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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.
A summary of the milliped faunas of Pakistan, Bangladesh, and Kashmir (Arthropoda: Diplopoda)
(2014)
Three female callipodidan samples from northern Pakistan are assigned to Bollmania kohalana (Attems, 1936) (Caspiopetalidae), the only ordinal representative documented from the country; a new record of Kaschmiriosoma loebli Jeekel, 2003 (Polydesmida: Paradoxosomatidae), is also provided. Localities are summarized for the 14 Pakistani, 6 Kashmirian, and 5 Bangladeshi diplopods. The last include one unidentifi able female of Zephronia Gray, 1832 (Sphaerotheriida: Zephroniidae), and two adventive species, Trachyjulus calvus (Pocock, 1893) (Spirostreptida: Cambalopsidae) and Asiomorpha coarctata (Saussure, 1860) (Polydesmida: Paradoxosomatidae); all constitute new country records. Two obscurely documented Bangladeshi diplopods are Gonoplectus cautus (Attems, 1936) (Spirostreptida: Harpagophoridae), and Trichopeltis watsoni Pocock, 1895 (Polydesmida: Cryptodesmidae). The Pakistani polydesmidan, Quasidesmus puschtun Golovatch, 1991, is transferred from Pyrgodesmidae to Cryptodesmidae.
CD4+CD25+ regulatory T cells (Tregs) represent a specialized subpopulation of T cells, which are essential for maintaining peripheral tolerance and preventing autoimmunity. The immunomodulatory effects of Tregs depend on their activation status. Here we show that, in contrast to conventional anti-CD4 monoclonal antibodies (mAbs), the humanized CD4-specific monoclonal antibody tregalizumab (BT-061) is able to selectively activate the suppressive properties of Tregs in vitro. BT-061 activates Tregs by binding to CD4 and activation of signaling downstream pathways. The specific functionality of BT-061 may be explained by the recognition of a unique, conformational epitope on domain 2 of the CD4 molecule that is not recognized by other anti-CD4 mAbs. We found that, due to this special epitope binding, BT-061 induces a unique phosphorylation of T-cell receptor complex-associated signaling molecules. This is sufficient to activate the function of Tregs without activating effector T cells. Furthermore, BT-061 does not induce the release of pro-inflammatory cytokines. These results demonstrate that BT-061 stimulation via the CD4 receptor is able to induce T-cell receptor-independent activation of Tregs. Selective activation of Tregs via CD4 is a promising approach for the treatment of autoimmune diseases where insufficient Treg activity has been described. Clinical investigation of this new approach is currently ongoing.
A second Yalta
(2014)
We explore the parameter space of the two-flavor thermal quark–meson model and its Polyakov loop-extended version under the influence of a constant external magnetic field B. We investigate the behavior of the pseudo critical temperature for chiral symmetry breaking taking into account the likely dependence of two parameters on the magnetic field: the Yukawa quark–meson coupling and the parameter T0 of the Polyakov loop potential. Under the constraints that magnetic catalysis is realized at zero temperature and the chiral transition at B=0 is a crossover, we find that the quark–meson model leads to thermal magnetic catalysis for the whole allowed parameter space, in contrast to the present picture stemming from lattice QCD.
Twenty six species of the genus Purenleon Stange (Neuroptera: Myrmeleontidae: Nemoleontini) are recognized from the New World, of which ten are described as new species: P. oaxacae, P. fernandezi, P. tibialis, P. adamsi, P. andinus, P. apache, P. aztecus, P. cavei, P. farri and P. toltecus. Neotypes are designated for Psammoleon banksi Esben-Petersen 1933 and for Formicaleo inaequalis Navás 1913. The larvae of sixteen species have been reared and are described with data on their biologies. The genus is subdivided into three species groups based mostly on leg structure. The inscriptus group consists of fi ve species, the tibialis group consists of two species and the rest of the species are in the bistictus group. Keys to the species based both on adults and larvae are provided and descriptions given.
