505 research outputs found
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 to today.
Measurements of galaxy rotation velocity , which quantify ordered
motions, and gas velocity dispersion , which quantify disordered
motions, are adopted from the DEEP2 and SIGMA surveys. This sample covers a
continuous baseline in redshift from to , spanning 10 Gyrs. At
low redshift, nearly all sufficiently massive star-forming galaxies are
rotationally supported (). By , the percentage of
galaxies with rotational support has declined to 50 at low stellar mass
() and 70 at high stellar mass
(). For , the percentage
drops below 35 for all masses. From 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 by a factor of 3 since a
redshift of 2, which is independent of mass. Over the same time period,
increases by a factor of 1.5 for low mass systems, but does not
evolve for high mass systems. These trends in and 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 decline with time as before, but
strongly increases with time for all galaxy masses. This enhances the
evolution in . These results indicate that 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
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