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Janssen, P.

Publications and source records attributed to Janssen, P..

At least 19 recordsLinked to original sources

Maps of historical forests in France and their temporal continuity since the first half of the 19th century

AbstractIntegrating environmental history is essential for understanding present-day ecosystem dynamics and guiding modern conservation strategies, particularly under the EU Biodiversity Strategy for 2030. This data paper presents the nationwide digitisation and vectorisation of the French General Ordnance survey map (1818-1866), capturing the countrys forest cover at its historical minimum (a pivotal moment known as the "forest transition"). The original manuscript sheets surveyed at a 1:40,000 scale (976 sheets) were scanned, georeferenced and vectorised. They offer higher thematic accuracy than the older Cassini map and are far more feasible for nationwide vectorisation than the highly detailed Napoleonic cadastre. The area-weighted mean survey date is 1843, and the dataset covers 99.6% of modern mainland France. To correct for paper deformation, historical surveying errors and coordinate system transformations, a rigorous workflow was established. This shifted from a global 6-parameter affine transformation (root mean square error of 60 m) to a local elastic transformation based on thousands of control points, for 21% of the territory, which reduced the positioning error to 34 m. We assessed data quality by comparing the General Ordnance Survey maps with the Napoleonic cadastre--the standard reference for 19th-century land-use data--across more than 600 municipalities. The correlation between the two sources regarding forest cover percentages was exceptionally high (r>0.9). Because forests formed large, compact blocks of significant strategic interest to military engineers, they were mapped with high precision. Localised inaccuracies were primarily found in remote areas, most notably in the mountains. The resulting historical vector layer was intersected with contemporary forest data (BD Foret(R) v2, 2005-2019). Historical polygons smaller than 0.5 ha were filtered out to comply with modern FAO forest definitions. This spatial overlay generated a new dataset detailing four distinct land-use trajectories: . ancient forests (44.8% of present day forest): land classified as forest in both the 19th century and the present day (indicating maximum temporal continuity). . recent forests (55.2% of present day forest): land that was non-forested in the 19th century but has since undergone reforestation. . deforested areas (18.9% of 19th-century forest): land recorded as forest in the 19th century but subsequently converted to other land uses. . stable non-forest areas: land that has remained unforested across both periods. Our results suggest that the forest area of mainland France at its historical minimum should be revised upward to 9.9 million ha. A preliminary analysis further indicates that current spatial variation in forest cover is explained more by land-use dynamics occurring since the forest transition than by the initial extent of forest cover. These two open-access national datasets (the 19th-century forest layer and the land-use transition map) open the door to a better understanding of present-day forests : e.g. their biodiversity, soil quality, tree growth and belowground water quality. Furthermore, they provide decision-support tools for conservation planning. Key messageIn this data paper, we provide a map of 19th-century forests in France based on the digitisation of the military topographic map (1818-1866). By overlaying this historical source with the present-day forest map, we built a second map which allows the identification of ancient forests, recent forests, and deforestation. These maps offer avenues for historical ecology and the design of conservation strategies.

ecology↗

Stabilization-Responsiveness Trade-offs in Continuous Shared-Control for Invasive Brain-Computer Interfaces

Intracortical brain-computer interfaces (iBCIs) can enable people with paralysis to control assistive devices, but reliable operation in dynamic environments remains limited by fluctuations in decoded neural commands. Here we develop a confidence-modulated AI-brain shared-control framework in which an artificial intelligence copilot adaptively integrates the decoded neural commands with a probabilistic temporal prior to stabilize execution while preserving user intent. In two macaques performing closed-loop virtual navigation tasks in complex environments, shared-control nearly eliminated execution-level failures, including obstacle collisions and target overshoot, while maintaining the directional structure of neural commands. Abrupt target changes revealed a boundary condition: temporal stabilization transiently delays responsiveness when recent history was no longer predictive. Offline replay showed that resetting the temporal prior eliminated this lag and restored performance, demonstrating that the impairment was algorithmic rather than a failure of neural decoding. These results provide a mechanistic characterization of confidence-modulated AI-brain shared control for continuous intracortical BCI navigation and identify design principles for safer and more reliable neuroprosthetic control in dynamic environments.

neuroscience↗

Epicranial electrical stimulation improves non-navigational spatial memory in macaque monkeys

