Surface textures of detrital pyroxenes in coastal dune sands (western Gulf of Mexico, Mexico): implications for their preservation and geoenvironmental processes

This work investigates how the surface textures and morphology of pyroxene grains evolve during their source‐to‐sink history. This study applies to detrital clinopyroxenes concentrated in coastal dune sands of the Gulf of Mexico which were sourced in the Trans Mexican Volcanic Belt then transported and deposited in environments subject to limited chemical weathering. The composition and morphology of the pyroxenes was characterised using single‐grain geochemical analysis and surface texture imagery with a novel approach based on the compactness property to assess the shape of minerals. This reveals heterogenous diopside‐augite populations, displaying mineral morphologies dominantly controlled by impact breakage along cleavages, little physical abrasion along their edges and with limited evidence for chemical weathering. Mechanical surface textures dominate over mechanical/chemical and chemical surface textures. These mechanical surface textures are preserved primarily as flat cleavage surfaces and rounded edges inherited from fluvial‐intertidal and aeolian transport, respectively. Mechanically/chemically induced surface textures are preserved as elongated depressions. Chemical surface textures are sparse and mostly represented by mammillated textures that suggest local dissolution under subaqueous conditions. The scarcity of chemical surface textures is attributed to frequent fragmentation of the clinopyroxenes along cleavages and limited chemical weathering during transport of the observed populations. Clinopyroxene grains in the coastal dune sands primarily retain surface characteristics from fluvial transport. Although the breakage of minerals along cleavages can obscure their original morphology under a weathering‐limited erosion regime, this study shows how surface textures and morphology of pyroxene grains is used to determine episodes of transport and deposition close to volcanic environments. The use of the compactness property as a shape descriptor measurement of particles provides an alternative approach to observe how clinopyroxene remains unaltered despite the high energy conditions of the coastal area

Minimum energy path planning for ad hoc networks

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 85-86).We introduce the problem of finding a path for a mobile node traveling from a source to a destination while communicating with at least one node from a set of stationary nodes in such a way that minimizes the transmission energy used in communication. We characterize this problem and introduce two algorithms. The first is a recursive algorithm useful for problems with one communication node. We show the limitations of this algorithm and how it can find suboptimal paths. The second algorithm, the discretized graph algorithm, can be applied to problems with more communication nodes. We find parameters that allow energy efficient paths to be found in suitable time. We demonstrate the applicability of the minimum energy path planning problem and how the discretized graph algorithm can be used in a more general context through an example.by Danjie Chen.M.Eng

Reitinhaku maastokartoilla

Reitinhakualgoritmien avulla voidaan etsiä optimaalisia polkuja monenlaisissa hakuavaruuksissa. Erilaiset kartat ovat tyypillisiä sovelluskohteita reitinhakualgoritmeille. Tässä tutkielmassa pyrin selvittämään, miten maastoa kuvaavaan paikkatietoaineistoon voidaan kohdistaa reitinhakualgoritmeja optimaalisen reitin löytämiseksi. Käsittelen myös korkeusmallien huomioimisen optimaalisten reittien haussa. Paikkatietoaineisto tarvitsee reitinhakua varten muuttaa reitinhakualgoritmille soveltuvaan muotoon. Keskityn aineiston käsittelyn suhteen erityisesti rasterointimenetelmään, johon liittyen esittelen erilaisia ruudukointitapoja ja soveltuvia reitinhakualgoritmeja. Käyn läpi myös rasterointimenetelmän kaltaiset navigointiverkot ja kulmariippumattoman reitinhaun. Esittelen toteuttamani sovelluksen, joka käyttää kuvailemiani menetelmiä reitinhakuun Maanmittauslaitoksen maastotietokannasta. Sovelluksen suorituskyky noudattaa rasterointimenetelmästä johdettavissa olevaa kompleksisuutta. Esimerkiksi 50 m x 50 m ruudukolla 37,9 kilometriä pitkän reitin laskeminen kestää noin kahdeksan sekuntia, aineiston esiprosessoinnin kestäessä muutamia minuutteja. Sovelluksen tuottamat reitit ovat käytettyjen parametrien ja karttatasojen suhteen optimaalisia, mutta vasta todellisia eri maastonkohtien liikkumiskustannuksia mittaamalla voitaisiin saavuttaa esimerkiksi metabolisten kustannusten suhteen optimaalisia reittejä

