Positron emission tomography (PET) tumor segmentation and quantification: Development of new algorithms

Tumor functional volume (FV) and its mean activity concentration (mAC) are the quantities derived from positron emission tomography (PET). These quantities are used for estimating radiation dose for a therapy, evaluating the progression of a disease and also use it as a prognostic indicator for predicting outcome. PET images have low resolution, high noise and affected by partial volume effect (PVE). Manually segmenting each tumor is very cumbersome and very hard to reproduce. To solve the above problem I developed an algorithm, called iterative deconvolution thresholding segmentation (IDTS) algorithm; the algorithm segment the tumor, measures the FV, correct for the PVE and calculates mAC. The algorithm corrects for the PVE without the need to estimate camera's point spread function (PSF); also does not require optimizing for a specific camera. My algorithm was tested in physical phantom studies, where hollow spheres (0.5-16 ml) were used to represent tumors with a homogeneous activity distribution. It was also tested on irregular shaped tumors with a heterogeneous activity profile which were acquired using physical and simulated phantom. The physical phantom studies were performed with different signal to background ratios (SBR) and with different acquisition times (1-5 min). The algorithm was applied on ten clinical data where the results were compared with manual segmentation and fixed percentage thresholding method called T50 and T60 in which 50% and 60% of the maximum intensity respectively is used as threshold. The average error in FV and mAC calculation was 30% and -35% for 0.5 ml tumor. The average error FV and mAC calculation were ~5% for 16 ml tumor. The overall FV error was ∼10% for heterogeneous tumors in physical and simulated phantom data. The FV and mAC error for clinical image compared to manual segmentation was around -17% and 15% respectively. In summary my algorithm has potential to be applied on data acquired from different cameras as its not dependent on knowing the camera's PSF. The algorithm can also improve dose estimation and treatment planning.^

Seawater carbonate chemistry and skeletal development, size, weight, total lipid and symbiont density of coral Favia fragum in a laboratory experiment

Ocean acidification (OA) threatens the existence of coral reefs by slowing the rate of calcium carbonate (CaCO3) production of framework-building corals thus reducing the amount of CaCO3 the reef can produce to counteract natural dissolution. Some evidence exists to suggest that elevated levels of dissolved inorganic nutrients can reduce the impact of OA on coral calcification. Here, we investigated the potential for enhanced energetic status of juvenile corals, achieved via heterotrophic feeding, to modulate the negative impact of OA on calcification. Larvae of the common Atlantic golf ball coral, Favia fragum, were collected and reared for 3 weeks under ambient (421 µatm) or significantly elevated (1,311 µatm) CO2 conditions. The metamorphosed, zooxanthellate spat were either fed brine shrimp (i.e., received nutrition from photosynthesis plus heterotrophy) or not fed (i.e., primarily autotrophic). Regardless of CO2 condition, the skeletons of fed corals exhibited accelerated development of septal cycles and were larger than those of unfed corals. At each CO2 level, fed corals accreted more CaCO3 than unfed corals, and fed corals reared under 1,311 µatm CO2 accreted as much CaCO3 as unfed corals reared under ambient CO2. However, feeding did not alter the sensitivity of calcification to increased CO2; Delta calcification/Delta Omega was comparable for fed and unfed corals. Our results suggest that calcification rates of nutritionally replete juvenile corals will decline as OA intensifies over the course of this century. Critically, however, such corals could maintain higher rates of skeletal growth and CaCO3 production under OA than those in nutritionally limited environments.

Early growth characteristics and the risk of reduced lung function and asthma : a meta-analysis of 25,000 children

Peer reviewed

Early growth characteristics and the risk of reduced lung function and asthma : a meta-analysis of 25,000 children

Peer reviewed

Colorado's Piceance Basin: Variation in the local public finance effects of oil and gas development

A large increase in natural gas production occurred in western Colorado’s Piceance basin in the mid- to late-2000s, generating a surge in population, economic activity, and heavy truck traffic in this rural region. We describe the fiscal effects related to this development for two county governments: Garfield and Rio Blanco, and two city governments: Grand Junction and Rifle. Counties maintain rural road networks in Colorado, and Garfield County’s ability to fashion agreements with operators to repair roads damaged during operations helped prevent the types of large new costs seen in Rio Blanco County, a neighboring county with less government capacity and where such agreements were not made. Rifle and Grand Junction experienced substantial oil- and gas-driven population growth, with greater challenges in the smaller, more isolated, and less economically diverse city of Rifle. Lessons from this case study include the value of crafting road maintenance agreements, fiscal risks for small and geographically isolated communities experiencing rapid population growth, challenges associated with limited infrastructure, and the desirability of flexibility in the allocation of oil- and gas-related revenue.

