CattleTickBase: An integrated Internet-based bioinformatics resource for Rhipicephalus (Boophilus) microplus

The Rhipicephalus micro plus genome is large and complex in structure, making it difficult to assemble a genome sequence and costly to resource the required bioinformatics. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome. We have acquired and assembled genomic DNA into contigs that represent over 1.8 Gigabase pairs of DNA from gene-enriched regions of the R. micro plus genome. We also have several datasets containing transcript sequences from a number of gene expression experiments conducted by the consortium. A web-based resource was developed to enable the scientific community to access our datasets and conduct analysis through a web-based bioinformatics environment called YABI. The collective bioinformatics resource is termed CattleTickBase. Our consortium has acquired genomic and transcriptomic sequence data at approximately 0.9X coverage of the gene-coding regions of the R. microplus genome. The YABI tool will facilitate access and manipulation of cattle tick genome sequence data as the genome sequencing of R. microplus proceeds. During this process the CattleTickBase resource will continue to be updated. Published by Elsevier Ltd. on behalf of Australian Society for Parasitology Inc.

Optimisation of resin extraction from an Australian arid grass ‘Triodia pungens’ and its preliminary evaluation as an anti-termite timber coating

Spinifex grasses are the dominant vegetative component in Australian grassland habitats, covering approximately 26% of the Australian landmass. Our ongoing work explores the utility of both the cellulosic and resinous components of this abundant biomass for modern applications and a potential economy for our Aboriginal collaborators. This study is focused on the optimisation of a resin extraction process using solvent, and the subsequent evaluation, via a field trial, of the potential use and efficacy of the resin as an anti-termite coating material. Termiticidal performance was evaluated by re-dissolving the extracted resin in acetone and coating on pine timber blocks. The resin-coated and control blocks were then exposed to a colony of Mastotermes darwiniensis’ (Froggatt) termites, which are the most primitive alive and destructive species in subterranean area, at a trial site in northeast Australia, for six months. The results clearly showed that spinifex resin effectively protected the timber from termite attack, while the uncoated control samples were extensively damaged. By demonstrating an enhanced termite resistance, we here report that plant resins that are produced by arid/semi-arid grasses could be potentially used as treatments to prevent termite attack.

Editorial of "International Journal of Critical Indigenous Studies, Volume 7, Number 1, 2014"

This edition testifies to the broad international reach of the journal, with contributions variously concerned with Arctic Indigenous communities, the Métis of Canada, Native Hawaiians and Māori of Aotearoa (New Zealand). Two articles stress the need to work collaboratively and respectfully with Indigenous populations whilst conducting research. The first, by Gwen Healey, notes the increased interest in health research in the Arctic, particularly with Inuit populations. Healy seeks to add to the growing body of literature concerned with Indigenous ways of knowing by highlighting Inuit concepts that inform an effective Arctic research model. The second, by primary author Peter Hutchinson and a range of co-contributors, highlights the ways in which Métis collaborators working in health developed a participatory Indigenous research method that was unique in that it foregrounded Métis relationships and relationality. In so doing, the researchers were able to give substance to otherwise staid policy statements about the need for good ethical research conduct.

