Learning Object-Independent Modes of Variation with Feature Flow Fields

We present a unifying framework in which "object-independent" modes of variation are learned from continuous-time data such as video sequences. These modes of variation can be used as "generators" to produce a manifold of images of a new object from a single example of that object. We develop the framework in the context of a well-known example: analyzing the modes of spatial deformations of a scene under camera movement. Our method learns a close approximation to the standard affine deformations that are expected from the geometry of the situation, and does so in a completely unsupervised (i.e. ignorant of the geometry of the situation) fashion. We stress that it is learning a "parameterization", not just the parameter values, of the data. We then demonstrate how we have used the same framework to derive a novel data-driven model of joint color change in images due to common lighting variations. The model is superior to previous models of color change in describing non-linear color changes due to lighting.

Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.)

Sk?t, L., Humphreys, J., Humphreys, M. O., Thorogood, D., Gallagher, J. A., Sanderson, R., Armstead, I. P., Thomas, I. D. (2007). Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne (L.). Genetics, 177 (1), 535-547. Sponsorship: BBSRC RAE2008

An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.)

Sk?t, L., Humphreys, M. O., Armstead, I. P., Heywood, S., Sk?t, K. P., Sanderson, R., Thomas, I. D., Chorlton, K. H., & Sackville Hamilton, N. R. (2005). An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Molecular Breeding, 15(3), 233-245. Sponsorship: BBSRC RAE2008

Skin Color-Based Video Segmentation under Time-Varying Illumination

A novel approach for real-time skin segmentation in video sequences is described. The approach enables reliable skin segmentation despite wide variation in illumination during tracking. An explicit second order Markov model is used to predict evolution of the skin-color (HSV) histogram over time. Histograms are dynamically updated based on feedback from the current segmentation and predictions of the Markov model. The evolution of the skin-color distribution at each frame is parameterized by translation, scaling and rotation in color space. Consequent changes in geometric parameterization of the distribution are propagated by warping and resampling the histogram. The parameters of the discrete-time dynamic Markov model are estimated using Maximum Likelihood Estimation, and also evolve over time. The accuracy of the new dynamic skin color segmentation algorithm is compared to that obtained via a static color model. Segmentation accuracy is evaluated using labeled ground-truth video sequences taken from staged experiments and popular movies. An overall increase in segmentation accuracy of up to 24% is observed in 17 out of 21 test sequences. In all but one case the skin-color classification rates for our system were higher, with background classification rates comparable to those of the static segmentation.

The impact of learning context on the acquisition of sociopragmatic variation patterns in non-native speaker teachers of English

The study is a cross-linguistic, cross-sectional investigation of the impact of learning contexts on the acquisition of sociopragmatic variation patterns and the subsequent enactment of compound identities. The informants are 20 non-native speaker teachers of English from a range of 10 European countries. They are all primarily mono-contextual foreign language learners/users of English: however, they differ with respect to the length of time accumulated in a target language environment. This allows for three groups to be established – those who have accumulated 60 days or less; those with between 90 days and one year and the final group, all of whom have accumulated in excess of one year. In order to foster the dismantling of the monolith of learning context, both learning contexts under consideration – i.e. the foreign language context and submersion context are broken down into micro-contexts which I refer to as loci of learning. For the purpose of this study, two loci are considered: the institutional and the conversational locus. In order to make a correlation between the impact of learning contexts and loci of learning on the acquisition of sociopragmatic variation patterns, a two-fold study is conducted. The first stage is the completion of a highly detailed language contact profile (LCP) questionnaire. This provides extensive biographical information regarding language learning history and is a powerful tool in illuminating the intensity of contact with the L2 that learners experience in both contexts as well as shedding light on the loci of learning to which learners are exposed in both contexts. Following the completion of the LCP, the informants take part in two role plays which require the enactment of differential identities when engaged in a speech event of asking for advice. The enactment of identities then undergoes a strategic and linguistic analysis in order to investigate if and how differences in the enactment of compound identities are indexed in language. Results indicate that learning context has a considerable impact not only on how identity is indexed in language, but also on the nature of identities enacted. Informants with very low levels of crosscontextuality index identity through strategic means – i.e. levels of directness and conventionality; however greater degrees of cross-contextuality give rise to the indexing of differential identities linguistically by means of speaker/hearer orientation and (non-) solidary moves. When it comes to the nature of identity enacted, it seems that more time spent in intense contact with native speakers in a range of loci of learning allows learners to enact their core identity; whereas low levels of contact with over-exposure to the institutional locus of learning fosters the enactment of generic identities.

