Biology subjects

Braun, D.

Publications and source records attributed to Braun, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Electroencephalographic activity patterns distinguish interdigitated default and frontoparietal networks

The brain is comprised of distributed functional networks that operate on diverse time scales. Evidence from precision fMRI shows that canonical networks, including default (DN), frontoparietal control (FPCN), and dorsal attention (dATN), each fractionate into multiple finely interdigitated networks. However, as fMRI is blind to fast processes underlying neural communication, there remains a need to neurophysiologically characterize individual-level network fractionation. To address this need, we conducted a simultaneous EEG-fMRI study, including multiple sessions per individual, resting-state and task conditions, and carbon wire loop sensors for optimized artifact correction. Using precision network mapping, we discovered dissociable electrophysiological correlates of blood-oxygen-level-dependent activity for two networks within the boundaries of the canonical DN. One (DNa) related more positively with alpha and high-beta power, while another (DNb) related more negatively with theta and low-beta power. Univariate and machine learning analyses further revealed electrophysiological dissociations between networks within the canonical FPCN (FPCNa versus FPCNb) but not dATN. The network-specific electrophysiological activity patterns were reliable across sessions, only modestly variable between resting-state and demanding task conditions, and observable for neighboring nodes of different networks across multiple cortical zones. Our findings provide insight into rhythmic neural processes that fine-grained networks may engage to support divergent cognitive operations.

neuroscience↗

bioRxiv2026

Real-time fMRI-triggered experience-sampling: a proof-of-concept study

Much of a typical individuals mental life is characterized by spontaneous thoughts that occur independently of external stimuli. In prior studies, ongoing mental experiences and their neural correlates have been captured using thought probes presented at random intervals during functional Magnetic Resonance Imaging (fMRI). However, this approach results in temporally imprecise estimates of brain activity relative to the arising of mental experience. In this preregistered, proof-of-concept study, we aimed to improve temporal precision using a novel method termed real-time fMRI-triggered experience-sampling (rt-fMRI-ES). We analyzed blood-oxygenation-level-dependent signals in real time during a wakeful resting state (n=60) to trigger thought probes from spontaneous activations within two regions: the dorsal anterior insular cortex (daIC; a key region within salience network) and posteromedial cortex (PMC; a key region within default mode network). We tested two preregistered hypotheses: (H1) Ratings of arousal time-locked to daIC-activation trials are higher than ratings time-locked to non-daIC-activation trials; (H2) Ratings of external-attention time-locked to PMC-activation trials are lower than ratings time-locked to non-PMC-activation trials. After applying preregistered exclusion criteria, 42 participants (1243 trials) and 49 participants (1429 trials) were included in H1 and H2 analyses, respectively. We did not find evidence in support of H1, but we did find evidence in support of H2, as external-attention ratings were significantly lower for trials triggered by PMC activation compared to other trial types. Taken together, we successfully developed and validated the rt-fMRI-ES method, offering a novel technique to efficiently capture spontaneous thoughts based on ongoing neural activity. Preregistered Stage 1 Recommendationhttps://osf.io/sd4hu (Date of in-principle acceptance: 07/24/2024; under temporary private embargo)

neuroscience↗

bioRxiv2026

Enhanced RNA Formation Under Amine-Rich Local Atmospheres from 2',3'- Cyclic Nucleotides

The core biopolymers (DNA, RNA and proteins) are assembled from their monomers under conditions that avoid water. RNA is crucial for the Origin of Life. When cleaved from its polymerized state, RNA first transitions to nucleoside 2,3-cyclic phosphates. In the reverse direction, RNA polymerizes from 2,3-cyclic monomers in dry states, creating short oligomers that then can ligate on a template under aqueous, alkaline conditions. We studied the role of the counterions in polymerization of 2,3-cyclic nucleotides under geologically plausible settings. Through experiments and simulations, we demonstrate that the presence of ammonium and alkylammonium counterions greatly improves RNA polymerization. The otherwise less reactive cytidine containing monomers formed polyC sequences of up to heptamers; copolymers of AU, GC, or GCAU were detected up to hexamers. Our findings suggest three reasons for this: (1) (Alkyl)ammonium cations form hydrogen bonds with phosphates, (2) their alkaline pKa value can trigger general base catalysis, and (3) (alkyl)ammonium salts naturally form dry, anhydrous materials. The findings indicate that pyrolyzed organic tars creating ammonia-rich gas pockets in subsurface rocks could have enhanced the early evolution of RNA. TOC image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/713775v1_ufig1.gif" ALT="Figure 1"> View larger version (112K): org.highwire.dtl.DTLVardef@1adc431org.highwire.dtl.DTLVardef@12b8da0org.highwire.dtl.DTLVardef@5f187dorg.highwire.dtl.DTLVardef@140ed1a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

