Parameter Estimation and Uncertainty Quantication for an Epidemic Model

We examine estimation of the parameters of Susceptible-Infective-Recovered (SIR) models in the context of least squares. We review the use of asymptotic statistical theory and sensitivity analysis to obtain measures of uncertainty for estimates of the model parameters and the basic reproductive number (R0 )—an epidemiologically significant parameter grouping. We find that estimates of different parameters, such as the transmission parameter and recovery rate, are correlated, with the magnitude and sign of this correlation depending on the value of R0. Situations are highlighted in which this correlation allows R0 to be estimated with greater ease than its constituent parameters. Implications of correlation for parameter identifiability are discussed. Uncertainty estimates and sensitivity analysis are used to investigate how the frequency at which data is sampled affects the estimation process and how the accuracy and uncertainty of estimates improves as data is collected over the course of an outbreak. We assess the informativeness of individual data points in a given time series to determine when more frequent sampling (if possible) would prove to be most beneficial to the estimation process. This technique can be used to design data sampling schemes in more general contexts

Stem, root, and older leaf N:P ratios are more responsive indicators of soil nutrient availability than new foliage

Author Posting. © Ecological Society of America, 2014. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecology 95 (2014): 2062–2068, doi:10.1890/13-1671.1.Foliar nitrogen to phosphorus (N:P) ratios are widely used to indicate soil nutrient availability and limitation, but the foliar ratios of woody plants have proven more complicated to interpret than ratios from whole biomass of herbaceous species. This may be related to tissues in woody species acting as nutrient reservoirs during active growth, allowing maintenance of optimal N:P ratios in recently produced, fully expanded leaves (i.e., “new” leaves, the most commonly sampled tissue). Here we address the hypothesis that N:P ratios of newly expanded leaves are less sensitive indicators of soil nutrient availability than are other tissue types in woody plants. Seedlings of five naturally established tree species were harvested from plots receiving two years of fertilizer treatments in a lowland tropical forest in the Republic of Panama. Nutrient concentrations were determined in new leaves, old leaves, stems, and roots. For stems and roots, N:P ratios increased after N addition and decreased after P addition, and trends were consistent across all five species. Older leaves also showed strong responses to N and P addition, and trends were consistent for four of five species. In comparison, overall N:P ratio responses in new leaves were more variable across species. These results indicate that the N:P ratios of stems, roots, and older leaves are more responsive indicators of soil nutrient availability than are those of new leaves. Testing the generality of this result could improve the use of tissue nutrient ratios as indices of soil nutrient availability in woody plants.Data are from Santiago et al. (2012), which was supported by a grant from the Andrew W. Mellon Foundation to S. J. Wright, a Smithsonian Institute Scholarly Studies grant to S. J. Wright and J. B. Yavitt, and a University of California Regent’s Faculty Fellowship to L. S. Santiago. L. A. Schreeg was partially supported through a Marine Biological Laboratory-Brown University SEED grant to Z. Cardon, S. Porder, and L. A. Schreeg

Seasonal changes in soil organic matter after a decade of nutrient addition in a lowland tropical forest

© 2015, US Government. Soil organic matter is an important pool of carbon and nutrients in tropical forests. The majority of this pool is assumed to be relatively stable and to turn over slowly over decades to centuries, although changes in nutrient status can influence soil organic matter on shorter timescales. We measured carbon, nitrogen, and phosphorus concentrations in soil organic matter and leaf litter over an annual cycle in a long-term nutrient addition experiment in lowland tropical rain forest in the Republic of Panama. Total soil carbon was not affected by a decade of factorial combinations of nitrogen, phosphorus, or potassium. Nitrogen addition increased leaf litter nitrogen concentration by 7 % but did not affect total soil nitrogen. Phosphorus addition doubled the leaf litter phosphorus concentration and increased soil organic phosphorus by 50 %. Surprisingly, concentrations of carbon, nitrogen, and phosphorus in soil organic matter declined markedly during the four-month dry season, and then recovered rapidly during the following wet season. Between the end of the wet season and the late dry season, total soil carbon declined by 16 %, total nitrogen by 9 %, and organic phosphorus by between 19 % in control plots and 25 % in phosphorus addition plots. The decline in carbon and nitrogen was too great to be explained by changes in litter fall, bulk density, or the soil microbial biomass. However, a major proportion of the dry-season decline in soil organic phosphorus was explained by a corresponding decline in the soil microbial biomass. These results have important implications for our understanding of the stability and turnover of organic matter in tropical forest soils, because they demonstrate that a considerable fraction of the soil organic matter is seasonally transient, despite the overall pool being relatively insensitive to long-term changes in nutrient status

Development and Application of a Functional Human Esophageal Mucosa Explant Platform to Eosinophilic Esophagitis.

There is an increasing prevalence of esophageal diseases but intact human tissue platforms to study esophageal function, disease mechanisms, and the interactions between cell types in situ are lacking. To address this, we utilized full thickness human donor esophagi to create and validate the ex vivo function of mucosa and smooth muscle (n = 25). Explanted tissue was tested for contractile responses to carbachol and histamine. We then treated ex vivo human esophageal mucosa with a cytokine cocktail to closely mimic the Th2 and inflammatory milieu of eosinophilic esophagitis (EoE) and assessed alterations in smooth muscle and extracellular matrix function and stiffening. We found that full thickness human esophagus as well as the individual layers of circular and longitudinal muscularis propria developed tension in response to carbachol ex vivo and that mucosa demonstrated squamous cell differentiation. Treatment of mucosa with Th2 and fibrotic cytokines recapitulated the majority of the clinical Eosinophilic Esophagitis Diagnostic Profile (EDP) on fluidic transcriptional microarray. Transforming growth factor-beta-1 (TGFβ1) increased gene expression of fibronectin, smooth muscle actin, and phospholamban (p < 0.001). The EoE cocktail also increased stiffness and decreased mucosal compliance, akin to the functional alterations in EoE (p = 0.001). This work establishes a new, transcriptionally intact and physiologically functional human platform to model esophageal tissue responses in EoE

