@book{7474, abstract = {This booklet is a collection of abstracts presented at the AHPC conference.}, editor = {Schlögl, Alois and Kiss, Janos and Elefante, Stefano}, isbn = {978-3-99078-004-6}, location = {Klosterneuburg, Austria}, pages = {72}, publisher = {IST Austria}, title = {{Austrian High-Performance-Computing meeting (AHPC2020)}}, doi = {10.15479/AT:ISTA:7474}, year = {2020}, } @article{7477, abstract = {We present conductance-matrix measurements of a three-terminal superconductor-semiconductor hybrid device consisting of two normal leads and one superconducting lead. Using a symmetry decomposition of the conductance, we find that antisymmetric components of pairs of local and nonlocal conductances qualitatively match at energies below the superconducting gap, and we compare this finding with symmetry relations based on a noninteracting scattering matrix approach. Further, the local charge character of Andreev bound states is extracted from the symmetry-decomposed conductance data and is found to be similar at both ends of the device and tunable with gate voltage. Finally, we measure the conductance matrix as a function of magnetic field and identify correlated splittings in low-energy features, demonstrating how conductance-matrix measurements can complement traditional single-probe measurements in the search for Majorana zero modes.}, author = {Ménard, G. C. and Anselmetti, G. L. R. and Martinez, E. A. and Puglia, D. and Malinowski, F. K. and Lee, J. S. and Choi, S. and Pendharkar, M. and Palmstrøm, C. J. and Flensberg, K. and Marcus, C. M. and Casparis, L. and Higginbotham, Andrew P}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {3}, publisher = {APS}, title = {{Conductance-matrix symmetries of a three-terminal hybrid device}}, doi = {10.1103/physrevlett.124.036802}, volume = {124}, year = {2020}, } @article{7478, abstract = {Two-terminal conductance spectroscopy of superconducting devices is a common tool for probing Andreev and Majorana bound states. Here, we study theoretically a three-terminal setup, with two normal leads coupled to a grounded superconducting terminal. Using a single-electron scattering matrix, we derive the subgap conductance matrix for the normal leads and discuss its symmetries. In particular, we show that the local and the nonlocal elements of the conductance matrix have pairwise identical antisymmetric components. Moreover, we find that the nonlocal elements are directly related to the local BCS charges of the bound states close to the normal probes and we show how the BCS charge of overlapping Majorana bound states can be extracted from experiments.}, author = {Danon, Jeroen and Hellenes, Anna Birk and Hansen, Esben Bork and Casparis, Lucas and Higginbotham, Andrew P and Flensberg, Karsten}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {3}, publisher = {APS}, title = {{Nonlocal conductance spectroscopy of Andreev bound states: Symmetry relations and BCS charges}}, doi = {10.1103/physrevlett.124.036801}, volume = {124}, year = {2020}, } @article{7488, abstract = {Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS.}, author = {Latorre-Pellicer, Ana and Ascaso, Ángela and Trujillano, Laura and Gil-Salvador, Marta and Arnedo, Maria and Lucia-Campos, Cristina and Antoñanzas-Pérez, Rebeca and Marcos-Alcalde, Iñigo and Parenti, Ilaria and Bueno-Lozano, Gloria and Musio, Antonio and Puisac, Beatriz and Kaiser, Frank J. and Ramos, Feliciano J. and Gómez-Puertas, Paulino and Pié, Juan}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, number = {3}, publisher = {MDPI}, title = {{Evaluating Face2Gene as a tool to identify Cornelia de Lange syndrome by facial phenotypes}}, doi = {10.3390/ijms21031042}, volume = {21}, year = {2020}, } @article{7490, abstract = {In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the plasma membrane but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.}, author = {Narasimhan, Madhumitha and Johnson, Alexander J and Prizak, Roshan and Kaufmann, Walter and Tan, Shutang and Casillas Perez, Barbara E and Friml, Jiří}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants}}, doi = {10.7554/eLife.52067}, volume = {9}, year = {2020}, } @article{7497, abstract = {Endophytic fungi can be beneficial to plant growth. However, the molecular mechanisms underlying colonization of Acremonium spp. remain unclear. In this study, a novel endophytic Acremonium strain was isolated from the buds of Panax notoginseng and named Acremonium sp. D212. The Acremonium sp. D212 could colonize the roots of P. notoginseng, enhance the resistance of P. notoginseng to root rot disease, and promote root growth and saponin biosynthesis in P. notoginseng. Acremonium sp. D212 could secrete indole‐3‐acetic acid (IAA) and jasmonic acid (JA), and inoculation with the fungus increased the endogenous levels of IAA and JA in P. notoginseng. Colonization of the Acremonium sp. D212 in the roots of the rice line Nipponbare was dependent on the concentration of methyl jasmonate (MeJA) (2 to 15 μM) and 1‐naphthalenacetic acid (NAA) (10 to 20 μM). Moreover, the roots of the JA signalling‐defective coi1‐18 mutant were colonized by Acremonium sp. D212 to a lesser degree than those of the wild‐type Nipponbare and miR393b‐overexpressing lines, and the colonization was rescued by MeJA but not by NAA. It suggests that the cross‐talk between JA signalling and the auxin biosynthetic pathway plays a crucial role in the colonization of Acremonium sp. D212 in host plants.