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Foti, M.

Publications and source records attributed to Foti, M..

3 recordsLinked to original sources

Towards Scalable Age-Grading of Aedes albopictus mosquito using Mid-Infrared Spectroscopy and Machine Learning

The age structure and dynamics of mosquito populations are crucial for understanding their ability to spread diseases and assessing the effectiveness of anti-mosquito control measures. However, available methods to age-grade mosquito populations are labour-intensive and imprecise, particularly for Aedes species. We investigated the potential of Mid-Infrared Spectroscopy (MIRS) combined with Supervised Machine Learning (ML) to rapidly and accurately predict the age of adult females and males of the arbovirus vector, Aedes albopictus. First, we demonstrated the ability of MIRS-ML to age male and female mosquitoes reared under laboratory conditions. Second, we optimised the model with adults emerged from wild collected eggs reared under natural conditions in a semi-field facility, to expose them to more realistic ambient conditions. For each sex we developed three ML models based on the resolution of the predicted adult age class: low (9 day interval), medium (6 days) and high resolution (3 days) from 1 to 15 or 33 days for males and females, respectively. The prediction accuracy decreased as the resolution increased. In males, the accuracy dropped from 99% (low) to 93% (medium) and 85.8% (low); in females the high and medium resolution models showed 89.4% and 78.5% accuracy, which decreased to 72.6% for the low resolution. In a simulated vector control intervention, the low-resolution models allowed to detect shifts in the age-structure of Ae. albopictus populations with minimal sampling effort (<100 specimens). Finally, we validated MIRS-ML on two unseen data and reconstructed plausible age structures in 1) laboratory-reared and 2) field-collected Ae. albopictus males and females. Overall, the results represent a first step towards the development of a sound and reproducible MIRS-ML approach for age-grading of Ae. albopictus populations in the wild. AUTHOR SUMMARYKnowing the age of mosquito populations is critical for understanding how effectively they can transmit viruses like dengue, chikungunya, and Zika, as older mosquitoes are more likely to be infectious. Also, comparing ages of mosquito population before and after a control intervention - such as insecticide aerial spraying - may allow to understand the impact of the intervention. However, existing methods to estimate mosquito age are time-consuming and imprecise. In this study, we tested whether a rapid and scalable method based on detection of age-related changes by mid-infrared spectroscopy (MIRS) coupled with machine learning (ML) could accurately estimate the age of Aedes albopictus, the Asian Tiger mosquito, an important arbovirus vector. We trained MIRS-ML models using mosquitoes reared in both laboratory and semi-field conditions to reflect realistic environmental variation. Our models were able to classify mosquito age with high accuracy, especially when grouping individuals into broader age categories. In simulated vector control scenarios, low-resolution models effectively detected shifts in population age structure with minimal sampling effort. We also applied our approach to field-collected mosquitoes that showed plausible age structures, suggesting potential of this approach for real-world surveillance. This method represents a promising, scalable, and non-destructive tool for monitoring mosquito population dynamics and could help monitor control strategies against Aedes-borne diseases.

ecology↗

Rhythms and Background (RnB): The Spectroscopy of Sleep Recordings

Non-rapid eye movement (NREM) sleep is characterized by the interaction of multiple coupled oscillations essential for various functions such as memory consolidation, alongside a pervasive and dynamic arrhythmic 1/f scale-free background that may also contribute to these functions. Although recent spectral parametrization methods such as FOOOF (Fitting-One-and-Over-f) allowed to dissociate rhythmic and arrhythmic components in the spectral domain, they fail to resolve these processes in the time domain, where instantaneous measures of frequency, amplitude, and phase-amplitude coupling are still confounded by arrhythmic activity. This limitation represents a significant pitfall for studies of NREM sleep, which often rely on phase-based analyses of specific oscillations. To address this limitation, we introduce Rhythms & Background (RnB), a novel wavelet-based methodology designed to dynamically denoise time-series data by correcting for arrhythmic interference. This enables the extraction of a purely rhythmic time-series suitable for enhanced time-domain analyses of sleep rhythms. We first validate RnB through simulations, demonstrating its robust performance in accurately estimating spectral profiles of individual and multiple oscillations across a range of arrhythmic conditions. We then apply RnB to publicly available intracranial EEG sleep recordings, showing that it provides an improved spectral and time-domain representation of hallmark NREM rhythms. Finally, we demonstrate that RnB significantly enhances the assessment of phase-amplitude coupling between cardinal NREM oscillations, outperforming traditional methods that conflate rhythmic and arrhythmic components. This methodological advance offers a substantial improvement in the analysis of sleep oscillations, providing greater precision in the study of rhythmic activity critical to NREM sleep functions. SIGNIFICANCE STATEMENTThe Rhythms and Background (RnB) algorithm introduces a novel approach to signal processing in electrophysiology by isolating rhythmic activity from the arrhythmic background at the time-series level. Unlike existing spectral decomposition methods, RnB enables more precise analysis of brain rhythms in both the time and spectral domains, providing clearer insights into cerebral oscillatory processes. This breakthrough has direct applications in studying brain connectivity and oscillation dynamics during sleep. Additionally, its application in clinical populations where pathological changes in arrhythmic activity are common, such as neurodevelopmental and neurodegenerative disorders, will help to better understand abnormal oscillatory processes. By improving the accuracy of rhythmic signal analysis, RnB opens new avenues for understanding brain function and dysfunction in research and clinical settings.

neuroscience↗

MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases

BackgroundMicroRNAs are crucial regulators of gene expression that participate in nearly every cellular process. Due to their central role, miRNAs are frequently implicated in the development of pathological conditions, as their dysregulation significantly disrupts normal cellular functioning. Consequently, a thorough characterization of the involvement of dysregulated miRNAs in disturbed pathways is imperative for understanding the mechanisms behind diseases. Nevertheless, the limited availability of analytical methods for joint multi-omic analysis of miRNA-mRNA datasets frequently yields inconclusive and contradictory findings. Specifically, the lack of statistical frame-works designed for integrated analysis of miRNA and mRNA data across biological conditions, as well as the insufficiency of methods suitable for non-sample-matched data, severely restricts the understanding of miRNA networks and the repro-ducibility of the conclusions drawn. To address these limitations, here we present MIRit, an open-source and all-in-one R package that enables integrative multi-omic miRNA analyses using various statistical approaches. ResultsTo showcase MIRits capabilities, we evaluated the pipeline on a thyroid cancer dataset, comparing 8 papillary thyroid carcinoma samples to contralateral healthy tissue, as well as on Alzheimers disease data, comparing temporal cortex samples from patients to those from healthy individuals. In the first case, MIRit revealed that upregulation of miR-146b-5p and miR-146b-3p caused downregulation of PAX8, resulting in decreased thyroid hormone transcription. In contrast, in the second dataset, MIRit showed that disrupted miRNA-mRNA networks in patients with Alzheimers disease impact neuroinflammation, glutamatergic signaling, and neuroprotection. In particular, overexpression of miR-320a-3p may reduce SERPINF1, potentially leading to the accumulation of A{beta}1-42 fragments. ConclusionsThe adoption of MIRits pipeline permits a comprehensive evaluation of perturbed regulatory networks in human diseases through a novel approach for integrative pathway analysis of miRNA-mRNA data. Specifically, MIRit enables the characterization of impaired networks at the molecular level, providing an outstanding advantage in the functional characterization of key dysregulated factors involved in disease pathogenesis and progression. In conclusion, our findings demonstrate the efficacy and usability of MIRit, making it a valuable tool for researchers in the field.

bioinformatics↗