BackgroundThe hippocampus and medial temporal lobe are crucial for spatial memory, and their dysfunction is linked to Alzheimers disease (AD), with changes detectable even in preclinical stages. Recently, neuromodulation has gained interest as a potential treatment due to its beneficial effects on AD pathology and cognitive performance. However, outcomes vary significantly based on stimulation parameters and study conditions, and evidence from large animal models remains limited. ObjectiveTo assess whether epicranial current stimulation (ECS) at 40 Hz can improve non-navigational spatial memory and hippocampal activations. MethodsThree rhesus macaques were implanted with spiral platinum electrodes bilaterally on the skull and were trained in a non-navigational spatial memory task. ECS was applied at 40 Hz or at 10 Hz and performance across multiple sessions was evaluated. We further performed ECS during fMRI to examine the spread of activations caused by ECS across the brain in a block-design experiment. ResultsECS at 40 Hz improved performance in a non-navigational spatial memory task, while 10 Hz ECS had minimal or negative effects. Concurrent ECS-fMRI showed extensive brain activations at 40 Hz, including significant hippocampal activations, which was not observed at 10 Hz. ConclusionsOur results show that ECS could be a minimally-invasive and effective approach to improve memory performance and activate the hippocampus. ECS could represent a potential treatment for patients suffering from memory impairment.

neuroscience↗

CroCoNet: a novel framework for cross-species network analysis reveals POU5F1 (OCT4) rewiring

BACKGROUNDGene regulatory changes play a central role in shaping cellular phenotypes across species. To understand how these phenotypes evolve, it is essential to investigate the underlying gene regulatory networks (GRNs). However, most comparative analyses of GRNs remain qualitative and are therefore sensitive to false positives and false negatives. RESULTSTo address this limitation, we introduce CroCoNet (Cross-species Comparison of Networks), an R package for the quantitative comparison of GRNs across species. CroCoNet constructs comparable network modules centered on known transcriptional regulators and quantifies the variability in module topology within and between species. By contrasting these levels of variability, CroCoNet can distinguish true evolutionary divergence from technical and biological confounders. Applying CroCoNet to scRNA-seq data from the early neural differentiation of human, gorilla, and cynomolgus macaque, we identified 20 conserved and 24 diverged modules. Despite the conserved expression pattern of the pluripotency factor POU5F1 (OCT4), its associated module was among the most diverged. This result was independently confirmed through cross-species CRISPRi perturbations coupled with single-cell RNA-seq as a readout. Moreover, we found that great ape- and human-specific LTR7 elements are enriched near POU5F1 module genes, potentially contributing to the cross-species differences in network topology. CONCLUSIONSThese findings demonstrate that CroCoNet can resolve regulatory rewiring and provides a robust framework for studying GRN evolution across closely related species. CroCoNet is available as an open-source R package at https://hellmann-lab.github.io/CroCoNet/.

evolutionary biology↗

An intracortical brain-machine interface based on macaque ventral premotor activity

The majority of brain-machine interface (BMI) studies have focused on decoding intended movements based on neural activity of primary motor (M1) and dorsal premotor cortex (PMd). The ventral premotor cortex (PMv), and more specifically area F5c, has been implicated in object grasping and action observation, and may represent an alternative for motor BMI control due to its phasic modulation during action observation. Using chronically implanted Utah arrays in F5c, PMd, and M1 in two male macaques, we compared the efficacy of controlling a motor BMI based on neural activity of each area. PMv decoding reached similar or even higher success rates than M1 and PMd in a 2D cursor control task, especially when controlling for the number of motion selective channels that were used by the decoder. We found similar results during a 2D robot avatar control task in a simulated 3D environment. At both the multi-unit and the population level, neural responses were highly similar during the training phase (passive observation of cursor movements) and the online decoding phase, and only a small subset of neurons modulated its selectivity for the direction of motion. Thus, ventral premotor area F5c may represent an alternative for online motor BMI control. Significance statementWe present the first study on online cursor and robot avatar control using neural activity of ventral premotor cortical area F5c. Known for decades for the presence of mirror neurons, which are active during both action execution and action observation, area F5c can support online BMI control with performance comparable to that of dorsal premotor and primary motor cortex. The population dynamics in all three areas were highly similar between the training phase and the online decoding phase.