Harvest: A biotextile future

- Description of the work Harvest: A biotextile future consists of four bags constructed from kombucha, each utilizing a different approach to this material. The kombucha material is a byproduct of the fermented green tea, kombucha, and is comprised of a symbiotic culture of bacteria and yeast (SCOBY) that forms a fast growing curd or pellicle on the surface of the tea. This pellicle is harvested, washed, and dried to make a material with characteristics that can range between leather and paper in handle. The pellicle is one hundred per cent cellulose, with the individual fibres growing together to produce a durable and strong non-woven textile. Techniques explored with the dry kombucha material include folding, stitching, and laser etching. The final bags were designed with reference to classic tropes of fashion accessories: the briefcase, the clutch, the valise and the handbag. The valise included three jars in which the kombucha was displayed as ‘growing’ within the bag. - Research Background This work sits within an emerging field of practice in which fashion design intersects with biotechnology. Designers such as Suzanne Lee have explored constructing garments from bacteria byproducts, and bio-artists Oron Catts and Ionat Zurr have created ‘victimless leather’ grown from cultured cells. Although still speculative, these collaborations between science and design point to new material applications for fashion. Our work contributes to this area through testing both the growing of the textile and its application to construct durable fashion artefacts. - Research Contribution Harvest: A biotextile future makes two contributions to new knowledge in the area of design for sustainability within fashion. The first contribution lies in extending the technical experimentation required to grow and manipulate the textile. For the briefcase, the pattern shape was ‘grown’ into the required shape, using a shaped container. Other techniques used in the bags included weaving, folding and laser etching the material to extend its functional and decorative properties. Experimentation with the growing and drying of the material led to the production of a wide range of physical properties, in which the material was more brittle or flexible as required. The second research contribution lies in the proposal of this material for use in durable fashion accessories. The material is still speculative and small-scale in production, however the four bags illustrate the potential for kombucha as a biodegradable alternative to leather or synthetic materials. - Research Significance This interplay of science and design research opens up an exploration for a speculative future of sustainable, biodegradable textiles using live bacteria to enable ‘homegrown’ vegan apparel. The collaborators on this project include scientist Peter Musk and fashion designers Alice Payne and Dean Brough. Harvest: A biotextile future was exhibited at the State Library of Queensland’s Asia Pacific Design Library, 1-5 November 2015, as part of The International Association of Societies of Design Research’s (IASDR) biannual design conference. The work was chosen for display by a panel of experts, based on the criteria of design innovation and contribution to new knowledge in design.

Conversation Pieces

This curated exhibition presented works by Australian artists Agatha Gothe-Snape, Alex Martinis Roe and Hannah Raisin and collaborative works by Catherine or Kate (Catherine Sagin and Kate Woodcroft), Scott Ferguson (Erika Scott and Brooke Ferguson) and Courtney Coombs and Caitlin Franzmann. These artists engage with ideas of contemporary feminism through processes of dialogue and exchange, exploring subjectivity, humour and intimacy in performance and installation artworks. These works are generated by physical, verbal or textual dialogues between collaborators, participants or the artist and audience; and spark a conversation about contemporary feminist art practice in Australia today.

Dissection of the genetic background of childhood onset progressive myoclonic epilepsies

The progressive myoclonic epilepsies (PMEs) are a clinically and etiologically heterogeneous group of symptomatic epilepsies characterized by myoclonus, tonic-clonic seizures, psychomotor regression and ataxia. Different disorders have been classified as PMEs. Of these, the group of neuronal ceroid lipofuscinoses (NCLs) comprise an entity that has onset in childhood, being the most common cause of neurodegeneration in children. The primary aim of this thesis was to dissect the molecular genetic background of patients with childhood onset PME by studying candidate genes and attempting to identify novel PME-associated genes. Another specific aim was to study the primary protein properties of the most recently identified member of the NCL-causing proteins, MFSD8. To dissect the genetic background of a cohort of Turkish patients with childhood onset PME, a screen of the NCL-associated genes PPT1, TPP1, CLN3, CLN5, CLN6, MFSD8, CLN8 and CTSD was performed. Altogether 49 novel mutations were identified, which together with 56 mutations found by collaborators raised the total number of known NCL mutations to 364. Fourteen of the novel mutations affect the recently identified MFSD8 gene, which had originally been identified in a subset of mainly Turkish patients as the underlying cause of CLN7 disease. To investigate the distribution of MFSD8 defects, a total of 211 patients of different ethnic origins were evaluated for mutations in the gene. Altogether 45 patients from nine different countries were provided with a CLN7 molecular diagnosis, denoting the wide geographical occurrence of MFSD8 defects. The mutations are private with only one having been established by a founder-effect in the Roma population from the former Czechoslovakia. All mutations identified except one are associated with the typical clinical picture of variant late-infantile NCL. To address the trafficking properties of MFSD8, lysosomal targeting of the protein was confirmed in both neuronal and non-neuronal cells. The major determinant for this lysosomal sorting was identified to be an N-terminal dileucine based signal (9-EQEPLL-14), recognized by heterotetrameric AP-1 adaptor proteins, suggesting that MFSD8 takes the direct trafficking pathway en route to the lysosomes. Expression studies revealed the neurons as the primary cell-type and the hippocampus and cerebellar granular cell layer as the predominant regions in which MFSD8 is expressed. To identify novel genes associated with childhood onset PME, a single nucleotide polymorphism (SNP) genomewide scan was performed in three small families and 18 sporadic patients followed by homozygosity mapping to determine the candidate loci. One of the families and a sporadic patient were positive for mutations in PLA2G6, a gene that had previously been shown to cause infantile neuroaxonal dystrophy. Application of next-generation sequencing of candidate regions in the remaining two families led to identification of a homozygous missense mutation in USP19 for the first and TXNDC6 for the second family. Analysis of the 18 sporadic cases mapped the best candidate interval in a 1.5 Mb region on chromosome 7q21. Screening of the positional candidate KCTD7 revealed six mutations in seven unrelated families. All patients with mutations in KCTD7 were reported to have early onset PME, rapid disease progression leading to dementia and no pathologic hallmarks. The identification of KCTD7 mutations in nine patients and the clinical delineation of their phenotype establish KCTD7 as a gene for early onset PME. The findings presented in this thesis denote MFSD8 and KCTD7 as genes commonly associated with childhood onset symptomatic epilepsy. The disease-associated role of TXNDC6 awaits verification through identification of additional mutations in patients with similar phenotypes. Completion of the genetic spectrum underlying childhood onset PMEs and understanding of the gene products functions will comprise important steps towards understanding the underlying pathogenetic mechanisms, and will possibly shed light on the general processes of neurodegeneration and nervous system regulation, facilitating the diagnosis, classification and possibly treatment of the affected cases.

