bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can spirometric norms be set using pre- or post- bronchodilator test results in older people?
Authors: Kato Bernet , Gulsvik Amund , Vollmer William , Janson Christer , Studnika Michael , Buist Sonia , Burney Peter 
Published: November 2012

Abstract

Background
Chronic Obstructive Pulmonary Disease (COPD) is defined by post-bronchodilator spirometry. Data on “normal values” come predominantly from pre-bronchodilator spirometry. The effects of this on diagnosis are unknown.

Methods
Lower limits of normal (LLN) were estimated from “normal” participants in the Burden of Obstructive Lung Disease (BOLD) programme. Values separately derived using pre- and post-bronchodilator spirometry were compared. Sensitivity and specificity of criteria derived from pre-bronchodilator spirometry and pre-bronchodilator spirometry adjusted by a constant were assessed in the remaining population. The “gold standard” was the LLN for the post-bronchodilator spirometry in the “normal population”. For FEV1/FVC, sensitivity and specificity of criteria were also assessed when a fixed value of < 70% was used rather than LLN.

Results
Of 6,600 participants with full data, 1,354 were defined as “normal”. Mean differences between pre- and post- bronchodilator measurements were small and the Bland-Altman plots showed no association between difference and mean value. Compared with using the gold standard, however, tests using pre-bronchodilator spirometry had a sensitivity and specificity of detecting a low FEV1 of 78.4% and 100%, a low FVC of 99.8% and 99.1% and a low FEV1/FVC ratio of 65% and 100%. Adjusting this by a constant improved the sensitivity without substantially altering the specificity for FEV1 (99%, 99.8%), FVC (97.4%, 99.9%) and FEV1/FVC (98.7%, 99.5%).

Conclusions
Using pre-bronchodilator spirometry to derive norms for lung function reduces sensitivity compared to a post-bronchodilator gold standard. Adjustment of these values by a constant can improve validity of the test.
Identification of proteins binding coding and non-coding human RNAs using protein microarrays
Authors: Siprashvili Zurab , Webster Dan E , Kretz Markus , Johnston Danielle , Rinn John L , Chang Howard Y , Khavari Paul A 
Published: November 2012

Abstract

Background
The regulation and function of mammalian RNAs has been increasingly appreciated to operate via RNA-protein interactions. With the recent discovery of thousands of novel human RNA molecules by high-throughput RNA sequencing, efficient methods to uncover RNA-protein interactions are urgently required. Existing methods to study proteins associated with a given RNA are laborious and require substantial amounts of cell-derived starting material. To overcome these limitations, we have developed a rapid and large-scale approach to characterize binding of in vitro transcribed labeled RNA to ~9,400 human recombinant proteins spotted on protein microarrays.

Results
We have optimized methodology to probe human protein microarrays with full-length RNA molecules and have identified 137 RNA-protein interactions specific for 10 coding and non-coding RNAs. Those proteins showed strong enrichment for common human RNA binding domains such as RRM, RBD, as well as K homology and CCCH type zinc finger motifs. Previously unknown RNA-protein interactions were discovered using this technique, and these interactions were biochemically verified between TP53 mRNA and Staufen1 protein as well as between HRAS mRNA and CNBP protein. Functional characterization of the interaction between Staufen 1 protein and TP53 mRNA revealed a novel role for Staufen 1 in preserving TP53 RNA stability.

Conclusions
Our approach demonstrates a scalable methodology, allowing rapid and efficient identification of novel human RNA-protein interactions using RNA hybridization to human protein microarrays. Biochemical validation of newly identified interactions between TP53-Stau1 and HRAS-CNBP using reciprocal pull-down experiments, both in vitro and in vivo, demonstrates the utility of this approach to study uncharacterized RNA-protein interactions.
Benefits of hyperthermic intraperitoneal chemotherapy for patients with serosal invasion in gastric cancer: a meta-analysis of the randomized controlled trials
Authors: Sun Jingxu , Song Yongxi , Wang Zhenning , Gao Peng , Chen Xiaowan , Xu Yingying , Liang Jiwang , Xu Huimian 
Published: November 2012

Abstract

Background
In this meta-analysis we aimed to determine the effectiveness and safety of hyperthermic intraperitoneal chemotherapy (HIPC) for patients with advanced gastric cancer who underwent gastrectomy.

