A Note on the Extinction Problem for Controlled Multitype Branching Processes

2000 Mathematics Subject Classification: 60J80, 60J10.

Recent Results for Supercritical Controlled Branching Processes with Control Random Functions

2000 Mathematics Subject Classification: 60J80, 60F05

Effects of in situ CO2 enrichment on structural characteristics, photosynthesis, and growth of the Mediterranean seagrass Posidonia oceanica

Seagrass is expected to benefit from increased carbon availability under future ocean acidification. This hypothesis has been little tested by in situ manipulation. To test for ocean acidification effects on seagrass meadows under controlled CO2/pH conditions, we used a Free Ocean Carbon Dioxide Enrichment (FOCE) system which allows for the manipulation of pH as continuous offset from ambient. It was deployed in a Posidonia oceanica meadow at 11 m depth in the Northwestern Mediterranean Sea. It consisted of two benthic enclosures, an experimental and a control unit both 1.7 m**3, and an additional reference plot in the ambient environment (2 m**2) to account for structural artifacts. The meadow was monitored from April to November 2014. The pH of the experimental enclosure was lowered by 0.26 pH units for the second half of the 8-month study. The greatest magnitude of change in P. oceanica leaf biometrics, photosynthesis, and leaf growth accompanied seasonal changes recorded in the environment and values were similar between the two enclosures. Leaf thickness may change in response to lower pH but this requires further testing. Results are congruent with other short-term and natural studies that have investigated the response of P. oceanica over a wide range of pH. They suggest any benefit from ocean acidification, over the next century (at a pH of 7.7 on the total scale), on Posidonia physiology and growth may be minimal and difficult to detect without increased replication or longer experimental duration. The limited stimulation, which did not surpass any enclosure or seasonal effect, casts doubts on speculations that elevated CO2 would confer resistance to thermal stress and increase the buffering capacity of meadows.

Understanding the role of transforming growth factor beta signalling and epigenomics in osteoarthritis

Osteoarthritis (OA) is the most common form of arthritis with a high socioeconomic burden, with an incompletely understood etiology. Evidence suggests a role for the transforming growth factor beta (TGF-ß) signalling pathway and epigenomics in OA. The aim of this thesis was to understand the involvement of the TGF-ß pathway in OA and to determine the DNA methylation patterns of OA-affected cartilage as compared to the OA-free cartilage. First, I found that a common SNP in the BMP2 gene, a ligand in the Bone morphogenetic protein (BMP) subunit of TGF-ß pathway, was associated with OA in the Newfoundland population. I also showed a genetic association between SMAD3 - a signal transducer in the TGF-ß subunit of the TGF-ß signalling pathway - and the total radiographic burden of OA. I further demonstrated that SMAD3 is over-expressed in OA cartilage, suggesting an over activation of the TGF-ß signalling in OA. Next, I examined the connection of these genes in the regulation of matrix metallopeptidase 13 (MMP13) - an enzyme known to destroy extracellular matrix in OA cartilage - in the context of the TGF-ß signalling. The analyses showed that TGF-ß, MMP13, and SMAD3 were overexpressed in OA cartilage, whereas the expression of BMP2 was significantly reduced. The expression of TGF-ß was positively correlated with that of SMAD3 and MMP13, suggesting that TGF-ß signalling is involved in up-regulation of MMP13. This regulation, however, appears not to be controlled by SMAD3 signals, possibly due to the involvement of collateral signalling, and to be suppressed by BMP regulation in healthy cartilage, whose levels were reduced in end-stage OA. In a genome-wide DNA methylation analysis, I reported CpG sites differentially methylated in OA and showed that the cartilage methylome has a potential to distinguish between OA-affected and non-OA cartilage. Functional clustering analysis of the genes harbouring differentially methylated loci revealed that they are enriched in the skeletal system morphogenesis pathway, which could be a potential candidate for further OA studies. Overall, the findings from the present thesis provide evidence that the TGF-ß signalling pathway is associated with the development of OA, and epigenomics might be involved as a potential mechanism in OA.

