MO-DE-207B-01: JACK FOWLER JUNIOR INVESTIGATOR COMPETITION WINNER: Between Somatic Mutations and PET-Based Radiomic Features in Non-Small Cell Lung Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yip, S; Coroller, T; Rios Velazquez, E

Purpose: Although PET-based radiomic features have been proposed to quantify tumor heterogeneity and shown promise in outcome prediction, little is known about their relationship with tumor genetics. This study assessed the association of [{sup 18}F]fluorodeoxyglucose (FDG)-PET-based radiomic features with non-small cell lung cancer (NSCLC) mutations. Methods: 348 NSCLC patients underwent FDG-PET/CT scans before treatment and were tested for genetic mutations. 13% (44/348) and 28% (96/348) patients were found to harbor EGFR (EGFR+) and KRAS (KRAS+) mutations, respectively. We evaluated nineteen PET-based radiomic features quantifying phenotypic traits, and compared them with conventional PET features (metabolic tumor volume (MTV) and maximum-SUV). Themore » association between the feature values and mutation status was evaluated using the Wilcoxcon-rank-sum-test. The ability of each measure to predict mutations was assessed by the area under the receiver operating curve (AUC). Noether’s test was used to determine if the AUCs were significantly from random (AUC=0.50). All p-values were corrected for multiple testing by controlling the false discovery rate (FDR{sub Wilcoxon} and FDR{sub Noether}) of 10%. Results: Eight radiomic features, MTV, and maximum-SUV, were significantly associated with the EGFR mutation (FDR{sub Wilcoxon}=0.01–0.10). However, KRAS+ demonstrated no significantly distinctive imaging features compared to KRAS− (FDR{sub Wilcoxon}≥0.92). EGFR+ and EGFR− were significantly discriminated by conventional PET features (AUC=0.61, FDR{sub Noether}=0.04 for MTV and AUC=0.64, FDR{sub Noether}=0.01 for maximum-SUV). Eight radiomic features were significantly predictive for EGFR+ compared to EGFR− (AUC=0.59–0.67, FDR{sub Noether}=0.0032–0.09). Normalized-inverse-difference-moment outperformed all features in predicting EGFR mutation (AUC=0.67, FDR{sub Noether}=0.0032). Moreover, only the radiomic feature normalized-inverse-difference-moment could significantly predict KRAS+ from EGFR+ (AUC=0.65, FDR{sub Noether}=0.05). All measures failed to predict KRAS+ from KRAS− (AUC=0.50–0.54, FDR{sub Noether}≥0.92). Conclusion: PET imaging features were strongly associated with EGFR mutations in NSCLC. Radiomic features have great potential in predicting EGFR mutations. Our study may help develop a non-invasive imaging biomarker for EGFR mutation. R.M. has consulting interests with Amgen.« less

Dihydropyrimidine dehydrogenase pharmacogenetics for predicting fluoropyrimidine-related toxicity in the randomised, phase III adjuvant TOSCA trial in high-risk colon cancer patients

PubMed Central

Ruzzo, A; Graziano, F; Galli, Fabio; Galli, Francesca; Rulli, E; Lonardi, S; Ronzoni, M; Massidda, B; Zagonel, V; Pella, N; Mucciarini, C; Labianca, R; Ionta, M T; Bagaloni, I; Veltri, E; Sozzi, P; Barni, S; Ricci, V; Foltran, L; Nicolini, M; Biondi, E; Bramati, A; Turci, D; Lazzarelli, S; Verusio, C; Bergamo, F; Sobrero, A; Frontini, L; Menghi, M; Magnani, M

2017-01-01

Background: Dihydropyrimidine dehydrogenase (DPD) catabolises ∼85% of the administered dose of fluoropyrimidines. Functional DPYD gene variants cause reduced/abrogated DPD activity. DPYD variants analysis may help for defining individual patients’ risk of fluoropyrimidine-related severe toxicity. Methods: The TOSCA Italian randomised trial enrolled colon cancer patients for 3 or 6 months of either FOLFOX-4 or XELOX adjuvant chemotherapy. In an ancillary pharmacogenetic study, 10 DPYD variants (*2A rs3918290 G>A, *13 rs55886062 T>G, rs67376798 A>T, *4 rs1801158 G>A, *5 rs1801159 A>G, *6 rs1801160 G>A, *9A rs1801265 T>C, rs2297595 A>G, rs17376848 T>C, and rs75017182 C>G), were retrospectively tested for associations with ⩾grade 3 fluoropyrimidine-related adverse events (FAEs). An association analysis and a time-to-toxicity (TTT) analysis were planned. To adjust for multiple testing, the Benjamini and Hochberg’s False Discovery Rate (FDR) procedure was used. Results: FAEs occurred in 194 out of 508 assessable patients (38.2%). In the association analysis, FAEs occurred more frequently in *6 rs1801160 A allele carriers (FDR=0.0083). At multivariate TTT analysis, significant associations were found for *6 rs1801160 A allele carriers (FDR<0.0001), *2A rs3918290 A allele carriers (FDR<0.0001), and rs2297595 GG genotype carriers (FDR=0.0014). Neutropenia was the most common FAEs (28.5%). *6 rs1801160 (FDR<0.0001), and *2A rs3918290 (FDR=0.0004) variant alleles were significantly associated with time to neutropenia. Conclusions: This study adds evidence on the role of DPYD pharmacogenetics for safety of patients undergoing fluoropyrimidine-based chemotherapy. PMID:29065426

Dihydropyrimidine dehydrogenase pharmacogenetics for predicting fluoropyrimidine-related toxicity in the randomised, phase III adjuvant TOSCA trial in high-risk colon cancer patients.

PubMed

Ruzzo, A; Graziano, F; Galli, Fabio; Galli, Francesca; Rulli, E; Lonardi, S; Ronzoni, M; Massidda, B; Zagonel, V; Pella, N; Mucciarini, C; Labianca, R; Ionta, M T; Bagaloni, I; Veltri, E; Sozzi, P; Barni, S; Ricci, V; Foltran, L; Nicolini, M; Biondi, E; Bramati, A; Turci, D; Lazzarelli, S; Verusio, C; Bergamo, F; Sobrero, A; Frontini, L; Menghi, M; Magnani, M

2017-10-24

Dihydropyrimidine dehydrogenase (DPD) catabolises ∼85% of the administered dose of fluoropyrimidines. Functional DPYD gene variants cause reduced/abrogated DPD activity. DPYD variants analysis may help for defining individual patients' risk of fluoropyrimidine-related severe toxicity. The TOSCA Italian randomised trial enrolled colon cancer patients for 3 or 6 months of either FOLFOX-4 or XELOX adjuvant chemotherapy. In an ancillary pharmacogenetic study, 10 DPYD variants (*2A rs3918290 G>A, *13 rs55886062 T>G, rs67376798 A>T, *4 rs1801158 G>A, *5 rs1801159 A>G, *6 rs1801160 G>A, *9A rs1801265 T>C, rs2297595 A>G, rs17376848 T>C, and rs75017182 C>G), were retrospectively tested for associations with ⩾grade 3 fluoropyrimidine-related adverse events (FAEs). An association analysis and a time-to-toxicity (TTT) analysis were planned. To adjust for multiple testing, the Benjamini and Hochberg's False Discovery Rate (FDR) procedure was used. FAEs occurred in 194 out of 508 assessable patients (38.2%). In the association analysis, FAEs occurred more frequently in *6 rs1801160 A allele carriers (FDR=0.0083). At multivariate TTT analysis, significant associations were found for *6 rs1801160 A allele carriers (FDR<0.0001), *2A rs3918290 A allele carriers (FDR<0.0001), and rs2297595 GG genotype carriers (FDR=0.0014). Neutropenia was the most common FAEs (28.5%). *6 rs1801160 (FDR<0.0001), and *2A rs3918290 (FDR=0.0004) variant alleles were significantly associated with time to neutropenia. This study adds evidence on the role of DPYD pharmacogenetics for safety of patients undergoing fluoropyrimidine-based chemotherapy.

Metabolic syndrome, diabetes and inadequate lifestyle in first-degree relatives of acute myocardial infarction survivors younger than 45 years old.

PubMed

Gurgel, Maria Helane C; Montenegro Junior, Renan M; Melo Ponte, Clarisse M; Sousa, Tamara Cristina S; Silva, Paulo Goberlanio B; de Sousa Belém, Lucia; Furtado, Frederico Luis Braz; de Araújo Batista, Lívia A; Pereira, Alexandre C; Santos, Raul D

2017-11-28

A premature myocardial infarction (PMI) is usually associated with a familial component. This study evaluated cardiovascular risk factors in first-degree relatives (FDR) of patients with PMI not presenting the familial hypercholesterolemia phenotype. A cross-sectional study comprising FDR of non-familial hypercholesterolemia patients who suffered a myocardial infarction <45-years age matched for age and sex with individuals without family history of cardiovascular disease. Subjects were evaluated for presence of the metabolic syndrome and its components, lifestyle, statin therapy, and laboratory parameters. The sample was composed of 166 FDR of 103 PMI patients and 111 controls. The prevalence of smoking (29.5 vs. 6.3%; p < 0.001), prediabetes (40.4 vs. 27%; p < 0.001), diabetes (19.9 vs. 1.8%; p < 0.001), metabolic syndrome (64.7 vs. 36%; p < 0.001), and dyslipidemia (84.2 vs. 31.2%; p = 0.001) was greater in FDR. There was no difference on the prevalence of abdominal obesity between groups. In addition, FDR presented higher triglycerides (179.0 ± 71.0 vs. 140.0 ± 74.0 mg/dL; p = 0.002), LDL-cholesterol (122.0 ± 36.0 vs. 113.0 ± 35 mg/dL; p = 0.031), non-HDL-cholesterol (157.0 ± 53.0 vs. 141.0 ± 41.0 mg/dL; p = 0.004), and lower HDL-cholesterol (39.0 ± 10.0 vs. 48.0 ± 14.0 mg/dL; p < 0.001) than controls. Thyrotropin levels (2.4 ± 1.6 vs. 1.9 ± 1.0 mUI/L; p = 0.002) were higher in FDR. The risk factor pattern was like the one of index cases. Only 5.9% (n = 10) of FDR were in use of statins. FDR of non-familial hypercholesterolemia patients with PMI presented an elevated prevalence of metabolic abnormalities, inadequate lifestyle and were undertreated for dyslipidemia.

Dr. Polio: Revisiting FDR's Medical Legacy.

PubMed

Dorfman, Robert G; Orkaby, Asher; Desai, Sukumar P

2018-01-01

The National Foundation for Infantile Paralysis (NFIP), the March of Dimes, and the Georgia Warm Springs Resort were reflections of Franklin D. Roosevelt's (FDR) complicated and personal relationship with polio. Between 1934 and 1957, significant advances were made in the care of polio survivors, and new and innovative medical fields gained both public attention and funding. The plight of disabled Americans and questions of accessibility also received widespread national attention. The NFIP helped establish a new prototype for grassroots philanthropy and personified FDR's vision for national health insurance. Drawing upon a variety of archival and primary sources, this article aims to revisit Roosevelt's contribution to the medical field. Rather than condone or defend FDR's public persona as a survivor of polio, this article argues that Roosevelt and his affiliated organizations played an important medical role during this period.

Testing jumps via false discovery rate control.

PubMed

Yen, Yu-Min

2013-01-01

Many recently developed nonparametric jump tests can be viewed as multiple hypothesis testing problems. For such multiple hypothesis tests, it is well known that controlling type I error often makes a large proportion of erroneous rejections, and such situation becomes even worse when the jump occurrence is a rare event. To obtain more reliable results, we aim to control the false discovery rate (FDR), an efficient compound error measure for erroneous rejections in multiple testing problems. We perform the test via the Barndorff-Nielsen and Shephard (BNS) test statistic, and control the FDR with the Benjamini and Hochberg (BH) procedure. We provide asymptotic results for the FDR control. From simulations, we examine relevant theoretical results and demonstrate the advantages of controlling the FDR. The hybrid approach is then applied to empirical analysis on two benchmark stock indices with high frequency data.

Pharmacovigilance data mining with methods based on false discovery rates: a comparative simulation study.

PubMed

Ahmed, I; Thiessard, F; Miremont-Salamé, G; Bégaud, B; Tubert-Bitter, P

2010-10-01

The early detection of adverse reactions caused by drugs that are already on the market is the prime concern of pharmacovigilance efforts; the methods in use for postmarketing surveillance are aimed at detecting signals pointing to potential safety concerns, on the basis of reports from health-care providers and from information available in various databases. Signal detection methods based on the estimation of false discovery rate (FDR) have recently been proposed. They address the limitation of arbitrary detection thresholds of the automatic methods in current use, including those last updated by the US Food and Drug Administration and the World Health Organization's Uppsala Monitoring Centre. We used two simulation procedures to compare the false-positive performances for three current methods: the reporting odds ratio (ROR), the information component (IC), the gamma Poisson shrinkage (GPS), and also for two FDR-based methods derived from the GPS model and Fisher's test. Large differences in FDR rates were associated with the signal-detection methods currently in use. These differences ranged from 0.01 to 12% in an analysis that was restricted to signals with at least three reports. The numbers of signals generated were also highly variable. Among fixed-size lists of signals, the FDR was lowered when the FDR-based approaches were used. Overall, the outcomes in both simulation studies suggest that improvement in effectiveness can be expected from use of the FDR-based GPS method.

Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes.

PubMed

Jiang, Lingjing; Amir, Amnon; Morton, James T; Heller, Ruth; Arias-Castro, Ery; Knight, Rob

2017-01-01

Differential abundance testing is a critical task in microbiome studies that is complicated by the sparsity of data matrices. Here we adapt for microbiome studies a solution from the field of gene expression analysis to produce a new method, discrete false-discovery rate (DS-FDR), that greatly improves the power to detect differential taxa by exploiting the discreteness of the data. Additionally, DS-FDR is relatively robust to the number of noninformative features, and thus removes the problem of filtering taxonomy tables by an arbitrary abundance threshold. We show by using a combination of simulations and reanalysis of nine real-world microbiome data sets that this new method outperforms existing methods at the differential abundance testing task, producing a false-discovery rate that is up to threefold more accurate, and halves the number of samples required to find a given difference (thus increasing the efficiency of microbiome experiments considerably). We therefore expect DS-FDR to be widely applied in microbiome studies. IMPORTANCE DS-FDR can achieve higher statistical power to detect significant findings in sparse and noisy microbiome data compared to the commonly used Benjamini-Hochberg procedure and other FDR-controlling procedures.

Field Measurements and Numerical Simulations of Temperature and Moisture in Highway Engineering Using a Frequency Domain Reflectometry Sensor.

PubMed

Yao, Yong-Sheng; Zheng, Jian-Long; Chen, Zeng-Shun; Zhang, Jun-Hui; Li, Yong

2016-06-10

This paper presents a systematic pioneering study on the use of agricultural-purpose frequency domain reflectometry (FDR) sensors to monitor temperature and moisture of a subgrade in highway extension and reconstruction engineering. The principle of agricultural-purpose FDR sensors and the process for embedding this kind of sensors for subgrade engineering purposes are introduced. Based on field measured weather data, a numerical analysis model for temperature and moisture content in the subgrade's soil is built. Comparisons of the temperature and moisture data obtained from numerical simulation and FDR-based measurements are conducted. The results show that: (1) the embedding method and process, data acquisition, and remote transmission presented are reasonable; (2) the temperature and moisture changes are coordinated with the atmospheric environment and they are also in close agreement with numerical calculations; (3) the change laws of both are consistent at positions where the subgrade is compacted uniformly. These results suggest that the data measured by the agricultural-purpose FDR sensors are reliable. The findings of this paper enable a new and effective real-time monitoring method for a subgrade's temperature and moisture changes, and thus broaden the application of agricultural-purpose FDR sensors.

cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate.

PubMed

Clevert, Djork-Arné; Mitterecker, Andreas; Mayr, Andreas; Klambauer, Günter; Tuefferd, Marianne; De Bondt, An; Talloen, Willem; Göhlmann, Hinrich; Hochreiter, Sepp

2011-07-01

Cost-effective oligonucleotide genotyping arrays like the Affymetrix SNP 6.0 are still the predominant technique to measure DNA copy number variations (CNVs). However, CNV detection methods for microarrays overestimate both the number and the size of CNV regions and, consequently, suffer from a high false discovery rate (FDR). A high FDR means that many CNVs are wrongly detected and therefore not associated with a disease in a clinical study, though correction for multiple testing takes them into account and thereby decreases the study's discovery power. For controlling the FDR, we propose a probabilistic latent variable model, 'cn.FARMS', which is optimized by a Bayesian maximum a posteriori approach. cn.FARMS controls the FDR through the information gain of the posterior over the prior. The prior represents the null hypothesis of copy number 2 for all samples from which the posterior can only deviate by strong and consistent signals in the data. On HapMap data, cn.FARMS clearly outperformed the two most prevalent methods with respect to sensitivity and FDR. The software cn.FARMS is publicly available as a R package at http://www.bioinf.jku.at/software/cnfarms/cnfarms.html.

Field and laboratory investigations for full depth reclamation projects.

DOT National Transportation Integrated Search

2011-03-01

Full-depth reclamation (FDR) offers a timely, cost-effective solution to restore a pavements condition. : However, FDR represents only one technique in the engineers toolkit available for addressing deteriorating : pavement conditions. The purp...

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry.

PubMed

Palmer, Andrew; Phapale, Prasad; Chernyavsky, Ilya; Lavigne, Regis; Fay, Dominik; Tarasov, Artem; Kovalev, Vitaly; Fuchser, Jens; Nikolenko, Sergey; Pineau, Charles; Becker, Michael; Alexandrov, Theodore

2017-01-01

High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for high-mass-resolution imaging mass spectrometry (https://github.com/alexandrovteam/pySM). We introduce a metabolite-signal match score and a target-decoy FDR estimate for spatial metabolomics.

Quantitative Profiling of Colorectal Cancer-Associated Bacteria Reveals Associations between Fusobacterium spp., Enterotoxigenic Bacteroides fragilis (ETBF) and Clinicopathological Features of Colorectal Cancer

PubMed Central

Viljoen, Katie S.; Dakshinamurthy, Amirtha; Goldberg, Paul; Blackburn, Jonathan M.

2015-01-01

Various studies have presented clinical or in vitro evidence linking bacteria to colorectal cancer, but these bacteria have not previously been concurrently quantified by qPCR in a single cohort. We quantify these bacteria (Fusobacterium spp., Streptococcus gallolyticus, Enterococcus faecalis, Enterotoxigenic Bacteroides fragilis (ETBF), Enteropathogenic Escherichia coli (EPEC), and afaC- or pks-positive E. coli) in paired tumour and normal tissue samples from 55 colorectal cancer patients. We further investigate the relationship between a) the presence and b) the level of colonisation of each bacterial species with site and stage of disease, age, gender, ethnicity and MSI-status. With the exception of S. gallolyticus, we detected all bacteria profiled here in both tumour and normal samples at varying frequencies. ETBF (FDR = 0.001 and 0.002 for normal and tumour samples) and afaC-positive E. coli (FDR = 0.03, normal samples) were significantly enriched in the colon compared to the rectum. ETBF (FDR = 0.04 and 0.002 for normal and tumour samples, respectively) and Fusobacterium spp. (FDR = 0.03 tumour samples) levels were significantly higher in late stage (III/IV) colorectal cancers. Fusobacterium was by far the most common bacteria detected, occurring in 82% and 81% of paired tumour and normal samples. Fusobacterium was also the only bacterium that was significantly higher in tumour compared to normal samples (p = 6e-5). We also identified significant associations between high-level colonisation by Fusobacterium and MSI-H (FDR = 0.05), age (FDR = 0.03) or pks-positive E. coli (FDR = 0.01). Furthermore, we exclusively identified atypical EPEC in our cohort, which has not been previously reported in association with colorectal cancer. By quantifying colorectal cancer-associated bacteria across a single cohort, we uncovered inter- and intra-individual patterns of colonization not previously recognized, as well as important associations with clinicopathological features, especially in the case of Fusobacterium and ETBF. PMID:25751261

Controlling the Rate of GWAS False Discoveries

PubMed Central

Brzyski, Damian; Peterson, Christine B.; Sobczyk, Piotr; Candès, Emmanuel J.; Bogdan, Malgorzata; Sabatti, Chiara

2017-01-01

With the rise of both the number and the complexity of traits of interest, control of the false discovery rate (FDR) in genetic association studies has become an increasingly appealing and accepted target for multiple comparison adjustment. While a number of robust FDR-controlling strategies exist, the nature of this error rate is intimately tied to the precise way in which discoveries are counted, and the performance of FDR-controlling procedures is satisfactory only if there is a one-to-one correspondence between what scientists describe as unique discoveries and the number of rejected hypotheses. The presence of linkage disequilibrium between markers in genome-wide association studies (GWAS) often leads researchers to consider the signal associated to multiple neighboring SNPs as indicating the existence of a single genomic locus with possible influence on the phenotype. This a posteriori aggregation of rejected hypotheses results in inflation of the relevant FDR. We propose a novel approach to FDR control that is based on prescreening to identify the level of resolution of distinct hypotheses. We show how FDR-controlling strategies can be adapted to account for this initial selection both with theoretical results and simulations that mimic the dependence structure to be expected in GWAS. We demonstrate that our approach is versatile and useful when the data are analyzed using both tests based on single markers and multiple regression. We provide an R package that allows practitioners to apply our procedure on standard GWAS format data, and illustrate its performance on lipid traits in the North Finland Birth Cohort 66 cohort study. PMID:27784720

Controlling the Rate of GWAS False Discoveries.

PubMed

Brzyski, Damian; Peterson, Christine B; Sobczyk, Piotr; Candès, Emmanuel J; Bogdan, Malgorzata; Sabatti, Chiara

2017-01-01

With the rise of both the number and the complexity of traits of interest, control of the false discovery rate (FDR) in genetic association studies has become an increasingly appealing and accepted target for multiple comparison adjustment. While a number of robust FDR-controlling strategies exist, the nature of this error rate is intimately tied to the precise way in which discoveries are counted, and the performance of FDR-controlling procedures is satisfactory only if there is a one-to-one correspondence between what scientists describe as unique discoveries and the number of rejected hypotheses. The presence of linkage disequilibrium between markers in genome-wide association studies (GWAS) often leads researchers to consider the signal associated to multiple neighboring SNPs as indicating the existence of a single genomic locus with possible influence on the phenotype. This a posteriori aggregation of rejected hypotheses results in inflation of the relevant FDR. We propose a novel approach to FDR control that is based on prescreening to identify the level of resolution of distinct hypotheses. We show how FDR-controlling strategies can be adapted to account for this initial selection both with theoretical results and simulations that mimic the dependence structure to be expected in GWAS. We demonstrate that our approach is versatile and useful when the data are analyzed using both tests based on single markers and multiple regression. We provide an R package that allows practitioners to apply our procedure on standard GWAS format data, and illustrate its performance on lipid traits in the North Finland Birth Cohort 66 cohort study. Copyright © 2017 by the Genetics Society of America.

Field Measurements and Numerical Simulations of Temperature and Moisture in Highway Engineering Using a Frequency Domain Reflectometry Sensor

PubMed Central

Yao, Yong-Sheng; Zheng, Jian-Long; Chen, Zeng-Shun; Zhang, Jun-Hui; Li, Yong

2016-01-01

This paper presents a systematic pioneering study on the use of agricultural-purpose frequency domain reflectometry (FDR) sensors to monitor temperature and moisture of a subgrade in highway extension and reconstruction engineering. The principle of agricultural-purpose FDR sensors and the process for embedding this kind of sensors for subgrade engineering purposes are introduced. Based on field measured weather data, a numerical analysis model for temperature and moisture content in the subgrade’s soil is built. Comparisons of the temperature and moisture data obtained from numerical simulation and FDR-based measurements are conducted. The results show that: (1) the embedding method and process, data acquisition, and remote transmission presented are reasonable; (2) the temperature and moisture changes are coordinated with the atmospheric environment and they are also in close agreement with numerical calculations; (3) the change laws of both are consistent at positions where the subgrade is compacted uniformly. These results suggest that the data measured by the agricultural-purpose FDR sensors are reliable. The findings of this paper enable a new and effective real-time monitoring method for a subgrade’s temperature and moisture changes, and thus broaden the application of agricultural-purpose FDR sensors. PMID:27294935

Family history of type 2 diabetes, abdominal adipocyte size and markers of the metabolic syndrome.

PubMed

Anthanont, P; Ramos, P; Jensen, M D; Hames, K C

2017-11-01

A major risk factor of type 2 diabetes mellitus (T2DM) is a positive family history of diabetes. First degree relatives (FDR) of patients with T2DM are more insulin resistant and are reported to have larger abdominal subcutaneous adipocytes than adults without a family history. Our objectives were to assess whether FDR of T2DM are associated with larger abdominal adipocytes independent of age, sex and abdominal subcutaneous fat and to assess whether a family history of T2DM is also independently related to femoral adipocyte size, as well as visceral fat and fasting plasma triglyceride (TG) concentrations. We extracted adipocyte size, body composition, plasma TG and demographic data of non-diabetic research participants of previous studies conducted in our laboratory. We ascertained the family history of T2DM from the electronic medical records. Multivariate regression analysis was used to assess whether FDR of T2DM are more likely to have other risk factors after adjusting for known covariates. Of 604 participants, 148 were FDR of T2DM. Although abdominal and femoral adipocyte size was greater in FDR of T2DM than those without a family history (0.74±0.33 vs 0.63±0.33 μg lipid per cell, P<0.001; 0.81±0.29 vs 0.72±0.33 μg lipid per cell, P=0.01, respectively), this was confounded by FDR of T2DM being older, having greater body mass index and percent body fat. A family history of T2DM was a significant predictor of abdominal adipocyte size after adjustment for age and body fat distribution parameters in females (total R 2 =0.5, P<0.0001), but not in males. A family history of T2DM was not independently predictive of femoral adipocyte size, visceral fat area or TG. Female FDR of T2DM have larger abdominal, but not femoral, adipocytes, even after accounting for age and body fat distribution.

Implementation of false discovery rate for exploring novel paradigms and trait dimensions with ERPs.

PubMed

Crowley, Michael J; Wu, Jia; McCreary, Scott; Miller, Kelly; Mayes, Linda C

2012-01-01

False discovery rate (FDR) is a multiple comparison procedure that targets the expected proportion of false discoveries among the discoveries. Employing FDR methods in event-related potential (ERP) research provides an approach to explore new ERP paradigms and ERP-psychological trait/behavior relations. In Study 1, we examined neural responses to escape behavior from an aversive noise. In Study 2, we correlated a relatively unexplored trait dimension, ostracism, with neural response. In both situations we focused on the frontal cortical region, applying a channel by time plots to display statistically significant uncorrected data and FDR corrected data, controlling for multiple comparisons.

Theory-of-mind understanding and theory-of-mind use in unaffected first-degree relatives of schizophrenia and bipolar disorder.

PubMed

Wang, Yong-Guang; Roberts, David L; Liang, Yan; Shi, Jian-Fei; Wang, Kai

2015-12-15

We assessed theory of mind (ToM) in unaffected first-degree relatives (FDR) of patients with schizophrenia (SC) and bipolar disorder (BD) compared to healthy controls with a revised computerized referential communication task. Results showed that FDR of SC performed worse than FDR of BD and controls on a task requiring ToM-use, but not on a task requiring ToM-understanding. This indicates that deficient ToM-use, rather than ToM-understanding impairments, may represent a potential candidate endophenotype for schizophrenia. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Incidence and mortality of colorectal cancer in individuals with a family history of colorectal cancer.

PubMed

Schoen, Robert E; Razzak, Anthony; Yu, Kelly J; Berndt, Sonja I; Firl, Kevin; Riley, Thomas L; Pinsky, Paul F

2015-11-01

Little is known about the change in risk conferred by family history of colorectal cancer (CRC) as a person ages. We evaluated the effect of family history on CRC incidence and mortality after 55 years of age, when the risk of early onset cancer had passed. We collected data from participants in the randomized, controlled Prostate, Lung, Colorectal and Ovarian cancer screening trial of flexible sigmoidoscopy versus usual care (55-74 years old, no history of CRC), performed at 10 US centers from 1993 to 2001. A detailed family history of colorectal cancer was obtained at enrollment, and subjects were followed for CRC incidence and mortality for up to 13 years. Among 144,768 participants, 14,961 subjects (10.3%) reported a family of CRC. Of 2090 incident cases, 273 cases (13.1%) had a family history of CRC; among 538 deaths from CRC, 71 (13.2%) had a family history of CRC. Overall, family history of CRC was associated with an increased risk of CRC incidence (hazard ratio [HR], 1.30; 95% confidence interval [CI], 1.10-1.50; P<.0001) and increased mortality (HR, 1.31; 95% CI, 1.02-1.69; P = .03). Subjects with 1 first degree relative (FDR) with CRC (n = 238; HR, 1.23; 95% CI, 1.07-1.42) or ≥2 FDRs with CRC (n = 35; HR, 2.04; 95% CI, 1.44-2.86) were at increased risk for incident CRC. However, among individuals with 1 FDR with CRC, there were no differences in risk based on age at diagnosis in the FDR (for FDR <60 years of age: HR, 1.27; 95% CI, 0.97-1.63; for FDR 60-70 years of age: HR, 1.33; 95% CI, 1.06-1.62; for FDR >70 years of age: HR, 1.14; 95% CI, 0.93-1.45; P trend = .59). After 55 years of age, subjects with 1 FDR with CRC had only a modest increase in risk for CRC incidence and death; age of onset in the FDR was not significantly associated with risk. Individuals with ≥2 FDRs with CRC had continued increased risk in older age. Guidelines and clinical practice for subjects with a family history of CRC should be modified to align CRC testing to risk. ClinicalTrials.gov number, NCT00002540. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

Separate class true discovery rate degree of association sets for biomarker identification.

PubMed

Crager, Michael R; Ahmed, Murat

2014-01-01

In 2008, Efron showed that biological features in a high-dimensional study can be divided into classes and a separate false discovery rate (FDR) analysis can be conducted in each class using information from the entire set of features to assess the FDR within each class. We apply this separate class approach to true discovery rate degree of association (TDRDA) set analysis, which is used in clinical-genomic studies to identify sets of biomarkers having strong association with clinical outcome or state while controlling the FDR. Careful choice of classes based on prior information can increase the identification power of the separate class analysis relative to the overall analysis.

Construction monitoring of full-depth reclamation in Madison County for MDOT project No. NH-0008-03(032).

DOT National Transportation Integrated Search

2011-10-01

This report presents the results of construction monitoring of the full-depth reclamation (FDR) process used on MDOT project number NH-0008-03(032) in Madison County on US49. FDR is a method of pavement rehabilitation in which the entire pavement str...

Construction monitoring of full-depth reclamation in Madison County for MDOT project no. NH-0008-03(032).

DOT National Transportation Integrated Search

2010-10-01

This report presents the results of construction monitoring of the full-depth reclamation (FDR) process used on MDOT project number NH-0008-03(032) in Madison County on US49. FDR is a method of pavement rehabilitation in which the entire pavement str...

Construction monitoring of full-depth reclamation in Madison County for MDOT project no. NH-0008-03(032)

DOT National Transportation Integrated Search

2010-10-01

This report presents the results of construction monitoring of the full-depth reclamation (FDR) process used on MDOT project number NH-0008-03(032) in Madison County on US49. FDR is a method of pavement rehabilitation in which the entire pavement str...

Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?

PubMed Central

Keich, Uri; Noble, William Stafford

2017-01-01

Estimating the false discovery rate (FDR) among a list of tandem mass spectrum identifications is mostly done through target-decoy competition (TDC). Here we offer two new methods that can use an arbitrarily small number of additional randomly drawn decoy databases to improve TDC. Specifically, “Partial Calibration” utilizes a new meta-scoring scheme that allows us to gradually benefit from the increase in the number of identifications calibration yields and “Averaged TDC” (a-TDC) reduces the liberal bias of TDC for small FDR values and its variability throughout. Combining a-TDC with “Progressive Calibration” (PC), which attempts to find the “right” number of decoys required for calibration we see substantial impact in real datasets: when analyzing the Plasmodium falciparum data it typically yields almost the entire 17% increase in discoveries that “full calibration” yields (at FDR level 0.05) using 60 times fewer decoys. Our methods are further validated using a novel realistic simulation scheme and importantly, they apply more generally to the problem of controlling the FDR among discoveries from searching an incomplete database. PMID:29326989

Effects of multiple genetic loci on the pathogenesis from serum urate to gout.

PubMed

Dong, Zheng; Zhou, Jingru; Jiang, Shuai; Li, Yuan; Zhao, Dongbao; Yang, Chengde; Ma, Yanyun; Wang, Yi; He, Hongjun; Ji, Hengdong; Yang, Yajun; Wang, Xiaofeng; Xu, Xia; Pang, Yafei; Zou, Hejian; Jin, Li; Wang, Jiucun

2017-03-02

Gout is a common arthritis resulting from increased serum urate, and many loci have been identified that are associated with serum urate and gout. However, their influence on the progression from elevated serum urate levels to gout is unclear. This study aims to explore systematically the effects of genetic variants on the pathogenesis in approximately 5,000 Chinese individuals. Six genes (PDZK1, GCKR, TRIM46, HNF4G, SLC17A1, LRRC16A) were determined to be associated with serum urate (P FDR  < 0.05) in the Chinese population for the first time. ABCG2 and a novel gene, SLC17A4, contributed to the development of gout from hyperuricemia (OR = 1.56, P FDR  = 3.68E-09; OR = 1.27, P FDR  = 0.013, respectively). Also, HNF4G is a novel gene associated with susceptibility to gout (OR = 1.28, P FDR  = 1.08E-03). In addition, A1CF and TRIM46 were identified as associated with gout in the Chinese population for the first time (P FDR  < 0.05). The present study systematically determined genetic effects on the progression from elevated serum urate to gout and suggests that urate-associated genes functioning as urate transporters may play a specific role in the pathogenesis of gout. Furthermore, two novel gout-associated genes (HNF4G and SLC17A4) were identified.

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets.

PubMed

Savitski, Mikhail M; Wilhelm, Mathias; Hahne, Hannes; Kuster, Bernhard; Bantscheff, Marcus

2015-09-01

Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target-decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target-decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The "picked" protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The "picked" target-decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used "classic" protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in proteomics analysis software. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

PubMed Central

Savitski, Mikhail M.; Wilhelm, Mathias; Hahne, Hannes; Kuster, Bernhard; Bantscheff, Marcus

2015-01-01

Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination. There are also limitations inherent to the widely used classic target–decoy strategy that particularly show when analyzing very large data sets and that lead to a strong over-representation of decoy identifications. In this study, we investigated the merits of the classic, as well as a novel target–decoy-based protein FDR estimation approach, taking advantage of a heterogeneous data collection comprised of ∼19,000 LC-MS/MS runs deposited in ProteomicsDB (https://www.proteomicsdb.org). The “picked” protein FDR approach treats target and decoy sequences of the same protein as a pair rather than as individual entities and chooses either the target or the decoy sequence depending on which receives the highest score. We investigated the performance of this approach in combination with q-value based peptide scoring to normalize sample-, instrument-, and search engine-specific differences. The “picked” target–decoy strategy performed best when protein scoring was based on the best peptide q-value for each protein yielding a stable number of true positive protein identifications over a wide range of q-value thresholds. We show that this simple and unbiased strategy eliminates a conceptual issue in the commonly used “classic” protein FDR approach that causes overprediction of false-positive protein identification in large data sets. The approach scales from small to very large data sets without losing performance, consistently increases the number of true-positive protein identifications and is readily implemented in proteomics analysis software. PMID:25987413

Determination of medium electrical properties through full-wave modelling of frequency domain reflectrometry data

NASA Astrophysics Data System (ADS)

André, Frédéric; Lambot, Sébastien

2015-04-01

Accurate knowledge of the shallow soil properties is of prime importance in agricultural, hydrological and environmental engineering. During the last decade, numerous geophysical techniques, either invasive or resorting to proximal or remote sensing, have been developed and applied for quantitative characterization of soil properties. Amongst them, time domain reflectrometry (TDR) and frequency domain reflectometry (FDR) are recognized as standard techniques for the determination of soil dielectric permittivity and electrical conductivity, based on the reflected electromagnetic waves from a probe inserted into the soil. TDR data were first commonly analyzed in the time domain using methods considering only a part of the waveform information. Later, advancements have led to the possibility of analyzing the TDR signal through full-wave inverse modeling either in the time or the frequency domains. A major advantage of FDR compared to TDR is the possibility to increase the bandwidth, thereby increasing the information content of the data and providing more detailed characterization of the medium. Amongst the recent works in this field, Minet et al. (2010) developed a modeling procedure for processing FDR data based on an exact solution of Maxwell's equations for wave propagation in one-dimensional multilayered media. In this approach, the probe head is decoupled from the medium and is fully described by characteristic transfer functions. The authors successfully validated the method for homogeneous sand subject to a range of water contents. In the present study, we further validated the modelling approach using reference liquids with well-characterized frequency-dependent electrical properties. In addition, the FDR model was coupled with a dielectric mixing model to investigate the ability of retrieving water content, pore water electrical conductivity and sand porosity from inversion of FDR data acquired in sand subject to different water content levels. Finally, the possibility of reconstructing the vertical profile of the properties by inversion of FDR data collected during progressive insertion of the probe into a vertically heterogeneous medium was also investigated. Index Terms: Frequency domain reflectrometry (FDR), frequency dependence, dielectric permittivity, electrical conductivity Reference: Minet J., Lambot S., Delaide G., Huisman J.A., Vereecken H., Vanclooster M., 2010. A generalized frequency domain reflectometry modeling technique for soil electrical properties determination. Vadose Zone Journal, 9: 1063-1072.

Single nucleotide variants in metastasis-related genes are associated with breast cancer risk, by lymph node involvement and estrogen receptor status, in women with European and African ancestry

PubMed Central

Roberts, Michelle R.; Sucheston-Campbell, Lara E.; Zirpoli, Gary R.; Higgins, Michael; Freudenheim, Jo L.; Bandera, Elisa V.; Ambrosone, Christine B.; Yao, Song

2017-01-01

Background Single nucleotide polymorphisms (SNPs) in pathways influencing lymph node (LN) metastasis and estrogen receptor (ER) status in breast cancer may partially explain inter-patient variability in prognosis. We examined 154 SNPs in 12 metastasis-related genes for associations with breast cancer risk, stratified by LN and ER status, in European-American (EA) and African-American (AA) women. Methods 2,671 women enrolled in the Women’s Circle of Health Study were genotyped. Pathway analyses were conducted using the adaptive rank truncated product (ARTP) method, with pARTP≤0.10 as significant. Multi-allelic risk scores were created for the ARTP-significant gene(s). Single-SNP and risk score associations were modeled using logistic regression, with false discovery rate (FDR) p-value adjustment. Results Although single-SNP associations were not significant at pFDR<0.05, several genes were significant in the ARTP analyses. In AA women, significant ARTP gene-level associations included CDH1 with LN+ (pARTP=0.10; multi-allelic OR=1.13, 95% CI 1.07–1.19, pFDR=0.0003) and SIPA1 with ER− breast cancer (pARTP=0.10; multi-allelic OR=1.16, 95% CI 1.02–1.31, pFDR=0.03). In EA women, MTA2 was associated with overall breast cancer risk (pARTP=0.004), regardless of ER status, and with LN− disease (pARTP=0.01). Also significant were SATB1 in ER− (pARTP=0.03; multi-allelic OR=1.12, 95% CI 1.05–1.20, pFDR=0.003) and KISS1 in LN− (pARTP=0.10; multi-allelic OR=1.18, 95% CI 1.08–1.29, pFDR=0.002) analyses. Among LN+ cases, significant ARTP associations were observed for SNAI1, CD82, NME1, and CTNNB1 (multi-allelic OR=1.09, 95% CI 1.04–1.14, pFDR=0.001). Conclusion Our findings suggest that variants in several metastasis genes may affect breast cancer risk by LN or ER status, although verification in larger studies is required. PMID:27597141

Fıbroblast growth factor 21 and ıts relatıonshıp wıth ınsulın sensıtıvıty ın fırst-degree relatıves of patıents wıth type 2 dıabetes mellıtus.

PubMed

Ors, Damla; Eroglu Altinova, Alev; Yalçın, Mehmet Muhittin; Gulbahar, Ozlem; Akturk, Mujde; Arslan, Metin; Balos Toruner, Fusun

2016-01-01

Fibroblast growth factor 21 (FGF 21) has been suggested as a predictor for the development of type 2 diabetes mellitus (T2DM). We aimed to determine FGF 21 levels in normoglycaemic (Group 1) and prediabetic (Group 2) first-degree relatives (FDR) of patients with T2DM in comparison with normoglycaemic subjects without a history of T2DM in their FDR (Group 3). There was a significant difference between Group 1, 2, and 3 with respect to plasma FGF 21 concentrations (143.3 ± 93.8, 221.9 ± ± 171.7 and 121.2 ± 119.8 pg/mL, respectively, p = 0.01). FGF 21 levels were significantly increased in prediabetic FDR of patients with T2DM compared to normoglycaemic subjects without a history of T2DM in their FDR (p = 0.02). FGF 21 levels did not differ between normoglycaemic FDR of patients with T2DM and normoglycaemic subjects without a history of T2DM in their FDR (p > 0.05). In the whole group, FGF 21 correlated positively with age (r = 0.31, p = 0.003), BMI (r = 0.38, p < 0.001), systolic blood pressure (r = 0.38, p = 0.001), diastolic blood pressure (r = 0.26, p = 0.02), fasting blood glucose (r = 0.24, p = 0.02), HOMA-IR (r = 0.23, p = 0.03), AUC glucose (r = 0.35, p = 0.001), and AUC insulin (r = 0.32, p = 0.003) and negatively with HDL cholesterol (r = -0.24, p = 0.02) and Matsuda ISI (r = -0.33, p = 0.002). In the regression analysis, BMI was the most predictive factor for FGF 21 levels (beta = 0.41, r2 = 0.17, p < 0.001). We showed that FGF 21 concentrations are increased in prediabetic FDR of patients with T2DM and that there is a significant association between FGF 21 and obesity and insulin sensitivity. (Endokrynol Pol 2016; 67 (3): 260-264).

Operational Use of the US Army Reserve in Foreign Disaster Relief to Support the United States Government’s Strategic Use of Humanitarian Assistance and Disaster Response

DTIC Science & Technology

2015-05-21

FDR). Global climate change , urbanization, growing natural resources scarcity, and other factors will increase the need for humanitarian assistance......additional military support to the United States Government’s agencies in Foreign Disaster Relief (FDR). Global climate change , urbanization, growing

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

PubMed

Lee, Woojoo; Alexeyenko, Andrey; Pernemalm, Maria; Guegan, Justine; Dessen, Philippe; Lazar, Vladimir; Lehtiö, Janne; Pawitan, Yudi

2015-01-01

Biological heterogeneity is common in many diseases and it is often the reason for therapeutic failures. Thus, there is great interest in classifying a disease into subtypes that have clinical significance in terms of prognosis or therapy response. One of the most popular methods to uncover unrecognized subtypes is cluster analysis. However, classical clustering methods such as k-means clustering or hierarchical clustering are not guaranteed to produce clinically interesting subtypes. This could be because the main statistical variability--the basis of cluster generation--is dominated by genes not associated with the clinical phenotype of interest. Furthermore, a strong prognostic factor might be relevant for a certain subgroup but not for the whole population; thus an analysis of the whole sample may not reveal this prognostic factor. To address these problems we investigate methods to identify and assess clinically interesting subgroups in a heterogeneous population. The identification step uses a clustering algorithm and to assess significance we use a false discovery rate- (FDR-) based measure. Under the heterogeneity condition the standard FDR estimate is shown to overestimate the true FDR value, but this is remedied by an improved FDR estimation procedure. As illustrations, two real data examples from gene expression studies of lung cancer are provided.

Development of Drag Reducing Polymer of FDR-SPC

NASA Astrophysics Data System (ADS)

Lee, Inwon; Park, Hyun; Chun, Ho Hwan

2015-11-01

In this study, a novel FDR-SPC (Frictional Drag Reduction Self-Polishing Copolymer) is first synthesized in this study. The drag reducing functional radical such as PEGMA (Poly(ethylene) glycol methacrylate) has been utilized to participate in the synthesis process of the SPC. The release mechanism of drag reducing radical is accounted for the hydrolysis reaction between the FDR-SPC and seawater. The types of the baseline SPC monomers, the molecular weight and the mole fraction of PEGMA were varied in the synthesis process. The resulting SPCs were coated to the substrate plates for the subsequent hydrodynamic test for skin friction measurement. A significant reduction in Reynolds stress was observed in a range of specimen, with the maximum drag reduction being 15.9% relative to the smooth surface for PRD3-1.

A modified error correction protocol for CCITT signalling system no. 7 on satellite links

NASA Astrophysics Data System (ADS)

Kreuer, Dieter; Quernheim, Ulrich

1991-10-01

Comite Consultatif International des Telegraphe et Telephone (CCITT) Signalling System No. 7 (SS7) provides a level 2 error correction protocol particularly suited for links with propagation delays higher than 15 ms. Not being originally designed for satellite links, however, the so called Preventive Cyclic Retransmission (PCR) Method only performs well on satellite channels when traffic is low. A modified level 2 error control protocol, termed Fix Delay Retransmission (FDR) method is suggested which performs better at high loads, thus providing a more efficient use of the limited carrier capacity. Both the PCR and the FDR methods are investigated by means of simulation and results concerning throughput, queueing delay, and system delay, respectively. The FDR method exhibits higher capacity and shorter delay than the PCR method.

Risk of Advanced Neoplasia in First-Degree Relatives with Colorectal Cancer: A Large Multicenter Cross-Sectional Study

PubMed Central

Quintero, Enrique; Gargallo, Carla; Lanas, Angel; Bujanda, Luis; Gimeno-García, Antonio Z.; Hernández-Guerra, Manuel; Nicolás-Pérez, David; Alonso-Abreu, Inmaculada; Morillas, Juan Diego; Balaguer, Francesc; Muriel, Alfonso

2016-01-01

Background First-degree relatives (FDR) of patients with colorectal cancer have a higher risk of developing colorectal cancer than the general population. For this reason, screening guidelines recommend colonoscopy every 5 or 10 y, starting at the age of 40, depending on whether colorectal cancer in the index-case is diagnosed at <60 or ≥60 y, respectively. However, studies on the risk of neoplastic lesions are inconclusive. The aim of this study was to determine the risk of advanced neoplasia (three or more non-advanced adenomas, advanced adenoma, or invasive cancer) in FDR of patients with colorectal cancer compared to average-risk individuals (i.e., asymptomatic adults 50 to 69 y of age with no family history of colorectal cancer). Methods and Findings This cross-sectional analysis includes data from 8,498 individuals undergoing their first lifetime screening colonoscopy between 2006 and 2012 at six Spanish tertiary hospitals. Of these individuals, 3,015 were defined as asymptomatic FDR of patients with colorectal cancer (“familial-risk group”) and 3,038 as asymptomatic with average-risk for colorectal cancer (“average-risk group”). The familial-risk group was stratified as one FDR, with one family member diagnosed with colorectal cancer at ≥60 y (n = 1,884) or at <60 y (n = 831), and as two FDR, with two family members diagnosed with colorectal cancer at any age (n = 300). Multiple logistic regression analysis was used for between-group comparisons after adjusting for potential confounders (age, gender, and center). Compared with the average-risk group, advanced neoplasia was significantly more prevalent in individuals having two FDR with colorectal cancer (odds ratio [OR] 1.90; 95% confidence interval [CI] 1.36–2.66, p < 0.001), but not in those having one FDR with colorectal cancer diagnosed at ≥60 y (OR 1.03; 95% CI 0.83–1.27, p = 0.77) and <60 y (OR 1.19; 95% CI 0.90–1.58, p = 0.20). After the age of 50 y, men developed advanced neoplasia over two times more frequently than women and advanced neoplasia appeared at least ten y earlier. Fewer colonoscopies by 2-fold were required to detect one advanced neoplasia in men than in women. Major limitations of this study were first that although average-risk individuals were consecutively included in a randomized control trial, this was not the case for all individuals in the familial-risk cohort; and second, the difference in age between the average-risk and familial-risk cohorts. Conclusions Individuals having two FDR with colorectal cancer showed an increased risk of advanced neoplasia compared to those with average-risk for colorectal cancer. Men had over 2-fold higher risk of advanced neoplasia than women, independent of family history. These data suggest that screening colonoscopy guidelines should be revised in the familial-risk population. PMID:27138769

Genetic Variations in Magnesium-Related Ion Channels May Affect Diabetes Risk among African American and Hispanic American Women123

PubMed Central

Chan, Kei Hang K; Chacko, Sara A; Song, Yiqing; Cho, Michele; Eaton, Charles B; Wu, Wen-Chih H; Liu, Simin

2015-01-01

Background: Prospective studies consistently link low magnesium intake to higher type 2 diabetes (T2D) risk. Objective: We examined the association of common genetic variants [single nucleotide polymorphisms (SNPs)] in genes related to magnesium homeostasis with T2D risk and potential interactions with magnesium intake. Methods: Using the Women's Health Initiative-SNP Health Association Resource (WHI-SHARe) study, we identified 17 magnesium-related ion channel genes (583 SNPs) and examined their associations with T2D risk in 7287 African-American (AA; n = 1949 T2D cases) and 3285 Hispanic-American (HA; n = 611 T2D cases) postmenopausal women. We performed both single- and multiple-locus haplotype analyses. Results: Among AA women, carriers of each additional copy of SNP rs6584273 in cyclin mediator 1 (CNNM1) had 16% lower T2D risk [OR: 0.84; false discovery rate (FDR)-adjusted P = 0.02]. Among HA women, several variants were significantly associated with T2D risk, including rs10861279 in solute carrier family 41 (anion exchanger), member 2 (SLC41A2) (OR: 0.54; FDR-adjusted P = 0.04), rs7174119 in nonimprinted in Prader-Willi/Angelman syndrome 1 (NIPA1) (OR: 1.27; FDR-adjusted P = 0.04), and 2 SNPs in mitochondrial RNA splicing 2 (MRS2) (rs7738943: OR = 1.55, FDR-adjusted P = 0.01; rs1056285: OR = 1.48, FDR-adjusted P = 0.02). Even with the most conservative Bonferroni adjustment, two 2-SNP-haplotypes in SLC41A2 and MRS2 region were significantly associated with T2D risk (rs12582312-rs10861279: P = 0.0006; rs1056285-rs7738943: P = 0.002). Among women with magnesium intake in the lowest 30% (AA: ≤0.164 g/d; HA: ≤0.185 g/d), 4 SNP signals were strengthened [rs11590362 in claudin 19 (CLDN19), rs823154 in SLC41A1, rs5929706 and rs5930817 in membra; HA: ≥0.313 g/d), rs6584273 in CNNM1 (OR: 0.71; FDR-adjusted P = 0.04) and rs1800467 in potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11) (OR: 2.50; FDR-adjusted P = 0.01) were significantly associated with T2D risk. Conclusions: Our findings suggest important associations between genetic variations in magnesium-related ion channel genes and T2D risk in AA and HA women that vary by amount of magnesium intake. PMID:25733456

Making the Stranger's Path Familiar: Environmental Communication that Turns Access into Participation

ERIC Educational Resources Information Center

Adelman, Clifford

2005-01-01

Visitors to the FDR Memorial in Washington, D.C., enter the area through ceremonial openings: from the pathway around the reflecting pond of the Jefferson Memorial, or across a small shaded plaza reached from a roadway parallel to the Potomac River. The FDR Memorial itself cannot be seen at the start of either of these paths. It is out there…

Type I and Type II error concerns in fMRI research: re-balancing the scale

PubMed Central

Cunningham, William A.

2009-01-01

Statistical thresholding (i.e. P-values) in fMRI research has become increasingly conservative over the past decade in an attempt to diminish Type I errors (i.e. false alarms) to a level traditionally allowed in behavioral science research. In this article, we examine the unintended negative consequences of this single-minded devotion to Type I errors: increased Type II errors (i.e. missing true effects), a bias toward studying large rather than small effects, a bias toward observing sensory and motor processes rather than complex cognitive and affective processes and deficient meta-analyses. Power analyses indicate that the reductions in acceptable P-values over time are producing dramatic increases in the Type II error rate. Moreover, the push for a mapwide false discovery rate (FDR) of 0.05 is based on the assumption that this is the FDR in most behavioral research; however, this is an inaccurate assessment of the conventions in actual behavioral research. We report simulations demonstrating that combined intensity and cluster size thresholds such as P < 0.005 with a 10 voxel extent produce a desirable balance between Types I and II error rates. This joint threshold produces high but acceptable Type II error rates and produces a FDR that is comparable to the effective FDR in typical behavioral science articles (while a 20 voxel extent threshold produces an actual FDR of 0.05 with relatively common imaging parameters). We recommend a greater focus on replication and meta-analysis rather than emphasizing single studies as the unit of analysis for establishing scientific truth. From this perspective, Type I errors are self-erasing because they will not replicate, thus allowing for more lenient thresholding to avoid Type II errors. PMID:20035017

Large-scale exploratory genetic analysis of cognitive impairment in Parkinson's disease.

PubMed

Mata, Ignacio F; Johnson, Catherine O; Leverenz, James B; Weintraub, Daniel; Trojanowski, John Q; Van Deerlin, Vivianna M; Ritz, Beate; Rausch, Rebecca; Factor, Stewart A; Wood-Siverio, Cathy; Quinn, Joseph F; Chung, Kathryn A; Peterson-Hiller, Amie L; Espay, Alberto J; Revilla, Fredy J; Devoto, Johnna; Yearout, Dora; Hu, Shu-Ching; Cholerton, Brenna A; Montine, Thomas J; Edwards, Karen L; Zabetian, Cyrus P

2017-08-01

Cognitive impairment is a common and disabling problem in Parkinson's disease (PD). Identification of genetic variants that influence the presence or severity of cognitive deficits in PD might provide a clearer understanding of the pathophysiology underlying this important nonmotor feature. We genotyped 1105 PD patients from the PD Cognitive Genetics Consortium for 249,336 variants using the NeuroX array. Participants underwent assessments of learning and memory (Hopkins Verbal Learning Test-Revised [HVLT-R]), working memory/executive function (Letter-Number Sequencing and Trail Making Test [TMT] A and B), language processing (semantic and phonemic verbal fluency), visuospatial abilities (Benton Judgment of Line Orientation [JoLO]), and global cognitive function (Montreal Cognitive Assessment). For common variants, we used linear regression to test for association between genotype and cognitive performance with adjustment for important covariates. Rare variants were analyzed using the optimal unified sequence kernel association test. The significance threshold was defined as a false discovery rate-corrected p-value (P FDR ) of 0.05. Eighteen common variants in 13 genomic regions exceeded the significance threshold for one of the cognitive tests. These included GBA rs2230288 (E326K; P FDR  = 2.7 × 10 -4 ) for JoLO, PARP4 rs9318600 (P FDR  = 0.006), and rs9581094 (P FDR  = 0.006) for HVLT-R total recall, and MTCL1 rs34877994 (P FDR  = 0.01) for TMT B-A. Analysis of rare variants did not yield any significant gene regions. We have conducted the first large-scale PD cognitive genetics analysis and nominated several new putative susceptibility genes for cognitive impairment in PD. These results will require replication in independent PD cohorts. Published by Elsevier Inc.

Prevalence of any size adenomas and advanced adenomas in 40- to 49-year-old individuals undergoing screening colonoscopy because of a family history of colorectal carcinoma in a first-degree relative.

PubMed

Gupta, Akshay K; Samadder, Jewel; Elliott, Eric; Sethi, Saurabh; Schoenfeld, Philip

2011-07-01

Per current guidelines, patients with a first-degree relative (FDR) with colorectal cancer (CRC) should get screened at least at age 40. Data about the prevalence of adenomas and advanced adenomas (AAs) in these patients are lacking. To examine the prevalence of adenomas and AAs in 40- to 49-year-old individuals undergoing screening colonoscopy for family history of CRC. Retrospective chart review. Asymptomatic patients 40 to 49 years of age undergoing their first screening colonoscopy at the University of Michigan during the period 1999 to 2009 because of an FDR with CRC. Prevalence of adenomas (any size), AAs, and risk factors associated with adenomas. Among 640 study patients, the prevalence of adenomas (any size) was 15.4% and 3.3% for AAs. Adenoma prevalence was lower if the FDR with CRC was younger than 60 years of age versus an FDR with CRC older than 60 years of age (12.4% vs 19%, P = .034). Male sex (odds ratio 2.6; 95% CI, 1.06-4.4) and advancing age (odds ratio 1.16; 95% CI, 1.03-1.31) were associated with adenomas. Limited data on risk factor exposure and insufficient sample size to assess risk factors for AAs. Among 40- to 49-year-old patients undergoing screening colonoscopy because of an FDR with CRC, the prevalence of adenomas and AAs is low. Further research should determine whether these individuals have a higher prevalence of adenomas compared with average-risk individuals. Copyright © 2011 American Society for Gastrointestinal Endoscopy. Published by Mosby, Inc. All rights reserved.

Epithelial-Mesenchymal Transition (EMT) Gene Variants and Epithelial Ovarian Cancer (EOC) Risk.

PubMed

Amankwah, Ernest K; Lin, Hui-Yi; Tyrer, Jonathan P; Lawrenson, Kate; Dennis, Joe; Chornokur, Ganna; Aben, Katja K H; Anton-Culver, Hoda; Antonenkova, Natalia; Bruinsma, Fiona; Bandera, Elisa V; Bean, Yukie T; Beckmann, Matthias W; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A; Brooks-Wilson, Angela; Bunker, Clareann H; Butzow, Ralf; Campbell, Ian G; Carty, Karen; Chen, Zhihua; Chen, Y Ann; Chang-Claude, Jenny; Cook, Linda S; Cramer, Daniel W; Cunningham, Julie M; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; du Bois, Andreas; Despierre, Evelyn; Dicks, Ed; Doherty, Jennifer A; Dörk, Thilo; Dürst, Matthias; Easton, Douglas F; Eccles, Diana M; Edwards, Robert P; Ekici, Arif B; Fasching, Peter A; Fridley, Brooke L; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G; Glasspool, Rosalind; Goodman, Marc T; Gronwald, Jacek; Harrington, Patricia; Harter, Philipp; Hasmad, Hanis N; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A T; Hillemanns, Peter; Hogdall, Claus K; Hogdall, Estrid; Hosono, Satoyo; Iversen, Edwin S; Jakubowska, Anna; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y; Jim, Heather; Kellar, Melissa; Kiemeney, Lambertus A; Krakstad, Camilla; Kjaer, Susanne K; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D; Lee, Alice W; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A; Liang, Dong; Lim, Boon Kiong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F A G; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R; McNeish, Ian; Menon, Usha; Milne, Roger L; Modugno, Francesmary; Moysich, Kirsten B; Ness, Roberta B; Nevanlinna, Heli; Eilber, Ursula; Odunsi, Kunle; Olson, Sara H; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Paul, James; Pearce, Celeste L; Pejovic, Tanja; Pelttari, Liisa M; Permuth-Wey, Jennifer; Pike, Malcolm C; Poole, Elizabeth M; Risch, Harvey A; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H; Rudolph, Anja; Runnebaum, Ingo B; Rzepecka, Iwona K; Salvesen, Helga B; Schernhammer, Eva; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C; Spiewankiewicz, Beata; Sucheston-Campbell, Lara; Teo, Soo-Hwang; Terry, Kathryn L; Thompson, Pamela J; Thomsen, Lotte; Tangen, Ingvild L; Tworoger, Shelley S; van Altena, Anne M; Vierkant, Robert A; Vergote, Ignace; Walsh, Christine S; Wang-Gohrke, Shan; Wentzensen, Nicolas; Whittemore, Alice S; Wicklund, Kristine G; Wilkens, Lynne R; Wu, Anna H; Wu, Xifeng; Woo, Yin-Ling; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Kelemen, Linda E; Berchuck, Andrew; Schildkraut, Joellen M; Ramus, Susan J; Goode, Ellen L; Monteiro, Alvaro N A; Gayther, Simon A; Narod, Steven A; Pharoah, Paul D P; Sellers, Thomas A; Phelan, Catherine M

2015-12-01

Epithelial-mesenchymal transition (EMT) is a process whereby epithelial cells assume mesenchymal characteristics to facilitate cancer metastasis. However, EMT also contributes to the initiation and development of primary tumors. Prior studies that explored the hypothesis that EMT gene variants contribute to epithelial ovarian carcinoma (EOC) risk have been based on small sample sizes and none have sought replication in an independent population. We screened 15,816 single-nucleotide polymorphisms (SNPs) in 296 genes in a discovery phase using data from a genome-wide association study of EOC among women of European ancestry (1,947 cases and 2,009 controls) and identified 793 variants in 278 EMT-related genes that were nominally (P < 0.05) associated with invasive EOC. These SNPs were then genotyped in a larger study of 14,525 invasive-cancer patients and 23,447 controls. A P-value <0.05 and a false discovery rate (FDR) <0.2 were considered statistically significant. In the larger dataset, GPC6/GPC5 rs17702471 was associated with the endometrioid subtype among Caucasians (odds ratio (OR) = 1.16, 95% CI = 1.07-1.25, P = 0.0003, FDR = 0.19), whereas F8 rs7053448 (OR = 1.69, 95% CI = 1.27-2.24, P = 0.0003, FDR = 0.12), F8 rs7058826 (OR = 1.69, 95% CI = 1.27-2.24, P = 0.0003, FDR = 0.12), and CAPN13 rs1983383 (OR = 0.79, 95% CI = 0.69-0.90, P = 0.0005, FDR = 0.12) were associated with combined invasive EOC among Asians. In silico functional analyses revealed that GPC6/GPC5 rs17702471 coincided with DNA regulatory elements. These results suggest that EMT gene variants do not appear to play a significant role in the susceptibility to EOC. © 2015 WILEY PERIODICALS, INC.

Epithelial-Mesenchymal Transition (EMT) gene variants and Epithelial Ovarian Cancer (EOC) risk

PubMed Central

Amankwah, Ernest K.; Lin, Hui-Yi; Tyrer, Jonathan P.; Lawrenson, Kate; Dennis, Joe; Chornokur, Ganna; Aben, Katja KH.; Anton-Culver, Hoda; Antonenkova, Natalia; Bruinsma, Fiona; Bandera, Elisa V.; Bean, Yukie T.; Beckmann, Matthias W.; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A.; Brooks-Wilson, Angela; Bunker, Clareann H.; Butzow, Ralf; Campbell, Ian G.; Carty, Karen; Chen, Zhihua; Chen, Y. Ann; Chang-Claude, Jenny; Cook, Linda S.; Cramer, Daniel W.; Cunningham, Julie M.; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; du Bois, Andreas; Despierre, Evelyn; Dicks, Ed; Doherty, Jennifer A.; Dörk, Thilo; Dürst, Matthias; Easton, Douglas F.; Eccles, Diana M.; Edwards, Robert P.; Ekici, Arif B.; Fasching, Peter A.; Fridley, Brooke L.; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G.; Glasspool, Rosalind; Goodman, Marc T.; Gronwald, Jacek; Harrington, Patricia; Harter, Philipp; Hasmad, Hanis N.; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A.T.; Hillemanns, Peter; Hogdall, Claus K.; Hogdall, Estrid; Hosono, Satoyo; Iversen, Edwin S.; Jakubowska, Anna; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y.; Jim, Heather; Kellar, Melissa; Kiemeney, Lambertus A.; Krakstad, Camilla; Kjaer, Susanne K.; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D.; Lee, Alice W.; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A.; Liang, Dong; Lim, Boon Kiong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F.A.G.; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R.; McNeish, Ian; Menon, Usha; Milne, Roger L.; Modugno, Francesmary; Moysich, Kirsten B.; Ness, Roberta B.; Nevanlinna, Heli; Eilber, Ursula; Odunsi, Kunle; Olson, Sara H.; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Paul, James; Pearce, Celeste L.; Pejovic, Tanja; Pelttari, Liisa M.; Permuth-Wey, Jennifer; Pike, Malcolm C.; Poole, Elizabeth M.; Risch, Harvey A.; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H.; Rudolph, Anja; Runnebaum, Ingo B.; Rzepecka, Iwona K.; Salvesen, Helga B.; Schernhammer, Eva; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B.; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C.; Spiewankiewicz, Beata; Sucheston-Campbell, Lara; Teo, Soo-Hwang; Terry, Kathryn L.; Thompson, Pamela J.; Thomsen, Lotte; Tangen, Ingvild L.; Tworoger, Shelley S.; van Altena, Anne M.; Vierkant, Robert A.; Vergote, Ignace; Walsh, Christine S.; Wang-Gohrke, Shan; Wentzensen, Nicolas; Whittemore, Alice S.; Wicklund, Kristine G.; Wilkens, Lynne R.; Wu, Anna H.; Wu, Xifeng; Woo, Yin-Ling; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Kelemen, Linda E.; Berchuck, Andrew; Schildkraut, Joellen M.; Ramus, Susan J.; Goode, Ellen L.; Monteiro, Alvaro N.A.; Gayther, Simon A.; Narod, Steven A.; Pharoah, Paul D. P.; Sellers, Thomas A.; Phelan, Catherine M.

2016-01-01

Introduction Epithelial-mesenchymal transition (EMT) is a process whereby epithelial cells assume mesenchymal characteristics to facilitate cancer metastasis. However, EMT also contributes to the initiation and development of primary tumors. Prior studies that explored the hypothesis that EMT gene variants contribute to EOC risk have been based on small sample sizes and none have sought replication in an independent population. Methods We screened 1254 SNPs in 296 genes in a discovery phase using data from a genome-wide association study of EOC among women of European ancestry (1,947 cases and 2,009 controls) and identified 793 variants in 278 EMT-related genes that were nominally (p<0.05) associated with invasive EOC. These SNPs were then genotyped in a larger study of 14,525 invasive-cancer patients and 23,447 controls. A p-value <0.05 and a false discovery rate (FDR) <0.2 was considered statistically significant. Results In the larger dataset, GPC6/GPC5 rs17702471 was associated with the endometrioid subtype among Caucasians (OR=1.16, 95%CI=1.07–1.25, p=0.0003, FDR=0.19), while F8 rs7053448 (OR=1.69, 95%CI=1.27–2.24, p=0.0003, FDR=0.12), F8 rs7058826 (OR=1.69, 95%CI=1.27–2.24, p=0.0003, FDR=0.12), and CAPN13 rs1983383 (OR=0.79, 95%CI=0.69–0.90, p=0.0005, FDR=0.12) were associated with combined invasive EOC among Asians. In silico functional analyses revealed that GPC6/GPC5 rs17702471 coincided with DNA regulatory elements. Conclusion These results suggest that EMT gene variants do not appear to play a significant role in the susceptibility to EOC. PMID:26399219

Empirical extensions of the lasso penalty to reduce the false discovery rate in high-dimensional Cox regression models.

