Advancing Bag-of-visual-words Representations For Lesion Classification In Retinal Images.

Diabetic Retinopathy (DR) is a complication of diabetes that can lead to blindness if not readily discovered. Automated screening algorithms have the potential to improve identification of patients who need further medical attention. However, the identification of lesions must be accurate to be useful for clinical application. The bag-of-visual-words (BoVW) algorithm employs a maximum-margin classifier in a flexible framework that is able to detect the most common DR-related lesions such as microaneurysms, cotton-wool spots and hard exudates. BoVW allows to bypass the need for pre- and post-processing of the retinographic images, as well as the need of specific ad hoc techniques for identification of each type of lesion. An extensive evaluation of the BoVW model, using three large retinograph datasets (DR1, DR2 and Messidor) with different resolution and collected by different healthcare personnel, was performed. The results demonstrate that the BoVW classification approach can identify different lesions within an image without having to utilize different algorithms for each lesion reducing processing time and providing a more flexible diagnostic system. Our BoVW scheme is based on sparse low-level feature detection with a Speeded-Up Robust Features (SURF) local descriptor, and mid-level features based on semi-soft coding with max pooling. The best BoVW representation for retinal image classification was an area under the receiver operating characteristic curve (AUC-ROC) of 97.8% (exudates) and 93.5% (red lesions), applying a cross-dataset validation protocol. To assess the accuracy for detecting cases that require referral within one year, the sparse extraction technique associated with semi-soft coding and max pooling obtained an AUC of 94.2 ± 2.0%, outperforming current methods. Those results indicate that, for retinal image classification tasks in clinical practice, BoVW is equal and, in some instances, surpasses results obtained using dense detection (widely believed to be the best choice in many vision problems) for the low-level descriptors.

Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

BACKGROUND: The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species. RESULTS: We sequenced the complete flagellin gene (flaA) in 18 different species and subspecies of Aeromonas. Sequences ranged in size from 870 (A. allosaccharophila) to 921 nucleotides (A. popoffii). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze flaA sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an omega ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence. CONCLUSION: The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection. REVIEWERS: This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).

Potential vorticity in warm conveyor belt outflow

Warm conveyor belts (WCBs) are the main ascending air masses within extratropical cyclones. They often exhibit strong condensation and precipitation, associated with ascent on large scales or embedded convection. Most of the air outflows into the upper troposphere as part of a ridge. Such ridges are an integral part of Rossby waves propagating along the tropopause and are identified with a negative potential vorticity (PV) anomaly and associated anticyclonic circulation. It has been argued that diabatic modification of PV in WCBs has an important influence on the extent of the ridge, propagation of Rossby waves and weather impacts downstream. Following the coherent ensemble of trajectories defining a WCB, PV is expected to increase with time while below the level of maximum latent heating and then decrease as trajectories ascend above the heating maximum. In models, it is found that the net change is approximately zero, so that the average PV of the WCB outflow is almost equal to the PV of its inflow. Here, the conditions necessary for this evolution are explored analytically using constraints arising from the conservation of circulation. It is argued that the net PV change is insensitive to the details of diabatic processes and the PV maximum midway along a WCB depends primarily on the net diabatic transport of mass from the inflow to the outflow layer. The main effect of diabatic processes within a WCB is to raise the isentropic level of the outflow, rather than to modify PV.

