bluuebunny/crossref_metadata_2025_split huggingface dataset:
To stratify or not to stratify: power considerations for population‐based genome‐wide association studies of quantitative traits
Authors: Behrens Gundula , Winkler Thomas W. , Gorski Mathias , Leitzmann Michael F. , Heid Iris M. 
Published: November 2011

AbstractMeta‐analyses of genome‐wide association studies require numerous study partners to conduct pre‐defined analyses and thus simple but efficient analyses plans. Potential differences between strata (e.g. men and women) are usually ignored, but often the question arises whether stratified analyses help to unravel the genetics of a phenotype or if they unnecessarily increase the burden of analyses. To decide whether to stratify or not to stratify, we compare general analytical power computations for the overall analysis with those of stratified analyses considering quantitative trait analyses and two strata. We also relate the stratification problem to interaction modeling and exemplify theoretical considerations on obesity and renal function genetics. We demonstrate that the overall analyses have better power compared to stratified analyses as long as the signals are pronounced in both strata with consistent effect direction. Stratified analyses are advantageous in the case of signals with zero (or very small) effect in one stratum and for signals with opposite effect direction in the two strata. Applying the joint test for a main SNP effect and SNP‐stratum interaction beats both overall and stratified analyses regarding power, but involves more complex models. In summary, we recommend to employ stratified analyses or the joint test to better understand the potential of strata‐specific signals with opposite effect direction. Only after systematic genome‐wide searches for opposite effect direction loci have been conducted, we will know if such signals exist and to what extent stratified analyses can depict loci that otherwise are missed. Genet. Epidemiol. 2011. © 2011 Wiley Periodicals, Inc.35:867‐879, 2011
Pitfalls of merging GWAS data: lessons learned in the eMERGE network and quality control procedures to maintain high data quality
Authors: Zuvich Rebecca L. , Armstrong Loren L. , Bielinski Suzette J. , Bradford Yuki , Carlson Christopher S. , Crawford Dana C. , Crenshaw Andrew T. , de Andrade Mariza , Doheny Kimberly F. , Haines Jonathan L. , Hayes M. Geoffrey , Jarvik Gail P. , Jiang Lan , Kullo Iftikhar J. , Li Rongling , Ling Hua , Manolio Teri A. , Matsumoto Martha E. , McCarty Catherine A. , McDavid Andrew N. , Mirel Daniel B. , Olson Lana M. , Paschall Justin E. , Pugh Elizabeth W. , Rasmussen Luke V. , Rasmussen‐Torvik Laura J. , Turner Stephen D. , Wilke Russell A. , Ritchie Marylyn D. 
Published: November 2011

AbstractGenome‐wide association studies (GWAS) are a useful approach in the study of the genetic components of complex phenotypes. Aside from large cohorts, GWAS have generally been limited to the study of one or a few diseases or traits. The emergence of biobanks linked to electronic medical records (EMRs) allows the efficient reuse of genetic data to yield meaningful genotype–phenotype associations for multiple phenotypes or traits. Phase I of the electronic MEdical Records and GEnomics (eMERGE‐I) Network is a National Human Genome Research Institute‐supported consortium composed of five sites to perform various genetic association studies using DNA repositories and EMR systems. Each eMERGE site has developed EMR‐based algorithms to comprise a core set of 14 phenotypes for extraction of study samples from each site's DNA repository. Each eMERGE site selected samples for a specific phenotype, and these samples were genotyped at either the Broad Institute or at the Center for Inherited Disease Research using the Illumina Infinium BeadChip technology. In all, approximately 17,000 samples from across the five sites were genotyped. A unified quality control (QC) pipeline was developed by the eMERGE Genomics Working Group and used to ensure thorough cleaning of the data. This process includes examination of sample and marker quality and various batch effects. Upon completion of the genotyping and QC analyses for each site's primary study, eMERGE Coordinating Center merged the datasets from all five sites. This larger merged dataset reentered the established eMERGE QC pipeline. Based on lessons learned during the process, additional analyses and QC checkpoints were added to the pipeline to ensure proper merging. Here, we explore the challenges associated with combining datasets from different genotyping centers and describe the expansion to eMERGE QC pipeline for merged datasets. These additional steps will be useful as the eMERGE project expands to include additional sites in eMERGE‐II, and also serve as a starting point for investigators merging multiple genotype datasets accessible through the National Center for Biotechnology Information in the database of Genotypes and Phenotypes. Our experience demonstrates that merging multiple datasets after additional QC can be an efficient use of genotype data despite new challenges that appear in the process. Genet. Epidemiol. 35:887–898, 2011. © 2011 Wiley Periodicals, Inc.
Uncertainty assessment of hydrologic and climate forecast models in Northeastern Brazil
Authors: Kwon Hyun‐Han , de Assis de Souza Filho Francisco , Block Paul , Sun Liqiang , Lall Upmanu , Reis Dirceu S. 
Published: November 2011

