bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role for the Paramyxovirus Genomic Promoter in Limiting Host Cell Antiviral Responses and Cell Killing
Authors: Manuse Mary J. , Parks Griffith D. 
Published: July 2009

ABSTRACT
The parainfluenza virus simian virus 5 (SV5) is a poor inducer of innate immune responses. In contrast, the naturally occurring SV5 variant Wake Forest parainfluenza virus (WF-PIV) activates the synthesis of proinflammatory cytokines and beta interferon (IFN-β). Comparison of SV5 and WF-PIV genome sequences revealed nine nucleotide differences within the viral genomic promoter, including two substitutions (U5C and A14G) in the most highly conserved 3′-end promoter element. To test the consequences of these promoter variations, a recombinant SV5 mutant [Le-(U5C, A14G)] was engineered to harbor the two WF-PIV genomic promoter substitutions in an otherwise wild-type (WT) SV5 background. Human lung epithelial cells infected with the Le-(U5C, A14G) mutant had higher rates of viral protein synthesis and levels of mRNA than cells infected with WT SV5, but levels of genomic RNA were not changed. Unlike WT SV5, the Le-(U5C, A14G) mutant was a potent inducer of interleukin-6 and IFN-β synthesis, despite expressing a functional V protein antagonist. Cytokine responses to Le-(U5C, A14G) infection were reduced either by small interfering RNA-mediated knockdown of retinoic acid-inducible gene I (RIG-I) or after infection of cells that were engineered to express the reovirus sigma3 double-stranded RNA-binding protein. Le-(U5C, A14G) induced cytopathic effects not seen with WT SV5, and the extent of cell killing correlated with elevated levels of viral F protein and cell-cell fusion. Our results support a model whereby the SV5 promoter has evolved to function at an attenuated level in order to limit (i) synthesis of aberrant RNAs which induce RIG-I-mediated responses and (ii) overproduction of mRNA for potentially toxic gene products, such as the F protein. Control of genomic promoter activity may be particularly important for viruses such as SV5, that express a V protein targeting mda-5 but do not encode antagonists such as the paramyxovirus C proteins, that specifically target RIG-I.
Prescribing antibiotics for sore throat: adherence to guidelines in patients admitted to hospital
Authors: Clifton N J , Raghavan U , Birkin J , Jones N S 
Published: July 2009

Abstract

Aim
We prospectively studied patients referred to secondary care with acute tonsillitis, peritonsillar cellulitis and quinsy (peritonsillar abscess) to see if recommended treatment guidelines were being followed and whether antibiotic resistance was contributing to admission.

Study design
Prospective observational study in a university teaching hospital of 90 consecutive patients admitted to secondary care over an 18 month period with acute tonsillitis, peritonsillar cellulitis or quinsy were studied. The geographical distribution by postcode, pre-admission history and treatment of each patient was recorded. The patients’ general practitioners (GPs) were questioned about the patients’ history, their use of antibiotics and prescribing guidelines and a patient questionnaire was completed. The result of hospital admission including throat swabs and blood cultures were recorded together with their treatment and outcome.

Results
58% (n = 28) of patients who were prescribed antibiotics before admission received an inadequate dose or inappropriate antibiotic. Only 56% (n = 45) of GPs said they used guidelines for the treatment of acute sore throat. In 34 cases an organism was isolated, with 33 (97%) being sensitive to penicillin. No resistant organisms were isolated. Hospital doctors prescribed antibiotics contrary to guidelines in 39% (n = 35) of cases.

