Quantifying uplift and denudation of a thermally heterogeneous crust: a detailed multi-thermochronometeric study of central west Britain

Topography is often thought as exclusively linked to mountain ranges formed by plates collision. It is now, however, known that apart from compression, uplift and denudation of rocks may be triggered by rifting, like it happens at elevated passive margins, and away from plate boundaries by both intra-plate stress causing reactivation of older structures, and by epeirogenic movements driven by mantle dynamics and initiating long-wavelength uplift. In the Cenozoic, central west Britain and other parts of the North Atlantic margins experienced multiple episodes of rock uplift and denudation that have been variable both at spatial and temporal scales. The origin of topography in central west Britain is enigmatic, and because of its location, it may be related to any of the processes mentioned above. In this study, three low temperature thermochronometers, the apatite fission track (AFT) and apatite and zircon (U-Th-Sm)/He (AHe and ZHe, respectively) methods were used to establish the rock cooling history from 200◦C to 30◦C. The samples were collected from the intrusive rocks in the high elevation, high relief regions of the Lake District (NW England), southern Scotland and northern Wales. AFT ages from the region are youngest (55–70 Ma) in the Lake District and increase northwards into southern Scotland and southwards in north Wales (>200 Ma). AHe and ZHe ages show no systematic pattern; the former range from 50 to 80 Ma and the latter tend to record the post-emplacement cooling of the intrusions (200–400 Ma). The complex, multi-thermochronometric inverse modelling suggests a ubiquitous, rapid Late Cretaceous/early Palaeogene cooling event that is particularly marked in Lake District and Criffell. The timing and rate of cooling in southern Scotland and in northern Wales is poorly resolved as the amount of cooling was less than 60◦C. The Lake District plutons were at >110◦C prior to the early Palaeogene; cooling due to a combined effect of high heat flow, from the heat producing granite batholith, and the blanketing effect of the overlying low conductivity Late Mesozoic limestones and mudstones. Modelling of the heat transfer suggests that this combination produced an elevated geothermal gradient within the sedimentary rocks (50–70◦C/km) that was about two times higher than at the present day. Inverse modelling of the AFT and AHe data taking the crustal structure into consideration suggests that denudation was the highest, 2.0–2.5 km, in the coastal areas of the Lake District and southern Scotland, gradually decreasing to less than 1 km in the northern Southern Uplands and northern Wales. Both the rift-related uplift and the intra-plate compression poorly correlate with the timing, location and spatial distribution of the early Palaeogene denudation. The pattern of early Palaeogene denudation correlates with the thickness of magmatic underplating, if the changes of mean topography, Late Cretaceous water depth and eroded rock density are taken into consideration. However, the uplift due to underplating alone cannot fully justify the total early Palaeogene denudation. The amount that is not ex- plained by underplating is, however, roughly spatially constant across the study area and can be referred to the transient thermal uplift induced by the mantle plume arrival. No other mechanisms are required to explain the observed pattern of denudation. The onset of denudation across the region is not uniform. Denudation started at 70–75 Ma in the central part of the Lake District whereas the coastal areas the rapid erosion appears to have initiated later (65–60 Ma). This is ~10 Ma earlier than the first vol- canic manifestation of the proto-Iceland plume and favours the hypothesis of the short period of plume incubation below the lithosphere before the volcanism. In most of the localities, the rocks had cooled to temperatures lower than 30◦C by the end of the Palaeogene, suggesting that the total Neogene denudation was, at a maximum, several hundreds of metres. Rapid cooling in the last 3 million years is resolved in some places in southern Scotland, where it could be explained by glacial erosion and post-glacial isostatic uplift.

Combined exposure to multiple mycotoxins in food: are we ready for risk assessment and risk management?

