Bio-inspired log-polar based color image pattern analysis in multiple frequency channels

The main topic addressed in this thesis is to implement color image pattern recognition based on the lateral inhibition subtraction phenomenon combined with a complex log-polar mapping in multiple spatial frequency channels. It is shown that the individual red, green and blue channels have different recognition performances when put in the context of former work done by Dragan Vidacic. It is observed that the green channel performs better than the other two channels, with the blue channel having the poorest performance. Following the application of a contrast stretching function the object recognition performance is improved in all channels. Multiple spatial frequency filters were designed to simulate the filtering channels that occur in the human visual system. Following these preprocessing steps Dragan Vidacic\u27s methodology is followed in order to determine the benefits that are obtained from the preprocessing steps being investigated. It is shown that performance gains are realized by using such preprocessing steps

Macroservers: An Execution Model for DRAM Processor-In-Memory Arrays

The emergence of semiconductor fabrication technology allowing a tight coupling between high-density DRAM and CMOS logic on the same chip has led to the important new class of Processor-In-Memory (PIM) architectures. Newer developments provide powerful parallel processing capabilities on the chip, exploiting the facility to load wide words in single memory accesses and supporting complex address manipulations in the memory. Furthermore, large arrays of PIMs can be arranged into a massively parallel architecture. In this report, we describe an object-based programming model based on the notion of a macroserver. Macroservers encapsulate a set of variables and methods; threads, spawned by the activation of methods, operate asynchronously on the variables' state space. Data distributions provide a mechanism for mapping large data structures across the memory region of a macroserver, while work distributions allow explicit control of bindings between threads and data. Both data and work distributuions are first-class objects of the model, supporting the dynamic management of data and threads in memory. This offers the flexibility required for fully exploiting the processing power and memory bandwidth of a PIM array, in particular for irregular and adaptive applications. Thread synchronization is based on atomic methods, condition variables, and futures. A special type of lightweight macroserver allows the formulation of flexible scheduling strategies for the access to resources, using a monitor-like mechanism

A social epidemiology of foodwork and home-prepared food

A significant amount of energy and resource has been devoted to promoting home food preparation, based on the hypothesis that it is an important, modifiable determinant of diet composition and quality. Ideas about the importance of home food preparation to good nutrition have permeated into policy, with a number of countries emphasising home food preparation and home-prepared food in their dietary guidelines and food guides. These policies encourage individuals to maintain ‘traditional’ domestic food practices in order to eat healthily, even while the food system, along with other dimensions of life such as working hours and leisure activities, are undergoing substantial change. Interventions have often focused on boosting skills, guided in part by public and academic discourse that posits that people are cooking less than they did in the past because they no longer know how. This idea persists despite evidence that most people feel their skill set to be adequate to their needs, and cite other barriers, including, notably, a lack of time. Concerns have been raised surrounding both the effectiveness of encouraging home food preparation as a strategy to improve dietary quality, and its repercussions for equity, with foodwork still being predominantly undertaken by women, and with those who are time-poor being potentially less able to adopt time-intensive approaches to food provisioning. Further, there is a certain lack of clarity surrounding what is being encouraged: not all foodwork produces foods that might be defined as ‘home-prepared’. This thesis aims to present a social epidemiology of foodwork and home-prepared food consumption, using nationally representative data from UK adults to: 1) Investigate how a ‘lack’ of time, in the form of competing demands on and other uses for time, is associated with time allocated to foodwork; and 2) Explore the association between home-prepared food consumption and diet quality. First, analysis of three waves of cross-sectional UK time use surveys, spanning three decades, demonstrated that both participation in foodwork and time spent on foodwork continued to decrease. A compositional data analysis approach was used to put this in the context of other daily activities, examining how time spent on activities such as work, sleep and leisure has evolved in tandem with time spent on foodwork. Results suggest that time devoted to work, paid and unpaid, has not increased substantially over this period. Instead, more time is spent on sleep and screen time. Second, analysis of the most recent wave of the UK time use survey compared how participants who did no foodwork, some foodwork, or a lot of foodwork allocated their time differently. Participants who spent more time on foodwork also spent less time on sleep, although not on screen time. Foodwork was predominantly done by women, and women who did more foodwork increased time spent on work (both paid and unpaid) and reduced time spent on leisure and personal care activities more substantially than their male counterparts. Third, a measure of home-prepared food consumption based on food diaries was developed using data from the UK National Diet and Nutrition Survey, and compared to a more orthodox measure: self-reported frequency of meals being prepared at home in participants’ households. These measures were significantly associated with one another, and this association did not vary systematically between most socioeconomic and demographic groups. Fourth, the food diary-based measure of home-prepared food was deployed to estimate consumption levels in the UK population (around a third of energy intake), and to determine the association between home-prepared food consumption and dietary quality. A moderate, though significant, association was found between the two. However, there was limited variation in the consumption of home-prepared food or its association with diet quality between different socio-demographic groups, suggesting that other components of diet may be responsible for consistently reported inequalities in diet quality. Finally, we explored the possibility of eating healthily where extensive foodwork was not possible or desirable by identifying individuals who ate healthily with minimal reliance on home-prepared food, describing their intake in terms of food and nutrients, as well as their socio-demographic characteristics. As a whole, this work suggests that, while foodwork and home food preparation continue to play a role in how people in the UK spend their time and provision their food, other ways of eating also play an important, and potentially growing, role, and may not always necessarily be detrimental to health. Interventions that seek to improve dietary quality at the population level must take a full account of contemporary life, supporting individuals in eating healthily through a diverse range of approaches to food.Funded by the Medical Research Council through the Centre for Diet and Activity Research, MRC Epidemiology Unit, University of Cambridg

