Big Data Processing in the Cloud: a Hydra/Sufia Experience

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

DSpace for Data Revisited

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

A Rights Expression Language for Federated Repositories

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Developing sustainable research data management services: an institutional collaboration

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Effect of epithelial debridement on human cornea proteoglycans

Corneal transparency is attributed to the regular spacing and diameter of collagen fibrils, and proteoglycans may play a role in fibrillogenesis and matrix assembly. Corneal scar tissue is opaque and this opacity is explained by decreased ultrastructural order that may be related to proteoglycan composition. Thus, the objectives of the present study were to characterize the proteoglycans synthesized by human corneal explants and to investigate the effect of mechanical epithelial debridement. Human corneas unsuitable for transplants were immersed in F-12 culture medium and maintained under tissue culture conditions. The proteoglycans synthesized in 24 h were labeled metabolically by the addition of 35S-sulfate to the medium. These compounds were extracted by 4 M GuHCl and identified by a combination of agarose gel electrophoresis, enzymatic degradation with protease and mucopolysaccharidases, and immunoblotting. Decorin was identified as the main dermatan sulfate proteoglycan and keratan sulfate proteoglycans were also prominent components. When the glycosaminoglycan side chains were analyzed, only keratan sulfate and dermatan sulfate were detected (~50% each). Nevertheless, when these compounds were 35S-labeled metabolically, the label in dermatan sulfate was greater than in keratan sulfate, suggesting a lower synthesis rate for keratan sulfate. 35S-Heparan sulfate also appeared. The removal of the epithelial layer caused a decrease in heparan sulfate labeling and induced the synthesis of dermatan sulfate by the stroma. The increased deposit of dermatan sulfate proteoglycans in the stroma suggests a functional relationship between epithelium and stroma that could be related to the corneal opacity that may appear after epithelial cell debridement.

Detection of immunoglobulin G in the lung and liver of hamsters with visceral leishmaniasis

Several organs are affected in visceral leishmaniasis, not only those rich in mononuclear phagocytes. Hypergammaglobulinemia occurs during visceral leishmaniasis; anti-Leishmania antibodies are not primarily important for protection but might be involved in the pathogenesis of tissue lesions. The glomerulonephritis occurring in visceral leishmaniasis has been attributed to immune complex deposition but in other organs the mechanism has not been studied. In the current study we demonstrated the presence of IgG in the lung and liver of hamsters with visceral leishmaniasis. Hamsters were injected intraperitoneally with 2 x 10(7) amastigotes of Leishmania (Leishmania) chagasi and the presence of IgG in the liver and lung was evaluated at 7, 15, 30, 45, 80 and 102 days postinfection (PI) by immunohistochemistry. The parasite burden in the spleen and liver increased progressively during infection. We observed a deposit of IgG from day 7 PI that increased progressively until it reached highest intensity around 30 and 45 days PI, declining at later times. The IgG deposits outlined the sinusoids. In the lung a deposit of IgG was observed in the capillary walls that was moderate at day 7 PI, but the intensity increased remarkably at day 30 PI and declined at later times of infection. No significant C3 deposits were observed in the lung or in the liver. We conclude that IgG may participate in the pathogenesis of the inflammatory process of the lung and liver occurring in experimental visceral leishmaniasis and we discuss an alternative mechanism other than immune complex deposition.

The role of complement in the early phase of Leishmania (Leishmania) amazonensis infection in BALB/c mice

Complement-depleted and -non-depleted BALB/c mice were inoculated with Leishmania (Leishmania) amazonensis promastigotes into the hind footpad to study the role of the complement system in cutaneous leishmaniasis. Total serum complement activity was measured by hemolytic assay and C3 fragment deposit at the inoculation site was determined by direct immunofluorescence in the early period of infection, i.e., at 3, 24, 48 h and 7 days post-infection. The inflammatory reaction and the parasite burden were evaluated in the skin lesion at 7 and 30 days post-infection. Total serum complement activity decreased in the early phase of infection, from 3 to 24 h, in non-depleted mice compared to non-infected and non-depleted mice. C3 fragment deposit at the site of parasite inoculation was present throughout the period of infection in non-depleted mice. In contrast, no C3 fragment deposit was observed at the inoculation site in complement-depleted mice. Complement-depleted mice showed a significant decrease in the inflammatory response and a significant increase in the number of parasites (70.0 ± 5.3 vs 5.3 ± 1.5) at 7 days of infection (P < 0.05). A higher number of parasites were also present at 30 days of infection at the inoculation site of complement-depleted mice (78.5 ± 24.9 vs 6.3 ± 5.7). These experiments indicate that complement has an important role at the beginning of experimental cutaneous leishmaniasis caused by L. (L.) amazonensis by controlling the number of parasites in the lesion.

