Biology subjects

Hoch, T.

Publications and source records attributed to Hoch, T..

5 recordsLinked to original sources

bioRxiv2025

Map simulator of tick abundance in heterogeneous agricultural landscapes

Among vector-borne diseases, tick-borne diseases (TBD) are a major concern for human health. Mapping the distribution of important tick species is thus a major challenge for efficient prevention. Due to its specific ecological requirements, Ixodes ricinus, the main tick species in Europe responsible for TBD transmission, lives mostly in woodlands but also at the interface between woodlands and pastures or crops and along hedgerows. At the landscape scale, extensive variations in tick densities are observed but remain poorly understood. In that aim, we built a statistical model to identify the landscape variables influencing the abundance of questing I. ricinus nymphs, using GLMM approaches and MCMC estimates. This model was fitted on a data set based on a field sampling of ticks conducted during 3 years in 2 different agricultural landscapes in northwest and southwest France, for a total of 5390 sampling units. Among 12 variables investigated, 4 were finally kept in the model: woodland perimeter, woodland distance, road distance and building perimeter. Then, we developed a R package that simulates the abundance of questing nymphs within a given agricultural landscape, taking into account the influence of the different habitats as determined by the above statistical model. The maps obtained as an output from this simulator will be a useful tool for visualizing TBD risk, notably for stake-holders involved in landscape management and public health decisions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/663759v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@f950aborg.highwire.dtl.DTLVardef@1f0f27org.highwire.dtl.DTLVardef@11bde05org.highwire.dtl.DTLVardef@8d2202_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsIxodes ricinus abondance is influenced by landscape characteristics Tick sampling was carried out in heterogeneous agricultural landscapes Informative variables related to habitats were identified by statistical analysis Woodlands, roads and buildings influence tick densities The resulting model was used to build a simulator of tick at-risk zones

ecology↗

bioRxiv2022

Seasonality of host-seeking Ixodes ricinus nymph abundance in relation to climate

There is growing concern about climate change and its impact on human health. Specifically, global warming could increase the probability of emerging infectious diseases, notably because of changes in the geographical and seasonal distributions of disease vectors such as mosquitoes and ticks. For example, the range of Ixodes ricinus, the most common and widespread tick species in Europe, is currently expanding northward and at higher altitudes. However, little is known about the seasonal variation in tick abundance in different climates. Seasonality of I. ricinus is often based on expert opinions while field surveys are usually limited in time. Our objective was to describe seasonal variations in I. ricinus abundance under different climates. To this end, a seven-year longitudinal study, with monthly collections of I. ricinus host-seeking nymphs, was carried out in France, in six locations corresponding to different climates. Tick data were log-transformed and grouped between years so as to obtain seasonal variations for a typical year. Daily average temperature was measured during the study period. Seasonal patterns of nymph abundance were established for the six different locations using linear harmonic regression. Model parameters were estimated separately for each location. Seasonal patterns appeared different depending on the climate considered. Western temperate sites showed an early spring peak, a summer minimum and a moderate autumn and winter abundance. More continental sites showed a later peak in spring, and a minimum in winter. The peak occurred in summer for the mountainous site, with an absence of ticks in winter. In all cases except the mountainous site, the timing of the spring peak could be related to the sum of degree days since the beginning of the year. Winter abundance was positively correlated to the corresponding temperature. Our results highlight clear patterns in the different sites corresponding to different climates, which allow further forecast of tick seasonality under changing climate conditions.

ecology↗

bioRxiv2021

Multiplexed Imaging Mass Cytometry of Chemokine Milieus in Metastatic Melanoma Characterizes Features of Response to Immunotherapy

