Parallel Sparse Matrix-Matrix Multiplication

The thesis investigates the BLAS-3 routine of sparse matrix-matrix multiplication (SpGEMM) based on the outer product method. Sev- eral algorithmic approaches have been implemented and empirically an- alyzed. The experiments have shown that an algorithm presented by Gustavson [22] outperforms other alternatives. In this work we propose optimization techniques that improve the scalability and the cache efficiency of the Gustavson’s algorithm for large matrices. Our approach succeeded to reduce the cache misses by more than a factor of five and to improve the net running time by 30% with some instances. The thesis also presents an algorithm for flops estima- tion, which can be used to determine an upper bound for the density of the result matrix. Furthermore, the work analyzes and empirically evaluates techniques for parallelization of the multiplication in a shared memory model by using Intel TBB and OpenMP. We investigate the cache efficiency of the algorithm in a parallel setting and compare several approaches for load balancing of the computation

Spatial analyses and growth of trees in selected bottomland hardwood stands

Sustainable management and conservation of the extensive bottomland hardwood forest resource in the southeastern U.S. requires a good understanding of basic structural and competitive relationships within these forests. To gain an insight into these relationships, plot information from stands in Arkansas, Louisiana, and Mississippi were analyzed. The effects of individual tree attributes, distance-dependant, and distance-independent competition measures on 5-yr radial growth of red oak crop trees were examined. Selected species included cherrybark oak (Quercus pagoda Raf.), water oak (Q. nigra L.), and Nuttall oak (Q. nuttallii Palmer). Spatial continuity of tree variables was explored through geostatistical analysis. Finally, spatial distribution patterns of all species, the intraspecific pattern of cherrybark oak, water oak, and sweetgum (Liquidambar styraciflua L.), and the interspecific pattern of their pairs was examined with point pattern analysis. In the analysis of 5-yr radial growth, the crown class score (from Meadows et al. 2001) accounted for a large portion of tree diameter growth. However, average plot-level characteristics failed to account for a significant proportion of the variability in tree growth. The basal area of trees taller than the crop trees and located within 2.5 mean crown radii had the highest negative correlation with crop tree 5-yr radial growth. Red oaks were likely exerting the greatest competition. Crop tree radial growth was also positively associated with the basal area of other red oaks taller than the crop tree and located between 3 and 4 mean crown radii from the crop tree (the indirect neighbors). Geostatistical analysis demonstrated that spatial continuity of unsuppressed tree attributes extended to a distance equal to 4 times the mean crown radius, suggesting that when resources are nonlimiting, multiple trees may be able to coexist and grow well in close proximity. Spatial point pattern analysis indicated that when species were combined, they were frequently aggregated and sometimes overdispersed. Plots with larger trees were more likely to exhibit overdispersion suggesting a shift to this pattern as trees grow. Interspecific and intraspecific pattern analyses suggested that strong interspecific competition resulted in species segregation, while weaker intraspecific competition led to aggregations of conspecifics

Pastor as Poet of the Soul

The church finds itself in a culture that challenges the idea of divine action in the world—one of the results of living in a secular age. We are more likely to talk about “good luck” or “coincidence” than we are about God acting in history. Charles Taylor calls this the immanent frame—that we have constructed a social view that frames our lives without the supernatural. In addition, Hartmut Rosa describes modernity as social acceleration, which puts us out-of-sync in our relationships to others and the world. For the pastor, these cultural and social forces at work often lead to malaise and alienation, which are also widespread in the church. But the pastor is uniquely called to name God’s action and invite the church to recognize it in their everyday lives. This paper proposes that understanding the role of the pastor as poet is a proactive and creative response to these secular developments

The epidemiology of hospital admissions in a general population: record linkage of hospital episode statistics to the European Prospective Investigation of Cancer (EPIC-Norfolk) cohort

