Coherent and incoherent ultrasound backscatter from cell aggregates

International audienceThe Effective Medium Theory (EMT) combined with the Structure Factor Model was recently developed to model the ultrasound backscatter from aggregating Red Blood Cells (RBCs) [Frances-chini, Metzger, Cloutier, IEEE UFFC, 2011]. The EMT assumes that aggregates can be treated as homogeneous effective spheres and the structure factor considers the interactions between the effective spheres. In this study, the EMT is further developed to decompose the differential backscattering cross section of a single cell aggregate into coherent and incoherent components. The coherent component corresponds to the average backscatter from the effective scatterer, and the incoherent component considers the fluctuation of the scattering wave around its average within the effective scatterer. A new theoretical expression for the incoherent component based on the structure factor is proposed and compared with another formulation based on the Gaussian direct correlation function. This theoretical improvement is assessed using computer simulations of ultrasound backscatter from aggregating cells. The consideration of the incoherent component based on the structure factor allows to approximate the simulations satisfactorily for a krag limit around 2, against a krag limit comprised between 1.07 and 1.47 with the former model considering only the coherent component

Beyond Paradigms in Cultural Astronomy. Proceedings of the 27th SEAC conference held together with the EAA

Proceedings of the 27th SEAC conference held together with the EAA.-- Editors: A. César González-García, Roslyn M. Frank, Lionel D. Sims, Michael A. Rappenglück, Georg Zotti, Juan A. Belmonte, Ivan Šprajc.Cultural Astronomy is the endeavour to understand the role of the sky in past and present societies, and how these societies incorporated the sky into their culture. This broad ranging discipline is closely related to archaeology when investigating material remains of the past. Cultural Astronomy also explores the role of the heavens from the perspectives of the anthropological sciences. In recent decades the discipline has been concerned with methodological and theoretical issues. This volume offers chapters based on presentations at the 27th SEAC meeting held in Bern (2019). These chapters provide a vivid image of front-line research in diverse areas, from Roman light and shadow effects to highlight power, to Maya city organization, Etruscan temple orientation or the ontology of the sky.Peer reviewe

Sequence-Specific Features of Short Double-Strand, Blunt-End RNAs Have RIG-I- and Type 1 Interferon-Dependent or -Independent Anti-Viral Effects

Pathogen-associated molecular patterns, including cytoplasmic DNA and double-strand (ds)RNA trigger the induction of interferon (IFN) and antiviral states protecting cells and organisms from pathogens. Here we discovered that the transfection of human airway cell lines or non-transformed fibroblasts with 24mer dsRNA mimicking the cellular micro-RNA (miR)29b-1* gives strong anti-viral effects against human adenovirus type 5 (AdV-C5), influenza A virus X31 (H3N2), and SARS-CoV-2. These anti-viral effects required blunt-end complementary RNA strands and were not elicited by corresponding single-strand RNAs. dsRNA miR-29b-1* but not randomized miR-29b-1* mimics induced IFN-stimulated gene expression, and downregulated cell adhesion and cell cycle genes, as indicated by transcriptomics and IFN-I responsive Mx1-promoter activity assays. The inhibition of AdV-C5 infection with miR-29b-1* mimic depended on the IFN-alpha receptor 2 (IFNAR2) and the RNA-helicase retinoic acid-inducible gene I (RIG-I) but not cytoplasmic RNA sensors MDA5 and ZNFX1 or MyD88/TRIF adaptors. The antiviral effects of miR29b-1* were independent of a central AUAU-motif inducing dsRNA bending, as mimics with disrupted AUAU-motif were anti-viral in normal but not RIG-I knock-out (KO) or IFNAR2-KO cells. The screening of a library of scrambled short dsRNA sequences identified also anti-viral mimics functioning independently of RIG-I and IFNAR2, thus exemplifying the diverse anti-viral mechanisms of short blunt-end dsRNAsThe work was supported by the Swiss National Science Foundation (31003A_179256/1 to UFG, and 320030_205097 to JPS), the Swiss National Science Foundation SystemsX RTD InfectX (51RT 0_126008 to UFG and CvM), and the University Research Priority Program of the University of Zurich (URPP) ITINERARE – Innovative Therapies in Rare Diseases to JPS.Peer reviewe

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Approche formelle pour la modélisation et la simulation à évènements discrets de systèmes multi-agents

