Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data

Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the information provided by this well-known hierarchical structure is rarely used by machine learning-based automatic microbial identification systems. Structured machine learning methods were recently proposed for taking into account the structure embedded in a hierarchy and using it as additional a priori information, and could therefore allow to improve microbial identification systems. We test and compare several state-of-the-art machine learning methods for microbial identification on a new Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset. We include in the benchmark standard and structured methods, that leverage the knowledge of the underlying hierarchical structure in the learning process. Our results show that although some methods perform better than others, structured methods do not consistently perform better than their "flat" counterparts. We postulate that this is partly due to the fact that standard methods already reach a high level of accuracy in this context, and that they mainly confuse species close to each other in the tree, a case where using the known hierarchy is not helpful

Universal amplitudes of the Casimir-like interactions between four types of rods in fluid membranes

The fluctuation-induced, Casimir-like interaction between two parallel rods of length L adsorbed on a fluid membrane is calculated analytically at short separations d<<L. The rods are modeled as constraints imposed on the membrane curvature along a straight line. This allows to define four types of rods, according to whether the membrane can twist along the rod and/or curve across it. For stiff constraints, all the interaction potentials between the different types of rods are attractive and proportional to L/d. Two of the four types of rods are then equivalent, which yields six universal Casimir amplitudes. Repulsion can occur between different rods for soft constraints. Numerical results obtained for all ranges of d/L show that the attraction potential reaches kT for d/L\simeq0.2. At separations smaller than d_c \approx L(L/l_p)^(1/3), where l_p is the rod persistence length, two rods with fixed ends will bend toward each other and finally come into contact because of the Casimir interaction.Comment: 6 pages, 3 figure

Evaluation of combustion concepts and scavenging configurations in a 2-Stroke compression-ignition engine for future automotive powerplants

