Gene expression variation between distinct areas of breast cancer measured from paraffin-embedded tissue cores

BACKGROUND: Diagnosis and prognosis in breast cancer are mainly based on histology and immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE) material. Recently, gene expression analysis was shown to elucidate the biological variance between tumors and molecular markers were identified that led to new classification systems that provided better prognostic and predictive parameters. Archived FFPE samples represent an ideal source of tissue for translational research, as millions of tissue blocks exist from routine diagnostics and from clinical studies. These should be exploited to provide clinicians with more accurate prognostic and predictive information. Unfortunately, RNA derived from FFPE material is partially degraded and chemically modified and reliable gene expression measurement has only become successful after implementing novel and optimized procedures for RNA isolation, demodification and detection. METHODS: In this study we used tissue cylinders as known from the construction of tissue microarrays. RNA was isolated with a robust protocol recently developed for RNA derived from FFPE material. Gene expression was measured by quantitative reverse transcription PCR. RESULTS: Sixteen tissue blocks from 7 patients diagnosed with multiple histological subtypes of breast cancer were available for this study. After verification of appropriate localization, sufficient RNA yield and quality, 30 tissue cores were available for gene expression measurement on TaqMan(R) Low Density Arrays (16 invasive ductal carcinoma (IDC), 8 ductal carcinoma in situ (DCIS) and 6 normal tissue), and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO), the estrogen receptor status and the HER2 status. The PRO scores measured from entire sections were similar to PRO scores determined from IDC tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores than cores derived from IDC or DCIS of the same block or from different blocks of the same patient. CONCLUSION: We have developed optimized protocols for RNA isolation from histologically distinct areas. RNA prepared from FFPE tissue cores is suitable for gene expression measurement by quantitative PCR. Distinct molecular scores could be determined from different cores of the same tumor specimen.

Pond-Breeding Amphibian Species Distributions in a Beaver-Modified Landscape, Acadia National Park, Mount Desert Island, Maine

In order to maintain pond-breeding amphibian species richness, it is important to understand how both natural and anthropogenic disturbances affect species assemblages and individual species distributions both at the scale of individual ponds and at a larger landscape scale. The goal of this project was to investigate what characteristics of ponds and the surrounding wetland landscape were most effective in predicting pond-breeding species richness and the individual occurrence of wood frog (Rana sylvatica), bullfrog (Rana catesbeiana) and pickerel frog (Rana palustris) breeding sites in a beaver-modified landscape and how this landscape has changed over time. The wetland landscape of Acadia National Park was historically modified by the natural disturbance cycles of beaver (Castor cazadensis), and since their reintroduction to the island in 1921, beaver have played a large role in creating and maintaining palustrine wetlands. In 2000 and 2001, I studied pond-breeding amphibian assemblages at 71 palustrine wetlands in Acadia National Park, Mount Desert Island, Maine. I determined breeding presence of 7 amphibian species and quantified 15 variables describing local pond conditions and characteristics of the wetland landscape. I developed a priori models to predict sites with high amphibian species and used model selection with Akaike's Information Criterion (AIC) to identify important variables. Single species models were also developed to predict wood frog, bullfrog and pickerel frogs breeding presence. The variables for wetland connectivity by stream corridors and the presence of beaver disturbance were the most effective variables to predict sites with high amphibian richness. Wood frog breeding was best predicted by local scale variables describing temporary, fishless wetlands and the absence of active beaver disturbance. Abandoned beaver sites provided wood frog breeding habitat (70%) in a similar proportion to that found in non beaver-influenced sites (79%). In contrast, bullfrog breeding presence was limited to active beaver wetlands with fish and permanent water, and 80% of breeding sites were large (≥2ha in size). Pickerel frog breeding site selection was predicted best by the connectivity of sites in the landscape by stream corridors. Models including the presence of beaver disturbance, greater wetland perimeter and greater depth were included in the confidence set of pickerel frog models but showed considerably less support. Analysis of historic aerial photographs showed an 89% increase in the total number of ponded wetlands available in the landscape between the years of 1944 and 1997. Beaver colonization generally converted forested wetlands and riparian areas to open water and emergent wetlands. Temporal colonization of beaver wetlands favored large sites low in the watersheds and sites that were impounded later were generally smaller, higher in the watershed, and more likely to be abandoned. These results suggest that beaver have not only increased the number of available breeding sites in the landscape for pond-breeding amphibians, but the resulting mosaic of active and abandoned beaver wetlands also provides suitable breeding habitat for species with differing habitat requirements.

