Task-driven neural network models predict neural dynamics of proprioception.

Proprioception tells the brain the state of the body based on distributed sensory neurons. Yet, the principles that govern proprioceptive processing are poorly understood. Here, we employ a task-driven modeling approach to investigate the neural code of proprioceptive neurons in cuneate nucleus (CN) and somatosensory cortex area 2 (S1). We simulated muscle spindle signals through musculoskeletal modeling and generated a large-scale movement repertoire to train neural networks based on 16 hypotheses, each representing different computational goals. We found that the emerging, task-optimized internal representations generalize from synthetic data to predict neural dynamics in CN and S1 of primates. Computational tasks that aim to predict the limb position and velocity were the best at predicting the neural activity in both areas. Since task optimization develops representations that better predict neural activity during active than passive movements, we postulate that neural activity in the CN and S1 is top-down modulated during goal-directed movements.

Neuronal Representation of Social Information in the Medial Amygdala of Awake Behaving Mice.

The medial amygdala (MeA) plays a critical role in processing species- and sex-specific signals that trigger social and defensive behaviors. However, the principles by which this deep brain structure encodes social information is poorly understood. We used a miniature microscope to image the Ca2+ dynamics of large neural ensembles in awake behaving mice and tracked the responses of MeA neurons over several months. These recordings revealed spatially intermingled subsets of MeA neurons with distinct temporal dynamics. The encoding of social information in the MeA differed between males and females and relied on information from both individual cells and neuronal populations. By performing long-term Ca2+ imaging across different social contexts, we found that sexual experience triggers lasting and sex-specific changes in MeA activity, which, in males, involve signaling by oxytocin. These findings reveal basic principles underlying the brain's representation of social information and its modulation by intrinsic and extrinsic factors.

Multi-animal pose estimation, identification and tracking with DeepLabCut.

Estimating the pose of multiple animals is a challenging computer vision problem: frequent interactions cause occlusions and complicate the association of detected keypoints to the correct individuals, as well as having highly similar looking animals that interact more closely than in typical multi-human scenarios. To take up this challenge, we build on DeepLabCut, an open-source pose estimation toolbox, and provide high-performance animal assembly and tracking-features required for multi-animal scenarios. Furthermore, we integrate the ability to predict an animal's identity to assist tracking (in case of occlusions). We illustrate the power of this framework with four datasets varying in complexity, which we release to serve as a benchmark for future algorithm development.

The Phlebotomine sand fly fauna of Switzerland revisited.

Sand flies (Diptera: Psychodidae, Phlebotominae; Newstead, 1911) are widespread in Europe, being particularly common in the Mediterranean region but rare north of the Alps. Thus, Switzerland is an opportune place to investigate the sand fly fauna on both sides of the Alpine crest, in southern sub-Mediterranean climate and northern oceanic temperate climate. We reinvestigated the Swiss sand fly fauna with the aim to assess changes in composition, altitudinal distribution, abundance and seasonality. Thirty-eight sites were investigated with light traps and/or interception sticky traps in 4 years. Ninety and 380 specimens were caught by light traps and sticky traps, respectively, at 15 collecting sites. Four species were identified. Phlebotomus mascittii (Grassi, 1908), Phlebotomus perniciosus (Newstead, 1911) and Sergentomyia minuta (Rondani, 1843) were confirmed in Ticino, and P. mascittii for the first time in neighbouring Grisons. Also, Phlebotomus neglectus (Tonnoir, 1921) is for the first time reported, though at a very low density compared to P. perniciosus at the same site. Its presence in Ticino supports the northward spread observed in Italy. Sand flies were detected north of the Alps at one site only, endorsing a historical report. Overall, the low density of P. perniciosus and very low density of P. neglectus suggest that canine leishmaniosis may not be an important disease risk in Switzerland.

Thermal preference of Culicoides biting midges in laboratory and semi-field settings.

Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are hematophagous insects, and some species can transmit a plethora of pathogens, e.g., bluetongue virus and African horse sickness virus, that mainly affect animals. The transmission of vector-borne pathogens is strongly temperature dependent, and recent studies pointed to the importance of including microclimatic data when modelling disease spread. However, little is known about the preferred temperature of biting midges. The present study addressed the thermal selection of field-caught Culicoides with two experiments. In a laboratory setup, sugar-fed or blood-fed midges were video tracked for 15 min while moving inside a 60 × 30 × 4 cm setup with a 15-25 °C temperature gradient. Culicoides spent over double the time in the coldest zone of the setup compared to the warmest one. This cold selection was significantly stronger for sugar-fed individuals. Calculated preferred temperatures were 18.3 °C and 18.9 °C for sugar-fed and blood-fed Culicoides, respectively. The effect of temperature on walking speed was significant but weak, indicating that their skewed distribution results from preference and not cold trapping. A second experiment consisted of a two-way-choice-setup, performed in a 90 × 45 × 45 cm net cage, placed outdoors in a sheltered environment. Two UV LED CDC traps were placed inside the setup, and a mean temperature difference of 2.2 °C was created between the two traps. Hundred-fifty Culicoides were released per experiment. Recapture rates were negatively correlated with ambient temperature and were on average three times higher in the cooled trap. The higher prevalence of biting midges in cooler environments influences fitness and ability to transmit pathogens and should be considered in models that predict Culicoides disease transmission.

Temperature preference of sugar- or blood-fed Aedes japonicus mosquitoes under semi-natural conditions.

Mosquito-borne diseases pose a major burden on humans and animals. Temperature strongly influences the physiology and life cycle of mosquitoes and also the pathogens they transmit. Thermoregulatory behaviour of mosquitoes has been addressed in a few laboratory studies. Here, we expand such studies by investigating the thermal preference when resting of Aedes japonicus, an invasive and putative vector species of many pathogens, in a semi-field setup during summers in a temperate climate. Blood-fed or sugar-fed Ae. japonicus females were released in the late afternoon in a large outdoor cage containing three resting boxes. The next morning, temperature treatments were applied to the boxes, creating a "cool" (over all experiments around 18 °C), and a "warm" (around 35 °C) microhabitat in addition to an untreated "ambient" (around 26 °C) one. The mosquitoes resting within the three boxes were counted five times, every 2 h between 9h and 17h. The highest proportions of mosquitoes (e.g. up to 21% of blood-fed ones) were found in the cool box while both blood-fed and sugar-fed mosquitoes avoided the warm box. The mean resting temperatures of Ae. japonicus were below the ambient temperatures measured by a nearby meteorological station, and this was more pronounced at higher outdoor temperatures and in blood-fed as compared to sugar-fed mosquitoes. Thus, over all experiments with blood-fed mosquitoes, the calculated average resting temperature was 4 °C below the outdoor temperature. As mosquitoes prefer cooler resting places than temperatures measured by weather stations in summer, models to predict mosquito-borne disease outbreaks need to account for the thermoregulatory behaviour of mosquitoes, especially in the wake of climate change.

Environment rather than breed or body site shapes the skin bacterial community of healthy sheep as revealed by metabarcoding.

