Statistical methods for polyhedral shape classification with incomplete data - application to cryo-electron tomographic images

A certain type of bacterial inclusion, known as a bacterial microcompartment, was recently identified and imaged through cryo-electron tomography. A reconstructed 3D object from single-axis limited angle tilt-series cryo-electron tomography contains missing regions and this problem is known as the missing wedge problem. Due to missing regions on the reconstructed images, analyzing their 3D structures is a challenging problem. The existing methods overcome this problem by aligning and averaging several similar shaped objects. These schemes work well if the objects are symmetric and several objects with almost similar shapes and sizes are available. Since the bacterial inclusions studied here are not symmetric, are deformed, and show a wide range of shapes and sizes, the existing approaches are not appropriate. This research develops new statistical methods for analyzing geometric properties, such as volume, symmetry, aspect ratio, polyhedral structures etc., of these bacterial inclusions in presence of missing data. These methods work with deformed and non-symmetric varied shaped objects and do not necessitate multiple objects for handling the missing wedge problem. The developed methods and contributions include: (a) an improved method for manual image segmentation, (b) a new approach to 'complete' the segmented and reconstructed incomplete 3D images, (c) a polyhedral structural distance model to predict the polyhedral shapes of these microstructures, (d) a new shape descriptor for polyhedral shapes, named as polyhedron profile statistic, and (e) the Bayes classifier, linear discriminant analysis and support vector machine based classifiers for supervised incomplete polyhedral shape classification. Finally, the predicted 3D shapes for these bacterial microstructures belong to the Johnson solids family, and these shapes along with their other geometric properties are important for better understanding of their chemical and biological characteristics.

Implication de la voie de dégradation ubiquitine-dépendante dans la pathologie des maladies de surchage lysosomale

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

The role of frameshifting and transcriptional dysregulation in spinocerebellar ataxia type-3

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

High-pressure experiments on a natural olivine gabbro from ODP Hole 176-735B

We have conducted high-pressure experiments on a natural oceanic gabbro composition (Gb108). Our aim was to test recent proposals that Sr-enrichment in rare primitive melt inclusions from Mauna Loa, Hawaii, may have resulted from melting of garnet pyroxenite formed in the magma source regions by reaction of peridotite with siliceous, Sr-enriched partial melts of eclogite of gabbroic composition. Gb108 is a natural, Sr-enriched olivine gabbro, which has a strong positive Sr anomaly superimposed on an overall depleted incompatible trace element pattern, reflecting its origin as a plagioclase-rich cumulate. At high pressures it crystallises as a coesite eclogite assemblage, with the solidus between 1,300 and 1,350°C at 3.5 GPa and 1,450 and 1,500°C at 4.5 GPa. Clinopyroxenes contain 4-9% Ca-eskolaite component, which varies systematically with pressure and temperature. Garnets are almandine and grossular-rich. Low degree partial melts are highly siliceous in composition, resembling dacites. Coesite is eliminated between 50 and 100°C above the solidus. The whole-rock Sr-enrichment is primarily hosted by clinopyroxene. This phase dominates the mode (>75 wt%) at all investigated PT conditions, and is the major contributor to partial melts of this eclogite composition. Hence the partial melts have trace element patterns sub-parallel to those of clinopyroxene with ~10* greater overall abundances and with strong positive Sr anomalies. Recent studies of primitive Hawaiian volcanics have suggested the incorporation into their source regions of eclogite, formerly gabbroic material recycled through the mantle at subduction zones. The models suggest that formerly gabbroic material, present as eclogite in the Hawaiian plume, partially melted earlier than surrounding peridotite (i.e. at higher pressure) because of the lower solidus temperature of eclogite compared with peridotite. This produced highly siliceous melts which reacted with surrounding peridotite producing hybrid pyroxene + garnet lithologies. The Sr-enriched nature of the formerly plagioclase-rich gabbro was present in the siliceous partial melts, as demonstrated by these experiments, and was transferred to the reactive pyroxenite. These in turn partially melted, producing Sr-enriched picritic liquids which mixed with normal picritic partial melts of peridotite before eruption. On rare occasions these mixed, relatively Sr-rich melts were trapped as melt inclusions in primitive olivine phenocrysts.Yaxley-Sobolev

Geochemical composition of calcite and aragonite, and characteristics of hydrothermal fluids of ODP Leg 168 sites

