Non-Gaussianity and Excursion Set Theory: Halo Bias

We study the impact of primordial non-Gaussianity generated during inflation on the bias of halos using excursion set theory. We recapture the familiar result that the bias scales as $k^{-2}$ on large scales for local type non-Gaussianity but explicitly identify the approximations that go into this conclusion and the corrections to it. We solve the more complicated problem of non-spherical halos, for which the collapse threshold is scale dependent.Comment: 13 pages, 3 figures. v2 references added. Matches published versio

Modelling environmental factors correlated with podoconiosis: a geospatial study of non-filarial elephantiasis

Introduction The precise trigger of podoconiosis — endemic non-filarial elephantiasis of the lower legs — is unknown. Epidemiological and ecological studies have linked the disease with barefoot exposure to red clay soils of volcanic origin. Histopathology investigations have demonstrated that silicon, aluminium, magnesium and iron are present in the lower limb lymph node macrophages of both patients and non-patients living barefoot on these clays. We studied the spatial variation (variations across an area) in podoconiosis prevalence and the associated environmental factors with a goal to better understanding the pathogenesis of podoconiosis. Methods Fieldwork was conducted from June 2011 to February 2013 in 12 kebeles (administrative units) in northern Ethiopia. Geo-located prevalence data and soil samples were collected and analysed along with secondary geological, topographic, meteorological and elevation data. Soil data were analysed for chemical composition, mineralogy and particle size, and were interpolated to provide spatially continuous information. Exploratory, spatial, univariate and multivariate regression analyses of podoconiosis prevalence were conducted in relation to primary (soil) and secondary (elevation, precipitation, and geology) covariates. Results Podoconiosis distribution showed spatial correlation with variation in elevation and precipitation. Exploratory analysis identified that phyllosilicate minerals, particularly clay (smectite and kaolinite) and mica groups, quartz (crystalline silica), iron oxide, and zirconium were associated with podoconiosis prevalence. The final multivariate model showed that the quantities of smectite (RR = 2.76, 95% CI: 1.35, 5.73; p = 0.007), quartz (RR = 1.16, 95% CI: 1.06, 1.26; p = 0.001) and mica (RR = 1.09, 95% CI: 1.05, 1.13; p < 0.001) in the soil had positive associations with podoconiosis prevalence. Conclusions More quantities of smectite, mica and quartz within the soil were associated with podoconiosis prevalence. Together with previous work indicating that these minerals may influence water absorption, potentiate infection and be toxic to human cells, the present findings suggest that these particles may play a role in the pathogenesis of podoconiosis and acute adenolymphangitis, a common cause of morbidity in podoconiosis patients

Phase behavior of weakly polydisperse sticky hard spheres: Perturbation theory for the Percus-Yevick solution

We study the effects of size polydispersity on the gas-liquid phase behaviour of mixtures of sticky hard spheres. To achieve this, the system of coupled quadratic equations for the contact values of the partial cavity functions of the Percus-Yevick solution is solved within a perturbation expansion in the polydispersity, i.e. the normalized width of the size distribution. This allows us to make predictions for various thermodynamic quantities which can be tested against numerical simulations and experiments. In particular, we determine the leading-order effects of size polydispersity on the cloud curve delimiting the region of two-phase coexistence and on the associated shadow curve; we also study the extent of size fractionation between the coexisting phases. Different choices for the size-dependence of the adhesion strengths are examined carefully; the Asakura-Oosawa model of a mixture of polydisperse colloids and small polymers is studied as a specific example.Comment: 43 pages, 12 figures, and 1 tabl

The Quantum Transverse Field Ising Model on an Infinite Tree from Matrix Product States

We give a generalization to an infinite tree geometry of Vidal's infinite time-evolving block decimation (iTEBD) algorithm for simulating an infinite line of quantum spins. We numerically investigate the quantum Ising model in a transverse field on the Bethe lattice using the Matrix Product State ansatz. We observe a second order phase transition, with certain key differences from the transverse field Ising model on an infinite spin chain. We also investigate a transverse field Ising model with a specific longitudinal field. When the transverse field is turned off, this model has a highly degenerate ground state as opposed to the pure Ising model whose ground state is only doubly degenerate.Comment: 28 pages, 23 figures, PDFlate

Regional avian species declines estimated from volunteer-collected long-term data using List Length Analysis

