Biology subjects

Zimmermann, E.

Publications and source records attributed to Zimmermann, E..

12 recordsLinked to original sources

bioRxiv2026

Movement planning predictions shape somatosensory sensitivity

Tactile sensitivity is reduced during limb movement, a phenomenon known as somatosensory gating. Here, across two experiments, we ask whether gating is driven by motor prediction or by motor execution. In a Go/NoGo paradigm, in which participants planned movements in every trial but on rare trials had to withhold them. Since previous work indicated that predictions about movement kinematics influence gating also during passive movements, we also tested a mechanical arm transport in a passive Go/NoGo paradigm. Perceived intensity was attenuated exclusively on Go trials, in both active and passive movements, and was indistinguishable from baseline on NoGo trials. However, discrimination precision was selectively degraded in Active NoGo trials when a movement was planned and then withheld. In Experiment 2, vibro-tactile probes delivered before movement onset already showed the same bias as probes delivered during movement, in both active and passive conditions, while precision remained unchanged. Our data demonstrates that the sensorimotor system predictively establishes tactile precision before movement onset. Such a mechanism might contribute to active texture exploration by separating tactile signals from the sensory signals arising through the self-produced movement.

neuroscience↗

bioRxiv2026

Vermeer: Autoregressive generative modeling of microscopy predicts protein localization

Fluorescent microscopy provides a rich view into how proteins localize within cells, but it remains experimentally infeasible to image human proteins across all of the different factors that can impact localization. We introduce Vermeer, a channel-adaptive autoregressive generative model for in silico generation of microscopy images of protein localization. Vermeer conditions generations on protein sequences and landmark stains showing the morphology of cells, which enables it to generalize to unseen proteins and cell lines. We show that Vermeer, trained on the Human Protein Atlas, can generate images with substantially improved perceptual quality and biological fidelity over previous proposals. Additionally, Vermeers autoregressive framework enables flexible generation using varying channel subsets and orderings, enabling zero-shot transfer to data collected under different imaging conditions and channel configurations than those used for training. These results position Vermeer to enable scalable modeling of protein localization and is a step towards generative foundation models that can operate over distinct microscopy datasets. Code is publicly accessible at https://github.com/microsoft/vermeer.git.

cell biology↗

bioRxiv2026

Effects of prediction and attention on tactile precision in somatosensory gating

Tactile sensitivity is reduced when the limb is in motion, a phenomenon known as somatosensory gating. In a previous study, we demonstrated that discrimination precision but not perceived intensity differed between active and passive movements. Here, we asked whether and how spatial attention modulates tactile precision in active and passive movements. Participants judged the relative intensity of two vibrations while the arm was still, actively moved, or passively transported by a movable platform. Visual attention was directed either to the movement start or goal position. Perceptual bias was reduced during both active and passive movement, independent of attentional allocation. In contrast, precision remained stable during active movement but declined during passive movement when attention was directed to the movement start. However, when attention was focused on the movement goals, precision was also high when doing passive movements. These findings indicate that during active movements, predictions based, likely on an efference copy, ensure tactile precision, whereas passive movements require spatial attention directed to the movement goal.

neuroscience↗

bioRxiv2026

Beyond alignment: synergistic integration is required for multimodal cell foundation models

The vision of a "virtual cell"--a computational model that simulates biological function across modalities and scales--has become a defining goal in computational biology. While powerful unimodal foundation models exist, the lack of large-scale paired data prohibits the joint training of multimodal approaches. This scarcity favors compositional foundation models (CFMs): architectures that fuse frozen unimodal experts via a learned interface. However, it remains unclear when this multimodal fusion adds task-relevant information beyond the strongest unimodal representation and when it merely aggregates redundant signal. Here, we introduce the Synergistic Information Score (SIS), a metric grounded in partial information decomposition (PID), that quantifies the information gain achievable only through cross-modal interactions. Extending theoretical results from self-supervised learning, we show that standard alignment-based fusion objectives on frozen encoders inherently collapse to detecting linear redundancies, limiting their ability to capture nonlinear synergistic states. This distinction is directly relevant for tasks aiming to link tissue morphology and gene expression. Benchmarking ten fusion methods on spatial transcriptomics datasets, we use SIS to demonstrate that tasks dominated by linear redundancies are sufficiently served by unimodal baselines, whereas complex niche definitions benefit from synergy-aware integration objectives that enable cross-modal interactions beyond linear alignment. Finally, we perform a scaling analysis which highlights that fine-tuning a dominant unimodal expert is the most sample-efficient path for standard tasks, suggesting that the benefits of multimodal frameworks only emerge when tasks depend on information distributed across modalities. Together, these results establish that building towards a virtual cell will require a fundamental shift from alignment objectives that emphasize shared structure to synergy-maximizing integration that preserves and exploits complementary cross-modal signal.

