Phosphorus recycling from human excreta in French agroecosystems and potential for food self-sufficiency

Phosphorus (P) is an essential constituent of life but large P losses from agroecosystems and sanitation systems are a major source of eutrophication in water bodies.These losses are doubly detrimental as P in human excretions can be used for crop fertilization.Through a unique dataset of 20,000 French WasteWater Treatment Plants (WWTPs) operational measurements over two decades and a P mass balance, we assess the fate of human excretions and their agricultural potential.Despite 75% of French WWTPs sludge being spread on crops, only 50% of the excreted P makes it back to agroecosystems. This is among the highest rate in Western countries where assessments have been made.Meanwhile, another 35% of the excreted P ends up in surface waters or the environment through WWTP discharge, individual autonomous systems diffuse losses, and sewers leaks.The remaining 15% is incinerated or sent to landfills.Moreover, while WWTP removal efficiency increased in the 2000s, reaching an 80% national average, it has been followed by a decade of stagnation in every French basin.The final removal efficiency for each basin, from 65% to 85%, closely matches whether the area was defined as P-sensitive in the European directive.Our results suggest that recycling all P in excretions could help supply 7 to 34% of French food supply without changing the current food system.Reshaping agricultural systems (shifting to more plant-based diets, decreasing P losses and food waste) would enable to go even further on the road to food sufficiency

Rich dynamics and functional organization on topographically designed neuronal networks in vitro

Neuronal cultures are a prominent experimental tool to understand complex functional organization in neuronal assemblies. However, neurons grown on flat surfaces exhibit a strongly coherent bursting behavior with limited functionality. To approach the functional richness of naturally formed neuronal circuits, here we studied neuronal networks grown on polydimethylsiloxane (PDMS) topographical patterns shaped as either parallel tracks or square valleys.We followed the evolution of spontaneous activity in these cultures along 20 days in vitro using fluorescence calcium imaging. The networks were characterized by rich spatiotemporal activity patterns that comprised from small regions of the culture to its whole extent. Effective connectivity analysis revealed the emergence of spatially compact functional modules that were associated with both the underpinned topographical features and predominant spatiotemporal activity fronts. Our results showthe capacity of spatial constraints tomold activity and functional organization, bringing new opportunities to comprehend the structure-function relationship in living neuronal circuits

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Croissance et activité de cultures neuronales : émergence de comportements organisés.

In this thesis, I provide models and numerical tools to better understand and predict the behavior and development of neuronal cultures and devices.Neuronal cultures have proven invaluable in improving our understanding of how the brain processes information, by enabling researchers to investigate neuronal and network response functions to various perturbations and stimuli.Furthermore, recent progress in microfluidics have opened the gate towards more elaborated neuronal devices, bringing us one step closer to complex signal processing with living in vitro neurons.In a first part, I propose a mechanism to explain the epileptiform bursts of activity present in cultures, mechanism which I formulate as a concise theoretical model. I subsequently test the predictions of this model on cultures and show that they are indeed compatible with the behavior observed in vitro.I further develop this description in the second part of the thesis, where I analyze its spatiotemporal dynamics and the fact that burst nucleate in specific areas in the network.Since predictions and analysis of these nucleation centers strongly depends on the network structure, I develop a simulation platform to enable efficient modeling of the network development. This software takes into account the interactions between the neurons and their environment and is the first platform to provide versatile and complete models to simulate the entire growth process of neurons. I demonstrate that this simulator is able to generate valid neuronal morphologies, then use it to propose new network topologies to describe neuronal cultures, as well as to reproduce existing neuronal devices. I then show that the activities sustained by these structures are compatible with the experimental recordings.Eventually, I discuss several future directions for which the use of neuronal devices would enable to circumvent current limitations of neuronal cultures, thus providing new information on the processes which underlie brain development and plasticity.Dans cette thèse, je propose plusieurs modèles et outils numériques afin de mieux comprendre et prédire le comportement et le développement de cultures et dispositifs neuronaux.Les cultures de neurones ont en effet été un outil précieux durant les 20 dernières années : elles ont permis de mieux comprendre la manière dont le cerveau traite les différentes informations qui lui parviennent en donnant aux scientifiques la possibilité de tester les effets de médicaments sur les neurones, ainsi que d'obtenir leurs réponses détaillées à diverses perturbations et stimuli.De plus, de récentes avancées en microfluidiques ont ouvert la voie à la conception de dispositifs neuronaux plus élaborés, rapprochant encore un peu plus la perspective du traitement de signaux complexes via des neurones in vitro.Dans une première partie, je propose un mécanisme pour expliquer les bouffées d'activité épileptiformes présentes dans les cultures, mécanisme que je formule via un modèle théorique concis. J'effectue ensuite une vérification expérimentale des prédictions du modèle sur des cultures et montre que celles-ci sont effectivement compatibles avec le comportement observé in vitro.Dans une seconde partie, je décris plus en détail la description de la dynamique spatio-temporelle du phénomène, notamment le fait que les bursts nucléent en des zones bien précises du réseau neuronal.Comme les prédictions et analyses effectuées dépendent fortement de la structure de ce réseau, je présente ensuite la réalisation d'une plateforme de simulation afin de permettre de modéliser efficacement le développement des réseaux neuronaux. Ce logiciel prend en compte les interactions entre les neurones et leur environnement et constitue la première plateforme à fournir des modèles polyvalents et complets pour décrire l'intégralité du processus de croissance neuronal. Je montre ensuite que ce simulateur est capable de générer des morphologies valides et l'utilise pour proposer des nouvelles topologies de réseaux afin de décrire les cultures de neurones. Je reproduis également des dispositifs neuronaux existants et montre que les activités entretenues par ces structures sont compatibles avec les observations expérimentales. Enfin, je discute plusieurs directions de recherche possibles, pour lesquelles l'utilisation de dispositifs neuronaux spécifiques permettrait de contourner les limitations des cultures neuronales et fournirait ainsi de nouvelles informations sur les processus sous-tendant le développement et la plasticité cérébral

