Seasonal Patterns Of Nitrogen Mineralization And Nitrification Following Harvesting In The White Spruce Forests Of Interior Alaska

Thesis (Ph.D.) University of Alaska Fairbanks, 1986The effects of commercial timber harvesting upon nitrogen transformations were evaluated for the forest floor and mineral soil of mature white spruce (Picea glauca (Moench.) Voss) forest sites in interior Alaska. Analyses of forest floor and mineral soil incubated in situ in mature forest and two recently harvested areas of different ages indicated an ammonium-dominated soil system for the unharvested area. Statistically, logging had no effect upon mineralization, nitrification or on the average NH(,4)-N or NO(,3)-N produced on incubation in the forest floor. In the mineral soil the same patterns were apparent with the exception that the NO(,3)-N produced on incubation was significantly greater in the harvested areas. However, the lack of a large number of incubation periods (n = 8), over the entire course of study (22 months of continuous incubation) likely contributed to this result. While mineralization (ammonification) rates did not differ between areas, there were times in mid-summer when nitrification rates in the clearcut areas far exceeded those in the control area. Thus, although the net amount of NH(,4)-N produced was not different between areas, the amount of nitrogen moved from the organic pool into available pools (net nitrogen mineralization) was greater in the harvested areas, primarily because of mid-summer nitrification in the latter. Increased soil moisture and temperature regimes due to harvesting were thought to be the prime factors responsible. Nitrogen cycling in the mature white spruce forest was typical of a steady-state system; cycling was very tight. Field estimates of mineralization for the forest floor (2.48 g/m('2)/yr) and the mineral soil (0.48 g/m('2)/yr) fit well into a schematic cycle developed around other estimates of N-pools and fluxes derived from the literature. This was also true of nitrification rates which were very low in both horizons. In the cleared areas, mineralization rates in the forest floor varied from 0.11 to 3.59 g/m('2)/yr and in the mineral horizon from 0.42 to 0.54 g/m('2)/yr. Nitrification rates varied from 1.49 to 3.01 g/m('2)/yr in the forest floor and from 0.24 to 0.27 g/m('2)/yr in the mineral soil. The effects of changes in abiotic and biotic controls on nitrogen mineralization and nitrification due to harvesting, and the implications of whole-tree vs. conventional logging are also discussed

Neural Likelihood Approximation for Integer Valued Time Series Data

Stochastic processes defined on integer valued state spaces are popular within the physical and biological sciences. These models are necessary for capturing the dynamics of small systems where the individual nature of the populations cannot be ignored and stochastic effects are important. The inference of the parameters of such models, from time series data, is difficult due to intractability of the likelihood; current methods, based on simulations of the underlying model, can be so computationally expensive as to be prohibitive. In this paper we construct a neural likelihood approximation for integer valued time series data using causal convolutions, which allows us to evaluate the likelihood of the whole time series in parallel. We demonstrate our method by performing inference on a number of ecological and epidemiological models, showing that we can accurately approximate the true posterior while achieving significant computational speed ups in situations where current methods struggle

Scoping review of current challenges and circumstances impacting Indigenous applications to Canadian medical schools

Introduction: Considering the relevant 2015 Truth and Reconciliation Commission recommendations, this paper reviews the current state of Canadian medical schools’ Indigenous admissions processes and explores continued barriers faced by Indigenous applicants. Methods: A summary of literature illustrating disadvantages for Indigenous applicants of current admissions tools is presented. A grey literature search of current admissions requirements, interview processes, and other relevant data from each medical school was performed. Tables comparing differences in their approaches are included. A calculation of Indigenous access to medical school seats compared to the broader Canadian population was conducted. Gaps in execution are explored, culminating in a table of recommendations. Results: Despite formal commitments to reduce barriers, Indigenous applicants to medical school in Canada still face barriers that non-Indigenous applicants do not. Most programs use tools for admission known to disadvantage Indigenous applicants. Indigenous applicants do not have equitable access to medical school seats. Facilitated Indigenous stream processes first ensure Indigenous applicants meet all minimum requirements of Canadian students, and then require further work. Discussion: Seven years after the Truth and Reconciliation Commission called on Canadian universities and governments to train more Indigenous health care providers, there has been limited progress to reduce the structural disadvantages Indigenous students face when applying to medical school. Based on best practices observed in Canada and coupled with relevant Indigenous-focused literature, recommendations are made for multiple stakeholders.  Conclusions: The study was limited by the data available on numbers of Indigenous applicants and matriculants. Where available, data are not encouraging as to equitable access to medical school for Indigenous populations in Canada. These findings were presented at the International Congress of Academic Medicine 2023 Conference, April 2023, Quebec City, Canada