BACKGROUND: The skin is inhabited by a variety of micro-organisms, with bacteria representing the predominant taxon of the skin microbiome. In sheep, the skin bacterial community of healthy animals has been addressed in few studies, only with culture-based methods or sequencing of cloned amplicons. OBJECTIVES: The objectives of this study were to determine the sheep skin bacterial community composition by using metabarcoding for a detailed characterisation and to determine the effect of body part, breed and environment. MATERIALS AND METHODS: Overall, 267 samples were taken from 89 adult female sheep, belonging to three different breeds and kept on nine different farms in Switzerland. From every individual, one sample each was taken from belly, left ear and left leg and metabarcoding of the 16S rRNA V3-V4 hypervariable region was performed. RESULTS: The main phyla identified were Actinobacteriota, Firmicutes, Proteobacteria and Bacteriodota. The alpha diversity as determined by Shannon's diversity index was significantly different between sheep from different farms. Beta diversity analysis by principal coordinate analysis (PCoA) showed clustering of the samples by farm and body site, while breed had only a marginal influence. A sparse partial least squares discriminant analysis (sPLS-DA) revealed seven main groups of operational taxonomic units (OTUs) of which groups of OTUs were specific for some farms. CONCLUSIONS AND CLINICAL RELEVANCE: These findings indicate that environment has a larger influence on skin microbial variability than breed, although the sampled breeds, the most abundant ones in Switzerland, are phenotypically similar. Future studies on the sheep skin microbiome may lead to novel insights in skin diseases and prevention.

Putative roles of mosquitoes (Culicidae) and biting midges (Culicoides spp.) as mechanical or biological vectors of lumpy skin disease virus.

The stable fly Stomoxys calcitrans (Diptera: Muscidae) is considered as the main mechanical vector of the lumpy skin disease virus (LSDV). In addition, the mosquito species Aedes aegypti (Diptera: Culicidae) was shown to transmit the virus from donor to receptor animals. Retention of the virus for several days was shown for two additional tropical mosquito species and the biting midge Culicoides nubeculosus (Diptera: Ceratopogonidae). In the present study, viral retention for 10- or 7-days post feeding on virus-spiked blood through a membrane was shown for field-collected Aedes japonicus and laboratory-reared Culex pipiens, two widely distributed mosquito species in temperate regions. Viral DNA could be detected from honey-coated Flinders Technology Associates (FTA) cards and shedded faeces for 1 or 4 days after an infectious blood meal was given to Ae. aegypti. Virus increase over time and virus dissemination was observed in laboratory-reared C. nubeculosus, but the virus could be isolated from field-collected biting midges only from the day of exposure to the blood meal. Thus, mosquitoes might serve as mechanical vectors of LSDV in case of interrupted feeding. A putative biological virus transmission by Culicoides biting midges, as suspected from field observations, deserves further investigations.

Video analysis of the locomotory behaviour of Aedes aegypti and Ae. japonicus mosquitoes under different temperature regimes in a laboratory setting.

Mosquito-borne diseases impose a high burden on human and animal health. Temperature strongly influences the physiology and life cycle of mosquitoes, but also the development and/or propagation of the pathogens they transmit. Thus, the vector capacity of mosquitoes depends strongly on temperature and their behavioural thermoregulation through microhabitat selection. Expanding on a previous study of static thermal preferences, the locomotory dynamics of temperate Aedes japonicus (reared from eggs collected in the field) and tropical Ae. aegypti (from a laboratory colony) was investigated at constant temperatures (10 °C, 25 °C, 40 °C) and in temperature gradients (10-20 °C, 20-30 °C, 30-40 °C). Blood-fed or non-blood-fed female mosquitoes were released in groups of 15 individuals into a Plexiglas box positioned on two thermoregulators connected by an aluminium plate to automatically monitor by video analysis mosquito flying, walking and resting duration, covered distances and velocity. Mosquitoes were predominantly resting, followed by walking and flying. At constant 10 °C, flights were rare and brief, and walking was slow. Most activity was observed at 25 °C for Ae. japonicus and 40 °C for Ae. aegypti. In the 30-40 °C gradient, activity of Ae. aegypti increased towards the cold end, suggesting active avoidance of very high temperatures. In the 20-30 °C gradient, edge effects were prominent, nevertheless revealing a greater proportion of mosquitoes gathered at the cooler end. Video analysis showed that this effect was not caused by a cold trap but represents true thermal preference. In the coolest gradient (10-20 °C), mosquitoes were active in all sectors without displaying a preference for either side. Overall, both the tropical and temperate mosquito species preferred cooler temperatures and actively avoided the hottest temperatures. Further studies with infected mosquitoes should provide important insights for developing models of vector-borne disease outbreaks.

