Modelling ecological niches with support vector machines

1. The ecological niche is a fundamental biological concept. Modelling species' niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species' ranges. 2. A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species' environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. 3. We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. 4. Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species' potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.

Continuous Quality Improvement Snow Plow Accident Study Report, 1995

Identify processes to modify in order to reduce snow plow accidents. Reviewed all [Iowa] D.O.T. snow plow accidents that occurred in calendar years 1992 and 1993.

Implementation of a Pilot Continuous Monitoring System: Iowa Falls Arch Bridge, HR-1088, 2015

The goal of this work was to move structural health monitoring (SHM) one step closer to being ready for mainstream use by the Iowa Department of Transportation (DOT) Office of Bridges and Structures. To meet this goal, the objective of this project was to implement a pilot multi-sensor continuous monitoring system on the Iowa Falls Arch Bridge such that autonomous data analysis, storage, and retrieval can be demonstrated. The challenge with this work was to develop the open channels for communication, coordination, and cooperation of various Iowa DOT offices that could make use of the data. In a way, the end product was to be something akin to a control system that would allow for real-time evaluation of the operational condition of a monitored bridge. Development and finalization of general hardware and software components for a bridge SHM system were investigated and completed. This development and finalization was framed around the demonstration installation on the Iowa Falls Arch Bridge. The hardware system focused on using off-the-shelf sensors that could be read in either “fast” or “slow” modes depending on the desired monitoring metric. As hoped, the installed system operated with very few problems. In terms of communications—in part due to the anticipated installation on the I-74 bridge over the Mississippi River—a hardline digital subscriber line (DSL) internet connection and grid power were used. During operation, this system would transmit data to a central server location where the data would be processed and then archived for future retrieval and use. The pilot monitoring system was developed for general performance evaluation purposes (construction, structural, environmental, etc.) such that it could be easily adapted to the Iowa DOT’s bridges and other monitoring needs. The system was developed allowing easy access to near real-time data in a format usable to Iowa DOT engineers.

Active deformation fields: dense deformation field estimation for atlas-based segmentation using the active contour framework.

This paper presents a new and original variational framework for atlas-based segmentation. The proposed framework integrates both the active contour framework, and the dense deformation fields of optical flow framework. This framework is quite general and encompasses many of the state-of-the-art atlas-based segmentation methods. It also allows to perform the registration of atlas and target images based on only selected structures of interest. The versatility and potentiality of the proposed framework are demonstrated by presenting three diverse applications: In the first application, we show how the proposed framework can be used to simulate the growth of inconsistent structures like a tumor in an atlas. In the second application, we estimate the position of nonvisible brain structures based on the surrounding structures and validate the results by comparing with other methods. In the final application, we present the segmentation of lymph nodes in the Head and Neck CT images, and demonstrate how multiple registration forces can be used in this framework in an hierarchical manner.

Continuous monitoring and quantification of multiple parameters of daily physical activity in ambulatory Duchenne muscular dystrophy patients.

Multiple motor function and strength assessment tools exist for the evaluation of neuromuscular diseases, but most do not directly assess functional ability in the patients' daily physical activity in their home environment. In this study our aim was to assess: 1) the feasibility and accuracy of physical activity monitoring during two days in a home environment of five DMD patients using a non-commercialized monitor containing a 3D accelerometer and a gyroscope, 2) if a difference in the physical activity parameters could be measured before and one month after starting prednisolone. We reliably quantified the time spend sitting, standing, lying, walking, the number of steps taken, the cadence, the number of walking episodes and their duration as well as how these were distributed over the day. Parameters possibly reflecting endurance, such as the duration of the walking episodes or the succession of two or three walking episodes lasting more than 30 s were the most improved after prednisolone treatment. This degree of detailed determination of physical activity in a home environment has not been previously reported in neuromuscular disorders to our knowledge and some of the reported parameters are potential new outcome measures in clinical trials.