PubMed

Ternès, Nils; Rotolo, Federico; Michiels, Stefan

2016-07-10

Correct selection of prognostic biomarkers among multiple candidates is becoming increasingly challenging as the dimensionality of biological data becomes higher. Therefore, minimizing the false discovery rate (FDR) is of primary importance, while a low false negative rate (FNR) is a complementary measure. The lasso is a popular selection method in Cox regression, but its results depend heavily on the penalty parameter λ. Usually, λ is chosen using maximum cross-validated log-likelihood (max-cvl). However, this method has often a very high FDR. We review methods for a more conservative choice of λ. We propose an empirical extension of the cvl by adding a penalization term, which trades off between the goodness-of-fit and the parsimony of the model, leading to the selection of fewer biomarkers and, as we show, to the reduction of the FDR without large increase in FNR. We conducted a simulation study considering null and moderately sparse alternative scenarios and compared our approach with the standard lasso and 10 other competitors: Akaike information criterion (AIC), corrected AIC, Bayesian information criterion (BIC), extended BIC, Hannan and Quinn information criterion (HQIC), risk information criterion (RIC), one-standard-error rule, adaptive lasso, stability selection, and percentile lasso. Our extension achieved the best compromise across all the scenarios between a reduction of the FDR and a limited raise of the FNR, followed by the AIC, the RIC, and the adaptive lasso, which performed well in some settings. We illustrate the methods using gene expression data of 523 breast cancer patients. In conclusion, we propose to apply our extension to the lasso whenever a stringent FDR with a limited FNR is targeted. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Tobacco exposure-related alterations in DNA methylation and gene expression in human monocytes: the Multi-Ethnic Study of Atherosclerosis (MESA)

PubMed Central

Reynolds, Lindsay M.; Lohman, Kurt; Pittman, Gary S.; Barr, R. Graham; Chi, Gloria C.; Kaufman, Joel; Wan, Ma; Bell, Douglas A.; Blaha, Michael J.; Rodriguez, Carlos J.; Liu, Yongmei

2017-01-01

ABSTRACT Alterations in DNA methylation and gene expression in blood leukocytes are potential biomarkers of harm and mediators of the deleterious effects of tobacco exposure. However, methodological issues, including the use of self-reported smoking status and mixed cell types have made previously identified alterations in DNA methylation and gene expression difficult to interpret. In this study, we examined associations of tobacco exposure with DNA methylation and gene expression, utilizing a biomarker of tobacco exposure (urine cotinine) and CD14+ purified monocyte samples from 934 participants of the community-based Multi-Ethnic Study of Atherosclerosis (MESA). Urine cotinine levels were measured using an immunoassay. DNA methylation and gene expression were measured with microarrays. Multivariate linear regression was used to test for associations adjusting for age, sex, race/ethnicity, education, and study site. Urine cotinine levels were associated with methylation of 176 CpGs [false discovery rate (FDR)<0.01]. Four CpGs not previously identified by studies of non-purified blood samples nominally replicated (P value<0.05) with plasma cotinine-associated methylation in 128 independent monocyte samples. Urine cotinine levels associated with expression of 12 genes (FDR<0.01), including increased expression of P2RY6 (Beta ± standard error = 0.078 ± 0.008, P = 1.99 × 10−22), a gene previously identified to be involved in the release of pro-inflammatory cytokines. No cotinine-associated (FDR<0.01) methylation profiles significantly (FDR<0.01) correlated with cotinine-associated (FDR<0.01) gene expression profiles. In conclusion, our findings i) identify potential monocyte-specific smoking-associated methylation patterns and ii) suggest that alterations in methylation may not be a main mechanism regulating gene expression in monocytes in response to cigarette smoking. PMID:29166816

Quantitative trait Loci analysis using the false discovery rate.

PubMed

Benjamini, Yoav; Yekutieli, Daniel

2005-10-01

False discovery rate control has become an essential tool in any study that has a very large multiplicity problem. False discovery rate-controlling procedures have also been found to be very effective in QTL analysis, ensuring reproducible results with few falsely discovered linkages and offering increased power to discover QTL, although their acceptance has been slower than in microarray analysis, for example. The reason is partly because the methodological aspects of applying the false discovery rate to QTL mapping are not well developed. Our aim in this work is to lay a solid foundation for the use of the false discovery rate in QTL mapping. We review the false discovery rate criterion, the appropriate interpretation of the FDR, and alternative formulations of the FDR that appeared in the statistical and genetics literature. We discuss important features of the FDR approach, some stemming from new developments in FDR theory and methodology, which deem it especially useful in linkage analysis. We review false discovery rate-controlling procedures--the BH, the resampling procedure, and the adaptive two-stage procedure-and discuss the validity of these procedures in single- and multiple-trait QTL mapping. Finally we argue that the control of the false discovery rate has an important role in suggesting, indicating the significance of, and confirming QTL and present guidelines for its use.

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population

PubMed Central

Lee, Woojoo; Alexeyenko, Andrey; Pernemalm, Maria; Guegan, Justine; Dessen, Philippe; Lazar, Vladimir; Lehtiö, Janne; Pawitan, Yudi

2015-01-01

Biological heterogeneity is common in many diseases and it is often the reason for therapeutic failures. Thus, there is great interest in classifying a disease into subtypes that have clinical significance in terms of prognosis or therapy response. One of the most popular methods to uncover unrecognized subtypes is cluster analysis. However, classical clustering methods such as k-means clustering or hierarchical clustering are not guaranteed to produce clinically interesting subtypes. This could be because the main statistical variability—the basis of cluster generation—is dominated by genes not associated with the clinical phenotype of interest. Furthermore, a strong prognostic factor might be relevant for a certain subgroup but not for the whole population; thus an analysis of the whole sample may not reveal this prognostic factor. To address these problems we investigate methods to identify and assess clinically interesting subgroups in a heterogeneous population. The identification step uses a clustering algorithm and to assess significance we use a false discovery rate- (FDR-) based measure. Under the heterogeneity condition the standard FDR estimate is shown to overestimate the true FDR value, but this is remedied by an improved FDR estimation procedure. As illustrations, two real data examples from gene expression studies of lung cancer are provided. PMID:26339613

Use of Metabolomics as a Complementary Omic Approach to Implement Risk Criteria for First-Degree Relatives of Gastric Cancer Patients

PubMed Central

Miolo, Gianmaria; Caggiari, Laura; De Zorzi, Mariangela; Steffan, Agostino

2018-01-01

A positive family history is a strong and consistently reported risk factor for gastric cancer (GC). So far, it has been demonstrated that serum pepsinogens (PGs), and gastrin 17 (G17) are useful for screening individuals at elevated risk to develop atrophic gastritis but they are suboptimal biomarkers to screen individuals for GC. The main purpose of this study was to investigate serum metabolomic profiles to find additional biomarkers that could be integrated with serum PGs and G17 to improve the diagnosis of GC and the selection of first-degree relatives (FDR) at higher risk of GC development. Serum metabolomic profiles included 188 serum metabolites, covering amino acids, biogenic amines, acylcarnitines, phosphatidylcholines, sphingomyelins and hexoses. Serum metabolomic profiles were performed with tandem mass spectrometry using the Biocrates AbsoluteIDQ p180 kit. The initial cohort (training set) consisted of n = 49 GC patients and n = 37 FDR. Differential metabolomic signatures among the two groups were investigated by univariate and multivariate partial least square differential analysis. The most significant metabolites were further selected and validated in an independent group of n = 22 GC patients and n = 17 FDR (validation set). Receiver operating characteristic (ROC) curves were used to evaluate the diagnostic power and the optimal cut-off for each of the discriminant markers. Multivariate analysis was applied to associate the selected serum metabolites, PGs, G17 and risk factors such as age, gender and Helicobacter pylori (H. pylori) infection with the GC and FDR has been performed and an integrative risk prediction algorithm was developed. In the training set, 40 metabolites mainly belonging to phospholipids and acylcarnitines classes were differentially expressed between GC and FDR. Out of these 40 metabolites, 9 were further confirmed in the validation set. Compared with FDR, GC patients were characterized by lower levels of hydroxylated sphingomyelins (SM(OH)22:1, SM(OH)22:2, SM(OH)24:1) and phosphatidylcholines (PC ae 40:1, PC ae 42:2, PC ae 42:3) and by higher levels of acylcarnitines derivatives (C2, C16, C18:1). The specificity and sensitivity of the integrative risk prediction analysis of metabolites for GC was 73.47% and 83.78% respectively with an area under the curve of the ROC curve of 0.811 that improves to 0.90 when metabolites were integrated with the serum PGs. The predictive risk algorithm composed of the C16, SM(OH)22:1 and PG-II serum levels according to the age of individuals, could be used to stratify FDR at high risk of GC development, and then this can be addressed with diagnostic gastroscopy. PMID:29518896

Flight State Information Inference with Application to Helicopter Cockpit Video Data Analysis Using Data Mining Techniques

NASA Astrophysics Data System (ADS)

Shin, Sanghyun

The National Transportation Safety Board (NTSB) has recently emphasized the importance of analyzing flight data as one of the most effective methods to improve eciency and safety of helicopter operations. By analyzing flight data with Flight Data Monitoring (FDM) programs, the safety and performance of helicopter operations can be evaluated and improved. In spite of the NTSB's effort, the safety of helicopter operations has not improved at the same rate as the safety of worldwide airlines, and the accident rate of helicopters continues to be much higher than that of fixed-wing aircraft. One of the main reasons is that the participation rates of the rotorcraft industry in the FDM programs are low due to the high costs of the Flight Data Recorder (FDR), the need of a special readout device to decode the FDR, anxiety of punitive action, etc. Since a video camera is easily installed, accessible, and inexpensively maintained, cockpit video data could complement the FDR in the presence of the FDR or possibly replace the role of the FDR in the absence of the FDR. Cockpit video data is composed of image and audio data: image data contains outside views through cockpit windows and activities on the flight instrument panels, whereas audio data contains sounds of the alarms within the cockpit. The goal of this research is to develop, test, and demonstrate a cockpit video data analysis algorithm based on data mining and signal processing techniques that can help better understand situations in the cockpit and the state of a helicopter by efficiently and accurately inferring the useful flight information from cockpit video data. Image processing algorithms based on data mining techniques are proposed to estimate a helicopter's attitude such as the bank and pitch angles, identify indicators from a flight instrument panel, and read the gauges and the numbers in the analogue gauge indicators and digital displays from cockpit image data. In addition, an audio processing algorithm based on signal processing and abrupt change detection techniques is proposed to identify types of warning alarms and to detect the occurrence times of individual alarms from cockpit audio data. Those proposed algorithms are then successfully applied to simulated and real helicopter cockpit video data to demonstrate and validate their performance.

Genetic variants in two pathways influence serum urate levels and gout risk: a systematic pathway analysis.

PubMed

Dong, Zheng; Zhou, Jingru; Xu, Xia; Jiang, Shuai; Li, Yuan; Zhao, Dongbao; Yang, Chengde; Ma, Yanyun; Wang, Yi; He, Hongjun; Ji, Hengdong; Zhang, Juan; Yuan, Ziyu; Yang, Yajun; Wang, Xiaofeng; Pang, Yafei; Jin, Li; Zou, Hejian; Wang, Jiucun

2018-03-01

The aims of this study were to identify candidate pathways associated with serum urate and to explore the genetic effect of those pathways on the risk of gout. Pathway analysis of the loci identified in genome-wide association studies (GWASs) showed that the ion transmembrane transporter activity pathway (GO: 0015075) and the secondary active transmembrane transporter activity pathway (GO: 0015291) were both associated with serum urate concentrations, with P FDR values of 0.004 and 0.007, respectively. In a Chinese population of 4,332 individuals, the two pathways were also found to be associated with serum urate (P FDR  = 1.88E-05 and 3.44E-04, separately). In addition, these two pathways were further associated with the pathogenesis of gout (P FDR  = 1.08E-08 and 2.66E-03, respectively) in the Chinese population and a novel gout-associated gene, SLC17A2, was identified (OR = 0.83, P FDR  = 0.017). The mRNA expression of candidate genes also showed significant differences among different groups at pathway level. The present study identified two transmembrane transporter activity pathways (GO: 0015075 and GO: 0015291) were associations with serum urate concentrations and the risk of gout. SLC17A2 was identified as a novel gene that influenced the risk of gout.

Frequency Domain Reflectometry NDE for Aging Cables in Nuclear Power Plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glass, Samuel W.; Jones, Anthony M.; Fifield, Leonard S.

Cable insulation polymers are among the more susceptible materials to age-related degradation within a nuclear power plant. This is recognized by both regulators and utilities, so all plants have developed cable aging management programs to detect damage before critical component failure in compliance with regulatory guidelines. Although a wide range of tools are available to evaluate cables and cable systems, cable aging management programs vary in how condition monitoring and nondestructive examinations are conducted as utilities search for the most reliable and cost-effective ways to assess cable system condition. Frequency domain reflectometry (FDR) is emerging as one valuable tool tomore » locate and assess damaged portions of a cable system with minimal cost and only requires access in most cases to one of the cable terminal ends. Since laboratory studies to evaluate the use of FDR for inspection of aged cables can be expensive and data interpretation may be confounded by multiple factors which influence results, a model-based approach is desired to parametrically investigate the effect of insulation material damage in a controlled manner. This work describes development of a physics-based FDR model which uses finite element simulations of cable segments in conjunction with cascaded circuit element simulations to efficiently study a cable system. One or more segments of the cable system model have altered physical or electrical properties which represent the degree of damage and the location of the damage in the system. This circuit model is then subjected to a simulated FDR examination. The modeling approach is verified using several experimental cases and by comparing it to a commercial simulator suitable for simulation of some cable configurations. The model is used to examine a broad range of parameters including defect length, defect profile, degree of degradation, number and location of defects, FDR bandwidth, and addition of impedance-matched extensions to minimize the end-shadow effect.« less

Frequency domain reflectometry modeling for nondestructive evaluation of nuclear power plant cables

NASA Astrophysics Data System (ADS)

Glass, S. W.; Fifield, L. S.; Jones, A. M.; Hartman, T. S.

2018-04-01

Cable insulation polymers are among the more susceptible materials to age-related degradation within a nuclear power plant. This is recognized by both regulators and utilities, so all plants have developed cable aging management programs to detect damage before critical component failure in compliance with regulatory guidelines. Although a wide range of tools are available to evaluate cables and cable systems, cable aging management programs vary in how condition monitoring and nondestructive examinations are conducted as utilities search for the most reliable and cost-effective ways to assess cable system condition. Frequency domain reflectometry (FDR) is emerging as one valuable tool to locate and assess damaged portions of a cable system with minimal cost and only requires access in most cases to one of the cable terminal ends. Since laboratory studies to evaluate the use of FDR for inspection of aged cables can be expensive and data interpretation may be confounded by multiple factors which influence results, a model-based approach is desired to parametrically investigate the effect of insulation material damage in a controlled manner. This work describes development of a physics-based FDR model which uses finite element simulations of cable segments in conjunction with cascaded circuit element simulations to efficiently study a cable system. One or more segments of the cable system model have altered physical or electrical properties which represent the degree of damage and the location of the damage in the system. This circuit model is then subjected to a simulated FDR examination. The modeling approach is verified using several experimental cases and by comparing it to a commercial simulator suitable for simulation of some cable configurations. The model is used to examine a broad range of parameters including defect length, defect profile, degree of degradation, number and location of defects, FDR bandwidth, and addition of impedance-matched extensions to minimize the end-shadow effect.

Milagro Observations of Potential TeV Emitters

NASA Astrophysics Data System (ADS)

Abeysekara, Anushka; Linnemann, James

2012-03-01

We searched for point sources in Milagro sky maps at the locations in four catalogs of potential TeV emitting sources. Our candidates are selected from the Fermi 2FGL pulsars, Fermi 2FGL extragalactic sources, TeVCat extragalactic sources, and from the BL Lac TeV Candidate list published by Costamante and Ghisellini in 2002. The False Discovery Rate (FDR) statistical procedure is used to select the sources. The FDR procedure controls the fraction of false detections. Our results are presented in this talk.

Use of the false discovery rate for evaluating clinical safety data.

PubMed

Mehrotra, Devan V; Heyse, Joseph F

2004-06-01

Clinical adverse experience (AE) data are routinely evaluated using between group P values for every AE encountered within each of several body systems. If the P values are reported and interpreted without multiplicity considerations, there is a potential for an excess of false positive findings. Procedures based on confidence interval estimates of treatment effects have the same potential for false positive findings as P value methods. Excess false positive findings can needlessly complicate the safety profile of a safe drug or vaccine. Accordingly, we propose a novel method for addressing multiplicity in the evaluation of adverse experience data arising in clinical trial settings. The method involves a two-step application of adjusted P values based on the Benjamini and Hochberg false discovery rate (FDR). Data from three moderate to large vaccine trials are used to illustrate our proposed 'Double FDR' approach, and to reinforce the potential impact of failing to account for multiplicity. This work was in collaboration with the late Professor John W. Tukey who coined the term 'Double FDR'.

Multiple testing with discrete data: Proportion of true null hypotheses and two adaptive FDR procedures.

PubMed

Chen, Xiongzhi; Doerge, Rebecca W; Heyse, Joseph F

2018-05-11

We consider multiple testing with false discovery rate (FDR) control when p values have discrete and heterogeneous null distributions. We propose a new estimator of the proportion of true null hypotheses and demonstrate that it is less upwardly biased than Storey's estimator and two other estimators. The new estimator induces two adaptive procedures, that is, an adaptive Benjamini-Hochberg (BH) procedure and an adaptive Benjamini-Hochberg-Heyse (BHH) procedure. We prove that the adaptive BH (aBH) procedure is conservative nonasymptotically. Through simulation studies, we show that these procedures are usually more powerful than their nonadaptive counterparts and that the adaptive BHH procedure is usually more powerful than the aBH procedure and a procedure based on randomized p-value. The adaptive procedures are applied to a study of HIV vaccine efficacy, where they identify more differentially polymorphic positions than the BH procedure at the same FDR level. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a high risk pancreatic screening clinic using 3.0 T MRI.

PubMed

Barnes, Chad A; Krzywda, Elizabeth; Lahiff, Shannon; McDowell, Dena; Christians, Kathleen K; Knechtges, Paul; Tolat, Parag; Hohenwalter, Mark; Dua, Kulwinder; Khan, Abdul H; Evans, Douglas B; Geurts, Jennifer; Tsai, Susan

2018-01-01

Selective screening for pancreatic cancer (PC) has been proposed. We describe the establishment of a comprehensive multidisciplinary screening program using 3.0 T MRI. Criteria for screening included the presence of PC in: ≥ 2 first degree relatives (FDR), 1 FDR and 1 s degree relative (SDR), ≥ 3 any degree relatives (ADR), or any known hereditary cancer syndrome with increased PC risk. Imaging with 3.0 T MRI was performed routinely and endoscopic ultrasound was used selectively. Screening was completed in 75 patients (pts). Hereditary cancer syndromes were present in 42 (56%) of the 75 pts: BRCA2 (18), ATM (8), BRCA1 (6), CDKN2A (4), PALB2 (3), Lynch (2), and Peutz-Jeghers (1). A family history of PC was present in ≥ 2 FDR in 12 (16%) pts, 1 FDR and 1 SDR in 5 (7) pts, and ≥ 3 ADR in 16 (21%) pts. Of the 65 pts who received screening MRI, 28 (43%) pts had pancreatic cystic lesions identified, including 1 (1%) patient in whom a cholangiocarcinoma was diagnosed as well. No patient underwent surgical resection. Using a 3.0 T MRI to screen patients at high risk for developing PC identified radiographic abnormalities in 43% of patients, which were stable on subsequent surveillance. Specific guidelines for the frequency of surveillance and indications for surgery remain areas of active investigation as the global experience with high risk screening continues to mature.

Genome-wide Association Study of Dermatomyositis Reveals Genetic Overlap with other Autoimmune Disorders

PubMed Central

Miller, Frederick W.; Cooper, Robert G.; Vencovsky, Jiri; Rider, Lisa G.; Danko, Katalin; Wedderburn, Lucy R.; Lundberg, Ingrid E.; Pachman, Lauren M.; Reed, Ann M.; Ytterberg, Steven R.; Padyukov, Leonid; Selva-O’Callaghan, Albert; Radstake, Timothy; Isenberg, David A.; Chinoy, Hector; Ollier, William E. R.; O’Hanlon, Terrance P.; Peng, Bo; Lee, Annette; Lamb, Janine A.; Chen, Wei; Amos, Christopher I.; Gregersen, Peter K.

2014-01-01

Objective To identify new genetic associations with juvenile and adult dermatomyositis (DM). Methods We performed a genome-wide association study (GWAS) of adult and juvenile DM patients of European ancestry (n = 1178) and controls (n = 4724). To assess genetic overlap with other autoimmune disorders, we examined whether 141 single nucleotide polymorphisms (SNPs) outside the major histocompatibility complex (MHC) locus, and previously associated with autoimmune diseases, predispose to DM. Results Compared to controls, patients with DM had a strong signal in the MHC region consisting of GWAS-level significance (P < 5x10−8) at 80 genotyped SNPs. An analysis of 141 non-MHC SNPs previously associated with autoimmune diseases showed that three SNPs linked with three genes were associated with DM, with a false discovery rate (FDR) < 0.05. These genes were phospholipase C like 1 (PLCL1, rs6738825, FDR=0.00089), B lymphoid tyrosine kinase (BLK, rs2736340, FDR=0.00031), and chemokine (C-C motif) ligand 21 (CCL21, rs951005, FDR=0.0076). None of these genes was previously reported to be associated with DM. Conclusion Our findings confirm the MHC as the major genetic region associated with DM and indicate that DM shares non-MHC genetic features with other autoimmune diseases, suggesting the presence of additional novel risk loci. This first identification of autoimmune disease genetic predispositions shared with DM may lead to enhanced understanding of pathogenesis and novel diagnostic and therapeutic approaches. PMID:23983088

Temperature Control in Radiatively Cooled Plasmas through Autoresonant Drive of TG-waves

NASA Astrophysics Data System (ADS)

Kabantsev, A. A.; Driscoll, C. F.

2013-10-01

We demonstrate accurate temperature control of pure electron plasmas, using driven wave heating ``autoresonantly'' in balance with cyclotron cooling. The mθ = 0 Trivelpiece-Gould wave frequencies are temperature-dependent, asfTG (T) =fTG (0) * [ 1 + ɛT ] ; and they exhibit a narrow Lorentzian absorption response R (f) with width γ ~10-3fTG . A continuous drive amplitude Adr then produces plasma heating power Ph ~Adr2 R (fdr) , which can exactly balance the cyclotron cooling powerPc ~ T /τc . This balance point is autoresonantly stable when fdr ~fTG (T) - γ : if T increases, then fTG (T) also increases and fdr gets further from resonance, so the heating power decreases and T decreases back to the balance point. (The second power-balance point at fdr ~fTG (T) + γ is unstable.) In practice, we use a mz = 3 TG wave having frequency range 5 . 2

In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing

DTIC Science & Technology

2015-07-24

remodeling & satellite cell activation. Fig. S8. a) Enriched KEGG pathways from differentially expressed genes for the late time points. The size of...Socs3, IL-1rn, IL-4rα, IL-10rα, IL-13rα1, FDR=4.31e-10 - GO:0050728, negative regulation of inflammatory response Invading immune cell genes: Cd68...Inflammatory States Several Days After Injury Innate immunity and microbial recognition: Tlr1, Tlr7, Tlr8, FDR=0.003 - GO:0034121, regulation of

Entropy and entropy production in Fokker–Plank equation under the generalized fluctuation–dissipation relation

NASA Astrophysics Data System (ADS)

Guo, Ran

2018-04-01

In this paper, we investigate the definition of the entropy in the Fokker–Planck equation under the generalized fluctuation–dissipation relation (FDR), which describes a Brownian particle moving in a complex medium with friction and multiplicative noise. The friction and the noise are related by the generalized FDR. The entropy for such a system is defined first. According to the definition of the entropy, we calculate the entropy production and the entropy flux. Lastly, we make a numerical calculation to display the results in figures.

The Parkinson Transcriptome Project: Roadmap to Personalized Care

DTIC Science & Technology

2015-08-01

these variants (although physically located in the proximity of the MAPT locus) do not regulate expression of the MAPT gene, but instead of three other...genes physically located nearby (i.e. RP11-707O23.5 with FDRs as low as 1.08-4, KANSL1-AS1 with FDR of 0.013, and LRRC37A2 with FDR of 0.0014...billion annually in the USA alone (O’Brien et al., 2009). There are no cures or disease-modifying therapies for Parkinson’s disease, and this may be due in

Frequency domain reflectometry NDE for aging cables in nuclear power plants

NASA Astrophysics Data System (ADS)

Glass, S. W.; Jones, A. M.; Fifield, L. S.; Hartman, T. S.

2017-02-01

Degradation of the cable jacket, electrical insulation, and other cable components of installed cables within nuclear power plants (NPPs) is known to occur as a function of age, temperature, radiation, and other environmental factors. Although system tests verify cable function under normal loads, demonstration of some cable's ability to perform under exceptional loads associated with design-basis events is essential to assuring plant integrity. The cable's ability to perform safely over the initial 40-year planned and licensed life has generally been demonstrated and there have been very few age-related cable failures. With greater than 1000 km of power, control, instrumentation, and other cables typically found in an NPP, replacing all the cables would be a severe cost burden. Justification for life extension to 60 and 80 years requires a cable aging management program that includes condition monitoring to justify cable performance under normal operation as well as accident conditions. A variety of tests are available to assess various aspects of electrical and mechanical cable performance, but none are suitable for all cable configurations nor does any single test confirm all features of interest. One particularly promising test that is beginning to be used more and more by utilities is frequency domain reflectometry (FDR). FDR is a nondestructive electrical inspection technique used to detect and localize faults in power and communication system conductors along the length of a cable from a single connection point. FDR detects discontinuities in the electrical impedance that arise due to cable splices or similar changes along the path of the conductor pair. In addition, FDR has the potential to provide sensitivity to insulation degradation by detecting small changes in impedance between the cable conductors being examined. The technique is also sensitive to cable bends, the particular lay of the cable in tray, proximity to other cable, and other factors that bear consideration when interpreting the test results. This paper examines various influences on the FDR approach and compares results of three different instruments to assess accelerated aging damage among several NPP representative cables.

A comparative review of estimates of the proportion unchanged genes and the false discovery rate

PubMed Central

Broberg, Per

2005-01-01

Background In the analysis of microarray data one generally produces a vector of p-values that for each gene give the likelihood of obtaining equally strong evidence of change by pure chance. The distribution of these p-values is a mixture of two components corresponding to the changed genes and the unchanged ones. The focus of this article is how to estimate the proportion unchanged and the false discovery rate (FDR) and how to make inferences based on these concepts. Six published methods for estimating the proportion unchanged genes are reviewed, two alternatives are presented, and all are tested on both simulated and real data. All estimates but one make do without any parametric assumptions concerning the distributions of the p-values. Furthermore, the estimation and use of the FDR and the closely related q-value is illustrated with examples. Five published estimates of the FDR and one new are presented and tested. Implementations in R code are available. Results A simulation model based on the distribution of real microarray data plus two real data sets were used to assess the methods. The proposed alternative methods for estimating the proportion unchanged fared very well, and gave evidence of low bias and very low variance. Different methods perform well depending upon whether there are few or many regulated genes. Furthermore, the methods for estimating FDR showed a varying performance, and were sometimes misleading. The new method had a very low error. Conclusion The concept of the q-value or false discovery rate is useful in practical research, despite some theoretical and practical shortcomings. However, it seems possible to challenge the performance of the published methods, and there is likely scope for further developing the estimates of the FDR. The new methods provide the scientist with more options to choose a suitable method for any particular experiment. The article advocates the use of the conjoint information regarding false positive and negative rates as well as the proportion unchanged when identifying changed genes. PMID:16086831

Effect of Tobacco Smoking on The Clinical, Histopathological, and Serological Manifestations of Sjögren’s Syndrome

PubMed Central

Stone, Donald U.; Fife, Dustin; Brown, Michael; Earley, Keith E.; Radfar, Lida; Kaufman, C. Erick; Lewis, David M.; Rhodus, Nelson L.; Segal, Barbara M.; Wallace, Daniel J.; Weisman, Michael H.; Venuturupalli, Swamy; Brennan, Michael T.; Lessard, Christopher J.; Montgomery, Courtney G.; Scofield, R. Hal; Sivils, Kathy L.

2017-01-01

Objectives To assess the association of smoking habits with the clinical, serological, and histopathological manifestations of Sjögren’s syndrome (SS) and non-Sjögren’s sicca (non-SS sicca). Methods Cross-sectional case-control study of 1288 patients with sicca symptoms (587 SS and 701 non-SS sicca) evaluated in a multi-disciplinary research clinic. Smoking patterns were obtained from questionnaire data and disease-related clinical and laboratory data were compared between current, past, ever, and never smokers. Results Current smoking rates were 4.6% for SS patients compared to 14.1% in non-SS sicca (p = 5.17x10E-09), 18% in a local lupus cohort (p = 1.13x10E-14) and 16.8% in the community (p = 4.12x10E-15). Current smoking was protective against SS classification (OR 0.35, 95%CI 0.22–0.56, FDR q = 1.9E10-05), focal lymphocytic sialadenitis (OR 0.26, 95%CI 0.15–0.44, FDR q = 1.52x10E-06), focus score ≥1 (OR 0.22, 95%CI 0.13–0.39, FDR q = 1.43x10E-07), and anti-Ro/SSA(+) (OR 0.36, 95%CI 0.2–0.64, FDR q = 0.0009); ever smoking was protective against the same features and against anti-La/SSB(+) (OR 0.52, 95%CI 0.39–0.70, FDR q = 5.82x10E-05). Duration of smoking was inversely correlated with SS even after controlling for socioeconomic status, BMI, alcohol and caffeine consumption. Conclusions Current tobacco smoking is negatively and independently associated with SS, protecting against disease-associated humoral and cellular autoimmunity. The overall smoking rate amongst SS patients is significantly lower than in matched populations and the effects of smoking are proportional to exposure duration. In spite of the protective effects of tobacco on SS manifestations, it is associated with other serious comorbidities such as lung disease, cardiovascular risk and malignancy, and should thus be strongly discouraged in patients with sicca. PMID:28166540

[Hyperspectral Remote Sensing Estimation Models for Pasture Quality].

PubMed

Ma, Wei-wei; Gong, Cai-lan; Hu, Yong; Wei, Yong-lin; Li, Long; Liu, Feng-yi; Meng, Peng

2015-10-01

Crude protein (CP), crude fat (CFA) and crude fiber (CFI) are key indicators for evaluation of the quality and feeding value of pasture. Hence, identification of these biological contents is an essential practice for animal husbandry. As current approaches to pasture quality estimation are time-consuming and costly, and even generate hazardous waste, a real-time and non-destructive method is therefore developed in this study using pasture canopy hyperspectral data. A field campaign was carried out in August 2013 around Qinghai Lake in order to obtain field spectral properties of 19 types of natural pasture using the ASD Field Spec 3, a field spectrometer that works in the optical region (350-2 500 nm) of the electromagnetic spectrum. In additional to the spectral data, pasture samples were also collected from the field and examined in laboratory to measure the relative concentration of CP (%), CFA (%) and CFI (%). After spectral denoising and smoothing, the relationship of pasture quality parameters with the reflectance spectrum, the first derivatives of reflectance (FDR), band ratio and the wavelet coefficients (WCs) was analyzed respectively. The concentration of CP, CFA and CFI of pasture was found closely correlated with FDR with wavebands centered at 424, 1 668, and 918 nm as well as with the low-scale (scale = 2, 4) Morlet, Coiflets and Gassian WCs. Accordingly, the linear, exponential, and polynomial equations between each pasture variable and FDR or WCs were developed. Validation of the developed equations indicated that the polynomial model with an independent variable of Coiflets WCs (scale = 4, wavelength =1 209 nm), the polynomial model with an independent variable of FDR, and the exponential model with an independent variable of FDR were the optimal model for prediction of concentration of CP, CFA and CFI of pasture, respectively. The R2 of the pasture quality estimation models was between 0.646 and 0.762 at the 0.01 significance level. Results suggest that the first derivatives or the wavelet coefficients of hyperspectral reflectance in visible and near-infrared regions can be used for pasture quality estimation, and that it will provide a basis for real-time prediction of pasture quality using remote sensing techniques.

Genome-wide association study of dermatomyositis reveals genetic overlap with other autoimmune disorders.

PubMed

Miller, Frederick W; Cooper, Robert G; Vencovský, Jiří; Rider, Lisa G; Danko, Katalin; Wedderburn, Lucy R; Lundberg, Ingrid E; Pachman, Lauren M; Reed, Ann M; Ytterberg, Steven R; Padyukov, Leonid; Selva-O'Callaghan, Albert; Radstake, Timothy R D J; Isenberg, David A; Chinoy, Hector; Ollier, William E R; O'Hanlon, Terrance P; Peng, Bo; Lee, Annette; Lamb, Janine A; Chen, Wei; Amos, Christopher I; Gregersen, Peter K

2013-12-01

To identify new genetic associations with juvenile and adult dermatomyositis (DM). We performed a genome-wide association study (GWAS) of adult and juvenile DM patients of European ancestry (n = 1,178) and controls (n = 4,724). To assess genetic overlap with other autoimmune disorders, we examined whether 141 single-nucleotide polymorphisms (SNPs) outside the major histocompatibility complex (MHC) locus, and previously associated with autoimmune diseases, predispose to DM. Compared to controls, patients with DM had a strong signal in the MHC region consisting of GWAS-level significance (P < 5 × 10(-8)) at 80 genotyped SNPs. An analysis of 141 non-MHC SNPs previously associated with autoimmune diseases showed that 3 SNPs linked with 3 genes were associated with DM, with a false discovery rate (FDR) of <0.05. These genes were phospholipase C-like 1 (PLCL1; rs6738825, FDR = 0.00089), B lymphoid tyrosine kinase (BLK; rs2736340, FDR = 0.0031), and chemokine (C-C motif) ligand 21 (CCL21; rs951005, FDR = 0.0076). None of these genes was previously reported to be associated with DM. Our findings confirm the MHC as the major genetic region associated with DM and indicate that DM shares non-MHC genetic features with other autoimmune diseases, suggesting the presence of additional novel risk loci. This first identification of autoimmune disease genetic predispositions shared with DM may lead to enhanced understanding of pathogenesis and novel diagnostic and therapeutic approaches. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.

A statistical method for the conservative adjustment of false discovery rate (q-value).

PubMed

Lai, Yinglei

2017-03-14

q-value is a widely used statistical method for estimating false discovery rate (FDR), which is a conventional significance measure in the analysis of genome-wide expression data. q-value is a random variable and it may underestimate FDR in practice. An underestimated FDR can lead to unexpected false discoveries in the follow-up validation experiments. This issue has not been well addressed in literature, especially in the situation when the permutation procedure is necessary for p-value calculation. We proposed a statistical method for the conservative adjustment of q-value. In practice, it is usually necessary to calculate p-value by a permutation procedure. This was also considered in our adjustment method. We used simulation data as well as experimental microarray or sequencing data to illustrate the usefulness of our method. The conservativeness of our approach has been mathematically confirmed in this study. We have demonstrated the importance of conservative adjustment of q-value, particularly in the situation that the proportion of differentially expressed genes is small or the overall differential expression signal is weak.

Genome-wide significant risk associations for mucinous ovarian carcinoma.

PubMed

Kelemen, Linda E; Lawrenson, Kate; Tyrer, Jonathan; Li, Qiyuan; Lee, Janet M; Seo, Ji-Heui; Phelan, Catherine M; Beesley, Jonathan; Chen, Xiaoqing; Spindler, Tassja J; Aben, Katja K H; Anton-Culver, Hoda; Antonenkova, Natalia

2015-08-01

Genome-wide association studies have identified several risk associations for ovarian carcinomas but not for mucinous ovarian carcinomas (MOCs). Our analysis of 1,644 MOC cases and 21,693 controls with imputation identified 3 new risk associations: rs752590 at 2q13 (P = 3.3 × 10(-8)), rs711830 at 2q31.1 (P = 7.5 × 10(-12)) and rs688187 at 19q13.2 (P = 6.8 × 10(-13)). We identified significant expression quantitative trait locus (eQTL) associations for HOXD9 at 2q31.1 in ovarian (P = 4.95 × 10(-4), false discovery rate (FDR) = 0.003) and colorectal (P = 0.01, FDR = 0.09) tumors and for PAX8 at 2q13 in colorectal tumors (P = 0.03, FDR = 0.09). Chromosome conformation capture analysis identified interactions between the HOXD9 promoter and risk-associated SNPs at 2q31.1. Overexpressing HOXD9 in MOC cells augmented the neoplastic phenotype. These findings provide the first evidence for MOC susceptibility variants and insights into the underlying biology of the disease.

A Non-parametric Cutout Index for Robust Evaluation of Identified Proteins*

PubMed Central

Serang, Oliver; Paulo, Joao; Steen, Hanno; Steen, Judith A.

2013-01-01

This paper proposes a novel, automated method for evaluating sets of proteins identified using mass spectrometry. The remaining peptide-spectrum match score distributions of protein sets are compared to an empirical absent peptide-spectrum match score distribution, and a Bayesian non-parametric method reminiscent of the Dirichlet process is presented to accurately perform this comparison. Thus, for a given protein set, the process computes the likelihood that the proteins identified are correctly identified. First, the method is used to evaluate protein sets chosen using different protein-level false discovery rate (FDR) thresholds, assigning each protein set a likelihood. The protein set assigned the highest likelihood is used to choose a non-arbitrary protein-level FDR threshold. Because the method can be used to evaluate any protein identification strategy (and is not limited to mere comparisons of different FDR thresholds), we subsequently use the method to compare and evaluate multiple simple methods for merging peptide evidence over replicate experiments. The general statistical approach can be applied to other types of data (e.g. RNA sequencing) and generalizes to multivariate problems. PMID:23292186

A low molecular weight proteome comparison of fertile and male sterile 8 anthers of Zea mays

PubMed Central

Wang, Dongxue; Adams, Christopher M.; Fernandes, John F.; Egger, Rachel L.; Walbot, Virginia

2014-01-01

Summary During maize anther development, somatic locular cells differentiate to support meiosis in the pollen mother cells. Meiosis is an important event during anther growth and is essential for plant fertility as pollen contains the haploid sperm. A subset of maize male sterile mutants exhibit meiotic failure, including ms8 (male sterile 8) in which meiocytes arrest as dyads and the locular somatic cells exhibit multiple defects. Systematic proteomic profiles were analysed in biological triplicates plus technical triplicates comparing ms8 anthers with fertile sibling samples at both the premeiotic and meiotic stages; proteins from 3.5 to 20 kDa were fractionated by 1-D PAGE, cleaved with Lys-C and then sequenced using a LTQ Orbitrap Velos MS paradigm. Three hundred and 59proteins were identified with two or more assigned peptides in which each of those peptides were counted at least two or more times (0.4% peptide false discovery rate (FDR) and 0.2% protein FDR); 2761 proteins were identified with one or more assigned peptides (0.4% peptide FDR and 7.6% protein FDR). Stage-specific protein expression provides candidate stage markers for early anther development, and proteins specifically expressed in fertile compared to sterile anthers provide important clues about the regulation of meiosis. 49% of the proteins detected by this study are new to an independent whole anther proteome, and many small proteins missed by automated maize genome annotation were validated; these outcomes indicate the value of focusing on low molecular weight proteins. The roles of distinctive expressed proteins and methods for mass spectrometry of low molecular weight proteins are discussed. PMID:22748129

Resampling-Based Empirical Bayes Multiple Testing Procedures for Controlling Generalized Tail Probability and Expected Value Error Rates: Focus on the False Discovery Rate and Simulation Study

PubMed Central

Dudoit, Sandrine; Gilbert, Houston N.; van der Laan, Mark J.

2014-01-01

Summary This article proposes resampling-based empirical Bayes multiple testing procedures for controlling a broad class of Type I error rates, defined as generalized tail probability (gTP) error rates, gTP(q, g) = Pr(g(Vn, Sn) > q), and generalized expected value (gEV) error rates, gEV(g) = E[g(Vn, Sn)], for arbitrary functions g(Vn, Sn) of the numbers of false positives Vn and true positives Sn. Of particular interest are error rates based on the proportion g(Vn, Sn) = Vn/(Vn + Sn) of Type I errors among the rejected hypotheses, such as the false discovery rate (FDR), FDR = E[Vn/(Vn + Sn)]. The proposed procedures offer several advantages over existing methods. They provide Type I error control for general data generating distributions, with arbitrary dependence structures among variables. Gains in power are achieved by deriving rejection regions based on guessed sets of true null hypotheses and null test statistics randomly sampled from joint distributions that account for the dependence structure of the data. The Type I error and power properties of an FDR-controlling version of the resampling-based empirical Bayes approach are investigated and compared to those of widely-used FDR-controlling linear step-up procedures in a simulation study. The Type I error and power trade-off achieved by the empirical Bayes procedures under a variety of testing scenarios allows this approach to be competitive with or outperform the Storey and Tibshirani (2003) linear step-up procedure, as an alternative to the classical Benjamini and Hochberg (1995) procedure. PMID:18932138

Liver functional genomics in beef cows on grazing systems: novel genes and pathways revealed.

PubMed

Laporta, Jimena; Rosa, Guilherme J M; Naya, Hugo; Carriquiry, Mariana

2014-02-15

The adaptation of the liver to periods of negative energy balance is largely unknown in beef cattle on grazing systems. We evaluated liver transcriptome throughout gestation and early lactation of purebred and crossbred beef cows [Angus, Hereford, and their F1 crossbreeds (CR)], grazing high or low herbage allowances (HA) of native grasslands (4 and 2.5 kg dry matter/kg body wt annual mean; n = 16) using an Agilent 4 × 44k bovine array. A total of 4,661 transcripts were affected by days [272 ≥ 2.5-fold difference, false discovery rate (FDR) ≤ 0.10] and 47 pathways were altered during winter gestation (-165 to -15 days relative to calving), when cows experienced decreased body condition score, decreased insulin, and increased nonesterified fatty acid concentrations. Gluconeogenesis and fatty acid oxidation pathways were upregulated, while cell growth, DNA replication, and transcription pathways were downregulated (FDR ≤ 0.25). We observed only small changes in the liver transcriptome during early lactation (+15 to +60 days). A total of 225 genes were differentially expressed (47 ≥ 2-fold difference, FDR ≤ 0.10) between HA. The majority of those were related to glucose and pyruvate metabolism and were upregulated in high HA, reflecting their better metabolic status. Two genes were upregulated in CR cows, but 148 transcripts (74 ≥ 2-fold change difference, FDR ≤ 0.10) were affected by the HA and cow genotype interaction. The transcriptional changes observed indicated a complex and previously unrecognized, hepatic adaptive program of grazing beef cows in different nutritional environments. Novel target candidate genes, metabolic pathways, and regulatory mechanisms were reported.

Neuroanatomical and Symptomatic Sex Differences in Individuals at Clinical High Risk for Psychosis.

PubMed

Guma, Elisa; Devenyi, Gabriel A; Malla, Ashok; Shah, Jai; Chakravarty, M Mallar; Pruessner, Marita

2017-01-01

Sex differences have been widely observed in clinical presentation, functional outcome and neuroanatomy in individuals with a first-episode of psychosis, and chronic patients suffering from schizophrenia. However, little is known about sex differences in the high-risk stages for psychosis. The present study investigated sex differences in cortical and subcortical neuroanatomy in individuals at clinical high risk (CHR) for psychosis and healthy controls (CTL), and the relationship between anatomy and clinical symptoms in males at CHR. Magnetic resonance images were collected in 26 individuals at CHR (13 men) and 29 CTLs (15 men) to determine total and regional brain volumes and morphology, cortical thickness, and surface area (SA). Clinical symptoms were assessed with the brief psychiatric rating scale. Significant sex-by-diagnosis interactions were observed with opposite directions of effect in male and female CHR subjects relative to their same-sex controls in multiple cortical and subcortical areas. The right postcentral, left superior parietal, inferior parietal supramarginal, and angular gyri [<5% false discovery rate (FDR)] were thicker in male and thinner in female CHR subjects compared with their same-sex CTLs. The same pattern was observed in the right superior parietal gyrus SA at the regional and vertex level. Using a recently developed surface-based morphology pipeline, we observed sex-specific shape differences in the left hippocampus (<5% FDR) and amygdala (<10% FDR). Negative symptom burden was significantly higher in male compared with female CHR subjects ( p  = 0.04) and was positively associated with areal expansion of the left amygdala in males (<5% FDR). Some limitations of the study include the sample size, and data acquisition at 1.5 T. This study demonstrates neuroanatomical sex differences in CHR subjects, which may be associated with variations in symptomatology in men and women with psychotic symptoms.

Enhancing performance of P300-Speller under mental workload by incorporating dual-task data during classifier training.

PubMed

Chen, Yuqian; Ke, Yufeng; Meng, Guifang; Jiang, Jin; Qi, Hongzhi; Jiao, Xuejun; Xu, Minpeng; Zhou, Peng; He, Feng; Ming, Dong

2017-12-01

As one of the most important brain-computer interface (BCI) paradigms, P300-Speller was shown to be significantly impaired once applied in practical situations due to effects of mental workload. This study aims to provide a new method of building training models to enhance performance of P300-Speller under mental workload. Three experiment conditions based on row-column P300-Speller paradigm were performed including speller-only, 3-back-speller and mental-arithmetic-speller. Data under dual-task conditions were introduced to speller-only data respectively to build new training models. Then performance of classifiers with different models was compared under the same testing condition. The results showed that when tasks of imported training data and testing data were the same, character recognition accuracies and round accuracies of P300-Speller with mixed-data training models significantly improved (FDR, p < 0.005). When they were different, performance significantly improved when tested on mental-arithmetic-speller (FDR, p < 0.05) while the improvement was modest when tested on n-back-speller (FDR, p < 0.1). The analysis of ERPs revealed that ERP difference between training data and testing data was significantly diminished when the dual-task data was introduced to training data (FDR, p < 0.05). The new method of training classifier on mixed data proved to be effective in enhancing performance of P300-Speller under mental workload, confirmed the feasibility to build a universal training model and overcome the effects of mental workload in its practical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

PubMed Central

Jones, Andrew R.; Siepen, Jennifer A.; Hubbard, Simon J.; Paton, Norman W.

2010-01-01

Tandem mass spectrometry, run in combination with liquid chromatography (LC-MS/MS), can generate large numbers of peptide and protein identifications, for which a variety of database search engines are available. Distinguishing correct identifications from false positives is far from trivial because all data sets are noisy, and tend to be too large for manual inspection, therefore probabilistic methods must be employed to balance the trade-off between sensitivity and specificity. Decoy databases are becoming widely used to place statistical confidence in results sets, allowing the false discovery rate (FDR) to be estimated. It has previously been demonstrated that different MS search engines produce different peptide identification sets, and as such, employing more than one search engine could result in an increased number of peptides being identified. However, such efforts are hindered by the lack of a single scoring framework employed by all search engines. We have developed a search engine independent scoring framework based on FDR which allows peptide identifications from different search engines to be combined, called the FDRScore. We observe that peptide identifications made by three search engines are infrequently false positives, and identifications made by only a single search engine, even with a strong score from the source search engine, are significantly more likely to be false positives. We have developed a second score based on the FDR within peptide identifications grouped according to the set of search engines that have made the identification, called the combined FDRScore. We demonstrate by searching large publicly available data sets that the combined FDRScore can differentiate between between correct and incorrect peptide identifications with high accuracy, allowing on average 35% more peptide identifications to be made at a fixed FDR than using a single search engine. PMID:19253293

Fetal death and reduced birth rates associated with exposure to lead-contaminated drinking water.

PubMed

Edwards, Marc

2014-01-01

This ecologic study notes that fetal death rates (FDR) during the Washington DC drinking water "lead crisis" (2000-2004) peaked in 2001 when water lead levels (WLLs) were highest, and were minimized in 2004 after public health interventions were implemented to protect pregnant women. Changes in the DC FDR vs neighboring Baltimore City were correlated to DC WLL (R(2) = 0.72). Birth rates in DC also increased versus Baltimore City and versus the United States in 2004-2006, when consumers were protected from high WLLs. The increased births in DC neighborhoods comparing 2004 versus 2001 was correlated to the incidence of lead pipes (R(2) = 0.60). DC birth rates from 1999 to 2007 correlated with proxies for maternal blood lead including the geometric mean blood lead in DC children (R(2) = 0.68) and the incidence of lead poisoning in children under age 1.3 years (R(2) = 0.64). After public health protections were removed in 2006, DC FDR spiked in 2007-2009 versus 2004-2006 (p < 0.05), in a manner consistent with high WLL health risks to consumers arising from partial lead service line replacements, and DC FDR dropped to historically low levels in 2010-2011 after consumers were protected and the PSLR program was terminated. Re-evaluation of a historic construction-related miscarriage cluster in the USA Today Building (1987-1988), demonstrates that high WLLs from disturbed plumbing were a possible cause. Overall results are consistent with prior research linking increased lead exposure to higher incidence of miscarriages and fetal death, even at blood lead elevations (≈5 μg/dL) once considered relatively low.

Cross-sectional study of the determinants and associations of sex hormone-binding globulin concentrations in first degree relatives (FDR) of patients with Type 2 Diabetes Mellitus.

PubMed

Abdella, N A; Mojiminiyi, O A

2017-11-01

This study explores the determinants of sex hormone binding globulin (SHBG) and associations with categories of glucose intolerance and undiagnosed diabetes in first-degree relatives (FDR) of patients with Type 2 Diabetes Mellitus (T2D). Anthropometric indices, fasting lipids, glucose, insulin, adiponectin, leptin, SHBG, estradiol (E2), testosterone (TT), androstenedione (AND), dehydroepiandrosterone sulphate (DHEA-S), high-sensitivity C-reactive protein (hs-CRP) and alanine aminotransferase (ALT) were measured in 584 FDR. Homeostasis model assessment-estimate of insulin resistance (HOMA-IR), beta cell function (%B), insulin sensitivity (%S) and free androgen index (FAI) were calculated. 266 subjects were normoglycemic; 237 had prediabetes and 81 had undiagnosed diabetes. SHBG decreased stepwise with worsening categories of glucose intolerance in females whereas FAI decreased stepwise with worsening categories in males only. SHBG showed significant positive correlations with adiponectin, and HDL-C and significant negative correlations with body mass index (BMI), waist circumference (WC), Waist:hip ratio (WHR), ALT, triglycerides (TG), %B, leptin and FAI. After adjustment for WHR, only HDL-C and FAI in men and FAI and HbA1c in females remained significantly associated with SHBG. Receiver Operating Characteristic (ROC) curve analysis for detection of diabetes showed that areas under the curve for FAI and SHBG were 0.711 and 0.386 for males and 0.430 and 0.660 for females respectively. Associations of SHBG with some anthropometric and metabolic variables in FDR suggests that lower levels is a marker for risk of developing T2D through obesity dependent metabolic pathways but low FAI is a better marker of state of diabetes in males. Copyright © 2017 Elsevier B.V. All rights reserved.

False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing.

PubMed

Xiao, Jian; Cao, Hongyuan; Chen, Jun

2017-09-15

Next generation sequencing technologies have enabled the study of the human microbiome through direct sequencing of microbial DNA, resulting in an enormous amount of microbiome sequencing data. One unique characteristic of microbiome data is the phylogenetic tree that relates all the bacterial species. Closely related bacterial species have a tendency to exhibit a similar relationship with the environment or disease. Thus, incorporating the phylogenetic tree information can potentially improve the detection power for microbiome-wide association studies, where hundreds or thousands of tests are conducted simultaneously to identify bacterial species associated with a phenotype of interest. Despite much progress in multiple testing procedures such as false discovery rate (FDR) control, methods that take into account the phylogenetic tree are largely limited. We propose a new FDR control procedure that incorporates the prior structure information and apply it to microbiome data. The proposed procedure is based on a hierarchical model, where a structure-based prior distribution is designed to utilize the phylogenetic tree. By borrowing information from neighboring bacterial species, we are able to improve the statistical power of detecting associated bacterial species while controlling the FDR at desired levels. When the phylogenetic tree is mis-specified or non-informative, our procedure achieves a similar power as traditional procedures that do not take into account the tree structure. We demonstrate the performance of our method through extensive simulations and real microbiome datasets. We identified far more alcohol-drinking associated bacterial species than traditional methods. R package StructFDR is available from CRAN. chen.jun2@mayo.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

DNA methylation changes at infertility genes in newborn twins conceived by in vitro fertilisation.

PubMed

Castillo-Fernandez, Juan E; Loke, Yuk Jing; Bass-Stringer, Sebastian; Gao, Fei; Xia, Yudong; Wu, Honglong; Lu, Hanlin; Liu, Yuan; Wang, Jun; Spector, Tim D; Saffery, Richard; Craig, Jeffrey M; Bell, Jordana T

2017-03-24

The association of in vitro fertilisation (IVF) and DNA methylation has been studied predominantly at regulatory regions of imprinted genes and at just thousands of the ~28 million CpG sites in the human genome. We investigated the links between IVF and DNA methylation patterns in whole cord blood cells (n = 98) and cord blood mononuclear cells (n = 82) from newborn twins using genome-wide methylated DNA immunoprecipitation coupled with deep sequencing. At a false discovery rate (FDR) of 5%, we identified one significant whole blood DNA methylation change linked to conception via IVF, which was located ~3 kb upstream of TNP1, a gene previously linked to male infertility. The 46 most strongly associated signals (FDR of 25%) included a second region in a gene also previously linked to infertility, C9orf3, suggesting that our findings may in part capture the effect of parental subfertility. Using twin modelling, we observed that individual-specific environmental factors appear to be the main overall contributors of methylation variability at the FDR 25% IVF-associated differentially methylated regions, although evidence for methylation heritability was also obtained at several of these regions. We replicated previous findings of differential methylation associated with IVF at the H19/IGF2 region in cord blood mononuclear cells, and we validated the signal at C9orf3 in monozygotic twins. We also explored the impact of intracytoplasmic sperm injection on the FDR 25% signals for potential effects specific to male or female infertility factors. To our knowledge, this is the most comprehensive study of DNA methylation profiles at birth and IVF conception to date, and our results show evidence for epigenetic modifications that may in part reflect parental subfertility.

Finding SDSS Galaxy Clusters in 4-dimensional Color Space Using the False Discovery Rate

NASA Astrophysics Data System (ADS)

Nichol, R. C.; Miller, C. J.; Reichart, D.; Wasserman, L.; Genovese, C.; SDSS Collaboration

2000-12-01

We describe a recently developed statistical technique that provides a meaningful cut-off in probability-based decision making. We are concerned with multiple testing, where each test produces a well-defined probability (or p-value). By well-known, we mean that the null hypothesis used to determine the p-value is fully understood and appropriate. The method is entitled False Discovery Rate (FDR) and its largest advantage over other measures is that it allows one to specify a maximal amount of acceptable error. As an example of this tool, we apply FDR to a four-dimensional clustering algorithm using SDSS data. For each galaxy (or test galaxy), we count the number of neighbors that fit within one standard deviation of a four dimensional Gaussian centered on that test galaxy. The mean and standard deviation of that Gaussian are determined from the colors and errors of the test galaxy. We then take that same Gaussian and place it on a random selection of n galaxies and make a similar count. In the limit of large n, we expect the median count around these random galaxies to represent a typical field galaxy. For every test galaxy we determine the probability (or p-value) that it is a field galaxy based on these counts. A low p-value implies that the test galaxy is in a cluster environment. Once we have a p-value for every galaxy, we use FDR to determine at what level we should make our probability cut-off. Once this cut-off is made, we have a final sample of galaxies that are cluster-like galaxies. Using FDR, we also know the maximum amount of field contamination in our cluster galaxy sample. We present our preliminary galaxy clustering results using these methods.

Combustion characteristics of an SI engine fueled with biogas fuel

NASA Astrophysics Data System (ADS)

Chen, Lei; Long, Wuqiang; Song, Peng

2017-04-01

An experimental research of the effect of H2 substitution and CO2 dilution on CH4 combustion has been carried out on a spark ignition engine. The results show that H2 addition could improve BMEP, thermal efficiency, CO and THC emissions. NOX emissions increased for higher low heating value (LHV) of H2 than CH4. CO2 dilution could effective reduce NOX emission of H2-CH4 combustion. Although engine performance, thermal efficiency and exhaust get unacceptable under high fuel dilution ratio (F.D.R.) conditions, it could be solved by decreasing F.D.R. and/or increasing hydrogen substitution ratio (H.S.R.).

How to talk about protein‐level false discovery rates in shotgun proteomics

PubMed Central

The, Matthew; Tasnim, Ayesha

2016-01-01

A frequently sought output from a shotgun proteomics experiment is a list of proteins that we believe to have been present in the analyzed sample before proteolytic digestion. The standard technique to control for errors in such lists is to enforce a preset threshold for the false discovery rate (FDR). Many consider protein‐level FDRs a difficult and vague concept, as the measurement entities, spectra, are manifestations of peptides and not proteins. Here, we argue that this confusion is unnecessary and provide a framework on how to think about protein‐level FDRs, starting from its basic principle: the null hypothesis. Specifically, we point out that two competing null hypotheses are used concurrently in today's protein inference methods, which has gone unnoticed by many. Using simulations of a shotgun proteomics experiment, we show how confusing one null hypothesis for the other can lead to serious discrepancies in the FDR. Furthermore, we demonstrate how the same simulations can be used to verify FDR estimates of protein inference methods. In particular, we show that, for a simple protein inference method, decoy models can be used to accurately estimate protein‐level FDRs for both competing null hypotheses. PMID:27503675

cit: hypothesis testing software for mediation analysis in genomic applications.

PubMed

Millstein, Joshua; Chen, Gary K; Breton, Carrie V

2016-08-01

The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data/models accommodated by the software and (iii) low power of common multiple testing approaches. The causal inference test (CIT) is based on hypothesis testing rather than estimation, allowing the testable assumptions to be evaluated in the determination of statistical significance. A user-friendly software package provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators. It can handle single and multiple binary and continuous instrumental variables, binary or continuous outcome variables and adjustment covariates. Also, the permutation-based FDR option provides a non-parametric implementation. Simulation studies demonstrate the validity of the cit package and show a substantial advantage of permutation-based FDR over other common multiple testing strategies. The cit open-source R package is freely available from the CRAN website (https://cran.r-project.org/web/packages/cit/index.html) with embedded C ++ code that utilizes the GNU Scientific Library, also freely available (http://www.gnu.org/software/gsl/). joshua.millstein@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Effect of early feed restriction on physiological responses, performance and ascites incidence in broiler chickens raised in normal or cold environment.

PubMed

Mohammadalipour, R; Rahmani, H R; Jahanian, R; Riasi, A; Mohammadalipour, M; Nili, N

2017-02-01

Intensive selection of broilers for faster growth and better feed efficiency resulted in greater susceptibility to metabolic disorders such as ascites syndrome, which is one of the major causes of mortality and economic loss in broiler industry. Whereas cool temperature is one of the primary triggers for ascites, early feed restriction (FDR) significantly alleviates its incidence and mortality. However, little is known about effects of FDR, cold environmental temperature and their interaction on physiological responses in broiler chickens. For this purpose, 320 one-day-old male broilers were divided into two treatment groups of Ad libitum (Ad) and feed restricted (FR) with eight pen replicates each. Chickens in FR group underwent feed access limitation from days 7 to 14 of age. On day 21 half of the birds (four pens) in each group exposed to the cold temperature (CT) and the other half (four pens) continued at normal temperature (NT). Average daily feed intake, average daily weight gain and feed conversion ratio (FCR) were measured at days 7, 14, 21, 28 and 42. At 39 and 46 days of age two chicks with a BW around the pen average were selected from each pen and slaughtered after collecting blood samples. Then, relative weight of internal organs and right ventricle weight per total ventricle weight (RV : TV) ratio were calculated. Compared with NT group, CT birds had higher daily feed intake and FCR (P<0.05) from day 28 to 42. Cumulative ascites mortality in CT chickens was higher (P<0.001) than NT chicks. Within the CT group, ascites mortality in FR chickens was reduced (P<0.001) to 1.25% compared with 8.75% in Ad chicks. Birds in CT group had significantly (P<0.05) thicker right ventricle and greater relative weight of heart, hematocrit and triiodothyronine concentration. However, none of these parameters were affected by FDR. Under cold stress conditions, FDR reduced activity of alanine aminotransferase and aspartate aminotransferase (P<0.05). Serum triglyceride, cholesterol, high-density lipoprotein and total protein were not influenced by either temperature or feeding regimen. In conclusion, these findings suggest that FDR reduces ascites incidence mainly by allowing better development of internal organs, which helps them to cope with the high metabolic pressure and suffer less damage.

Reduced deep regional cerebral venous oxygen saturation in hemodialysis patients using quantitative susceptibility mapping.

PubMed

Chai, Chao; Liu, Saifeng; Fan, Linlin; Liu, Lei; Li, Jinping; Zuo, Chao; Qian, Tianyi; Haacke, E Mark; Shen, Wen; Xia, Shuang

2018-02-01

Cerebral venous oxygen saturation (SvO 2 ) is an important indicator of brain function. There was debate about lower cerebral oxygen metabolism in hemodialysis patients and there were no reports about the changes of deep regional cerebral SvO 2 in hemodialysis patients. In this study, we aim to explore the deep regional cerebral SvO 2 from straight sinus using quantitative susceptibility mapping (QSM) and the correlation with clinical risk factors and neuropsychiatric testing . 52 hemodialysis patients and 54 age-and gender-matched healthy controls were enrolled. QSM reconstructed from original phase data of 3.0 T susceptibility-weighted imaging was used to measure the susceptibility of straight sinus. The susceptibility was used to calculate the deep regional cerebral SvO 2 and compare with healthy individuals. Correlation analysis was performed to investigate the correlation between deep regional cerebral SvO 2 , clinical risk factors and neuropsychiatric testing. The deep regional cerebral SvO 2 of hemodialysis patients (72.5 ± 3.7%) was significantly lower than healthy controls (76.0 ± 2.1%) (P < 0.001). There was no significant difference in the measured volume of interests of straight sinus between hemodialysis patients (250.92 ± 46.65) and healthy controls (249.68 ± 49.68) (P = 0.859). There were no significant correlations between the measured susceptibility and volume of interests in hemodialysis patients (P = 0.204) and healthy controls (P = 0.562), respectively. Hematocrit (r = 0.480, P < 0.001, FDR corrected), hemoglobin (r = 0.440, P < 0.001, FDR corrected), red blood cell (r = 0.446, P = 0.003, FDR corrected), dialysis duration (r = 0.505, P = 0.002, FDR corrected) and parathyroid hormone (r = -0.451, P = 0.007, FDR corrected) were risk factors for decreased deep regional cerebral SvO 2 in patients. The Mini-Mental State Examination (MMSE) scores of hemodialysis patients were significantly lower than healthy controls (P < 0.001). However, the deep regional cerebral SvO 2 did not correlate with MMSE scores (P = 0.630). In summary, the decreased deep regional cerebral SvO 2 occurred in hemodialysis patients and dialysis duration, parathyroid hormone, hematocrit, hemoglobin and red blood cell may be clinical risk factors.

Multi-state time-varying reliability evaluation of smart grid with flexible demand resources utilizing Lz transform

NASA Astrophysics Data System (ADS)

Jia, Heping; Jin, Wende; Ding, Yi; Song, Yonghua; Yu, Dezhao

2017-01-01

With the expanding proportion of renewable energy generation and development of smart grid technologies, flexible demand resources (FDRs) have been utilized as an approach to accommodating renewable energies. However, multiple uncertainties of FDRs may influence reliable and secure operation of smart grid. Multi-state reliability models for a single FDR and aggregating FDRs have been proposed in this paper with regard to responsive abilities for FDRs and random failures for both FDR devices and information system. The proposed reliability evaluation technique is based on Lz transform method which can formulate time-varying reliability indices. A modified IEEE-RTS has been utilized as an illustration of the proposed technique.

Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics.

PubMed

Keich, Uri; Kertesz-Farkas, Attila; Noble, William Stafford

2015-08-07

Interpreting the potentially vast number of hypotheses generated by a shotgun proteomics experiment requires a valid and accurate procedure for assigning statistical confidence estimates to identified tandem mass spectra. Despite the crucial role such procedures play in most high-throughput proteomics experiments, the scientific literature has not reached a consensus about the best confidence estimation methodology. In this work, we evaluate, using theoretical and empirical analysis, four previously proposed protocols for estimating the false discovery rate (FDR) associated with a set of identified tandem mass spectra: two variants of the target-decoy competition protocol (TDC) of Elias and Gygi and two variants of the separate target-decoy search protocol of Käll et al. Our analysis reveals significant biases in the two separate target-decoy search protocols. Moreover, the one TDC protocol that provides an unbiased FDR estimate among the target PSMs does so at the cost of forfeiting a random subset of high-scoring spectrum identifications. We therefore propose the mix-max procedure to provide unbiased, accurate FDR estimates in the presence of well-calibrated scores. The method avoids biases associated with the two separate target-decoy search protocols and also avoids the propensity for target-decoy competition to discard a random subset of high-scoring target identifications.