Thermal preferences of subtropical Aedes aegypti and temperate Ae. japonicus mosquitoes.

Temperature is an important determinant affecting the capacity of disease vectors like mosquitoes (Culicidae) to transmit disease agents. Although the impact of temperature on vector-borne disease dynamics has been studied intensively, the actual temperature encountered by the vector in a heterogeneous landscape is rarely taken into account. If disease vectors have temperature preferences and therefore select specific microhabitats, this would substantially influence key life history traits that determine transmission intensity. The thermal preferences of subtropical Aedes aegypti and temperate Ae. japonicus mosquitoes were investigated in a temperature gradient set-up consisting of a Plexiglas box on top of an aluminium plate on two thermal regulators. Blood-fed (one day after feeding) and unfed (non-blood-fed) mosquitoes were released in small (15-20 °C, 20-25 °C, 25-30 °C) and large (15-30 °C, 30-45 °C) temperature gradients to assess their thermal preferences after 15 min. Additionally, the effect of humidity was investigated in a two-choice chamber setup. Both mosquito species avoided higher temperatures, pronouncedly dangerously high temperatures in the 30-45 °C gradient. At lower temperatures, blood-fed mosquitoes preferred the cooler sides of the 20-25 °C and 25-30 °C gradient, which were all below their rearing temperature. In the lowest gradient of 15-20 °C, no preferences were found. The thermal preference of unfed mosquitoes was similar to that of the blood-fed mosquitoes. No humidity preference or effect of humidity on temperature preferences was observed within the tested range (40-90%). The set-up allows for assessing the thermal preference of mosquitoes under controlled conditions. The observed preference of mosquitoes for cooler temperatures would increase their longevity and slow down pathogen development. If similar microhabitat selection is observed in the field, vector borne disease models should be adjusted accordingly.

Experimental evaluation of infection, dissemination, and transmission rates for two West Nile virus strains in European Aedes japonicus under a fluctuating temperature regime.

West Nile virus (WNV) is continuously spreading in Eastern and Southern Europe. However, the extent of vector competence of Aedes japonicus (Theobald, 1901) is controversial. In this work, we elucidated the dynamics of virus growth in this invasive mosquito species. Females of Ae. japonicus were reared from eggs collected in the field in Switzerland and fed on bovine blood spiked with two WNV lineage 1 strains (FIN, Italy; NY99, USA). Fully engorged females were incubated for 14 days under a fluctuating temperature regime of 24 ± 7 °C (average 24 °C), 45-90% relative humidity, which is realistic for a Central European mid-summer day. Infection, dissemination, and transmission rates were assessed from individual mosquitoes by analyzing the abdomen, legs and wings, and saliva for the presence of viral RNA. Saliva was also investigated for the presence of infectious virus particles. Overall, 302 females were exposed to WNV strain FIN and 293 to strain NY99. A higher infection rate was observed for NY99 (57.4%) compared to FIN (30.4%) (p = 0.003). There was no statistical evidence that the dissemination rate (viral RNA in legs and wings) was different between females infected with FIN (57.1%) compared to NY99 (35.5%) (p = 0.16). Viral RNA load of FIN compared to NY99 was significantly higher in the hemocoel (p = 0.031) of exposed females but not at other sites (legs and wings, saliva). This is the first study describing the vector competence parameters for two WNV strains in a European population of Ae. japonicus. The high dissemination and transmission rates for WNV under a realistic temperature regime in Ae. japonicus together with recent findings on its opportunistic feeding behavior (mammals and birds) indicate its potential role in WNV transmission in Central Europe where it is highly abundant.

Effects of Pyriproxifen on Aedes japonicus Development and Its Auto-Dissemination by Gravid Females in Laboratory Trials.

