bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteriophage PhiX174's Ecological Niche and the Flexibility of Its
Escherichia coli
Lipopolysaccharide Receptor
Authors: Michel Alix , Clermont Olivier , Denamur Erick , Tenaillon Olivier 
Published: September 2010

ABSTRACT

To determine bacteriophage PhiX174's ecological niche, 783
Escherichia coli
isolates were screened for susceptibility. Sensitive strains are diverse regarding their phylogenies and core lipopolysaccharides (LPS), but all have rough phenotypes. Further analysis of
E. coli
K-12 LPS mutants revealed that PhiX174 can use a wide diversity of LPS structures to initiate its infectious process.
Anaerobic Expression of the Ferredoxin-Encoding
FDX5
Gene of Chlamydomonas reinhardtii Is Regulated by the Crr1 Transcription Factor
Authors: Lambertz Camilla , Hemschemeier Anja , Happe Thomas 
Published: September 2010

ABSTRACT

The unicellular green alga
Chlamydomonas reinhardtii
has a complex anaerobic metabolism and reacts to hypoxic or anaerobic conditions with the induced expression of many genes. One gene which is upregulated particularly strongly is the
FDX5
gene, encoding one of at least six ferredoxin isoforms in
C. reinhardtii
. Fdx5 is a typical plant-type 2Fe2S protein that is located in the chloroplast. The
FDX5
promoter region contains three GTAC motifs, which are known to be the binding sites for copper response regulator 1 (Crr1) and other
SQUAMOSA
promoter binding proteins (SBPs). This study shows that two of these GTAC sites are essential to confer oxygen and also copper responsiveness to a reporter gene. The SBP domain of Crr1 is able to bind to both of these GTAC sites in
in vitro
binding assays. Moreover, in a Crr1-deficient
C. reinhardtii
strain,
FDX5
is not expressed. These results clearly indicate that Crr1 is involved in the transcriptional regulation of the
FDX5
gene in the absence of oxygen or copper.
Glycosylation of Pilin and Nonpilin Protein Constructs byPseudomonas aeruginosa1244
Authors: Qutyan Mohammed , Henkel Matthew , Horzempa Joseph , Quinn Michael , Castric Peter 
Published: September 2010

ABSTRACTPilO is an oligosaccharyl transferase (OTase) that catalyzes the O-glycosylation ofPseudomonas aeruginosa1244 pilin by adding a single O-antigen repeating unit to the β carbon of the C-terminal residue (a serine). While PilO has an absolute requirement for Ser/Thr at this position, it is unclear if this enzyme must recognize other pilin features. To test this, pilin constructs containing peptide extensions terminating with serine were tested for the ability to support glycosylation. It was found that a 15-residue peptide, which had been modeled on the C-proximal region of strain 1244 pilin, served as a PilO substrate when it was expressed on either group II or group III pilins. In addition, adding a 3-residue extension culminating in serine to the C terminus of a group III pilin supported PilO activity. A protein fusion composed of strain 1244 pilin linked at its C terminus withEscherichia colialkaline phosphatase (which, in turn, contained the above-mentioned 15 amino acids at its C terminus) was glycosylated by PilO.E. colialkaline phosphatase lacking the pilin membrane anchor and containing the 15-residue peptide was also glycosylated by PilO. Addition of the 3-residue extension did not allow glycosylation of either of these constructs. Site-directed mutagenesis of strain 1244 pilin residues of the C-proximal region common to the group I proteins showed that this structure was not required for glycosylation. These experiments indicate that pilin common sequence is not required for glycosylation and show that nonpilin protein can be engineered to be a PilO substrate.
Evidence that thesupE44Mutation ofEscherichia coliIs an Amber Suppressor Allele ofglnXand that It Also Suppresses Ochre and Opal Nonsense Mutations
Authors: Singaravelan B. , Roshini B. R. , Munavar M. Hussain 
Published: September 2010