During Leg 168 a transect was drilled across the eastern flank of the Juan de Fuca Ridge in an area where the volcanic basement is covered by sediments of variable thickness. Samples of basement volcanic rocks were recovered from nine locations along the transect, where the basement sediment interface is presently heated to temperatures varying from 15° to 64°C. Altered rocks with secondary calcium carbonate were common at four of the sites, where present-day temperatures range from 38° to 64°C. Fluid inclusions in aragonite suggest that the mineral precipitated from an aqueous fluid of seawater salinity at temperatures well below 100°C. The chemical compositions of secondary calcite and aragonite were determined with both an electron microprobe and a laser-ablation inductively coupled plasma-mass spectroscopy (LA-ICP-MS) microprobe. These two techniques yielded consistent analyses of the same minor elements (Mg and Sr) in the same specimens. The combined results show that secondary aragonites contain very little Mg, Mn, Fe, Co, Ni, Cu, Zn, Rb, La, Ce, Pb, or U, yet they contain significant Sr. In contrast, secondary calcites contain significant Mg, Mn, Fe, Ni, Cu, Zn, and Pb, yet very little Co, Rb, Sr, La, Ce, or U. Secondary calcium carbonates provide subseafloor reservoirs for some minor and trace elements. Replacement of aragonite by calcite should result in a release of Sr, Rb, and Zn to solution, and it provides a sink for Mg, Mn, Ni, Cu, Zn, and Pb.

Helium and oxygen isotope ratios of ODP Sites 193-1188 and 193-1189

Fluid mixing processes and thermal regimes within the Snowcap and Roman Ruins vent sites of the PACMANUS hydrothermal system, Papua New Guinea, were investigated using 3He/4He ratios from fluid inclusions within pyrite and anhydrite and the d18O signature of anhydrite. Depressed 3He/4He ratios of 0.2-6.91RA appear to be caused by significant atmospheric diffusive exchange, whilst He-Ne diffusive fractionation precludes correction using 20Ne. 40Ar/36Ar ratios of 295-310 are elevated above seawater, indicating the majority of argon is seawater derived but with a magmatic component. d18O anhydrite ratios are 6.5 per mil to 11 per mil for Snowcap and 6.4 per mil to 11.9 per mil for Roman Ruins. Using oxygen isotope fractionation factors for the anhydrite-water system, the temperatures calculated assuming isotopic equilibrium at depth are up to 100 °C cooler than fluid inclusion trapping temperatures. It is likely that anhydrite is precipitated rapidly, preventing d18O equilibration. By comparing new d18O values for anhydrite with corresponding published 87Sr/86Sr ratios, seawater is inferred to penetrate deep into the Snowcap system with little conductive heating. A simple fluid mixing model has been constructed whereby the differing venting styles can be explained by a plumbing system at depth which favors delivery of end-member hydrothermal fluid to the high temperature sites.

Magnetic extracts of three gravity cores located at the Ceará Rise, the Mid-Atlantic Ridge and the Sierra Leone Rise

The magnetic microparticle and nanoparticle inventories of marine sediments from equatorial Atlantic sites were investigated by scanning and transmission electron microscopy to classify all present detrital and authigenic magnetic mineral species and to investigate their regional distribution, origin, transport, and preservation. This information is used to establish source-to-sink relations and to constrain environmental magnetic proxy interpretations for this area. Magnetic extracts were prepared from sediments of three supralysoclinal open ocean gravity cores located at the Ceará Rise (GeoB 1523-1; 3°49.9'N/41°37.3'W), the Mid-Atlantic Ridge (GeoB 4313-2; 4°02.8'N/33°26.3'W), and the Sierra Leone Rise (GeoB 2910-1; 4°50.7'N/21°03.2'W). Sediments from two depths corresponding to marine isotope stages 4 and 5.5 were processed. This selection represents glacial and interglacial conditions of sedimentation for the western, central, and eastern equatorial Atlantic and avoids interferences from subsurface and anoxic processes. Crystallographic, elemental, morphological, and granulometric data of more than 2000 magnetic particles were collected by scanning and transmission electron microscopy. On basis of these properties, nine particle classes could be defined: detrital magnetite, titanomagnetite (fragmental and euhedral), titanomagnetite-hemoilmentite intergrowths, silicates with magnetic inclusions, microcrystalline hematite, magnetite spherules, bacterial magnetite, goethite needles, and nanoparticle clusters. Each class can be associated with fluvial, eolian, subaeric, and submarine volcanic, biogenic, or chemogenic sources. Large-scale sedimentation patterns are delineated as well: detrital magnetite is typical of Amazon discharge, fragmental titanomagnetite is a submarine weathering product of mid-ocean ridge basalts, and titanomagnetite-hemoilmenite intergrowths are common magnetic particles in West African dust. This clear regionalization underlines that magnetic petrology is an excellent indicator of source-to-sink relations. Hematite encrustations, magnetic spherules, and nanoparticle clusters were found at all investigated sites, while bacterial magnetite and authigenic hematite were only detected at the more oxic western site. At the eastern site, surface pits and crevices were seen on the crystal faces indicating subtle early diagenetic reductive dissolution. It was observed that paleoclimatic signatures of magnetogranulometric parameters such as the ratio of anhysteretic and isothermal remanent magnetizations can be formed either by mixing of multiple sources with separate, relatively narrow grain size ranges (western site) or by variable sorting of a single source with a broad grain size distribution (eastern site). Hematite, goethite, and possibly ferrihydrite nanoparticles occur in all sediment cores studied and have either high-coercive or superparamagnetic properties depending on their partly ultrafine grain sizes. These two magnetic fractions are generally discussed as separate fractions, but we suggest that they could actually be genetically linked.