In a series of laboratory experiments, we investigated the effects of the juvenile-hormone analog pyriproxyfen on the inhibition of Aedes japonicus adult emergence after exposure of late-stage (3rd/4th) larvae (either field-collected or lab-reared from field-collected eggs) to pyriproxyfen. Emergence inhibition was 74%, 83%, 86%, and 92% at 0.01, 0.5, 2.5, and 5 µg/liter, respectively. Additionally, following a 1-day exposure of larvae to pyriproxyfen-containing water (5 µg/liter), and for a separate cohort exposed to that same water 10 days later, significantly more pupae died resulting in fewer adults emerged in the treatment versus control group. In 4 tent trials, gravid adult females were able to auto-disseminate a 5% pyriproxyfen powder to larval development habitats at high enough concentrations to cause a significant increase in inhibition of adult emergence. Therefore, we conclude that pyriproxyfen has a great potential for use in controlling this invasive cryptic breeder.

Babesia spp. in European wild ruminant species: parasite diversity and risk factors for infection.

Babesia are tick-borne parasites that are increasingly considered as a threat to animal and public health. We aimed to assess the role of European free-ranging wild ruminants as maintenance mammalian hosts for Babesia species and to determine risk factors for infection. EDTA blood was collected from 222 roe deer (Capreolus c. capreolus), 231 red deer (Cervus e. elaphus), 267 Alpine chamois (Rupicapra r. rupicapra) and 264 Alpine ibex (Capra i. ibex) from all over Switzerland and analysed by PCR with pan-Babesia primers targeting the 18S rRNA gene, primers specific for B. capreoli and Babesia sp. EU1, and by sequencing. Babesia species, including B. divergens, B. capreoli, Babesia sp. EU1, Babesia sp. CH1 and B. motasi, were detected in 10.7% of all samples. Five individuals were co-infected with two Babesia species. Infection with specific Babesia varied widely between host species. Cervidae were significantly more infected with Babesia spp. than Caprinae. Babesia capreoli and Babesia sp. EU1 were mostly found in roe deer (prevalences 17.1% and 7.7%, respectively) and B. divergens and Babesia sp. CH1 only in red deer. Factors significantly associated with infection were low altitude and young age. Identification of Babesia sp. CH1 in red deer, co-infection with multiple Babesia species and infection of wild Caprinae with B. motasi and Babesia sp. EU1 are novel findings. We propose wild Caprinae as spillover or accidental hosts for Babesia species but wild Cervidae as mammalian reservoir hosts for B. capreoli, possibly Babesia sp. EU1 and Babesia sp. CH1, whereas their role regarding B. divergens is more elusive.

Altered thermal preferences of infected or immune-challenged Aedes aegypti and Aedes japonicus mosquitoes.

Temperature is a critical factor shaping physiology, life cycle, and behaviour of ectothermic vector insects, as well as the development and multiplication of pathogens within them. However, the influence of pathogen infections on thermal preferences (behavioural thermoregulation) is not well-understood. The present study examined the thermal preferences of mosquitoes (Aedes aegypti and Ae. japonicus) infected with either Sindbis virus (SINV) or Dirofilaria immitis over 12 days post exposure (p.e.) or injected with a non-pathogenic Sephadex bead over 24 h in a thermal gradient (15-30 °C). SINV-infected Ae. aegypti preferred 5 °C warmer temperatures than non-infected ones at day 6 p.e., probably the time of highest innate immune response. In contrast, D. immitis-infected Ae. japonicus preferred 4 °C cooler temperatures than non-infected ones at day 9 p.e., presumably a stress response during the migration of third instar larvae from their development site to the proboscis. Sephadex bead injection also induced a cold preference in the mosquitoes but to a level that did not differ from control-injections. The cold preference thus might be a strategy to escape the risk of desiccation caused by the wound created by piercing the thorax. Further research is needed to uncover the genetic and physiological mechanisms underlying these behaviours.

SuperAnimal pretrained pose estimation models for behavioral analysis.

