Estimates of sex- and age-class-specific survival probabilities for a southern Great Barrier Reef green sea turtle population

Sex- and age-class-specific survival probabilities of a southern Great Barrier Reef green sea turtle population were estimated using a capture - mark - recapture (CMR) study and a Cormack - Jolly - Seber (CJS) modelling approach. The CMR history profiles for 954 individual turtles tagged over a 9-year period ( 1984 - 1992) were classified into three age classes ( adult, subadult, juvenile) based on somatic growth and reproductive traits. Reduced-parameter CJS models, accounting for constant survival and time-specific recapture, fitted best for all age classes. There were no significant sex-specific differences in either survival or recapture probabilities for any age class. Mean annual adult survival was estimated at 0.9482 (95% CI: 0.92 - 0.98) and was significantly higher than survival for either subadults or juveniles. Mean annual subadult survival was 0.8474 ( 95% CI: 0.79 - 0.91), which was not significantly different from mean annual juvenile survival estimated at 0.8804 ( 95% CI: 0.84 - 0.93). The time-specific adult recapture probabilities were a function of sampling effort but this was not the case for either juveniles or subadults. The sampling effort effect was accounted for explicitly in the estimation of adult survival and recapture probabilities. These are the first comprehensive sex- and age-class-specific survival and recapture probability estimates for a green sea turtle population derived from a long-term CMR program.

Social inequalities in male mortality, and in male mortality from smoking: indirect estimation from national death rates in England and Wales, Poland, and North America

Background There are substantial social inequalities in adult male mortality in many countries. Smoking is often more prevalent among men of lower social class, education, or income. The contribution of smoking to these social inequalities in mortality remains uncertain. Methods The contribution of smoking to adult mortality in a population can be estimated indirectly from disease-specific death rates in that population (using absolute lung cancer rates to indicate proportions due to smoking of mortality from certain other diseases). We applied these methods to 1996 death rates at ages 35-69 years in men in three different social strata in four countries, based on a total of 0.6 million deaths. The highest and lowest social strata were based on social class (professional vs unskilled manual) in England and Wales, neighbourhood income (top vs bottom quintile) in urban Canada, and completed years of education (more than vs less than 12 years) in the USA and Poland. Results In each country, there was about a two-fold difference between the highest and the lowest social strata in overall risks of dying among men aged 35-69 years (England and Wales 21% vs 43%, USA 20% vs 37%, Canada 21% vs 34%, Poland 26% vs 50%: four-country mean 22% vs 41%, four-country mean absolute difference 19%). More than half of this difference in mortality between the top and bottom social strata involved differences in risks of being killed at age 35-69 years by smoking (England and Wales 4% vs 19%, USA 4% vs 15%, Canada 6% vs 13%, Poland 5% vs 22%: four-country mean 5% vs 17%, four-country mean absolute difference 12%). Smoking-attributed mortality accounted for nearly half of total male mortality in the lowest social stratum of each country. Conclusion In these populations, most, but not all, of the substantial social inequalities in adult male mortality during the 1990s were due to the effects of smoking. Widespread cessation of smoking could eventually halve the absolute differences between these social strata in the risk of premature death.

Spatial aspects of MRSA epidemiology:A case study using stochastic simulation, kernel estimation and SaTScan

The identification of disease clusters in space or space-time is of vital importance for public health policy and action. In the case of methicillin-resistant Staphylococcus aureus (MRSA), it is particularly important to distinguish between community and health care-associated infections, and to identify reservoirs of infection. 832 cases of MRSA in the West Midlands (UK) were tested for clustering and evidence of community transmission, after being geo-located to the centroids of UK unit postcodes (postal areas roughly equivalent to Zip+4 zip code areas). An age-stratified analysis was also carried out at the coarser spatial resolution of UK Census Output Areas. Stochastic simulation and kernel density estimation were combined to identify significant local clusters of MRSA (p<0.025), which were supported by SaTScan spatial and spatio-temporal scan. In order to investigate local sampling effort, a spatial 'random labelling' approach was used, with MRSA as cases and MSSA (methicillin-sensitive S. aureus) as controls. Heavy sampling in general was a response to MRSA outbreaks, which in turn appeared to be associated with medical care environments. The significance of clusters identified by kernel estimation was independently supported by information on the locations and client groups of nursing homes, and by preliminary molecular typing of isolates. In the absence of occupational/ lifestyle data on patients, the assumption was made that an individual's location and consequent risk is adequately represented by their residential postcode. The problems of this assumption are discussed, with recommendations for future data collection.