neuroscience↗

Action observation responses in macaque frontal cortex

Neurons that are active during action execution and action observation (i.e. Action Observation/Execution Neurons, AOENs) are distributed across the brain in a network of parietal, motor, and prefrontal areas. In a previous study, we showed that most AOENs in ventral premotor area F5c, where they were discovered three decades ago, responded in a highly phasic way during the observation of a grasping action, did not require the perception of causality or a meaningful action, and even responded to static frames of the action videos. To assess whether these characteristics are shared with AOENs in other areas of the AOE network, we performed the first large-scale neural recordings during action execution and action observation in multiple frontal areas including dorsal premotor (PMd) area F2, primary motor (M1) cortex, ventral premotor area F5p, frontal eye field (FEF) and 45B. In all areas, AOENs displayed highly phasic responses during specific epochs of the action video and strong responses to simple movements of an object, similar to F5c. In addition, the population dynamics in PMv, PMd and M1 showed a shared representation between action execution and action observation, with an overlap that was as large as the overlap between action execution and passive viewing of simple translation movements. These results pose important constraints on the interpretation of action observation responses in frontal cortical areas.

neuroscience↗

An intracortical brain-computer interface for navigation in virtual reality in macaque monkeys

We present an innovative intracortical Brain-Computer Interface (BCI) to bridge the gap between laboratory settings and real-world applications. This BCI approach introduces three key advancements. First, we utilized neural signals from three macaque brain regions - primary motor, dorsal and ventral premotor cortex - enabling precise and flexible decoding of real-time three-dimensional (3D) sphere/avatar velocities. Second, we developed a realistic, immersive 3D virtual reality setup with dynamic camera tracking, allowing continuous navigation and obstacle avoidance that closely mimic real-world scenarios. Finally, our BCI approach is very well suited for use by paralyzed patients, featuring a brief passive fixation without overt movements and closed-loop operation without retraining of the decoder during online decoding, relying on the users neural plasticity and the decoders robust generalization across tasks. Our BCI adapted to different environments, targets, and obstacles, illustrating its potential to substantially enhance the quality of life for paralyzed patients by enabling natural, reliable and flexible control in complex settings.

neuroscience↗

Identification and comparison of orthologous celltypes from primate embryoid bodies shows limits of marker gene transferability

The identification of cell types remains a major challenge. Even after a decade of single-cell RNA sequencing (scRNA-seq), reasonable cell type annotations almost always include manual non-automated steps. The identification of orthologous cell types across species complicates matters even more, but at the same time strengthens the confidence in the assignment. Here, we generate and analyze a dataset consisting of embryoid bodies (EBs) derived from induced pluripotent stem cells (iPSCs) of four primate species: humans, orangutans, cynomolgus, and rhesus macaques. This kind of data includes a continuum of developmental cell types, multiple batch effects (i.e. species and individuals) and uneven cell type compositions and hence poses many challenges. We developed a semi-automated computational pipeline combining classification and marker based cluster annotation to identify orthologous cell types across primates. This approach enabled the investigation of cross-species conservation of gene expression. Consistent with previous studies, our data confirm that broadly expressed genes are more conserved than cell type-specific genes, raising the question how conserved - inherently cell type-specific - marker genes are. Our analyses reveal that human marker genes are less effective in macaques and vice versa, highlighting the limited transferability of markers across species. Overall, our study advances the identification of orthologous cell types across species, provides a well-curated cell type reference for future in vitro studies and informs the transferability of marker genes across species.

cell biology↗

Fine-grained neural coding of bodies and body parts in human visual cortex

The visual image of a human body provides a valuable source of socially relevant information. However, our understanding of the neuronal mechanisms underlying body perception in humans remains limited given the spatiotemporal constraints of functional imaging. Here we recorded multi-unit spiking activity in two neurosurgical patients in or near the extrastriate body area (EBA), a critical region for body perception. Our recordings revealed a strong preference for human bodies over a large range of control stimuli. Notably, this preference was driven by a distinct selectivity for body parts. Moreover, the observed body selectivity generalized to non-photographic depictions of bodies such as silhouettes and stick figures. Overall, our study provides an unprecedented access into the representation of bodies in the human visual cortex to bridge the gap between human neuroimaging and macaque electrophysiology studies, and form a solid basis for computational models of human body processing.

neuroscience↗

Visual selectivity and motor role of action observation/execution neurons in macaque ventral premotor cortex

Neurons responding during action execution and action observation were discovered in the ventral premotor cortex three decades ago. However, neither the minimum visual features nor the motor involvement of Action Observation/Execution Neurons (AOENs) have been revealed at present. We investigated the minimal visual stimulus for activation and the involvement in motor behavior of AOENs in ventral premotor area F5c of four macaques. The large majority of AOENs showed highly phasic responses during the action videos, and also responded to an abstract shape moving towards but not interacting with an object, even when the shape moved on a scrambled background, implying that most AOENs in F5c do not require the perception of causality or a meaningful action. Additionally, electrical microstimulation of AOEN sites invariably elicited motor responses and frequently interfered with visually guided object grasping. Our findings suggest that an important role of F5c AOENs in visuomotor control during object grasping.

neuroscience↗

Neuronal tuning and population representations of shape and category in human visual cortex.

