Emissió de compostos orgànics volàtils en vegetació mediterrània : COVs oxigenats de cadena curta, interacció entre organismes i impacte atmosfèric /

Descripció del recurs: el 19 setembre 2011Els compostos orgànics volàtils (COVs) presents a l'atmosfera poden tenir fonts naturals o antròpiques. Els COVs estan implicats en reaccions químiques que afecten la química atmosfèrica i poden tenir impactes indirectes sobre el clima a través de la generació d'aerosols i compostos oxidants. Globalment, la vegetació és la font principal de COVs naturals, mentre que els COVs antropogènics són la majoria de vegades producte d'emissions industrials i de motors de vehicles. D'entre els COVs biogènics, els isoprenoids són els més coneguts i estudiats. La nostra recerca es va centrar en el grup de COVs de cadena curta oxigenats (oxCOVs), un grup poc conegut format per metanol, etanol, formaldehid, acetaldehid, acids fòrmic i acètic, i acetona. Els oxCOVs poden ser emesos directament tant per les plantes com per les activitats humanes, i també es poden formar per la degradació atmosfèrica d'altres COVs de major massa molecular. Entre d'altres raons, han estat menys estudiats degut a problemes analítics, que s'han resolt en part recentment amb l'aparició de noves tecnologies, especialment l'espectrometria de masses per transferència de protons. Els oxCOVs tenen diverses propietats que els diferencien d'altres COVs com els isoprenoids. Els oxCOVs són més solubles en aigua i això fa la seva emissió en plantes depenent dels estomes. També tenen una vida atmosfèrica relativament llarga i presenten concentracions considerables a l'atmosfera en el nivell de ppbv (1 part en 109 en volum). Les emissions d'oxCOVs en plantes mediterrànies són molt poc conegudes, per això vam estudiar-ne l'intercanvi en els arbres típicament mediterranis Quercus ilex i Pinus halepensis. Es va confirmar el control estomàtic i de la concentració atmosfèrica del seu intercanvi. Per exemple, es va observar un punt de compensació de 20 ppbv pel formaldehid en les dues espècies d'arbre, mentre que per l'acetaldehid va ser de 6 ppbv en P. halepensis. Un tractament de sequera i posterior reg va mostrar que la sequera afecta l'intercanvi d'oxCOVs perquè afecta la conductància estomàtica. A més, es va confirmar que Q. ilex emet isoprè, encara que amb taxes petites, i que l'emissió d'isoprenoids en Q. ilex va disminuir per la sequera. Els COVs poden tenir també un paper ecològic molt important: participar en les comunicacions entre organismes. En interaccions planta-planta la nostra hipòtesi era que el metanol podia jugar un paper senyalitzador, ja que el metanol s'emet en grans quantitats des de les fulles quan són atacades per un herbívor. Un experiment de fumigació amb metanol va mostrar que les respostes de Q. ilex al metanol arribat per l'aire eren similars a les respostes a l'herbivoria i també que l'emissió de monoterpens es va incrementar lleugerament. En la comunicació entre animals, vam identificar alguns components volàtils emesos pels capolls i els excrements d'una espècie d'abella solitària (Osmia cornuta), essent-ne l'àcid acètic un dels més abundants. Llavors vam provar l'atracció exercida per l'àcid acètic sobre femelles de Monodontomerus aeneus, una vespa parasitoide d'O. cornuta, que busquen capolls per ovipositar-hi. Encara que l'àcid acètic sol atreia M. aeneus, probablement un senyal volàtil complex intervé en el procés d'atracció, ja que la ràtio àcid acètic-acetaldehid característica dels excrements va resultar més atractiva que altres ràtios. L'objectiu final de la tesi va ser observar quin impacte tenen les emissions de COVs en l'atmosfera mediterrània, ja sigui pel nivell de concentració que atanyen els COVs a l'aire com també per la seva participació en la formació de compostos com l'ozó. Per això vam mesurar (hivern i estiu) les concentracions d'oxCOVs, isoprenoids i COVs aromàtics en una zona boscosa situada dins del parc natural del Montseny, a uns 60 km al NE de la ciutat de Barcelona. Mentre que els COVs aromàtics no varen presentar gairebé cap variació estacional, les concentracions dels oxCOVs van assolir nivells més alts a l'estiu degut a les majors emissions de la vegetació i a l'increment de les reaccions fotoquímiques resultants de les altes temperatures i radiació solar de l'estiu. Els COVs isoprenoids van mostrar el canvi entre estacions més gran: les concentracions van augmentar un ordre de magnitud a l'estiu, degut a l'increment de l'activitat fisiològica de la vegetació i de les seves taxes d'emissió. També les concentracions diürnes màximes d'ozó van augmentar a l'estiu, per la major activitat fotoquímica i la presència de més COVs a l'aire. La variació diària de concentracions de COVs seguia bàsicament el règim de vent de la muntanya. La brisa marina que es desenvolupa quan surt el sol transporta cap a la muntanya masses d'aire que prèviament han passat sobre la regió metropolitana de Barcelona, on han estat enriquides en NO2 i en COVs d'origen biòtic i abiòtic. A més, aquestes masses d'aire contaminades poden reaccionar amb els COVs biogènics emesos de forma local per la vegetació, tot afavorint la formació d'O3 en aquesta zona boscosa. L'únic tipus