Soil characterization via methods of functional data analysis

Soil is a fundamental natural resource which is relied upon globally for its vital ecological and economic functions. It is important for many reasons including the production of food, support of wildlife and in supporting the mitigation of global warming. With an increasing world population, tremendous pressure is placed on the world’s natural resources. In order to keep up with the agricultural needs of a growing global population, soil management and monitoring practices need to be put in place. However, the standard procedures for monitoring soil quality are prohibitively expensive and slow, with an additional hazard to the environment through use of harmful chemicals. Thus, there has been a widespread interest into the use of diffuse reflectance spectroscopy for the prediction of physical and chemical properties in the soil. This method of recording soil data is cost-effective, rapid, requires minimal sample preparation and does not involve the use of hazardous chemicals. Currently, multivariate analyses such as partial least squares regression are routinely used to predict a wide range of soil properties from spectral data obtained from a mid- and near-infrared diffuse reflectance spectroscopy of soil samples. Whilst this method has been shown to successfully predict a multitude of soil quantities, methods of functional data analysis provide an alternate way of studying continuous data, recognising that it is sometimes more natural, and often fruitful, to view a collection of data points as observed realisations of random functions. In this thesis, the main focus is to compare standard multivariate techniques of analysing soil spectra to methods of functional data analysis. Chapter 1 provides an introduction to the importance of soil monitoring, mid-infrared spectroscopy, a description of the data and the objectives of the thesis. Following this, Chapter 2 demonstrates the performances of principal component analysis, linear discriminant analysis and support vector machines in investigating the variability of the soil spectra across the mid-infrared range. These multivariate methods are assessed on their ability to distinguish differences between groups of spectra based on various grouping variables. In Chapter 3, functional data analysis is introduced and methods of functional principal component analysis and functional hypothesis testing are implemented. Functional principal component analysis is applied to identify regions of the spectra which contain the principal modes of variation which could be pertinent to explaining differences between samples of different land-uses or sampling sites. Functional hypothesis tests are used to directly test for differences between groups of spectra and pointwise permutation F-tests are used to locate regions of the spectra where these group differences are prominent. Chapter 4 introduces functional linear regression as an alternative to the industry standard of partial least squares regression for relating the spectra to the physical wet chemistry properties of the soil. In this chapter, it is of interest to identify physical soil properties which can be successfully predicted by functional and partial least squares regression; and what the achievable performances of these predictions are. Comparisons between the two approaches are made and the advantages of each approach are considered. Finally, Chapter 5 provides a summary of the work presented and discusses the limitations and remaining challenges for the use of functional data analysis for the characterization of soil

Assessment of commercially available computerized neurocognitive testing in the adolescent concussed athlete: A retrospective analysis.

Background: Clinicians frequently use computer-based neurocognitive assessments to aid in the diagnosis and management of Sport Related Concussion (SRC). With practitioners using varied Neuro-Cognitive Assessment Tools (NCAT), questions arise concerning among NCAT and how these differences may affect patient care. The purpose of the current study is to offer a comparative analysis of two widely accepted, commercially available computer-based neurocognitive testing modalities in the adolescent concussed athlete. Hypothesis: There will be a difference between the C3 Logix® vs ImPACT® scoring in the IRPT and RTP Study Design: Retrospective chart review. Methods: In order to identify patients that were diagnosed with SRC, the records of patients reporting to a Sports Medicine practice were reviewed from a period of 18 months. All patients were assessed with either the ImPACT® or C3 Logix NCAT®. The date of the injury (DOI) as well as the patient’s symptom level (IVAL), time to initiation of the return to play protocol (IRTP), and time to the return to play (RTP) were recorded. Results: Two hundred and twenty-two records (222) were identified. There was no difference in the symptom score (P = 0.22) at the IEVAL between C3 Logix® (31.5±27.0) and ImPACT® (23.2±21.9), in the IRTP (P = 0.22) between the C3 Logix® (6.2±4.3 days) and ImPACT® (5.1±4.3 days) or RTP (P = 0.46) between C3 Logix (12.1±4.9 days) and ImPACT (15.6±19.8 days). Weak to moderate correlations were found between symptom scores, IRTP, and RTP. Conclusions: Clinicians made similar recommendations, independent of the NCAT used, as when to initiate the return to play protocol and when the patient could ultimately return to play. Clinical Relevance: The particular NCAT utilized by clinician was not a primary factor in the clinical judgement towards the management of the patient with SRC

Stellar Spin-Orbit Misalignment in a Multiplanet System

Stars hosting hot Jupiters are often observed to have high obliquities, whereas stars with multiple co-planar planets have been seen to have low obliquities. This has been interpreted as evidence that hot-Jupiter formation is linked to dynamical disruption, as opposed to planet migration through a protoplanetary disk. We used asteroseismology to measure a large obliquity for Kepler-56, a red giant star hosting two transiting co-planar planets. These observations show that spin-orbit misalignments are not confined to hot-Jupiter systems. Misalignments in a broader class of systems had been predicted as a consequence of torques from wide-orbiting companions, and indeed radial-velocity measurements revealed a third companion in a wide orbit in the Kepler-56 system.Comment: Accepted for publication in Science, published online on October 17 2013; PDF includes main article and supplementary materials (65 pages, 27 figures, 7 tables); v2: small correction to author lis