Conclusions
Antibiotic resistance was not demonstrated in this study. Adherence to guidelines for prescribing antibiotics in patients with features of group A β-haemolytic streptococcal sore throat is poor. Information support may help to improve prescribing.
A review of novel biological tools used in screening for the early detection of lung cancer
Authors: Ghosal R , Kloer P , Lewis K E 
Published: July 2009

Abstract
Lung cancer is the most common cancer worldwide and causes more deaths per year than any other cancer. It has a very poor 5-year survival rate of 8–16%, partly because of comorbidity preventing curative treatments but mainly because of the disease presenting with symptoms only when it is at an advanced and incurable stage. When lung cancer is detected earlier and is amenable to radical treatments such as potentially curative surgery and radical radiotherapy, 5-year survival rates are much higher (up to 67%). Therefore reliable detection of lung cancer at this earlier (usually asymptomatic) stage of disease should be an important way to improve outcomes. This review discusses the principles of screening with respect to lung cancer, concentrating mainly on the biological modalities used to detect it. The lack of impact achieved by early studies using sputum cytology (in conjunction with chest radiographs) is described, and then newer technology used to measure other biomarkers in sputum, serum, exhaled breath and bronchial mucosa to diagnose (early) lung cancer is detailed. Many techniques show promise, but debate continues about which population to screen and what is the most (cost) effective modality to use. Moreover, no single biomarker or combination of biomarkers in screening has yet been shown to reduce lung cancer mortality in large prospective randomised studies.
Response of coastal Douglas-fir and competing vegetation to repeated and delayed weed control treatments during early plantation development
Authors: Maguire Douglas A. , Mainwaring Douglas B. , Rose Robin , Garber Sean M. , Dinger Eric J. 
Published: July 2009

A key silvicultural decision in managing young conifer plantations is determining the number and timing of release treatments to control competing vegetation. Three coastal Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) plantations were treated under eight alternative herbicide regimes during the first 5 years after planting to test treatment effects on vegetation dynamics and seedling growth. After termination of herbicide treatments, competing vegetation developed at a rate similar to that of check plots, reaching 40%–60% cover in the first growing season and approaching 100% by the third. Recovery of competing vegetation was slightly more rapid with greater number of previous releases. Annual volume growth of seedlings was negatively correlated with current cover of competing vegetation, but competitive effects from previous years were fully accounted for by initial tree size. Under 4 years of release, delaying treatment by 1 year reduced volume attained at the end of 5 years by about 15%. Plots receiving 5 consecutive years of weed control reached the 5 year volume of check plots in only 3.9 years, implying an age shift of 1.1 years. Increasing the number of operational release treatments significantly improved seedling growth in the short term, but long-term growth effects must be monitored to determine the economically optimal regime.
Ectomycorrhizal fungal communities and soil chemistry in harvested and unharvested temperate Nothofagus rainforests
Authors: Dickie I.A. , Richardson S.J. , Wiser S.K. 
Published: July 2009

The composition of ectomycorrhizal (EcM) fungal communities in Nothofagus rainforests and the responses of the fungal communities to timber harvesting have been unknown. We investigated EcM communities in two sites, 9 to 11 years after timber harvesting, and tested whether changes in the communities were driven by soil chemistry. The fungal communities in both sites were highly diverse, yet 53 out of 140 distinct terminal restriction fragment length polymorphism (T-RFLP) patterns were shared between the sites. At both sites, timber harvesting reduced the presence of EcM roots and caused shifts in the fungal community in the organic soil horizons. At one site, Laccaria spp. increased in harvested areas, which partially correlated with an increase in soil mineralizable nitrogen. The other site showed a decreased abundance of Russula sp. (cf. R. purpureotincta , R. roseostipitata ) in harvested areas, which correlated with declines in soil carbon and organic horizon depth, and a decline in the abundance of rare species at the edge of harvested areas, which was related to inorganic phosphorus. The results show that EcM fungal communities in Nothofagus temperate rainforest are highly diverse at the local scale, yet have a high degree of similarity across sites. These communities are directly affected by timber harvesting and by shifts in soil chemistry following timber harvesting.
Oral Contraceptive Use and BRCA Penetrance: A Case-Only Study
Authors: Pasanisi Patrizia , Hédelin Guy , Berrino Jacopo , Chang-Claude Jenny , Hermann Silke , Steel Michael , Haites Neva , Hart Jacob , Peled Ronit , Gafà Lorenzo , Leggio Laura , Traina Adele , Amodio Rosalba , Primic-Zakelj Maja , Zadnik Vesna , Veidebaum Toomas , Tekkel Mare , Berrino Franco 
Published: July 2009