Methods
In accordance with standard meta-analysis procedures, our study included patients who underwent resection for advanced gastric cancer and were randomly allocated to receive either hyperthermic intraperitoneal chemotherapy or control. We searched PubMed (up to November 2011), EMBASE (up to November 2011), Cochrane Database of Systematic Reviews (CDSR), and Cochrane Central Register of Controlled Trials (CCTR) (up to November 2011). Both published and unpublished trials were included in the analysis, and no search restrictions were imposed. There was no language restriction. The results were analyzed using RevMan 5.1 software, which was provided by Cochrane Collaboration.

Results
There were ten randomized controlled trials included in the analysis. A total of 1062 patients with gastric cancer in these studies were divided into the HIPC group (n = 518) and control group (n = 544). A significant improvement in survival was observed in the HIPC groups compared to the control group in the mitomycin C (MMC) subgroup (RR = 0.75, 95%CI 0.65-0.86; P < 0.00001) and the 5-FU group (RR = 0.69, 95%CI 0.52-0.90; P < 0.00001); the total RR was 0.73 (95%CI 0.64-0.83; P < 0.00001). Our findings indicated that HIPC potentially exhibited a lower peritoneal recurrence rate in the HIPC group compared to the control group (RR = 0.45, 95%CI 0.28-0.72; P = 0.001).

Conclusions
Our meta-analysis demonstrated that HIPC may improve the overall survival rate for patients who receive resection for advance gastric cancer potentially, and help to prevent peritoneal local recurrence among patients with serosal invasion in gastric cancer.
Antioxidant activity, total phenolic and total flavonoid contents of whole plant extracts Torilis leptophylla L
Authors: Saeed Naima , Khan Muhammad R , Shabbir Maria 
Published: November 2012

AbstractBackgroundThe aim of this study was to screen various solvent extracts of whole plant ofTorilis leptophyllato display potent antioxidant activityin vitroandin vivo, total phenolic and flavonoid contents in order to find possible sources for future novel antioxidants in food and pharmaceutical formulations.Material and methodsA detailed study was performed on the antioxidant activity of the methanol extract of whole plant ofTorilis leptophylla(TLM) and its derived fractions {n-hexane (TLH), chloroform (TLC) ethyl acetate (TLE)n-butanol (TLB) and residual aqueous fraction (TLA)} byin vitrochemical analyses and carbon tetrachloride (CCl4) induced hepatic injuries (lipid peroxidation and glutathione contents) in male Sprague-Dawley rat. The total yield, total phenolic (TPC) and total flavonoid contents (TFC) of all the fractions were also determined. TLM was also subjected to preliminary phytochemical screening test for various constituents.ResultsThe total phenolic contents (TPC) (121.9±3.1 mg GAE/g extract) of TLM while total flavonoid contents (TFC) of TLE (60.9 ±2.2 mg RTE/g extract) were found significantly higher as compared to other solvent fractions. Phytochemical screening of TLM revealed the presence of alkaloids, anthraquinones, cardiac glycosides, coumarins, flavonoids, saponins, phlobatannins, tannins and terpenoids. The EC50values based on the DPPH (41.0±1 μg/ml), ABTS (10.0±0.9 μg/ml) and phosphomolybdate (10.7±2 μg/ml) for TLB, hydroxyl radicals (8.0±1 μg/ml) for TLC, superoxide radicals (57.0±0.3 μg/ml) for TLM and hydrogen peroxide radicals (68.0±2 μg/ml) for TLE were generally lower showing potential antioxidant properties. A significant but marginal positive correlation was found between TPC and EC50values for DPPH, hydroxyl, phosphomolybdate and ABTS, whereas another weak and positive correlation was determined between TFC and EC50values for superoxide anion and hydroxyl radicals. Results ofin vivoexperiment revealed that administration of CCl4caused a significant increase in lipid peroxidation (TBARS) while decrease in GSH contents of liver. In contrast, TLM (200 mg/kg bw) and silymarin (50 mg/kg bw) co-treatment effectively prevented these alterations and maintained the antioxidant status.ConclusionData from present results revealed thatTorilis leptophyllaact as an antioxidant agent due to its free radical scavenging and cytoprotective activity.
Plasmonic enhancements of photoluminescence in hybrid Si nanostructures with Au fabricated by fully top-down lithography
Authors: Nakaji Koudo , Li Hao , Kiba Takayuki , Igarashi Makoto , Samukawa Seiji , Murayama Akihiro 
Published: November 2012