ABSTRACTTranslational readthrough of nonsense codons is seen not only in organisms possessing one or more tRNA suppressors but also in strains lacking suppressors. Amber suppressor tRNAs have been reported to suppress only amber nonsense mutations, unlike ochre suppressors, which can suppress both amber and ochre mutations, essentially due to wobble base pairing. In anEscherichia colistrain carrying thelacZU118episome (an ochre mutation in thelacZgene) and harboring thesupE44allele, suppression of the ochre mutation was observed after 7 days of incubation. The presence of thesupE44lesion in the relevant strains was confirmed by sequencing, and it was found to be in the duplicate copy of theglnVtRNA gene,glnX. To investigate this further, anin vivoluciferase assay developed by D. W. Schultz and M. Yarus (J. Bacteriol. 172:595-602, 1990) was employed to evaluate the efficiency of suppression of amber (UAG), ochre (UAA), and opal (UGA) mutations bysupE44. We have shown here thatsupE44suppresses ochre as well as opal nonsense mutations, with comparable efficiencies. The readthrough of nonsense mutations in a wild-typeE. colistrain was much lower than that in asupE44strain when measured by the luciferase assay. Increased suppression of nonsense mutations, especially ochre and opal, bysupE44was found to be growth phase dependent, as this phenomenon was only observed in stationary phase and not in logarithmic phase. These results have implications for the decoding accuracy of the translational machinery, particularly in stationary growth phase.
Functional Characterization of a Cyanobacterial OmpR/PhoB Class Transcription Factor Binding Site Controlling Light Color Responses
Authors: Bezy Ryan P. , Kehoe David M. 
Published: September 2010

ABSTRACT

Complementary chromatic acclimation (CCA) allows many cyanobacteria to change the composition of their light-harvesting antennae for maximal absorption of different wavelengths of light. In the freshwater species
Fremyella diplosiphon
, this process is controlled by the ratio of red to green light and allows the differential regulation of two subsets of genes in the genome. This response to ambient light color is controlled in part by a two-component system that includes a phytochrome class photoreceptor and a response regulator with an OmpR/PhoB class DNA binding domain called RcaC. During growth in red light, RcaC is able to simultaneously activate expression of red light-induced genes and repress expression of green light-induced genes through binding to the L box promoter element. Here we investigate how the L box functions as both an activator and a repressor under the same physiological conditions by analyzing the effects of changing the position, orientation, and sequence of the L box. We demonstrate that changes in the local sequences surrounding the L box affect the strength of its activity and that the activating and repressing functions of the L box are orientation dependent. Also, the spacing between the L box and the transcription start site is critical for it to work as an activator, while its repressing role during light regulation requires additional upstream and downstream DNA sequence elements. The latter result suggests that the repressing function of RcaC requires it to operate in association with multiple additional DNA binding proteins, at least one of which is functioning as an activator.
SepL Resembles an Aberrant Effector in Binding to a Class 1 Type III Secretion Chaperone and Carrying an N-Terminal Secretion Signal
Authors: Younis Rasha , Bingle Lewis E. H. , Rollauer Sarah , Munera Diana , Busby Stephen J. , Johnson Steven , Deane Janet E. , Lea Susan M. , Frankel Gad , Pallen Mark J. 
Published: September 2010

ABSTRACTHere we show that the type III secretion gatekeeper protein SepL resembles an aberrant effector protein in binding to a class 1 type III secretion chaperone (Orf12, here renamed CesL). We also show that short N-terminal fragments (≤70 amino acids) from SepL are capable of targeting fusion proteins for secretion and translocation.
Genistein alters coagulation gene expression in ovariectomised rats treated with phytoestrogens
Authors: Kelly Lynne A. , O’Leary John J. , Seidlova-Wuttke Dana , Wuttke Wolfgang , Norris Lucy A. 
Published: September 2010