Estimation and prediction of average vehicle occupancies using traffic accident records

As congestion management strategies begin to put more emphasis on person trips than vehicle trips, the need for vehicle occupancy data has become more critical. The traditional methods of collecting these data include the roadside windshield method and the carousel method. These methods are labor-intensive and expensive. An alternative to these traditional methods is to make use of the vehicle occupancy information in traffic accident records. This method is cost effective and may provide better spatial and temporal coverage than the traditional methods. However, this method is subject to potential biases resulting from under- and over-involvement of certain population sectors and certain types of accidents in traffic accident records. In this dissertation, three such potential biases, i.e., accident severity, driver’s age, and driver’s gender, were investigated and the corresponding bias factors were developed as needed. The results show that although multi-occupant vehicles are involved in higher percentages of severe accidents than are single-occupant vehicles, multi-occupant vehicles in the whole accident vehicle population were not overrepresented in the accident database. On the other hand, a significant difference was found between the distributions of the ages and genders of drivers involved in accidents and those of the general driving population. An information system that incorporates adjustments for the potential biases was developed to estimate the average vehicle occupancies (AVOs) for different types of roadways on the Florida state roadway system. A reasonableness check of the results from the system shows AVO estimates that are highly consistent with expectations. In addition, comparisons of AVOs from accident data with the field estimates show that the two data sources produce relatively consistent results. While accident records can be used to obtain the historical AVO trends and field data can be used to estimate the current AVOs, no known methods have been developed to project future AVOs. Four regression models for the purpose of predicting weekday AVOs on different levels of geographic areas and roadway types were developed as part of this dissertation. The models show that such socioeconomic factors as income, vehicle ownership, and employment have a significant impact on AVOs.

Estimation and Prediction of Average Vehicle Occupancies using Traffic Accident Records

As congestion management strategies begin to put more emphasis on person trips than vehicle trips, the need for vehicle occupancy data has become more critical. The traditional methods of collecting these data include the roadside windshield method and the carousel method. These methods are labor-intensive and expensive. An alternative to these traditional methods is to make use of the vehicle occupancy information in traffic accident records. This method is cost effective and may provide better spatial and temporal coverage than the traditional methods. However, this method is subject to potential biases resulting from under- and over-involvement of certain population sectors and certain types of accidents in traffic accident records. In this dissertation, three such potential biases, i.e., accident severity, driver¡¯s age, and driver¡¯s gender, were investigated and the corresponding bias factors were developed as needed. The results show that although multi-occupant vehicles are involved in higher percentages of severe accidents than are single-occupant vehicles, multi-occupant vehicles in the whole accident vehicle population were not overrepresented in the accident database. On the other hand, a significant difference was found between the distributions of the ages and genders of drivers involved in accidents and those of the general driving population. An information system that incorporates adjustments for the potential biases was developed to estimate the average vehicle occupancies (AVOs) for different types of roadways on the Florida state roadway system. A reasonableness check of the results from the system shows AVO estimates that are highly consistent with expectations. In addition, comparisons of AVOs from accident data with the field estimates show that the two data sources produce relatively consistent results. While accident records can be used to obtain the historical AVO trends and field data can be used to estimate the current AVOs, no known methods have been developed to project future AVOs. Four regression models for the purpose of predicting weekday AVOs on different levels of geographic areas and roadway types were developed as part of this dissertation. The models show that such socioeconomic factors as income, vehicle ownership, and employment have a significant impact on AVOs.