Detection of changes of high-frequency activity by statistical time-frequency analysis in epileptic spikes

PubMed Central

Kobayashi, Katsuhiro; Jacobs, Julia; Gotman, Jean

2013-01-01

Objective A novel type of statistical time-frequency analysis was developed to elucidate changes of high-frequency EEG activity associated with epileptic spikes. Methods The method uses the Gabor Transform and detects changes of power in comparison to background activity using t-statistics that are controlled by the false discovery rate (FDR) to correct type I error of multiple testing. The analysis was applied to EEGs recorded at 2000 Hz from three patients with mesial temporal lobe epilepsy. Results Spike-related increase of high-frequency oscillations (HFOs) was clearly shown in the FDR-controlled t-spectra: it was most dramatic in spikes recorded from the hippocampus when the hippocampus was the seizure onset zone (SOZ). Depression of fast activity was observed immediately after the spikes, especially consistently in the discharges from the hippocampal SOZ. It corresponded to the slow wave part in case of spike-and-slow-wave complexes, but it was noted even in spikes without apparent slow waves. In one patient, a gradual increase of power above 200 Hz preceded spikes. Conclusions FDR-controlled t-spectra clearly detected the spike-related changes of HFOs that were unclear in standard power spectra. Significance We developed a promising tool to study the HFOs that may be closely linked to the pathophysiology of epileptogenesis. PMID:19394892

Genome-wide significant risk associations for mucinous ovarian carcinoma

PubMed Central

Kelemen, Linda E.; Lawrenson, Kate; Tyrer, Jonathan; Li, Qiyuan; M. Lee, Janet; Seo, Ji-Heui; Phelan, Catherine M.; Beesley, Jonathan; Chen, Xiaoqin; Spindler, Tassja J.; Aben, Katja K.H.; Anton-Culver, Hoda; Antonenkova, Natalia; Baker, Helen; Bandera, Elisa V.; Bean, Yukie; Beckmann, Matthias W.; Bisogna, Maria; Bjorge, Line; Bogdanova, Natalia; Brinton, Louise A.; Brooks-Wilson, Angela; Bruinsma, Fiona; Butzow, Ralf; Campbell, Ian G.; Carty, Karen; Chang-Claude, Jenny; Chen, Y. Ann; Chen, Zhihua; Cook, Linda S.; Cramer, Daniel W.; Cunningham, Julie M.; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; Dennis, Joe; Dicks, Ed; Doherty, Jennifer A.; Dörk, Thilo; du Bois, Andreas; Dürst, Matthias; Eccles, Diana; Easton, Douglas T.; Edwards, Robert P.; Eilber, Ursula; Ekici, Arif B.; Engelholm, Svend Aage; Fasching, Peter A.; Fridley, Brooke L.; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G.; Glasspool, Rosalind; Goode, Ellen L.; Goodman, Marc T.; Grownwald, Jacek; Harrington, Patricia; Harter, Philipp; Hasmad, Hanis Nazihah; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A.T.; Hillemanns, Peter; Hogdall, Estrid; Hogdall, Claus; Hosono, Satoyo; Iversen, Edwin S.; Jakubowska, Anna; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y; Kellar, Melissa; Kelley, Joseph L.; Kiemeney, Lambertus A.; Krakstad, Camilla; Kjaer, Susanne K.; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D.; Lee, Alice W.; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A.; Liang, Dong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon F.A.G.; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R.; McNeish, Iain; Menon, Usha; Modugno, Francesmary; Moes-Sosnowska, Joanna; Moysich, Kirsten B.; Narod, Steven A.; Nedergaard, Lotte; Ness, Roberta B.; Nevanlinna, Heli; Azmi, Mat Adenan Noor; Odunsi, Kunle; Olson, Sara H.; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Paul, James; Pearce, Celeste Leigh; Pejovic, Tanja; Pelttari, Liisa M.; Permuth-Wey, Jennifer; Pike, Malcolm C.; Poole, Elizabeth M.; Ramus, Susan J.; Risch, Harvey A.; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H.; Rudolph, Anja; Runnebaum, Ingo B.; Rzepecka, Iwona K.; Salvesen, Helga B.; Schildkraut, Joellen M.; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C.; Sucheston, Lara; Tangen, Ingvild L.; Teo, Soo-Hwang; Terry, Kathryn L.; Thompson, Pamela J; Tworoger, Shelley S.; van Altena, Anne M.; Van Nieuwenhuysen, Els; Vergote, Ignace; Vierkant, Robert A.; Wang-Gohrke, Shan; Walsh, Christine; Wentzensen, Nicolas; Whittemore, Alice S.; Wicklund, Kristine G.; Wilkens, Lynne R.; Wlodzimierz, Sawicki; Woo, Yin-Ling; Wu, Xifeng; Wu, Anna H.; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Sellers, Thomas A.; Freedman, Matthew L.; Chenevix-Trench, Georgia; Pharoah, Paul D.; Gayther, Simon A.; Berchuck, Andrew

2015-01-01

Genome-wide association studies have identified several risk associations for ovarian carcinomas (OC) but not for mucinous ovarian carcinomas (MOC). Genotypes from OC cases and controls were imputed into the 1000 Genomes Project reference panel. Analysis of 1,644 MOC cases and 21,693 controls identified three novel risk associations: rs752590 at 2q13 (P = 3.3 × 10−8), rs711830 at 2q31.1 (P = 7.5 × 10−12) and rs688187 at 19q13.2 (P = 6.8 × 10−13). Expression Quantitative Trait Locus (eQTL) analysis in ovarian and colorectal tumors (which are histologically similar to MOC) identified significant eQTL associations for HOXD9 at 2q31.1 in ovarian (P = 4.95 × 10−4, FDR = 0.003) and colorectal (P = 0.01, FDR = 0.09) tumors, and for PAX8 at 2q13 in colorectal tumors (P = 0.03, FDR = 0.09). Chromosome conformation capture analysis identified interactions between the HOXD9 promoter and risk SNPs at 2q31.1. Overexpressing HOXD9 in MOC cells augmented the neoplastic phenotype. These findings provide the first evidence for MOC susceptibility variants and insights into the underlying biology of the disease. PMID:26075790

Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics

PubMed Central

2016-01-01

Interpreting the potentially vast number of hypotheses generated by a shotgun proteomics experiment requires a valid and accurate procedure for assigning statistical confidence estimates to identified tandem mass spectra. Despite the crucial role such procedures play in most high-throughput proteomics experiments, the scientific literature has not reached a consensus about the best confidence estimation methodology. In this work, we evaluate, using theoretical and empirical analysis, four previously proposed protocols for estimating the false discovery rate (FDR) associated with a set of identified tandem mass spectra: two variants of the target-decoy competition protocol (TDC) of Elias and Gygi and two variants of the separate target-decoy search protocol of Käll et al. Our analysis reveals significant biases in the two separate target-decoy search protocols. Moreover, the one TDC protocol that provides an unbiased FDR estimate among the target PSMs does so at the cost of forfeiting a random subset of high-scoring spectrum identifications. We therefore propose the mix-max procedure to provide unbiased, accurate FDR estimates in the presence of well-calibrated scores. The method avoids biases associated with the two separate target-decoy search protocols and also avoids the propensity for target-decoy competition to discard a random subset of high-scoring target identifications. PMID:26152888

A phase II trial of fixed-dosed rate gemcitabine in platinum-resistant ovarian cancer: a GEICO (Grupo Español de Investigación en Cáncer de Ovario) Trial.

PubMed

Ojeda Gonzalez, Belen; Gonzalez Martin, Antonio; Bover Barcelo, Isabel; Fabregat i Mayol, Xavier; Mellado, Begoña; Rubio Perez, María Jesus; Alonso Carrion, Lorenzo; Casado Herraez, Antonio; Calvo Garcia, Elisa; Churruca Galaz, Cristina; Arcusa Lanza, Angels; Herrero Ibañez, Ana; Adrover Cebrian, Encarna; Poveda Velasco, Andres

2008-10-01

Gemcitabine has well-recognized activity in the treatment of ovarian cancer. Fixed-dose rate (FDR) delivery has been proposed as a more rationale way to administer gemcitabine, to avoid saturation of the enzyme that catalyzes its intracellular transformation into the active metabolites, difluorodeoxycitidine biphosphate, and triphosphate. Our aim was to assess clinical activity of gemcitabine delivered by FDR infusion in patients with platinum resistant ovarian cancer. Patients with platinum-resistant ovarian cancer received gemcitabine 1000 mg/m(2) over 120 minutes on days 1 and 8 of each cycle. Cycles were repeated every 3 weeks, and up to 6 cycles were delivered. Forty-eight patients were included in the study. Among 41 patients evaluable for response, 9 clinical responses (1 complete response and 8 partial responses) were observed, achieving a global response rate of 22%. Grade 3 to 4 hematological toxicity consisted of anemia (15% of patients), neutropenia (24%), and thrombopenia (10%). One patient died due to septic shock. The main grade 3 to 4 nonhematological toxicity was asthenia (7 patients, 17%). Activity of gemcitabine administered by FDR infusion in patients with platinum-resistant ovarian cancer seems similar to that achieved using 30-minute infusions, with higher toxicity.

How to talk about protein-level false discovery rates in shotgun proteomics.

PubMed

The, Matthew; Tasnim, Ayesha; Käll, Lukas

2016-09-01

A frequently sought output from a shotgun proteomics experiment is a list of proteins that we believe to have been present in the analyzed sample before proteolytic digestion. The standard technique to control for errors in such lists is to enforce a preset threshold for the false discovery rate (FDR). Many consider protein-level FDRs a difficult and vague concept, as the measurement entities, spectra, are manifestations of peptides and not proteins. Here, we argue that this confusion is unnecessary and provide a framework on how to think about protein-level FDRs, starting from its basic principle: the null hypothesis. Specifically, we point out that two competing null hypotheses are used concurrently in today's protein inference methods, which has gone unnoticed by many. Using simulations of a shotgun proteomics experiment, we show how confusing one null hypothesis for the other can lead to serious discrepancies in the FDR. Furthermore, we demonstrate how the same simulations can be used to verify FDR estimates of protein inference methods. In particular, we show that, for a simple protein inference method, decoy models can be used to accurately estimate protein-level FDRs for both competing null hypotheses. © 2016 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monitoring water content dynamics of biological soil crusts

USGS Publications Warehouse

Young, Michael H.; Fenstermaker, Lynn F.; Belnap, Jayne

2017-01-01

Biological soil crusts (hereafter, “biocrusts”) dominate soil surfaces in nearly all dryland environments. To better understand the influence of water content on carbon (C) exchange, we assessed the ability of dual-probe heat-pulse (DPHP) sensors, installed vertically and angled, to measure changes in near-surface water content. Four DPHP sensors were installed in each of two research plots (eight sensors total) that differed by temperature treatment (control and heated). Responses were compared to horizontally installed water content measurements made with three frequency-domain reflectometry (FDR) sensors in each plot at 5-cm depth. The study was conducted near Moab, Utah, from April through September 2009. Results showed significant differences between sensor technologies: peak water content differences from the DPHP sensors were approximately three times higher than those from the FDR sensors; some of the differences can be explained by the targeted monitoring of biocrust material in the shorter DPHP sensor and by potential signal loss from horizontally installed FDR sensors, or by an oversampling of deeper soil. C-exchange estimates using the DPHP sensors showed a net C loss of 69 and 76 g C m−2 in control and heated plots, respectively. The study illustrates the potential for using the more sensitive data from shallow installations for estimating C exchange in biocrusts.

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

PubMed Central

Klambauer, Günter; Schwarzbauer, Karin; Mayr, Andreas; Clevert, Djork-Arné; Mitterecker, Andreas; Bodenhofer, Ulrich; Hochreiter, Sepp

2012-01-01

Quantitative analyses of next-generation sequencing (NGS) data, such as the detection of copy number variations (CNVs), remain challenging. Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate (FDR), even upon correction for GC content. In the context of association studies between CNVs and disease, a high FDR means many false CNVs, thereby decreasing the discovery power of the study after correction for multiple testing. We propose ‘Copy Number estimation by a Mixture Of PoissonS’ (cn.MOPS), a data processing pipeline for CNV detection in NGS data. In contrast to previous approaches, cn.MOPS incorporates modeling of depths of coverage across samples at each genomic position. Therefore, cn.MOPS is not affected by read count variations along chromosomes. Using a Bayesian approach, cn.MOPS decomposes variations in the depth of coverage across samples into integer copy numbers and noise by means of its mixture components and Poisson distributions, respectively. The noise estimate allows for reducing the FDR by filtering out detections having high noise that are likely to be false detections. We compared cn.MOPS with the five most popular methods for CNV detection in NGS data using four benchmark datasets: (i) simulated data, (ii) NGS data from a male HapMap individual with implanted CNVs from the X chromosome, (iii) data from HapMap individuals with known CNVs, (iv) high coverage data from the 1000 Genomes Project. cn.MOPS outperformed its five competitors in terms of precision (1–FDR) and recall for both gains and losses in all benchmark data sets. The software cn.MOPS is publicly available as an R package at http://www.bioinf.jku.at/software/cnmops/ and at Bioconductor. PMID:22302147

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate.

PubMed

Klambauer, Günter; Schwarzbauer, Karin; Mayr, Andreas; Clevert, Djork-Arné; Mitterecker, Andreas; Bodenhofer, Ulrich; Hochreiter, Sepp

2012-05-01

Quantitative analyses of next-generation sequencing (NGS) data, such as the detection of copy number variations (CNVs), remain challenging. Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate (FDR), even upon correction for GC content. In the context of association studies between CNVs and disease, a high FDR means many false CNVs, thereby decreasing the discovery power of the study after correction for multiple testing. We propose 'Copy Number estimation by a Mixture Of PoissonS' (cn.MOPS), a data processing pipeline for CNV detection in NGS data. In contrast to previous approaches, cn.MOPS incorporates modeling of depths of coverage across samples at each genomic position. Therefore, cn.MOPS is not affected by read count variations along chromosomes. Using a Bayesian approach, cn.MOPS decomposes variations in the depth of coverage across samples into integer copy numbers and noise by means of its mixture components and Poisson distributions, respectively. The noise estimate allows for reducing the FDR by filtering out detections having high noise that are likely to be false detections. We compared cn.MOPS with the five most popular methods for CNV detection in NGS data using four benchmark datasets: (i) simulated data, (ii) NGS data from a male HapMap individual with implanted CNVs from the X chromosome, (iii) data from HapMap individuals with known CNVs, (iv) high coverage data from the 1000 Genomes Project. cn.MOPS outperformed its five competitors in terms of precision (1-FDR) and recall for both gains and losses in all benchmark data sets. The software cn.MOPS is publicly available as an R package at http://www.bioinf.jku.at/software/cnmops/ and at Bioconductor.

Observations of stem water storage in trees of opposing hydraulic strategies

DOE PAGES

Matheny, Ashley M.; Bohrer, Gil; Garrity, Steven R.; ...

2015-09-29

Hydraulic capacitance and water storage form a critical buffer against cavitation and loss of conductivity within the xylem system. Withdrawal from water storage in leaves, branches, stems, and roots significantly impacts sap flow, stomatal conductance, and transpiration. Storage quantities differ based on soil water availability, tree size, wood anatomy and density, drought tolerance, and hydraulic strategy (anisohydric or isohydric). However, the majority of studies focus on the measurement of storage in conifers or tropical tree species. We demonstrate a novel methodology using frequency domain reflectometry (FDR) to make continuous, direct measurements of wood water content in two hardwood species inmore » a forest in Michigan. We present results of a two month study comparing the water storage dynamics between a mature red oak and red maple, two species with differing wood densities, hydraulic architecture, and hydraulic strategy. We also include results pertaining to the use of different probe lengths to sample water content only within the active sapwood and over the entire conductive sapwood and the outer portion of heartwood in red oak. Both species studied exhibited diurnal cycles of storage that aligned well with the dynamics of sap flux. Red maple, a diffuse porous, relatively isohydric species showed a strong dependence on stored water during both wet and dry periods. Red oak, a ring porous relatively anisohydric species, was less reliant on storage, and did not demonstrate a dependence on soil water potential. Comparison between long and short FDR probes in the oak revealed that oaks may utilize water stored in the innermost layers of the xylem when soil moisture conditions are limiting. We found the FDR probes to be a reliable, functional means for continuous automated measurement of wood water content in hardwoods at a fast time scale. Application of FDR technology for the measurement of tree water storage will benefit forest ecologists as well as the modeling community as we improve our understanding and simulations of plant hydrodynamic processes on a large scale.« less

Sleep spindle and K-complex detection using tunable Q-factor wavelet transform and morphological component analysis

PubMed Central

Lajnef, Tarek; Chaibi, Sahbi; Eichenlaub, Jean-Baptiste; Ruby, Perrine M.; Aguera, Pierre-Emmanuel; Samet, Mounir; Kachouri, Abdennaceur; Jerbi, Karim

2015-01-01

A novel framework for joint detection of sleep spindles and K-complex events, two hallmarks of sleep stage S2, is proposed. Sleep electroencephalography (EEG) signals are split into oscillatory (spindles) and transient (K-complex) components. This decomposition is conveniently achieved by applying morphological component analysis (MCA) to a sparse representation of EEG segments obtained by the recently introduced discrete tunable Q-factor wavelet transform (TQWT). Tuning the Q-factor provides a convenient and elegant tool to naturally decompose the signal into an oscillatory and a transient component. The actual detection step relies on thresholding (i) the transient component to reveal K-complexes and (ii) the time-frequency representation of the oscillatory component to identify sleep spindles. Optimal thresholds are derived from ROC-like curves (sensitivity vs. FDR) on training sets and the performance of the method is assessed on test data sets. We assessed the performance of our method using full-night sleep EEG data we collected from 14 participants. In comparison to visual scoring (Expert 1), the proposed method detected spindles with a sensitivity of 83.18% and false discovery rate (FDR) of 39%, while K-complexes were detected with a sensitivity of 81.57% and an FDR of 29.54%. Similar performances were obtained when using a second expert as benchmark. In addition, when the TQWT and MCA steps were excluded from the pipeline the detection sensitivities dropped down to 70% for spindles and to 76.97% for K-complexes, while the FDR rose up to 43.62 and 49.09%, respectively. Finally, we also evaluated the performance of the proposed method on a set of publicly available sleep EEG recordings. Overall, the results we obtained suggest that the TQWT-MCA method may be a valuable alternative to existing spindle and K-complex detection methods. Paths for improvements and further validations with large-scale standard open-access benchmarking data sets are discussed. PMID:26283943

SUSCEPTIBILITY LOCI FOR UMBILICAL HERNIA IN SWINE DETECTED BY GENOME-WIDE ASSOCIATION.

PubMed

Liao, X J; Lia, L; Zhang, Z Y; Long, Y; Yang, B; Ruan, G R; Su, Y; Ai, H S; Zhang, W C; Deng, W Y; Xiao, S J; Ren, J; Ding, N S; Huang, L S

2015-10-01

Umbilical hernia (UH) is a complex disorder caused by both genetic and environmental factors. UH brings animal welfare problems and severe economic loss to the pig industry. Until now, the genetic basis of UH is poorly understood. The high-density 60K porcine SNP array enables the rapid application of genome-wide association study (GWAS) to identify genetic loci for phenotypic traits at genome wide scale in pigs. The objective of this research was to identify susceptibility loci for swine umbilical hernia using the GWAS approach. We genotyped 478 piglets from 142 families representing three Western commercial breeds with the Illumina PorcineSNP60 BeadChip. Then significant SNPs were detected by GWAS using ROADTRIPS (Robust Association-Detection Test for Related Individuals with Population Substructure) software base on a Bonferroni corrected threshold (P = 1.67E-06) or suggestive threshold (P = 3.34E-05) and false discovery rate (FDR = 0.05). After quality control, 29,924 qualified SNPs and 472 piglets were used for GWAS. Two suggestive loci predisposing to pig UH were identified at 44.25MB on SSC2 (rs81358018, P = 3.34E-06, FDR = 0.049933) and at 45.90MB on SSC17 (rs81479278, P = 3.30E-06, FDR = 0.049933) in Duroc population, respectively. And no SNP was detected to be associated with pig UH at significant level in neither Landrace nor Large White population. Furthermore, we carried out a meta-analysis in the combined pure-breed population containing all the 472 piglets. rs81479278 (P = 1.16E-06, FDR = 0.022475) was identified to associate with pig UH at genome-wide significant level. SRC was characterized as plausible candidate gene for susceptibility to pig UH according to its genomic position and biological functions. To our knowledge, this study gives the first description of GWAS identifying susceptibility loci for umbilical hernia in pigs. Our findings provide deeper insights to the genetic architecture of umbilical hernia in pigs.

Cortical thickness and surface area in neonates at high risk for schizophrenia.

PubMed

Li, Gang; Wang, Li; Shi, Feng; Lyall, Amanda E; Ahn, Mihye; Peng, Ziwen; Zhu, Hongtu; Lin, Weili; Gilmore, John H; Shen, Dinggang

2016-01-01

Schizophrenia is a neurodevelopmental disorder associated with subtle abnormal cortical thickness and cortical surface area. However, it is unclear whether these abnormalities exist in neonates associated with genetic risk for schizophrenia. To this end, this preliminary study was conducted to identify possible abnormalities of cortical thickness and surface area in the high-genetic-risk neonates. Structural magnetic resonance images were acquired from offspring of mothers (N = 21) who had schizophrenia (N = 12) or schizoaffective disorder (N = 9), and also matched healthy neonates of mothers who were free of psychiatric illness (N = 26). Neonatal cortical surfaces were reconstructed and parcellated as regions of interest (ROIs), and cortical thickness for each vertex was computed as the shortest distance between the inner and outer surfaces. Comparisons were made for the average cortical thickness and total surface area in each of 68 cortical ROIs. After false discovery rate (FDR) correction, it was found that the female high-genetic-risk neonates had significantly thinner cortical thickness in the right lateral occipital cortex than the female control neonates. Before FDR correction, the high-genetic-risk neonates had significantly thinner cortex in the left transverse temporal gyrus, left banks of superior temporal sulcus, left lingual gyrus, right paracentral cortex, right posterior cingulate cortex, right temporal pole, and right lateral occipital cortex, compared with the control neonates. Before FDR correction, in comparison with control neonates, male high-risk neonates had significantly thicker cortex in the left frontal pole, left cuneus cortex, and left lateral occipital cortex; while female high-risk neonates had significantly thinner cortex in the bilateral paracentral, bilateral lateral occipital, left transverse temporal, left pars opercularis, right cuneus, and right posterior cingulate cortices. The high-risk neonates also had significantly smaller cortical surface area in the right pars triangularis (before FDR correction), compared with control neonates. This preliminary study provides the first evidence that early development of cortical thickness and surface area might be abnormal in the neonates at genetic risk for schizophrenia.

Risk of childhood mortality in family members of men with poor semen quality.

PubMed

Hanson, Heidi A; Mayer, Erik N; Anderson, Ross E; Aston, Kenneth I; Carrell, Douglas T; Berger, Justin; Lowrance, William T; Smith, Ken R; Hotaling, James M

2017-01-01

What is the familial childhood mortality in first-degree (FDR) and second-degree relatives (SDR) of patients undergoing semen analysis (SA)? The relationship between infertility and congenital malformations (CM) in offspring is complex, with an increased risk of death due to CM in FDR, but not SDR, of men with lower semen parameters. Semen quality is an established predictor of men's somatic health. We can gain a better understanding of possible genetic or environmental determinants of the infertility phenotype by exploring familial aggregation of childhood mortality in relatives of men with poor semen quality. Retrospective cohort study from the Subfertility, Health and Assisted Reproduction study (cohort compiled 1996-2011) linked with patient/familial information from the Utah Population Database (UPDB). Index cases included a clinic-referred sample of 12 889 men who underwent SA and had adequate familial and follow-up data in the UPDB. Parameters of semen quality included: semen concentration, sperm count, motility, total motile count, sperm head morphology, sperm tail morphology and vitality. SA data were collected from two tertiary medical center andrology laboratories that have captured ~90% of all SA performed in Utah since 2004. Age- and sex-matched fertile controls were selected to create the comparison group for determining risk of childhood death (to age 20 years) in family members. A total of 79 750 siblings and 160 016 aunts/uncles were used to investigate the familial aggregation of childhood mortality. The main outcome was childhood mortality in FDR and SDR of men with SA and their matched controls. All-cause and cause-specific Cox proportional hazard models were used to test the association between semen quality and childhood mortality in family members. Cause-specific models were considered for cancer and CM. In the cohort of men with SA, there were 406 (1.0%) deaths in FDR and 772 (1.1%) deaths in SDR due to any cause. There was no significant difference in the risk of all-cause childhood mortality between the relatives of men with SA and the fertile control group [hazard ratio (HR) Female = 1.08, 95% CI = 0.88, 1.32; HR Male = 0.88, 95% CI = 0.75, 1.04]. We found no association between semen quality and risk for childhood cancer mortality in FDR or SDR (HR FDR = 0.98, 95% CI = 0.62, 1.54; HR SDR = 1.12, 95% CI = 0.83, 1.50). The FDR of men with SA and fertile controls were followed on average for 19.71 and 19.73 years, respectively. During this period of follow-up, FDR of men with SA had an unadjusted 40% relative risk of increased CM-related death. After stratifying by semen parameters and adjusting for birth year, we found FDR of men with worse semen quality, and notably azoospermic men (HR = 2.69, 95% CI = 1.24,5.84), were at higher risk of CM-related death. A large proportion of men with SA in the study had normal semen parameters. It is important to note that these men themselves may not be subfertile, but they were subfertile at the couple level (i.e. the female partner may be infertile). In addition, care is needed when interpreting our results, as we do not have semen measures on our sample of fertile men. Second, we were unable to include potential confounders such as medical comorbidities, smoking status, or environmental exposures. Third, men with SA were seen at the University of Utah or Intermountain Health Care clinics for a fertility evaluation thereby suggesting a more select population. Fourth, we chose to categorize morphology into equally distributed quartiles as a response to the fact that the World Health Organization threshold for normal motility changed multiple times during our study period. Lastly, we do not know the proportion of female partners with diagnosed infertility. We chose not to subcategorize each infertile male by infertile diagnosis because our goal was to understand how semen parameters influenced familial childhood mortality. We are not the first study to show a relationship between fertility and CMs. Children conceived through ART may be at higher risk of birth defects, however it is not known if the relationship is causal or if there is some underlying factor linking infertility and birth outcomes. This study provides further evidence that the increased risk of congenital birth defects may not be due to the ART, but rather genetic or environmental factors that link the two outcomes. We encourage further research in order to confirm a relationship between semen quality and increased risk for CM. This work was supported by the National Institutes of Health - National Institute of Aging [Grant numbers 1R21AG036938-01, 2R01 AG022095 and 1K12HD085852-01]. Authors have no competing interests to disclose. Not applicable. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Significant Correlation Between the Infant Gut Microbiome and Rotavirus Vaccine Response in Rural Ghana

PubMed Central

Harris, Vanessa C.; Armah, George; Fuentes, Susana; Korpela, Katri E.; Parashar, Umesh; Victor, John C.; Tate, Jacqueline; de Weerth, Carolina; Giaquinto, Carlo; Wiersinga, Willem Joost; Lewis, Kristen D. C.; de Vos, Willem M.

2017-01-01

Background. Rotavirus (RV) is the leading cause of diarrhea-related death in children worldwide and 95% of RV-associated deaths occur in Africa and Asia where RV vaccines (RVVs) have lower efficacy. We hypothesize that differences in intestinal microbiome composition correlate with the decreased RVV efficacy observed in poor settings. Methods. We conducted a nested, case-control study comparing prevaccination, fecal microbiome compositions between 6-week old, matched RVV responders and nonresponders in rural Ghana. These infants' microbiomes were then compared with 154 age-matched, healthy Dutch infants' microbiomes, assumed to be RVV responders. Fecal microbiome analysis was performed in all groups using the Human Intestinal Tract Chip. Results. We analyzed findings in 78 Ghanaian infants, including 39 RVV responder and nonresponder pairs. The overall microbiome composition was significantly different between RVV responders and nonresponders (FDR, 0.12), and Ghanaian responders were more similar to Dutch infants than nonresponders (P = .002). RVV response correlated with an increased abundance of Streptococcus bovis and a decreased abundance of the Bacteroidetes phylum in comparisons between both Ghanaian RVV responders and nonresponders (FDR, 0.008 vs 0.003) and Dutch infants and Ghanaian nonresponders (FDR, 0.002 vs 0.009). Conclusions. The intestinal microbiome composition correlates significantly with RVV immunogenicity and may contribute to the diminished RVV immunogenicity observed in developing countries. PMID:27803175

Ethnic specificity of lupus-associated loci identified in a genome-wide association study in Korean women.

PubMed

Lee, Hye-Soon; Kim, Taehyeung; Bang, So Young; Na, Young Ji; Kim, Il; Kim, Kwangwoo; Kim, Jae-Hoon; Chung, Yeun-Jun; Shin, Hyoung Doo; Kang, Young Mo; Shim, Seung-Cheol; Suh, Chang-Hee; Park, Yong-Beom; Kim, Jong-Sung; Kang, Changwon; Bae, Sang-Cheol

2014-06-01

To identify novel genetic candidates for systemic lupus erythematosus (SLE) in the Korean population, and to validate the risk loci for SLE identified in previous genome-wide association studies (GWAS). We performed a GWAS in 400 Korean female SLE patients and 445 controls. Selected single-nucleotide polymorphisms (SNP) were then replicated in an independent cohort of 385 SLE patients and 583 controls (replication cohort 1), and in a further 811 SLE patients and 1502 controls (replication cohort 2). In the GWAS phase, rs9275428 located near HLA-DQB1 showed the strongest association with SLE (OR 0.50, false discovery rate (FDR) p=3.07×10(-6)). Although no loci reached genome-wide significance outside major histocompatibility complex (MHC), C8orf13-BLK, STAT4, CSMD1, DIAPH3, GLDC and TNFSF4 showed FDR p < 0.05. Our results suggest that STAT4, BLK, IRF5, PTTG1-miR-146a, UBE2L3 and TNFAIP3 are shared susceptibility loci among Caucasians and Asians, while ETS1, IKZF1, SLC15A4 are likely to be Asian-specific loci. In a combined analysis of 1596 SLE patients and 2540 controls for selected 22 candidate SNP, STAT4 and BLK as positive controls showed a strong association with SLE (FDR p=9.85×10(-13) and 2.28×10(-8), respectively). Of these, 16 candidates (PEX5L, TRAJ50, MYO18B, SOS1, ARHGAP26, SMURF1, CADPS, HAND1, FAM78B, DIAPH3, TBL1XR1, CSMD1, ZBTB20, C3orf21, HIPK1 and AP001042.1) showed only nominal significance (7.05×10(-4)≤FDR p≤4.38×10(-2)). There are similarities and differences in genetic susceptibility for SLE between Caucasian and Asian ethnic groups. Although 16 putative novel loci for SLE have been suggested in the Korean population, further research on a larger sample is required to discriminate truth from error.

A Phase I/II Trial of Intensity Modulated Radiation (IMRT) Dose Escalation With Concurrent Fixed-dose Rate Gemcitabine (FDR-G) in Patients With Unresectable Pancreatic Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ben-Josef, Edgar, E-mail: edgar.ben-josef@uphs.upenn.edu; Schipper, Mathew; Francis, Isaac R.

2012-12-01

Purpose: Local failure in unresectable pancreatic cancer may contribute to death. We hypothesized that intensification of local therapy would improve local control and survival. The objectives were to determine the maximum tolerated radiation dose delivered by intensity modulated radiation with fixed-dose rate gemcitabine (FDR-G), freedom from local progression (FFLP), and overall survival (OS). Methods and Materials: Eligibility included pathologic confirmation of adenocarcinoma, radiographically unresectable, performance status of 0-2, absolute neutrophil count of {>=}1500/mm{sup 3}, platelets {>=}100,000/mm{sup 3}, creatinine <2 mg/dL, bilirubin <3 mg/dL, and alanine aminotransferase/aspartate aminotransferase {<=}2.5 Multiplication-Sign upper limit of normal. FDR-G (1000 mg/m{sup 2}/100 min intravenously) wasmore » given on days -22 and -15, 1, 8, 22, and 29. Intensity modulated radiation started on day 1. Dose levels were escalated from 50-60 Gy in 25 fractions. Dose-limiting toxicity was defined as gastrointestinal toxicity grade (G) {>=}3, neutropenic fever, or deterioration in performance status to {>=}3 between day 1 and 126. Dose level was assigned using TITE-CRM (Time-to-Event Continual Reassessment Method) with the target dose-limiting toxicity (DLT) rate set to 0.25. Results: Fifty patients were accrued. DLTs were observed in 11 patients: G3/4 anorexia, nausea, vomiting, and/or dehydration (7); duodenal bleed (3); duodenal perforation (1). The recommended dose is 55 Gy, producing a probability of DLT of 0.24. The 2-year FFLP is 59% (95% confidence interval [CI]: 32-79). Median and 2-year overall survival are 14.8 months (95% CI: 12.6-22.2) and 30% (95% CI 17-45). Twelve patients underwent resection (10 R0, 2 R1) and survived a median of 32 months. Conclusions: High-dose radiation therapy with concurrent FDR-G can be delivered safely. The encouraging efficacy data suggest that outcome may be improved in unresectable patients through intensification of local therapy.« less

Assessment of soil water use by grassland by frequency domain reflectometry in the humid area of Spain

NASA Astrophysics Data System (ADS)

Mestas Valero, R. M.; Báez Bernal, D.; García Pomar, M. I.; Paz González, A.

2009-04-01

Frequency domain reflectometry (FDR) is becoming increasingly used for indirect water content determination in soils. In Galica, located in NW Spain, the humid region of this country, annual precipitation exceeds evapotranspiration. However, the yearly distribution of rainfall is irregular, so that supplementary irrigation during the dry warm summer is required often. This study aims to evaluate soil water use by grasslands and soil water regime patterns during the warm season from soil moisture measured at successive depths using FDR. The study sity is located at the experimental field of the Centre for Agricultural Research (CIAM) in Mabegondo, latitude 43°14' N and longitude 08°15' W. Soil moisture was monitored at six experimental plots from July to October 2008 two times per week using a portable FDR sensor. Measurements were made from 10 to 160 cm depth at 10 cm intervals. Moreover one of the plots was equipped with a continuous recording FDR-EnviroSCAN probe. Crop potential evapotranspiration (ETc) was estimated according to the of FAO version of the Penman-Monteith equation and the meteorological information required to apply this method was provided by a station located in the place experimental field. Cumulative rainfall along the study period was 195 mm, which is above the long-term mean and cumulative potential evapotranspiration was 264.7 mm. Using the water balance method the total value of actual evapotranspiration was estimated at 205.2 mm. Analysis of soil moisture content profiles allowed a description of soil water regime and main soil water withdrawal patterns under grassland. In general, grassland roots extracted most soil water from the 0-40 cm depth. In contrast, moisture content at the bottom of the profile was close to saturation, even the driest weeks of the study period. Continuous monitoring of soil water content allowed a more detailed characterization of dry and wet periods during the study season. The study data set may be useful for assessing draught risks and supplementary irrigation needs.

Full depth reclamation : workshop materials.

DOT National Transportation Integrated Search

2011-01-01

Rehabilitating an old pavement by pulverizing and stabilizing the existing pavement is a process referred to as Full Depth Reclamation (FDR). This process shows great potential as an economical rehabilitation alternative that provides deep structural...

Adaptation of Decoy Fusion Strategy for Existing Multi-Stage Search Workflows

NASA Astrophysics Data System (ADS)

Ivanov, Mark V.; Levitsky, Lev I.; Gorshkov, Mikhail V.

2016-09-01

A number of proteomic database search engines implement multi-stage strategies aiming at increasing the sensitivity of proteome analysis. These approaches often employ a subset of the original database for the secondary stage of analysis. However, if target-decoy approach (TDA) is used for false discovery rate (FDR) estimation, the multi-stage strategies may violate the underlying assumption of TDA that false matches are distributed uniformly across the target and decoy databases. This violation occurs if the numbers of target and decoy proteins selected for the second search are not equal. Here, we propose a method of decoy database generation based on the previously reported decoy fusion strategy. This method allows unbiased TDA-based FDR estimation in multi-stage searches and can be easily integrated into existing workflows utilizing popular search engines and post-search algorithms.

Reconstruction of the 1994 Pittsburgh Airplane Accident Using a Computer Simulation

NASA Technical Reports Server (NTRS)

Parks, Edwin K.; Bach, Ralph E., Jr.; Shin, Jae Ho

1998-01-01

On September 8, 1994, a Boeing 737-300 passenger airplane was on a downwind approach to the Pittsburgh International Airport at an altitude of 5000 feet above ground level (6000 feet MSL). While in a shallow left turn onto a downwind approach heading, the airplane crossed into the vortex trail of a Boeing 727 flying in the same approach pattern about 4 miles ahead. The B-737 airplane rolled and turned sharply to the left, exited the vortex wake and plunged into the ground. Weather was not a factor in the accident. The airplane was equipped with a 11+ channel digital Flight Data Recorder (FDR) and a multiple channel Cockpit Voice Recorder (CVR). Both recorders were recovered from the crash site and provided excellent data for the development of an accident scenario. Radar tracking of the two airplanes as well as the indicated air speed (IAS) perturbations clearly visible on the B-737 FDR recordings indicate that the upset was apparently initiated by the airplane's crossing into the wake of the B-727 flying ahead in the same traffic pattern. A 6 degree-of-freedom simulation program for the B-737 airplane using MATLAB and SIMULINK was constructed. The simulation was initialized at the stabilized flight conditions of the airplane about 13 seconds prior to its entry into the vortex trail of the B-727 airplane. By assuming a certain combination of control inputs, it was possible to produce a simulated motion that closely matched that recorded on the FDR.

Potential association of vacuum cleaning frequency with an altered gut microbiota in pregnant women and their 2-year-old children.

PubMed

Avershina, Ekaterina; Ravi, Anuradha; Storrø, Ola; Øien, Torbjørn; Johnsen, Roar; Rudi, Knut

2015-12-21

Westernized lifestyle and hygienic behavior have contributed to dramatic changes in the human-associated microbiota. This particularly relates to indoor activities such as house cleaning. We therefore investigated the associations between washing and vacuum cleaning frequency and the gut microbiota composition in a large longitudinal cohort of mothers and their children. The gut microbiota composition was determined using 16S ribosomal RNA (rRNA) gene Illumina deep sequencing. We found that high vacuum cleaning frequency about twice or more a week was associated with an altered gut microbiota composition both during pregnancy and for 2-year-old children, while there were no associations with house washing frequency. In total, six Operational Taxonomic Units (OTUs) showed significant False Discovery Rate (FDR) corrected associations with vacuum cleaning frequency for mothers (two positive and four negative) and five for 2-year-old children (four positive and one negative). For mothers and the 2-year-old children, OTUs among the dominant microbiota (average >5 %) showed correlation to vacuum cleaning frequency, with an increase in Faecalibacterium prausnitzii for mothers (p = 0.013, FDR corrected), and Blautia sp. for 2-year children (p = 0.012, FDR corrected). Bacteria showing significant associations are among the dominant gut microbiota, which may indicate indirect immunomodulation of the gut microbiota possibly through increased allergen (dust mites) exposure as a potential mechanism. However, further exploration is needed to unveil mechanistic details.

Significant Correlation Between the Infant Gut Microbiome and Rotavirus Vaccine Response in Rural Ghana.

PubMed

Harris, Vanessa C; Armah, George; Fuentes, Susana; Korpela, Katri E; Parashar, Umesh; Victor, John C; Tate, Jacqueline; de Weerth, Carolina; Giaquinto, Carlo; Wiersinga, Willem Joost; Lewis, Kristen D C; de Vos, Willem M

2017-01-01

 Rotavirus (RV) is the leading cause of diarrhea-related death in children worldwide and 95% of RV-associated deaths occur in Africa and Asia where RV vaccines (RVVs) have lower efficacy. We hypothesize that differences in intestinal microbiome composition correlate with the decreased RVV efficacy observed in poor settings.  We conducted a nested, case-control study comparing prevaccination, fecal microbiome compositions between 6-week old, matched RVV responders and nonresponders in rural Ghana. These infants' microbiomes were then compared with 154 age-matched, healthy Dutch infants' microbiomes, assumed to be RVV responders. Fecal microbiome analysis was performed in all groups using the Human Intestinal Tract Chip.  We analyzed findings in 78 Ghanaian infants, including 39 RVV responder and nonresponder pairs. The overall microbiome composition was significantly different between RVV responders and nonresponders (FDR, 0.12), and Ghanaian responders were more similar to Dutch infants than nonresponders (P = .002). RVV response correlated with an increased abundance of Streptococcus bovis and a decreased abundance of the Bacteroidetes phylum in comparisons between both Ghanaian RVV responders and nonresponders (FDR, 0.008 vs 0.003) and Dutch infants and Ghanaian nonresponders (FDR, 0.002 vs 0.009).  The intestinal microbiome composition correlates significantly with RVV immunogenicity and may contribute to the diminished RVV immunogenicity observed in developing countries. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America.

Virtual Reality Therapy for the Treatment of Alcohol Dependence: A Preliminary Investigation With Positron Emission Tomography/Computerized Tomography.

PubMed

Son, Ji Hyun; Lee, Sang Hoon; Seok, Ju Won; Kee, Baik Seok; Lee, Hyun Woong; Kim, Hyung Joon; Lee, Tae Kyung; Han, Doug Hyun

2015-07-01

Virtual reality therapy (VRT) uses multimodal stimulation that includes visual, auditory, olfactory, and gustatory stimuli. The aim of this study was to assess the effectiveness of VRT in treating subjects with alcohol dependence (AD) by evaluating changes in brain metabolism. The VRT protocol consisted of three steps: relaxation, presentation of a high-risk situation, and presentation of an aversive situation. Twelve alcohol-dependent subjects underwent 10 sessions of VRT. The alcohol-dependent subjects were assessed with 18F-fluorodeoxyglucose positron emission tomography images before and after VRT, whereas the control group underwent imaging according to the same protocol only at baseline. Compared with the healthy control group, AD subjects showed higher metabolism in the right lentiform nucleus and right temporal lobe (BA20) at baseline (P(FDR < .05) = .026). In addition, the metabolism in the left anterior cingulate was lower in subjects with AD (P(uncorr) = .001). After VRT, alcohol-dependent subjects showed decreased brain metabolism in the right lentiform nucleus (P(FDR < .05) = .026) and right temporal lobe (BA38, P(FDR < .05) = .032) relative to that at baseline. Our results suggest a neurobiological imbalance, notably, a high sensitivity to stimuli, in the limbic system in subjects with AD. Furthermore, we determined that metabolism decreased in the basal ganglia after VRT, which may explain the limbic-regulated responses of reward and regulation. Therefore, we tentatively recommend VRT to treat AD through its regulating effect on limbic circuits.

Maternal nutrition induces gene expression changes in fetal muscle and adipose tissues in sheep.

PubMed

Peñagaricano, Francisco; Wang, Xin; Rosa, Guilherme Jm; Radunz, Amy E; Khatib, Hasan

2014-11-28

Maternal nutrition during different stages of pregnancy can induce significant changes in the structure, physiology, and metabolism of the offspring. These changes could have important implications on food animal production especially if these perturbations impact muscle and adipose tissue development. Here, we evaluated the impact of different maternal isoenergetic diets, alfalfa haylage (HY; fiber), corn (CN; starch), and dried corn distillers grains (DG; fiber plus protein plus fat), on the transcriptome of fetal muscle and adipose tissues in sheep. Prepartum diets were associated with notable gene expression changes in fetal tissues. In longissimus dorsi muscle, a total of 224 and 823 genes showed differential expression (FDR ≤0.05) in fetuses derived from DG vs. CN and HY vs. CN maternal diets, respectively. Several of these significant genes affected myogenesis and muscle differentiation. In subcutaneous and perirenal adipose tissues, 745 and 208 genes were differentially expressed (FDR ≤0.05), respectively, between CN and DG diets. Many of these genes are involved in adipogenesis, lipogenesis, and adipose tissue development. Pathway analysis revealed that several GO terms and KEGG pathways were enriched (FDR ≤0.05) with differentially expressed genes associated with tissue and organ development, chromatin biology, and different metabolic processes. These findings provide evidence that maternal nutrition during pregnancy can alter the programming of fetal muscle and fat tissues in sheep. The ramifications of the observed gene expression changes, in terms of postnatal growth, body composition, and meat quality of the offspring, warrant future investigation.

Fecal Microbiota Differences According to the Risk of Advanced Colorectal Neoplasms.

PubMed

Yang, Hyo-Joon; Kwon, Min-Jung; Chang, Yoosoo; Song, Seul-Ki; Ahn, Kwang-Sung; Kim, Han-Na; Yun, Yeojun; Kim, Hyung-Lae; Park, Dong Il

2018-02-09

This study aimed to compare differences in the fecal microbiota according to the risk of advanced colorectal neoplasia (ACN) based on a risk-score model in a large Korean cohort. Stool samples were collected from 1122 health screening recipients: 404 enrolled in the average risk (AR) group, 514 in the moderate risk (MR) group, and 204 in the high risk (HR) group, in accordance with their risk of ACN. The fecal microbiota was characterized using pyrosequencing of the V3-V4 region of the 16S rRNA genes. The overall microbial diversity was significantly reduced with an increased risk of ACN [false discovery rate (FDR), P<0.001], and the composition was significantly different between the risk groups (Bonferroni corrected, P<0.05). On taxonomic comparison, 6 of 11 phyla and 39 of 88 genera were significantly different among the risk groups (all FDR P<0.05). These included under-representation of Bacteroides, Ruminococcus, and Bifidobacterium, and over-representation of Prevotella and Fusobacterium with an increased risk of ACN. In particular, we observed that the unknown genus of Ruminococcaceae were relatively abundant (16.2%) in the AR group and significantly depleted with an increased risk of ACN (13.5% in the HR group; FDR P<0.001). These findings support the hypothesis that the fecal microbiota is different according to the risk of ACN. An unknown genus of Ruminococcaceae, as novel potential butyrate producers, might have a possible role in colorectal tumorigenesis in the Korean population.

Comparison of clinical and biochemical variables in type 2 diabetes mellitus patients and their first-degree relatives with metabolic syndrome in Benin City, Nigeria: A cross sectional case controlled study.

PubMed

Ogedengbe, S; Ezeani, I U; Aihanuwa, E

2016-01-01

Type 2 diabetes mellitus (T2DM) is characterized by a relative insulin deficiency or insulin resistance. It is also associated with a cluster of metabolic abnormalities, including hyper-tension and dyslipidemia. Although there are many studies that have studied the metabolic abnormalities in T2DM patients with metabolic syndrome (MetS), only few of them have assessed the metabolic abnormalities in their first-degree relatives (FDRs) who had MetS. The aim of this study is to compare the clinical and biochemical variables in T2DM subjects and their FDRs without diabetes in Benin City, Nigeria. This is a cross sectional case control study including 124 T2DM patients, 96 FDR of T2DM subjects, and 96 controls recruited using convenience sampling. Data were collected using a questionnaire-administered technique. Variables of interest that were assessed included anthropometric indices like waist circumference (WC), hip circumference (HC), waist:hip ratio (WHR), body mass index (BMI), systolic blood pressure (SBP), diastolic blood pressure (DBP), serum lipid profile, fasting plasma glucose (FPG), hemoglobin A1c (HbA1c), proteinuria, and microalbuminuria. The 1999 World Health Organization (WHO) criteria were used to make a diagnosis of metabolic syndrome. The Chi-square test was used for comparison of proportions. P-value of less than 0.05 was taken as statistically significant. The student t-test was used to compare means and test for significant differences in the anthropometric and the metabolic indices. The prevalence of the MetS in T2DM persons was 87.1%, 16.7% in the FDR group, and 13.5% in the control group according to the WHO criteria. The mean value of HbA1c was significantly higher in T2DM subjects with MetS (p<0.05). The mean values of WC, FPG, total cholesterol, HDL cholesterol, and LDL cholesterol were higher in subjects with MetS in the T2DM group than in persons with MetS in the FDR group though not significant (p>0.05). The mean values of WHR, BMI, SBP, DBP, and triglyceride were higher in persons with the MetS in the FDR group than in persons with the MetS in the T2DM group. The difference in the BMI and SBP was significant (p<0.05). The prevalence of MetS in subjects with T2DM in Nigeria is very high. Though, all the biochemical and clinical indices were higher in T2DM subjects with MetS, the mean HbA1c, BMI, and SBP was significantly higher when compared to their FDR who also have MetS.

Photosystem I from plants as a bacterial cytochrome P450 surrogate electron donor: terminal hydroxylation of branched hydrocarbon chains.

PubMed

Jensen, Kenneth; Johnston, Jonathan B; de Montellano, Paul R Ortiz; Møller, Birger Lindberg

2012-02-01

The ability of cytochrome P450 enzymes to catalyze highly regio- and stereospecific hydroxylations makes them attractive alternatives to approaches based on chemical synthesis but they require expensive cofactors, e.g. NAD(P)H, which limits their commercial potential. Ferredoxin (Fdx) is a multifunctional electron carrier that in plants accepts electrons from photosystem I (PSI) and facilitates photoreduction of NADP(+) to NADPH mediated by ferredoxin-NAD(P)H oxidoreductase (FdR). In bacteria, the electron flow is reversed and Fdx accepts electrons from NADPH via FdR and serves as the direct electron donor to bacterial P450s. By combining the two systems, we demonstrate that irradiation of PSI can drive the activity of a bacterial P450, CYP124 from Mycobacterium tuberculosis. The substitution of the costly cofactor NADPH with sunlight illustrates the potential of the light-driven hydroxylation system for biotechnology applications.

Synaptic, transcriptional and chromatin genes disrupted in autism.

PubMed

De Rubeis, Silvia; He, Xin; Goldberg, Arthur P; Poultney, Christopher S; Samocha, Kaitlin; Cicek, A Erucment; Kou, Yan; Liu, Li; Fromer, Menachem; Walker, Susan; Singh, Tarinder; Klei, Lambertus; Kosmicki, Jack; Shih-Chen, Fu; Aleksic, Branko; Biscaldi, Monica; Bolton, Patrick F; Brownfeld, Jessica M; Cai, Jinlu; Campbell, Nicholas G; Carracedo, Angel; Chahrour, Maria H; Chiocchetti, Andreas G; Coon, Hilary; Crawford, Emily L; Curran, Sarah R; Dawson, Geraldine; Duketis, Eftichia; Fernandez, Bridget A; Gallagher, Louise; Geller, Evan; Guter, Stephen J; Hill, R Sean; Ionita-Laza, Juliana; Jimenz Gonzalez, Patricia; Kilpinen, Helena; Klauck, Sabine M; Kolevzon, Alexander; Lee, Irene; Lei, Irene; Lei, Jing; Lehtimäki, Terho; Lin, Chiao-Feng; Ma'ayan, Avi; Marshall, Christian R; McInnes, Alison L; Neale, Benjamin; Owen, Michael J; Ozaki, Noriio; Parellada, Mara; Parr, Jeremy R; Purcell, Shaun; Puura, Kaija; Rajagopalan, Deepthi; Rehnström, Karola; Reichenberg, Abraham; Sabo, Aniko; Sachse, Michael; Sanders, Stephan J; Schafer, Chad; Schulte-Rüther, Martin; Skuse, David; Stevens, Christine; Szatmari, Peter; Tammimies, Kristiina; Valladares, Otto; Voran, Annette; Li-San, Wang; Weiss, Lauren A; Willsey, A Jeremy; Yu, Timothy W; Yuen, Ryan K C; Cook, Edwin H; Freitag, Christine M; Gill, Michael; Hultman, Christina M; Lehner, Thomas; Palotie, Aaarno; Schellenberg, Gerard D; Sklar, Pamela; State, Matthew W; Sutcliffe, James S; Walsh, Christiopher A; Scherer, Stephen W; Zwick, Michael E; Barett, Jeffrey C; Cutler, David J; Roeder, Kathryn; Devlin, Bernie; Daly, Mark J; Buxbaum, Joseph D

2014-11-13

The genetic architecture of autism spectrum disorder involves the interplay of common and rare variants and their impact on hundreds of genes. Using exome sequencing, here we show that analysis of rare coding variation in 3,871 autism cases and 9,937 ancestry-matched or parental controls implicates 22 autosomal genes at a false discovery rate (FDR) < 0.05, plus a set of 107 autosomal genes strongly enriched for those likely to affect risk (FDR < 0.30). These 107 genes, which show unusual evolutionary constraint against mutations, incur de novo loss-of-function mutations in over 5% of autistic subjects. Many of the genes implicated encode proteins for synaptic formation, transcriptional regulation and chromatin-remodelling pathways. These include voltage-gated ion channels regulating the propagation of action potentials, pacemaking and excitability-transcription coupling, as well as histone-modifying enzymes and chromatin remodellers-most prominently those that mediate post-translational lysine methylation/demethylation modifications of histones.

Fourier phase retrieval with a single mask by Douglas-Rachford algorithms.

PubMed

Chen, Pengwen; Fannjiang, Albert

2018-05-01

The Fourier-domain Douglas-Rachford (FDR) algorithm is analyzed for phase retrieval with a single random mask. Since the uniqueness of phase retrieval solution requires more than a single oversampled coded diffraction pattern, the extra information is imposed in either of the following forms: 1) the sector condition on the object; 2) another oversampled diffraction pattern, coded or uncoded. For both settings, the uniqueness of projected fixed point is proved and for setting 2) the local, geometric convergence is derived with a rate given by a spectral gap condition. Numerical experiments demonstrate global, power-law convergence of FDR from arbitrary initialization for both settings as well as for 3 or more coded diffraction patterns without oversampling. In practice, the geometric convergence can be recovered from the power-law regime by a simple projection trick, resulting in highly accurate reconstruction from generic initialization.

Neuropeptide S Receptor Induces Neuropeptide Expression and Associates with Intermediate Phenotypes of Functional Gastrointestinal Disorders

PubMed Central

Camilleri, Michael; Carlson, Paula; Zinsmeister, Alan R.; McKinzie, Sanna; Busciglio, Irene; Burton, Duane; Zucchelli, Marco; D’Amato, Mauro

2009-01-01

Background & Aims NPSR1, the receptor for neuropeptide S (NPS), is expressed by gastrointestinal (GI) enteroendocrine (EE) cells, and is involved in inflammation, anxiety and nociception. NPSR1 polymorphisms are associated with asthma and inflammatory bowel disease. We aimed to determine whether NPS induces expression of GI neuropeptides; and to associate NPSR1 single nucleotide polymorphisms (SNPs) with symptom phenotype and GI functions in health and functional GI disorders (FGID). Methods The effect of NPS on mRNA expression of neuropeptides was assessed using real-time PCR in NPSR1-tranfected HEK293 cells. Seventeen NPSR1 SNPs were successfully genotyped in 699 subjects from a regional cohort of 466 FGID patients and 233 healthy controls. Associations were sought using sex-adjusted regression analysis and false discovery rate (FDR) correction. Results NPS-NPSR1 signaling induced increased expression of CCK, VIP, PYY, and somatostatin. There were no significant associations with phenotypes of FGID symptoms. There were several NPSR1 SNPs associated with individual motor or sensory functions; the associations of SNPs rs2609234, rs6972158 and rs1379928 with colonic transit rate remained significant after FDR correction. The rs1379928 polymorphism was also associated with pain, gas and urgency sensory ratings at 36 mm Hg distension, the level pre-specified for formal testing. Associations with rectal sensory ratings were not significant after FDR correction. Conclusions Expression of several neuropeptides is induced upon NPS-NPSR1 signaling; NPSR1 variants are associated with colonic transit in FGID. The role of the NPS system in FGID deserves further study. PMID:19732772

Cerebrovascular risk factors and brain microstructural abnormalities on diffusion tensor images in HIV-infected individuals.

PubMed

Nakamoto, Beau K; Jahanshad, Neda; McMurtray, Aaron; Kallianpur, Kalpana J; Chow, Dominic C; Valcour, Victor G; Paul, Robert H; Marotz, Liron; Thompson, Paul M; Shikuma, Cecilia M

2012-08-01

HIV-associated neurocognitive disorder remains prevalent in HIV-infected individuals despite effective antiretroviral therapy. As these individuals age, comorbid cerebrovascular disease will likely impact cognitive function. Effective tools to study this impact are needed. This study used diffusion tensor imaging (DTI) to characterize brain microstructural changes in HIV-infected individuals with and without cerebrovascular risk factors. Diffusion-weighted MRIs were obtained in 22 HIV-infected subjects aged 50 years or older (mean age = 58 years, standard deviation = 6 years; 19 males, three females). Tensors were calculated to obtain fractional anisotropy (FA) and mean diffusivity (MD) maps. Statistical comparisons accounting for multiple comparisons were made between groups with and without cerebrovascular risk factors. Abnormal glucose metabolism (i.e., impaired fasting glucose, impaired glucose tolerance, or diabetes mellitus) was associated with significantly higher MD (false discovery rate (FDR) critical p value = 0.008) and lower FA (FDR critical p value = 0.002) in the caudate and lower FA in the hippocampus (FDR critical p value = 0.004). Pearson correlations were performed between DTI measures in the caudate and hippocampus and age- and education-adjusted composite scores of global cognitive function, memory, and psychomotor speed. There were no detectable correlations between the neuroimaging measures and measures of cognition. In summary, we demonstrate that brain microstructural abnormalities are associated with abnormal glucose metabolism in the caudate and hippocampus of HIV-infected individuals. Deep gray matter structures and the hippocampus may be vulnerable in subjects with comorbid abnormal glucose metabolism, but our results should be confirmed in further studies.

Smoke-related DNA methylation changes in the etiology of human disease.

PubMed

Besingi, Welisane; Johansson, Asa

2014-05-01

Exposure to environmental and lifestyle factors, such as cigarette smoking, affect the epigenome and might mediate risk for diseases and cancers. We have performed a genome-wide DNA methylation study to determine the effect of smoke and snuff (smokeless tobacco) on DNA methylation. A total of 95 sites were differentially methylated [false discovery rate (FDR) q-values < 0.05] in smokers and a subset of the differentially methylated loci were also differentially expressed in smokers. We found no sites, neither any biological functions nor molecular processes enriched for smoke-less tobacco-related differential DNA methylation. This suggests that methylation changes are not caused by the basic components of the tobacco but from its burnt products. Instead, we see a clear enrichment (FDR q-value < 0.05) for genes, including CPOX, CDKN1A and PTK2, involved in response to arsenic-containing substance, which agrees with smoke containing small amounts of arsenic. A large number of biological functions and molecular processes with links to disease conditions are also enriched (FDR q-value < 0.05) for smoke-related DNA methylation changes. These include 'insulin receptor binding', and 'negative regulation of glucose import' which are associated with diabetes, 'positive regulation of interleukin-6-mediated signaling pathway', 'regulation of T-helper 2 cell differentiation', 'positive regulation of interleukin-13 production' which are associated with the immune system and 'sertoli cell fate commitment' which is important for male fertility. Since type 2 diabetes, repressed immune system and infertility have previously been associated with smoking, our results suggest that this might be mediated by DNA methylation changes.

25-Hydroxyvitamin D in pregnancy and genome wide cord blood DNA methylation in two pregnancy cohorts (MoBa and ALSPAC).

PubMed

Suderman, M; Stene, L C; Bohlin, J; Page, C M; Holvik, K; Parr, C L; Magnus, M C; Håberg, S E; Joubert, B R; Wu, M C; London, S J; Relton, C; Nystad, W

2016-05-01

The aim of the study was to investigate whether maternal mid-pregnancy 25-hydroxyvitamin D concentrations are associated with cord blood DNA methylation. DNA methylation was assessed using the Illumina HumanMethylation450 BeadChip, and maternal plasma 25-hydroxyvitamin D was measured in 819 mothers/newborn pairs participating in the Norwegian Mother and Child Cohort (MoBa) and 597 mothers/newborn pairs participating in the Avon Longitudinal Study of Parents and Children (ALSPAC). Across 473,731CpG DNA methylation sites in cord blood DNA, none were strongly associated with maternal 25-hydroxyvitamin D after adjusting for multiple tests (false discovery rate (FDR)>0.5; 473,731 tests). A meta-analysis of the results from both cohorts, using the Fisher method for combining p-values, also did not strengthen findings (FDR>0.2). Further exploration of a set of CpG sites in the proximity of four a priori defined candidate genes (CYP24A1, CYP27B1, CYP27A1 and CYP2R1) did not result in any associations with FDR<0.05 (56 tests). In this large genome wide assessment of the potential influence of maternal vitamin D status on DNA methylation, we did not find any convincing associations in 1416 newborns. If true associations do exist, their identification might require much larger consortium studies, expanded genomic coverage, investigation of alternative cell types or measurements of 25-hydroxyvitamin D at different gestational time points. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Omnisphero: a high-content image analysis (HCA) approach for phenotypic developmental neurotoxicity (DNT) screenings of organoid neurosphere cultures in vitro.

PubMed

Schmuck, Martin R; Temme, Thomas; Dach, Katharina; de Boer, Denise; Barenys, Marta; Bendt, Farina; Mosig, Axel; Fritsche, Ellen

2017-04-01

Current developmental neurotoxicity (DNT) testing in animals faces major limitations, such as high cost and time demands as well as uncertainties in their methodology, evaluation and regulation. Therefore, the use of human-based 3D in vitro systems in combination with high-content image analysis (HCA) might contribute to DNT testing with lower costs, increased throughput and enhanced predictivity for human hazard identification. Human neural progenitor cells (hNPCs) grown as 3D neurospheres mimic basic processes of brain development including hNPC migration and differentiation and are therefore useful for DNT hazard identification. HCA of migrated neurospheres creates new challenges for automated evaluations because it encompasses variable cell densities, inconsistent z-layers and heterogeneous cell populations. We tackle those challenges with our Omnisphero software, which assesses multiple endpoints of the 'Neurosphere Assay.' For neuronal identification, Omnisphero reaches a true positive rate (TPR) of 83.8 % and a false discovery rate (FDR) of 11.4 %, thus being comparable to the interindividual difference among two researchers (TPR = 94.3, FDR = 11.0 %) and largely improving the results obtained by an existing HCA approach, whose TPR does not exceed 50 % at a FDR above 50 %. The high FDR of existing methods results in incorrect measurements of neuronal morphological features accompanied by an overestimation of compound effects. Omnisphero additionally includes novel algorithms to assess 'neurosphere-specific' endpoints like radial migration and neuronal density distribution within the migration area. Furthermore, a user-assisted parameter optimization procedure makes Omnisphero accessible to non-expert end users.

Structural evaluation of asphalt pavements with full-depth reclaimed base.

DOT National Transportation Integrated Search

2012-12-01

Currently, MnDOT pavement design recommends granular equivalency, GE = 1.0 for non-stabilized full-depth : reclamation (FDR) material, which is equivalent to class 5 material. For stabilized full-depth reclamation (SFDR), : there was no guideline for...

A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data.

PubMed

Li, Xiaohong; Brock, Guy N; Rouchka, Eric C; Cooper, Nigel G F; Wu, Dongfeng; O'Toole, Timothy E; Gill, Ryan S; Eteleeb, Abdallah M; O'Brien, Liz; Rai, Shesh N

2017-01-01

Normalization is an essential step with considerable impact on high-throughput RNA sequencing (RNA-seq) data analysis. Although there are numerous methods for read count normalization, it remains a challenge to choose an optimal method due to multiple factors contributing to read count variability that affects the overall sensitivity and specificity. In order to properly determine the most appropriate normalization methods, it is critical to compare the performance and shortcomings of a representative set of normalization routines based on different dataset characteristics. Therefore, we set out to evaluate the performance of the commonly used methods (DESeq, TMM-edgeR, FPKM-CuffDiff, TC, Med UQ and FQ) and two new methods we propose: Med-pgQ2 and UQ-pgQ2 (per-gene normalization after per-sample median or upper-quartile global scaling). Our per-gene normalization approach allows for comparisons between conditions based on similar count levels. Using the benchmark Microarray Quality Control Project (MAQC) and simulated datasets, we performed differential gene expression analysis to evaluate these methods. When evaluating MAQC2 with two replicates, we observed that Med-pgQ2 and UQ-pgQ2 achieved a slightly higher area under the Receiver Operating Characteristic Curve (AUC), a specificity rate > 85%, the detection power > 92% and an actual false discovery rate (FDR) under 0.06 given the nominal FDR (≤0.05). Although the top commonly used methods (DESeq and TMM-edgeR) yield a higher power (>93%) for MAQC2 data, they trade off with a reduced specificity (<70%) and a slightly higher actual FDR than our proposed methods. In addition, the results from an analysis based on the qualitative characteristics of sample distribution for MAQC2 and human breast cancer datasets show that only our gene-wise normalization methods corrected data skewed towards lower read counts. However, when we evaluated MAQC3 with less variation in five replicates, all methods performed similarly. Thus, our proposed Med-pgQ2 and UQ-pgQ2 methods perform slightly better for differential gene analysis of RNA-seq data skewed towards lowly expressed read counts with high variation by improving specificity while maintaining a good detection power with a control of the nominal FDR level.

A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data

PubMed Central

Li, Xiaohong; Brock, Guy N.; Rouchka, Eric C.; Cooper, Nigel G. F.; Wu, Dongfeng; O’Toole, Timothy E.; Gill, Ryan S.; Eteleeb, Abdallah M.; O’Brien, Liz

2017-01-01

Normalization is an essential step with considerable impact on high-throughput RNA sequencing (RNA-seq) data analysis. Although there are numerous methods for read count normalization, it remains a challenge to choose an optimal method due to multiple factors contributing to read count variability that affects the overall sensitivity and specificity. In order to properly determine the most appropriate normalization methods, it is critical to compare the performance and shortcomings of a representative set of normalization routines based on different dataset characteristics. Therefore, we set out to evaluate the performance of the commonly used methods (DESeq, TMM-edgeR, FPKM-CuffDiff, TC, Med UQ and FQ) and two new methods we propose: Med-pgQ2 and UQ-pgQ2 (per-gene normalization after per-sample median or upper-quartile global scaling). Our per-gene normalization approach allows for comparisons between conditions based on similar count levels. Using the benchmark Microarray Quality Control Project (MAQC) and simulated datasets, we performed differential gene expression analysis to evaluate these methods. When evaluating MAQC2 with two replicates, we observed that Med-pgQ2 and UQ-pgQ2 achieved a slightly higher area under the Receiver Operating Characteristic Curve (AUC), a specificity rate > 85%, the detection power > 92% and an actual false discovery rate (FDR) under 0.06 given the nominal FDR (≤0.05). Although the top commonly used methods (DESeq and TMM-edgeR) yield a higher power (>93%) for MAQC2 data, they trade off with a reduced specificity (<70%) and a slightly higher actual FDR than our proposed methods. In addition, the results from an analysis based on the qualitative characteristics of sample distribution for MAQC2 and human breast cancer datasets show that only our gene-wise normalization methods corrected data skewed towards lower read counts. However, when we evaluated MAQC3 with less variation in five replicates, all methods performed similarly. Thus, our proposed Med-pgQ2 and UQ-pgQ2 methods perform slightly better for differential gene analysis of RNA-seq data skewed towards lowly expressed read counts with high variation by improving specificity while maintaining a good detection power with a control of the nominal FDR level. PMID:28459823

EFICAz2: enzyme function inference by a combined approach enhanced by machine learning.

