bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the PhoB Regulon and Role of PhoU in the Phosphate Starvation Response of Caulobacter crescentus
Authors: Lubin Emma A. , Henry Jonathan T. , Fiebig Aretha , Crosson Sean , Laub Michael T. 
Published: October 2015

ABSTRACT

An ability to sense and respond to changes in extracellular phosphate is critical for the survival of most bacteria. For
Caulobacter crescentus
, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria,
Caulobacter
responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here we used chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB under phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes under phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help
Caulobacter
scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in
Caulobacter
, as PhoU depletion has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit striking accumulation of large polyphosphate granules, suggesting that PhoU participates in controlling intracellular phosphate metabolism.

IMPORTANCE
The transcription factor PhoB is widely conserved throughout the bacterial kingdom, where it helps organisms respond to phosphate limitation by driving the expression of a battery of genes. Most of what is known about PhoB and its target genes is derived from studies of
Escherichia coli
. Our work documents the PhoB regulon in
Caulobacter crescentus
, and comparison to the regulon in
E. coli
reveals significant differences, highlighting the evolutionary plasticity of transcriptional responses driven by highly conserved transcription factors. We also demonstrated that the conserved protein PhoU, which is implicated in bacterial persistence, does not regulate PhoB activity, as previously suggested. Instead, our results favor a model in which PhoU affects intracellular phosphate accumulation, possibly through the high-affinity phosphate transporter.
Dispersal from Microbial Biofilms
Authors: Barraud Nicolas , Kjelleberg Staffan , Rice Scott A. 
Published: October 2015

ABSTRACT
One common feature of biofilm development is the active dispersal of cells from the mature biofilm, which completes the biofilm life cycle and allows for the subsequent colonization of new habitats. Dispersal is likely to be critical for species survival and appears to be a precisely regulated process that involves a complex network of genes and signal transduction systems. Sophisticated molecular mechanisms control the transition of sessile biofilm cells into dispersal cells and their coordinated detachment and release in the bulk liquid. Dispersal cells appear to be specialized and exhibit a unique phenotype different from biofilm or planktonic bacteria. Further, the dispersal population is characterized by a high level of heterogeneity, reminiscent of, but distinct from, that in the biofilm, which could potentially allow for improved colonization under various environmental conditions. Here we review recent advances in characterizing the molecular mechanisms that regulate biofilm dispersal events and the impact of dispersal in a broader ecological context. Several strategies that exploit the mechanisms controlling biofilm dispersal to develop as applications for biofilm control are also presented.
Interrupting transmission of soil-transmitted helminths: a study protocol for cluster randomised trials evaluating alternative treatment strategies and delivery systems in Kenya
Authors: Brooker Simon J , Mwandawiro Charles S , Halliday Katherine E , Njenga Sammy M , Mcharo Carlos , Gichuki Paul M , Wasunna Beatrice , Kihara Jimmy H , Njomo Doris , Alusala Dorcas , Chiguzo Athuman , Turner Hugo C , Teti Caroline , Gwayi-Chore Claire , Nikolay Birgit , Truscott James E , Hollingsworth T Déirdre , Balabanova Dina , Griffiths Ulla K , Freeman Matthew C , Allen Elizabeth , Pullan Rachel L , Anderson Roy M 
Published: October 2015

IntroductionIn recent years, an unprecedented emphasis has been given to the control of neglected tropical diseases, including soil-transmitted helminths (STHs). The mainstay of STH control is school-based deworming (SBD), but mathematical modelling has shown that in all but very low transmission settings, SBD is unlikely to interrupt transmission, and that new treatment strategies are required. This study seeks to answer the question: is it possible to interrupt the transmission of STH, and, if so, what is the most cost-effective treatment strategy and delivery system to achieve this goal?Methods and analysisTwo cluster randomised trials are being implemented in contrasting settings in Kenya. The interventions are annual mass anthelmintic treatment delivered to preschool- and school-aged children, as part of a national SBD programme, or to entire communities, delivered by community health workers. Allocation to study group is by cluster, using predefined units used in public health provision—termed community units (CUs). CUs are randomised to one of three groups: receiving either (1) annual SBD; (2) annual community-based deworming (CBD); or (3) biannual CBD. The primary outcome measure is the prevalence of hookworm infection, assessed by four cross-sectional surveys. Secondary outcomes are prevalence ofAscaris lumbricoidesandTrichuris trichiura, intensity of species infections and treatment coverage. Costs and cost-effectiveness will be evaluated. Among a random subsample of participants, worm burden and proportion of unfertilised eggs will be assessed longitudinally. A nested process evaluation, using semistructured interviews, focus group discussions and a stakeholder analysis, will investigate the community acceptability, feasibility and scale-up of each delivery system.Ethics and disseminationStudy protocols have been reviewed and approved by the ethics committees of the Kenya Medical Research Institute and National Ethics Review Committee, and London School of Hygiene and Tropical Medicine. The study has a dedicated web site.Trial registration numberNCT02397772.
Expectations and perceptions of care among victims of sexual assault who first seek care from emergency, primary care and gynaecological doctors
Authors: Denis Céline , Seyller Marie , Chariot Patrick 
Published: October 2015

