Detection of clusters using space-time scan statistics

This paper aims at detecting spatio-temporal clustering in fire sequences using space?time scan statistics, a powerful statistical framework for the analysis of point processes. The methodology is applied to active fire detection in the state of Florida (US) identified by MODIS (Moderate Resolution Imaging Spectroradiometer) during the period 2003?06. Results of the present study show that statistically significant clusters can be detected and localized in specific areas and periods of the year. Three out of the five most likely clusters detected for the entire frame period are localized in the north of the state, and they cover forest areas; the other two clusters cover a large zone in the south, corresponding to agricultural land and the prairies in the Everglades. In order to analyze if the wildfires recur each year during the same period, the analyses have been performed separately for the 4 years: it emerges that clusters of forest fires are more frequent in hot seasons (spring and summer), while in the southern areas, they are widely present during the whole year. The recognition of overdensities of events and the ability to locate them in space and in time can help in supporting fire management and focussing on prevention measures.

Sex-chromosome evolution of Palearctic tree frogs in space and time

Sexual reproduction is nearly universal in eukaryotes and genetic determination of sex prevails among animals. The astonishing diversity of sex-determining systems and sex chromosomes is yet bewildering. Some taxonomic groups possess conserved and dimorphic sex chromosomes, involving a functional copy (e.g. mammals' X, birds' Z) and a degenerated copy (mammals' Y, birds' W), implying that sex- chromosomes are expected to decay. In contrast, others like amphibians, reptiles and fishes yet maintained undifferentiated sex chromosomes. Why such different evolutionary trajectories? In this thesis, we empirically test and characterize the main hypotheses proposed to prevent the genetic decay of sex chromosomes, namely occasional X-Y recombination and frequent sex-chromosome transitions, using the Palearctic radiation of Hyla tree frogs as a model system. We take a phylogeographic and phylogenetic approach to relate sex-chromosome recombination, differentiation, and transitions in a spatial and temporal framework. By reconstructing the recent evolutionary history of the widespread European tree frog H. arborea, we showed that sex chromosomes can recombine in males, preventing their differentiation, a situation that potentially evolves rapidly. At the scale of the entire radiation, X-Y recombination combines with frequent transitions to prevent sex-chromosome degeneration in Hyla: we traced several turnovers of sex-determining system within the last 10My. These rapid changes seem less random than usually assumed: we gathered evidences that one chromosome pair is a sex expert, carrying genes with key role in animal sex determination, and which probably specialized through frequent reuse as a sex chromosome in Hyla and other amphibians. Finally, we took advantage of secondary contact zones between closely-related Hyla lineages to evaluate the consequences of sex chromosome homomorphy on the genetics of speciation. In comparison with other systems, the evolution of sex chromosomes in Hyla emphasized the existence of consistent evolutionary patterns within the chaotic diversity of flexibility of cold-blooded vertebrates' sex-determining systems, and provides insights into the evolution of recombination. Beyond sex-chromosome evolution, this work also significantly contributed to speciation, phylogeography and applied conservation research. -- La reproduction sexuée est quasi-universelle chez les eucaryotes et le sexe est le plus souvent déterminé génétiquement au sein du règne animal. L'incroyable diversité des systèmes de reproduction et des chromosomes sexuels est particulièrement étonnante. Certains groupes taxonomiques possèdent des chromosomes sexuels dimorphiques et très conservés, avec une copie entièrement fonctionnelle (ex : le X des mammifères, le Z des oiseaux) et une copie dégénérée (ex : le Y des mammifères, le W des oiseaux), suggérant que les chromosomes sexuels sont voués à se détériorer. Cependant les chromosomes sexuels d'autres groupes tels que les amphibiens, les reptiles et les poissons sont pour la plupart indifférenciés. Comment expliquer des trajectoires évolutives si différentes? Au cours de cette thèse, nous avons étudié empiriquement les processus évolutifs pouvant maintenir les chromosomes sexuels intacts, à savoir la recombinaison X-Y occasionnel ainsi que les substitutions fréquentes de chromosomes sexuels, en utilisant les rainettes Paléarctiques du genre Hyla comme modèle d'étude. Nous avons adopté une approche phylogéographique et phylogénétique pour appréhender les événements de recombinaison, de différenciation et de transitions de chromosomes sexuels dans un contexte spatio-temporel. En retraçant l'histoire évolutive récente de la rainette verte H. arborea, nous avons mis en évidence que les chromosomes sexuels pouvaient recombiner chez les mâles, empêchant ainsi leur différenciation, et que ce processus avait le potentiel d'évoluer très rapidement. A l'échelle plus globale de la radiation, il apparait que les phénomènes de recombinaison X-Y soient également accompagnés de substitutions de chromosomes sexuels, et participent de concert au maintien de chromosomes sexuels intacts dans les populations: le système de détermination du sexe des rainettes a changé plusieurs fois au cours des 10 derniers millions d'années. Ces transitions fréquentes ne semblent pas aléatoires: nous avons identifié une paire de chromosomes qui présente des caractéristiques présageant d'une spécialisation dans le déterminisme du sexe (notamment car elle possède des gènes importants pour cette fonction), et qui a été réutilisée plusieurs fois comme tel chez les rainettes ainsi que d'autres amphibiens. Enfin, nous avons étudié l'hybridation entre différentes espèces dans leurs zones de contact, afin d'évaluer si l'absence de différenciation entre X et Y jouaient un rôle dans les processus génétiques de spéciation. Outre son intérêt pour la compréhension de l'évolution des chromosomes sexuels, ce travail contribue de manière significative à d'autres domaines de recherche tels que la spéciation, la phylogéographie, ainsi que la biologie de la conservation.