Magnetic and petrographic properties of ODP Site 120-747 (Table 1)

Carbonate sediments from the Kerguelen Plateau (ODP Leg 120) of Eocene to Pliocene age were investigated with rock magnetic, petrographic and geochemical methods to determine the carriers of remanent magnetization. Magnetic methods showed that the major magnetic minerals were titanomagnetites slightly larger than single domain particles. Submicrometre to micrometre-size grains of titanomagnetite were identified as inclusions in volcanic glass particles or as crystals in lithic clasts. Volcanic fallout ash particles formed the major fraction of the magnetic extract from each sediment sample. Three groups of volcanic ashes were identified: trachytic ashes, basaltic ashes with sideromelane and tachylite shards, and palagonitic ashes. These three groups could be equally well defined based on their magnetic hysteresis properties and alternating field demagnetization curves. The highest coercivities of all samples were found for the tachylite, due to the submicrometre-size titanomagnetite inclusions in the matrix. Trachytic ashes had intermediate magnetic properties between the single-domain-type tachylites and the palagonitic (altered) basaltic ashes with low coercivities. Samples which contained mixtures of these different volcanic ashes could be distinguished from the three types of ashes based on their magnetic characteristics. There was neither evidence of biogenic magnetofossils in the transmission electron micrographs nor did we find magnetic particles derived from continental Antarctica. The presence of dispersed volcanic fallout ashes between visible ash layers suggests continuous explosive volcanic activity on the Kerguelen Plateau in the South Indian Ocean since the early Eocene. The continuous fallout of volcanic ash from explosive volcanism on the Kerguelen Archipelago is the source of the magnetic particles and thus responsible for the magnetostratigraphy of the nannofossil oozes drilled during Leg 120.

(Table 2) Contents of U, P2O5, CO2, and TOC in phosphorites from Pacific seamounts

Uranium content of in phosphorites from Pacific seamounts does not exceed 10ppm; it is significantly lower than in phosphorites from submarine continental margins and deposits on land. Phosphate is not the main carrier of uranium, which is inhomogeneously distributed in ferromanganese hydroxide-, phosphate-, silicate- and carbonate materials. Uranium associated with phosphate is not isomorphic admixture. Uranium occurs in rocks in fine particles of unknown composition. Ultramicroscopic inclusions of U(IV) oxides have been also found.

Age determination on monazite from Forefinger Point granulites, East Antarctica (Table 2.6-1)

Electron microprobe (EMP) dating on monazite in granulite- facies rocks from Forefinger Point, East Antarctica, yielded dominant ages of 500 Ma on matrix monazites.They are associated with secondary cordierite, biotite and sapphirine, formed during nearly isothermal decompression after the high P-T assemblages involving garnet, orthopyroxene and sillimanite. Older ages around 750-1000 Ma are detected in monazite cores and in monazite inclusions in garnet porphyroblast. Combining the available age data and the reaction textures, it becomes evident that the Forefinger Point granulites have been overprinted by a granulite-facies decompressional event of Pan-African age. Moreover, EMP monazite dating imply that the Forefinger Point granulites have experienced at least two stages of metamorphic evolution.

