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  1. Free, publicly-accessible full text available March 18, 2023
  2. Aims. An interplanetary coronal mass ejection (ICME) event was observed by the Solar Orbiter at 0.8 AU on 2020 April 19 and by Wind at 1 AU on 2020 April 20. Futhermore, an interplanetary shock wave was driven in front of the ICME. Here, we focus on the transmission of the magnetic fluctuations across the shock and we analyze the characteristic wave modes of solar wind turbulence in the vicinity of the shock observed by both spacecraft. Methods. The observed ICME event is characterized by a magnetic helicity-based technique. The ICME-driven shock normal was determined by magnetic coplanarity method formore »the Solar Orbiter and using a mixed plasma and field approach for Wind. The power spectra of magnetic field fluctuations were generated by applying both a fast Fourier transform and Morlet wavelet analysis. To understand the nature of waves observed near the shock, we used the normalized magnetic helicity as a diagnostic parameter. The wavelet-reconstructed magnetic field fluctuation hodograms were used to further study the polarization properties of waves. Results. We find that the ICME-driven shock observed by Solar Orbiter and Wind is a fast, forward oblique shock with a more perpendicular shock angle at the Wind position. After the shock crossing, the magnetic field fluctuation power increases. Most of the magnetic field fluctuation power resides in the transverse fluctuations. In the vicinity of the shock, both spacecraft observe right-hand polarized waves in the spacecraft frame. The upstream wave signatures fall within a relatively broad and low frequency band, which might be attributed to low frequency MHD waves excited by the streaming particles. For the downstream magnetic wave activity, we find oblique kinetic Alfvén waves with frequencies near the proton cyclotron frequency in the spacecraft frame. The frequency of the downstream waves increases by a factor of ∼7–10 due to the shock compression and the Doppler effect.« less
    Free, publicly-accessible full text available December 1, 2022
  3. DenseNets introduce concatenation-type skip connections that achieve state-of-the-art accuracy in several computer vision tasks. In this paper, we reveal that the topology of the concatenation-type skip connections is closely related to the gradient propagation which, in turn, enables a predictable behavior of DNNs’ test performance. To this end, we introduce a new metric called NN-Mass to quantify how effectively information flows through DNNs. Moreover, we empirically show that NN-Mass also works for other types of skip connections, e.g., for ResNets, Wide-ResNets (WRNs), and MobileNets, which contain addition-type skip connections (i.e., residuals or inverted residuals). As such, for both DenseNet-like CNNsmore »and ResNets/WRNs/MobileNets, our theoretically grounded NN-Mass can identify models with similar accuracy, despite having significantly different size/compute requirements. Detailed experiments on both synthetic and real datasets (e.g., MNIST, CIFAR-10, CIFAR-100, ImageNet) provide extensive evidence for our insights. Finally, the closed-form equation of our NN-Mass enables us to design significantly compressed DenseNets (for CIFAR-10) and MobileNets (for ImageNet) directly at initialization without time-consuming training and/or searching.« less
  4. Free, publicly-accessible full text available November 1, 2022
  5. Jacob, S. (Ed.)
    Protein–protein interactions underlie cellular structure and function. In recent years, a number of methods have been developed for the identification of protein complexes and component proteins involved in the control of various biological pathways. Tandem affinity purification (TAP) coupled with mass spectrometry (MS) is a powerful method enabling the isolation of high-purity native protein complexes under mild conditions by performing two sequential purification steps using two different epitope tags. In this protocol, we describe a TAP-MS methodology for identifying protein-protein interactions present at very low levels in the fungal cell. Using the 6xHis-3xFLAG double tag, we start the affinity purificationmore »process for our protein of interest using high-capacity Ni²⁺ columns. This allows for greatly increased sample input compared to antibody-based first-step purification in conventional TAP protocols and provides a large amount of highly concentrated and preliminarily purified protein complexes to be used in a second purification step involving FLAG immunoprecipitation. The second step greatly facilitates the capture of low-level interacting partners under in vivo conditions. Our TAP-MS method has been proven to secure the characterization of low-abundance protein complexes under physiological conditions with high efficiency, specificity, and economy in the filamentous fungus Magnaporthe oryzae and might benefit gene function and proteomics studies in plants and other research fields.« less
  6. Eukaryotic filamentous plant pathogens with biotrophic growth stages like the devastating hemibiotrophic rice blast fungus Magnaporthe oryzae grow for extended periods in living host plant cells without eliciting defense responses. M. oryzae elaborates invasive hyphae (IH) that grow in and between living rice cells while separated from host cytoplasm by plant-derived membrane interfaces. However, although critical to the plant infection process, the molecular mechanisms and metabolic strategies underpinning this intracellular growth phase are poorly understood. Eukaryotic cell growth depends on activated target-of-rapamycin (TOR) kinase signaling, which inhibits autophagy. Here, using live-cell imaging coupled with plate growth tests and RNAseq, proteomic,more »quantitative phosphoproteomics and metabolic approaches, we show how cycles of autophagy in IH modulate TOR reactivation via α-ketoglutarate to sustain biotrophic growth and maintain biotrophic interfacial membrane integrity in host rice cells. Deleting the M. oryzae serine-threonine protein kinase Rim15-encoding gene attenuated biotrophic growth, disrupted interfacial membrane integrity and abolished the in planta autophagic cycling we observe here for the first time in wild type. Δrim15 was also impaired for glutaminolysis and depleted for α-ketoglutarate. α-ketoglutarate treatment of Δrim15-infected leaf sheaths remediated Δrim15 biotrophic growth. In WT, α-ketoglutarate treatment suppressed autophagy. α-ketoglutarate signaling is amino acid prototrophy- and GS-GOGAT cycle-dependent. We conclude that, following initial IH elaboration, cycles of Rim15- dependent autophagic flux liberate α-ketoglutarate – via the GS-GOGAT cycle – as an amino acid-sufficiency signal to trigger TOR reactivation and promote fungal biotrophic growth in nutrient-restricted host rice cells.« less