Abstract
Background: Women with deleterious mutations in BRCA genes are at increased risk of breast cancer. However, the penetrance of the genetic trait may be regulated through environmental factors. This multinational case-only study tested the interaction between oral contraceptive use and genetic susceptibility in the occurrence of breast cancer.
Methods: We recruited 3,123 patients diagnosed with breast cancer before the age of 45 years. Participants were classified according to their probability of carrying a BRCA mutation on the basis of their family history of breast and ovarian cancer. According to a case-only approach, the frequency of relevant exposures among breast cancer cases with high probability of BRCA mutation (“genetic cases”) was compared with the frequency of the same exposures among breast cancer cases with a low probability of BRCA mutation (“sporadic cases”). The interaction odds ratios (OR) and 95% confidence intervals (CI) for oral contraceptive use were estimated by unconditional logistic regression, after controlling for potentially confounding variables.
Results: The analysis was carried out comparing 382 “genetic” and 1,333 “sporadic” cases. We found a borderline significant interaction between genetic breast cancer and oral contraceptive use for ever users compared with never users (OR, 1.3; 95% CI, 1.0-1.7). The greatest interaction OR was found for women who started using pill at 18 to 20 years (OR, 1.6; 95% CI, 1.1-2.3).
Conclusion: These results suggest that BRCA mutation carriers, as well as women with a significant family history of breast and ovarian cancer are more vulnerable to exogenous hormones in oral contraceptives. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2107–13)
Test Sensitivity in the European Prostate Cancer Screening Trial: Results from Finland, Sweden, and the Netherlands
Authors: Auvinen Anssi , Raitanen Jani , Moss Sue , de Koning Harry J. , Hugosson Jonas , Tammela Teuvo , Roobol Monique , Lilja Hans , Hakama Matti 
Published: July 2009

Abstract
Test sensitivity pertains to the ability of a test to identify subjects with the target disorder. In cancer screening, test sensitivity can be estimated using interval cancer incidence as an indicator of false-negative result. A randomized trial provides the optimal approach for estimating test sensitivity, as the control arm provides the expected rates. We estimated the sensitivity of the prostate-specific antigen test using incidence method, i.e., based on incidence of interval cancer among subjects with negative screening results, compared with that in the control arm. Data from three centers in the European randomized screening trial were used to estimate interval cancer incidence (II) among 39,389 men with negative screening tests. This was compared with incidence among the 79,525 men in the control arm of the trial (Ic) to estimate test sensitivity (S = 1 − II / IC). Confidence intervals were calculated using simulations, assuming that the number of cases follows a Poisson distribution. The estimated test sensitivity following the first screen was 0.87 (0.83-0.92) in Finland, 0.87 (0.62-1.00) in Sweden, and 0.93 (95% confidence interval, 0.90-0.96) in the Netherlands. There was some indication of a higher test sensitivity for aggressive cancers (0.85-0.98 for non–organ-confined cases or Gleason 8-10) and for the second screening round (approximately 0.85-0.95). Test sensitivity varied to some extent between the three centers in the European trial, probably reflecting variation in screening protocols, but was acceptable in the first screening round, and may be better for aggressive cancers and in the second screening round. (Cancer Epidemiol Biomarkers Prev 2009;18(7):2000–5)
Encoding in the Visual Word Form Area: An fMRI Adaptation Study of Words versus Handwriting
Authors: Barton Jason J. S. , Fox Christopher J. , Sekunova Alla , Iaria Giuseppe 
Published: July 2009