Roll-to-roll atomic layer deposition process for flexible electronics applications

Atomic Layer Deposition (ALD) is the technology of choice where very thin and highquality films are required. Its advantage is its ability to deposit dense and pinhole-free coatings in a controllable manner. It has already shown promising results in a range of applications, e.g. diffusion barrier coatings for OLED displays, surface passivation layers for solar panels. Spatial Atomic Layer Deposition (SALD) is a concept that allows a dramatic increase in ALD throughput. During the SALD process, the substrate moves between spatially separated zones filled with the respective precursor gases and reagents in such a manner that the exposure sequence replicates the conventional ALD cycle. The present work describes the development of a high-throughput ALD process. Preliminary process studies were made using an SALD reactor designed especially for this purpose. The basic properties of the ALD process were demonstrated using the wellstudied Al2O3 trimethyl aluminium (TMA)+H2O process. It was shown that the SALD reactor is able to deposit uniform films in true ALD mode. The ALD nature of the process was proven by demonstrating self-limiting behaviour and linear film growth. The process behaviour and properties of synthesized films were in good agreement with previous ALD studies. Issues related to anomalous deposition at low temperatures were addressed as well. The quality of the coatings was demonstrated by applying 20 nm of the Al2O3 on to polymer substrate and measuring its moisture barrier properties. The results of tests confirmed the superior properties of the coatings and their suitability for flexible electronics encapsulation. Successful results led to the development of a pilot scale roll-to-roll coating system. It was demonstrated that the system is able to deposit superior quality films with a water transmission rate of 5x10-6 g/m2day at a web speed of 0.25 m/min. That is equivalent to a production rate of 180 m2/day and can be potentially increased by using wider webs. State-of-art film quality, high production rates and repeatable results make SALD the technology of choice for manufacturing ultra-high barrier coatings for flexible electronics.

Protein turnover, amino acid requirements and recommendations for athletes and active populations

Skeletal muscle is the major deposit of protein molecules. As for any cell or tissue, total muscle protein reflects a dynamic turnover between net protein synthesis and degradation. Noninvasive and invasive techniques have been applied to determine amino acid catabolism and muscle protein building at rest, during exercise and during the recovery period after a single experiment or training sessions. Stable isotopic tracers (13C-lysine, 15N-glycine, ²H5-phenylalanine) and arteriovenous differences have been used in studies of skeletal muscle and collagen tissues under resting and exercise conditions. There are different fractional synthesis rates in skeletal muscle and tendon tissues, but there is no major difference between collagen and myofibrillar protein synthesis. Strenuous exercise provokes increased proteolysis and decreased protein synthesis, the opposite occurring during the recovery period. Individuals who exercise respond differently when resistance and endurance types of contractions are compared. Endurance exercise induces a greater oxidative capacity (enzymes) compared to resistance exercise, which induces fiber hypertrophy (myofibrils). Nitrogen balance (difference between protein intake and protein degradation) for athletes is usually balanced when the intake of protein reaches 1.2 g·kg-1·day-1 compared to 0.8 g·kg-1·day-1 in resting individuals. Muscular activities promote a cascade of signals leading to the stimulation of eukaryotic initiation of myofibrillar protein synthesis. As suggested in several publications, a bolus of 15-20 g protein (from skimmed milk or whey proteins) and carbohydrate (± 30 g maltodextrine) drinks is needed immediately after stopping exercise to stimulate muscle protein and tendon collagen turnover within 1 h.

