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

Ultrafast internal conversion and photochromism in gas-phase salicylideneaniline

Salicylideneaniline (SA) is an archetypal system for excited-state intramolecular proton transfer (ESIPT) in non-planar systems. Multiple channels for relaxation involving both the keto and enol forms have been proposed after excitation to S1 with near-UV light. Here, we present transient absorption measurements of hot gas-phase SA, jet-cooled SA, and SA in Ar clusters using cavity-enhanced transient absorption spectroscopy (CE-TAS). Assignment of the spectra is aided by simulated TAS spectra, computed by applying time-dependent complete active space configuration interaction (TD-CASCI) to structures drawn from nonadiabatic molecular dynamics simulations. We find prompt ESIPT in all conditions followed by the rapid generation of the trans keto metastable photochrome state and fluorescent keto state in parallel. Increasing the internal energy increases the photochrome yield and decreases the fluorescent yield and fluorescent state lifetime observed in TAS. In Ar clusters, internal conversion of SA is severely hindered, but the photochrome yield is unchanged. Taken together, these results are consistent with the photochrome being produced via the vibrationally excited keto population after ESIPT

Ultrafast internal conversion and photochromism in gas-phase salicylideneaniline

Salicylidenaniline (SA) is an archetypal system for excited-state intramolecular proton transfer (ESIPT) in non-planar systems. Multiple channels for relaxation involving both the keto and enol forms have been proposed after excitation to S$_1$ with near-UV light. Here we present transient absorption measurements of hot gas-phase SA, jet-cooled SA, and SA in Ar clusters using cavity-enhanced transient absorption spectroscopy (CE-TAS). Assignment of the spectra is aided by simulated TAS spectra, computed by applying time-dependent complete active space configuration interaction (TD-CASCI) to structures drawn from nonadiabatic molecular dynamics simulations. We find prompt ESIPT in all conditions followed by the rapid parallel generation of the trans-keto metastable photochrome state and fluorescent keto state in parallel. Increasing the internal energy increases the photochrome yield and decreases the fluorescent yield and fluorescent state lifetime observed in TAS. In Ar clusters, internal conversion of SA is severely hindered but the photochrome yield is unchanged. Taken together, these results are consistent with the photochrome being produced via the vibrationally excited keto population after ESIPT

Translational Research and Medicine at NASA: From Earth to Space and Back Again

The Space Environment provides many challenges to the human physiology and therefore to extended habitation and exploration. Translational research and medical strategies are meeting these challenges by combining Earth based medical solutions with innovative and developmental engineering approaches. Translational methodologies are current applied to spaceflight related dysregulations in the areas of: (1) cardiovascular fluid shifts, intracranial hypertension and neuro-ocular impairment 2) immune insufficiency and suppression/viral re-expression, 3) bone loss and fragility (osteopenia/osteoporosis) and muscle wasting, and finally 4) radiation sensitivity and advanced ageing. Over 40 years of research into these areas have met with limited success due to lack of tools and basic understanding of central issues that cause physiologic maladaptaion and distrupt homeostatis. I will discuss the effects of living in space (reduced gravity, increased radiation and varying atmospheric conditions [EVA]) during long-duration, exploration-class missions and how translational research has benefited not only space exploration but also Earth based medicine. Modern tools such as telemedicine advances in genomics, proteomics, and metabolomics (Omicssciences) has helped address syndromes, at the systemic level by enlisting a global approach to assessing spaceflight physiology and to develop countermeasures thereby permitting our experience in space to be translated to the Earth's medical community

The overlooked significance of plasma volume for successful adaptation to high altitude in Sherpa and Andean natives