Object recognition and categorization are essential cognitive processes which engage considerable neural resources in the human ventral visual stream. However, the tuning properties of human ventral stream neurons for object shape and category are virtually unknown. We performed the first large-scale recordings of spiking activity in human Lateral Occipital Complex in response to stimuli in which the shape dimension was dissociated from the category dimension. Consistent with studies in nonhuman primates, the neuronal representations were primarily shape-based, although we also observed category-like encoding for images of animals. Surprisingly, linear decoders could reliably classify stimulus category even in data sets that were entirely shape-based. In addition, many tuning curves showed an interaction between shape and category tuning. These results represent the first detailed study on shape and category coding at the neuronal level in the human ventral visual stream, furnishing essential evidence that reconciles human imaging and macaque single-cell studies.

neuroscience↗

The effect of background noise and its removal on the analysis of single-cell expression data

BACKGROUNDIn droplet-based single-cell and single-nucleus RNA-seq experiments, not all reads associated with one cell barcode originate from the encapsulated cell. Such background noise is attributed to spillage from cell-free ambient RNA or barcode swapping events. Here, we characterize this background noise exemplified by three single-cell RNA-seq (scRNA-seq) and two single-nucleus RNA-seq (snRNA-seq) replicates of mouse kidney cells. For each experiment, kidney cells from two mouse subspecies were pooled, allowing to identify cross-genotype contaminating molecules and estimate the levels of background noise. RESULTSWe find that background noise is highly variable across replicates and individual cells, making up on average 3-35% of the total counts (UMIs) per cell and show that this has a considerable impact on the specificity and detectability of marker genes. In search of the source of background noise, we find that expression profiles of cell-free droplets are very similar to expression profiles of cross-genotype contamination and hence that the majority of background molecules originates from ambient RNA. Finally, we use our genotype-based estimates to evaluate the performance of three methods (CellBender, DecontX, SoupX) that are designed to quantify and remove background noise. We find that CellBender provides the most precise estimates of background noise levels and also yields the highest improvement for marker gene detection. By contrast, clustering and classification of cells are fairly robust towards background noise and only small improvements can be achieved by background removal that may come at the cost of distortions in fine structure. CONCLUSIONOur findings help to better understand the extent, sources and impact of background noise in single-cell experiments and provide guidance on how to deal with it.

bioinformatics↗

Neural effects of continuous theta-burst stimulation in macaque parietal neurons

Theta-burst transcranial magnetic stimulation (TBS) has become a standard non-invasive technique to induce offline changes in cortical excitability in human volunteers. Yet, TBS suffers from a high variability across subjects. A better knowledge about how TBS affects neural activity in vivo could uncover its mechanisms of action and ultimately allow its mainstream use in basic science and clinical applications. To address this issue, we applied continuous TBS (cTBS, 300 pulses) in awake behaving rhesus monkeys and quantified its after-effects on neuronal recordings and behavior. Guided by anatomical MRI, we recorded single-cell activity in parietal area PFG during passive fixation of real-world objects. Overall, we observed a pronounced, long-lasting and highly reproducible reduction in neuronal excitability after cTBS in individual parietal neurons, with some neurons exhibiting periods of hyperexcitability during the recovery phase. We applied the same stimulation protocol during visually-guided grasping of objects, and observed a significant grasping impairment. These results provide the first experimental evidence on the effects of cTBS on single neurons in awake behaving monkeys.

neuroscience↗

Face neurons in human visual cortex

The exquisite capacity of primates to detect and recognize faces is crucial for social interactions. Although disentangling the neural basis of human face recognition remains a key goal in neuroscience, direct evidence at the single-neuron level is virtually nonexistent. We recorded from face-selective neurons in human visual cortex, in a region characterized by functional magnetic resonance imaging (fMRI) activations for faces compared to objects (i.e. the occipital face area, OFA). The majority of visually responsive neurons in this fMRI activation showed strong selectivity at short latencies for faces compared to objects. Feature scrambled faces and face-like objects could also drive these neurons, suggesting that the OFA is not tightly-tuned to the visual attributes that typically define whole human faces. These single-cell recordings within the human face processing system provide vital experimental evidence linking previous imaging studies in humans and invasive studies in animal models.

neuroscience↗

Temporal dynamics of neural activity in macaque frontal cortex assessed with large-scale recordings