A Mineralogical Study of a Dravitic Tourmaline from the Grenville Province

Tourmaline from a gem-quality deposit in the Grenville province has been studied with X-ray diffraction, visible-near infrared spectroscopy, Fourier transform infrared spectroscopy, scanning electron microscopy, electron microprobe and optical measurements. The tourmaline is found within tremolite-rich calc-silicate pods hosted in marble of the Central Metasedimentary Belt. The crystals are greenish-greyish-brown and have yielded facetable material up to 2.09 carats in size. Using the classification of Henry et al. 2011 the tourmaline is classified as a dravite, with a representative formula shown to be (Na0.73Ca0.2380.032)(Mg2+2.913Fe2+0.057Ti4+0.030) (Al3+5.787Fe3+0.017Mg2+0.14)(Si6.013O18)(BO3)3(OH)3((OH,O)0.907F0.093). Rietveld analysis of powder diffraction data gives a = 15.9436(8) Å, c = 7.2126(7) Å and a unit cell volume of 1587.8 Å3. A polished thin section was cut perpendicular to the c-axis of one tourmaline crystal, which showed zoning from a dark brown core into a lighter rim into a thin darker rim and back into lighter zonation. Through the geochemical data, three key stages of crystal growth can be seen within this thin section. The first is the core stage which occurs from the dark core to the first colourless zone; the second is from this colourless zone increasing in brown colour to the outer limit before a sudden absence of colour is noted; the third is a sharp change from the end of the second and is entirely colourless. These events are the result of metamorphism and hydrothermal fluids resulting from nearby felsic intrusive plutons. Scanning electron microscope, and electron microprobe traverses across this cross-section revealed that the green colour is the result of iron present throughout the system while the brown colour is correlated with titanium content. Crystal inclusions in the tourmaline of chlorapatite, and zircon were identified by petrographic analysis and confirmed using scanning electron microscope data and occur within the third stage of formation.

Alteration mineralogy and pathfinder element inventory of the McArthur River unconformity-related uranium deposit, Canada

The chemical compositions, modal mineralogy, and textural variability of interstitial minerals in sandstones of the Athabasca Group strata in the vicinity of the McArthur River unconformity-related uranium deposit were characterized using a combination of short wave infrared spectroscopy (SWIR), lithogeochemistry, scanning electron microscopy (SEM), electron probe microanalysis (EPMA) and laser ablation mass spectrometry (LA-ICP-MS) to determine the residence sites of pathfinder trace elements. The importance of integrating in-situ mineral chemistry with whole-rock analyses resides in the possibility to establish the mineralogical and paragenetic context of geochemical signatures in defining the footprint of the deposit. Located in the Athabasca Basin, Saskatchewan, Canada, the deposit is situated below ~550 m of quartz arenitic sandstones that are strongly silicified between depths of approximately 200-400 m. The silicified layer exhibits significant control on the distribution of alteration minerals, and appears to have restricted both the primary and secondary dispersion of pathfinder trace elements, which include U, radiogenic Pb isotopes, V, Ni, Co, Cu, Mo, As, Zn, and REEs. Diagenetic background sandstones contain assemblages of illite, dickite, aluminum-phosphate-sulfate (APS) minerals, apatite, and Fe-Ti oxide minerals. Altered sandstones contain assemblages of Al-Mg chlorite (sudoite), alkali-deficient dravite, APS minerals, kaolinite, illite, and oxide minerals. Throughout the sandstones, APS minerals account for the majority of the Sr and LREE concentrations, whereas late pre-ore chlorite, containing up to 0.1 wt.% Ni, accounts for the majority of Ni concentrations. Cobalt, Cu, Mo, and Zn occur predominantly in cryptic sub-micron sulfide and sulfarsenide inclusions in clay mineral aggregates and in association with paragenetically-late Fe-Ti oxides. Uranium occurs predominantly in cryptic micro-inclusions associated with pyrite in late-stage quartz overgrowths, and with paragenetically late Fe-Ti oxide micro-inclusions in kaolinite. Additionally, up to 0.2 wt.% U is cryptically distributed in post-ore Fe-oxide veins. Early diagenetic apatite, monazite and apatite inclusions in detrital quartz, and detrital zircon also contribute significant U and HREE to samples analyzed with an aggressive leach such as Aqua Regia. Detailed LA-ICP-MS chemical mapping of interstitial assemblages, detrital grains, and cements provides new insights into the distribution and inventory of pathfinder elements in the footprint of the McArthur River uranium deposit.

