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.

La conception néolibérale de la justice: les cas comparés de Friedrich A. von Hayek et de Walter Lippmann

Le néolibéralisme, un terme qui désigne couramment la raison d’état contemporaine, est largement associé à un désinvestissement de l’État pour la cause sociale ainsi qu’à un discours de légitimation des disparités socio-économiques. Il s’agit, pour plusieurs, d’une idéologie qui ne considère pas la justice comme un idéal collectif à poursuivre. Un retour sur certains penseurs à qui l’on attribue la formulation des idées néolibérales permet toutefois de constater que la justice fut, au sein de leurs travaux, l’un des thèmes majeurs. L’objectif général de ce mémoire est donc de présenter la conception de la justice chez deux penseurs du néolibéralisme : le journaliste américain Walter Lippmann et l’économiste autrichien Friedrich A. von Hayek. Cette perspective comparée me permettra d’identifier ce que je nomme la «conception néolibérale» de la justice, conception qui s’articule à partir d’une compréhension singulière du marché. Dans le premier chapitre, je présente le problème central de la conception néolibérale de la justice, en abordant la posture épistémologique privilégiée par Hayek et Lippmann. Dans le deuxième chapitre, je présente certaines modalités de cette conception et soulève ses principales apories. Je soutiens aussi qu’une rupture survient entre Hayek et Lippmann autour de la notion de «responsabilité». Finalement, je compare la conception néolibérale de la justice avec la conception libertarienne présentée par Nozick. C’est à partir des critères de justice respectifs de chaque théorie que j’avance la distinction, au troisième chapitre, entre les deux conceptions pourtant similaires. Contrairement à une analyse courante qui fait du néolibéralisme un projet amoral, je soutiens que la reconnaissance de la dimension morale du discours néolibéral ouvre une fenêtre à partir de laquelle il devient possible de critiquer le projet sur des bases éthiques. C’est en identifiant la notion de justice à l’oeuvre dans le discours néolibéral contemporain et en l’inscrivant dans la tradition morale présentée dans le cadre de ce mémoire que nous sommes mieux à même de comprendre l’idéologie du néolibéralisme.

Le processus de thermo-érosion du pergélisol dans la zone de pergélisol continu

Les polygones à coin de glace sont très répandus dans la zone du pergélisol continu. Lorsque le ruissellement d’eau de fonte nivale s’infiltre de façon concentrée dans une cavité, il peut initier le processus de thermo-érosion du pergélisol (notamment des coins de glace) pouvant mener à la formation de ravins. Dans la vallée de Qalikturvik sur l’Ile Bylot (NU, Canada), le développement de ravins de thermo-érosion dans un milieu de polygones à coins de glace entraîne comme impact : i. la réorganisation des réseaux de drainage impliquant un assèchement des milieux humides en marge des chenaux d’érosion, ii. des variations dans le régime thermique et de l’humidité de proche-surface et iii. la prise en charge et le déplacement des sédiments vers l’extérieur du bassin-versant. L’objectif de cette thèse vise à approfondir les connaissances géomorphologiques propres au ravinement par thermo-érosion, d’examiner, caractériser et quantifier les impacts du ravinement (tel que sus-mentionné en i. ii. iii.) et le rôle de celui-ci dans une optique d’évolution du paysage périglaciaire à l’échelle temporelle de l’année à la décennie. Les ravins sont dynamiques : un ravin en particulier déclenché en 1999 et étudié depuis s’érodait à une vitesse de 38 à 50 m/a durant sa première décennie d’existence, pour atteindre une longueur totale de ~750 m et une surface érodée de ~25 000 m² en 2009. Des puits sont localisés près des zones de ravinement actives ; des levées alluviale, mares et polygones effondrés dans les zones stabilisées post-perturbation. Sur la terrasse de polygones recouvrant le plancher de la vallée au site à l’étude, 35 ravins furent identifiés et 1401 polygones furent perturbés avec 200 000 m³ de sols transportés. Une amélioration du drainage, une dégradation de la capacité de rétention de l’humidité, une transition d’un écoulement de ruissellement vers un écoulement canalisé caractérise les aires ravinées et leurs environs. Les polygones intacts sont homogènes d’un à l’autre et dans leurs centres ; les polygones perturbés ont une réponse hétérogène (flore, humidité et régime thermique). Les milieux érodés hétérogènes succèdent aux milieux homogènes et deviennent le nouvel état d’équilibre pour plusieurs décennies.