We make eye movements to objects before grasping these objects, and the gaze direction generally indicates where the object will be grasped. Hence, the brain has to coordinate eye-, arm- and hand movements. We performed large-scale recordings (more than 2000 responsive sites) in frontal cortex of monkeys during a saccade-reach-grasp task. When an object appeared in peripheral vision, the first burst of activity emerged in prearcuate areas (the FEF and area 45B), followed by dorsal and ventral premotor cortex, and a buildup of activity in primary motor cortex. After the saccade, prearcuate activity remained elevated while primary motor and premotor activity rose in anticipation of the upcoming arm and hand movement. Some premotor and prearcuate sites were equally active when the object appeared in peripheral vision and at the fovea, suggesting a role in eye-hand coordination. Thus, a large part of lateral frontal cortex is active during a saccade-reach-grasp task.

neuroscience↗

The causal role of three frontal cortical areas in grasping

Efficient object grasping requires the continuous control of arm and hand movements based on visual information. Previous studies have identified a network of parietal and frontal areas that is crucial for the visual control of prehension movements. Electrical microstimulation of 3D shape-selective clusters in AIP during fMRI activates areas F5a and 45B, suggesting that these frontal areas may represent important downstream areas for object processing during grasping, but the role of area F5a and 45B in grasping is unknown. To assess their causal role in the frontal grasping network, we reversibly inactivated 45B, F5a and F5p during visually-guided grasping in macaque monkeys. First, we recorded single neuron activity in 45B, F5a and F5p to identify sites with object responses during grasping. Then, we injected muscimol or saline to measure the grasping deficit induced by the temporary disruption of each of these three nodes in the grasping network. The inactivation of all three areas resulted in a significant increase in the grasping time in both animals, with the strongest effect observed in area F5p. These results not only confirm a clear involvement of F5p, but also indicate causal contributions of area F5a and 45B in visually-guided object grasping.

neuroscience↗

Effect of viewing distance on object responses in macaque areas 45B, F5a and F5p

To perform real-world tasks like grasping, the primate brain has to process visual object information so that the grip aperture can be adjusted before contact with the object is made. Previous studies have demonstrated that the posterior subsector of the Anterior Intraparietal area (pAIP) is connected to frontal area 45B, and the anterior subsector of AIP (aAIP) to F5a (Premereur et al., 2015). However, the role of area 45B and F5a in visually-guided object grasping is poorly understood. Here, we investigated the role of area 45B, F5a and F5p in visually-guided grasping. If a neuronal response to an object during passive fixation represents the activation of a motor command related to the preshaping of the hand, such neurons should prefer objects presented within reachable distance. Conversely, neurons encoding a pure visual representation of an object should be less affected by viewing distance. Contrary to our expectations, we found that the majority of neurons in area 45B were object- and viewing distance selective, with a clear preference for the near viewing distance. Area F5a showed much weaker object selectivity compared to 45B, with a similar preference for objects presented at the Near position emerging mainly in the late epoch. Finally, F5p neurons were less object selective and frequently preferred objects presented at the Far position. Therefore, contrary to our expectations, neurons in area 45B - but not F5p neurons - prefer objects presented in peripersonal space. Significance statementThe current experiment provides the first evidence on the neural representation of distance in frontal areas that are active during visually-guided grasping. Area 45B and F5a neurons were object- and distance-selective, and preferred the near viewing distance even for objects with identical retinal size. In area F5p we observed strong visual responses with an unexpected preference for the Far viewing distance, suggesting that the motor-related object representation was still active during the presentation of objects outside reaching distance.

neuroscience↗

Single-cell selectivity and functional architecture of human lateral occipital complex.

The human lateral occipital complex (LOC) is more strongly activated by images of objects compared to scrambled controls, but detailed information at the neuronal level is currently lacking. We recorded with microelectrode arrays in the LOC of two patients, and obtained highly selective single-unit, multi-unit and high-gamma responses to images of objects. Contrary to predictions derived from functional imaging studies, all neuronal properties indicated that the subsector of LOC we recorded from occupies an unexpectedly high position in the hierarchy of visual areas. Notably, the response latencies of LOC neurons were long, the shape selectivity was spatially clustered, LOC receptive fields were large and bilateral, and a number of LOC neurons exhibited 3D-structure selectivity (a preference for convex or concave stimuli), which are all properties typical of end-stage ventral stream areas. Thus, our results challenge prevailing ideas about the position of the LOC in the hierarchy of visual areas.

neuroscience↗