It is nowadays recognized that the risk of human co-exposure to multiple mycotoxins is real. In the last years, a number of studies have approached the issue of co-exposure and the best way to develop a more precise and realistic assessment. Likewise, the growing concern about the combined effects of mycotoxins and their potential impact on human health has been reflected by the increasing number of toxicological studies on the combined toxicity of these compounds. Nevertheless, risk assessment of these toxins, still follows the conventional paradigm of single exposure and single effects, incorporating only the possibility of additivity but not taking into account the complex dynamics associated to interactions between different mycotoxins or between mycotoxins and other food contaminants. Considering that risk assessment is intimately related to the establishment of regulatory guidelines, once the risk assessment is completed, an effort to reduce or manage the risk should be followed to protect public health. Risk assessment of combined human exposure to multiple mycotoxins thus poses several challenges to scientists, risk assessors and risk managers and opens new avenues for research. This presentation aims to give an overview of the different challenges posed by the likelihood of human co-exposure to mycotoxins and the possibility of interactive effects occurring after absorption, towards knowledge generation to support a more accurate human risk assessment and risk management. For this purpose, a physiologically-based framework that includes knowledge on the bioaccessibility, toxicokinetics and toxicodynamics of multiple toxins is proposed. Regarding exposure assessment, the need of harmonized food consumption data, availability of multianalyte methods for mycotoxin quantification, management of left-censored data and use of probabilistic models will be highlight, in order to develop a more precise and realistic exposure assessment. On the other hand, the application of predictive mathematical models to estimate mycotoxins’ combined effects from in vitro toxicity studies will be also discussed. Results from a recent Portuguese project aimed at exploring the toxic effects of mixtures of mycotoxins in infant foods and their potential health impact will be presented as a case study, illustrating the different aspects of risk assessment highlighted in this presentation. Further studies on hazard and exposure assessment of multiple mycotoxins, using harmonized approaches and methodologies, will be crucial towards an improvement in data quality and contributing to holistic risk assessment and risk management strategies for multiple mycotoxins in foodstuffs.

Methods matter: computational modelling in public health policy and planning

This work is aimed at understanding and unifying information on epidemiological modelling methods and how those methods relate to public policy addressing human health, specifically in the context of infectious disease prevention, pandemic planning, and health behaviour change. This thesis employs multiple qualitative and quantitative methods, and presents as a manuscript of several individual, data-driven projects that are combined in a narrative arc. The first chapter introduces the scope and complexity of this interdisciplinary undertaking, describing several topical intersections of importance. The second chapter begins the presentation of original data, and describes in detail two exercises in computational epidemiological modelling pertinent to pandemic influenza planning and policy, and progresses in the next chapter to present additional original data on how the confidence of the public in modelling methodology may have an effect on their planned health behaviour change as recommended in public health policy. The thesis narrative continues in the final data-driven chapter to describe how health policymakers use modelling methods and scientific evidence to inform and construct health policies for the prevention of infectious diseases, and concludes with a narrative chapter that evaluates the breadth of this data and recommends strategies for the optimal use of modelling methodologies when informing public health policy in applied public health scenarios.

The experience of teaching statistics to non-specialist students in Saudi universities

Undoubtedly, statistics has become one of the most important subjects in the modern world, where its applications are ubiquitous. The importance of statistics is not limited to statisticians, but also impacts upon non-statisticians who have to use statistics within their own disciplines. Several studies have indicated that most of the academic departments around the world have realized the importance of statistics to non-specialist students. Therefore, the number of students enrolled in statistics courses has vastly increased, coming from a variety of disciplines. Consequently, research within the scope of statistics education has been able to develop throughout the last few years. One important issue is how statistics is best taught to, and learned by, non-specialist students. This issue is controlled by several factors that affect the learning and teaching of statistics to non-specialist students, such as the use of technology, the role of the English language (especially for those whose first language is not English), the effectiveness of statistics teachers and their approach towards teaching statistics courses, students’ motivation to learn statistics and the relevance of statistics courses to the main subjects of non-specialist students. Several studies, focused on aspects of learning and teaching statistics, have been conducted in different countries around the world, particularly in Western countries. Conversely, the situation in Arab countries, especially in Saudi Arabia, is different; here, there is very little research in this scope, and what there is does not meet the needs of those countries towards the development of learning and teaching statistics to non-specialist students. This research was instituted in order to develop the field of statistics education. The purpose of this mixed methods study was to generate new insights into this subject by investigating how statistics courses are currently taught to non-specialist students in Saudi universities. Hence, this study will contribute towards filling the knowledge gap that exists in Saudi Arabia. This study used multiple data collection approaches, including questionnaire surveys from 1053 non-specialist students who had completed at least one statistics course in different colleges of the universities in Saudi Arabia. These surveys were followed up with qualitative data collected via semi-structured interviews with 16 teachers of statistics from colleges within all six universities where statistics is taught to non-specialist students in Saudi Arabia’s Eastern Region. The data from questionnaires included several types, so different techniques were used in analysis. Descriptive statistics were used to identify the demographic characteristics of the participants. The chi-square test was used to determine associations between variables. Based on the main issues that are raised from literature review, the questions (items scales) were grouped and five key groups of questions were obtained which are: 1) Effectiveness of Teachers; 2) English Language; 3) Relevance of Course; 4) Student Engagement; 5) Using Technology. Exploratory data analysis was used to explore these issues in more detail. Furthermore, with the existence of clustering in the data (students within departments within colleges, within universities), multilevel generalized linear models for dichotomous analysis have been used to clarify the effects of clustering at those levels. Factor analysis was conducted confirming the dimension reduction of variables (items scales). The data from teachers’ interviews were analysed on an individual basis. The responses were assigned to one of the eight themes that emerged from within the data: 1) the lack of students’ motivation to learn statistics; 2) students' participation; 3) students’ assessment; 4) the effective use of technology; 5) the level of previous mathematical and statistical skills of non-specialist students; 6) the English language ability of non-specialist students; 7) the need for extra time for teaching and learning statistics; and 8) the role of administrators. All the data from students and teachers indicated that the situation of learning and teaching statistics to non-specialist students in Saudi universities needs to be improved in order to meet the needs of those students. The findings of this study suggested a weakness in the use of statistical software applications in these courses. This study showed that there is lack of application of technology such as statistical software programs in these courses, which would allow non-specialist students to consolidate their knowledge. The results also indicated that English language is considered one of the main challenges in learning and teaching statistics, particularly in institutions where English is not used as the main language. Moreover, the weakness of mathematical skills of students is considered another major challenge. Additionally, the results indicated that there was a need to tailor statistics courses to the needs of non-specialist students based on their main subjects. The findings indicate that statistics teachers need to choose appropriate methods when teaching statistics courses.