FIN-CLARIN: A Framework for Depositing and Disseminating Language Resources for R&D

Researchers and developers in academia and industry would benefit from a facility that enables them to easily locate, licence and use the kind of empirical data they need for testing and refining their hypotheses and to deposit and disseminate their data e.g. to support replication and validation of reported scientific experiments. To answer these needs initially in Finland, there is an ongoing project at University of Helsinki and its collaborators to create a user-friendly web service for researchers and developers in Finland and other countries. In our talk, we describe ongoing work to create a palette of extensive but easily available Finnish language resources and technologies for the research community, including lexical resources, wordnets, morphologically tagged corpora, dependency syntactic treebanks and parsebanks, open-source finite state toolkits and libraries and language models to support text analysis and processing at customer site. Also first publicly available results are presented.

Cavitation in holographic sQGP

We study the possibility of cavitation in the non-conformal N = 2* SU(N) theory which is a mass deformation of N = 4 SU(N) Yang-Mills theory. The second order transport coefficients are known from the numerical work using AdS/CFT by Buchel and collaborators. Using these and the approach of Rajagopal and Tripuraneni, we investigate the flow equations in a (1 + 1)-dimensional boost invariant set up. We find that the string theory model does not exhibit cavitation before phase transition is reached. We give a semi-analytic explanation of this finding. (C) 2011 Elsevier B.V. All rights reserved.

Shear Localization In Dynamic Deformation: Microstructural Evolution

Investigations made by the authors and collaborators into the microstructural aspects of adiabatic shear localization are critically reviewed. The materials analyzed are low-carbon steels, 304 stainless steel, monocrystalline Fe-Ni-Cr, Ti and its alloys, Al-Li alloys, Zircaloy, copper, and Al/SiCp composites. The principal findings are the following: (a) there is a strain-rate-dependent critical strain for the development of shear bands; (b) deformed bands and white-etching bands correspond to different stages of deformation; (c) different slip activities occur in different stages of band development; (d) grain refinement and amorphization occur in shear bands; (e) loss of stress-carrying capability is more closely associated with microdefects rather than with localization of strain; (f) both crystalline rotation and slip play important roles; and (g) band development and band structures are material dependent. Additionally, avenues for new research directions are suggested.

Estrategias y fundamentos del discurso alfonsí : una tentativa de romper con el topos literario de la especularidad