Strontium isotopes and sedimentology of a marine Triassic succession (upper Ladinian) of the westernmost Tethys, Spain

Chemical Stratigraphy, or the study of the variation of chemical elements within sedimentary sequences, has gradually become an experienced tool in the research and correlation of global geologic events. In this paper 87Sr/ 86Sr ratios of the Triassic marine carbonates (Muschelkalk facies) of southeast Iberian Ranges, Iberian Peninsula, are presented and the representative Sr-isotopic curve constructed for the upper Ladinian interval. The studied stratigraphic succession is 102 meters thick, continuous, and well preserved. Previous paleontological data from macro and micro, ammonites, bivalves, foraminifera, conodonts and palynological assemblages, suggest a Fassanian-Longobardian age (Late Ladinian). Although diagenetic minerals are present in small amounts, the elemental data content of bulk carbonate samples, especially Sr contents, show a major variation that probably reflects palaeoenvironmental changes. The 87Sr/86Sr ratios curve shows a rise from 0.707649 near the base of the section to 0.707741 and then declines rapidly to 0.707624, with a final values rise up to 0.70787 in the upper part. The data up to meter 80 in the studied succession is broadly concurrent with 87Sr/86Sr ratios of sequences of similar age and complements these data. Moreover, the sequence stratigraphic framework and its key surfaces, which are difficult to be recognised just based in the facies analysis, are characterised by combining variations of the Ca, Mg, Mn, Sr and CaCO3 contents

Understandings of transnational families in debates on Migration and development

International migration sets in motion a range of significant transnational processes that connect countries and people. How migration interacts with development and how policies might promote and enhance such interactions have, since the turn of the millennium, gained attention on the international agenda. The recognition that transnational practices connect migrants and their families across sending and receiving societies forms part of this debate. The ways in which policy debate employs and understands transnational family ties nevertheless remain underexplored. This article sets out to discern the understandings of the family in two (often intermingled) debates concerned with transnational interactions: The largely state and policydriven discourse on the potential benefits of migration on economic development, and the largely academic transnational family literature focusing on issues of care and the micro-politics of gender and generation. Emphasizing the relation between diverse migration-development dynamics and specific family positions, we ask whether an analytical point of departure in respective transnational motherhood, fatherhood or childhood is linked to emphasizing certain outcomes. We conclude by sketching important strands of inclusions and exclusions of family matters in policy discourse and suggest ways to better integrate a transnational family perspective in global migration-development policy.

Combining histology, stable isotope analysis and ZooMS collagen fingerprinting to investigate the taphonomic history and dietary behaviour of extinct giant tortoises from the Mare aux Songes deposit on Mauritius

Taphonomic research of bones can provide additional insight into a site's formation and development, the burial environment and ongoing post-mortem processes. A total of 30 tortoise (Cylindraspis) femur bone samples from the Mare aux Songes site (Mauritius)were studied histologically, assessing parameters such as presence and type of microbial alteration, inclusions, staining/infiltrations, the degree of microcracking and birefringence. The absence of microbial attack in the 4200 year old Mare aux Songes bones suggests the animals rapidly entered the soil whole-bodied and were sealed anoxically, although they suffered frombiological and chemical degradation (i.e. pyrite formation/oxidation, mineral dissolution and staining) related to changes in the site's hydrology. Additionally, carbon and nitrogen stable isotopeswere analysed to obtain information on the animals' feeding behaviour. The results show narrowly distributed δ13C ratios, indicating a terrestrial C3 plant-based diet, combined with a wide range in δ15N ratios. This is most likely related to the tortoises' drought-adaptive ability to change their metabolic processes, which can affect the δ15N ratios. Furthermore, ZooMS collagen fingerprinting analysis successfully identified two tortoise species (C. triserrata and C. inepta) in the bone assemblage,which,when combined with stable isotope data, revealed significantly different δ15N ratios between the two tortoise species. As climatic changes around this period resulted in increased aridity in the Mascarene Islands, this could explain the extremely elevated δ15N ratio in our dataset. The endemic fauna was able to endure the climatic changes 4200 years ago, although human arrival in the 17th century changed the original habitat to such an extent that it resulted in the extinction of several species. Fortunately we are still able to study these extinct tortoises due to the beneficial conditions of their burial environment, resulting in excellent bone preservation.