Restoration ecology of coastal lagoons: new methods for the prediction of ecological trajectories and economic valuation

Conservation of the seven lagoons of the Palavas complex (southern France) has been severely impaired by nutrient over-enrichment during at least four decades. The effluents of the Montpellier wastewater treatment plant (WWTP) represented the main nutrient input. To improve the water quality of these lagoons, this WWTP was renovated and upgraded and, since the end of 2005, its effluents have been discharged 11 km offshore into the Mediterranean (total investment €150 M). Possibilities of ecosystem restoration as part of a conservation programme were explored by a focus group of experts. Their tasks were: (i) to evaluate the impact of the reduction of the nutrient input; (ii) if necessary, to design additional measures for an active restoration programme; and (iii) to predict ecosystem trajectories for the different cases. Extension of Magnoliophyta meadows can be taken as a proxy for ecosystem restoration as they favour the increase of several fish (seahorse) and bird (ducks, swans, herons) species, albeit they represent a trade-off for greater flamingos. Additional measures for active ecosystem restoration were only recommended for the most impaired lagoon Méjean, while the least impaired lagoon Ingril is already on a trajectory of spontaneous recovery. A multiple contingent valuation considering four different management options for the Méjean lagoon was used in a pilot study based on face-to-face interviews with 159 respondents. Three levels of ecosystem restoration were expressed in terms of recovery of Magnoliophyta meadows, including their impact on emblematic fish and avifauna. These were combined with different options for access (status quo, increasing access, increasing access with measures to reduce disturbance). The results show a willingness of local populations to pay per year about €25 for the highest level of ecological restoration, while they were only willing to allocate about €5 for additional footpaths and hides.

Balancing the demands of two tasks: an investigation of cognitive-motor dual-tasking in relapsing remitting multiple sclerosis

Background: People with relapsing remitting MS (PwRRMS) suffer disproportionate decrements in gait under dual-task conditions, when walking and a cognitive task are combined. There has been much less investigation of the impact of cognitive demands on balance. This study investigated whether: (1) PwRRMS show disproportionate decrements in postural stability under dual-task conditions compared to healthy controls; (2) dual-task decrements are associated with everyday dual-tasking difficulties. In addition, the impact of mood, fatigue and disease severity on dual-tasking were also examined. Methods: 34 PwRRMS and 34 matched controls completed cognitive (digit span) and balance (movement of centre of pressure on a Biosway, on stable and unstable surfaces) tasks under single and dual-task conditions. Everyday dual-tasking was measured using the DTQ. Mood was measured by the HADS. Fatigue was measured via the MFIS. Results: No differences in age, gender, years of education, estimated pre-morbid IQ or baseline digit span between the groups. Compared to healthy controls, PwRRMS showed a significantly greater decrement in postural stability under dual-task conditions on an unstable surface (p=0.007), but not a stable surface (p=0.679). PwRRMS reported higher levels of everyday dual-tasking difficulties (p<0.001). Balance decrement scores were not correlated with everyday dual-tasking difficulties, or with fatigue. Stable surface balance decrement scores were significantly associated with levels of anxiety (rho=0.527, p=0.001) and depression (rho=0.451, p=0.007). Conclusion: RRMS causes difficulties with dual-tasking, impacting balance, particularly under challenging conditions, which may contribute to an increased risk of gait difficulties and falls. The striking relationship between anxiety/depression and dual-task decrement suggests that worry may be contributing to dual-task difficulties.