The UK National Health Service (NHS) is primarily funded by taxation free at the point of delivery. Hospitals account for approximately 50% of overall NHS spending. Two-thirds of people admitted to hospital are over 65 with those over 85 accounting for 25% of bed days. This thesis aims to quantify hospital usage in a general population of middle-aged and older men and women over a 20-year follow-up period and to examine related demographic and behavioural factors. Patterns of hospital usage are described using two main hospital usage measures: admission numbers and length of stay. Socioeconomic factors such as education, occupational social class and residential area deprivation that may predict future hospital usage are examined. I assess the relationships between potentially modifiable factors such as cigarette smoking, the consumption of alcohol, body mass index and physical activity and future hospital usage while the implications for clinical and public health planning, policy and practice are also considered. The thesis is based on the European Prospective Investigation of Cancer in Norfolk (EPIC-Norfolk), a community-based cohort of 25,639 men and women aged 40-79 at recruitment between 1993-1997 and followed up to the present. Participants completed a lifestyle questionnaire and attended a clinic where measurements and blood were taken at baseline and again at a second time-point after 12 years. All participants were linked to hospital records using their unique NHS numbers and to census data using their postcode. Episode statistics including admission and discharge dates were used to create numbers of admissions and length of stay outcomes. ICD-10 diagnosis codes were used to construct a hospital multimorbidity outcome using the Charlson Comorbidity Index above the level of 3. Logistic regression was the primary statistical model used throughout the analyses. Exposures were examined prospectively, prior to any hospital admission. The current analyses were conducted on 25,014 participants in the cohort still alive in 1999 when hospital admission data were first available. Over the first 10 years of follow-up, 73% of study participants had at least one admission to hospital, 14% with ≥7 admissions and 20% with >20 hospital days. After 20 years, 90% of participants had a hospital admission, 65% had ≥7 admissions and 59% had >20 hospital days. High numbers of admissions and hospital days were positively associated with male sex, age, manual social class, current cigarette smoking and body mass index (BMI) >30 kg/m². The thesis examined levels of deprivation both at individual level, using education and occupational social class, and residential area level using the Townsend Area Deprivation Index. Compared with those having Townsend Index lower than the average for England and Wales, those with a higher than average deprivation index had a higher likelihood of spending >20 days in hospital. Occupational social class and educational attainment modified the association between area deprivation and hospitalisation; those with manual social class and lower education level were at greater risk of hospitalisation when living in an area with higher deprivation index. The thesis also examined potentially modifiable behavioural factors. Compared with current non-drinkers, men and women who reported any alcohol drinking had a lower risk of spending >20 days in hospital. Participants with a baseline physical activity score of at least moderately inactive had fewer hospital admissions and fewer days in hospital over 10 years, than those who were inactive. Similar associations were observed over 10 years from time-point two (TP2) and similar but attenuated results were observed for 20-year follow-up. Participants who remained physically active or became active between baseline and TP2 had lower risk of subsequent hospital usage than those who remained inactive or became inactive. An additional hospital-based outcome measure, hospital admission with multimorbidity (HAWM), was used to examine incident multimorbidity for participants free of the condition at baseline. Baseline 5-year and 10-year incident HAWM were observed in 11% and 21% of participants, respectively. More men had incident HAWM than women and those aged >75 years had the highest proportion of multimorbid conditions with 29% at 5 years and 47% at 10 years. HAWM rates at TP2 were similar to baseline. Longer duration of hospital stay and number of admissions, age, male sex and prevalent diseases, smoking, physical inactivity, high BMI and low fruit and vegetable intake were associated with incident HAWM. Simple demographic and behavioural indicators are related to the future probability of cumulative hospital admissions, length of stay and hospital admissions with multimorbidity. Increasing age, male sex and modifiable factors such as smoking, body mass index and usual physical activity are all strongly associated with subsequent hospital usage. Modest feasible differences in lifestyles in the general population may potentially mitigate the future impact of long hospital stay and multimorbidity and have a substantial impact on hospital usage and costs. The social determinants of health are well recognised. While some of the socioeconomic gradient in ill health has been attributed to differences in behavioural factors, there is also a socioeconomic gradient in hospital usage for individually measured social class and education and for area level deprivation apparently independently of measured behavioural factors and reported prevalent disease which warrant further exploration