Abstract
The authors study plasmonic enhancements of photoluminescence (PL) in Si nanodisk (ND) arrays hybridized with nanostructures such as nanoplates of Au, where these hybrid nanostructures are fabricated by fully top-down lithography: neutral-beam etching using bio-nano-templates and high-resolution electron-beam lithography. The separation distance between the Si ND and Au nanostructure surfaces is precisely controlled by inserting a thin SiO2 layer with a thickness of 3 nm. We observe that PL intensities in the Si NDs are enhanced by factors up to 5 depending on the wavelength by integrating with the Au nanoplates. These enhancements also depend on the size and shape of the Au nanoplates.
Iterative joint frequency offset and channel estimation for OFDM systems using first and second order approximation algorithms
Authors: Yen Rainfield Y , Liu Hong-Yu , Tsai Chia-Sheng 
Published: November 2012

Abstract
To implement an algorithm for joint estimation of carrier frequency offset (CFO) and channel impulse response (CIR) in orthogonal frequency division multiplexing (OFDM) systems, the maximum-likelihood criterion is commonly adopted. A major difficulty arises from the highly nonlinear nature of the log-likelihood function which renders local extrema or multiple solutions for the CFO and CIR estimators. Use of an approximation method coupled with an adaptive iteration algorithm has been a popular approach to ease problem solving. The approximation used in those existing methods is usually of the first order level. Here, in addition to a new first order approximation method, we also propose a second order approximation method. Further, for the part of the adaptive iteration algorithm, we adopt a new technique which will enable performance improvement. Our first order approximation method is found to outperform the existing ones in terms of estimation accuracies, tracking range, computation complexity, and convergence speed. As expected, our second order approximation method provides an even further improvement at the expense of higher computation complication.
Association between circulating ascorbic acid, α-tocopherol, 25-hydroxyvitamin D, and plasma cytokine concentrations in young adults: a cross-sectional study
Authors: García-Bailo Bibiana , Roke Kaitlin , Mutch David M , El-Sohemy Ahmed , Badawi Alaa 
Published: November 2012

Abstract

Background
Inflammation and oxidative stress are associated with the development of numerous chronic diseases. Circulating ascorbic acid, α-tocopherol, and 25-hydroxyvitamin D (25(OH)D) may help reduce concentrations of pro-inflammatory cytokines through their antioxidant and anti-inflammatory properties. These micronutrients may act synergistically, and they may have different anti-inflammatory effects, but previous studies have assessed the link between each of these micronutrients and inflammation in isolation without controlling for the other micronutrients. Our objective was to examine the association between circulating concentrations of ascorbic acid, α-tocopherol, and 25(OH) D and a panel of pro-inflammatory cytokines in an ethnically diverse population of young adults.

Methods
Participants (n = 1,007) from the Toronto Nutrigenomics and Health study provided fasting blood samples for biomarker measurements and were subsequently categorized into tertiles for each micronutrient based on their circulating concentrations. We conducted Pearson’s correlation analyses across all micronutrients and cytokines. The associations between individual micronutrients and cytokines were examined using analysis of covariance with age, sex, waist circumference, ethnicity, physical activity, season of blood collection, total cholesterol, hormonal contraceptive use among women, and the other two micronutrients as covariates.

Results
We observed weak micronutrient-cytokine correlations, moderate correlations between certain cytokines, and strong correlations between specific cytokines, particularly interleukin 1- receptor antagonist (IL-1RA), interferon-γ (IFN-γ), and platelet-derived growth factor BB (PDGF-bb). After full covariate adjustment, circulating α-tocopherol was inversely associated with IFN-γ and regulated upon activation normal T-cell expressed and secreted (RANTES). We observed an unexpected positive association between ascorbic acid and IFN-γ. 25(OH)D was not associated with altered concentrations of any inflammatory biomarkers.