Abstract
Written texts are not just words but complex multidimensional stimuli, including aspects such as case, font, and handwriting style, for example. Neuropsychological reports suggest that left fusiform lesions can impair the reading of text for word (lexical) content, being associated with alexia, whereas right-sided lesions may impair handwriting recognition. We used fMRI adaptation in 13 healthy participants to determine if repetition–suppression occurred for words but not handwriting in the left visual word form area (VWFA) and the reverse in the right fusiform gyrus. Contrary to these expectations, we found adaptation for handwriting but not for words in both the left VWFA and the right VWFA homologue. A trend to adaptation for words but not handwriting was seen only in the left middle temporal gyrus. An analysis of anterior and posterior subdivisions of the left VWFA also failed to show any adaptation for words. We conclude that the right and the left fusiform gyri show similar patterns of adaptation for handwriting, consistent with a predominantly perceptual contribution to text processing.
Electrophysiological Evidence for Endogenous Control of Attention in Switching between Languages in Overt Picture Naming
Authors: Verhoef Kim M. W. , Roelofs Ardi , Chwilla Dorothee J. 
Published: July 2009

AbstractLanguage switching in bilingual speakers requires attentional control to select the appropriate language, for example, in picture naming. Previous language-switch studies used the color of pictures to indicate the required language thereby confounding endogenous and exogenous control. To investigate endogenous language control, our language cues preceded picture stimuli by 750 msec. Cue-locked event-related potentials (ERPs) were measured while Dutch–English bilingual speakers overtly named pictures. The response language on consecutive trials could be the same (repeat trials) or different (switch trials). Naming latencies were longer on switch than on repeat trials, independent of the response language. Cue-locked ERPs showed an early posterior negativity for switch compared to repeat trials for L2 but not for L1, and a late anterior negativity for switch compared to repeat trials for both languages. The early switch–repeat effect might reflect disengaging from the nontarget native language, whereas the late switch–repeat effect reflects engaging in the target language. Implications for models of bilingual word production are discussed.
Fifty Years of the Indonesian Throughflow*
Authors: Tillinger Debra , Gordon Arnold L. 
Published: July 2009

Abstract
Simple Ocean Data Assimilation (SODA) reanalysis data are used to produce a 50-yr record of flow through the Makassar Strait, the primary conduit for the Indonesian Throughflow (ITF). Two time series are constructed for comparison to the flow through the Makassar Strait as observed during 1997–98 and 2004–06: SODA along-channel speed within the Makassar Strait and Pacific to Indian Ocean interocean pressure difference calculated on isopycnal layers from SODA hydrology. These derived time series are compared to the total ITF as well as to the vertical distribution and frequency bands of ITF variability. The pressure difference method displays higher skill in replicating the observed Makassar ITF time series at periods longer than 9 months, particularly within the thermocline layer (50–200 m), the location of maximum flow. This is attributed to the connection between the thermocline layer and large-scale wind forcing, which affects the hydrology of the ITF inflow and outflow regions. In contrast, the surface layer (0–50 m) is more strongly correlated with local wind flow, and it is better predicted by SODA along-channel velocity. The pressure difference time series is extended over the 50-yr period of SODA and displays a strong correlation with ENSO as well as a correlation at the decadal scale with the island rule.
Clouds in Tropical Cyclones
Authors: Houze Robert A. 
Published: July 2009

AbstractClouds within the inner regions of tropical cyclones are unlike those anywhere else in the atmosphere. Convective clouds contributing to cyclogenesis have rotational and deep intense updrafts but tend to have relatively weak downdrafts. Within the eyes of mature tropical cyclones, stratus clouds top a boundary layer capped by subsidence. An outward-sloping eyewall cloud is controlled by adjustment of the vortex toward gradient-wind balance, which is maintained by a slantwise current transporting boundary layer air upward in a nearly conditionally symmetric neutral state. This balance is intermittently upset by buoyancy arising from high-moist-static-energy air entering the base of the eyewall because of the radial influx of low-level air from the far environment, supergradient wind in the eyewall zone, and/or small-scale intense subvortices. The latter contain strong, erect updrafts. Graupel particles and large raindrops produced in the eyewall fall out relatively quickly while ice splinters left aloft surround the eyewall, and aggregates are advected radially outward and azimuthally up to 1.5 times around the cyclone before melting and falling as stratiform precipitation. Electrification of the eyewall cloud is controlled by its outward-sloping circulation. Outside the eyewall, a quasi-stationary principal rainband contains convective cells with overturning updrafts and two types of downdrafts, including a deep downdraft on the band’s inner edge. Transient secondary rainbands exhibit propagation characteristics of vortex Rossby waves. Rainbands can coalesce into a secondary eyewall separated from the primary eyewall by a moat that takes on the structure of an eye. Distant rainbands, outside the region dominated by vortex dynamics, consist of cumulonimbus clouds similar to non–tropical storm convection.
Introduction of the GSI into the NCEP Global Data Assimilation System
Authors: Kleist Daryl T. , Parrish David F. , Derber John C. , Treadon Russ , Wu Wan-Shu , Lord Stephen 
Published: July 2009