The effect of Me2SO overexposure during cryopreservation on HOS TE85 and hMSC viability, growth and quality

With the cell therapy industry continuing to grow, the ability to preserve clinical grade cells, including mesenchymal stem cells (MSCs), whilst retaining cell viability and function remains critical for the generation of off-the-shelf therapies. Cryopreservation of MSCs, using slow freezing, is an established process at lab scale. However, the cytotoxicity of cryoprotectants, like Me2SO, raises questions about the impact of prolonged cell exposure to cryoprotectant at temperatures >0 °C during processing of large cell batches for allogenic therapies prior to rapid cooling in a controlled rate freezer or in the clinic prior to administration. Here we show that exposure of human bone marrow derived MSCs to Me2SO for ≥1 h before freezing, or after thawing, degrades membrane integrity, short-term cell attachment efficiency and alters cell immunophenotype. After 2 h's exposure to Me2SO at 37 °C post-thaw, membrane integrity dropped to ∼70% and only ∼50% of cells retained the ability to adhere to tissue culture plastic. Furthermore, only 70% of the recovered MSCs retained an immunophenotype consistent with the ISCT minimal criteria after exposure. We also saw a similar loss of membrane integrity and attachment efficiency after exposing osteoblast (HOS TE85) cells to Me2SO before, and after, cryopreservation. Overall, these results show that freezing medium exposure is a critical determinant of product quality as process scale increases. Defining and reporting cell sensitivity to freezing medium exposure, both before and after cryopreservation, enables a fair judgement of how scalable a particular cryopreservation process can be, and consequently whether the therapy has commercial feasibility.

Nanoporous InP: anodic formation and growth mechanism in aqueous electrolytes

Porous layers can be formed electrochemically on (100) oriented n-InP substrates in aqueous KOH. A nanoporous layer is obtained underneath a dense near-surface layer and the pores appear to propagate from holes through the near-surface layer. In the early stages of the anodization transmission electron microscopy (TEM) clearly shows individual porous domains that appear to have a square-based pyramidal shape. Each domain appears to develop from an individual surface pit which forms a channel through this near-surface layer. We suggest that the pyramidal structure arises as a result of preferential pore propagation along the <100> directions. AFM measurements show that the density of surface pits increases with time. Each of these pits acts as a source for a pyramidal porous domain. When the domains grow, the current density increases correspondingly. Eventually the domains meet, forming a continuous porous layer, the interface between the porous and bulk InP becomes relatively flat and its total effective surface area decreases resulting in a decrease in the current density. Current-time curves at constant potential exhibit a peak and porous layers are observed to form beneath the electrode surface. The density of pits formed on the surface increases with time and approaches a plateau value. Porous layers are also observed in highly doped InP but are not observed in wafers with doping densities below ~5 × 1017 cm-3. Numerical models of this process have been developed invoking a mechanism of directional selectivity of pore growth preferentially along the <100> lattice directions. Manipulation of the parameters controlling these curves shows that the fall-off in current is controlled by the rate of diffusion of electrolyte through the pore structure with the final decline in current being caused by the termination of growth at the pore tips through the formation of passivating films or some other irreversible modification of the pore tips.

Growth and characterization of anodic Films on InP in KOH and (NH4)2S

The current-voltage characteristics of InP were investigated in (NH4)2S and KOH electrolytes. In both solutions, the observation of current peaks in the cyclic voltammetric curves was attributed to the growth of passivating films. The relationship between the peak currents and the scan rates suggests that the film formation process is diffusion controlled in both cases. The film thickness required to inhibit current flow was found to be much lower on samples anodized in the sulphide solution. Focused ion beam (FIB) secondary electron images of the surface films show that film cracking of the type reported previously for films grown in (NH4)2S is also observed for films grown in KOH. X-ray and electron diffraction measurements indicate the presence of In2O3 and InPO4 in films grown in KOH and In2S3 in films grown in (NH4)2S.