Conclusions
These findings suggest that α-tocopherol, but not ascorbic acid or 25(OH)D, is inversely associated with inflammation in healthy young adults.
Female partners of opioid-injecting men in the Republic of Georgia: an initial characterization
Authors: Lund Ingunn O , Kirtadze Irma , Otiashvili David , O’Grady Kevin E , Jones Hendrée E 
Published: November 2012

Abstract

Background
HIV and Hepatitis C virus (HCV) infections are strongly related to injection drug use in the Republic of Georgia. Little information is available about HIV and HCV status, sexual risk, support for their partner, and risk for physical violence among the female partners of opioid-injecting men in the Republic of Georgia, many of whom may not be using drugs, yet may be at high risk of being infected with HIV and HCV from their drug-using partners.

Methods
In order to better understand the risks for females whose partners are injecting drugs, the present study conducted an initial investigation of the non-substance-using female partners of 40 opioid-injecting men who were participating in a clinical trial examining the feasibility and efficacy of a 22-week comprehensive intervention that paired behavioral treatment with naltrexone. The 40 female partners were assessed at their male partners’ study intake.

Results
The female sample was 32.3 years old (SD=6.7), 37 (93%) were married, with 15.5 years of education. A majority reported at least partial employment the majority of the time during the past 3 years, with only one woman reported being unemployed most of the time during the past 3 years. They self-reported they were 3% HIV-positive and 8% HCV-positive. Their HIV sex risk scores indicated a relatively low risk. However, only 4 (10%) women reported using a condom most of the time while having sex and 15 (38%) report not having had sex during the last 30 days. Experiences of interpersonal violence were common, with 42% reporting physical abuse by their partner during the last year and 48% reporting feeling unsafe in their current relationship.

Conclusions
The alarmingly high rate of failure to use barrier protection methods, together with the high percentage who did not know their HIV and HCV status, suggest that it may be beneficial to include non-substance-using female partners in prevention programs along with their partners to reduce the risk of HIV and HCV spreading from the population of injection-drug–using males into the general population. [This secondary analysis study was funded by an international supplement to the parent randomized clinical trial “Treating the Partners of Drug Using Pregnant Women: Stage II (HOPE)”. ClinicalTrials.gov Identifier: NCT00496990.]
A prevalence-based approach to societal costs occurring in consequence of child abuse and neglect
Authors: Habetha Susanne , Bleich Sabrina , Weidenhammer Jörg , Fegert Jörg M 
Published: November 2012

Abstract

Background
Traumatization in childhood can result in lifelong health impairment and may have a negative impact on other areas of life such as education, social contacts and employment as well. Despite the frequent occurrence of traumatization, which is reflected in a 14.5 percent prevalence rate of severe child abuse and neglect, the economic burden of the consequences is hardly known. The objective of this prevalence-based cost-of-illness study is to show how impairment of the individual is reflected in economic trauma follow-up costs borne by society as a whole in Germany and to compare the results with other countries’ costs.

Methods
From a societal perspective trauma follow-up costs were estimated using a bottom-up approach. The literature-based prevalence rate includes emotional, physical and sexual abuse as well as physical and emotional neglect in Germany. Costs are derived from individual case scenarios of child endangerment presented in a German cost-benefit-analysis. A comparison with trauma follow-up costs in Australia, Canada and the USA is based on purchasing power parity.

Results
The annual trauma follow-up costs total to a margin of EUR 11.1 billion for the lower bound and to EUR 29.8 billion for the upper bound. This equals EUR 134.84 and EUR 363.58, respectively, per capita for the German population. These results conform to the ones obtained from cost studies conducted in Australia (lower bound) and Canada (upper bound), whereas the result for the United States is much lower.

Conclusion
Child abuse and neglect result in trauma follow-up costs of economically relevant magnitude for the German society. Although the result is well in line with other countries’ costs, the general lack of data should be fought in order to enable more detailed future studies. Creating a reliable cost data basis in the first place can pave the way for long-term cost savings.
Cell Line Derived Multi-Gene Predictor of Pathologic Response to Neoadjuvant Chemotherapy in Breast Cancer: A Validation Study on US Oncology 02-103 Clinical Trial
Authors: Shen Kui , Qi Yuan , Song Nan , Tian Chunqiao , Rice Shara D , Gabrin Michael J , Brower Stacey L , Symmans William Fraser , O’Shaughnessy Joyce A , Holmes Frankie A , Asmar Lina , Pusztai Lajos 
Published: November 2012

Abstract

Background
The purpose of this study is to assess the predictive accuracy of a multi-gene predictor of response to docetaxel, 5-fluorouracil, epirubicin and cyclophosphamide combination chemotherapy on gene expression data from patients who received these drugs as neoadjuvant treatment.

