bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correction of Polarimetric Radar Reflectivity Measurements and Rainfall Estimates for Apparent Vertical Profile in Stratiform Rain
Authors: Kalogiros John , Anagnostou Marios N. , Anagnostou Emmanouil N. , Montopoli Mario , Picciotti Errico , Marzano Frank S. 
Published: December 2012

AbstractA method for correcting the vertical profile of reflectivity measurements and rainfall estimates (VPR) in plan position indicator (PPI) scans of polarimetric weather radars in the melting layer and the snow layer during stratiform rain is presented. The method for the detection of the boundaries of the melting layer is based on the well-established characteristic of local minimum of copolar correlation coefficient in the melting layer. This method is applied to PPI scans instead of a beam-by-beam basis with the addition of new acceptance criteria adapted to the radar used in this study. An apparent vertical profile of reflectivity measurements, or rainfall estimate, is calculated by averaging the range profiles from all of the available azimuth directions in each PPI scan. The height of each profile is properly scaled with melting-layer boundaries, and the reflectivity, or rainfall estimate, is normalized with respect to its value at the lower boundary of the melting layer. This approach allows variations of the melting-layer boundaries in space and time and variations of the shape of the apparent VPR in time. The application of the VPR correction to reflectivity and rainfall estimates from a reflectivity–rainfall algorithm and a polarimetric algorithm showed that this VPR correction method effectively removes the bias that is due to the brightband effect in PPI scans. It performs also satisfactorily in the snow region, removing the decrease of the observed VPR with range but with an overestimation by 2 dB or more. This method does not require a tuning using climatological data, and it can be applied on any algorithm for rainfall estimation.
Evaluation of Weather Noise and Its Role in Climate Model Simulations*
Authors: Chen Hua , Schneider Edwin K. , Kirtman Ben P. , Colfescu Ioana 
Published: December 2012

Abstract
The relationship between coupled atmosphere–ocean general circulation model simulations and uncoupled simulations made with specified SST and sea ice is investigated using the Community Climate System Model, version 3. Experiments are carried out in a perfect model framework. Two closely related questions are investigated: 1) whether the statistics of the atmospheric weather noise in the atmospheric model are the same as in the coupled model, and 2) whether the atmospheric model reproduces the SST-forced response of the coupled model.
The weather noise in both the coupled and uncoupled simulations is found by removing the forced response, as determined from the uncoupled ensemble, from the atmospheric field. The weather-noise variance is generally not distinguishable between the coupled and uncoupled simulations. However, variances of the total fields differ between the coupled and uncoupled simulations, since there is constructive or destructive interference between the SST-forced response and weather noise in the coupled model but no correlation between the SST-forced and weather-noise components in the uncoupled model simulations.
Direct regression estimates of the forced response show little difference between the coupled and uncoupled simulations. Differences in local correlations are explained by weather noise because weather noise forces SST in the coupled simulation only.
The results demonstrate and explain an important intrinsic difference in precipitation statistics between the coupled and uncoupled simulations. This difference could have consequences for the design of dynamical downscaling experiments and for tuning general circulation models.
Is It Really Necessary to Delay Intranasal Steroid Treatment after FESS? An Animal Study
Authors: Bayraktar Cem , Atmaca Sinan , Guvenc Dilek , Karayigit M. Onder , Atmaca Enes , Yarim Murat , Aksoy Abdurrahman 
Published: December 2012

ObjectivesThe aim of this study is to investigate the effect of early intranasal steroid administration on wound healing after sinus surgery.Study DesignRandomized, placebo‐controlled, blinded animal study.SettingAnimal laboratory.Subjects and MethodsForty‐two male New Zealand rabbits underwent bilateral 3‐mm punch resection of the concha nasalis ventralis. The animals were divided into 3 groups: saline, late steroid, and early steroid. The saline group received saline drops, the late steroid group received saline drops for 7 days followed by intranasal mometasone furoate 50 µg/nostril/d, and the early steroid group received intranasal mometasone furoate (same dose) starting on postoperative day 1. The animals were sacrificed on postoperative days 10 and 21. Left nasal specimens were examined histopathologically with hematoxylin‐eosin and matrix metalloproteinase–9 (MMP‐9) stains. Right nasal specimens were examined with high‐performance liquid chromatography, and hydroxyproline levels were measured as mg/g in wet tissue.ResultsLate steroid and early steroid groups were similar with regard to MMP‐9 staining on days 10 and 21. On day 10, the early steroid group revealed significantly intense MMP‐9 staining when compared with the saline group, and the late steroid and early steroid groups revealed significant fibrosis when compared with the saline group. Hydroxyproline levels were similar in all groups on day 10. The early steroid group revealed significantly higher hydroxyproline levels when compared with the late steroid group on day 21.ConclusionOur findings showed that early intranasal steroid administration after sinus surgery in an animal model has no detrimental effects with regard to wound‐healing parameters.
Comparison of Repair Integrity and Functional Outcomes for 3 Arthroscopic Suture Bridge Rotator Cuff Repair Techniques
Authors: Kim Kyung Cheon , Shin Hyun Dae , Cha Soo Min , Lee Woo Yong 
Published: December 2012

