Detection of trend changes in time series using Bayesian inference

Change points in time series are perceived as isolated singularities where two regular trends of a given signal do not match. The detection of such transitions is of fundamental interest for the understanding of the system's internal dynamics. In practice observational noise makes it difficult to detect such change points in time series. In this work we elaborate a Bayesian method to estimate the location of the singularities and to produce some confidence intervals. We validate the ability and sensitivity of our inference method by estimating change points of synthetic data sets. As an application we use our algorithm to analyze the annual flow volume of the Nile River at Aswan from 1871 to 1970, where we confirm a well-established significant transition point within the time series.Comment: 9 pages, 12 figures, submitte

Elevated H2AX Phosphorylation Observed with kINPen Plasma Treatment Is Not Caused by ROS-Mediated DNA Damage but Is the Consequence of Apoptosis

Phosphorylated histone 2AX (γH2AX) is a long-standing marker for DNA double-strand breaks (DSBs) from ionizing radiation in the field of radiobiology. This led to the perception of γH2AX being a general marker of direct DNA damage with the treatment of other agents such as low-dose exogenous ROS that unlikely act on cellular DNA directly. Cold physical plasma confers biomedical effects majorly via release of reactive oxygen and nitrogen species (ROS). In vitro, increase of γH2AX has often been observed with plasma treatment, leading to the conclusion that DNA damage is a direct consequence of plasma exposure. However, increase in γH2AX also occurs during apoptosis, which is often observed with plasma treatment as well. Moreover, it must be questioned if plasma-derived ROS can reach into the nucleus and still be reactive enough to damage DNA directly. We investigated γH2AX induction in a lymphocyte cell line upon ROS exposure (plasma, hydrogen peroxide, or hypochlorous acid) or UV-B light. Cytotoxicity and γH2AX induction was abrogated by the use of antioxidants with all types of ROS treatment but not UV radiation. H2AX phosphorylation levels were overall independent of analyzing either all nucleated cells or segmenting γH2AX phosphorylation for each cell cycle phase. SB202190 (p38-MAPK inhibitor) and Z-VAD-FMK (pan-caspase inhibitor) significantly inhibited γH2AX induction upon ROS but not UV treatment. Finally, and despite γH2AX induction, UV but not plasma treatment led to significantly increased micronucleus formation, which is a functional read-out of genotoxic DNA DSBs. We conclude that plasma-mediated and low-ROS γH2AX induction depends on caspase activation and hence is not the cause but consequence of apoptosis induction. Moreover, we could not identify lasting mutagenic effects with plasma treatment despite phosphorylation of H2AX

An Antiherpesviral Host-Directed Strategy Based on CDK7 Covalently Binding Drugs: Target-Selective, Picomolar-Dose, Cross-Virus Reactivity

The repertoire of currently available antiviral drugs spans therapeutic applications against a number of important human pathogens distributed worldwide. These include cases of the pandemic severe acute respiratory coronavirus type 2 (SARS-CoV-2 or COVID-19), human immunodeficiency virus type 1 (HIV-1 or AIDS), and the pregnancy- and posttransplant-relevant human cytomegalovirus (HCMV). In almost all cases, approved therapies are based on direct-acting antivirals (DAAs), but their benefit, particularly in long-term applications, is often limited by the induction of viral drug resistance or side effects. These issues might be addressed by the additional use of host-directed antivirals (HDAs). As a strong input from long-term experiences with cancer therapies, host protein kinases may serve as HDA targets of mechanistically new antiviral drugs. The study demonstrates such a novel antiviral strategy by targeting the major virus-supportive host kinase CDK7. Importantly, this strategy focuses on highly selective, 3D structure-derived CDK7 inhibitors carrying a warhead moiety that mediates covalent target binding. In summary, the main experimental findings of this study are as follows: (1) the in vitro verification of CDK7 inhibition and selectivity that confirms the warhead covalent-binding principle (by CDK-specific kinase assays), (2) the highly pronounced antiviral efficacies of the hit compounds (in cultured cell-based infection models) with half-maximal effective concentrations that reach down to picomolar levels, (3) a particularly strong potency of compounds against strains and reporter-expressing recombinants of HCMV (using infection assays in primary human fibroblasts), (4) additional activity against further herpesviruses such as animal CMVs and VZV, (5) unique mechanistic properties that include an immediate block of HCMV replication directed early (determined by Western blot detection of viral marker proteins), (6) a substantial drug synergism in combination with MBV (measured by a Loewe additivity fixed-dose assay), and (7) a strong sensitivity of clinically relevant HCMV mutants carrying MBV or ganciclovir resistance markers. Combined, the data highlight the huge developmental potential of this host-directed antiviral targeting concept utilizing covalently binding CDK7 inhibitors

