Direct Optical Detection of Microorganisms in Exoplanet Atmospheres: Methods

The purpose of this project is to develop an optical method for detecting the presence of life, specifically microorganisms, in the atmosphere of an exoplanet. We are developing algorithms that distinguish between aerosols of biological origin (microorganisms) from aerosols of non-biological origin (dust, hydrosols, etc.) using analysis of their respective and combined extinction spectra. The method uses large databases of computer-modeled spectra to analyze optical measurements and identify biological aerosols. Whereas most exoplanet researchers focus on detecting molecular spectral signatures, we are focusing on detecting the microorganisms directly rather than their molecular by-products. This method holds significant potential for detecting microorganisms from light scattered from an exoplanet’s atmosphere. In order to simulate exoplanet atmospheres using information available today, Jupiter’s atmosphere was used as a model. This was accomplished by creating a MATLAB program that simulates the scattering of light using complex mathematical models. The optical information for clouds of different types was programmed into MATLAB, as well as the optical data for different kinds of microorganisms. Extinction spectra were simulated using many different size distributions; these distributions were centered at particle sizes typical of microorganisms, liquid clouds, and ice clouds. Many experiment were carried out in order to analyze the effects of different variables on the resulting extinction spectra. These experiments and their results are detailed in our second poster, entitled “Direct Optical Detection of Microorganisms in Exoplanet Atmospheres: Models & Results.

Direct Optical Detection of Microorganisms in Exoplanet Atmospheres: Models & Results

This poster will focus on the analysis of extinction spectra obtained from simulations of exoplanet atmospheres; these spectra have been simulated using a variety of particle types and size distributions. To simulate these spectra, we have created a MATLAB program that uses mathematical models and complex algorithms to model Mie and spherical scattering. This scattering of light from aerosols has been modeled in the ultraviolet to near infrared band (200-1100 nm). We have modeled atmospheric compositions that are typical of Jovian planets, using known information about the atmosphere of Jupiter (see our first poster, entitled “Direct Optical Detection of Microorganisms in Exoplanet Atmospheres: Methods”). Extinction spectra were simulated for six particle types: Erwinia herbicola (EH), Bacillus atrophaeus (BG), ovalbumin (OV), ammonia ice, water, and water ice. Initial results show that the extinction spectra of microorganisms are distinctly different from those of water and ammonia ice clouds; all spectra resemble complex polynomial functions, but the size and location of the peaks vary according to the composition of the particles simulated. These differences are amplified when the size of the particles tested is proportional to the wavelength of the light. There are many variables that could affect this change in extinction spectra. The resulting data from the simulations detailed above has been analyzed to determine which variables most affect the spectra. This analysis focused on the variation of four parameters: refractive index, average particle size, percent volume, and standard deviation

Understanding the viability of impurity-band photovoltaics : a case study of S-doped Si

