Quantitative Imaging in Electron and Confocal Microscopies for Applications in Biology

Among the large number of topics related to the quantification of images in electron and confocal microscopies for applications in biology, we selected four subjects that we consider to be representative of some recent tendencies. The first is the quantification of three-dimensional data sets recorded routinely in scanning confocal microscopy. The second is the quantification of the textural and fractal appearance of images. The two other topics are related to image series, which are more and more often provided by imaging instruments. The first kind of series concerns electron energy-filtered images. We show that the parametric (modelling) approach can be complemented by non-parametric approaches (e.g., different variants of multivariate statistical techniques). The other kind of series consists of multiple mappings of a specimen. We describe several new tools for the study and quantification of the co-location, with potential application to multiple mappings in microanalysis or in fluorescence microscopy

Improving tropical forest aboveground biomass estimations:: insights from canopy trees structure and spatial organization

Tropical forests store more than half of the world’s forest carbon and are particularly threatened by deforestation and degradation processes, which together represent the second largest source of anthropogenic CO2 emissions. Consequently, tropical forests are the focus of international climate policies (i.e. Reducing emissions from deforestation and forest degradation, REDD) aiming at reducing forest-related CO2 emissions. The REDD initiative lies on our ability to map forest carbon stocks (i.e. spatial dynamics) and to detect deforestation and degradations (i.e. temporal dynamics) at large spatial scales (e.g. national, forested basin), with accuracy and precision. Remote-sensing is as a key tool for this purpose, but numerous sources of error along the carbon mapping chain makes meeting REDD criteria an outstanding challenge. In the present thesis, we assessed carbon (quantified through aboveground biomass, AGB) estimation error at the tree- and plot-level using a widely used pantropical AGB model, and at the landscape-level using a remote sensing method based on canopy texture features from very high resolution (VHR) optical data. Our objective was to better understand and reduce AGB estimation error at each level using information on large canopy tree structure, distribution and spatial organization. Although large trees disproportionally contributed to forest carbon stock, they are under-represented in destructive datasets and subject to an under-estimation bias with the pantropical AGB model. We destructively sampled 77 very large tropical trees and assembled a large (pantropical) dataset to study how variation in tree form (through crown sizes and crown mass ratio) contributed to this error pattern. We showed that the source of bias in the pantropical model was a systematic increase in the proportion of tree mass allocated to the crown in canopy trees. An alternative AGB model accounting for this phenomenon was proposed. We also propagated the AGB model bias at the plot-level and showed that the interaction between forest structure and model bias, although often overlooked, might in fact be substantial. We further analyzed the structural properties of crown branching networks in light of the assumptions and predictions of the Metabolic Theory of Ecology, which supports the power-form of the pantropical AGB model. Important deviations were observed, notably from Leonardo’s rule (i.e. the principle of area conservation), which, all else being equal, could support the higher proportion of mass in large tree crowns. A second part of the thesis dealt with the extrapolation of field-plot AGB via canopy texture features of VHR optical data. A major barrier for the development of a broad-scale forest carbon monitoring method based on canopy texture is that relationships between canopy texture and stand structure parameters (including AGB) vary among forest types and regions of the world. We investigated this discrepancy using a simulation approach: virtual canopy scenes were generated for 279 1-ha plots distributed on contrasted forest types across the tropics. We showed that complementing FOTO texture with additional descriptors of forest structure, notably on canopy openness (from a lacunarity analysis) and tree slenderness (from a bioclimatic proxy) allows developing a stable inversion frame for forest AGB at large scale. Although the approach we proposed requires further empirical validation, a first case study on a forests mosaic in the Congo basin gave promising results. Overall, this work increased our understanding of mechanisms behind AGB estimation errors at the tree-, plot- and landscape-level. It stresses the need to better account for variation patterns in tree structure (e.g. ontogenetic pattern of carbon allocation) and forest structural organization (across forest types, under different environmental conditions) to improve general AGB models, and in fine our ability to accurately map forest AGB at large scale

Satires et parodies du Moyen Âge grec, introd., trad. et notes de René Bouchet

L’époque Comnène (1057‑1185), marquée par un grand classicisme et par la redécouverte enthousiaste des auteurs anciens, est connue pour avoir vu s’épanouir l’une des plus brillantes renaissances littéraires, culturelles et artistiques qu’ait connues l’Empire byzantin. L’Alexiade, vaste épopée d’inspiration homérique consacrée par la princesse Anne Comnène à la geste de son père, l’empereur Alexis, reste à juste titre le texte le plus célèbre et le plus étudié de cette époque ; mais on oublie ..