SummaryRecent data has shown that hormone therapy (HT) increases the risk of cardiovascular and thromboembolic disease, particularly in users of oral HT. Phytoestrogens are popular alternatives to oestrogen therapy; however, their effects on cardiovascular risk are unknown. We investigated the effect of the phytoestrogen, genistein on the expression of genes and proteins from the haemostatic system in the liver in an ovariectomised rat model. Fifty-nine virgin female Sprague-Dawley rats were fed with soy-free chow supplemented with 17β estradiol (E2) (daily uptake 0.19 or 0.75 mg/kg body weight), or genistein (daily up-take 6 or 60 mg/kg body weight), for three months and compared to soy-free control rats. Gene expression of prothrombin, factor VII, fibrinogen alpha and fibrinogen beta was increased with E2 and genistein compared to the soy-free control group (p<0.001). Genistein increased factor VII significantly more than E2 (p<0.005). Plasminogen mRNA was increased in both treatment groups compared to the soy-free control, with genistein expression significantly higher than E2 (p<0.001). Tissue plasminogen inhibitor (tPA), plasminogen activator inhibitor-1 (PAI-1) and C-reactive protein (CRP) expression were also increased in both groups relative the soy-free control. Results of protein analysis largely concurred with those of the mRNA. Oestrogen receptor β (ERβ) was undetected while oestrogen receptor α (ERα) was detected in each sample group. Genistein can increase the expression of coagulation and fibrinolytic genes. This effect was similar and in some cases higher than 17β estradiol. These results suggest that genistein may not be neutral with respect to the haemostatic system.
The inter-rater reliability of the Pulmonary Embolism Severity Index
Authors: Fraga Montserrat , Taffé Patrick , Méan Marie , Hugli Olivier , Witzig Stéphanie , Waeber Gérard , Aujesky Drahomir 
Published: September 2010

SummaryThe Pulmonary Embolism Severity Index (PESI) is a validated clinical prognostic model for patients with acute pulmonary embolism (PE). Our goal was to assess the PESI’s inter-rater reliability in patients diagnosed with PE. We prospectively identified consecutive patients diagnosed with PE in the emergency department of a Swiss teaching hospital. For all patients, resident and attending physician raters independently collected the 11 PESI variables. The raters then calculated the PESI total point score and classified patients into one of five PESI risk classes (I-V) and as low (risk classes I/II) versus higher-risk (risk classes III-V). We examined the inter-rater reliability for each of the 11 PESI variables, the PESI total point score, assignment to each of the five PESI risk classes, and classification of patients as low versus higher-risk using kappa (κ) and intra-class correlation coefficients (ICC). Among 48 consecutive patients with an objective diagnosis of PE, reliability coefficients between resident and attending physician raters were > 0.60 for 10 of the 11 variables comprising the PESI. The inter-rater reliability for the PESI total point score (ICC: 0.89, 95% CI: 0.81–0.94), PESI risk class assignment (κ: 0.81, 95% CI: 0.66–0.94), and the classification of patients as low versus higher-risk (κ: 0.92, 95% CI: 0.72–0.98) was near perfect. Our results demonstrate the high reproducibility of the PESI, supporting the use of the PESI for risk stratification of patients with PE.
Ventricular Remodeling and Survival Are More Favorable for Myocarditis Than For Idiopathic Dilated Cardiomyopathy in Childhood
Authors: Foerster Susan R. , Canter Charles E. , Cinar Amy , Sleeper Lynn A. , Webber Steven A. , Pahl Elfriede , Kantor Paul F. , Alvarez Jorge A. , Colan Steven D. , Jefferies John L. , Lamour Jacqueline M. , Margossian Renee , Messere Jane E. , Rusconi Paolo G. , Shaddy Robert E. , Towbin Jeffrey A. , Wilkinson James D. , Lipshultz Steven E. 
Published: September 2010

Background—
Myocarditis is a cause of a new-onset dilated cardiomyopathy phenotype in children, with small studies reporting high rates of recovery of left ventricular (LV) function.