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2013.Cataloged from PDF version of thesis.Includes bibliographical references (p. 137-149).This thesis explores the electronic structure, optical properties, and carrier lifetimes in silicon that is doped with sulfur beyond the equilibrium solid solubility limit, with a focus on applications as an absorber layer for an impurity-band photovoltaic device. The concept of an impurity-band material envisions the creation of a band of electronic states by incorporating high concentrations of deep-level dopants, which enable the generation of free carriers using photons with energy less than that of the band gap of the host semiconductor. The investigations reported in this thesis provide a framework for the appropriate selection of impurity-band candidate materials. The thesis is divided into three primary sections, one for each of three experimental techniques, respectively. First, the electronic band structure is studied using synchrotron-based x-ray emission spectroscopy. These spectra provide the first insights into how the electronic structure changes as the sulfur concentration is increased across the metal-insulator transition, and how the electronic structure is linked to the anomalously high subband gap absorption. A discrete change in local electronic structure is seen that corresponds to the macroscopic change in electronic behavior. Additionally, a direct correlation is seen between sulfur-induced states and the sub-band gap absorption. Next, the optical properties are studied using Fourier transform infrared spectroscopy. Extraction of the complex index of refraction is performed using numerical models that simulate both the transmission and reflection measurements. Analysis of the absorption coefficient determines the position of the sulfur-induced states within the band gap and their optical cross section for different sulfur concentrations and annealing conditions. At sulfur concentrations above the metal-insulator transition, the sulfur states become degenerate or near-degenerate with the conduction band, and such high concentrations are deemed to have an electronic structure unsuitable for an impurity-band photovoltaic material. Third, low-temperature photoconductivity experiments determine the mobility-lifetime product for carriers generated via sub-band gap photons. Combining both the FTIR optical results with the mobility-lifetime product measured from photoconductivity experiments provide the first empirical determination of the impurity-band figure of merit for sulfur-doped silicon. The figure of merit is found to be over an order of magnitude too low to be suitable as an impurity band absorber layer. Finally, in the conclusion, future directions and a predictive methodology for selecting new candidate impurity band materials that hold promise are discussed. The predictive methodology describes a simple way to estimate the figure of merit for super-saturated materials solely using literature values of the optical and electrical capture cross sections at dilute concentrations.by Joseph Timothy Sullivan.Ph.D

Synthesis of monodisperse chitosan nanoparticles

The objectives of this study were to evaluate the effects of the initial concentrations of chitosan (CS) and sodium tripolyphosphate (TPP), the CS:TPP mass ratio, the CS molecular weight (MW) and pH on the synthesis of CS nanoparticles (CS NPs). The particle size of the synthesised CS NPs was significantly affected (P 300 nm. While both native CS and CS NPs showed antimicrobial activity, no significant antimicrobial enhancement was observed for the NP form. The findings of this study have shown that monodisperse CS NPs can be obtained using a combination of bottom-up and top-down techniques and the unique physiochemical properties of these nanomaterials have the potential for applications in developing of antimicrobial active packaging materials

Wilson River Watershed Assessment : final report

The purpose of this watershed assessment is to provide an inventory and characterization of watershed conditions in the Wilson River watershed and to provide recommendations that address the issues of water quality, fisheries and fish habitat, and watershed hydrology

Miami River watershed assessment : final report

The purpose of this watershed assessment is to inventory and characterize watershed conditions of the Miami River watershed and to provide recommendations that address the issues of water quality, fisheries and fish habitat, and watershed hydrology. This assessment was conducted by reviewing and synthesizing existing data sets and some new data collected by the watershed council, following the guidelines outlined in the Oregon Watershed Enhancement Board (OWEB) watershed assessment manual (WPN 1999)

PATRIC, the bacterial bioinformatics database and analysis resource

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issu

Identification of KIF21A mutations as a rare cause of congenital fibrosis of the extraocular muscles type 3 (CFEOM3).

PURPOSE. Three congenital fibrosis of the extraocular muscles phenotypes (CFEOM1-3) have been identified. Each represents a specific form of paralytic strabismus characterized by congenital restrictive ophthalmoplegia, often with accompanying ptosis. It has been demonstrated that CFEOM1 results from mutations in KIF21A and CFEOM2 from mutations in PHOX2A. This study was conducted to determine the incidence of KIF21A and PHOX2A mutations among individuals with the third CFEOM phenotype, CFEOM3. METHODS. All pedigrees and sporadic individuals with CFEOM3 in the authors' database were identified, whether the pedigrees were linked or consistent with linkage to the FEOM1, FEOM2, and/or FEOM3 loci was determined, and the appropriate pedigrees and the sporadic individuals were screened for mutations in KIF21A and PHOX2A. RESULTS. Twelve CFEOM3 pedigrees and 10 CFEOM3 sporadic individuals were identified in the database. The structures of eight of the pedigrees permitted the generation of meaningful linkage data. KIF21A was screened in 17 probands, and mutations were identified in two CFEOM3 pedigrees. One pedigree harbored a novel mutation (2841G-->A, M947I) and one harbored the most common and recurrent of the CFEOM1 mutations identified previously (2860C-->T, R954W). None of CFEOM3 pedigrees or sporadic individuals harbored mutations in PHOX2A. CONCLUSIONS. The results demonstrate that KIF21A mutations are a rare cause of CFEOM3 and that KIF21A mutations can be nonpenetrant. Although KIF21A is the first gene to be associated with CFEOM3, the results imply that mutations in the unidentified FEOM3 gene are the more common cause of this phenotype

