282 research outputs found
Genetic analysis and prevalence studies of the brp exopolysaccharide locus of Vibrio vulnificus
Phase variation in the Gram-negative human pathogen Vibrio vulnificus involves three colonial morphotypes- smooth opaque colonies due to production of capsular polysaccharide (CPS), smooth translucent colonies as the result of little or no CPS expression, and rugose colonies due to production of a separate extracellular polysaccharide (EPS), which greatly enhances biofilm formation. Previously, it was shown that the brp locus, which consists of nine genes arranged as an operon, is up-regulated in rugose strains in a c-di-GMP-dependent manner, and that plasmid insertions into the locus resulted in loss of rugosity and efficient biofilm production. Here, we have used non-polar mutagenesis to assess the involvement of individual brp genes in production of EPS and related phenotypes. Inactivation of genes predicted to be involved in various stages of EPS biosynthesis eliminated both the rugose colonial appearance and production of EPS, while knockout of a predicted flippase function involved in EPS transport resulted in a dry, lightly striated phenotype, which was associated with a reduction of brp-encoded EPS on the cell surface. All brp mutants retained the reduced motility characteristic of rugose strains. Lastly, we provide evidence that the brp locus is highly prevalent among strains of V. vulnificus. © 2014 Garrison-Schilling et al
SeaTrack: Ground station orbit prediction and planning software for sea-viewing satellites
An orbit prediction software package (Sea Track) was designed to assist High Resolution Picture Transmission (HRPT) stations in the acquisition of direct broadcast data from sea-viewing spacecraft. Such spacecraft will be common in the near future, with the launch of the Sea viewing Wide Field-of-view Sensor (SeaWiFS) in 1994, along with the continued Advanced Very High Resolution Radiometer (AVHRR) series on NOAA platforms. The Brouwer-Lyddane model was chosen for orbit prediction because it meets the needs of HRPT tracking accuracies, provided orbital elements can be obtained frequently (up to within 1 week). Sea Track requires elements from the U.S. Space Command (NORAD Two-Line Elements) for the satellite's initial position. Updated Two-Line Elements are routinely available from many electronic sources (some are listed in the Appendix). Sea Track is a menu-driven program that allows users to alter input and output formats. The propagation period is entered by a start date and end date with times in either Greenwich Mean Time (GMT) or local time. Antenna pointing information is provided in tabular form and includes azimuth/elevation pointing angles, sub-satellite longitude/latitude, acquisition of signal (AOS), loss of signal (LOS), pass orbit number, and other pertinent pointing information. One version of Sea Track (non-graphical) allows operation under DOS (for IBM-compatible personal computers) and UNIX (for Sun and Silicon Graphics workstations). A second, graphical, version displays orbit tracks, and azimuth-elevation for IBM-compatible PC's, but requires a VGA card and Microsoft FORTRAN
A novel phase variant of the cholera pathogen shows stress-adaptive cryptic transcriptomic signatures
© 2016 The Author(s). Background: In a process known as phase variation, the marine bacterium and cholera pathogen Vibrio cholerae alternately expresses smooth or rugose colonial phenotypes, the latter being associated with advanced biofilm architecture and greater resistance to ecological stress. To define phase variation at the transcriptomic level in pandemic V. cholerae O1 El Tor strain N16961, we compared the RNA-seq-derived transcriptomes among the smooth parent N16961, its rugose derivative (N16961R) and a smooth form obtained directly from the rugose at high frequencies consistent with phase variation (N16961SD). Results: Differentially regulated genes which clustered into co-expression groups were identified for specific cellular functions, including acetate metabolism, gluconeogenesis, and anaerobic respiration, suggesting an important link between these processes and biofilm formation in this species. Principal component analysis separated the transcriptome of N16961SD from the other phase variants. Although N16961SD was defective in biofilm formation, transcription of its biofilm-related vps and rbm gene clusters was nevertheless elevated as judged by both RNA-seq and RT-qPCR analyses. This transcriptome signature was shared with N16961R, as were others involving two-component signal transduction, chemotaxis, and c-di-GMP synthesis functions. Conclusions: Precise turnarounds in gene expression did not accompany reversible phase transitions (i.e., smooth to rugose to smooth) in the cholera pathogen. Transcriptomic signatures consisting of up-regulated genes involved in biofilm formation, environmental sensing and persistence, chemotaxis, and signal transduction, which were shared by N16961R and N16961SD variants, may implicate a stress adaptation in the pathogen that facilitates transition of the N16961SD smooth form back to rugosity should environmental conditions dictate