Local fiscal effects of oil and gas development in eight states

Oil and gas production in the United States has increased dramatically in the past 10 years. This growth has important implications for local governments, which often see new revenues from a variety of sources: property taxes on oil and gas property, sales taxes driven by the oil and gas workforce, allocations of state revenues from severance taxes or state and federal leases, leases on local government land, and contributions from oil and gas companies to support local services. At the same time, local governments tend to experience a range of new costs such as road damage caused by heavy industry truck traffic, increased demand for emergency services and law enforcement, and challenges with workforce retention. This report examines county and municipal fiscal effects in 14 oil- and gas-producing regions of eight states: AK, CA, KS, OH, OK, NM, UT, and WV. We find that for most local governments, oil and gas development—whether new or longstanding—has a positive effect on local public finances. However, effects can vary substantially due to a variety of local factors and policy issues. For some local governments, particularly those in rural regions experiencing large increases in development, revenues have not kept pace with rapidly increased costs and demand for services, particularly on road repair.

Seawater carbonate chemistry, length, mass and otholith development of spiny damselfish Acanthochromis polyacanthus during experiments, 2011

Determining which marine species are sensitive to elevated CO2 and reduced pH, and which species tolerate these changes, is critical for predicting the impacts of ocean acidification on marine biodiversity and ecosystem function. Although adult fish are thought to be relatively tolerant to higher levels of environmental CO2, very little is known about the sensitivity of juvenile stages, which are usually much more vulnerable to environmental change. We tested the effects of elevated environmental CO2 on the growth, survival, skeletal development and otolith (ear bone) calcification of a common coral reef fish, the spiny damselfish Acanthochromis polyacanthus. Newly hatched juveniles were reared for 3 wk at 4 different levels of PCO2(seawater) spanning concentrations already experienced in near-reef waters (450 µatm CO2) to those predicted to occur over the next 50 to 100 yr in the IPCC A2 emission scenario (600, 725, 850 µatm CO2). Elevated PCO2 had no effect on juvenile growth or survival. Similarly, there was no consistent variation in the size of 29 different skeletal elements that could be attributed to CO2 treatments. Finally, otolith size, shape and symmetry (between left and right side of the body) were not affected by exposure to elevated PCO2, despite the fact that otoliths are composed of aragonite. This is the first comprehensive assessment of the likely effects of ocean acidification on the early life history development of a marine fish. Our results suggest that juvenile A. polyacanthus are tolerant of moderate increases in environmental CO2 and that further acidification of the ocean will not, in isolation, have a significant effect on the early life history development of this species, and perhaps other tropical reef fishes

Hypoxia-induced epigenetic modifications are associated with cardiac tissue fibrosis and the development of a myofibroblast-like phenotype