Resumen: Incluso antes de su llegada al trono, Alfonso X (1252-1284) emprendió una amplia labor de recopilación, traducción y reescritura de obras, tanto jurídicas, históricas como científicas. Numerosos estudios han subrayado tanto la coherencia de este proyecto como su funcionalidad política, en la medida en que dibuja un nuevo marco de relaciones en el reino y en la corte. En este trabajo, basado en la producción historiográfica y en parte de las obras científicas elaboradas en el scriptorium de Alfonso X, se intentará mostrar que esta producción textual supone una renovación, no sólo en el ámbito político sino también discursivo, y no sólo por la ruptura que supone la utilización del castellano. El análisis de prácticas tales como la compilación, la reescritura y la traducción, que remitirían en principio a una clara continuidad con la tradición textual anterior, permite por el contrario tomar la medida del salto cualitativo que representa la obra alfonsí en cuanto al sentido mismo que se la da a la escritura. La interpretación a la que se pretende llegar es que, si bien los colaboradores regios compilan, reescriben y traducen, la perspectiva desde la que el rey, considerado como autor de las obras, ordena los saberes que estas actividades producen, supone romper con el topos fundador de gran parte de la literatura medieval, la metáfora del espejo, según la cual el libro revela la verdad en la medida en que revela y refleja el mundo, es decir el orden divino

Quantum Interference and Entanglement of Surface Plasmons

Surface plasma waves arise from the collective oscillations of billions of electrons at the surface of a metal in unison. The simplest way to quantize these waves is by direct analogy to electromagnetic fields in free space, with the surface plasmon, the quantum of the surface plasma wave, playing the same role as the photon. It follows that surface plasmons should exhibit all of the same quantum phenomena that photons do, including quantum interference and entanglement.

Unlike photons, however, surface plasmons suffer strong losses that arise from the scattering of free electrons from other electrons, phonons, and surfaces. Under some circumstances, these interactions might also cause “pure dephasing,” which entails a loss of coherence without absorption. Quantum descriptions of plasmons usually do not account for these effects explicitly, and sometimes ignore them altogether. In light of this extra microscopic complexity, it is necessary for experiments to test quantum models of surface plasmons.

In this thesis, I describe two such tests that my collaborators and I performed. The first was a plasmonic version of the Hong-Ou-Mandel experiment, in which we observed two-particle quantum interference between plasmons with a visibility of 93 ± 1%. This measurement confirms that surface plasmons faithfully reproduce this effect with the same visibility and mutual coherence time, to within measurement error, as in the photonic case.

The second experiment demonstrated path entanglement between surface plasmons with a visibility of 95 ± 2%, confirming that a path-entangled state can indeed survive without measurable decoherence. This measurement suggests that elastic scattering mechanisms of the type that might cause pure dephasing must have been weak enough not to significantly perturb the state of the metal under the experimental conditions we investigated.

These two experiments add quantum interference and path entanglement to a growing list of quantum phenomena that surface plasmons appear to exhibit just as clearly as photons, confirming the predictions of the simplest quantum models.

Quantum Mechanics Studies of Fuel Cell Catalysts and Proton Conducting Ceramics with Validation by Experiment

We carried out quantum mechanics (QM) studies aimed at improving the performance of hydrogen fuel cells. This led to predictions of improved materials, some of which were subsequently validated with experiments by our collaborators.

In part I, the challenge was to find a replacement for the Pt cathode that would lead to improved performance for the Oxygen Reduction Reaction (ORR) while remaining stable under operational conditions and decreasing cost. Our design strategy was to find an alloy with composition Pt3M that would lead to surface segregation such that the top layer would be pure Pt, with the second and subsequent layers richer in M. Under operating conditions we expect the surface to have significant O and/or OH chemisorbed on the surface, and hence we searched for M that would remain segregated under these conditions. Using QM we examined surface segregation for 28 Pt₃M alloys, where M is a transition metal. We found that only Pt₃Os and Pt₃Ir showed significant surface segregation when O and OH are chemisorbed on the catalyst surfaces. This result indicates that Pt₃Os and Pt3Ir favor formation of a Pt-skin surface layer structure that would resist the acidic electrolyte corrosion during fuel cell operation environments. We chose to focus on Os because the phase diagram for Pt-Ir indicated that Pt-Ir could not form a homogeneous alloy at lower temperature. To determine the performance for ORR, we used QM to examine all intermediates, reaction pathways, and reaction barriers involved in the processes for which protons from the anode reactions react with O₂ to form H₂O. These QM calculations used our Poisson-Boltzmann implicit solvation model include the effects of the solvent (water with dielectric constant 78 with pH 7 at 298K). We found that the rate determination step (RDS) was the O_ad hydration reaction (O_ad + H₂O_ad -> OH_ad + OH_ad) in both cases, but that the barrier for pure Pt of 0.50 eV is reduced to 0.48 eV for Pt₃Os, which at 80 degrees C would increase the rate by 218%. We collaborated with the Pu-Wei Wu’s group to carry out experiments, where we found that the dealloying process-treated Pt2Os catalyst showed two-fold higher activity at 25 degrees C than pure Pt and that the alloy had 272% improved stability, validating our theoretical predictions.