Classification of very high spatial resolution imagery using mathematical morphology and support vector machines

We investigate the relevance of morphological operators for the classification of land use in urban scenes using submetric panchromatic imagery. A support vector machine is used for the classification. Six types of filters have been employed: opening and closing, opening and closing by reconstruction, and opening and closing top hat. The type and scale of the filters are discussed, and a feature selection algorithm called recursive feature elimination is applied to decrease the dimensionality of the input data. The analysis performed on two QuickBird panchromatic images showed that simple opening and closing operators are the most relevant for classification at such a high spatial resolution. Moreover, mixed sets combining simple and reconstruction filters provided the best performance. Tests performed on both images, having areas characterized by different architectural styles, yielded similar results for both feature selection and classification accuracy, suggesting the generalization of the feature sets highlighted.

Lentiviral vector-mediated gene transfer in adult mouse photoreceptors is impaired by the presence of a physical barrier

RESUME L'utilisation de la thérapie génique dans l'approche d'un traitement des maladies oculaires dégénératives, plus particulièrement de la rétinite pigmentaire, semble être très prometteuse (Acland et al. 2001). Parmi les vecteurs développés, les vecteurs lentiviraux (dérivé du virus humain HIV-1), permettent la transduction des photorécepteurs après injection sous-rétinienne chez la souris durant les premiers jours de vie. Cependant l'efficacité du transfert de gène est nettement plus limitée dans ce type cellulaire après injection chez l'adulte (Kostic et al. 2003). L'objet de notre étude est de déterminer si la présence d'une barrière physique produite au cours du développement, située entre les photorécepteurs et l'épithélium pigmentaire ainsi qu'entre les photorécepteurs eux-mêmes, est responsable de: la diminution de l'entrée en masse du virus dans les photorécepteurs, minimisant ainsi son efficacité chez la souris adulte. De précédentes recherches, chez le lapin, ont décrit la capacité d'enzymes spécifiques comme la Chondroïtinase ABC et la Neuraminidase X de modifier la structure de la matrice entourant les photorécepteurs (Inter Photoreceptor Matrix, IPM) par digestion de certains de ses constituants suite à leur injection dans l'espace sous-rétinien (Yao et al. 1990). Considérant l'IPM comme une barrière physique, capable de réduire l'efficacité de transduction des photorécepteurs chez la souris adulte, nous avons associé différentes enzymes simultanément à l'injection sous-rétinienne de vecteurs lentiviraux afin d'améliorer la transduction virale en fragilisant I'IPM, la rendant ainsi plus perméable à la diffusion du virus. L'injection sous-rétinienne de Neuraminidase X et de Chondroïtinase ABC chez la souris induit des modifications structurales de l'IPM qui se manifestent respectivement par la révélation ou la disparition de sites de liaison de la peanut agglutinin sur les photorécepteurs. L'injection simultanée de Neuraminidase X avec le vecteur viral contenant le transgène thérapeutique augmente significativement le nombre de photorécepteurs transduits (environ cinq fois). Nous avons en fait démontré que le traitement enzymatique augmente principalement la diffusion du lentivirus dans l'espace situé entre l'épithélium pigmentaire et les photorécepteurs. Le traitement à la Chondroïtinase ABC n'entraîne quant à elle qu'une légère amélioration non significative de la transduction. Cette étude montre qu'une meilleure connaissance de l'IPM ainsi que des substances capables de la modifier (enzymes, drogues etc.) pourrait aider à élaborer de nouvelles stratégies afin d'améliorer la distribution de vecteurs viraux dans la rétine adulte.

Nocturnal hypoglycaemias in type 1 diabetic patients : what can we learn with continuous glucose monitoring ?