Abstract
At the National Centers for Environmental Prediction (NCEP), a new three-dimensional variational data assimilation (3DVAR) analysis system was implemented into the operational Global Data Assimilation System (GDAS) on 1 May 2007. The new analysis system, the Gridpoint Statistical Interpolation (GSI), replaced the Spectral Statistical Interpolation (SSI) 3DVAR system, which had been operational since 1991. The GSI was developed at the Environmental Modeling Center at NCEP as part of an effort to create a more unified, robust, and efficient analysis scheme. The key aspect of the GSI is that it formulates the analysis in model grid space, which allows for more flexibility in the application of the background error covariances and makes it straightforward for a single analysis system to be used across a broad range of applications, including both global and regional modeling systems and domains.
Due to the constraints of working with an operational system, the final GDAS package included many changes other than just a simple replacing of the SSI with the new GSI. The new GDAS package contained an upgrade to the Global Forecast System model, including a new vertical coordinate, as well as new features in the GSI that were never developed for the SSI. Some of these new features included changes to the observation selection, quality control, minimization algorithm, dynamic balance constraint, and assimilation of new observation types. The evaluation of the new system relative to the SSI-based system was performed for nearly an entire year of analyses and forecasts. The objective and subjective evaluations showed that the new package exhibited superior forecast performance relative to the old SSI-based system. The new system has been shown to improve forecast skill in the tropics and substantially reduce the short-term forecast error in the extratropics. This implementation has laid the groundwork for future scientific advancements in data assimilation at NCEP.
Evaluation of WRF Model Output for Severe Weather Forecasting from the 2008 NOAA Hazardous Weather Testbed Spring Experiment
Authors: Coniglio Michael C. , Elmore Kimberly L. , Kain John S. , Weiss Steven J. , Xue Ming , Weisman Morris L. 
Published: July 2009

Abstract
This study assesses forecasts of the preconvective and near-storm environments from the convection-allowing models run for the 2008 National Oceanic and Atmospheric Administration (NOAA) Hazardous Weather Testbed (HWT) spring experiment. Evaluating the performance of convection-allowing models (CAMs) is important for encouraging their appropriate use and development for both research and operations. Systematic errors in the CAM forecasts included a cold bias in mean 2-m and 850-hPa temperatures over most of the United States and smaller than observed vertical wind shear and 850-hPa moisture over the high plains. The placement of airmass boundaries was similar in forecasts from the CAMs and the operational North American Mesoscale (NAM) model that provided the initial and boundary conditions. This correspondence contributed to similar characteristics for spatial and temporal mean error patterns. However, substantial errors were found in the CAM forecasts away from airmass boundaries. The result is that the deterministic CAMs do not predict the environment as well as the NAM. It is suggested that parameterized processes used at convection-allowing grid lengths, particularly in the boundary layer, may be contributing to these errors.
It is also shown that mean forecasts from an ensemble of CAMs were substantially more accurate than forecasts from deterministic CAMs. If the improvement seen in the CAM forecasts when going from a deterministic framework to an ensemble framework is comparable to improvements in mesoscale model forecasts when going from a deterministic to an ensemble framework, then an ensemble of mesoscale model forecasts could predict the environment even better than an ensemble of CAMs. Therefore, it is suggested that the combination of mesoscale (convection parameterizing) and CAM configurations is an appropriate avenue to explore for optimizing the use of limited computer resources for severe weather forecasting applications.