Spatiotemporal Variations in the Fire Regimes of Whitebark Pine (\u3cem\u3ePinus albicaulis\u3c/em\u3e Engelm.) Forests, Western Montana, USA, and Their Management Implications

Whitebark pine (Pinus albicaulis) is a long-lived tree species that exists throughout high elevation forest communities of western North America. It is the foundation of a diminishing ecosystem that supports Clark’s nutcrackers, red squirrels, grizzly bears, and black bears. The decline of this species is directly related to mortality from widespread mountain pine beetle outbreaks and infestation by the invasive white pine blister rust, and may be exacerbated by fire suppression. Prescribed fire will be a primary management tool in efforts to preserve whitebark pine on the landscape. My research used dendrochronology to investigate the fire history of whitebark pine stands on three mountains in the Lolo National Forest, Montana, via fire-scar and age structure analyses. I then used these data to assess the USDA Fire Regime Condition Classification (FRCC) fire regime types for my sites. Additionally, I utilized traditional superposed epoch analysis techniques in a novel manner to develop a multi-decadal superposed epoch analysis for fire-climate and fire-tree establishment analyses. I sampled between 40 and 50 fire-scarred trees, snags, and remnants, and collected age structure data in two 0.5 ha plots at each site. Samples at all sites recorded a frost event in AD 1601 related to southern hemisphere volcanic activity. The fire-history and stand-structure data indicate all three sites were characterized by mixed-severity fire regimes and generally agreed with the FRCC classifications. However, fires occurred with greater frequency than previously found in whitebark pine forests and distinct differences existed between the fire regimes of each of the three sites that are likely related to topography, forest cover, and climate conditions. A period of widespread fire activity at all three sites occurred from the mid-1700s to the early 1800s and may be the expression of interactions between several climate variables. Fire suppression led to a decline in fire activity in the 1900s, but subalpine fir trees began establishing between 300 and 140 years ago at all three sites. This suggests fire suppression may not be responsible for the advanced succession found in these whitebark pine forests and management decisions based on that assumption are inappropriate for these sites. In addition, the spatial and temporal variability in fire activity between these sites requires a refinement in the Fire Regime Condition Classification methods if they are to be used for managing whitebark pine forests

Uncovering the effects of interface-induced ordering of liquid on crystal growth using machine learning

The process of crystallization is often understood in terms of the fundamental microstructural elements of the crystallite being formed, such as surface orientation or the presence of defects. Considerably less is known about the role of the liquid structure on the kinetics of crystal growth. Here atomistic simulations and machine learning methods are employed together to demonstrate that the liquid adjacent to solid-liquid interfaces presents significant structural ordering, which effectively reduces the mobility of atoms and slows down the crystallization kinetics. Through detailed studies of silicon and copper we discover that the extent to which liquid mobility is affected by interface-induced ordering (IIO) varies greatly with the degree of ordering and nature of the adjacent interface. Physical mechanisms behind the IIO anisotropy are explained and it is demonstrated that incorporation of this effect on a physically-motivated crystal growth model enables the quantitative prediction of the growth rate temperature dependence

Study of autoimmune reactions in rheumatoid arthritis

Rheumatoid arthritis (RA) is a systemic autoimmune disease that affects approximately 1% of the population worldwide. Despite being rather common, the etiopathology of RA remains unclear. Approximately two-thirds of patients have antibodies to citrullinated proteins (ACPAs), generally detected using the 2nd generation cyclic citrullinated peptide (CCP2) ELISA. A wealth of evidence implicates ACPA in the etiology of RA: the major risk factors - a group of HLA-DRB1 alleles referred to as the shared epitope (SE), and smoking - have been described to associate primarily with the ACPA-positive subset of RA. Moreover, ACPAs can be detected years before clinical onset, and their presence are highly predictive of progression to RA. However, the mechanism by which ACPAs might contribute to disease, as well as the definitive in vivo target, is not understood. The aim of this thesis was therefore to better characterize the ACPA response in RA, in terms of antigen specificity, association with genetic and environmental risk factors, cross-reactivity with carbamylated antigens, presence in CCP2-negative RA, and finally the antigen specificity and functional characteristics of ACPA-positive B cells. Through studies using affinity purified anti-CCP2 IgG, we could demonstrate that the CCP2 ELISA directly captures the ACPA response, and that ACPA purified in this manner bound a variety of citrullinated peptide epitopes and exhibited binding to RA synovial tissue and immune cells (Study I). We also discovered that purified ACPA could bind both carbamylated and citrullinated proteins, and peptide absorption experiments confirmed extensive cross-reactivity between ACPA and anti-carbamylated protein (CarP) antibodies in the context of the candidate autoantigen α-enolase, casting doubt on the specificity of the anti-CarP response, which we posit may be cross-reactive ACPA (Study II). By screening 2,836 serum samples from the population-based case-control cohort EIRA on an autoantigen multiplex array, we then showed that “seronegative” RA is not truly a seronegative disease subset. Autoantibodies - including ACPA and rheumatoid factor (RF) - were present in a substantial proportion, and this subset resembled seropositive RA in terms of associations with risk factors (Study III). This study highlights the need for new biomarkers, better classification of seronegative RA, and more sensitive clinical tests for seropositive RA. Finally, we utilized a method of B cell immortalization to derive ACPA-producing B cell clones from RA synovial fluid that retained surface immunoglobulin expression. We successfully generated a CEP-1-positive B cell clone from a SE-positive RA patient, and visualized surface binding to citrullinated (but not native) protein (Study IV). This pilot study lays the ground for in-depth investigation of the characteristics of the ACPA lymphocyte population, specifically in regards to HLA-DRB1 SE-mediated antigen presentation. It is my hope that the data presented in this thesis can provide a basis for future studies into the putative specificity and mechanism of the ACPA response, in order to elucidate disease processes in RA and ultimately improve the diagnosis and treatment of the diseas

Supply Shock Versus Demand Shock: The Local Effects of New Housing in Low-Income Areas

We study the local effects of new market-rate housing in low-income areas using microdata on large apartment buildings, rents, and migration. New buildings decrease nearby rents by 5 to 7 percent relative to locations slightly farther away or developed later, and they increase in-migration from low-income areas. Results are driven by a large supply effect—we show that new buildings absorb many high-income households—that overwhelms any offsetting endogenous amenity effect. The latter may be small because most new buildings go into already-changing areas. Contrary to common concerns, new buildings slow local rent increases rather than initiate or accelerate them

Adiabatically controlled motional states of a ground-state cooled CaO+^{+} and Ca+^{+} trapped ion chain

Control of the external degree of freedom of trapped molecular ions is a prerequisite for their promising applications to spectroscopy, precision measurements of fundamental constants, and quantum information technology. Here, we demonstrate near ground-state cooling of the axial motional modes of a calcium mono-oxide ion via sympathetic sideband cooling with a co-trapped calcium ion. We also show that the phonon state of the axial out-of-phase mode of the ion chain is maintained while the mode frequency is adiabatically ramped up and down. The adiabatic ramping of the motional mode frequency is a prerequisite for searching for the proposed molecular dipole-phonon interaction