Analysis, modelling and visualisation of spatiotemporal data for urban studies

The proportion of population living in or around cites is more important than ever. Urban sprawl and car dependence have taken over the pedestrian-friendly compact city. Environmental problems like air pollution, land waste or noise, and health problems are the result of this still continuing process. The urban planners have to find solutions to these complex problems, and at the same time insure the economic performance of the city and its surroundings. At the same time, an increasing quantity of socio-economic and environmental data is acquired. In order to get a better understanding of the processes and phenomena taking place in the complex urban environment, these data should be analysed. Numerous methods for modelling and simulating such a system exist and are still under development and can be exploited by the urban geographers for improving our understanding of the urban metabolism. Modern and innovative visualisation techniques help in communicating the results of such models and simulations. This thesis covers several methods for analysis, modelling, simulation and visualisation of problems related to urban geography. The analysis of high dimensional socio-economic data using artificial neural network techniques, especially self-organising maps, is showed using two examples at different scales. The problem of spatiotemporal modelling and data representation is treated and some possible solutions are shown. The simulation of urban dynamics and more specifically the traffic due to commuting to work is illustrated using multi-agent micro-simulation techniques. A section on visualisation methods presents cartograms for transforming the geographic space into a feature space, and the distance circle map, a centre-based map representation particularly useful for urban agglomerations. Some issues on the importance of scale in urban analysis and clustering of urban phenomena are exposed. A new approach on how to define urban areas at different scales is developed, and the link with percolation theory established. Fractal statistics, especially the lacunarity measure, and scale laws are used for characterising urban clusters. In a last section, the population evolution is modelled using a model close to the well-established gravity model. The work covers quite a wide range of methods useful in urban geography. Methods should still be developed further and at the same time find their way into the daily work and decision process of urban planners. La part de personnes vivant dans une région urbaine est plus élevé que jamais et continue à croître. L'étalement urbain et la dépendance automobile ont supplanté la ville compacte adaptée aux piétons. La pollution de l'air, le gaspillage du sol, le bruit, et des problèmes de santé pour les habitants en sont la conséquence. Les urbanistes doivent trouver, ensemble avec toute la société, des solutions à ces problèmes complexes. En même temps, il faut assurer la performance économique de la ville et de sa région. Actuellement, une quantité grandissante de données socio-économiques et environnementales est récoltée. Pour mieux comprendre les processus et phénomènes du système complexe "ville", ces données doivent être traitées et analysées. Des nombreuses méthodes pour modéliser et simuler un tel système existent et sont continuellement en développement. Elles peuvent être exploitées par le géographe urbain pour améliorer sa connaissance du métabolisme urbain. Des techniques modernes et innovatrices de visualisation aident dans la communication des résultats de tels modèles et simulations. Cette thèse décrit plusieurs méthodes permettant d'analyser, de modéliser, de simuler et de visualiser des phénomènes urbains. L'analyse de données socio-économiques à très haute dimension à l'aide de réseaux de neurones artificiels, notamment des cartes auto-organisatrices, est montré à travers deux exemples aux échelles différentes. Le problème de modélisation spatio-temporelle et de représentation des données est discuté et quelques ébauches de solutions esquissées. La simulation de la dynamique urbaine, et plus spécifiquement du trafic automobile engendré par les pendulaires est illustrée à l'aide d'une simulation multi-agents. Une section sur les méthodes de visualisation montre des cartes en anamorphoses permettant de transformer l'espace géographique en espace fonctionnel. Un autre type de carte, les cartes circulaires, est présenté. Ce type de carte est particulièrement utile pour les agglomérations urbaines. Quelques questions liées à l'importance de l'échelle dans l'analyse urbaine sont également discutées. Une nouvelle approche pour définir des clusters urbains à des échelles différentes est développée, et le lien avec la théorie de la percolation est établi. Des statistiques fractales, notamment la lacunarité, sont utilisées pour caractériser ces clusters urbains. L'évolution de la population est modélisée à l'aide d'un modèle proche du modèle gravitaire bien connu. Le travail couvre une large panoplie de méthodes utiles en géographie urbaine. Toutefois, il est toujours nécessaire de développer plus loin ces méthodes et en même temps, elles doivent trouver leur chemin dans la vie quotidienne des urbanistes et planificateurs.

Resting-brain functional connectivity predicted by analytic measures of network communication.

