Regression Methods for Group Testing Data

Group testing is an efficient method of disease screening, whereby individual specimens (e.g., blood, urine, etc.) are pooled together and tested as a whole for the presence of disease. A common goal is to use data arising from these testing protocols to better understand the relationship between disease status and potential risk factors (e.g., age, symptom status, etc.). Numerous statistical methodologies have been developed for this purpose, most of which are built within the framework of a generalized linear model. Recent authors have suggested the inadequacy of such regression methods to capture the true functional relationships when nonlinear effects are present. In this dissertation, we develop new parametric and nonparametric regression methods for group testing data using the expectation-maximization algorithm. Our methods can be implemented with any group testing algorithm and have the flexibility to seamlessly account for both linear and nonlinear covariate effects. In addition, our methods are the first within the group testing literature to integrate machine learning techniques. A growing number of assays have the ability to detect multiple diseases simultaneously. One such assay is the Aptima Combo 2 Assay (AC2A), which is able to simultaneously test for the presence of chlamydia and gonorrhea. With this as our motivating example, we generalize our regression methods to allow for a bivariate response. We use simulation to demonstrate the estimation performance of our algorithms and provide a real data application of our methods using disease screening data obtained from the University of Iowa

The Spitzer c2d Survey of Nearby Dense Cores. IX. Discovery of a Very Low Luminosity Object Driving a Molecular Outflow in the Dense Core L673-7

We present new infrared, submillimeter, and millimeter observations of the dense core L673-7 and report the discovery of a low-luminosity, embedded Class 0 protostar driving a molecular outflow. L673-7 is seen in absorption against the mid-infrared background in 5.8, 8, and 24 micron Spitzer images, allowing for a derivation of the column density profile and total enclosed mass of L673-7, independent of dust temperature assumptions. Estimates of the core mass from these absorption profiles range from 0.2-4.5 solar masses. Millimeter continuum emission indicates a mass of about 2 solar masses, both from a direct calculation assuming isothermal dust and from dust radiative transfer models constrained by the millimeter observations. We use dust radiative transfer models to constrain the internal luminosity of L673-7, defined to be the luminosity of the central source and excluding the luminosity from external heating, to be 0.01-0.045 solar luminosities, with 0.04 solar luminosities the most likely value. L673-7 is thus classified as a very low luminosity object (VeLLO), and is among the lowest luminosity VeLLOs yet studied. We calculate the kinematic and dynamic properties of the molecular outflow in the standard manner, and we show that the expected accretion luminosity based on these outflow properties is greater than or equal to 0.36 solar luminosities. The discrepancy between this expected accretion luminosity and the internal luminosity derived from dust radiative transfer models indicates that the current accretion rate is much lower than the average rate over the lifetime of the outflow. Although the protostar embedded within L673-7 is consistent with currently being substellar, it is unlikely to remain as such given the substantial mass reservoir remaining in the core.Comment: 19 pages, 14 figures. Accepted by Ap

Spitzer and HHT observations of starless cores: masses and environments

We present Spitzer observations of a sample of 12 starless cores selected to have prominent 24 micron shadows. The Spitzer images show 8 and 24 micron shadows and in some cases 70 micron shadows; these spatially resolved absorption features trace the densest regions of the cores. We have carried out a 12CO (2-1) and 13CO (2-1) mapping survey of these cores with the Heinrich Hertz Telescope (HHT). We use the shadow features to derive optical depth maps. We derive molecular masses for the cores and the surrounding environment; we find that the 24 micron shadow masses are always greater than or equal to the molecular masses derived in the same region, a discrepancy likely caused by CO freeze--out onto dust grains. We combine this sample with two additional cores that we studied previously to bring the total sample to 14 cores. Using a simple Jeans mass criterion we find that ~ 2/3 of the cores selected to have prominent 24 micron shadows are collapsing or near collapse, a result that is supported by millimeter line observations. Of this subset at least half have indications of 70 micron shadows. All cores observed to produce absorption features at 70 micron are close to collapse. We conclude that 24 micron shadows, and even more so the 70 micron ones, are useful markers of cloud cores that are approaching collapse.Comment: 41 pages, 28 figures, 5 tables; accepted by Ap

Bedside Measurement of Volatile Organic Compounds in the Atmosphere of Neonatal Incubators Using Ion Mobility Spectrometry