Intratumoral immune cells are crucial for tumor control and anti-tumor responses during immunotherapy. Immune cell trafficking into tumors is mediated by chemokines, which are expressed and secreted upon various stimuli and interact with specific receptors. To broadly characterize chemokine expression and function in tumors, we have used multiplex mass cytometry-based imaging of protein markers and RNA transcripts to analyze the chemokine landscape and immune infiltration in metastatic melanoma samples. Tumors that lacked immune infiltration were devoid of most chemokines and exhibited particularly low levels of antigen presentation and inflammation. Infiltrated tumors were characterized by expression of multiple chemokines. CXCL9 and CXCL10 were often localized in patches associated with dysfunctional T cells expressing CXCL13 which was strongly associated with B cell patches and follicles. TCF7+ naive-like T cells, which predict response to immunotherapy, were enriched in the vicinity of B cell patches and follicles. Our data highlight the strength of RNA and protein co-detection which was critical to deconvolve specialized immune microenvironments in inflamed tumors based on chemokine expression. Our findings further suggest that the formation of tertiary lymphoid structures is accompanied by naive and naive- like T cell recruitment, which ultimately boosts anti-tumor activity. One sentence summaryInflammatory chemokine milieus in metastatic melanoma are hotspots of T cell dysfunction and CXCL13 expression, which likely guide the recruitment of B cells and the formation of B cell follicles responsible for anti-tumor immunity.

cancer biology↗

bioRxiv2020

cytomapper: an R/Bioconductor package for visualisation of highly multiplexed imaging data

Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Standard data processing pipelines quantify cell-specific features and generate object segmentation masks as well as multi-channel images. Therefore, multiplexed imaging data can be visualised across two layers of information: pixel-intensities represent the spatial expression of biomarkers across an image while segmented objects visualise cellular morphology, interactions and cell phenotypes in their microenvironment. Here we describe cytomapper, a computational tool that enables visualisation of pixel- and cell-level information obtained by multiplexed imaging. The package is written in the statistical programming language R, integrates with the image and single-cell analysis infrastructure of the Bioconductor project, and allows visualisation of single to hundreds of images in parallel. Using cytomapper, expression of multiple markers is displayed as composite images, segmentation masks are coloured based on cellular features, and selected cells can be outlined in images based on their cell type, among other functions. We illustrate the utility of cytomapper by analysing 100 images obtained by imaging mass cytometry from a cohort of type 1 diabetes patients and healthy individuals. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells based on marker expression and visualisation of selected cells in corresponding images. Together, cytomapper offers tools for diverse image and single-cell visualisation approaches and supports robust cell phenotyping via gating.

bioinformatics↗

bioRxiv2018

A generic multi-level stochastic modelling framework in computational epidemiology

There is currently an overwhelming increased interest in predictive biology and computational modelling. The development of reliable, reproducible and revisable simulation models in computational life sciences is often pointed out as a challenging issue. Population dynamics, including epidemiology, has not yet developed a language to formalize complex models in a univocal and automatable way, hence hindering the capability to implement in short time reliable, revisable and expert-friendly models intended for realistic mechanistic simulations. In epidemiology specifically, models aim not only at understanding pathogen spread but also at assessing control measures at several scales. To achieve this goal efficiently, best software practices should be supported by Artificial Intelligence methods to handle experts knowledge. The framework EMULSION presented here intends to both tackle multiple modelling paradigms in epidemiology and facilitate the automation of model design. We therefore built both a domain-specific language (DSL) for the modular description of complex epidemiological models, and a generic simulation engine designed to embed existing modelling paradigms within a homogeneous architecture based on adaptive software agents. The diversity of concerns (biology, economics, human activities) involved in real pathosystems requires an explicit, comprehensive and intelligible way to describe epidemiological models, to involve experts without computer science skills throughout the modelling, simulation and output analysis steps. This approach was applied to compare hypotheses in modelling a zoonosis (Q fever), to study its transmission dynamics within and between cattle herds at a regional scale, and to assess the contribution of transmission pathways. Separating model description from the simulation engine allowed epidemiologists to be involved in assumption revision, while guaranteeing very few code modifications. We assessed the added value of EMULSION by applying the DSL and the simulation engine to a concrete disease. Future extensions of EMULSION towards a broader range of epidemiological concerns will reduce significantly the time required to design and assess models and control measures against endemic and epidemic diseases. Ultimately, we believe this effort is a major lever to increase scientists preparedness to face emerging threats for public health and provide rapid, reliable, and reasoned assessments of control measures.

epidemiology↗