Transient but not genetic loss of miR-451 attenuates the development of pulmonary arterial hypertension

<b>Rationale:</b> MicroRNAs are small non-coding RNAs involved in the regulation of gene expression and have recently been implicated in the development of pulmonary arterial hypertension (PAH). Previous work established that miR-451 is up-regulated in rodent models of PAH.<p></p> <b>Objectives:</b> The role of miR-451 in the pulmonary circulation is unknown. We therefore sought to assess the involvement of miR-451 in the development of pulmonary arterial hypertension.<p></p> <b>Methods:</b> Silencing of miR-451 was performed in vivo using miR-451 knockout mice and an antimiR targeting mature miR-451 in rats. Coupled with exposure to hypoxia, indices of pulmonary arterial hypertension were assessed. The effect of modulating miR-451 on human pulmonary artery smooth muscle cell proliferation and migration was analysed.<p></p> <b>Measurements and Main Results:</b> We observed a reduction in systolic right ventricular pressure in hypoxic rats pre-treated with antimiR-451 compared to hypoxia alone (47.7 ± 1.36mmHg and 56.0 ± 2.03mmHg respectively, p<0.01). In miR-451 knockout mice following exposure to chronic hypoxia, no significant differences were observed compared to wild type hypoxic mice. In vitro analysis demonstrated that over-expression of miR-451 in human pulmonary artery smooth muscle cells promoted migration under serum-free conditions. No effect on cellular proliferation was observed.<p></p> <b>Conclusions:</b> Transient inhibition of miR-451 attenuated the development of pulmonary arterial hypertension in hypoxia exposed rats. Genetic deletion of miR-451 had no beneficial effect on indices of pulmonary arterial hypertension, potentially due to pathway redundancy compensating for the loss of miR-451.<p></p&gt

The function of respiratory complex I in plants and in human disease

Complex I is the largest complex in the mitochondrial respiratory chain. Defects in complex I are a major cause of mitochondrial disease in humans. Mutations in the assembly factor NUBPL have been implicated in causing complex I deficiency. To assign pathogenicity to patient NUBPL variants, I used a yeast model, Yarrowia lipolytica, and recreated the corresponding amino acid changes in the Ind1 homolog. Using a combination of BN-PAGE, Western blotting and enzymatic analysis I was able to assign pathogenicity to four of the six variants as well as furthering our understanding of the role of Ind1 in complex I assembly. Complex I has been lost in the course of evolution in several unicellular eukaryotes, but never in multicellular eukaryotes. Recently, two studies found that the mitochondrial genes encoding complex I subunits were lacking in the genus Viscum. To investigate if complex I has been lost, I isolated mitochondria from European Mistletoe, Viscum album. My results from BN-PAGE and proteomic analysis indicate that complex I has been lost. Complex I requires FeS clusters, which are delivered by the mitochondrial ISC pathway. To better understand this process in plants, I characterised the role of FeS carrier proteins NFU4, NFU5 and GRXS15 in Arabidopsis thaliana. NFU4 and NFU5 were found to be genetically redundant but when combined as a double mutant were embryo lethal. This suggest that NFU4 and NFU5 play an important role in FeS assembly. Mutants in GRXS15 had a severe growth phenotype, but normal levels of respiratory complexes, suggesting GRXS15 plays a secondary role in FeS cluster assembly. Understanding complex I will be important in the future for helping to treat human mitochondrial disorders. In addition, studying complex I in plants, including in non-model organisms, helps further our understanding of its function and evolution

Welcome to the Front Page: An Ethnographic Exploration of Free Speech within Reddit