Voimalaitosten kattilaputkien sisäpuolisten kerrostumien paksuuden mittaaminen ultraäänimenetelmällä

Höyryvoimalaitoksen käyttöönotossa muodostuu kattilaputkien sisäpinnoille niitä korroosiolta suojaava ohut metallioksidikerros. Tämän kerroksen päälle kasvaa kattilan käytön aikana haitallista kerrostumaa paikallisen korroosion tai kattilavedessä olevien epäpuhtauksien kerääntymisen tai kiteytymisen seurauksena. Kerrostuma haittaa lämmönsiirtoa tulipesästä putkiseinämän läpi kattilaveteen. Putkien lämpötilan nousu suunniteltua korkeammaksi kasvattaa putkivaurioiden ja sisäpuolisen korroosion riskiä. Tästä johtuen paksuksi kasvaneet kerrostumat pyritään poistamaan happokäsittelyllä eli peittauksella ennen vaurioiden syntyä. Perinteisesti kerrostumapaksuus on määritetty kattilasta irrotetuista näyteputkista mikroskoopilla. Työn tavoitteena oli tutkia uudenlaisen ultraäänimittauksen teoriaa ja selvittää sen toimivuus höyrystinputkien kerrostumapaksuusmittauksissa. Lisäksi tavoitteena oli tutkia voimalaitoksen höyrystimen sisäpuolisten kerrostumien muodostumista ja niiden vaikutuksia sekä kattilan peittaustarpeen arviointia. Höyrystimen kerrostumien kasvunopeuteen vaikuttavat eniten voimalaitostyyppi, käytetty vesikemia ja kattilaveteen kulkeutuvien epäpuhtauksien määrä. Kasvunopeus vaihtelee laitosten välillä suuresti ja eroaa myös tulipesän eri kohdissa. Kattilaveden epäpuhtauspitoisuus ja kerrostumapaksuus vaikuttavat molemmat korroosiovaurioiden todennäköisyyteen. Peittauspaksuuden ohjearvoissa tulisi huomioida kattilan käyttöpaine, kattilatyyppi ja riski kattilaveden laadun heikkenemiselle. Putkinäytteistä ja laitoksilla suoritettujen mittauksien perusteella uusi ultraäänitekniikka tuottaa luotettavia tuloksia tavanomaisten kerrostumien mittauksessa. Vain yhdellä laitoksella esiintyi irtonaisen sakan kaltaista kerrostumaa, jota mittaus ei kyennyt havaitsemaan. Mittaustulokset kerrostumista tulipesän eri osissa antavat hyvän perustan peittaustarpeen arviointiin.

Drift dispersal in central Southern Ontario /

Two tills are readily identi-f i able in central Southern Ontario, a very stony, loose deposit o-f variable matrix (Dummer till) and a moderately stony, fissile and compact deposit that is more homogeneous (drumlinized till). The quantity o-f Precambr i an, Paleozoic and Shadow Lake Formation (Paleozoic) rock types were determined and corresponding isopleth maps drawn. The changes in lithology content occurred in the direction o-f transport, there-fore, compositional isopleths o-f till may be considered equipotential lines for the reconstruction of glacier flow paths. Areal gradations of drift lithology indicated that the prime agents of dispersal were ice and glacial meltwaters. The down-ice abundance trend of till components indicated a dispersal pattern showing the concentration of a given lithology type peaking within a few kilometres of the source followed by a rapid decline and thereafter, a more gradual decrease with increasing distance. Within the esker deposits, igneous rocks may form the major component and can extend further onto the limestone plain than in the adjacent till. Evidence is presented that indicates the "style" of dispersal was one in which glacial ice may have been strongly influenced by local bedrock topography and the regional structural trends. The ice tended to follow pre-existing valleys and lows, depositing till composed mainly of local bedrock. Gradations in Paleozoic clast content showed that the local bedrock lithology became the primary till component within 3 km of down-ice transport. Evidence is presented that indicated the last glaciation may have occurred as a relatively thin ice mass, followed by stagnation and recession. No evidence of a lateglacial re-advance was found within the study area. Because of the lack of a contact between the Dummer and drumlinized till, and because of results showing gradation of the Dummer till into the drumlinized till (as indicated by lithology content and grain size), it is suggested that no re-advance occurred.

