Analysis of Synthetic Diamond Wafer Interferograms Using a Parallelized Simulated Annealing Algorithm

Diamonds are known for both their beauty and their durability. Jefferson National Lab in Newport News, VA has found a way to utilize the diamond's strength to view the beauty of the inside of the atomic nucleus with the hopes of finding exotic forms of matter. By firing very fast electrons at a diamond sheet no thicker than a human hair, high energy particles of light known as photons are produced with a high degree of polarization that can illuminate the constituents of the nucleus known as quarks. The University of Connecticut Nuclear Physics group has responsibility for crafting these extremely thin, high quality diamond wafers. These wafers must be cut from larger stones that are about the size of a human finger, and then carefully machined down to the final thickness. The thinning of these diamonds is extremely challenging, as the diamond's greatest strength also becomes its greatest weakness. The Connecticut Nuclear Physics group has developed a novel technique to assist industrial partners in assessing the quality of the final machining steps, using a technique based on laser interferometry. The images of the diamond surface produced by the interferometer encode the thickness and shape of the diamond surface in a complex way that requires detailed analysis to extract. We have developed a novel software application to analyze these images based on the method of simulated annealing. Being able to image the surface of these diamonds without requiring costly X-ray diffraction measurements allows rapid feedback to the industrial partners as they refine their thinning techniques. Thus, by utilizing a material found to be beautiful by many, the beauty of nature can be brought more clearly into view.

Application of stellar photometry to the analysis of microarray images

Improvements in the analysis of microarray images are critical for accurately quantifying gene expression levels. The acquisition of accurate spot intensities directly influences the results and interpretation of statistical analyses. This dissertation discusses the implementation of a novel approach to the analysis of cDNA microarray images. We use a stellar photometric model, the Moffat function, to quantify microarray spots from nylon microarray images. The inherent flexibility of the Moffat shape model makes it ideal for quantifying microarray spots. We apply our novel approach to a Wilms' tumor microarray study and compare our results with a fixed-circle segmentation approach for spot quantification. Our results suggest that different spot feature extraction methods can have an impact on the ability of statistical methods to identify differentially expressed genes. We also used the Moffat function to simulate a series of microarray images under various experimental conditions. These simulations were used to validate the performance of various statistical methods for identifying differentially expressed genes. Our simulation results indicate that tests taking into account the dependency between mean spot intensity and variance estimation, such as the smoothened t-test, can better identify differentially expressed genes, especially when the number of replicates and mean fold change are low. The analysis of the simulations also showed that overall, a rank sum test (Mann-Whitney) performed well at identifying differentially expressed genes. Previous work has suggested the strengths of nonparametric approaches for identifying differentially expressed genes. We also show that multivariate approaches, such as hierarchical and k-means cluster analysis along with principal components analysis, are only effective at classifying samples when replicate numbers and mean fold change are high. Finally, we show how our stellar shape model approach can be extended to the analysis of 2D-gel images by adapting the Moffat function to take into account the elliptical nature of spots in such images. Our results indicate that stellar shape models offer a previously unexplored approach for the quantification of 2D-gel spots. ^

An analysis of Texas's school based HPV vaccine mandate: A public health risk communication failure: HPVETO!

Genital human papillomavirus (HPV) is of public health concern because persistent infection with certain HPV types can cause cervical cancer. In response to a nationwide push for cervical cancer legislation, Texas Governor Rick Perry bypassed the traditional legislative process and issued an executive order mandating compulsory HPV vaccinations for all female public school students prior to their entrance in the sixth grade. By bypassing the legislative process Governor Perry did not effectively mitigate the risk perception issues that arose around the need for and usefulness of the vaccine mandate. This policy paper uses a social policy paradigm to identify perception as the key intervening factor on how the public responds to risk information. To demonstrate how the HPV mandate failed, it analyzes four factors, economics, politics, knowledge and culture, that shape perception and influence the public's response. By understanding the factors that influence the public's perception, public health practitioners and policy makers can more effectively create preventive health policy at the state level. ^