Bases metodológicas para un sistema de apoyo a la selección de especies en la restauración de la vegetación

RESUMEN El apoyo a la selección de especies a la restauración de la vegetación en España en los últimos 40 años se ha basado fundamentalmente en modelos de distribución de especies, también llamados modelos de nicho ecológico, que estiman la probabilidad de presencia de las especies en función de las condiciones del medio físico (clima, suelo, etc.). Con esta tesis se ha intentado contribuir a la mejora de la capacidad predictiva de los modelos introduciendo algunas propuestas metodológicas adaptadas a los datos disponibles actualmente en España y enfocadas al uso de los modelos en la selección de especies. No siempre se dispone de datos a una resolución espacial adecuada para la escala de los proyectos de restauración de la vegetación. Sin embrago es habitual contar con datos de baja resolución espacial para casi todas las especies vegetales presentes en España. Se propone un método de recalibración que actualiza un modelo de regresión logística de baja resolución espacial con una nueva muestra de alta resolución espacial. El método permite obtener predicciones de calidad aceptable con muestras relativamente pequeñas (25 presencias de la especie) frente a las muestras mucho mayores (más de 100 presencias) que requería una estrategia de modelización convencional que no usara el modelo previo. La selección del método estadístico puede influir decisivamente en la capacidad predictiva de los modelos y por esa razón la comparación de métodos ha recibido mucha atención en la última década. Los estudios previos consideraban a la regresión logística como un método inferior a técnicas más modernas como las de máxima entropía. Los resultados de la tesis demuestran que esa diferencia observada se debe a que los modelos de máxima entropía incluyen técnicas de regularización y la versión de la regresión logística usada en las comparaciones no. Una vez incorporada la regularización a la regresión logística usando penalización, las diferencias en cuanto a capacidad predictiva desaparecen. La regresión logística penalizada es, por tanto, una alternativa más para el ajuste de modelos de distribución de especies y está a la altura de los métodos modernos con mejor capacidad predictiva como los de máxima entropía. A menudo, los modelos de distribución de especies no incluyen variables relativas al suelo debido a que no es habitual que se disponga de mediciones directas de sus propiedades físicas o químicas. La incorporación de datos de baja resolución espacial proveniente de mapas de suelo nacionales o continentales podría ser una alternativa. Los resultados de esta tesis sugieren que los modelos de distribución de especies de alta resolución espacial mejoran de forma ligera pero estadísticamente significativa su capacidad predictiva cuando se incorporan variables relativas al suelo procedente de mapas de baja resolución espacial. La validación es una de las etapas fundamentales del desarrollo de cualquier modelo empírico como los modelos de distribución de especies. Lo habitual es validar los modelos evaluando su capacidad predictiva especie a especie, es decir, comparando en un conjunto de localidades la presencia o ausencia observada de la especie con las predicciones del modelo. Este tipo de evaluación no responde a una cuestión clave en la restauración de la vegetación ¿cuales son las n especies más idóneas para el lugar a restaurar? Se ha propuesto un método de evaluación de modelos adaptado a esta cuestión que consiste en estimar la capacidad de un conjunto de modelos para discriminar entre las especies presentes y ausentes de un lugar concreto. El método se ha aplicado con éxito a la validación de 188 modelos de distribución de especies leñosas orientados a la selección de especies para la restauración de la vegetación en España. Las mejoras metodológicas propuestas permiten mejorar la capacidad predictiva de los modelos de distribución de especies aplicados a la selección de especies en la restauración de la vegetación y también permiten ampliar el número de especies para las que se puede contar con un modelo que apoye la toma de decisiones. SUMMARY During the last 40 years, decision support tools for plant species selection in ecological restoration in Spain have been based on species distribution models (also called ecological niche models), that estimate the probability of occurrence of the species as a function of environmental predictors (e.g., climate, soil). In this Thesis some methodological improvements are proposed to contribute to a better predictive performance of such models, given the current data available in Spain and focusing in the application of the models to selection of species for ecological restoration. Fine grained species distribution data are required to train models to be used at the scale of the ecological restoration projects, but this kind of data are not always available for every species. On the other hand, coarse grained data are available for almost every species in Spain. A recalibration method is proposed that updates a coarse grained logistic regression model using a new fine grained updating sample. The method allows obtaining acceptable predictive performance with reasonably small updating sample (25 occurrences of the species), in contrast with the much larger samples (more than 100 occurrences) required for a conventional modeling approach that discards the coarse grained data. The choice of the statistical method may have a dramatic effect on model performance, therefore comparisons of methods have received much interest in the last decade. Previous studies have shown a poorer performance of the logistic regression compared to novel methods like maximum entropy models. The results of this Thesis show that the observed difference is caused by the fact that maximum entropy models include regularization techniques and the versions of logistic regression compared do not. Once regularization has been added to the logistic regression using a penalization procedure, the differences in model performance disappear. Therefore, penalized logistic regression may be considered one of the best performing methods to model species distributions. Usually, species distribution models do not consider soil related predictors because direct measurements of the chemical or physical properties are often lacking. The inclusion of coarse grained soil data from national or continental soil maps could be a reasonable alternative. The results of this Thesis suggest that the performance of the models slightly increase after including soil predictors form coarse grained soil maps. Model validation is a key stage of the development of empirical models, such as species distribution models. The usual way of validating is based on the evaluation of model performance for each species separately, i.e., comparing observed species presences or absence to predicted probabilities in a set of sites. This kind of evaluation is not informative for a common question in ecological restoration projects: which n species are the most suitable for the environment of the site to be restored? A method has been proposed to address this question that estimates the ability of a set of models to discriminate among present and absent species in a evaluation site. The method has been successfully applied to the validation of 188 species distribution models used to support decisions on species selection for ecological restoration in Spain. The proposed methodological approaches improve the predictive performance of the predictive models applied to species selection in ecological restoration and increase the number of species for which a model that supports decisions can be fitted.