Characterisation of disuse-related osteoporosis in an animal model of spinal cord injury

Injury to the spinal cord can result in paralysis below the level of injury. A secondary complication of the removal of muscle-driven bone stimulation is the development of rapid osteoporosis in the bones of the paralysed limbs. The severe deterioration of both bone quantity and quality means that spinal cord injury (SCI) patients are at a significantly higher risk of fragility fractures in the lower extremities than the able-bodied population.;These fractures occur most commonly around the knee (distal femur and proximal tibia). This thesis presents a characterisation of the time-course effects a complete SCI has on the fracture-prone distal femur in a rat model. The aims are to characterise the quality and distribution of bone and to provide a uniquely detailed description of its response to SCI at various time points post-injury.;Bone quality is assessed using i) ex vivo micro-Computed Tomography (μCT) for global and site-specific analysis of both trabecular and cortical bone morphometry and densitometry, and ii) three-point bending and torsional mechanical testing to provide whole-bone structural and material level properties.;Evidence is presented that SCI-induced osteoporosis is site-specific within the same appendicular bone. A rapid and severe deterioration of metaphyseal trabecular bone was observed, after just 2 weeks trabecular volume fraction (BV/TV) had decreased by 59% compared to age-matched sham-operated controls. This resulted in a compromised structure composed of on average 53% fewer and 15% thinner trabeculae compared to control.;At later time points post-SCI there were no further significant reductions in metaphyseal BV/TV, although significant microstructural changes did occur. On the other hand, the more distally located epiphyseal trabecular bone was structurally more resistant to SCI-induced osteoporosis. There was a 23% decrease in BV/TV at 2 weeks post-SCI compared to control, characterised by a 15% decrease in trabecular thickness, thus unlike metaphyseal trabecular structures, the epiphyseal structure's connectivity was maintained. At later time points post-SCI there was a growth-related increase in epiphyseal BV/TV.;Rapid changes to cortical bone were also seen, with distal-metaphyseal regions experiencing the most severe decrease in cortical area at 2 weeks post-SCI compared to control. The varying degrees of change in the amount of both trabecular and cortical bone appears concomitant with each region's bone surface to volume ratio. Analysis of more chronic time points post-SCI (6, 10 and 16 weeks) highlights that caution must be exercised when interpreting results from rodent studies.;The analysis performed here indicates that SCI-induced bone changes are a combination of bone loss and suppressed bone growth. No difference in cortical tissue mineral density was observed between SCI and control groups at any time-points assessed, indicating that the decreases in whole-bone mechanical properties observed due to SCI were primarily a result of changes to the spatial distribution of bone.;Cumulatively, this thesis illustrates that SCI-induced osteoporosis has detrimentally affected the spatial distribution of both trabecular and cortical bone in site-specific ways, but the bone material itself does not appear affected.Injury to the spinal cord can result in paralysis below the level of injury. A secondary complication of the removal of muscle-driven bone stimulation is the development of rapid osteoporosis in the bones of the paralysed limbs. The severe deterioration of both bone quantity and quality means that spinal cord injury (SCI) patients are at a significantly higher risk of fragility fractures in the lower extremities than the able-bodied population.;These fractures occur most commonly around the knee (distal femur and proximal tibia). This thesis presents a characterisation of the time-course effects a complete SCI has on the fracture-prone distal femur in a rat model. The aims are to characterise the quality and distribution of bone and to provide a uniquely detailed description of its response to SCI at various time points post-injury.;Bone quality is assessed using i) ex vivo micro-Computed Tomography (μCT) for global and site-specific analysis of both trabecular and cortical bone morphometry and densitometry, and ii) three-point bending and torsional mechanical testing to provide whole-bone structural and material level properties.;Evidence is presented that SCI-induced osteoporosis is site-specific within the same appendicular bone. A rapid and severe deterioration of metaphyseal trabecular bone was observed, after just 2 weeks trabecular volume fraction (BV/TV) had decreased by 59% compared to age-matched sham-operated controls. This resulted in a compromised structure composed of on average 53% fewer and 15% thinner trabeculae compared to control.;At later time points post-SCI there were no further significant reductions in metaphyseal BV/TV, although significant microstructural changes did occur. On the other hand, the more distally located epiphyseal trabecular bone was structurally more resistant to SCI-induced osteoporosis. There was a 23% decrease in BV/TV at 2 weeks post-SCI compared to control, characterised by a 15% decrease in trabecular thickness, thus unlike metaphyseal trabecular structures, the epiphyseal structure's connectivity was maintained. At later time points post-SCI there was a growth-related increase in epiphyseal BV/TV.;Rapid changes to cortical bone were also seen, with distal-metaphyseal regions experiencing the most severe decrease in cortical area at 2 weeks post-SCI compared to control. The varying degrees of change in the amount of both trabecular and cortical bone appears concomitant with each region's bone surface to volume ratio. Analysis of more chronic time points post-SCI (6, 10 and 16 weeks) highlights that caution must be exercised when interpreting results from rodent studies.;The analysis performed here indicates that SCI-induced bone changes are a combination of bone loss and suppressed bone growth. No difference in cortical tissue mineral density was observed between SCI and control groups at any time-points assessed, indicating that the decreases in whole-bone mechanical properties observed due to SCI were primarily a result of changes to the spatial distribution of bone.;Cumulatively, this thesis illustrates that SCI-induced osteoporosis has detrimentally affected the spatial distribution of both trabecular and cortical bone in site-specific ways, but the bone material itself does not appear affected

