Respiration | EPFL Graph Search

vignette|Le souffle constitue chez les humains la phase externe d'évacuation des gaz issus du processus respiratoire. La respiration est une fonction biologique qui permet aux êtres vivants d'utiliser leurs réserves énergétiques grâce à des échanges gazeux avec le milieu extérieur. De très nombreux organismes respirent : bactéries, végétaux, champignons, animaux, etc. La respiration fait à la fois référence :

au processus biochimique qui se déroule à l'intérieur de la cellule, la respiration cellulaire ;
au transfert des gaz de l'extérieur de l'organisme vers la cellule ou inversement.

Autant la respiration est une fonction qui accompagne la vie depuis ses origines, autant elle ne s'est pas exprimée dans les mêmes conditions au cours de l'histoire de la Terre, connaissant ou induisant parfois de profonds bouleversements. Elle contribue de manière déterminante aux principaux cycles biogéochimiques. En physiologie humaine et en médecine, la respiration concerne directement ou tran

On-site biostimulation evaluation of a remediated perchloroethene-contaminated acquifer located in Jablunkov, Czech Republic

Isabelle Fäh

Chlorinated ethenes solvents (CEs) are one of the most common contaminants identified in groundwater ecosystems. Long used as a degreaser in industry, perchloroethene (PCE) and trichloroethene (TCE) are particularly persistent in the environment as recalcitrant to oxic degradation, and classified as unhealthy and dangerous for the environment. Under anaerobic conditions, CEs can be degraded naturally in the environment by organohalide respiring bacteria (OHRB) through dehalogenase enzymes reducing them into ethene, a non-hazardous end product. However, toxicity of the intermediate daughter compounds of the degradation (TCE, DCE and VC) is higher than PCE. As this natural attenuation is a slow process, intermediate compounds accumulate in the environment and biostimulation is often used to enhance the complete degradation of CEs. Substrates are added to the contaminated aquifer and used by fermentative bacteria releasing by-product such as H2 that is essential for the dehalorespiration of CEs. Biostimulation has been studied in a PCE contaminated-aquifer located in Jablunkov (Czech Republic). Cheese whey (CW) has been injected into the groundwater in November 2012 and June 2013. The objective of the current project is to evaluate the efficiency of the CW applications by analysing microbiologic and physico-chemical parameters describing the aquifer at six sampling dates from September 2012 to December 2013 within six wells allocated over the aquifer. Global bacterial community structures were analysed in laboratory using Polymerase Chain Reaction (PCR) and T-RFLP (Terminal Restriction Fragment Length Polymorphism). OHRB were analysed as well by specific PCR targeting 16S rRNA and dehalogenase genes of bacteria known to degrade completely the CEs. Then, contaminants and ethene concentrations as well as others Terminal Electron Acceptors implicated in the respiratory processes (Terminal Electron Accepting Processes – TEAPs) were measured to give information about the redox conditions within the aquifer. Finally, others hydrogeological parameters such as pH and temperature were measured. All data were analysed using Multiple Factor Analysis (MFA) in the R software. Interpretations provided a global model indicating the characteristics and functioning of the aquifer. The successive CW applied on-site have a gradual impact on the environmental conditions and on the structures of bacterial communities. After the two CW applications, the aquifer has partly changed to conditions favourable for complete dechlorination. It was the case for three wells over six. Two CW injections have been necessary to allow the production of ethene for two wells whereas only one was needed for the other one. Biostimulation were efficient but not sufficient to completely degrade the CEs on the whole aquifer. In one well, the accumulation of DCE were more important than the production of ethene. In two other wells, ethene was not produced but the statistical analysis showed that they tend toward complete dechlorination conditions. New CW applications would be necessary to completely remediate this aquifer.

2014

A lightweight learning-based decoding algorithm for intraneural vagus nerve activity classification in pigs

Silvestro Micera, Leonardo Pollina, Ivo Strauss

Objective. Bioelectronic medicine is an emerging field that aims at developing closed-loop neuromodulation protocols for the autonomic nervous system (ANS) to treat a wide range of disorders. When designing a closed-loop protocol for real time modulation of the ANS, the computational execution time and the memory and power demands of the decoding step are important factors to consider. In the context of cardiovascular and respiratory diseases, these requirements may partially explain why closed-loop clinical neuromodulation protocols that adapt stimulation parameters on patient's clinical characteristics are currently missing. Approach. Here, we developed a lightweight learning-based decoder for the classification of cardiovascular and respiratory functional challenges from neural signals acquired through intraneural electrodes implanted in the cervical vagus nerve (VN) of five anaesthetized pigs. Our algorithm is based on signal temporal windowing, nine handcrafted features, and random forest (RF) model for classification. Temporal windowing ranging from 50 ms to 1 s, compatible in duration with cardio-respiratory dynamics, was applied to the data in order to mimic a pseudo real-time scenario. Main results. We were able to achieve high balanced accuracy (BA) values over the whole range of temporal windowing duration. We identified 500 ms as the optimal temporal windowing duration for both BA values and computational execution time processing, achieving more than 86% for BA and a computational execution time of only similar to 6.8 ms. Our algorithm outperformed in terms of BA and computational execution time a state of the art decoding algorithm tested on the same dataset (Vallone et al 2021 J. Neural Eng. 18 0460a2). We found that RF outperformed other machine learning models such as support vector machines, K-nearest neighbors, and multi-layer perceptrons. Significance. Our approach could represent an important step towards the implementation of a closed-loop neuromodulation protocol relying on a single intraneural interface able to perform real-time decoding tasks and selective modulation of the VN.

IOP Publishing Ltd2022

Neuromodulation of neocortical microcircuitry: a multi-scale framework to model the effects of cholinergic release

Cristina Colangelo

Neuromodulation of neocortical microcircuits is one of the most fascinatingand mysterious aspects of brain physiology. Despite over a century of research,the neuroscientific community has yet to uncover the fundamentalbiological organizing principles underlying neuromodulatory release. Phylogenetically,Acetylcholine (ACh) is perhaps the oldest neuromodulator,and one of the most well-studied. ACh regulates the physiology of neuronsand synapses, and modulates neural microcircuits to bring about areconfiguration of global network states. ACh is known to support cognitiveprocesses such as learning and memory, and is involved in the regulationof arousal, attention and sensory processing. While the effects of ACh inthe neocortex have been characterized extensively, integrated knowledge ofits mechanisms of action is lacking. Furthermore, the ways in which AChis released from en-passant axons originating in subcortical nuclei are stilldebatable. Simulation-based paradigms play an important role in testingscientific hypotheses, and provide a useful framework to integrate what isalready known and systematically explore previously uncharted territory.Importantly, data-driven computational approaches highlight gaps in currentknowledge and guide experimental research. To this end, I developed amulti-scale model of cholinergic innervation of rodent somatosensory cortexcomprising two distinct sets of ascending projections implementing eithersynaptic (ST) or volumetric transmission (VT). The model enables the projectiontypes to be combined in arbitrary proportions, thus permitting investigationsof the relative contributions of these two transmission modalities.Using our ACh model, we find that the two modes of cholinergic release actin concert and have powerful desynchronizing effects on microcircuit activity.Furthermore we show that this modeling framework can be extendedto other neuromodulators, such as dopamine and serotonin, with minimalconstraining data. In summary, our results suggest a more nuanced view ofneuromodulation in which multiple modes of transmitter release - ST vs VT- are required to produce synergistic functional effects.

EPFL2022