Sistemas de diálogo con aplicaciones en Educación

En este proyecto se investigan 3 subáreas de Inteligencia Artificial y sus aplicaciones en contextos educativos. Las 3 áreas son 1) agentes conversacionales automatizados que actúan como instructores virtuales o sistemas de tutoring automatizado, 2) asistentes virtuales que llevan a cabo una tarea dada bajo la instrucción de un aprendiz avanzado, y 3) plataformas de programación de chatbots como una herramienta educativa para enseñar conceptos básicos de ciencias de la computación. La hipótesis de este proyecto es que tanto los tutores como los asistentes conversacionales automatizados deben incluir una representación contextual rica que identifique lo entendido por el aprendiz hasta el momento y ser capaces de realizar inferencias sobre ella para poder guiar mejor su aprendizaje. Los objetivos de este proyecto incluyen el desarrollo de algoritmos de inferencia contextuales apropiados para instructores y asistentes virtuales, el desarrollo de algoritmos para la programación simplificada de chatbots, la evaluación de estos algoritmos en pruebas piloto en escuelas y la realización de un curso online abierto masivo para estudiantes de secundario del programa Conectar Igualdad que quieran aprender sobre Inteligencia Artificial y Ciencias de la Computación. El método a utilizar será la realización de recolección de corpus (interacciones humano-humano de las interacciones tutor-aprendiz), la aplicación de técnicas de procesamiento de lenguaje natural como la generación por selección y la interpretación por clustering y maximum entropy models usando características sintácticas, semánticas y pragmáticas. Se desarrollarán los algoritmos siguiendo una metodología estándar de Ingeniería de Software y se evaluarán en experiencias piloto en escuelas secundarias así como en un curso online abierto y masivo. Además se dictará un curso de capacitación docente para la incorporación de las tecnologías producidas a sus cursos. Como resultado se espera la contribución al área de Inteligencia Artificial con aplicaciones en Educación de algoritmos evaluados empíricamente en entornos educativos reales del nivel medio. Además, se espera contribuir a las metodologías de enseñanza de Ciencias de la Computación en el nivel medio. Este proyecto es relevante a la realidad nacional y mundial de falta de recursos humanos formados en las Ciencias de la Computación y al crecimiento mundial que el área de Inteligencia Artificial en general y de Sistemas de diálogo (o interfaces conversacionales) en particular ha tenido en los últimos años con el crecimiento exponencial de la tecnología en la vida diaria.