PubMed

Arakaki, Adrian K; Huang, Ying; Skolnick, Jeffrey

2009-04-13

We previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on the detection of functionally discriminating residues (FDRs). FDRs distinguish between member of an enzyme family that are homofunctional (classified under the EC number of interest) or heterofunctional (annotated with another EC number or lacking enzymatic activity). Each of the two FDR-based components is associated to one of two specific kinds of enzyme families. EFICAz exhibits high precision performance, except when the maximal test to training sequence identity (MTTSI) is lower than 30%. To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment. We have developed two new EFICAz components, analogs to the two FDR-based components, where the discrimination between homo and heterofunctional members is based on the evaluation, via Support Vector Machine models, of all the aligned positions between the query sequence and the multiple sequence alignments associated to the enzyme families. Benchmark results indicate that: i) the new SVM-based components outperform their FDR-based counterparts, and ii) both SVM-based and FDR-based components generate unique predictions. We developed classification tree models to optimally combine the results from the six EFICAz components into a final EC number prediction. The new implementation of our approach, EFICAz2, exhibits a highly improved prediction precision at MTTSI < 30% compared to the original EFICAz, with only a slight decrease in prediction recall. A comparative analysis of enzyme function annotation of the human proteome by EFICAz2 and KEGG shows that: i) when both sources make EC number assignments for the same protein sequence, the assignments tend to be consistent and ii) EFICAz2 generates considerably more unique assignments than KEGG. Performance benchmarks and the comparison with KEGG demonstrate that EFICAz2 is a powerful and precise tool for enzyme function annotation, with multiple applications in genome analysis and metabolic pathway reconstruction. The EFICAz2 web service is available at: http://cssb.biology.gatech.edu/skolnick/webservice/EFICAz2/index.html.

Franklin Delano Roosevelt: The Diagnosis of Poliomyelitis Revisited.

PubMed

Ditunno, John F; Becker, Bruce E; Herbison, Gerald J

2016-09-01

Revisiting the ailments of famous historical persons in light of contemporary medical understanding has become a common academic hobby. Public discussion of Franklin Delano Roosevelt's (FDR) diagnosis of poliomyelitis after his sudden onset of paralysis in 1921 has received just such a revisitation. Recently, this 2003 historical analysis has been referenced widely on the Internet and in biographies, raising speculation that his actual diagnosis should have been Guillain-Barré Syndrome, a noncontagious disease of the peripheral nervous system rather than poliomyelitis. The authors of that 2003 analysis used a statistical analysis of his case by selectively choosing some of his reported symptoms. FDR's diagnosis of poliomyelitis, however, was fully supported by the findings of leading expert physicians of that time, who were very knowledgeable in the then-common disease and who periodically examined him during the period of 1921-1924. The most significant diagnostic features of polio are the absence of objective sensory findings in the presence of flaccid motor paralysis. These features are consistent with diagnostic criteria extant during the periods of major poliomyelitis epidemics as well as those of the Center for Disease Control 90 years later. Additional findings of fever, prodromal hyperesthesia, more severe residual proximal muscle weakness, and extensive lower extremity impairment requiring mobility with long leg braces or a wheelchair give further evidence for the diagnosis in FDR's case. Nonbulbar Guillain-Barré Syndrome, which shares the features of a flaccid paralysis and thus mimicking the initial presentation of poliomyelitis, has more than an 80% complete recovery with no reported cases of eventual wheelchair use. The most severe cases of Guillain-Barré Syndrome often have persistent objective sensory loss, associated with greater weakness in the feet and hands, which show no resemblance to FDR's impairment and disability. In light of the expert initial assessments by physicians completely familiar with the signs and symptoms of the then-common disease, review of his initial and subsequent disease course, and residual symptoms in comparison with those of Guillain-Barré syndrome, we find no reason to question the diagnostic accuracy of poliomyelitis and wish to put this debate to rest. Copyright © 2016 American Academy of Physical Medicine and Rehabilitation. Published by Elsevier Inc. All rights reserved.

Novel Genetic Variants Associated With Increased Vertebral Volumetric BMD, Reduced Vertebral Fracture Risk, and Increased Expression of SLC1A3 and EPHB2

PubMed Central

Nielson, Carrie M; Liu, Ching-Ti; Smith, Albert V; Ackert-Bicknell, Cheryl L; Reppe, Sjur; Jakobsdottir, Johanna; Wassel, Christina; Register, Thomas C; Oei, Ling; Alonso, Nerea; Oei, Edwin H; Parimi, Neeta; Samelson, Elizabeth J; Nalls, Mike A; Zmuda, Joseph; Lang, Thomas; Bouxsein, Mary; Latourelle, Jeanne; Claussnitzer, Melina; Siggeirsdottir, Kristin; Srikanth, Priya; Lorentzen, Erik; Vandenput, Liesbeth; Langefeld, Carl; Raffield, Laura; Terry, Greg; Cox, Amanda J; Allison, Matthew A; Criqui, Michael H; Bowden, Don; Ikram, M Arfan; Mellstrom, Dan; Karlsson, Magnus K; Carr, John; Budoff, Matthew; Phillips, Caroline; Cupples, L Adrienne; Chou, Wen-Chi; Myers, Richard H; Ralston, Stuart H; Gautvik, Kaare M; Cawthon, Peggy M; Cummings, Steven; Karasik, David; Rivadeneira, Fernando; Gudnason, Vilmundur; Orwoll, Eric S; Harris, Tamara B; Ohlsson, Claes; Kiel, Douglas P; Hsu, Yi-Hsiang

2017-01-01

Genome-wide association studies (GWASs) have revealed numerous loci for areal bone mineral density (aBMD). We completed the first GWAS meta-analysis (n = 15,275) of lumbar spine volumetric BMD (vBMD) measured by quantitative computed tomography (QCT), allowing for examination of the trabecular bone compartment. SNPs that were significantly associated with vBMD were also examined in two GWAS meta-analyses to determine associations with morphometric vertebral fracture (n = 21,701) and clinical vertebral fracture (n = 5893). Expression quantitative trait locus (eQTL) analyses of iliac crest biopsies were performed in 84 postmenopausal women, and murine osteoblast expression of genes implicated by eQTL or by proximity to vBMD-associated SNPs was examined. We identified significant vBMD associations with five loci, including: 1p36.12, containing WNT4 and ZBTB40; 8q24, containing TNFRSF11B; and 13q14, containing AKAP11 and TNFSF11. Two loci (5p13 and 1p36.12) also contained associations with radiographic and clinical vertebral fracture, respectively. In 5p13, rs2468531 (minor allele frequency [MAF] = 3%) was associated with higher vBMD (β = 0.22, p = 1.9 × 10−8) and decreased risk of radiographic vertebral fracture (odds ratio [OR] = 0.75; false discovery rate [FDR] p = 0.01). In 1p36.12, rs12742784 (MAF = 21%) was associated with higher vBMD (β = 0.09, p = 1.2 × 10−10) and decreased risk of clinical vertebral fracture (OR = 0.82; FDR p = 7.4 × 10−4). Both SNPs are noncoding and were associated with increased mRNA expression levels in human bone biopsies: rs2468531 with SLC1A3 (β = 0.28, FDR p = 0.01, involved in glutamate signaling and osteogenic response to mechanical loading) and rs12742784 with EPHB2 (β = 0.12, FDR p = 1.7 × 10−3, functions in bone-related ephrin signaling). Both genes are expressed in murine osteoblasts. This is the first study to linkSLC1A3 and EPHB2 to clinically relevant vertebral osteoporosis phenotypes. These results may help elucidate vertebral bone biology and novel approaches to reducing vertebral fracture incidence. © 2016 American Society for Bone and Mineral Research. PMID:27476799

Full-depth reclamation : new test procedures and recommended updates to specifications.

DOT National Transportation Integrated Search

2012-07-01

Rehabilitating an old pavement by pulverizing and stabilizing the existing pavement is a process referred to : as Full Depth Reclamation (FDR). The stabilized layer becomes either the base or sub-base of the new : pavement structure. This process has...

Altered Methylation in Tandem Repeat Element and Elemental Component Levels in Inhalable Air Particles

PubMed Central

Hou, Lifang; Zhang, Xiao; Zheng, Yinan; Wang, Sheng; Dou, Chang; Guo, Liqiong; Byun, Hyang-Min; Motta, Valeria; McCracken, John; Díaz, Anaité; Kang, Choong-Min; Koutrakis, Petros; Bertazzi, Pier Alberto; Li, Jingyun; Schwartz, Joel; Baccarelli, Andrea A.

2014-01-01

Exposure to particulate matter (PM) has been associated with lung cancer risk in epidemiology investigations. Elemental components of PM have been suggested to have critical roles in PM toxicity, but the molecular mechanisms underlying their association with cancer risks remain poorly understood. DNA methylation has emerged as a promising biomarker for environmental-related diseases, including lung cancer. In this study, we evaluated the effects of PM elemental components on methylation of three tandem repeats in a highly-exposed population in Beijing, China. The Beijing Truck Driver Air Pollution Study was conducted shortly before the 2008 Beijing Olympic Games (June 15-July 27, 2008) and included 60 truck drivers and 60 office workers. On two days separated by 1-2 weeks, we measured blood DNA methylation of SATα, NBL2, D4Z4, and personal exposure to eight elemental components in PM2.5, including aluminum (Al), silicon (Si), sulfur (S), potassium (K), calcium (Ca) titanium (Ti), iron (Fe), and zinc (Zn). We estimated the associations of individual elemental component with each tandem repeat methylation in generalized estimating equations (GEE) models adjusted for PM2.5 mass and other covariates. Out of the eight examined elements, NBL2 methylation was positively associated with concentrations of Si (0.121, 95%CI: 0.030; 0.212, FDR=0.047) and Ca (0.065, 95%CI: 0.014; 0.115, FDR=0.047) in truck drivers. In office workers, SATα methylation was positively associated with concentrations of S (0.115, 95%CI: 0.034; 0.196, FDR=0.042). PM-associated differences in blood tandem-repeat methylation may help detect biological effects of the exposure and identify individuals who may eventually experience higher lung cancer risk. PMID:24273195

Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions.

PubMed

Biscarini, Filippo; Cozzi, Paolo; Casella, Laura; Riccardi, Paolo; Vattari, Alessandra; Orasen, Gabriele; Perrini, Rosaria; Tacconi, Gianni; Tondelli, Alessandro; Biselli, Chiara; Cattivelli, Luigi; Spindel, Jennifer; McCouch, Susan; Abbruscato, Pamela; Valé, Giampiero; Piffanelli, Pietro; Greco, Raffaella

2016-01-01

In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions. In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011). We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.

Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment

PubMed Central

Le Hellard, Stéphanie; Wang, Yunpeng; Witoelar, Aree; Zuber, Verena; Bettella, Francesco; Hugdahl, Kenneth; Espeseth, Thomas; Steen, Vidar M.; Melle, Ingrid; Desikan, Rahul; Schork, Andrew J.; Thompson, Wesley K.; Dale, Anders M.; Djurovic, Srdjan

2017-01-01

Abstract There is evidence for genetic overlap between cognitive abilities and schizophrenia (SCZ), and genome-wide association studies (GWAS) demonstrate that both SCZ and general cognitive abilities have a strong polygenic component with many single-nucleotide polymorphisms (SNPs) each with a small effect. Here we investigated the shared genetic architecture between SCZ and educational attainment, which is regarded as a “proxy phenotype” for cognitive abilities, but may also reflect other traits. We applied a conditional false discovery rate (condFDR) method to GWAS of SCZ (n = 82 315), college completion (“College,” n = 95 427), and years of education (“EduYears,” n = 101 069). Variants associated with College or EduYears showed enrichment of association with SCZ, demonstrating polygenic overlap. This was confirmed by an increased replication rate in SCZ. By applying a condFDR threshold <0.01, we identified 18 genomic loci associated with SCZ after conditioning on College and 15 loci associated with SCZ after conditioning on EduYears. Ten of these loci overlapped. Using conjunctional FDR, we identified 10 loci shared between SCZ and College, and 29 loci shared between SCZ and EduYears. The majority of these loci had effects in opposite directions. Our results provide evidence for polygenic overlap between SCZ and educational attainment, and identify novel pleiotropic loci. Other studies have reported genetic overlap between SCZ and cognition, or SCZ and educational attainment, with negative correlation. Importantly, our methods enable identification of bi-directional effects, which highlight the complex relationship between SCZ and educational attainment, and support polygenic mechanisms underlying both cognitive dysfunction and creativity in SCZ. PMID:27338279

Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment.

PubMed

Le Hellard, Stéphanie; Wang, Yunpeng; Witoelar, Aree; Zuber, Verena; Bettella, Francesco; Hugdahl, Kenneth; Espeseth, Thomas; Steen, Vidar M; Melle, Ingrid; Desikan, Rahul; Schork, Andrew J; Thompson, Wesley K; Dale, Anders M; Djurovic, Srdjan; Andreassen, Ole A

2017-05-01

There is evidence for genetic overlap between cognitive abilities and schizophrenia (SCZ), and genome-wide association studies (GWAS) demonstrate that both SCZ and general cognitive abilities have a strong polygenic component with many single-nucleotide polymorphisms (SNPs) each with a small effect. Here we investigated the shared genetic architecture between SCZ and educational attainment, which is regarded as a "proxy phenotype" for cognitive abilities, but may also reflect other traits. We applied a conditional false discovery rate (condFDR) method to GWAS of SCZ (n = 82 315), college completion ("College," n = 95 427), and years of education ("EduYears," n = 101 069). Variants associated with College or EduYears showed enrichment of association with SCZ, demonstrating polygenic overlap. This was confirmed by an increased replication rate in SCZ. By applying a condFDR threshold <0.01, we identified 18 genomic loci associated with SCZ after conditioning on College and 15 loci associated with SCZ after conditioning on EduYears. Ten of these loci overlapped. Using conjunctional FDR, we identified 10 loci shared between SCZ and College, and 29 loci shared between SCZ and EduYears. The majority of these loci had effects in opposite directions. Our results provide evidence for polygenic overlap between SCZ and educational attainment, and identify novel pleiotropic loci. Other studies have reported genetic overlap between SCZ and cognition, or SCZ and educational attainment, with negative correlation. Importantly, our methods enable identification of bi-directional effects, which highlight the complex relationship between SCZ and educational attainment, and support polygenic mechanisms underlying both cognitive dysfunction and creativity in SCZ. © The Author 2016. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci.

PubMed

Kar, Siddhartha P; Adler, Emily; Tyrer, Jonathan; Hazelett, Dennis; Anton-Culver, Hoda; Bandera, Elisa V; Beckmann, Matthias W; Berchuck, Andrew; Bogdanova, Natalia; Brinton, Louise; Butzow, Ralf; Campbell, Ian; Carty, Karen; Chang-Claude, Jenny; Cook, Linda S; Cramer, Daniel W; Cunningham, Julie M; Dansonka-Mieszkowska, Agnieszka; Doherty, Jennifer Anne; Dörk, Thilo; Dürst, Matthias; Eccles, Diana; Fasching, Peter A; Flanagan, James; Gentry-Maharaj, Aleksandra; Glasspool, Rosalind; Goode, Ellen L; Goodman, Marc T; Gronwald, Jacek; Heitz, Florian; Hildebrandt, Michelle A T; Høgdall, Estrid; Høgdall, Claus K; Huntsman, David G; Jensen, Allan; Karlan, Beth Y; Kelemen, Linda E; Kiemeney, Lambertus A; Kjaer, Susanne K; Kupryjanczyk, Jolanta; Lambrechts, Diether; Levine, Douglas A; Li, Qiyuan; Lissowska, Jolanta; Lu, Karen H; Lubiński, Jan; Massuger, Leon F A G; McGuire, Valerie; McNeish, Iain; Menon, Usha; Modugno, Francesmary; Monteiro, Alvaro N; Moysich, Kirsten B; Ness, Roberta B; Nevanlinna, Heli; Paul, James; Pearce, Celeste L; Pejovic, Tanja; Permuth, Jennifer B; Phelan, Catherine; Pike, Malcolm C; Poole, Elizabeth M; Ramus, Susan J; Risch, Harvey A; Rossing, Mary Anne; Salvesen, Helga B; Schildkraut, Joellen M; Sellers, Thomas A; Sherman, Mark; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa; Terry, Kathryn L; Tworoger, Shelley S; Walsh, Christine; Wentzensen, Nicolas; Whittemore, Alice S; Wu, Anna H; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Freedman, Matthew L; Gayther, Simon A; Pharoah, Paul D P; Lawrenson, Kate

2017-02-14

Genome-wide association studies (GWAS) have identified 18 loci associated with serous ovarian cancer (SOC) susceptibility but the biological mechanisms driving these findings remain poorly characterised. Germline cancer risk loci may be enriched for target genes of transcription factors (TFs) critical to somatic tumorigenesis. All 615 TF-target sets from the Molecular Signatures Database were evaluated using gene set enrichment analysis (GSEA) and three GWAS for SOC risk: discovery (2196 cases/4396 controls), replication (7035 cases/21 693 controls; independent from discovery), and combined (9627 cases/30 845 controls; including additional individuals). The PAX8-target gene set was ranked 1/615 in the discovery (P GSEA <0.001; FDR=0.21), 7/615 in the replication (P GSEA =0.004; FDR=0.37), and 1/615 in the combined (P GSEA <0.001; FDR=0.21) studies. Adding other genes reported to interact with PAX8 in the literature to the PAX8-target set and applying an alternative to GSEA, interval enrichment, further confirmed this association (P=0.006). Fifteen of the 157 genes from this expanded PAX8 pathway were near eight loci associated with SOC risk at P<10 -5 (including six with P<5 × 10 -8 ). The pathway was also associated with differential gene expression after shRNA-mediated silencing of PAX8 in HeyA8 (P GSEA =0.025) and IGROV1 (P GSEA =0.004) SOC cells and several PAX8 targets near SOC risk loci demonstrated in vitro transcriptomic perturbation. Putative PAX8 target genes are enriched for common SOC risk variants. This finding from our agnostic evaluation is of particular interest given that PAX8 is well-established as a specific marker for the cell of origin of SOC.

Bon-EV: an improved multiple testing procedure for controlling false discovery rates.

PubMed

Li, Dongmei; Xie, Zidian; Zand, Martin; Fogg, Thomas; Dye, Timothy

2017-01-03

Stability of multiple testing procedures, defined as the standard deviation of total number of discoveries, can be used as an indicator of variability of multiple testing procedures. Improving stability of multiple testing procedures can help to increase the consistency of findings from replicated experiments. Benjamini-Hochberg's and Storey's q-value procedures are two commonly used multiple testing procedures for controlling false discoveries in genomic studies. Storey's q-value procedure has higher power and lower stability than Benjamini-Hochberg's procedure. To improve upon the stability of Storey's q-value procedure and maintain its high power in genomic data analysis, we propose a new multiple testing procedure, named Bon-EV, to control false discovery rate (FDR) based on Bonferroni's approach. Simulation studies show that our proposed Bon-EV procedure can maintain the high power of the Storey's q-value procedure and also result in better FDR control and higher stability than Storey's q-value procedure for samples of large size(30 in each group) and medium size (15 in each group) for either independent, somewhat correlated, or highly correlated test statistics. When sample size is small (5 in each group), our proposed Bon-EV procedure has performance between the Benjamini-Hochberg procedure and the Storey's q-value procedure. Examples using RNA-Seq data show that the Bon-EV procedure has higher stability than the Storey's q-value procedure while maintaining equivalent power, and higher power than the Benjamini-Hochberg's procedure. For medium or large sample sizes, the Bon-EV procedure has improved FDR control and stability compared with the Storey's q-value procedure and improved power compared with the Benjamini-Hochberg procedure. The Bon-EV multiple testing procedure is available as the BonEV package in R for download at https://CRAN.R-project.org/package=BonEV .

Asbestos-associated genome-wide DNA methylation changes in lung cancer.

PubMed

Kettunen, Eeva; Hernandez-Vargas, Hector; Cros, Marie-Pierre; Durand, Geoffroy; Le Calvez-Kelm, Florence; Stuopelyte, Kristina; Jarmalaite, Sonata; Salmenkivi, Kaisa; Anttila, Sisko; Wolff, Henrik; Herceg, Zdenko; Husgafvel-Pursiainen, Kirsti

2017-11-15

Previous studies have revealed a robust association between exposure to asbestos and human lung cancer. Accumulating evidence has highlighted the role of epigenome deregulation in the mechanism of carcinogen-induced malignancies. We examined the impact of asbestos on DNA methylation. Our genome-wide studies (using Illumina HumanMethylation450K BeadChip) of lung cancer tissue and paired normal lung from 28 asbestos-exposed or non-exposed patients, mostly smokers, revealed distinctive DNA methylation changes. We identified a number of differentially methylated regions (DMR) and differentially variable, differentially methylated CpGs (DVMC), with individual CpGs further validated by pyrosequencing in an independent series of 91 non-small cell lung cancer and paired normal lung. We discovered and validated BEND4, ZSCAN31 and GPR135 as significantly hypermethylated in lung cancer. DMRs in genes such as RARB (FDR 1.1 × 10 -19 , mean change in beta [Δ] -0.09), GPR135 (FDR 1.87 × 10 -8 , mean Δ -0.09) and TPO (FDR 8.58 × 10 -5 , mean Δ -0.11), and DVMCs in NPTN, NRG2, GLT25D2 and TRPC3 (all with p <0.05, t-test) were significantly associated with asbestos exposure status in exposed versus non-exposed lung tumors. Hypomethylation was characteristic to DVMCs in lung cancer tissue from asbestos-exposed subjects. When DVMCs related to asbestos or smoking were analyzed, 96% of the elements were unique to either of the exposures, consistent with the concept that the methylation changes in tumors may be specific for risk factors. In conclusion, we identified novel DNA methylation changes associated with lung tumors and asbestos exposure, suggesting that changes may be present in causal pathway from asbestos exposure to lung cancer. © 2017 UICC.

Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate.

PubMed

Park, Gun Wook; Hwang, Heeyoun; Kim, Kwang Hoe; Lee, Ju Yeon; Lee, Hyun Kyoung; Park, Ji Yeong; Ji, Eun Sun; Park, Sung-Kyu Robin; Yates, John R; Kwon, Kyung-Hoon; Park, Young Mok; Lee, Hyoung-Joo; Paik, Young-Ki; Kim, Jin Young; Yoo, Jong Shin

2016-11-04

In the Chromosome-Centric Human Proteome Project (C-HPP), false-positive identification by peptide spectrum matches (PSMs) after database searches is a major issue for proteogenomic studies using liquid-chromatography and mass-spectrometry-based large proteomic profiling. Here we developed a simple strategy for protein identification, with a controlled false discovery rate (FDR) at the protein level, using an integrated proteomic pipeline (IPP) that consists of four engrailed steps as follows. First, using three different search engines, SEQUEST, MASCOT, and MS-GF+, individual proteomic searches were performed against the neXtProt database. Second, the search results from the PSMs were combined using statistical evaluation tools including DTASelect and Percolator. Third, the peptide search scores were converted into E-scores normalized using an in-house program. Last, ProteinInferencer was used to filter the proteins containing two or more peptides with a controlled FDR of 1.0% at the protein level. Finally, we compared the performance of the IPP to a conventional proteomic pipeline (CPP) for protein identification using a controlled FDR of <1% at the protein level. Using the IPP, a total of 5756 proteins (vs 4453 using the CPP) including 477 alternative splicing variants (vs 182 using the CPP) were identified from human hippocampal tissue. In addition, a total of 10 missing proteins (vs 7 using the CPP) were identified with two or more unique peptides, and their tryptic peptides were validated using MS/MS spectral pattern from a repository database or their corresponding synthetic peptides. This study shows that the IPP effectively improved the identification of proteins, including alternative splicing variants and missing proteins, in human hippocampal tissues for the C-HPP. All RAW files used in this study were deposited in ProteomeXchange (PXD000395).

MicroRNA signatures of colonic polyps on screening and histology

PubMed Central

Tsikitis, Vassiliki L.; Potter, Amiee; Mori, Motomi; Buckmeier, Julie A.; Preece, Christina R.; Harrington, Christina A.; Bartley, Angela N.; Bhattacharyya, Achyut K.; Hamilton, Stanley R.; Lance, M. Peter; Thompson, Patricia A.

2016-01-01

Colorectal cancer (CRC) and adenoma adjacent to cancer exhibit distinct microRNA (miR) alterations in an apparent mucosa-to-adenocarcinoma sequence. The pattern of microRNAs in screen-detected polyps in relation to histologic features and cancer risk has not been investigated. miR expression analysis was performed on normal mucosa (NM), hyperplastic polyps (HPs), tubular adenomas (TAs), tubulovillous adenomas or high-grade dysplasia (TVHGs), and serrated polyps (sessile serrated adenoma/polyps, SSA/Ps, and traditional serrated adenomas, TSAs) in biopsy specimens from 109 patients undergoing screening/surveillance colonoscopy. Generalized linear models were used to identify differentially expressed miRs by histologic type and logistic regression to identify miR predictors of histopathology. False discovery rate (FDR) was used to control for multiple comparisons. We identified 99 miRs differing in at least one of five histopathologic groups (FDR ≤ 0.05). In a comparison of HPNM vs. TVHG, the top most up- and down-regulated miRs in HPNM included miR-145, -143, -107, -194, and -26a (upregulated), and miR-663, -1268, -320b, -1275, and -320b (down-regulated) (FDR P-value < 0.05). miR-145 and -619 showed high accuracy to discriminate low- from high-risk polyps without serrated histology (TVHG vs. HPNM+TA) (CI= 95.6%), whereas miRs-124, -143, and -30a showed high accuracy of separating high-risk polyps (TVHG+TSA) from low-risk polyps (HPNM+TA+SSA/P) (CI=96.0%). For TSAs, miRs-125b and -199a were uniquely downregulated relative to HPNMs, and miR-335, -222 and -214 discriminated between non-serrated and serrated histology. Our data support the presence of CRC-associated miR alterations in screen-detected adenomas that may be useful for risk stratification for surveillance interval planning. PMID:27658891

Role of Re-entry Tears on the Dynamics of Type B Dissection Flap.

PubMed

Canchi, Saranya; Guo, Xiaomei; Phillips, Matt; Berwick, Zachary; Kratzberg, Jarin; Krieger, Joshua; Roeder, Blayne; Haulon, Stephan; Chambers, Sean; Kassab, Ghassan S

2018-01-01

Mortality during follow-up after acute Type B aortic dissection is substantial with aortic expansion observed in over 59% of the patients. Lumen pressure differential is considered a prime contributing factor for aortic dilation after propagation. The objective of the study was to evaluate the relationship between changes in vessel geometry with and without lumen pressure differential post propagation in an ex vivo porcine model with comparison with patient clinical data. A pulse duplicator system was utilized to propagate the dissection within descending thoracic porcine aortic vessels for set proximal (%circumference of the entry tear: 40%, axial length: 2 cm) and re-entry (50% of distal vessel circumference) tear geometry. Measurements of lumen pressure differential were made along with quantification of vessel geometry (n = 16). The magnitude of mean lumen pressure difference measured after propagation was low (~ 5 mmHg) with higher pressures measured in false lumen and as anticipated the pressure difference approached zero after the creation of distal re-entry tear. False lumen Dissection Ratio (FDR) defined as arc length of dissected wall divided by arc length of dissection flap, had mean value of 1.59 ± 0.01 at pressure of 120/80 mmHg post propagation with increasing values with increase in pulse pressure that was not rescued with the creation of distal re-entry tear (p < 0.01). An average FDR of 1.87 ± 0.27 was measured in patients with acute Type B dissection. Higher FDR value (FDR = 1 implies zero dissection) in the presence of distal re-entry tear demonstrates an acute change in vessel morphology in response to the dissection independent of local pressure changes challenges the re-apposition of the aortic wall.

Genetic Overlap Between Schizophrenia and Volumes of Hippocampus, Putamen, and Intracranial Volume Indicates Shared Molecular Genetic Mechanisms.

PubMed

Smeland, Olav B; Wang, Yunpeng; Frei, Oleksandr; Li, Wen; Hibar, Derrek P; Franke, Barbara; Bettella, Francesco; Witoelar, Aree; Djurovic, Srdjan; Chen, Chi-Hua; Thompson, Paul M; Dale, Anders M; Andreassen, Ole A

2018-06-06

Schizophrenia (SCZ) is associated with differences in subcortical brain volumes and intracranial volume (ICV). However, little is known about the underlying etiology of these brain alterations. Here, we explored whether brain structure volumes and SCZ share genetic risk factors. Using conditional false discovery rate (FDR) analysis, we integrated genome-wide association study (GWAS) data on SCZ (n = 82315) and GWAS data on 7 subcortical brain volumes and ICV (n = 11840). By conditioning the FDR on overlapping associations, this statistical approach increases power to discover genetic loci. To assess the credibility of our approach, we studied the identified loci in larger GWAS samples on ICV (n = 26577) and hippocampal volume (n = 26814). We observed polygenic overlap between SCZ and volumes of hippocampus, putamen, and ICV. Based on conjunctional FDR < 0.05, we identified 2 loci shared between SCZ and ICV implicating genes FOXO3 (rs10457180) and ITIH4 (rs4687658), 2 loci shared between SCZ and hippocampal volume implicating SLC4A10 (rs4664442) and SPATS2L (rs1653290), and 2 loci shared between SCZ and volume of putamen implicating DCC (rs4632195) and DLG2 (rs11233632). The loci shared between SCZ and hippocampal volume or ICV had not reached significance in the primary GWAS on brain phenotypes. Proving our point of increased power, 2 loci did reach genome-wide significance with ICV (rs10457180) and hippocampal volume (rs4664442) in the larger GWAS. Three of the 6 identified loci are novel for SCZ. Altogether, the findings provide new insights into the relationship between SCZ and brain structure volumes, suggesting that their genetic architectures are not independent.

Are obesity, ACPAs and periodontitis conditions that influence the risk of developing rheumatoid arthritis in first-degree relatives?

PubMed

Unriza-Puin, Sonia; Bautista-Molano, Wilson; Lafaurie, Gloria I; Valle-Oñate, Rafael; Chalem, Philippe; Chila-Moreno, Lorena; Bello-Gualtero, Juan Manuel; Romero-Sánchez, Consuelo

2017-04-01

The aim of this study was to investigate the body mass index (BMI), anti-citrullinated protein antibodies (ACPAs) status and the presence of periodontitis and IgG-1/IgG-2 antibodies against Porphyromonas gingivalis (Pg) in the first-degree relatives (FDRs) of rheumatoid arthritis (RA) patients and compare these variables with a control group of healthy individuals from the general population. In total, 100 FDR individuals and 200 healthy controls matched by age and gender were included. Rheumatologic and periodontal assessment was performed, and the presence of ACPAs and anti-P. gingivalis antibodies was evaluated. Groupwise comparisons were analysed using the McNemar and Wilcoxon tests. A conditional logistic regression analysis was performed to establish the associations between BMI, ACPAs and periodontitis in both groups. In the FDR group, 70% of the subjects were female, with a mean age of 37.3 ± 13 years. Obesity was observed in 17 and 7% of the FDRs and controls, respectively. ACPAs were found in 7% of the FDRs vs. 2.5% of the controls. Periodontitis was diagnosed in 79 and 56% of the FDRs and controls, respectively. Among the FDRs, 15% had severe periodontitis. There were associations in the FDR group related to the presence of obesity (OR 2.93, 95% CI 1.03-8.28), ACPAs (OR 2.45, 95% CI 0.7-8.32) and periodontitis (OR 3.70 95% CI 1.89-7.29). Regarding anti-P. gingivalis antibodies and smoking history, no differences were found between the groups. Obesity, ACPAs and periodontitis (diagnosis and severity) can be considered as relevant conditions associated with the development of RA in FDRs.

Frequency of a positive family history of colorectal cancer in general practice: a cross-sectional study.

PubMed

Plath, Jasper; Siebenhofer, Andrea; Koné, Insa; Hechtner, Marlene; Schulz-Rothe, Sylvia; Beyer, Martin; Gerlach, Ferdinand M; Guethlin, Corina

2017-02-01

Evidence on the frequency of a positive family history of colorectal cancer (CRC) among individuals aged <55 years is lacking. General practice setting might be well suited for the identification of individuals in this above-average risk group. To determine the frequency of a reported positive family history of CRC among patients aged 40 to 54 years in a general practice setting. We conducted a cross-sectional study in 21 general practices in Germany. Patients aged 40 to 54 years were identified by means of the practice software and interviewed by health care assistants using a standardized four-item questionnaire. Outcome was occurrence of a positive family history of CRC, defined as at least one first-degree relative (FDR: parents, siblings, or children) with CRC. Further measurements were FDRs with CRC / colorectal polyps (adenomas) diagnosed before the age of 50 and occurrence of three or more relatives with colorectal, stomach, cervical, ovarian, urethel or renal pelvic cancer. Out of 6723 participants, 7.2% (95% confidence interval [CI] 6.6% to 7.8%) reported at least one FDR with CRC and 1.2% (95% CI 0.9% to 1.5%) reported FDRs with CRC diagnosed before the age of 50. A further 2.6% (95% CI 2.3% to 3.0%) reported colorectal polyps in FDRs diagnosed before the age of 50 and 2.1% (95% CI 1.8% to 2.5%) reported three or more relatives with entities mentioned above. One in 14 patients reported at least one FDR with CRC. General practice should be considered when defining requirements of risk-adapted CRC screening. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Attentional bias modification alters intrinsic functional network of attentional control: A randomized controlled trial.

PubMed

Hakamata, Yuko; Mizukami, Shinya; Komi, Shotaro; Sato, Eisuke; Moriguchi, Yoshiya; Motomura, Yuki; Maruo, Kazushi; Izawa, Shuhei; Kim, Yoshiharu; Hanakawa, Takashi; Inoue, Yusuke; Tagaya, Hirokuni

2018-06-05

Attentional bias modification (ABM) alleviates anxiety by moderating biased attentional processing toward threat; however, its neural mechanisms remain unclear. We examined how ABM changes functional connectivity (FC) and functional network measures, leading to anxiety reduction. Fifty-four healthy anxious individuals received either ABM or sham training for 1 month in a double-blind randomized controlled trial. Anxious traits, attentional control, and attentional bias were assessed. Thirty-five participants completed resting-state functional magnetic resonance imaging (MRI) scans before and after training. ABM significantly mitigated an anxious traits regarding physical stress vulnerability (η 2  = 0.12, p = 0.009). As compared to sham training, ABM significantly strengthened FC between the pulvinar and transverse gyrus along the temporoparietal junction (T = 3.90, FDR-corrected p = 0.010), whereas it decreased FC between the postCG and ventral fronto-parietal network (vFPN) regions such as the anterior insula and ventrolateral prefrontal cortex (all T ≤ - 3.19, FDR-corrected p ≤ 0.034). Although ABM diminished network measures of the postcentral gyrus (postCG) (all T ≤ - 4.30, FDR-corrected p ≤ 0.006), only the pulvinar-related FC increase was specifically correlated with anxiety reduction (r = - 0.46, p = 0.007). Per-protocol analysis and reduced sample size in MRI analysis. ABM might augment the pulvinar's control over vFPN to maintain endogenous attention to a behavioral goal, while diminishing the information exchanges of the postCG with vFPN to inhibit the capture of exogenous attention by potential threats. The pulvinar might play a critical role in ABM anxiolytic efficacy. Copyright © 2018 Elsevier B.V. All rights reserved.

Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci

PubMed Central

Kar, Siddhartha P; Adler, Emily; Tyrer, Jonathan; Hazelett, Dennis; Anton-Culver, Hoda; Bandera, Elisa V; Beckmann, Matthias W; Berchuck, Andrew; Bogdanova, Natalia; Brinton, Louise; Butzow, Ralf; Campbell, Ian; Carty, Karen; Chang-Claude, Jenny; Cook, Linda S; Cramer, Daniel W; Cunningham, Julie M; Dansonka-Mieszkowska, Agnieszka; Doherty, Jennifer Anne; Dörk, Thilo; Dürst, Matthias; Eccles, Diana; Fasching, Peter A; Flanagan, James; Gentry-Maharaj, Aleksandra; Glasspool, Rosalind; Goode, Ellen L; Goodman, Marc T; Gronwald, Jacek; Heitz, Florian; Hildebrandt, Michelle A T; Høgdall, Estrid; Høgdall, Claus K; Huntsman, David G; Jensen, Allan; Karlan, Beth Y; Kelemen, Linda E; Kiemeney, Lambertus A; Kjaer, Susanne K; Kupryjanczyk, Jolanta; Lambrechts, Diether; Levine, Douglas A; Li, Qiyuan; Lissowska, Jolanta; Lu, Karen H; Lubiński, Jan; Massuger, Leon F A G; McGuire, Valerie; McNeish, Iain; Menon, Usha; Modugno, Francesmary; Monteiro, Alvaro N; Moysich, Kirsten B; Ness, Roberta B; Nevanlinna, Heli; Paul, James; Pearce, Celeste L; Pejovic, Tanja; Permuth, Jennifer B; Phelan, Catherine; Pike, Malcolm C; Poole, Elizabeth M; Ramus, Susan J; Risch, Harvey A; Rossing, Mary Anne; Salvesen, Helga B; Schildkraut, Joellen M; Sellers, Thomas A; Sherman, Mark; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa; Terry, Kathryn L; Tworoger, Shelley S; Walsh, Christine; Wentzensen, Nicolas; Whittemore, Alice S; Wu, Anna H; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Freedman, Matthew L; Gayther, Simon A; Pharoah, Paul D P; Lawrenson, Kate

2017-01-01

Background: Genome-wide association studies (GWAS) have identified 18 loci associated with serous ovarian cancer (SOC) susceptibility but the biological mechanisms driving these findings remain poorly characterised. Germline cancer risk loci may be enriched for target genes of transcription factors (TFs) critical to somatic tumorigenesis. Methods: All 615 TF-target sets from the Molecular Signatures Database were evaluated using gene set enrichment analysis (GSEA) and three GWAS for SOC risk: discovery (2196 cases/4396 controls), replication (7035 cases/21 693 controls; independent from discovery), and combined (9627 cases/30 845 controls; including additional individuals). Results: The PAX8-target gene set was ranked 1/615 in the discovery (PGSEA<0.001; FDR=0.21), 7/615 in the replication (PGSEA=0.004; FDR=0.37), and 1/615 in the combined (PGSEA<0.001; FDR=0.21) studies. Adding other genes reported to interact with PAX8 in the literature to the PAX8-target set and applying an alternative to GSEA, interval enrichment, further confirmed this association (P=0.006). Fifteen of the 157 genes from this expanded PAX8 pathway were near eight loci associated with SOC risk at P<10−5 (including six with P<5 × 10−8). The pathway was also associated with differential gene expression after shRNA-mediated silencing of PAX8 in HeyA8 (PGSEA=0.025) and IGROV1 (PGSEA=0.004) SOC cells and several PAX8 targets near SOC risk loci demonstrated in vitro transcriptomic perturbation. Conclusions: Putative PAX8 target genes are enriched for common SOC risk variants. This finding from our agnostic evaluation is of particular interest given that PAX8 is well-established as a specific marker for the cell of origin of SOC. PMID:28103614

Integrative genomics analysis identifies ancestral-related eQTLs on POLB, and supports the association of genetic ancestry with survival disparity in HNSCC

PubMed Central

Ramakodi, Meganathan P.; Devarajan, Karthik; Blackman, Elizabeth; Gibbs, Denise; Luce, Danièle; Deloumeaux, Jacqueline; Duflo, Suzy; Liu, Jeffrey C.; Mehra, Ranee; Kulathinal, Rob J.; Ragin, Camille C.

2016-01-01

BACKGROUND African-Americans (Afr-Amr) with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than Caucasians (Cau). This study investigates the functional importance of ancestry-informative SNPs in HNSCC and also examines the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS Ancestry-informative SNPs, RNAseq, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes. The results of eQTL analyses were also replicated using a Gene Expression Omnibus (GEO) dataset. The effects of eQTLs on overall survival (OS) and disease-free survival (DFS) were evaluated. RESULTS Five ancestry-related SNPs were identified as cis-eQTLs in the POLB gene (FDR<0.01). The homozygous/ heterozygous genotypes containing the Afr-allele showed higher POLB expression relative to the homozygous Cau-allele genotype (P<0.001). A replication study using a GEO dataset validated all five eQTLs, also showing a statistically significant difference in POLB expression based on genetic ancestry (P=0.002). An association was observed between these eQTLs and OS (P<0.037; FDR<0.0363) as well as DFS of oral cavity and laryngeal cancer patients treated with platinum-based chemotherapy and/or radiotherapy (P=0.018 to 0.0629; FDR<0.079). Genotypes containing the Afr-allele were associated with poor OS/DFS compared to homozygous genotypes harboring the Cau-allele. CONCLUSIONS Our analyses show that ancestry-related alleles could act as eQTLs in HNSCC and support the association of ancestry-related genetic factors with survival disparity in patients diagnosed with oral cavity and laryngeal cancer. PMID:27906459

Assessing associations between the AURKA-HMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers.

PubMed

Blanco, Ignacio; Kuchenbaecker, Karoline; Cuadras, Daniel; Wang, Xianshu; Barrowdale, Daniel; de Garibay, Gorka Ruiz; Librado, Pablo; Sánchez-Gracia, Alejandro; Rozas, Julio; Bonifaci, Núria; McGuffog, Lesley; Pankratz, Vernon S; Islam, Abul; Mateo, Francesca; Berenguer, Antoni; Petit, Anna; Català, Isabel; Brunet, Joan; Feliubadaló, Lidia; Tornero, Eva; Benítez, Javier; Osorio, Ana; Ramón y Cajal, Teresa; Nevanlinna, Heli; Aittomäki, Kristiina; Arun, Banu K; Toland, Amanda E; Karlan, Beth Y; Walsh, Christine; Lester, Jenny; Greene, Mark H; Mai, Phuong L; Nussbaum, Robert L; Andrulis, Irene L; Domchek, Susan M; Nathanson, Katherine L; Rebbeck, Timothy R; Barkardottir, Rosa B; Jakubowska, Anna; Lubinski, Jan; Durda, Katarzyna; Jaworska-Bieniek, Katarzyna; Claes, Kathleen; Van Maerken, Tom; Díez, Orland; Hansen, Thomas V; Jønson, Lars; Gerdes, Anne-Marie; Ejlertsen, Bent; de la Hoya, Miguel; Caldés, Trinidad; Dunning, Alison M; Oliver, Clare; Fineberg, Elena; Cook, Margaret; Peock, Susan; McCann, Emma; Murray, Alex; Jacobs, Chris; Pichert, Gabriella; Lalloo, Fiona; Chu, Carol; Dorkins, Huw; Paterson, Joan; Ong, Kai-Ren; Teixeira, Manuel R; Hogervorst, Frans B L; van der Hout, Annemarie H; Seynaeve, Caroline; van der Luijt, Rob B; Ligtenberg, Marjolijn J L; Devilee, Peter; Wijnen, Juul T; Rookus, Matti A; Meijers-Heijboer, Hanne E J; Blok, Marinus J; van den Ouweland, Ans M W; Aalfs, Cora M; Rodriguez, Gustavo C; Phillips, Kelly-Anne A; Piedmonte, Marion; Nerenstone, Stacy R; Bae-Jump, Victoria L; O'Malley, David M; Ratner, Elena S; Schmutzler, Rita K; Wappenschmidt, Barbara; Rhiem, Kerstin; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Plendl, Hansjoerg J; Niederacher, Dieter; Sutter, Christian; Wang-Gohrke, Shan; Steinemann, Doris; Preisler-Adams, Sabine; Kast, Karin; Varon-Mateeva, Raymonda; Gehrig, Andrea; Bojesen, Anders; Pedersen, Inge Sokilde; Sunde, Lone; Jensen, Uffe Birk; Thomassen, Mads; Kruse, Torben A; Foretova, Lenka; Peterlongo, Paolo; Bernard, Loris; Peissel, Bernard; Scuvera, Giulietta; Manoukian, Siranoush; Radice, Paolo; Ottini, Laura; Montagna, Marco; Agata, Simona; Maugard, Christine; Simard, Jacques; Soucy, Penny; Berger, Andreas; Fink-Retter, Anneliese; Singer, Christian F; Rappaport, Christine; Geschwantler-Kaulich, Daphne; Tea, Muy-Kheng; Pfeiler, Georg; John, Esther M; Miron, Alex; Neuhausen, Susan L; Terry, Mary Beth; Chung, Wendy K; Daly, Mary B; Goldgar, David E; Janavicius, Ramunas; Dorfling, Cecilia M; van Rensburg, Elisabeth J; Fostira, Florentia; Konstantopoulou, Irene; Garber, Judy; Godwin, Andrew K; Olah, Edith; Narod, Steven A; Rennert, Gad; Paluch, Shani Shimon; Laitman, Yael; Friedman, Eitan; Liljegren, Annelie; Rantala, Johanna; Stenmark-Askmalm, Marie; Loman, Niklas; Imyanitov, Evgeny N; Hamann, Ute; Spurdle, Amanda B; Healey, Sue; Weitzel, Jeffrey N; Herzog, Josef; Margileth, David; Gorrini, Chiara; Esteller, Manel; Gómez, Antonio; Sayols, Sergi; Vidal, Enrique; Heyn, Holger; Stoppa-Lyonnet, Dominique; Léoné, Melanie; Barjhoux, Laure; Fassy-Colcombet, Marion; de Pauw, Antoine; Lasset, Christine; Ferrer, Sandra Fert; Castera, Laurent; Berthet, Pascaline; Cornelis, François; Bignon, Yves-Jean; Damiola, Francesca; Mazoyer, Sylvie; Sinilnikova, Olga M; Maxwell, Christopher A; Vijai, Joseph; Robson, Mark; Kauff, Noah; Corines, Marina J; Villano, Danylko; Cunningham, Julie; Lee, Adam; Lindor, Noralane; Lázaro, Conxi; Easton, Douglas F; Offit, Kenneth; Chenevix-Trench, Georgia; Couch, Fergus J; Antoniou, Antonis C; Pujana, Miguel Angel

2015-01-01

While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood approach. The association of HMMR rs299290 with breast cancer risk in BRCA1 mutation carriers was confirmed: per-allele hazard ratio (HR) = 1.10, 95% confidence interval (CI) 1.04-1.15, p = 1.9 x 10(-4) (false discovery rate (FDR)-adjusted p = 0.043). Variation in CSTF1, located next to AURKA, was also found to be associated with breast cancer risk in BRCA2 mutation carriers: rs2426618 per-allele HR = 1.10, 95% CI 1.03-1.16, p = 0.005 (FDR-adjusted p = 0.045). Assessment of pairwise interactions provided suggestions (FDR-adjusted pinteraction values > 0.05) for deviations from the multiplicative model for rs299290 and CSTF1 rs6064391, and rs299290 and TUBG1 rs11649877 in both BRCA1 and BRCA2 mutation carriers. Following these suggestions, the expression of HMMR and AURKA or TUBG1 in sporadic breast tumors was found to potentially interact, influencing patients' survival. Together, the results of this study support the hypothesis of a causative link between altered function of AURKA-HMMR-TPX2-TUBG1 and breast carcinogenesis in BRCA1/2 mutation carriers.

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data

DOE PAGES

Woo, Sunghee; Cha, Seong Won; Na, Seungjin; ...

2014-11-17

Cancer is driven by the acquisition of somatic DNA lesions. Distinguishing the early driver mutations from subsequent passenger mutations is key to molecular sub-typing of cancers, and the discovery of novel biomarkers. The availability of genomics technologies (mainly wholegenome and exome sequencing, and transcript sampling via RNA-seq, collectively referred to as NGS) have fueled recent studies on somatic mutation discovery. However, the vision is challenged by the complexity, redundancy, and errors in genomic data, and the difficulty of investigating the proteome using only genomic approaches. Recently, combination of proteomic and genomic technologies are increasingly employed. However, the complexity and redundancymore » of NGS data remains a challenge for proteogenomics, and various trade-offs must be made to allow for the searches to take place. This paperprovides a discussion of two such trade-offs, relating to large database search, and FDR calculations, and their implication to cancer proteogenomics. Moreover, it extends and develops the idea of a unified genomic variant database that can be searched by any mass spectrometry sample. A total of 879 BAM files downloaded from TCGA repository were used to create a 4.34 GB unified FASTA database which contained 2,787,062 novel splice junctions, 38,464 deletions, 1105 insertions, and 182,302 substitutions. Proteomic data from a single ovarian carcinoma sample (439,858 spectra) was searched against the database. By applying the most conservative FDR measure, we have identified 524 novel peptides and 65,578 known peptides at 1% FDR threshold. The novel peptides include interesting examples of doubly mutated peptides, frame-shifts, and non-sample-recruited mutations, which emphasize the strength of our approach.« less

Potential benefits of adding emulsion to reclaimed base material : interim report - fourth year.

DOT National Transportation Integrated Search

2003-05-01

Rehabilitation of deteriorated asphalt pavements has become one of the primary tools utilized by the : Maine Department of Transportation (MDOT). One method used to achieve this task is the use of full : depth reclamation (FDR). : In an effort to imp...

Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls.

PubMed

Meijer, Rosa J; Goeman, Jelle J

2016-09-01

The use of multiple testing procedures in the context of gene-set testing is an important but relatively underexposed topic. If a multiple testing method is used, this is usually a standard familywise error rate (FWER) or false discovery rate (FDR) controlling procedure in which the logical relationships that exist between the different (self-contained) hypotheses are not taken into account. Taking those relationships into account, however, can lead to more powerful variants of existing multiple testing procedures and can make summarizing and interpreting the final results easier. We will show that, from the perspective of interpretation as well as from the perspective of power improvement, FWER controlling methods are more suitable than FDR controlling methods. As an example of a possible power improvement, we suggest a modified version of the popular method by Holm, which we also implemented in the R package cherry. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Target-decoy Based False Discovery Rate Estimation for Large-scale Metabolite Identification.

PubMed

Wang, Xusheng; Jones, Drew R; Shaw, Timothy I; Cho, Ji-Hoon; Wang, Yuanyuan; Tan, Haiyan; Xie, Boer; Zhou, Suiping; Li, Yuxin; Peng, Junmin

2018-05-23

Metabolite identification is a crucial step in mass spectrometry (MS)-based metabolomics. However, it is still challenging to assess the confidence of assigned metabolites. In this study, we report a novel method for estimating false discovery rate (FDR) of metabolite assignment with a target-decoy strategy, in which the decoys are generated through violating the octet rule of chemistry by adding small odd numbers of hydrogen atoms. The target-decoy strategy was integrated into JUMPm, an automated metabolite identification pipeline for large-scale MS analysis, and was also evaluated with two other metabolomics tools, mzMatch and mzMine 2. The reliability of FDR calculation was examined by false datasets, which were simulated by altering MS1 or MS2 spectra. Finally, we used the JUMPm pipeline coupled with the target-decoy strategy to process unlabeled and stable-isotope labeled metabolomic datasets. The results demonstrate that the target-decoy strategy is a simple and effective method for evaluating the confidence of high-throughput metabolite identification.

Frequency Domain Reflectometry Modeling and Measurement for Nondestructive Evaluation of Nuclear Power Plant Cables

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glass, Samuel W.; Fifield, Leonard S.; Jones, Anthony M.

Cable insulation polymers are among the more susceptible materials to age-related degradation within a nuclear power plant. This is recognized by both regulators and utilities, so all plants have developed cable aging management programs to detect damage before critical component failure in compliance with regulatory guidelines. Although a wide range of tools are available to evaluate cables and cable systems, cable aging management programs vary in how condition monitoring and NDE is conducted as utilities search for the most reliable and cost-effective ways to assess cable system condition. Frequency domain reflectometry (FDR) is emerging as one valuable tool to locatemore » and assess damaged portions of a cable system with minimal cost and only requires access in most cases to one of the cable terminal ends. This work examines a physics-based model of a cable system and relates it to FDR measurements for a better understanding of specific damage influences on defect detectability.« less

Testability analysis on a hydraulic system in a certain equipment based on simulation model

NASA Astrophysics Data System (ADS)

Zhang, Rui; Cong, Hua; Liu, Yuanhong; Feng, Fuzhou

2018-03-01

Aiming at the problem that the complicated structure and the shortage of fault statistics information in hydraulic systems, a multi value testability analysis method based on simulation model is proposed. Based on the simulation model of AMESim, this method injects the simulated faults and records variation of test parameters ,such as pressure, flow rate, at each test point compared with those under normal conditions .Thus a multi-value fault-test dependency matrix is established. Then the fault detection rate (FDR) and fault isolation rate (FIR) are calculated based on the dependency matrix. Finally the system of testability and fault diagnosis capability are analyzed and evaluated, which can only reach a lower 54%(FDR) and 23%(FIR). In order to improve testability performance of the system,. number and position of the test points are optimized on the system. Results show the proposed test placement scheme can be used to solve the problems that difficulty, inefficiency and high cost in the system maintenance.

Flight Test of GL-1 Glider Half Scale Prototype

NASA Astrophysics Data System (ADS)

Fikri Zulkarnain, Muhammad; Fazlur Rahman, Muhammad; Luthfi Imam Nurhakim, Muhammad; Arifianto, Ony; Mulyanto, Taufiq

2018-04-01

GL-1 is a single-seat mid-performance glider, designed to be Indonesian National Glider. The Glider have been developing since 2014. The development produced a half scale prototype called BL-1, which had accomplished static test in 2016, then followed by first flight test at April 20th 2017, and second flight test at May 21st 2017. The purpose of the flight test was to obtain familiarization of the aircraft, aerodynamics characteristics and flow visualization, with data from flight recorded in FDR. The flight test resulted in two flights with total length of 21 minutes. The data from FDR and flight test documents extracted to analyze the characteristics and behavior of the aircraft during flight test. The aerodynamics characteristic was close to analytical results. The control was good; however, the effectiveness of control surface may need to be further analyzed. The result of the flight test will be used as a reference for further improvements and may need further testing.

Farm scale application of EMI and FDR sensors to measuring and mapping soil water content

NASA Astrophysics Data System (ADS)

Rallo, Giovanni; Provenzano, Giuseppe

2017-04-01

Soil water content (SWC) controls most water exchange processes within and between the soil-plants-atmosphere continuum and can therefore be considered as a practical variable for irrigation farmer choices. A better knowledge of spatial SWC patterns could improve farmer's awareness about critical crop water status conditions and enhance their capacity to characterize their behavior at the field or farm scale. However, accurate soil moisture measurement across spatial and temporal scales is still a challenging task and, specifically at intermediate spatial (0.1-100 ha) and temporal (minutes to days) scales, a data gap remains that limits our understanding over reliability of the SWC spatial measurements and its practical applicability in irrigation scheduling. In this work we compare the integrated EM38 (Geonics Ltd. Canada) response, collected at different sensor positions above ground to that obtained by integrating the depth profile of volumetric SWC measured with Diviner 2000 (Sentek) in conjunction with the depth response function of the EM38 when operated in both horizontal and vertical dipole configurations. On a 1.0-ha Olive grove site in Sicliy (Italy), 200 data points were collected before and after irrigation or precipitation events following a systematic sampling grid with focused measurements around the tree. Inside two different zone of the field, characterized from different soil physical properties, two Diviner 2000 access tube (1.2 m) were installed and used for the EM38 calibration. After calibration, the work aimed to propose the combined use of the FDR and EMI sensors to measuring and mapping root zone soil water content. We found strong correlations (R2 = 0.66) between Diviner 2000 SWC averaged to a depth of 1.2 m and ECa from an EM38 held in the vertical mode above the soil surface. The site-specific relationship between FDR-based SWC and ECa was linear for the purposes of estimating SWC over the explored range of ECa monitored at field levels. Volumetric SWC changes in the root zone were observed by differencing the maps, where differences in the observed ECa are primarily the result of changes in soil water status. As with the data showed in the research, more structured patterns occur after wetting event, indicating the presence of subsurface flow or root water uptake paths. A vision for the future at hydrological watershed scale is to combine EMI measurements with FDR-based sensor networks, the last with the scope to constrain calibration of the EMI measurements.

Assessment of NDE for key indicators of aging cables in nuclear power plants - Interim status

NASA Astrophysics Data System (ADS)

Glass, S. W.; Ramuhalli, P.; Fifield, L. S.; Prowant, M. S.; Dib, G.; Tedeschi, J. R.; Suter, J. D.; Jones, A. M.; Good, M. S.; Pardini, A. F.; Hartman, T. S.

2016-02-01

Degradation of the cable jacket, electrical insulation, and other cable components of installed cables within nuclear power plants (NPPs) is known to occur as a function of age, temperature, radiation, and other environmental factors. System tests verify cable function under normal loads; however, the concern is over cable performance under exceptional loads associated with design-basis events (DBEs). The cable's ability to perform safely over the initial 40-year planned and licensed life has generally been demonstrated and there have been very few age-related cable failures. With greater than 1000 km of power, control, instrumentation, and other cables typically found in an NPP, replacing all the cables would be a severe cost burden. Justification for life extension to 60 and 80 years requires a cable aging management program to justify cable performance under normal operation as well as accident conditions. Currently the gold standard for determining cable insulation degradation is the elongation-at-break (EAB). This, however, is an ex-situ measurement and requires removal of a sample for laboratory investigation. A reliable nondestructive examination (NDE) in-situ approach is desirable to objectively determine the suitability of the cable for service. A variety of tests are available to assess various aspects of electrical and mechanical cable performance, but none of these tests are suitable for all cable configurations nor does any single test confirm all features of interest. Nevertheless, the complete collection of test possibilities offers a powerful range of tools to assure the integrity of critical cables. Licensees and regulators have settled on a practical program to justify continued operation based on condition monitoring of a lead sample set of cables where test data is tracked in a database and the required test data are continually adjusted based on plant and fleet-wide experience. As part of the Light Water Reactor Sustainability program sponsored by the U.S. Nuclear Regulatory Commission, the U.S. Department of Energy, and industry (represented by the Electric Power Research Institute), an assessment of cable NDE methods was commissioned. Technologies include both bulk electrical measurements (Tan δ, time domain reflectometry, frequency domain reflectometry (FDR), partial discharge, and other techniques) and local insulation measurement (indenter, dynamic mechanical analysis interdigital capacitance, infrared spectral measurement, etc.). This aging cable NDE program update reviews the full range of techniques but focuses on the most interesting test approaches that have a chance to be deployed in-situ, particularly including Tan δ, FDR, and ultrasound methods that have been reviewed most completely in this progress period.

History Microcomputer Games: Update 2.

ERIC Educational Resources Information Center

Sargent, James E.

1985-01-01

Provides full narrative reviews of B-1 Nuclear Bomber (Avalon, 1982); American History Adventure (Social Science Microcomputer Review Software, 1985); Government Simulations (Prentice-Hall, 1985); and The Great War, FDR and the New Deal, and Hitler's War, all from New Worlds Software, 1985. Lists additional information on five other history and…

75 FR 24965 - Mormon Island Auxiliary Dam (MIAD) Modification Project, Sacramento and El Dorado Counties, CA

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-06

... Folsom DS/FDR EIS/EIR considered several methods to modify MIAD to achieve Reclamation's risk standards... availability of the Final Supplemental Environmental Impact Statement/Environmental Impact Report (EIS/EIR). SUMMARY: Pursuant to the National Environmental Policy Act and the California Environmental Quality Act...

Short, multi-needle FDR sensor suitable for measuring soil water content

USDA-ARS?s Scientific Manuscript database

Time domain reflectometry (TDR) is a well-established electromagnetic technique used to measure soil water content. TDR sensors have been combined with heat pulse sensors to produce thermo-TDR sensors. Thermo-TDR sensors are restricted to having relatively short needles in order to accurately measur...

Why Study about F.D.R. and Hitler?

ERIC Educational Resources Information Center

Gross, Richard E.

1983-01-01

Both Franklin Delano Roosevelt and Adolf Hitler came to power in 1933. This 50th anniversary issue contains articles analyzing the two men, and the different political, social, moral, and artistic directions taken by the United States and Germany in the 1930's. American youth have much to learn from what occurred. (CS)

Checked Out: Ohioans' Views on Education 2009

ERIC Educational Resources Information Center

Thomas B. Fordham Institute, 2009

2009-01-01

In collaboration with the Thomas B. Fordham Institute and Catalyst Ohio, the FDR Group conducted a telephone survey of 1,002 randomly selected Ohio residents between April 1 and April 9, 2009 (margin of error +/- 3 percentage points). The survey--the third in a series--reports Ohioans' views on critical education issues, including school funding,…

Learning Early Twentieth-Century History through First-Person Interviews

ERIC Educational Resources Information Center

Lark, Lisa A.

2007-01-01

For many of the students in the author's American history class, early twentieth-century American history seems far removed from their daily lives. Being first and second-generation American citizens, many of the students do not have the luxury of hearing grandparents and great-grandparents telling stories about FDR and Henry Ford. More…

Using the Internet To Create Primary Source Teaching Packets.

ERIC Educational Resources Information Center

VanFossen, Phillip J.; Shiveley, James M.

2000-01-01

Describes strategies and guidelines for creating age- and content-appropriate primary source documents using the Internet. Discusses the value of using topic-specific primary source teaching packets, or jackdaws. Provides three Internet generated jackdaws: New Deal/FDR, Home Front during World War II, and the Gilded Age. Addresses fair use issues.…

Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci

PubMed Central

Thompson, Wesley K.; McEvoy, Linda K.; Schork, Andrew J.; Zuber, Verena; LeBlanc, Marissa; Bettella, Francesco; Mills, Ian G.; Desikan, Rahul S.; Djurovic, Srdjan; Gautvik, Kaare M.; Dale, Anders M.; Andreassen, Ole A.

2015-01-01

Bone Mineral Density (BMD) is a highly heritable trait, but genome-wide association studies have identified few genetic risk factors. Epidemiological studies suggest associations between BMD and several traits and diseases, but the nature of the suggestive comorbidity is still unknown. We used a novel genetic pleiotropy-informed conditional False Discovery Rate (FDR) method to identify single nucleotide polymorphisms (SNPs) associated with BMD by leveraging cardiovascular disease (CVD) associated disorders and metabolic traits. By conditioning on SNPs associated with the CVD-related phenotypes, type 1 diabetes, type 2 diabetes, systolic blood pressure, diastolic blood pressure, high density lipoprotein, low density lipoprotein, triglycerides and waist hip ratio, we identified 65 novel independent BMD loci (26 with femoral neck BMD and 47 with lumbar spine BMD) at conditional FDR < 0.01. Many of the loci were confirmed in genetic expression studies. Genes validated at the mRNA levels were characteristic for the osteoblast/osteocyte lineage, Wnt signaling pathway and bone metabolism. The results provide new insight into genetic mechanisms of variability in BMD, and a better understanding of the genetic underpinnings of clinical comorbidity. PMID:26695485

Global transcriptional analysis of psoriatic skin and blood confirms known disease-associated pathways and highlights novel genomic "hot spots" for differentially expressed genes.

PubMed

Coda, Alvin B; Icen, Murat; Smith, Jason R; Sinha, Animesh A

2012-07-01

There are major gaps in our knowledge regarding the exact mechanisms and genetic basis of psoriasis. To investigate the pathogenesis of psoriasis, gene expression in 10 skin (5 lesional, 5 nonlesional) and 11 blood (6 psoriatic, 5 nonpsoriatic) samples were examined using Affymetrix HG-U95A microarrays. We detected 535 (425 upregulated, 110 downregulated) DEGs in lesional skin at 1% false discovery rate (FDR). Combining nine microarray studies comparing lesional and nonlesional psoriatic skin, 34.5% of dysregulated genes were overlapped in multiple studies. We further identified 20 skin and 2 blood associated transcriptional "hot spots" at specified genomic locations. At 5% FDR, 11.8% skin and 10.4% blood DEGs in our study mapped to one of the 12 PSORS loci. DEGs that overlap with PSORS loci may offer prioritized targets for downstream genetic fine mapping studies. Novel DEG "hot spots" may provide new targets for defining susceptibility loci in future studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Multiple testing corrections in quantitative proteomics: A useful but blunt tool.

PubMed

Pascovici, Dana; Handler, David C L; Wu, Jemma X; Haynes, Paul A

2016-09-01

Multiple testing corrections are a useful tool for restricting the FDR, but can be blunt in the context of low power, as we demonstrate by a series of simple simulations. Unfortunately, in proteomics experiments low power can be common, driven by proteomics-specific issues like small effects due to ratio compression, and few replicates due to reagent high cost, instrument time availability and other issues; in such situations, most multiple testing corrections methods, if used with conventional thresholds, will fail to detect any true positives even when many exist. In this low power, medium scale situation, other methods such as effect size considerations or peptide-level calculations may be a more effective option, even if they do not offer the same theoretical guarantee of a low FDR. Thus, we aim to highlight in this article that proteomics presents some specific challenges to the standard multiple testing corrections methods, which should be employed as a useful tool but not be regarded as a required rubber stamp. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

PubMed Central

Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.; Chain, Patrick S. G.

2015-01-01

A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools. PMID:25765641

Research on lettuce growth technology onboard Chinese Tiangong II Spacelab

NASA Astrophysics Data System (ADS)

Shen, Yunze; Guo, Shuangsheng; Zhao, Pisheng; Wang, Longji; Wang, Xiaoxia; Li, Jian; Bian, Qiang

2018-03-01

Lettuce was grown in a space vegetable cultivation facility onboard the Tiangong Ⅱ Spacelab during October 18 to November 15, 2016, in order to testify the key cultivating technology in CELSS under spaceflight microgravity condition. Potable water was used for irrigation of rooting substrate and the SRF (slowly released fertilizer) offered mineral nutrition for plant growth. Water content and electric conductivity in rooting substrate were measured based on FDR(frequency domain reflectometry) principle applied first in spaceflight. Lettuce germinated with comparative growth vigor as the ground control, showing that the plants appeared to be not stressed by the spaceflight environment. Under microgravity, lettuce grew taller and showed deeper green color than the ground control. In addition, the phototropism of the on-orbit plants was more remarkable. The nearly 30-d spaceflight test verified the seed fixation technology and water& nutrition management technology, which manifests the feasibility of FDR being used for measuring moisture content and electric conductivity in rooting zone under microgravity. Furthermore, the edibility of the space-grown vegetable was proved, providing theoretical support for astronaut to consume the space vegetable in future manned spaceflight.

Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics.

PubMed

Blank-Landeshammer, Bernhard; Kollipara, Laxmikanth; Biß, Karsten; Pfenninger, Markus; Malchow, Sebastian; Shuvaev, Konstantin; Zahedi, René P; Sickmann, Albert

2017-09-01

Complex mass spectrometry based proteomics data sets are mostly analyzed by protein database searches. While this approach performs considerably well for sequenced organisms, direct inference of peptide sequences from tandem mass spectra, i.e., de novo peptide sequencing, oftentimes is the only way to obtain information when protein databases are absent. However, available algorithms suffer from drawbacks such as lack of validation and often high rates of false positive hits (FP). Here we present a simple method of combining results from commonly available de novo peptide sequencing algorithms, which in conjunction with minor tweaks in data acquisition ensues lower empirical FDR compared to the analysis using single algorithms. Results were validated using state-of-the art database search algorithms as well specifically synthesized reference peptides. Thus, we could increase the number of PSMs meeting a stringent FDR of 5% more than 3-fold compared to the single best de novo sequencing algorithm alone, accounting for an average of 11 120 PSMs (combined) instead of 3476 PSMs (alone) in triplicate 2 h LC-MS runs of tryptic HeLa digestion.