Epitaxial growth of visible to infra-red transparent conducting In2O3 nanodot dispersions and reversible charge storage as a Li-ion battery anode

Unique bimodal distributions of single crystal epitaxially grown In2O3 nanodots on silicon are shown to have excellent IR transparency greater than 87% at IR wavelengths up to 4 μm without sacrificing transparency in the visible region. These broadband antireflective nanodot dispersions are grown using a two-step metal deposition and oxidation by molecular beam epitaxy, and backscattered diffraction confirms a dominant (111) surface orientation. We detail the growth of a bimodal size distribution that facilitates good surface coverage (80%) while allowing a significant reduction in In2O3 refractive index. This unique dispersion offers excellent surface coverage and three-dimensional volumetric expansion compared to a thin film, and a step reduction in refractive index compared to bulk active materials or randomly porous composites, to more closely match the refractive index of an electrolyte, improving transparency. The (111) surface orientation of the nanodots, when fully ripened, allows minimum lattice mismatch strain between the In2O3 and the Si surface. This helps to circumvent potential interfacial weakening caused by volume contraction due to electrochemical reduction to lithium, or expansion during lithiation. Cycling under potentiodynamic conditions shows that the transparent anode of nanodots reversibly alloys lithium with good Coulombic efficiency, buffered by co-insertion into the silicon substrate. These properties could potentially lead to further development of similarly controlled dispersions of a range of other active materials to give transparent battery electrodes or materials capable of non-destructive in situ spectroscopic characterization during charging and discharging.

AuxAg1-x alloy seeds: A way to control growth, morphology and defect formation in Ge nanowires

Germanium (Ge) nanowires are of current research interest for high speed nanoelectronic devices due to the lower band gap and high carrier mobility compatible with high K-dielectrics and larger excitonic Bohr radius ensuing a more pronounced quantum confinement effect [1-6]. A general way for the growth of Ge nanowires is to use liquid or a solid growth promoters in a bottom-up approach which allow control of the aspect ratio, diameter, and structure of 1D crystals via external parameters, such as precursor feedstock, temperature, operating pressure, precursor flow rate etc [3, 7-11]. The Solid-phase seeding is preferred for more control processing of the nanomaterials and potential suppression of the unintentional incorporation of high dopant concentrations in semiconductor nanowires and unrequired compositional tailing of the seed-nanowire interface [2, 5, 9, 12]. There are therefore distinct features of the solid phase seeding mechanism that potentially offer opportunities for the controlled processing of nanomaterials with new physical properties. A superior control over the growth kinetics of nanowires could be achieved by controlling the inherent growth constraints instead of external parameters which always account for instrumental inaccuracy. The high dopant concentrations in semiconductor nanowires can result from unintentional incorporation of atoms from the metal seed material, as described for the Al catalyzed VLS growth of Si nanowires [13] which can in turn be depressed by solid-phase seeding. In addition, the creation of very sharp interfaces between group IV semiconductor segments has been achieved by solid seeds [14], whereas the traditionally used liquid Au particles often leads to compositional tailing of the interface [15] . Korgel et al. also described the superior size retention of metal seeds in a SFSS nanowire growth process, when compared to a SFLS process using Au colloids [12]. Here in this work we have used silver and alloy seed particle with different compositions to manipulate the growth of nanowires in sub-eutectic regime. The solid seeding approach also gives an opportunity to influence the crystallinity of the nanowires independent of the substrate. Taking advantage of the readily formation of stacking faults in metal nanoparticles, lamellar twins in nanowires could be formed.