Temporary antimetabolite treatment hold boosts SARS-CoV-2 vaccination–specific humoral and cellular immunity in kidney transplant recipients

Transplant recipients exhibit an impaired protective immunity after SARS-CoV-2 vaccination, potentially caused by mycophenolate (MPA) immunosuppression. Recent data from patients with autoimmune disorders suggest that temporary MPA hold might greatly improve booster vaccination outcomes. We applied a fourth dose of SARS-CoV-2 vaccine to 29 kidney transplant recipients during a temporary (5 weeks) MPA/azathioprine hold, who had not mounted a humoral immune response to previous vaccinations. Seroconversion until day 32 after vaccination was observed in 76% of patients, associated with acquisition of virus-neutralizing capacity. Interestingly, 21/25 (84%) calcineurin inhibitor-treated patients responded, but only 1/4 belatacept-treated patients responded. In line with humoral responses. counts and relative frequencies of spike receptor binding domain-specific (RBD-specific) B cells were markedly increased on day 7 after vaccination, with an increase in RBD-specific CD27(++)CD38(+) plasmablasts. Whereas overall proportions of spike-reactive CD4(+) T cells remained unaltered after the fourth dose, frequencies were positively correlated with specific IgG levels. Importantly, antigen-specific proliferating Ki67(+) and in vivo-activated programmed cell death 1-positive T cells significantly increased after revaccination during MPA hold, whereas cytokine production and memory differentiation remained unaffected. In summary, antimetabolite hold augmented all arms of immunity during booster vaccination. These data suggest further studies of antimetabolite hold in kidney transplant recipients

AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor.

peer reviewedProtein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.LabEx IBEID (Biologie Intégrative des Maladies Infectieuses Emergentes

Évaluer l’impact d’installations sonores sur la perception du paysage sonore urbain : cas d’étude d’une place publique parisienne

Dans nos sociétés urbaines, il est courant de considérer l’environnement sonore comme une pollution qu’il convient de réduire. Pourtant, diminuer le niveau sonore n’entraîne pas forcément une amélioration de la qualité d’un environnement sonore, car la nature des sources qui y sont présentes est d’une importance critique pour son appréciation. Plutôt que de considérer le son comme une nuisance, il est ainsi possible de l’envisager comme une ressource pouvant avoir un impact positif sur la qualité de vie urbaine. Dans ce cadre, mon projet doctoral consiste à planifier et étudier l’impact d’installations sonores sur le paysage sonore urbain. Mon premier cas d’étude s’incarne dans une collaboration scientifique et artistique autour du projet Niches Acoustiques, conçu par la compositrice Nadine Schütz. Ce projet vise la mise en place d’une installation sonore pérenne dans une place publique, le parvis du Tribunal de Grande Instance de Paris. Notre objectif est double : au moyen d’évaluations perceptives impliquant des simulations de paysages sonores en laboratoire, nous cherchons à informer la composition de cette œuvre et à anticiper son impact sur la perception du lieu où elle sera déployée. Nous présentons ici la première phase de ce projet, une session de mesures permettant la simulation spatialisée de l’environnement sonore du parvis et des futures interventions sonores qui s’opèreront dans le cadre du projet artistique. Deux séries de mesure ont été effectuées : des mesures acoustiques et des prises de son de type High-Order Ambisonics à différentes positions et périodes d’activité, puis, en collaboration avec Bruitparif, des mesures de niveau sonore continues pendant plusieurs semaines. Les données de cette double campagne seront présentées. Elles fournissent à la fois le matériau nécessaire à la simulation du paysage sonore du site, mais permettent aussi des analyses préliminaires qui caractérisent et identifient l’activité et la signature acoustique du lieu

Landwirtschaftliche Nutztierhaltung: Begriffsdefinition zum zentralen Untersuchungsobjekt im Projekt SocialLab²