Characteristics of Kepler Planetary Candidates Based on the First Data Set: The Majority are Found to be Neptune-Size and Smaller

In the spring of 2009, the Kepler Mission commenced high-precision photometry on nearly 156,000 stars to determine the frequency and characteristics of small exoplanets, conduct a guest observer program, and obtain asteroseismic data on a wide variety of stars. On 15 June 2010 the Kepler Mission released data from the first quarter of observations. At the time of this publication, 706 stars from this first data set have exoplanet candidates with sizes from as small as that of the Earth to larger than that of Jupiter. Here we give the identity and characteristics of 306 released stars with planetary candidates. Data for the remaining 400 stars with planetary candidates will be released in February 2011. Over half the candidates on the released list have radii less than half that of Jupiter. The released stars include five possible multi-planet systems. One of these has two Neptune-size (2.3 and 2.5 Earth-radius) candidates with near-resonant periods.Comment: Paper to accompany Kepler's June 15, 2010 data release; submitted to Astrophysical Journal Figures 1,2,& 3 revised. Improved labeling on all figures. Slight changes to planet frequencies in result

Discovery and Rossiter-McLaughlin Effect of Exoplanet Kepler-8b

We report the discovery and the Rossiter-McLaughlin effect of Kepler-8b, a transiting planet identified by the NASA Kepler Mission. Kepler photometry and Keck-HIRES radial velocities yield the radius and mass of the planet around this F8IV subgiant host star. The planet has a radius RP = 1.419 RJ and a mass, MP = 0.60 MJ, yielding a density of 0.26 g cm^-3, among the lowest density planets known. The orbital period is P = 3.523 days and orbital semima jor axis is 0.0483+0.0006/-0.0012 AU. The star has a large rotational v sin i of 10.5 +/- 0.7 km s^-1 and is relatively faint (V = 13.89 mag), both properties deleterious to precise Doppler measurements. The velocities are indeed noisy, with scatter of 30 m s^-1, but exhibit a period and phase consistent with the planet implied by the photometry. We securely detect the Rossiter-McLaughlin effect, confirming the planet's existence and establishing its orbit as prograde. We measure an inclination between the projected planetary orbital axis and the projected stellar rotation axis of lambda = -26.9 +/- 4.6 deg, indicating a moderate inclination of the planetary orbit. Rossiter-McLaughlin measurements of a large sample of transiting planets from Kepler will provide a statistically robust measure of the true distribution of spin-orbit orientations for hot jupiters in general.Comment: 26 pages, 8 figures, 2 tables; In preparation for submission to the Astrophysical Journa

Planet Occurrence within 0.25 AU of Solar-type Stars from Kepler

We report the distribution of planets as a function of planet radius (R_p), orbital period (P), and stellar effective temperature (Teff) for P < 50 day orbits around GK stars. These results are based on the 1,235 planets (formally "planet candidates") from the Kepler mission that include a nearly complete set of detected planets as small as 2 Earth radii (Re). For each of the 156,000 target stars we assess the detectability of planets as a function of R_p and P. We also correct for the geometric probability of transit, R*/a. We consider first stars within the "solar subset" having Teff = 4100-6100 K, logg = 4.0-4.9, and Kepler magnitude Kp < 15 mag. We include only those stars having noise low enough to permit detection of planets down to 2 Re. We count planets in small domains of R_p and P and divide by the included target stars to calculate planet occurrence in each domain. Occurrence of planets varies by more than three orders of magnitude and increases substantially down to the smallest radius (2 Re) and out to the longest orbital period (50 days, ~0.25 AU) in our study. For P < 50 days, the radius distribution is given by a power law, df/dlogR= k R^\alpha. This rapid increase in planet occurrence with decreasing planet size agrees with core-accretion, but disagrees with population synthesis models. We fit occurrence as a function of P to a power law model with an exponential cutoff below a critical period P_0. For smaller planets, P_0 has larger values, suggesting that the "parking distance" for migrating planets moves outward with decreasing planet size. We also measured planet occurrence over Teff = 3600-7100 K, spanning M0 to F2 dwarfs. The occurrence of 2-4 Re planets in the Kepler field increases with decreasing Teff, making these small planets seven times more abundant around cool stars than the hottest stars in our sample. [abridged]Comment: Submitted to ApJ, 22 pages, 10 figure

Masses, radii, and orbits of small Kepler planets : The transition from gaseous to rocky planets