Methane emissions in East Asia for 2000-2011 estimated using an atmospheric Bayesian inversion
Abstract We present methane (CH4) emissions for East Asia from a Bayesian inversion of CH4 mole fraction and stable isotope (ÎŽ13C-CH4) measurements. Emissions were estimated at monthly resolutio
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Reference-dependent analysis of capital structure and REIT performance
Using prospect theory, we develop a theoretical framework to examine the relationship between leverage and Real Estate Investment Trust (REIT) returns by introducing the concept of reference point. We postulate that firmsâ capital structure decisions are affected by target leverage (i.e., the reference point) as well as the observed leverage. Market conditions combined with firmsâ capital structure will put firms in either loss or gain domains, where firms behave differently. In general, the leverage-return relationship is positive in the gain domain and negative in the loss domain. Firms are then subject to asymmetric risk preference in different domains. Our empirical evidence shows strong support for the theoretical model. Compared to the conventional approach where only observed leverage is used, our model is more flexible and realistic in revealing the underlying structure of the leverageâreturns relationship.We are grateful for financial support from the National Natural Science Foundation of China (Project #71231005) and the Senior Membersâ Research Grant from Newnham College, University of Cambridge
LSST: from Science Drivers to Reference Design and Anticipated Data Products
(Abridged) We describe here the most ambitious survey currently planned in
the optical, the Large Synoptic Survey Telescope (LSST). A vast array of
science will be enabled by a single wide-deep-fast sky survey, and LSST will
have unique survey capability in the faint time domain. The LSST design is
driven by four main science themes: probing dark energy and dark matter, taking
an inventory of the Solar System, exploring the transient optical sky, and
mapping the Milky Way. LSST will be a wide-field ground-based system sited at
Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m
effective) primary mirror, a 9.6 deg field of view, and a 3.2 Gigapixel
camera. The standard observing sequence will consist of pairs of 15-second
exposures in a given field, with two such visits in each pointing in a given
night. With these repeats, the LSST system is capable of imaging about 10,000
square degrees of sky in a single filter in three nights. The typical 5
point-source depth in a single visit in will be (AB). The
project is in the construction phase and will begin regular survey operations
by 2022. The survey area will be contained within 30,000 deg with
, and will be imaged multiple times in six bands, ,
covering the wavelength range 320--1050 nm. About 90\% of the observing time
will be devoted to a deep-wide-fast survey mode which will uniformly observe a
18,000 deg region about 800 times (summed over all six bands) during the
anticipated 10 years of operations, and yield a coadded map to . The
remaining 10\% of the observing time will be allocated to projects such as a
Very Deep and Fast time domain survey. The goal is to make LSST data products,
including a relational database of about 32 trillion observations of 40 billion
objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures
available from https://www.lsst.org/overvie
Coping with stress: a pilot study of a self-help stress management intervention for patients with epileptic or psychogenic non-epileptic seizures
Purpose: Many patients with epilepsy or psychogenic non-epileptic seizures (PNES) experience high levels of stress. Although psychological interventions have been developed for seizure disorders, few patients can currently access them. We aimed to assess the acceptability and feasibility of a self-help intervention targeting stress in patients with seizures, and to provide preliminary evidence for its effectiveness.