Methods
Tumor samples were obtained from patients with stage II-III breast cancer before starting neoadjuvant chemotherapy with four cycles of 5-fluorouracil/epirubicin/cyclophosphamide (FEC) followed by four cycles of docetaxel/capecitabine (TX) on US Oncology clinical trial 02-103. Most patients with HER-2-positive cancer also received trastuzumab (H). The chemotherapy predictor (TFEC-MGP) was developed from publicly available gene expression data of 42 breast cancer cell-lines with corresponding in vitro chemotherapy sensitivity results for the four chemotherapy drugs. No predictor was developed for treatment with trastuzumab. The predictive performance of TFEC-MGP in distinguishing cases with pathologic complete response from those with residual disease was evaluated for the FEC/TX and FEC/TX plus H group separately. The area under the receiver-operating characteristic curve (AU-ROC) was used as the metric of predictive performance. Genomic predictions were performed blinded to clinical outcome.

Results
The AU-ROC was 0.70 (95% CI: 0.57-0.82) for the FEC/TX group (n=66) and 0.43 (95% CI: 0.20-0.66) for the FEC/TX plus H group (n=25). Among the patients treated with FEC/TX, the AU-ROC was 0.69 (95% CI: 0.52-0.86) for estrogen receptor (ER)-negative (n=28) and it was 0.59 (95% CI: 0.36-0.82) for ER-positive cancers (n=37). ER status was not reported for one patient.

Conclusions
Our results indicate that the cell line derived 291-probeset genomic predictor of response to FEC/TX combination chemotherapy shows good performance in a blinded validation study, particularly in ER-negative patients.
An algorithm for longitudinal registration of PET/CT images acquired during neoadjuvant chemotherapy in breast cancer: preliminary results
Authors: Li Xia , Abramson Richard G , Arlinghaus Lori R , Chakravarthy Anuradha Bapsi , Abramson Vandana , Mayer Ingrid , Farley Jaime , Delbeke Dominique , Yankeelov Thomas E 
Published: November 2012

Abstract

Background
By providing estimates of tumor glucose metabolism, 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) can potentially characterize the response of breast tumors to treatment. To assess therapy response, serial measurements of FDG-PET parameters (derived from static and/or dynamic images) can be obtained at different time points during the course of treatment. However, most studies track the changes in average parameter values obtained from the whole tumor, thereby discarding all spatial information manifested in tumor heterogeneity. Here, we propose a method whereby serially acquired FDG-PET breast data sets can be spatially co-registered to enable the spatial comparison of parameter maps at the voxel level.

Methods
The goal is to optimally register normal tissues while simultaneously preventing tumor distortion. In order to accomplish this, we constructed a PET support device to enable PET/CT imaging of the breasts of ten patients in the prone position and applied a mutual information-based rigid body registration followed by a non-rigid registration. The non-rigid registration algorithm extended the adaptive bases algorithm (ABA) by incorporating a tumor volume-preserving constraint, which computed the Jacobian determinant over the tumor regions as outlined on the PET/CT images, into the cost function. We tested this approach on ten breast cancer patients undergoing neoadjuvant chemotherapy.

Results
By both qualitative and quantitative evaluation, our constrained algorithm yielded significantly less tumor distortion than the unconstrained algorithm: considering the tumor volume determined from standard uptake value maps, the post-registration median tumor volume changes, and the 25th and 75th quantiles were 3.42% (0%, 13.39%) and 16.93% (9.21%, 49.93%) for the constrained and unconstrained algorithms, respectively (p = 0.002), while the bending energy (a measure of the smoothness of the deformation) was 0.0015 (0.0005, 0.012) and 0.017 (0.005, 0.044), respectively (p = 0.005).

Conclusion
The results indicate that the constrained ABA algorithm can accurately align prone breast FDG-PET images acquired at different time points while keeping the tumor from being substantially compressed or distorted.

Trial registration
NCT00474604