The Essential Roles of the Chromatin Factor Gon4l in Heart Development

Heart development and the genetic pathways underlying it are highly conserved among vertebrates. During heart development, an embryo must induce mesoderm formation, pattern the mesoderm, specify cardiomyocytes, increase the population of cardiomyocytes through proliferation, and pattern the cardiac chambers. It is becoming increasingly clear that chromatin modifications help mediate the complex processes of heart development by providing spatiotemporal regulation of gene expression. My thesis work focuses on characterizing functions of the chromatin factor Gonad-4-like (Gon4l), encoded by the gene ugly duckling (udu), in zebrafish heart development. Previous works established a requirement for Gon4l in the formation of many mesoderm derivatives including somites and blood. My studies define novel roles for maternal and zygotic Gon4l function in zebrafish heart development. Embryos lacking both maternal and zygotic udu (MZudu) expression have perturbations in the formation of all three germ layers, but this thesis focused on the disruptions in mesoderm development. MZudu-/- embryos have abnormal mesoderm patterning that results in defects in the development of mesoderm derived tissues and organs. MZudu mutant embryos present an almost complete loss of anterior lateral plate mesoderm formation, and subsequently heart development. RNA-sequencing performed on MZudu /- embryos uncovered broad misregulation of genes including morphogens and transcription factors. Cell autonomy transplants indicated that Gon4l has both cell-autonomous and non-cell-autonomous functions in heart development, which suggests that disruption of multiple signaling pathways contributes to the defects in heart development. In addition, this work establishes separate zygotic functions for Gon4l in cardiomyocyte proliferation and maintenance of ventricular identity. Notably, these deficiencies in heart development are not due to increased expression of tp53, unlike the hematopoiesis defects in zygotic udu (Zudu) mutant embryos. Cardiomyocyte proliferation is reduced in Zudu-/- embryos. Differential expression of ccnd3 and ccne2 and evidence that Gon4l associates with regulatory regions of these cyclins posits that Gon4l may be required for progression through the G1/S cell cycle checkpoint. Analysis of nkx2.5;udu compound mutant phenotypes revealed that nkx2.5 and udu genetically interact in the maintenance of ventricular identity. However, ectopic expression of nkx2.5 failed to restore ventricular patterning in udu-/- embryos, which indicates that Gon4l could regulate multiple pathways to maintain ventricular identity. Altogether my work establishes novel roles for Gon4l in regulating mesoderm patterning, cardiomyocyte proliferation, and maintenance of ventricular identity during vertebrate heart development

RNA Methylation and Ythdf Readers in Posttranscriptional Regulation and Development