Method: Patients were recruited from outpatient neurology clinics and randomised to an immediate intervention group (n=39), who received the intervention at baseline, or a delayed intervention group (n=43), who received the intervention one month post-baseline. Participants completed self-report questionnaires measuring stress (SSSI), anxiety (GAD-7), depression (NDDI-E), quality of life (EQ-5D), seizure severity and frequency (LSSS-3) at baseline, and at one- and two-month follow-up. Participants also provided telephone feedback. The intervention consisted of a self-help stress management workbook based on an integrative stress model framework.
Results: Although the rate of participants failing to return follow-up information at two months was approximately 50%, those who completed the trial found the intervention acceptable; with the majority rating it as helpful (63.6%) and that they would recommend it to others with seizures (88.1%). A significant reduction in self-reported stress (p = 0.01) with a medium effect size (dz = 0.51) was observed one-month post-intervention. There were no significant changes in any other measures.
Conclusion: The intervention was perceived to be acceptable, safe and helpful by participants. It could be a useful complementary treatment option for reducing stress experienced by patients living with seizure disorders. Further evaluation in a larger trial is warranted
Spintronics: Fundamentals and applications
Spintronics, or spin electronics, involves the study of active control and
manipulation of spin degrees of freedom in solid-state systems. This article
reviews the current status of this subject, including both recent advances and
well-established results. The primary focus is on the basic physical principles
underlying the generation of carrier spin polarization, spin dynamics, and
spin-polarized transport in semiconductors and metals. Spin transport differs
from charge transport in that spin is a nonconserved quantity in solids due to
spin-orbit and hyperfine coupling. The authors discuss in detail spin
decoherence mechanisms in metals and semiconductors. Various theories of spin
injection and spin-polarized transport are applied to hybrid structures
relevant to spin-based devices and fundamental studies of materials properties.
Experimental work is reviewed with the emphasis on projected applications, in
which external electric and magnetic fields and illumination by light will be
used to control spin and charge dynamics to create new functionalities not
feasible or ineffective with conventional electronics.Comment: invited review, 36 figures, 900+ references; minor stylistic changes
from the published versio
Large-scale mapping of human proteinâprotein interactions by mass spectrometry
Mapping proteinâprotein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of proteinâprotein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24 540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel proteinâprotein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations
Some behavioral aspects of energy descent: How a biophysical psychology might help people transition through the lean times ahead
This article is part of the Research Topic: Nature and environment: The psychology of its benefits and its protection.We may soon face biophysical limits to perpetual growth. Energy supplies may tighten and then begin a long slow descent while defensive expenditures rise to address problems caused by past resource consumption. The outcome may be significant changes in daily routines at the individual and community level. It is difficult to know when this scenario might begin to unfold but it clearly would constitute a new behavioral context, one that the behavioral sciences least attends to. Even if one posits a less dramatic scenario, people may still need to make many urgent and perhaps unsettling transitions. And while a robust response would be needed, it is not at all clear what should be the details of that response. Since it is likely that no single response will fix things everywhere, for all people or for all time, it would be useful to conduct many social experiments. Indeed, a culture of small experiments should be fostered which, at the individual and small group level, can be described as behavioral entrepreneurship. This may have begun, hidden in plain sight, but more social experiments are needed. To be of help, it may be useful to both package behavioral insights in a way that is practitioner-oriented and grounded in biophysical trends and to propose a few key questions that need attention. This paper begins the process of developing a biophysical psychology, incomplete as it is at this early stage.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109261/1/De Young, R. (2014) Some behavioral aspects of energy descent, How a biophysical psychology might help people transition through the lean times ahead, Frontiers in Psychology, 5, 1255.pdfDescription of De Young, R. (2014) Some behavioral aspects of energy descent, How a biophysical psychology might help people transition through the lean times ahead, Frontiers in Psychology, 5, 1255.pdf : Main articl
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