SINGLE-MOLECULE STUDIES ON DNA COMPACTION & GENE REGULATION IN BACTERIA CELLS

Ph.DDOCTOR OF PHILOSOPH

Image analysis for gene expression based phenotype characterization in yeast cells

  Image analysis of objects in the microscope scale requires accuracy so that measurements can be used to differentiate between groups of objects that are being studied. This thesis deals with measurements in yeast biology that are obtained through microscope images. We study the algorithms and workflow of image analysis of yeast cells in order to understand and improve the measurement accuracy. The Saccharomyces cerevisiae cell is widely used as a model organism in the life sciences. It is essential to study the gene and protein behaviour within these cells, and consequently making it possible to find treatment and solutions for genetic and hereditary diseases. This is possible since many processes that occurs at the molecular level in this organism are similar to those in human cells. In the research group Imaging and Bioinformatics, we have developed a framework for analysis of yeast cells. This framework is intended to serve as a support for research in yeast biology. The framework is integrated in one application and presented via a GUI. The application integrates modules and algorithms including segmentation, measurement, analysis and visualization.  Erasmus-Mundus, Raymond-Sackler, LSBSLIACS - OU

X-ray computed microtomography applications for complex geometries and multiphase flow

In all fields, fundamental and applied research seek to produce experimental measurements without causing interferences to the process being observed. This capability is of paramount importance, since small perturbations of the phenomenon can alter it to the point of producing biased or even incorrect results. Xray techniques, based on synchrotron or laboratory X-ray sources, have attracted the attention of the research and industrial R&D community thanks to their characteristic of having little to no detectable influence on the subject under study. Moreover, if declined as tomography, this technique can provide localized full volume information at the micrometre scale, from which arbitrary shaped geometries and material densities can be deduced. During this thesis an X-ray microtomography instrument, based on a laboratory X-ray source, has been exploited to gain three main objectives. The first one is the analysis of how a liquid drop, of water or glycol, adapts its shape to reach an equilibrium state when gently deposed on a flat or patterned surface. So far this has been done using 2D techniques but introducing the knowledge of the third dimension and being able to see the drop shape even in not optically accessible locations, opens new possibilities to better understand the physics that regulate it. The second one is the reconstruction of the internal geometries of automotive diesel injectors with high resolution to detect and highlight differences between nominal and real geometries, key information to produce more realistic CFD simulations of the flow inside production grade injectors geometries. A scaled -up model made of PEEK was also studied, producing successive tomographies, to detect small geometrical changes induced by part usage, giving an in-depth view of the locations more prone to be damaged by cavitation flow. The third one is the study of a multiphase flow inside the same scaled-up model injection channel with flowing conditions exhibiting cavitation. The geometry of the non-axisymmetric model mimics the flow pattern of a real diesel injection channel and automotive grade diesel was consequently selected as fluid. Understanding the dependence of cavitation development on flow characteristics in a three-dimensional way, through the determination of the localized void fraction of the multiphase flow, can lead to improvements in the knowledge of such a phenomenon that can guide the design of future fuel injection equipment