Development in animals requires precise and coordinated changes in gene expression. This genetic remodeling is achieved through extensive regulatory networks of proteins and RNAs that function together to specify new cell fates and patterns. One developmental event heavily reliant on these regulatory networks is the maternal-to-zygotic transition (MZT), a universal step in metazoan embryogenesis in which a fertilized oocyte is reprogrammed into a pluripotent embryo. The earliest stages of the MZT are governed by maternally inherited gene products, which are required for cellular functions in the initially transcriptionally silent embryo. To shift developmental control to the zygote, these maternal mRNAs are massively degraded through multiple posttranscriptional mechanisms. The RNA modification, N6-methyladenosine (m6A) has been proposed as a master regulator of mRNA decay during developmental transitions, but the direct effects of this pathway on maternal transcript clearance remain unclear. To determine whether m6A facilitates gene expression changes during the MZT, I employed zebrafish embryos as a model system to dissect the contributions of RNA methylation and its reader proteins to maternal transcript fate. Through transcriptome analysis and reporter assays, I found that m6A controls maternal mRNA degradation by promoting deadenylation. To understand how RNA methylation fits into the framework of known decay pathways, I compared transcripts co-targeted by m6A and miR-430, a microRNA that controls mRNA clearance in zebrafish. This revealed that these mechanisms function independently but additively to promote mRNA degradation, reflecting that methylation modulates transcript abundance in concert with known regulators. To disentangle the roles of the Ythdf proteins that mediate the effects of m6A on mRNA, I generated zebrafish genetic mutants of Ythdf1, Ythdf2, and Ythdf3. Through transcriptomic and phenotypic analysis of these mutants, I determined that global maternal mRNA clearance, zygotic genome activation, and development proceed normally in the absence of any one reader. This revealed that individual Ythdf protein have limited effects on the removal of methylated maternal mRNAs during the MZT. To test if this restricted impact of single Ythdf loss stems from functional redundancy between the readers, I produced double mutants of Ythdf2 and Ythdf3. Double Ythdf deletion prevents female gonad development, indicating that these factors exert overlapping activities during oogenesis. Finally, to fully establish functionally redundancy, I created triple Ythdf mutants, which were larval lethal. I observed this same phenotype in zebrafish lacking the methylases that add m6A to mRNA, indicating that RNA methylation is essential for developmental viability. Together, this work provides insight into the contributions of the m6A modification and its Ythdf effectors to maternal mRNA clearance, and establishes how these key regulators coordinate the gene expression changes that underlie embryonic reprogramming

Improving filtering methods based on the Fast Fourier Transform to delineate objective relief domains: An application to Mare Ingenii lunar area

A recent study has proven that high-pass filtering (HPF) based on the Fast Fourier Transform (FFT) is a rapid and efficient computational method for the semi-automated detection of geomorphic features from high-resolution digital elevation models (DEM). Although this new approach shows great potential for cartographic purposes using remote sensing data, some methodological improvements are still required in the following areas: (i) to develop a robust criteria for filter radius selection; (ii) to test the relationship between filter vectors and landscape form, and explore how DEM artefacts (vegetation, anthropic structures, etc.) can interfere with landform detection; and (iii) to explore filter response regarding generalisation and blurring effects when working with landscapes composed of landforms of different scales that are superimposed on one another. These topics are addressed here through two experiments (Experiment_1 and Experiment_2) with synthetic digital relief models inspired in the lunar landscape. Finally, the improved methodology was applied on the Mare Ingenii lunar relief (Experiment_3) using the Lunar Orbiter Laser Altimeter DEM and the results were tested against ground truths (GTs) developed using the extensive database available at Astropedia website and an ad hoc crater map. The analysis of existing frequencies in a 2D DEM signal through the true magnitude-true frequency plot provides an objective method for filter radius selection, and the use of a Butterworth transference function enables a more versatile filtering. Experiment_1 demonstrates a close correspondence between vectors obtained by filtering called Filtered Geomorphic References (FGRs) and the synthetic landform selected. The accuracy indicators from Experiment_1 and 2 show the good results obtained in the correspondence between FGRs and crater depressions, either from flat-bottomed to bowl shapes. Experiments 2 and 3 confirm that in landscapes generated by superimposed geomorphic features of different sizes, the smaller the crater, the better the filters detect its boundaries. Moreover, the spatial repeatability of FGRs can be used as a cartographic criterion in the identification of crater shape depressions or hills. Besides, the criterion is useful to assess true reality mapped in the GT employed. Finally, the objective geomorphic units obtained by combining the FGRs demonstrate their usefulness for the objective characterisation of the moonscape. Using the synthetic landscapes, the FGRs identify those relief domains composed of depressions and hills.This work was carried out as part of the Projects: 29.P114.64004 (UC); 29.P203.64004 (UC); RECORNISA (FLTQ-UC)

A BIOLOGICAL BASED MODEL OF THE HUMAN VISUAL SYSTEM INCORPORATING LATERAL SUBTRACTIVE INHIBITION WITH NON-UNIFORM SAMPLING AND MULTIPLE SPATIAL FREQUENCY FILTERS

The human visual system has been an interesting topic of scientific research for decades. It is known that the cone photo-receptors are arrayed in a non-linear fashion and that a lateral subtractive inhibitory process is occurring in the visual pathway. This thesis outlines for the first time how lateral subtractive inhibition manifests itself in the context of a non-uniform sensor distribution where the distance between cone photo-receptors, and size of the receptors, are varying in a log manner when moving radially away from the foveal area. Range limits on the parameters that control the non-uniform sampling and coupling coefficients are presented and optimal values are identified for specific image resolutions. The results of this analysis are then coupled to a proposed model of spatial frequency filtering to assist in subsequent studies of feature extraction and pattern analysis. The filters generated are based on three spatial-frequency channels that are designed to model the human eye contrast sensitivity curve. Simulated results are presented