Discovering visual concept structure with sparse and incomplete tags

This work was partially supported by the China Scholarship Council, Vision Semantics Limited, and Royal Society Newton Advanced Fellowship Programme (NA150459)

Understanding the Structural and Functional Importance of Early Folding Residues in Protein Structures

Proteins adopt three-dimensional structures which serve as a starting point to understand protein function and their evolutionary ancestry. It is unclear how proteins fold in vivo and how this process can be recreated in silico in order to predict protein structure from sequence. Contact maps are a possibility to describe whether two residues are in spatial proximity and structures can be derived from this simplified representation. Coevolution or supervised machine learning techniques can compute contact maps from sequence: however, these approaches only predict sparse subsets of the actual contact map. It is shown that the composition of these subsets substantially influences the achievable reconstruction quality because most information in a contact map is redundant. No strategy was proposed which identifies unique contacts for which no redundant backup exists. The StructureDistiller algorithm quantifies the structural relevance of individual contacts and identifies crucial contacts in protein structures. It is demonstrated that using this information the reconstruction performance on a sparse subset of a contact map is increased by 0.4 A, which constitutes a substantial performance gain. The set of the most relevant contacts in a map is also more resilient to false positively predicted contacts: up to 6% of false positives are compensated before reconstruction quality matches a naive selection of contacts without any false positive contacts. This information is invaluable for the training to new structure prediction methods and provides insights into how robustness and information content of contact maps can be improved. In literature, the relevance of two types of residues for in vivo folding has been described. Early folding residues initiate the folding process, whereas highly stable residues prevent spontaneous unfolding events. The structural relevance score proposed by this thesis is employed to characterize both types of residues. Early folding residues form pivotal secondary structure elements, but their structural relevance is average. In contrast, highly stable residues exhibit significantly increased structural relevance. This implies that residues crucial for the folding process are not relevant for structural integrity and vice versa. The position of early folding residues is preserved over the course of evolution as demonstrated for two ancient regions shared by all aminoacyl-tRNA synthetases. One arrangement of folding initiation sites resembles an ancient and widely distributed structural packing motif and captures how reverberations of the earliest periods of life can still be observed in contemporary protein structures

Analisis orientado a objetos de imágenes de teledetección para cartografia forestal : bases conceptuales y un metodo de segmentacion para obtener una particion inicial para la clasificacion = Object-oriented analysis of remote sensing images for land cover mapping : Conceptual foundations and a segmentation method to derive a baseline partition for classification

El enfoque comúnmente usado para analizar las imágenes de satélite con fines cartográficos da lugar a resultados insatisfactorios debido principalmente a que únicamente utiliza los patrones espectrales de los píxeles, ignorando casi por completo la estructura espacial de la imagen. Además, la equiparación de las clases de cubierta a tipos de materiales homogéneos permite que cualquier parte arbitrariamente delimitada dentro de una tesela del mapa siga siendo un referente del concepto definido por su etiqueta. Esta posibilidad es incongruente con el modelo jerárquico del paisaje cada vez más aceptado en Ecología del Paisaje, que asume que la homogeneidad depende de la escala de observación y en cualquier caso es más semántica que biofísica, y que por tanto los paisajes son intrínsecamente heterogéneos y están compuestos de unidades (patches) que funcionan simultáneamente como un todo diferente de lo que les rodea y como partes de un todo mayor. Por tanto se hace necesario un nuevo enfoque (orientado a objetos) que sea compatible con este modelo y en el que las unidades básicas del análisis sean delimitadas de acuerdo a la variación espacial del fenómeno estudiado. Esta tesis pretende contribuir a este cambio de paradigma en teledetección, y sus objetivos concretos son: 1.- Poner de relieve las deficiencias del enfoque tradicionalmente empleado en la clasificación de imágenes de satélite. 2.- Sentar las bases conceptuales de un enfoque alternativo basado en zonas básicas clasificables como objetos. 3.- Desarrollar e implementar una versión demostrativa de un método automático que convierte una imagen multiespectral en una capa vectorial formada por esas zonas. La estrategia que se propone es producir, basándose en la estructura espacial de las imágenes, una partición de estas en la que cada región puede considerarse relativamente homogénea y diferente de sus vecinas y que además supera (aunque no por mucho) el tamaño de la unidad mínima cartografiable. Cada región se asume corresponde a un rodal que tras la clasificación será agregado junto a otros rodales vecinos en una región mayor que en conjunto pueda verse como una instancia de un cierto tipo de objetos que más tarde son representados en el mapa mediante teselas de una clase particular