[ES] El trabajo de investigación presentado en esta tesis es el resultado de varios años dedicados al desarrollo, la implementación y la optimización de dos tecnologías combinadas: un concepto de combustión innovador y una arquitectura de motor de nuevo diseño. Esta investigacion se ha realizado en el marco de una colaboración con Renault SA, como continuación de las actividades realizadas en el proyecto europeo POWERFUL (POWERtrain for FUture Light-duty vehicles) por un lado,y en el marco del proyecto europeo REWARD (Real World Advanced technologies foR Diesel engines), devenido como continuación del proyecto POWERFUL en el marco del programa de investigación Horizonte 2020, por otro lado. Los principales objetivos de estos estudios eran evaluar el potencial del concepto de combustión parcialmente premezclada (PPC) operando con gasolina como combustible en un innovador motor de 2 tiempos de válvulas en culata, y luego diseñar una nueva geometría de motor de 2 tiempos utilizando la arquitectura Uniflujo para superar los principales problemas y limitaciones observados durante la primera etapa, que se pueden resumir principalmente en el rendimiento de barrido (especialmente trabajando en cargas elevadas). La metodología diseñada para este trabajo de investigación sigue un enfoque teórico-experimental. La evaluación del concepto de combustión PPC operando con gasolina se llevó a cabo principalmente con un enfoque experimental con el apoyo del análisis en línea directamente en el banco de ensayo, seguido de un exhaustivo tratamiento posterior de los datos y de un análisis detallado del proceso de combustión utilizando herramientas de diagnóstico. Por el contrario, el desarrollo del nuevo motor Uniflujo de 2 tiempos consistió principalmente en iteraciones sobre modelado 3D-CFD, si bien las actividades experimentales fueron fundamentales para validar las diferentes soluciones propuestas y evaluar su sensibilidad ante diferentes parámetros de interés utilizando una metodología de Diseño de Experimentos (DoE). La primera parte del trabajo se ha dedicado a la comprensión de los procesos termodinámicos involucrados en la combustión operando con el concepto PPC en un motor de 2 tiempos de válvulas en culata utilizando gasolina como combustible, y a evaluar su potencial en términos de emisiones contaminantes, consumo de combustible y ruido. Por último, se ha realizado un trabajo de exploración para ampliar en la medida de lo posible el rango de funcionamiento de este concepto de combustión en esta configuración específica del motor, investigando especialmente el rendimiento en cargas bajas en todo el rango de regímenes de giro del motor, y estableciendo también las principales limitaciones para la operación en cargas altas. La segunda parte de la tesis se ha centrado en el desarrollo y optimización teórica de un motor Uniflujo de 2 tiempos de nuevo diseño, incluyendo su fabricación y validación experimental. El objetivo principal era optimizar, utilizando principalmente simulaciones 3D-CFD, el rendimiento de barrido de esta arquitectura de 2 tiempos mediante el diseño de nuevas geometrías de puertos de admisión, permitiendo un gran control sobre el flujo de aire hacia y a través del cilindro para barrer al máximo los gases quemados y minimizar el cortocircuito de aire fresco hacia el escape. Las soluciones óptimas se evaluaron experimentalmente siguiendo la metodología DoE, antes de comparar finalmente los resultados de rendimiento de barrido con la anterior arquitectura de motor de 2 tiempos con válvulas en culata.[CA] El treball de recerca presentat en aquesta tesi és el resultat de diversos anys dedicats al desenvolupament, la implementació i l'optimització de dues tecnologies combinades: un concepte de combustió innovador i una arquitectura de motor de nou disseny. Aquesta recerca s'ha realitzat en el marc d'una col·laboració amb Renault SA, com a continuació de les activitats del projecte europeu *POWERFUL (*POWERtrain *for *FUture Light-*duty *vehicles) d'una banda, i en el marc del projecte europeu *REWARD (Real *World *Advanced *technologies *foR Dièsel *engines), es devingut com a continuació del projecte *POWERFUL en el marc del programa d'investigació Horitzó 2020, d'altra banda. Els principals objectius d'aquests estudis eren avaluar el potencial del concepte de combustió parcialment premesclada (PPC) operant amb gasolina com a combustible en un innovador motor de 2 temps de vàlvules en culata, i després dissenyar una nova geometria de motor de 2 temps utilitzant l'arquitectura Uniflux per a superar els principals problemes i limitacions observats durant la primera etapa, que es poden resumir principalment en el rendiment d'escombratge (especialment treballant en càrregues elevades). La metodologia dissenyada per a realitzar aquests treballs de recerca segueix un enfocament tant experimental com teòric. L'avaluació del concepte de combustió PPC operant amb gasolina es va dur a terme principalment amb un enfocament experimental, però sempre amb el suport de l'anàlisi en línia directament en el banc d'assaig, seguit d'un exhaustiu tractament posterior de les dades combinat amb una anàlisi detallada del procés de combustió utilitzant eines de diagnòstic. Per contra, el desenvolupament i el disseny del nou motor Uniflux de 2 temps va consistir principalment en iteracions sobre modelatge 3D-CFD, si bé les activitats experimentals van ser fonamentals per a validar les diferents solucions proposades i avaluar la seua sensibilitat davant una sèrie de paràmetres d'interés utilitzant una metodologia de Disseny d'Experiments (DoE). La primera part del treball s'ha dedicat a la comprensió dels processos termodinàmics involucrats en la combustió operant amb el concepte de combustió PPC en un motor de 2 temps de vàlvules en culata utilitzant gasolina com a combustible, i a avaluar el seu potencial en termes d'emissions contaminants, consum de combustible i també de soroll. Finalment, s'ha fet un treball d'exploració per a ampliar en la mesura que siga possible el rang de funcionament d'aquest concepte de combustió utilitzant eixa configuració específica del motor, investigant especialment el rendiment en càrregues baixes en tot el rang de règims de gir del motor, i establint també les principals limitacions per a l'operació en càrregues altes. La segona part de la tesi s'ha centrat en el desenvolupament i optimització teòrica d'un motor Uniflux de 2 temps de nou disseny, incloent la seua fabricació i validació experimental. L'objectiu principal era optimitzar, utilitzant principalment simulacions 3D-CFD, el rendiment d'escombratge d'aquesta arquitectura de 2 temps mitjançant el disseny de noves geometries de ports d'admissió, permetent un gran control sobre el flux d'aire cap a i a través del cilindre per a escombrar al màxim els gasos cremats i minimitzar el curtcircuit d'aire fresc cap a l'escapament. Les solucions òptimes es van fabricar i van avaluar experimentalment seguint la metodologia DoE, abans de comparar finalment els resultats de rendiment d'escombratge amb l'anterior arquitectura de motor de 2 temps amb vàlvules en culata.[EN] The research work presented in this thesis is the result of several years dedicated to the development, implementation and optimization of two combined technologies: an innovative combustion concept and a newly designed engine architecture. These investigations have been performed in the framework of a research collaboration with Renault SA following up the activities performed along the European POWERFUL project (POWERtrain for FUture Light-duty vehicles) on the one hand, and in the framework of the European REWARD project (REal World Advanced technologies foR Diesel engines), brought as a continuation of the POWERFUL project in the frame of the Horizon 2020 research program, on the other hand. The main objectives of these studies were to evaluate the potential of the Partially Premixed Combustion (PPC) concept operating with gasoline fuel in an innovative 2-Stroke poppet-valve engine, and then to design a new 2-Stroke engine geometry using the Uniflow architecture to overcome the main problems and limitations observed during the first stage, which can be mainly summarized to the scavenging performance (especially at high loads). The methodology designed for performing these investigation is based on both experimental and theoretical approaches. The evaluation of the gasoline PPC concept was carried out mainly experimentally, but always supported by online analysis directly on the test-bench and followed by a thorough post-processing of the data combined with a detailed analysis of the combustion using combustion diagnostic tools. On the contrary, the development and design of the new 2-Stroke Uniflow engine consisted mainly of 3D-CFD iterations, but experimental testing was crucial to validate the different solutions proposed and evaluate their sensitivity to a set of parameters of interest using a Design of Experiments (DoE) methodology. The first part of the work has been dedicated to the understanding of the thermodynamical processes involved in the combustion in a poppet-valve 2-Stroke engine operating with the gasoline PPC concept, and to evaluate its potential in terms of pollutant emissions, fuel consumption and also noise. Finally, a wide exploration has been performed to extend as much as possible the operating range of this combustion concept using that specific engine configuration, especially investigating the low loads performance throughout the full range of engine speeds, and also laying out the main limitations for high-to-full load operations. The second part of the thesis has been focused on the development and theoretical optimization of a newly designed 2-Stroke Uniflow engine, leading to manufacture and experimental validation. The main objective was to optimize, using mainly 3D-CFD modeling simulations, the scavenging performance of this 2-Stroke architecture by designing new intake ports geometries and to enable a great control over the air flow into and through the cylinder in order to scavenge the burnt gases as much as possible while minimizing the fresh air short-circuit to the exhaust. The optimum solutions were then manufactured and experimentally tested following a DoE methodology, before finally comparing the results of the scavenging performance to the previous 2-Stroke poppet-valve engine architecture.Thein, KJL. (2021). Evaluation of combustion concepts and scavenging configurations in a 2-Stroke compression-ignition engine for future automotive powerplants [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/164044TESI