Trends in socioeconomic inequalities in amenable mortality in urban areas of Spanish cities, 1996-2007

Background: While research continues into indicators such as preventable and amenable mortality in order to evaluate quality, access, and equity in the healthcare, it is also necessary to continue identifying the areas of greatest risk owing to these causes of death in urban areas of large cities, where a large part of the population is concentrated, in order to carry out specific actions and reduce inequalities in mortality. This study describes inequalities in amenable mortality in relation to socioeconomic status in small urban areas, and analyses their evolution over the course of the periods 1996–99, 2000–2003 and 2004–2007 in three major cities in the Spanish Mediterranean coast (Alicante, Castellón, and Valencia). Methods: All deaths attributed to amenable causes were analysed among non-institutionalised residents in the three cities studied over the course of the study periods. Census tracts for the cities were grouped into 3 socioeconomic status levels, from higher to lower levels of deprivation, using 5 indicators obtained from the 2001 Spanish Population Census. For each city, the relative risks of death were estimated between socioeconomic status levels using Poisson’s Regression models, adjusted for age and study period, and distinguishing between genders. Results: Amenable mortality contributes significantly to general mortality (around 10%, higher among men), having decreased over time in the three cities studied for men and women. In the three cities studied, with a high degree of consistency, it has been seen that the risks of mortality are greater in areas of higher deprivation, and that these excesses have not significantly modified over time. Conclusions: Although amenable mortality decreases over the time period studied, the socioeconomic inequalities observed are maintained in the three cities. Areas have been identified that display excesses in amenable mortality, potentially attributable to differences in the healthcare system, associated with areas of greater deprivation. Action must be taken in these areas of greater inequality in order to reduce the health inequalities detected. The causes behind socioeconomic inequalities in amenable mortality must be studied in depth.

Trends in socioeconomic inequalities in preventable mortality in urban areas of 33 Spanish cities, 1996–2007 (MEDEA project)

Background: Preventable mortality is a good indicator of possible problems to be investigated in the primary prevention chain, making it also a useful tool with which to evaluate health policies particularly public health policies. This study describes inequalities in preventable avoidable mortality in relation to socioeconomic status in small urban areas of thirty three Spanish cities, and analyses their evolution over the course of the periods 1996–2001 and 2002–2007. Methods: We analysed census tracts and all deaths occurring in the population residing in these cities from 1996 to 2007 were taken into account. The causes included in the study were lung cancer, cirrhosis, AIDS/HIV, motor vehicle traffic accidents injuries, suicide and homicide. The census tracts were classified into three groups, according their socioeconomic level. To analyse inequalities in mortality risks between the highest and lowest socioeconomic levels and over different periods, for each city and separating by sex, Poisson regression were used. Results: Preventable avoidable mortality made a significant contribution to general mortality (around 7.5%, higher among men), having decreased over time in men (12.7 in 1996–2001 and 10.9 in 2002–2007), though not so clearly among women (3.3% in 1996–2001 and 2.9% in 2002–2007). It has been observed in men that the risks of death are higher in areas of greater deprivation, and that these excesses have not modified over time. The result in women is different and differences in mortality risks by socioeconomic level could not be established in many cities. Conclusions: Preventable mortality decreased between the 1996–2001 and 2002–2007 periods, more markedly in men than in women. There were socioeconomic inequalities in mortality in most cities analysed, associating a higher risk of death with higher levels of deprivation. Inequalities have remained over the two periods analysed. This study makes it possible to identify those areas where excess preventable mortality was associated with more deprived zones. It is in these deprived zones where actions to reduce and monitor health inequalities should be put into place. Primary healthcare may play an important role in this process.