FDR Soil Moisture Sensor for Environmental Testing and Evaluation

NASA Astrophysics Data System (ADS)

Linmao, Ye; longqin, Xue; guangzhou, Zhang; haibo, Chen; likuai, Shi; zhigang, Wu; gouhe, Yu; yanbin, Wang; sujun, Niu; Jin, Ye; Qi, Jin

To test the affect of environmental stresses on a adaptability of soil moisture capacitance sensor(FDR) a number of stresses were induced including vibrational shock as well as temperature and humidity through the use of a CH-I constant humidity chamber with variable temperature. A Vibrational platform was used to exam the resistance and structural integrity of the sensor after vibrations simulating the process of using, transporting and handling the sensor. A Impactive trial platform was used to test the resistance and structural integrity of the sensor after enduring repeated mechanical shocks. An CH-I constant humidity chamber with high-low temperature was used to test the adaptability of sensor in different environments with high temperature, low temperature and constant humidity. Otherwise, scope of magnetic force line of sensor was also tested in this paper. Test show:the capacitance type soil moisture sensor spread a feeling machine to bear heat, high wet and low temperature, at bear impact and vibration experiment in pass an examination, is a kind of environment to adapt to ability very strong instrument;Spread a feeling machine moreover electric field strength function radius scope 7 cms.

Characterizing the Joint Effect of Diverse Test-Statistic Correlation Structures and Effect Size on False Discovery Rates in a Multiple-Comparison Study of Many Outcome Measures

NASA Technical Reports Server (NTRS)

Feiveson, Alan H.; Ploutz-Snyder, Robert; Fiedler, James

2011-01-01

In their 2009 Annals of Statistics paper, Gavrilov, Benjamini, and Sarkar report the results of a simulation assessing the robustness of their adaptive step-down procedure (GBS) for controlling the false discovery rate (FDR) when normally distributed test statistics are serially correlated. In this study we extend the investigation to the case of multiple comparisons involving correlated non-central t-statistics, in particular when several treatments or time periods are being compared to a control in a repeated-measures design with many dependent outcome measures. In addition, we consider several dependence structures other than serial correlation and illustrate how the FDR depends on the interaction between effect size and the type of correlation structure as indexed by Foerstner s distance metric from an identity. The relationship between the correlation matrix R of the original dependent variables and R, the correlation matrix of associated t-statistics is also studied. In general R depends not only on R, but also on sample size and the signed effect sizes for the multiple comparisons.

Lower Relative Contribution of Positive Family History to Colorectal Cancer Risk with Increasing Age: A Systematic Review and Meta-Analysis of 9.28 Million Individuals.

PubMed

Wong, Martin C S; Chan, C H; Lin, Jiayan; Huang, Jason L W; Huang, Junjie; Fang, Yuan; Cheung, Wilson W L; Yu, C P; Wong, John C T; Tse, Gary; Wu, Justin C Y; Chan, Francis K L

2018-06-05

Existing algorithms predicting the risk of colorectal cancer (CRC) assign a fixed score for family history of CRC. Whether the increased CRC risk attributed to family history of CRC was higher in younger patients remains inconclusive. We examined the risk of CRC associated with family history of CRC in first-degree relative (FDR) according to the age of index subjects (<40 vs. ≥40; <50 vs. ≥50; and <60 vs. ≥60 years). Ovid Medline, EMBASE, and gray literature from the reference lists of all identified studies were searched from their inception to March 2017. We included case-control/cohort studies that investigated the relationship between family history of CRC in FDR and prevalence of CRC. Two reviewers independently selected articles according to the PRISMA guideline. A random effects meta-analysis pooled relative risks (RR). We analyzed 9.28 million subjects from 63 studies. A family history of CRC in FDR confers a higher risk of CRC (RR = 1.76, 95% CI = 1.57-1.97, p < 0.001). This increased risk was higher in younger individuals (RR = 3.29, 95% CI = 1.67-6.49 for <40 years versus RR = 1.42, 95% CI = 1.24-1.62 for ≥40 years, p = 0.017; RR = 2.81, 95% CI = 1.94-4.07 for <50 years versus RR = 1.47, 95% CI = 1.28-1.69 for ≥50 years, p = 0.001). No publication bias was identified, and the findings are robust in subgroup analyses. The increase in relative risk of CRC attributed to family history was found to be higher in younger individuals. Family history of CRC could be assigned a higher score for younger subjects in CRC risk prediction algorithms. Future studies should examine if such approach may improve their predictive capability.

Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions

DOE PAGES

Shatsky, Maxim; Dong, Ming; Liu, Haichuan; ...

2016-04-20

Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification ofmore » endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.« less

Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods

PubMed Central

Shen, Yufeng; Tolić, Nikola; Xie, Fang; Zhao, Rui; Purvine, Samuel O.; Schepmoes, Athena A.; Ronald, J. Moore; Anderson, Gordon A.; Smith, Richard D.

2011-01-01

We report on the effectiveness of CID, HCD, and ETD for LC-FT MS/MS analysis of peptides using a tandem linear ion trap-Orbitrap mass spectrometer. A range of software tools and analysis parameters were employed to explore the use of CID, HCD, and ETD to identify peptides isolated from human blood plasma without the use of specific “enzyme rules”. In the evaluation of an FDR-controlled SEQUEST scoring method, the use of accurate masses for fragments increased the numbers of identified peptides (by ~50%) compared to the use of conventional low accuracy fragment mass information, and CID provided the largest contribution to the identified peptide datasets compared to HCD and ETD. The FDR-controlled Mascot scoring method provided significantly fewer peptide identifications than with SEQUEST (by 1.3–2.3 fold) at the same confidence levels, and CID, HCD, and ETD provided similar contributions to identified peptides. Evaluation of de novo sequencing and the UStags method for more intense fragment ions revealed that HCD afforded more sequence consecutive residues (e.g., ≥7 amino acids) than either CID or ETD. Both the FDR-controlled SEQUEST and Mascot scoring methods provided peptide datasets that were affected by the decoy database and mass tolerances applied (e.g., the identical peptides between the datasets could be limited to ~70%), while the UStags method provided the most consistent peptide datasets (>90% overlap) with extremely low (near zero) numbers of false positive identifications. The m/z ranges in which CID, HCD, and ETD contributed the largest number of peptide identifications were substantially overlapping. This work suggests that the three peptide ion fragmentation methods are complementary, and that maximizing the number of peptide identifications benefits significantly from a careful match with the informatics tools and methods applied. These results also suggest that the decoy strategy may inaccurately estimate identification FDRs. PMID:21678914

Cerebral Small Vessel Disease Burden Is Associated with Motor Performance of Lower and Upper Extremities in Community-Dwelling Populations

PubMed Central

Su, Ning; Zhai, Fei-Fei; Zhou, Li-Xin; Ni, Jun; Yao, Ming; Li, Ming-Li; Jin, Zheng-Yu; Gong, Gao-Lang; Zhang, Shu-Yang; Cui, Li-Ying; Tian, Feng; Zhu, Yi-Cheng

2017-01-01

Objective: To investigate the correlation between cerebral small vessel disease (CSVD) burden and motor performance of lower and upper extremities in community-dwelling populations. Methods: We performed a cross-sectional analysis on 770 participants enrolled in the Shunyi study, which is a population-based cohort study. CSVD burden, including white matter hyperintensities (WMH), lacunes, cerebral microbleeds (CMBs), perivascular spaces (PVS), and brain atrophy were measured using 3T magnetic resonance imaging. All participants underwent quantitative motor assessment of lower and upper extremities, which included 3-m walking speed, 5-repeat chair-stand time, 10-repeat pronation–supination time, and 10-repeat finger-tapping time. Data on demographic characteristics, vascular risk factors, and cognitive functions were collected. General linear model analysis was performed to identify potential correlations between motor performance measures and imaging markers of CSVD after controlling for confounding factors. Results: For motor performance of the lower extremities, WMH was negatively associated with gait speed (standardized β = -0.092, p = 0.022) and positively associated with chair-stand time (standardized β = 0.153, p < 0.0001, surviving FDR correction). For motor performance of the upper extremities, pronation–supination time was positively associated with WMH (standardized β = 0.155, p < 0.0001, surviving FDR correction) and negatively with brain parenchymal fraction (BPF; standardized β = -0.125, p = 0.011, surviving FDR correction). Only BPF was found to be negatively associated with finger-tapping time (standardized β = -0.123, p = 0.012). However, lacunes, CMBs, or PVS were not found to be associated with motor performance of lower or upper extremities in multivariable analysis. Conclusion: Our findings suggest that cerebral microstructural changes related to CSVD may affect motor performance of both lower and upper extremities. WMH and brain atrophy are most strongly associated with motor function deterioration in community-dwelling populations. PMID:29021757

Automated video-based detection of nocturnal convulsive seizures in a residential care setting.

PubMed

Geertsema, Evelien E; Thijs, Roland D; Gutter, Therese; Vledder, Ben; Arends, Johan B; Leijten, Frans S; Visser, Gerhard H; Kalitzin, Stiliyan N

2018-06-01

People with epilepsy need assistance and are at risk of sudden death when having convulsive seizures (CS). Automated real-time seizure detection systems can help alert caregivers, but wearable sensors are not always tolerated. We determined algorithm settings and investigated detection performance of a video algorithm to detect CS in a residential care setting. The algorithm calculates power in the 2-6 Hz range relative to 0.5-12.5 Hz range in group velocity signals derived from video-sequence optical flow. A detection threshold was found using a training set consisting of video-electroencephalogaphy (EEG) recordings of 72 CS. A test set consisting of 24 full nights of 12 new subjects in residential care and additional recordings of 50 CS selected randomly was used to estimate performance. All data were analyzed retrospectively. The start and end of CS (generalized clonic and tonic-clonic seizures) and other seizures considered desirable to detect (long generalized tonic, hyperkinetic, and other major seizures) were annotated. The detection threshold was set to the value that obtained 97% sensitivity in the training set. Sensitivity, latency, and false detection rate (FDR) per night were calculated in the test set. A seizure was detected when the algorithm output exceeded the threshold continuously for 2 seconds. With the detection threshold determined in the training set, all CS were detected in the test set (100% sensitivity). Latency was ≤10 seconds in 78% of detections. Three/five hyperkinetic and 6/9 other major seizures were detected. Median FDR was 0.78 per night and no false detections occurred in 9/24 nights. Our algorithm could improve safety unobtrusively by automated real-time detection of CS in video registrations, with an acceptable latency and FDR. The algorithm can also detect some other motor seizures requiring assistance. © 2018 The Authors. Epilepsia published by Wiley Periodicals, Inc. on behalf of International League Against Epilepsy.

Identification of candidate genes in osteoporosis by integrated microarray analysis.

PubMed

Li, J J; Wang, B Q; Fei, Q; Yang, Y; Li, D

2016-12-01

In order to screen the altered gene expression profile in peripheral blood mononuclear cells of patients with osteoporosis, we performed an integrated analysis of the online microarray studies of osteoporosis. We searched the Gene Expression Omnibus (GEO) database for microarray studies of peripheral blood mononuclear cells in patients with osteoporosis. Subsequently, we integrated gene expression data sets from multiple microarray studies to obtain differentially expressed genes (DEGs) between patients with osteoporosis and normal controls. Gene function analysis was performed to uncover the functions of identified DEGs. A total of three microarray studies were selected for integrated analysis. In all, 1125 genes were found to be significantly differentially expressed between osteoporosis patients and normal controls, with 373 upregulated and 752 downregulated genes. Positive regulation of the cellular amino metabolic process (gene ontology (GO): 0033240, false discovery rate (FDR) = 1.00E + 00) was significantly enriched under the GO category for biological processes, while for molecular functions, flavin adenine dinucleotide binding (GO: 0050660, FDR = 3.66E-01) and androgen receptor binding (GO: 0050681, FDR = 6.35E-01) were significantly enriched. DEGs were enriched in many osteoporosis-related signalling pathways, including those of mitogen-activated protein kinase (MAPK) and calcium. Protein-protein interaction (PPI) network analysis showed that the significant hub proteins contained ubiquitin specific peptidase 9, X-linked (Degree = 99), ubiquitin specific peptidase 19 (Degree = 57) and ubiquitin conjugating enzyme E2 B (Degree = 57). Analysis of gene function of identified differentially expressed genes may expand our understanding of fundamental mechanisms leading to osteoporosis. Moreover, significantly enriched pathways, such as MAPK and calcium, may involve in osteoporosis through osteoblastic differentiation and bone formation.Cite this article: J. J. Li, B. Q. Wang, Q. Fei, Y. Yang, D. Li. Identification of candidate genes in osteoporosis by integrated microarray analysis. Bone Joint Res 2016;5:594-601. DOI: 10.1302/2046-3758.512.BJR-2016-0073.R1. © 2016 Fei et al.

Genetic Polymorphisms in Host Antiviral Genes: Associations with Humoral and Cellular Immunity to Measles Vaccine

PubMed Central

Haralambieva, Iana H.; Ovsyannikova, Inna G.; Umlauf, Benjamin J.; Vierkant, Robert A.; Pankratz, V. Shane; Jacobson, Robert M.; Poland, Gregory A.

2014-01-01

Host antiviral genes are important regulators of antiviral immunity and plausible genetic determinants of immune response heterogeneity after vaccination. We genotyped and analyzed 307 common candidate tagSNPs from 12 antiviral genes in a cohort of 745 schoolchildren immunized with two doses of measles-mumps-rubella vaccine. Associations between SNPs/haplotypes and measles virus-specific immune outcomes were assessed using linear regression methodologies in Caucasians and African-Americans. Genetic variants within the DDX58/RIG-I gene, including a coding polymorphism (rs3205166/Val800Val), were associated as single-SNPs (p≤0.017; although these SNPs did not remain significant after correction for false discovery rate/FDR) and in haplotype-level analysis, with measles-specific antibody variations in Caucasians (haplotype allele p-value=0.021; haplotype global p-value=0.076). Four DDX58 polymorphisms, in high LD, demonstrated also associations (after correction for FDR) with variations in both measles-specific IFN-γ and IL-2 secretion in Caucasians (p≤0.001, q=0.193). Two intronic OAS1 polymorphisms, including the functional OAS1 SNP rs10774671 (p=0.003), demonstrated evidence of association with a significant allele-dose-related increase in neutralizing antibody levels in African-Americans. Genotype and haplotype-level associations demonstrated the role of ADAR genetic variants, including a non-synonymous SNP (rs2229857/Arg384Lys; p=0.01), in regulating measles virus-specific IFN-γ Elispot responses in Caucasians (haplotype global p-value=0.017). After correction FDR, 15 single-SNP associations (11 SNPs in Caucasians and 4 SNPs in African-Americans) still remained significant at the q-value<0.20. In conclusion, our findings strongly point to genetic variants/genes, involved in antiviral sensing and antiviral control, as critical determinants, differentially modulating the adaptive immune responses to live attenuated measles vaccine in Caucasians and African-Americans. PMID:21939710

Fixed-dose-rate gemcitabine: a viable first-line treatment option for advanced pancreatic and biliary tract cancer.

PubMed

Milella, Michele; Gelibter, Alain J; Pino, Maria Simona; Bossone, Giandominik; Marolla, Paolo; Sperduti, Isabella; Cognetti, Francesco

2010-01-01

We have already reported on fixed-dose-rate gemcitabine (FDR-Gem) in advanced, inoperable pancreatic ductal adenocarcinoma (PDAC) and biliary tract cancer (BTC) in the context of a formal phase II study; building on that experience, we have now expanded the study to reach a cumulative accrual of 106 patients. One hundred six patients (PDAC/BTC, 75/31) were treated with weekly FDR-Gem (1,000 mg/m(2) infused at 10 mg/m(2) per minute). Patient characteristics included: male-to-female ratio, 0.83; median age, 63 years (range, 28-82); metastatic disease in 66% of patients; and an Eastern Cooperative Oncology Group performance status (ECOG PS) score of 0-1 in 81% of patients. The median and total number of treatment weeks delivered were 8 (range, 2-22) and 1,154, respectively. Thirteen percent of patients achieved an objective response, 42% experienced a positive clinical benefit response, and 54% achieved a >50% reduction in serum cancer antigen (CA)19.9 levels. The median progression-free survival (PFS) and overall survival (OS) times for the entire population were 4.4 months (95% confidence interval [CI], 3.5-5.1 months) and 7.7 months (95% CI, 6.3-8.8 months), respectively, with 20% of patients alive at 1 year. On multivariate analysis, a CA19.9 reduction >50% and baseline ECOG PS score of 0 were the only independent predictors of PFS and OS, respectively. Treatment was well tolerated, with grade 3-4 neutropenia in 47 of 1,154 treatment weeks (4.1%), and grade 3 anemia and thrombocytopenia in 8 of 1,154 (0.7%) and 16 of 1,154 (1.4%) treatment weeks, respectively. Currently available evidence, including this updated analysis, supports the use of FDR-Gem as a first-line option in advanced PDAC, and possibly in BTC, patients and prompts the continued evaluation of this approach in combination regimens.

Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shatsky, Maxim; Dong, Ming; Liu, Haichuan

Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification ofmore » endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR.« less

Obese First-Degree Relatives of Patients with Type 2 Diabetes with Elevated Triglyceride Levels Exhibit Increased β-Cell Function

PubMed Central

Torres-Rasgado, Enrique; Porchia, Leonardo M.; Ruiz-Vivanco, Guadalupe; Gonzalez-Mejia, M. Elba; Báez-Duarte, Blanca G.; Pulido-Pérez, Patricia; Rivera, Alicia; Romero, Jose R.

2015-01-01

Abstract Background: Type 2 diabetes mellitus (T2DM) is characterized as a disease continuum that is marked by metabolic changes that are present for several years, sometimes well before frank diagnosis of T2DM. Genetic predisposition, ethnicity, geography, alterations in BMI, and lipid profile are considered important markers for the pathogenesis of T2DM through mechanisms that remain unresolved and controversial. The aim of this study was to investigate the relationship between triglycerides (TGs) and β-cell function, insulin resistance (IR), and insulin sensitivity (IS) in obese first-degree relatives of patients with T2DM (FDR-T2DM) among subjects from central Mexico with normal glucose tolerance (NGT). Methods: We studied 372 FDR-T2DM subjects (ages,18–65) and determined body mass index (BMI), fasting plasma glucose (FPG), oral glucose tolerance test (OGTT), insulin, and TGs levels. Subjects were categorized based on glycemic control [NGT, prediabetes (PT2DM), or T2DM]. NGT subjects were further categorized by BMI [normal weight (Ob−) or obese (Ob+)] and TGs levels (TG−, <150 mg/dL, or TG+, ≥150 mg/dL). β-cell function, IR, and IS were determined by the homeostasis model assessment of β-cell function (HOMA2-β), homeostasis model assessment of insulin resistance (HOMA2-IR), and Quantitative Insulin Sensitivity Check Index (QUICKI) indices, respectively. Results: The obese subjects with elevated TGs levels had 21%–60% increased β-cell function when compared to all groups (P<0.05). In addition, this group had insulin levels, IS, and IR similar to PT2DM. Furthermore, only in obese subjects did TGs correlate with β-cell function (ρ=0.502, P<0.001). Conclusion: We characterized FDR-T2DM subjects from central Mexico with NGT and revealed a class of obese subjects with elevated TGs and β-cell function, which may precede PT2DM. PMID:25423015

Assessing Associations between the AURKA-HMMR-TPX2-TUBG1 Functional Module and Breast Cancer Risk in BRCA1/2 Mutation Carriers

PubMed Central

Blanco, Ignacio; Kuchenbaecker, Karoline; Cuadras, Daniel; Wang, Xianshu; Barrowdale, Daniel; de Garibay, Gorka Ruiz; Librado, Pablo; Sánchez-Gracia, Alejandro; Rozas, Julio; Bonifaci, Núria; McGuffog, Lesley; Pankratz, Vernon S.; Islam, Abul; Mateo, Francesca; Berenguer, Antoni; Petit, Anna; Català, Isabel; Brunet, Joan; Feliubadaló, Lidia; Tornero, Eva; Benítez, Javier; Osorio, Ana; Cajal, Teresa Ramón y; Nevanlinna, Heli; Aittomäki, Kristiina; Arun, Banu K.; Toland, Amanda E.; Karlan, Beth Y.; Walsh, Christine; Lester, Jenny; Greene, Mark H.; Mai, Phuong L.; Nussbaum, Robert L.; Andrulis, Irene L.; Domchek, Susan M.; Nathanson, Katherine L.; Rebbeck, Timothy R.; Barkardottir, Rosa B.; Jakubowska, Anna; Lubinski, Jan; Durda, Katarzyna; Jaworska-Bieniek, Katarzyna; Claes, Kathleen; Van Maerken, Tom; Díez, Orland; Hansen, Thomas V.; Jønson, Lars; Gerdes, Anne-Marie; Ejlertsen, Bent; de la Hoya, Miguel; Caldés, Trinidad; Dunning, Alison M.; Oliver, Clare; Fineberg, Elena; Cook, Margaret; Peock, Susan; McCann, Emma; Murray, Alex; Jacobs, Chris; Pichert, Gabriella; Lalloo, Fiona; Chu, Carol; Dorkins, Huw; Paterson, Joan; Ong, Kai-Ren; Teixeira, Manuel R.; Hogervorst, Frans B. L.; van der Hout, Annemarie H.; Seynaeve, Caroline; van der Luijt, Rob B.; Ligtenberg, Marjolijn J. L.; Devilee, Peter; Wijnen, Juul T.; Rookus, Matti A.; Meijers-Heijboer, Hanne E. J.; Blok, Marinus J.; van den Ouweland, Ans M. W.; Aalfs, Cora M.; Rodriguez, Gustavo C.; Phillips, Kelly-Anne A.; Piedmonte, Marion; Nerenstone, Stacy R.; Bae-Jump, Victoria L.; O'Malley, David M.; Ratner, Elena S.; Schmutzler, Rita K.; Wappenschmidt, Barbara; Rhiem, Kerstin; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Plendl, Hansjoerg J.; Niederacher, Dieter; Sutter, Christian; Wang-Gohrke, Shan; Steinemann, Doris; Preisler-Adams, Sabine; Kast, Karin; Varon-Mateeva, Raymonda; Gehrig, Andrea; Bojesen, Anders; Pedersen, Inge Sokilde; Sunde, Lone; Jensen, Uffe Birk; Thomassen, Mads; Kruse, Torben A.; Foretova, Lenka; Peterlongo, Paolo; Bernard, Loris; Peissel, Bernard; Scuvera, Giulietta; Manoukian, Siranoush; Radice, Paolo; Ottini, Laura; Montagna, Marco; Agata, Simona; Maugard, Christine; Simard, Jacques; Soucy, Penny; Berger, Andreas; Fink-Retter, Anneliese; Singer, Christian F.; Rappaport, Christine; Geschwantler-Kaulich, Daphne; Tea, Muy-Kheng; Pfeiler, Georg; John, Esther M.; Miron, Alex; Neuhausen, Susan L.; Terry, Mary Beth; Chung, Wendy K.; Daly, Mary B.; Goldgar, David E.; Janavicius, Ramunas; Dorfling, Cecilia M.; van Rensburg, Elisabeth J.; Fostira, Florentia; Konstantopoulou, Irene; Garber, Judy; Godwin, Andrew K.; Olah, Edith; Narod, Steven A.; Rennert, Gad; Paluch, Shani Shimon; Laitman, Yael; Friedman, Eitan; Liljegren, Annelie; Rantala, Johanna; Stenmark-Askmalm, Marie; Loman, Niklas; Imyanitov, Evgeny N.; Hamann, Ute; Spurdle, Amanda B.; Healey, Sue; Weitzel, Jeffrey N.; Herzog, Josef; Margileth, David; Gorrini, Chiara; Esteller, Manel; Gómez, Antonio; Sayols, Sergi; Vidal, Enrique; Heyn, Holger; Stoppa-Lyonnet, Dominique; Léoné, Melanie; Barjhoux, Laure; Fassy-Colcombet, Marion; de Pauw, Antoine; Lasset, Christine; Ferrer, Sandra Fert; Castera, Laurent; Berthet, Pascaline; Cornelis, François; Bignon, Yves-Jean; Damiola, Francesca; Mazoyer, Sylvie; Maxwell, Christopher A.; Vijai, Joseph; Robson, Mark; Kauff, Noah; Corines, Marina J.; Villano, Danylko; Cunningham, Julie; Lee, Adam; Lindor, Noralane; Lázaro, Conxi; Easton, Douglas F.; Offit, Kenneth; Chenevix-Trench, Georgia; Couch, Fergus J.; Antoniou, Antonis C.; Pujana, Miguel Angel

2015-01-01

While interplay between BRCA1 and AURKA-RHAMM-TPX2-TUBG1 regulates mammary epithelial polarization, common genetic variation in HMMR (gene product RHAMM) may be associated with risk of breast cancer in BRCA1 mutation carriers. Following on these observations, we further assessed the link between the AURKA-HMMR-TPX2-TUBG1 functional module and risk of breast cancer in BRCA1 or BRCA2 mutation carriers. Forty-one single nucleotide polymorphisms (SNPs) were genotyped in 15,252 BRCA1 and 8,211 BRCA2 mutation carriers and subsequently analyzed using a retrospective likelihood approach. The association of HMMR rs299290 with breast cancer risk in BRCA1 mutation carriers was confirmed: per-allele hazard ratio (HR) = 1.10, 95% confidence interval (CI) 1.04 – 1.15, p = 1.9 x 10−4 (false discovery rate (FDR)-adjusted p = 0.043). Variation in CSTF1, located next to AURKA, was also found to be associated with breast cancer risk in BRCA2 mutation carriers: rs2426618 per-allele HR = 1.10, 95% CI 1.03 – 1.16, p = 0.005 (FDR-adjusted p = 0.045). Assessment of pairwise interactions provided suggestions (FDR-adjusted pinteraction values > 0.05) for deviations from the multiplicative model for rs299290 and CSTF1 rs6064391, and rs299290 and TUBG1 rs11649877 in both BRCA1 and BRCA2 mutation carriers. Following these suggestions, the expression of HMMR and AURKA or TUBG1 in sporadic breast tumors was found to potentially interact, influencing patients’ survival. Together, the results of this study support the hypothesis of a causative link between altered function of AURKA-HMMR-TPX2-TUBG1 and breast carcinogenesis in BRCA1/2 mutation carriers. PMID:25830658

Cerebral Small Vessel Disease Burden Is Associated with Motor Performance of Lower and Upper Extremities in Community-Dwelling Populations.

PubMed

Su, Ning; Zhai, Fei-Fei; Zhou, Li-Xin; Ni, Jun; Yao, Ming; Li, Ming-Li; Jin, Zheng-Yu; Gong, Gao-Lang; Zhang, Shu-Yang; Cui, Li-Ying; Tian, Feng; Zhu, Yi-Cheng

2017-01-01

Objective: To investigate the correlation between cerebral small vessel disease (CSVD) burden and motor performance of lower and upper extremities in community-dwelling populations. Methods: We performed a cross-sectional analysis on 770 participants enrolled in the Shunyi study, which is a population-based cohort study. CSVD burden, including white matter hyperintensities (WMH), lacunes, cerebral microbleeds (CMBs), perivascular spaces (PVS), and brain atrophy were measured using 3T magnetic resonance imaging. All participants underwent quantitative motor assessment of lower and upper extremities, which included 3-m walking speed, 5-repeat chair-stand time, 10-repeat pronation-supination time, and 10-repeat finger-tapping time. Data on demographic characteristics, vascular risk factors, and cognitive functions were collected. General linear model analysis was performed to identify potential correlations between motor performance measures and imaging markers of CSVD after controlling for confounding factors. Results: For motor performance of the lower extremities, WMH was negatively associated with gait speed (standardized β = -0.092, p = 0.022) and positively associated with chair-stand time (standardized β = 0.153, p < 0.0001, surviving FDR correction). For motor performance of the upper extremities, pronation-supination time was positively associated with WMH (standardized β = 0.155, p < 0.0001, surviving FDR correction) and negatively with brain parenchymal fraction (BPF; standardized β = -0.125, p = 0.011, surviving FDR correction). Only BPF was found to be negatively associated with finger-tapping time (standardized β = -0.123, p = 0.012). However, lacunes, CMBs, or PVS were not found to be associated with motor performance of lower or upper extremities in multivariable analysis. Conclusion: Our findings suggest that cerebral microstructural changes related to CSVD may affect motor performance of both lower and upper extremities. WMH and brain atrophy are most strongly associated with motor function deterioration in community-dwelling populations.

After the War: Nation-Building from FDR to George W. Bush

DTIC Science & Technology

2008-01-01

vet analysis, as well as to develop policy options that were not mere regurgitations of departmental positions. The deputies, having known each other...think that important U.S. interests were involved and declared, “We don’t have a dog in this fight.”55 President Bush and Baker felt that Europe could

Genome-wide genetic analyses highlight mitogen-activated protein kinase (MAPK) signaling in the pathogenesis of endometriosis.

PubMed

Uimari, Outi; Rahmioglu, Nilufer; Nyholt, Dale R; Vincent, Katy; Missmer, Stacey A; Becker, Christian; Morris, Andrew P; Montgomery, Grant W; Zondervan, Krina T

2017-04-01

Do genome-wide association study (GWAS) data for endometriosis provide insight into novel biological pathways associated with its pathogenesis? GWAS analysis uncovered multiple pathways that are statistically enriched for genetic association signals, analysis of Stage A disease highlighted a novel variant in MAP3K4, while top pathways significantly associated with all endometriosis and Stage A disease included several mitogen-activated protein kinase (MAPK)-related pathways. Endometriosis is a complex disease with an estimated heritability of 50%. To date, GWAS revealed 10 genomic regions associated with endometriosis, explaining <4% of heritability, while half of the heritability is estimated to be due to common risk variants. Pathway analyses combine the evidence of single variants into gene-based measures, leveraging the aggregate effect of variants in genes and uncovering biological pathways involved in disease pathogenesis. Pathway analysis was conducted utilizing the International Endogene Consortium GWAS data, comprising 3194 surgically confirmed endometriosis cases and 7060 controls of European ancestry with genotype data imputed up to 1000 Genomes Phase three reference panel. GWAS was performed for all endometriosis cases and for Stage A (revised American Fertility Society (rAFS) I/II, n = 1686) and B (rAFS III/IV, n = 1364) cases separately. The identified significant pathways were compared with pathways previously investigated in the literature through candidate association studies. The most comprehensive biological pathway databases, MSigDB (including BioCarta, KEGG, PID, SA, SIG, ST and GO) and PANTHER were utilized to test for enrichment of genetic variants associated with endometriosis. Statistical enrichment analysis was performed using the MAGENTA (Meta-Analysis Gene-set Enrichment of variaNT Associations) software. The first genome-wide association analysis for Stage A endometriosis revealed a novel locus, rs144240142 (P = 6.45 × 10-8, OR = 1.71, 95% CI = 1.23-2.37), an intronic single-nucleotide polymorphism (SNP) within MAP3K4. This SNP was not associated with Stage B disease (P = 0.086). MAP3K4 was also shown to be differentially expressed in eutopic endometrium between Stage A endometriosis cases and controls (P = 3.8 × 10-4), but not with Stage B disease (P = 0.26). A total of 14 pathways enriched with genetic endometriosis associations were identified (false discovery rate (FDR)-P < 0.05). The pathways associated with any endometriosis were Grb2-Sos provides linkage to MAPK signaling for integrins pathway (P = 2.8 × 10-5, FDR-P = 3.0 × 10-3), Wnt signaling (P = 0.026, FDR-P = 0.026) and p130Cas linkage to MAPK signaling for integrins pathway (P = 6.0 × 10-4, FDR-P = 0.029); with Stage A endometriosis: extracellular signal-regulated kinase (ERK)1 ERK2 MAPK (P = 5.0 × 10-4, FDR-P = 5.0 × 10-4) and with Stage B endometriosis: two overlapping pathways that related to extracellular matrix biology-Core matrisome (P = 1.4 × 10-3, FDR-P = 0.013) and ECM glycoproteins (P = 1.8 × 10-3, FDR-P = 7.1 × 10-3). Genes arising from endometriosis candidate gene studies performed to date were enriched for Interleukin signaling pathway (P = 2.3 × 10-12), Apoptosis signaling pathway (P = 9.7 × 10-9) and Gonadotropin releasing hormone receptor pathway (P = 1.2 × 10-6); however, these pathways did not feature in the results based on GWAS data. Not applicable. The analysis is restricted to (i) variants in/near genes that can be assigned to pathways, excluding intergenic variants; (ii) the gene-based pathway definition as registered in the databases; (iii) women of European ancestry. The top ranked pathways associated with overall and Stage A endometriosis in particular involve integrin-mediated MAPK activation and intracellular ERK/MAPK acting downstream in the MAPK cascade, both acting in the control of cell division, gene expression, cell movement and survival. Other top enriched pathways in Stage B disease include ECM glycoprotein pathways important for extracellular structure and biochemical support. The results highlight the need for increased efforts to understand the functional role of these pathways in endometriosis pathogenesis, including the investigation of the biological effects of the genetic variants on downstream molecular processes in tissue relevant to endometriosis. Additionally, our results offer further support for the hypothesis of at least partially distinct causal pathophysiology for minimal/mild (rAFS I/II) vs. moderate/severe (rAFS III/IV) endometriosis. The genome-wide association data and Wellcome Trust Case Control Consortium (WTCCC) were generated through funding from the Wellcome Trust (WT084766/Z/08/Z, 076113 and 085475) and the National Health and Medical Research Council (NHMRC) of Australia (241944, 339462, 389927, 389875, 389891, 389892, 389938, 443036, 442915, 442981, 496610, 496739, 552485 and 552498). N.R. was funded by a grant from the Medical Research Council UK (MR/K011480/1). A.P.M. is a Wellcome Trust Senior Fellow in Basic Biomedical Science (grant WT098017). All authors declare there are no conflicts of interest. © The Author 2017. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology.

Genome-wide genetic analyses highlight mitogen-activated protein kinase (MAPK) signaling in the pathogenesis of endometriosis

PubMed Central

Uimari, Outi; Rahmioglu, Nilufer; Nyholt, Dale R.; Vincent, Katy; Missmer, Stacey A.; Becker, Christian; Morris, Andrew P.; Montgomery, Grant W.

2017-01-01

Abstract STUDY QUESTION Do genome-wide association study (GWAS) data for endometriosis provide insight into novel biological pathways associated with its pathogenesis? SUMMARY ANSWER GWAS analysis uncovered multiple pathways that are statistically enriched for genetic association signals, analysis of Stage A disease highlighted a novel variant in MAP3K4, while top pathways significantly associated with all endometriosis and Stage A disease included several mitogen-activated protein kinase (MAPK)-related pathways. WHAT IS KNOWN ALREADY Endometriosis is a complex disease with an estimated heritability of 50%. To date, GWAS revealed 10 genomic regions associated with endometriosis, explaining <4% of heritability, while half of the heritability is estimated to be due to common risk variants. Pathway analyses combine the evidence of single variants into gene-based measures, leveraging the aggregate effect of variants in genes and uncovering biological pathways involved in disease pathogenesis. STUDY DESIGN, SIZE, DURATION Pathway analysis was conducted utilizing the International Endogene Consortium GWAS data, comprising 3194 surgically confirmed endometriosis cases and 7060 controls of European ancestry with genotype data imputed up to 1000 Genomes Phase three reference panel. GWAS was performed for all endometriosis cases and for Stage A (revised American Fertility Society (rAFS) I/II, n = 1686) and B (rAFS III/IV, n = 1364) cases separately. The identified significant pathways were compared with pathways previously investigated in the literature through candidate association studies. PARTICIPANTS/MATERIALS, SETTING, METHODS The most comprehensive biological pathway databases, MSigDB (including BioCarta, KEGG, PID, SA, SIG, ST and GO) and PANTHER were utilized to test for enrichment of genetic variants associated with endometriosis. Statistical enrichment analysis was performed using the MAGENTA (Meta-Analysis Gene-set Enrichment of variaNT Associations) software. MAIN RESULTS AND THE ROLE OF CHANCE The first genome-wide association analysis for Stage A endometriosis revealed a novel locus, rs144240142 (P = 6.45 × 10−8, OR = 1.71, 95% CI = 1.23–2.37), an intronic single-nucleotide polymorphism (SNP) within MAP3K4. This SNP was not associated with Stage B disease (P = 0.086). MAP3K4 was also shown to be differentially expressed in eutopic endometrium between Stage A endometriosis cases and controls (P = 3.8 × 10−4), but not with Stage B disease (P = 0.26). A total of 14 pathways enriched with genetic endometriosis associations were identified (false discovery rate (FDR)-P < 0.05). The pathways associated with any endometriosis were Grb2-Sos provides linkage to MAPK signaling for integrins pathway (P = 2.8 × 10−5, FDR-P = 3.0 × 10−3), Wnt signaling (P = 0.026, FDR-P = 0.026) and p130Cas linkage to MAPK signaling for integrins pathway (P = 6.0 × 10−4, FDR-P = 0.029); with Stage A endometriosis: extracellular signal-regulated kinase (ERK)1 ERK2 MAPK (P = 5.0 × 10−4, FDR-P = 5.0 × 10−4) and with Stage B endometriosis: two overlapping pathways that related to extracellular matrix biology—Core matrisome (P = 1.4 × 10−3, FDR-P = 0.013) and ECM glycoproteins (P = 1.8 × 10−3, FDR-P = 7.1 × 10−3). Genes arising from endometriosis candidate gene studies performed to date were enriched for Interleukin signaling pathway (P = 2.3 × 10−12), Apoptosis signaling pathway (P = 9.7 × 10−9) and Gonadotropin releasing hormone receptor pathway (P = 1.2 × 10−6); however, these pathways did not feature in the results based on GWAS data. LARGE SCALE DATA Not applicable. LIMITATIONS, REASONS FOR CAUTION The analysis is restricted to (i) variants in/near genes that can be assigned to pathways, excluding intergenic variants; (ii) the gene-based pathway definition as registered in the databases; (iii) women of European ancestry. WIDER IMPLICATIONS OF THE FINDINGS The top ranked pathways associated with overall and Stage A endometriosis in particular involve integrin-mediated MAPK activation and intracellular ERK/MAPK acting downstream in the MAPK cascade, both acting in the control of cell division, gene expression, cell movement and survival. Other top enriched pathways in Stage B disease include ECM glycoprotein pathways important for extracellular structure and biochemical support. The results highlight the need for increased efforts to understand the functional role of these pathways in endometriosis pathogenesis, including the investigation of the biological effects of the genetic variants on downstream molecular processes in tissue relevant to endometriosis. Additionally, our results offer further support for the hypothesis of at least partially distinct causal pathophysiology for minimal/mild (rAFS I/II) vs. moderate/severe (rAFS III/IV) endometriosis. STUDY FUNDING/COMPETING INTEREST(S) The genome-wide association data and Wellcome Trust Case Control Consortium (WTCCC) were generated through funding from the Wellcome Trust (WT084766/Z/08/Z, 076113 and 085475) and the National Health and Medical Research Council (NHMRC) of Australia (241944, 339462, 389927, 389875, 389891, 389892, 389938, 443036, 442915, 442981, 496610, 496739, 552485 and 552498). N.R. was funded by a grant from the Medical Research Council UK (MR/K011480/1). A.P.M. is a Wellcome Trust Senior Fellow in Basic Biomedical Science (grant WT098017). All authors declare there are no conflicts of interest. PMID:28333195

To Mrs. Roosevelt, Who "Looks for the Poor" and to FDR: The CCC Is "A Vain Effort to Placate Youth." Teaching Ideas.

ERIC Educational Resources Information Center

Cohen, Robert

1996-01-01

Utilizes letters to the First Lady and President Roosevelt as primary sources for a series of activities supporting a unit on the Great Depression. The letter to Mrs. Roosevelt asks for some old clothes for a needy family. The letter to President Roosevelt expresses dissatisfaction with his efforts. (MJP)

Polymorphisms of inflammatory markers and risk of essential hypertension in Tatars from Russia.

PubMed

Timasheva, Yanina R; Nasibullin, Timur R; Imaeva, Elvira B; Erdman, Vera V; Kruzliak, Peter; Tuktarova, Ilsiyar A; Nikolaeva, Irina E; Mustafina, Olga E

2015-01-01

Essential hypertension (EH) is a common disease with a clear genetic component. Inflammation and endothelial dysfunction play a prominent role in the development of persistent blood pressure elevation. The aim of the current study was to detect an association between EH and polymorphic markers in genes encoding for molecules involved in the control of intercellular interactions during the inflammation process. We analysed SNPs in SELE, SELP, SELL, ICAM1, VEGFA, IL1B, IL6, IL10 and IL12B genes in a group of 534 men of Tatar ethnicity (217 patients with EH and 317 controls). Using a Markov chain Monte-Carlo-based approach (APSampler), we found genotype and allelic combinations associated with EH. The most significant associations were observed for SELE rs2076059*C-SELP rs6131*A-VEGFA -2549*I-IL1B rs16944*C (p = 3.42 × 10(-5), FDR q = 0.035) and SELE rs2076059*C-SELP rs6131*A-IL12B rs3212227*C-IL1B rs16944*C (p = 323 × 10(-4), FDR q = 0.035).

Structural Impairments of Hippocampus in Coal Mine Gas Explosion-Related Posttraumatic Stress Disorder

PubMed Central

Lang, Xu; Li, Huabing; Qin, Wen; Yu, Chunshui

2014-01-01

Investigations on hippocampal and amygdalar volume have revealed inconsistent results in patients with posttraumatic stress disorder (PTSD). Little is known about the structural covariance alterations between the hippocampus and amygdala in PTSD. In this study, we evaluated the alteration in the hippocampal and amygdalar volume and their structural covariance in the coal mine gas explosion related PTSD. High resolution T1-weighted magnetic resonance imaging (MRI) was performed on coal mine gas explosion related PTSD male patients (n = 14) and non-traumatized coalminers without PTSD (n = 25). The voxel-based morphometry (VBM) method was used to test the inter-group differences in hippocampal and amygdalar volume as well as the inter-group differences in structural covariance between the ipsilateral hippocampus and amygdala. PTSD patients exhibited decreased gray matter volume (GMV) in the bilateral hippocampi compared to controls (p<0.05, FDR corrected). GMV covariances between the ipsilateral hippocampus and amygdala were significantly reduced in PTSD patients compared with controls (p<0.05, FDR corrected). The coalminers with gas explosion related PTSD had decreased hippocampal volume and structural covariance with the ipsilateral amygdala, suggesting that the structural impairment of the hippocampus may implicate in the pathophysiology of PTSD. PMID:25000505

Chapter 8: Plasma operation and control

NASA Astrophysics Data System (ADS)

ITER Physics Expert Group on Disruptions, Control, Plasma, and MHD; ITER Physics Expert Group on Energetic Particles, Heating, Current and Drive; ITER Physics Expert Group on Diagnostics; ITER Physics Basis Editors

1999-12-01

Wall conditioning of fusion devices involves removal of desorbable hydrogen isotopes and impurities from interior device surfaces to permit reliable plasma operation. Techniques used in present devices include baking, metal film gettering, deposition of thin films of low-Z material, pulse discharge cleaning, glow discharge cleaning, radio frequency discharge cleaning, and in situ limiter and divertor pumping. Although wall conditioning techniques have become increasingly sophisticated, a reactor scale facility will involve significant new challenges, including the development of techniques applicable in the presence of a magnetic field and of methods for efficient removal of tritium incorporated into co-deposited layers on plasma facing components and their support structures. The current status of various approaches is reviewed, and the implications for reactor scale devices are summarized. Creation and magnetic control of shaped and vertically unstable elongated plasmas have been mastered in many present tokamaks. The physics of equilibrium control for reactor scale plasmas will rely on the same principles, but will face additional challenges, exemplified by the ITER/FDR design. The absolute positioning of outermost flux surface and divertor strike points will have to be precise and reliable in view of the high heat fluxes at the separatrix. Long pulses will require minimal control actions, to reduce accumulation of AC losses in superconducting PF and TF coils. To this end, more complex feedback controllers are envisaged, and the experimental validation of the plasma equilibrium response models on which such controllers are designed is encouraging. Present simulation codes provide an adequate platform on which equilibrium response techniques can be validated. Burning plasmas require kinetic control in addition to traditional magnetic shape and position control. Kinetic control refers to measures controlling density, rotation and temperature in the plasma core as well as in plasma periphery and divertor. The planned diagnostics (Chapter 7) serve as sensors for kinetic control, while gas and pellet fuelling, auxiliary power and angular momentum input, impurity injection, and non-inductive current drive constitute the control actuators. For example, in an ignited plasma, core density controls fusion power output. Kinetic control algorithms vary according to the plasma state, e.g. H- or L-mode. Generally, present facilities have demonstrated the kinetic control methods required for a reactor scale device. Plasma initiation - breakdown, burnthrough and initial current ramp - in reactor scale tokamaks will not involve physics differing from that found in present day devices. For ITER, the induced electric field in the chamber will be ~0.3V· m-1 - comparable to that required by breakdown theory but somewhat smaller than in present devices. Thus, a start-up 3MW electron cyclotron heating system will be employed to assure burnthrough. Simulations show that plasma current ramp up and termination in a reactor scale device can follow procedures developed to avoid disruption in present devices. In particular, simulations remain in the stable area of the li-q plane. For design purposes, the resistive V·s consumed during initiation is found, by experiments, to follow the Ejima expression, 0.45μ0 RIp. Advanced tokamak control has two distinct goals. First, control of density, auxiliary power, and inductive current ramping to attain reverse shear q profiles and internal transport barriers, which persist until dissipated by magnetic flux diffusion. Such internal transport barriers can lead to transient ignition. Second, combined use poloidal field shape control with non-inductive current drive and NBI angular momentum injection to create and control steady state, high bootstrap fraction, reverse shear discharges. Active n = 1 magnetic feedback and/or driven rotation will be required to suppress resistive wall modes for steady state plasmas that must operate in the wall stabilized regime for reactor levels of β >= 0.03.

[Role of visfatin in the pathogenesis of gestational diabetes mellitus and its relationship with insulin resistance].

PubMed

Huo, Yan; Liu, Suxin; Feng, Jing; Li, Hongyan; Fan, Yanli; Jin, Ying; Li, Li

2014-08-01

To investigate the role of visfatin in the pathogenesis of gestational diabetes mellitus (GDM) and its correlation with insulin resistance. The study recruited 58 pregnant women of 24 to 28 gestational weeks in People's Hospital of Hebei Province from January to June 2013. Among them, 30 were patients with GDM (GDM group), 28 had normal oral glucose tolerance test and was referred as healthy pregnancy group (NGT group). Fourteen age-matched female who were first-degree relatives (FDR1) of type 2 diabetes mellitus patients, and 27 healthy nonpregnant women with normal oral glucose tolerance test were referred as high-risk group and normal controls (NC), respectively. The fasting plasma glucose (FPG), 1 hour and 2 hours postprandial glucose levels were measured by glucose oxidase method. The fasting insulin (FIN) levels were measured by radioimmunoassay and the homeostatic model assessment-insulin resistance index (HOMA- IR) was calculated. The levels of total cholesterol (TC), triglycerdes (TG), high density lipoprotein cholesterol (HDL) and low density lipoprotein cholesterol (LDL) were determined. The visfatin levels were measured by ELISA. (1)The levels of FPG were significantly higher in GDM, FDR1 and NC group [(5.5 ± 0.7), (5.1 ±0.6), (5.2 ± 0.4)mmol/L] than that in NGT group [(4.5 ± 0.3) mmol/L], respectively (P < 0.05). (2) The levels of INS [(14 ± 6)mU/L], HOMA- IR (4.0 ± 2.0), 1 hour [(10.9 ± 1.8) mmol/L] and 2 hours [(8.6 ± 1.8) mmol/L] postprandial glucose levels of GDM group were significantly higher than those in NGT group [(12 ± 4) mU/L, 2.0 ± 1.0, (7. 4 ± 1.3) and (6.2 ± 0.9) mmol/L], respectively (P < 0.05). (3) The levels of TC, TG, HDL and LDL levels in GDM group were (5.5 ± 0.9), (2.8 ± 0.8), (1.8 ± 0.4) and (3.3 ± 0.8) mmol/L, and were(5.9 ± 0.8), (2.5 ± 0.7), (1.9 ± 0.4) and (3.4 ± 0.6) mmol/L in NGT group. The levels of lipid in the two groups were significantly higher than those in FDR1 or NC group, respectively(P < 0.05).(4)The levels of visfatin in GDM group and NGT group [(43 ± 10), (45 ± 12) µg/L] were significantly higher than that in FDR1 or NC group [(29 ± 9), (36 ± 7) µg/L], respectively (P < 0.05), but the visfatin levels in FDR1 group were significantly lower than that in NC group (P < 0.05). The visfatin levels in GDM group were slightly lower than that in NGT group, but the difference was not statistically significant (P > 0.05). (5)The visfatin levels in NGT group were negatively correlated to the levels of FPG, HOMA-IR and TC (r = -0.38, -0.44, -0.47, respectively, P < 0.05). But the visfatin levels in GDM group were not correlated with the levels of FPG, HOMA-IR, TC (r = -0.16, -0.01, 0.33, respectively, P > 0.05). While in NC group, the levels of visfatin were negatively correlated with FPG and 2 hours postprandial glucose(r = -0.48, -0.42, respectively, P < 0.05). Visfatin may be an important adipokine that involved in the carbohydrate and lipid metabolism in GDM, and is related to the pathogensis of GDM and insulin resistance.

Advanced Digital Signal Processing for Hybrid Lidar

DTIC Science & Technology

2014-10-30

obtain range measurements . A MATLAB- based system developed at Clarkson University in FY14 has been used to perform real-time FDR ranging... measurement accuracy. There have been various methods that attempt to reduce the backscatter. One method is to increase the modulation frequency beyond...an unambiguous range measurement . In general, it is desired to determine which combination of Radio Frequency (RF) modulation frequencies, modulation

Large Scale Mass Spectrometry-based Identifications of Enzyme-mediated Protein Methylation Are Subject to High False Discovery Rates*

PubMed Central

Hart-Smith, Gene; Yagoub, Daniel; Tay, Aidan P.; Pickford, Russell; Wilkins, Marc R.

2016-01-01

All large scale LC-MS/MS post-translational methylation site discovery experiments require methylpeptide spectrum matches (methyl-PSMs) to be identified at acceptably low false discovery rates (FDRs). To meet estimated methyl-PSM FDRs, methyl-PSM filtering criteria are often determined using the target-decoy approach. The efficacy of this methyl-PSM filtering approach has, however, yet to be thoroughly evaluated. Here, we conduct a systematic analysis of methyl-PSM FDRs across a range of sample preparation workflows (each differing in their exposure to the alcohols methanol and isopropyl alcohol) and mass spectrometric instrument platforms (each employing a different mode of MS/MS dissociation). Through 13CD3-methionine labeling (heavy-methyl SILAC) of Saccharomyces cerevisiae cells and in-depth manual data inspection, accurate lists of true positive methyl-PSMs were determined, allowing methyl-PSM FDRs to be compared with target-decoy approach-derived methyl-PSM FDR estimates. These results show that global FDR estimates produce extremely unreliable methyl-PSM filtering criteria; we demonstrate that this is an unavoidable consequence of the high number of amino acid combinations capable of producing peptide sequences that are isobaric to methylated peptides of a different sequence. Separate methyl-PSM FDR estimates were also found to be unreliable due to prevalent sources of false positive methyl-PSMs that produce high peptide identity score distributions. Incorrect methylation site localizations, peptides containing cysteinyl-S-β-propionamide, and methylated glutamic or aspartic acid residues can partially, but not wholly, account for these false positive methyl-PSMs. Together, these results indicate that the target-decoy approach is an unreliable means of estimating methyl-PSM FDRs and methyl-PSM filtering criteria. We suggest that orthogonal methylpeptide validation (e.g. heavy-methyl SILAC or its offshoots) should be considered a prerequisite for obtaining high confidence methyl-PSMs in large scale LC-MS/MS methylation site discovery experiments and make recommendations on how to reduce methyl-PSM FDRs in samples not amenable to heavy isotope labeling. Data are available via ProteomeXchange with the data identifier PXD002857. PMID:26699799

Pregnancy exposure to atmospheric pollution and meteorological conditions and placental DNA methylation.

PubMed

Abraham, Emilie; Rousseaux, Sophie; Agier, Lydiane; Giorgis-Allemand, Lise; Tost, Jörg; Galineau, Julien; Hulin, Agnès; Siroux, Valérie; Vaiman, Daniel; Charles, Marie-Aline; Heude, Barbara; Forhan, Anne; Schwartz, Joel; Chuffart, Florent; Bourova-Flin, Ekaterina; Khochbin, Saadi; Slama, Rémy; Lepeule, Johanna

2018-06-19

Air pollution exposure represents a major health threat to the developing foetus. DNA methylation is one of the most well-known molecular determinants of the epigenetic status of cells. Blood DNA methylation has been proven sensitive to air pollutants, but the molecular impact of air pollution on new-borns has so far received little attention. We investigated whether nitrogen dioxide (NO 2 ), particulate matter (PM 10 ), temperature and humidity during pregnancy are associated with differences in placental DNA methylation levels. Whole-genome DNA-methylation was measured using the Illumina's Infinium HumanMethylation450 BeadChip in the placenta of 668 newborns from the EDEN cohort. We designed an original strategy using a priori biological information to focus on candidate genes with a specific expression pattern in placenta (active or silent) combined with an agnostic epigenome-wide association study (EWAS). We used robust linear regression to identify CpGs and differentially methylated regions (DMR) associated with each exposure during short- and long-term time-windows. The candidate genes approach identified nine CpGs mapping to 9 genes associated with prenatal NO 2 and PM 10 exposure [false discovery rate (FDR) p < 0.05]. Among these, the methylation level of 2 CpGs located in ADORA2B remained significantly associated with NO 2 exposure during the 2nd trimester and whole pregnancy in the EWAS (FDR p < 0.05). EWAS further revealed associations between the environmental exposures under study and variations of DNA methylation of 4 other CpGs. We further identified 27 DMRs significantly (FDR p < 0.05) associated with air pollutants exposure and 13 DMRs with meteorological conditions. The methylation of ADORA2B, a gene whose expression was previously associated with hypoxia and pre-eclampsia, was consistently found here sensitive to atmospheric pollutants. In addition, air pollutants were associated to DMRs pointing towards genes previously implicated in preeclampsia, hypertensive and metabolic disorders. These findings demonstrate that air pollutants exposure at levels commonly experienced in the European population are associated with placental gene methylation and provide some mechanistic insight into some of the reported effects of air pollutants on preeclampsia. Copyright © 2018 Elsevier Ltd. All rights reserved.

EDITORIAL: The FDR Prize The FDR Prize

NASA Astrophysics Data System (ADS)

Funakoshi, Mitsuaki

2011-08-01

From the 56 papers published in 2010 in Fluid Dynamics Research the following paper has been selected for the fourth FDR prize: 'Baroclinic multipole formation from heton interaction' by M A Sokolovskiy and X J Carton, published in volume 42 (August 2010) 045501. Coherent vortices are a universal feature of fluids at moderate and large Reynolds number, and have particular relevance to the quasi-two-dimensional flows used to model phenomena in the atmosphere and ocean. The structure and interaction of such vortices have proved a fascinating area for the researchers of fluid dynamics, including thoreticians, observers and experimentalists, together with related problems of how they mix fluids and how they transport scalars such as temperature and salinity. In this paper 'hetons' are considered; they are vortices of dipolar structures in a multilayer rotating fluid, carry thermal anomalies, and are relevant to transport in flows such as the Gulf Stream. The paper is a comprehensive study of the structure, invariants and interactions of two opposite-signed hetons in a two-layer fluid for several initial configurations and for several values of the Rossby radius of deformation, using models based on point vortex dynamics and contour dynamics of finite-area vortex regions. Different types of coupling and interactions are isolated and discussed. Depending on the initial configuration and the value of the radius of deformation, the time evolutions toward horizonal dipoles, vertically tilted dipoles, L-shaped dipoles, and Z-shaped tripoles are observed in the case of finite-area vortices. Using point vortex dynamics a rigorous analysis based on trilinear coordinates is performed, and the appearance of similar structures is shown analytically, except for the L-shaped dipoles. The contribution of this paper to the important problem of heton interaction is both profound and substantial. The study will be of great interest to a wide variety of readers and is likely to inspire further numerical and experimental work, as well being helpful in the interpretation and analysis of observations. Overall, the paper will undoubtedly have a large impact on the fluid dynamics community.

Fixed-Dose-Rate Gemcitabine: A Viable First-Line Treatment Option for Advanced Pancreatic and Biliary Tract Cancer

PubMed Central

Milella, Michele; Pino, Maria Simona; Bossone, Giandominik; Marolla, Paolo; Sperduti, Isabella; Cognetti, Francesco

2010-01-01

Background. We have already reported on fixed-dose-rate gemcitabine (FDR-Gem) in advanced, inoperable pancreatic ductal adenocarcinoma (PDAC) and biliary tract cancer (BTC) in the context of a formal phase II study; building on that experience, we have now expanded the study to reach a cumulative accrual of 106 patients. Methods. One hundred six patients (PDAC/BTC, 75/31) were treated with weekly FDR-Gem (1,000 mg/m2 infused at 10 mg/m2 per minute). Patient characteristics included: male-to-female ratio, 0.83; median age, 63 years (range, 28–82); metastatic disease in 66% of patients; and an Eastern Cooperative Oncology Group performance status (ECOG PS) score of 0–1 in 81% of patients. Results. The median and total number of treatment weeks delivered were 8 (range, 2–22) and 1,154, respectively. Thirteen percent of patients achieved an objective response, 42% experienced a positive clinical benefit response, and 54% achieved a >50% reduction in serum cancer antigen (CA)19.9 levels. The median progression-free survival (PFS) and overall survival (OS) times for the entire population were 4.4 months (95% confidence interval [CI], 3.5–5.1 months) and 7.7 months (95% CI, 6.3–8.8 months), respectively, with 20% of patients alive at 1 year. On multivariate analysis, a CA19.9 reduction >50% and baseline ECOG PS score of 0 were the only independent predictors of PFS and OS, respectively. Treatment was well tolerated, with grade 3–4 neutropenia in 47 of 1,154 treatment weeks (4.1%), and grade 3 anemia and thrombocytopenia in 8 of 1,154 (0.7%) and 16 of 1,154 (1.4%) treatment weeks, respectively. Conclusions. Currently available evidence, including this updated analysis, supports the use of FDR-Gem as a first-line option in advanced PDAC, and possibly in BTC, patients and prompts the continued evaluation of this approach in combination regimens. PMID:20189980

Fixed dose-rate gemcitabine infusion as first-line treatment for advanced-stage carcinoma of the pancreas and biliary tree.

PubMed

Gelibter, Alain; Malaguti, Paola; Di Cosimo, Serena; Bria, Emilio; Ruggeri, Enzo Maria; Carlini, Paolo; Carboni, Fabio; Ettorre, Giuseppe Maria; Pellicciotta, Mario; Giannarelli, Diana; Terzoli, Edmondo; Cognetti, Francesco; Milella, Michele

2005-09-15

Gemcitabine infusion at the fixed dose rate of 10 mg/m(2) per minute (FDR-gemcitabine) has pharmacokinetic advantages and may result in improved therapeutic efficacy. Between April 2002 and September 2003, 40 patients with advanced-stage pancreatic adenocarcinoma (PDAC; n = 27) or biliary tree carcinoma (BTC; n = 13) were treated with weekly FDR-gemcitabine (1000 mg/m(2)). The primary end point was the response rate. The secondary end points were progression-free and overall survival (PFS and OS), tumor marker response, and clinical benefit response (CBR). The overall response rate (ORR) on an intent-to-treat basis was 15% (95% confidence interval [95% CI], 4-26%). A positive CBR was obtained in 14 of 29 (48%) patients. Seventeen of 25 (68%) patients had a reduction in carbohydrate antigen 19-9 (CA 19-9) of > 25%. The median time to treatment failure and the median PFS were 17 weeks (95% CI, 13-22 weeks) and 19 weeks (95% CI, 15-23 weeks), respectively. The median OS was 40 weeks (95% CI, 36-45 weeks) and the 1-year actuarial survival rate was 25.8%. Multivariate analysis showed that a performance status score of 0-1 at study entry and locally advanced disease were the only independent predictors of longer PFS and OS, whereas a reduction in CA 19-9 serum levels > 75% was an independent predictor of longer PFS, but had no impact on OS. Toxicity was mild with Grade 3-4 neutropenia (according to the National Cancer Institute-Common Toxicity Criteria [version 2.0]) in 18 of 427 treatment weeks (4.2%), and Grade 3 anemia and thrombocytopenia in 6 of 427 treatment weeks (1.4%) and 9 of 427 treatment weeks (2.1%), respectively, and asymptomatic Grade 3-4 transaminase elevation in 21 of 427 treatment weeks (4.9%). FDR-gemcitabine at the weekly dose of 1000 mg/m(2) demonstrated promising activity, despite negligible toxicity, in patients with advanced-stage PDAC and BTC. Copyright 2005 American Cancer Society.

Bulk Electrical Cable Non-Destructive Examination Methods for Nuclear Power Plant Cable Aging Management Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glass, Samuel W.; Jones, Anthony M.; Fifield, Leonard S.

This Pacific Northwest National Laboratory milestone report describes progress to date on the investigation of nondestructive test methods focusing particularly on bulk electrical test methods that provide key indicators of cable aging and damage. The work includes a review of relevant literature as well as hands-on experimental verification of inspection capabilities. As nuclear power plants consider applying for second, or subsequent, license renewal to extend their operating period from 60 years to 80 years, it is important to understand how the materials installed in plant systems and components will age during that time and develop aging management programs to assuremore » continued safe operation under normal and design basis events (DBE). Normal component and system tests typically confirm the cables can perform their normal operational function. The focus of the cable test program, however, is directed toward the more demanding challenge of assuring the cable function under accident or DBE. The industry has adopted 50% elongation at break (EAB) relative to the un-aged cable condition as the acceptability standard. All tests are benchmarked against the cable EAB test. EAB, however, is a destructive test so the test programs must apply an array of other nondestructive examination (NDE) tests to assure or infer the overall set of cable’s system integrity. Assessment of cable integrity is further complicated in many cases by vendor’s use of dissimilar material for jacket and insulation. Frequently the jacket will degrade more rapidly than the underlying insulation. Although this can serve as an early alert to cable damage, direct test of the cable insulation without violating the protective jacket becomes problematic. This report addresses the range of bulk electrical NDE cable tests that are or could be practically implemented in a field-test situation with a particular focus on frequency domain reflectometry (FDR). The FDR test method offers numerous advantages over many other bulk electrical tests. Two commercial FDR systems plus a laboratory vector network analyzer are used to test an array of aged and un-aged cables under identical conditions. Several conclusions are set forth, and a number of knowledge gaps are identified.« less

FDR's First Inaugural Address: Declaring "War" on the Great Depression. The Constitution Community: The Great Depression and World War II (1929-1945).

ERIC Educational Resources Information Center

Lawlor, John M., Jr.

By late winter 1933, the United States had already endured more than 3 years of economic depression. During the previous summer, the Democratic Party platform had unveiled a generalized plan for economic recovery. President Franklin D. Roosevelt set about to prepare the nation to accept expansion of federal power since he recognized that the…

The Meaning of Freedom of Speech: First Amendment Freedoms from Wilson to FDR. Contributions in American History No. 15.

ERIC Educational Resources Information Center

Murphy, Paul L.

Using the Jazz Age as his frame of reference, the author analyzes the role of dissent and its suppression in American life. The crisis in civil liberties which began with a wartime restriction of freedom of speech in 1918 evoked a counteraction from concerned citizens during the 1920s. Their efforts were vindicated in 1931 when a…

FOCJ as a Means of Regional Cooperation (FOCJ als Mittel regionaler Kooperation)

DTIC Science & Technology

2008-03-01

Zinssicherungsin- strumente wie Swap-Geschdfte und Optionsgeschdifte (Rehm 2001) sogenannte De- rivatgeschdifte sollten ffir FOCJ an die engen Voraussetzungen, die...Fehler behoben werden mUissen und auf spezielle Wilnsche des noch engen Kundenkreises eingegangen werden muss, ist der finan- zielle Aufwand fdr Forschung...selbst Cluster entwickeln, z.B. Dow Chemicals mit ,,value 57 park", oder gernischtwirtschaftlicher Unternehmen, z.B. Volkswagen" (Detig, Feng, Friedrich

Subgrouping Chronic Fatigue Syndrome Patients By Genetic and Immune Profiling

DTIC Science & Technology

2015-12-01

participant inclusion was also verified against our master demographic file. This process revealed that only a small percentage of participants (...the ! ! − !!! , ∈ ℤ!| ≤ 7 , is a cubic -spline basis on three knots, ! is value of outcome for batch control, and is residual ...tests. Specifically, -value adjustments will employ an 8 adaptive two- stage linear step-up procedure to control the FDR at 5% (Benjamani et al. 2006

Consensus QSAR model for identifying novel H5N1 inhibitors.

PubMed

Sharma, Nitin; Yap, Chun Wei

2012-08-01

Due to the importance of neuraminidase in the pathogenesis of influenza virus infection, it has been regarded as the most important drug target for the treatment of influenza. Resistance to currently available drugs and new findings related to structure of the protein requires novel neuraminidase 1 (N1) inhibitors. In this study, a consensus QSAR model with defined applicability domain (AD) was developed using published N1 inhibitors. The consensus model was validated using an external validation set. The model achieved high sensitivity, specificity, and overall accuracy along with low false positive rate (FPR) and false discovery rate (FDR). The performance of model on the external validation set and training set were comparable, thus it was unlikely to be overfitted. The low FPR and low FDR will increase its accuracy in screening large chemical libraries. Screening of ZINC library resulted in 64,772 compounds as probable N1 inhibitors, while 173,674 compounds were defined to be outside the AD of the consensus model. The advantage of the current model is that it was developed using a large and diverse dataset and has a defined AD which prevents its use on compounds that it is not capable of predicting. The consensus model developed in this study is made available via the free software, PaDEL-DDPredictor.