Can population-level variation in early childhood development be measured in a manner that supports service planning and intervention?

Background: The Early Development Instrument (EDI) is a population-level measure of five developmental domains at school-entry age. The overall aim of this thesis was to explore the potential of the EDI as an indicator of early development in Ireland. Methods: A cross-sectional study was conducted in 47 primary schools in 2011 using the EDI and a linked parental questionnaire. EDI (teacher completed) scores were calculated for 1,344 children in their first year of full-time education. Those scoring in the lowest 10% of the sample population in one or more domains were deemed to be 'developmentally vulnerable'. Scores were correlated with contextual data from the parental questionnaire and with indicators of area and school-level deprivation. Rasch analysis was used to determine the validity of the EDI. Results: Over one quarter (27.5%) of all children in the study were developmentally vulnerable. Individual characteristics associated with increased risk of vulnerability were being male; under 5 years old; and having English as a second language. Adjusted for these demographics, low birth weight, poor parent/child interaction and mother’s lower level of education showed the most significant odds ratios for developmental vulnerability. Vulnerability did not follow the area-level deprivation gradient as measured by a composite index of material deprivation. Children considered by the teacher to be in need of assessment also had lower scores, which were not significantly different from those of children with a clinical diagnosis of special needs. all domains showed at least reasonable fit to the Rasch model supporting the validity of the instrument. However, there was a need for further refinement of the instrument in the Irish context. Conclusion: This thesis provides a unique snapshot of early development in Ireland. The EDI and linked parental questionnaires are promising indicators of the extent, distribution and determinants of developmental vulnerability.

A longitudinal study of epigenetic variation in twins.

DNA methylation is a key epigenetic mechanism involved in the developmental regulation of gene expression. Alterations in DNA methylation are established contributors to inter-individual phenotypic variation and have been associated with disease susceptibility. The degree to which changes in loci-specific DNA methylation are under the influence of heritable and environmental factors is largely unknown. In this study, we quantitatively measured DNA methylation across the promoter regions of the dopamine receptor 4 gene (DRD4), the serotonin transporter gene (SLC6A4/SERT) and the X-linked monoamine oxidase A gene (MAOA) using DNA sampled at both ages 5 and 10 years in 46 MZ twin-pairs and 45 DZ twin-pairs (total n=182). Our data suggest that DNA methylation differences are apparent already in early childhood, even between genetically identical individuals, and that individual differences in methylation are not stable over time. Our longitudinal-developmental study suggests that environmental influences are important factors accounting for interindividual DNA methylation differences, and that these influences differ across the genome. The observation of dynamic changes in DNA methylation over time highlights the importance of longitudinal research designs for epigenetic research.

Variation in use of surveillance colonoscopy among colorectal cancer survivors in the United States.

BACKGROUND: Clinical practice guidelines recommend colonoscopies at regular intervals for colorectal cancer (CRC) survivors. Using data from a large, multi-regional, population-based cohort, we describe the rate of surveillance colonoscopy and its association with geographic, sociodemographic, clinical, and health services characteristics. METHODS: We studied CRC survivors enrolled in the Cancer Care Outcomes Research and Surveillance (CanCORS) study. Eligible survivors were diagnosed between 2003 and 2005, had curative surgery for CRC, and were alive without recurrences 14 months after surgery with curative intent. Data came from patient interviews and medical record abstraction. We used a multivariate logit model to identify predictors of colonoscopy use. RESULTS: Despite guidelines recommending surveillance, only 49% of the 1423 eligible survivors received a colonoscopy within 14 months after surgery. We observed large regional differences (38% to 57%) across regions. Survivors who received screening colonoscopy were more likely to: have colon cancer than rectal cancer (OR = 1.41, 95% CI: 1.05-1.90); have visited a primary care physician (OR = 1.44, 95% CI: 1.14-1.82); and received adjuvant chemotherapy (OR = 1.75, 95% CI: 1.27-2.41). Compared to survivors with no comorbidities, survivors with moderate or severe comorbidities were less likely to receive surveillance colonoscopy (OR = 0.69, 95% CI: 0.49-0.98 and OR = 0.44, 95% CI: 0.29-0.66, respectively). CONCLUSIONS: Despite guidelines, more than half of CRC survivors did not receive surveillance colonoscopy within 14 months of surgery, with substantial variation by site of care. The association of primary care visits and adjuvant chemotherapy use suggests that access to care following surgery affects cancer surveillance.