Background: No reported study has compared the clinical outcomes of suture bridge techniques. Purpose: To compare the functional outcomes and repair integrity of the arthroscopic single-mattress (SM), double-pulley (DP), and double-mattress (DM) suture bridge (SB) techniques for full-thickness rotator cuff tears. Study Design: Cohort study; Level of evidence, 2. Methods: Seventy-eight consecutive shoulders with full-thickness rotator cuff tears and a 1- to 4-cm anteroposterior dimension underwent arthroscopic SB repairs. The SM-SB technique was used in the first 26 consecutive shoulders, the DP-SB method was used in the second 26 consecutive shoulders, and the DM-SB repair was used in the final 26 consecutive shoulders. Seventy-four shoulders (94.9%) underwent postoperative evaluation for cuff integrity using MRI or ultrasound. Clinical outcomes were evaluated in 76 shoulders (97.4%) at a minimum of 2 years postoperatively. Clinical outcomes were evaluated using the shoulder rating scale of the University of California, Los Angeles (UCLA), American Shoulder and Elbow Surgeons (ASES), and Constant scores at an average of 31 months postoperatively. Results: At final follow-up, the average ASES, UCLA, and Constant scores improved significantly: respective scores were 88.46, 30.58, and 73.96 in the SM-SB group ( P < .001); 87.19, 31.35, and 72.50 in the DP-SB group ( P < .001); and 87.19, 32.81, and 75.35 in the DM-SB group ( P < .001). However, there were no significant differences among the 3 groups in terms of the ASES, UCLA, or Constant scores ( P = .954, .210, and .755, respectively). The retear rate of repaired rotator cuffs was 20% in the SM-SB group, 12.5% in the DP-SB group, and 12% in the DM-SB group; however, the differences among the 3 groups were not statistically significant ( P = .674). The number of suture anchors (mean ± SD) used for repair was 4.31 ± 0.47 in the SM-SB group, 4.00 ± 0.00 in the DP-SB group, and 3.38 ± 0.50 in the DM-SB group ( P < .001). Conclusion: Arthroscopic rotator cuff repair yielded successful functional outcomes without significant differences among the 3 SB techniques. Additionally, no significant differences in repair integrity were observed among the 3 methods postoperatively.
High cereblon expression is associated with better survival in patients with newly diagnosed multiple myeloma treated with thalidomide maintenance
Authors: Broyl Annemiek , Kuiper Rowan , van Duin Mark , van der Holt Bronno , el Jarari Laila , Bertsch Uta , Zweegman Sonja , Buijs Arjan , Hose Dirk , Lokhorst Henk M. , Goldschmidt Hartmut , Sonneveld Pieter 
Published: December 2012

Abstract
Recently, cereblon (CRBN) expression was found to be essential for the activity of thalidomide and lenalidomide. In the present study, we investigated whether the clinical efficacy of thalidomide in multiple myeloma is associated with CRBN expression in myeloma cells. Patients with newly diagnosed multiple myeloma were included in the HOVON-65/GMMG-HD4 trial, in which postintensification treatment in 1 arm consisted of daily thalidomide (50 mg) for 2 years. Gene-expression profiling, determined at the start of the trial, was available for 96 patients who started thalidomide maintenance. In this patient set, increase of CRBN gene expression was significantly associated with longerprogression-free survival (P = .005). In contrast, no association between CRBN expression and survival was observed in the arm with bortezomib maintenance. We conclude that CRBN expression may be associated with the clinical efficacy of thalidomide. This trial has been registered at the Nederlands Trial Register (www.trialregister.nl) as NTR213; at the European Union Drug Regulating Authorities Clinical Trials (EudraCT) as 2004-000944-26; and at the International Standard Randomized Controlled Trial Number (ISRCTN) as 64455289.
An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales
Authors: Le Phuong Thi , Ramulu Hemalatha Golaconda , Guijarro Laurent , Paganini Julien , Gouret Philippe , Chabrol Olivier , Raoult Dider , Pontarotti Pierre 
Published: December 2012

AbstractBackgroundHorizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent inRickettsialesgenomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species intoRickettsialesspecies.ResultsWe developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) intoRickettsialesgenomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 completeRickettsialesgenomes, of which 38 were previously unidentified instances of HGT fromAnaplasma,Wolbachia,CandidatusPelagibacter ubique andRickettsiagenomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as “rhizome-like”.ConclusionsOur analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.
Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe
Authors: Carter-O’Connell Ian , Peel Michael T , Wykoff Dennis D , O’Shea Erin K 
Published: December 2012

Abstract

Background
Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway, leading to expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1

+
) via a non-orthologous PHO pathway involving genetically identified positive (pho7

+
) and negative (csk1
+) regulators. The genes induced by phosphate limitation and the molecular mechanism by which pho7

+
and csk1
+ function are unknown. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7

+
and csk1

+
in the PHO response.

Results
We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response that contains the ScPHO5 (pho1

+
), ScPHO84 (SPBC8E4.01c), and ScGIT1 (SPBC1271.09) orthologs. We identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1

+
requires Pho7 binding to a UAS in the pho1

+
promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7

+
for maximal induction.

Conclusions
We provide a global analysis of the transcriptional response to phosphate limitation in S. pombe. Our results elucidate the conserved core regulon induced in response to phosphate starvation in this ascomycete distantly related to S. cerevisiae and provide a better understanding of flexibility in environmental stress response networks.
Risk of esophagus cancer in diabetes mellitus: a population-based case-control study in Taiwan
Authors: Cheng Kao-Chi , Chen Yu-Lung , Lai Shih-Wei , Tsai Pang-Yao , Sung Fung-Chang 
Published: December 2012

Abstract

Background
Diabetes mellitus (DM) has been associated with the cancer risk. This study investigated relationship between DM and esophageal cancer using Taiwan’s insurance data.

Methods
We identified 549 patients with esophageal cancer newly diagnosed in 2000-2009 and randomly selected 2196 controls without any cancer, frequency matched by sex, age and diagnosis year of cases. Logistic regression model estimated odds ratios (ORs) and 95% confidence intervals (CI) of esophageal cancer associated with DM, sex, age. co-morbidities and medications.

Results
Cases were more prevalent than controls for alcoholism and esophageal disorders and using nonsteroidal anti-inflammatory drugs (NSAIDs) and cyclooxygenase-2 inhibitors but not DM. Esophageal cancer had no association with DM (OR 0.99, 95% CI 0.71-1.37), but significantly associated with alcoholism (OR 14.1, 95% CI 7.87-25.4), esophageal ulcer (OR 10.1, 95% CI 5.70-17.9), esophageal reflux (OR 3.47, 95% CI 2.14-5.26) and uses of NSAIDs (OR 2.73, 95% CI 1.80-4.13). An elevated risk of esophageal cancer appeared in DM patients taking insulin (OR 2.57, 95% CI 1.08-6.15) or sulfonyurea (OR 3.80, 95% CI 1.16-12.5).

Conclusions
Patients with DM are not at higher risk for esophagus cancer. However, esophageal disorders and anti-diabetic drugs are associated with the risk of the disease.
Menopause and the influence of culture: another gap for Indigenous Australian women?
Authors: Jones Emma K , Jurgenson Janelle R , Katzenellenbogen Judith M , Thompson Sandra C 
Published: December 2012

Abstract

Background
There is great variation in experience of menopause in women around the world. The purpose of this study was to review current understanding of Australian Aboriginal and Torres Strait Islander (Indigenous) women’s experiences of menopause. The literature pertaining to the perception, significance and experience of menopause from a number of cultural groups around the world has been included to provide context for why Indigenous women’s experience might be important for their health and differ from that reported in other studies of Australian women and menopause.

Methods
A search of databases including Ovid Medline, Pubmed, Web of Science, AUSThealth, AMED, EMBASE, Global Health and PsychINFO was undertaken from January 2011 to April 2011 using the search terms menopause, Indigenous, Aboriginal, attitudes, and perceptions and repeated in September 2012.

Results
Considerable research shows significant variation across cultures in the menopausal experience. Biological, psychological, social and cultural factors are associated with either positive or negative attitudes, perceptions or experiences of menopause in various cultures. Comparative international literature shows that neither biological nor social factors alone are sufficient to explain the variation in experiences of the menopausal transition. However, a strong influence of culture on the menopause experience can be found. The variation in women’s experience of menopause indicates that different cultural groups of women may have different understandings and needs during the menopausal transition. While considerable literature exists for Australian women as a whole, there has been little investigation of Australian Indigenous women, with only two research studies related to Indigenous women’s experiences of menopause identified.