A multi-session simultaneous EEG-fMRI dataset with repeated experience sampling

The integration of electroencephalography (EEG) and functional Magnetic Resonance Imaging (fMRI) can be used to characterize temporal and spatial components of neural activity during unfolding mental experience. Here we introduce a multi-session simultaneous EEG-fMRI dataset with measures of continuous behavior and spontaneous mental experience. Data components, organized in Brain Imaging Dataset Structure (BIDS) format, include fMRI, EEG with carbon wire loop sensors for artifact removal, continuous performance task responses, experience sampling ratings, and mental health surveys, from 24 healthy adults. Tasks included the gradual-onset continuous performance task and resting state with intermittent experience sampling of 13 unique thought dimensions (36 repetitions, including 468 total ratings, per participant). The same protocol was completed on two different days, yielding approximately 1.33 hours of simultaneous EEG-fMRI data per individual. The dataset may be used to explore the behavioral and experiential relevance of brain activity during the wakeful resting state. The dataset also provides a means to study the reliability of relationships between fMRI and EEG features across sessions within individuals.

neuroscience↗

bioRxiv2025

CNS-penetrant NLRP3 inhibitor achieves durable weight loss and reverses hypothalamic inflammation in diet-induced obesity

The NLRP3 inflammasome is a key mediator of innate immunity that integrates inflammatory and metabolic stress signals. Increased and/or chronic activation of this critical pathway has been implicated in obesity, with hypothalamic neuroinflammation linked to dysregulation of energy balance. TN-783 is an investigational, CNS-penetrant, small-molecule NLRP3 inhibitor that potently suppressed inflammasome activation across multiple in vitro assays. In diet-induced obese (DIO) mice, only TN-783, and not the peripherally restricted NLRP3 inhibitor TN-101, produced progressive and sustained weight loss, underscoring the requirement for central target engagement. Weight loss was driven by a persistent reduction in food intake across both acute and chronic phases, without altering energy expenditure. This effect was further characterized by selective reduction of fat mass, with minimal impact on lean tissues. Mechanistically, NLRP3 inhibition attenuated DIO-induced hypothalamic neuroinflammation and partially reversed obesity-associated molecular changes based on transcriptomic and proteomic profiling of the hypothalamus. Beyond monotherapy, TN-783 enhanced the effects of the GLP-1 receptor agonist semaglutide by amplifying weight loss, reinitiating weight loss after semaglutide effect had plateaued, and maintaining the weight loss benefit after semaglutide withdrawal. Discontinuation of TN-783 resulted in reversal of both weight and feeding effects, indicating that its therapeutic activity requires ongoing target engagement rather than permanent remodeling of metabolic pathways. Collectively, these observations support central NLRP3 inhibition as a distinct and promising approach for obesity treatment, offering robust induction and sustained maintenance of weight loss while preserving reversibility.

neuroscience↗

bioRxiv2025

Scaling Large Language Models for Next-Generation Single-Cell Analysis

AO_SCPLOWBSTRACTC_SCPLOWSingle-cell RNA sequencing has transformed our understanding of cellular diversity, yet current single-cell foundation models (scFMs) remain limited in their scalability, flexibility across diverse tasks, and ability to natively integrate textual information. In this work, we build upon the Cell2Sentence (C2S) framework, which represents scRNA-seq profiles as textual "cell sentences," to train Large Language Models (LLMs) on a corpus comprising over one billion tokens of transcriptomic data, biological text, and metadata. Scaling the model to 27 billion parameters yields consistent improvements in predictive and generative capabilities and supports advanced downstream tasks that require synthesis of information across multi-cellular contexts. Targeted fine-tuning with modern reinforcement learning techniques produces strong performance in perturbation response prediction, natural language interpretation, and complex biological reasoning. This predictive strength enabled a dual-context virtual screen that nominated the kinase inhibitor silmitasertib (CX-4945) as a candidate for context-selective upregulation of antigen presentation. Experimental assessment in human cell models unseen during training supported this prediction, demonstrating that C2S-Scale can effectively guide the discovery of context-conditioned biology. C2S-Scale unifies transcriptomic and textual data at unprecedented scales, surpassing both specialized single-cell models and general-purpose LLMs to provide a platform for next-generation single-cell analysis and the development of "virtual cells."