Body Mass Index, Smoking, and Alcohol and Risks of Barrett’s Esophagus and Esophageal Adenocarcinoma: A UK Prospective Cohort Study

BACKGROUND: The timing of the risk factors cigarette smoking, alcohol and obesity in the development of Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) is unclear. AIMS: To investigate these exposures in the aetiology of BE and EAC in the same population. METHODS: The cohort included 24,068 men and women, aged 39–79 years, recruited between 1993 and 1997 into the prospective EPIC-Norfolk Study who provided information on anthropometry, smoking and alcohol intake. The cohort was monitored until December 2008 and incident cases identified. RESULTS: One hundred and four participants were diagnosed with BE and 66 with EAC. A body mass index (BMI) above 23 kg/m(2) was associated with a greater risk of BE [BMI ≥23 vs. 18.5 to <23, hazard ratio (HR) 3.73, 95 % CI 1.37–10.16], and within a normal BMI, the risk was greater in the higher category (HR 3.76, 95 % CI 1.30–10.85, BMI 23–25 vs. 18.5 to >23 kg/m(2)). Neither smoking nor alcohol intake were associated with risk for BE. For EAC, all BMI categories were associated with risk, although statistically significant for only the highest (BMI >35 vs. BMI 18.5 to <23, HR 4.95, 95 % CI 1.11–22.17). The risk was greater in the higher category of a normal BMI (HR 2.73, 95 % CI 0.93–8.00, p = 0.07, BMI 23–25 vs. 18.5 to >23 kg/m(2)). There was an inverse association with ≥7 units alcohol/week (HR 0.51, 95 % CI 0.29–0.88) and with wine (HR 0.49, 95 % CI 0.23–1.04, p = 0.06, drinkers vs. non-drinkers). CONCLUSIONS: Obesity may be involved early in carcinogenesis and the association with EAC and wine should be explored. The data have implications for aetiological investigations and prevention strategies

Contribution of cod liver oil-related nutrients (vitamins A, D, E and eicosapentaenoic acid and docosahexaenoic acid) to daily nutrient intake and their associations with plasma concentrations in the EPIC-Norfolk cohort

Total nutrient intake (TNI) is intake from food and supplements. This provides an assessment of nutrient adequacy and the prevalence of excessive intake, as well as the response with respect to biomarkers. Cod liver oil (CLO) is the most frequently consumed supplement in the UK, containing nutrients that might have varying influences on health. We calculated TNI for vitamins A, D and E, as well as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), and assessed associations with the respective blood concentrations

Dietary dairy product intake and incident type 2 diabetes: a prospective study using dietary data from a 7-day food diary

The consumption of specific dairy types may be beneficial for the prevention of diabetes. Abstract: The aim of this study was to investigate the association between total and types of dairy product intake and risk of developing incident type 2 diabetes, using a food diary. Methods: A nested case-cohort within the EPIC-Norfolk Study was examined, including a random subcohort (n=4,000) and cases of incident diabetes (n=892, including 143 cases in the subcohort) followed-up for 11 years. Diet was assessed using a prospective 7-day food diary. Total dairy intake (g/day) was estimated and categorised into high-fat (≥3.9%) and low-fat (&lt;3.9% fat) dairy, and by subtype into yoghurt, cheese and milk. Combined fermented dairy product intake (yoghurt, cheese, sour cream) was estimated and categorised into high- and low-fat. Prentice-weighted Cox regression HRs were calculated. Results: Total dairy, high-fat dairy, milk, cheese and high-fat fermented dairy product intakes were not associated with the development of incident diabetes. Low-fat dairy intake was inversely associated with diabetes in age- and sex-adjusted analyses (tertile [T] 3 vs T1, HR 0.81 [95% CI 0.66, 0.98]), but further adjustment for anthropometric, dietary and diabetes risk factors attenuated this association. In addition, an inverse association was found between diabetes and low-fat fermented dairy product intake (T3 vs T1, HR 0.76 [95% CI 0.60, 0.99]; ptrend=0.049) and specifically with yoghurt intake (HR 0.72 [95% CI 0.55, 0.95]; ptrend=0.017) in multivariable adjusted analyses. Conclusions/interpretation: Greater low-fat fermented dairy product intake, largely driven by yoghurt intake, was associated with a decreased risk of type 2 diabetes development in prospective analyses. These findings suggest that the consumption of specific dairy types may be beneficial for the prevention of diabetes, highlighting the importance of food group subtypes for public health messages

Predicting admissions and time spent in hospital over a decade in a population-based record linkage study: the EPIC-Norfolk cohort.