Weighted directed clustering: interpretations and requirements for heterogeneous, inferred, and measured networks

Weights and directionality of the edges carry a large part of the information we can extract from a complex network. However, many network measures were formulated initially for undirected binary networks. The necessity to incorporate information about the weights led to the conception of multiple extensions, particularly for definitions of the local clustering coefficient discussed here. We uncover that not all of these extensions are fully weighted; some depend on the degree and thus change a lot when an infinitely-small-weight edge is exchanged for the absence of an edge, a feature that is not always desirable. We call these methods “hybrid” and argue that, in many situations, one should prefer fully weighted definitions. After listing the necessary requirements for a method to analyze many various weighted networks properly, we propose a fully weighted continuous clustering coefficient that satisfies all the previously proposed criteria while also being continuous with respect to vanishing weights. We demonstrate that the behavior and meaning of the Zhang-Horvath clustering and our proposed continuous definition provide complementary results and significantly outperform other definitions in multiple relevant conditions. We demonstrate, using synthetic and real-world networks, that when the network is inferred, noisy, or very heterogeneous, it is essential to use the fully weighted clustering definitions

Vers de nouveaux engrais d'origine humaine ?

Face à un contexte d’instabilité du coût de l’unité d’azote et de tension sur l’accès à la matière organique, des engrais alternatifs émergent comme ceux issus des urines et matières fécales humaines. Cette tribune aborde les enjeux relatifs au déploiement de ces engrais humains

Phosphorus recycling from human excreta in French agroecosystems and potential for food self-sufficiency

Phosphorus (P) is an essential constituent of life but large P losses from agroecosystems and sanitation systems are a major source of eutrophication in water bodies.These losses are doubly detrimental as P in human excretions can be used for crop fertilization.Through a unique dataset of 20,000 French WasteWater Treatment Plants (WWTPs) operational measurements over two decades and a P mass balance, we assess the fate of human excretions and their agricultural potential.Despite 75% of French WWTPs sludge being spread on crops, only 50% of the excreted P makes it back to agroecosystems. This is among the highest rate in Western countries where assessments have been made.Meanwhile, another 35% of the excreted P ends up in surface waters or the environment through WWTP discharge, individual autonomous systems diffuse losses, and sewers leaks.The remaining 15% is incinerated or sent to landfills.Moreover, while WWTP removal efficiency increased in the 2000s, reaching an 80% national average, it has been followed by a decade of stagnation in every French basin.The final removal efficiency for each basin, from 65% to 85%, closely matches whether the area was defined as P-sensitive in the European directive.Our results suggest that recycling all P in excretions could help supply 7 to 34% of French food supply without changing the current food system.Reshaping agricultural systems (shifting to more plant-based diets, decreasing P losses and food waste) would enable to go even further on the road to food sufficiency