bioinformatics↗

bioRxiv2025

Neural sensitivity to the heartbeat is modulated by spontaneous fluctuations in subjective arousal during wakeful rest

Spontaneous thoughts, occupying much of ones awake time in daily life, are often colored by emotional qualities. While spontaneous thoughts have been associated with various neural correlates, the relationship between subjective qualities of ongoing experiences and the brains sensitivity to bodily signals (i.e., interoception) remains largely unexplored. Given the well-established role of interoception in emotion, clarifying this relationship may elucidate how processes relevant to mental health, such as arousal and anxiety, are regulated. We used EEG and ECG to measure the heartbeat evoked potential (HEP), an index of interoceptive processing, while 51 adult participants (34 male, 20 female) visually fixated on a cross image and let their minds wander freely. At pseudo-random intervals, participants reported their momentary level of arousal. This measure of affective arousal was highly variable within and between individuals but was statistically unrelated to several markers of physiological arousal, including heart rate, heart rate variability, time on task, and EEG alpha power at posterior electrodes. A cluster-based permutation analysis revealed that the HEP amplitude was increased during low relative to high affective arousal in a set of frontal electrodes during the 340 - 356 millisecond window after heartbeat onset. This HEP effect was more pronounced in individuals who reported high, relative to low, levels of trait anxiety. Together, our results offer novel evidence that at varying levels of trait anxiety, the brain differentially modulates sensitivity to bodily signals in coordination with the momentary, spontaneous experience of affective arousal--a mechanism that may operate independently of physiological arousal. Significance StatementOur findings highlight the relationships between spontaneous fluctuations in affective arousal, brain-body interactions, and anxiety, offering new insights into how interoception fluctuates with changes in internal states. By showing that interoceptive processing is heightened during lower affective arousal and that this effect is amplified in individuals with higher trait anxiety, our study suggests the brain adaptively downregulates interoceptive sensitivity in response to fluctuating internal states. These results have implications for understanding how spontaneous thoughts shape interoception and emotion, particularly in clinical contexts where dysregulated interoception is linked to anxiety and mood disorders. More broadly, our work underscores the need to distinguish between different forms of arousal, advancing understanding of the taxonomy and ways of measuring arousal.

neuroscience↗

bioRxiv2024

The challenge of sequencing Chlamydia trachomatis and other bacterial STI genomes directly from clinical swabs: the optimum solution

Rates of bacterial sexually transmitted infections (STIs) are rising and accessing their genomes provides information on strain evolution, circulating strains, and encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Treponema pallidum (TP), globally the most common bacterial STIs. Mycoplasma genitalium (MG) is also a bacterial STI which is of concern due to AMR development. These bacteria are also fastidious or hard to culture, and standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts of human and other microbiota DNA. These factors hinder the sequencing of bacterial STI genomes. We aimed to overcome these challenges in obtaining whole genome sequences, and evaluated four approaches using clinical samples from Argentina (39), Switzerland (14), and cultured samples from Finland (2) and Argentina (1). First, direct genome sequencing from swab samples was attempted through Illumina deep metagenomic sequencing, showing extremely low levels of target DNA, with under 0.01% of the sequenced reads being from the target pathogens. Second, host DNA depletion followed by Illumina sequencing was not found to produce enrichment in these very low load samples. Third, we tried a selective long-read approach with the new adaptive sequencing from Oxford Nanopore Technologies (ONT), which also did not improve enrichment sufficiently to provide genomic information. Finally, target enrichment using a novel pan-genome set of custom SureSelect probes targeting CT, NG, TP, and MG followed by Illumina sequencing was successful. We produced whole genomes from 64% of CT positive samples; from 36% of NG positive samples, and from 60% of TP positive samples. Additionally, we enriched MG DNA to gain partial genomes from 60% of samples. This is the first publication to date to utilize a pan-genome STI panel in target enrichment. Target enrichment, though costly, proved essential for obtaining genomic data from clinical samples. This data can be utilized to examine circulating strains, genotypic resistance, and guide public health strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/624631v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@578aeborg.highwire.dtl.DTLVardef@16185f9org.highwire.dtl.DTLVardef@1a2ae87org.highwire.dtl.DTLVardef@1703fa7_HPS_FORMAT_FIGEXP M_FIG C_FIG Impact statementGenome data on circulating sexually transmitted infections (STIs) is important to better understand transmission networks, antimicrobial resistance and to guide treatment decisions. For many bacterial STIs, this information is difficult to obtain, as the bacteria are fastidious, in some cases intracellular, and often recalcitrant to culture. We have developed and tested a target enrichment STI panel of baits to capture whole genomes of Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, and Mycoplasma genitalium with approximately 50% success in genome sequencing for the first three pathogens. We compare this against other sequencing and enrichment methods, which did not provide sufficient data for genome analysis. This panel approach shows potential for clinical samples carrying these pathogens and can potentially also be developed for further pathogen groups. Data summaryAll illumina sequence data, with human read data removed using Hostile (1) and KrakenTools (https://github.com/jenniferlu717/KrakenTools), is deposited with the European Nucleotide Archive (ENA) under project number PRJEB72167.