Vécu et perception des soins en milieu carcéral (étude qualitative auprès des personnes incarcérées à la maison d'arrêt de Grenoble-Varces)

Depuis la réforme de 1994, la responsabilité des soins aux personnes incarcérées a été transférée de l'administration pénitentiaire au service public hospitalier dans le but de leur garantir l'accès à des soins comparables à ceux dispensés à la population générale. Le point de vue des personnes incarcérées sur le système de soin en milieu carcéral n'a jamais été exploré en France. Nous avons étudié le vécu et la perception par les personnes détenues des soins dispensés en milieu carcéral. Nous avons réalisé une étude qualitative par entretiens individuels semi-dirigés réalisés auprès des personnes incarcérées à la maison d'arrêt de Grenoble-Varces. Quinze personnes ont été interrogées. De manière générale, les participants trouvaient les soins de qualité satisfaisante et avaient de bonnes relations avec le personnel soignant. Par contre, ils jugeaient les soins dentaires de mauvaise qualité, critiquaient la prescription excessive de médicaments psychotropes et la mauvaise prise en charge de la douleur. Bien que les soins semblaient être accessibles en routine, les participants relevaient de graves lacunes d'accès aux soins en situation d'urgence en particulier la nuit. Le passage obligé par les surveillants apparaissait comme le principal obstacle à l'accès aux soins. Enfin, l'importance des soins pour les participants était relativisée par la place ambiguë qu'ils occupent dans l univers carcéral. Les conditions d'incarcération, l'enfermement et l hygiène représentaient autant de mises en danger de leur santé. L'accès à des soins de qualité est une condition indispensable mais non suffisante pour garantir aux personnes incarcérées la protection de leur santé.Since the 1994 reform, the responsibility of prisoner's health care has been transferred from penitentiary administration to public hospital health services. The aim of this reform was to guarantee to guarantee prisoners the same health care access as the general population. The prisoner's point of view about the prison health care has never been explored in France. We studied prisoners' experiences and perception of health care in prison. A qualitative approach was performed using semi-structured interviews which were carried out with prisoners in Grenoble-Varces's prison. Fifteen people were interviewed. Generally, participants were satisfied with health care quality and had a good relationship with the healthcare professionals. On the other hand, they poorly judged dental healthcare, they thought psychoactive drugs were over-prescribed, and thought that pain was not relieved well enough. Although access to health care seemed to be usually satisfying, access to emergency care seemed to be difficult particularly at night. The main obstacle to health care appeared to be the prison guards. Although the role of health care services seemed important for the prisoners, its position within the prison was ambiguous. Their health was endangered by prison leaving conditions, imprisonment, hygiene. The quality and accessibility of health care is essential but is not sufficient to guarantee protection of prisoner's health. Indeed, in the participant's view, leaving conditions in prison and freedom deprivation were irreconcilable with this aim.GRENOBLE1-BU Médecine pharm. (385162101) / SudocSudocFranceF

Closing a gap in tropical forest biomass estimation : taking crown mass variation into account in pantropical allometries