We also carried out similar QM studies followed by experimental validation for the Os/Pt core-shell catalyst fabricated by the underpotential deposition (UPD) method. The QM results indicated that the RDS for ORR is a compromise between the OOH formation step (0.37 eV for Pt, 0.23 eV for Pt_2ML/Os core-shell) and H₂O formation steps (0.32 eV for Pt, 0.22 eV for Pt_2ML/Os core-shell). We found that Pt_2ML/Os has the highest activity (compared to pure Pt and to the Pt₃Os alloy) because the 0.37 eV barrier decreases to 0.23 eV. To understand what aspects of the core shell structure lead to this improved performance, we considered the effect on ORR of compressing the alloy slab to the dimensions of pure Pt. However this had little effect, with the same RDS barrier 0.37 eV. This shows that the ligand effect (the electronic structure modification resulting from the Os substrate) plays a more important role than the strain effect, and is responsible for the improved activity of the core- shell catalyst. Experimental materials characterization proves the core-shell feature of our catalyst. The electrochemical experiment for Pt_2ML/Os/C showed 3.5 to 5 times better ORR activity at 0.9V (vs. NHE) in 0.1M HClO₄ solution at 25 degrees C as compared to those of commercially available Pt/C. The excellent correlation between experimental half potential and the OH binding energies and RDS barriers validate the feasibility of predicting catalyst activity using QM calculation and a simple Langmuir–Hinshelwood model.

In part II, we used QM calculations to study methane stream reforming on a Ni-alloy catalyst surfaces for solid oxide fuel cell (SOFC) application. SOFC has wide fuel adaptability but the coking and sulfur poisoning will reduce its stability. Experimental results suggested that the Ni4Fe alloy improves both its activity and stability compared to pure Ni. To understand the atomistic origin of this, we carried out QM calculations on surface segregation and found that the most stable configuration for Ni₄Fe has a Fe atom distribution of (0%, 50%, 25%, 25%, 0%) starting at the bottom layer. We calculated that the binding of C atoms on the Ni4Fe surface is 142.9 Kcal/mol, which is about 10 Kcal/mol weaker compared to the pure Ni surface. This weaker C binding energy is expected to make coke formation less favorable, explaining why Ni₄Fe has better coking resistance. This result confirms the experimental observation. The reaction energy barriers for CHx decomposition and C binding on various alloy surface, Ni₄X (X=Fe, Co, Mn, and Mo), showed Ni₄Fe, Ni₄Co, and Fe₄Mn all have better coking resistance than pure Ni, but that only Ni₄Fe and Fe₄Mn have (slightly) improved activity compared to pure Ni.

In part III, we used QM to examine the proton transport in doped perovskite-ceramics. Here we used a 2x2x2 supercell of perovskite with composition Ba₈X₇M₁(OH)₁O₂₃ where X=Ce or Zr and M=Y, Gd, or Dy. Thus in each case a 4⁺ X is replace by a 3⁺ M plus a proton on one O. Here we predicted the barriers for proton diffusion allowing both includes intra-octahedron and inter-octahedra proton transfer. Without any restriction, we only observed the inter-octahedra proton transfer with similar energy barrier as previous computational work but 0.2 eV higher than experimental result for Y doped zirconate. For one restriction in our calculations is that the O_donor-O_acceptor atoms were kept at fixed distances, we found that the barrier difference between cerates/zirconates with various dopants are only 0.02~0.03 eV. To fully address performance one would need to examine proton transfer at grain boundaries, which will require larger scale ReaxFF reactive dynamics for systems with millions of atoms. The QM calculations used here will be used to train the ReaxFF force field.

The complex angular momentum theory of the production of three particles in collisions of two strongly interacting particles at high energy

The problem of the continuation to complex values of the angular momentum of the partial wave amplitude is examined for the simplest production process, that of two particles → three particles. The presence of so-called "anomalous singularities" complicates the procedure followed relative to that used for quasi two-body scattering amplitudes. The anomalous singularities are shown to lead to exchange degenerate amplitudes with possible poles in much the same way as "normal" singularities lead to the usual signatured amplitudes. The resulting exchange-degenerate trajectories would also be expected to occur in two-body amplitudes.

