179 research outputs found
hp-version time domain boundary elements for the wave equation on quasi-uniform meshes
Solutions to the wave equation in the exterior of a polyhedral domain or a
screen in exhibit singular behavior from the edges and corners.
We present quasi-optimal -explicit estimates for the approximation of the
Dirichlet and Neumann traces of these solutions for uniform time steps and
(globally) quasi-uniform meshes on the boundary. The results are applied to an
-version of the time domain boundary element method. Numerical examples
confirm the theoretical results for the Dirichlet problem both for screens and
polyhedral domains.Comment: 41 pages, 11 figure
Boundary elements with mesh refinements for the wave equation
The solution of the wave equation in a polyhedral domain in
admits an asymptotic singular expansion in a neighborhood of the corners and
edges. In this article we formulate boundary and screen problems for the wave
equation as equivalent boundary integral equations in time domain, study the
regularity properties of their solutions and the numerical approximation.
Guided by the theory for elliptic equations, graded meshes are shown to recover
the optimal approximation rates known for smooth solutions. Numerical
experiments illustrate the theory for screen problems. In particular, we
discuss the Dirichlet and Neumann problems, as well as the Dirichlet-to-Neumann
operator and applications to the sound emission of tires.Comment: 45 pages, to appear in Numerische Mathemati
Histopathological Image Classification based on Self-Supervised Vision Transformer and Weak Labels
Whole Slide Image (WSI) analysis is a powerful method to facilitate the
diagnosis of cancer in tissue samples. Automating this diagnosis poses various
issues, most notably caused by the immense image resolution and limited
annotations. WSIs commonly exhibit resolutions of 100Kx100K pixels. Annotating
cancerous areas in WSIs on the pixel level is prohibitively labor-intensive and
requires a high level of expert knowledge. Multiple instance learning (MIL)
alleviates the need for expensive pixel-level annotations. In MIL, learning is
performed on slide-level labels, in which a pathologist provides information
about whether a slide includes cancerous tissue. Here, we propose Self-ViT-MIL,
a novel approach for classifying and localizing cancerous areas based on
slide-level annotations, eliminating the need for pixel-wise annotated training
data. Self-ViT- MIL is pre-trained in a self-supervised setting to learn rich
feature representation without relying on any labels. The recent Vision
Transformer (ViT) architecture builds the feature extractor of Self-ViT-MIL.
For localizing cancerous regions, a MIL aggregator with global attention is
utilized. To the best of our knowledge, Self-ViT- MIL is the first approach to
introduce self-supervised ViTs in MIL-based WSI analysis tasks. We showcase the
effectiveness of our approach on the common Camelyon16 dataset. Self-ViT-MIL
surpasses existing state-of-the-art MIL-based approaches in terms of accuracy
and area under the curve (AUC)
Single-Cell Tracking Reveals Antibiotic-Induced Changes in Mycobacterial Energy Metabolism
ATP is a key molecule of cell physiology, but despite its importance, there are currently no methods for monitoring single-cell ATP fluctuations in live bacteria. This is a major obstacle in studies of bacterial energy metabolism, because there is a growing awareness that bacteria respond to stressors such as antibiotics in a highly individualistic manner. Here, we present a method for long-term single-cell tracking of ATP levels in Mycobacterium smegmatis based on a combination of microfluidics, time-lapse microscopy, and Forster resonance energy transfer (FRET)-based ATP biosensors. Upon treating cells with antibiotics, we observed that individual cells undergo an abrupt and irreversible switch from high to low intracellular ATP levels. The kinetics and extent of ATP switching clearly discriminate between an inhibitor of ATP synthesis and other classes of antibiotics. Cells that resume growth after 24 h of antibiotic treatment maintain high ATP levels throughout the exposure period. In contrast, antibiotic-treated cells that switch from ATP-high to ATP-low states never resume growth after antibiotic washout. Surprisingly, only a subset of these nongrowing ATP-low cells stains with propidium iodide (PI), a widely used live/dead cell marker. These experiments also reveal a cryptic subset of cells that do not resume growth after antibiotic washout despite remaining ATP high and PI negative. We conclude that ATP tracking is a more dynamic, sensitive, reliable, and discriminating marker of cell viability than staining with PI. This method could be used in studies to evaluate antimicrobial effectiveness and mechanism of action, as well as for high-throughput screening. IMPORTANCE New antimicrobials are urgently needed to stem the rising tide of antibiotic-resistant bacteria. All antibiotics are expected to affect bacterial energy metabolism, directly or indirectly, yet tools to assess the impact of antibiotics on the ATP content of individual bacterial cells are lacking. The method described here for single-cell tracking of intracellular ATP in live bacteria has many advantages compared to conventional ensemble-averaged assays. It provides a continuous real-time readout of bacterial ATP content, cell vitality, and antimicrobial mechanism of action with high temporal resolution at the single-cell level. In combination with high-throughput microfluidic devices and automated microscopy, this method also has the potential to serve as a novel screening tool in antimicrobial drug discovery