AbstractSeasonal streamflow forecasts based on climate information can guide water managers toward superior reservoir operations, leading to improved water resources management efficiency. Uncertainty, however, is always present in seasonal streamflow forecasts, affecting the forecast value. Thus, a forecast should not be considered complete without a description of its uncertainty, which is critical for climate risk and water resources management. This study investigates the uncertainties of a seasonal streamflow forecast system for Northeastern Brazil based on climate precipitation forecasts and hydrologic modeling. These two sources of uncertainty are treated independently and then compared in order to guide future investments in the forecast system. Sea surface temperature is considered to be the primary source of uncertainty for the seasonal precipitation forecasts, based upon a 10‐member climate model ensemble. Parameter uncertainty is considered to be the only source of uncertainty for the hydrologic model. Estimation of parameter uncertainty is estimated by the Shuffled Complex Evolution Metropolis algorithm, which employs a Markov Chain Monte Carlo scheme to provide the posterior distribution of the parameters and form uncertainty bounds on streamflow forecasts. Results indicate that uncertainties associated with the climate forecast are much larger than those from parameter estimation in the hydrologic model. Although model structure has not been considered in the evaluation of hydrologic uncertainties, this study indicates that future efforts to address the predominant source of uncertainty should focus on the climate prediction models. Copyright © 2011 John Wiley & Sons, Ltd.
Estimated phytanic acid intake and prostate cancer risk: A prospective cohort study
Authors: Wright Margaret E. , Bowen Phyllis , Virtamo Jarmo , Albanes Demetrius , Gann Peter H. 
Published: November 2011

AbstractPhytanic acid is a saturated fatty acid found predominantly in red meat and dairy products and may contribute to increases in prostate cancer risk that are observed with higher intakes of these foods. We constructed a novel summary measure of phytanic acid intake and prospectively examined its association with prostate cancer risk in the Alpha‐Tocopherol, Beta‐Carotene Cancer Prevention Study—a cohort of Finnish male smokers aged 50–69 years. Diet was assessed at baseline in 27,111 participants using a validated 276‐item dietary questionnaire. Since phytanic acid is not currently included in food composition tables, we used the published phytanic acid content of 151 major food items to estimate total daily intake. During up to 21 years of follow‐up, a total of 1,929 incident prostate cancer cases (including 438 advanced cases) were identified. Higher phytanic acid intake, though unrelated to the risk of localized disease [relative risks (RR) and 95% confidence intervals (CI) for increasing quartiles of intake = 1.00 (ref), 0.83 (0.68–1.01), 0.76 (0.62–0.94) and 0.91 (0.74–1.13); p trend = 0.23], was associated with increased risks of advanced prostate cancer [RR and 95% CI = 1.00 (ref), 1.43 (1.09–1.89), 1.31 (0.99–1.75) and 1.38 (1.02–1.89); p trend = 0.06]. This association appeared to be driven predominantly by phytanic acid obtained from dairy products (particularly butter). Our study indicates that phytanic acid may contribute to previously observed associations between high‐fat animal foods (particularly dairy products) and prostate cancer risk, although some caution is warranted as it may be acting as a surrogate marker of dairy fat.
Using biofilms as initial inocula in animal models of biofilm‐related infections
Authors: Williams Dustin L. , Costerton J. William 
Published: November 2011