Accurately monitoring tropical forest carbon stocks is a challenge that remains outstanding. Allometric models that consider tree diameter, height and wood density as predictors are currently used in most tropical forest carbon studies. In particular, a pantropical biomass model has been widely used for approximately a decade, and its most recent version will certainly constitute a reference model in the coming years. However, this reference model shows a systematic bias towards the largest trees. Because large trees are key drivers of forest carbon stocks and dynamics, understanding the origin and the consequences of this bias is of utmost concern. In this study, we compiled a unique tree mass data set of 673 trees destructively sampled in five tropical countries (101 trees > 100 cm in diameter) and an original data set of 130 forest plots (1 ha) from central Africa to quantify the prediction error of biomass allometric models at the individual and plot levels when explicitly taking crown mass variations into account or not doing so. We first showed that the proportion of crown to total tree aboveground biomass is highly variable among trees, ranging from 3 to 88 %. This proportion was constant on average for trees = 45 Mg. This increase coincided with a progressive deviation between the pantropical biomass model estimations and actual tree mass. Taking a crown mass proxy into account in a newly developed model consistently removed the bias observed for large trees (> 1 Mg) and reduced the range of plot- level error (in %) from [-23; 16] to [0; 10]. The disproportionally higher allocation of large trees to crown mass may thus explain the bias observed recently in the reference pantropical model. This bias leads to far- from- negligible, but often overlooked, systematic errors at the plot level and may be easily corrected by taking a crown mass proxy for the largest trees in a stand into account, thus suggesting that the accuracy of forest carbon estimates can be significantly improved at a minimal cost

Allometric equations for integrating remote sensing imagery into forest monitoring programmes.

Remote sensing is revolutionizing the way we study forests, and recent technological advances mean we are now able - for the first time - to identify and measure the crown dimensions of individual trees from airborne imagery. Yet to make full use of these data for quantifying forest carbon stocks and dynamics, a new generation of allometric tools which have tree height and crown size at their centre are needed. Here, we compile a global database of 108753 trees for which stem diameter, height and crown diameter have all been measured, including 2395 trees harvested to measure aboveground biomass. Using this database, we develop general allometric models for estimating both the diameter and aboveground biomass of trees from attributes which can be remotely sensed - specifically height and crown diameter. We show that tree height and crown diameter jointly quantify the aboveground biomass of individual trees and find that a single equation predicts stem diameter from these two variables across the world's forests. These new allometric models provide an intuitive way of integrating remote sensing imagery into large-scale forest monitoring programmes and will be of key importance for parameterizing the next generation of dynamic vegetation models.T.J. was funded by NERC (grant number: NE/K016377/1). This work has benefited from ANR grants to J.C. (CEBA, ref. ANR-10-LABX-25-01 and TULIP, ref. ANR-10-LABX-0041). The Sustainable Landscapes Brazil project was supported by the Brazilian Agricultural Research Corporation (EMBRAPA), the US Forest Service, and USAID, and the US Department of State. Data collection for the UNECE ICP Forests PCC Collaborative Database was cofinanced by national or regional organizations and by the European Commission under regulations (EEC) No 2158/86, Forest Focus (EC) No 2152/200, FutMon (EC) LIFE07 ENV/D/218.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1111/gcb.1338

Keep an ear out for Francisella tularensis: otomastoiditis Cases after Canyoneering

We report here three unusual cases of otomastoiditis due to Francisella tularensis, complicated by cervical abscesses and persistent hearing loss, plus facial paralysis for one patient. Intriguingly, the three patients had practiced canyoneering independently in the same French river, between 2009 and 2014, several days before clinical symptoms onset. The results point out that fresh water exposure may be a potential contamination route for tularemia. Besides, due to the frequent complications and sequelae, we believe that F. tularensis should be considered as a possible etiology in case of otitis media, failure of the conventional antibiotic treatment, and suspicious exposure of the bacteria

Elastin Peptides Signaling Relies on Neuraminidase-1-Dependent Lactosylceramide Generation

The sialidase activity of neuraminidase-1 (Neu-1) is responsible for ERK 1/2 pathway activation following binding of elastin peptide on the elastin receptor complex. In this work, we demonstrate that the receptor and lipid rafts colocalize at the plasma membrane. We also show that the disruption of these microdomains as well as their depletion in glycolipids blocks the receptor signaling. Following elastin peptide treatment, the cellular GM3 level decreases while lactosylceramide (LacCer) content increases consistently with a GM3/LacCer conversion. The use of lactose or Neu-1 siRNA blocks this process suggesting that the elastin receptor complex is responsible for this lipid conversion. Flow cytometry analysis confirms this elastin peptide-driven LacCer generation. Further, the use of a monoclonal anti-GM3 blocking antibody shows that GM3 is required for signaling. In conclusion, our data strongly suggest that Neu-1-dependent GM3/LacCer conversion is the key event leading to signaling by the elastin receptor complex. As a consequence, we propose that LacCer is an early messenger for this receptor