Comparative Microbial Dynamics in Crassostrea virginica and Crassostrea ariakensis

Considerations to introduce the Suminoe or Asian oyster Crassostrea ariakensis along the East Coast have raised many questions regarding ecology, economics, and human health. To date, research has focused primarily on the ecological and socioeconomic implications of this initiative, yet few studies have assessed its potential impact on public health. Our work compares the rates of bioaccumulation, depuration and post harvest decay of indicator organisms (such as E. coli) and Vibrio sp. between Crassostrea virginica and Crassostrea ariakensis in the laboratory. Preliminary results suggest that the rates of bioaccumulation of E. coli in Crassostrea ariakensis were significantly lower than those for Crassostrea virginica, depuration of E. coli was variable between the two species, and Crassostrea ariakensis post harvest decay rates of Vibrio sp. were significantly lower than Crassostrea virginica. This research provides coastal managers with insight into the response of Crassostrea ariakensis to bacteria, an important consideration for determining appropriate management strategies for this species. Further field-based studies will be necessary to elucidate the mechanisms responsible for the differences in rates of bioaccumulation and depuration. (PDF contains 40 pages

Gemini/GMOS Transmission Spectral Survey: Complete Optical Transmission Spectrum of the hot Jupiter WASP-4b

We present the complete optical transmission spectrum of the hot Jupiter WASP-4b from 440-940 nm at R ~ 400-1500 obtained with the Gemini Multi-Object Spectrometers (GMOS); this is the first result from a comparative exoplanetology survey program of close-in gas giants conducted with GMOS. WASP-4b has an equilibrium temperature of 1700 K and is favorable to study in transmission due to a large scale height (370 km). We derive the transmission spectrum of WASP-4b using 4 transits observed with the MOS technique. We demonstrate repeatable results across multiple epochs with GMOS, and derive a combined transmission spectrum at a precision about twice above photon noise, which is roughly equal to to one atmospheric scale height. The transmission spectrum is well fitted with a uniform opacity as a function of wavelength. The uniform opacity and absence of a Rayleigh slope from molecular hydrogen suggest that the atmosphere is dominated by clouds with condensate grain size of ~1 um. This result is consistent with previous observations of hot Jupiters since clouds have been seen in planets with similar equilibrium temperatures to WASP-4b. We describe a custom pipeline that we have written to reduce GMOS time-series data of exoplanet transits, and present a thorough analysis of the dominant noise sources in GMOS, which primarily consist of wavelength- and time- dependent displacements of the spectra on the detector, mainly due to a lack of atmospheric dispersion correction.Comment: 23 pages, 12 figures, accepted for publication in AJ, 2017 July

Kinetics of n-Butoxy and 2-Pentoxy Isomerization and Detection of Primary Products by Infrared Cavity Ringdown Spectroscopy