Numerical methods for solar tomography in the STEREO era

In this thesis, we propose several advances in the numerical and computational algorithms that are used to determine tomographic estimates of physical parameters in the solar corona. We focus on methods for both global dynamic estimation of the coronal electron density and estimation of local transient phenomena, such as coronal mass ejections, from empirical observations acquired by instruments onboard the STEREO spacecraft. We present a first look at tomographic reconstructions of the solar corona from multiple points-of-view, which motivates the developments in this thesis. In particular, we propose a method for linear equality constrained state estimation that leads toward more physical global dynamic solar tomography estimates. We also present a formulation of the local static estimation problem, i.e., the tomographic estimation of local events and structures like coronal mass ejections, that couples the tomographic imaging problem to a phase field based level set method. This formulation will render feasible the 3D tomography of coronal mass ejections from limited observations. Finally, we develop a scalable algorithm for ray tracing dense meshes, which allows efficient computation of many of the tomographic projection matrices needed for the applications in this thesis.

SHIFTING SCALES, ADJUSTING LENSES: A FRAMEWORK FOR INVESTIGATING BALTIMORE’S URBAN VACANCY

This thesis addresses contemporary gaps of vacancy within literature by using qualitative and quantitative methods and tools to determine the quantity, location, and interspatial relationships of vacant buildings and lots located in Baltimore Maryland. Spatial analyses were conducted to answer three questions of vacancy: 1) how many vacant lots and buildings exist, 2) whether there are spatial patterns of vacancy, such as clustering around geographic locations or within watersheds, and 3) how to prioritize intervention opportunities that respond to the city's larger issues? Using the city’s vacant lot and building data-sets, two concepts emerged from these investigations. First, Utilized Landscapes as a classification system that identifies lands that serve a function but have un-traditional qualities that make them susceptible to being labeled “vacant.” Second, the development of Transitional Zones, geographical areas with a high density of vacant buildings or lots that should be prioritized.

EXAMINING SECONDARY MATHEMATICS TEACHER CANDIDATES’ LEARNING AND ENACTMENT OF MATHEMATICS TEACHING PRACTICES: A MULTIPLE CASE STUDY

This qualitative case study explored three teacher candidates’ learning and enactment of discourse-focused mathematics teaching practices. Using audio and video recordings of their teaching practice this study aimed to identify the shifts in the way in which the teacher candidates enacted the following discourse practices: elicited and used evidence of student thinking, posed purposeful questions, and facilitated meaningful mathematical discourse. The teacher candidates’ written reflections from their practice-based coursework as well as interviews were examined to see how two mathematics methods courses influenced their learning and enactment of the three discourse focused mathematics teaching practices. These data sources were also used to identify tensions the teacher candidates encountered. All three candidates in the study were able to successfully enact and reflect on these discourse-focused mathematics teaching practices at various time points in their preparation programs. Consistency of use and areas of improvement differed, however, depending on various tensions experienced by each candidate. Access to quality curriculum materials as well as time to formulate and enact thoughtful lesson plans that supported classroom discourse were tensions for these teacher candidates. This study shows that teacher candidates are capable of enacting discourse-focused teaching practices early in their field placements and with the support of practice-based coursework they can analyze and reflect on their practice for improvement. This study also reveals the importance of assisting teacher candidates in accessing rich mathematical tasks and collaborating during lesson planning. More research needs to be explored to identify how specific aspects of the learning cycle impact individual teachers and how this can be used to improve practice-based teacher education courses.