We report on the masses, sizes, and orbits of the planets orbiting 22 Kepler stars. There are 49 planet candidates around these stars, including 42 detected through transits and 7 revealed by precise Doppler measurements of the host stars. Based on an analysis of the Kepler brightness measurements, along with high-resolution imaging and spectroscopy, Doppler spectroscopy, and (for 11 stars) asteroseismology, we establish low false-positive probabilities (FPPs) for all of the transiting planets (41 of 42 have an FPP under 1%), and we constrain their sizes and masses. Most of the transiting planets are smaller than three times the size of Earth. For 16 planets, the Doppler signal was securely detected, providing a direct measurement of the planet's mass. For the other 26 planets we provide either marginal mass measurements or upper limits to their masses and densities; in many cases we can rule out a rocky composition. We identify six planets with densities above 5 g cm-3, suggesting a mostly rocky interior for them. Indeed, the only planets that are compatible with a purely rocky composition are smaller than 2 R ⊕. Larger planets evidently contain a larger fraction of low-density material (H, He, and H2O).Peer reviewedFinal Accepted Versio

Planetary Candidates Observed by Kepler, III: Analysis of the First 16 Months of Data

New transiting planet candidates are identified in sixteen months (May 2009 - September 2010) of data from the Kepler spacecraft. Nearly five thousand periodic transit-like signals are vetted against astrophysical and instrumental false positives yielding 1,091 viable new planet candidates, bringing the total count up to over 2,300. Improved vetting metrics are employed, contributing to higher catalog reliability. Most notable is the noise-weighted robust averaging of multi-quarter photo-center offsets derived from difference image analysis which identifies likely background eclipsing binaries. Twenty-two months of photometry are used for the purpose of characterizing each of the new candidates. Ephemerides (transit epoch, T_0, and orbital period, P) are tabulated as well as the products of light curve modeling: reduced radius (Rp/R*), reduced semi-major axis (d/R*), and impact parameter (b). The largest fractional increases are seen for the smallest planet candidates (197% for candidates smaller than 2Re compared to 52% for candidates larger than 2Re) and those at longer orbital periods (123% for candidates outside of 50-day orbits versus 85% for candidates inside of 50-day orbits). The gains are larger than expected from increasing the observing window from thirteen months (Quarter 1-- Quarter 5) to sixteen months (Quarter 1 -- Quarter 6). This demonstrates the benefit of continued development of pipeline analysis software. The fraction of all host stars with multiple candidates has grown from 17% to 20%, and the paucity of short-period giant planets in multiple systems is still evident. The progression toward smaller planets at longer orbital periods with each new catalog release suggests that Earth-size planets in the Habitable Zone are forthcoming if, indeed, such planets are abundant.Comment: Submitted to ApJS. Machine-readable tables are available at http://kepler.nasa.gov, http://archive.stsci.edu/kepler/results.html, and the NASA Exoplanet Archiv

In focus: perplexing increase of urinary stone disease in children, adolescent and young adult women and its economic impact

Background Urinary stone disease (USD) historically has affected older men, but studies suggest recent increases in women, leading to a near identical sex incidence ratio. USD incidence has doubled every 10 years, with disproportionate increases amongst children, adolescent, and young adult (AYA) women. USD stone composition in women is frequently apatite (calcium phosphate), which forms in a higher urine pH, low urinary citrate, and an abundance of urinary uric acid, while men produce more calcium oxalate stones. The reasons for this epidemiological trend are unknown. Methods This perspective presents the extent of USD with data from a Canadian Province and a North American institution, explanations for these findings and offers potential solutions to decrease this trend. We describe the economic impact of USD. Findings There was a significant increase of 46% in overall surgical interventions for USD in Ontario. The incidence rose from 47.0/100,000 in 2002 to 68.7/100,000 population in 2016. In a single United States institution, the overall USD annual unique patient count rose from 10,612 to 17,706 from 2015 to 2019, and the proportion of women with USD was much higher than expected. In the 10–17-year-old patients, 50.1% were girls; with 57.5% in the 18–34 age group and 53.6% in the 35–44 age group. The roles of obesity, diet, hormones, environmental factors, infections, and antibiotics, as well as the economic impact, are discussed. Interpretation We confirm the significant increase in USD among women. We offer potential explanations for this sex disparity, including microbiological and pathophysiological aspects. We also outline innovative solutions – that may require steps beyond typical preventive and treatment recommendations

Kepler-63b: A Giant Planet in a Polar Orbit around a Young Sun-like Star

We present the discovery and characterization of a giant planet orbiting the young Sun-like star Kepler-63 (KOI-63, m_(Kp) = 11.6, T_(eff) = 5576 K, M_★ = 0.98 M_☉). The planet transits every 9.43 days, with apparent depth variations and brightening anomalies caused by large starspots. The planet's radius is 6.1 ± 0.2 R_⊕, based on the transit light curve and the estimated stellar parameters. The planet's mass could not be measured with the existing radial-velocity data, due to the high level of stellar activity, but if we assume a circular orbit, then we can place a rough upper bound of 120 M_⊕ (3σ). The host star has a high obliquity (ψ = 104°), based on the Rossiter-McLaughlin effect and an analysis of starspot-crossing events. This result is valuable because almost all previous obliquity measurements are for stars with more massive planets and shorter-period orbits. In addition, the polar orbit of the planet combined with an analysis of spot-crossing events reveals a large and persistent polar starspot. Such spots have previously been inferred using Doppler tomography, and predicted in simulations of magnetic activity of young Sun-like stars