Analysis of life expectancy using linear and nonlinear models

Life expectancy has consistently increased over the last 150 years due to improvements in nutrition, medicine, and public health. Several studies found that in many developed countries, life expectancy continued to rise following a nearly linear trend, which was contrary to a common belief that the rate of improvement in life expectancy would decelerate and was fit with an S-shaped curve. Using samples of countries that exhibited a wide range of economic development levels, we explored the change in life expectancy over time by employing both nonlinear and linear models. We then observed if there were any significant differences in estimates between linear models, assuming an auto-correlated error structure. When data did not have a sigmoidal shape, nonlinear growth models sometimes failed to provide meaningful parameter estimates. The existence of an inflection point and asymptotes in the growth models made them inflexible with life expectancy data. In linear models, there was no significant difference in the life expectancy growth rate and future estimates between ordinary least squares (OLS) and generalized least squares (GLS). However, the generalized least squares model was more robust because the data involved time-series variables and residuals were positively correlated. ^

Age analysis, aragonite and high magnesium calcite content from different IODP Holes from Exp 310

The widespread occurrence of microbialites in the last deglacial reef frameworks (16-6 Ka BP) implies that the accurate study of their development patterns is of prime importance to unravel the evolution of reef architecture through time and to reconstruct the reef response to sea-level variations and environmental changes. The present study is based on the sedimentological and chronological analysis (14C AMS dating) of drill cores obtained during the IODP Expedition #310 "Tahiti Sea Level" on the successive terraces which typify the modern reef slopes from Tahiti. It provides a comprehensive data base to investigate the microbialite growth patterns (i.e. growth rates and habitats), to analyze their roles in reef frameworks and to reconstruct the evolution of the reef framework architecture during sea-level rise. The last deglacial reefs from Tahiti are composed of two distinctive biological communities: (1) the coralgal communities including seven assemblages characterized by various growth forms (branching, robust branching, massive, tabular and encrusting) that form the initial frameworks and (2) the microbial communities developed in the primary cavities of those frameworks, a few meters (1.5 to 6 m) below the living coral reef surface, where they heavily encrusted the coralgal assemblages to form microbialite crusts. The dating results demonstrate the occurrence of two distinctive generations of microbialites: the "reefal microbialites" which developed a few hundred years after coralgal communities in shallow-water environments, whereas the "slope microbialites" grew a few thousands of years later in significantly deeper water conditions after the demise of coralgal communities. The development of microbialites was controlled by the volume and the shape of the primary cavities of the initial reef frameworks determined by the morphology and the packing of coral colonies. The most widespread microbialite development occurred in frameworks dominated by branching, thin encrusting, tabular and robust branching coral colonies which built loose and open frameworks typified by a high porosity (> 50%). In contrast, their growth was minimal in compact coral frameworks formed by massive and thick encrusting corals where primary cavities yielded a low porosity (~ 30%) and could not host a significant microbialite expansion.

The Chilean wheat market and its price support mechanism : a spatial market integration analysis

This research investigates the spatial market integration of the Chilean wheat market in relation with its most representative international markets by using a vector error correction model (VECM) and how a price support policy, as a price band, affect it. The international market was characterized by two relevant wheat prices: PAN from Argentina and Hard Red Winter from the United States. The spatial market integration level, expressed in the error correction term (ECT), allowed concluding that there is a high integration degree among these markets with a variable influence of the price band mechanism mainly related with its estimation methodology. Moreover, this paper showed that Chile can be seen as price taker as long as the speed of its adjustment to international shocks, being these reactions faster than in the United States and Argentina. Finally, the results validated the "Law of the One Price", which assumes price equalization across all local markets in the long run.

Geochemical analysis of minerals from sediment core CRP-2 in the Ross Sea, Antarctica

Distribution patterns, petrography, whole-rock and mineral chemistry, and shape and fabric data are described for the most representative basement lithologies occurring as clasts (granule to bolder grain-size class) from the 625 m deep CRP-2/2A drillcore. A major change in the distribution pattern of the clast types occurs at c. 310 mbsf., with granitoid-dominated clasts above and mainly dolerite clasts below; moreover, compositional and modal data suggest a further division into seven main detrital assemblages or petrofacies. In spite of this variability, most granitoid pebbles consist of either pink or grey biotite±hornblende monzogranites. Other less common and ubiquitous lithologies include biotite syenogranite, biotite-hornblende granodiorite, tonalite, monzogranitic porphyries (very common below 310 mbsf), microgranite, and subordinately, monzogabbro, Ca-silicate rocks, biotite-clinozoisite schist and biotite orthogneiss (restricted to the pre-Pliocene strata). The ubiquitous occurrence of biotite±hornblende monzogranite pebbles in both the Quaternary-Pliocene and Miocene-Oligocene sections, apparently reflects the dominance of these lithologies in the onshore basement, and particularly in the Cambro-Ordovician Granite Harbour Igneous Complex which forms the most extensive outcrop in southern Victoria Land. The petrographical features of the other CRP-2/2A pebble lithologies are consistent with a supply dominantly from areas of the Transantarctic Mountains facing the CRP-2/2A site, and they thus provide further evidence of a local provenance for the supply of basement clasts to the CRP-2/2A sedimentary strata.

Climate sensitivity across marine domains of life: limits to evolutionary adaptation shape species interactions, supplementary material

Organisms in all domains, Archaea, Bacteria, and Eukarya will respond to climate change with differential vulnerabilities resulting in shifts in species distribution, coexistence, and interactions. The identification of unifying principles of organism functioning across all domains would facilitate a cause and effect understanding of such changes and their implications for ecosystem shifts. For example, the functional specialization of all organisms in limited temperature ranges leads us to ask for unifying functional reasons. Organisms also specialize in either anoxic or various oxygen ranges, with animals and plants depending on high oxygen levels. Here, we identify thermal ranges, heat limits of growth, and critically low (hypoxic) oxygen concentrations as proxies of tolerance in a meta-analysis of data available for marine organisms, with special reference to domain-specific limits. For an explanation of the patterns and differences observed, we define and quantify a proxy for organismic complexity across species from all domains. Rising complexity causes heat (and hypoxia) tolerances to decrease from Archaea to Bacteria to uni- and then multicellular Eukarya. Within and across domains, taxon-specific tolerance limits likely reflect ultimate evolutionary limits of its species to acclimatization and adaptation. We hypothesize that rising taxon-specific complexities in structure and function constrain organisms to narrower environmental ranges. Low complexity as in Archaea and some Bacteria provide life options in extreme environments. In the warmest oceans, temperature maxima reach and will surpass the permanent limits to the existence of multicellular animals, plants and unicellular phytoplankter. Smaller, less complex unicellular Eukarya, Bacteria, and Archaea will thus benefit and predominate even more in a future, warmer, and hypoxic ocean.

Grain size and XRD analysis on Site 162-983

The grain size of deep-sea sediments provides an apparently simple proxy for current speed. However, grain size-based proxies may be ambiguous when the size distribution reflects a combination of processes, with current sorting only one of them. In particular, such sediment mixing hinders reconstruction of deep circulation changes associated with ice-rafting events in the glacial North Atlantic because variable ice-rafted detritus (IRD) input may falsely suggest current speed changes. Inverse modeling has been suggested as a way to overcome this problem. However, this approach requires high-precision size measurements that register small changes in the size distribution. Here we show that such data can be obtained using electrosensing and laser diffraction techniques, despite issues previously raised on the low precision of electrosensing methods and potential grain shape effects on laser diffraction. Down-core size patterns obtained from a sediment core from the North Atlantic are similar for both techniques, reinforcing the conclusion that both techniques yield comparable results. However, IRD input leads to a coarsening that spuriously suggests faster current speed. We show that this IRD influence can be accounted for using inverse modeling as long as wide size spectra are taken into account. This yields current speed variations that are in agreement with other proxies. Our experiments thus show that for current speed reconstruction, the choice of instrument is subordinate to a proper recognition of the various processes that determine the size distribution and that by using inverse modeling meaningful current speed reconstructions can be obtained from mixed sediments.

Grain shape of sediment from the Weddell Sea

Very fine quartz sand was examined from Paleogene and Neogene sediments of ODP Sites 693, 694, 695, 696, and 697 to determine their grain roundness using Fourier analysis and SEM surface texture characteristics. The objective of this study was to identify grain roundness and surface texture characteristics unique to East (Site 693) and West (Sites 695, 696, and 697) Antarctica and to glacial regimes. Once identified, these distinguishing features could then be used to determine changes in source area and glacial conditions in the central Weddell Sea Basin (Site 694). Three end members of very fine quartz sand are recognized in the Oligocene to Pleistocene sediments of the Weddell Sea: angular, rounded, and intermediate. End member 1 (angular) consists of extremely angular grains with numerous fracture textures. Previous investigations suggested that these sands are derived from crystalline rocks that fractured during formation or deformation and/or were exposed to weathering by ice. In this study, however, the correlation of angularity with ice activity is problematical as the most angular sands were recovered in the lower Oligocene sediments of the South Orkney Microcontinent, a period of temperate climatic conditions. End member 3 (rounded) consists of rounded grains with chemically and mechanically produced surface textures. These sands are presumed to be derived from the Beacon-type rocks in East Antarctica and the sedimentary deposits of the Northern Antarctic Peninsula. End member 2 (intermediate) grains display crystalline nodes and grain embayments. They are thought to be derived from felsic intrusives, East Antarctic quartzites, basement metamorphics of the South Orkney Microcontinent, and/or the Andean intrusive series of West Antarctica. Unfortunately, no features unique to either the East or West Antarctic sediment sources or to glacial conditions could be isolated. Therefore, the objective of determining provenance changes and sediment erosion and transport mechanisms could not be achieved using this approach.

Pollen analysis of a peat profile from the Rieseberger Moor, Lower Saxony, Germany

The Rieseberger Moor is a fen, 145 hectares in size, situated about 20 km east of Brunswick (Braunschweig), Lower Saxony, Germany. Peat was dug in the fen - with changing intensity - since the mid-18th century until around AD 1955. According to Schneekloth & Schneider (1971) the remaining peat (fen and wood peat) is predominantly 1.5 to 2 m thick (maximum 2.7 m). Part of the fen - now a nature reserve (NSG BR 005) - is wooded (Betula, Salix, Alnus). For more information on the Rieseberger Moor see http://de.wikipedia.org/wiki/Rieseberger_Moor. Willi Selle was the first to publish pollen diagrams from this site (Selle 1935, profiles Rieseberger Torfmoor I and II). This report deals with a 2.2 m long profile from the wooded south-eastern part of the fen consisting of strongly decomposed fen peat taken A.D. 1965 and studied by pollen analysis in the same year. The peat below 1.45 m contained silt and clay, samples 1.48 and 1.58 m even fine sand. These samples had to be treated with HF (hydrofluoric acid) in addition to the treatment with hot caustic potash solution. The coring ended in sandy material. The new pollen data reflect the early part of the known postglacial development of the vegetation of this area: the change from a birch dominated forest to a pine forest and the later spreading of Corylus and of the thermophilous deciduous tree genera Quercus, Ulmus, Tilia and Fraxinus followed by the expansion of Alnus. The new data are in agreement with Selle's results, except for Alnus, which in Selle's pollen diagram II shows high values (up to 42% of the arboreal pollen sum) even in samples deposited before Corylus and Quercus started to spread. On contrary the new pollen diagram shows that alder pollen - although present in all samples - is frequent in the three youngest pollen spectra only. A period with dominating Alnus as seen in the uppermost part of Selle's pollen diagrams is missing. The latter is most likely the result of peat cutting at the later coring site, whereas the early, unusually high alder values of Selle's pollen study are probably caused by contamination of the pollen samples with younger peat. Selle took peat samples usually with a "Torfbohrer" (= Hiller sampler). This side-filling type of sampler with an inner chamber and an outer loose jacket offers - if not handled with appropriate care - ample opportunities to contaminate older peat with carried off younger material. Pollen grains of Fagus (2 % of the arboreal pollen sum) were found in two samples only, namely in the uppermost samples of the new profile (0.18 m) and of Selle's profile I (0.25 m). If this pollen is autochthonous, with other words: if this surface-near peat was not disturbed by human activities, the Fagus pollen indicates an Early Subboreal age of this part of the profile. The accumulation of the Rieseberg peat started during the Preboreal. Increased values of Corylus, Quercus and Ulmus indicate that sample 0.78 m of the new profile is the oldest Boreal sample. The high Alnus values prove the Atlantic age of the younger peat. Whether Early Subboreal peat exists at the site is questionable, but evidently none of the three profiles reaches to Late Subboreal time, when Fagus spread in the region. Did peat-growth end during the Subboreal? Did younger peat exist, but got lost by peat cutting or has younger peat simply not yet been found in the Rieseberg fen? These questions cannot be answered with this study. The temporary decline of the curve of Pinus for the benefit of Betula during the Preboreal, unusual for this period, is contemporaneous with the deposition of sand (Rieseberger Moor II, 1.33 - 1,41 m; samples 1.48 and 1.58 m of the new profile) and must be considered a local phenomenon. Literature: Schneekloth, Heinrich & Schneider, Siegfried (1971). Die Moore in Niedersachsen. 2. Teil. Bereich des Blattes Braunschweig der Geologischen Karte der Bundesrepublik Deutschland (1:200000). - Schriften der wirtschaftswissenschaftlichen Gesellschaft zum Studium Niedersachsens e.V. Reihe A I., Band 96, Heft 2, 83 Seiten, Göttingen. Selle, Willi (1935) Das Torfmoor bei Rieseberg. - Jahresbericht des Vereins für Naturwissenschaft zu Braunschweig, 23, 46-58, Braunschweig.

Grain size analysis of sediment core GeoB1510-2

Detailed information about the sediment properties and microstructure can be provided through the analysis of digital ultrasonic P wave seismograms recorded automatically during full waveform core logging. The physical parameter which predominantly affects the elastic wave propagation in water-saturated sediments is the P wave attenuation coefficient. The related sedimentological parameter is the grain size distribution. A set of high-resolution ultrasonic transmission seismograms (-50-500 kHz), which indicate downcore variations in the grain size by their signal shape and frequency content, are presented. Layers of coarse-grained foraminiferal ooze can be identified by highly attenuated P waves, whereas almost unattenuated waves are recorded in fine-grained areas of nannofossil ooze. Color -encoded pixel graphics of the seismograms and instantaneous frequencies present full waveform images of the lithology and attenuation. A modified spectral difference method is introduced to determine the attenuation coefficient and its power law a = kF. Applied to synthetic seismograms derived using a "constant Q" model, even low attenuation coefficients can be quantified. A downcore analysis gives an attenuation log which ranges from -700 dB/m at 400 kHz and a power of n=1-2 in coarse-grained sands to few decibels per meter and n :s; 0.5 in fine-grained clays. A least squares fit of a second degree polynomial describes the mutual relationship between the mean grain size and the attenuation coefficient. When it is used to predict the mean grain size, an almost perfect coincidence with the values derived from sedimentological measurements is achieved.

Application of photoluminescence and electroluminescence techniques to the characterization of intermediate band solar cells

The intermediatebandsolarcell (IBSC) is a photovoltaic device with a theoretical conversion efficiency limit of 63.2%. In recent years many attempts have been made to fabricate an intermediateband material which behaves as the theory states. One characteristic feature of an IBSC is its luminescence spectrum. In this work the temperature dependence of the photoluminescence (PL) and electroluminescence (EL) spectra of InAs/GaAs QD-IBSCs together with their reference cell have been studied. It is shown that EL measurements provide more reliable information about the behaviour of the IB material inside the IBSC structure than PL measurements. At low temperatures, the EL spectra are consistent with the quasi-Fermi level splits described by the IBSC model, whereas at room temperature they are not. This result is in agreement with previously reported analysis of the quantum efficiency of the solarcells