K2-231 b: A sub-Neptune exoplanet transiting a solar twin in Ruprecht 147

We identify a sub-Neptune exoplanet ($R_p = 2.5 \pm 0.2$ R$_\oplus$) transiting a solar twin in the Ruprecht 147 star cluster (3 Gyr, 300 pc, [Fe/H] = +0.1 dex). The ~81 day light curve for EPIC 219800881 (V = 12.71) from K2 Campaign 7 shows six transits with a period of 13.84 days, a depth of ~0.06%, and a duration of ~4 hours. Based on our analysis of high-resolution MIKE spectra, broadband optical and NIR photometry, the cluster parallax and interstellar reddening, and isochrone models from PARSEC, Dartmouth, and MIST, we estimate the following properties for the host star: $M_\star = 1.01 \pm 0.03$ M$_\odot$, $R_\star= 0.95 \pm 0.03$ R$_\odot$, and $T_{\rm eff} = 5695 \pm 50$ K. This star appears to be single, based on our modeling of the photometry, the low radial velocity variability measured over nearly ten years, and Keck/NIRC2 adaptive optics imaging and aperture-masking interferometry. Applying a probabilistic mass-radius relation, we estimate that the mass of this planet is $M_p = 7 +5 -3$ M$_\oplus$, which would cause a RV semi-amplitude of $K = 2 \pm 1$ m s$^{-1}$ that may be measurable with existing precise RV facilities. After statistically validating this planet with BLENDER, we now designate it K2-231 b, making it the second sub-stellar object to be discovered in Ruprecht 147 and the first planet; it joins the small but growing ranks of 23 other planets found in open clusters.Comment: 24 pages, 7 figures, light curve included as separate fil

Physical Characterization of Active Asteroid (6478) Gault

Main belt asteroid (6478) Gault has been dynamically linked with two overlapping asteroid families: Phocaea, dominated by S-type asteroids, and Tamara, dominated by low-albedo C-types. This object has recently become an interesting case for study, after images obtained in late 2018 revealed that it was active and displaying a comet-like tail. Previous authors have proposed that the most likely scenarios to explain the observed activity on Gault were rotational excitation or merger of near-contact binaries. Here we use new photometric and spectroscopic data of Gault to determine its physical and compositional properties. Lightcurves derived from the photometric data showed little variation over three nights of observations, which prevented us from determining the rotation period of the asteroid. Using WISE observations of Gault and the near-Earth Asteroid Thermal Model (NEATM) we determined that this asteroid has a diameter $<$6 km. NIR spectroscopic data obtained with the Infrared Telescope Facility (IRTF) showed a spectrum similar to that of S-complex asteroids, and a surface composition consistent with H chondrite meteorites. These results favor a compositional affinity between Gault and asteroid (25) Phocaea, and rules out a compositional link with the Tamara family. From the spectroscopic data we found no evidence of fresh material that could have been exposed during the outburst episodes.Comment: 9 pages, 4 figures, accepted for publication in ApJ

Highly multimode visible squeezed light with programmable spectral correlations through broadband up-conversion

Multimode squeezed states of light have been proposed as a resource for achieving quantum advantage in computing and sensing. Recent experiments that demonstrate multimode Gaussian states to this end have most commonly opted for spatial or temporal modes, whereas a complete system based on frequency modes has yet to be realized. Instead, we show how to use the frequency modes simultaneously squeezed in a conventional, single-spatial-mode, optical parametric amplifier when pumped by ultrashort pulses. Specifically, we show how adiabatic frequency conversion can be used not only to convert the quantum state from infrared to visible wavelengths, but to concurrently manipulate the joint spectrum. This near unity-efficiency quantum frequency conversion, over a bandwidth >45 THz and, to our knowledge, the broadest to date, allows us to measure the state with an electron-multiplying CCD (EMCCD) camera-based spectrometer, at non-cryogenic temperatures. We demonstrate the squeezing of >400 frequency modes, with a mean of approximately 700 visible photons per shot. Our work shows how many-mode quantum states of light can be generated, manipulated, and measured with efficient use of hardware resources -- in our case, using one pulsed laser, two nonlinear crystals, and one camera. This ability to produce, with modest hardware resources, large multimode squeezed states with partial programmability motivates the use of frequency encoding for photonics-based quantum information processing

Tycho 2 stars with infrared excess in the MSX Point Source Catalogue

Stars of all evolutionary phases have been found to have excess infrared emission due to the presence of circumstellar material. To identify such stars, we have positionally correlated the infrared MSX point source catalogue and the Tycho 2 optical catalogue. A near/mid infrared colour criteria has been developed to select infrared excess stars. The search yielded 1938 excess stars, over half (979) have never previously been detected by IRAS. The excess stars were found to be young objects such as Herbig Ae/Be and Be stars, and evolved objects such as OH/IR and carbon stars. A number of B type excess stars were also discovered whose infrared colours could not be readily explained by known catalogued objects.Comment: Added Comment: 16 pages, 9 figures, accepted for publication in MNRA

Clinical Management of Food Allergy

Food allergies have become a growing public health concern. Currently the standard of care focuses on avoidance of trigger foods, education, and treatment of symptoms following accidental ingestions. Here we provide a framework for primary care physicians and allergists for the diagnosis, management, and treatment of pediatric food allergy