Molecular Signatures in Skin Associated with Clinical Improvement During Mycophenolate Treatment in Systemic Sclerosis

PubMed Central

Hinchcliff, Monique; Huang, Chiang-Ching; Wood, Tammara A.; Mahoney, J. Matthew; Martyanov, Viktor; Bhattacharyya, Swati; Tamaki, Zenshiro; Lee, Jungwha; Carns, Mary; Podlusky, Sofia; Sirajuddin, Arlene; Shah, Sanjiv J; Chang, Rowland W.; Lafyatis, Robert; Varga, John; Whitfield, Michael L.

2013-01-01

Heterogeneity in systemic sclerosis/SSc confounds clinical trials. We previously identified ‘intrinsic’ gene expression subsets by analysis of SSc skin. Here we test the hypotheses that skin gene expression signatures including intrinsic subset are associated with skin score/MRSS improvement during mycophenolate mofetil (MMF) treatment. Gene expression and intrinsic subset assignment were measured in 12 SSc patients’ biopsies and ten controls at baseline, and from serial biopsies of one cyclophosphamide-treated patient, and nine MMF-treated patients. Gene expression changes during treatment were determined using paired t-tests corrected for multiple hypothesis testing. MRSS improved in four of seven MMF-treated patients classified as the inflammatory intrinsic subset. Three patients without MRSS improvement were classified as normal-like or fibroproliferative intrinsic subsets. 321 genes (FDR <5%) were differentially expressed at baseline between patients with and without MRSS improvement during treatment. Expression of 571 genes (FDR <10%) changed between pre- and post-MMF treatment biopsies for patients demonstrating MRSS improvement. Gene expression changes in skin are only seen in patients with MRSS improvement. Baseline gene expression in skin, including intrinsic subset assignment, may identify SSc patients whose MRSS will improve during MMF treatment, suggesting that gene expression in skin may allow targeted treatment in SSc. PMID:23677167

Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry.

PubMed

Kitata, Reta Birhanu; Dimayacyac-Esleta, Baby Rorielyn T; Choong, Wai-Kok; Tsai, Chia-Feng; Lin, Tai-Du; Tsou, Chih-Chiang; Weng, Shao-Hsing; Chen, Yi-Ju; Yang, Pan-Chyr; Arco, Susan D; Nesvizhskii, Alexey I; Sung, Ting-Yi; Chen, Yu-Ju

2015-09-04

Despite significant efforts in the past decade toward complete mapping of the human proteome, 3564 proteins (neXtProt, 09-2014) are still "missing proteins". Over one-third of these missing proteins are annotated as membrane proteins, owing to their relatively challenging accessibility with standard shotgun proteomics. Using nonsmall cell lung cancer (NSCLC) as a model study, we aim to mine missing proteins from disease-associated membrane proteome, which may be still largely under-represented. To increase identification coverage, we employed Hp-RP StageTip prefractionation of membrane-enriched samples from 11 NSCLC cell lines. Analysis of membrane samples from 20 pairs of tumor and adjacent normal lung tissue was incorporated to include physiologically expressed membrane proteins. Using multiple search engines (X!Tandem, Comet, and Mascot) and stringent evaluation of FDR (MAYU and PeptideShaker), we identified 7702 proteins (66% membrane proteins) and 178 missing proteins (74 membrane proteins) with PSM-, peptide-, and protein-level FDR of 1%. Through multiple reaction monitoring using synthetic peptides, we provided additional evidence of eight missing proteins including seven with transmembrane helix domains. This study demonstrates that mining missing proteins focused on cancer membrane subproteome can greatly contribute to map the whole human proteome. All data were deposited into ProteomeXchange with the identifier PXD002224.

FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.

PubMed

Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R; Hubbard, Simon J

2011-04-01

Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the postprocessing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server and a downloadable application that makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline also provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download.

FDRAnalysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines

PubMed Central

Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R.; Hubbard, Simon J.

2013-01-01

Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the post-processing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server, and a downloadable application, which makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download. PMID:21222473

Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay.

PubMed

Reiner-Benaim, Anat; Yekutieli, Daniel; Letwin, Noah E; Elmer, Gregory I; Lee, Norman H; Kafkafi, Neri; Benjamini, Yoav

2007-09-01

Gene expression and phenotypic functionality can best be associated when they are measured quantitatively within the same experiment. The analysis of such a complex experiment is presented, searching for associations between measures of exploratory behavior in mice and gene expression in brain regions. The analysis of such experiments raises several methodological problems. First and foremost, the size of the pool of potential discoveries being screened is enormous yet only few biologically relevant findings are expected, making the problem of multiple testing especially severe. We present solutions based on screening by testing related hypotheses, then testing the hypotheses of interest. In one variant the subset is selected directly, in the other one a tree of hypotheses is tested hierarchical; both variants control the False Discovery Rate (FDR). Other problems in such experiments are in the fact that the level of data aggregation may be different for the quantitative traits (one per animal) and gene expression measurements (pooled across animals); in that the association may not be linear; and in the resolution of interest only few replications exist. We offer solutions to these problems as well. The hierarchical FDR testing strategies presented here can serve beyond the structure of our motivating example study to any complex microarray study. Supplementary data are available at Bioinformatics online.

Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis.

PubMed

Kremer, Lukas P M; Leufken, Johannes; Oyunchimeg, Purevdulam; Schulze, Stefan; Fufezan, Christian

2016-03-04

Proteomics data integration has become a broad field with a variety of programs offering innovative algorithms to analyze increasing amounts of data. Unfortunately, this software diversity leads to many problems as soon as the data is analyzed using more than one algorithm for the same task. Although it was shown that the combination of multiple peptide identification algorithms yields more robust results, it is only recently that unified approaches are emerging; however, workflows that, for example, aim to optimize search parameters or that employ cascaded style searches can only be made accessible if data analysis becomes not only unified but also and most importantly scriptable. Here we introduce Ursgal, a Python interface to many commonly used bottom-up proteomics tools and to additional auxiliary programs. Complex workflows can thus be composed using the Python scripting language using a few lines of code. Ursgal is easily extensible, and we have made several database search engines (X!Tandem, OMSSA, MS-GF+, Myrimatch, MS Amanda), statistical postprocessing algorithms (qvality, Percolator), and one algorithm that combines statistically postprocessed outputs from multiple search engines ("combined FDR") accessible as an interface in Python. Furthermore, we have implemented a new algorithm ("combined PEP") that combines multiple search engines employing elements of "combined FDR", PeptideShaker, and Bayes' theorem.

A permutation-based non-parametric analysis of CRISPR screen data.

PubMed

Jia, Gaoxiang; Wang, Xinlei; Xiao, Guanghua

2017-07-19

Clustered regularly-interspaced short palindromic repeats (CRISPR) screens are usually implemented in cultured cells to identify genes with critical functions. Although several methods have been developed or adapted to analyze CRISPR screening data, no single specific algorithm has gained popularity. Thus, rigorous procedures are needed to overcome the shortcomings of existing algorithms. We developed a Permutation-Based Non-Parametric Analysis (PBNPA) algorithm, which computes p-values at the gene level by permuting sgRNA labels, and thus it avoids restrictive distributional assumptions. Although PBNPA is designed to analyze CRISPR data, it can also be applied to analyze genetic screens implemented with siRNAs or shRNAs and drug screens. We compared the performance of PBNPA with competing methods on simulated data as well as on real data. PBNPA outperformed recent methods designed for CRISPR screen analysis, as well as methods used for analyzing other functional genomics screens, in terms of Receiver Operating Characteristics (ROC) curves and False Discovery Rate (FDR) control for simulated data under various settings. Remarkably, the PBNPA algorithm showed better consistency and FDR control on published real data as well. PBNPA yields more consistent and reliable results than its competitors, especially when the data quality is low. R package of PBNPA is available at: https://cran.r-project.org/web/packages/PBNPA/ .

Understanding of real alternative redox partner of Streptomyces peucetius DoxA: Prediction and validation using in silico and in vitro analyses.

PubMed

Rimal, Hemraj; Lee, Seung-Won; Lee, Joo-Ho; Oh, Tae-Jin

2015-11-01

Streptomyces peucetius ATCC27952 contains the cytochrome P450 monoxygenase DoxA that is responsible for the hydroxylation of daunorubicin into doxorubicin. Although S. peucetius ATCC27952 contains several potential redox partners, the most suitable endogenous electron-transport system is still unclear; therefore, we conducted a study of potential redox partners using Accelrys Discovery Studio 3.5. Recombinant DoxA along with its redox partners from S. peucetius FDX1, FDR2, and FDX3, and the putidaredoxin and putidaredoxin reductase from Pseudomonas putida that are essential equivalents of the class I type of bacterial electron-transport system were over-expressed and purified. The successful development of an efficient redox system was achieved by an in vitro enzymatic catalysis reaction with DoxA. The optimal pH for the activation of the heme was 7.6 and the optimal temperature was 30 °C. Our findings suggest a two-fold increase of DoxA activity via the NADH → FDR2 → FDX1 → DoxA pathway for the hydroxylation of the daunorubicin, and indicate that the usage of a native redox partner may increase daunorubicin-derived doxorubicin production due to the inclusion of DoxA. Copyright © 2015 Elsevier Inc. All rights reserved.

Analysis of 30 Genes (355 SNPS) Related to Energy Homeostasis for Association with Adiposity in European-American and Yup'ik Eskimo Populations

PubMed Central

Chung, Wendy K.; Patki, Amit; Matsuoka, Naoki; Boyer, Bert B.; Liu, Nianjun; Musani, Solomon K.; Goropashnaya, Anna V.; Tan, Perciliz L.; Katsanis, Nicholas; Johnson, Stephen B.; Gregersen, Peter K.; Allison, David B.; Leibel, Rudolph L.; Tiwari, Hemant K.

2009-01-01

Objective Human adiposity is highly heritable, but few of the genes that predispose to obesity in most humans are known. We tested candidate genes in pathways related to food intake and energy expenditure for association with measures of adiposity. Methods We studied 355 genetic variants in 30 candidate genes in 7 molecular pathways related to obesity in two groups of adult subjects: 1,982 unrelated European Americans living in the New York metropolitan area drawn from the extremes of their body mass index (BMI) distribution and 593 related Yup'ik Eskimos living in rural Alaska characterized for BMI, body composition, waist circumference, and skin fold thicknesses. Data were analyzed by using a mixed model in conjunction with a false discovery rate (FDR) procedure to correct for multiple testing. Results After correcting for multiple testing, two single nucleotide polymorphisms (SNPs) in Ghrelin (GHRL) (rs35682 and rs35683) were associated with BMI in the New York European Americans. This association was not replicated in the Yup'ik participants. There was no evidence for gene × gene interactions among genes within the same molecular pathway after adjusting for multiple testing via FDR control procedure. Conclusion Genetic variation in GHRL may have a modest impact on BMI in European Americans. PMID:19077438

Analysis of 30 genes (355 SNPS) related to energy homeostasis for association with adiposity in European-American and Yup'ik Eskimo populations.

PubMed

Chung, Wendy K; Patki, Amit; Matsuoka, Naoki; Boyer, Bert B; Liu, Nianjun; Musani, Solomon K; Goropashnaya, Anna V; Tan, Perciliz L; Katsanis, Nicholas; Johnson, Stephen B; Gregersen, Peter K; Allison, David B; Leibel, Rudolph L; Tiwari, Hemant K

2009-01-01

Human adiposity is highly heritable, but few of the genes that predispose to obesity in most humans are known. We tested candidate genes in pathways related to food intake and energy expenditure for association with measures of adiposity. We studied 355 genetic variants in 30 candidate genes in 7 molecular pathways related to obesity in two groups of adult subjects: 1,982 unrelated European Americans living in the New York metropolitan area drawn from the extremes of their body mass index (BMI) distribution and 593 related Yup'ik Eskimos living in rural Alaska characterized for BMI, body composition, waist circumference, and skin fold thicknesses. Data were analyzed by using a mixed model in conjunction with a false discovery rate (FDR) procedure to correct for multiple testing. After correcting for multiple testing, two single nucleotide polymorphisms (SNPs) in Ghrelin (GHRL) (rs35682 and rs35683) were associated with BMI in the New York European Americans. This association was not replicated in the Yup'ik participants. There was no evidence for gene x gene interactions among genes within the same molecular pathway after adjusting for multiple testing via FDR control procedure. Genetic variation in GHRL may have a modest impact on BMI in European Americans.

Evaluation of Second-Level Inference in fMRI Analysis

PubMed Central

Roels, Sanne P.; Loeys, Tom; Moerkerke, Beatrijs

2016-01-01

We investigate the impact of decisions in the second-level (i.e., over subjects) inferential process in functional magnetic resonance imaging on (1) the balance between false positives and false negatives and on (2) the data-analytical stability, both proxies for the reproducibility of results. Second-level analysis based on a mass univariate approach typically consists of 3 phases. First, one proceeds via a general linear model for a test image that consists of pooled information from different subjects. We evaluate models that take into account first-level (within-subjects) variability and models that do not take into account this variability. Second, one proceeds via inference based on parametrical assumptions or via permutation-based inference. Third, we evaluate 3 commonly used procedures to address the multiple testing problem: familywise error rate correction, False Discovery Rate (FDR) correction, and a two-step procedure with minimal cluster size. Based on a simulation study and real data we find that the two-step procedure with minimal cluster size results in most stable results, followed by the familywise error rate correction. The FDR results in most variable results, for both permutation-based inference and parametrical inference. Modeling the subject-specific variability yields a better balance between false positives and false negatives when using parametric inference. PMID:26819578

Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study.

PubMed

Zhao, Zhongming; Guo, An-Yuan; van den Oord, Edwin J C G; Aliev, Fazil; Jia, Peilin; Edenberg, Howard J; Riley, Brien P; Dick, Danielle M; Bettinger, Jill C; Davies, Andrew G; Grotewiel, Michael S; Schuckit, Marc A; Agrawal, Arpana; Kramer, John; Nurnberger, John I; Kendler, Kenneth S; Webb, Bradley T; Miles, Michael F

2012-01-01

A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation. In this study, we performed a unique multi-species evidence-based data integration using three microarray experiments in mice or humans that generated an initial alcohol dependence (AD) related genes list, human linkage and association results, and gene sets implicated in C. elegans and Drosophila. We then used permutation and false discovery rate (FDR) analyses on the genome-wide association studies (GWAS) dataset from the Collaborative Study on the Genetics of Alcoholism (COGA) to evaluate the ranking results and weighting matrices. We found one weighting score matrix could increase FDR based q-values for a list of 47 genes with a score greater than 2. Our follow up functional enrichment tests revealed these genes were primarily involved in brain responses to ethanol and neural adaptations occurring with alcoholism. These results, along with our experimental validation of specific genes in mice, C. elegans and Drosophila, suggest that a cross-species evidence-based approach is useful to identify candidate genes contributing to alcoholism.

Mechanical Component Diagnostic System

DTIC Science & Technology

1991-01-01

Control and Display Unit ( CADU ) executes the system software and controls data acquisition that is carried out by 6 the Data Acquisition Unit (DAU... CADU screen. Displays intended for the CD are also echoed on the CADU in the FDR backup mode. If initialization is successful, clocks are synchronized...and normal MCDS monitoring mode is entered. If there is no display on the CD, the user may manually switch to the backup CD display on the CADU . Hence

FDR's Fireside Chat on the Purposes and Foundations of the Recovery Program. The Constitution Community: The Great Depression and World War II (1929-1945).

ERIC Educational Resources Information Center

Clark, Linda Darus

When Franklin Delano Roosevelt was elected U.S. President in 1932, it was with the promise to restore U.S. confidence and to bring the country out of the Great Depression. After his election, Roosevelt formulated his New Deal policies to bring about relief from economic hardships. He created the National Recovery Administration (NRA) which had two…

Underbody Blast Models of TBI Caused by Hyper-Acceleration and Secondary Head Impact

DTIC Science & Technology

2016-02-01

discovery rate (FDR), which controls for the expected proportion of false rejected hypotheses. ANOVA was performed to evaluate the significance in gene...acceleration/deceleration11,27 and blast4,13 have also been designed for the purpose of evaluating coup-contrecoup and blast wave energies potentially... evaluation of different angles/ locations of the projectile impact to the surface of the rat head. Finally, pilot studies were conducted to provide further

A Brief Survey of Democracy Promotion in U.S. Foreign Policy

DTIC Science & Technology

2014-03-01

highlight that economic and security concerns both pre-dated active democracy promotion efforts. 2 For its first centennial , the United States was...the troubles of the world. The 1930s brought the Great Depression and the perception that democracy and capitalism might not be such good ideas after...peacetime foreign policy on democracy was somewhat constrained by the Great Depression and World War II. As World War II raged, FDR eloquently

Targeted Feature Detection for Data-Dependent Shotgun Proteomics

PubMed Central

2017-01-01

Label-free quantification of shotgun LC–MS/MS data is the prevailing approach in quantitative proteomics but remains computationally nontrivial. The central data analysis step is the detection of peptide-specific signal patterns, called features. Peptide quantification is facilitated by associating signal intensities in features with peptide sequences derived from MS2 spectra; however, missing values due to imperfect feature detection are a common problem. A feature detection approach that directly targets identified peptides (minimizing missing values) but also offers robustness against false-positive features (by assigning meaningful confidence scores) would thus be highly desirable. We developed a new feature detection algorithm within the OpenMS software framework, leveraging ideas and algorithms from the OpenSWATH toolset for DIA/SRM data analysis. Our software, FeatureFinderIdentification (“FFId”), implements a targeted approach to feature detection based on information from identified peptides. This information is encoded in an MS1 assay library, based on which ion chromatogram extraction and detection of feature candidates are carried out. Significantly, when analyzing data from experiments comprising multiple samples, our approach distinguishes between “internal” and “external” (inferred) peptide identifications (IDs) for each sample. On the basis of internal IDs, two sets of positive (true) and negative (decoy) feature candidates are defined. A support vector machine (SVM) classifier is then trained to discriminate between the sets and is subsequently applied to the “uncertain” feature candidates from external IDs, facilitating selection and confidence scoring of the best feature candidate for each peptide. This approach also enables our algorithm to estimate the false discovery rate (FDR) of the feature selection step. We validated FFId based on a public benchmark data set, comprising a yeast cell lysate spiked with protein standards that provide a known ground-truth. The algorithm reached almost complete (>99%) quantification coverage for the full set of peptides identified at 1% FDR (PSM level). Compared with other software solutions for label-free quantification, this is an outstanding result, which was achieved at competitive quantification accuracy and reproducibility across replicates. The FDR for the feature selection was estimated at a low 1.5% on average per sample (3% for features inferred from external peptide IDs). The FFId software is open-source and freely available as part of OpenMS (www.openms.org). PMID:28673088

A two-step hierarchical hypothesis set testing framework, with applications to gene expression data on ordered categories

PubMed Central

2014-01-01

Background In complex large-scale experiments, in addition to simultaneously considering a large number of features, multiple hypotheses are often being tested for each feature. This leads to a problem of multi-dimensional multiple testing. For example, in gene expression studies over ordered categories (such as time-course or dose-response experiments), interest is often in testing differential expression across several categories for each gene. In this paper, we consider a framework for testing multiple sets of hypothesis, which can be applied to a wide range of problems. Results We adopt the concept of the overall false discovery rate (OFDR) for controlling false discoveries on the hypothesis set level. Based on an existing procedure for identifying differentially expressed gene sets, we discuss a general two-step hierarchical hypothesis set testing procedure, which controls the overall false discovery rate under independence across hypothesis sets. In addition, we discuss the concept of the mixed-directional false discovery rate (mdFDR), and extend the general procedure to enable directional decisions for two-sided alternatives. We applied the framework to the case of microarray time-course/dose-response experiments, and proposed three procedures for testing differential expression and making multiple directional decisions for each gene. Simulation studies confirm the control of the OFDR and mdFDR by the proposed procedures under independence and positive correlations across genes. Simulation results also show that two of our new procedures achieve higher power than previous methods. Finally, the proposed methodology is applied to a microarray dose-response study, to identify 17 β-estradiol sensitive genes in breast cancer cells that are induced at low concentrations. Conclusions The framework we discuss provides a platform for multiple testing procedures covering situations involving two (or potentially more) sources of multiplicity. The framework is easy to use and adaptable to various practical settings that frequently occur in large-scale experiments. Procedures generated from the framework are shown to maintain control of the OFDR and mdFDR, quantities that are especially relevant in the case of multiple hypothesis set testing. The procedures work well in both simulations and real datasets, and are shown to have better power than existing methods. PMID:24731138

Altered resting brain connectivity in persistent cancer related fatigue

PubMed Central

Hampson, Johnson P.; Zick, Suzanna M.; Khabir, Tohfa; Wright, Benjamin D.; Harris, Richard E.

2015-01-01

There is an estimated 3 million women in the US living as breast cancer survivors and persistent cancer related fatigue (PCRF) disrupts the lives of an estimated 30% of these women. PCRF is associated with decreased quality of life, decreased sleep quality, impaired cognition and depression. The mechanisms of cancer related fatigue are not well understood; however, preliminary findings indicate dysfunctional activity in the brain as a potential factor. Here we investigate the relationship between PCRF on intrinsic resting state connectivity in this population. Twenty-three age matched breast cancer survivors (15 fatigued and 8 non-fatigued) who completed all cancer-related treatments at least 12 weeks prior to the study, were recruited to undergo functional connectivity magnetic resonance imaging (fcMRI). Intrinsic resting state networks were examined with both seed based and independent component analysis methods. Comparisons of brain connectivity patterns between groups as well as correlations with self-reported fatigue symptoms were performed. Fatigued patients displayed greater left inferior parietal lobule to superior frontal gyrus connectivity as compared to non-fatigued patients (P < 0.05 FDR corrected). This enhanced connectivity was associated with increased physical fatigue (P = 0.04, r = 0.52) and poor sleep quality (P = 0.04, r = 0.52) in the fatigued group. In contrast greater connectivity in the non-fatigued group was found between the right precuneus to the periaqueductal gray as well as the left IPL to subgenual cortex (P < 0.05 FDR corrected). Mental fatigue scores were associated with greater default mode network (DMN) connectivity to the superior frontal gyrus (P = 0.05 FDR corrected) among fatigued subjects (r = 0.82) and less connectivity in the non-fatigued group (r = −0.88). These findings indicate that there is enhanced intrinsic DMN connectivity to the frontal gyrus in breast cancer survivors with persistent fatigue. As the DMN is a network involved in self-referential thinking we speculate that enhanced connectivity between the DMN and the frontal gyrus may be related to mental fatigue and poor sleep quality. In contrast, enhanced connectivity between the DMN and regions in the subgenual cingulate and brainstem may serve a protective function in the non-fatigued group. PMID:26106555

Calibration of a geophysically based model using soil moisture measurements in mountainous terrains

NASA Astrophysics Data System (ADS)

Pellet, Cécile; Hilbich, Christin; Marmy, Antoine; Hauck, Christian

2016-04-01

The use of geophysical methods in the field of permafrost research is well established and crucial since it is the only way to infer the composition of the subsurface material. Since geophysical measurements are indirect, ambiguities in the interpretation of the results can arise, hence the simultaneous use of several methods (e.g. electrical resistivity tomography and refraction seismics) is often necessary. The so-called four-phase model, 4PM (Hauck et al., 2011) constitutes a further step towards clarification of interpretation from geophysical measurements. It uses two well-known petrophysical relationships, namely Archie's law and an extension of Timur's time-averaged equation for seismic P-wave velocities, to quantitatively estimate the different phase contents (air, water and ice) in the ground from tomographic electric and seismic measurements. In this study, soil moisture measurements were used to calibrate the 4PM in order to assess the spatial distribution of water, ice and air content in the ground at three high elevation sites with different ground properties and thermal regimes. The datasets used here were collected as part of the SNF-project SOMOMOUNT. Within the framework of this project a network of six entirely automated soil moisture stations was installed in Switzerland along an altitudinal gradient ranging from 1'200 m. a.s.l. to 3'400 m. a.s.l. The standard instrumentation of each station comprises the installation of Frequency Domain Reflectometry (FDR) and Time Domain Reflectometry (TDR) sensors for long term monitoring coupled with repeated Electrical Resistivity Tomography (ERT) and Refraction Seismic Tomography (RST) as well as spatial FDR (S-FDR) measurements. The use of spatially distributed soil moisture data significantly improved the 4PM calibration process and a semi-automatic calibration scheme was developed. This procedure was then tested at three different locations, yielding satisfactory two dimensional distributions of water-, ice- and air content (Pellet et al., 2016). REFERENCES Hauck, C., Böttcher, M., & Maurer, H. 2011: A new model for estimating subsurface ice content based on combined electrical and seismic data sets, The Cryosphere, 5(2), 453-468. Pellet, C., Hilbich, C., Marmy, A., & Hauck, C. 2016: Soil moisture data for the validation of permafrost models using direct and indirect measurement approaches at three alpine sites, Front. Earth Sci., 3(91).

Altered resting brain connectivity in persistent cancer related fatigue.

PubMed

Hampson, Johnson P; Zick, Suzanna M; Khabir, Tohfa; Wright, Benjamin D; Harris, Richard E

2015-01-01

There is an estimated 3 million women in the US living as breast cancer survivors and persistent cancer related fatigue (PCRF) disrupts the lives of an estimated 30% of these women. PCRF is associated with decreased quality of life, decreased sleep quality, impaired cognition and depression. The mechanisms of cancer related fatigue are not well understood; however, preliminary findings indicate dysfunctional activity in the brain as a potential factor. Here we investigate the relationship between PCRF on intrinsic resting state connectivity in this population. Twenty-three age matched breast cancer survivors (15 fatigued and 8 non-fatigued) who completed all cancer-related treatments at least 12 weeks prior to the study, were recruited to undergo functional connectivity magnetic resonance imaging (fcMRI). Intrinsic resting state networks were examined with both seed based and independent component analysis methods. Comparisons of brain connectivity patterns between groups as well as correlations with self-reported fatigue symptoms were performed. Fatigued patients displayed greater left inferior parietal lobule to superior frontal gyrus connectivity as compared to non-fatigued patients (P < 0.05 FDR corrected). This enhanced connectivity was associated with increased physical fatigue (P = 0.04, r = 0.52) and poor sleep quality (P = 0.04, r = 0.52) in the fatigued group. In contrast greater connectivity in the non-fatigued group was found between the right precuneus to the periaqueductal gray as well as the left IPL to subgenual cortex (P < 0.05 FDR corrected). Mental fatigue scores were associated with greater default mode network (DMN) connectivity to the superior frontal gyrus (P = 0.05 FDR corrected) among fatigued subjects (r = 0.82) and less connectivity in the non-fatigued group (r = -0.88). These findings indicate that there is enhanced intrinsic DMN connectivity to the frontal gyrus in breast cancer survivors with persistent fatigue. As the DMN is a network involved in self-referential thinking we speculate that enhanced connectivity between the DMN and the frontal gyrus may be related to mental fatigue and poor sleep quality. In contrast, enhanced connectivity between the DMN and regions in the subgenual cingulate and brainstem may serve a protective function in the non-fatigued group.

Using multifractal analysis of ultra-weak photon emission from germinating wheat seedlings to differentiate between two grades of intoxication with potassium dichromate

NASA Astrophysics Data System (ADS)

Scholkmann, Felix; Cifra, Michal; Alexandre Moraes, Thiago; de Mello Gallep, Cristiano

2011-12-01

The aim of the present study was to test whether the multifractal properties of ultra-weak photon emission (UPE) from germinating wheat seedlings (Triticum aestivum) change when the seedlings are treated with different concentrations of the toxin potassium dichromate (PD). To this end, UPE was measured (50 seedlings in one Petri dish, duration: approx. 16.6- 28 h) from samples of three groups: (i) control (group C, N = 9), (ii) treated with 25 ppm of PD (group G25, N = 32), and (iii) treated with 150 ppm of PD (group G150, N = 23). For the multifractal analysis, the following steps where performed: (i) each UPE time series was trimmed to a final length of 1000 min; (ii) each UPE time series was filtered, linear detrended and normalized; (iii) the multifractal spectrum (f(α)) was calculated for every UPE time series using the backward multifractal detrended moving average (MFDMA) method; (iv) each multifractal spectrum was characterized by calculating the mode (αmode) of the spectrum and the degree of multifractality (Δα) (v) for every UPE time series its mean, skewness and kurtosis were also calculated; finally (vi) all obtained parameters where analyzed to determine their ability to differentiate between the three groups. This was based on Fisher's discriminant ratio (FDR), which was calculated for each parameter combination. Additionally, a non-parametric test was used to test whether the parameter values are significantly different or not. The analysis showed that when comparing all the three groups, FDR had the highest values for the multifractal parameters (αmode, Δα). Furthermore, the differences in these parameters between the groups were statistically significant (p < 0.05). The classical parameters (mean, skewness and kurtosis) had lower FDR values than the multifractal parameters in all cases and showed no significant difference between the groups (except for the skewness between group C and G150). In conclusion, multifractal analysis enables changes in UPE time series to be detected even when they are hidden for normal linear signal analysis methods. The analysis of changes in the multifractal properties might be a basis to design a classification system enabling the intoxication of cell cultures to be quantified based on UPE measurements.

A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification.

PubMed

Tu, Chengjian; Shen, Shichen; Sheng, Quanhu; Shyr, Yu; Qu, Jun

2017-01-30

Reliable quantification of low-abundance proteins in complex proteomes is challenging largely owing to the limited number of spectra/peptides identified. In this study we developed a straightforward method to improve the quantitative accuracy and precision of proteins by strategically retrieving the less confident peptides that were previously filtered out using the standard target-decoy search strategy. The filtered-out MS/MS spectra matched to confidently-identified proteins were recovered, and the peptide-spectrum-match FDR were re-calculated and controlled at a confident level of FDR≤1%, while protein FDR maintained at ~1%. We evaluated the performance of this strategy in both spectral count- and ion current-based methods. >60% increase of total quantified spectra/peptides was respectively achieved for analyzing a spike-in sample set and a public dataset from CPTAC. Incorporating the peptide retrieval strategy significantly improved the quantitative accuracy and precision, especially for low-abundance proteins (e.g. one-hit proteins). Moreover, the capacity of confidently discovering significantly-altered proteins was also enhanced substantially, as demonstrated with two spike-in datasets. In summary, improved quantitative performance was achieved by this peptide recovery strategy without compromising confidence of protein identification, which can be readily implemented in a broad range of quantitative proteomics techniques including label-free or labeling approaches. We hypothesize that more quantifiable spectra and peptides in a protein, even including less confident peptides, could help reduce variations and improve protein quantification. Hence the peptide retrieval strategy was developed and evaluated in two spike-in sample sets with different LC-MS/MS variations using both MS1- and MS2-based quantitative approach. The list of confidently identified proteins using the standard target-decoy search strategy was fixed and more spectra/peptides with less confidence matched to confident proteins were retrieved. However, the total peptide-spectrum-match false discovery rate (PSM FDR) after retrieval analysis was still controlled at a confident level of FDR≤1%. As expected, the penalty for occasionally incorporating incorrect peptide identifications is negligible by comparison with the improvements in quantitative performance. More quantifiable peptides, lower missing value rate, better quantitative accuracy and precision were significantly achieved for the same protein identifications by this simple strategy. This strategy is theoretically applicable for any quantitative approaches in proteomics and thereby provides more quantitative information, especially on low-abundance proteins. Published by Elsevier B.V.

EDITORIAL: The FDR Prize The FDR Prize

NASA Astrophysics Data System (ADS)

Kida, Shigeo

2009-06-01

From the 45 papers published in the year 2008 in Fluid Dynamics Research the following paper has been selected for the second FDR prize: 'Propagation of very long water waves, with vorticity, over variable depth, with applications to tsunamis' by Adrian Constantin and Robin S Johnson, published in volume 40 (March 2008) pp 175-211. This paper takes, as its main theme, the analysis of the propagation of very long gravity waves in the ocean environment, with the possibility of applying the results to tsunamis. Both variable depth and some pre-existing vorticity are allowed in the model, but under the over-arching assumption of long waves; indeed, it is argued, the waves are so long that it is impossible for classical soliton theory to be the appropriate description of a developing tsunami. This aspect is supported by some simple scaling arguments, together with some observations associated with the tsunami of Boxing Day 2004. The formulation is based on two small scales: the slow scale on which the depth varies and the small amplitude of the wave (as initially generated in deep water). The technique adopted is that of matched asymptotic expansions. The solution, constructed for deep water, is not valid in suitably reduced depth of water; the solution in this shallow region (close inshore) is then matched to the deep-water solution. A novel feature of this work is the inclusion of a general distribution of vorticity in the absence of waves—intended to model the realistic ocean—which is based on the slow evolution scale for the bottom topography. Some general properties of such background flows are proved, and two specific examples have been obtained: constant vorticity everywhere (as far as the shoreline), and regions of isolated vorticity (for appropriate bottom profiles). The way in which the wave properties are modified in the presence of vorticity is described. The significant overall proposal in this theory, specifically applicable to tsunamis, is that it is the profile of the initial disturbance (generated by the seismic activity) that is the single most important ingredient in the formation of tsunami waves (provided, of course, the familiar requirement of a long, gently shelving beach is also present). This contention is described and developed, and supported by some graphical examples of the various types of solution that can be obtained; these include contributions from variable depth and suitable background vorticity.

A novel multidimensional protein identification technology approach combining protein size exclusion prefractionation, peptide zwitterion-ion hydrophilic interaction chromatography, and nano-ultraperformance RP chromatography/nESI-MS2 for the in-depth analysis of the serum proteome and phosphoproteome: application to clinical sera derived from humans with benign prostate hyperplasia.

PubMed

Garbis, Spiros D; Roumeliotis, Theodoros I; Tyritzis, Stavros I; Zorpas, Kostas M; Pavlakis, Kitty; Constantinides, Constantinos A

2011-02-01

The current proof-of-principle study was aimed toward development of a novel multidimensional protein identification technology (MudPIT) approach for the in-depth proteome analysis of human serum derived from patients with benign prostate hyperplasia (BPH) using rational chromatographic design principles. This study constituted an extension of our published work relating to the identification and relative quantification of potential clinical biomarkers in BPH and prostate cancer (PCa) tissue specimens. The proposed MudPIT approach encompassed the use of three distinct yet complementary liquid chromatographic chemistries. High-pressure size-exclusion chromatography (SEC) was used for the prefractionation of serum proteins followed by their dialysis exchange and solution phase trypsin proteolysis. The tryptic peptides were then subjected to offline zwitterion-ion hydrophilic interaction chromatography (ZIC-HILIC) fractionation followed by their online analysis with reversed-phase nano-ultraperformance chromatography (RP-nUPLC) hyphenated to nanoelectrospray ionization-tandem mass spectrometry using an ion trap mass analyzer. For the spectral processing, the sequential use of the SpectrumMill, Scaffold, and InsPecT software tools was applied for the tryptic peptide product ion MS(2) spectral processing, false discovery rate (FDR) assessment, validation, and protein identification. This milestone serum analysis study allowed the confident identification of over 1955 proteins (p ≤ 0.05; FDR ≤ 5%) with a broad spectrum of biological and physicochemical properties including secreted, tissue-specific proteins spanning approximately 12 orders of magnitude as they occur in their native abundance levels in the serum matrix. Also encompassed in this proteome was the confident identification of 375 phosphoproteins (p ≤ 0.05; FDR ≤ 5%) with potential importance to cancer biology. To demonstrate the performance characteristics of this novel MudPIT approach, a comparison was made with the proteomes resulting from the immunodepletion of the high abundant albumin and IgG proteins with offline first dimensional tryptic peptide separation with both ZIC-HILIC and strong cation exchange (SCX) chromatography and their subsequent online RP-nUPLC-nESI-MS(2) analysis.

Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate.

PubMed

Buschmann, Tilo; Zhang, Rong; Brash, Douglas E; Bystrykh, Leonid V

2014-08-07

DNA barcodes are short unique sequences used to label DNA or RNA-derived samples in multiplexed deep sequencing experiments. During the demultiplexing step, barcodes must be detected and their position identified. In some cases (e.g., with PacBio SMRT), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives.For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements. In our analysis, barcode sequences showed high rates of coincidental similarities with the Mus musculus reference DNA. This problem became more acute when the length of the barcode sequence decreased and the number of barcodes in the set increased. The method presented in this paper controls the tail area-based false discovery rate to distinguish between barcoded and unbarcoded reads. This method helps to establish the highest acceptable minimal distance between reads and barcode sequences. In a proof of concept experiment we correctly detected barcodes in 83% of the reads with a precision of 89%. Sensitivity improved to 99% at 99% precision when the adjacent primer sequence was incorporated in the analysis. The analysis was further improved using a paired end strategy. Following an analysis of the data for sequence variants induced in the Atp1a1 gene of C57BL/6 murine melanocytes by ultraviolet light and conferring resistance to ouabain, we found no evidence of cross-contamination of DNA material between samples. Our method offers a proper quantitative treatment of the problem of detecting barcoded reads in a noisy sequencing environment. It is based on the false discovery rate statistics that allows a proper trade-off between sensitivity and precision to be chosen.

Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene

PubMed Central

2010-01-01

Background DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map indicated that the DIP-locus lacks suppression of recombination, which is unique among all other map-based cloning efforts of apomeiosis to date. FDR as well as apomixis as a whole are of interest in plant breeding, allowing for polyploidization and fixation of hybrid vigor, respectively. No dominant FDR or apomixis genes have yet been isolated. Here, we zoom-in to the DIP-locus by largely extending our initial mapping population, and by analyzing (local) suppression of recombination and allele sequence divergence (ASD). Results We identified 24 recombinants between two most closely linked molecular markers to DIP in an F1-population of 2227 plants that segregates for diplospory and lacks parthenogenesis. Both markers segregated c. 1:1 in the entire population, indicating a 1:1 segregation rate of diplospory. Fine-mapping showed three amplified fragment length polymorphisms (AFLPs) closest to DIP at 0.2 cM at one flank and a single AFLP at 0.4 cM at the other flank. Our data lacked strong evidence for ASD at marker regions close to DIP. An unexpected bias towards diplosporous plants among the recombinants (20 out of 24) was found. One third of these diplosporous recombinants showed incomplete penetrance of 50-85% diplospory. Conclusions Our data give interesting new insights into the structure of the diplospory locus in Taraxacum. We postulate a locus with a minimum of two DIP-genes and possibly including one or two enhancers or cis-regulatory elements on the basis of the bias towards diplosporous recombinants and incomplete penetrance of diplospory in some of them. We define the DIP-locus to 0.6 cM, which is estimated to cover ~200-300 Kb, with the closest marker at 0.2 cM. Our results confirm the minor role of suppression of recombination and ASD around DIP, making it an excellent candidate to isolate via a chromosome-walking approach. PMID:20659311

Genetic fine-mapping of DIPLOSPOROUS in Taraxacum (dandelion; Asteraceae) indicates a duplicated DIP-gene.

PubMed

Vijverberg, Kitty; Milanovic-Ivanovic, Slavica; Bakx-Schotman, Tanja; van Dijk, Peter J

2010-07-26

DIPLOSPOROUS (DIP) is the locus for diplospory in Taraxacum, associated to unreduced female gamete formation in apomicts. Apomicts reproduce clonally through seeds, including apomeiosis, parthenogenesis, and autonomous or pseudogamous endosperm formation. In Taraxacum, diplospory results in first division restitution (FDR) nuclei, and inherits as a dominant, monogenic trait, independent from the other apomixis elements. A preliminary genetic linkage map indicated that the DIP-locus lacks suppression of recombination, which is unique among all other map-based cloning efforts of apomeiosis to date. FDR as well as apomixis as a whole are of interest in plant breeding, allowing for polyploidization and fixation of hybrid vigor, respectively. No dominant FDR or apomixis genes have yet been isolated. Here, we zoom-in to the DIP-locus by largely extending our initial mapping population, and by analyzing (local) suppression of recombination and allele sequence divergence (ASD). We identified 24 recombinants between two most closely linked molecular markers to DIP in an F1-population of 2227 plants that segregates for diplospory and lacks parthenogenesis. Both markers segregated c. 1:1 in the entire population, indicating a 1:1 segregation rate of diplospory. Fine-mapping showed three amplified fragment length polymorphisms (AFLPs) closest to DIP at 0.2 cM at one flank and a single AFLP at 0.4 cM at the other flank. Our data lacked strong evidence for ASD at marker regions close to DIP. An unexpected bias towards diplosporous plants among the recombinants (20 out of 24) was found. One third of these diplosporous recombinants showed incomplete penetrance of 50-85% diplospory. Our data give interesting new insights into the structure of the diplospory locus in Taraxacum. We postulate a locus with a minimum of two DIP-genes and possibly including one or two enhancers or cis-regulatory elements on the basis of the bias towards diplosporous recombinants and incomplete penetrance of diplospory in some of them. We define the DIP-locus to 0.6 cM, which is estimated to cover approximately 200-300 Kb, with the closest marker at 0.2 cM. Our results confirm the minor role of suppression of recombination and ASD around DIP, making it an excellent candidate to isolate via a chromosome-walking approach.

Targeted Feature Detection for Data-Dependent Shotgun Proteomics.

PubMed

Weisser, Hendrik; Choudhary, Jyoti S

2017-08-04

Label-free quantification of shotgun LC-MS/MS data is the prevailing approach in quantitative proteomics but remains computationally nontrivial. The central data analysis step is the detection of peptide-specific signal patterns, called features. Peptide quantification is facilitated by associating signal intensities in features with peptide sequences derived from MS2 spectra; however, missing values due to imperfect feature detection are a common problem. A feature detection approach that directly targets identified peptides (minimizing missing values) but also offers robustness against false-positive features (by assigning meaningful confidence scores) would thus be highly desirable. We developed a new feature detection algorithm within the OpenMS software framework, leveraging ideas and algorithms from the OpenSWATH toolset for DIA/SRM data analysis. Our software, FeatureFinderIdentification ("FFId"), implements a targeted approach to feature detection based on information from identified peptides. This information is encoded in an MS1 assay library, based on which ion chromatogram extraction and detection of feature candidates are carried out. Significantly, when analyzing data from experiments comprising multiple samples, our approach distinguishes between "internal" and "external" (inferred) peptide identifications (IDs) for each sample. On the basis of internal IDs, two sets of positive (true) and negative (decoy) feature candidates are defined. A support vector machine (SVM) classifier is then trained to discriminate between the sets and is subsequently applied to the "uncertain" feature candidates from external IDs, facilitating selection and confidence scoring of the best feature candidate for each peptide. This approach also enables our algorithm to estimate the false discovery rate (FDR) of the feature selection step. We validated FFId based on a public benchmark data set, comprising a yeast cell lysate spiked with protein standards that provide a known ground-truth. The algorithm reached almost complete (>99%) quantification coverage for the full set of peptides identified at 1% FDR (PSM level). Compared with other software solutions for label-free quantification, this is an outstanding result, which was achieved at competitive quantification accuracy and reproducibility across replicates. The FDR for the feature selection was estimated at a low 1.5% on average per sample (3% for features inferred from external peptide IDs). The FFId software is open-source and freely available as part of OpenMS ( www.openms.org ).

Carbon Fiber TOW Angle Determination Using Microwave Reflectometry

NASA Technical Reports Server (NTRS)

Wilson, William C.; Moore, Jason P.; Juarez, Peter D.

2016-01-01

NASA's Advanced Composites Project is investigating technologies that increase automated remote inspection of aircraft composite structures. Therefore, microwave Frequency Domain Reflectometry (FDR) is being investigated as a method of enabling rapid remote inspection of angular orientation of the tow using microwave radiation. This work will present preliminary data demonstrating that frequency shifts in the reflection spectrum of a carbon fiber tow sample are indicative of the angle of the tow with respect to an interrogating antenna's linear polarized output.

Insurgency and Counterinsurgency in Central America

DTIC Science & Technology

1983-06-01

broadly based. In Guatemala, the revolution is at a different stage, and in Honduras, it is an embryo , although the condition? "üJ" ’"MwMfc Jh...who declared "The people of this continent alone have, the right to decide their own destiny ," and by President Theodore Roosevelt in 1904 when he...becoming an embryo government-in-exile. Although in many respects an international propaganda organization, the FDR does have one Important body--the

Laboratory Performance of Five Selected Soil Moisture Sensors Applying Factory and Own Calibration Equations for Two Soil Media of Different Bulk Density and Salinity Levels.

PubMed

Matula, Svatopluk; Báťková, Kamila; Legese, Wossenu Lemma

2016-11-15

Non-destructive soil water content determination is a fundamental component for many agricultural and environmental applications. The accuracy and costs of the sensors define the measurement scheme and the ability to fit the natural heterogeneous conditions. The aim of this study was to evaluate five commercially available and relatively cheap sensors usually grouped with impedance and FDR sensors. ThetaProbe ML2x (impedance) and ECH₂O EC-10, ECH₂O EC-20, ECH₂O EC-5, and ECH₂O TE (all FDR) were tested on silica sand and loess of defined characteristics under controlled laboratory conditions. The calibrations were carried out in nine consecutive soil water contents from dry to saturated conditions (pure water and saline water). The gravimetric method was used as a reference method for the statistical evaluation (ANOVA with significance level 0.05). Generally, the results showed that our own calibrations led to more accurate soil moisture estimates. Variance component analysis arranged the factors contributing to the total variation as follows: calibration (contributed 42%), sensor type (contributed 29%), material (contributed 18%), and dry bulk density (contributed 11%). All the tested sensors performed very well within the whole range of water content, especially the sensors ECH₂O EC-5 and ECH₂O TE, which also performed surprisingly well in saline conditions.

Laboratory Performance of Five Selected Soil Moisture Sensors Applying Factory and Own Calibration Equations for Two Soil Media of Different Bulk Density and Salinity Levels

PubMed Central

Matula, Svatopluk; Báťková, Kamila; Legese, Wossenu Lemma

2016-01-01

Non-destructive soil water content determination is a fundamental component for many agricultural and environmental applications. The accuracy and costs of the sensors define the measurement scheme and the ability to fit the natural heterogeneous conditions. The aim of this study was to evaluate five commercially available and relatively cheap sensors usually grouped with impedance and FDR sensors. ThetaProbe ML2x (impedance) and ECH2O EC-10, ECH2O EC-20, ECH2O EC-5, and ECH2O TE (all FDR) were tested on silica sand and loess of defined characteristics under controlled laboratory conditions. The calibrations were carried out in nine consecutive soil water contents from dry to saturated conditions (pure water and saline water). The gravimetric method was used as a reference method for the statistical evaluation (ANOVA with significance level 0.05). Generally, the results showed that our own calibrations led to more accurate soil moisture estimates. Variance component analysis arranged the factors contributing to the total variation as follows: calibration (contributed 42%), sensor type (contributed 29%), material (contributed 18%), and dry bulk density (contributed 11%). All the tested sensors performed very well within the whole range of water content, especially the sensors ECH2O EC-5 and ECH2O TE, which also performed surprisingly well in saline conditions. PMID:27854263

Mining Missing Membrane Proteins by High-pH Reverse Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry

PubMed Central

Kitata, Reta Birhanu; Dimayacyac-Esleta, Baby Rorielyn T.; Choong, Wai-Kok; Tsai, Chia-Feng; Lin, Tai-Du; Tsou, Chih-Chiang; Weng, Shao-Hsing; Chen, Yi-Ju; Yang, Pan-Chyr; Arco, Susan D.; Nesvizhskii, Alexey I.; Sung, Ting-Yi; Chen, Yu-Ju

2016-01-01

Despite significant efforts in the past decade towards complete mapping of the human proteome, 3564 proteins (neXtProt, 09-2014) are still “missing proteins”. Over one-third of these missing proteins are annotated as membrane proteins, owing to their relatively challenging accessibility with standard shotgun proteomics. Using non-small cell lung cancer (NSCLC) as a model study, we aim to mine missing proteins from disease-associated membrane proteome, which may be still largely under-represented. To increase identification coverage, we employed Hp-RP StageTip pre-fractionation of membrane-enriched samples from 11 NSCLC cell lines. Analysis of membrane samples from 20 pairs of tumor and adjacent normal lung tissue were incorporated to include physiologically expressed membrane proteins. Using multiple search engines (X!Tandem, Comet and Mascot) and stringent evaluation of FDR (MAYU and PeptideShaker), we identified 7702 proteins (66% membrane proteins) and 178 missing proteins (74 membrane proteins) with PSM-, peptide-, and protein-level FDR of 1%. Through multiple reaction monitoring (MRM) using synthetic peptides, we provided additional evidences for 8 missing proteins including 7 with transmembrane helix domains (TMH). This study demonstrates that mining missing proteins focused on cancer membrane sub-proteome can greatly contribute to map the whole human proteome. All data were deposited into ProteomeXchange with the identifier PXD002224. PMID:26202522

ProteinInferencer: Confident protein identification and multiple experiment comparison for large scale proteomics projects.

PubMed

Zhang, Yaoyang; Xu, Tao; Shan, Bing; Hart, Jonathan; Aslanian, Aaron; Han, Xuemei; Zong, Nobel; Li, Haomin; Choi, Howard; Wang, Dong; Acharya, Lipi; Du, Lisa; Vogt, Peter K; Ping, Peipei; Yates, John R

2015-11-03

Shotgun proteomics generates valuable information from large-scale and target protein characterizations, including protein expression, protein quantification, protein post-translational modifications (PTMs), protein localization, and protein-protein interactions. Typically, peptides derived from proteolytic digestion, rather than intact proteins, are analyzed by mass spectrometers because peptides are more readily separated, ionized and fragmented. The amino acid sequences of peptides can be interpreted by matching the observed tandem mass spectra to theoretical spectra derived from a protein sequence database. Identified peptides serve as surrogates for their proteins and are often used to establish what proteins were present in the original mixture and to quantify protein abundance. Two major issues exist for assigning peptides to their originating protein. The first issue is maintaining a desired false discovery rate (FDR) when comparing or combining multiple large datasets generated by shotgun analysis and the second issue is properly assigning peptides to proteins when homologous proteins are present in the database. Herein we demonstrate a new computational tool, ProteinInferencer, which can be used for protein inference with both small- or large-scale data sets to produce a well-controlled protein FDR. In addition, ProteinInferencer introduces confidence scoring for individual proteins, which makes protein identifications evaluable. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015. Published by Elsevier B.V.

Genome-Wide Meta-Analysis of Longitudinal Alcohol Consumption Across Youth and Early Adulthood.

PubMed

Adkins, Daniel E; Clark, Shaunna L; Copeland, William E; Kennedy, Martin; Conway, Kevin; Angold, Adrian; Maes, Hermine; Liu, Youfang; Kumar, Gaurav; Erkanli, Alaattin; Patkar, Ashwin A; Silberg, Judy; Brown, Tyson H; Fergusson, David M; Horwood, L John; Eaves, Lindon; van den Oord, Edwin J C G; Sullivan, Patrick F; Costello, E J

2015-08-01

The public health burden of alcohol is unevenly distributed across the life course, with levels of use, abuse, and dependence increasing across adolescence and peaking in early adulthood. Here, we leverage this temporal patterning to search for common genetic variants predicting developmental trajectories of alcohol consumption. Comparable psychiatric evaluations measuring alcohol consumption were collected in three longitudinal community samples (N=2,126, obs=12,166). Consumption-repeated measurements spanning adolescence and early adulthood were analyzed using linear mixed models, estimating individual consumption trajectories, which were then tested for association with Illumina 660W-Quad genotype data (866,099 SNPs after imputation and QC). Association results were combined across samples using standard meta-analysis methods. Four meta-analysis associations satisfied our pre-determined genome-wide significance criterion (FDR<0.1) and six others met our 'suggestive' criterion (FDR<0.2). Genome-wide significant associations were highly biological plausible, including associations within GABA transporter 1, SLC6A1 (solute carrier family 6, member 1), and exonic hits in LOC100129340 (mitofusin-1-like). Pathway analyses elaborated single marker results, indicating significant enriched associations to intuitive biological mechanisms, including neurotransmission, xenobiotic pharmacodynamics, and nuclear hormone receptors (NHR). These findings underscore the value of combining longitudinal behavioral data and genome-wide genotype information in order to study developmental patterns and improve statistical power in genomic studies.

Characterization of Visceral and Subcutaneous Adipose Tissue Transcriptome and Biological Pathways in Pregnant and Non-Pregnant Women: Evidence for Pregnancy-Related Regional-Specific Differences in Adipose Tissue

PubMed Central

Mazaki-Tovi, Shali; Vaisbuch, Edi; Tarca, Adi L.; Kusanovic, Juan Pedro; Than, Nandor Gabor; Chaiworapongsa, Tinnakorn; Dong, Zhong; Hassan, Sonia S.; Romero, Roberto

2015-01-01

Objective The purpose of this study was to compare the transcriptome of visceral and subcutaneous adipose tissues between pregnant and non-pregnant women. Study Design The transcriptome of paired visceral and abdominal subcutaneous adipose tissues from pregnant women at term and matched non-pregnant women (n = 11) was profiled with the Affymetrix Human Exon 1.0 ST array. Differential expression of selected genes was validated with the use of quantitative reverse transcription–polymerase chain reaction. Results Six hundred forty-four transcripts from 633 known genes were differentially expressed (false discovery rate (FDR) <0.1; fold-change >1.5), while 42 exons from 36 genes showed differential usage (difference in FIRMA scores >2 and FDR<0.1) between the visceral and subcutaneous fat of pregnant women. Fifty-six known genes were differentially expressed between pregnant and non-pregnant subcutaneous fat and three genes in the visceral fat. Enriched biological processes in the subcutaneous adipose tissue of pregnant women were mostly related to inflammation. Conclusion The transcriptome of visceral and subcutaneous fat depots reveals pregnancy-related gene expression and splicing differences in both visceral and subcutaneous adipose tissue. Furthermore, for the first time, alternative splicing in adipose tissue has been associated with regional differences and human parturition. PMID:26636677

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

DOE PAGES

Orellana, Luis H.; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

2016-10-07

Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific, most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles andmore » related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N 2O, to inert N 2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes.« less

Brain structure in schizophrenia vs. psychotic bipolar I disorder: A VBM study.

PubMed

Nenadic, Igor; Maitra, Raka; Langbein, Kerstin; Dietzek, Maren; Lorenz, Carsten; Smesny, Stefan; Reichenbach, Jürgen R; Sauer, Heinrich; Gaser, Christian

2015-07-01

While schizophrenia and bipolar disorder have been assumed to share phenotypic and genotypic features, there is also evidence for overlapping brain structural correlates, although it is unclear whether these relate to shared psychotic features. In this study, we used voxel-based morphometry (VBM8) in 34 schizophrenia patients, 17 euthymic bipolar I disorder patients (with a history of psychotic symptoms), and 34 healthy controls. Our results indicate that compared to healthy controls schizophrenia patients show grey matter deficits (p<0.05, FDR corrected) in medial and right dorsolateral prefrontal, as well as bilaterally in ventrolateral prefrontal and insular cortical areas, thalamus (bilaterally), left superior temporal cortex, and minor medial parietal and parietooccipital areas. Comparing schizophrenia vs. bipolar I patients (p<0.05, FDR corrected) yielded a similar pattern, however, there was an additional significant reduction in schizophrenia patients in the (posterior) hippocampus bilaterally, left dorsolateral prefrontal cortex, and left cerebellum. Compared to healthy controls, the deficits in bipolar I patients only reached significance at p<0.001 (uncorr.) for a minor parietal cluster, but not for prefrontal areas. Our results suggest that the more extensive prefrontal, thalamic, and hippocampal deficits that might set apart schizophrenia and bipolar disorder might not be related to mere appearance of psychotic symptoms at some stage of the disorders. Copyright © 2015 Elsevier B.V. All rights reserved.

Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shen, Yufeng; Tolic, Nikola; Purvine, Samuel O.

2011-11-07

The peptidome (i.e. processed and degraded forms of proteins) of e.g. blood can potentially provide insights into disease processes, as well as a source of candidate biomarkers that are unobtainable using conventional bottom-up proteomics approaches. MS dissociation methods, including CID, HCD, and ETD, can each contribute distinct identifications using conventional peptide identification methods (Shen et al. J. Proteome Res. 2011), but such samples still pose significant analysis and informatics challenges. In this work, we explored a simple approach for better utilization of high accuracy fragment ion mass measurements provided e.g. by FT MS/MS and demonstrate significant improvements relative to conventionalmore » descriptive and probabilistic scores methods. For example, at the same FDR level we identified 20-40% more peptides than SEQUEST and Mascot scoring methods using high accuracy fragment ion information (e.g., <10 mass errors) from CID, HCD, and ETD spectra. Species identified covered >90% of all those identified from SEQUEST, Mascot, and MS-GF scoring methods. Additionally, we found that the merging the different fragment spectra provided >60% more species using the UStags method than achieved previously, and enabled >1000 peptidome components to be identified from a single human blood plasma sample with a 0.6% peptide-level FDR, and providing an improved basis for investigation of potentially disease-related peptidome components.« less

How functional connectivity between emotion regulation structures can be disrupted: preliminary evidence from adolescents with moderate to severe traumatic brain injury.

PubMed

Newsome, Mary R; Scheibel, Randall S; Mayer, Andrew R; Chu, Zili D; Wilde, Elisabeth A; Hanten, Gerri; Steinberg, Joel L; Lin, Xiaodi; Li, Xiaoqi; Merkley, Tricia L; Hunter, Jill V; Vasquez, Ana C; Cook, Lori; Lu, Hanzhang; Vinton, Kami; Levin, Harvey S

2013-09-01

Outcome of moderate to severe traumatic brain injury (TBI) includes impaired emotion regulation. Emotion regulation has been associated with amygdala and rostral anterior cingulate (rACC). However, functional connectivity between the two structures after injury has not been reported. A preliminary examination of functional connectivity of rACC and right amygdala was conducted in adolescents 2 to 3 years after moderate to severe TBI and in typically developing (TD)control adolescents, with the hypothesis that the TBI adolescents would demonstrate altered functional connectivity in the two regions. Functional connectivity was determined by correlating fluctuations in the blood oxygen level dependent(BOLD) signal of the rACC and right amygdala with that of other brain regions. In the TBI adolescents, the rACC was found to be significantly less functionally connected to medial prefrontal cortices and to right temporal regions near the amygdala (height threshold T = 2.5, cluster level p < .05, FDR corrected), while the right amygdala showed a trend in reduced functional connectivity with the rACC (height threshold T = 2.5, cluster level p = .06, FDR corrected). Data suggest disrupted functional connectivity in emotion regulation regions. Limitations include small sample sizes. Studies with larger sample sizes are necessary to characterize the persistent neural damage resulting from moderate to severe TBI during development.

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

PubMed Central

Theis, Corinna; Zirbel, Craig L.; zu Siederdissen, Christian Höner; Anthon, Christian; Hofacker, Ivo L.; Nielsen, Henrik; Gorodkin, Jan

2015-01-01

Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D module prediction tools and apply them on a 13-way vertebrate sequence-based alignment. We find that RNA 3D modules predicted by metaRNAmodules and JAR3D are significantly enriched in the screened windows compared to their shuffled counterparts. The initially estimated FDR of 47.0% is lowered to below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence. PMID:26509713

Sparse representation and Bayesian detection of genome copy number alterations from microarray data.

PubMed

Pique-Regi, Roger; Monso-Varona, Jordi; Ortega, Antonio; Seeger, Robert C; Triche, Timothy J; Asgharzadeh, Shahab

2008-02-01

Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) that are associated with the development and behavior of tumors. Advances in microarray technology have allowed for greater resolution in detection of DNA copy number changes (amplifications or deletions) across the genome. However, the increase in number of measured signals and accompanying noise from the array probes present a challenge in accurate and fast identification of breakpoints that define CNA. This article proposes a novel detection technique that exploits the use of piece wise constant (PWC) vectors to represent genome copy number and sparse Bayesian learning (SBL) to detect CNA breakpoints. First, a compact linear algebra representation for the genome copy number is developed from normalized probe intensities. Second, SBL is applied and optimized to infer locations where copy number changes occur. Third, a backward elimination (BE) procedure is used to rank the inferred breakpoints; and a cut-off point can be efficiently adjusted in this procedure to control for the false discovery rate (FDR). The performance of our algorithm is evaluated using simulated and real genome datasets and compared to other existing techniques. Our approach achieves the highest accuracy and lowest FDR while improving computational speed by several orders of magnitude. The proposed algorithm has been developed into a free standing software application (GADA, Genome Alteration Detection Algorithm). http://biron.usc.edu/~piquereg/GADA

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orellana, Luis H.; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific, most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles andmore » related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N 2O, to inert N 2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes.« less

Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening

PubMed Central

2017-01-01

Microfluidic droplet-based screening of DNA-encoded one-bead-one-compound combinatorial libraries is a miniaturized, potentially widely distributable approach to small molecule discovery. In these screens, a microfluidic circuit distributes library beads into droplets of activity assay reagent, photochemically cleaves the compound from the bead, then incubates and sorts the droplets based on assay result for subsequent DNA sequencing-based hit compound structure elucidation. Pilot experimental studies revealed that Poisson statistics describe nearly all aspects of such screens, prompting the development of simulations to understand system behavior. Monte Carlo screening simulation data showed that increasing mean library sampling (ε), mean droplet occupancy, or library hit rate all increase the false discovery rate (FDR). Compounds identified as hits on k > 1 beads (the replicate k class) were much more likely to be authentic hits than singletons (k = 1), in agreement with previous findings. Here, we explain this observation by deriving an equation for authenticity, which reduces to the product of a library sampling bias term (exponential in k) and a sampling saturation term (exponential in ε) setting a threshold that the k-dependent bias must overcome. The equation thus quantitatively describes why each hit structure’s FDR is based on its k class, and further predicts the feasibility of intentionally populating droplets with multiple library beads, assaying the micromixtures for function, and identifying the active members by statistical deconvolution. PMID:28682059

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

PubMed Central

2017-01-01

Abstract Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific, most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles and related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N2O, to inert N2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes. PMID:28180325

Association of urinary metal profiles with altered glucose levels and diabetes risk: a population-based study in China.

PubMed

Feng, Wei; Cui, Xiuqing; Liu, Bing; Liu, Chuanyao; Xiao, Yang; Lu, Wei; Guo, Huan; He, Meian; Zhang, Xiaomin; Yuan, Jing; Chen, Weihong; Wu, Tangchun

2015-01-01

Elevated heavy metals and fasting plasma glucose (FPG) levels were both associated with increased risk of cardiovascular diseases. However, studies on the associations of heavy metals and essential elements with altered FPG and diabetes risk were limited or conflicting. The objective of this study was to evaluate the potential associations of heavy metals and essential trace elements with FPG and diabetes risk among general Chinese population. We conducted a cross-sectional study to investigate the associations of urinary concentrations of 23 metals with FPG, impaired fasting glucose (IFG) and diabetes among 2242 community-based Chinese adults in Wuhan. We used the false discovery rate (FDR) method to correct for multiple hypothesis tests. After adjusting for potential confounders, urinary aluminum, titanium, cobalt, nickel, copper, zinc, selenium, rubidium, strontium, molybdenum, cadmium, antimony, barium, tungsten and lead were associated with altered FPG, IFG or diabetes risk (all P< 0.05); arsenic was only dose-dependently related to diabetes (P< 0.05). After additional adjustment for multiple testing, titanium, copper, zinc, selenium, rubidium, tungsten and lead were still significantly associated with one or more outcomes (all FDR-adjusted P< 0.05). Our results suggest that multiple metals in urine are associated with FPG, IFG or diabetes risk. Because the cross-sectional design precludes inferences about causality, further prospective studies are warranted to validate our findings.

Cadherin-13 gene is associated with hyperactive/impulsive symptoms in attention/deficit hyperactivity disorder.

PubMed

Salatino-Oliveira, Angélica; Genro, Julia Pasqualini; Polanczyk, Guilherme; Zeni, Cristian; Schmitz, Marcelo; Kieling, Christian; Anselmi, Luciana; Menezes, Ana Maria Baptista; Barros, Fernando Cde; Polina, Evelise Regina; Mota, Nina R; Grevet, Eugênio Horácio; Bau, Claiton Henrique Dotto; Rohde, Luis Augusto; Hutz, Mara Helena

2015-04-01

Several efforts have been made to find new genetic risk variants which explain the high heritability of ADHD. At the genome level, genes involved in neurodevelopmental pathways were pointed as candidates. CDH13 and CTNNA2 genes are within GWAS top hits in ADHD and there are emerging notions about their contribution to ADHD pathophysiology. The main goal of this study is to test the association between SNPs in CDH13 and CTNNA2 genes and ADHD across the life cycle in subjects with ADHD. This study included 1,136 unrelated ADHD cases and 946 individuals without ADHD. No significant association between CDH13 and CTNNA2 was observed between cases and controls across different samples (P ≥ 0.096 for all comparisons). No allele was significantly more transmitted than expected from parents to ADHD probands. The CDH13 rs11150556 CC genotype was associated with more hyperactive/impulsive symptoms in youths with ADHD (children/adolescents clinical sample: F = 7.666, P = 0.006, FDR P-value = 0.032; Pelotas Birth Cohort sample: F = 6.711, P = 0.011, FDR P-value = 0.032). Although there are many open questions regarding the role of neurodevelopmental genes in ADHD symptoms, the present study suggests that CDH13 is associated with hyperactive/impulsive symptoms in youths with ADHD. © 2015 Wiley Periodicals, Inc.

Grandmaternal stress during pregnancy and DNA methylation of the third generation: an epigenome-wide association study

PubMed Central

Serpeloni, F; Radtke, K; de Assis, S G; Henning, F; Nätt, D; Elbert, T

2017-01-01

Stress during pregnancy may impact subsequent generations, which is demonstrated by an increased susceptibility to childhood and adulthood health problems in the children and grandchildren. Although the importance of the prenatal environment is well reported with regards to future physical and emotional outcomes, little is known about the molecular mechanisms that mediate the long-term consequences of early stress across generations. Recent studies have identified DNA methylation as a possible mediator of the impact of prenatal stress in the offspring. Whether psychosocial stress during pregnancy also affects DNA methylation of the grandchildren is still not known. In the present study we examined the multigenerational hypothesis, that is, grandmaternal exposure to psychosocial stress during pregnancy affecting DNA methylation of the grandchildren. We determined the genome-wide DNA methylation profile in 121 children (65 females and 56 males) and tested for associations with exposure to grandmaternal interpersonal violence during pregnancy. We observed methylation variations of five CpG sites significantly (FDR<0.05) associated with the grandmother’s report of exposure to violence while pregnant with the mothers of the children. The results revealed differential methylation of genes previously shown to be involved in circulatory system processes (FDR<0.05). This study provides support for DNA methylation as a biological mechanism involved in the transmission of stress across generations and motivates further investigations to examine prenatal-dependent DNA methylation as a potential biomarker for health problems. PMID:28809857

Biological Systems of Vitamin K: A Plasma Nutriproteomics Study of Subclinical Vitamin K Deficiency in 500 Nepalese Children.