Site controlled red-yellow-green light emitting InGaN quantum discs on nano-tipped GaN rods

We report a method of growing site controlled InGaN multiple quantum discs (QDs) at uniform wafer scale on coalescence free ultra-high density (>80%) nanorod templates by metal organic chemical vapour deposition (MOCVD). The dislocation and coalescence free nature of the GaN space filling nanorod arrays eliminates the well-known emission problems seen in InGaN based visible light sources that these types of crystallographic defects cause. Correlative scanning transmission electron microscopy (STEM), energy-dispersive X-ray (EDX) mapping and cathodoluminescence (CL) hyperspectral imaging illustrates the controlled site selection of the red, yellow and green (RYG) emission at these nano tips. This article reveals that the nanorod tips' broad emission in the RYG visible range is in fact achieved by manipulating the InGaN QD's confinement dimensions, rather than significantly increasing the In%. This article details the easily controlled method of manipulating the QDs dimensions producing high crystal quality InGaN without complicated growth conditions needed for strain relaxation and alloy compositional changes seen for bulk planar GaN templates.

Seawater carbonate chemistry, larval settlement and growth rate during experiments with coral Porites astreoides, 2008

In response to the increases in pCO2 projected in the 21st century, adult coral growth and calcification are expected to decrease significantly. However, no published studies have investigated the effect of elevated pCO2 on earlier life history stages of corals. Porites astreoides larvae were collected from reefs in Key Largo, Florida, USA, settled and reared in controlled saturation state seawater. Three saturation states were obtained, using 1 M HCl additions, corresponding to present (380 ppm) and projected pCO2 scenarios for the years 2065 (560 ppm) and 2100 (720 ppm). The effect of saturation state on settlement and post-settlement growth was evaluated. Saturation state had no significant effect on percent settlement; however, skeletal extension rate was positively correlated with saturation state, with ~50% and 78% reductions in growth at the mid and high pCO2 treatments compared to controls, respectively.

(Table S1) Stable isotope record and growth rates of cultured Mytilus edulis

To study the effects of temperature, salinity, and life processes (growth rates, size, metabolic effects, and physiological/genetic effects) on newly precipitated bivalve carbonate, we quantified shell isotopic chemistry of adult and juvenile animals of the intertidal bivalve Mytilus edulis (Blue mussel) collected alive from western Greenland and the central Gulf of Maine and cultured them under controlled conditions. Data for juvenile and adult M. edulis bivalves cultured in this study, and previously by Wanamaker et al. (2006, doi:10.1029/2005GC001189), yielded statistically identical paleotemperature relationships. On the basis of these experiments we have developed a species-specific paleotemperature equation for the bivalve M. edulis [T °C = 16.28 (±0.10) - 4.57 (±0.15) {d18Oc VPBD - d18Ow VSMOW} + 0.06 (±0.06) {d18Oc VPBD - d18Ow VSMOW}**2; r**2 = 0.99; N = 323; p < 0.0001]. Compared to the Kim and O'Neil (1997) inorganic calcite equation, M. edulis deposits its shell in isotope equilibrium (d18Ocalcite) with ambient water. Carbon isotopes (d13Ccalcite) from sampled shells were substantially more negative than predicted values, indicating an uptake of metabolic carbon into shell carbonate, and d13Ccalcite disequilibrium increased with increasing salinity. Sampled shells of M. edulis showed no significant trends in d18Ocalcite based on size, cultured growth rates, or geographic collection location, suggesting that vital effects do not affect d18Ocalcite in M. edulis. The broad modern and paleogeographic distribution of this bivalve, its abundance during the Holocene, and the lack of an intraspecies physiologic isotope effect demonstrated here make it an ideal nearshore paleoceanographic proxy throughout much of the North Atlantic Ocean.

Hormonal factors and insulin-like growth factor-1 in North American postmenopausal women

