267 research outputs found
A Machine Learning Tutorial for Operational Meteorology, Part II: Neural Networks and Deep Learning
Over the past decade the use of machine learning in meteorology has grown
rapidly. Specifically neural networks and deep learning have been used at an
unprecedented rate. In order to fill the dearth of resources covering neural
networks with a meteorological lens, this paper discusses machine learning
methods in a plain language format that is targeted for the operational
meteorological community. This is the second paper in a pair that aim to serve
as a machine learning resource for meteorologists. While the first paper
focused on traditional machine learning methods (e.g., random forest), here a
broad spectrum of neural networks and deep learning methods are discussed.
Specifically this paper covers perceptrons, artificial neural networks,
convolutional neural networks and U-networks. Like the part 1 paper, this
manuscript discusses the terms associated with neural networks and their
training. Then the manuscript provides some intuition behind every method and
concludes by showing each method used in a meteorological example of diagnosing
thunderstorms from satellite images (e.g., lightning flashes). This paper is
accompanied with an open-source code repository to allow readers to explore
neural networks using either the dataset provided (which is used in the paper)
or as a template for alternate datasets
Separation of VUV/UV photons and reactive particles in the effluent of a He/O2 atmospheric pressure plasma jet
Cold atmospheric pressure plasmas can be used for treatment of living tissues
or for inactivation of bacteria or biological macromolecules. The treatment is
usually characterized by a combined effect of UV and VUV radiation, reactive
species, and ions. This combination is usually beneficial for the effectiveness
of the treatment but it makes the study of fundamental interaction mechanisms
very difficult. Here we report on an effective separation of VUV/UV photons and
heavy reactive species in the effluent of a micro scale atmospheric pressure
plasma jet (-APPJ). The separation is realized by an additional flow of
helium gas under well-defined flow conditions, which deflects heavy particles
in the effluent without affecting the VUV and UV photons. Both components of
the effluent, the photons and the reactive species, can be used separately or
in combination for sample treatment. The results of treatment of a model plasma
polymer film and vegetative Bacillus subtilis and Escherichia coli cells are
shown and discussed. A simple model of the He gas flow and reaction kinetics of
oxygen atoms in the gas phase and at the surface is used to provide a better
understanding of the processes in the plasma effluent. The new jet
modification, called X-Jet for its appearance, will simplify the investigation
of interaction mechanisms of atmospheric pressure plasmas with biological
samples.Comment: 10 pages, 7 figures, submitted to Journal of Physics D: Applied
Physic
Recommended from our members
Chemical fingerprints of cold physical plasmas – an experimental and computational study using cysteine as tracer compound
Reactive oxygen and nitrogen species released by cold physical plasma are being proposed as effectors in various clinical conditions connected to inflammatory processes. As these plasmas can be tailored in a wide range, models to compare and control their biochemical footprint are desired to infer on the molecular mechanisms underlying the observed effects and to enable the discrimination between different plasma sources. Here, an improved model to trace short-lived reactive species is presented. Using FTIR, high-resolution mass spectrometry, and molecular dynamics computational simulation, covalent modifications of cysteine treated with different plasmas were deciphered and the respective product pattern used to generate a fingerprint of each plasma source. Such, our experimental model allows a fast and reliable grading of the chemical potential of plasmas used for medical purposes. Major reaction products were identified to be cysteine sulfonic acid, cystine, and cysteine fragments. Less-abundant products, such as oxidized cystine derivatives or S-nitrosylated cysteines, were unique to different plasma sources or operating conditions. The data collected point at hydroxyl radicals, atomic O, and singlet oxygen as major contributing species that enable an impact on cellular thiol groups when applying cold plasma in vitro or in vivo
EPHA3 (EPH receptor A3)
Review on EPHA3 (EPH receptor A3), with data on DNA, on the protein encoded, and where the gene is implicated
UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells
The paralogous human proteins UPF3A and UPF3B are involved in recognizing mRNAs targeted by nonsense-mediated mRNA decay (NMD). While UPF3B has been demonstrated to support NMD, contradicting reports describe UPF3A either as an NMD activator or inhibitor. Here, we present a comprehensive functional analysis of UPF3A and UPF3B in human cells using combinatory experimental approaches. Overexpression or knockout of UPF3A as well as knockout of UPF3B did not detectably change global NMD activity. In contrast, the co-depletion of UPF3A and UPF3B resulted in a marked NMD inhibition and a transcriptome-wide upregulation of NMD substrates, demonstrating a functional redundancy between both NMD factors. Although current models assume that UPF3 bridges NMD-activating exon-junction complexes (EJC) to the NMD factor UPF2, UPF3B exhibited normal NMD activity in rescue experiments when UPF2 or EJC binding was impaired. Further rescue experiments revealed partially redundant functions of UPF3B domains in supporting NMD, involving both UPF2 and EJC interaction sites and the central region of UPF3. Collectively, UPF3A and UPF3B serve as fault-tolerant NMD activators in human cells
Exon junction complex-associated multi-adapter RNPS1 nucleates splicing regulatory complexes to maintain transcriptome surveillance
The exon junction complex (EJC) is an RNA-binding multi-protein complex with critical functions in post-transcriptional gene regulation. It is deposited on the mRNA during splicing and regulates diverse processes including pre-mRNA splicing and nonsense-mediated mRNA decay (NMD) via various interacting proteins. The peripheral EJC-binding protein RNPS1 was reported to serve two insufficiently characterized functions: suppressing mis-splicing of cryptic splice sites and activating NMD in the cytoplasm. The analysis of transcriptome-wide effects of EJC and RNPS1 knockdowns in different human cell lines supports the conclusion that RNPS1 can moderately influence NMD activity, but is not a globally essential NMD factor. However, numerous aberrant splicing events strongly suggest that the main function of RNPS1 is splicing regulation. Rescue analyses revealed that the RRM and C-terminal domain of RNPS1 both contribute partially to regulate RNPS1-dependent splicing events. We defined the RNPS1 core interactome using complementary immunoprecipitations and proximity labeling, which identified interactions with splicing-regulatory factors that are dependent on the C-terminus or the RRM domain of RNPS1. Thus, RNPS1 emerges as a multifunctional splicing regulator that promotes correct and efficient splicing of different vulnerable splicing events via the formation of diverse splicing-promoting complexes
Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay
The paralogous human proteins UPF3A and UPF3B are involved in recognizing mRNAs targeted by nonsense-mediated mRNA decay (NMD). UPF3B has been demonstrated to support NMD, presumably by bridging an exon junction complex (EJC) to the NMD factor UPF2. The role of UPF3A has been described either as a weak NMD activator or an NMD inhibitor. Here, we present a comprehensive functional analysis of UPF3A and UPF3B in human cells using combinatory experimental approaches. Overexpression or knockout of UPF3A as well as knockout of UPF3B did not substantially change global NMD activity. In contrast, the co-depletion of UPF3A and UPF3B resulted in a marked NMD inhibition and a transcriptome-wide upregulation of NMD substrates, demonstrating a functional redundancy between both NMD factors. In rescue experiments, UPF2 or EJC binding-deficient UPF3B largely retained NMD activity. However, combinations of different mutants, including deletion of the middle domain, showed additive or synergistic effects and therefore failed to maintain NMD. Collectively, UPF3A and UPF3B emerge as fault-tolerant, functionally redundant NMD activators in human cells
In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation
In humans, aggregation of polyglutamine repeat (polyQ) proteins causes disorders such as Huntington’s disease. Although plants express hundreds of polyQ-containing proteins, no pathologies arising from polyQ aggregation have been reported. To investigate this phenomenon, we expressed an aggregation-prone fragment of human huntingtin (HTT) with an expanded polyQ stretch (Q69) in Arabidopsis thaliana plants. In contrast to animal models, we find that Arabidopsis sp. suppresses Q69 aggregation through chloroplast proteostasis. Inhibition of chloroplast proteostasis diminishes the capacity of plants to prevent cytosolic Q69 aggregation. Moreover, endogenous polyQ-containing proteins also aggregate on chloroplast dysfunction. We find tha
- …