Analysis of coupled heat and moisture transfer in masonry structures
Evaluation of effective or macroscopic coefficients of thermal conductivity
under coupled heat and moisture transfer is presented. The paper first gives a
detailed summary on the solution of a simple steady state heat conduction
problem with an emphasis on various types of boundary conditions applied to the
representative volume element -- a periodic unit cell. Since the results
essentially suggest no superiority of any type of boundary conditions, the
paper proceeds with the coupled nonlinear heat and moisture problem subjecting
the selected representative volume element to the prescribed macroscopically
uniform heat flux. This allows for a direct use of the academic or commercially
available codes. Here, the presented results are derived with the help of the
SIFEL (SIimple Finite Elements) system.Comment: 23 pages, 11 figure
MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis
Artificial Intelligence methods are powerful tools for biological image
analysis and processing. High-quality annotated images are key to training and
developing new methods, but access to such data is often hindered by the lack
of standards for sharing datasets. We brought together community experts in a
workshop to develop guidelines to improve the reuse of bioimages and
annotations for AI applications. These include standards on data formats,
metadata, data presentation and sharing, and incentives to generate new
datasets. We are positive that the MIFA (Metadata, Incentives, Formats, and
Accessibility) recommendations will accelerate the development of AI tools for
bioimage analysis by facilitating access to high quality training data.Comment: 16 pages, 3 figure
Identification and Engineering of Transporters for Efficient Melatonin Production in Escherichia coli
Transporter discovery and engineering play an important role in cell factory development. Decreasing the intracellular concentration of the product reduces product inhibition and/or toxicity. Lowering intracellular concentrations is especially beneficial for achieving a robust strain at high titers. However, the identification of transporters for xenobiotic chemicals in the host strain is challenging. Here we present a high-throughput workflow to discover Escherichia coli transporters responsible for the efflux of the inhibitory xenobiotic compound melatonin. We took advantage of the Keio collection and screened about 400 transporter knockouts in the presence of a high concentration of melatonin. We found five transporters that when knocked out showed decreased tolerance to melatonin, indicating they are exporters of melatonin. We overexpressed these five genes individually in the production strain and found that one of them, yhjV, encoding a transporter with unknown substrates, resulted in a 27% titer increase in cultivation mimicking fed-batch fermentation. This study demonstrates how microbial cell factories can be improved through transporter identification and engineering. Further, these results lay the foundation for the scale-up of melatonin production in E. coli
FCC-hh: The Hadron Collider: Future Circular Collider Conceptual Design Report Volume 3
In response to the 2013 Update of the European Strategy for Particle Physics (EPPSU), the Future Circular Collider (FCC) study was launched as a world-wide international collaboration hosted by CERN. The FCC study covered an energy-frontier hadron collider (FCC-hh), a highest-luminosity high-energy lepton collider (FCC-ee), the corresponding 100 km tunnel infrastructure, as well as the physics opportunities of these two colliders, and a high-energy LHC, based on FCC-hh technology. This document constitutes the third volume of the FCC Conceptual Design Report, devoted to the hadron collider FCC-hh. It summarizes the FCC-hh physics discovery opportunities, presents the FCC-hh accelerator design, performance reach, and staged operation plan, discusses the underlying technologies, the civil engineering and technical infrastructure, and also sketches a possible implementation. Combining ingredients from the Large Hadron Collider (LHC), the high-luminosity LHC upgrade and adding novel technologies and approaches, the FCC-hh design aims at significantly extending the energy frontier to 100 TeV. Its unprecedented centre of-mass collision energy will make the FCC-hh a unique instrument to explore physics beyond the Standard Model, offering great direct sensitivity to new physics and discoveries
- âŠ