Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis.

We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following segmental removal of the colon (resection) and its reconnection (anastomosis). Here we hypothesized that comparative genetic analysis of E. faecalis isolates present at the anastomotic wound site before and after surgery would shed insight into the mechanisms by which collagenolytic strains are selected for and predominate at sites of anastomotic disruption. Whole genome optical mapping of four pairs of isolates from rat colonic tissue obtained following surgical resection (herein named "pre-op" isolates) and then 6 days later from the anastomotic site (herein named "post-op" isolates) demonstrated that the isolates with higher collagenolytic activity formed a distinct cluster. In order to perform analysis at a deeper level, a single pair of E. faecalis isolates (16A pre-op and 16A post-op) was selected for whole genome sequencing and assembled using a hybrid assembly algorithm. Comparative genomics demonstrated absence of multiple gene clusters, notably a pathogenicity island in the post-op isolate. No differences were found in the fsr-gelE-sprE genes (EF1817-1822) responsible for regulation and production of collagenolytic activity. Analysis of unique genes among the 16A pre-op and post-op isolates revealed the predominance of transporter systems-related genes in the pre-op isolate and phage-related and hydrolytic enzyme-encoding genes in the post-op isolate. Despite genetic differences observed between pre-op and post-op isolates, the precise genetic determinants responsible for their differential expression of collagenolytic activity remains unknown

The DEEP2 Galaxy Redshift Survey: Redshift Identification of Single-Line Emission Galaxies

We present two methods for determining spectroscopic redshifts of galaxies in the DEEP2 survey which display only one identifiable feature, an emission line, in the observed spectrum ("single-line galaxies"). First, we assume each single line is one of the four brightest lines accessible to DEEP2: Halpha, [OIII] 5007, Hbeta, or [OII] 3727. Then, we supplement spectral information with BRI photometry. The first method, parameter space proximity (PSP), calculates the distance of a single-line galaxy to galaxies of known redshift in (B-R), (R-I), R, observed wavelength parameter space. The second method is an artificial neural network (ANN). Prior information, such as allowable line widths and ratios, rules out one or more of the four lines for some galaxies in both methods. Based on analyses of evaluation sets, both methods are nearly perfect at identifying blended [OII] doublets. Of the lines identified as Halpha in the PSP and ANN methods, 91.4% and 94.2% respectively are accurate. Although the methods are not this accurate at discriminating between [OIII] and Hbeta, they can identify a single line as one of the two, and the ANN method in particular unambiguously identifies many [OIII] lines. From a sample of 640 single-line spectra, the methods determine the identities of 401 (62.7%) and 472 (73.8%) single lines, respectively, at accuracies similar to those found in the evaluation sets.Comment: 11 pages, 6 figures, accepted to Ap

A meta-language for systems architecting

Thesis (Ph. D.)--Massachusetts Institute of Technology, Engineering Systems Division, 2005.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (leaves 164-168).(cont.) To demonstrate its practical value in large-scale engineering systems, the research applied OPN to two space exploration programs and one aircraft design problem. In our experiments, OPN was able to significantly change the modeling and architectural reasoning process by automating a number of manual model construction, manipulation, and simulation tasks.The aim of this research is to design an executable meta-language that supports system architects' modeling process by automating certain model construction, manipulation and simulation tasks. This language specifically addresses the needs in systematically communicating architects' intent with a wide range of stakeholders and to organize knowledge from various domains. Our investigation into existing architecting approaches and technologies has pointed out the need to develop a simple and intuitive, yet formal language, that expresses multiple layers of abstractions, provides reflexive knowledge about the models, mechanizes data exchange and manipulation, while allowing integration with legacy infrastructures. A small set of linguistic primitives, stateful objects and processes that transform them were identified as both required and sufficient building blocks of the meta-language, specified as an Object-Process Network (OPN). To demonstrate the applicability of OPN, a software environment has been developed and applied to define meta-models of large-scale complex system architectures such as space transportation systems. OPN provides three supporting aspects of architectural modeling. As a declarative language, OPN provides a diagrammatic formal language to help architects specify the space of architectural options. As an imperative language, OPN automates the process of creating architectural option instances and computes associated performance metrics for those instances. As a simulation language, OPN uses a function-algebraic model to subsume and compose discrete, continuous, and probabilistic events within one unified execution engine.by Hsueh-Yung Benjamin Koo.Ph.D

The Patient's Guide to Psoriasis Treatment. Part 4: Goeckerman Therapy.

BackgroundThe Goeckerman regimen remains one of the oldest, most reliable treatment options for patients with moderate to severe psoriasis. Goeckerman therapy currently consists of exposure to ultraviolet B light and application of crude coal tar. The details of the procedure can be confusing and challenging to understand for the first-time patient or provider.ObjectiveTo present a freely available online guide and video on Goeckerman treatment that explains the regimen in a patient-oriented manner.MethodsThe Goeckerman protocol used at the University of California-San Francisco Psoriasis and Skin Treatment Center as well as available information from the literature were reviewed to design a comprehensive guide for patients receiving Goeckerman treatment.ResultsWe created a printable guide and video resource that covers the supplies needed for Goeckerman regimen, the treatment procedure, expected results, how to monitor for adverse events, and discharge planning.ConclusionThis new resource is beneficial for prospective patients planning to undergo Goeckerman treatment, healthcare providers, and trainees who want to learn more about this procedure. Online media and video delivers material in a way that is flexible and often familiar to patients

The Patient's Guide to Psoriasis Treatment. Part 2: PUVA Phototherapy.