Ischemia caused by coronary artery disease and myocardial infarction leads to aberrant ventricular remodeling and cardiac fibrosis. This occurs partly through accumulation of gene expression changes in resident fibroblasts, resulting in an overactive fibrotic phenotype. Long-term adaptation to a hypoxic insult is likely to require significant modification of chromatin structure in order to maintain the fibrotic phenotype. Epigenetic changes may play an important role in modulating hypoxia-induced fibrosis within the heart. Therefore, the aim of the study was to investigate the potential pro-fibrotic impact of hypoxia on cardiac fibroblasts and determine whether alterations in DNA methylation could play a role in this process. This study found that within human cardiac tissue, the degree of hypoxia was associated with increased expression of collagen 1 and alpha-smooth muscle actin (ASMA). In addition, human cardiac fibroblast cells exposed to prolonged 1% hypoxia resulted in a pro-fibrotic state. These hypoxia-induced pro-fibrotic changes were associated with global DNA hypermethylation and increased expression of the DNA methyltransferase (DNMT) enzymes DNMT1 and DNMT3B. Expression of these methylating enzymes was shown to be regulated by hypoxia-inducible factor (HIF)-1α. Using siRNA to block DNMT3B expression significantly reduced collagen 1 and ASMA expression. In addition, application of the DNMT inhibitor 5-aza-2'-deoxycytidine suppressed the pro-fibrotic effects of TGFβ. Epigenetic modifications and changes in the epigenetic machinery identified in cardiac fibroblasts during prolonged hypoxia may contribute to the pro-fibrotic nature of the ischemic milieu. Targeting up-regulated expression of DNMTs in ischemic heart disease may prove to be a valuable therapeutic approach.

Land, Power and Technology : Essays on Political Economy and Historical Development

Land Ownership and Development: Evidence from Postwar Japan This paper analyzes the effect of land ownership on technology adoption and structural transformation. A large-scale land reform in postwar Japan enforced a large number of tenant farmers who were cultivating land to become owners of this land. I find that the municipalities which had many owner farmers after the land reform tended to experience a quick entry of new agricultural machines which became available after the reform. The adoption of the machines reduced the dependence on family labor, and led to a reallocation of labor from agriculture to industries and service sectors in urban centers when these sectors were growing. I also analyze the aggregate impact of labor reallocation on economic growth by using a simple growth model and micro data. I find that it increased GDP by about 12 percent of the GDP in 1974 during 1955-74. I also find a large and positive effect on agricultural productivity. Loyalty and Treason: Theory and Evidence from Japan's Land Reform A historically large-scale land reform in Japan after World War II enforced by the occupation forces redistributed a large area of farmlands to tenant farmers. The reform demolished hierarchical structures by weakening landlords' power in villages and towns. This paper investigates how the change in the social and economic structure of small communities affects electoral outcomes in the presence of clientelism. I find that there was a considerable decrease in the vote share of conservative parties in highly affected areas after the reform. I find the supporting evidence that the effect was driven by the fact that the tenant farmers who had obtained land exited from the long-term tenancy contract and became independent landowners. The effect was relatively persistent. Finally, I also find the surprising result that there was a decrease, rather than an increase, in turnout in these areas after the reform.  Geography and State Fragmentation We examine how geography affects the location of borders between sovereign states in Europe and surrounding areas from 1500 until today at the grid-cell level. This is motivated by an observation that the richest places in this region also have the highest historical border presence, suggesting a hitherto unexplored link between geography and modern development, working through state fragmentation. The raw correlations show that borders tend to be located on mountains, by rivers, closer to coasts, and in areas suitable for rainfed, but not irrigated, agriculture. Many of these patterns also hold with rigorous spatial controls. For example, cells with more rivers and more rugged terrain than their neighboring cells have higher border densities. However, the fragmenting effects of suitability for rainfed agriculture are reversed with such neighbor controls. Moreover, we find that borders are less likely to survive over time when they separate large states from small, but this size-difference effect is mitigated by, e.g., rugged terrain.

The effect of garlic extract on growth, haematology and cell-mediated immune response of newborn goat kids

The present study was carried out to evaluate the effect of different levels of garlic extract supplemented in milk on growth rate, haematology and cell–mediated immune response of Markhoz newborn goat kids. Twenty four newborn goat kids (aged 7+/-3days) were randomly assigned to four groups. The groups consisted of control (received milk without garlic extract), T1, T2 and T3 which received milk supplemented with 62.5, 125 and 250 mg aqueous garlic extract per kg live weight per day for 42 days, respectively. Body weights were measured weekly throughout the experimental period. At day 42, about 10 ml blood samples were collected from each kid via the jugular vein for haematological study. Cell–mediated immune response was evaluated through double skin thickness after intradermal injection of phyto-hematogglutinin (PHA) at day 21 and 42. Total gain was significantly higher for kids in T3 (P<0.05) compared with the control group. Average daily gain (ADG) in T3 group in week 4–5 was higher (P<0.05). Significant differences in globulin (P<0.01), hemoglobin (Hb; P<0.001), hematocrit (PCV; P<0.001), erythrocyte (RBC; P<0.001), neutrophil (P<0.001), lymphocyte (P<0.001) and leukocyte (WBC; P<0.001) were observed among groups. Hb, PCV, RBC, lymphocytes and WBC were higher in kids given garlic extract supplementation. There was a significant difference of double skin thickness among the groups at day 42 (P<0.01). In conclusion, this study indicated that milk supplemented with aqueous garlic extract improved growth rate and immunity of newborn goat kids.