The complex relationship between structural and functional connectivity, as measured by noninvasive imaging of the human brain, poses many unresolved challenges and open questions. Here, we apply analytic measures of network communication to the structural connectivity of the human brain and explore the capacity of these measures to predict resting-state functional connectivity across three independently acquired datasets. We focus on the layout of shortest paths across the network and on two communication measures-search information and path transitivity-which account for how these paths are embedded in the rest of the network. Search information is an existing measure of information needed to access or trace shortest paths; we introduce path transitivity to measure the density of local detours along the shortest path. We find that both search information and path transitivity predict the strength of functional connectivity among both connected and unconnected node pairs. They do so at levels that match or significantly exceed path length measures, Euclidean distance, as well as computational models of neural dynamics. This capacity suggests that dynamic couplings due to interactions among neural elements in brain networks are substantially influenced by the broader network context adjacent to the shortest communication pathways.

Citrus fruit and cancer risk in a network of case-control studies.

BACKGROUND: Citrus fruit has shown a favorable effect against various cancers. To better understand their role in cancer risk, we analyzed data from a series of case-control studies conducted in Italy and Switzerland. PATIENTS AND METHODS: The studies included 955 patients with oral and pharyngeal cancer, 395 with esophageal, 999 with stomach, 3,634 with large bowel, 527 with laryngeal, 2,900 with breast, 454 with endometrial, 1,031 with ovarian, 1,294 with prostate, and 767 with renal cell cancer. All cancers were incident and histologically confirmed. Controls were admitted to the same network of hospitals for acute, nonneoplastic conditions. Odds ratios (OR) were estimated by multiple logistic regression models, including terms for major identified confounding factors for each cancer site, and energy intake. RESULTS: The ORs for the highest versus lowest category of citrus fruit consumption were 0.47 (95% confidence interval, CI, 0.36-0.61) for oral and pharyngeal, 0.42 (95% CI, 0.25-0.70) for esophageal, 0.69 (95% CI, 0.52-0.92) for stomach, 0.82 (95% CI, 0.72-0.93) for colorectal, and 0.55 (95% CI, 0.37-0.83) for laryngeal cancer. No consistent association was found with breast, endometrial, ovarian, prostate, and renal cell cancer. CONCLUSIONS: Our findings indicate that citrus fruit has a protective role against cancers of the digestive and upper respiratory tract.

Endocytic and secretory traffic in Arabidopsis merge in the trans-Golgi network/early endosome, an independent and highly dynamic organelle.

Plants constantly adjust their repertoire of plasma membrane proteins that mediates transduction of environmental and developmental signals as well as transport of ions, nutrients, and hormones. The importance of regulated secretory and endocytic trafficking is becoming increasingly clear; however, our knowledge of the compartments and molecular machinery involved is still fragmentary. We used immunogold electron microscopy and confocal laser scanning microscopy to trace the route of cargo molecules, including the BRASSINOSTEROID INSENSITIVE1 receptor and the REQUIRES HIGH BORON1 boron exporter, throughout the plant endomembrane system. Our results provide evidence that both endocytic and secretory cargo pass through the trans-Golgi network/early endosome (TGN/EE) and demonstrate that cargo in late endosomes/multivesicular bodies is destined for vacuolar degradation. Moreover, using spinning disc microscopy, we show that TGN/EEs move independently and are only transiently associated with an individual Golgi stack.

Outcome and prognostic factors in olfactory neuroblastoma: a rare cancer network study.

Purpose: To assess the outcome in patients with olfactory neuroblastoma (ONB). Methods and Materials: Seventy-seven patients treated for nonmetastatic ONB between 1971 and 2004 were included. According to Kadish classification, there were 11 patients with Stage A, 29 with Stage B, and 37 with Stage C. T-classification included 9 patients with T1, 26 with T2, 16 with T3, 15 with T4a, and 11 with T4b tumors. Sixty-eight patients presented with N0 (88%) disease. Results: Most of the patients (n = 56, 73 %) benefited from surgery (S), and total excision was possible in 44 patients (R0 in 32, R1 in 13, R2 in 11). All but five patients benefited from RT, and chemotherapy was given in 21(27%). Median follow-up period was 72 months (range, 6-315). The 5-year overall survival (OS), disease-free survival (DES), locoregional control, and local control were 64%, 57%, 62%, and 70%, respectively. In univariate analyses, favorable factors were Kadish A or B disease, T1 T3 tumors, no nodal involvement, curative surgery, R0/R1 resection, and RT-dose 54 Gy or higher. Multivariate analysis revealed that the best independent factors predicting the outcome were T1 T3, N0, R0/R1 resection, and total RT dose (54 Gy or higher). Conclusion: In this multicenter retrospective study, patients with ONB treated with R0 or R1 surgical resection followed by at least 54-Gy postoperative RT had the best outcome. Novel strategies including concomitant chemotherapy and/or higher dose RT should be prospectively investigated in this rare disease for which local failure remains a problem.