PubMed

Lee, Sun Eun; Schulze, Kerry J; Cole, Robert N; Wu, Lee S F; Yager, James D; Groopman, John; Christian, Parul; West, Keith P

2016-04-01

Vitamin K (VK) is a fat-soluble vitamin whose deficiency disrupts coagulation and may disturb bone and cardiovascular health. However, the scale and systems affected by VK deficiency in pediatric populations remains unclear. We conducted a study of the plasma proteome of 500 Nepalese children 6-8 years of age (male/female ratio = 0.99) to identify proteins associated with VK status. We measured the concentrations of plasma lipids and protein induced by VK absence-II (PIVKA-II) and correlated relative abundance of proteins quantified by mass spectrometry with PIVKA-II. VK deficiency (PIVKA-II>2 μg/L) was associated with a higher abundance of low-density lipoproteins, total cholesterol, and triglyceride concentrations (p<0.01). Among 978 proteins observed in >10% of the children, five proteins were associated with PIVKA-II and seven proteins were differentially abundant between VK deficient versus sufficient children, including coagulation factor-II, hemoglobin, and vascular endothelial cadherin, passing a false discovery rate (FDR) threshold of 10% (q<0.10). Among 27 proteins associated with PIVKA-II or VK deficiency at a less stringent FDR (q<0.20), a network comprised of hemoglobin subunits and erythrocyte anti-oxidative enzymes were highly and positively correlated each other (all r>0.7). Untargeted proteomics offers a novel systems approach to elucidating biological processes of coagulation, vascularization, and erythrocyte oxidative stress related to VK status. The results may help elucidate subclinical metabolic disturbances related to VK deficiency in populations.

Filtering genetic variants and placing informative priors based on putative biological function.

PubMed

Friedrichs, Stefanie; Malzahn, Dörthe; Pugh, Elizabeth W; Almeida, Marcio; Liu, Xiao Qing; Bailey, Julia N

2016-02-03

High-density genetic marker data, especially sequence data, imply an immense multiple testing burden. This can be ameliorated by filtering genetic variants, exploiting or accounting for correlations between variants, jointly testing variants, and by incorporating informative priors. Priors can be based on biological knowledge or predicted variant function, or even be used to integrate gene expression or other omics data. Based on Genetic Analysis Workshop (GAW) 19 data, this article discusses diversity and usefulness of functional variant scores provided, for example, by PolyPhen2, SIFT, or RegulomeDB annotations. Incorporating functional scores into variant filters or weights and adjusting the significance level for correlations between variants yielded significant associations with blood pressure traits in a large family study of Mexican Americans (GAW19 data set). Marker rs218966 in gene PHF14 and rs9836027 in MAP4 significantly associated with hypertension; additionally, rare variants in SNUPN significantly associated with systolic blood pressure. Variant weights strongly influenced the power of kernel methods and burden tests. Apart from variant weights in test statistics, prior weights may also be used when combining test statistics or to informatively weight p values while controlling false discovery rate (FDR). Indeed, power improved when gene expression data for FDR-controlled informative weighting of association test p values of genes was used. Finally, approaches exploiting variant correlations included identity-by-descent mapping and the optimal strategy for joint testing rare and common variants, which was observed to depend on linkage disequilibrium structure.

[Active search of celiac disease among first degree relatives of known celiac patients].

PubMed

Bejares, Marcela; Oyarzún, Amaya; Lucero, Yalda; Espinoza, Nelly; Bascuñán, Karla; Araya, Magdalena

2015-12-01

Active search of celiac disease (CD) among risk groups has significantly increased the scope of known clinical variants. To measure the frequency and clinical characteristics of CD among first degree relatives (FDR) of known celiac cases. Between January 2012-August 2013, 37 patients with celiac disease brought 113 FDR for assessment. Their clinical data was recorded and a blood sample was obtained to measure serum Immunoglobulin A (IgA) levels, anti-transglutaminase (tTG) and anti-endomisial (EMA) antibodies. Cases with positive serology were advised to have an intestinal biopsy. Fourteen relatives (12.4%) had positive serological results and none had IgA deficiency. Among IgA-tTG (-) cases, measurement of IgA/IgG-tTG identified an additional case. Two of the 14 relatives were EMA positive. All 14 cases were advised to have an intestinal biopsy, but only 6 accepted the procedure. In two, the intestinal lesion was classified Marsh ≥ 2 and active CD was diagnosed. Histology in the remaining four was Marsh 0/1 and were diagnosed potential CD, remaining under control, without gluten free diet. Serological prevalence of CD among first degree relatives of known celiac cases was 15 fold greater than in THE general Chilean population, strongly supporting the idea of implementing active search to customary clinical practice. Determination of IgA/IgG-tTG may be useful to improve the yield of active search. Intestinal biopsies were crucial to differentiate active classic CD from potential CD.

Second generation sequencing of microRNA in Human Bone Cells treated with Parathyroid Hormone or Dexamethasone.

PubMed

Laxman, Navya; Rubin, Carl-Johan; Mallmin, Hans; Nilsson, Olle; Tellgren-Roth, Christian; Kindmark, Andreas

2016-03-01

We investigated the impact of treatment with parathyroid hormone (PTH) and dexamethasone (DEX) for 2 and 24h by RNA sequencing of miRNAs in primary human bone (HOB) cells. A total of 207 million reads were obtained, and normalized absolute expression retrieved for 373 most abundant miRNAs. In naïve control cells, 7 miRNAs were differentially expressed (FDR<0.05) between the two time points. Ten miRNAs exhibited differential expression (FDR <0.05) across two time points and treatments after adjusting for expression in controls and were selected for downstream analyses. Results show significant effects on miRNA expression when comparing PTH with DEX at 2h with even more pronounced effects at 24h. Interestingly, several miRNAs exhibiting differences in expression are predicted to target genes involved in bone metabolism e.g. miR-30c2, miR-203 and miR-205 targeting RUNX2, and miR-320 targeting β-catenin (CTNNB1) mRNA expression. CTNNB1and RUNX2 levels were decreased after DEX treatment and increased after PTH treatment. Our analysis also identified 2 putative novel miRNAs in PTH and DEX treated cells at 24h. RNA sequencing showed that PTH and DEX treatment affect miRNA expression in HOB cells and that regulated miRNAs in turn are correlated with expression levels of key genes involved in bone metabolism. Copyright © 2016 Elsevier Inc. All rights reserved.

Grandmaternal stress during pregnancy and DNA methylation of the third generation: an epigenome-wide association study.

PubMed

Serpeloni, F; Radtke, K; de Assis, S G; Henning, F; Nätt, D; Elbert, T

2017-08-15

Stress during pregnancy may impact subsequent generations, which is demonstrated by an increased susceptibility to childhood and adulthood health problems in the children and grandchildren. Although the importance of the prenatal environment is well reported with regards to future physical and emotional outcomes, little is known about the molecular mechanisms that mediate the long-term consequences of early stress across generations. Recent studies have identified DNA methylation as a possible mediator of the impact of prenatal stress in the offspring. Whether psychosocial stress during pregnancy also affects DNA methylation of the grandchildren is still not known. In the present study we examined the multigenerational hypothesis, that is, grandmaternal exposure to psychosocial stress during pregnancy affecting DNA methylation of the grandchildren. We determined the genome-wide DNA methylation profile in 121 children (65 females and 56 males) and tested for associations with exposure to grandmaternal interpersonal violence during pregnancy. We observed methylation variations of five CpG sites significantly (FDR<0.05) associated with the grandmother's report of exposure to violence while pregnant with the mothers of the children. The results revealed differential methylation of genes previously shown to be involved in circulatory system processes (FDR<0.05). This study provides support for DNA methylation as a biological mechanism involved in the transmission of stress across generations and motivates further investigations to examine prenatal-dependent DNA methylation as a potential biomarker for health problems.

MAFsnp: A Multi-Sample Accurate and Flexible SNP Caller Using Next-Generation Sequencing Data

PubMed Central

Hu, Jiyuan; Li, Tengfei; Xiu, Zidi; Zhang, Hong

2015-01-01

Most existing statistical methods developed for calling single nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS) data are based on Bayesian frameworks, and there does not exist any SNP caller that produces p-values for calling SNPs in a frequentist framework. To fill in this gap, we develop a new method MAFsnp, a Multiple-sample based Accurate and Flexible algorithm for calling SNPs with NGS data. MAFsnp is based on an estimated likelihood ratio test (eLRT) statistic. In practical situation, the involved parameter is very close to the boundary of the parametric space, so the standard large sample property is not suitable to evaluate the finite-sample distribution of the eLRT statistic. Observing that the distribution of the test statistic is a mixture of zero and a continuous part, we propose to model the test statistic with a novel two-parameter mixture distribution. Once the parameters in the mixture distribution are estimated, p-values can be easily calculated for detecting SNPs, and the multiple-testing corrected p-values can be used to control false discovery rate (FDR) at any pre-specified level. With simulated data, MAFsnp is shown to have much better control of FDR than the existing SNP callers. Through the application to two real datasets, MAFsnp is also shown to outperform the existing SNP callers in terms of calling accuracy. An R package “MAFsnp” implementing the new SNP caller is freely available at http://homepage.fudan.edu.cn/zhangh/softwares/. PMID:26309201

Spatial feature analysis of a cosmic-ray sensor for measuring the soil water content: Comparison of four weighting methods

NASA Astrophysics Data System (ADS)

Cai, Jingya; Pang, Zhiguo; Fu, Jun'e.

2018-04-01

To quantitatively analyze the spatial features of a cosmic-ray sensor (CRS) (i.e., the measurement support volume of the CRS and the weight of the in situ point-scale soil water content (SWC) in terms of the regionally averaged SWC derived from the CRS) in measuring the SWC, cooperative observations based on CRS, oven drying and frequency domain reflectometry (FDR) methods are performed at the point and regional scales in a desert steppe area of the Inner Mongolia Autonomous Region. This region is flat with sparse vegetation cover consisting of only grass, thereby minimizing the effects of terrain and vegetation. Considering the two possibilities of the measurement support volume of the CRS, the results of four weighting methods are compared with the SWC monitored by FDR within an appropriate measurement support volume. The weighted average calculated using the neutron intensity-based weighting method (Ni weighting method) best fits the regionally averaged SWC measured by the CRS. Therefore, we conclude that the gyroscopic support volume and the weights determined by the Ni weighting method are the closest to the actual spatial features of the CRS when measuring the SWC. Based on these findings, a scale transformation model of the SWC from the point scale to the scale of the CRS measurement support volume is established. In addition, the spatial features simulated using the Ni weighting method are visualized by developing a software system.

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs

PubMed Central

Yang, Hui; Huang, Xiaochang; Fang, Shaoming; He, Maozhang; Zhao, Yuanzhang; Wu, Zhenfang; Yang, Ming; Zhang, Zhiyan; Chen, Congying; Huang, Lusheng

2017-01-01

Gut microbiota plays fundamental roles in energy harvest, nutrient digestion, and intestinal health, especially in processing indigestible components of polysaccharides in diet. Unraveling the microbial taxa and functional capacity of gut microbiome associated with feed efficiency can provide important knowledge to improve pig feed efficiency in swine industry. In the current research, we studied the association of fecal microbiota with feed efficiency in 280 commercial Duroc pigs. All experimental pigs could be clustered into two enterotype-like groups. Different enterotypes showed the tendency of association with the feed efficiency (P = 0.07). We further identified 31 operational taxonomic units (OTUs) showing the potential associations with porcine feed efficiency. These OTUs were mainly annotated to the bacteria related to the metabolisms of dietary polysaccharides. Although we did not identify the RFI-associated bacterial species at FDR < 0.05 level, metagenomic sequencing analysis did find the distinct function capacities of gut microbiome between the high and low RFI pigs (FDR < 0.05). The KEGG orthologies related to nitrogen metabolism, amino acid metabolism, and transport system, and eight KEGG pathways including glycine, serine, and threonine metabolism were positively associated with porcine feed efficiency. We inferred that gut microbiota might improve porcine feed efficiency through promoting intestinal health by the SCFAs produced by fermenting dietary polysaccharides and improving the utilization of dietary protein. The present results provided important basic knowledge for improving porcine feed efficiency through modulating gut microbiome. PMID:28861066

Characterization of a Genomic Signature of Pregnancy in the Breast

PubMed Central

Belitskaya-Lévy, Ilana; Zeleniuch-Jacquotte, Anne; Russo, Jose; Russo, Irma H.; Bordás, Pal; Åhman, Janet; Afanasyeva, Yelena; Johansson, Robert; Lenner, Per; Li, Xiaochun; de Cicco, Ricardo López; Peri, Suraj; Ross, Eric; Russo, Patricia A.; Santucci-Pereira, Julia; Sheriff, Fathima S.; Slifker, Michael; Hallmans, Göran; Toniolo, Paolo; Arslan, Alan A.

2012-01-01

The objective of the current study was to comprehensively compare the genomic profiles in the breast of parous and nulliparous postmenopausal women to identify genes that permanently change their expression following pregnancy. The study was designed as a two-phase approach. In the discovery phase, we compared breast genomic profiles of 37 parous with 18 nulliparous postmenopausal women. In the validation phase, confirmation of the genomic patterns observed in the discovery phase was sought in an independent set of 30 parous and 22 nulliparous postmenopausal women. RNA was hybridized to Affymetrix HG_U133 Plus 2.0 oligonucleotide arrays containing probes to 54,675 transcripts; scanned and the images analyzed using Affymetrix GCOS software. Surrogate variable analysis, logistic regression and significance analysis for microarrays were used to identify statistically significant differences in expression of genes. The False Discovery Rate (FDR) approach was used to control for multiple comparisons. We found that 208 genes (305 probe sets) were differentially expressed between parous and nulliparous women in both discovery and validation phases of the study at a FDR of 10% and with at least a 1.25-fold change. These genes are involved in regulation of transcription, centrosome organization, RNA splicing, cell cycle control, adhesion and differentiation. The results provide persuasive evidence that full-term pregnancy induces long-term genomic changes in the breast. The genomic signature of pregnancy could be used as an intermediate marker to assess potential chemopreventive interventions with hormones mimicking the effects of pregnancy for prevention of breast cancer. PMID:21622728

Detecting differentially expressed genes in heterogeneous diseases using half Student's t-test.

PubMed

Hsu, Chun-Lun; Lee, Wen-Chung

2010-12-01

Microarray technology provides information about hundreds and thousands of gene-expression data in a single experiment. To search for disease-related genes, researchers test for those genes that are differentially expressed between the case subjects and the control subjects. The authors propose a new test, the 'half Student's t-test', specifically for detecting differentially expressed genes in heterogeneous diseases. Monte-Carlo simulation shows that the test maintains the nominal α level quite well for both normal and non-normal distributions. Power of the half Student's t is higher than that of the conventional 'pooled' Student's t when there is heterogeneity in the disease under study. The power gain by using the half Student's t can reach ∼10% when the standard deviation of the case group is 50% larger than that of the control group. Application to a colon cancer data reveals that when the false discovery rate (FDR) is controlled at 0.05, the half Student's t can detect 344 differentially expressed genes, whereas the pooled Student's t can detect only 65 genes. Or alternatively, if only 50 genes are to be selected, the FDR for the pooled Student's t has to be set at 0.0320 (false positive rate of ∼3%), but for the half Student's t, it can be at as low as 0.0001 (false positive rate of about one per ten thousands). The half Student's t-test is to be recommended for the detection of differentially expressed genes in heterogeneous diseases.

Knowledge-driven binning approach for rare variant association analysis: application to neuroimaging biomarkers in Alzheimer's disease.

PubMed

Kim, Dokyoon; Basile, Anna O; Bang, Lisa; Horgusluoglu, Emrin; Lee, Seunggeun; Ritchie, Marylyn D; Saykin, Andrew J; Nho, Kwangsik

2017-05-18

Rapid advancement of next generation sequencing technologies such as whole genome sequencing (WGS) has facilitated the search for genetic factors that influence disease risk in the field of human genetics. To identify rare variants associated with human diseases or traits, an efficient genome-wide binning approach is needed. In this study we developed a novel biological knowledge-based binning approach for rare-variant association analysis and then applied the approach to structural neuroimaging endophenotypes related to late-onset Alzheimer's disease (LOAD). For rare-variant analysis, we used the knowledge-driven binning approach implemented in Bin-KAT, an automated tool, that provides 1) binning/collapsing methods for multi-level variant aggregation with a flexible, biologically informed binning strategy and 2) an option of performing unified collapsing and statistical rare variant analyses in one tool. A total of 750 non-Hispanic Caucasian participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort who had both WGS data and magnetic resonance imaging (MRI) scans were used in this study. Mean bilateral cortical thickness of the entorhinal cortex extracted from MRI scans was used as an AD-related neuroimaging endophenotype. SKAT was used for a genome-wide gene- and region-based association analysis of rare variants (MAF (minor allele frequency) < 0.05) and potential confounding factors (age, gender, years of education, intracranial volume (ICV) and MRI field strength) for entorhinal cortex thickness were used as covariates. Significant associations were determined using FDR adjustment for multiple comparisons. Our knowledge-driven binning approach identified 16 functional exonic rare variants in FANCC significantly associated with entorhinal cortex thickness (FDR-corrected p-value < 0.05). In addition, the approach identified 7 evolutionary conserved regions, which were mapped to FAF1, RFX7, LYPLAL1 and GOLGA3, significantly associated with entorhinal cortex thickness (FDR-corrected p-value < 0.05). In further analysis, the functional exonic rare variants in FANCC were also significantly associated with hippocampal volume and cerebrospinal fluid (CSF) Aβ 1-42 (p-value < 0.05). Our novel binning approach identified rare variants in FANCC as well as 7 evolutionary conserved regions significantly associated with a LOAD-related neuroimaging endophenotype. FANCC (fanconi anemia complementation group C) has been shown to modulate TLR and p38 MAPK-dependent expression of IL-1β in macrophages. Our results warrant further investigation in a larger independent cohort and demonstrate that the biological knowledge-driven binning approach is a powerful strategy to identify rare variants associated with AD and other complex disease.

Parallel epigenomic and transcriptomic responses to viral infection in honey bees (Apis mellifera).

PubMed

Galbraith, David A; Yang, Xingyu; Niño, Elina Lastro; Yi, Soojin; Grozinger, Christina

2015-03-01

Populations of honey bees are declining throughout the world, with US beekeepers losing 30% of their colonies each winter. Though multiple factors are driving these colony losses, it is increasingly clear that viruses play a major role. However, information about the molecular mechanisms mediating antiviral immunity in honey bees is surprisingly limited. Here, we examined the transcriptional and epigenetic (DNA methylation) responses to viral infection in honey bee workers. One-day old worker honey bees were fed solutions containing Israeli Acute Paralysis Virus (IAPV), a virus which causes muscle paralysis and death and has previously been associated with colony loss. Uninfected control and infected, symptomatic bees were collected within 20-24 hours after infection. Worker fat bodies, the primary tissue involved in metabolism, detoxification and immune responses, were collected for analysis. We performed transcriptome- and bisulfite-sequencing of the worker fat bodies to identify genome-wide gene expression and DNA methylation patterns associated with viral infection. There were 753 differentially expressed genes (FDR<0.05) in infected versus control bees, including several genes involved in epigenetic and antiviral pathways. DNA methylation status of 156 genes (FDR<0.1) changed significantly as a result of the infection, including those involved in antiviral responses in humans. There was no significant overlap between the significantly differentially expressed and significantly differentially methylated genes, and indeed, the genomic characteristics of these sets of genes were quite distinct. Our results indicate that honey bees have two distinct molecular pathways, mediated by transcription and methylation, that modulate protein levels and/or function in response to viral infections.

Effects of Long-Term Treatment on Brain Volume in Patients with Obstructive Sleep Apnea Syndrome

PubMed Central

Kim, Hosung; Joo, Eun Yeon; Suh, Sooyeon; Kim, Jae-Hun; Kim, Sung Tae; Hong, Seung Bong

2015-01-01

We assessed structural brain damage in obstructive sleep apnea syndrome (OSA) patients (21 males) and the effects of long-term continuous positive airway pressure (CPAP) treatment (18.2 ± 12.4 months; 8-44 months) on brain structures and investigated the relationship between severity of OSA and effects of treatment. Using deformation-based morphometry to measure local volume changes, we identified widespread neocortical and cerebellar atrophy in untreated patients compared to controls (59 males; Cohen's D = 0.6; FDR < 0.05). Analysis of longitudinally scanned magnetic resonance imaging (MRI) scans both before and after treatment showed increased brain volume following treatment (FDR < 0.05). Volume increase was correlated with longer treatment in the cortical areas that largely overlapped with the initial atrophy. The areas overlying the hippocampal dentate gyrus and the cerebellar dentate nucleus displayed a volume increase after treatment. Patients with very severe OSA (AHI > 64) presented with prefrontal atrophy and displayed an additional volume increase in this area following treatment. Higher impairment of working memory in patients prior to treatment correlated with prefrontal volume increase after treatment. The large overlap between the initial brain damage and the extent of recovery after treatment suggests partial recovery of non-permanent structural damage. Volume increases in the dentate gyrus and the dentate nucleus possibly likely indicate compensatory neurogenesis in response to diminishing oxidative stress. Such changes in other brain structures may explain gliosis, dendritic volume increase, or inflammation. This study provides neuroimaging evidence that revealed the positive effects of long-term CPAP treatment in patients with OSA. PMID:26503297

Effects of chronic cobalt and chromium exposure after metal‐on‐metal hip resurfacing: An epigenome‐wide association pilot study

PubMed Central

Steinberg, Julia; Shah, Karan M.; Gartland, Alison; Zeggini, Eleftheria

2017-01-01

ABSTRACT Metal‐on‐metal (MOM) hip resurfacing has recently been a popular prosthesis choice for the treatment of symptomatic arthritis, but results in the release of cobalt and chromium ions into the circulation that can be associated with adverse clinical effects. The mechanism underlying these effects remains unclear. While chromosomal aneuploidy and translocations are associated with this exposure, the presence of subtle structural epigenetic modifications in patients with MOM joint replacements remains unexplored. Consequently, we analyzed whole blood DNA methylation in 34 OA patients with MOM hip resurfacing (MOM HR) compared to 34 OA patients with non‐MOM total hip replacements (non‐MOM THR), using the genome‐wide Illumina HumanMethylation 450k BeadChip. No probes showed differential methylation significant at 5% false‐discovery rate (FDR). We also tested association of probe methylation levels with blood chromium and cobalt levels directly; there were no significant associations at 5% FDR. Finally, we used the “epigenetic clock” to compare estimated to actual age at sample for all individuals. We found no significant difference between MOM HR and non‐MOM THR, and no correlation of age acceleration with blood metal levels. Our results suggest the absence of large methylation differences systemically following metal exposure, however, larger sample sizes will be required to identify potential small effects. Any DNA methylation changes that may occur in the local periprosthetic tissues remain to be elucidated. © 2017 The Authors. Orthopaedic Research Society. Published by Wiley Periodicals, Inc. on behalf of Orthopaedic Research Society. J Orthop Res 35:2323–2328, 2017. PMID:28098396

Effects of marijuana use on prefrontal and parietal volumes and cognition in emerging adults.

PubMed

Price, Jenessa S; McQueeny, Tim; Shollenbarger, Skyler; Browning, Erin L; Wieser, Jon; Lisdahl, Krista M

2015-08-01

Chronic marijuana (MJ) use among adolescents has been associated with structural and functional abnormalities, particularly in developing regions responsible for higher order cognition. This study investigated prefrontal (PFC) and parietal volumes and executive function in emerging adult MJ users and explored potential gender differences. Participants (ages 18-25) were 27 MJ users and 32 controls without neurologic or psychiatric disorders or heavy other drug use. A series of multiple regressions examined whether group status, past year MJ use, and their interactions with gender predicted ROI volumes. Post hoc analyses consisted of brain-behavior correlations between volumes and cognitive variables and Fisher's z tests to assess group differences. MJ users demonstrated significantly smaller medial orbitofrontal (mOFC; p = 0.004, FDR p = 0.024) and inferior parietal volumes (p = 0.04, FDR p = 0.12); follow-up regressions found that increased past year MJ use did not significantly dose-dependently predict smaller mOFC volume in a sub-sample of individuals with at least one past year MJ use. There were no significant gender interactions. There was a significant brain-behavior difference by group, such that smaller mOFC volumes were associated with poorer complex attention for MJ users (p < 0.05). Smaller mOFC volumes among MJ users suggest disruption of typical neurodevelopmental processes associated with regular MJ use for both genders. These results highlight the need for longitudinal, multi-modal imaging studies providing clearer information on timing of neurodevelopmental processes and neurocognitive impacts of youth MJ initiation.

Initial validation and results of the Symptoms in Persons At Risk of Rheumatoid Arthritis (SPARRA) questionnaire: a EULAR project

PubMed Central

van Beers-Tas, Marian H; ter Wee, Marieke M; van Tuyl, Lilian H; Maat, Bertha; Hoogland, Wijnanda; Hensvold, Aase H; Catrina, Anca I; Mosor, Erika; Finckh, Axel; Courvoisier, Delphine S; Filer, Andrew; Sahbudin, Ilfita; Stack, Rebecca J; Raza, Karim; van Schaardenburg, Dirkjan

2018-01-01

Objectives To describe the development and assess the psychometric properties of the novel ‘Symptoms in Persons At Risk of Rheumatoid Arthritis’ (SPARRA) questionnaire in individuals at risk of rheumatoid arthritis (RA) and to quantify their symptoms. Methods The questionnaire items were derived from a qualitative study in patients with seropositive arthralgia. The questionnaire was administered to 219 individuals at risk of RA on the basis of symptoms or autoantibody positivity: 74% rheumatoid factor and/or anticitrullinated protein antibodies positive, 26% seronegative. Validity, reliability and responsiveness were assessed. Eighteen first degree relatives (FDR) of patients with RA were used for comparison. Results Face and content validity were high. The test-retest showed good agreement and reliability (1 week and 6 months). Overall, construct validity was low to moderate, with higher values for concurrent validity, suggesting that some questions reflect symptom content not captured with regular Visual Analogue Scale pain/well-being. Responsiveness was low (small subgroup). Finally, the burden of symptoms in both seronegative and seropositive at risk individuals was high, with pain, stiffness and fatigue being the most common ones with a major impact on daily functioning. The FDR cohort (mostly healthy individuals) showed a lower burden of symptoms; however, the distribution of symptoms was similar. Conclusions The SPARRA questionnaire has good psychometric properties and can add information to currently available clinical measures in individuals at risk of RA. The studied group had a high burden and impact of symptoms. Future studies should evaluate whether SPARRA data can improve the prediction of RA in at risk individuals.

Quantum statistical effects in the mass transport of interstitial solutes in a crystalline solid

NASA Astrophysics Data System (ADS)

Woo, C. H.; Wen, Haohua

2017-09-01

The impact of quantum statistics on the many-body dynamics of a crystalline solid at finite temperatures containing an interstitial solute atom (ISA) is investigated. The Mori-Zwanzig theory allows the many-body dynamics of the crystal to be formulated and solved analytically within a pseudo-one-particle approach using the Langevin equation with a quantum fluctuation-dissipation relation (FDR) based on the Debye model. At the same time, the many-body dynamics is also directly solved numerically via the molecular dynamics approach with a Langevin heat bath based on the quantum FDR. Both the analytical and numerical results consistently show that below the Debye temperature of the host lattice, quantum statistics significantly impacts the ISA transport properties, resulting in major departures from both the Arrhenius law of diffusion and the Einstein-Smoluchowski relation between the mobility and diffusivity. Indeed, we found that below one-third of the Debye temperature, effects of vibrations on the quantum mobility and diffusivity are both orders-of-magnitude larger and practically temperature independent. We have shown that both effects have their physical origin in the athermal lattice vibrations derived from the phonon ground state. The foregoing theory is tested in quantum molecular dynamics calculation of mobility and diffusivity of interstitial helium in bcc W. In this case, the Arrhenius law is only valid in a narrow range between ˜300 and ˜700 K. The diffusivity becomes temperature independent on the low-temperature side while increasing linearly with temperature on the high-temperature side.

A family-based study of gene variants and maternal folate and choline in neuroblastoma: A Report from the Children’s Oncology Group

PubMed Central

Mazul, Angela L; Siega-Riz, Anna Maria; Weinberg, Clarice R; Engel, Stephanie M.; Zou, Fei; Carrier, Kathryn S.; Basta, Patricia V; Vaksman, Zalman; Maris, John M; Diskin, Sharon J; Maxen, Charlene; Naranjo, Arlene; Olshan, Andrew F

2016-01-01

Purpose Neuroblastoma is a childhood cancer of the sympathetic nervous system with embryonic origins. Previous epidemiologic studies suggest maternal vitamin supplementation during pregnancy reduces the risk of neuroblastoma. We hypothesized offspring and maternal genetic variants in folate-related and choline-related genes are associated with neuroblastoma and modify the effects of maternal intake of folate, choline and folic acid. Methods The Neuroblastoma Epidemiology in North America (NENA) study recruited 563 affected children and their parents through the Children’s Oncology Group’s Childhood Cancer Research Network. We used questionnaires to ascertain pre-pregnancy supplementation and estimate usual maternal dietary intake of folate, choline and folic acid. We genotyped 955 genetic variants related to folate or choline using DNA extracted from saliva samples and used a log-linear model to estimate both child and maternal risk ratios and stratum-specific risk ratios for gene-environment interactions. Results Overall, no maternal or offspring genotypic results met criteria for a false discovery rate (FDR) Q-value <0.2. Associations were also null for gene-environment interaction with pre-pregnancy vitamin supplementation, dietary folic acid and folate. FDR significant gene-choline interactions were found for offspring SNPs rs10489810 and rs9966612 located in MTHFD1L and TYMS, respectively, with maternal choline dietary intake dichotomized at the first quartile. Conclusion These results suggest that variants related to one-carbon metabolism are not strongly associated with neuroblastoma. Choline-related variants may play a role; however, the functional consequences of the interacting variants are unknown and require independent replication. PMID:27541142

A family-based study of gene variants and maternal folate and choline in neuroblastoma: a report from the Children's Oncology Group.

PubMed

Mazul, Angela L; Siega-Riz, Anna Maria; Weinberg, Clarice R; Engel, Stephanie M; Zou, Fei; Carrier, Kathryn S; Basta, Patricia V; Vaksman, Zalman; Maris, John M; Diskin, Sharon J; Maxen, Charlene; Naranjo, Arlene; Olshan, Andrew F

2016-10-01

Neuroblastoma is a childhood cancer of the sympathetic nervous system with embryonic origins. Previous epidemiologic studies suggest maternal vitamin supplementation during pregnancy reduces the risk of neuroblastoma. We hypothesized offspring and maternal genetic variants in folate-related and choline-related genes are associated with neuroblastoma and modify the effects of maternal intake of folate, choline, and folic acid. The Neuroblastoma Epidemiology in North America (NENA) study recruited 563 affected children and their parents through the Children's Oncology Group's Childhood Cancer Research Network. We used questionnaires to ascertain pre-pregnancy supplementation and estimate usual maternal dietary intake of folate, choline, and folic acid. We genotyped 955 genetic variants related to folate or choline using DNA extracted from saliva samples and used a log-linear model to estimate both child and maternal risk ratios and stratum-specific risk ratios for gene-environment interactions. Overall, no maternal or offspring genotypic results met criteria for a false discovery rate (FDR) Q-value <0.2. Associations were also null for gene-environment interaction with pre-pregnancy vitamin supplementation, dietary folic acid, and folate. FDR-significant gene-choline interactions were found for offspring SNPs rs10489810 and rs9966612 located in MTHFD1L and TYMS, respectively, with maternal choline dietary intake dichotomized at the first quartile. These results suggest that variants related to one-carbon metabolism are not strongly associated with neuroblastoma. Choline-related variants may play a role; however, the functional consequences of the interacting variants are unknown and require independent replication.

POWER-ENHANCED MULTIPLE DECISION FUNCTIONS CONTROLLING FAMILY-WISE ERROR AND FALSE DISCOVERY RATES.

PubMed

Peña, Edsel A; Habiger, Joshua D; Wu, Wensong

2011-02-01

Improved procedures, in terms of smaller missed discovery rates (MDR), for performing multiple hypotheses testing with weak and strong control of the family-wise error rate (FWER) or the false discovery rate (FDR) are developed and studied. The improvement over existing procedures such as the Šidák procedure for FWER control and the Benjamini-Hochberg (BH) procedure for FDR control is achieved by exploiting possible differences in the powers of the individual tests. Results signal the need to take into account the powers of the individual tests and to have multiple hypotheses decision functions which are not limited to simply using the individual p -values, as is the case, for example, with the Šidák, Bonferroni, or BH procedures. They also enhance understanding of the role of the powers of individual tests, or more precisely the receiver operating characteristic (ROC) functions of decision processes, in the search for better multiple hypotheses testing procedures. A decision-theoretic framework is utilized, and through auxiliary randomizers the procedures could be used with discrete or mixed-type data or with rank-based nonparametric tests. This is in contrast to existing p -value based procedures whose theoretical validity is contingent on each of these p -value statistics being stochastically equal to or greater than a standard uniform variable under the null hypothesis. Proposed procedures are relevant in the analysis of high-dimensional "large M , small n " data sets arising in the natural, physical, medical, economic and social sciences, whose generation and creation is accelerated by advances in high-throughput technology, notably, but not limited to, microarray technology.

Context-Sensitive Markov Models for Peptide Scoring and Identification from Tandem Mass Spectrometry

PubMed Central

Grover, Himanshu; Wallstrom, Garrick; Wu, Christine C.

2013-01-01

Abstract Peptide and protein identification via tandem mass spectrometry (MS/MS) lies at the heart of proteomic characterization of biological samples. Several algorithms are able to search, score, and assign peptides to large MS/MS datasets. Most popular methods, however, underutilize the intensity information available in the tandem mass spectrum due to the complex nature of the peptide fragmentation process, thus contributing to loss of potential identifications. We present a novel probabilistic scoring algorithm called Context-Sensitive Peptide Identification (CSPI) based on highly flexible Input-Output Hidden Markov Models (IO-HMM) that capture the influence of peptide physicochemical properties on their observed MS/MS spectra. We use several local and global properties of peptides and their fragment ions from literature. Comparison with two popular algorithms, Crux (re-implementation of SEQUEST) and X!Tandem, on multiple datasets of varying complexity, shows that peptide identification scores from our models are able to achieve greater discrimination between true and false peptides, identifying up to ∼25% more peptides at a False Discovery Rate (FDR) of 1%. We evaluated two alternative normalization schemes for fragment ion-intensities, a global rank-based and a local window-based. Our results indicate the importance of appropriate normalization methods for learning superior models. Further, combining our scores with Crux using a state-of-the-art procedure, Percolator, we demonstrate the utility of using scoring features from intensity-based models, identifying ∼4-8 % additional identifications over Percolator at 1% FDR. IO-HMMs offer a scalable and flexible framework with several modeling choices to learn complex patterns embedded in MS/MS data. PMID:23289783

Phylogenetic comparative methods complement discriminant function analysis in ecomorphology.

PubMed

Barr, W Andrew; Scott, Robert S

2014-04-01

In ecomorphology, Discriminant Function Analysis (DFA) has been used as evidence for the presence of functional links between morphometric variables and ecological categories. Here we conduct simulations of characters containing phylogenetic signal to explore the performance of DFA under a variety of conditions. Characters were simulated using a phylogeny of extant antelope species from known habitats. Characters were modeled with no biomechanical relationship to the habitat category; the only sources of variation were body mass, phylogenetic signal, or random "noise." DFA on the discriminability of habitat categories was performed using subsets of the simulated characters, and Phylogenetic Generalized Least Squares (PGLS) was performed for each character. Analyses were repeated with randomized habitat assignments. When simulated characters lacked phylogenetic signal and/or habitat assignments were random, <5.6% of DFAs and <8.26% of PGLS analyses were significant. When characters contained phylogenetic signal and actual habitats were used, 33.27 to 45.07% of DFAs and <13.09% of PGLS analyses were significant. False Discovery Rate (FDR) corrections for multiple PGLS analyses reduced the rate of significance to <4.64%. In all cases using actual habitats and characters with phylogenetic signal, correct classification rates of DFAs exceeded random chance. In simulations involving phylogenetic signal in both predictor variables and predicted categories, PGLS with FDR was rarely significant, while DFA often was. In short, DFA offered no indication that differences between categories might be explained by phylogenetic signal, while PGLS did. As such, PGLS provides a valuable tool for testing the functional hypotheses at the heart of ecomorphology. Copyright © 2013 Wiley Periodicals, Inc.

Genome-Wide Association Mapping Reveals Novel QTL for Seedling Leaf Rust Resistance in a Worldwide Collection of Winter Wheat.

PubMed

Li, Genqiao; Xu, Xiangyang; Bai, Guihua; Carver, Brett F; Hunger, Robert; Bonman, J Michael; Kolmer, James; Dong, Hongxu

2016-11-01

Leaf rust of wheat ( L.) is a major disease that causes significant yield losses worldwide. The short-lived nature of leaf rust resistance () genes necessitates a continuous search for novel sources of resistance. We performed a genome-wide association study (GWAS) on a panel of 1596 wheat accessions. The panel was evaluated for leaf rust reaction by testing with a bulk of Eriks. () isolates collected from multiple fields of Oklahoma in 2013 and two predominant races in the fields of Oklahoma in 2015. The panel was genotyped with a set of 5011 single-nucleotide polymorphism (SNP) markers. A total of 14 quantitative trait loci (QTL) for leaf rust resistance were identified at a false discovery rate (FDR) of 0.01 using the mixed linear model (MLM). Of these, eight QTL reside in the vicinity of known genes or QTL, and more studies are needed to determine their relationship with known loci. is a new QTL to bread wheat but is close to a locus previously identified in durum wheat [ L. subsp. (Desf.) Husn.]. The other five QTL, including , , , , and , are likely novel loci for leaf rust resistance. The uneven distribution of the 14 QTL in the six subpopulations of the panel suggests that wheat breeders can enhance leaf rust resistance by selectively introgressing some of these QTL into their breeding materials. In addition, another 31 QTL were significantly associated with leaf rust resistance at a FDR of 0.05. Copyright © 2016 Crop Science Society of America.

Malaria rapid diagnostic test evaluation at private retail pharmacies in Kumasi, Ghana.

PubMed

Audu, Rauf; Anto, Berko Panyin; Koffuor, George Asumeng; Abruquah, Akua Afriyie; Buabeng, Kwame Ohene

2016-01-01

Malaria rapid diagnostic test (MRDT) provides a good alternative to malaria microscopy diagnosis, particularly in resource-constrained settings. This study therefore evaluated MRDT in private retail pharmacies (PRPs) as a critical step in community case malaria management. In a prospective, cross-over, validation survey at six PRPs in the Ashanti Region of Ghana, 1200 patients presenting with fever in the preceding 48 h were sampled. Fingerstick blood samples were collected for preparation of thick and thin blood films for malaria microscopy. Categorized patients (600 each) went through the processes of MRDT or presumptive diagnosis (PD) of malaria. The malaria disease prevalence of the study area was established. Selectivity (Se), specificity (Sp), positive predictive value (PPV) along with false discovery rate (FDR), and negative predictive value (NPV) along with the false omission rate (FOR), and diagnostic odds ratio (DOR) of MRDT were then calculated. While 43.0% tested positive using the MRDT, 57.0% tested negative. However, 62.0% MRDT-negative patients in addition to all the MRDT positives were given artemether-lumefantrine. Of those diagnosed by PD, 98.2% were prescribed with an antimalarial (microscopy however confirmed only 70.3% as positive). Se and Sp of the MRDT were 90.68 ± 11.18% and 98.68 ± 1.19%, respectively. Malaria prevalence was estimated to be 43.3%. PPV was 98.0%, FDR was 2.0%, NPV was 98.0%, FOR was 2.0%, and DOR was 2366.43. Results highlighted good performance of MRDTs at PRPs which could inform decision toward its implementation.

Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation.

PubMed

Arnardottir, Erna S; Nikonova, Elena V; Shockley, Keith R; Podtelezhnikov, Alexei A; Anafi, Ron C; Tanis, Keith Q; Maislin, Greg; Stone, David J; Renger, John J; Winrow, Christopher J; Pack, Allan I

2014-10-01

To address whether changes in gene expression in blood cells with sleep loss are different in individuals resistant and sensitive to sleep deprivation. Blood draws every 4 h during a 3-day study: 24-h normal baseline, 38 h of continuous wakefulness and subsequent recovery sleep, for a total of 19 time-points per subject, with every 2-h psychomotor vigilance task (PVT) assessment when awake. Sleep laboratory. Fourteen subjects who were previously identified as behaviorally resistant (n = 7) or sensitive (n = 7) to sleep deprivation by PVT. Thirty-eight hours of continuous wakefulness. We found 4,481 unique genes with a significant 24-h diurnal rhythm during a normal sleep-wake cycle in blood (false discovery rate [FDR] < 5%). Biological pathways were enriched for biosynthetic processes during sleep. After accounting for circadian effects, two genes (SREBF1 and CPT1A, both involved in lipid metabolism) exhibited small, but significant, linear changes in expression with the duration of sleep deprivation (FDR < 5%). The main change with sleep deprivation was a reduction in the amplitude of the diurnal rhythm of expression of normally cycling probe sets. This reduction was noticeably higher in behaviorally resistant subjects than sensitive subjects, at any given P value. Furthermore, blood cell type enrichment analysis showed that the expression pattern difference between sensitive and resistant subjects is mainly found in cells of myeloid origin, such as monocytes. Individual differences in behavioral effects of sleep deprivation are associated with differences in diurnal amplitude of gene expression for genes that show circadian rhythmicity. © 2014 Associated Professional Sleep Societies, LLC.

T174. STRUCTURAL ABNORMALITIES IN THE CINGULATE CORTEX IN ADOLESCENTS AT ULTRA-HIGH RISK WHO LATER DEVELOP PSYCHOSIS

PubMed Central

Fortea, Adriana; van Eindhjoven, Phillip; Pariente, Jose; Calvo, Anna; Batalla, Albert; de la Serna, Elena; Ilzarbe, Daniel; Tor, Jordina; Dolz, Montserrat; Baeza, Inmaculada; Sugranyes, Gisela

2018-01-01

Abstract Background Identification of biomarkers of transition to psychosis in individuals at ultra-high risk (UHR) has the potential to improve future outcomes (McGorry, 2008). Structural MRI studies with UHR samples have revealed steeper rates of cortical thinning in temporal, prefrontal and cingulate cortices in individuals who later develop psychosis in both baseline and longitudinal comparisons (Fusar-Poli, 2011; Cannon, 2014). However, little is known about how onset of prodromal symptoms during adolescence impacts on changes in cortical thickness (CTH) (Ziermans, 2012). Methods Multicentre cross-sectional case-control study, including youth aged 10–17 years, recruited from two child and adolescent mental health centres. UHR individuals were identified using the Structured Interview for Prodromal Syndromes criteria with some modifications. Healthy controls (HC) were recruited from the same geographical area. Exclusion criteria comprised personal history of psychotic symptoms, IQ<70, autism spectrum disorder, presence of neurological disorder, or antecedents of head trauma with loss of consciousness. The study was approved by the local Ethical Review Boards. All participants underwent a comprehensive socio-demographic and clinical evaluation at baseline and after 6, 12 and 18 months follow-up to identify which individuals converted to psychosis (UHR-P) and which did not (UHR-NP). High-resolution magnetic resonance structural images were acquired at baseline on a 3Tesla and 1.5Tesla scanners. An inter-site compatibility study was conducted with healthy controls which revealed high inter-site correlation coefficients (r>.6) for CTH measures. Images were pre-processed employing automated procedures implemented in FreeSurfer 5.3.0, cortical parcellation employed the Desikan-Killiany brain atlas. Analyses: First, mean global and lobar (frontal, parietal, temporal, occipital, insula and cingulate) CTH measurements were computed. Then, within lobes showing group effects, CTH was measured for each parcellation. ANCOVA was performed to test differences between groups in SPSS 22.0, including gender, age, total intracranial volume and site as covariates. Significance was set at p<.05, corrected using the false discovery rate (FDR). Results 122 subjects were included (59 UHR-NP vs. 18 UHR-P vs. 45 HC, mean ages: 15.2 ± 1.5 vs. 15.0 ± 1.8 vs. 15.8 ± 1.5, F=1.9, p=.15; gender (%female): 61.0% vs 61.1% vs 68.9%, χ2=.76, p=.68). There were no significant differences in case-control proportion between centres: χ2=1.3, p=.25. No significant differences in global CTH in UHR-P (2.57 ± 0.13mm) relative to UHR-NP (2.56 ± 0.11mm) and HC (2.58 ± 0.09mm) were found. There was a significant group effect on the right cingulate cortex (F=6.6, pFDR=.024): UHR-P showed lower CTH in this area relative to controls (p=.007 uncorrected). Within the right cingulate cortex, a significant group effect was found in the posterior cingulate (F=5.7, pFDR=.016) and isthmus (F=4.6, pFDR=.024), and a trend level in the caudal anterior cingulate (F=2.9, p=.057): with smaller CTH in UHR-P relative to HC in the isthmus cingulate (p=.025) and the posterior cingulate (p=.066). No significant differences were observed between UHR-P and UHR-NP groups. Discussion UHR-P showed significant cortical thinning in several regions of the right cingulate cortex in comparison to HC, giving support to the notion that structural alterations in the cingulate cortex may be present in children and adolescents prior the onset of psychosis. Longitudinal changes in CTH have the potential to increase understanding of changes related to transition to clinical illness.

A test data compression scheme based on irrational numbers stored coding.

PubMed

Wu, Hai-feng; Cheng, Yu-sheng; Zhan, Wen-fa; Cheng, Yi-fei; Wu, Qiong; Zhu, Shi-juan

2014-01-01

Test question has already become an important factor to restrict the development of integrated circuit industry. A new test data compression scheme, namely irrational numbers stored (INS), is presented. To achieve the goal of compress test data efficiently, test data is converted into floating-point numbers, stored in the form of irrational numbers. The algorithm of converting floating-point number to irrational number precisely is given. Experimental results for some ISCAS 89 benchmarks show that the compression effect of proposed scheme is better than the coding methods such as FDR, AARLC, INDC, FAVLC, and VRL.

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

PubMed Central

Freedman, Adam H.; Schweizer, Rena M.; Ortega-Del Vecchyo, Diego; Han, Eunjung; Davis, Brian W.; Gronau, Ilan; Silva, Pedro M.; Galaverni, Marco; Fan, Zhenxin; Marx, Peter; Lorente-Galdos, Belen; Ramirez, Oscar; Hormozdiari, Farhad; Alkan, Can; Vilà, Carles; Squire, Kevin; Geffen, Eli; Kusak, Josip; Boyko, Adam R.; Parker, Heidi G.; Lee, Clarence; Tadigotla, Vasisht; Siepel, Adam; Bustamante, Carlos D.; Harkins, Timothy T.; Nelson, Stanley F.; Marques-Bonet, Tomas; Ostrander, Elaine A.; Wayne, Robert K.; Novembre, John

2016-01-01

Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the domestication, we examined patterns of polymorphism in six canid genomes that were previously used to infer a demographic model of dog domestication. Using an inferred demographic model, we computed false discovery rates (FDR) and identified 349 outlier regions consistent with positive selection at a low FDR. The signals in the top 100 regions were frequently centered on candidate genes related to brain function and behavior, including LHFPL3, CADM2, GRIK3, SH3GL2, MBP, PDE7B, NTAN1, and GLRA1. These regions contained significant enrichments in behavioral ontology categories. The 3rd top hit, CCRN4L, plays a major role in lipid metabolism, that is supported by additional metabolism related candidates revealed in our scan, including SCP2D1 and PDXC1. Comparing our method to an empirical outlier approach that does not directly account for demography, we found only modest overlaps between the two methods, with 60% of empirical outliers having no overlap with our demography-based outlier detection approach. Demography-aware approaches have lower-rates of false discovery. Our top candidates for selection, in addition to expanding the set of neurobehavioral candidate genes, include genes related to lipid metabolism, suggesting a dietary target of selection that was important during the period when proto-dogs hunted and fed alongside hunter-gatherers. PMID:26943675

Disrupted rich club network in behavioral variant frontotemporal dementia and early-onset Alzheimer's disease

PubMed Central

Daianu, Madelaine; Mezher, Adam; Mendez, Mario F.; Jahanshad, Neda; Jimenez, Elvira E.; Thompson, Paul M.

2016-01-01

In network analysis, the so-called ‘rich club’ describes the core areas of the brain that are more densely interconnected among themselves than expected by chance, and has been identified as a fundamental aspect of the human brain connectome. This is the first in-depth diffusion imaging study to investigate the rich club along with other organizational changes in the brain's anatomical network in behavioral frontotemporal dementia (bvFTD), and a matched cohort with early-onset Alzheimer's disease (EOAD). Our study sheds light on how bvFTD and EOAD affect connectivity of white matter fiber pathways in the brain, revealing differences and commonalities in the connectome among the dementias. To analyze the breakdown in connectivity, we studied 3 groups: 20 bvFTD, 23 EOAD and 37 healthy elderly controls. All participants were scanned with diffusion-weighted MRI, and based on whole-brain probabilistic tractography and cortical parcellations, we analyzed the rich club of the brain's connectivity network. This revealed distinct patterns of disruption in both forms of dementia. In the connectome, we detected less disruption overall in EOAD than in bvFTD (False Discovery Rate (FDR) critical Pperm=5.7×10−3, 10,000 permutations), with more involvement of richly interconnected areas of the brain (chi-squared PΧ2=1.4×10−4) – predominantly posterior cognitive alterations. In bvFTD, we found a greater spread of disruption including the rich club (FDR critical Pperm=6×10−4), but especially more peripheral alterations (PΧ2=6.5×10−3), particularly in medial frontal areas of the brain, in line with the known behavioral socioemotional deficits seen in these patients. PMID:26678225

Evidence for gene-gene epistatic interactions among susceptibility loci for systemic lupus erythematosus.

PubMed

Hughes, Travis; Adler, Adam; Kelly, Jennifer A; Kaufman, Kenneth M; Williams, Adrienne H; Langefeld, Carl D; Brown, Elizabeth E; Alarcón, Graciela S; Kimberly, Robert P; Edberg, Jeffrey C; Ramsey-Goldman, Rosalind; Petri, Michelle; Boackle, Susan A; Stevens, Anne M; Reveille, John D; Sanchez, Elena; Martín, Javier; Niewold, Timothy B; Vilá, Luis M; Scofield, R Hal; Gilkeson, Gary S; Gaffney, Patrick M; Criswell, Lindsey A; Moser, Kathy L; Merrill, Joan T; Jacob, Chaim O; Tsao, Betty P; James, Judith A; Vyse, Timothy J; Alarcón-Riquelme, Marta E; Harley, John B; Richardson, Bruce C; Sawalha, Amr H

2012-02-01

Several confirmed genetic susceptibility loci for lupus have been described. To date, no clear evidence for genetic epistasis in lupus has been established. The aim of this study was to test for gene-gene interactions in a number of known lupus susceptibility loci. Eighteen single-nucleotide polymorphisms tagging independent and confirmed lupus susceptibility loci were genotyped in a set of 4,248 patients with lupus and 3,818 normal healthy control subjects of European descent. Epistasis was tested by a 2-step approach using both parametric and nonparametric methods. The false discovery rate (FDR) method was used to correct for multiple testing. We detected and confirmed gene-gene interactions between the HLA region and CTLA4, IRF5, and ITGAM and between PDCD1 and IL21 in patients with lupus. The most significant interaction detected by parametric analysis was between rs3131379 in the HLA region and rs231775 in CTLA4 (interaction odds ratio 1.19, Z = 3.95, P = 7.8 × 10(-5) [FDR ≤0.05], P for multifactor dimensionality reduction = 5.9 × 10(-45)). Importantly, our data suggest that in patients with lupus, the presence of the HLA lupus risk alleles in rs1270942 and rs3131379 increases the odds of also carrying the lupus risk allele in IRF5 (rs2070197) by 17% and 16%, respectively (P = 0.0028 and P = 0.0047, respectively). We provide evidence for gene-gene epistasis in systemic lupus erythematosus. These findings support a role for genetic interaction contributing to the complexity of lupus heritability. Copyright © 2012 by the American College of Rheumatology.

Predictors of Overweight During Childhood in Offspring of Parents With Type 1 Diabetes

PubMed Central

Hummel, Sandra; Pflüger, Maren; Kreichauf, Susanne; Hummel, Michael; Ziegler, Anette-G.

2009-01-01

OBJECTIVE To study which perinatal factors affect the risk of childhood overweight in offspring with a first-degree relative (FDR) with type 1 diabetes and to determine whether maternal diabetes is an independent contributor to overweight risk. RESEARCH DESIGN AND METHODS Data on a child's weight and height were collected at age 2, 5, and 8 years from 1,214 children participating in the prospective BABYDIAB study. All children had an FDR with type 1 diabetes, including 783 whose mothers had type 1 diabetes. Overweight was defined as BMI percentile ≥90. Data on birth size, breast-feeding, maternal age, and smoking during pregnancy were collected by questionnaires. Risk estimates were calculated by logistic regression analyses. RESULTS Breastfeeding duration and birth size both contributed significantly to overweight risk at all age intervals. Full breast-feeding >4 months or any breast-feeding >6 months reduced risk of overweight (aged 8 years: odds ratio 0.3 [95% CI 0.2–0.7], P = 0.004; and 0.3 [0.1–0.6], P = 0.001). Large-for-gestational-age status increased risk of overweight (aged 8 years: 2.4 [1.4–4.3], P = 0.002). Importantly, no evidence was found for an independent contribution of maternal type 1 diabetes to childhood overweight. CONCLUSIONS Our findings indicate that maternal type 1 diabetes is not an independent risk factor for overweight during childhood in offspring of type 1 diabetic mothers but that factors associated with maternal type 1 diabetes, such as short breast-feeding duration and high birth size, predispose children to overweight during childhood. PMID:19228867

Risk modeling in prospective diabetes studies: Association and predictive value of anthropometrics.

PubMed

Jafari-Koshki, Tohid; Arsang-Jang, Shahram; Aminorroaya, Ashraf; Mansourian, Marjan; Amini, Masoud

2018-04-03

This study aimed to introduce and apply modern statistical techniques for assessing association and predictive value of risk factors in first-degree relatives (FDR) of patients with diabetes from repeatedly measured diabetes data. We used data from 1319 FDR's of patients with diabetes followed for 8 years. Association and predictive performance of weight (Wt), body mass index (BMI), waist and hip circumferences (WC and HC) and their ratio (WHR), waist-height ratio (WHtR) and a body shape index (ABSI) in relation to future diabetes were evaluated by using Cox regression and joint longitudinal-survival modeling. According to Cox regression, in total sample, WC, HC, Wt, WHtR and BMI had significant direct association with diabetes (all p < 0.01) with the best predictive ability for WHtR (concordance probability estimate = 0.575). Joint modeling suggested direct associations between diabetes and WC, WHR, Wt, WHtR and BMI in total sample (all p < 0.05). According to LPML criterion, WHtR was the best predictor in both total sample and females with LPML of -2666.27 and -2185.67, respectively. However, according to AUC criteria, BMI had the best predictive performance with AUC-JM = 0.7629 and dAUC-JM = 0.5883 in total sample. In females, both AUC criteria indicated that WC was the best predictor followed by WHtR. WC, WHR, Wt, WHtR and BMI are among candidate anthropometric measures to be monitored in diabetes prevention programs. Larger multi-ethnic and multivariate research are warranted to assess interactions and identify the best predictors in subgroups. Copyright © 2018 Diabetes India. Published by Elsevier Ltd. All rights reserved.

The effect of fecal microbiota transplantation on psychiatric symptoms among patients with irritable bowel syndrome, functional diarrhea and functional constipation: An open-label observational study.

PubMed

Kurokawa, Shunya; Kishimoto, Taishiro; Mizuno, Shinta; Masaoka, Tatsuhiro; Naganuma, Makoto; Liang, Kuo-Ching; Kitazawa, Momoko; Nakashima, Moeko; Shindo, Chie; Suda, Wataru; Hattori, Masahira; Kanai, Takanori; Mimura, Masaru

2018-08-01

The intestinal microbiota is considered as a potential common underpinning pathophysiology of Functional Gastrointestinal Disorders (FGIDs) and psychiatric disorders such as depression and anxiety. Fecal Microbiota Transplantation (FMT) has been reported to have therapeutic effects on diseases related to dysbiosis, but few studies have evaluated its effect on psychiatric symptoms. We followed 17 patients with either Irritable Bowel Syndrome (IBS), Functional Diarrhea (FDr) or Functional Constipation (FC) who underwent FMT for the treatment of gastrointestinal symptoms and observation of psychiatric symptoms. Changes in Hamilton Rating Scale for Depression (HAM-D) and subscale of sleep-related items, Hamilton Rating Scale for Anxiety (HAM-A) and Quick Inventory for Depressive Symptoms (QIDS) between baseline and 4 weeks after FMT, and relationship with the intestinal microbiota were measured. At baseline, 12 out of 17 patients were rated with HAM-D ≥ 8. Significant improvement in HAM-D total and sleep subscale score, HAM-A and QIDS were observed (p = 0.007, p = 0.007, p = 0.01, p = 0.007, respectively). Baseline Shannon index indicated that microbiota showed lower diversity in patients with HAM-D ≥ 8 compared to those of healthy donors and patients with HAM-D < 8. There was a significant correlation between baseline Shannon index and HAM-D score, and a correlation between Shannon index change and HAM-D improvement after FMT. The small sample size with no control group. Our results suggest that depression and anxiety symptoms may be improved by FMT regardless of gastrointestinal symptom change in patients with IBS, FDr and FC, and the increase of microbiota diversity may help to improve patient's mood. Copyright © 2018 Elsevier B.V. All rights reserved.

Maternal Choline Supplementation during Normal Murine Pregnancy Alters the Placental Epigenome: Results of an Exploratory Study.

PubMed

Kwan, Sze Ting Cecilia; King, Julia H; Grenier, Jennifer K; Yan, Jian; Jiang, Xinyin; Roberson, Mark S; Caudill, Marie A

2018-03-28

The placental epigenome regulates processes that affect placental and fetal development, and could be mediating some of the reported effects of maternal choline supplementation (MCS) on placental vascular development and nutrient delivery. As an extension of work previously conducted in pregnant mice, the current study sought to explore the effects of MCS on various epigenetic markers in the placenta. RNA and DNA were extracted from placentas collected on embryonic day 15.5 from pregnant mice fed a 1X or 4X choline diet, and were subjected to genome-wide sequencing procedures or mass-spectrometry-based assays to examine placental imprinted gene expression, DNA methylation patterns, and microRNA (miRNA) abundance. MCS yielded a higher (fold change = 1.63-2.25) expression of four imprinted genes ( Ampd3 , Tfpi2 , Gatm and Aqp1 ) in the female placentas and a lower (fold change = 0.46-0.62) expression of three imprinted genes ( Dcn , Qpct and Tnfrsf23 ) in the male placentas (false discovery rate (FDR) ≤ 0.05 for both sexes). Methylation in the promoter regions of these genes and global placental DNA methylation were also affected ( p ≤ 0.05). Additionally, a lower (fold change = 0.3; P unadjusted = 2.05 × 10 -4 ; FDR = 0.13) abundance of miR-2137 and a higher (fold change = 1.25-3.92; p < 0.05) expression of its target genes were detected in the 4X choline placentas. These data demonstrate that the placental epigenome is responsive to maternal choline intake during murine pregnancy and likely mediates some of the previously described choline-induced effects on placental and fetal outcomes.

Maternal obesity programs mitochondrial and lipid metabolism gene expression in infant umbilical vein endothelial cells.

PubMed

Costa, S M R; Isganaitis, E; Matthews, T J; Hughes, K; Daher, G; Dreyfuss, J M; da Silva, G A P; Patti, M-E

2016-11-01

Maternal obesity increases risk for childhood obesity, but molecular mechanisms are not well understood. We hypothesized that primary umbilical vein endothelial cells (HUVEC) from infants of overweight and obese mothers would harbor transcriptional patterns reflecting offspring obesity risk. In this observational cohort study, we recruited 13 lean (pre-pregnancy body mass index (BMI) <25.0 kg m -2 ) and 24 overweight-obese ('ov-ob', BMI⩾25.0 kg m -2 ) women. We isolated primary HUVEC, and analyzed both gene expression (Primeview, Affymetrix) and cord blood levels of hormones and adipokines. A total of 142 transcripts were differentially expressed in HUVEC from infants of overweight-obese mothers (false discovery rate, FDR<0.05). Pathway analysis revealed that genes involved in mitochondrial and lipid metabolism were negatively correlated with maternal BMI (FDR<0.05). To test whether these transcriptomic patterns were associated with distinct nutrient exposures in the setting of maternal obesity, we analyzed the cord blood lipidome and noted significant increases in the levels of total free fatty acids (lean: 95.5±37.1 μg ml -1 , ov-ob: 124.1±46.0 μg ml -1 , P=0.049), palmitate (lean: 34.5±12.7 μg ml -1 , ov-ob: 46.3±18.4 μg ml -1 , P=0.03) and stearate (lean: 20.8±8.2 μg ml -1 , ov-ob: 29.7±17.2 μg ml -1 , P=0.04), in infants of overweight-obese mothers. Prenatal exposure to maternal obesity alters HUVEC expression of genes involved in mitochondrial and lipid metabolism, potentially reflecting developmentally programmed differences in oxidative and lipid metabolism.

Maternal obesity programs mitochondrial and lipid metabolism gene expression in infant umbilical vein endothelial cells

PubMed Central

Ramos Costa, Suzana Maria; Isganaitis, Elvira; Matthews, Tucker; Hughes, Katelyn; Daher, Grace; Dreyfuss, Jonathan M.; Pontes da Silva, Giselia Alves; Patti, Mary-Elizabeth

2016-01-01

Background/Objectives Maternal obesity increases risk for childhood obesity, but molecular mechanisms are not well understood. We hypothesized that primary umbilical vein endothelial cells (HUVEC) from infants of overweight and obese mothers would harbor transcriptional patterns reflecting offspring obesity risk. Subjects/Methods In this observational cohort study, we recruited 13 lean (pre-pregnancy BMI <25.0 kg/m2) and 24 overweight-obese (‘ov-ob’, BMI ≥25.0 kg/m2) women. We isolated primary HUVEC, and analyzed both gene expression (Primeview, Affymetrix) and cord blood levels of hormones and adipokines. Results 142 transcripts were differentially expressed in HUVEC from infants of overweight-obese mothers (false discovery rate, FDR <0.05). Pathway analysis revealed that genes involved in mitochondrial and lipid metabolism were negatively correlated with maternal BMI (FDR <0.05). To test whether these transcriptomic patterns were associated with distinct nutrient exposures in the setting of maternal obesity, we analyzed the cord blood lipidome and noted significant increases in levels of total free fatty acids (lean: 95.5 ± 37.1 ug/ml, ov-ob: 124.1 ± 46.0 ug/ml, P=0.049), palmitate (lean: 34.5 ± 12.7 ug/ml, ov-ob: 46.3 ± 18.4 ug/ml, P=0.03) and stearate (lean: 20.8 ± 8.2 ug/ml, ov-ob: 29.7 ± 17.2 ug/ml, P=0.04), in infants of overweight-obese mothers. Conclusion Prenatal exposure to maternal obesity alters HUVEC expression of genes involved in mitochondrial and lipid metabolism, potentially reflecting developmentally-programmed differences in oxidative and lipid metabolism. PMID:27531045

Gene Expression in Accumbens GABA Neurons from Inbred Rats with Different Drug-Taking Behavior

PubMed Central

Sharp, B.M.; Chen, H.; Gong, S.; Wu, X.; Liu, Z.; Hiler, K.; Taylor, W.L.; Matta, S.G.

2011-01-01

Inbred Lewis and Fisher 344 rat strains differ greatly in drug self-administration; Lewis rats operantly self-administer drugs of abuse including nicotine, whereas Fisher self-administer poorly. As shown herein, operant food self-administration is similar. Based on their pivotal role in drug reward, we hypothesized that differences in basal gene expression in GABAergic neurons projecting from nucleus accumbens (NAcc) to ventral pallidum (VP) play a role in vulnerability to drug taking behavior. The transcriptomes of NAcc shell-VP GABAergic neurons from these two strains were analyzed in adolescents, using a multidisciplinary approach that combined stereotaxic ionotophoretic brain microinjections, laser-capture microdissection (LCM) and microarray measurement of transcripts. LCM enriched the gene transcripts detected in GABA neurons compared to the residual NAcc tissue: a ratio of neuron/residual > 1 and false discovery rate (FDR) <5% yielded 6,623 transcripts, whereas a ratio of >3 yielded 3,514. Strain-dependent differences in gene expression within GABA neurons were identified; 322 vs. 60 transcripts showed 1.5-fold vs. 2-fold differences in expression (FDR<5%). Classification by gene ontology showed these 322 transcripts were widely distributed, without categorical enrichment. This is most consistent with a global change in GABA neuron function. Literature-mining by Chilibot found 38 genes related to synaptic plasticity, signaling and gene transcription, all of which determine drug-abuse; 33 genes have no known association with addiction or nicotine. In Lewis rats, upregulation of Mint-1, Cask, CamkIIδ, Ncam1, Vsnl1, Hpcal1 and Car8 indicates these transcripts likely contribute to altered signaling and synaptic function in NAcc GABA projection neurons to VP. PMID:21745336

Augmentation of Heroin Seeking Following Chronic Food Restriction in the Rat: Differential Role for Dopamine Transmission in the Nucleus Accumbens Shell and Core.