Genome-wide scan of copy number variation in late-onset Alzheimer's disease.

Alzheimer's disease is a complex and progressive neurodegenerative disease leading to loss of memory, cognitive impairment, and ultimately death. To date, six large-scale genome-wide association studies have been conducted to identify SNPs that influence disease predisposition. These studies have confirmed the well-known APOE epsilon4 risk allele, identified a novel variant that influences disease risk within the APOE epsilon4 population, found a SNP that modifies the age of disease onset, as well as reported the first sex-linked susceptibility variant. Here we report a genome-wide scan of Alzheimer's disease in a set of 331 cases and 368 controls, extending analyses for the first time to include assessments of copy number variation. In this analysis, no new SNPs show genome-wide significance. We also screened for effects of copy number variation, and while nothing was significant, a duplication in CHRNA7 appears interesting enough to warrant further investigation.

Variation in pediatric traumatic brain injury outcomes in the United States.

OBJECTIVE: To ascertain the degree of variation, by state of hospitalization, in outcomes associated with traumatic brain injury (TBI) in a pediatric population. DESIGN: A retrospective cohort study of pediatric patients admitted to a hospital with a TBI. SETTING: Hospitals from states in the United States that voluntarily participate in the Agency for Healthcare Research and Quality's Healthcare Cost and Utilization Project. PARTICIPANTS: Pediatric (age ≤ 19 y) patients hospitalized for TBI (N=71,476) in the United States during 2001, 2004, 2007, and 2010. INTERVENTIONS: None. MAIN OUTCOME MEASURES: Primary outcome was proportion of patients discharged to rehabilitation after an acute care hospitalization among alive discharges. The secondary outcome was inpatient mortality. RESULTS: The relative risk of discharge to inpatient rehabilitation varied by as much as 3-fold among the states, and the relative risk of inpatient mortality varied by as much as nearly 2-fold. In the United States, approximately 1981 patients could be discharged to inpatient rehabilitation care if the observed variation in outcomes was eliminated. CONCLUSIONS: There was significant variation between states in both rehabilitation discharge and inpatient mortality after adjusting for variables known to affect each outcome. Future efforts should be focused on identifying the cause of this state-to-state variation, its relationship to patient outcome, and standardizing treatment across the United States.

A Quantitative Analysis of Growth and Size Regulation in Manduca sexta: The Physiological Basis of Variation in Size and Age at Metamorphosis.

Body size and development time are important life history traits because they are often highly correlated with fitness. Although the developmental mechanisms that control growth have been well studied, the mechanisms that control how a species-characteristic body size is achieved remain poorly understood. In insects adult body size is determined by the number of larval molts, the size increment at each molt, and the mechanism that determines during which instar larval growth will stop. Adult insects do not grow, so the size at which a larva stops growing determines adult body size. Here we develop a quantitative understanding of the kinetics of growth throughout larval life of Manduca sexta, under different conditions of nutrition and temperature, and for genetic strains with different adult body sizes. We show that the generally accepted view that the size increment at each molt is constant (Dyar's Rule) is systematically violated: there is actually a progressive increase in the size increment from instar to instar that is independent of temperature. In addition, the mass-specific growth rate declines throughout the growth phase in a temperature-dependent manner. We show that growth within an instar follows a truncated Gompertz trajectory. The critical weight, which determines when in an instar a molt will occur, and the threshold size, which determines which instar is the last, are different in genetic strains with different adult body sizes. Under nutrient and temperature stress Manduca has a variable number of larval instars and we show that this is due to the fact that more molts at smaller increments are taken before threshold size is reached. We test whether the new insight into the kinetics of growth and size determination are sufficient to explain body size and development time through a mathematical model that incorporates our quantitative findings.

Coccolithophore bloom size variation in response to the regional environment of the subarctic North Atlantic

Several environmental/physical variables derived from satellite and in situ data sets were used to understand the variability of coccolithophore abundance in the subarctic North Atlantic. The 7-yr (1997–2004) time-series analysis showed that the combined effects of high solar radiation, shallow mixed layer depth (<20 m), and increased temperatures explained >89% of the coccolithophore variation. The June 1998 bloom, which was associated with high light intensity, unusually high sea-surface temperature, and a very shallow mixed layer, was found to be one of the most extensive (>995,000 km2) blooms ever recorded. There was a pronounced sea-surface temperature shift in the mid-1990s with a peak in 1998, suggesting that exceptionally large blooms are caused by pronounced environmental conditions and the variability of the physical environment strongly affects the spatial extent of these blooms. Consequently, if the physical environment varies, the effects of these blooms on the atmospheric and oceanic environment will vary as well.