bioinformatics↗

bioRxiv2025

Impact of Group Size and Habitat Disturbance on Parasitic Infection in Free-ranging Proboscis Monkeys

Group-living primates experience the benefits and costs associated with sociality, including an elevated risk of parasite transmission. However, the relative influence of group type (i.e., social structure), group size, and habitat disturbance on parasitic infection remains unclear, particularly in Southeast Asian primates. In this study, the abundance of intestinal parasites in proboscis monkeys (Nasalis larvatus) inhabiting a riverine forest along the Menanggul River, Sabah, Malaysian Borneo, was investigated. Fecal samples (n = 160) were collected from one-male-multifemale and all-male groups in areas with varying levels of anthropogenic disturbance, with efforts made to ensure that each sample originated from a different individual. In addition, the effects of group type, group size, and sampling location on parasite abundance were evaluated using fecal egg counts and Bayesian models. Three dominant parasite species groups (Trichuris sp., Strongyloides fuelleborni, and Oesophagostomum aculeatum) with an overall infection prevalence of 81.25% were identified. Results showed that group type did not significantly affect parasite abundance. However, group size showed a positive correlation with the abundance of Trichuris sp. and a negative correlation with S. fuelleborni and O. aculeatum. In addition, our models revealed that the infection load of Trichuris sp. decreased with increasing distance from the river mouth, which was used as a proxy for a disturbance gradient, whereas O. aculeatum exhibited higher infection load at greater distances, indicating lower prevalence in more disturbed downstream areas. Thus, parasite abundance in proboscis monkeys may be shaped by social and environmental factors, with taxa-specific responses likely reflecting differences in environmental persistence and transmission ecology.

ecology↗

bioRxiv2023

Visuo-motor updating in autism symptomatology

Autism Spectrum Disorder (ASD) presents a range of challenges, including heightened sensory sensitivities. Here, we examine the idea that sensory overload in ASD may be linked to issues with efference copy mechanisms, which predict the sensory outcomes of self-generated actions, such as eye movements. Efference copies play a vital role in maintaining visual and motor stability. Disrupted efference copies hinder precise predictions, leading to increased reliance on actual feedback and potential distortions in perceptions across eye movements. In our first experiment, we tested how well healthy individuals with varying levels of autistic traits updated their mental map after making eye movements. We found that those with more autistic traits had difficulty using information from their eye movements to update the spatial representation of their mental map, resulting in significant errors in object localization. In the second experiment, we looked at how participants perceived an object displacement after making eye movements. Using a trans-saccadic spatial updating task, we found that those with higher autism scores exhibited a greater bias, indicating under-compensation of eye movements and a failure to maintain spatial stability during saccades. Overall, our study underscores efference copys vital role in visuo-motor stability, aligning with Bayesian theories of autism, potentially informing interventions for improved action-perception integration in autism.

neuroscience↗

bioRxiv2023

Time is Confidence: Monetary Incentives Metacognitive Profile on Duration Judgment

The question we addressed in the current study is whether the mere prospect of monetary reward affects subjective time perception. To test this question, we collected trail-based confidence reports in a task in which subjects made categorical decisions about probe durations relative to the reference duration. When there was a potential to gain monetary reward, the duration was perceived to be longer than in the neutral condition, and confidence, which reflects the perceived probability of being correct, was higher in the reward condition than in the neutral condition. We found that confidence influences the sense of time in different individuals: subjects with high-confidence reported that they perceived the duration signaled by the monetary gain condition as longer than subjects with low-confidence. Our results showed that only high-confidence individuals overestimated the monetary gain context. Finally, we found a negative relationship between confidence and time perception, and that confidence bias at the maximum uncertainty duration of 450 ms is predictive of time perception. Taken together, the current study demonstrates that subjective measure of the confidence profile caused overestimation of time rather than by the outcome valence of reward expectancy.

neuroscience↗

bioRxiv2022

Statistical Learning Emerges from Temporally Preparing What Action to Perform Where