BackgroundThe role of health professionals is pivotal in providing support to victims of sexual assault. Our aim was to identify patient expectations of doctors after a sexual assault and to assess how they rated the doctors’ responses.MethodsWe conducted a prospective observational study (May 2010–December 2012) involving victims of sexual assault (age >10 years) in a Department of Forensic Medicine near Paris, France. The patients included were those who had first sought care from a doctor prior to arriving at the Department of Forensic Medicine. Victims were asked by questionnaire and interviewed by the forensic physician about medical consultations before arriving at the Department, their expectations about those consultations and their feelings about the quality of support provided. Each patient's feelings were rated on a five-point scale.ResultsAmong 1112 victims reporting sexual assault, 232 previously had a consultation, and were included in the study. Patients expected trauma care in 44% of cases, and received it in 40% (p=0.42), psychological support in 31% of cases, and received it in 21% (p=0.02), gynaecological care in 28%, and received it in 31% (p=0.52) and forensic support in 21%, and received it in 54% (p<0.001). The patients more frequently considered the provided support to be crucial when they received both forensic support and trauma care, psychological support or gynaecological care than when they only received trauma care, psychological support or gynaecological care (25% vs 3%, p=0.001).ConclusionsPhysicians who are the first medical provider to see a patient after a sexual assault often fail to meet patients’ expectations, particularly with regard to psychological support. Care received was perceived as best when physicians provided both forensic support and trauma care, psychological support or gynaecological care.
Leptospirosis acquisition following the reintroduction of wildlife
Authors: Gelling M. , Zochowski W. , Macdonald D. W. , Johnson A. , Palmer M. , Mathews F. 
Published: October 2015

Potential risks posed to domestic animals and human beings by zoonotic diseases in reintroduced animals can reduce the acceptability of reintroductions. The authors investigated the role of endangered water voles, Arvicola amphibius, as a host for leptospirosis, a waterborne zoonosis affecting a range of mammals. Based on samples from 112 individuals from across the UK, a 6.2 per cent exposure rate was found (7 animals were microscopic agglutination test (MAT) positive for serum antibodies), with 4 of 11 sites having positive animals. No individual was actively excreting leptospires in urine (PCR urine test, 0 per cent positive). The acquisition of Leptospira species by a cohort of ‘clean’ captive‐bred voles reintroduced to one site in the wild was then examined. By four months postrelease the maximum exposure prevalence (by either MAT or culture) was 42.9 per cent. Thirty‐five per cent were actively excreting leptospires. The rapidity of leptospire acquisition and comparatively high prevalence of infectious individuals is notable, exceeding expectation based on wild voles. One possible explanation is a lack of immunocompetence in reintroduced voles. Analyses of haematological parameters from reintroduced voles suggest a link between prior condition and disease acquisition. There may be potential to select the fittest animals before release to maximise reintroduction success.
Inflation with non-minimally derivative coupling
Authors: Yang Nan , Gao Qing , Gong Yungui 
Published: October 2015

We derive the second order correction to the scalar and tensor spectral tilts for the inflationary models with non-minimally derivative coupling. In the high friction limit, the quartic power law potential is consistent with the observational constraint at 95% CL because the amplitude of the primordial gravitational waves is smaller, and the inflaton excursion is sub-Planckian.
Petrographic characteristics of intrusive rocks as an evaluation tool of their technical properties
Authors: Johansson Eva , Miškovský Karel , Bergknut Magnus , Šachlová Šárka 
Published: October 2015

Abstract
The main petrographic variables of intrusive rocks that influence the technical test methods common used within the aggregate industry were identified and evaluated, the aim being to investigate whether petrographic description could be used as a tool for the preliminary quality evaluation of different rock groups. Evaluation of the dependence of the technical test methods on petrographic variables covered 26 intrusive rocks, including some of their altered varieties (orthogneisses), divided into two groups: 17 granitoids and 9 gabbroids. The selective designated samples were analysed to determine their petrographic characteristics and resistance to fragmentation, wear and wear by abrasion from studded tyres. In order to identify the complicated associations between the petrographic and technical properties, multivariate statistical evaluation was performed. The results of statistical evaluation highlighted that mean grain size of mica minerals, grain size distribution, content of mica minerals and mean grain size were the main variables influencing the technical properties of granitoid rocks, while for gabbroid rocks, the main influences were the frequency of microcracks, mica content, grain size distribution and mean grain size.
c-Myc Alterations Confer Therapeutic Response and Acquired Resistance to c-Met Inhibitors in MET-Addicted Cancers
Authors: Shen Aijun , Wang Lu , Huang Min , Sun Jingya , Chen Yi , Shen Yan-Yan , Yang Xinying , Wang Xin , Ding Jian , Geng Meiyu 
Published: October 2015