Methods and Results—

The presenting characteristics and outcomes of children with myocarditis diagnosed clinically and with biopsy confirmation (n=119) or with probable myocarditis diagnosed clinically or by biopsy alone (n=253) were compared with children with idiopathic dilated cardiomyopathy (n=1123). Characteristics at presentation were assessed as possible predictors of outcomes. The distributions of time to death, transplantation, and echocardiographic normalization in the biopsy-confirmed myocarditis and probable myocarditis groups did not differ (
P
≥0.5), but both groups differed significantly from the idiopathic dilated cardiomyopathy group (all
P
≤0.003). In children with myocarditis, lower LV fractional shortening
z
-score at presentation predicted greater mortality (hazard ratio, 0.85; 95% confidence interval, 0.73 to 0.98;
P
=0.03) and greater LV posterior wall thickness predicted transplantation (hazard ratio, 1.17; 95% confidence interval, 1.02 to 1.35;
P
=0.03). In those with decreased LV fractional shortening at presentation, independent predictors of echocardiographic normalization were presentation with an LV end-diastolic dimension
z
-score >2 (hazard ratio, 0.36; 95% confidence interval, 0.22 to 0.58;
P
<0.001) and greater septal wall thickness (hazard ratio, 1.16; 95% confidence interval, 1.01 to 1.34;
P
=0.04).

Conclusions—
Children with biopsy-confirmed or probable myocarditis had similar proportions of death, transplantation, and echocardiographic normalization 3 years after presentation and better outcomes than those of children with idiopathic dilated cardiomyopathy. In children with myocarditis who had impaired LV ejection at presentation, rates of echocardiographic normalization were greater in those without LV dilation and in those with greater septal wall thickness at presentation.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00005391.
The Codex of a Companion of the Prophet and the Qurān of the Prophet
Authors: Sadeghi Behnam , Bergmann Uwe 
Published: September 2010

AbstractThe essay discusses a manuscript of the Qurān dating from the first half of the seventh century AD. The text does not belong to the Utmānic textual tradition, making this the only known manuscript of a non-Utmānic text type. The essay compares this text type with those of the Utmānic and other Companion textual traditions in order to shed light on the Prophetic prototype.
Conditional Threats
Authors: Øverland Gerhard 
Published: September 2010

AbstractIn this paper I ponder the moral status of conditional threats, in particular the extent to which a threatened party would be permitted to use (lethal) defensive force. I first investigate a mugger case before turning briefly to the more complicated issue of national defence in the face of an invading army. One should not exaggerate the level of protection people under threat owe their conditioned killers simply because what is extorted is of little value. After all, either the conditional threat is willing to kill for something she has no claim on at all, or, if she has a just claim on it – or good reason to believe that she has – she is willing to kill to (re)acquire something of not much worth. In both cases the moral culpability of the conditional threat could be seen as reducing her claim on protection from harm.
Local-Scale Urban Meteorological Parameterization Scheme (LUMPS): Longwave Radiation Parameterization and Seasonality-Related Developments
Authors: Loridan Thomas , Grimmond C. S. B. , Offerle Brian D. , Young Duick T. , Smith Thomas E. L. , Järvi Leena , Lindberg Fredrik 
Published: September 2010

Abstract
Recent developments to the Local-scale Urban Meteorological Parameterization Scheme (LUMPS), a simple model able to simulate the urban energy balance, are presented. The major development is the coupling of LUMPS to the Net All-Wave Radiation Parameterization (NARP). Other enhancements include that the model now accounts for the changing availability of water at the surface, seasonal variations of active vegetation, and the anthropogenic heat flux, while maintaining the need for only commonly available meteorological observations and basic surface characteristics. The incoming component of the longwave radiation (L↓) in NARP is improved through a simple relation derived using cloud cover observations from a ceilometer collected in central London, England. The new L↓ formulation is evaluated with two independent multiyear datasets (Łódź, Poland, and Baltimore, Maryland) and compared with alternatives that include the original NARP and a simpler one using the National Climatic Data Center cloud observation database as input. The performance for the surface energy balance fluxes is assessed using a 2-yr dataset (Łódź). Results have an overall RMSE &lt; 34 W m−2 for all surface energy balance fluxes over the 2-yr period when using L↓ as forcing, and RMSE &lt; 43 W m−2 for all seasons in 2002 with all other options implemented to model L↓.
Can Global Warming Strengthen the East Asian Summer Monsoon?
Authors: Li Jianping , Wu Zhiwei , Jiang Zhihong , He Jinhai 
Published: September 2010