Risk Factors for Incisional and Organ Space Surgical Site Infections After Liver Resection are Different.

BACKGROUND: Surgical site infection (SSI) is a common cause of major morbidity after liver resection. This study aimed to identify the risk factors for incisional and organ/space SSIs after liver resection. METHODS: Our liver surgery database was retrospectively analyzed for patients treated between January 2009 and November 2012 in a tertiary care Swiss hospital. Univariate and multivariate analyses were conducted on preoperative, intraoperative, and postoperative variables to identify risk factors for incisional and organ/space SSIs. RESULTS: In a total of 226 patients, SSI incidences were 12.8 % (incisional), 4.0 % (organ/space), and 1.8 % (both). Univariate analysis showed that incisional SSIs were associated with high American Society of Anesthesiologists (ASA) scores, preoperative anemia, hypoalbuminemia, low prothrombin time, viral or alcoholic chronic hepatitis, liver cirrhosis, and prolonged operation times. Organ/space SSIs were associated with high rates of red blood cell transfusions, concomitant bowel surgery, and prolonged operation times. Multivariate analysis revealed that risk factors for incisional SSIs were anemia [odds ratio (OR) 2.82], high ASA scores (OR 2.88), presence of hepatitis or cirrhosis (OR 5.07), and prolonged operation times (OR 9.61). The only risk factor for organ/space SSIs was concomitant bowel surgery (OR 5.53). Hospital stays were similar in organ/space and incisional SSI groups, but significantly longer for those with both organ/space and incisional SSIs. CONCLUSIONS: High ASA scores, anemia, chronic hepatitis or liver cirrhosis, and prolonged operations increased the risk of incisional SSIs; concomitant bowel surgery increased the risk of organ/space SSI. Specific precautions to prevent organ/space and incisional SSIs may shorten hospital stays.

Wiki-supported collaborative learning in primary education. How a dialogic space is created for thinking together

This paper explores how wikis may be used to support primary education students’ collaborative interaction and how such an interaction process can be characterised. The overall aim of this study is to analyse the collaborative processes of students working together in a wiki environment, in order to see how primary students can actively create a shared context for learning in the wiki. Educational literature has already reported that wikis may support collaborative knowledge-construction processes, but in our study we claim that a dialogic perspective is needed to accomplish this. Students must develop an intersubjective orientation towards each others’ perspectives, to co-construct knowledge about a topic. For this purpose, our project utilised a ‘Thinking Together’ approach to help students develop an intersubjective orientation towards one another and to support the creation of a ‘dialogic space’ to co-construct new understanding in a wiki science project. The students’ asynchronous interaction process in a primary classroom -- which led to the creation of a science text in the wiki -- was analysed and characterised, using a dialogic approach to the study of CSCL practices. Our results illustrate how the Thinking Together approach became embedded within the wiki environment and in the students’ collaborative processes. We argue that a dialogic approach for examining interaction can be used to help design more effective pedagogic approaches related to the use of wikis in education and to equip learners with the competences they need to participate in the global knowledge-construction era.

Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking.

We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2×2×3 factorial design with the following factors: PMC on or off; 3.0mm or 1.5mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p<0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies.

Diagnosis of the nutrient compositional space of fruit crops

Tissue analysis is a useful tool for the nutrient management of fruit orchards. The mineral composition of diagnostic tissues expressed as nutrient concentration on a dry weight basis has long been used to assess the status of 'pure' nutrients. When nutrients are mixed and interact in plant tissues, their proportions or concentrations change relatively to each other as a result of synergism, antagonism, or neutrality, hence producing resonance within the closed space of tissue composition. Ternary diagrams and nutrient ratios are early representations of interacting nutrients in the compositional space. Dual and multiple interactions were integrated by the Diagnosis and Recommendation Integrated System (DRIS) into nutrient indexes and by Compositional Nutrient Diagnosis into centered log ratios (CND-clr). DRIS has some computational flaws such as using a dry matter index that is not a part as well as nutrient products (e.g. NxCa) instead of ratios. DRIS and CND-clr integrate all possible nutrient interactions without defining an ad hoc interactive model. They diagnose D components while D-1 could be diagnosed in the D-compositional Hilbert space. The isometric log ratio (ilr) coordinates overcome these problems using orthonormal binary nutrient partitions instead of dual ratios. In this study, it is presented a nutrient interactive model as well as computation methods for DRIS and CND-clr and CND-ilr coordinates (CND-ilr) using leaf analytical data from an experimental apple orchard in Southwestern Quebec, Canada. It was computed the Aitchison and Mahalanobis distances across ilr coordinates as measures of nutrient imbalance. The effect of changing nutrient concentrations on ilr coordinates are simulated to identify the ones contributing the most to nutrient imbalance.