Befragungen sind in der Wissenschaft ein gerne als auch häufig eingesetztes Instrument, um Erkenntnisse über einen Forschungsgegenstand zu erhalten. Davon auszugehen, dass eine Befragung schnell und einfach konzipiert ist, ist jedoch ein Trugschluss. Befragte können auf vielfältige Art und Weise bewusst oder unbewusst beeinflusst werden: Fragenreihenfolge, Herleitung zu einem Thema aber auch die Wortwahl sind entscheidend dafür, ob Befragte wirklich die eigene Meinung zu einem Thema äußern oder sich in eine bestimmte Richtung haben leiten lassen. In Bezug auf die Nutztierhaltung können unterschiedliche Formulierungen gewählt werden: Während 'Massentierhaltung' in den meisten Fällen negativ wahrgenommen wird, ist es im Falle der 'bäuerlichen Landwirtschaft' in der Regel genau anders herum. Der Frage, welcher Begriff am neutralsten die derzeit am häufigsten praktizierte Form der landwirtschaftlichen Nutztierhaltung beschreibt, widmet sich dieser Beitrag. Mit Hilfe qualitativer (u.a. Think Aloud, Information Retrieval Probing, Sortiertechnik, Paraphrasierung) und quantitativer Pretestverfahren (u.a. univariate Varianzanalyse, Normalitätsverteilung, Shapiro-Wilk-Test) wurden unterschiedliche Begrifflichkeiten systematisch untersucht. Ergebnis der unterschiedlichen Analysen ist, dass der Begriff 'vorrangig praktizierte landwirtschaftliche Nutztierhaltung nach gesetzlichem Mindeststandard' (Langform) bzw. 'landwirtschaftliche Nutztierhaltung' (Kurzform) das Thema am neutralsten darstellt.Surveys are a popular and frequently used instrument in science to gain knowledge about a research subject. However, it is a fallacy to assume that a survey can be designed quickly and easily. Respondents can be influenced consciously or unconsciously in many ways: Question order, derivation to a topic but also the choice of words are decisive for whether respondents really express their own opinion on a topic or have allowed themselves to be led in a certain direction. With regard to livestock farming, different formulations can be chosen: While "factory farming" is perceived negatively in most cases, it is usually the other way round in the case of "peasant farming". The question of which term most neutrally describes the currently most frequently practised form of farm animal husbandry is the subject of this article. With the help of qualitative (including think aloud, information retrieval probing, sorting technique, paraphrasing) and quantitative pretest procedures (including univariate analysis of variance, normality distribution, Shapiro-Wilk test), different terms were systematically examined. The result of the different analyses is that the term "primarily practised farm animal husbandry according to legal minimum standards" (long form) or "farm animal husbandry" (short form) represents the topic in the most neutral way

Recombinant Human Cytomegalovirus Expressing an Analog-Sensitive Kinase pUL97 as Novel Tool for Functional Analyses

The human cytomegalovirus (HCMV) is a member of the beta-herpesvirus family and inflicts life-long latent infections in its hosts. HCMV has been shown to manipulate and dysregulate many cellular processes. One major interactor with the cellular host is the viral kinase pUL97. The UL97 gene is essential for viral replication, and kinase-deficient mutants of pUL97 display a severe replication defect. Recently, another group established an analog-sensitive version of the pUL97 protein. This mutant kinase can be treated with a non-hydrolysable ATP analog, thereby inhibiting its kinase function. This process is reversible by removing the ATP analog by media change. We introduced this mutant version of the pUL97 protein into the laboratory strain Ad169 of HCMV, BADwt, creating a BAD-UL97-as1 viral mutant. This mutant virus replicated normally in infected cells in the absence of the ATP analog and maintained its ability to phosphorylate its cellular substrates. However, when treated with the ATP analog, BAD-UL97-as1 displayed a defect in the production of intra- and extracellular viral DNA and in the production of viral progeny. Furthermore, in the presence of 3MB-PP1, a well-established substrate of pUL97 was no longer hyperphosphorylated. This effect was detectable as early as 4 h post treatment, which allows for studies on pUL97 without the complication of low viral titers. Nevertheless, we observed off-target effects of 3MB-PP1 on several cellular processes, which should be considered with this approach

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models

Pristionchus pacificus is a nematode model organism whose genome has recently been sequenced. To refine the genome annotation we performed transcriptome and proteome analysis and gathered comprehensive experimental information on gene expression. Transcriptome analysis on a 454 Life Sciences (Roche) FLX platform generated >700,000 expressed sequence tags (ESTs) from two normalized EST libraries, whereas proteome analysis on an LTQ-Orbitrap mass spectrometer detected >27,000 nonredundant peptide sequences from more than 4000 proteins at sub-parts-per-million (ppm) mass accuracy and a false discovery rate of <1%. Retraining of the SNAP gene prediction algorithm using the gene expression data led to a decrease in the number of previously predicted protein-coding genes from 29,000 to 24,000 and refinement of numerous gene models. The P. pacificus proteome contains a high proportion of small proteins with no known homologs in other species (“pioneer” proteins). Some of these proteins appear to be products of highly homologous genes, pointing to their common origin. We show that >50% of all pioneer genes are transcribed under standard culture conditions and that pioneer proteins significantly contribute to a unimodal distribution of predicted protein sizes in P. pacificus, which has an unusually low median size of 240 amino acids (26.8 kDa). In contrast, the predicted proteome of Caenorhabditis elegans follows a distinct bimodal protein size distribution, with significant functional differences between small and large protein populations. Combined, these results provide the first catalog of the expressed genome of P. pacificus, refinement of its genome annotation, and the first comparison of related nematode models at the proteome level