The primary products of n-butoxy and 2-pentoxy isomerization in the presence and absence of O_2 have been detected using pulsed laser photolysis-cavity ringdown spectroscopy (PLP-CRDS). Alkoxy radicals n-butoxy and 2-pentoxy were generated by photolysis of alkyl nitrite precursors (n-butyl nitrite or 2-pentyl nitrite, respectively), and the isomerization products with and without O_2 were detected by infrared cavity ringdown spectroscopy 20 μs after the photolysis. We report the mid-IR OH stretch (ν_1) absorption spectra for δ-HO-1-C_4H_8•, δ-HO-1-C_4H_8OO•, δ-HO-1-C_5H_(10)•, and δ-HO-1-C_5H_(10)OO•. The observed ν_1 bands are similar in position and shape to the related alcohols (n-butanol and 2-pentanol), although the HOROO• absorption is slightly stronger than the HOR• absorption. We determined the rate of isomerization relative to reaction with O_2 for the n-butoxy and 2-pentoxy radicals by measuring the relative ν_1 absorbance of HOROO• as a function of [O_2]. At 295 K and 670 Torr of N_2 or N_2/O_2, we found rate constant ratios of k_(isom)/k_(O2) = 1.7 (±0.1) × 10^(19) cm^(–3) for n-butoxy and k_(isom)/k_(O2) = 3.4(±0.4) × 10^(19) cm^(–3) for 2-pentoxy (2σ uncertainty). Using currently known rate constants k_(O2), we estimate isomerization rates of k_(isom) = 2.4 (±1.2) × 10^5 s^(–1) and k_(isom) ≈ 3 × 10^5 s^(–1) for n-butoxy and 2-pentoxy radicals, respectively, where the uncertainties are primarily due to uncertainties in k_(O2). Because isomerization is predicted to be in the high pressure limit at 670 Torr, these relative rates are expected to be the same at atmospheric pressure. Our results include corrections for prompt isomerization of hot nascent alkoxy radicals as well as reaction with background NO and unimolecular alkoxy decomposition. We estimate prompt isomerization yields under our conditions of 4 ± 2% and 5 ± 2% for n-butoxy and 2-pentoxy formed from photolysis of the alkyl nitrites at 351 nm. Our measured relative rate values are in good agreement with and more precise than previous end-product analysis studies conducted on the n-butoxy and 2-pentoxy systems. We show that reactions typically neglected in the analysis of alkoxy relative kinetics (decomposition, recombination with NO, and prompt isomerization) may need to be included to obtain accurate values of k_(isom)/k_(O2)

The tree cut and merge algorithm for estimation of network reliability

This article presents Monte Carlo techniques for estimating network reliability. For highly reliable networks, techniques based on graph evolution models provide very good performance. However, they are known to have significant simulation cost. An existing hybrid scheme (based on partitioning the time space) is available to speed up the simulations; however, there are difficulties with optimizing the important parameter associated with this scheme. To overcome these difficulties, a new hybrid scheme (based on partitioning the edge set) is proposed in this article. The proposed scheme shows orders of magnitude improvement of performance over the existing techniques in certain classes of network. It also provides reliability bounds with little overhead.K.P. Hui, N. Bean, M. Kraetzl and D. Kroes

Metallicities of M Dwarf Planet Hosts from Spectral Synthesis

We present the first spectroscopic metallicities of three M dwarfs with known or candidate planetary mass companions. We have analyzed high resolution, high signal-to-noise spectra of these stars which we obtained at McDonald Observatory. Our analysis technique is based on spectral synthesis of atomic and molecular features using recently revised cool-star model atmospheres and spectrum synthesis code. The technique has been shown to yield results consistent with the analyses of solar-type stars and allows measurements of M dwarf [M/H] values to 0.12 dex precision. From our analysis, we find [M/H] = -0.12, -0.32, and -0.33 for GJ 876, GJ 436, and GJ 581 respectively. These three M dwarf planet hosts have sub-solar metallicities, a surprising departure from the trend observed in FGK-type stars. This study is the first part of our ongoing work to determine the metallicities of the M dwarfs included in the McDonald Observatory planet search program.Comment: 13 pages, 2 figures, accepted for publication in ApJ

Application of Gene Shaving and Mixture Models to Cluster Microarray Gene Expression Data

