperature heat sources using wide range of organic working fluids like R123, R134a, R141b, R152a, R245fa, R290 and isobutene. The work involves detailed turbine analysis including 1D mean line approach, extensive 3D CFD simulations and ORC cycle analysis at inlet total pressure ranging from 2–5 bar corresponding to temperature range from 275K–365K to achieve the best turbine and cycle performance. This work provides a more reliable data base for small scale organic working fluids instead of using the map of large scale gas turbine. The numerical simulation was performed using 3D RANS with SST turbulence model in ANSYS-CFX. Using iterative CFD simulations with various working fluids with subsonic inlet conditions, Mach number ranging from 0.6–0.65, results showed that using working fluid R123 for a turbine with mean diameter of 70mm, the maximum isentropic efficiency was 82% and power output 5.66 kW leading to cycle efficiency of 9.5%.

Sign in / Sign up

Export Citation Format

Share Document