The effect of landscape complexity and microclimate on the thermal tolerance of a pest insect

Landscape changes are known to exacerbate the impacts of climate change. As such, understanding the combined effect of climate and landscape on agroecosystems is vital if we are to maintain the function of agroecosystems. This study aimed to elucidate the effects of agricultural landscape complexity on the microclimate and thermal tolerance of an aphid pest to better understand how landscape and climate may interact to affect the thermal tolerance of pest species within the context of global climate change. Meteorological data were measured at the landscape level, and cereal aphids (Sitobion avenae, Metopolophium dirhodum and Rhopalosiphum padi) sampled, from contrasting landscapes (simple and complex) in winter 2013/2014 and spring 2014 in cereal fields of Brittany, France. Aphids were returned to the laboratory and the effect of landscape of origin on aphid cold tolerance (as determined by CTmin ) was investigated. Results revealed that local landscape complexity significantly affected microclimate, with simple homogenous landscapes being on average warmer, but with greater temperature variation. Landscape complexity was shown to impact aphid cold tolerance, with aphids from complex landscapes being more cold tolerant than those from simple landscapes in both winter and spring, but with differences among species. This study highlights that future changes to land use could have implications for the thermal tolerance and adaptability of insects. Furthermore, not all insect species respond in a similar way to microhabitat and microclimate, which could disrupt important predator-prey relationships and the ecosystem service they provide

L’influence des organismes communautaires à titre d’acteurs intermédiaires de prestation de biens et de services sur la confiance institutionnelle des personnes s’y impliquant : le cas québécois

