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Acceleration of Biomedical Image Processing and Reconstruction with FPGAs
Increasing chip sizes and better programming tools have made it possible to increase the boundaries of application acceleration with reconfigurable computer chips. In this thesis the potential of acceleration with Field Programmable Gate Arrays (FPGAs) is examined for applications that perform biomedical image processing and reconstruction. The dataflow paradigm was used to port the analysis of image data for localization microscopy and for 3D electron tomography from an imperative description towards the FPGA for the first time.
After the primitives of image processing on FPGAs are presented, a general workflow is given for analyzing imperative source code and converting it to a hardware pipeline where every node processes image data in parallel. The theoretical foundation is then used to accelerate both example applications. For localization microscopy, an acceleration of 185 compared to an Intel i5 450 CPU was achieved, and electron tomography could be sped up by a factor of 5 over an Nvidia Tesla C1060 graphics card while maintaining full accuracy in both cases.
In this article, the author shows that progress of info-communications is a key factor of society changes, as it radically changes the key aspects of human life. Studying the time of progress and comparing it with the most important anthropic characteristic - length of human life, he comes to the conclusion that our generation has witnessed the tipping point in the rate of development of human civilization. This showing up in the fact that the present stage of the scientific and technological advance lead to the transformation, perhaps on the same scale, what were the appearance of written language and publishing, but these multiple fundamental changes in the life of society occur within the life of a single generation. In these circumstances, the task of forecasting, in its traditional setting, is becoming increasingly inaccurate. According to the author, the only possibility is to venture outside the framework of formal logic and technocratic approaches and try to find answers to these questions by generating new meanings of the realities surrounding us and in this context philosophy has a special role.
Acacia pendula, Weeping Myall, (family Fabaceae) is the most legislatively protected plant species in the New South Wales Hunter Valley. Under the NSW Threatened Species Conservation Act 1995 it is listed as an Endangered Population (in the Hunter Valley) and as a component of two Endangered Ecological Communities (one in the Hunter, one elsewhere in NSW); it is also listed as a Critically Endangered Ecological Community (in the Hunter Valley) on the Commonwealth Environment Protection and Biodiversity Conservation Act 1999 and listed as threatened in three other eastern Australian States.
To ascertain the likely original distribution of stands of Acacia pendula in the Hunter Valley, this paper examines the writings of early Australian explorers, herbarium and database records, and the species habitat attributes across NSW. None of the journals examined, including those of botanist/explorer Allan Cunningham (who originally collected Acacia pendula from the Lachlan River in 1817), Thomas Mitchell or Ludwig Leichhardt, make note of the species for the Hunter Valley. Several explorers do, however, record Acacia pendula regularly (>100 times) across other parts of NSW, Queensland, and South Australia.
Historical herbarium and database records show a paucity of records from the Hunter prior to the year 2000, after which a 37-fold increase in observations since 1951 is apparent. For the first 128 years of botanical exploration (1823 to 1951), there are no validated collections or records of Acacia pendula from the Hunter Valley. The single exception is a specimen collected by Cunningham from 1825 (lodged at Kew, UK), purported to be from ‘Hunters River’, but which is morphologically different to other collections of Acacia pendula from that time. There is some uncertainty over the origins of this specimen.
Analysis of habitats supporting Acacia pendula in NSW outside of the Hunter show them to differ significantly in geological age, soil type, rainfall and elevation from those in the Hunter.
Collectively, these findings provide a strong circumstantial case that Acacia pendula was absent from the Hunter at the time of European settlement; this has important implications for the conservation and management of Hunter stands. Rather than being a threatened species in the Hunter Valley, it is postulated that Acacia pendula has been intentionally and/or accidentally introduced to the region, and may now be imposing a new and emerging threat to the endangered grassy woodlands and forests there. There is now an urgent need for genetic studies to clarify the origins of the current Hunter Valley stands, and to define the taxonomic limits of Acacia pendula and its close relatives.
Acacia
(2014)
Acacia is a strong and independent woman whose heart and heritage like rooted in Africa, while her reality in contemporary America finds itself in a very different time and place. In living her life, she must breach the distance between her current space and the ties that bind her. Straddling two sometimes opposing worlds of medicine and dance, Dr Acacia Graeme must find the balance between feeding her mind through work and study, and nourishing her soul and spirit through dance. And what happened when the music stops? Because it does, often. How will she get through the silence of her every day? This is the story of a flawed heroine whose intentions are pure, her truth perhaps less so. Torn between the enduring innocence of her first love and the life-long search that is her longing for one true love, she is compelled to come to terms with her own free nature and independent spirit and, in so doing, turn tragedy to triumph.