Background: Mechanisms underlying the effect of estrogen exposure on breast cancer risk remain unclear. Insulin-like growth factor-1 (IGF-1) levels have been positively associated with breast cancer and are a potential mechanism. Objectives: The objectives of this thesis are: 1) to explore whether the reproductive risk factors and the lifetime cumulative number of menstrual cycles (LCMC), as measures for long-term estrogen exposure, are associated with IGF-1 levels, and 2) to examine the effect of an aromatase inhibitor (AI) on IGF-1 levels, and the potential interaction with BMI. Methods: A cross sectional study and a randomized controlled trial nested with the MAP.3 chemoprevention trial were used to address objective 1 and 2, respectively. 567 postmenopausal women were selected. Anthropometric measurements, lifestyle factors, reproductive characteristics and serum IGF-1 concentrations were collected at baseline and one year. Objective 1. The LCMC was computed as a composite measure of the reproductive characteristics. Multivariable linear regression models were used to assess the association between IGF-1 levels and LCMC and the hormonal risk factors, while adjusting for potential covariates. Objective 2. Changes in IGF-1 were compared between the exemestane and placebo, and effect modification by BMI was tested with an interaction term. Results: Objective 1. Women aged 55 years or older at menopause had 16.26 ng/mL (95% CI: 1.76, 30.75) higher IGF-1 compared to women aged less than 50 years at menopause. Women in the highest category of menstrual cycles (≥500 cycles) had an average 19.00 ng/mL (95%CI: 5.86, 32.14) higher concentration of IGF-1 compared to women in the lowest category (<350). Exogenous hormones had no effect on postmenopausal IGF-1 levels. Objective 2. Exemestane significantly increased IGF-1 levels by 18% (95% CI: 14%-22%); while, placebo had no effect on IGF-1. The changes in IGF-1 were significantly different between the treatment arms (P<0.0001) and no significant interaction was observed between treatment and BMI on IGF-1 changes (P=0.1327). Conclusion: Objective 1. Larger number of menstrual cycles and a later age at menopause are positively associated with IGF-1. IGF-1 may be one mechanism by which prolonged estrogen exposure increases cancer risk. Objective 2. We conclude that the reduced cancer risk observed with AI therapy likely occurs in an IGF-1 independent mechanism. Further studies exploring the clinical consequences of increased IGF-1 on AI therapy are needed.

On the microstructure, growth pattern and original porosity of belemnite rostra: insights from calcitic Jurassic belemnites

Calcitic belemnite rostra are usually employed to perform paleoenvironmental studies based on geochemical data. However, several questions, such as their original porosity and microstructure, remain open, despite they are essential to make accurate interpretations based on geochemical analyses.This paper revisits and enlightens some of these questions. Petrographic data demonstrate that calcite crystals of the rostrum solidum of belemnites grow from spherulites that successively develop along the apical line, resulting in a “regular spherulithic prismatic” microstructure. Radially arranged calcite crystals emerge and diverge from the spherulites: towards the apex, crystals grow until a new spherulite is formed; towards the external walls of the rostrum, the crystals become progressively bigger and prismatic. Adjacent crystals slightly vary in their c-axis orientation, resulting in undulose extinction. Concentric growth layering develops at different scales and is superimposed and traversed by a radial pattern, which results in the micro-fibrous texture that is observed in the calcite crystals in the rostra.Petrographic data demonstrate that single calcite crystals in the rostra have a composite nature, which strongly suggests that the belemnite rostra were originally porous. Single crystals consistently comprise two distinct zones or sectors in optical continuity: 1) the inner zone is fluorescent, has relatively low optical relief under transmitted light (TL) microscopy, a dark-grey color under backscatter electron microscopy (BSEM), a commonly triangular shape, a “patchy” appearance and relatively high Mg and Na contents; 2) the outer sector is non-fluorescent, has relatively high optical relief under TL, a light-grey color under BSEM and low Mg and Na contents. The inner and fluorescent sectors are interpreted to have formed first as a product of biologically controlled mineralization during belemnite skeletal growth and the non-fluorescent outer sectors as overgrowths of the former, filling the intra- and inter-crystalline porosity. This question has important implications for making paleoenvironmental and/or paleoclimatic interpretations based on geochemical analyses of belemnite rostra.Finally, the petrographic features of composite calcite crystals in the rostra also suggest the non-classical crystallization of belemnite rostra, as previously suggested by other authors.

Size-selective mortality and environmental factors affecting early marine growth during early marine life stages of sub-yearling Chinook salmon in Puget Sound, Washington

Thesis (Master's)--University of Washington, 2016-08