Rapport de synthèse : Hypoglycémies nocturnes chez les patients diabétiques de type 1 : que pouvons-nous apprendre de la mesure de la glycémie en continu ? But : les hypoglycémies nocturnes sont une complication majeure du traitement des patients diabétiques de type 1; des autocontrôles de la glycémie capillaire sont donc recommandés pour les détecter. Cependant, la majorité des hypoglycémies nocturnes ne sont pas décelées par un autocontrôle glycémique durant la nuit. La mesure de la glycémie en continu (CGMS) est une alternative intéressante. Les buts de cette étude rétrospective étaient d'évaluer la véritable incidence des hypoglycémies nocturnes chez des patients diabétiques de type 1, la meilleure période pour effectuer un autocontrôle permettant de prédire une hypoglycémie nocturne, la relation entre les hyperglycémies matinales et les hypoglycémies nocturnes (phénomène de Somogyi) ainsi que l'utilité du CGMS pour réduire les hypoglycémies nocturnes. Méthode : quatre-vingt-huit patients diabétiques de type 1 qui avaient bénéficié d'un CGMS ont été inclus. Les indications au CGMS, les hypoglycémies nocturnes et diurnes ainsi que la corrélation entre les hypoglycémies nocturnes et les hyperglycémies matinales durant le CGMS ont été enregistrées. L'efficacité du CGMS pour réduire les hypoglycémies nocturnes a été évaluée six à neuf mois après. Résultats : la prévalence des hypoglycémies nocturnes était de 67% (32% non suspectées). La sensibilité d'une hypoglycémie à prédire une hypoglycémie nocturne était de 37% (OR = 2,37, P = 0,001) lorsqu'elle survient au coucher (22-24 h) et de 43% lorsqu'elle survient à 3 h (OR = 4,60, P < 0,001). Les hypoglycémies nocturnes n'étaient pas associées à des hyperglycémies matinales, mais à des hypoglycémies matinales (OR = 3.95, P < 0.001). Six à neuf mois après le CGMS, les suspicions cliniques d'hypoglycémies nocturnes ont diminué de 60% à 14% (P < 0.001). Abstract : Aim. - In type 1 diabetic patients (TIDM), nocturnal hypoglycaemias (Nlï) are a serious complication of T1DM treatment; self-monitoring of blood glucose (SMBG) is recommended to detect them. However, the majority of NH remains undetected on an occasional SMBG done during the night. An alternative strategy is the Continuous glucose monitoring (CGMS), which retrospectively shows the glycaemic profile. The aims of this retrospective study were to evaluate the true incidence of NH in TiDM, the bèst SMBG time to predict NH, the relationship between morning hyperglycaemia and N$ (Somogyi phenomenon) and the utility of CGMS to reduce NH. Methods. -Eighty-eight T1DM who underwent a CGMS exam were included. Indications for CGMS evaluarion, hypoglycaemias and correlation with morning hyperglycaemias were recorded. The efficiency of CGMS to reduce the suspected NH was evaluated after 6-9 months. Results. -The prevalence of NH was 67% (32% of them unsuspected). A measured hypoglycaemia at bedtime (22-24 h) had a sensitivity of 37% to detect NH (OR = 2.37, P = 0.001), while a single measure <_ 4 mmol/l at 3-hour had a sensitivity of 43% (OR = 4.60, P < 0.001). NH were not associated with morning hyperglycaemias but with morning hypoglycaemias (OR = 3.95, P < 0.001). After 6-9 months, suspicions of NH decreased from 60 to 14% (P < 0.001). Conclusion. - NH were highly prevalent and often undetected. SMBG at bedtime, which detected hypoglycaemia had sensitivity almost equal to that of 3-hour and should be preferred because it is easier to perform. Somogyi phenomenon was not observed. CGMS is useful to reduce the risk of NH in 75% of patients.