de COV que presentava un cicle diari diferent dels demés van ser els monoterpens, perquè tenien un origen biogènic local. L'isoprè també compartia parcialment el cicle diari dels monoterpens, però només a l'estiu quan les seves fonts biòtiques eren més fortes.Volatile organic compounds (VOCs) present in the atmosphere can have natural or anthropic sources. VOCs are involved in atmospheric chemistry reactions that can have indirect climatic impacts through the generation of aerosols and oxidant compounds. Globally, vegetation is the main source of natural VOC emission, while anthropogenic VOCs are in most cases product of vehicle exhaust and industry emissions. Within biogenic VOCs, isoprenoids are the most studied and known group. Our research was focused in a group of short-chain oxygenated VOCs (oxVOCs), a poorly known group composed by methanol, ethanol, formaldehyde, acetaldehyde, formic and acetic acids, and acetone. They can be emitted directly either by plants or by human activities, and they can also be formed through degradation in the air of other higher molecular mass VOCs. Among other reasons, they have been less studied due to analytical problems than have been partly solved in recent years with the advent of new technologies, specially proton transfer reaction mass spectrometry. OxVOCs have several properties that set them apart of other VOCs like isoprenoids. OxVOCs are more soluble in water and this fact makes their release from plants stomatal-dependent. In addition, these compounds have relatively long atmospheric halflives and reach considerable concentrations in the atmosphere in the range of parts per billion in volume (ppbv). Emissions of oxVOCs in Mediterranean plants are scarcely known, for this reason we studied oxVOCs exchange in the typically Mediterranean tree species Quercus ilex and Pinus halepensis. The stomatal and atmospheric mixing ratios control of their exchange was confirmed. For instance, a compensation point of 20 ppbv for formaldehyde was observed for both tree species, while for acetaldehyde it was of 6 ppbv in P. halepensis. A treatment of drought and posterior re-watering showed that drought affects oxVOC exchange because it affects stomatal conductance. In addition, it was confirmed that Q. ilex emits isoprene, although at small rates, and that isoprenoid emission in Q. ilex decreased due to drought. VOCs can also have an important ecological role: taking part in the communication between organisms. In plant-plant interaction our hypothesis was that methanol could have a signalling role, given that methanol is emitted in big amounts from leaves upon herbivore attack. An experiment of fumigation with methanol showed that Q. ilex responses to airborne methanol were similar to responses to herbivory and also that monoterpene emission was slightly increased. In communication between animals, we identified some volatile components emitted by the cocoons and frass of a solitary bee species (Osmia cornuta), being acetic acid an abundant one among them. We then tested acetic acid attractiveness for Monodontomerus aeneus female wasps, parasitoids of O. cornuta, that look for cocoons to oviposit. Although acetic acid alone attracted M. aeneus, a complex volatile signal is probably involved in the attraction process since the ratio acetic acid-acetaldehyde characteristic of the frass was more attractive than other ratios. The last objective of this thesis was to observe the impact that VOC emissions have on the Mediterranean atmosphere, either by the mixing ratios that VOC reach in the air or also by their participation in the formation of compounds like ozone. To achieve this, the mixing ratios of oxVOCs, isoprenoids, and aromatic VOCs were measured (winter and summer) in a forest site located within a densely forested natural park (Montseny) about 60 km NE of the city of Barcelona. While aromatic VOCs showed almost no seasonal variability, short-chain oxygenated VOCs presented higher mixing ratios in summer due to the increased emission by vegetation and the increased photochemistry, both enhanced by the high temperatures and solar radiation in summer. Isoprenoid VOCs showed the biggest seasonal change in mixing ratios:they increased by one order of magnitude in summer, as a result of the increased vegetation physiological activity and emission rates. Ozone highest diurnal concentrations increased in summer too, due to more photochemical activity and the presence of more VOCs in the air. The daily variation of the VOC mixing ratios was mainly governed by the wind regime of the mountain. Sea breeze that develops after sunrise advects to the mountain polluted air masses that previously had passed over the Barcelona metropolitan region, where they were enriched in NO2 and in VOCs of biotic and abiotic origin. Furthermore, these polluted air masses can react with biogenic VOCs emitted at the local valley by the vegetation, thus enhancing O3 formation in this forest site. The only VOC species that showed a different daily pattern were monoterpenes because of their local biogenic emission. Isoprene also shared partially the daily pattern of monoterpenes, but only in summer when its biotic sources were stronger