microbiology↗

bioRxiv2024

Global and compartmentalized serotonergic control of sensorimotor integration underlying motor adaptation

The vertebrate serotonergic system plays a critical role in modulating adaptive behavior. Yet, it has been challenging to unravel the downstream targets and the effects of serotonin on ongoing neural dynamics due to its widespread innervation and the complex nature of receptor signaling. Here, we show that the serotonergic system controls brain-wide neural dynamics in a spatially dualistic manner, global and compartmentalized, during motor adaptation behavior in zebrafish. Larval zebrafish adapt the vigor of tail motions depending on environmental drag force during visual pursuit behavior in a serotonin-dependent manner. Whole-brain imaging of serotonin release and systematic spatial mapping of serotonin receptors showed highly compartmentalized patterns that span multiple brain areas. Interestingly, whole-brain neural activity imaging combined with the perturbation of tph2+ raphe serotonin neurons revealed dualistic modulation of neural activity depending on behavioral encoding: global suppression of locomotor networks and the compartmentalized enhancement of midbrain sensory networks, both of which synergistically enabled motor adaptation. The compartmentalized modulation resulted from local serotonin release and receptor expression, while the global effect was due to modulation of a key network hub that broadcasts behavioral state signals. Our results reveal how the serotonergic system interacts with brain-wide neural dynamics through its parallel interactions and provide a conceptual framework for understanding the neural mechanisms of widespread serotonergic behavioral control.

neuroscience↗

bioRxiv2024

Heat flows solubilize apatite to boost phosphate availability for prebiotic chemistry

Phosphorus is an essential building block of the most prominent biomolecules, such as polynucleic acids, and has likely played that role since the beginning of life. Despite this importance for prebiotic chemistry, phosphate could not be supplied by the atmosphere, and had to be fueled mainly by geological phosphate sources. However, phosphorus was scarce in Earths rock record and often bound in poorly soluble minerals, with the calcium phosphate mineral apatite as key example. While specific chemical boundary conditions that bind calcium have been used to address this so-called phosphate problem, a fundamental process that solubilizes and enriches phosphate from geological sources remains elusive. Here, we show that ubiquitous heat flows through rock cracks can liberate phosphate from apatite by the selective removal of calcium. Phosphates surprisingly strong thermophoresis not only achieves its 100-fold up-concentration in aqueous solution, in particular it also boosts its solubility by two orders of magnitude. We show that the heat-flow-solubilized phosphate can feed the synthesis of trimetaphosphate, increasing the conversion 260-fold compared to the thermal equilibrium case. Heat flows thus enhance solubility as a geological parameter to unlock apatites as phosphate source for prebiotic chemistry, providing a key element in solving early lifes phosphate problem.

biophysics↗

bioRxiv2024

Prebiotic gas flow environment enables isothermal nucleic acid replication

Nucleic acid replication is a central process at the origin of life. On early Earth, replication is challenged by the dilution of molecular building blocks and the difficulty of separating daughter from parent strands, a necessity for exponential replication. While thermal gradient systems have been shown to address these problems, elevated temperatures lead to degradation. Also, compared to constant temperature environments, such systems are rare. The isothermal system studied here models an abundant geological environment of the prebiotic Earth, in which water is continuously evaporated at the point of contact with the gas flows, inducing up-concentration and circular flow patterns at the gas-water interface through momentum transfer. We show experimentally that this setting drives a 30-fold accumulation of nucleic acids and their periodic separation by a 3-fold reduction in salt and product concentration. Fluid dynamic simulations agree with observations from tracking fluorescent beads. In this isothermal system, we were able to drive exponential DNA replication with Taq polymerase. The results provide a model for a ubiquitous non-equilibrium system to host early Darwinian molecular evolution at constant temperature.