Resilience and the cultural landscape : the case of the Lower Ninth Ward after Hurricane Katrina

Le but de cette recherche est d’évaluer l’importance du paysage culturel dans la résilience des communautés urbaines post-catastrophes. Ce travail se concentre sur le quartier du Lower Ninth Ward dans la ville de La Nouvelle-Orléans (États-Unis) après le passage de l’ouragan Katrina en 2005. Les catastrophes naturelles prennent une envergure et causent des dommages considérables lorsqu’elles touchent des villes. La reconstruction post -désastre est donc très dispendieuse pour les villes et les gouvernements, d’autant que certaines régions sont dévastées au point qu’elles doivent être reconstruites au complet. Cependant, le coût le plus lourd à assumer reste celui en vies humaines et si rebâtir les éléments concrets d’une ville est une tâche difficile à entreprendre, reconstruire une communauté est considérablement plus complexe. Dans le but de comprendre une telle démarche, cette recherche se concentre sur les éléments intangibles, comme l’attachement au lieu et les réseaux sociaux, dont une communauté a besoin pour se reconstituer de façon durable et résiliente. Le concept de résilience est très contesté dans la littérature et plusieurs chercheurs se sont essayés à le mesurer. Cette recherche adopte une perspective critique sur le concept et le revisite d’un point de vue holistique pour mettre en lumière sa complexité. Cette démarche permet de remettre en question l’importance de mesurer un concept finalement en perpétuelle redéfinition dans le temps et selon les échelles géographiques. De plus, en établissant une relation entre résilience et paysage culturel, il a été possible de mieux comprendre la complexité de la résilience. Touchant à plusieurs disciplines (architecture de paysage, urbanisme et sociologie), cette recherche utilise une méthodologie qui reflète son aspect multidisciplinaire : les méthodes mixtes. Ces dernières permettent la collecte de données quantitatives et qualitatives qui produisent une vue globale de la situation post-Katrina à travers le regroupement de recensions statistiques, d’observations de terrain et d’articles de journaux. Parallèlement, des entretiens ont été réalisés avec des résidents du quartier ainsi qu’avec des professionnels pour mieux comprendre les différents points de vue. Cette méthodologie a permis de produire des résultats au niveau du cas d’étude autant qu’au niveau théorique. La recherche valide l’importance de prendre en compte le paysage culturel dans les situations post-catastrophes, (en particulier) dans la mesure où il s’agit d’un élément souvent négligé par les urbanistes et les acteurs locaux. En effet, les éléments constitutifs du paysage culturel tels que l’attachement au lieu et les réseaux sociaux, participent d’un sentiment d'appartenance (« home ») et d’une volonté, pour les résidents, de reconstruire leurs habitations, leur communauté ainsi que leur quartier. Toutefois, il faut reconnaître que ces éléments ne suffisent pas à retrouver ce qu’ils ont perdu. Ainsi, l’étude du paysage culturel permet non seulement de mieux comprendre la complexité de la résilience, mais démontre également que cette dernière est une construction sociale.

Iterated responsive threshold search for the quadratic multiple knapsack problem

International audience

Using a Combination of Phylogenetic Comparative and Paleobotanical Methods to Elucidate Patterns of Lineage Selection in Rosales (Plantae: Anthophyta)

An increasing focus in evolutionary biology is on the interplay between mesoscale ecological and evolutionary processes such as population demographics, habitat tolerance, and especially geographic distribution, as potential drivers responsible for patterns of diversification and extinction over geologic time. However, few studies to date connect organismal processes such as survival and reproduction through mesoscale patterns to long-term macroevolutionary trends. In my dissertation, I investigate how mechanism of seed dispersal, mediated through geographic range size, influences diversification rates in the Rosales (Plantae: Anthophyta). In my first chapter, I validate the phylogenetic comparative methods that I use in my second and third chapters. Available state speciation and extinction (SSE) models assumptions about evolution known to be false through fossil data. I show, however, that as long as net diversification rates remain positive – a condition likely true for the Rosales – these violations of SSE’s assumptions do not cause significantly biased results. With SSE methods validated, my second chapter reconstructs three associations that appear to increase diversification rate for Rosalean genera: (1) herbaceous habit; (2) a three-way interaction combining animal dispersal, high within-genus species richness, and geographic range on multiple continents; (3) a four-way interaction combining woody habit with the other three characteristics of (2). I suggest that the three- and four-way interactions represent colonization ability and resulting extinction resistance in the face of late Cenozoic climate change; however, there are other possibilities as well that I hope to investigate in future research. My third chapter reconstructs the phylogeographic history of the Rosales using both non-fossil-assisted SSE methods as well as fossil-informed traditional phylogeographic analysis. Ancestral state reconstructions indicate that the Rosaceae diversified in North America while the other Rosalean families diversified elsewhere, possibly in Eurasia. SSE is able to successfully identify groups of genera that were likely to have been ancestrally widespread, but has poorer taxonomic resolution than methods that use fossil data. In conclusion, these chapters together suggest several potential causal links between organismal, mesoscale, and geologic scale processes, but further work will be needed to test the hypotheses that I raise here.