Quantification of behavior is critical in diverse applications from neuroscience, veterinary medicine to animal conservation. A common key step for behavioral analysis is first extracting relevant keypoints on animals, known as pose estimation. However, reliable inference of poses currently requires domain knowledge and manual labeling effort to build supervised models. We present SuperAnimal, a method to develop unified foundation models that can be used on over 45 species, without additional manual labels. These models show excellent performance across six pose estimation benchmarks. We demonstrate how to fine-tune the models (if needed) on differently labeled data and provide tooling for unsupervised video adaptation to boost performance and decrease jitter across frames. If fine-tuned, SuperAnimal models are 10-100× more data efficient than prior transfer-learning-based approaches. We illustrate the utility of our models in behavioral classification and kinematic analysis. Collectively, we present a data-efficient solution for animal pose estimation.

Sense the moist and feel the heat: mosquito host and oviposition site detection.

Laursen et al. identified coreceptor Ir93a that is required for humidity and thermal sensing in the mosquito species Anopheles gambiae and Aedes aegypti. Behavioural studies with mutant mosquitoes with disrupted Ir93a revealed that they were less attracted to a blood meal source and oviposition site at close distance.

NeuroAI: If grid cells are the answer, is path integration the question?

Spatially modulated neurons known as grid cells are thought to play an important role in spatial cognition. A new study has found that units with grid-cell-like properties can emerge within artificial neural networks trained to path integrate, and developed a unifying theory explaining the formation of these cells which shows what circuit constraints are necessary and how learned systems carry out path integration.

Contrasting action and posture coding with hierarchical deep neural network models of proprioception.

Biological motor control is versatile, efficient, and depends on proprioceptive feedback. Muscles are flexible and undergo continuous changes, requiring distributed adaptive control mechanisms that continuously account for the body's state. The canonical role of proprioception is representing the body state. We hypothesize that the proprioceptive system could also be critical for high-level tasks such as action recognition. To test this theory, we pursued a task-driven modeling approach, which allowed us to isolate the study of proprioception. We generated a large synthetic dataset of human arm trajectories tracing characters of the Latin alphabet in 3D space, together with muscle activities obtained from a musculoskeletal model and model-based muscle spindle activity. Next, we compared two classes of tasks: trajectory decoding and action recognition, which allowed us to train hierarchical models to decode either the position and velocity of the end-effector of one's posture or the character (action) identity from the spindle firing patterns. We found that artificial neural networks could robustly solve both tasks, and the networks' units show tuning properties similar to neurons in the primate somatosensory cortex and the brainstem. Remarkably, we found uniformly distributed directional selective units only with the action-recognition-trained models and not the trajectory-decoding-trained models. This suggests that proprioceptive encoding is additionally associated with higher-level functions such as action recognition and therefore provides new, experimentally testable hypotheses of how proprioception aids in adaptive motor control.

Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics.

Keypoint tracking algorithms have revolutionized the analysis of animal behavior, enabling investigators to flexibly quantify behavioral dynamics from conventional video recordings obtained in a wide variety of settings. However, it remains unclear how to parse continuous keypoint data into the modules out of which behavior is organized. This challenge is particularly acute because keypoint data is susceptible to high frequency jitter that clustering algorithms can mistake for transitions between behavioral modules. Here we present keypoint-MoSeq, a machine learning-based platform for identifying behavioral modules ("syllables") from keypoint data without human supervision. Keypoint-MoSeq uses a generative model to distinguish keypoint noise from behavior, enabling it to effectively identify syllables whose boundaries correspond to natural sub-second discontinuities inherent to mouse behavior. Keypoint-MoSeq outperforms commonly used alternative clustering methods at identifying these transitions, at capturing correlations between neural activity and behavior, and at classifying either solitary or social behaviors in accordance with human annotations. Keypoint-MoSeq therefore renders behavioral syllables and grammar accessible to the many researchers who use standard video to capture animal behavior.