biophysics↗

bioRxiv2024

Individual variability in neural representations of mind-wandering

Mind-wandering is a frequent, daily mental activity, experienced in unique ways in each person. Yet neuroimaging evidence relating mind-wandering to brain activity, for example in the default mode network (DMN), has relied on population-rather than individual-based inferences due to limited within-individual sampling. Here, three densely-sampled individuals each reported hundreds of mind-wandering episodes while undergoing multi-session functional magnetic resonance imaging. We found reliable associations between mind-wandering and DMN activation when estimating brain networks within individuals using precision functional mapping. However, the timing of spontaneous DMN activity relative to subjective reports, and the networks beyond DMN that were activated and deactivated during mind-wandering, were distinct across individuals. Connectome-based predictive modeling further revealed idiosyncratic, whole-brain functional connectivity patterns that consistently predicted mind-wandering within individuals but did not fully generalize across individuals. Predictive models of mind-wandering and attention that were derived from larger-scale neuroimaging datasets largely failed when applied to densely-sampled individuals, further highlighting the need for personalized models. Our work offers novel evidence for both conserved and variable neural representations of self-reported mind-wandering in different individuals. The previously-unrecognized inter-individual variations reported here underscore the broader scientific value and potential clinical utility of idiographic approaches to brain-experience associations.

neuroscience↗

bioRxiv2023

Replication elongates short DNA, reduces sequence bias, and develops trimer structure

The origin of molecular evolution required the replication of short oligonucleotides to form longer polymers. Prebiotically plausible oligonucleotide pools tend to contain more of some nucleotide bases than others. It has been unclear whether this initial bias persists and how it affects replication. To investigate this, we examined the evolution of 12 mer biased short DNA pools during enzymatic templated polymerization. Our analysis using next-generation sequencing from different time points revealed that the initial nucleotide bias of the pool disappeared in the elongated pool after isothermal replication. In contrast, the nucleotide composition at each position in the elongated sequences remained biased and varied with both position and initial bias. Furthermore, we observed the emergence of highly periodic dimer and trimer motifs in the rapidly elongated sequences. This shift in nucleotide composition and the emergence of structure through templated replication could help explain how biased prebiotic pools could undergo molecular evolution and lead to complex functional nucleic acids.

biophysics↗

bioRxiv2023

High-resolution tracking of unconfined zebrafish behavior reveals stimulatory and anxiolytic effects of psilocybin

Serotonergic psychedelics are emerging therapeutics for psychiatric disorders, yet their underlying mechanisms of action in the brain remain largely elusive. Zebrafish have evolutionarily conserved serotonergic circuits and subcortical targets such as the brainstem regions and the cerebellum, providing a promising model for studying the subcortical effects of serotonergic drugs. Here, we developed a wide-field behavioral tracking system for larval zebrafish and investigated the effects of psilocybin, a psychedelic serotonin receptor agonist. Machine learning analyses of precise body kinematics identified latent behavioral states reflecting spontaneous exploration, visually-driven rapid swimming, and irregular swim patterns following stress exposure. Using this method, we identified two main behavioral effects of acute psilocybin treatment: [i] increased rapid swimming in the absence of visual stimuli and [ii] prevention of irregular swim patterns following stress exposure. Together, these effects indicate that psilocybin induces a brain state that is both stimulatory and anxiolytic. These findings pave the way for using larval zebrafish to elucidate subcortical mechanisms underlying the behavioral effects of serotonergic psychedelics.