Early stage primary bone lymphoma - a retrospective, multicenter rare cancer network (rcn) study

Purpose: Primary bone lymphoma (PBL) accounts for less than 1% of all malignant lymphomas, and 4-5% of all extra-nodal lymphomas. In this study, the disease profile, outcome, and prognostic factors were assessed in patients with stage I and II PBL.Patients and Methods: Thirteen Rare Cancer Network (RCN) institutions enrolled 116 consecutive patients with PBL treated between 1987 and 2008 in this study. Inclusion criteria were age > 16 years, stage I and II, minimum 6 months follow-up and a biopsy-proven confirmation of non-Hodgkin's lymphoma (NHL). Eighty-seven patients underwent chemoradiotherapy (CXRT), 15 radiotherapy (RT) without (13) or with (2) surgery, 14 chemotherapy (CXT) without (9) or with (5) surgery. Median RT dose was 40 Gy (range: 4-60). The median number of CXT cycles was 6 (range: 2-8). Median follow-up was 41 months (range: 6-242).Results: The overall response rate at the end of treatment was 91% (CR 74%, PR 17%). Local recurrence or progression was observed in 12 (10%) patients, and systemic recurrence in 17 (15%). Causes of death included disease progression in 21, unrelated in 5, CXT-related toxicity in 1, and second primary cancer in 2 patients. The 5-yr overall survival (OS), lymphoma-specific survival (LSS), and local control (LC) were 76%, 78% and 92%, respectively. In univariate analyses (log-rank test), favorable prognostic factors for OS were age <50 years (P=0.008), international prognostic index (IPI) score ≤1 (P=0.009), high grade histology (P=0.04), CXRT (P=0.05), CXT (P=0,0004), complete response (CR) (P<0.0001), number of CXT cycles ( ≥6 ) (P=0.01), and RT dose > 40 Gy (P=0.005). All above-mentioned parameters were also significant for LSS except for age and number of chemotherapy cycles. For LC, only CR and stage I were favorable factors. In multivariate analysis, IPI score, RT dose, complete response, and chemotherapy were independently influencing the outcome (OS and LSS). Complete response at the end of treatment was the only predicting factor for LC. Six patients developed grade 3 or more toxicities, according to Common Terminology Criteria for Adverse Events (CTCAE) V3.0.Conclusion: This large multicenter study confirms the relatively good prognosis of early stage PBL treated with combined CXRT. Local control was excellent, while systemic failures were rare. An adequate dose of RT (40 Gy or more) and complete CXT regime (≥ 6 cycles) were associated with better outcome.

Diffusion Spectrum Imaging after stroke shows structural changes in the contra-lateral motor network correlating with functional recovery

There is growing interest in understanding the role of the non-injured contra-lateral hemisphere in stroke recovery. In the experimental field, histological evidence has been reported that structural changes occur in the contra-lateral connectivity and circuits during stroke recovery. In humans, some recent imaging studies indicated that contra-lateral sub-cortical pathways and functional and structural cortical networks are remodeling, after stroke. Structural changes in the contra-lateral networks, however, have never been correlated to clinical recovery in patients. To determine the importance of the contra-lateral structural changes in post-stroke recovery, we selected a population of patients with motor deficits after stroke affecting the motor cortex and/or sub-cortical motor white matter. We explored i) the presence of Generalized Fractional Anisotropy (GFA) changes indicating structural alterations in the motor network of patientsâeuro? contra-lateral hemisphere as well as their longitudinal evolution ii) the correlation of GFA changes with patientsâeuro? clinical scores, stroke size and demographics data iii) and a predictive model.

Représentations institutionnelles du cancer [Institutional representations of cancer]

Current institutional and official representations of cancer are: coordination, integration, team approaches, quality management, full informed consent, patient centered communication and empowerment. Web access, comprehensive care plan summaries patient centered healthcare interactions and evidence-based programs are different ways of delivering the comprehensive care and follow-up cancer survivors deserve. The question remains, how to best explore and respect, in the meantime, more subjective dimensions such as patient beliefs, values, the meaning of the illness, preferences and needs. These aspects are fundamental elements in the construction of a trusting relationship, so as to find common ground, to be open to discuss anxiety and doubts and to provide information tailored to suit the patient's level of understanding, in order to reduce vulnerability to the feeling of being "lost in transition".

Online teaching of inflammatory skin pathology by a French-speaking international university network