Long-term systematic population monitoring data sets are rare but are essential in identifying changes in species abundance. In contrast, community groups and natural history organizations have collected many species lists. These represent a large, untapped source of information on changes in abundance but are generally considered of little value. The major problem with using species lists to detect population changes is that the amount of effort used to obtain the list is often uncontrolled and usually unknown. It has been suggested that using the number of species on the list, the "list length,'' can be a measure of effort. This paper significantly extends the utility of Franklin's approach using Bayesian logistic regression. We demonstrate the value of List Length Analysis to model changes in species prevalence (i.e., the proportion of lists on which the species occurs) using bird lists collected by a local bird club over 40 years around Brisbane, southeast Queensland, Australia. We estimate the magnitude and certainty of change for 269 bird species and calculate the probabilities that there have been declines and increases of given magnitudes

Impact of pharmacologic inhibition of tooth movement on periodontal and tooth root tissues during orthodontic force application

ObjectiveThe goal of this study was to investigate potential negative sequelae of orthodontic force application ±delivery of an osteoclast inhibitor, recombinant osteoprotegerin protein (OPG‐Fc), on periodontal tissues.Setting and Sample PopulationSprague Dawley rats from a commercial supplier were investigated in a laboratory setting.Materials and MethodsRats were randomly divided into four groups (n = 7 each): one group with no orthodontic appliances and injected once prior to the experimental period with empty polymer microspheres, one group with orthodontic appliances and injected once with empty microspheres, one group with orthodontic appliances and injected once with polymer microspheres containing 1 mg/kg of OPG‐Fc, and one group with orthodontic appliances and injected with non‐encapsulated 5 mg/kg of OPG‐Fc every 3 days during the experimental period. The animals were euthanized after 28 days of tooth movement for histomorphometric analyses.ResultsRoot resorption, PDL area and widths were similar in animals without appliances and animals with appliances plus high‐dose OPG‐Fc. PDL blood vessels were compressed and decreased in number in all animals that received orthodontic appliances, regardless of OPG‐Fc. Hyalinization was significantly increased only in animals with orthodontic appliances plus multiple injections of 5 mg/kg non‐encapsulated OPG‐Fc when compared to animals without appliances.ConclusionsResults of this study indicate that while pharmacological modulation of tooth movement through osteoclast inhibition is feasible when delivered in a locally controlled low‐dose manner, high‐dose levels that completely prevent tooth movement through bone may decrease local blood flow and increase the incidence of hyalinization.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153668/1/ocr12350_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153668/2/ocr12350-sup-0001-FigS1-S2.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/153668/3/ocr12350.pd

Optimal allocation of conservation effort among subpopulations of a threatened species: How important is patch quality?

Money is often a limiting factor in conservation, and attempting to conserve endangered species can be costly. Consequently, a framework for optimizing fiscally constrained conservation decisions for a single species is needed. In this paper we find the optimal budget allocation among isolated subpopulations of a threatened species to minimize local extinction probability. We solve the problem using stochastic dynamic programming, derive a useful and simple alternative guideline for allocating funds, and test its performance using forward simulation. The model considers subpopulations that persist in habitat patches of differing quality, which in our model is reflected in different relationships between money invested and extinction risk. We discover that, in most eases, subpopulations that are less efficient to manage should receive more money than those that are more efficient to manage, due to higher investment needed to reduce extinction risk. Our simple investment guideline performs almost as well as the exact optimal strategy. We illustrate our approach with a case study of the management of the Sumatran tiger, Panthera tigris sumatrae, in Kerinei Seblat National Park (KSNP), Indonesia. We find that different budgets should be allocated to the separate tiger subpopulations in KSNP. The subpopulation that is not at risk of extinction does not require any management investment. Based on the combination of risks of extinction and habitat quality, the optimal allocation for these particular tiger subpopulations is an unusual case: subpopulations that occur in higher-quality habitat (more efficient to manage) should receive more funds than the remaining subpopulation that is in lower-quality habitat. Because the yearly budget allocated to the KSNP for tiger conservation is small, to guarantee the persistence of all the subpopulations that are currently under threat we need to prioritize those that are easier to save. When allocating resources among subpopulations of a threatened species, the combined effects of differences in habitat quality, cost of action, and current subpopulation probability of extinction need to be integrated. We provide a useful guideline for allocating resources among isolated subpopulations of any threatened species

Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research