La confiance institutionnelle est la clé de la santé de toute entité législative. Deux groupes de facteurs sont à la source de l’émanation de confiance institutionnelle chez les individus : les facteurs liés à la représentativité et ceux liés à l’expertise des institutions. L’État est le principal récipiendaire de la confiance institutionnelle issue de ces deux groupes. Toutefois, il n’est pas le seul acteur à pouvoir s’en réclamer, en particulier dans un contexte de multiplication de nouveaux acteurs socio-économiques dans la diffusion de biens et de services relevant traditionnellement du domaine public et de retrait progressif de l’intervention étatique. Les organismes communautaires sont l’un de ces nouveaux acteurs dont la présence et l’importance sociale sont en forte augmentation. Or, ils peuvent également être, au même titre que l’État, les récipiendaires de la confiance des individus. Dans le contexte de diminution de la confiance institutionnelle envers l’État au fil des dernières décennies, les organismes communautaires ont-ils un rôle à jouer et un impact vis-à-vis de cette situation par rapport aux personnes qui s’y impliquent ? À partir d’un sondage auprès des personnes responsables des organismes communautaires québécois dédiés aux individus en situation de handicap physique ou/et psychologique, nous tentons de répondre à ce questionnement. Les résultats démontrent une diminution de la confiance institutionnelle à la faveur d’une hausse de confiance envers les organismes communautaires à la suite de l’implication des individus dans ce type d’acteur et ce, particulièrement au niveau des deux groupes de facteurs explicatifs (représentativité et expertise). Institutional trust is the key to every healthy legislative entity. Two groups of factor are the source of emanation of people’s institutional trust : factors about representativeness and about expertise. The state is the main recipient of institutional trust from these two groups. However, he is not the only actor who can claim it, particularly in a context of multiplication of new socio-economic actors in the distribution of goods and services traditionally made by the public sector and progressive withdrawal of state intervention. Community-based organizations are one of those new actors whose presence and social importance are sharply increasing. However, they can be, on the same level than the state, the recipients of people’s trust. In the context of a decline of institutional trust in the state over the last decades, do community-based organisms have a role to play and an impact over this situation for the people who are involved in those organizations ? Based on a survey of people in charge of Quebec community-based organizations dedicated to individuals with physical and/or psychological disabilities, we tried to answer this question. The results demonstrate a decrease of institutional trust in favor of higher trust in community-based organizations as a result of being involved in this type of actor, particularly at the level of the two groups of explanatory factors (representativeness and expertise).Institutional trust is the key to every healthy legislative entity. Two groups of factor are the source of emanation of people’s institutional trust : factors about representativeness and about expertise. The state is the main recipient of institutional trust from these two groups. However, he is not the only actor who can claim it, particularly in a context of multiplication of new socio-economic actors in the distribution of goods and services traditionally made by the public sector and progressive withdrawal of state intervention. Community-based organizations are one of those new actors whose presence and social importance are sharply increasing. However, they can be, on the same level than the state, the recipients of people’s trust. In the context of a decline of institutional trust in the state over the last decades, do community-based organisms have a role to play and an impact over this situation for the people who are involved in those organizations ? Based on a survey of people in charge of Quebec community-based organizations dedicated to individuals with physical and/or psychological disabilities, we tried to answer this question. The results demonstrate a decrease of institutional trust in favor of higher trust in community-based organizations as a result of being involved in this type of actor, particularly at the level of the two groups of explanatory factors (representativeness and expertise)

Early earthquake detection capabilities of different types of future-generation gravity gradiometers

Since gravity propagates at the speed of light, gravity perturbations induced by earthquake deformation have the potential to enable faster alerts than the current earthquake early warning systems based on seismic waves. Additionally, for large earthquakes (M_w > 8), gravity signals may allow for a more reliable magnitude estimation than seismic-based methods. Prompt elastogravity signals induced by earthquakes of magnitude larger than 7.9 have been previously detected with seismic arrays and superconducting gravimeters. For smaller earthquakes, down to M_w ≃ 7, it has been proposed that detection should be based on measurements of the gradient of the gravitational field, in order to mitigate seismic vibration noise and to avoid the canceling effect of the ground motions induced by gravity signals. Here we simulate the five independent components of the gravity gradient signals induced by earthquakes of different focal mechanisms. We study their spatial amplitude distribution to determine what kind of detectors is preferred (which components of the gravity gradient are more informative), how detectors should be arranged, and how earthquake source parameters can be estimated. The results show that early earthquake detections, within 10 seconds of the rupture onset, using only the horizontal gravity strain components are achievable up to about 140 km distance from the epicenter. Depending on the earthquake focal mechanism and on the detector location, additional measurement of the vertical gravity strain components can enhance the detectable range by 10–20 km. These results are essential for the design of gravity-based earthquake early warning systems