Introduction: Developments in technology, webbased teaching and whole slide imaging have broadened the teaching horizon in anatomic pathology. Creating online learning material including many types of media like radiologic images, videos, clinical and macroscopic photographs and whole slides imaging is now accessible to almost every university. Unfortunately, a major limiting factor to maintain and update the learning material is the amount of work, time and resources needed. In this perspective, a French national university network was initiated in 2011 to build mutualised online teaching pathology modules with clinical cases and tests. This network has been extended to an international level in 2012-2014 (Quebec, Switzerland and Ivory Coast). Method: One of the first steps of the international project was to build a learning module on inflammatory skin pathology intended for interns and residents of pathology and dermatology. A pathology resident from Quebec spent 6 weeks in France and Switzerland to develop the contents and build the module on an e-learning Moodle platform (http: //moodle.sorbonne-paris-cite.fr) under the supervision of two dermatopathologists (BV, MB). The learning module contains text, interactive clinical cases, tests with feedback, whole slides images (WSI), images and clinical photographs. For that module, the virtual slides are decentralized in 2 universities (Bordeaux and Paris 7). Each university is responsible of its own slide scanning, image storage and online display with virtual slide viewers. Results: The module on inflammatory skin pathology includes more than 50 web pages with French original content, tests and clinical cases, links to over 45 WSI and more than 50 micro and clinical photographs. The whole learning module is currently being revised by four dermatopathologists and two senior pathologists. It will be accessible to interns and residents in spring 2014. The experience and knowledge gained from that work will be transferred to the next international fellowship intern whose work will be aimed at creating lung and breast pathology learning modules. Conclusion: The challenges of sustaining a project of this scope are numerous. The technical aspect of whole-slide imaging and storage needs to be developed by each university or group. The content needs to be regularly updated, completed and its use and existence needs to be promoted by the different actors in pathology. Of the great benefits of that kind of project are the international partnerships and connections that have been established between numerous Frenchspeaking universities and pathologists with the common goals of promoting education in pathology and the use of technology including whole slide imaging. * The Moodle website is hosted by PRES Sorbonne Paris Cité, and financial supports for hardware have been obtained from UNF3S (http://www.unf3s.org/) and PRES Sorbonne Paris Cité. Financial support for international fellowships has been obtained from CFQCU (http://www.cfqcu.org/).

Extreme prematurity and intra uterine growth restriction effects in brain network topology at school age

Higher risk for long-term behavioral and emotional sequelae, with attentional problems (with or without hyperactivity) is now becoming one of the hallmarks of extreme premature (EP) birth and birth after pregancy conditions leading to poor intra uterine growth restriction (IUGR) [1,2]. However, little is know so far about the neurostructural basis of these complexe brain functional abnormalities that seem to have their origins in early critical periods of brain development. The development of cortical axonal pathways happens in a series of sequential events. The preterm phase (24-36 post conecptional weeks PCW) is known for being crucial for growth of the thalamocortical fiber bundles as well as for the development of long projectional, commisural and projectional fibers [3]. Is it logical to expect, thus, that being exposed to altered intrauterine environment (altered nutrition) or to extrauterine environment earlier that expected, lead to alterations in the structural organization and, consequently, alter the underlying white matter (WM) structure. Understanding rate and variability of normal brain development, and detect differences from typical development may offer insight into the neurodevelopmental anomalies that can be imaged at later stages. Due to its unique ability to non-invasively visualize and quantify in vivo white matter tracts in the brain, in this study we used diffusion MRI (dMRI) tractography to derive brain graphs [4,5,6]. This relatively simple way of modeling the brain enable us to use graph theory to study topological properties of brain graphs in order to study the effects of EP and IUGR on childrens brain connectivity at age 6 years old.

The Poor Representation of the Poor in a Comparative Perspective

Due to diverging levels of political influence of various income groups, political institutions likely reflect¦the policy preferences of certain groups of citizens better than others, independently of their numerical¦weight. This runs counter the egalitarian principle of 'one citizen, one vote'. The present article documents¦a general trend of underrepresentation of the preferences of relatively poor citizens both by¦parties and by governments across Western democracies, although important cross-national differences¦exist.

Treatment results and prognostic factors in primary thyroid lymphoma patients: a rare cancer network study.

Background: This study analyzed prognostic factors and treatment outcomes of primary thyroid lymphoma. Patients and Methods: Data were retrospectively collected for 87 patients (53 stage I and 34 stage II) with median age 65 years. Fifty-two patients were treated with single modality (31 with chemotherapy alone and 21 with radiotherapy alone) and 35 with combined modality treatment. Median follow-up was 51 months. Results: Sixty patients had aggressive lymphoma and 27 had indolent lymphoma. The 5- and 10-year overall survival (OS) rates were 74% and 71%, respectively, and the disease-free survival (DFS) rates were 68% and 64%. Univariate analysis revealed that age, tumor size, stage, lymph node involvement, B symptoms, and treatment modality were prognostic factors for OS, DFS, and local control (LC). Patients with thyroiditis had significantly better LC rates. In multivariate analysis, OS was influenced by age, B symptoms, lymph node involvement, and tumor size, whereas DFS and LC were influenced by B symptoms and tumor size. Compared with single modality treatment, patients treated with combined modality had better 5-year OS, DFS, and LC. Conclusions: Combined modality leads to an excellent prognosis for patients with aggressive lymphoma but does not improve OS and LC in patients with indolent lymphoma.