This thesis addresses questions related to the reproducibility of numerical experiments in the context of complex environmental systems, and more specifically in the context of agent-based modeling. The activity can be seen to a numerical experiment, just like any other scientific experiment in an experimental discipline. Therefore, the description of MAS models should be shared in an unambiguous manner. To this end, we headed to a formal approach to describe models of structural and semantic point of view. We present in this manuscript two major contributions : an agent paradigm formalization proposal combined to design methods for models developments and an implementation of abstractions to facilitate the MAS development, according to the concepts defined by the formal approach through the Quartz tool. We also propose an implementation of the approach through two examples, in which the definition of a model is established from the informal description to its implementation.Cette thèse aborde les problématiques liées à la reproductibilité des expériences numériques dans le cadre des systèmes complexes environnementaux, et plus particulièrement dans la cadre de la modélisation de systèmes multi-agents. L’activité de M&S peut s’apparenter à une expérience numérique, au même titre qu’une expérience scientifique menée dans une discipline expérimentale, c’est pourquoi la description des modèles SMA doit être partagée de façon non ambigüe. Dans cet objectif, nous nous sommes dirigés vers une approche formelle, qui permet de décrire les modèles d’un point de vue structurel et sémantique. Nous présentons dans ce manuscrit deux contributions majeures : une proposition de formalisation du paradigme agent associant des méthodes de conception pour l’élaboration des modèles et une mise en œuvre des abstractions permettant de faciliter le développement de SMA, d’après les concepts définis par l’approche formelle à travers l’outil Quartz. Nous proposons également une mise en application de l’approche à travers deux exemples, dans lesquels la définition d’un modèle est établie, de la description informelle à son implémentation

Formal approach to discrete event modeling and simulation of multi-agent systems

Cette thèse aborde les problématiques liées à la reproductibilité des expériences numériques dans le cadre des systèmes complexes environnementaux, et plus particulièrement dans le cadre de la modélisation de systèmes multi-agents. L'activité de M&S peut s'apparenter à une expérience numérique, au même titre qu'une expérience scientifique menée dans une discipline expérimentale, c'est pourquoi la description des modèles SMA doit être partagée de façon non ambigüe. Dans cet objectif, nous nous sommes dirigés vers une approche formelle, qui permet de décrire les modèles d'un point de vue structurel et sémantique. Nous présentons dans ce manuscrit deux contributions majeures : une proposition de formalisation du paradigme agent associant des méthodes de conception pour l'élaboration des modèles et une mise en oeuvre des abstractions permettant de faciliter le développement de SMA, d’après les concepts définis par l’approche formelle à travers l'outil Quartz. Nous proposons également une mise en application de l'approche à travers deux exemples, dans lesquels la définition d'un modèle est établie, de la description informelle à son implémentation.This thesis addresses questions related to the reproducibility of numerical experiments in the context of complex environmental systems, and more specifically in the context of agent-based modeling. The activity can be seen to a numerical experiment, just like any other scientific experiment in an experimental discipline. Therefore, the description of MAS models should be shared in an unambiguous manner. To this end, we headed to a formal approach to describe models of structural and semantic point of view. We present in this manuscript two major contributions: an agent paradigm formalization proposal combined to design methods for models developments and an implementation of abstractions to facilitate the MAS development, according to the concepts defined by the formal approach through the Quartz tool. We also propose an implementation of the approach through two examples, in which the definition of a model is established from the informal description to its implementation

Quantitative characterization of tissue microstructure in concentrated cell pellet biophantoms based on the structure factor model

International audienceQuantitative ultrasound (QUS) methods based on the backscatter coefficient (BSC) are typically model-based. The BSC is estimated from experiments and is fit to a model. The fit parameters often are termed QUS estimates and are used to characterize the scattering properties of the tissue under investigation. Nevertheless, for physical interpretation of QUS estimates to be accurate, the scattering model chosen must also be accurate. The goal of this work was to investigate the use of the structure factor model (SFM) to take into account coherent scattering from dense concentration of scatterers. The study focuses on comparing the performance of two sparse models (fluid-filled sphere and Gaussian) and one concentrated model (SFM) to estimate QUS parameters from simulations and cell pellet biophantoms with a range of scatterer volume fractions. Results demonstrated the superiority of the SFM for all investigated volume fractions (i.e., from 0.006 to 0.30). In particular, the sparse models underestimated scatterer size and overestimated acoustic concentration when the volume fraction was greater than 0.12. In addition, the SFM has the ability to provide the volume fraction and the relative impedance contrast (instead of only the acoustic concentration provided by the sparse models), which could have a great benefit for tissue characterization. This study demonstrates that the SFM could prove to be an invaluable tool for QUS and could help to more accurately characterize tissue from ultrasound measurements