AbstractOne of the most practical strategies that has been undertaken to fight biofilm implant‐related infections has been the development of coatings on biomaterial devices that can elute antimicrobials into regions of patients' tissues. To date, the majority of animal studies that have been developed to model infections that accompany the use of these materials have primarily involved an initial inoculum of planktonic bacterial cells from batch cultures. Although valuable, data that have been derived from these experiments may not provide important clinical insight into how bacteria in well‐established, mature biofilms impact device‐related and other clinical infections when they contaminate a patient site or implanted device. In this review, a discussion is presented on the impact that a shift in biofilm research may have if initial inocula of well‐established, mature biofilms are used to model biomaterial device‐related infections in animal models. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
A fully degradable tracheal stent: In vitro and in vivo characterization of material degradation
Authors: Ng Anthony H. C. , Ng Nelson S. P. , Zhu G. H. , Lim Lynne H. Y. , Venkatraman Subbu S. 
Published: November 2011

AbstractWe report on the testing of materials for a fully degradable tracheal stent. Such a stent has several advantages over currently used permanent stents made of metal or silicone polymers. However, the mode of degradation in the trachea is expected to be different from a fully submerged device, because of the uniqueness of the tracheal environment. A physical model was developed to allow an in‐depth study of degradation of bioabsorbable polymers exposed to two differing media; namely 70 wt % water (gel) on one side and humidified air on the other, simulating conditions in a tracheal passage. Longitudinal microtome slices were obtained from both polymer surfaces and degradation kinetics data were derived from size exclusion chromatography. On the basis of the data obtained, it is observed that well‐studied bulk‐degrading polymers might show surface‐eroding properties in such an environment. Generally, hydrophobic polymers retard the formation of a water concentration gradient and exhibit bulk‐degradation kinetics. However, addition of specific plasticizers can influence the water uptake gradient, and force the polymer towards a pseudo “surface‐eroding” behavior. In vivo studies in a rabbit model of degradable stents made from a selected polymer, demonstrate the feasibility of a fully bioabsorbable tracheal stent. This study aims to improve understanding of degradation of polymers under heterogeneous environments. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2012.
Association of participation in a mindfulness program with measures of PTSD, depression and quality of life in a veteran sample
Authors: Kearney David J. , McDermott Kelly , Malte Carol , Martinez Michelle , Simpson Tracy L. 
Published: November 2011

AbstractObjectives: To assess outcomes of veterans who participated in mindfulness‐based stress reduction (MBSR). Design: Posttraumatic stress disorder (PTSD) symptoms, depression, functional status, behavioral activation, experiential avoidance, and mindfulness were assessed at baseline, and 2 and 6 months after enrollment. Results: At 6 months, there were significant improvements in PTSD symptoms (standardized effect size, d = ‐0.64, p< 0.001); depression (d = ‐0.70, p<0.001); behavioral activation (d = 0.62, p<0.001); mental component summary score of the Short Form‐8 (d = 0.72, p<0.001); acceptance (d = 0.67, p<0.001); and mindfulness (d = 0.78, p<0.001), and 47.7% of veterans had clinically significant improvements in PTSD symptoms. Conclusions: MBSR shows promise as an intervention for PTSD and warrants further study in randomized controlled trials. © 2011 Wiley Periodicals, Inc. J Clin Psychol 68:1–16, 2012.
Matrix metalloproteinase3 gene promoter polymorphisms and their haplotypes are associated with gastric cancer risk in eastern Indian population
Authors: Dey Sanjib , Stalin Sami , Gupta Arnab , Saha Debjit , Kesh Kousik , Swarnakar Snehasikta 
Published: November 2011