Abstract
Use of kinase inhibitors in cancer therapy leads invariably to acquired resistance stemming from kinase reprogramming. To overcome the dynamic nature of kinase adaptation, we asked whether a signal-integrating downstream effector might exist that provides a more applicable therapeutic target. In this study, we reported that the transcriptional factor c-Myc functions as a downstream effector to dictate the therapeutic response to c-Met inhibitors in c-Met–addicted cancer and derived resistance. Dissociation of c-Myc from c-Met control, likely overtaken by a variety of reprogrammed kinases, led to acquisition of drug resistance. Notably, c-Myc blockade by RNA interference or pharmacologic inhibition circumvented the acquired resistance to c-Met inhibition. Combining c-Myc blockade and c-Met inhibition in MET-amplified patient-derived xenograft mouse models heightened therapeutic activity. Our findings offer a preclinical proof of concept for the application of c-Myc–blocking agents as a tactic to thwart resistance to kinase inhibitors. Cancer Res; 75(21); 4548–59. ©2015 AACR.
ST-Segment Elevation and Fractionated Electrograms in Brugada Syndrome Patients Arise From the Same Structurally Abnormal Subepicardial RVOT Area but Have a Different Mechanism
Authors: ten Sande Judith N. , Coronel Ruben , Conrath Chantal E. , Driessen Antoine H.G. , de Groot Joris R. , Tan Hanno L. , Nademanee Koonlawee , Wilde Arthur A.M. , de Bakker Jacques M.T. , van Dessel Pascal F.H.M. 
Published: October 2015

Background—
Brugada syndrome (BrS) is characterized by a typical ECG pattern. We aimed to determine the pathophysiologic basis of the ST-segment in the BrS-ECG with data from various epicardial and endocardial right ventricular activation mapping procedures in 6 BrS patients and in 5 non-BrS controls.

Methods and Results—
In 7 patients (2 BrS and 5 controls) with atrial fibrillation, an epicardial 8×6 electrode grid (interelectrode distance 1 mm) was placed epicardially on the right ventricular outflow tract (RVOT) before video-assisted thoracoscopic surgical pulmonary vein isolation. In 2 other BrS patients, endocardial, epicardial RV (CARTO), and body surface mapping was performed. In 2 additional BrS patients, we performed decremental preexcitation of the RVOT before endocardial RV mapping. During video-assisted thoracoscopic surgical pulmonary vein isolation and CARTO mapping, BrS patients (n=4) showed greater activation delay and more fractionated electrograms in the RVOT region than controls. Ajmaline administration increased the region with fractionated electrograms, as well as ST-segment elevation. Preexcitation of the RVOT (n=2) resulted in ECGs that supported the current-to-load mismatch hypothesis for ST-segment elevation. Body surface mapping showed that the area with ST-segment elevation anatomically correlated with the area of fractionated electrograms and activation delay at the RVOT epicardium.

Conclusions—
ST-segment elevation and epicardial fractionation/conduction delay in BrS patients are most likely related to the same structural subepicardial abnormalities, but the mechanism is different. ST-segment elevation may be caused by current-to-load mismatch, whereas fractionated electrograms and conduction delay are expected to be caused by discontinuous conduction in the same area with abnormal myocardium.
Adjusting for Risk Associated With Pediatric and Congenital Cardiac Catheterization
Authors: Jayaram Natalie , Beekman Robert H. , Benson Lee , Holzer Ralf , Jenkins Kathy , Kennedy Kevin F. , Martin Gerard R. , Moore John W. , Ringel Richard , Rome Jonathan , Spertus John A. , Vincent Robert , Bergersen Lisa 
Published: October 2015

Background—
As US health care increasingly focuses on outcomes as a means for quantifying quality, there is a growing demand for risk models that can account for the variability of patients treated at different hospitals so that equitable comparisons between institutions can be made. We sought to apply aspects of prior risk-standardization methodology to begin development of a risk-standardization tool for the National Cardiovascular Data Registry (NCDR) IMPACT (Improving Pediatric and Adult Congenital Treatment) Registry.