Background: Early and non-invasive diagnosis of common diseases is of great importance in the care of preterm infants. We hypothesized that volatile organic compounds (VOC) can be successfully measured in the neonatal incubator atmosphere. Methods: This is a feasibility study to investigate whether the discrimination of occupied and unoccupied neonatal incubators is possible by bedside measurement of volatile organic compounds (VOCs) on the neonatal intensive care unit. VOC profiles were measured in the incubator air using ion mobility spectrometry coupled to multi-capillary columns (BreathDiscovery B&S Analytik GmbH, Dortmund, Germany). Results: Seventeen incubators occupied by preterm infants (50 measurements) and nine unoccupied neonatal incubators were sampled, using 37 room air measurements as controls. Three VOC signals that allow the discrimination between occupied and unoccupied incubators were identified. The best discrimination was reached by peak P20 exhibiting a sensitivity, specificity, positive predictive value and negative predictive value of 94.0, 88.9, 97.3, and 72.3%, respectively. Use of a decision tree improved these values to 100.0, 88.9, 98.0, and 100.0%, respectively. Discussion: A bedside method that allows the characterization of VOC profiles in the neonatal incubator atmosphere using ion mobility spectrometry was established. Occupied and unoccupied incubators could be discriminated by characterizing VOC profiles. This technique has the potential to yield results within minutes. Thus, future studies are recommended to test the hypothesis that VOCs within neonatal incubators are useful biomarkers for non-invasive diagnostics in preterm neonates

Contrasting soil dynamics in a formerly glaciated and non-glaciated Mediterranean mountain plateau (Serra da Estrela, Portugal)

Few data are available on how soil erosion rates compare between surfaces of different ages because short-term processes often overprint the longer-term erosion signal. This study investigated the soil dynamics among two end-member sites, a formerly glaciated ('young', maximum glacial extent at 22-30 ka BP) and a non-glaciated ('old') area at the Serra da Estrela (Portugal). To disentangle soil distribution rates over different timeframes, isotopes for long-term (10Be), mid-term (delta C-13) and short-term (239+240Pu) periods were applied together with principles of the percolation theory.& nbsp;The formerly glaciated area has soils with a lower degree of weathering and lower carbon content compared to soils of the 'old', non-glaciated area. The selected isotopes and their distribution along the soil profiles revealed temporal differences in soil mixing process. It is hypothesised that the slightly higher elevation and formerly glaciated sites experienced cryoturbation effects over a longer period, while being less active or absent for the last few decades at the older, non-glaciated soils.& nbsp;The average long-term (millennia) soil erosion rates correspond to the expected higher rates at the younger surface and lower rates at the older surface. Once the formerly glaciated area became ice-free, soil erosion rates were high and decreased giving rise to average long-term rates of 101-140 [t km(-2) yr(-1)] for the older surfaces and 176-248 [t km(-2) yr(-1)] for the younger surfaces. In addition, seasonal freeze-thaw of the soils has persisted over a long period and affected the younger soils more intensively than the older soils. The current (last decades) soil redistribution rates, however, are up to one order of magnitude higher than the millennia rates and are controlled by surface angle and vegetation cover and less by soil texture. The more undulated, non-glaciated older surface had the highest short-term (decades) soil erosion rates in the range of 900-1700 [t km(-2 & nbsp;)yr(-1)], exhibits degrading conditions and relatively shallow soils. The younger soils, however, showed short-term (last few decades) average soil deposition rates of ~ 230 [t km(-2) yr(-1)]. Human impact (bush fires, grazing) is the cause for the currently strong soil degradation at the non-glaciated area.info:eu-repo/semantics/publishedVersio

Patterns of volatile organic compounds in excrements of preterm neonates

Background: As neonates are susceptible for many diseases, establishing noninvasive diagnostic methods is desirable. We hypothesized that volatile organic compounds (VOCs) could be successfully measured in diaper samples. Methods: We performed a feasibility study to investigate whether ambient airindependent headspace measurements of the VOC profiles of diapers from premature infants can be conducted using ion mobility spectrometer coupled with multi-capillary columns (B & S Analytik GmbH). Results: We analysed 39 diapers filled with stool (n = 10) or urine (n = 20) respectively, using empty diapers as a control (n = 9). A total of 158 different VOCs were identified, and we classified the content of the diapers (urine or stool) according to their VOC profiles with a significance level of p<0.05. Conclusions: We have developed a novel method to study headspace VOC profiles of biosamples using ion mobility spectrometry coupled with multi-capillary columns. Using this method, we have characterized the VOC profiles of stool and urine of preterm neonates. Future studies are warranted to characterize specific VOC profiles in infections and other diseases of the preterm neonate, thus establishing quick and noninvasive diagnostics in the routine care of the highly vulnerable preterm and term neonates

Attenuated asthma phenotype in mice with a fetal-like antigen receptor repertoire