Contributions to gait recognition using multiple views

Esta tesis se centra en la identificación de personas a través de la forma de caminar. El problema del reconocimiento del paso ha sido tratado mediante diferentes enfoques, en los dominios 2D y 3D, y usando una o varias vistas. Sin embargo, la dependencia con respecto al punto de vista, y por tanto de la trayectoria del sujeto al caminar sigue siendo aún un problema abierto. Se propone hacer frente al problema de la dependencia con respecto a la trayectoria por medio de reconstrucciones 3D de sujetos caminando. El uso de reconstrucciones varias ventajas que cabe destacar. En primer lugar, permite explotar una mayor cantidad de información en contraste con los métodos que extraen los descriptores de la marcha a partir de imágenes, en el dominio 2D. En segundo lugar, las reconstrucciones 3D pueden ser alineadas a lo largo de la marcha como si el sujeto hubiera caminado en una cinta andadora, proporcionando así una forma de analizar el paso independientemente de la trayectoria seguida. Este trabajo propone tres enfoques para resolver el problema de la dependencia a la vista: 1. Mediante la utilización de reconstrucciones volumétricas alineadas. 2. Mediante el uso de reconstrucciones volumétricas no alineadas. 3. Sin usar reconstrucciones. Se proponen además tres tipos de descriptores. El primero se centra en describir el paso mediante análisis morfológico de los volúmenes 3D alineados. El segundo hace uso del concepto de entropa de la información para describir la dinámica del paso humano. El tercero persigue capturar la dinámica de una forma invariante a rotación, lo cual lo hace especialmente interesante para ser aplicado tanto en trayectorias curvas como rectas, incluyendo cambios de dirección. Estos enfoques han sido probados sobre dos bases de datos públicas. Ambas están especialmente diseñadas para tratar el problema de la dependencia con respecto al punto de vista, y por tanto de la dependencia con respecto a la trayectoria. Los resultados experimentales muestran que para el enfoque basado en reconstrucciones volumétricas alineadas, el descriptor del paso basado en entropa consigue los mejores resultados, en comparación con métodos estrechamente relacionados del Estado del Arte actual. No obstante, el descriptor invariante a rotación consigue una tasa de reconocimiento que supera a los métodos actuales sin requerir la etapa previa de alineamiento de las reconstrucciones 3D.

Noninvasive imaging of three-dimensional micro and nanostructures by topological methods

We present topological derivative and energy based procedures for the imaging of micro and nano structures using one beam of visible light of a single wavelength. Objects with diameters as small as 10 nm can be located and their position tracked with nanometer precision. Multiple objects dis-tributed either on planes perpendicular to the incidence direction or along axial lines in the incidence direction are distinguishable. More precisely, the shape and size of plane sections perpendicular to the incidence direction can be clearly determined, even for asymmetric and nonconvex scatterers. Axial resolution improves as the size of the objects decreases. Initial reconstructions may proceed by gluing together two-dimensional horizontal slices between axial peaks or by locating objects at three-dimensional peaks of topological energies, depending on the effective wavenumber. Below a threshold size, topological derivative based iterative schemes improve initial predictions of the lo-cation, size, and shape of objects by postprocessing fixed measured data. For larger sizes, tracking the peaks of topological energy fields that average information from additional incident light beams seems to be more effective.

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization

Background: Statistical analysis of DNA microarray data provides a valuable diagnostic tool for the investigation of genetic components of diseases. To take advantage of the multitude of available data sets and analysis methods, it is desirable to combine both different algorithms and data from different studies. Applying ensemble learning, consensus clustering and cross-study normalization methods for this purpose in an almost fully automated process and linking different analysis modules together under a single interface would simplify many microarray analysis tasks. Results: We present ArrayMining.net, a web-application for microarray analysis that provides easy access to a wide choice of feature selection, clustering, prediction, gene set analysis and cross-study normalization methods. In contrast to other microarray-related web-tools, multiple algorithms and data sets for an analysis task can be combined using ensemble feature selection, ensemble prediction, consensus clustering and cross-platform data integration. By interlinking different analysis tools in a modular fashion, new exploratory routes become available, e.g. ensemble sample classification using features obtained from a gene set analysis and data from multiple studies. The analysis is further simplified by automatic parameter selection mechanisms and linkage to web tools and databases for functional annotation and literature mining. Conclusion: ArrayMining.net is a free web-application for microarray analysis combining a broad choice of algorithms based on ensemble and consensus methods, using automatic parameter selection and integration with annotation databases.