neuroscience↗

bioRxiv2023

Variant-specific Mendelian Risk Prediction Model

Many pathogenic sequence variants (PSVs) have been associated with increased risk of cancers. Mendelian risk prediction models use Mendelian laws of inheritance to predict the probability of having a PSV based on family history, as well as specified PSV frequency and penetrance (agespecific probability of developing cancer given genotype). Most existing models assume penetrance is the same for any PSVs in a certain gene. However, for some genes (for example, BRCA1/2), cancer risk does vary by PSV. We propose an extension of Mendelian risk prediction models to relax the assumption that risk is the same for any PSVs in a certain gene by incorporating variant-specific penetrances and illustrating these extensions on two existing Mendelian risk prediction models, BRCAPRO and PanelPRO. Our proposed BRCAPRO-variant and PanelPRO-variant models incorporate variant-specific BRCA1/2 PSVs through the region classifications. Due to the sparsity of the variant information we classify BRCA1/2 PSVs into three regions; the breast cancer clustering region (BCCR), the ovarian cancer clustering region (OCCR), and an other region. Simulations were conducted to evaluate the performance of the proposed BRCAPRO-variant model compared to the existing BRCAPRO model which assumes the penetrance is the same for any PSVs in BRCA1 (and respectively BRCA2). Simulation results showed that the BRCAPRO-variant model was well calibrated to predict region-specific BRCA1/2 carrier status with high discrimination and accuracy on the region-specific level. In addition, we showed that the BRCAPRO-variant model achieved performance gains over the existing risk prediction models in terms of calibration without loss in discrimination and accuracy. We also evaluated the performance of the two proposed models, BRCAPRO-variant and PanelPRO-variant, on a cohort of 1,961 families from the Cancer Genetics Network (CGN). We showed that our proposed models provide region-specific PSV carrier probabilities with high accuracy, while the calibration, discrimination and accuracy of gene-specific PSV carrier probabilities were comparable to the existing gene-specific models. As more variant-specific PSV penetrances become available, we have shown that Mendelian risk prediction models can be extended to integrate the additional information, providing precise variant or region-specific PSV carrier probabilities and improving future cancer risk predictions.

genetics↗

bioRxiv2022

Selection of the Early Genetic Code by Ultraviolet Light

The DNA sequences available in the prebiotic era were the genomic building blocks of the first life forms on Earth and have therefore been a matter of intense debate.1,2 On the surface of the Early Earth, ultraviolet (UV) light is a key energy source3, which is known to damage nucleic acids4. However, a systematic study of the sequence selectivity upon UV exposure under Early Earth conditions is still missing. In this work, we quantify the UV stability of all possible canonical DNA sequences and derive information on codon appearance under UV irradiation as selection pressure. We irradiate a model system of random 8mers at 266 nm and determine its UV stability via next-generation sequencing. As a result, we obtain the formation rates of the dominant dimer lesions as a function of their neighboring sequences and find a strong sequence selectivity. On the basis of our experimental results, we simulate the photodamage of short proto-genomes of 150 bases length by a Monte Carlo approach. Our results strongly argue for UV compatibility of early life and allow the ranking of codon evolutionary models with respect to their UV resistance.

biophysics↗

bioRxiv2022

Sequence Dependent UV Damage of Complete Pools of Oligonucleotides

Understanding the sequence-dependent DNA damage formation requires to probe a complete pool of sequences over a wide dose range of the damage causing exposure. We used high throughput sequencing to simultaneously obtain the dose dependence and quantum yields for oligonucleotide damages for all possible 4096 DNA sequences with hexamer length. We exposed the DNA with ultraviolet radiation at 266 nm and doses of up to 500 photons per base. At the dimer level our results confirm existing literature values, whereas we now quantified the susceptibility of sequence motifs to UV irradiation up to previously inaccessible polymer lengths. This revealed the protective effect of the sequence context in preventing the formation of UV-lesions. For example, the rate to form dipyrimidine lesions is strongly reduced by nearby guanine bases. Our results provide a complete picture of the sensitivity of oligonucleotides to UV irradiation and allow to predict their survival chances in high-UV environments.

biophysics↗

bioRxiv2022

Sensing the Full Dynamics of the Human Hand with a Neural Interface and Deep Learning

Theories about the neural control of movement are largely based on movement-sensing devices that capture the dynamics of predefined anatomical landmarks. However, neuromuscular interfaces such as surface electromyography (sEMG) can potentially overcome the limitations of these technologies by directly sensing the motor commands transmitted to the muscles. This allows for the continuous, real-time prediction of kinematics and kinetics without being limited by the biological and physical constraints that affect motion-based technologies. In this work, we present a deep learning method that can decode and map the electrophysiological activity of the forearm muscles into movements of the human hand. We recorded the kinematics and kinetics of the human hand during a wide range of grasping and individual digit movements covering more than 20 degrees of freedom of the hand at slow (0.5 Hz) and fast (1.5 Hz) movement speeds in healthy participants. The input of the model consists of three-hundred EMG sensors placed only on the extrinsic hand muscles. We demonstrate that our neural network can accurately predict the kinematics and contact forces of the hand even during unseen movements and with simulated real-time resolution. By examining the latent space of the network, we find evidence that it has learned the underlying anatomical and neural features of the sEMG that drive all hand motor behaviours.

neuroscience↗