We hypothesized that the scarcity of N-nucleotides might contribute to the inability of the neonate to mount a robust allergic immune response. To test this, we used terminal deoxyribunucleotidyl Transferase defcient (TdT−/−) mice, which express “fetal-like” T cell receptor and immunoglobulin repertoires with largely germline-encoded CDR3 regions. Intraperitoneal sensitization was followed by aerosol provocation with either PBS or the allergen OVA in both TdT−/− mice and wild-type mice to develop allergic respiratory infammation. The efects of this procedure were investigated by lung function test, immunological analysis of serum and brochoalveolar lavage. The local TH2 cytokine milieu was signifcantly attenuated in TdT−/− mice. Within this group, the induction of total IgE levels was also signifcantly reduced after sensitization. TdT−/− mice showed a tendency toward reduced eosinophilic infow into the bronchial tubes, which was associated with the elimination of respiratory hyperreactivity. In conclusion, in a murine model of allergic airway infammation, the expression of fetal-like antigen receptors was associated with potent indications of a reduced ability to mount an asthma phenotype. This underlines the importance of somatically-generated antigen-receptor repertoire diversity in type one allergic immune responses and suggests that the fetus may be protected from allergic responses, at least in part, by controlling N addition

KELT-1b: A Strongly Irradiated, Highly Inflated, Short Period, 27 Jupiter-mass Companion Transiting a mid-F Star

We present the discovery of KELT-1b, the first transiting low-mass companion from the wide-field Kilodegree Extremely Little Telescope-North (KELT-North) survey. The V=10.7 primary is a mildly evolved, solar-metallicity, mid-F star. The companion is a low-mass brown dwarf or super-massive planet with mass of 27.23+/-0.50 MJ and radius of 1.110+0.037-0.024 RJ, on a very short period (P=1.21750007) circular orbit. KELT-1b receives a large amount of stellar insolation, with an equilibrium temperature assuming zero albedo and perfect redistribution of 2422 K. Upper limits on the secondary eclipse depth indicate that either the companion must have a non-zero albedo, or it must experience some energy redistribution. Comparison with standard evolutionary models for brown dwarfs suggests that the radius of KELT-1b is significantly inflated. Adaptive optics imaging reveals a candidate stellar companion to KELT-1, which is consistent with an M dwarf if bound. The projected spin-orbit alignment angle is consistent with zero stellar obliquity, and the vsini of the primary is consistent with tidal synchronization. Given the extreme parameters of the KELT-1 system, we expect it to provide an important testbed for theories of the emplacement and evolution of short-period companions, and theories of tidal dissipation and irradiated brown dwarf atmospheres.Comment: 30 pages, 19 figures. Submitted to Ap

KELT-2Ab: A Hot Jupiter Transiting the Bright (V=8.77) Primary Star of a Binary System

We report the discovery of KELT-2Ab, a hot Jupiter transiting the bright (V=8.77) primary star of the HD 42176 binary system. The host is a slightly evolved late F-star likely in the very short-lived "blue-hook" stage of evolution, with \teff=6148\pm48{\rm K}, $\log{g}=4.030_{-0.026}^{+0.015}$ and \feh=0.034\pm0.78. The inferred stellar mass is $M_*=1.314_{-0.060}^{+0.063}$\msun\ and the star has a relatively large radius of $R_*=1.836_{-0.046}^{+0.066}$\rsun. The planet is a typical hot Jupiter with period $4.11379\pm0.00001$ days and a mass of $M_P=1.524\pm0.088$\mj\ and radius of $R_P=1.290_{-0.050}^{+0.064}$\rj. This is mildly inflated as compared to models of irradiated giant planets at the $\sim$4 Gyr age of the system. KELT-2A is the third brightest star with a transiting planet identified by ground-based transit surveys, and the ninth brightest star overall with a transiting planet. KELT-2Ab's mass and radius are unique among the subset of planets with $V<9$ host stars, and therefore increases the diversity of bright benchmark systems. We also measure the relative motion of KELT-2A and -2B over a baseline of 38 years, robustly demonstrating for the first time that the stars are bound. This allows us to infer that KELT-2B is an early K-dwarf. We hypothesize that through the eccentric Kozai mechanism KELT-2B may have emplaced KELT-2Ab in its current orbit. This scenario is potentially testable with Rossiter-McLaughlin measurements, which should have an amplitude of $\sim$44 m s$^{-1}$.Comment: 9 pages, 2 tables, 4 figures. A short video describing this paper is available at http://www.youtube.com/watch?v=wVS8lnkXXlE. Revised to reflect the ApJL version. Note that figure 4 is not in the ApJL versio