Researchers are frequently faced with the analysis of microarray data of a relatively large number of genes using a small number of tissue samples. We examine the application of two statistical methods for clustering such microarray expression data: EMMIX-GENE and GeneClust. EMMIX-GENE is a mixture-model based clustering approach, designed primarily to cluster tissue samples on the basis of the genes. GeneClust is an implementation of the gene shaving methodology, motivated by research to identify distinct sets of genes for which variation in expression could be related to a biological property of the tissue samples. We illustrate the use of these two methods in the analysis of Affymetrix oligonucleotide arrays of well-known data sets from colon tissue samples with and without tumors, and of tumor tissue samples from patients with leukemia. Although the two approaches have been developed from different perspectives, the results demonstrate a clear correspondence between gene clusters produced by GeneClust and EMMIX-GENE for the colon tissue data. It is demonstrated, for the case of ribosomal proteins and smooth muscle genes in the colon data set, that both methods can classify genes into co-regulated families. It is further demonstrated that tissue types (tumor and normal) can be separated on the basis of subtle distributed patterns of genes. Application to the leukemia tissue data produces a division of tissues corresponding closely to the external classification, acute myeloid meukemia (AML) and acute lymphoblastic leukemia (ALL), for both methods. In addition, we also identify genes specific for the subgroup of ALL-Tcell samples. Overall, we find that the gene shaving method produces gene clusters at great speed; allows variable cluster sizes and can incorporate partial or full supervision; and finds clusters of genes in which the gene expression varies greatly over the tissue samples while maintaining a high level of coherence between the gene expression profiles. The intent of the EMMIX-GENE method is to cluster the tissue samples. It performs a filtering step that results in a subset of relevant genes, followed by gene clustering, and then tissue clustering, and is favorable in its accuracy of ranking the clusters produced

Detecting Planets Around Very Low Mass Stars with the Radial Velocity Method

The detection of planets around very low-mass stars with the radial velocity method is hampered by the fact that these stars are very faint at optical wavelengths where the most high-precision spectrometers operate. We investigate the precision that can be achieved in radial velocity measurements of low mass stars in the near infrared (nIR) Y-, J-, and H-bands, and we compare it to the precision achievable in the optical. For early-M stars, radial velocity measurements in the nIR offer no or only marginal advantage in comparison to optical measurements. Although they emit more flux in the nIR, the richness of spectral features in the optical outweighs the flux difference. We find that nIR measurement can be as precise than optical measurements in stars of spectral type ~M4, and from there the nIR gains in precision towards cooler objects. We studied potential calibration strategies in the nIR finding that a stable spectrograph with a ThAr calibration can offer enough wavelength stability for m/s precision. Furthermore, we simulate the wavelength-dependent influence of activity (cool spots) on radial velocity measurements from optical to nIR wavelengths. Our spot simulations reveal that the radial velocity jitter does not decrease as dramatically towards longer wavelengths as often thought. The jitter strongly depends on the details of the spots, i.e., on spot temperature and the spectral appearance of the spot. Forthcoming nIR spectrographs will allow the search for planets with a particular advantage in mid- and late-M stars. Activity will remain an issue, but simultaneous observations at optical and nIR wavelengths can provide strong constraints on spot properties in active stars.Comment: accepted by ApJ, v2 accepted revision with new precision calculations, abstract abride

A semi-analytical approach to perturbations in mutated hilltop inflation

We study cosmological perturbations and observational aspects for mutated hilltop model of inflation. Employing mostly analytical treatment, we evaluate observable parameters during inflation as well as post-inflationary perturbations. This further leads to exploring observational aspects related to Cosmic Microwave Background (CMB) radiation. This semi-analytical treatment reduces complications related to numerical computation to some extent for studying the different phenomena related to CMB angular power spectrum for mutated hilltop inflation.Comment: 7 pages, 2 figures. Improved version to appear in IJMP

Vortices in small superconducting disks

We study the Ginzburg-Landau equations in order to describe a two-dimensional superconductor in a bounded domain. Using the properties of a particular integrability point ($\kappa = 1/ \sqrt2$) of these nonlinear equations which allows vortex solutions, we obtain a closed expression for the energy of the superconductor. The presence of the boundary provides a selection mechanism for the number of vortices. A perturbation analysis around $\kappa = 1/ \sqrt2$ enables us to include the effects of the vortex interactions and to describe quantitatively the magnetization curves recently measured on small superconducting disks. We also calculate the optimal vortex configuration and obtain an expression for the confining potential away from the London limit.Comment: 4 pages, to be published in Physica C (Superconductivity