Estimation of sea surface temperatures and salinity of ODP Site 177-1089 (Appendix A)

ODP Site 1089 is optimally located in order to monitor the occurrence of maxima in Agulhas heat and salt spillage from the Indian to the Atlantic Ocean. Radiolarian-based paleotemperature transfer functions allowed to reconstruct the climatic history for the last 450 kyr at this location. A warm sea surface temperature anomaly during Marine Isotope Stage (MIS) 10 was recognized and traced to other oceanic records along the surface branch of the global thermohaline (THC) circulation system, and is particularly marked at locations where a strong interaction between oceanic and atmospheric overturning cells and fronts occurs. This anomaly is absent in the Vostok ice core deuterium, and in oceanic records from the Antarctic Zone. However, it is present in the deuterium excess record from the Vostok ice core, interpreted as reflecting the temperature at the moisture source site for the snow precipitated at Vostok Station. As atmospheric models predict a subtropical Indian source for such moisture, this provides the necessary teleconnection between East Antarctica and ODP Site 1089, as the subtropical Indian is also the source area of the Agulhas Current, the main climate agent at our study location. The presence of the MIS 10 anomaly in the delta13C foraminiferal records from the same core supports its connection to oceanic mechanisms, linking stronger Agulhas spillover intensity to increased productivity in the study area. We suggest, in analogy to modern oceanographic observations, this to be a consequence of a shallow nutricline, induced by eddy mixing and baroclinic tide generation, which are in turn connected to the flow geometry, and intensity, of the Agulhas Current as it flows past the Agulhas Bank. We interpret the intensified inflow of Agulhas Current to the South Atlantic as responding to the switch between lower and higher amplitude in the insolation forcing in the Agulhas Current source area. This would result in higher SSTs in the Cape Basin during the glacial MIS 10, due to the release into the South Atlantic of the heat previously accumulating in the subtropical and equatorial Indian and Pacific Ocean. If our explanation for the MIS 10 anomaly in terms of an insolation variability switch is correct, we might expect that a future Agulhas SSST anomaly event will further delay the onset of next glacial age. In fact, the insolation forcing conditions for the Holocene (the current interglacial) are very similar to those present during MIS 11 (the interglacial preceding MIS 10), as both periods are characterized by a low insolation variability for the Agulhas Current source area. Natural climatic variability will force the Earth system in the same direction as the anthropogenic global warming trend, and will thus lead to even warmer than expected global temperatures in the near future.

Prospective Estimation of Radiation Dose and Image Quality for Optimized CT Performance

X-ray computed tomography (CT) is a non-invasive medical imaging technique that generates cross-sectional images by acquiring attenuation-based projection measurements at multiple angles. Since its first introduction in the 1970s, substantial technical improvements have led to the expanding use of CT in clinical examinations. CT has become an indispensable imaging modality for the diagnosis of a wide array of diseases in both pediatric and adult populations [1, 2]. Currently, approximately 272 million CT examinations are performed annually worldwide, with nearly 85 million of these in the United States alone [3]. Although this trend has decelerated in recent years, CT usage is still expected to increase mainly due to advanced technologies such as multi-energy [4], photon counting [5], and cone-beam CT [6].

Despite the significant clinical benefits, concerns have been raised regarding the population-based radiation dose associated with CT examinations [7]. From 1980 to 2006, the effective dose from medical diagnostic procedures rose six-fold, with CT contributing to almost half of the total dose from medical exposure [8]. For each patient, the risk associated with a single CT examination is likely to be minimal. However, the relatively large population-based radiation level has led to enormous efforts among the community to manage and optimize the CT dose.

As promoted by the international campaigns Image Gently and Image Wisely, exposure to CT radiation should be appropriate and safe [9, 10]. It is thus a responsibility to optimize the amount of radiation dose for CT examinations. The key for dose optimization is to determine the minimum amount of radiation dose that achieves the targeted image quality [11]. Based on such principle, dose optimization would significantly benefit from effective metrics to characterize radiation dose and image quality for a CT exam. Moreover, if accurate predictions of the radiation dose and image quality were possible before the initiation of the exam, it would be feasible to personalize it by adjusting the scanning parameters to achieve a desired level of image quality. The purpose of this thesis is to design and validate models to quantify patient-specific radiation dose prospectively and task-based image quality. The dual aim of the study is to implement the theoretical models into clinical practice by developing an organ-based dose monitoring system and an image-based noise addition software for protocol optimization.

More specifically, Chapter 3 aims to develop an organ dose-prediction method for CT examinations of the body under constant tube current condition. The study effectively modeled the anatomical diversity and complexity using a large number of patient models with representative age, size, and gender distribution. The dependence of organ dose coefficients on patient size and scanner models was further evaluated. Distinct from prior work, these studies use the largest number of patient models to date with representative age, weight percentile, and body mass index (BMI) range.

