Neuro-explicit semantic segmentation of the diffusion cloud chamber

For decades, in diffusion cloud chambers, different types of subatomic particle tracks from radioactive sources or cosmic radiation had to be identified with the naked eye which limited the amount of data that could be processed. In order to allow these classical particle detectors to enter the digital era, we successfully developed a neuro-explicit artificial intelligence model that, given an image from the cloud chamber, automatically annotates most of the particle tracks visible in the image according to the type of particle or process that created it. To achieve this goal, we combined the attention U-Net neural network architecture with methods that model the shape of the detected particle tracks. Our experiments show that the model effectively detects particle tracks and that the neuro-explicit approach decreases the misclassification rate of rare particles by 73% compared with solely using the attention U-Net

Associations between oxytocin and vasopressin concentrations, traumatic event exposure and posttraumatic stress disorder symptoms: group comparisons, correlations, and courses during an internet-based cognitive-behavioural treatment

Background: Posttraumatic stress disorder (PTSD) is characterized by impairments in extinction learning and social behaviour, which are targeted by trauma-focused cognitive behavioural treatment (TF-CBT). The biological underpinnings of TF-CBT can be better understood by adding biomarkers to the clinical evaluation of interventions. Due to their involvement in social functioning and fear processing, oxytocin and arginine vasopressin might be informative biomarkers for TF-CBT, but to date, this has never been tested. Objective: To differentiate the impact of traumatic event exposure and PTSD symptoms on blood oxytocin and vasopressin concentrations. Further, to describe courses of PTSD symptoms, oxytocin and vasopressin during an internet-based TF-CBT and explore interactions between these parameters. Method: We compared oxytocin and vasopressin between three groups of active and former male service members of the German Armed Forces (n = 100): PTSD patients (n = 39), deployed healthy controls who experienced a deployment-related traumatic event (n = 33) and non-deployed healthy controls who never experienced a traumatic event (n = 28). PTSD patients underwent a 5-week internet-based TF-CBT. We correlated PTSD symptoms with oxytocin and vasopressin before treatment onset. Further, we analysed courses of PTSD symptoms, oxytocin and vasopressin from pre- to post-treatment and 3 months follow-up, as well as interactions between the three parameters. Results: Oxytocin and vasopressin did not differ between the groups and were unrelated to PTSD symptoms. PTSD symptoms were highly stable over time, whereas the endocrine parameters were not, and they also did not change in mean. Oxytocin and vasopressin were not associated with PTSD symptoms longitudinally. Conclusions: Mainly due to their insufficient intraindividual stability, single measurements of endogenous oxytocin and vasopressin concentrations are not informative biomarkers for TF-CBT. We discuss how the stability of these biomarkers might be increased and how they could be better related to the specific impairments targeted by TF-CBT

isomiRdb : microRNA expression at isoform resolution

A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients’ samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 × 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland.de/isomirdb

Viewpoints. 75 Sides to Freie Universität Berlin

Das Buch mit 75 Illustrationen und Kurztexten ist eine Reise durch die Geschichte und Welt der Freien Universität Berlin und entstand im April 2023 anlässlich ihres 75-jährigen Gründungsjubiläums. Die Bilder zeigen, ohne Anspruch auf Vollständigkeit, mit Augenzwinkern, eine vernetzte und internationale Universität, die sich seit ihren Anfängen und fortwährend ihren Leitwerten Freiheit, Gerechtigkeit und Wahrheit verpflichtet fühlt und zu einem bedeutenden Teil der Stadt und des Wissenschaftsraums Berlin geworden ist. Aspekte ihrer Geschichte und Gegenwart wurden künstlerisch interpretiert von Yves Haltner, einem Schweizer Illustrator und Grafiker, der in Berlin lebt und arbeitet.The book containing 75 illustrations and short texts is a journey through the history and world of Freie Universität Berlin. It was created in April 2023 to mark the occasion of the 75th anniversary of the university’s founding. With a hint of irony and pointed fragmentary playfulness, the images depict a connected, international university deeply committed to its core values: freedom, justice, truth. The university has become an important part of Berlin as a city and research hub. Various aspects of the past and present of the university were artistically interpreted by Yves Haltner, a Swiss illustrator and graphic designer who lives and works in Berlin

