A hidden Markov model for matching spatial networks

Datasets of the same geographic space at different scales and temporalities are increasingly abundant, paving the way for new scientific research. These datasets require data integration, which implies linking homologous entities in a process called data matching that remains a challenging task, despite a quite substantial literature, because of data imperfections and heterogeneities. In this paper, we present an approach for matching spatial networks based on a hidden Markov model (HMM) that takes full benefit of the underlying topology of networks. The approach is assessed using four heterogeneous datasets (streets, roads, railway, and hydrographic networks), showing that the HMM algorithm is robust in regards to data heterogeneities and imperfections (geometric discrepancies and differences in level of details) and adaptable to match any type of spatial networks. It also has the advantage of requiring no mandatory parameters, as proven by a sensitivity exploration, except a distance threshold that filters potential matching candidates in order to speed-up the process. Finally, a comparison with a commonly cited approach highlights good matching accuracy and completeness

Historical collaborative geocoding

The latest developments in digital have provided large data sets that can increasingly easily be accessed and used. These data sets often contain indirect localisation information, such as historical addresses. Historical geocoding is the process of transforming the indirect localisation information to direct localisation that can be placed on a map, which enables spatial analysis and cross-referencing. Many efficient geocoders exist for current addresses, but they do not deal with the temporal aspect and are based on a strict hierarchy (..., city, street, house number) that is hard or impossible to use with historical data. Indeed historical data are full of uncertainties (temporal aspect, semantic aspect, spatial precision, confidence in historical source, ...) that can not be resolved, as there is no way to go back in time to check. We propose an open source, open data, extensible solution for geocoding that is based on the building of gazetteers composed of geohistorical objects extracted from historical topographical maps. Once the gazetteers are available, geocoding an historical address is a matter of finding the geohistorical object in the gazetteers that is the best match to the historical address. The matching criteriae are customisable and include several dimensions (fuzzy semantic, fuzzy temporal, scale, spatial precision ...). As the goal is to facilitate historical work, we also propose web-based user interfaces that help geocode (one address or batch mode) and display over current or historical topographical maps, so that they can be checked and collaboratively edited. The system is tested on Paris city for the 19-20th centuries, shows high returns rate and is fast enough to be used interactively.Comment: WORKING PAPE

The impact of long-term water stress on tree architecture and production is related to changes in transitions between vegetative and reproductive growth in the ‘Granny Smith’ apple cultivar

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitièresInternational audienceWater stress (WS) generates a number of physiological and morphological responses in plants that depend on the intensity and duration of stress as well as the plant species and development stage. In perennial plants, WS may affect plant development through cumulative effects that modify plant functions, architecture and production over time. Plant architecture depends on the fate of the terminal and axillary buds that can give rise, in the particular case of apple, to reproductive or vegetative growth units (GUs) of different lengths. In this study, the impact of long-term WS (7 years) on the fate of terminal and axillary buds was investigated in relation to flowering occurrence and production pattern (biennial vs regular) in the ‘Granny Smith’ cultivar. It was observed that WS decreased the total number of GUs per branch, regardless of their type. Conversely, WS did not modify the timing of the two successive developmental phases characterized by the production of long and medium GUs and an alternation of floral GUs over time, respectively. The analysis of GU successions over time using a variable-order Markov chain that included both the effects of the predecessor and water treatment revealed that WS reduced the transition towards long and medium GUs and increased the transition toward floral, short and dead GUs. WS also slightly increased the proportion of axillary floral GUs. The higher relative frequency of floral GUs compared with vegetative ones reduced the tendency to biennial bearing under WS. The accelerated ontogenetic trend observed under WS suggests lower vegetative growth that could, in turn, be beneficial to floral induction and fruit set

Experiencing a significant win and its sociodemographic and motivational predictors: A comparative analysis of pure-chance gamblers from Poland and France

Research on the relationship between wins and gambling behavior often focuses on winning considerably large amounts of money. It seems, however, that it is not the amount of the win, but the significance that the player assigns to the win, that exerts a decisive influence on gambling behavior. Therefore, in this study we adopted the concept of significant win: a win perceived by gamblers as important to them. The research aimed to discover what kind of wins are experienced as significant and what factors explain experiencing wins as significant. This study, conducted in Poland (N = 3,143) and France (N = 5,692), also had a comparative goal: discovering intercultural differences in experiencing significant wins. A computer-assisted web survey was administered to gamblers who engaged in pure-chance gambling, where the participant does not influence the outcome of the gamble after the initial bet is placed - selected from representative samples in both countries. We used logistic regression models to examine predictors of significant win experience in both countries and the differences between the countries. The results demonstrated that Polish gamblers more frequently considered a win significant when it was accompanied by strong, often negative emotions and was higher in monetary value normalized in terms of average monthly personal income, than French gamblers. French gamblers more frequently associated a significant win with a positive experience. The common predictors of a significant win experience in both countries were: being in debt, experiencing the win of a close person, gambling in a game of pure chance other than lotteries, more systematic pursuit of gambling, self-enhancement motivation, and coping motivation to gamble. Age at initiation into gambling was a significant predictor only in the French sample, whereas a financial motivation was a significant predictor in the Polish one. The results confirmed that the subjective perception of gambling wins is only partially related to the amounts of wins, which has practical implications for planning prevention strategies