BackgroundPUVA treatment is photochemotherapy for psoriasis that combines psoralen with UVA radiation. Although PUVA is a very effective treatment option for psoriasis, there is an absence of patient resources explaining and demonstrating the process of PUVA. Studies have shown that patients who viewed videos explaining the treatment procedures for various medical conditions had a greater understanding of their treatment and were more active participants in their health.ObjectiveTo present a freely available online guide and video on PUVA treatment designed for patient education on PUVA.MethodsThe PUVA treatment protocol used at the University of California-San Francisco Psoriasis and Skin Treatment Center as well as available information from the literature was reviewed to design a comprehensive guide for patients receiving PUVA treatment.ResultsWe created a printable guide and video resource that reviews the benefits and risks of PUVA, discusses the three types of PUVA (hand-foot soak, full body soak, and systemic), demonstrates the PUVA process, and provides practical tips for safe use.ConclusionOnline media and video delivers material in a way that is flexible and often familiar to patients. This new format is beneficial for prospective patients planning to undergo PUVA treatment, health-care providers, and trainees who want to learn more about this treatment

The DEEP2 Redshift Survey: Lyman Alpha Emitters in the Spectroscopic Database

We present the first results of a search for Lyman-alpha emitters (LAEs) in the DEEP2 spectroscopic database that uses a search technique that is different from but complementary to traditional narrowband imaging surveys. We have visually inspected ~20% of the available DEEP2 spectroscopic data and have found nine high-quality LAEs with clearly asymmetric line profiles and an additional ten objects of lower quality, some of which may also be LAEs. Our survey is most sensitive to LAEs at z=4.4-4.9 and that is indeed where all but one of our high-quality objects are found. We find the number density of our spectroscopically-discovered LAEs to be consistent with those found in narrowband imaging searches. The combined, averaged spectrum of our nine high-quality objects is well fit by a two-component model, with a second, lower-amplitude component redshifted by ~420 km/s with respect to the primary Lyman-alpha line, consistent with large-scale outflows from these objects. We conclude by discussing the advantages and future prospects of blank-sky spectroscopic surveys for high-z LAEs.Comment: Accepted for publication in Ap

z~2: An Epoch of Disk Assembly

We explore the evolution of the internal gas kinematics of star-forming galaxies from the peak of cosmic star-formation at $z\sim2$ to today. Measurements of galaxy rotation velocity $V_{rot}$, which quantify ordered motions, and gas velocity dispersion $\sigma_g$, which quantify disordered motions, are adopted from the DEEP2 and SIGMA surveys. This sample covers a continuous baseline in redshift from $z=2.5$ to $z=0.1$, spanning 10 Gyrs. At low redshift, nearly all sufficiently massive star-forming galaxies are rotationally supported ($V_{rot}>\sigma_g$). By $z=2$, the percentage of galaxies with rotational support has declined to 50$\%$ at low stellar mass ($10^{9}-10^{10}\,M_{\odot}$) and 70$\%$ at high stellar mass ($10^{10}-10^{11}M_{\odot}$). For $V_{rot}\,>\,3\,\sigma_g$, the percentage drops below 35$\%$ for all masses. From $z\,=\,2$ to now, galaxies exhibit remarkably smooth kinematic evolution on average. All galaxies tend towards rotational support with time, and it is reached earlier in higher mass systems. This is mostly due to an average decline in $\sigma_g$ by a factor of 3 since a redshift of 2, which is independent of mass. Over the same time period, $V_{rot}$ increases by a factor of 1.5 for low mass systems, but does not evolve for high mass systems. These trends in $V_{rot}$ and $\sigma_g$ with time are at a fixed stellar mass and should not be interpreted as evolutionary tracks for galaxy populations. When galaxy populations are linked in time with abundance matching, not only does $\sigma_g$ decline with time as before, but $V_{rot}$ strongly increases with time for all galaxy masses. This enhances the evolution in $V_{rot}/\sigma_g$. These results indicate that $z\,=\,2$ is a period of disk assembly, during which the strong rotational support present in today's massive disk galaxies is only just beginning to emerge.Comment: 12 pages, 8 figures, submitted to Ap

Testing Diagnostics of Nuclear Activity and Star Formation in Galaxies at z>1

We present some of the first science data with the new Keck/MOSFIRE instrument to test the effectiveness of different AGN/SF diagnostics at z~1.5. MOSFIRE spectra were obtained in three H-band multi-slit masks in the GOODS-S field, resulting in two hour exposures of 36 emission-line galaxies. We compare X-ray data with the traditional emission-line ratio diagnostics and the alternative mass-excitation and color-excitation diagrams, combining new MOSFIRE infrared data with previous HST/WFC3 infrared spectra (from the 3D-HST survey) and multiwavelength photometry. We demonstrate that a high [OIII]/Hb ratio is insufficient as an AGN indicator at z>1. For the four X-ray detected galaxies, the classic diagnostics ([OIII]/Hb vs. [NII]/Ha and [SII]/Ha) remain consistent with X-ray AGN/SF classification. The X-ray data also suggest that "composite" galaxies (with intermediate AGN/SF classification) host bona-fide AGNs. Nearly 2/3 of the z~1.5 emission-line galaxies have nuclear activity detected by either X-rays or the classic diagnostics. Compared to the X-ray and line ratio classifications, the mass-excitation method remains effective at z>1, but we show that the color-excitation method requires a new calibration to successfully identify AGNs at these redshifts.Comment: 7 pages, 4 figures. Accepted to ApJ Letter