Towards Empowerment: Narrative Study of Counselling Psychology Trainees and How They Make Sense of Their Personal and Professional Development in the Context of Their Past Experiences

The discipline of counselling psychology continues to grow and change in response to social, economic and political pressures. It has been argued that its quest for a coherent and distinct identity, which emphasises the possibility of the coexistence of multiple approaches, creates an inherently uncertain and dilemmatic training environment that may hinder the development of trainees’ professional identities. In order to gain a deeper understanding of the issue at hand, the aim was to explore how final year trainees and newly qualified counselling psychologists constructed and made sense of their emerging professional identities and what experiences, past and present, they drew upon in the context of their training to shape those identities. Applying narrative inquiry to analyse eight open-ended interviews, eight preliminary themes were originally identified in participants’ narratives, which with further refinements lead to stories of struggle and marginalisation, growth and discovery, and power and resilience. Participants’ stories of struggle and marginalisation emerged in reference to early family dynamics and stressful life experiences, which seemed to also foster a strong identification with the counselling psychology profession, while stories of growth and discovery focused on the importance of having supportive figures, who helped to instill a sense of security and create an atmosphere of openness. It was in this learning environment that participants felt it was possible to develop a more resilient, empowered professional self, which allowed them to shed an earlier sense of struggle and vulnerability. However, where more of an emphasis was placed on power and resilience, there seemed to be less room for participants to express other feelings that came into conflict with their preferred sense of professional self. While there seems to be a need for a ‘safer’ climate, in which trainees could voice and acknowledge anxieties, vulnerabilities and limitations, addressing concerns around power and vulnerability that may be contributing to the silencing of particular voices and identities may be equally important if trainees are to develop coherent and distinct counselling psychologist identities.

Territorial innovation, social ventures and local development: An exploratory case study

Social innovation is recognized as an important driver of growth and social value creation. Social innovative strategies are often pursued at the local level, by (social) organizations which have a more comprehensive knowledge of the complex social problems that a specific community is facing. The objective of the present study is to analyse the extent to which innovative social ventures are able to contribute to local development. By means of a qualitative approach, based on the case study method, we attempt to illustrate the innovative strategies conceived on the ground by a social venture specifically created to foster the local development of its inhabitants. The results shows that social innovation is a viable strategy to revitalize the economic growth of a region, through the creation of local employment on the basis of village’s traditional activities that are redefined in a new and competitive way. However, to be successful the strategy demands the deep knowledge of existing social problems as well as the availability of endogenous local resources and capabilities that could be used by social entrepreneurs. Therefore, social innovation ensures that local development and social cohesion are achieved in a sustainable way, at the same time that cultural and environmental heritage are also preserved.