Geochemistry and age models of sediments from the Celtic margin

The sedimentary sections of three cores from the Celtic margin provide high-resolution records of the terrigenous fluxes during the last glacial cycle. A total of 21 14C AMS dates allow us to define age models with a resolution better than 100 yr during critical periods such as Heinrich events 1 and 2. Maximum sedimentary fluxes occurred at the Meriadzek Terrace site during the Last Glacial Maximum (LGM). Detailed X-ray imagery of core MD95-2002 from the Meriadzek Terrace shows no sedimentary structures suggestive of either deposition from high-density turbidity currents or significant erosion. Two paroxysmal terrigenous flux episodes have been identified. The first occurred after the deposition of Heinrich event 2 Canadian ice-rafted debris (IRD) and includes IRD from European sources. We suggest that the second represents an episode of deposition from turbid plumes, which precedes IRD deposition associated with Heinrich event 1. At the end of marine isotopic stage 2 (MIS 2) and the beginning of MIS 1 the highest fluxes are recorded on the Whittard Ridge where they correspond to deposition from turbidity current overflows. Canadian icebergs have rafted debris at the Celtic margin during Heinrich events 1, 2, 4 and 5. The high-resolution records of Heinrich events 1 and 2 show that in both cases the arrival of the Canadian icebergs was preceded by a European ice rafting precursor event, which took place about 1-1.5 kyr before. Two rafting episodes of European IRD also occurred immediately after Heinrich event 2 and just before Heinrich event 1. The terrigenous fluxes recorded in core MD95-2002 during the LGM are the highest reported at hemipelagic sites from the northwestern European margin. The magnitude of the Canadian IRD fluxes at Meriadzek Terrace is similar to those from oceanic sites.

FORAMINIFERAL RECORD OF CHANGES IN SUMMER MONSOON PRECIPITATION AT THE SOUTHEASTERN BRAZILIAN CONTINENTAL MARGIN SINCE THE LAST GLACIAL MAXIMUM

Changes in the oxygen isotopic composition of the planktonic foraminifer Globigerinoides ruber and in the foraminifera faunal composition in a core retrieved from the southeastern Brazilian continental margin were used to infer past changes in the hydrological balance and monsoon precipitation in the western South Atlantic since the Last Glacial Maximum (LGM). The results suggest a first-order orbital (precessional) control on the South American Monsoon precipitation. This agrees with previous studies based on continental proxies except for LGM estimates provided by pollen records. The causes for this disagreement are discussed.

Depositional models of lacustrine evaporites in the SE margin of the Ebro basin (Paleogene, NE Spain)

An important evaporitic sedimentation occurred during the Paleogene (Eocene to lower Oligocene) in the Barberà sector of the southeastern margin of the Tertiary Ebro Basin. This sedimentation took place in shallow lacustrine environments and was controlled by a number of factors: 1) the tectonic structuration of the margin; 2) the high calcium sulphate content in the meteoric waters coming from the marginal reliefs; 3) the semiarid climate; and 4) the development of large alluvial fans along the basin margin, which also conditioned the location of the saline lakes. The evaporites are currently composed of secondary gypsum in surface and anhydrite at depth. There are, however, vestiges of the local presence of sodium sulphates. The evaporite units, with individual thicknesses ranging between 50 and 100 m, are intercalated within various lithostratigraphic formations and exhibit a paleogeographical pattern. The units located closer to the basin margin are characterized by a massive gypsum lithofacies (originally, bioturbated gypsum) bearing chert, and also by meganodular gypsum locally (originally, meganodules of anhydrite) in association with red lutites and clastic intercalations (gypsarenites, sandstones and conglomerates). Chert, which is only linked to the thickest gypsum layers, seems to be an early diagenetic, lacustrine product. Cyclicity in these proximal units indicates the progressive development of lowsalinity, lacustrine bodies on red mud flats. At the top of some cycles, exposure episodes commonly resulted in dissolution, erosion, and the formation of edaphic features. In contrast, the units located in a more distal position with regard to the basin margin are formed by an alternation of banded-nodular gypsum and laminated gypsum layers in association with grey lutites and few clastic intercalations. These distal units formed in saline lakes with a higher ionic concentration. Exposure episodes in these lakes resulted in the formation of synsedimentary anhydrite and sabkha cycles. In some of these units, however, outer rims characterized by a lithofacies association similar to that of the proximal units occur (nodular gypsum, massive gypsum and chert nodules).

