SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

Background: Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated. Results: We analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that the

The sense of agency as tracking control

Does sense of agency (SoA) arise merely from action-outcome associations, or does an additional real-time process track each step along the chain? Tracking control predicts that deviant intermediate steps between action and outcome should reduce SoA. In two experiments, participants learned mappings between two finger actions and two tones. In later test blocks, actions triggered a robot hand moving either the same or a different finger, and also triggered tones, which were congruent or incongruent with the mapping. The perceived delay between actions and tones gave a proxy measure for SoA. Action-tone binding was stronger for congruent than incongruent tones, but only when the robot movement was also congruent. Congruent tones also had reduced N amplitudes, but again only when the robot movement was congruent.We suggest that SoA partly depends on a real time tracking control mechanism, since deviant intermediate action of the robot reduced SoA over the tone

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Do Research Software Engineers and Software Engineering Researchers Speak the Same Language?

Anecdotal evidence suggests that Research Software Engineers (RSEs) and Software Engineering Researchers (SERs) often use different terminologies for similar concepts, creating communication challenges. To better understand these divergences, we have started investigating how SE fundamentals from the SER community are interpreted within the RSE community, identifying aligned concepts, knowledge gaps, and areas for potential adaptation. Our preliminary findings reveal opportunities for mutual learning and collaboration, and our systematic methodology for terminology mapping provides a foundation for a crowd-sourced extension and validation in the future

Rapid and Precise Semi-Automatic Axon Quantification in Human Peripheral Nerves

We developed a time-efficient semi-automated axon quantification method using freeware in human cranial nerve sections stained with paraphenylenediamine (PPD). It was used to analyze a total of 1238 facial and masseteric nerve biopsies. The technique was validated by comparing manual and semi-automated quantification of 129 (10.4%) randomly selected biopsies. The software-based method demonstrated a sensitivity of 94% and a specificity of 87%. Semi-automatic axon counting was significantly faster (p<0.001) than manual counting. It took 1hour and 47minutes for all 129 biopsies (averaging 50sec per biopsy, 0.04seconds per axon). The counting process is automatic and does not need to be supervised. Manual counting took 21hours and 6minutes in total (average 9minutes and 49seconds per biopsy, 0.52seconds per axon). Our method showed a linear correlation to the manual counts (R=0.944 Spearman rho). Attempts have been made by several research groups to automate axonal load quantification. These methods often require specific hard- and software and are therefore only accessible to a few specialized laboratories. Our semi-automated axon quantification is precise, reliable and time-sparing using publicly available software and should be useful for an effective axon quantification in various human peripheral nerves