Biology subjects

Dekker, T.

Publications and source records attributed to Dekker, T..

9 recordsLinked to original sources

bioRxiv2026

Allocating resources across time in a cumulative allocation game

We investigate an alternative to decision under risk where players begin with an endowment of wealth, and their goal is to increase this wealth as rapidly as possible by repeatedly investing part of it. In such a Cumulative Allocation Game (CAG), expected wealth can grow exponentially but - if wealth ever goes to zero - the game is over and the participant wins nothing (ruin). CAGs can be used to model a wide range of biological and economic activity from casino gambling to animal foraging to stock market investment (Kelly Criterion). However, there is little previous research concerning human performance in CAGs and how it relates to human performance in similar decision-under-risk tasks. In two experiments we asked participants to complete four CAGs designed to allow us to test a series of hypotheses about human performance and compare it to normative play maximizing their log rate of growth. In the main experimental conditions, participants performance was initially close to normative but their proportion bet decreased by almost a factor of two over the course of the experiment. This reduction in proportion-bet decreased their expected rate of growth by roughly 25% - a substantial deviation from optimal. Why would participants systematically abandon a normative strategy? We conjecture that a possible reason is loss aversion, well documented in decision under risk. We conjecture that while loss aversion in decision under risk is sub-optimal, there is an intrinsic asymmetry between losses and gains in CAGs that could explain the loss aversion we observe.

animal behavior and cognition↗

bioRxiv2025

Deep Learning-Based 3D Leukocyte Differentiation Using Label-Free Higher Harmonic Generation Microscopy

Both in clinical practice and translational research, cell differentiation of leukocytes provides important information used for diagnostics or insights into pathophysiological mechanisms. The current gold-standard method for bronchoalveolar lavage fluid (BALF) analysis involves histochemical staining of cytospins, followed by manual morphological quantification. However, this approach is labor-intensive, time-consuming, and highly operator-dependent, limiting its efficiency and throughput. This study proposes a deep learning framework for rapid, automated 3D leukocyte differentiation using label-free higher harmonic generation microscopy (HHGM). 3D leukocyte characterization was performed with label-free HHGM. Two deep learning models, ResNet 3D-50 and Vision Transformer (ViT) 3D, were trained, validated and tested for leucocyte differentiation on both BALF and blood fraction samples from 14 interstitial lung disease (ILDs) and 12 acute respiratory distress syndrome (ARDS) patients. Deep-learning model-prediction and cytospin analysis were performed by separate investigators. Results were compared using Bland-Altman analysis. The deep learning algorithm achieved >96% accuracy in quantifying neutrophils, eosinophils, lymphocytes, and macrophages/monocytes. Bland-Altman analysis showed mean differences of less than 3% between cytospin analysis and the deep learning based approach across all cell types. By integrating the label-free imaging capabilities of HHGM with deep learning, this study established a fast, accurate and high-throughput leukocyte differentiation in fresh BALF and blood samples. By significantly improving efficiency and reproducibility, this technology has the potential to transform clinical workflows and advance precision medicine.

biophysics↗

bioRxiv2024

Hierarchical cortical plasticity in congenital sight impairment

A robust learning system balances adaptability to new experiences with stability of its foundational architecture. To investigate how the human brain implements this we used a new approach to study plasticity and stability across hierarchical processing stages in visual cortex. We compare the rod system of individuals born with rod-only photoreceptor inputs (achromatopsia) to the typically developed rod system, allowing us to dissociate impacts of life-long versus transient responses to altered input. Cortical input stages (V1) exhibited high stability, with input-deprived cortex showing no retinotopic remapping and exhibiting structural hallmarks of deprivation. However, plasticity manifested as reorganised read-out of these inputs by higher-order cortex, in a pattern that could compensate for the lower resolution of a rod-only system and its lack of high-density foveal input. We propose that these hierarchical dynamics robustly optimize processing of available input and could reflect a broader principle of brain organisation with important implications for emerging sight-rescue therapies.