Reddit, the self-described Font Page of the Internet, presents a front row seat to the commodification of the internet’s earliest aspiration into a marketable good. Yet unlike other platforms in the web 2.0 era, Reddit’s users resist, finding means to counter the prevailing trend. The platform with its long, and often tortured relationship to free speech suggests the means towards locating the root of such resistance. Expressing a desire for autonomy, free speech within Reddit highlights the clash between competing directions for Reddit. Like much of the internet, Reddit’s future can be distilled to a single question, does it exist as a private property, or a public good? Welcome to the front page is an ethnographic exploration of the role that free speech plays within Reddit. Addressing how free speech is understood and deployed by users, moderators, and administrators, the following thesis contends that to understand Reddit’s successes and failures, one must first begin by understanding the importance of free speech, and the direction such an attachment portends

Connexin 43 plays a role in pulmonary vascular reactivity in mice

Pulmonary arterial hypertension (PAH) is a chronic condition characterized by vascular remodeling and increased vaso-reactivity. PAH is more common in females than in males (~3:1). Connexin (Cx)43 has been shown to be involved in cellular communication within the pulmonary vasculature. Therefore, we investigated the role of Cx43 in pulmonary vascular reactivity using Cx43 heterozygous (Cx43+/−) mice and 37,43Gap27, which is a pharmacological inhibitor of Cx37 and Cx43. Contraction and relaxation responses were studied in intra-lobar pulmonary arteries (IPAs) derived from normoxic mice and hypoxic mice using wire myography. IPAs from male Cx43+/− mice displayed a small but significant increase in the contractile response to endothelin-1 (but not 5-hydroxytryptamine) under both normoxic and hypoxic conditions. There was no difference in the contractile response to endothelin-1 (ET-1) or 5-hydroxytryptamine (5-HT) in IPAs derived from female Cx43+/−mice compared to wildtype mice. Relaxation responses to methacholine (MCh) were attenuated in IPAs from male and female Cx43+/− mice or by pre-incubation of IPAs with 37,43Gap27. Nω-Nitro-L-arginine methyl ester (l-NAME) fully inhibited MCh-induced relaxation. In conclusion, Cx43 is involved in nitric oxide (NO)-induced pulmonary vascular relaxation and plays a gender-specific and agonist-specific role in pulmonary vascular contractility. Therefore, reduced Cx43 signaling may contribute to pulmonary vascular dysfunction

Lattice Boltzmann Magnetohydrodynamics

Understanding the dynamics of plasmas presents a formidable challenge in theoretical physics. Being governed by a complicated set of non-linear equations, analytic descriptions of their behaviour are only possible in the simplest of cases and therefore numerical methods are essential to understand any realistic situation. This thesis presents an application of the lattice Boltzmann (LB) method to the solution of the magnetohydrodynamic (MHD) equations, which model the low frequency motions of plasmas. The lattice Boltzmann method, which has been developed over the past decade or so, is a kinetic model of fluid like systems, derived from the statistical mechanics of lattice gas cellular automata. In chapter 1, after a brief derivation of the equations to be modelled and discussion of standard numerical methods, the basic ideas of cellular automata (CA) are reviewed along with some examples. Special attention is given to lattice gas models of hydrodynamics and magnetohy- drodynamics (MHD), with a discussion of the particular problem that an MHD model faces, namely the representation of the essentially non-local Lorentz force, and how this was overcome. In chapter 2 the lattice Boltzmann method is discussed in some detail. The LB models of two dimensional hydrodynamics and magnetohydrodynamics are explained and the Navier-Stokes and MHD equations are derived from these models. The derivation is standard in the literature and bears important similarities to the theory discussed in chapter 1 despite, in the case of the MHD model, the fundamentally different means by which the interactions between the particles and magnetic field are represented. An improvement of the Mill) model is proposed and a linear stability analysis is carried out. Alternative methods of discretising the lattice Boltzmann equation are also discussed. Various tests are presented in chapter 3. The simulations of Hartmann flow confirm previously published results, although we also model the evolution of the flow towards a steady state in the case of an unmagnetised fluid. Damped Alfven waves are also modelled. Both of these linear problems show good agreement between the numerical lattice Boltzmann solutions and the analytic solutions. Simulations of a non-linear reconnection problem are also presented, namely the coalescence of magnetic islands. The simulations reproduce correctly the qualitative features of island coalescence found in the literature. The lattice Boltzmann method is applied to a practical problem in chapter 4, namely the shedding of vortices in the wake of an obstacle. This problem is relevant to the dynamics of solar active regions, in which the photosphere is either stirred by or drags along an erupting magnetic flux tube. The observed vorticity in such regions is greater than can be accounted for by the action of the Coriolis force on the upwelling or downwelling fluid. The effect of a magnetic field on the vortex shedding process is investigated, and it is found that if the magnetic field is strong enough, then Alfven waves transport vorticity sufficiently fast to supress the vortex shedding process. In the case of a perpendicular magnetic field, reconnection is also observed in the wake. Generalisations of the lattice Boltzmann MHD model are proposed in chapter T). A thermal MHD model and a three dimensional model are presented, and the thermal model is tested by simulating magnetosonic waves, which show good agreement with the analytic solutions. Conclusions and suggestions for future work are discussed in chapter 6. The computer code for the numerical simulations is contained in the appendix. The original work for this thesis is the modification of the lattice Boltzmann MHD model in section 2.4.4, the stability analysis of section 2.4.5 and the work which appears in chapters 3, 4 and 5