With effective quantification of organ dose under constant tube current condition, Chapter 4 aims to extend the organ dose prediction system to tube current modulated (TCM) CT examinations. The prediction, applied to chest and abdominopelvic exams, was achieved by combining a convolution-based estimation technique that quantifies the radiation field, a TCM scheme that emulates modulation profiles from major CT vendors, and a library of computational phantoms with representative sizes, ages, and genders. The prospective quantification model is validated by comparing the predicted organ dose with the dose estimated based on Monte Carlo simulations with TCM function explicitly modeled.

Chapter 5 aims to implement the organ dose-estimation framework in clinical practice to develop an organ dose-monitoring program based on a commercial software (Dose Watch, GE Healthcare, Waukesha, WI). In the first phase of the study we focused on body CT examinations, and so the patient’s major body landmark information was extracted from the patient scout image in order to match clinical patients against a computational phantom in the library. The organ dose coefficients were estimated based on CT protocol and patient size as reported in Chapter 3. The exam CTDIvol, DLP, and TCM profiles were extracted and used to quantify the radiation field using the convolution technique proposed in Chapter 4.

With effective methods to predict and monitor organ dose, Chapters 6 aims to develop and validate improved measurement techniques for image quality assessment. Chapter 6 outlines the method that was developed to assess and predict quantum noise in clinical body CT images. Compared with previous phantom-based studies, this study accurately assessed the quantum noise in clinical images and further validated the correspondence between phantom-based measurements and the expected clinical image quality as a function of patient size and scanner attributes.

Chapter 7 aims to develop a practical strategy to generate hybrid CT images and assess the impact of dose reduction on diagnostic confidence for the diagnosis of acute pancreatitis. The general strategy is (1) to simulate synthetic CT images at multiple reduced-dose levels from clinical datasets using an image-based noise addition technique; (2) to develop quantitative and observer-based methods to validate the realism of simulated low-dose images; (3) to perform multi-reader observer studies on the low-dose image series to assess the impact of dose reduction on the diagnostic confidence for multiple diagnostic tasks; and (4) to determine the dose operating point for clinical CT examinations based on the minimum diagnostic performance to achieve protocol optimization.

Chapter 8 concludes the thesis with a summary of accomplished work and a discussion about future research.

Sea surface temperature estimation of sediment core 86014-12PC51

A recently developed technique for determining past sea surface temperatures (SST), based on an analysis of the unsaturation ratio of long chain C37 methyl alkenones produced by Prymnesiophyceae phytoplankton (U37 k' ), has been applied to an upper Quaternary sediment core from the equatorial Atlantic. U37 k' temperature estimates were compared to those obtained from delta18O of the planktonic foraminifer Globigerinoides sacculifer and of planktonic foraminiferal assemblages for the last glacial cycle. The alkenone method showed 1.8°C cooling at the last glacial maximum, about 1/2 to 1/3 of the decrease shown by the isotopic method (6.3°C) and foraminiferal modern analogue technique estimates for the warm season (3.8°C). Warm season foraminiferal assemblage estimates based on transfer functions are out of phase with the other estimates, showing a 1.4°C drop at the last glacial maximum with an additional 0.9°C drop in the deglaciation. Increased alkenone abundances, total organic carbon percentage and foraminiferal accumulation rates in the last glaciation indicate an increase in productivity of as much as 4 times over present day. These changes are thought to be due to increased upwelling caused by enhanced winds during the glaciation. If U37 k' estimates are correct, as much as 50-70% (up to 4.5°C) of estimated delta18O and modern analogue temperature changes in the last glaciation may have been due to changes in thermocline depth, whereas transfer functions seem more strongly influenced by seasonality changes. This indicates these estimates may be influenced as strongly by other factors as they are by SST, which in the equatorial Atlantic was only reduced slightly in the last glaciation.