Walking Back the System Trope: Reimagining Incarceration and the State Through a Spatial Theory Approach

This dissertation critiques the systems theory approach to incarceration policy, practice, and research and proposes a rhetorically informed spatial theory approach as an alternative. Offering a non-hierarchical complexity theory as a bridge between systems and space, I then integrate rhetorical listening as a strategy for navigating and operationalizing our proposed spatial theory approach. I then apply our proposed methodology to archival research, focusing on the South Carolina Penitentiary as a case study, and offer two heuretic experiments to explore the range of this methodology for archival research. I also explore potential applications of this rhetorically informed spatial theory approach in terms of civic engagement among incarcerated populations through deliberative democracy theory. Finally, I conclude that this methodology offers an avenue for elaborating the ambiguity in myriad social organizational practices that are conceived in terms of systems, crucial insights into uses of complexity in contemporary rhetorical studies, and a valuable approach for argument analysis and civic engagement in composition classrooms

Association of Protein Helices and Assembly of Foldamers: Stories in Membrane and Aqueous Environments

Solvents play an important role in association and assembly of molecules. Here we studied solvent effects on proteins and organic chemicals in different contexts. First, X-ray crystal structures show that helix dimers in membrane- and water-soluble proteins have distinct behaviors in packing and sequence selection. Transmembrane dimers are stabilized by compact packing and hydrogen bonding between small residues. Meanwhile, water-soluble dimers utilize hydrophobic residues for packing irrespective of the size of the interface and tight dimers are rare. Secondly, we apply the results learned above to a complex system in which a designed protein binds to single-walled carbon-nanotube in aqueous environments. Previous designs of the hexameric helical bundles utilized leucine and alanine residues to make two distinct helix-helix interfaces. Our molecular dynamics simulations showed that the alanine-comprising interface is much more labile than the leucine-comprising one. This result can be interpreted by the scarcity of tight soluble helix dimers as mentioned above. Thus more stable modular helix-helix interfaces have to be employed to design peptides binding to carbon-nanotubes with higher affinities. Lastly, we describe a serendipitous discovery of the crystalline framework structure by an amphiphilic triarylamide foldamer. Foldamers are peptide-like polymers of non-natural monomers arranged in defined sequence and chain length that are able to adopt protein-like secondary and tertiary structures. In contrast with traditional metal-organic and organic frameworks, which exploit strong directional coordination and hydrogen bonding for assembly in organic solvents, the crystal herein is built up from a combination of noncovalent hydrophobic, hydrogen-bonded, and electrostatic interactions in aqueous solution. The structure is in honeycomb geometry with each cubicle as a truncated octahedron. A new supramolecular synthon, in which hydrogen bonding and π-π stacking are encompassed, was discovered in the crystal structure. Through NMR experiments we probed the oligomeric states of the foldamer in the early stages prior to crystallization. The hierarchic crystal structure was discussed in terms of supramolecular synthons in crystal engineering

Recognition and Early Stage Detection of <em>Phytophthora</em> in a Crop Farm Using IoT

Detection of agricultural plant pests is seen as one of the farmers’ problems. Automated Pest Detection Machine enables early detection of crop insects with advanced computer vision and image recognition. Innovative research in the field of agriculture has demonstrated a new direction by Internet of Things (IoT). IoT needs to be widely experienced at the early stage, so that it is widely used in different farming applications. It allows farmers increase their crop yield with reduced time and greater precision. For the past decade, climate change and precipitation have been unpredictable. Due to this, many Indian farmers are adopting smart methods for environment known as intelligent farming. Smart farming is an automated and IOT-based information technology (Internet of Things). In all wireless environments IOT is developing quickly and widely. The Internet of Things helps to monitor agricultural crops and thus quickly and effectively increase farmers’ income. This paper presents a literature review on IoT devices for recognizing and detecting insects in crop fields. Different types of framework/models are present which are explaining the procedure of insect detection

Modeling Habitat Attributes of Cavity-Nesting Birds in the Uinta Mountains, Utah: A Hierarchical Approach