neuroscience↗

bioRxiv2024

Olfaction in Tephritidae: a balance between detection and discrimination

Phytophagous insects are capable of detecting and locating suitable hosts, which emit volatile compounds. Polyphagous species appear to have a complex olfactory strategy given that their numerous hosts have diverse emission profiles. In particular, their hosts volatile emissions share some of the same compounds, providing chemical bridges between them. However, the behavioural plasticity observed in insect host selection suggests that other volatiles have a complementary role. Here we explore how the specialization of polyphagous Tephritidae fruit fly in detecting and discriminating between host fruits has driven their chemical selectivity. The volatile emissions from intact or mechanically damaged fruit of 28 different species were analysed using gas chromatography-mass spectrometry and fed into a neuronal model of an olfactory system. We predicted in silico a functional trade-off between the two tasks, with optimal performance depending on detecting a higher proportion of shared fruit compounds, but with lower sensitivity compared to unshared compounds, or vice-versa. Using triple point electroantennography and a behavioural assay, we studied the olfactory response of Tephritidae fruit fly species that oviposit on fruit. Amplitude of the olfactory responses of eight species were negatively correlated with the compounds degree of sharedness among fruit emissions, while response probability was previously shown to correlate positively with a similar metric. A dose-dependent switch in the flys preference confirmed the ecological importance of both shared and unshared fruit compounds. Thus, we propose that insect olfactory systems are chemically tuned to detect suitable hosts and accurately discriminate between them.

ecology↗

bioRxiv2024

Cardiovascular risk in ANCA-associated vasculitis: monocyte phenotyping reveals distinctive signatures between serological subsets

ObjectivesAnti-neutrophil cytoplasmic antibodies (ANCA)-associated vasculitides (AAV) is associated with an increased cardiovascular risk, particularly the myeloperoxidase AAV serotype (MPO-AAV). Distinct alterations in monocyte phenotypes may cause accelerated atherosclerotic disease in AAV. MethodsA cohort including 43 AAV patients and 19 healthy controls were included for downstream analyses. Extensive phenotyping of monocytes and monocyte-derived macrophages was performed using bulk RNA-sequencing and flow cytometry. An in vitro transendothelial migration assay reflecting intrinsic adhesive and migratory capacities of monocytes was employed. Subsequent sub-analyses were performed to investigate differences between serological subtypes. ResultsMonocyte subset analysis showed increased classical monocytes during active disease, whereas non-classical monocytes were decreased. RNA-sequencing revealed upregulation of distinct inflammatory pathways and lipid metabolism-related markers in monocytes of active AAV patients. No differences were detected in the intrinsic monocyte adhesion and migration capacity. Monocytes of MPO-AAV patients in remission expressed genes related to inflammation, coagulation, platelet-binding and interferon signalling, whereas the expression of chemokine receptors indicative of acute inflammation and monocyte extravasation (i.e., CCR2 and CCR5) was increased in monocytes of proteinase-3(PR3)-AAV patients. During active disease, PR3-AAV was linked with elevated serum CRP and increased platelet counts compared to MPO-AAV. ConclusionThese findings highlight changes in monocyte subset composition and activation, but not in the intrinsic migration capacity of AAV monocytes. MPO-AAV monocytes are associated with sustained upregulation of inflammatory genes, whereas PR3-AAV monocytes exhibit chemokine receptor upregulation. These molecular changes may play a role in elevating cardiovascular risk as well as in the underlying pathophysiology of AAV. Key messages- Monocytes are activated during active ANCA-associated vasculitis (AAV) and upregulate lipid metabolism-related markers - AAV monocytes have a normal intrinsic adhesion and migration capacity, although overall monocyte migration likely rises by other mechanisms - The two serological subsets MPO-AAV and PR3-AAV exhibit differences in monocyte activation and chemokine receptor expression

immunology↗

bioRxiv2023

A comparative study on the impact of five Desmodium species on soil microbiome reveals enrichment of selected bacterial and fungal taxa

IntroductionSeveral Desmodium spp. are used as intercrops in push-pull pest management systems to repel insect herbivores. In addition, Desmodium suppresses the parasitic weed Striga, and diversifies the soil microbiome with negative impacts on fungi. We investigated the impact of a 2-year cropping of five Desmodium species on soil microbiome populations. MethodologyTotal DNA was obtained from root zone soil samples collected from a two-years-old common garden experiment with replicated plots of five Desmodium spp. at the international centre for insect physiology and ecology (ICIPE), Mbita, Kenya. Subsequently, 16S and ITS DNA sequencing were performed and the data was analysed by using QIIME2 and Calypso. ResultsOur findings show significant differences in composition and abundance of specific microbial taxa among the Desmodium plots and the bulk soil, with a stronger shift observed for fungal community profiles than bacteria. There was, however, no significant difference in overall diversity, richness and evenness of microbial communities among the Desmodium plots and the bulk soil. Similarly, beta diversity analysis did not reveal a significant association of variation to specific Desmodium spp. plots. Discussion and conclusionThis is the first study to compare impact and association of whole soil microbiomes to different Desmodium species. Whereas long-term Desmodium cropping clearly shifts whole microbiome communities, no significant difference in overall diversity and richness of microbial populations was observed among the studied plots. However, there was a divergence of individual taxa reflected on their increased abundance in association to specific Desmodium spp., pointing towards potential impact on ecosystem services. These findings indicate that significant shifts in whole microbial populations due to Desmodium spp. and thus potentially provision of associated ecosystem services require longer cultivation periods to solidify. Future studies should focus on techniques that monitor real-time changes in microbial populations such as RNA-seq to ascertain live and dead microbes, and thus infer ecological services.