Dynamic and static circulating cancer microRNA biomarkers : a validation study

For cancers and other pathologies, early diagnosis remains the most promising path to survival. Profiling of longitudinal cohorts facilitates insights into trajectories of biomarkers. We measured microRNA expression in 240 serum samples from patients with colon, lung, and breast cancer and from cancerfree controls. Each patient provided at least two serum samples, one prior to diagnosis and one following diagnosis. The median time interval between the samples was 11.6 years. Using computational models, we evaluated the circulating profiles of 21 microRNAs. The analysis yielded two sets of biomarkers, static ones that show an absolute difference between certain cancer types and controls and dynamic ones where the level over time provided higher diagnostic information content. In the first group, miR-99a-5p stands out for all three cancer types. In the second group, miR-155-5p allows to predict lung cancers and colon cancers. Classification in samples from cancer and non-cancer patients using gradient boosted trees reached an average accuracy of 79.9%. The results suggest that individual change over time or an absolute value at one time point may predict a disease with high specificity and sensitivity

How symptoms of simple acute infections affect the SSS-8 and SSD-12 as screening instruments for somatic symptom disorder in the primary care setting

ObjectiveSomatic symptom disorder (SSD) is one of the most common reasons for consultations in primary care, in addition to simple acute infections. Questionnaire-based screening instruments to identify patients at high risk of SSD are thus of great clinical relevance. Although screening instruments are frequently used, it is currently unclear to what extent they are influenced by the concurrent presence of simple acute infections. Therefore, this study aimed to investigate how symptoms of simple acute infections affect the two established questionnaires as screening instruments for somatic symptom disorder in the primary care setting.MethodsIn our cross-sectional, multicenter design, a total of 1,000 patients in primary care practices were screened using the two most established SSD screening questionnaires, the 8-item Somatic Symptom Scale (SSS-8) and the 12-item Somatic Symptom Disorder—B Criteria Scale (SSD-12), followed by clinical assessment by the primary care physician.ResultsA total of 140 patients with a simple acute infection (acute infection group, AIG) and 219 patients with chronic somatic symptoms (somatic symptom group, SSG) were included. The patients in the SSG showed higher total SSS-8 and SSD-12 scores than the patients in the AIG; however, the SSS-8 was more susceptible to changes triggered by symptoms of a simple acute infection than the SSD-12.ConclusionThese results suggest that the SSD-12 is less susceptible to symptoms of a simple acute infection. Its total score and corresponding cutoff value provide a more specific and thus less susceptible screening tool for identifying SSD in primary care

Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues

Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specifc except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specifc ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling

Background: Precision medicine approaches aim to tackle diseases on an individual level through molecular profiling. Despite the growing knowledge about diseases and the reported diversity of molecular phenotypes, the descriptions of human health on an individual level have been far less elaborate. Methods: To provide insights into the longitudinal protein signatures of well-being, we profiled blood plasma collected over one year from 101 clinically healthy individuals using multiplexed antibody assays. After applying an antibody validation scheme, we utilized > 700 protein profiles for in-depth analyses of the individuals’ short-term health trajectories. <p<Findings: We found signatures of circulating proteomes to be highly individual-specific. Considering technical and longitudinal variability, we observed that 49% of the protein profiles were stable over one year. We also identified eight networks of proteins in which 11 242 proteins covaried over time. For each participant, there were unique protein profiles of which some could be explained by associations to genetic variants. Interpretation: This observational and non-interventional study identifyed noticeable diversity among clinically healthy subjects, and facets of individual-specific signatures emerged by monitoring the variability of the circulating proteomes over time. To enable more personal hence precise assessments of health states, longitudinal profiling of circulating proteomes can provide a valuable component for precision medicine approaches

Ageing-associated small RNA cargo of extracellular vesicles

Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2–18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR