A covariance analysis to optimize the optical follow-up strategies

The Astronomical Institute of the University of Bern (AIUB) is conducting several search campaigns for space debris using optical sensors. The debris objects are discovered during systematic survey observations. In general, the result of a discovery consists in only a short observation arc, or tracklet, which is used to perform a first orbit determination in order to be able to observe t he object again in subsequent follow-up observations. The additional observations are used in the orbit improvement process to obtain accurate orbits to be included in a catalogue. In order to obtain the most accurate orbit within the time available it is necessary to optimize the follow-up observations strategy. In this paper an in‐depth study, using simulations and covariance analysis, is performed to identify the optimal sequence of follow-up observations to obtain the most accurate orbit propagation to be used for the space debris catalogue maintenance. The main factors that determine the accuracy of the results of an orbit determination/improvement process are: tracklet length, number of observations, type of orbit, astrometric error of the measurements, time interval between tracklets, and the relative position of the object along its orbit with respect to the observing station. The main aim of the covariance analysis is to optimize the follow-up strategy as a function of the object-observer geometry, the interval between follow-up observations and the shape of the orbit. This an alysis can be applied to every orbital regime but particular attention was dedicated to geostationary, Molniya, and geostationary transfer orbits. Finally the case with more than two follow-up observations and the influence of a second observing station are also analyzed.

PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

Fast Prediction of Femoral Biomechanics Using Supervised Machine Learning and Statistical Shape Modeling

Finite element (FE) analysis is an important computational tool in biomechanics. However, its adoption into clinical practice has been hampered by its computational complexity and required high technical competences for clinicians. In this paper we propose a supervised learning approach to predict the outcome of the FE analysis. We demonstrate our approach on clinical CT and X-ray femur images for FE predictions ( FEP), with features extracted, respectively, from a statistical shape model and from 2D-based morphometric and density information. Using leave-one-out experiments and sensitivity analysis, comprising a database of 89 clinical cases, our method is capable of predicting the distribution of stress values for a walking loading condition with an average correlation coefficient of 0.984 and 0.976, for CT and X-ray images, respectively. These findings suggest that supervised learning approaches have the potential to leverage the clinical integration of mechanical simulations for the treatment of musculoskeletal conditions.

Post-colonial (American?) English Presence on the North-Western Pacific Island of Kosrae: A cross-linguistic analysis of the overlaps and divergences of Kosraean English compared to standard American English

Kosrae is the most remote island of the Federated States of Micronesia (FSM), with a population of less than 7,000 inhabitants, located in the Pacific Ocean between Hawaii and Guam. FSM is an independent sovereign nation consisting of four states in total: Pohnpei, Chuuk, Yap, and Kosrae. Having passed through the hands of Spain, Germany and Japan, the United States gained administrative control of FSM after WWII, as commissioned by the UN. The FSM became an independent nation in 1986 while still retaining affiliation with the US under a ‘Compact of Free Association’. Now both Kosraean and English are considered to be the two official languages and the variety of Kosraean English which has arisen proves for an interesting comparative study. In order to obtain the relevant data, I spent three months on the island of Kosrae, interviewing 90 local speakers, ranging in age (16-70), occupation, sex and time spent off island. The 45 minute long interviews were informal but supported by participant information to capture relevant data and conversations were guided in a way that aimed to reveal language and cultural attitudes. With reference to these samples, I examine the effects of American English on the language use in Kosrae. This paper aims to present a broad analysis of phonological, morphosyntactic and pragmatic features, such as pro-dropping, discourse markers and other practices in order to demonstrate the similarities and differences between the two varieties, which are coming to shape the variety developing on Kosrae. Having transcribed conversations using the tool Elan, I will put particular focus on [h] deletion and insertion, a rare occurrence found in a variety of post-colonial American English which I believe is of particular interest. I assess the presence of English in Kosrae with reference to sociological influences, past and present. First, I discuss the extralinguistic factors which have shaped the English that is currently used on Kosrae, including migration between US and FSM, and English as a language of administration, social media usage and visual media presence. Secondly, I assess the use of English in this community in light of Schneider’s (2007) ‘Dynamic Model’, with reference to America’s contribution as an ‘exploitation colony’ as defined by Mufwene (2001). Finally, an overview of the salient linguistic characteristics of Kosraean English, based on the data collected will be presented and compared to features associated with standard American English in view of examining overlap and divergence. The overall objective is to present a cross-linguistic description of a hitherto unexamined English emerging in a postcolonial environment with a juxtaposed contact variety. Mufwene, Salikoko S. 2001. The ecology of language evolution. Cambridge: Cambridge University Press. Schneider, E. (2007). Postcolonial Englishes. Cambridge: Cambridge University Press. Segal, H.G. (1989) Kosrae, The Sleeping Lady Awakens. Kosrae: Kosrae Tourist Division, Dept. Of Conservation and Development. Keywords: American English, Global English, Pacific English, Morphosyntactic, Phonological, Variation, Discourse

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.

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.