Timing studies on statistical learning predominantly present temporal regularities in a discrete, trial-by-trial manner. This, however, is a simplified representation of natures complex temporal structure in which regularities are embedded in a continuous stream of interrupting, irregular events. Recent studies using more complex, dynamic experimental tasks have nevertheless replicate the ubiquitous finding of a performance benefit for regular versus irregular timed events. This regularity benefit is commonly interpreted to emerge from a mechanism that detects and subsequently exploits the regularity as it would be impossible for irregular timed events. In contrast, here we show that this interpretation overlooks the influence of learning various time-related factors that contribute to the regularity benefit in such complex temporal environments. Instead of only learning the temporal regularity, participants exploited the temporal properties of targets that we initially considered as irregular and uninformative. Participants temporally prepared, in parallel, for different actions to perform and locations to attend, irrespective of targets regularity. In fact, this temporal preparation explained regularity benefits without assuming statistical learning of the regular target. Using a computational model, f MTP, we illustrate that such adaptation can arise from associative memory processes underlying temporal preparation.

neuroscience↗

bioRxiv2022

Proteome coverage after simultaneous proteo-metabolome liquid-liquid extraction

Proteo-metabolomics is essential in systems biology and simultaneous proteo-metabolome extraction by liquid-liquid extraction (SPM-LLE) allows extraction of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE it must be solubilized for quantitative proteomics. Solubilization and proteome extraction is a critical factor in the information that can be obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea with respect to proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated the extent to which the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were very similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants (SDC, SDS) for quantitative proteomics is better when the proteome was extracted by direct cell lysis and not from an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet and by direct cell lysis.

systems biology↗

bioRxiv2021

Sensory attenuation for external events is produced by a competition for attentional resources

Sensory events appear reduced in intensity when we actively produce them. Here, we investigated sensory attenuation in a virtual reality setup that allowed us to manipulate the time of tactile feedback when pressing a virtual button. We asked whether tactile motor attention might shift to the tactile location that makes contact with the button. In experiment one, we found that a tactile impulse was perceived as more intense when button pressing. In a second experiment, participants pushed a button and estimated the intensity of sounds. We found sensory attenuation for sounds only when tactile feedback was provided at the time the movement goal was reached. These data indicate that attentional prioritization for the tactile modality during a goal-directed hand movement might lead to a transient reduction in sensitivity in other modalities, resulting in sensory attenuation for sounds.

neuroscience↗

bioRxiv2021

Global Temporal Movement Control

Complex, goal-directed and time-critical movements require the processing of temporal features in sensory information as well as the fine-tuned temporal interplay of several effectors. Temporal estimates used to produce such behavior may thus be obtained through perceptual or motor processes. To disentangle the two options, we tested whether adaptation to a temporal perturbation in an interval reproduction task transfers to interval reproduction tasks with varying sensory information (visual appearance of targets, modality, virtual reality (VR) environment or real-world) or varying movement types (continuous arm movements or brief clicking movements). Halfway through the experiments we introduced a temporal perturbation, such that continuous pointing movements were artificially slowed down in VR, causing participants to adapt their behavior to sustain performance. In four experiments, we found that sensorimotor adaptation to temporal perturbations is independent of environment context and movement type, but modality specific. Our findings suggest that motor errors induced by temporal sensorimotor adaptation affect the modality specific perceptual processing of temporal estimates.

neuroscience↗

bioRxiv2020

Pointing in depth is shaped by a natural grasping distance prior

Vision in depth is distorted. A similar distortion can be observed for pointing to visual targets in depth. It has been suggested that pointing errors in depth reflect the visual distortion. However, much research has suggested that in case visual information is not rich enough, the sensorimotor system involves prior knowledge to optimally plan movement trajectories. Here, we show that pointing in depth is guided by a prior that biases movements toward the natural grasping distance at which object manipulation is usually performed. To dissociate whether pointing is guided by distorted vision only or whether it takes into account a natural grasping distance prior, we adapted pointing movements. Participants received visual feedback about the success of their pointing once the movement was finished. We distorted the feedback to signal either that pointing was not far enough or in separate sessions that pointing was too far. Participants adapted to this artificial error by either extending or shortening their pointing movements. The generalization of pointing adaptation revealed a bias in movement planning that is inconsistent with pointing being guided only by distorted vision but with the involvement of knowledge about the natural grasping distance. Adaptation was strongest for pointing movements to a middle position that corresponds to the natural grassing distance and it was weakest for movements leading away from it. It has been demonstrated that pointing adaptation in depth changes visual perception (Volcic et al., 2013). We also wondered how effects of pointing adaptation on visual space would generalize in depth.

neuroscience↗