The impact of social housing on health in Glasgow and Baltimore, 1930-1980

This dissertation seeks to discern the impact of social housing on public health in the cities of Glasgow, Scotland and Baltimore, Maryland in the twentieth century. Additionally, this dissertation seeks to compare the impact of social housing policy implementation in both cities, to determine the efficacy of social housing as a tool of public health betterment. This is accomplished through the exposition and evaluation of the housing and health trends of both cities over the course of the latter half of the twentieth century. Both the cities of Glasgow and Baltimore had long struggled with both overcrowded slum districts and relatively unhealthy populations. Early commentators had noticed the connection between insanitary housing and poor health, and sought a solution to both of these problems. Beginning in the 1940s, housing reform advocates (self-dubbed ‘housers') pressed for the development of social housing, or municipally-controlled housing for low-income persons, to alleviate the problems of overcrowded slum dwellings in both cities. The impetus for social housing was twofold: to provide affordable housing to low-income persons and to provide housing that would facilitate healthy lives for tenants. Whether social housing achieved these goals is the crux of this dissertation. In the immediate years following the Second World War, social housing was built en masse in both cities. Social housing provided a reprieve from slum housing for both working-class Glaswegians and Baltimoreans. In Baltimore specifically, social housing provided accommodation for the city’s Black residents, who found it difficult to occupy housing in White neighbourhoods. As the years progressed, social housing developments in both cities faced unexpected problems. In Glasgow, stable tenant flight (including both middle class and skilled artisan workers)+ resulted in a concentration of poverty in the city’s housing schemes, and in Baltimore, a flight of White tenants of all income levels created a new kind of state subsidized segregated housing stock. The implementation of high-rise tower blocks in both cities, once heralded as a symbol of housing modernity, also faced increased scrutiny in the 1960s and 1970s. During the period of 1940-1980, before policy makers in the United States began to eschew social housing for subsidized private housing vouchers and community based housing associations had truly taken off in Britain, public health professionals conducted academic studies of the impact of social housing tenancy on health. Their findings provide the evidence used to assess the second objective of social housing provision, as outlined above. Put simply, while social housing units were undoubtedly better equipped than slum dwellings in both cities, the public health investigations into the impact of rehousing slum dwellers into social housing revealed that social housing was not a panacea for each city’s social and public health problems.

Effect of temperature on genomic and some biological indices during embryonic and larval development of Caspian trout Salmo trutta caspius Kessler, 1877

Since 1966 especially recent decade, Caspian trout (Salmo trutta caspius Kessler, 1877) considered as a strategic endemic species for Caspian Sea fisheries resources also coldwater aquaculture in Iran. Nowadays habitat condition effects on this subspecies during life stages, artificial breeding and incubation period noticed by research and execution sessions of fisheries in Iran. Incubation duration of Caspian trout from artificial fertilization followed by green egg and eyed egg, hatching and yolk sac absorption identified as most sensitive stages for fish and any pollution, stress and deviation by natural life conditions of embryo up to larvae could provide possible mortalities and observable or hidden alterations. Among all vital factors for Caspian trout welfare even in conservation plans and stocks rehabilitation programs or recent attempts for domestication of this fish for introduction to cold water aquaculture industry, water temperature as the most important physical factor which might conserve or induce stress to rearing environment condition is not considered yet. In hatcheries activities, the temperature for incubation and rearing Caspian trout eggs is determining by available water temperature and wide range of temperatures in governmental or private farms is using depend on the water resources availability. Also global climate change consideration and increase temperature trend accompany with group of physical and chemical factors provided by fish farm discharges and other source points entered to the migration pathway of Caspian trout in spawning season were not investigated before. Natural spawning migration pathway is upstream of Caspian tout south and south west rivers especially in Cheshmehkileh upstream in Tonekabon, Iran directed this research focus on the mentioned location. For simulation of natural spawning bed for Caspian trout, water supplied from the upstream of Daryasar branch as headwater of Cheshmehkileh River which provided REDD water condition for in vitro incubation. Green eggs treatments of wild and F1 cultured brooders both 3+ were incubated. Incubation implemented in dark, constant temperature (4, 8, 12 degree centigrade) and DO–pH–temperature digital monitoring in 3 recycling incubators ended to yolk sac absorption and entering larval stage. Hatching success, possible genome alterations by HSP70 gene expression and comet assay implemented as diagnostic tools in 3 life stages of eyed egg– Alevin and Larvae. Numbers and diameters of larvae white fiber muscles measured by histology experiment and Hematoxylin–eosine staining. Results stated significant effect of incubation temperature on hatching success, genome and white fiber muscles of wild and F1 samples. Hatching success measured as 31% and 38% for cultured and wild cold treatments, 79% and 91% for normal and 64% and 73% for warm cultured and wild treatments respectively. Considerable mortality occurred for cold treatment and 8 degree centigrade stated the best thermal condition in normal incubator according to hatching success in wild Caspian trout samples.