Land cover classification of Samoylov Island and Landsat subpixel water cover of Lena River Delta, Siberia, with links to ESRI grid files

Ignoring small-scale heterogeneities in Arctic land cover may bias estimates of water, heat and carbon fluxes in large-scale climate and ecosystem models. We investigated subpixel-scale heterogeneity in CHRIS/PROBA and Landsat-7 ETM+ satellite imagery over ice-wedge polygonal tundra in the Lena Delta of Siberia, and the associated implications for evapotranspiration (ET) estimation. Field measurements were combined with aerial and satellite data to link fine-scale (0.3 m resolution) with coarse-scale (upto 30 m resolution) land cover data. A large portion of the total wet tundra (80%) and water body area (30%) appeared in the form of patches less than 0.1 ha in size, which could not be resolved with satellite data. Wet tundra and small water bodies represented about half of the total ET in summer. Their contribution was reduced to 20% in fall, during which ET rates from dry tundra were highest instead. Inclusion of subpixel-scale water bodies increased the total water surface area of the Lena Delta from 13% to 20%. The actual land/water proportions within each composite satellite pixel was best captured with Landsat data using a statistical downscaling approach, which is recommended for reliable large-scale modelling of water, heat and carbon exchange from permafrost landscapes.

Geochemistry and radiogenic isotope ratios of the volcanic sequences from Izu-Bonin Arc, Japan

New radiogenic isotope and trace element data are presented for the volcanic sequences along 600 km of the active Izu-Bonin arc, the Oligocene Izu arc, and their associated rift basins. As with many intra-oceanic island arcs, the Pliocene-Recent Izu-Bonin frontal-arc lavas are highly depleted in Zr, Nb and the rare-earth elements relative to typical mid-ocean ridge basalt (MORB), indicating that the mantle wedge source has undergone a previous episode of melting. Ratios between these elements (such as Nb/Zr and La/Sm), as well as 143Nd/144Nd, do not vary significantly along the length of the frontal-arc. These parameters suggest that each of the arc volcanoes is derived from similar melt fractions of the mantle wedge. However, Ba/Zr, Ba/Rb and 87Sr/86Sr increase along the frontal-arc to the north. This leads us to propose that a variable enrichment in Ba and radiogenic Sr is superimposed on the mantle wedge. Sr-Nd and Pb-Nd isotope variation indicate that both Sr and Pb become more radiogenic after fluid addition. However, Pb isotope ratios do not correlate with increases in Pb concentration or ratios such as Ba/Zr and Nb/Pb. In other words, the Pb isotopic composition of the arc lavas appears to be independent of the amount of Pb introduced by subduction fluids into the mantle source. This buffering of Pb isotopes along the frontal-arc means that the isotopic composition of the lavas is indistinguishable from that of the fluid. Isotopic mixing models presented for the arc are only illustrative of the many plausible combinations of components and quantities. Despite this, we are able to determine that the mantle wedge has isotopic characteristics similar to Indian Ocean MORB, and that the subduction-fluid solute is primarily derived from subducted oceanic basalt with a <2% contribution from subducted sediment. Lavas in the Oligocene Izu arc and fore-arc basin were derived from a mantle wedge of similar composition to the active arc. Despite levels of Pb enrichment comparable to those of the modern arc, the Pb isotopes of the Oligocene volcanics indicate a lower sediment input into the melting region.