Simple In Vitro Assay for Determining the Sensitivity of Plasmodium vivax Isolates from Fresh Human Blood to Antimalarials in Areas where P. vivax Is Endemic

The aim of this study was to develop a simple, field-practical, and effective in vitro method for determining the sensitivity of fresh erythrocytic Plasmodium vivax isolates to a range of antimalarials. The method used is a modification of the standard World Health Organization (WHO) microtest for determination of P.falciparum drug sensitivity. The WHO method was modified by removing leukocytes and using a growth medium supplemented with AB(+) serum. We successfully carried out 34 in vitro drug assays on 39 P. vivax isolates collected from the Mae Sod malaria clinic, Tak Province, Thailand. The mean percentage of parasites maturing to schizonts (six or more merozoites) in control wells was 66.5% +/- 5.9% (standard deviation). This level of growth in the control wells enabled rapid microscopic determination (5 min per isolate per drug) of the MICs of chloroquine, dihydroartemisinin, WR238605 (tafenoquine), and sulfadoxine. P. vivax was relatively sensitive to chloroquine (MIC = 160 ng/ml, 50% inhibitory concentration [IC50] = 49.8 ng/ml) and dihydroartemisinin (MIC = 0.5 ng/ml, IC50 = 0.47 ng/ml). The poor response of P. vivax to both tafenoquine (MIC = 14,000 ng/ml, IC50 = 9,739 ng/ml) and sulfadoxine (MIC = 500,000 ng/ml, IC50 = 249,000 ng/ml) was due to the slow action of these drugs and the innate resistance of P. vivax to sulfadoxine. The in vitro assay developed in our study should be useful both for assessing the antimalarial sensitivity of P. vivax populations and for screening new antimalarials in the absence of long-term P. vivax cultures.

Equilibrium adsorption in cylindrical mesopores: A modified Broekhoff and de boer theory versus density functional theory

This paper presents a thermodynamic analysis of capillary condensation phenomena in cylindrical pores. Here, we modified the Broekhoff and de Boer (BdB) model for cylindrical pores accounting for the effect of the pore radius on the potential exerted by the pore walls. The new approach incorporates the recently published standard nitrogen and argon adsorption isotherm on nonporous silica LiChrospher Si-1000. The developed model is tested against the nonlocal density functional theory (NLDFT), and the criterion for this comparison is the condensation/evaporation pressure versus the pore diameter. The quantitative agreement between the NLDFT and the refined version of the BdB theory is ascertained for pores larger than 2 nm. The modified BdB theory was applied to the experimental adsorption branch of adsorption isotherms of a number of MCM-41 samples to determine their pore size distributions (PSDs). It was found that the PSDs determined with the new BdB approach coincide with those determined with the NLDFT (also using the experimental adsorption branch). As opposed to the NLDFT, the modified BdB theory is very simple in its utilization and therefore can be used as a convenient tool to obtain PSDs of all mesoporous solids from the analysis of the adsorption branch of adsorption isotherms of any subcritical fluids.

(Table 3, page 280) Chemical composition of micronodules from a series of stations and sediment depths from Areas C, F, G and K in the Pacific Ocean from R/V Sonne Cruise SO06

Compositional data for coexisting manganese nodules, micronodules, sediments and pore waters from five areas in the equatorial and S.W. Pacific have been obtained. This represents the largest study of its type ever undertaken to establish the distribution of elements between the various phases within the sediment column. The composition of manganese nodules, micronodules and sediments (on a carbonate-free basis) shows marked differences between the equatorial high productivity zone and the low productivity region of the S.W. Pacific. In the case of the nodules, th is reflects an increased supply of transition elements (notably Ni, Cu and Zn) to the nodules as a result of the in situ dissolution of siliceous tests within the sediment column in the equatorial Pacific high productivity zone. Micronodules display similar, but somewhat different, compositions to those of the associated nodules in each area. Micronodule composition is therefore influenced by the same basic factors that control nodule composition, but is modified by dissolution of the micronodules in situ within the sediment column. Locally, as in the area immediately south of the Marquesas Fracture Zone, the micronodule population is contaminated by small, angular volcanic rock fragments; this leads to apparently anomalous micronodule compositions. Micronodules appear to be a transient feature in the sediment column, especially in the equatorial Pacific. Dissolution of micronodules in the sediment column therefore represents an important source of elements for the growth of manganese nodules in the equatorial Pacific. Sediment composition is markedly influenced by the carbonate content. On a carbonate-free basis, the sediments from the equatorial high productivity zone are quite distinct in composition from those in the S.W. Pacific. This reflects differences in the lithology of the sediments. In the Aitutaki Passage, the local influence of volcanoclastic material in sediment composition has been established. The major cations and anions in pore waters measured here show no major differences between equatorial and S.W. Pacific sediments. Silica is, however, higher in equatorial Pacific pore waters reflecting the dissolution of siliceous tests in these sediments.

The Performance Characteristics of a Surface-Modified Cutting Tool

In the past, many papers have been presented which show that the coating of cutting tools often yields decreased wear rates and reduced coefficients of friction. Although different theories are proposed, covering areas such as hardness theory, diffusion barrier theory, thermal barrier theory, and reduced friction theory, most have not dealt with the question of how and why the coating of tool substrates with hard materials such as Titanium Nitride (TiN), Titanium Carbide (TiC) and Aluminium Oxide (Al203) transforms the performance and life of cutting tools. This project discusses the complex interrelationship that encompasses the thermal barrier function and the relatively low sliding friction coefficient of TiN on an undulating tool surface, and presents the result of an investigation into the cutting characteristics and performance of EDMed surface-modified carbide cutting tool inserts. The tool inserts were coated with TiN by the physical vapour deposition (PVD) method. PVD coating is also known as Ion-plating which is the general term of the coating method in which the film is created by attracting ionized metal vapour in this the metal was Titanium and ionized gas onto negatively biased substrate surface. Coating by PVD was chosen because it is done at a temperature of not more than 5000C whereas chemical Vapour Deposition CVD process is done at very high temperature of about 8500C and in two stages of heating up the substrates. The high temperatures involved in CVD affects the strength of the (tool) substrates. In this study, comparative cutting tests using TiN-coated control specimens with no EDM surface structures and TiN-coated EDMed tools with a crater-like surface topography were carried out on mild steel grade EN-3. Various cutting speeds were investigated, up to an increase of 40% of the tool manufacturer’s recommended speed. Fifteen minutes of cutting were carried out for each insert at the speeds investigated. Conventional tool inserts normally have a tool life of approximately 15 minutes of cutting. After every five cuts (passes) microscopic pictures of the tool wear profiles were taken, in order to monitor the progressive wear on the rake face and on the flank of the insert. The power load was monitored for each cut taken using an on-board meter on the CNC machine to establish the amount of power needed for each stage of operation. The spindle drive for the machine is an 11 KW/hr motor. Results obtained confirmed the advantages of cutting at all speeds investigated using EDMed coated inserts, in terms of reduced tool wear and low power loads. Moreover, the surface finish on the workpiece was consistently better for the EDMed inserts. The thesis discusses the relevance of the finite element method in the analysis of metal cutting processes, so that metal machinists can design, manufacture and deliver goods (tools) to the market quickly and on time without going through the hassle of trial and error approach for new products. Improvements in manufacturing technologies require better knowledge of modelling metal cutting processes. Technically the use of computational models has a great value in reducing or even eliminating the number of experiments traditionally used for tool design, process selection, machinability evaluation, and chip breakage investigations. In this work, much interest in theoretical and experimental investigations of metal machining were given special attention. Finite element analysis (FEA) was given priority in this study to predict tool wear and coating deformations during machining. Particular attention was devoted to the complicated mechanisms usually associated with metal cutting, such as interfacial friction; heat generated due to friction and severe strain in the cutting region, and high strain rates. It is therefore concluded that Roughened contact surface comprising of peaks and valleys coated with hard materials (TiN) provide wear-resisting properties as the coatings get entrapped in the valleys and help reduce friction at chip-tool interface. The contributions to knowledge: a. Relates to a wear-resisting surface structure for application in contact surfaces and structures in metal cutting and forming tools with ability to give wear-resisting surface profile. b. Provide technique for designing tool with roughened surface comprising of peaks and valleys covered in conformal coating with a material such as TiN, TiC etc which is wear-resisting structure with surface roughness profile compose of valleys which entrap residual coating material during wear thereby enabling the entrapped coating material to give improved wear resistance. c. Provide knowledge for increased tool life through wear resistance, hardness and chemical stability at high temperatures because of reduced friction at the tool-chip and work-tool interfaces due to tool coating, which leads to reduced heat generation at the cutting zones. d. Establishes that Undulating surface topographies on cutting tips tend to hold coating materials longer in the valleys, thus giving enhanced protection to the tool and the tool can cut faster by 40% and last 60% longer than conventional tools on the markets today.