Abstract
The Indian summer monsoon (ISM) tends to be intensified in a global-warming scenario, with a weakened linkage with El Niño–Southern Oscillation (ENSO), but how the East Asian summer monsoon (EASM) responds is still an open question. This study investigates the responses of the EASM from observations, theoretical, and modeling perspectives. Observational and theoretical evidence demonstrates that, in contrast to the dramatic global-warming trend within the past 50 years, the regional-mean EASM rainfall is basically dominated by considerable interannual-to-decadal fluctuations, concurrent with enhanced precipitation over the middle and lower reaches of the Yangtze River and over southern Japan and suppressed rainfall amount over the South China and Philippine Seas. From 1958 through 2008, the EASM circulation exhibits a southward shift in its major components (the subtropical westerly jet stream, the western Pacific Ocean subtropical high, the subtropical mei-yu–baiu–changma front, and the tropical monsoon trough). Such a southward shift is very likely or in part due to the meridional asymmetric warming with the most prominent surface warming in the midhigh latitudes (45°–60°N), which induces a weakened meridional thermal contrast over eastern Asia. Another notable feature is the enhanced ENSO–EASM relationship within the past 50 years, which is opposite to the ISM. Fourteen state-of-the-art coupled models from the Intergovernmental Panel on Climate Change show that the EASM strength does not respond with any pronounced trend to the global-warming “A1B” forcing scenario (with an atmospheric CO2 concentration of 720 ppm) but shows interannual-to-decadal variations in the twenty-first century (2000–99). These results indicate that the primary response of the EASM to a warming climate may be a position change instead of an intensity change, and such position change may lead to spatial coexistence of floods and droughts over eastern Asia as has been observed in the past 50 years.
Drought Monitoring for Washington State: Indicators and Applications
Authors: Shukla Shraddhanand , Steinemann Anne C. , Lettenmaier Dennis P. 
Published: September 2010

Abstract
A drought monitoring system (DMS) can help to detect and characterize drought conditions and reduce adverse drought impacts. The authors evaluate how a DMS for Washington State, based on a land surface model (LSM), would perform. The LSM represents current soil moisture (SM), snow water equivalent (SWE), and runoff over the state. The DMS incorporates the standardized precipitation index (SPI), standardized runoff index (SRI), and soil moisture percentile (SMP) taken from the LSM. Four historical drought events (1976–77, 1987–89, 2000–01, and 2004–05) are constructed using DMS indicators of SPI/SRI-3, SPI/SRI-6, SPI/SRI-12, SPI/SRI-24, SPI/SRI-36, and SMP, with monthly updates, in each of the state’s 62 Water Resource Inventory Areas (WRIAs). The authors also compare drought triggers based on DMS indicators with the evolution of drought conditions and management decisions during the four droughts. The results show that the DMS would have detected the onset and recovery of drought conditions, in many cases, up to four months before state declarations.
Causes of death among patients with multiple sclerosis
Authors: Sumelahti Marja-Liisa , Hakama Matti , Elovaara Irina , Pukkala Eero 
Published: September 2010

Background: Several studies show a high mortality risk among patients with multiple sclerosis (MS). Objectives: In this study, mortality and underlying causes of death were analysed among patients with MS diagnosed between 1964—1993 in Finland ( n = 1595). Methods: Standardized mortality ratios (SMRs) were calculated for both genders. The follow-up was based on linkage to the national computerized Cause-of-Death Register of Statistics Finland. Results: Altogether, 464 deaths were recorded by the end of 2006. The SMR as compared with the general population among females was 3.4 (95% confidence interval 3.0—3.9) and among males 2.2 (1.9—2.6). In total, 270 patients (58%) died from MS; only one of these deaths occurred during the first 2 years after the MS diagnosis. Mortality was also increased for other natural causes of death ( n = 160) in patients followed for more than 10 years (SMR 1.4, 1.2—1.7), with a significant increase in deaths from influenza (29, 6.0—85), pneumonia (4.7, 2.5—8.0) and gastrointestinal causes (4.4, 2.3—7.7). The SMR for violent causes was 1.2 (0.7—1.9) and for alcohol-related deaths 0.2 (0.02—0.7). The SMR for suicides was 1.7 (0.9—2.7). Conclusions: The MS population has an increased disease mortality, while the increase in the risk of accidents and suicides is not significantly increased among patients with MS in Finland.