Steroid modulation of neutrophil function

Dexamethasone, a glucocorticoid, is used extensively in clinical medicine in the treatment of respiratory diseases, notably asthma. This medical effect is probably due in part to a down-regulation of many cytokines e.g.. IL-8. However, the side effects of steroids often may outweigh the beneficial effects, especially if the disease in question is of a chronic nature. This combined with steroid resistance has led to an increase in the use of non-steroidal anti-inflammatory drugs. These tend to be aspirin derivatives, and many have side-effects. I have investigated a factor that is naturally produced by the body which may alleviate the symptoms of inflammation without many of the side- effects, with an aim to providing a viable alternative. A novel steroid induced monocyte derived factor was described twenty years ago by Stevenson as part of an MD thesis submitted to this university. This remains an unusual phenomenon, as most of the effects of steroids are due to a down-regulation of release; here is one of the few examples of the reverse. Although it raised many interesting points about dispersive motility of populations of polymorphonuclear leukocytes (PMN) it did not look at individual cells, nor at many of the interesting properties of neutrophils. One of the known effects of some steroids (though not Dexamethasone), and many NSAIDs, is a reduction of adhesion of PMN to venous endothelium. Human umbilical vein endothelial cells (and bovine aorta endothelium) were used as an ex vivo model for this, and my results show there is a marked decrease in this adhesion. This effect was observed not only on resting endothelium, but also when the endothelial cells had been pre-treated with ILip or thrombin. This decreased adhesion was due to an interaction with the PMN and the factor, as shown by adhesion being reduced when protein coated coverslips were used as the substrate for adhesion. It is suspected that the reasons for this may be due to an inactivation of integrins such as Mac-1, although a role for selectins cannot be ruled out. Recent work by Diaz-Gonzalez suggests that some NSAIDs act by inducing PMN to shed L-selectin. Other effects of this steroid induced monocyte derived factor on human PMN were determined using biological and biochemical techniques. Previous work has shown a novel dispersive effect of this factor on PMN when used in a uniform concentration, and so I decided to look at the moiphology of treated PMN. Using scanning electron microscopy I observed a polarisation of the PMN, but without any raffling of the membrane, a feature that is normally observed with polarisation. This morphology was not observed with control supernatants taken from monocytes cultured in the absence of Dexamethasone. This moiphology was conserved using cells in suspension and adhered to bovine aorta endothelium. The underlying actin cytoskeleton was examined using confocal microscopy, and the microfilamentous airay was noted as being devoid of spikes, observed with activation, for example with fMLP. Late cytoskeletal controlled effects, the release of granule contents, were also investigated, and it was noted that the release of primary granule contents could be inhibited by this factor in a dose dependent manner. This fusion of granules with the plasma membrane is controlled by the activation of numerous tyrosine kinases, and follows a strict order. Secondary granule release was shown to be inhibited also, as assayed by the cleavage of type I collagen, and analysis of SDS gels. The effects on the metabolic burst showed conflicting results with inhibition being present, again in a dose dependent manner, but much of this activity was removed with increasing purification, leaving only very slight inhibition