OBJECTIVE: To quantify hospital use in a general population over 10 years follow-up and to examine related factors in a general population-based cohort. DESIGN: A prospective population-based study of men and women. SETTING: Norfolk, UK. PARTICIPANTS: 11,228 men and 13,786 women aged 40-79 years in 1993-1997 followed between 1999 and 2009. MAIN OUTCOMES MEASURES: Number of hospital admissions and total bed days for individuals over a 10-year follow-up period identified using record linkage; five categories for admissions (from zero to highest ≥ 7) and hospital bed days (from zero to highest ≥ 20 nights). RESULTS: Over a period of 10 years, 18,179 (72.7%) study participants had at least one admission to hospital, 13.8% with 7 or more admissions and 19.9% with 20 or more nights in hospital. In logistic regression models with outcome ≥ 7 admissions, low education level OR 1.14 (1.05 to 1.24), age OR per 10-year increase 1.75 (1.67 to 1.82), male sex OR 1.32 (1.22 to 1.42), manual social class 1.22 (1.13 to 1.32), current cigarette smoker OR 1.53 (1.37 to 1.71) and body mass index >30 kg/m² OR 1.41 (1.28 to 1.56) all independently predicted the outcome with p30 kg/m², estimated percentages of the cohort in the categories of admission numbers and hospital bed days in stratified age bands with twofold to threefold differences in future hospital use between those with high-risk and low-risk scores. CONCLUSIONS: The future probability of cumulative hospital admissions and bed days appears independently related to a range of simple demographic and behavioural indicators. The strongest of these is increasing age with high body mass index and smoking having similar magnitudes for predicting risk of future hospital usage.The design and conduct of the EPIC-Norfolk study and collection and management of the data was supported by programme grants from the Medical Research Council UK (G9502233, G0401527) and Cancer Research UK (C864/A8257, C864/A2883).This is the final version of the article. It first appeared from the BMJ Group via http://dx.doi.org/10.1136/bmjopen-2015-00946

The association between physical activity and the risk of symptomatic Barrett’s oesophagus: a UK prospective cohort study

Background: Physical activity affects the functioning of the gastrointestinal system through both local and systemic effects and may play an important role in the aetiology of gastroesophageal reflux disease, Barrett’s oesophagus and oesophageal adenocarcinoma. We investigated, for the first time in a large prospective cohort study, associations between recreational and occupational levels of physical activity and the incidence of Barrett’s oesophagus. Participants and methods: The European Prospective Investigation of Cancer-Norfolk recruited 30 445 men and women between 1993 and 1997. Occupational and recreational levels of physical activity were measured using a baseline questionnaire. The cohort was followed up until 2015 to identify symptomatic cases of Barrett’s oesophagus. Cox proportional hazard regression estimated hazard ratios (HR) for physical activity and the development of disease. Results: Two hundred and three participants developed Barrett’s oesophagus (mean age: 70.6 years) the majority of whom were men (70.9%). There was an inverse association between standing occupations and disease risk [HR: 0.50, 95% confidence interval (CI): 0.31–0.82, P=0.006] when compared with sedentary jobs. Heavy manual occupations were positively associated with disease risk (HR: 1.66, 95% CI: 0.91–3.00), but conventional statistical significance was not reached (P=0.09). No associations were found between recreational activity and the risk of Barrett’s oesophagus (HR: 1.34, 95% CI: 0.72–2.50, P=0.35, highest vs. lowest levels of activity). Conclusion: Our study suggests that occupational levels of physical activity may be associated with the risk Barrett’s oesophagus. However, further work is required to confirm and describe specific occupations that may be protective