The Parallel Distributed Image Search Engine (ParaDISE)

Image retrieval is a complex task that differs according to the context and the user requirements in any specific field, for example in a medical environment. Search by text is often not possible or optimal and retrieval by the visual content does not always succeed in modelling high-level concepts that a user is looking for. Modern image retrieval techniques consists of multiple steps and aim to retrieve information from large–scale datasets and not only based on global image appearance but local features and if possible in a connection between visual features and text or semantics. This paper presents the Parallel Distributed Image Search Engine (ParaDISE), an image retrieval system that combines visual search with text–based retrieval and that is available as open source and free of charge. The main design concepts of ParaDISE are flexibility, expandability, scalability and interoperability. These concepts constitute the system, able to be used both in real–world applications and as an image retrieval research platform. Apart from the architecture and the implementation of the system, two use cases are described, an application of ParaDISE in retrieval of images from the medical literature and a visual feature evaluation for medical image retrieval. Future steps include the creation of an open source community that will contribute and expand this platform based on the existing parts

Overview of the ImageCLEF 2016 Medical Task

ImageCLEF is the image retrieval task of the Conference and Labs of the Evaluation Forum (CLEF). ImageCLEF has historically focused on the multimodal and language–independent retrieval of images. Many tasks are related to image classification and the annotation of image data as well. The medical task has focused more on image retrieval in the beginning and then retrieval and classification tasks in subsequent years. In 2016 a main focus was the creation of meta data for a collection of medical images taken from articles of the the biomedical scientific literature. In total 8 teams participated in the four tasks and 69 runs were submitted. No team participated in the caption prediction task, a totally new task. Deep learning has now been used for several of the ImageCLEF tasks and by many of the participants obtaining very good results. A majority of runs was submitting using deep learning and this follows general trends in machine learning. In several of the tasks multimodal approaches clearly led to best results

Using Crowdsourcing for Multi-label Biomedical Compound Figure Annotation

Information analysis or retrieval for images in the biomedical literature needs to deal with a large amount of compound figures (figures containing several subfigures), as they constitute probably more than half of all images in repositories such as PubMed Central, which was the data set used for the task. The ImageCLEFmed benchmark proposed among other tasks in 2015 and 2016 a multi-label classification task, which aims at evaluating the automatic classification of figures into 30 image types. This task was based on compound figures and thus the figures were distributed to participants as compound figures but also in a separated form. Therefore, the generation of a gold standard was required, so that algorithms of participants can be evaluated and compared. This work presents the process carried out to generate the multi-labels of ∼2650 compound figures using a crowdsourcing approach. Automatic algorithms to separate compound figures into subfigures were used and the results were then validated or corrected via crowdsourcing. The image types (MR, CT, X–ray, ...) were also annotated by crowdsourcing including detailed quality control. Quality control is necessary to insure quality of the annotated data as much as possible. ∼625 h were invested with a cost of ∼870$

Comparing Fusion Techniques for the ImageCLEF 2013 Medical Case Retrieval Task

Retrieval systems can supply similar cases with a proven diagnosis to a new example case under observation to help clinicians during their work. The ImageCLEFmed evaluation campaign proposes a framework where research groups can compare case-based retrieval approaches. This paper focuses on the case-based task and adds results of the compound figure separation and modality classification tasks. Several fusion approaches are compared to identify the approaches best adapted to the heterogeneous data of the task. Fusion of visual and textual features is analyzed, demonstrating that the selection of the fusion strategy can improve the best performance on the case-based retrieval task