ecology↗

bioRxiv2022

The push-pull intercrop Desmodium does not repel, but intercepts and kills pests

Over two decades ago, scientists developed a push-pull intercropping strategy that received critical acclaim for synergizing food security with ecosystem resilience in smallholder farming. The strategy suppresses Lepidopteran pests in maize through a combination of a repellent intercrop (push), commonly Desmodium spp., and an attractive, dead-end border crop (pull). Key is the intercrops constitutive release of volatiles that repel herbivores. Surprisingly, however, we found that Desmodium does not constitutively release volatiles, and only minimally upon herbivory. Further, in oviposition choice settings, Spodoptera frugiperda, a devastating invasive pest, was not repelled by Desmodium volatiles. In search of an alternative mechanism, we found that neonate larvae strongly preferred Desmodium over maize. However, their development stagnated and none survived. In addition, larvae were frequently seen impaled and immobilized by the dense network of silica-fortified, non-glandular trichomes. Thus, entirely different from repelling adult moths, Desmodium intercepts and decimates dispersing offspring. As a hallmark of sustainable pest control, maize-Desmodium intercropping has inspired countless efforts trying to emulate a stimulo-deterrent diversion in other cropping systems. However, detailed knowledge of the actual mechanisms is required to rationally improve the strategy, and translate the concept into other cropping systems.

ecology↗

bioRxiv2019

Loss of adaptive capacity in asthmatics revealed by biomarker fluctuation dynamics on experimental rhinovirus challenge

Asthma is a dynamic disease, in which lung mechanical and inflammatory processes often interact in a complex, unpredictable manner. We hypothesize that this may be explained by respiratory disease-related systems instability and loss of adaptability to changing environmental conditions, resulting in highly fluctuating biomarkers and symptoms. Using time series of inflammatory (eosinophils, neutrophils, FeNO), clinical and lung function biomarkers (PEF, FVC, and FEV1), we estimated this loss of adaptive capacity (AC) during an experimental perturbation with a rhinovirus in 24 healthy and asthmatic volunteers. Loss of AC was estimated by comparing similarities between pre- and post-challenge time series. Unlike healthy participants, the asthmatics post-viral-challenge state resembled significantly more other rhinovirus-infected asthmatics than their own pre-viral-challenge state (hypergeometric-test: p=0.029). This reveals loss of AC, and supports the novel concept that not only single physiological mechanisms, but interacting dynamic disease properties are altered in asthma and contribute to a more vulnerable phenotype.

physiology↗

bioRxiv2018

Trace impurities in test stimuli can seriously compromise chemosensory studies

The discovery of olfactory receptors and major technological advances have greatly accelerated our understanding of chemosensory mechanisms. However, some of this rapid progress may be compromised by inadequate knowledge or characterization of the purity of chemical stimuli used to challenge olfactory or other chemoreceptors when mapping their response profiles. Here, we provide strong evidence that the presence of trace impurities in test stimuli can completely obscure true ligand-receptor relationships. DmOR7a, an olfactory receptor of the vinegar fly (Drosophila melanogaster) has been reported to respond to several long-chain aliphatic ligands such as a putative Drosophila pheromone1, the pheromone of the silkworm moth Bombyx mori2, and a common fatty acid, linoleic acid3. By contrast, we show that DmOR7a responds with high sensitivity to volatile impurities and degradation products present in minute quantities in authentic standards of those compounds, but not to the standards themselves. Responses to impurities can easily go unnoticed due to two main factors. First, the sensitivity of receptors to key ligands may be greater than that of analytical chemistry instruments used to check sample purity. Second, the concentration of highly volatile impurities in an odour puff may be orders of magnitude higher than the main component of a sample, due to the large differences in vapour pressures between the impurities and the main component. Issues concerning impurities are not limited to studies on olfaction that use odour puffs to characterize receptor-ligand interactions, but may affect all studies on chemosensation, from molecular biology and in-silico predictions to behaviour. Purity, which is crucial in receptor-ligand studies, is always implied, but rarely checked rigorously. To avoid misinterpretations, a proper account of all compounds present in test stimuli and an unequivocal confirmation of ligand affinity should accompany chemosensory studies.

neuroscience↗