A revision of the genus Acentroptera Guérin-Méneville, 1844 (Coleoptera: Chrysomelidae: Cassidinae)
(2014)
The species of the genus Acentroptera Guérin-Méneville, 1844 are revised. Thirteen species are treated as valid and are illustrated. A neotype is designated for A. tessellata Baly. Acentroptera maculata Pic from Brazil and A. rubronotata Pic from Brazil are treated as incertae sedis. Acentroptera bita n. sp. and A. lineata n. sp. both from Panama are described as new. A key to the 13 treated species is presented. Five species appear to be associated with bromeliads (Bromeliaceae).
The fauna of the small carrion beetles and round fungus beetles (Leiodidae) of the oceanic islands of the West Indies is reviewed with 11 genera and 81 species recorded. Keys to adults of all genera and species, descriptions, and figures are provided to aid in identification. All species are endemic to the islands of the West Indies. Most species are endemic to a single island, but some species in the Lesser Antilles occur on more than one island. It is certain that more species remain to be discovered, especially on larger and less explored islands. Two new genera are described: Parvocyrtusa (type species Parvocyrtusa hispaniolensis), and Pseudolionothus (type species Pseudolionothus insularis). The genus Pseudoagathidium Angelini is reported from the New World for the first time with one species. The higher taxa and 61 new species and their island distributions are as follows: Cholevinae, Eucatopini, Eucatops Portevin (first West Indian record): E. annulus, Hispaniola. Ptomaphagini, Proptomaphaginus Szymczakowski (four species, no new taxa), Greater Antilles and Bahamas (new genus record). Anemadini, Dissochaetus Reitter (five species, one new species): D. santalucia, St. Lucia. Leiodinae, Agathidiini, Agathidium Panzer (first West Indian record): A. minutum, Hispaniola. Pseudoagathidium Angelini (first New World record): P. ignotum, St. Vincent. Leiodini, Isoplastus Horn (first West Indian record): I. hispaniolensis, Hispaniola. Zeadolopus Broun (five known species, 28 new species): Z. acinaces, Hispaniola; Z. angulatus, St. Vincent; Z. antiguensis, Antigua, Saba, Montserrat; Z. atratus, Cuba; Z. bahamensis, Bahamas Islands (Andros Island); Z. caborojo, Hispaniola; Z. carinatus, Jamaica; Z caymanensis, Cayman Islands (Grand Cayman); Z. cubensis, Cuba; Z. dominica, Dominica; Z. exiguus, Hispaniola; Z. flavidus, Cuba; Z. hatomayor, Hispaniola; Z. hispaniolensis, Hispaniola; Z. iviei, Hispaniola; Z. jarabacoa, Hispaniola; Z. lavega, Hispaniola; Z. longipes, Hispaniola; Z. lucidus, Cuba; Z. miniusculus, Hispaniola; Z. nanus, Hispaniola; Z. nesiotes, St. Lucia and Martinique; Z. oviedoensis, Hispaniola; Z. parvantilliensis, Montserrat, Guadeloupe, Dominica, Martinique, St. Lucia, St. Vincent, Grenada; Z. paulus, Hispaniola; Z. pedernales, Hispaniola; Z. pusillus, Cuba. Parvocyrtusa (new genus, one new species): P. hispaniolensis, Hispaniola. Pseudolionothus (new genus, two new species): P. andersoni, Cuba; P. insularis, Hispaniola. Scotocryptini, Aglyptinus Cockerell (five known species, 19 new species): A. angulatus, Hispaniola; A. bahamensis, Bahamas Islands (Andros Island); A. biserriatus, Cuba; A. capitaneus, Cuba; A. dominica, Dominica; A. fortipunctatus, Cuba; A. grandis, Hispaniola; A. grenadensis, Grenada; A. hemipterus, Jamaica; A. hispaniolensis, Hispaniola; A. longipalpus, Hispaniola; A. luciae, St. Lucia; A. maculatus, Jamaica; A. martiniquensis, Martinique; A. minutus, Cuba; A. parvoculus, Jamaica; A. parvus, St. Lucia; A. sinuatus, Cuba; A. vincentii, St. Vincent. Creagrophorus Matthews (one known species, seven new species): C. bicolor, Martinique; C. cubensis, Cuba; C. dominica, Dominica; C. hispaniolensis, Hispaniola; C. microdentatus, Hispaniola; C. santalucia, St. Lucia; C. unidentatus, St. Vincent and Grenada.