In contrast to Andean natives, high altitude Tibetans present with a lower hemoglobin concentration that correlates with reproductive success and exercise capacity. Decades of physiological and genomic research have assumed that the lower hemoglobin concentration in Himalayan natives results from a blunted erythropoietic response to hypoxia (i.e. no increase in total hemoglobin mass). In contrast, herein we test the hypothesis that the lower hemoglobin concentration is the result of greater plasma volume, rather than an absence of increased hemoglobin production. We assessed hemoglobin mass, plasma volume and blood volume in lowlanders at sea level, lowlanders acclimatized to high altitude, Himalayan Sherpa and Andean Quechua, and explored the functional relevance of volumetric hematological measures to exercise capacity. Hemoglobin mass was highest in Andeans, but also elevated in Sherpa compared to lowlanders. Sherpa demonstrated a larger plasma volume than Andeans, resulting in a comparable total blood volume at a lower hemoglobin concentration. Hemoglobin mass was positively related to exercise capacity in lowlanders at sea level and Sherpa at high altitude, but not in Andean natives. Collectively, our findings demonstrate a unique adaptation in Sherpa that reorientates attention away from hemoglobin concentration and towards a paradigm where hemoglobin mass and plasma volume may represent phenotypes with adaptive significance at high altitude

Second harmonic generation in SiC polytypes

LMTO calculations are presented for the frequency dependent second harmonic generation (SHG) in the polytypes 2H, 4H, 6H, 15R and 3C of SiC. All independent tensor components are calculated. The spectral features and the ratios of the 333 to 311 tensorial components are studied as a function of the degree of hexagonality. The relationship to the linear optical response and the underlying band structure are investigated. SHG is suggested to be a sensitive tool for investigating the near band edge interband excitations.Comment: 12 pages, 10 figure

Weak lensing power spectra for precision cosmology: Multiple-deflection, reduced shear and lensing bias corrections

It is usually assumed that the ellipticity power spectrum measured in weak lensing observations can be expressed as an integral over the underlying matter power spectrum. This is true at second order in the gravitational potential. We extend the standard calculation, constructing all corrections to fourth order in the gravitational potential. There are four types of corrections: corrections to the lensing shear due to multiple-deflections; corrections due to the fact that shape distortions probe the reduced shear $\gamma/(1-\kappa)$ rather than the shear itself; corrections associated with the non-linear conversion of reduced shear to mean ellipticity; and corrections due to the fact that observational galaxy selection and shear measurement is based on galaxy brightnesses and sizes which have been (de)magnified by lensing. We show how the previously considered corrections to the shear power spectrum correspond to terms in our analysis, and highlight new terms that were not previously identified. All correction terms are given explicitly as integrals over the matter power spectrum, bispectrum, and trispectrum, and are numerically evaluated for the case of sources at z=1. We find agreement with previous works for the ${\mathcal O}(\Phi^3)$ terms. We find that for ambitious future surveys, the ${\mathcal O}(\Phi^4)$ terms affect the power spectrum at the ~ 1-5 $\sigma$ level; they will thus need to be accounted for, but are unlikely to represent a serious difficulty for weak lensing as a cosmological probe.Comment: 14 pages, 3 figures; matches A & A accepted versio

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

Invisible Belfast:Flat ontologies and remediation of the post-conflict city

[in]visible Belfast was a research-driven indie alternate reality game (ARG) that ran for 6 weeks during the spring of 2011 in Belfast and was subsequently adapted, 5 years later into a fictional documentary for BBC Radio 4. The ARG is a participatory and dispersed narrative, which the audience play through. The text expands outward across both physical and digital platforms to create a mystery for the players using everyday platforms. The ARG is a product of media convergence and at its heart transmedial, defined by its complexity and modes of participation. The fictional radio documentary which remediated the ARG into a more simple linear structure, but possibly a more complex narrative form, retells parts of the story for new audiences. The premise of [in]visible belfast – the game and later the documentary – is itself an adaptation of writer Ciaran Carson’s novel The Star Factory (1997): a postmodern adventure through the complex psychogeography of Belfast. A trail through the labyrinthine text, which paints the history of Belfast in poetic prose. This article will map the concept’s journey from novel to game to radio, contextualising its development within its political and urban landscape and charting the remediation of the narratives as they fold out across multiple media and complex story arches. The article will draw together ideas from previous publications on ARG, transmediality and complex textualities from the authors and reflect on the textual trajectories that the remediation of the narrative has taken from the original book, through the ARG, into the radio documentary. Building upon recent approaches from environmental philosopher Tim Morton and games theorist Ian Bogost, the authors argue that Belfast’s history propels medial adaptations of a particular kind, characterised by a ‘flat’ ontology of space and time and a sort of diffuse and dark urban experience for designers/producers and players/listeners