Estimated HIV Incidence in the United States, 2006–2009

Background The estimated number of new HIV infections in the United States reflects the leading edge of the epidemic. Previously, CDC estimated HIV incidence in the United States in 2006 as 56,300 (95% CI: 48,200–64,500). We updated the 2006 estimate and calculated incidence for 2007–2009 using improved methodology. Methodology We estimated incidence using incidence surveillance data from 16 states and 2 cities and a modification of our previously described stratified extrapolation method based on a sample survey approach with multiple imputation, stratification, and extrapolation to account for missing data and heterogeneity of HIV testing behavior among population groups. Principal Findings Estimated HIV incidence among persons aged 13 years and older was 48,600 (95% CI: 42,400–54,700) in 2006, 56,000 (95% CI: 49,100–62,900) in 2007, 47,800 (95% CI: 41,800–53,800) in 2008 and 48,100 (95% CI: 42,200–54,000) in 2009. From 2006 to 2009 incidence did not change significantly overall or among specific race/ethnicity or risk groups. However, there was a 21% (95% CI:1.9%–39.8%; p = 0.017) increase in incidence for people aged 13–29 years, driven by a 34% (95% CI: 8.4%–60.4%) increase in young men who have sex with men (MSM). There was a 48% increase among young black/African American MSM (12.3%–83.0%; p<0.001). Among people aged 13–29, only MSM experienced significant increases in incidence, and among 13–29 year-old MSM, incidence increased significantly among young, black/African American MSM. In 2009, MSM accounted for 61% of new infections, heterosexual contact 27%, injection drug use (IDU) 9%, and MSM/IDU 3%. Conclusions/Significance Overall, HIV incidence in the United States was relatively stable 2006–2009; however, among young MSM, particularly black/African American MSM, incidence increased. HIV continues to be a major public health burden, disproportionately affecting several populations in the United States, especially MSM and racial and ethnic minorities. Expanded, improved, and targeted prevention is necessary to reduce HIV incidence

The Primordial Inflation Polarization Explorer (PIPER): Current Status and Performance of the First Flight

The Primordial Inflation Polarization ExploreR (PIPER) is a balloon-borne instrument optimized to measure the polarization of the CMB at large angular scales. It will map 85% of the sky over a series of conventional balloon flights from the Northern and Southern hemispheres, measuring the B-mode polarization power spectrumover a range of multipoles from 2-300 covering both the reionization bump and the recombination peak, with sensitivity to measure the tensor-to-scalar ratio down to r = 0.007. PIPER will observe in four frequency bands centered at 200, 270, 350, and 600 GHz to characterize dust foregrounds. The instrument has background-limited sensitivity provided by fully cryogenic (1.7 K) optics focusing the sky signal onto kilo-pixel arrays of time-domain multiplexed Transition-Edge Sensor (TES) bolometers held at 100 mK. Polarization sensitivity and systematiccontrol are provided by front-end Variable-delay Polarization Modulators (VPMs). PIPER had its engineering flight in October 2017 from Fort Sumner, New Mexico. This papers outlines the major components in the PIPER system discussing the conceptual design as well as specific choices made for PIPER. We also report on the results of the engineering flight, looking at the functionality of the payload systems, particularly VPM, as well as pointing out areas of improvement