The Afrotropical Rhyssinae are reviewed. A total of 12 species are reported from the region, including five new species: Epirhyssa brianfisheri sp. nov., E. gavinbroadi sp. nov., E. shaka sp. nov., E. villemantae sp. nov. and E. tombeaodiba sp. nov. The generic status of E. brianfisheri sp. nov. is discussed since this species could also be considered to be an extra-limital Triancyra species, emphasizing the putative paraphyletic status of Epirhyssa. Epirhyssa ghesquierei Seyrig, 1937, E. overlaeti Seyrig, 1937 and E. uelensis Benoit, 1951 are newly reported from Cameroon. We provide illustrated diagnoses and identification notes. Finally, we discuss the apparent scarcity of African rhyssines compared to other regions.
Eleven Neotropical species of Laemophloeus Dejean with antennal clubs composed of three antennomeres are reviewed, diagnosed, and illustrated. Six of the species are described as new: L. capitesculptus Thomas, n. sp., L. corporeflavus Thomas, n. sp., L. dozieri Thomas, n. sp., L. insulatestudinorum Thomas, n. sp., L. planaclavatus Thomas, n. sp., and L. taurus Thomas, n. sp. Four new synonymies are proposed: L. catharinensis Kessel (=L. incisus Sharp), new synonym; L. similans Kessel (=L. incisus Sharp), new synonym; L. distinguendus Sharp (=L. megacephalus Grouvelle), new synonym, and L. chevrolati Grouvelle (=L. lecontei Grouvelle), new synonym. A key to the species is provided.
Orientation: Publishing methodologically sound, empirically based studies in reputable accredited scientific journals are essential in order to advance knowledge and evidence-based practice in the field of industrial and organisational psychology.
Research purpose: The purpose of the research was to conduct a broad content analysis of the articles published in the South African Journal of Industrial Psychology (SAJIP) between 2004 and 2013. The study aimed to provide a descriptive overview of the most frequent content themes,published authors and institutions, research approaches, strategies, designs and analysis techniques, software packages and sample sizes in industrial and organisational (I-O) psychology utilised in the publications.
Motivation for study: The periodic analyses of published content in scholarly journals provide an index of the extent to which the publications reflect the scope of practice in a given discipline and broaden insight into the direction and relevance of research published in a journal.
Research design, approach and method: A broad systematic content analysis was conducted of 342 documented articles published in the SAJIP between 2004 and 2013. Descriptive data(frequencies and percentages) were used to report the findings.
Main findings: The publishing pattern of the SAJIP appeared to correspond with its focus and scope. Manuscripts utilising mostly cross-sectional quantitative correlational research designs with large samples (n > 201) were published in the SAJIP. The University of Johannesburg and Professor Sebastiaan (Ian) Rothmann were the largest contributors to publications between 2004 and 2013. Organisational psychology and psychometrics were the most prominent domains in I-O psychology research. Data were predominantly processed utilising SPSS.
Practical implications: The insights derived from the findings can be employed to plan future research initiatives in the field of I-O psychology.
Contribution/value-add: The findings provide valuable insight into the current status of the foci of I-O psychology research as published in the SAJIP between 2004 and 2013 and the contribution made by the SAJIP to advancing knowledge and evidence-based practice in I-O psychology.