AbstractSingle nucleotide polymorphisms (SNPs) of matrix metalloproteinase3 (MMP3) promoter in the development and progression of gastric cancer of whole stomach has never been investigated in any population. We conducted a hospital‐based case‐control study to explore the MMP3 SNPs and their haplotypes with the risk of gastric cancer for the first time in eastern Indian population. A total of 218 gastric cancer patients and 175 healthy controls were genotyped for MMP3‐1612 5A/6A (rs3025058) by PCR–RFLP and rechecked 10% by DNA sequencing. MMP3‐707 A/G (rs522616) and MMP3‐375 C/G (rs617819) were genotyped by DNA sequencing among 209 patients and 154 controls. MMP3‐1612 5A6A genotype (P = 0.026, odds ratio (OR) = 1.756, confidence interval (CI) = 1.070–2.883), combined 5A5A and 5A6A genotype (P = 0.015, OR = 1.791, CI = 1.122–2.858) and 5A allele (P = 0.002, OR = 1.75, CI = 1.21–2.53) and; MMP3‐707 GG genotype (P = < 0.0001; OR = 9.612; 95% CI = 3.403–27.147), combined GG and AG genotype (P = 0.001, OR = 2.201, CI = 1.385–3.498) and G allele (P = <0.0001, OR = 2.189, CI = 1.582–3.033) conferred significant risk for gastric cancer development. Also, tobacco addicted individuals with combined 5A5A and 5A6A genotype (P = 0.005, OR = 2.952, CI = 1.377–6.327) at −1612 position of MMP3 promoter displayed a higher risk to gastric cancer development. The genotypic combinations of all three MMP3 promoter polymorphisms and their haplotypes with increasing risk allele in a dose‐dependent manner showed a potential risk for developing gastric cancer. The analyses suggested that the MMP3‐707 G/G and MMP3‐1612 5A/6A polymorphisms are potential independent predictors of gastric cancer risk development. © 2011 Wiley Periodicals, Inc.
Processed nerve allografts for peripheral nerve reconstruction: A multicenter study of utilization and outcomes in sensory, mixed, and motor nerve reconstructions
Authors: Brooks Darrell N. , Weber Renata V. , Chao Jerome D. , Rinker Brian D. , Zoldos Jozef , Robichaux Michael R. , Ruggeri Sebastian B. , Anderson Kurt A. , Bonatz Ekkehard E. , Wisotsky Scott M. , Cho Mickey S. , Wilson Christopher , Cooper Ellis O. , Ingari John V. , Safa Bauback , Parrett Brian M. , Buncke Gregory M. 
Published: November 2011

AbstractPurpose: As alternatives to autograft become more conventional, clinical outcomes data on their effectiveness in restoring meaningful function is essential. In this study we report on the outcomes from a multicenter study on processed nerve allografts (Avance® Nerve Graft, AxoGen, Inc). Patients and Methods: Twelve sites with 25 surgeons contributed data from 132 individual nerve injuries. Data was analyzed to determine the safety and efficacy of the nerve allograft. Sufficient data for efficacy analysis were reported in 76 injuries (49 sensory, 18 mixed, and 9 motor nerves). The mean age was 41 ± 17 (18–86) years. The mean graft length was 22 ± 11 (5–50) mm. Subgroup analysis was performed to determine the relationship to factors known to influence outcomes of nerve repair such as nerve type, gap length, patient age, time to repair, age of injury, and mechanism of injury. Results: Meaningful recovery was reported in 87% of the repairs reporting quantitative data. Subgroup analysis demonstrated consistency, showing no significant differences with regard to recovery outcomes between the groups (P > 0.05 Fisher's Exact Test). No graft related adverse experiences were reported and a 5% revision rate was observed. Conclusion: Processed nerve allografts performed well and were found to be safe and effective in sensory, mixed and motor nerve defects between 5 and 50 mm. The outcomes for safety and meaningful recovery observed in this study compare favorably to those reported in the literature for nerve autograft and are higher than those reported for nerve conduits. © 2011 Wiley Periodicals, Inc. Microsurgery, 2012.
Dispersion of carbon nanotubes through amphiphilic block copolymers: Rheological and dielectrical characterizations of poly(ethylene oxide) composites
Authors: Semaan Chantal , Schappacher Michèle , Soum Alain 
Published: November 2011

AbstractIn this article, we report on some properties of polymer nanocomposites prepared from dispersions of multiwall carbon nanotubes (CNT) in aqueous solution prepared using amphiphilic block copolymers. These nanocomposites are made of polyethylene oxide as matrix and CNT wrapped with copolymers as fillers. We investigated the rheological and electrical behavior of such composites with the objectives of underlined the effect of wrapping. Two rheological and only one electrical percolation thresholds have been observed and related to polymer–CNT and CNT–CNT networks. The low values of these percolation thresholds agree with a homogeneous dispersion of CNT in the matrix. We also demonstrated that specific wrapping may induce an increase of electrical conductivity without affecting too much the viscosity of the melt. POLYM. COMPOS., 2012. © 2011 Society of Plastics Engineers
Zero‐valent bimetallic iron/copper catalyzed SET‐LRP: A dual activation by zero‐valent iron
Authors: Zhou Lili , Zhang Zhengbiao , Wang Wenxiang , Cheng Zhenping , Zhou Nianchen , Zhu Jian , Zhang Wei , Zhu Xiulin 
Published: November 2011