Conclusions
Differences in biocultural experience of menopause around the world suggest the importance of biocultural research. For the Indigenous women of Australia, the relative contribution of culture, social disadvantage and poor general health compared with non-Indigenous women to the experience of menopause is unknown. As such, further research and understanding of the experience of Indigenous women around Australia is needed. This information could assist individuals, families, cultural groups and healthcare providers to enhance management and support for Indigenous Australian women.
Yeast prions form infectious amyloid inclusion bodies in bacteria
Authors: Espargaró Alba , Villar-Piqué Anna , Sabaté Raimon , Ventura Salvador 
Published: December 2012

Abstract

Background
Prions were first identified as infectious proteins associated with fatal brain diseases in mammals. However, fungal prions behave as epigenetic regulators that can alter a range of cellular processes. These proteins propagate as self-perpetuating amyloid aggregates being an example of structural inheritance. The best-characterized examples are the Sup35 and Ure2 yeast proteins, corresponding to [PSI+] and [URE3] phenotypes, respectively.

Results
Here we show that both the prion domain of Sup35 (Sup35-NM) and the Ure2 protein (Ure2p) form inclusion bodies (IBs) displaying amyloid-like properties when expressed in bacteria. These intracellular aggregates template the conformational change and promote the aggregation of homologous, but not heterologous, soluble prionogenic molecules. Moreover, in the case of Sup35-NM, purified IBs are able to induce different [PSI+] phenotypes in yeast, indicating that at least a fraction of the protein embedded in these deposits adopts an infectious prion fold.

Conclusions
An important feature of prion inheritance is the existence of strains, which are phenotypic variants encoded by different conformations of the same polypeptide. We show here that the proportion of infected yeast cells displaying strong and weak [PSI+] phenotypes depends on the conditions under which the prionogenic aggregates are formed in E. coli, suggesting that bacterial systems might become useful tools to generate prion strain diversity.
100% Orange juice consumption is associated with better diet quality, improved nutrient adequacy, decreased risk for obesity, and improved biomarkers of health in adults: National Health and Nutrition Examination Survey, 2003-2006
Authors: O’Neil Carol E , Nicklas Theresa A , Rampersaud Gail C , Fulgoni III Victor L 
Published: December 2012

AbstractBackgroundConsumption of 100% orange juice (OJ) has been positively associated with nutrient adequacy and diet quality, with no increased risk of overweight/obesity in children; however, no one has examined these factors in adults. The purpose of this study was to examine the association of 100% OJ consumption with nutrient adequacy, diet quality, and risk factors for metabolic syndrome (MetS) in a nationally representative sample of adults.MethodsData from adults 19+ years of age (n = 8,861) participating in the National Health and Nutrition Examination Survey 2003-2006 were used. The National Cancer Institute method was used to estimate the usual intake (UI) of 100% OJ consumption, selected nutrients, and food groups. Percentages of the population below the Estimated Average Requirement (EAR) or above the Adequate Intake (AI) were determined. Diet quality was measured by the Healthy Eating Index-2005 (HEI-2005). Covariate adjusted logistic regression was used to determine if consumers had a lower odds ratio of being overweight or obese or having risk factors of MetS or MetS.ResultsUsualper capitaintake of 100% OJ was 50.3 ml/d. Among consumers (n = 2,310; 23.8%), UI was 210.0 ml/d. Compared to non-consumers, consumers had a higher (p < 0.05) percentage (% ± SE) of the population meeting the EAR for vitamin A (39.7 ± 2.5 vs 54.0 ± 1.2), vitamin C (0.0 ± 0.0 vs 59.0 ± 1.4), folate (5.8 ± 0.7 vs 15.1 ± 0.9), and magnesium (51.6 ± 1.6 vs 63.7 ± 1.2). Consumers were also more likely to be above the AI for potassium (4.1 ± 0.8 vs 1.8 ± 0.2). HEI-2005 was significantly (p < 0.05) higher in consumers (55.0 ± 0.4 vs 49.7 ± 0.3). Consumers also had higher intakes of total fruit, fruit juice, whole fruit, and whole grain. Consumers had a lower (p < 0.05) mean body mass index (27.6 ± 0.2 vs 28.5 ± 0.1), total cholesterol levels (197.6 ± 1.2 vs 200.8 ± 0.75 mg/dL), and low density lipoprotein-cholesterol levels (112.5 ± 1.4 vs 116.7 ± 0.93 mg/dL). Finally, compared to non-consumers of 100% OJ, consumers were 21% less likely to be obese and male consumers were 36% less likely to have MetS.ConclusionThe results suggest that moderate consumption of 100% OJ should be encouraged to help individuals meet the USDA daily recommendation for fruit intake and as a component of a healthy diet.