Identification of new biomarkers for sarcopenia and characterization of cathepsin D biomarker

peer reviewedBackground Sarcopenia is the progressive generalized loss of skeletal muscle mass, strength, and function that occurs with aging. This study was undertaken to identify new biomarkers of sarcopenia by proteomics analysis of female sera. Methods A case–control study was set up, for which 19 sarcopenic subjects and 20 control subjects, according to the European Working Group on Sarcopenia Older People criteria published in 2010 (EWGSOP1), were enrolled. All the subjects were at least 65 years old and in majority female. Biomarker screening was performed by a comparative mass spectrometry analysis. Protein expression levels between the two groups were compared. One of the identified biomarkers, cathepsin D, was measured by immunoassay on the serum of the full sample set (n = 39). Its diagnostic performance was evaluated with a receiver operating characteristic curve (ROC curve). Results Two biomarkers were identified: fructose-biphosphate aldolase A (P ≤ 0.05) and cathepsin D (P ≤ 0.05). The levels of all of them were higher in sarcopenic patients. It was confirmed by immunoassay that cathepsin D levels in serum were significantly higher in the sarcopenic group of patients (P = 0.038). An inverse correlation (−0.385) was observed between cathepsin D levels in serum and gait speed. The area under the ROC curve measurement (AUC = 0.696) demonstrated that cathepsin D levels could discriminate between sarcopenic and non-sarcopenic subjects. A predictive model including cathepsin D, age, and body mass index was established to improve the diagnostic performance (AUC = 0.908). Conclusions Cathepsin D has been identified as a diagnostic biomarker of sarcopenia

Exploring carbon allocation with a multi-scale model: the case of apple

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitièresUnderstanding the allocation of carbohydrates among organs is necessary to predict plant growth in relation to climatic conditions and agronomic practices. Despite the large number of studies on the subject of carbon allocation, no clear consensus exists on (i) the most appropriate topological scale (organ, metamer, compartment...) to represent this process on complex plant structures, and (ii) the importance of distances between organs in carbon transport. In this study, we implemented a generic source-sink based carbon allocation model, following the equation of the SIMWAL model, that takes into account the distances between sources and sinks, the sink strength and the availability of carbohydrates from photosynthesis. Our model makes use of multi-scale tree graph (MTG) to represent geometry and topology of a tree structure at different scales. Starting from the description of a plant at a given scale (e.g. metamer and growing unit scales), we defined additional grouping criteria (fruiting branches and main axis) that were used to represent the plant structure, and the process of carbon allocation at different spatial resolutions. Generic functions to determine the biomass and carbon demand of the individual organs described in an MTG were implemented and calibrated for apple trees (Fuji variety) by means of age and organ type dependent allometric equations and maximum potential Relative Growth Rate curves (RGR) obtained in a field experiment. Photosynthesis for individual leaves of the input MTG was estimated by means of a radiative model (RATP). The model was then applied to architectural mock-ups in the MTG format produced by the MappleT model, representing trees with high and low fruit loads. Simulations on simplified plant structures qualitatively showed the influence of the scale of representation and of the distance parameter on the predicted carbon allocation. In order to test assumptions regarding the effect of distance, the source-sink behavior and the suitability of the alternative scales of representation for predicting carbon allocation, the variability and spatial distribution of the simulated RGR were compared to field observations. Finally, a benchmarking was performed to compare the computational efficiency of the model when running at different scales. The presented multiscale model provides a framework to re-interpret the plant topology in order to test the influence of some assumptions at the basis of the carbon allocation process, such as branch autonomy or the effect of distance. It is also a mean to investigate the trade-offs between the detail at which a plant is described, and the accuracy and computational efficiency in predicting carbon allocation. The present work was developed on the OpenAlea platform, and will provide existing Functional Structural Plant Models with a new generic model to simulate carbon allocation in plants

Tissue Localization and Extracellular Matrix Degradation by PI, PII and PIII Snake Venom Metalloproteinases: Clues on the Mechanisms of Venom-Induced Hemorrhage

20 páginas, 4 figuras, 3 tablas y 7 tablas en material suplementario.Snake venom hemorrhagic metalloproteinases (SVMPs) of the PI, PII and PIII classes were compared in terms of tissue localization and their ability to hydrolyze basement membrane components in vivo, as well as by a proteomics analysis of exudates collected in tissue injected with these enzymes. Immunohistochemical analyses of co-localization of these SVMPs with type IV collagen revealed that PII and PIII enzymes co-localized with type IV collagen in capillaries, arterioles and post-capillary venules to a higher extent than PI SVMP, which showed a more widespread distribution in the tissue. The patterns of hydrolysis by these three SVMPs of laminin, type VI collagen and nidogen in vivo greatly differ, whereas the three enzymes showed a similar pattern of degradation of type IV collagen, supporting the concept that hydrolysis of this component is critical for the destabilization of microvessel structure leading to hemorrhage. Proteomic analysis of wound exudate revealed similarities and differences between the action of the three SVMPs. Higher extent of proteolysis was observed for the PI enzyme regarding several extracellular matrix components and fibrinogen, whereas exudates from mice injected with PII and PIII SVMPs had higher amounts of some intracellular proteins. Our results provide novel clues for understanding the mechanisms by which SVMPs induce damage to the microvasculature and generate hemorrhage.This work was performed in partial fulfillment of the requirements for the PhD degree for Cristina Herrera at Universidad de Costa Rica.Peer reviewe

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Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Nurses' perceptions of aids and obstacles to the provision of optimal end of life care in ICU

Contains fulltext : 172380.pdf (publisher's version ) (Open Access