Evolution of an Archean greenstone belt in the Stormy Lake - Kawashegamuk Lake area (stratigraphy, structure and geochemistry) - Western Wabigoon Subprovince, Northwest Ontario /

330 km 2 of the easter-n part of the Archean Manitou Lakes - Stormy Lake metavolcanic - metasedimentary belt have been mapped and sampled. A large number of rocks ~.vere analyzed for the major and trace constituents including the rare-earth elements (REE). The Stormy Lake - Kawashegamuk Lake area may be subdivided into four major lithological groups of supracrustal rocks 1) A north-facing mafic assemblage, consisting of pillowed tholeiitic basalts and gabbro sills characterized by flat REE profiles, is exposed in the south part of the map area and belongs to a 8000 m thick homoclinal assemblage outside the map area. Felsic pyroclastic rocks believed to have been issued from a large central vent conformably overlie the tholeiites. 2) A dominantly epiclastic group facing to the north consists of terrestrial deposits interpreted to be an alluvial fan deposit ; a submarine facies is represented by turbiditic sediments. 3) The northeastern part of the study area consists of volcanic rocks belonging to two mafic - felsic cycles facing to the southuest ; andesitic flows with fractionated REE patterns make up a large part of the upper cycle, whereas the lower cycle has a stronger chemical polarity being represented by tholeiitic flows, with flat REE, which a r e succeeded by dacitic and rhyolitic pyroclasti cs. iii 4) A thick monotonous succession of tholeiitic pillmled basalt f lows and gabbro sills with flat REE represent the youngest supracrustal rocks. TIle entire belt underwent folding, faulting and granitic plutonism during a tectono-thermal event around 2700 Ma ago. Rocks exposed in the map area were subjected to regional greenschist facies metamorphism, but higher metamorphic grades are present near late granitic intrusions. Geochemical studies have been useful in 1) distinguishing the various rock units ; 2) relating volcanic and intrusive rocks 3) studying the significance of chemical changes due to post magmatic processes 4) determining the petrogenesis of the major volcanic rock types. In doing so, two major volcanic suites have been recognized : a) a tholeiitic suite, mostly represented by mafic rocks, was derived from partial melting of upper mantle material depleted in Ti, K and the light REE ; b) a calc-alkalic suite which evolved from partial melting of amphibolite in the lower crust. The more differentiated magma types have been produced by a multistage process involving partial melting and fractional crystallization to yield a continuum of compos i t i ons ranging from basaltic andesite to rhyolite. A model for the development of the eastern part of the Manitou Lakes - Stormy Lake belt has been proposed.

Development of hypogene and supergene alteration and copper mineralization patterns, Sar Cheshmeh porphyry copper deposits, Iran /

The formation of the Sar Cheshmeh porphyry Cu-Mo deposit is related to the culmination of calc-alkaline igneous activity in the Kerman region. The deposit comprises a suite of Late Cenozoic intrusive sub-volcanic and extrusive rocks emplaced into a folded series of Eocene andesitic lavas and pyroclastic sediments. The earliest stage of magmatism was emplacement of a large granodiorite stock about 29 m.y.b.p. This was followed by intrusion of two separate porphyritic bodies at 15 (Sar Cheshrneh porphyry) and 12 m.y.b.p. (Late porphyry) and a series of sub-volcanic dikes between 12 and 9 m.y.b.p. Magmatic activity terminated with multi-phase extrusion of a Pelean dacitic dome complex between 10 and 2.8 m.y.b.p. The country rocks and the earlier porphyritic intrusions are pervasively altered to biotite-rich potassium silicate (metasomatic and hydrothermal) sericite-clay, phyllic and chlorite-clay, argillic assemblages. These grade outwards to an extensive propylitic zone. Within the ore body, the later intra-. and post-mineral dikes only reach the propylitic grade. At least three different sets of quartz veins are present, including a sericite-chlorite-quartz set which locally retrogrades pervasive secondary biotite to sericite. In the hypogene zone, metasomatic and hydrothermal alteration is related to all stages of magmatism but copper mineralization and veining are restricted to a period of 15 to 9 m.y.b.p.related to the early intrusive phases. The copper mineralization and silicate alteration do not fit a simple annular ring model but have been greatly modified by, 1. The existence of an ititial, outer ring, of metasomatic alteration overprinted by an inner.ring of hydrothermal alteration and, 2. later extensive dilating effects of intra- and post-mineral dikes. The hydrothermal clay mineral assemblage in the hypogene zone is illite-chlorite-kaolinite-smectite (beidellite). Preliminary studies indicate that the amount of each of these clays varies vertically and that hydrothermal zonation of clay minerals is possible. However, these minerals alter to illite-kaolinite assemblages in the supergene sulfide zone and to more kaolinite-rich assemblages in the supergene leached zone. Hydrothermal biotite breaks down readily in the supergene zone and is not well preserved in surface outcrops. The distribution of copper minerals in the supergene sulfide enrichment zone is only partly related to rock type being more dependent on topography and the availability of fractures.