Bode's maximum available feedback and phase margin

'Maximum Available Feedback' is Bode's term for the highest possible loop gain over a given bandwidth, with specified stability margins, in a single loop feedback system. His work using asymptotic analysis allowed Bode to develop a methodology for achieving this. However, the actual system performance differs from that specified, due to the use of asymptotic approximations, and the author[2] has described how, for instance, the actual phase margin is often much lower than required when the bandwidth is high, and proposed novel modifications to the asymptotes to address the issue. This paper gives some new analysis of such systems, showing that the method also contravenes Bode's definition of phase margin, and shows how the author's modifications can be used for different amounts of bandwidth.

Lower intercanine width and gingival margin changes. A retrospective study.

OBJECTIVE: To determine if changes in the lower intercanine widths during orthodontic treatment with fixed appliances result in gingival margin changes around the lower canines and incisors. METHOD: Pre- and post-treatment intra-oral photographs and orthodontic study models of 178 Caucasian adolescents (101 female, 77 male) were used. All subjects were treated with fixed appliances. The subjects had mean ages of 11.41 (SD: 1.83) years and 14.91 (SD: 1.78) years on their initial and final records respectively. The latter were taken 28 days or more after the appliances had been removed. The inclusion criteria were: Angle Class I or Class II malocclusion (with or without transverse and/or vertical discrepancies); nonextraction treatment; less than 4 mm crowding or spacing; fully erupted lower incisors and good periodontal health. The intercanine widths and the positions of the gingival margins relative to the maximum curvatures of the labial surfaces of the lower canines and incisors were measured with digital calipers. RESULTS: A significant association was found between unaltered intercanine widths and coronal migration of the gingival margins (p = 0.045). There were no significant associations between either increased or reduced intercanine widths and changes in the gingival margins. CONCLUSIONS: Following orthodontic treatment coronal migration of the gingival margins around the lower incisors and canines is more likely to be associated with an unaltered intercanine width.

Age models of ODP sites from the Barents Sea-Svalbard region

Based on a revised chronostratigraphy, and compilation of borehole data from the Barents Sea continental margin, a coherent glaciation model is proposed for the Barents Sea ice sheet over the past 3.5 million years (Ma). Three phases of ice growth are suggested: (1) The initial build-up phase, covering mountainous regions and reaching the coastline/shelf edge in the northern Barents Sea during short-term glacial intensification, is concomitant with the onset of the Northern Hemisphere Glaciation (3.6-2.4 Ma). (2) A transitional growth phase (2.4-1.0 Ma), during which the ice sheet expanded towards the southern Barents Sea and reached the northwestern Kara Sea. This is inferred from step-wise decrease of Siberian river-supplied smectite-rich sediments, likely caused by ice sheet blockade and possibly reduced sea ice formation in the Kara Sea as well as glacigenic wedge growth along the northwestern Barents Sea margin hampering entrainment and transport of sea ice sediments to the Arctic-Atlantic gateway. (3) Finally, large-scale glaciation in the Barents Sea occurred after 1 Ma with repeated advances to the shelf edge. The timing is inferred from ice grounding on the Yermak Plateau at about 0.95 Ma, and higher frequencies of gravity-driven mass movements along the western Barents Sea margin associated with expansive glacial growth.