Avalanche-like vortex penetration driven by pulsed microwave fields in an epitaxial LaSrCuO thin film

Different vortex penetration regimes have been registered in the output voltage signal of a magnetometer when single microwave pulses are applied to an epitaxial overdoped La2− x Sr x CuO4 thin film in a perpendicular dc magnetic field. The onset of a significant variation in the sample magnetization which exists below threshold values of temperature, dc magnetic field, and pulse duration is interpreted as an avalanche-type flux penetration. The microwave contribution to the background electric field suggests that the nucleation of this fast vortex motion is of electric origin, which also guarantees the occurrence of vortex instabilities under adiabatic conditions via the enhancement of the flux flow resistivity. Flux creep phenomena and heat transfer effects act as stabilizing factors against the microwave-pulse-induced fast flux diffusion.

Childhood epilepsy with neuropsychological regression and continuous spike waves during sleep: epilepsy surgery in a young adult.

We describe the case of a man with a history of complex partial seizures and severe language, cognitive and behavioural regression during early childhood (3.5 years), who underwent epilepsy surgery at the age of 25 years. His early epilepsy had clinical and electroencephalogram features of the syndromes of epilepsy with continuous spike waves during sleep and acquired epileptic aphasia (Landau-Kleffner syndrome), which we considered initially to be of idiopathic origin. Seizures recurred at 19 years and presurgical investigations at 25 years showed a lateral frontal epileptic focus with spread to Broca's area and the frontal orbital regions. Histopathology revealed a focal cortical dysplasia, not visible on magnetic resonance imaging. The prolonged but reversible early regression and the residual neuropsychological disorders during adulthood were probably the result of an active left frontal epilepsy, which interfered with language and behaviour during development. Our findings raise the question of the role of focal cortical dysplasia as an aetiology in the syndromes of epilepsy with continuous spike waves during sleep and acquired epileptic aphasia.

Remote Continuous Evaluation of a Bridge Constructed Using High-Performance Steel, 2006

Of the approximately 25,000 bridges in Iowa, 28% are classified as structurally deficient, functionally obsolete, or both. The state of Iowa thus follows the national trend of an aging infrastructure in dire need of repair or replacement with a relatively limited funding base. Therefore, there is a need to develop new materials with properties that may lead to longer life spans and reduced life-cycle costs. In addition, new methods for determining the condition of structures are needed to monitor the structures effectively and identify when the useful life of the structure has expired or other maintenance is needed. High-performance steel (HPS) has emerged as a material with enhanced weldability, weathering capabilities, and fracture toughness compared to conventional structural steels. In 2004, the Iowa Department of Transportation opened Iowa's first HPS girder bridge, the East 12th Street Bridge over I-235 in Des Moines, Iowa. The objective of this project was to evaluate HPS as a viable option for use in Iowa bridges with a continuous structural health monitoring (SHM) system. The scope of the project included documenting the construction of the East 12th Street Bridge and concurrently developing a remote, continuous SHM system using fiber-optic sensing technology to evaluate the structural performance of the bridge. The SHM system included bridge evaluation parameters, similar to design parameters used by bridge engineers, for evaluating the structure. Through the successful completion of this project, a baseline of bridge performance was established that can be used for continued long-term monitoring of the structure. In general, the structural performance of the HPS bridge exceeded the design parameters and is performing well. Although some problems were encountered with the SHM system, the system functions well and recommendations for improving the system have been made.

A new disruption vector (pDHO) to obtain heterothallic strains from both Saccharomyces cerevisiae and Saccharomyces pastorianus

Yeasts are responsible for several traits in fermented beverages, including wine and beer, and their genetic manipulation is often necessary to improve the quality of the fermentation product. Improvement of wild-type strains of Saccharomyces cerevisiae and Saccharomyces pastorianus is difficult due to their homothallic character and variable ploidy level. Homothallism is determined by the HO gene in S. cerevisiae and the Sc-HO gene in S. pastorianus. In this work, we describe the construction of an HO disruption vector (pDHO) containing an HO disruption cassette and discuss its use in generating heterothallic yeast strains from homothallic Saccharomyces species.