Characterization of the defined MDC types and compilation of MDC initiation times (excel-file 19 kB)

Mud accumulates on continental shelves under a variety of environmental conditions and results in a diverse formation of mud depocenters (MDCs). Their three-dimensional architectures have been in the focus of several recent studies. Due to some terminological confusion concerning MDCs, the present study sets out to define eight individual MDC types in terms of surface sediment distribution and internal geometry. Under conditions of substantial sediment supply, prodeltas (distal zones off river deltas; triangular sheets), subaqueous deltas (disconnected from deltas by strong normal-to-shore currents; wedge-like clinoforms), and mud patches (scattered distribution) and mud blankets (widespread covers) are formed. Forced by hydrodynamic conditions, mud belts in the strict sense (detached from source; elongated bodies), and shallow-water contourite drifts (detached from source; growing normal to prevailing current direction; triangular clinoforms) develop. Controlled by local morphology, mud entrapments (in depressions, behind morphological steps) and mud wedges (triangular clinoforms growing in flow direction) are deposited. Shelf mud deposition took place (1) during early outer-shelf drowning (~14 ka), (2) after inner-shelf inundation to maximum flooding (9.5-6.5 ka), and (3) in sub-recent times (<2 ka). Subsequent expansion may be (1) concentric, in cases where the depocenter formed near the fluvial source, (2) uni-directional, extending along advective current transport paths, and (3) progradational, forming clinoforms that grow either parallel or normal to the bottom current direction. Classical mud belts may be initiated around defined nuclei, the remote sites of which are determined by seafloor morphology rather than the location of the source. From a stratigraphic perspective, mud depocenters coincide with sea-level highstand-related, shelf-wide condensed sections. They often show a conformable succession from transgressive to highstand systems tract stages.

Characteristics of samples obtained during Pokhodsk 2012-2013 campaigns in the joint Russian-German POLYGON Project

Polygonal tundra, thermokarst basins and pingos are common and characteristic periglacial features of arctic lowlands underlain by permafrost in Northeast Siberia. Modern polygonal mires are in the focus of biogeochemical, biological, pedological, and cryolithological research with special attention to their carbon stocks and greenhouse-gas fluxes, their biodiversity and their dynamics and functioning under past, present and future climate scenarios. Within the frame of the joint German-Russian DFG-RFBR project Polygons in tundra wetlands: state and dynamics under climate variability in Polar Regions (POLYGON) field studies of recent and of late Quaternary environmental dynamics were carried out in the Indigirka lowland and in the Kolyma River Delta in summer 2012 and summer 2013. Using a multidisciplinary approach, several types of polygons and thermokarst lakes were studied in different landscapes units in the Kolyma Delta in 2012 around the small fishing settlement Pokhodsk. The floral and faunal associations of polygonal tundra were described during the fieldwork. Ecological, hydrological, meteorological, limnological, pedological and cryological features were studied in order to evaluate modern and past environmental conditions and their essential controlling parameters. The ecological monitoring and collection program of polygonal ponds were undertaken as in 2011 in the Indigirka lowland by a former POLYGON expedition (Schirrmeister et al. [eds.] 2012). Exposures, pits and drill cores in the Kolyma Delta were studied to understand the cryolithological structures of frozen ground and to collect samples for detailed paleoenvironmental research of the late Quaternary past. Dendrochronological and ecological studies were carried out in the tree line zone south of the Kolyma Delta. Based on previous work in the Indigirka lowland in 2011 (Schirrmeister et al. [eds.] 2012), the environmental monitoring around the Kytalyk research station was continued until the end of August 2012. In addition, a classical exposure of the late Pleistocene permafrost at the Achchaygy Allaikha River near Chokurdakh was studied. The ecological studies near Pokhodsk were continued in 2013 (chapter 13). Other fieldwork took place at the Pokhodsk-Yedoma-Island in the northwestern part of the Kolyma Delta.

Phospholipid fatty acid and quinone composition of sediments from ODP Leg 205 sites

Assessing the habitability of deep-sea sediments undergoing compaction, compression, and subduction at convergent margins adds to our understanding of the limits of the terrestrial biosphere. In this work, we report exploratory biomarker data on sediments obtained at Ocean Drilling Program (ODP) Sites 1253, 1254, and 1255 during drilling at the Costa Rica subduction trench and forearc sedimentary wedge. The samples selected for postcruise biomarker analyses were located within intervals of potentially enhanced fluid flow within the décollement and sedimentary wedge fault zones (Sites 1254 and 1255) and within basal carbonates at the reference site (Site 1253). The passage of fluids that are geochemically distinct from ambient interstitial water provides a disequilibrium setting that may enhance habitability. Biomarker data show low levels of microbial biomass in subseafloor sediments sampled at the Costa Rica convergent margin as deep as ~370 meters below seafloor.