AbstractIn this work, bimetallic zero‐valent metal (Fe(0) powder and Cu(0) powder) was used to mediate the single electron transfer‐living radical polymerization (SET‐LRP) of methyl methacrylate at 25 °C in dimethyl sulfoxide. Different feed ratios of [Fe(0)]0/[Cu(0)]0 (0/1.5, 0.5/1, 0.75/0.75, 1/0.5, and 1.3/0.2) were explored. With the increase of Fe(0) feed, the polymerization rate was mildly depressed with a prolonged induction period. While, the control over the molecular weights was improved upon the increase of Fe(0). A best control (initiation efficiency = 91%) was achieved at [Fe(0)]0/[Cu(0)]0 = 1/0.5. A further increase of Fe(0) to the feed ratio of [Fe(0)]0:[Cu(0)]0 = 1.3: 0.2 led to a uncontrolled polymerization. Explorations of available solvents and ligands for this polymerization confirmed the SET‐LRP mechanism. It was suggested that Fe(0) might act as a dual role in this process: one was the activation agent for Cu(0), which favored a better control over the molecular weights; The other was an alternative catalyst for the activation of R‐X or Pn‐X to generate radicals, which assured a comparable polymerization rate as that of Cu(0). This work provided an alternative and economical catalyst for SET‐LRP, and would eventually reinforce the SET‐LRP technique. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Ultraviolet to near‐infrared downconversion in Yb3+‐doped Sr2CeO4
Authors: Zhou Ru , Wei Xiantao , Chen Yonghu , Duan Changkui , Yin Min 
Published: November 2011

AbstractEfficient blue–green emission is observed for Sr2CeO4 under ultraviolet excitation ranging from 250 to 400 nm and this is ascribed to the emission of the O2−–Ce4+ charge transfer (CT) states. Under the excitation of ultraviolet light in the broad absorption band, an intense near‐infrared (NIR) emission of Yb3+: 2F5/2 → 2F7/2 around 1 µm is observed for Yb3+‐doped Sr2CeO4. The Yb3+ concentration‐dependent luminescence properties and the lifetimes of both the visible CT emission and the NIR Yb3+ emission are investigated under the excitation of a 266‐nm pulsed laser beam. The fast decline of the lifetimes of the CT emission with the increasing Yb3+ concentration suggests efficient energy transfer from the host to Yb3+ ions. A cooperative energy transfer (CET) mechanism is proposed to explain the NIR downconversion process. The Sr2CeO4:Yb3+ phosphors can convert ultraviolet photons into NIR photons around 1 µm with a twofold increase in the photon number via CET, which has potential application in enhancing the photovoltaic conversion efficiency of silicon‐based solar cells.
Stress Effects: A Study of Salivary Cortisol Levels in Third‐year Medical Students
Authors: Tseng Teresa , Iosif Ana‐Maria , Seritan Andreea L. 
Published: November 2011

AbstractThe physical, mental and emotional stresses experienced during the training and careers of physicians have been linked to increased rates of anxiety, depression and suicide. Increased stress leads to alterations in the hypothalamic–pituitary–adrenal (HPA) axis, which can determine multisystem modulations with acute and chronic consequences. This study investigated salivary cortisol patterns in third‐year medical students performing clinical work at a US medical school. Morning and evening salivary cortisol samples were collected from students during the last 2 weeks of each of three successive clinical rotations and while on vacation. Salivary cortisol levels were measured using Siemens radioimmunoassay kits (Siemens Medical Solutions Diagnostics, Los Angeles, CA, USA). Statistical analysis used mixed‐effects regression models. Eleven students submitted 64 salivary samples. Statistically significant blunting of the diurnal cortisol variation was observed in students on inpatient rotations. HPA axis changes occur in third‐year medical students performing inpatient clinical work. These findings can inform curriculum planning, rotation‐specific guidelines and the development of student wellness programmes. Copyright © 2011 John Wiley & Sons, Ltd.