From room for books to room for users: an old infantry barrack as an answer to the lack of space

At the beginning of the 21st century, some Catalan university libraries detected a need stemming from the lack of space and the reconversion of physical libraries within the new European educational panorama. With the same cooperative spirit that characterized previous CBUC (Consortium of Academic Libraries of Catalonia) programs and services, the Consortium set in motion a project to address this need. An initial study was commissioned in 2002, and in 2003 a suitable building (old infantry barracks) was found in Lleida. The official opening took place in 2008. GEPA (Guaranteed Space for the Preservation of Access) facility is a cooperative repository, whose objectives are to store and preserve low use documents, ensuring their future access when needed, to convert room for books into room for library users, and doing it saving both space and money. The paper presents a brief historical introduction about the physical management of collections in libraries, and a short overview about high density library repositories all over the world, as an answer to the pressing problem of lack of spaces. The main goals of the communication are to comment the architectural project and its librarian issues, and to show how the GEPA facility allowed to change the spaces in university libraries in Catalonia. On the one hand, the paper deals with the selection of an old building to be renovated, the determination of the librarian needs, the compact shelving system chosen to store the documents in the building, the relation between physical space and information management, and the logistics involved in the load of low use documents from the libraries into the facility. On the other hand, we will show some examples of physical changes in Catalan libraries after large loads of documents to GEPA.

Time and space: genetic structure of the common sea urchin paracentrotus lividus in the south-eastern iberian coast

Spatio-temporal variability in settlement and recruitment, high mortality during the first life-history stages, and selection may determine the genetic structure of cohorts of long-lived marine invertebrates at small scales. We conducted a spatial and temporal analysis of the common Mediterranean Sea urchin Paracentrotus lividus to determine the genetic structure of cohorts at different scales. In Tossa de Mar (NW Mediterranean), recruitment was followed over 5 consecutive springs (2006-2010). In spring 2008, recruits and two-year-old individuals were collected at 6 locations along East and South Iberian coasts separated from 200 to over 1,100 km. All cohorts presented a high genetic diversity based on a fragment of mtCOI. Our results showed a marked genetic homogeneity in the temporal monitoring and a low degree of spatial structure in 2006. In 2008, coupled with an abnormality in the usual circulation patterns in the area, the genetic structure of the southern populations studied changed markedly, with arrival of many private haplotypes. This fact highlights the importance of point events in renewing the genetic makeup of populations, which can only be detected through analysis of the cohort structure coupling temporal and spatial perspectives.

Paper Surface Image Processing for Roughness Quality Measurement

Diplomityössä on käsitelty paperin pinnankarkeuden mittausta, joka on keskeisimpiä ongelmia paperimateriaalien tutkimuksessa. Paperiteollisuudessa käytettävät mittausmenetelmät sisältävät monia haittapuolia kuten esimerkiksi epätarkkuus ja yhteensopimattomuus sileiden papereiden mittauksissa, sekä suuret vaatimukset laboratorio-olosuhteille ja menetelmien hitaus. Työssä on tutkittu optiseen sirontaan perustuvia menetelmiä pinnankarkeuden määrittämisessä. Konenäköä ja kuvan-käsittelytekniikoita tutkittiin karkeilla paperipinnoilla. Tutkimuksessa käytetyt algoritmit on tehty Matlab® ohjelmalle. Saadut tulokset osoittavat mahdollisuuden pinnankarkeuden mittaamiseen kuvauksen avulla. Parhaimman tuloksen perinteisen ja kuvausmenetelmän välillä antoi fraktaaliulottuvuuteen perustuva menetelmä.

Level Set Methods in Image Processing

This thesis gives an overview of the use of the level set methods in the field of image science. The similar fast marching method is discussed for comparison, also the narrow band and the particle level set methods are introduced. The level set method is a numerical scheme for representing, deforming and recovering structures in an arbitrary dimensions. It approximates and tracks the moving interfaces, dynamic curves and surfaces. The level set method does not define how and why some boundary is advancing the way it is but simply represents and tracks the boundary. The principal idea of the level set method is to represent the N dimensional boundary in the N+l dimensions. This gives the generality to represent even the complex boundaries. The level set methods can be powerful tools to represent dynamic boundaries, but they can require lot of computing power. Specially the basic level set method have considerable computational burden. This burden can be alleviated with more sophisticated versions of the level set algorithm like the narrow band level set method or with the programmable hardware implementation. Also the parallel approach can be used in suitable applications. It is concluded that these methods can be used in a quite broad range of image applications, like computer vision and graphics, scientific visualization and also to solve problems in computational physics. Level set methods and methods derived and inspired by it will be in the front line of image processing also in the future.