The medGIFT Group in ImageCLEFmed 2013

This article presents the participation of the medGIFT groupin ImageCLEFmed 2013. Since 2004, the group has participated in themedical image retrieval tasks of ImageCLEF each year. There are fourtypes of tasks for ImageCLEFmed 2013: modality classi cation, image{based retrieval, case{based retrieval and a new task on compound gureseparation. The medGIFT group participated in all four tasks. MedGIFTis developing a system named ParaDISE (Parallel Distributed ImageSearch Engine), which is the successor of GIFT (GNU Image FindingTool). The alpha version of ParaDISE was used to run the experimentsin the competition. The focus was on the use of multiple features incombinations with novel strategies, i.e, compound gure separation formodality classi cation or modality ltering for ad{hoc image and case{based retrieval

Les plantes s'avisen del perill imminent

Les plantes envien senyals a l'atmosfera per comunicar-se amb altres plantes i amb els animals: quan una planta és atacada per un patogen o per un herbívor allibera certs compostos a l'aire que "avisen" les altres del perill imminent, de manera que puguin preparar-se per rebre'l. Són substàncies que activen el metabolisme defensiu de les plantes com l'emissió de compostos repel·lents contra els herbívors, de reclam pels parasitoides dels herbívors o la segregació d'antioxidants o estabilitzadors de les membranes cel·lulars. Investigadors de la UAB han investigat si el metanol podria comptar-se entre aquestes substàncies de comunicació ja que s'ha detectat que en la sega dels camps de cultiu o en l'atac per herbívors s'alliberen grans quantitats d'aquest compost a l'atmosfera detectables per les plantes de la rodalia.Las plantas envían señales a la atmósfera para comunicarse con otras plantas y con los animales: cuando una planta es atacada por un patógeno o por un herbívoro libera ciertos compuestos en el aire que "avisan" a las demás del peligro inminente, de manera que puedan prepararse para recibirlo. Son sustancias que activan el metabolismo defensivo de las plantas como la emisión de compuestos repelentes contra los herbívoros, de reclamo para los parasitoides de los herbívoros o la segregación de antioxidantes o estabilizadores de las membranas celulares. Investigadores de la UAB han investigado si el metanol podría estar entre estas sustancias de comunicación ya que se ha detectado que en la siega de los campos de cultivo o en el ataque por herbívoros se liberan grandes cantidades de este compuesto a la atmósfera detectables por las plantas de los alrededores

Photosynthesis, stomatal conductance and terpene emission response to water availability in dry and mesic Mediterranean forests

Water stress results in a reduction of the metabolism of plants and in a reorganization of their use of resources geared to survival. In the Mediterranean region, periods of drought accompanied by high temperatures and high irradiance occur in summer. Plants have developed various mechanisms to survive in these conditions by resisting, tolerating or preventing stress. We used three typical Mediterranean tree species in Israel, Pinus halepensis L., Quercus calliprinos and Quercus ithaburensis Webb, as models for studying some of these adaptive mechanisms. We measured their photosynthetic rates (A), stomatal conductance (g s), and terpene emission rates during spring and summer in a geophysical gradient from extremely dry to mesic from Yatir (south, arid) to Birya (north, moist) with intermediate conditions in Solelim. A and g s of P. halepensis were threefold higher in Birya than in Yatir where they remained very low both seasons. Quercus species presented 2-3-fold higher A and g s but with much more variability between seasons, especially for Q. ithaburensis with A and g s that decreased 10-30-fold from spring to summer. Terpene emission rates for pine were not different regionally in spring but they were 5-8-fold higher in Birya than in Yatir in summer (P < 0.05). Higher emissions were also observed in Solelim for the drought resistant Q. ithaburensis (P < 0.001) but not for Q. calliprinos. α-Pinene followed by limonene and 3-carene were the dominant terpenes. Warmer summer conditions result in increased Terpene emission rates except under severe drought, in which case they strongly decreas

Semi–Supervised Learning for Image Modality Classification

Searching for medical image content is a regular task for many physicians, especially in radiology. Retrieval of medical images from the scientific literature can benefit from automatic modality classification to focus the search and filter out non–relevant items. Training datasets are often unevenly distributed regarding the classes resulting sometimes in a less than optimal classification performance. This article proposes a semi–supervised learning approach applied using a k–Nearest Neighbour (k–NN) classifier to exploit unlabelled data and to expand the training set. The algorithmic implementation is described and the method is evaluated on the ImageCLEFmed modality classification benchmark. Results show that this approach achieves an improved performance over supervised k–NN and Random Forest classifiers. Moreover, medical case–based retrieval benefits from the modality filter