(Table 2) Age determination of sediment cores from the Portuguese Margin

We demonstrate that changes in the behavior of the Mediterranean Outflow Water (MOW) prior to and through the last deglaciation played an important role in promoting Meridional Overturning Circulation (MOC). Estimation of past MOW salt and heat fluxes indicates that they gradually increased through the last deglaciation. Between 17.5 and 14.6 thousand years ago (ka B.P., where B.P. references year 1950), net evaporation from the Mediterranean exported sufficient fresh water from the North Atlantic catchment to cause an average salinity increase of 0.5 psu throughout the upper 2000 m of the entire North Atlantic to the north of 25°N. Combined with rapid intensification and shoaling of the MOW plume, which we identify around 15-14.5 ka B.P., this deglacial MOW-related salt accumulation preconditioned the North Atlantic for abrupt resumption of the MOC at 14.6 ka B.P.

Estimation of whole body muscle, adipose/fat mass, validation in health and during weight loss. Development of prediction equations using MRI as reference method

Background: Body composition is affected by diseases, and affects responses to medical treatments, dosage of medicines, etc., while an abnormal body composition contributes to the causation of many chronic diseases. While we have reliable biochemical tests for certain nutritional parameters of body composition, such as iron or iodine status, and we have harnessed nuclear physics to estimate the body’s content of trace elements, the very basic quantification of body fat content and muscle mass remains highly problematic. Both body fat and muscle mass are vitally important, as they have opposing influences on chronic disease, but they have seldom been estimated as part of population health surveillance. Instead, most national surveys have merely reported BMI and waist, or sometimes the waist/hip ratio; these indices are convenient but do not have any specific biological meaning. Anthropometry offers a practical and inexpensive method for muscle and fat estimation in clinical and epidemiological settings; however, its use is imperfect due to many limitations, such as a shortage of reference data, misuse of terminology, unclear assumptions, and the absence of properly validated anthropometric equations. To date, anthropometric methods are not sensitive enough to detect muscle and fat loss. Aims: The aim of this thesis is to estimate Adipose/fat and muscle mass in health disease and during weight loss through; 1. evaluating and critiquing the literature, to identify the best-published prediction equations for adipose/fat and muscle mass estimation; 2. to derive and validate adipose tissue and muscle mass prediction equations; and 3.to evaluate the prediction equations along with anthropometric indices and the best equations retrieved from the literature in health, metabolic illness and during weight loss. Methods: a Systematic review using Cochrane Review method was used for reviewing muscle mass estimation papers that used MRI as the reference method. Fat mass estimation papers were critically reviewed. Mixed ethnic, age and body mass data that underwent whole body magnetic resonance imaging to quantify adipose tissue and muscle mass (dependent variable) and anthropometry (independent variable) were used in the derivation/validation analysis. Multiple regression and Bland-Altman plot were applied to evaluate the prediction equations. To determine how well the equations identify metabolic illness, English and Scottish health surveys were studied. Statistical analysis using multiple regression and binary logistic regression were applied to assess model fit and associations. Also, populations were divided into quintiles and relative risk was analysed. Finally, the prediction equations were evaluated by applying them to a pilot study of 10 subjects who underwent whole-body MRI, anthropometric measurements and muscle strength before and after weight loss to determine how well the equations identify adipose/fat mass and muscle mass change. Results: The estimation of fat mass has serious problems. Despite advances in technology and science, prediction equations for the estimation of fat mass depend on limited historical reference data and remain dependent upon assumptions that have not yet been properly validated for different population groups. Muscle mass does not have the same conceptual problems; however, its measurement is still problematic and reference data are scarce. The derivation and validation analysis in this thesis was satisfactory, compared to prediction equations in the literature they were similar or even better. Applying the prediction equations in metabolic illness and during weight loss presented an understanding on how well the equations identify metabolic illness showing significant associations with diabetes, hypertension, HbA1c and blood pressure. And moderate to high correlations with MRI-measured adipose tissue and muscle mass before and after weight loss. Conclusion: Adipose tissue mass and to an extent muscle mass can now be estimated for many purposes as population or groups means. However, these equations must not be used for assessing fatness and categorising individuals. Further exploration in different populations and health surveys would be valuable.

Indirect child mortality estimation technique to identify trends of under-five mortality in Ethiopia.