The ab-initio molecular dynamics framework has been the cornerstone of computational solid state physics in the last few decades. Although it is already a mature field it is still rapidly developing to accommodate the growth in solid state research as well as to efficiently utilize the increase in computing power. Starting from the first principles, the ab-initio molecular dynamics provides essential information about structural and electronic properties of matter under various external conditions. In this thesis we use the ab-initio molecular dynamics to study the behavior of BaFe2As2 and CaFe2As2 under the application of external pressure. BaFe2As2 and CaFe2As2 belong to the family of iron based superconductors which are a novel and promising superconducting materials. The application of pressure is one of two key methods by which electronic and structural properties of iron based superconductors can be modified, the other one being doping (or chemical pressure). In particular, it has been noted that pressure conditions have an important effect, but their exact role is not fully understood. To better understand the effect of different pressure conditions we have performed a series of ab-initio simulations of pressure application. In order to apply the pressure with arbitrary stress tensor we have developed a method based on the Fast Inertial Relaxation Engine, whereby the unit cell and the atomic positions are evolved according to the metadynamical equations of motion. We have found that the application of hydrostatic and c axis uniaxial pressure induces a phase transition from the magnetically ordered orthorhombic phase to the non-magnetic collapsed tetragonal phase in both BaFe2As2 and CaFe2As2. In the case of BaFe2As2, an intermediate tetragonal non-magnetic tetragonal phase is observed in addition. Application of the uniaxial pressure parallel to the c axis reduces the critical pressure of the phase transition by an order of magnitude, in agreement with the experimental findings. The in-plane pressure application did not result in transition to the non-magnetic tetragonal phase and instead, rotation of the magnetic order direction could be observed. This is discussed in the context of Ginzburg-Landau theory. We have also found that the magnetostructural phase transition is accompanied by a change in the Fermi surface topology, whereby the hole cylinders centered around the Gamma point disappear, restricting the possible Cooper pair scattering channels in the tetragonal phase. Our calculations also permit us to estimate the bulk moduli and the orthorhombic elastic constants of BaFe2As2 and CaFe2As2.
To study the electronic structure in systems with broken translational symmetry, such as doped iron based superconductors, it is necessary to develop a method to unfold the complicated bandstructures arising from the supercell calculations. In this thesis we present the unfolding method based on group theoretical techniques. We achieve the unfolding by employing induced irreducible representations of space groups. The unique feature of our method is that it treats the point group operations on an equal footing with the translations. This permits us to unfold the bandstructures beyond the limit of translation symmetry and also formulate the tight-binding models of reduced dimensionality if certain conditions are met. Inclusion of point group operations in the unfolding formalism allows us to reach important conclusions about the two versus one iron picture in iron based superconductors.
And finally, we present the results of ab-initio structure prediction in the cases of giant volume collapse in MnS2 and alkaline doped picene. In the case of MnS2, a previously unobserved high pressure arsenopyrite structure of MnS2 is predicted and stability regions for the two competing metastable phases under pressure are determined. In the case of alkaline doped picene, crystal structures with different levels of doping were predicted and used to study the role of electronic correlations.
A Torrent of Terror
(2014)
Rome Aboh's poetry unmistakably enwraps the condition of the politically and socially cannibalised segment of his society; and the beauty of the verse radiates from his facility with language as the stylist and linguist. The section 'patriotism' with such poems as 'hour of truth' aptly brings out the socially obligatory role of the poets whose mission goes beyond versifying and sharing their personal fantasies and urges. Similarly the poem 'letter to the mp' echoes the agonies of the common masses who feel deceived by the ruling elite in their so-called democratic nations.
Characterized by small body size, apically rounded/lobed anterior gonopod telopodites, long slender posterior gonopod telopodites, and torsion in the cyphopod receptacles, Floridobolus fl oydi, n. sp., is described from the southern sector of the Brooksville Ridge in northwestern peninsular Florida. It inhabits sandy “Big Scrub” environments like F. penneri Causey, 1957, and F. orini Shelley, 2014, and is documented from the sector’s center and northern periphery, in Hernando and Citrus Counties, respectively, with a sight record from the eastern periphery. Its discovery supports the thesis that each sand ridge in peninsular Florida may harbor a unique species of this endemic genus.
A revision of the genus Asterostegus Mortensen, 1933 (Echinodermata: Ophiuroidea: Euryalidae) is based on seven specimens, including the holotype of Asterostegus maini McKnight, 2003. A new species, Asterostegus sabineae sp. nov., is described from off Reunion Island and two other species, A. tuberculatus Mortensen, 1933 and A. maini, are redescribed. A tabular key to the three species of the genus Asterostegus is provided. Some terminology of the taxonomy of euryalid ophiuroids is revised.
Based on a meta-analysis, Redick and Lindsey (2013) found that complex span and n-back tasks show an average correlation of r = 0.20, and concluded that "complex span and n-back tasks cannot be used interchangeably as working memory measures in research applications" (p. 1102). Here, we comment on this conclusion from a psychometric perspective. In addition to construct variance, performance on a test contains measurement error, task-specific variance, and paradigm-specific variance. Hence, low correlations among dissimilar indicators do not provide strong evidence for the existence, or absence, of a construct common to both indicators. One way to arrive at such evidence is to fit hierarchical latent factors that model task-specific, paradigm-specific, and construct variance. We report analyses for 101 younger and 103 older adults who worked on nine different working memory tasks. The data are consistent with a hierarchical model of working memory, according to which both complex span and n-back tasks are valid indicators of working memory. The working memory factor predicts 71% of the variance in a factor of reasoning among younger adults (83% for among older adults). When the working memory factor was restricted to any possible triplet of working memory tasks, the correlation between working memory and reasoning was inversely related to the average magnitude of the correlations among the indicators, indicating that more highly intercorrelated indicators may provide poorer coverage of the construct space. We stress the need to go beyond specific tasks and paradigms when studying higher-order cognitive constructs, such as working memory.