Urban Ponds as an Aquatic Biodiversity Resource in Modified Landscapes

Urbanization is a global process contributing to the loss and fragmentation of natural habitats. Many studies have focused on the biological response of terrestrial taxa and habitats to urbanization. However, little is known regarding the consequences of urbanization on freshwater habitats, especially small lentic systems. In this study we examined aquatic macroinvertebrate diversity (family and species level) and variation in community composition between 240 urban and 782 non-urban ponds distributed across the UK. Contrary to predictions, urban ponds supported similar numbers of invertebrate species and families compared to non-urban ponds. Similar gamma diversity was found between the two groups at both family and species taxonomic levels. The biological communities of urban ponds were markedly different to those of non-urban ponds and the variability in urban pond community composition was greater than that in non-urban ponds, contrary to previous work showing homogenisation of communities in urban areas. Positive spatial autocorrelation was recorded for urban and non-urban ponds at 0-50 km (distance between pond study sites) and negative spatial autocorrelation was observed at 100-150 km, and was stronger in urban ponds in both cases. Ponds do not follow the same ecological patterns as terrestrial and lotic habitats (reduced taxonomic richness) in urban environments; in contrast they support high taxonomic richness and contribute significantly to regional faunal diversity. Individual cities are complex structural mosaics which evolve over long periods of time and are managed in diverse ways, promoting the development of a wide-range of environmental conditions and habitat niches in urban ponds which can promote greater heterogeneity between pond communities at larger scales. Ponds provide an opportunity for managers and environmental regulators to conserve and enhance freshwater biodiversity in urbanized landscapes whilst also facilitating key ecosystem services including storm water storage and water treatment.

Urban ponds as an aquatic biodiversity resource in modified landscapes.

Urbanization is a global process contributing to the loss and fragmentation of natural habitats. Many studies have focused on the biological response of terrestrial taxa and habitats to urbanization. However, little is known regarding the consequences of urbanization on freshwater habitats, especially small lentic systems. In this study we examined aquatic macroinvertebrate diversity (family and species level) and variation in community composition between 240 urban and 784 non-urban ponds distributed across the UK. Contrary to predictions, urban ponds supported similar numbers of invertebrate species and families compared to non-urban ponds. Similar gamma diversity was found between the two groups at a family level, and while at a species level gamma diversity was higher in non-urban ponds, this difference was not statistically significant. The biological communities of urban ponds were markedly different to those of non-urban ponds and the variability in urban pond community composition was greater than that in non-urban ponds, contrary to previous work showing homogenisation of communities in urban areas. Positive spatial autocorrelation was recorded for urban and non-urban ponds at 0-50 km (distance between pond study sites) and negative spatial autocorrelation was observed at 100-150 km, and was stronger in urban ponds in both cases. Ponds do not follow the same ecological patterns as terrestrial and lotic habitats (reduced taxonomic richness) in urban environments; in contrast they support high taxonomic richness and contribute significantly to regional faunal diversity. Individual cities are complex structural mosaics which evolve over long periods of time and are managed in diverse ways, promoting the development of a wide-range of environmental conditions and habitat niches in urban ponds which can promote greater heterogeneity between pond communities at larger scales. Ponds provide an opportunity for managers and environmental regulators to conserve and enhance freshwater biodiversity in urbanized landscapes whilst also facilitating key ecosystem services including storm water storage and water treatment.

Design for placement of modified optodes to non-invasively map cerebral function

By using near infrared spectroscopy (NIRS) and by modifying the current Somanetics® optodes being used with the INVOS oximeter, the modified optodes are made to be fairly functional not only across the forehead, but across the hairy regions of the scalp as well. A major problem arises in the positioning of these optodes on the patients scalp and holding them in place while recording data. Another problem arises in the inconsistent repeatability of the trends displayed in the recorded data. A method was developed to facilitate the easy placement of these optodes on the patients scalp keeping in mind thepatient's comfort. The sensitivity of the optodes, too, was improved by incorporating better refined techniques for manufacturing the fiber optic brushes and fixing the same to the optode transmitting and receiving windows. The modified and improved optodes, in the single as well as in the multiplexed modes, were subjected to various tests on different areas of the brain to determine their efficiency and functionality.