The representation of the production amplitude in terms of the singularities of the partial wave amplitude is then developed and applied to the high energy region, with attention being paid to the emergence of "double Regge" terms. Certain new results are obtained for the behavior of the amplitude at zero momentum transfer, and some predictions of polarization and minima in momentum transfer distributions are made. A calculation of the polarization of the ρ^o meson in the reaction π ^- p → π ^- ρ^op at high energy with small momentum transfer to the proton is compared with data taken at 25 Gev by W. D. Walker and collaborators. The result is favorable, although limited by the statistics of the available data.

Gestão por competências: as implicações sobre o comprometimento e a cidadania organizacional

Neste estudo foram verificadas as implicações da gestão por competências nos comportamentos de cidadania organizacional (CCO) e no comprometimento organizacional. Buscamos verificar até que ponto os modelos de gestão de pessoas baseados em competências podem influenciar positiva ou negativamente os CCO e o comprometimento, ou seja, até que ponto estas práticas funcionam como um elemento que estimula ou auxilia na desintegração, reduzindo a adoção dos comportamentos de cidadania organizacional e também o comprometimento com a organização. A pesquisa foi realizada em uma organização multinacional fabricante de produtos óticos, que utiliza os modelos de gestão baseados em competências para seleção, avaliação e remuneração variável de seus funcionários há três anos. Para investigação do comprometimento organizacional adotamos como referencial o Modelo de Três Componentes de Meyer e Allen. Para a investigação dos comportamentos de cidadania organizacional utilizamos como referência as quatro dimensões encontradas a partir dos estudos de Armênio Rego e seus colaboradores. A metodologia adotada combinou métodos quantitativos e qualitativos. Nos levantamentos quantitativos usamos a escala para mensurar o comprometimento desenvolvida por Meyer Allen e Smith, traduzida e validada para o contexto brasileiro por Medeiros, e a escala de comportamentos de cidadania organizacional desenvolvida por Armênio Rego e colaboradores. Os resultados alcançados indicam que a população estudada apresenta um grau satisfatório de comprometimento global, com maior presença da dimensão afetiva. Com relação aos CCO, os mesmos também encontram-se presentes em um grau adequado nesta amostra com maior destaque nas dimensões harmonia interpessoal e iniciativa. Dentre as conclusões obtidas a partir do estudo, destacamos que os resultados indicam a existência de variáveis organizacionais que parecem estar contribuindo para neutralizar a competição e o individualimo, por vezes potencializado pelas práticas de gestão baseadas em competências.

A leitura das salas

Focalizando as Salas de Leitura Polo do Município do Rio de Janeiro, este trabalho empreende uma leitura que visa a analisar as concepções que têm sustentado a configuração destes espaços e as práticas neles desenvolvidas, dialogando com as concepções de leitura em circulação na literatura específica, enfatizando a contribuição da perspectiva discursiva para o encaminhamento das questões relativas à ruptura com o modelo de ensino tradicional, baseado na administração do sentido supostamente único. Para tanto, examina os dispositivos legais que regem as Salas de Leitura e as condições concretas de realização das práticas, buscando articular os níveis macro e micro de análise através do ciclo de políticas, formulado por Stephen Ball e colaboradores, privilegiando as relações entre os contextos de influência, da produção textual e da prática. Assume a abordagem qualitativa e, nela, o estudo de caso, ciente da impossibilidade de generalizações, com o objetivo de aprofundar as observações sistemáticas cotidianas e a interlocução constante com os professores responsáveis pela implementação da proposta, em duas escolas municipais. A descrição minuciosa dos dois contextos da prática remete a considerações acerca das reconfigurações das Salas de Leitura, seus determinantes e as ressignificações produzidas pelos sujeitos envolvidos. Na medida em que o período do trabalho de campo coincidiu com mudança significativa no contexto de influência e de produção textual, a pretensão é sistematizar elementos para a análise dos modos pelos quais esta chega ao contexto da prática e das possibilidades de reconfiguração do espaço das Salas de Leitura.