A 3.6 Ma sedimentological, geochemical and palynological record of sediment core ICDP5011-1 in Lake Elgygytgyn, NE Russia

Understanding the evolution of Arctic polar climate from the protracted warmth of the middle Pliocene into the earliest glacial cycles in the Northern Hemisphere has been hindered by the lack of continuous, highly resolved Arctic time series. Evidence from Lake El'gygytgyn, NE Arctic Russia, shows that 3.6-3.4 million years ago, summer temperatures were ~8°C warmer than today when pCO2 was ~400 ppm. Multiproxy evidence suggests extreme warmth and polar amplification during the middle Pliocene, sudden stepped cooling events during the Pliocene-Pleistocene transition, and warmer than present Arctic summers until ~2.2 Ma, after the onset of Northern Hemispheric glaciation. Our data are consistent with sea-level records and other proxies indicating that Arctic cooling was insufficient to support large-scale ice sheets until the early Pleistocene.

Radiocarbon dating, carbon storage and soil properties of samples from Tulemalu Lake, central Canadian Arctic

We investigated total storage and landscape partitioning of soil organic carbon (SOC) in continuous permafrost terrain, central Canadian Arctic. The study is based on soil chemical analyses of pedons sampled to 1 m depth at 35 individual sites along three transects. Radiocarbon dating of cryoturbated soil pockets, basal peat and fossil wood shows that cryoturbation processes have been occurring since the Middle Holocene and that peat deposits started to accumulate in a forest-tundra environment where spruce was present (~6000 cal yrs BP). Detailed partitioning of SOC into surface organic horizons, cryoturbated soil pockets and non-cryoturbated mineral soil horizons is calculated (with storage in active layer and permafrost calculated separately) and explored using principal component analysis. The detailed partitioning and mean storage of SOC in the landscape are estimated from transect vegetation inventories and a land cover classification based on a Landsat satellite image. Mean SOC storage in the 0-100 cm depth interval is 33.8 kg C/m**2, of which 11.8 kg C/m**2 is in permafrost. Fifty-six per cent of the total SOC mass is stored in peatlands (mainly bogs), but cryoturbated soil pockets in Turbic Cryosols also contribute significantly (17%). Elemental C/N ratios indicate that this cryoturbated soil organic matter (SOM) decomposes more slowly than SOM in surface O-horizons.

Chlorine concentrations and stable isotope ratios in Izu Bonin tephra

d37Cl values were determined for Izu Bonin arc magmas erupted 0-44 Ma in order to better understand the time-dependent processing of volatiles in subduction zones. Pristine ash-sized particles (glass, pumice, scoria, and rock fragments) were handpicked from tephra drilled at ODP Site 782. d37Cl values for these particles span a large range from -2.1 to +1.7 per mil (error = ± 0.3 per mil) vs. SMOC (Standard Mean Ocean Chloride, defined as 0 per mil). The temporal data extend the previously reported range of d37Cl values of -2.6 to 0.4 per mil (bulk ash) and -5.4 to -0.1 per mil (volcanic gases) from the Quaternary Izu Bonin-Mariana volcanic front to more positive values. Overall, the temporal data indicate a time-progressive evolution, from isotopically negative Eocene and Oligocene magmas (-0.7 ± 1.1 per mil, n = 10) to Neogene magmas that have higher ?37Cl values on average (+0.3 ± 1.1 per mil; n = 13). The increase is due to the emergence of positive d37Cl values in the Neogene, while minimum d37Cl values are similar through time. The range in d37Cl values cannot be attributed to fractionation during melt formation and differentiation, and must reflect the diversity of Cl present in the arc magma sources. Cl clearly derives from the slab (> 96% Cl in arc magmas), but d37Cl values do not correlate with isotope tracers (e.g. 207Pb/204Pb and 87Sr/86Sr) that are indicative of the flux from subducting sedimentary and igneous crust. Given the steady, high Cl flux since at least 42 Ma, the temporal variability of d37Cl values is best explained by a flux from subducting isotopically positive and negative serpentinite formed in the ocean basins that mingles with and possibly overprints the isotopically negative flux from sediment and igneous crust at arc front depths. The change in the d37Cl values before and after backarc spreading may reflect either a tectonically induced change in the mechanism of serpentinite formation on the oceanic plate, or possibly the integration of isotopically positive wedge serpentinite as arc fluid source during the Neogene. Our study suggests that serpentinites are important fluid sources at arc front depth, and implies the return of isotopically positive and negative Cl from the Earth surface to the mantle.