Birds may have the ability to view their environments at a wide range of spatial scales; accordingly, they may make habitat-selection decisions at multiple spatial scales. I investigated the implications of hierarchy theory and a landscape perspective on nestsite selection in cavity-nesting birds in the Uinta Mountains in northeastern Utah. I used · three different approaches to address the concept of a multi-scaled nest-site selection Ill process. First, I conducted an exploratory study in which I investigated nest-site selection at three spatial scales for Red-naped Sapsucker (Sphyrapicus nuchalis), Northern Flicker (Colaptes auratus), Tree Swallow (Tachycineta bicolor), and Mountain Chickadee (Parus gambeli). By conducting a hierarchically structured analysis, I was able to investigate the habitat relationships that might result from a hierarchically organized nest site selection process . I found that the four species were associated with patterns of vegetation at three spatial scales and that these associations combined in such a way as to imply a process of nest-site selection that may be more complex than that posited by the niche-gestalt concept. Second, I conducted an experiment in which I investigated nest-site selection at two spatial scales. I compared the use of four types of aspen stands in a two-by-two factorial design according to within-stand structure and landscape context. Stands were classified as either dense or sparse and as having predominantly meadow or forested edges. To address nest-site selection by secondary cavity nesters , who may be limited by cavity availability, I augmented the natural cavities with nest boxes. I found that birds predominantly nested in sparse stands and in stands with meadow edges. Although only five nest boxes were used for nesting, all five of these boxes were in sparse stands with meadow edges. The third way in which I investigated the process of nest-site selection was to build and test predictive models using associations between birds and landscape patterns. By using landscape patterns to predict habitat, I was able to build models that were easily applied ; predictions could be made without any additional data collection in the field. The models were very accurate for both Red-naped Sapsuckers and Tree Swallows (86- 98% and 53-93% nests correctly predicted, respectively) but were less accurate for Mountain Chickadees and Northern Flickers (33-42% and 19-37%, respectively)

MATLAB

A well-known statement says that the PID controller is the "bread and butter" of the control engineer. This is indeed true, from a scientific standpoint. However, nowadays, in the era of computer science, when the paper and pencil have been replaced by the keyboard and the display of computers, one may equally say that MATLAB is the "bread" in the above statement. MATLAB has became a de facto tool for the modern system engineer. This book is written for both engineering students, as well as for practicing engineers. The wide range of applications in which MATLAB is the working framework, shows that it is a powerful, comprehensive and easy-to-use environment for performing technical computations. The book includes various excellent applications in which MATLAB is employed: from pure algebraic computations to data acquisition in real-life experiments, from control strategies to image processing algorithms, from graphical user interface design for educational purposes to Simulink embedded systems

Homes of Healing: The Medical Utilisation of British Country Houses in the Second World War. A Spatial History of Alternative Spaces

This thesis focuses on the history of Britain's stately homes and country houses during the Second World War. It will explore the ways these historic properties shaped the wartime experiences of those who lived, worked, and recovered within and how the transitional nature of the space resulted in divergent identities forming around the properties' popular representation. It builds upon the scholarly research of Peter Mandler and Adrian Tinniswood and attempts to rectify the often overlooked and underappreciated contribution of country houses to the provision of medical care and to the wider war effort. The thesis will understand the wartime representation of the properties in accordance with the interwar attitudes towards the city and the countryside. It examines the ways in which the idealisation of rurality impacted the popular representation of the auxiliary hospital and convalescent home. Furthermore, it will explore the way new and existing identities shaped the relationships that developed between aristocratic homeowners, medical personnel, and military patients. Ultimately, it will argue that the military-medico utilisation of country houses during the Second World War added new layers of cultural meaning to what were already palimpsest-like spaces. The thesis will consult an array of sources from a variety of repositories. Firstly, it will draw on the lived experience of patients, staff and homeowners through their diaries, letters, and memoirs. Secondly, it will explore the representational value and understanding of these institutions and their occupants through an analysis of local and national newspapers as well as popular periodicals and magazines. Finally, it will consult with parliamentary records and medical journals to provide essential context to the changes being made to these historic monuments

Development of a R package to facilitate the learning of clustering techniques

This project explores the development of a tool, in the form of a R package, to ease the process of learning clustering techniques, how they work and what their pros and cons are. This tool should provide implementations for several different clustering techniques with explanations in order to allow the student to get familiar with the characteristics of each algorithm by testing them against several different datasets while deepening their understanding of them through the explanations. Additionally, these explanations should adapt to the input data, making the tool not only adept for self-regulated learning but for teaching too.Grado en Ingeniería Informátic