Methods and Results—
Using IMPACT, we identified all patients undergoing diagnostic or interventional cardiac catheterization between January 2011 and March 2013. Multivariable hierarchical logistic regression was used to identify patient and procedural characteristics predictive of experiencing a major adverse event after cardiac catheterization. A total of 19 608 cardiac catheterizations were performed between January 2011 and March 2013. Among all cases, a major adverse event occurred in 378 of all cases (1.9%). After multivariable adjustment, 8 variables were identified as critical for risk standardization: patient age, renal insufficiency, single-ventricle physiology, procedure-type risk group, low systemic saturation, low mixed venous saturation, elevated systemic ventricular end-diastolic pressure, and elevated main pulmonary artery pressures. The model had good discrimination (C statistic, 0.70), confirmed by bootstrap validation (validation C statistic, 0.69).

Conclusions—
Using prior risk-standardization efforts as a foundation, we developed and internally validated a model to predict the occurrence of a major adverse event after cardiac catheterization for congenital heart disease. Future efforts should be directed toward further refinement of the model variables within this large, multicenter data set.
Notes on Carex (Cyperaceae) from China (III): the description of four new species
Authors: Jin Xiao-Feng , CHEN WEI-JIE , CEN JIA-MENG 
Published: October 2015

Carex scopulus, C. bamaensis, C. pararadicalis and C. tingnungii, four new species from China, are described with illustrations in the present paper. Carex scopulus is similar to C. chungii (sect. Mitratae) in having achenes with angles constricted at the middle, but differs by having pistillate scales pale reddish brown and acuminate at apex, staminate scales reddish brown, and perigynia glabrous. Carex bamaensis is similar to C. lancifolia (sect. Clandestinae) in having culms lateral and leaf blades 2.5–6 mm wide, but differs in having culms, leaves and bracts all pilose, and pistillate spikes fairly densely flowered. Carex pararadicalis resembles C. handelii (sect. Chlorostachyae) in having rhizomes long and creeping, but differs by having the terminal spike gynecandrous, lateral spikes pistillate, and pistillate scales obtuse at apex and shorter than the perigynia. Carex tingnungii resembles C. plectobasis (subsect. Ferrugineae) in having 3 stigmas and perigynia that are compressed trigonous and densely whitish hispidulous, but differs in having a solitary staminate spike with 1–4 pistillate flowers at the base, achenes oblong-ellipsoid, and styles that are densely crisped-pilose.
Coreopsis bakeri (Asteraceae; Coreopsideae), a new species from Florida, USA
Authors: Schilling Edward E. , Johnson Ann F. , Iacona Gwenllian D. 
Published: October 2015

Coreopsis bakeri (Asteraceae; Coreopsideae), an early blooming and very narrow-leaved perennial restricted to rare limestone glade habitats in northern Florida, is described as new. The plants most closely resemble Coreopsis lanceolata, a common species of the southeastern U.S., but have narrower, glabrous, and infolded leaves. In addition to phenotypic differences, the two species show divergence at two nuclear genes, the nuclear ITS and ETS regions, and for two chloroplast intergenic spacers (psbA-trnH and rpl32-trnL). Because of the rarity of C. bakeri and the very limited extent of its distinctive habitat, this species is in urgent need of protection. In addition, C. lanceolata is found in open areas near the limestone glades, and poses a potential threat through competition or hybridization.
Impact of Soil Moisture Assimilation on Land Surface Model Spinup and Coupled Land–Atmosphere Prediction
Authors: Santanello Joseph A. , Kumar Sujay V. , Peters-Lidard Christa D. , Lawston Patricia M. 
Published: October 2015

Abstract
Advances in satellite monitoring of the terrestrial water cycle have led to a concerted effort to assimilate soil moisture observations from various platforms into offline land surface models (LSMs). One principal but still open question is that of the ability of land data assimilation (LDA) to improve LSM initial conditions for coupled short-term weather prediction. In this study, the impact of assimilating Advanced Microwave Scanning Radiometer for EOS (AMSR-E) soil moisture retrievals on coupled WRF Model forecasts is examined during the summers of dry (2006) and wet (2007) surface conditions in the southern Great Plains. LDA is carried out using NASA’s Land Information System (LIS) and the Noah LSM through an ensemble Kalman filter (EnKF) approach. The impacts of LDA on the 1) soil moisture and soil temperature initial conditions for WRF, 2) land–atmosphere coupling characteristics, and 3) ambient weather of the coupled LIS–WRF simulations are then assessed. Results show that impacts of soil moisture LDA during the spinup can significantly modify LSM states and fluxes, depending on regime and season. Results also indicate that the use of seasonal cumulative distribution functions (CDFs) is more advantageous compared to the traditional annual CDF bias correction strategies. LDA performs consistently regardless of atmospheric forcing applied, with greater improvements seen when using coarser, global forcing products. Downstream impacts on coupled simulations vary according to the strength of the LDA impact at the initialization, where significant modifications to the soil moisture flux–PBL–ambient weather process chain are observed. Overall, this study demonstrates potential for future, higher-resolution soil moisture assimilation applications in weather and climate research.