Phenotypic variation in shell form in the intertidal acorn barnacle Chthamalus montagui: distribution, response to predators and life history trade-offs.

The acorn barnacle Chthamalus montagui can present strong variation in shell morphology, ranging from flat conic to a highly bent form, caused by a substantial overgrowth of the rostrum plate. Shell shape distribution was investigated between January and May 2004 from geographical to microhabitat spatial scales along the western coast of Britain. Populations studied in the north (Scotland and Isle of Man) showed a higher degree of shell variation compared to those in the south (Wales and south-west England). In the north, C. montagui living at lower tidal levels and in proximity to the predatory dogwhelk, Nucella lapillus, were more bent in profile. Laboratory experiments were conducted to examine behavioural responses, and vulnerability of bent and conic barnacles to predation by N. lapillus. Dogwhelks did not attack one morphotype more than the other, but only 15 % of attacks on bent forms were successful compared to 75 % in conic forms. Dogwhelk effluent reduced the time spent feeding by C. montagui (11 %), but there was no significant difference between conic and bent forms. Examination of barnacle morphology indicated a trade-off in investment in shell structure and feeding appendages associated with being bent, but none with egg or somatic tissue mass. These results are consistent with C. montagui showing an induced defence comparable to that found in its congeners Chthamalus anisopoma and Chthamalus fissus on the Pacific coast of North America, but further work to demonstrate inducibility is required.

How does Calanus helgolandicus maintain its population in a variable environment? Analysis of a 25-year time series from the English Channel

Calanus helgolandicus is a key copepod of the NE Atlantic and fringing shelves, with a distribution that is expanding northwards with oceanic warming. The Plymouth L4 site has warmed over the past 25-years, and experiences large variations in the timing and availability of food for C. helgolandicus. Here we examine the degree to which these changes translate into variation in reproductive output and subsequently C. helgolandicus population size. Egg production rates (eggs female−1 day−1) were maximal in the spring to early-summer period of diatom blooms and high ciliate abundance, rather than during the equally large autumn blooms of autotrophic dinoflagellates. Egg hatch success was lower in spring however, with a greater proportion of naupliar deformities then also. Both the timing and the mean summer abundance of C. helgolandicus (CI–CVI) reflected those of spring total reproductive output. However this relationship was driven by inter-annual variability in female abundance and not that of egg production per female, which ranged only two-fold. Winter abundance of C. helgolandicus at L4 was much more variable than abundance in other seasons, and reflected conditions from the previous growing season. However, these low winter abundances had no clear carry-over signal to the following season’s population size. Overall, the C. helgolandicus population appears to be surprisingly resilient at this dynamic, inshore site, showing no long-term phenology shift and only a four-fold variation in mean abundance between years. This dampening effect may reflect a series of mortality sources, associated with the timing of stratification in the early part of the season, likely affecting egg sinking and loss, plus intense, density-dependent mortality of early stages in mid-summer likely through predation.

A reliable externally fixated murine femoral fracture model that accounts for variation in movement between animals.

Fifty-two CFLP mice had an open femoral diaphyseal osteotomy held in compression by a four-pin external fixator. The movement of 34 of the mice in their cages was quantified before and after operation, until sacrifice at 4, 8, 16 or 24 days. Thirty-three specimens underwent histomorphometric analysis and 19 specimens underwent torsional stiffness measurement. The expected combination of intramembranous and endochondral bone formation was observed, and the model was shown to be reliable in that variation in the histological parameters of healing was small between animals at the same time point, compared to the variation between time-points. There was surprisingly large individual variation in the amount of animal movement about the cage, which correlated with both histomorphometric and mechanical measures of healing. Animals that moved more had larger external calluses containing more cartilage and demonstrated lower torsional stiffness at the same time point. Assuming that movement of the whole animal predicts, at least to some extent, movement at the fracture site, this correlation is what would be expected in a model that involves similar processes to those in human fracture healing. Models such as this, employed to determine the effect of experimental interventions, will yield more information if the natural variation in animal motion is measured and included in the analysis.