}, author = {Han, L and Zhou, X and Zhao, Y and Zhu, S and Wu, L and He, Y and Ping, X and Lu, X and Huang, W and Qian, J and Zhang, L and Jiang, X and Zhu, D and Luo, C and Li, S and Dong, Q and Fu, Q and Deng, K and Wang, X and Wang, L and Peng, S and Wu, J and Li, W and Friml, Jiří and Zhu, Y and He, X and Du, Y}, issn = {1744-7909}, journal = {Journal of Integrative Plant Biology}, number = {9}, pages = {1433--1451}, publisher = {Wiley}, title = {{Colonization of endophyte Acremonium sp. D212 in Panax notoginseng and rice mediated by auxin and jasmonic acid}}, doi = {10.1111/jipb.12905}, volume = {62}, year = {2020}, } @inproceedings{7505, abstract = {Neural networks have demonstrated unmatched performance in a range of classification tasks. Despite numerous efforts of the research community, novelty detection remains one of the significant limitations of neural networks. The ability to identify previously unseen inputs as novel is crucial for our understanding of the decisions made by neural networks. At runtime, inputs not falling into any of the categories learned during training cannot be classified correctly by the neural network. Existing approaches treat the neural network as a black box and try to detect novel inputs based on the confidence of the output predictions. However, neural networks are not trained to reduce their confidence for novel inputs, which limits the effectiveness of these approaches. We propose a framework to monitor a neural network by observing the hidden layers. We employ a common abstraction from program analysis - boxes - to identify novel behaviors in the monitored layers, i.e., inputs that cause behaviors outside the box. For each neuron, the boxes range over the values seen in training. The framework is efficient and flexible to achieve a desired trade-off between raising false warnings and detecting novel inputs. We illustrate the performance and the robustness to variability in the unknown classes on popular image-classification benchmarks.}, author = {Henzinger, Thomas A and Lukina, Anna and Schilling, Christian}, booktitle = {24th European Conference on Artificial Intelligence}, location = {Santiago de Compostela, Spain}, pages = {2433--2440}, publisher = {IOS Press}, title = {{Outside the box: Abstraction-based monitoring of neural networks}}, doi = {10.3233/FAIA200375}, volume = {325}, year = {2020}, } @article{7508, abstract = {In this paper, we introduce a novel method for deriving higher order corrections to the mean-field description of the dynamics of interacting bosons. More precisely, we consider the dynamics of N d-dimensional bosons for large N. The bosons initially form a Bose–Einstein condensate and interact with each other via a pair potential of the form (N−1)−1Ndβv(Nβ·)forβ∈[0,14d). We derive a sequence of N-body functions which approximate the true many-body dynamics in L2(RdN)-norm to arbitrary precision in powers of N−1. The approximating functions are constructed as Duhamel expansions of finite order in terms of the first quantised analogue of a Bogoliubov time evolution.}, author = {Bossmann, Lea and Pavlović, Nataša and Pickl, Peter and Soffer, Avy}, issn = {1572-9613}, journal = {Journal of Statistical Physics}, pages = {1362--1396}, publisher = {Springer Nature}, title = {{Higher order corrections to the mean-field description of the dynamics of interacting bosons}}, doi = {10.1007/s10955-020-02500-8}, volume = {178}, year = {2020}, } @article{7509, abstract = {In this paper we study the joint convexity/concavity of the trace functions Ψp,q,s(A,B)=Tr(Bq2K∗ApKBq2)s, p,q,s∈R, where A and B are positive definite matrices and K is any fixed invertible matrix. We will give full range of (p,q,s)∈R3 for Ψp,q,s to be jointly convex/concave for all K. As a consequence, we confirm a conjecture of Carlen, Frank and Lieb. In particular, we confirm a weaker conjecture of Audenaert and Datta and obtain the full range of (α,z) for α-z Rényi relative entropies to be monotone under completely positive trace preserving maps. We also give simpler proofs of many known results, including the concavity of Ψp,0,1/p for 0