Heavy mineral and bulk mineral compositions of cores from Kumano Basin

Coring during Integrated Ocean Drilling Program Expeditions 315, 316, and 333 recovered turbiditic sands from the forearc Kumano Basin (Site C0002), a Quaternary slope basin (Site C0018), and uplifted trench wedge (Site C0006) along the Kumano Transect of the Nankai Trough accretionary wedge offshore of southwest Japan. The compositions of the submarine turbiditic sands here are investigated in terms of bulk and heavy mineral modal compositions to identify their provenance and dispersal mechanisms, as they may reflect changes in regional tectonics during the past ca. 1.5 Myrs. The results show a marked change in the detrital signature and heavy mineral composition in the forearc and slope basin facies around 1 Ma. This sudden change is interpreted to reflect a major change in the sand provenance, rather than heavy mineral dissolution and/or diagenetic effects, in response to changing tectonics and sedimentation patterns. In the trench-slope basin, the sands older than 1 Ma were probably eroded from the exposed Cretaceous-Tertiary accretionary complex of the Shimanto Belt and transported via the former course of the Tenryu submarine canyon system, which today enters the Nankai Trough northeast of the study area. In contrast, the high abundance of volcanic lithics and volcanic heavy mineral suites of the sands younger than 1 Ma points to a strong volcanic component of sediment derived from the Izu-Honshu collision zones and probably funnelled to this site through the Suruga Canyon. However, sands in the forearc basin show persistent presence of blue sodic amphiboles across the 1 Ma boundary, indicating continuous flux of sediments from the Kumano/Kinokawa River. This implies that the sands in the older turbidites were transported by transverse flow down the slope. The slope basin facies then switched to reflect longitudinal flow around 1 Ma, when the turbiditic sand tapped a volcanic provenance in the Izu-Honshu collision zone, while the sediments transported transversely became confined in the Kumano Basin. Therefore, the change in the depositional systems around 1 Ma is a manifestation of the decoupling of the sediment routing pattern from transverse to long-distance axial flow in response to forearc high uplift along the megasplay fault.

(Table 1) Results of pore water analyses, including boron content and boron isotope ratios

Drilling a transect of holes across the Costa Rica forearc during ODP Leg 170 demonstrated the margin wedge to be of continental, non accretionary origin, which is intersected by permeable thrust faults. Pore waters from four drillholes, two of which penetrated the décollement zone and reached the underthrust lower plate sedimentary sequence of the Cocos Plate, were examined for boron contents and boron isotopic signatures. The combined results show dilution of the uppermost sedimentary cover of the forearc, with boron contents lower than half of the present-day seawater values. Pore fluid "refreshening" suggests that gas hydrate water has been mixed with the sediment interstitial water, without profoundly affecting the d11B values. Fault-related flux of a deeply generated fluid is inferred from high B concentration in the interval beneath the décollement, being released from the underthrust sequence with incipient burial. First-order fluid budget calculations over a cross-section across the Costa Rica forearc indicate that no significant fluid transfer from the lower to the upper plate is inferred from boron fluid profiles, at least within the frontal 40 km studied. Expulsed lower plate pore water, which is estimated to be 0.26-0.44 km3 per km trench, is conducted efficiently along and just beneath the décollement zone, indicating effective shear-enhanced compaction. In the upper plate forearc wedge, dewatering occurs as diffuse transport as well as channelled flow. A volume of approximately 2 km3 per km trench is expulsed due to compaction and, to a lesser extent, lateral shortening. Pore water chemistry is influenced by gas hydrate instability, so that it remains unknown whether deep processes like mineral dehydration or hydrocarbon formation may play a considerable role towards the hinterland.