First tests of a 800 kJ HTS SMES

SMES using high critical temperature superconductors are interesting for high power pulsed sources. Operation at temperatures above 20 K makes cryogenics easier, enhances stability and improves operation as pulsed power source. In the context of a DGA (Delegation Generate pour l'Armement) project, we have designed and constructed a 800 kJ SMES. The coil is wound with Nexans conductors made of Bi-2212 PIT tapes soldered in parallel. The coil consists in 26 superposed simple pancakes wound and bonded on sliced copper plates coated with epoxy. The rated current is 315 A for an energy of 814 kJ. The external diameter of the coil is 814 mm and its height 222 mm. The cooling at 20 K is only performed by conduction from cryocoolers to make cryogenics very friendly and invisible for the SMES users. The cooling down has been successfully carried out and the thermal system works as designed. After a brief description of the SMES design and construction, some tests will be presented. From a current of 244 A, the SMES delivered 425 kJ to a resistance with a maximum power of 175 kW.Comment: 5 page

Dating the emergence of the divaricate habit in the New Zealand flora

The New Zealand divaricates are a collection of shrubs, short trees and tree juveniles whose crowns are made of tough interlaced twigs branching at wide angles and bearing small leaves. These species represent c. 13% of the native woody flora, a proportion not seen in any other region of the world. Since the late 19ᵗʰ century, ecologists and botanists have sought to understand the of drivers this unique case of convergent evolution. Debate has been dominated by two main competing hypotheses invoking (1) the effect of browsing by now-extinct avian herbivores (moa) and (2) a response to frosty and droughty Plio-Pleistocene climates. Observational and experimental evidence, as well as theoretical discussions, have not clearly favoured one over the other. More recently, a synthetic hypothesis involving both climate and browsing has been proposed, but has not been specifically tested yet: the divaricate habit did not become advantageous as an anti-browsing defence until Plio-Pleistocene climatic constraints prevented young trees and shrubs from growing quickly out of reach of ground-dwelling herbivores. These hypotheses imply different expected divergence periods between divaricate species and their non-divaricate relatives. The focus of this PhD project is to produce a dated phylogeny including as many divaricates as possible, with the aim of bringing new evidence to help tease apart the various hypotheses about their evolution. This PhD thesis is built from a previously published paper and draft manuscripts intended for submission to scientific journals. The first two papers report phylogenies of small genera (Pennantia J.R.Forst. & G.Forst. and Corokia A.Cunn.) that include divaricate species. These studies helped develop lab methods and offered the opportunity to test diverse phylogenetic methods on a smaller scale in preparation for the third paper, which is the core dating work of this PhD. The phylogenies of Pennantia and Corokia provided in this thesis (Chapter 2 and 3, respectively) are the first published dated phylogenies of all the species of each genus. Building the phylogeny of Corokia was also the occasion to discuss two theories trying to explain the distribution of extant species on landmasses formerly part of Gondwana: vicariance and long-distance dispersal—Corokia appears to be one of an increasing number of cases where long-distance dispersal is indicated. The dated phylogeny of most New Zealand divaricate species presented in Chapter 4 reveals that, in the great majority of genera with divaricate representatives, the divaricate habit appeared in New Zealand within the last 5 My, i.e. since the beginning of the Pliocene. On one hand, this research constitutes a valuable methodological addition to the field of molecular phylogenetics by (1) disseminating a method for retrieving extra genetic markers, at no marginal cost, from Next Generation Sequencing shotgun sequencing data of DNA samples enriched for a specific set of markers, and (2) developing a guide to using a piece of phylogenetic reconstruction software (treePL), which was missing from the literature and needed by users. On the other hand, dating the emergence of the divaricate habit brought new and crucial evidence to the debate over what promoted the evolution of the divaricate habit in New Zealand: the findings are clearly consistent with a major effect of Plio-Pleistocene climates—and given evidence and discussion from past studies of these plants and similar plants around the world, the effect of browsing by moa was also probably involved