Geology of the Sand Creek porphyry molybdenum prospect /

The Sand Creek Prospect is located within the eastern exposed margin of the Coast Plutonic Complex. The occurrence is a plug and dyke porphyry molybdenum deposit. The rock types, listed in decreasing age: 1) metamorphlc schists and gneisses; 2) diorite suite rocks - diorite, quartz diorite, tonalite; 3) rocks of andesitic composition; 4) granodiorites, coarse porphyritic granodiorite, quartzfeldspar porphyry, feldspar porphyry; and 5) lamprophyre. Hydrothermal alteration is known to have resulted from emplacement of the hornblende-feldspar porphyry through to the quartz-feldspar porphyry. Molybdenum mineralization is chiefly associated with the quartz-feldspar porphyry. Ore mineralogy is dominated by pyrite with subordinate molybdenite, chalcopyrite, covelline, sphalerite, galena, scheelite, cassiterite and wolframite. Molybdenite exhibits a textural gradation outward from the quartz-feldspar porphyry. That is, disseminated rosettes and rosettes in quartz veins to fine-grained molybdenite in quartz veins and potassic altered fractures to fine-grained molybdenite paint or 6mears in the peripheral zones. The quartz-feldspar porphyry dykes were emplaced in an inhomogeneous stress field. The trend of dykes, faults and shear zones is 0^1° to 063° and dips between 58° NW and 86* SE. Joint Pole distribution reflects this fault orientation. These late deformatior maxima are probably superimposed upon annuli representing diapiric emplacement of the plutons. A model of emplacement involving two magmatic pulses is given in the following sequence: Diorite pulse (i) dioritequartz diorite, (ii) tonalites; granodiorite pulse (iii) hornblende-fildspar microporphyry, hornblende/biotite porphyry, (iv) coarse grained granodiorite, (v) quartz-feldspar porphyry, (vi) feldspar porphyry, and (vii) lamprophyre. The combination of plutonic and coarse porphyritic textures, extensive propylitic overprinting of potassic alteration assemblages suggests that the. prospect represents the lower reaches of a porphyry system.

A reconnaissance study of the metamorphic petrology and volcanic geochemistry of a portion of the Island Lake greenstone belt, Manitoba /

The Island Lake greenstone belt is one of the major Archean supracrustal exposures in the northwestern part of the Superior Province of the Canadian Shield. This belt is subdivided into two units: 1) a lower sequence characterised by pillowed to massive, locally pyroclastic, basalt to andesite with a thin central zone of felsic derivatives, all of which are interbedded with and overlain by thick sequences of turbidite facies rock; 2) the upper unit which consists of thick stratified conglomerate overlain by thickly bedded arkose and feldspathic greywacke. Reconnaissance sampling traverses were completed across both the strike of the belt and along its margins with adjacent granitoids. Most of the belt is within the greenschist metamorphic f acies with amphibolite facies occurring in certain areas near t he margins. A post-tectonic, low pressure thermal event may be responsible for the development of a unit of cordierite schi s t which stretches southeastwards from the east end of Cochrane Bay. Volcanism is cyclical in nature changing from tholeiitic to calc-alkaline. There is a general progression in the character of the lavas from mafic t o felsic with stratigraphic height. Chemica l d a ta sugges t that h i gh level fractionation of a mantle- derived ' dry' magma i s t he s ource of the thole i iti c lavas. Contamination of this magma with 'we t' sia l and subsequent fractionation may be r esponsi b l e for the calcalkaline phases .Observations of stratigraphic relationships (in particular the contact between the supracrustals and the granitoids) coupled with the metamorphic and chemical studies, allow the construction of a preliminary model for the evolution of the Island Lake greenstone belt. The following sequential development is suggested: 1) a platform stage characterised by the subaqueous effusion of mafic to intermediate lavas of alternating tholeiitic and calc-alkaline affinities; 2) an edifice stage marked by the eruption of felsic calc-alkaline rocks; 3) an erosional stage characterised by the deposit~on of thick sequences of turbidite facies rocks; 4) the impingement of granitic masses into the margins of the greenstone belt, which was probably related to a downward warping of the supracrustal pilei 5) the erosion of sialic massifs surrounding and within the greenstone belt and of early supracrustal piles, to give the clastic upper unit.