Background: In sub-Saharan African countries, the chance of a child dying before the age of five years is high. The problem is similar in Ethiopia, but it shows a decrease over years. Methods: The 2000; 2005 and 2011 Ethiopian Demographic and Health Survey results were used for this work. The purpose of the study is to detect the pattern of under-five child mortality overtime. Indirect child mortality estimation technique is adapted to examine the under-five child mortality trend in Ethiopia. Results: From the result, it was possible to see the trend of under-five child mortality in Ethiopia. The under-five child mortality shows a decline in Ethiopia. Conclusion: From the study, it can be seen that there is a positive correlation between mother and child survival which is almost certain in any population. Therefore, this study shows the trend of under-five mortality in Ethiopia and decline over time.

Written in bones: Anthropological study of skeletal remains from middle age population of Leopoli Cencelle, (Viterbo)"

[en] Anthropological study of the human remains of a medieval cemetery in Leopoli-Cencelle in which the sex attribution, the estimation of age at death and the estimation of stature are taken into account.

Configuring a Better Estimation of Kidney Size in Obese Children and Adolescents

Background: Obesity ignites numerous health and psychosocial problems and is associated with various comorbidities. Body mass index (BMI) is also independently associated with improved risk for numerous kidney disorders. As renal length is considered a vital parameter in the clinical assessment of renal patients, normal renal length has to be defined in accordance to BMI. Objectives: The aim of this study was to define normal kidney length in obese children, comparing ultrasound measurements of the kidney length in obese and non-obese children and adolescents, in order to reduce unnecessary evaluations for nephromegaly. Patients and Methods: Fifty obese children and adolescents and 50 non-obese children and adolescents, aged 1-19 years, were selected from patients of pediatric clinics in two hospitals (Rasoul-e-Akram and Shahid Fahmideh) in Tehran between June 2010 and 2012. After the nephrologist’s and endocrinologist’s approval, the largest longitudinal renal dimension was measured in deep inspiration position by abdomino-pelvic ultrasonography in both groups. Results: It was revealed that both kidneys in obese group were significantly larger than in control group (P = 0.044 and 0.040, respectively). Obesity status, height and age were proven to be significant and independent predictors of length of both kidneys. In both groups length of left kidney was significantly larger than that of right kidney (P < 0.001). Conclusions: A specific standard cut-point limit or norm gram has to be formulated for obese children and adolescents in order to facilitate the diagnosis of kidney diseases, including organomegaly, in these patients.

Landscape strategies in Bronze Age Southwestern Cyprus (2500-1100 B.C.)

This thesis concerns the analysis of the socio-economic transformation of communities in Bronze Age southwestern Cyprus. Through the adoption of a dialectical perspective of analysis, individuals and environment are considered part of the same unity: they are cooperating agents in shaping society and culture. The Bronze Age is a period of intense transformation in the organization of local communities, made of a continuous renegotiation of the socio-economic roles and interactions. The archaeological record from this portion of the island allows one to go beyond the investigation of the complex and articulated transition from the EBA-MBA agro-pastoral and self-sufficient communities to the LBA centralized and trade-oriented urban-centres. Through a shifting of analytical scales, the emerging picture suggests major transformations in the individual-community-territory dialectical relations. A profound change in the materials conditions of social life, as well as in the superstructural realm, was particularly entailed by the dissolution of the relation to the earth, due to the emergence of new forms of land exploitation/ownership and to the shift of the settlement pattern in previously unknown areas. One of the key points of this thesis is the methodological challenge of working with legacy survey data as I re-analysed a diverse archaeological legacy, which is the result of more than fifty years of survey projects, rescue and research-oriented excavations, as well as casual discoveries. Source critique and data evaluation are essential requirements in an integrative and cross-disciplinary regional perspective, in the comprehensive processing of heterogeneous archaeological and environmental datasets. Through the estimation of data precision and certainty, I developed an effective - but simple - method to critically evaluate existing datasets and to inter-correlate them without losing their original complexity. This powerful method for data integration can be applied to similar datasets belonging to other regions and other periods as it originates from the evaluation of larger methodological and theoretical issues that are not limited to my spatial and temporal focus. As I argue in this thesis, diverse archaeological legacies can be efficiently re-analysed through an integrative and regional methodology. The adoption of a regional scale of analysis can provide an excellent perspective on the complexity of transformations in ancient societies, thus creating a fundamental bridge between the local stories and grand landscape narratives.