PubMed

D'Cunha, Tracey M; Daoud, Emilie; Rizzo, Damaris; Bishop, Audrey B; Russo, Melissa; Mourra, Gabrielle; Hamel, Laurie; Sedki, Firas; Shalev, Uri

2017-04-01

Caloric restriction during drug abstinence increases the risk for relapse in addicts. In rats, chronic food restriction during a period of withdrawal following heroin self-administration augments heroin seeking. The mechanisms underlying this effect are largely unknown. Here, we investigated the role of nucleus accumbens (NAc) shell and core dopamine (DA) in food restriction-induced augmentation of heroin seeking. Rats were trained to self-administer heroin (0.1 mg/kg/infusion) for 10 days. Next, rats were moved to the animal colony for a withdrawal period, during which rats were food restricted to 90% of their original body weight (FDR group) or given unrestricted access to food (sated group). On day 14 of food restriction, rats were returned to the operant conditioning chambers for a heroin-seeking test under extinction conditions. Extracellular DA levels were assessed using in vivo microdialysis. In separate experiments, the DA D1-like receptor antagonist SCH39166 (12.5, 25.0, or 50.0 ng/side) was administered into the NAc before the heroin-seeking test. In the NAc shell, pre-test exposure to the heroin-associated context increased DA only in FDR rats; but in the NAc core, DA increased regardless of feeding condition. Food restriction significantly augmented heroin seeking and increased DA in the NAc shell and core during the test. Intra-NAc shell administration of SCH39166 decreased heroin seeking in all rats. In contrast, in the NAc core, SCH39166 selectively decreased the augmentation of heroin-seeking induced by chronic food restriction. Taken together, these results suggest that activation of the DA D1-like receptor in the NAc core is important for food restriction-induced augmentation of heroin seeking.

DNA-Methylation Patterns in Trisomy 21 Using Cells from Monozygotic Twins

PubMed Central

Sailani, M. Reza; Santoni, Federico A.; Letourneau, Audrey; Borel, Christelle; Makrythanasis, Periklis; Hibaoui, Youssef; Popadin, Konstantin; Bonilla, Ximena; Guipponi, Michel; Gehrig, Corinne; Vannier, Anne; Carre-Pigeon, Frederique; Feki, Anis; Nizetic, Dean; Antonarakis, Stylianos E.

2015-01-01

DNA methylation is essential in mammalian development. We have hypothesized that methylation differences induced by trisomy 21 (T21) contribute to the phenotypic characteristics and heterogeneity in Down syndrome (DS). In order to determine the methylation differences in T21 without interference of the interindividual genomic variation, we have used fetal skin fibroblasts from monozygotic (MZ) twins discordant for T21. We also used skin fibroblasts from MZ twins concordant for T21, normal MZ twins without T21, and unrelated normal and T21 individuals. Reduced Representation Bisulfite Sequencing (RRBS) revealed 35 differentially methylated promoter regions (DMRs) (Absolute methylation differences = 25%, FDR < 0.001) in MZ twins discordant for T21 that have also been observed in comparison between unrelated normal and T21 individuals. The identified DMRs are enriched for genes involved in embryonic organ morphogenesis (FDR = 1.60 e -03) and include genes of the HOXB and HOXD clusters. These DMRs are maintained in iPS cells generated from this twin pair and are correlated with the gene expression changes. We have also observed an increase in DNA methylation level in the T21 methylome compared to the normal euploid methylome. This observation is concordant with the up regulation of DNA methyltransferase enzymes (DNMT3B and DNMT3L) and down regulation of DNA demethylation enzymes (TET2 and TET3) observed in the iPSC of the T21 versus normal twin. Altogether, the results of this study highlight the epigenetic effects of the extra chromosome 21 in T21 on loci outside of this chromosome that are relevant to DS associated phenotypes. PMID:26317209

Empirical null estimation using zero-inflated discrete mixture distributions and its application to protein domain data.

PubMed

Gauran, Iris Ivy M; Park, Junyong; Lim, Johan; Park, DoHwan; Zylstra, John; Peterson, Thomas; Kann, Maricel; Spouge, John L

2017-09-22

In recent mutation studies, analyses based on protein domain positions are gaining popularity over gene-centric approaches since the latter have limitations in considering the functional context that the position of the mutation provides. This presents a large-scale simultaneous inference problem, with hundreds of hypothesis tests to consider at the same time. This article aims to select significant mutation counts while controlling a given level of Type I error via False Discovery Rate (FDR) procedures. One main assumption is that the mutation counts follow a zero-inflated model in order to account for the true zeros in the count model and the excess zeros. The class of models considered is the Zero-inflated Generalized Poisson (ZIGP) distribution. Furthermore, we assumed that there exists a cut-off value such that smaller counts than this value are generated from the null distribution. We present several data-dependent methods to determine the cut-off value. We also consider a two-stage procedure based on screening process so that the number of mutations exceeding a certain value should be considered as significant mutations. Simulated and protein domain data sets are used to illustrate this procedure in estimation of the empirical null using a mixture of discrete distributions. Overall, while maintaining control of the FDR, the proposed two-stage testing procedure has superior empirical power. 2017 The Authors. Biometrics published by Wiley Periodicals, Inc. on behalf of International Biometric Society This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cortical thickness and low insight into symptoms in enduring schizophrenia.

PubMed

Emami, Seema; Guimond, Synthia; Mallar Chakravarty, M; Lepage, Martin

2016-01-01

Poor insight is a common, multidimensional phenomenon in patients with schizophrenia, associated with poorer outcomes and treatment non-adherence. Yet scant research has investigated the neuronal correlates of insight into symptoms (IS), a dimension of insight that may be particularly significant in enduring schizophrenia. Sixty-six patients with enduring schizophrenia (duration >4years) and 33 healthy controls completed MRI scanning and IQ, depression, and anxiety assessments. The Scale to Assess Insight-Expanded (SAI-E) measured insight into patients' four most prominent symptoms and patients were classified into two groups: low IS (0-2; n=33), and high IS (>2; n=33). We evaluated the association between cortical thickness (CT) and insight into symptoms using two methods: (1) a between-patients region-of-interest analysis in the insula, superior temporal gyrus (STG) and frontal lobe; and (2) a whole-brain exploratory regression between patient and controls. Brain regions were segmented using a neuroanatomical atlas and vertex-wise CT analyses were conducted with CIVET, covaried for age and sex. ROI analysis revealed thinner insula cortex in patients with low IS (p<0.05, surviving FDR correction). Patients with low IS also showed significantly thinner right insula, STG, and parahippocampal cortex compared to healthy controls (p<0.05, surviving FDR correction). Regions of observed CT reductions have been hypothesized to subserve self-monitoring, error awareness, and ability to identify hallucinations. Results highlight an important association between right insula abnormalities and impaired IS in schizophrenia. The diverse clinical presentation of patients further suggests an independent relationship between symptomology and insight-related differences in CT that has been previously unexplored in enduring schizophrenia. Copyright © 2015 Elsevier B.V. All rights reserved.

Method for evaluation of laboratory craters using crater detection algorithm for digital topography data

NASA Astrophysics Data System (ADS)

Salamunićcar, Goran; Vinković, Dejan; Lončarić, Sven; Vučina, Damir; Pehnec, Igor; Vojković, Marin; Gomerčić, Mladen; Hercigonja, Tomislav

In our previous work the following has been done: (1) the crater detection algorithm (CDA) based on digital elevation model (DEM) has been developed and the GT-115225 catalog has been assembled [GRS, 48 (5), in press, doi:10.1109/TGRS.2009.2037750]; and (2) the results of comparison between explosion-induced laboratory craters in stone powder surfaces and GT-115225 have been presented using depth/diameter measurements [41stLPSC, Abstract #1428]. The next step achievable using the available technology is to create 3D scans of such labo-ratory craters, in order to compare different properties with simple Martian craters. In this work, we propose a formal method for evaluation of laboratory craters, in order to provide objective, measurable and reproducible estimation of the level of achieved similarity between these laboratory and real impact craters. In the first step, the section of MOLA data for Mars (or SELENE LALT for Moon) is replaced with one or several 3D-scans of laboratory craters. Once embedment was done, the CDA can be used to find out whether this laboratory crater is similar enough to real craters, as to be recognized as a crater by the CDA. The CDA evaluation using ROC' curve represents how true detection rate (TDR=TP/(TP+FN)=TP/GT) depends on the false detection rate (FDR=FP/(TP+FP)). Using this curve, it is now possible to define the measure of similarity between laboratory and real impact craters, as TDR or FDR value, or as a distance from the bottom-right origin of the ROC' curve. With such an approach, the reproducible (formally described) method for evaluation of laboratory craters is provided.

Tissue-specific impact of FADS cluster variants on FADS1 and FADS2 gene expression.

PubMed

Reynolds, Lindsay M; Howard, Timothy D; Ruczinski, Ingo; Kanchan, Kanika; Seeds, Michael C; Mathias, Rasika A; Chilton, Floyd H

2018-01-01

Omega-6 (n-6) and omega-3 (n-3) long (≥ 20 carbon) chain polyunsaturated fatty acids (LC-PUFAs) play a critical role in human health and disease. Biosynthesis of LC-PUFAs from dietary 18 carbon PUFAs in tissues such as the liver is highly associated with genetic variation within the fatty acid desaturase (FADS) gene cluster, containing FADS1 and FADS2 that encode the rate-limiting desaturation enzymes in the LC-PUFA biosynthesis pathway. However, the molecular mechanisms by which FADS genetic variants affect LC-PUFA biosynthesis, and in which tissues, are unclear. The current study examined associations between common single nucleotide polymorphisms (SNPs) within the FADS gene cluster and FADS1 and FADS2 gene expression in 44 different human tissues (sample sizes ranging 70-361) from the Genotype-Tissue Expression (GTEx) Project. FADS1 and FADS2 expression were detected in all 44 tissues. Significant cis-eQTLs (within 1 megabase of each gene, False Discovery Rate, FDR<0.05, as defined by GTEx) were identified in 12 tissues for FADS1 gene expression and 23 tissues for FADS2 gene expression. Six tissues had significant (FDR< 0.05) eQTLs associated with both FADS1 and FADS2 (including artery, esophagus, heart, muscle, nerve, and thyroid). Interestingly, the identified eQTLs were consistently found to be associated in opposite directions for FADS1 and FADS2 expression. Taken together, findings from this study suggest common SNPs within the FADS gene cluster impact the transcription of FADS1 and FADS2 in numerous tissues and raise important questions about how the inverse expression of these two genes impact intermediate molecular (such a LC-PUFA and LC-PUFA-containing glycerolipid levels) and ultimately clinical phenotypes associated with inflammatory diseases and brain health.

Analysis of genetic composition and transmitted parental heterozygosity of natural 2n gametes in Populus tomentosa based on SSR markers.

PubMed

Han, Zhiqiang; Geng, Xining; Du, Kang; Xu, Congping; Yao, Pengqiang; Bai, Fengying; Kang, Xiangyang

2018-06-01

Natural 2n female gametes and transmission of parental heterozygosity by natural 2n gametes in Populus tomentosa are reported for the first time, which provides a new approach to polyploid breeding. Naturally occurring 2n pollen is widespread in Populus tomentosa and plays an important role in polyploid breeding. However, the competitiveness of 2n pollen is lower than that of haploid pollen during pollination and fertilization, so 2n pollen is less efficient at fertilizing haploid female gametes to produce polyploids. In theory, polyploids can also be obtained when 2n female gametes are fertilized by haploid pollen. Thus, the question becomes whether natural 2n female gametes exist in P. tomentosa, which can be answered by examining the genetic composition of natural 2n gametes. In this study, the origin of 87 triploids from the hybrid combination "X-2 × Z-5" was identified by SSR markers and 21% of natural 2n gametes were found to originate from female parents. Four SSR loci with low recombination rates were used to identify the genetic composition of natural 2n gametes. The results showed that the genetic composition of 2n female gametes was mainly characterized by SDR, while 2n male gametes were mainly produced by FDR. Moreover, the transmission of parental heterozygosity by natural 2n gametes, which is significantly different between female and male parents in FDR and SDR types, was analysed using 42 SSR primers. Here, we report naturally occurring 2n female gametes for the first time in P. tomentosa and reveal the genetic constitution and transmitted parental heterozygosity of these gametes. Our results provide a foundation for theoretical research into 2n gametes and their application in new polyploid breeding strategies.

Blood cell gene expression associated with cellular stress defense is modulated by antioxidant-rich food in a randomised controlled clinical trial of male smokers.

PubMed

Bøhn, Siv K; Myhrstad, Mari C; Thoresen, Magne; Holden, Marit; Karlsen, Anette; Tunheim, Siv Haugen; Erlund, Iris; Svendsen, Mette; Seljeflot, Ingebjørg; Moskaug, Jan O; Duttaroy, Asim K; Laake, Petter; Arnesen, Harald; Tonstad, Serena; Collins, Andrew; Drevon, Christan A; Blomhoff, Rune

2010-09-16

Plant-based diets rich in fruit and vegetables can prevent development of several chronic age-related diseases. However, the mechanisms behind this protective effect are not elucidated. We have tested the hypothesis that intake of antioxidant-rich foods can affect groups of genes associated with cellular stress defence in human blood cells. NCT00520819 http://clinicaltrials.gov. In an 8-week dietary intervention study, 102 healthy male smokers were randomised to either a diet rich in various antioxidant-rich foods, a kiwifruit diet (three kiwifruits/d added to the regular diet) or a control group. Blood cell gene expression profiles were obtained from 10 randomly selected individuals of each group. Diet-induced changes on gene expression were compared to controls using a novel application of the gene set enrichment analysis (GSEA) on transcription profiles obtained using Affymetrix HG-U133-Plus 2.0 whole genome arrays. Changes were observed in the blood cell gene expression profiles in both intervention groups when compared to the control group. Groups of genes involved in regulation of cellular stress defence, such as DNA repair, apoptosis and hypoxia, were significantly upregulated (GSEA, FDR q-values < 5%) by both diets compared to the control group. Genes with common regulatory motifs for aryl hydrocarbon receptor (AhR) and AhR nuclear translocator (AhR/ARNT) were upregulated by both interventions (FDR q-values < 5%). Plasma antioxidant biomarkers (polyphenols/carotenoids) increased in both groups. The observed changes in the blood cell gene expression profiles suggest that the beneficial effects of a plant-based diet on human health may be mediated through optimization of defence processes.

Clinical and Metabolic Characterization of Lean Caucasian Subjects With Non-alcoholic Fatty Liver.

PubMed

Feldman, Alexandra; Eder, Sebastian K; Felder, Thomas K; Kedenko, Lyudmyla; Paulweber, Bernhard; Stadlmayr, Andreas; Huber-Schönauer, Ursula; Niederseer, David; Stickel, Felix; Auer, Simon; Haschke-Becher, Elisabeth; Patsch, Wolfgang; Datz, Christian; Aigner, Elmar

2017-01-01

Non-alcoholic fatty liver disease (NAFLD) is closely linked to obesity; however, 5-8% of lean subjects also have evidence of NAFLD. We aimed to investigate clinical, genetic, metabolic and lifestyle characteristics in lean Caucasian subjects with NAFLD. Data from 187 subjects allocated to one of the three groups according to body mass index (BMI) and hepatic steatosis on ultrasound were obtained: lean healthy (BMI≤25 kg/m 2 , no steatosis, N=71), lean NAFLD (BMI≤25 kg/m 2 , steatosis, N=55), obese NAFLD (BMI≥30 kg/m 2 , steatosis; N=61). All subjects received a detailed clinical and laboratory examination including oral glucose tolerance test. The serum metabolome was assessed using the Metabolomics AbsoluteIDQ p180 kit (BIOCRATES Life Sciences). Genotyping for single-nucleotide polymorphisms (SNPs) associated with NAFLD was performed. Lean NAFLD subjects had fasting insulin concentrations similar to lean healthy subjects but had markedly impaired glucose tolerance. Lean NAFLD subjects had a higher rate of the mutant PNPLA3 CG/GG variant compared to lean controls (P=0.007). Serum adiponectin concentrations were decreased in both NAFLD groups compared to controls (P<0.001 for both groups) The metabolomics study revealed a potential role for various lysophosphatidylcholines (lyso-PC C18:0, lyso-PC C17:0) and phosphatidylcholines (PCaa C36:3; false discovery rate (FDR)-corrected P-value<0.001) as well as lysine, tyrosine, and valine (FDR<0.001). Lean subjects with evidence of NAFLD have clinically relevant impaired glucose tolerance, low adiponectin concentrations and a distinct metabolite profile with an increased rate of PNPLA3 risk allele carriage.

Relative Risks for Lethal Prostate Cancer Based on Complete Family History of Prostate Cancer Death.

PubMed

Albright, Frederick S; Stephenson, Robert A; Agarwal, Neeraj; Cannon-Albright, Lisa A

2017-01-01

There are few published familial relative risks (RR) for lethal prostate cancer. This study estimates RRs for lethal prostate cancer based on comprehensive family history data, with the goal of improving identification of those men at highest risk of dying from prostate cancer. We used a population-based genealogical resource linked to a statewide electronic SEER cancer registry and death certificates to estimate relative risks (RR) for death from prostate cancer based upon family history. Over 600,000 male probands were analyzed, representing a variety of family history constellations of lethal prostate cancer. RR estimates were based on the ratio of the observed to the expected number of lethal prostate cancer cases using internal rates. RRs for lethal prostate cancer based on the number of affected first-degree relatives (FDR) ranged from 2.49 (95% CI: 2.27, 2.73) for exactly 1 FDR to 5.30 (2.13, 10.93) for ≥3 affected FDRs. In an absence of affected FDRs, increased risk was also significant for increasing numbers of affected second-degree or third degree relatives. Equivalent risks were observed for similar maternal and paternal family history. This study provides population-based estimates of lethal prostate cancer risk based on lethal prostate cancer family history. Many family history constellations associated with two to greater than five times increased risk for lethal prostate cancer were identified. These lethal prostate cancer risk estimates hold potential for use in identification, screening, early diagnosis, and treatment of men at high risk for death from prostate cancer. Prostate77:41-48, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Protein differences between human trapezius and vastus lateralis muscles determined with a proteomic approach.

PubMed

Hadrévi, Jenny; Hellström, Fredrik; Kieselbach, Thomas; Malm, Christer; Pedrosa-Domellöf, Fatima

2011-08-10

The trapezius muscle is a neck muscle that is susceptible to chronic pain conditions associated with repetitive tasks, commonly referred to as chronic work-related myalgia, hence making the trapezius a muscle of clinical interest. To provide a basis for further investigations of the proteomic traits of the trapezius muscle in disease, two-dimensional difference gel electrophoresis (2D-DIGE) was performed on the healthy trapezius using vastus lateralis as a reference. To obtain as much information as possible from the vast proteomic data set, both one-way ANOVA, with and without false discovery rate (FDR) correlation, and partial least square projection to latent structures with discriminant analysis (PLS-DA) were combined to compare the outcome of the analysis. The trapezius and vastus lateralis showed significant differences in metabolic, contractile and regulatory proteins, with different results depending on choice of statistical approach and pre-processing technique. Using the standard method, FDR correlated one-way ANOVA, 42 protein spots differed significantly in abundance between the two muscles. Complementary analysis using immunohistochemistry and western blot confirmed the results from the 2D-DIGE analysis. The proteomic approach used in the present study combining 2D-DIGE and multivariate modelling provided a more comprehensive comparison of the protein profiles of the human trapezius and vastus lateralis muscle, than previously possible to obtain with immunohistochemistry or SDS-PAGE alone. Although 2D-DIGE has inherent limitations it is particularly useful to comprehensively screen for important structural and metabolic proteins, and appears to be a promising tool for future studies of patients suffering from chronic work related myalgia or other muscle diseases.

Proteomics Indicators of the Rapidly Shifting Physiology from Whole Mountain Pine Beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), Adults during Early Host Colonization

PubMed Central

Pitt, Caitlin; Robert, Jeanne A.; Bonnett, Tiffany R.; Keeling, Christopher I.; Bohlmann, Jörg; Huber, Dezene P. W.

2014-01-01

We developed proteome profiles for host colonizing mountain pine beetle adults, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). Adult insects were fed in pairs on fresh host lodgepole pine, Pinus contorta Dougl. ex Loud, phloem tissue. The proteomes of fed individuals were monitored using iTRAQ and compared to those of starved beetles, revealing 757 and 739 expressed proteins in females and males, respectively, for which quantitative information was obtained. Overall functional category distributions were similar for males and females, with the majority of proteins falling under carbohydrate metabolism (glycolysis, gluconeogenesis, citric acid cycle), structure (cuticle, muscle, cytoskeleton), and protein and amino acid metabolism. Females had 23 proteins with levels that changed significantly with feeding (p<0.05, FDR<0.20), including chaperones and enzymes required for vitellogenesis. In males, levels of 29 proteins changed significantly with feeding (p<0.05, FDR<0.20), including chaperones as well as motor proteins. Only two proteins, both chaperones, exhibited a significant change in both females and males with feeding. Proteins with differential accumulation patterns in females exhibited higher fold changes with feeding than did those in males. This difference may be due to major and rapid physiological changes occurring in females upon finding a host tree during the physiological shift from dispersal to reproduction. The significant accumulation of chaperone proteins, a cytochrome P450, and a glutathione S-transferase, indicate secondary metabolite-induced stress physiology related to chemical detoxification during early host colonization. The females' activation of vitellogenin only after encountering a host indicates deliberate partitioning of resources and a balancing of the needs of dispersal and reproduction. PMID:25360753

Proteomics indicators of the rapidly shifting physiology from whole mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), adults during early host colonization.

PubMed

Pitt, Caitlin; Robert, Jeanne A; Bonnett, Tiffany R; Keeling, Christopher I; Bohlmann, Jörg; Huber, Dezene P W

2014-01-01

We developed proteome profiles for host colonizing mountain pine beetle adults, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). Adult insects were fed in pairs on fresh host lodgepole pine, Pinus contorta Dougl. ex Loud, phloem tissue. The proteomes of fed individuals were monitored using iTRAQ and compared to those of starved beetles, revealing 757 and 739 expressed proteins in females and males, respectively, for which quantitative information was obtained. Overall functional category distributions were similar for males and females, with the majority of proteins falling under carbohydrate metabolism (glycolysis, gluconeogenesis, citric acid cycle), structure (cuticle, muscle, cytoskeleton), and protein and amino acid metabolism. Females had 23 proteins with levels that changed significantly with feeding (p<0.05, FDR<0.20), including chaperones and enzymes required for vitellogenesis. In males, levels of 29 proteins changed significantly with feeding (p<0.05, FDR<0.20), including chaperones as well as motor proteins. Only two proteins, both chaperones, exhibited a significant change in both females and males with feeding. Proteins with differential accumulation patterns in females exhibited higher fold changes with feeding than did those in males. This difference may be due to major and rapid physiological changes occurring in females upon finding a host tree during the physiological shift from dispersal to reproduction. The significant accumulation of chaperone proteins, a cytochrome P450, and a glutathione S-transferase, indicate secondary metabolite-induced stress physiology related to chemical detoxification during early host colonization. The females' activation of vitellogenin only after encountering a host indicates deliberate partitioning of resources and a balancing of the needs of dispersal and reproduction.

Central and non-central networks, cognition, clinical symptoms, and polygenic risk scores in schizophrenia.

PubMed

Alloza, Clara; Bastin, Mark E; Cox, Simon R; Gibson, Jude; Duff, Barbara; Semple, Scott I; Whalley, Heather C; Lawrie, Stephen M

2017-12-01

Schizophrenia is a complex disorder that may be the result of aberrant connections between specific brain regions rather than focal brain abnormalities. Here, we investigate the relationships between brain structural connectivity as described by network analysis, intelligence, symptoms, and polygenic risk scores (PGRS) for schizophrenia in a group of patients with schizophrenia and a group of healthy controls. Recently, researchers have shown an interest in the role of high centrality networks in the disorder. However, the importance of non-central networks still remains unclear. Thus, we specifically examined network-averaged fractional anisotropy (mean edge weight) in central and non-central subnetworks. Connections with the highest betweenness centrality within the average network (>75% of centrality values) were selected to represent the central subnetwork. The remaining connections were assigned to the non-central subnetwork. Additionally, we calculated graph theory measures from the average network (connections that occur in at least 2/3 of participants). Density, strength, global efficiency, and clustering coefficient were significantly lower in patients compared with healthy controls for the average network (p FDR  < 0.05). All metrics across networks were significantly associated with intelligence (p FDR  < 0.05). There was a tendency towards significance for a correlation between intelligence and PGRS for schizophrenia (r = -0.508, p = 0.052) that was significantly mediated by central and non-central mean edge weight and every graph metric from the average network. These results are consistent with the hypothesis that intelligence deficits are associated with a genetic risk for schizophrenia, which is mediated via the disruption of distributed brain networks. Hum Brain Mapp 38:5919-5930, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A fish-based diet intervention improves endothelial function in postmenopausal women with type 2 diabetes mellitus: a randomized crossover trial.

PubMed

Kondo, Keiko; Morino, Katsutaro; Nishio, Yoshihiko; Kondo, Motoyuki; Nakao, Keiko; Nakagawa, Fumiyuki; Ishikado, Atsushi; Sekine, Osamu; Yoshizaki, Takeshi; Kashiwagi, Atsunori; Ugi, Satoshi; Maegawa, Hiroshi

2014-07-01

The beneficial effects of fish and n-3 polyunsaturated fatty acids (PUFAs) consumption on atherosclerosis have been reported in numerous epidemiological studies. However, to the best of our knowledge, the effects of a fish-based diet intervention on endothelial function have not been investigated. Therefore, we studied these effects in postmenopausal women with type 2 diabetes mellitus (T2DM). Twenty-three postmenopausal women with T2DM were assigned to two four-week periods of either a fish-based diet (n-3 PUFAs ≧ 3.0 g/day) or a control diet in a randomized crossover design. Endothelial function was measured with reactive hyperemia using strain-gauge plethysmography and compared with the serum levels of fatty acids and their metabolites. Endothelial function was determined with peak forearm blood flow (Peak), duration of reactive hyperemia (Duration) and flow debt repayment (FDR). A fish-based dietary intervention improved Peak by 63.7%, Duration by 27.9% and FDR by 70.7%, compared to the control diet. Serum n-3 PUFA levels increased after the fish-based diet period and decreased after the control diet, compared with the baseline (1.49 vs. 0.97 vs. 1.19 mmol/l, p < 0.0001). There was no correlation between serum n-3 PUFA levels and endothelial function. An increased ratio of epoxyeicosatrienoic acid/dihydroxyeicosatrienoic acid was observed after a fish-based diet intervention, possibly due to the inhibition of the activity of soluble epoxide hydrolase. A fish-based dietary intervention improves endothelial function in postmenopausal women with T2DM. Dissociation between the serum n-3 PUFA concentration and endothelial function suggests that the other factors may contribute to this phenomenon. Copyright © 2014 Elsevier Inc. All rights reserved.

Transcription of PR3 and Related Myelopoiesis Genes in Peripheral Blood Mononuclear Cells in Active Wegener's Granulomatosis

PubMed Central

Cheadle, Chris; Berger, Alan E.; Andrade, Felipe; James, Regina; Johnson, Kristen; Watkins, Tonya; Park, Jin Kyun; Chen, Yu-Chi; Ehrlich, Eva; Mullins, Marissa; Chrest, Francis; Barnes, Kathleen C.; Levine, Stuart M.

2010-01-01

Objective Wegener's granulomatosis (WG) is a systemic inflammatory disease causing substantial morbidity. This study seeks to understand the biology underlying WG, and to discover markers of disease activity useful in prognosis and treatment guidance. Methods Gene expression profiling was performed using total RNA from PBMC and granulocyte fractions from 41 WG patients and 23 healthy controls. Gene set enrichment analysis (GSEA) was performed to search for candidate WG-associated molecular pathways and disease activity biomarkers. Principal component analysis (PCA) was used to visualize relationships between subgroups of WG patients and controls. Longitudinal changes in PR3 expression were evaluated using RT-PCR, and clinical outcomes including remission status and disease activity were determined using the BVAS-WG. Results We identified 86 genes significantly up-regulated in WG PBMCs and 40 in WG PMNs relative to controls. Genes up-regulated in WG PBMCs were involved in myeloid differentiation, and included the WG autoantigen, PR3. The coordinated regulation of myeloid differentiation genes was confirmed by gene set analysis. Median expression values of the 86 WG PBMC genes were associated with disease activity (p=1.3 × 10−4), and patients expressing these genes at a lower level were only modestly different from healthy controls (p=0.07). PR3 transcription was significantly up-regulated in the PBMCs (p=1.3 ×10−5, FDR=0.002), but not in the PMNs (p=0.03, FDR=0.28) of WG patients, and changes in BVAS-WG tracked with PBMC PR3 RNA levels in a preliminary longitudinal analysis. Conclusion Transcription of PR3 and related myeloid differentiation genes in PBMCs may represent novel markers of disease activity in WG. PMID:20155833

Genetic correlates of insight in schizophrenia.

PubMed

Xavier, Rose Mary; Vorderstrasse, Allison; Keefe, Richard S E; Dungan, Jennifer R

2018-05-01

Insight in schizophrenia is clinically important as it is associated with several adverse outcomes. Genetic contributions to insight are unknown. We examined genetic contributions to insight by investigating if polygenic risk scores (PRS) and candidate regions were associated with insight. Schizophrenia case-only analysis of the Clinical Antipsychotics Trials of Intervention Effectiveness trial. Schizophrenia PRS was constructed using Psychiatric Genomics Consortium (PGC) leave-one out GWAS as discovery data set. For candidate regions, we selected 105 schizophrenia-associated autosomal loci and 11 schizophrenia-related oligodendrocyte genes. We used regressions to examine PRS associations and set-based testing for candidate analysis. We examined data from 730 subjects. Best-fit PRS at p-threshold of 1e-07 was associated with total insight (R 2 =0.005, P=0.05, empirical P=0.054) and treatment insight (R 2 =0.005, P=0.048, empirical P=0.048). For models that controlled for neurocognition, PRS significantly predicted treatment insight but at higher p-thresholds (0.1 to 0.5) but did not survive correction. Patients with highest polygenic burden had 5.9 times increased risk for poor insight compared to patients with lowest burden. PRS explained 3.2% (P=0.002, empirical P=0.011) of variance in poor insight. Set-based analyses identified two variants associated with poor insight- rs320703, an intergenic variant (within-set P=6e-04, FDR P=0.046) and rs1479165 in SOX2-OT (within-set P=9e-04, FDR P=0.046). To the best of our knowledge, this is the first study examining genetic basis of insight. We provide evidence for genetic contributions to impaired insight. Relevance of findings and necessity for replication are discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

In silico pathway analysis in cervical carcinoma reveals potential new targets for treatment

PubMed Central

van Dam, Peter A.; van Dam, Pieter-Jan H. H.; Rolfo, Christian; Giallombardo, Marco; van Berckelaer, Christophe; Trinh, Xuan Bich; Altintas, Sevilay; Huizing, Manon; Papadimitriou, Kostas; Tjalma, Wiebren A. A.; van Laere, Steven

2016-01-01

An in silico pathway analysis was performed in order to improve current knowledge on the molecular drivers of cervical cancer and detect potential targets for treatment. Three publicly available Affymetrix gene expression data-sets (GSE5787, GSE7803, GSE9750) were retrieved, vouching for a total of 9 cervical cancer cell lines (CCCLs), 39 normal cervical samples, 7 CIN3 samples and 111 cervical cancer samples (CCSs). Predication analysis of microarrays was performed in the Affymetrix sets to identify cervical cancer biomarkers. To select cancer cell-specific genes the CCSs were compared to the CCCLs. Validated genes were submitted to a gene set enrichment analysis (GSEA) and Expression2Kinases (E2K). In the CCSs a total of 1,547 probe sets were identified that were overexpressed (FDR < 0.1). Comparing to CCCLs 560 probe sets (481 unique genes) had a cancer cell-specific expression profile, and 315 of these genes (65%) were validated. GSEA identified 5 cancer hallmarks enriched in CCSs (P < 0.01 and FDR < 0.25) showing that deregulation of the cell cycle is a major component of cervical cancer biology. E2K identified a protein-protein interaction (PPI) network of 162 nodes (including 20 drugable kinases) and 1626 edges. This PPI-network consists of 5 signaling modules associated with MYC signaling (Module 1), cell cycle deregulation (Module 2), TGFβ-signaling (Module 3), MAPK signaling (Module 4) and chromatin modeling (Module 5). Potential targets for treatment which could be identified were CDK1, CDK2, ABL1, ATM, AKT1, MAPK1, MAPK3 among others. The present study identified important driver pathways in cervical carcinogenesis which should be assessed for their potential therapeutic drugability. PMID:26701206

Prior to extension, Transcriptomes of fibroblast-like Synoviocytes from extended and Polyarticular juvenile idiopathic arthritis are indistinguishable.

PubMed

Brescia, AnneMarie C; Simonds, Megan M; McCahan, Suzanne M; Sullivan, Kathleen E; Rose, Carlos D

2018-01-08

Our intent was to identify differences between the transcriptome of fibroblast-like synoviocytes (FLS) in oligoarticular juvenile idiopathic arthritis (JIA) before extension when compared to persistent subtype of JIA, when the two are clinically indistinguishable. Additionally, we sought to determine if differences between the transcriptomes of FLS from extended-to-be and polyarticular course JIA could be detected. Our hypothesis was that intrinsic differences in the transcriptome of the FLS from extended-to-be JIA would distinguish them from persistent oligoarticular JIA, before the course is clinically apparent. Global gene expression was defined in cultured FLS from 6 controls, 12 JIA with persistent course, 7 JIA prior to extension (extended-to-be), 4 JIA with extended course and 6 polyarticular onset, using Affymetrix Human GeneChips 133plus2.0. Bioconductor Linear Models for Microarray Analysis revealed 22 probesets with differential expression between persistent and extended-to-be FLS at 15% FDR, however only 2 probesets distinguished extended-to-be from extended and none distinguished extended-to-be and polyarticular at 15% FDR. Differences in extended and polyarticular gene expression profiles were not detected. Confirmation of select genes was done on the RNA level by RT-qPCR and on the protein level in synovial fluid by ELISA. The transcriptome of FLS from extended-to-be juvenile idiopathic arthritis is distinct from persistent course before a clinical distinction can be made. Additionally, the transcriptome of extended-to-be and polyarticular course, including those who have already extended, are indistinguishable. These gene expression data suggest that FLS already reflect a polyarticular behavior early in disease course, suggesting that extended-to-be may be "latent polyarticular" at onset. These differences can be used to develop early biomarkers of disease course, allowing for better-informed treatment decisions.

Marginal Vitamin B-6 Deficiency Decreases Plasma (n-3) and (n-6) PUFA Concentrations in Healthy Men and Women123

PubMed Central

Zhao, Mei; Lamers, Yvonne; Ralat, Maria A.; Coats, Bonnie S.; Chi, Yueh-Yun; Muller, Keith E.; Bain, James R.; Shankar, Meena N.; Newgard, Christopher B.; Stacpoole, Peter W.; Gregory, Jesse F.

2012-01-01

Previous animal studies showed that severe vitamin B-6 deficiency altered fatty acid profiles of tissue lipids, often with an increase of linoleic acid and a decrease of arachidonic acid. However, little is known about the extent to which vitamin B-6 deficiency affects human fatty acid profiles. The aim of this study was to determine the effects of marginal vitamin B-6 deficiency on fatty acid profiles in plasma, erythrocytes, and peripheral blood mononuclear cells (PBMC) of healthy adults fed a 28-d, low-vitamin B-6 diet. Healthy participants (n = 23) received a 2-d, controlled, vitamin B-6–adequate diet followed by a 28-d, vitamin B-6–restricted diet to induce a marginal deficiency. Plasma HDL and LDL cholesterol concentrations, FFA concentrations, and erythrocyte and PBMC membrane fatty acid compositions did not significantly change from baseline after the 28-d restriction. Plasma total arachidonic acid, EPA, and DHA concentrations decreased from (mean ± SD) 548 ± 96 to 490 ± 94 μmol/L, 37 ± 13 to 32 ± 13 μmol/L, and 121 ± 28 to 109 ± 28 μmol/L [positive false discovery rate (pFDR) adjusted P < 0.05], respectively. The total (n-6):(n-3) PUFA ratio in plasma exhibited a minor increase from 15.4 ± 2.8 to 16.6 ± 3.1 (pFDR adjusted P < 0.05). These data indicate that short-term vitamin B-6 restriction decreases plasma (n-3) and (n-6) PUFA concentrations and tends to increase the plasma (n-6):(n-3) PUFA ratio. Such changes in blood lipids may be associated with the elevated risk of cardiovascular disease in vitamin B-6 insufficiency. PMID:22955512

Efficacy of family mediation and the role of family violence: study protocol.

PubMed

Cleak, Helen; Schofield, Margot; Bickerdike, Andrew

2014-01-21

Family law reforms in Australia require separated parents in dispute to attempt mandatory family dispute resolution (FDR) in community-based family services before court attendance. However, there are concerns about such services when clients present with a history of high conflict and family violence. This study protocol describes a longitudinal study of couples presenting for family mediation services. The study aims to describe the profile of family mediation clients, including type of family violence, and determine the impact of violence profiles on FDR processes and outcomes, such as the type and durability of shared parenting arrangements and clients' satisfaction with mediated agreements. A mixed method, naturalistic longitudinal design is used. The sampling frame is clients presenting at nine family mediation centres across metropolitan, outer suburban, and regional/rural sites in Victoria, Australia. Data are collected at pre-test, completion of mediation, and six months later. Self-administered surveys are administered at the three time points, and a telephone interview at the final post-test. The key study variable is family violence. Key outcome measures are changes in the type and level of acrimony and violent behaviours, the relationship between violence and mediated agreements, the durability of agreements over six months, and client satisfaction with mediation. Family violence is a major risk to the physical and mental health of women and children. This study will inform debates about the role of family violence and how to manage it in the family mediation context. It will also inform decision-making about mediation practices by better understanding how mediation impacts on parenting agreements, and the implications for children, especially in the context of family violence.

Epigenetic Signatures of Cigarette Smoking

PubMed Central

Joehanes, Roby; Just, Allan C.; Marioni, Riccardo E.; Pilling, Luke C.; Reynolds, Lindsay M.; Mandaviya, Pooja R.; Guan, Weihua; Xu, Tao; Elks, Cathy E.; Aslibekyan, Stella; Moreno-Macias, Hortensia; Smith, Jennifer A.; Brody, Jennifer A.; Dhingra, Radhika; Yousefi, Paul; Pankow, James S.; Kunze, Sonja; Shah, Sonia; McRae, Allan F.; Lohman, Kurt; Sha, Jin; Absher, Devin M.; Ferrucci, Luigi; Zhao, Wei; Demerath, Ellen W.; Bressler, Jan; Grove, Megan L.; Huan, Tianxiao; Liu, Chunyu; Mendelson, Michael M.; Yao, Chen; Kiel, Douglas P.; Peters, Annette; Wang-Sattler, Rui; Visscher, Peter M.; Wray, Naomi R.; Starr, John M.; Ding, Jingzhong; Rodriguez, Carlos J.; Wareham, Nicholas J.; Irvin, Marguerite R.; Zhi, Degui; Barrdahl, Myrto; Vineis, Paolo; Ambatipudi, Srikant; Uitterlinden, André G.; Hofman, Albert; Schwartz, Joel; Colicino, Elena; Hou, Lifang; Vokonas, Pantel S.; Hernandez, Dena G.; Singleton, Andrew B.; Bandinelli, Stefania; Turner, Stephen T.; Ware, Erin B.; Smith, Alicia K.; Klengel, Torsten; Binder, Elisabeth B.; Psaty, Bruce M.; Taylor, Kent D.; Gharib, Sina A.; Swenson, Brenton R.; Liang, Liming; DeMeo, Dawn L.; O'Connor, George T.; Herceg, Zdenko; Ressler, Kerry J.; Conneely, Karen N.; Sotoodehnia, Nona; Kardia, Sharon L. R.; Melzer, David; Baccarelli, Andrea A.; van Meurs, Joyce B. J.; Romieu, Isabelle; Arnett, Donna K.; Ong, Ken K.; Liu, Yongmei; Waldenberger, Melanie; Deary, Ian J.; Fornage, Myriam; Levy, Daniel; London, Stephanie J.

2016-01-01

Background DNA methylation leaves a long-term signature of smoking exposure and is one potential mechanism by which tobacco exposure predisposes to adverse health outcomes, such as cancers, osteoporosis, lung, and cardiovascular disorders. Methods and Results To comprehensively determine the association between cigarette smoking and DNA methylation, we conducted a meta-analysis of genome-wide DNA methylation assessed using the Illumina BeadChip 450K array on 15,907 blood derived DNA samples from participants in 16 cohorts (including 2,433 current, 6,518 former, and 6,956 never smokers). Comparing current versus never smokers, 2,623 CpG sites (CpGs), annotated to 1,405 genes, were statistically significantly differentially methylated at Bonferroni threshold of p<1×10−7 (18,760 CpGs at False Discovery Rate (FDR)<0.05). Genes annotated to these CpGs were enriched for associations with several smoking-related traits in genome-wide studies including pulmonary function, cancers, inflammatory diseases and heart disease. Comparing former versus never smokers, 185 of the CpGs that differed between current and never smokers were significant p<1×10−7 (2,623 CpGs at FDR<0.05), indicating a pattern of persistent altered methylation, with attenuation, after smoking cessation. Transcriptomic integration identified effects on gene expression at many differentially methylated CpGs. Conclusions Cigarette smoking has a broad impact on genome-wide methylation that, at many loci, persists many years after smoking cessation. Many of the differentially methylated genes were novel genes with respect to biologic effects of smoking, and might represent therapeutic targets for prevention or treatment of tobacco-related diseases. Methylation at these sites could also serve as sensitive and stable biomarkers of lifetime exposure to tobacco smoke. PMID:27651444

Associations of body mass index and waist circumference with: energy intake and percentage energy from macronutrients, in a cohort of australian children

PubMed Central

2011-01-01

Background It is evident from previous research that the role of dietary composition in relation to the development of childhood obesity remains inconclusive. Several studies investigating the relationship between body mass index (BMI), waist circumference (WC) and/or skin fold measurements with energy intake have suggested that the macronutrient composition of the diet (protein, carbohydrate, fat) may play an important contributing role to obesity in childhood as it does in adults. This study investigated the possible relationship between BMI and WC with energy intake and percentage energy intake from macronutrients in Australian children and adolescents. Methods Height, weight and WC measurements, along with 24 h food and drink records (FDR) intake data were collected from 2460 boys and girls aged 5-17 years living in the state of Queensland, Australia. Results Statistically significant, yet weak correlations between BMI z-score and WC with total energy intake were observed in grades 1, 5 and 10, with only 55% of subjects having a physiologically plausible 24 hr FDR. Using Pearson correlations to examine the relationship between BMI and WC with energy intake and percentage macronutrient intake, no significant correlations were observed between BMI z-score or WC and percentage energy intake from protein, carbohydrate or fat. One way ANOVAs showed that although those with a higher BMI z-score or WC consumed significantly more energy than their lean counterparts. Conclusion No evidence of an association between percentage macronutrient intake and BMI or WC was found. Evidently, more robust longitudinal studies are needed to elucidate the relationship linking obesity and dietary intake. PMID:21615883

Screening the molecular targets of ovarian cancer based on bioinformatics analysis.

PubMed

Du, Lei; Qian, Xiaolei; Dai, Chenyang; Wang, Lihua; Huang, Ding; Wang, Shuying; Shen, Xiaowei

2015-01-01

Ovarian cancer (OC) is the most lethal gynecologic malignancy. This study aims to explore the molecular mechanisms of OC and identify potential molecular targets for OC treatment. Microarray gene expression data (GSE14407) including 12 normal ovarian surface epithelia samples and 12 OC epithelia samples were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) between 2 kinds of ovarian tissue were identified by using limma package in R language (|log2 fold change| gt;1 and false discovery rate [FDR] lt;0.05). Protein-protein interactions (PPIs) and known OC-related genes were screened from COXPRESdb and GenBank database, respectively. Furthermore, PPI network of top 10 upregulated DEGs and top 10 downregulated DEGs was constructed and visualized through Cytoscape software. Finally, for the genes involved in PPI network, functional enrichment analysis was performed by using DAVID (FDR lt;0.05). In total, 1136 DEGs were identified, including 544 downregulated and 592 upregulated DEGs. Then, PPI network was constructed, and DEGs CDKN2A, MUC1, OGN, ZIC1, SOX17, and TFAP2A interacted with known OC-related genes CDK4, EGFR/JUN, SRC, CLI1, CTNNB1, and TP53, respectively. Moreover, functions about oxygen transport and embryonic development were enriched by the genes involved in the network of downregulated DEGs. We propose that 4 DEGs (OGN, ZIC1, SOX17, and TFAP2A) and 2 functions (oxygen transport and embryonic development) might play a role in the development of OC. These 4 DEGs and known OC-related genes might serve as therapeutic targets for OC. Further studies are required to validate these predictions.

Exercise training causes differential changes in gene expression in diaphragm arteries and 2A arterioles of obese rats.

PubMed

Laughlin, M Harold; Padilla, Jaume; Jenkins, Nathan T; Thorne, Pamela K; Martin, Jeffrey S; Rector, R Scott; Akter, Sadia; Davis, J Wade

2015-09-15

We employed next-generation, transcriptome-wide RNA sequencing (RNA-Seq) technology to assess the effects of two different exercise training protocols on transcriptional profiles in diaphragm second-order arterioles (D2a) and in the diaphragm feed artery (DFA) from Otsuka Long Evans Tokushima Fatty (OLETF) rats. Arterioles were isolated from the diaphragm of OLETF rats that underwent an endurance exercise training program (EX; n = 13), interval sprint training program (SPRINT; n = 14), or remained sedentary (Sed; n = 12). Our hypothesis was that exercise training would have similar effects on gene expression in the diaphragm and soleus muscle arterioles because diaphragm blood flow increases during exercise to a similar extent as in soleus. Results reveal that several canonical pathways that were significantly altered by exercise in limb skeletal muscles were not among the pathways significantly changed in the diaphragm arterioles including actin cytoskeleton signaling, role of NFAT in regulation of immune response, protein kinase A signaling, and protein ubiquitination pathway. EX training altered the expression of a smaller number of genes than did SPRINT in the DFA but induced a larger number of genes with altered expression in the D2a than did SPRINT. In fact, FDR differential expression analysis (FDR, 10%) indicated that only two genes exhibited altered expression in D2a of SPRINT rats. Very few of the genes that exhibited altered expression in the DFA or D2a were also altered in limb muscle arterioles. Finally, results indicate that the 2a arterioles of soleus muscle (S2a) from endurance-trained animals and the DFA of SPRINT animals exhibited the largest number of genes with altered expression.

The interaction of early life experiences with COMT val158met affects anxiety sensitivity.

PubMed

Baumann, C; Klauke, B; Weber, H; Domschke, K; Zwanzger, P; Pauli, P; Deckert, J; Reif, A

2013-11-01

The pathogenesis of anxiety disorders is considered to be multifactorial with a complex interaction of genetic factors and individual environmental factors. Therefore, the aim of this study was to examine gene-by-environment interactions of the genes coding for catechol-O-methyltransferase (COMT) and monoamine oxidase A (MAOA) with life events on measures related to anxiety. A sample of healthy subjects (N = 782; thereof 531 women; mean age M = 24.79, SD = 6.02) was genotyped for COMT rs4680 and MAOA-uVNTR (upstream variable number of tandem repeats), and was assessed for childhood adversities [Childhood Trauma Questionnaire (CTQ)], anxiety sensitivity [Anxiety Sensitivity Index (ASI)] and anxious apprehension [Penn State Worry Questionnaire (PSWQ)]. Main and interaction effects of genotype, environment and gender on measures related to anxiety were assessed by means of regression analyses. Association analysis showed no main gene effect on either questionnaire score. A significant interactive effect of childhood adversities and COMT genotype was observed: Homozygosity for the low-active met allele and high CTQ scores was associated with a significant increment of explained ASI variance [R(2) = 0.040, false discovery rate (FDR) corrected P = 0.04]. A borderline interactive effect with respect to MAOA-uVNTR was restricted to the male subgroup. Carriers of the low-active MAOA allele who reported more aversive experiences in childhood exhibited a trend for enhanced anxious apprehension (R(2) = 0.077, FDR corrected P = 0.10). Early aversive life experiences therefore might increase the vulnerability to anxiety disorders in the presence of homozygosity for the COMT 158met allele or low-active MAOA-uVNTR alleles. © 2013 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Leaf and canopy reflectance spectrometry applied to the estimation of angular leaf spot disease severity of common bean crops

PubMed Central

Martínez-Martínez, Víctor; Machado, Marley L.; Pinto, Francisco A. C.

2018-01-01

This study is aimed at (i) estimating the angular leaf spot (ALS) disease severity in common beans crops in Brazil, caused by the fungus Pseudocercospora griseola, employing leaf and canopy spectral reflectance data, (ii) evaluating the informative spectral regions in the detection, and (iii) comparing the estimation accuracy when the reflectance or the first derivative reflectance (FDR) is employed. Three data sets of useful spectral reflectance measurements in the 440 to 850 nm range were employed; measurements were taken over the leaves and canopy of bean crops with different levels of disease. A system based in Principal Component Analysis (PCA) and Artificial Neural Networks (ANN) was developed to estimate the disease severity from leaf and canopy hyperspectral reflectance spectra. Levels of disease to be taken as true reference were determined from the proportion of the total leaf surface covered by necrotic lesions on RGB images. When estimating ALS disease severity in bean crops by using hyperspectral reflectance spectrometry, this study suggests that (i) successful estimations with coefficients of determination up to 0.87 can be achieved if the spectra is acquired by the spectroradiometer in contact with the leaves, (ii) unsuccessful estimations are obtained when the spectra are acquired by the spectroradiometer from one or more meters above the crop, (iii) the red to near-infrared spectral region (630–850 nm) offers the same precision in the estimation as the blue to near-infrared spectral region (440–850), and (iv) neither significant improvements nor significant detriments are achieved when the input data to the estimation processing system are the FDR spectra, instead of the reflectance spectra. PMID:29698420

Genetic variants in endotoxin signalling pathway, domestic endotoxin exposure and asthma exacerbations.

PubMed

Kljaic-Bukvic, Blazenka; Blekic, Mario; Aberle, Neda; Curtin, John A; Hankinson, Jenny; Semic-Jusufagic, Aida; Belgrave, Danielle; Simpson, Angela; Custovic, Adnan

2014-10-01

We investigated the interaction between genetic variants in endotoxin signalling pathway and domestic endotoxin exposure in relation to asthma presence, and amongst children with asthma, we explored the association of these genetic variants and endotoxin exposure with hospital admissions due to asthma exacerbations. In a case-control study, we analysed data from 824 children (417 asthmatics, 407 controls; age 5-18 yr). Amongst asthmatics, we extracted data on hospitalization for asthma exacerbation from medical records. Endotoxin exposure was measured in dust samples collected from homes. We included 26 single-nucleotide polymorphisms (SNPs) in the final analysis (5 CD14, 7LY96 and 14 TLR4). Two variants remained significantly associated with hospital admissions with asthma exacerbations after correction for multiple testing: for CD14 SNP rs5744455, carriers of T allele had decreased risk of repeated hospital admissions compared with homozygotes for C allele [OR (95% CI), 0.42 (0.25-0.88), p = 0.01, False Discovery Rate (FDR) p = 0.02]; for LY96 SNP rs17226566, C-allele carriers were at a lower risk of hospital admissions compared with T-allele homozygotes [0.59 (0.38-0.90), p = 0.01, FDR p = 0.04]. We observed two interactions between SNPs in CD14 and LY96 with environmental endotoxin exposure in relation to hospital admissions due to asthma exacerbation which remained significant after correction for multiple testing (CD14 SNPs rs2915863 and LY96 SNP rs17226566). Amongst children with asthma, genetic variants in CD14 and LY96 may increase the risk of hospital admissions with acute exacerbations. Polymorphisms in endotoxin pathway interact with domestic endotoxin exposure in further modification of the risk of hospitalization. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Investigation of dietary factors and endometrial cancer risk using a nutrient-wide association study approach in the EPIC and Nurses' Health Study (NHS) and NHSII.

PubMed

Merritt, Melissa A; Tzoulaki, Ioanna; Tworoger, Shelley S; De Vivo, Immaculata; Hankinson, Susan E; Fernandes, Judy; Tsilidis, Konstantinos K; Weiderpass, Elisabete; Tjønneland, Anne; Petersen, Kristina E N; Dahm, Christina C; Overvad, Kim; Dossus, Laure; Boutron-Ruault, Marie-Christine; Fagherazzi, Guy; Fortner, Renée T; Kaaks, Rudolf; Aleksandrova, Krasimira; Boeing, Heiner; Trichopoulou, Antonia; Bamia, Christina; Trichopoulos, Dimitrios; Palli, Domenico; Grioni, Sara; Tumino, Rosario; Sacerdote, Carlotta; Mattiello, Amalia; Bueno-de-Mesquita, H Bas; Onland-Moret, N Charlotte; Peeters, Petra H; Gram, Inger T; Skeie, Guri; Quirós, J Ramón; Duell, Eric J; Sánchez, María-José; Salmerón, D; Barricarte, Aurelio; Chamosa, Saioa; Ericson, Ulrica; Sonestedt, Emily; Nilsson, Lena Maria; Idahl, Annika; Khaw, Kay-Tee; Wareham, Nicholas; Travis, Ruth C; Rinaldi, Sabina; Romieu, Isabelle; Patel, Chirag J; Riboli, Elio; Gunter, Marc J

2015-02-01

Data on the role of dietary factors in endometrial cancer development are limited and inconsistent. We applied a "nutrient-wide association study" approach to systematically evaluate dietary risk associations for endometrial cancer while controlling for multiple hypothesis tests using the false discovery rate (FDR) and validating the results in an independent cohort. We evaluated endometrial cancer risk associations for dietary intake of 84 foods and nutrients based on dietary questionnaires in three prospective studies, the European Prospective Investigation into Cancer and Nutrition (EPIC; N = 1,303 cases) followed by validation of nine foods/nutrients (FDR ≤ 0.10) in the Nurses' Health Studies (NHS/NHSII; N = 1,531 cases). Cox regression models were used to estimate HRs and 95% confidence intervals (CI). In multivariate adjusted comparisons of the extreme categories of intake at baseline, coffee was inversely associated with endometrial cancer risk (EPIC, median intake 750 g/day vs. 8.6; HR, 0.81; 95% CI, 0.68-0.97, Ptrend = 0.09; NHS/NHSII, median intake 1067 g/day vs. none; HR, 0.82; 95% CI, 0.70-0.96, Ptrend = 0.04). Eight other dietary factors that were associated with endometrial cancer risk in the EPIC study (total fat, monounsaturated fat, carbohydrates, phosphorus, butter, yogurt, cheese, and potatoes) were not confirmed in the NHS/NHSII. Our findings suggest that coffee intake may be inversely associated with endometrial cancer risk. Further data are needed to confirm these findings and to examine the mechanisms linking coffee intake to endometrial cancer risk to develop improved prevention strategies. ©2015 American Association for Cancer Research.

RNA sequencing data from neutrophils of patients with cystic fibrosis reveals potential for developing biomarkers for pulmonary exacerbations.

PubMed

Jiang, Kaiyu; Poppenberg, Kerry E; Wong, Laiping; Chen, Yanmin; Borowitz, Drucy; Goetz, Danielle; Sheehan, Daniel; Frederick, Carla; Tutino, Vincent M; Meng, Hui; Jarvis, James N

2018-06-22

There is no effective way to predict cystic fibrosis (CF) pulmonary exacerbations (CFPE) before they become symptomatic or to assess satisfactory treatment responses. RNA sequencing of peripheral blood neutrophils from CF patients before and after therapy for CFPE was used to create transcriptome profiles. Transcripts with an average transcripts per million (TPM) level > 1.0 and a false discovery rate (FDR) < 0.05 were used in a cosine K-nearest neighbor (KNN) model. Real time PCR was used to corroborate RNA sequencing expression differences in both neutrophils and whole blood samples from an independent cohort of CF patients. Furthermore, sandwich ELISA was conducted to assess plasma levels of MRP8/14 complexes in CF patients before and after therapy. We found differential expression of 136 transcripts and 83 isoforms when we compared neutrophils from CF patients before and after therapy (>1.5 fold change, FDR-adjusted P < 0.05). The model was able to successfully separate CF flare samples from those taken from the same patients in convalescence with an accuracy of 0.75 in both the training and testing cohorts. Six differently expressed genes were confirmed by real time PCR using both isolated neutrophils and whole blood from an independent cohort of CF patients before and after therapy, even though levels of myeloid related protein MRP8/14 dimers in plasma of CF patients were essentially unchanged by therapy. Our findings demonstrate the potential of machine learning approaches for classifying disease states and thus developing sensitive biomarkers that can be used to monitor pulmonary disease activity in CF. Copyright © 2018 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Efficacy of family mediation and the role of family violence: study protocol

PubMed Central

2014-01-01

Background Family law reforms in Australia require separated parents in dispute to attempt mandatory family dispute resolution (FDR) in community-based family services before court attendance. However, there are concerns about such services when clients present with a history of high conflict and family violence. This study protocol describes a longitudinal study of couples presenting for family mediation services. The study aims to describe the profile of family mediation clients, including type of family violence, and determine the impact of violence profiles on FDR processes and outcomes, such as the type and durability of shared parenting arrangements and clients’ satisfaction with mediated agreements. Methods A mixed method, naturalistic longitudinal design is used. The sampling frame is clients presenting at nine family mediation centres across metropolitan, outer suburban, and regional/rural sites in Victoria, Australia. Data are collected at pre-test, completion of mediation, and six months later. Self-administered surveys are administered at the three time points, and a telephone interview at the final post-test. The key study variable is family violence. Key outcome measures are changes in the type and level of acrimony and violent behaviours, the relationship between violence and mediated agreements, the durability of agreements over six months, and client satisfaction with mediation. Discussion Family violence is a major risk to the physical and mental health of women and children. This study will inform debates about the role of family violence and how to manage it in the family mediation context. It will also inform decision-making about mediation practices by better understanding how mediation impacts on parenting agreements, and the implications for children, especially in the context of family violence. PMID:24443936

Exploratory plasma proteomic analysis in a randomized crossover trial of aspirin among healthy men and women.

PubMed

Wang, Xiaoliang; Shojaie, Ali; Zhang, Yuzheng; Shelley, David; Lampe, Paul D; Levy, Lisa; Peters, Ulrike; Potter, John D; White, Emily; Lampe, Johanna W

2017-01-01

Long-term use of aspirin is associated with lower risk of colorectal cancer and other cancers; however, the mechanism of chemopreventive effect of aspirin is not fully understood. Animal studies suggest that COX-2, NFκB signaling and Wnt/β-catenin pathways may play a role, but no clinical trials have systematically evaluated the biological response to aspirin in healthy humans. Using a high-density antibody array, we assessed the difference in plasma protein levels after 60 days of regular dose aspirin (325 mg/day) compared to placebo in a randomized double-blinded crossover trial of 44 healthy non-smoking men and women, aged 21-45 years. The plasma proteome was analyzed on an antibody microarray with ~3,300 full-length antibodies, printed in triplicate. Moderated paired t-tests were performed on individual antibodies, and gene-set analyses were performed based on KEGG and GO pathways. Among the 3,000 antibodies analyzed, statistically significant differences in plasma protein levels were observed for nine antibodies after adjusting for false discoveries (FDR adjusted p-value<0.1). The most significant protein was succinate dehydrogenase subunit C (SDHC), a key enzyme complex of the mitochondrial tricarboxylic acid (TCA) cycle. The other statistically significant proteins (NR2F1, MSI1, MYH1, FOXO1, KHDRBS3, NFKBIE, LYZ and IKZF1) are involved in multiple pathways, including DNA base-pair repair, inflammation and oncogenic pathways. None of the 258 KEGG and 1,139 GO pathways was found to be statistically significant after FDR adjustment. This study suggests several chemopreventive mechanisms of aspirin in humans, which have previously been reported to play a role in anti- or pro-carcinogenesis in cell systems; however, larger, confirmatory studies are needed.

RNA sequencing confirms similarities between PPI-responsive oesophageal eosinophilia and eosinophilic oesophagitis.

PubMed

Peterson, K A; Yoshigi, M; Hazel, M W; Delker, D A; Lin, E; Krishnamurthy, C; Consiglio, N; Robson, J; Yandell, M; Clayton, F

2018-06-04

Although current American guidelines distinguish proton pump inhibitor-responsive oesophageal eosinophilia (PPI-REE) from eosinophilic oesophagitis (EoE), these entities are broadly similar. While two microarray studies showed that they have similar transcriptomes, more extensive RNA sequencing studies have not been done previously. To determine whether RNA sequencing identifies genetic markers distinguishing PPI-REE from EoE. We retrospectively examined 13 PPI-REE and 14 EoE biopsies, matched for tissue eosinophil content, and 14 normal controls. Patients and controls were not PPI-treated at the time of biopsy. We did RNA sequencing on formalin-fixed, paraffin-embedded tissue, with differential expression confirmation by quantitative polymerase chain reaction (PCR). We validated the use of formalin-fixed, paraffin-embedded vs RNAlater-preserved tissue, and compared our formalin-fixed, paraffin-embedded EoE results to a prior EoE study. By RNA sequencing, no genes were differentially expressed between the EoE and PPI-REE groups at the false discovery rate (FDR) ≤0.01 level. Compared to normal controls, 1996 genes were differentially expressed in the PPI-REE group and 1306 genes in the EoE group. By less stringent criteria, only MAPK8IP2 was differentially expressed between PPI-REE and EoE (FDR = 0.029, 2.2-fold less in EoE than in PPI-REE), with similar results by PCR. KCNJ2, which was differentially expressed in a prior study, was similar in the EoE and PPI-REE groups by both RNA sequencing and real-time PCR. Eosinophilic oesophagitis and PPI-REE have comparable transcriptomes, confirming that they are part of the same disease continuum. © 2018 John Wiley & Sons Ltd.

Evaluation of Candidate Genes for Cholinesterase Activity in Farmworkers Exposed to Organophosphorus Pesticides: Association of Single Nucleotide Polymorphisms in BCHE

PubMed Central

Howard, Timothy D.; Hsu, Fang-Chi; Grzywacz, Joseph G.; Chen, Haiying; Quandt, Sara A.; Vallejos, Quirina M.; Whalley, Lara E.; Cui, Wei; Padilla, Stephanie; Arcury, Thomas A.

2010-01-01

Background Organophosphate pesticides act as cholinesterase inhibitors. For those with agricultural exposure to these chemicals, risk of potential exposure-related health effects may be modified by genetic variability in cholinesterase metabolism. Cholinesterase activity is a useful, indirect measurement of pesticide exposure, especially in high-risk individuals such as farmworkers. To understand fully the links between pesticide exposure and potential human disease, analyses must be able to consider genetic variability in pesticide metabolism. Objectives We studied participants in the Community Participatory Approach to Measuring Farmworker Pesticide Exposure (PACE3) study to determine whether cholinesterase levels are associated with single-nucleotide polymorphisms (SNPs) involved in pesticide metabolism. Methods Cholinesterase levels were measured from blood samples taken from 287 PACE3 participants at up to four time points during the 2007 growing season. We performed association tests of cholinesterase levels and 256 SNPs in 30 candidate genes potentially involved in pesticide metabolism. A false discovery rate (FDR) p-value was used to account for multiple testing. Results Thirty-five SNPs were associated (unadjusted p < 0.05) based on at least one of the genetic models tested (general, additive, dominant, and recessive). The strongest evidence of association with cholinesterase levels was observed with two SNPs, rs2668207 and rs2048493, in the butyrylcholinesterase (BCHE) gene (FDR adjusted p = 0.15 for both; unadjusted p = 0.00098 and 0.00068, respectively). In participants with at least one minor allele, cholinesterase levels were lower by 4.3–9.5% at all time points, consistent with an effect that is independent of pesticide exposure. Conclusions Common genetic variation in the BCHE gene may contribute to subtle changes in cholinesterase levels. PMID:20529763

Negative mood influences default mode network functional connectivity in chronic low back pain patients: Implications for functional neuroimaging biomarkers

PubMed Central

Letzen, Janelle E.; Robinson, Michael E.

2016-01-01

The default mode network (DMN) has been proposed as a biomarker for several chronic pain conditions. DMN functional connectivity (fcMRI) is typically examined during resting-state fMRI, in which participants are instructed to let thoughts wander. However, factors at the time of data collection (e.g., negative mood) that might systematically impact pain perception and its brain activity, influencing the application of the DMN as a pain biomarker, are rarely reported. The present study measured whether positive and negative moods altered DMN fcMRI patterns in chronic low back pain (CLBP) patients, specifically focusing on negative mood due to its clinical-relevance. Thirty-three participants (CLBP = 17) underwent resting-state fMRI scanning before and after sad and happy mood inductions, and rated levels of mood and pain intensity at the time of scanning. Two-way repeated measures ANOVAs were conducted on resting-state functional connectivity data. Significant group (CLBP > HC) X condition (sadness > baseline) interaction effects were identified in clusters spanning parietal operculum/postcentral gyrus, insular cortices, anterior cingulate cortex, frontal pole, and a portion of the cerebellum (pFDR < .05). However, only one significant cluster covering a portion of the cerebellum was identified examining a two-way repeated measures ANOVA for happiness > baseline (pFDR < .05). Overall, these findings suggest that DMN fcMRI is affected by negative mood in individuals with and without CLBP. It is possible that DMN fcMRI seen in chronic pain patients is related to an affective dimension of pain, which is important to consider in future neuroimaging biomarker development and implementation. PMID:27583568

A population based cohort study of patients with multiple colon and endometrial cancer: correlation of microsatellite instability (MSI) status, age at diagnosis and cancer risk.

PubMed

Cederquist, K; Golovleva, I; Emanuelsson, M; Stenling, R; Grönberg, H

2001-02-15

Hereditary non-polyposis colorectal cancer, HNPCC, is an autosomal dominant condition predisposing to cancers of primarily the colorectum and the endometrium. The aim of our study was to identify persons at a high risk of hereditary colorectal cancer and to estimate their risk of colon and other HNPCC-associated tumours. Family histories of cancer were obtained on 89 persons with double primary (DP) cancers of the colon and the endometrium. The cancer risks in their 649 first-degree-relatives (FDR) were analysed. The microsatellite instability (MSI) status of the tumour of the proband was also analysed and the cancer risks were estimated in relation to MSI status and age at diagnosis in the proband (over or under 50 years). The overall standardised incidence ratio (SIR) was 1.69 (95% CI; 1.39-2.03). In the =50-year-old cohort the SIR was 2.67 (95% CI; 2.08-3.38). Colon, rectal and uterus cancer exhibited significantly increased risks. This risk was further increased in the =50-year-old MSI positive families. Several =50-year-old MSI negative HNPCC-like families with increased risks were also identified. In conclusion a FDR to a person with a DP cancer of the colorectum or the colon/endometrium have a significantly increased risk of having a colorectal or other HNPCC-associated cancers if the proband is diagnosed with one of the cancers before age 50. These families are candidates for genetic counselling and colorectal screening programmes. Mutations in mismatch repair genes can explain some of the increased risk in these families, but mutations in MSI negative families are probably due to other colon cancer susceptibility genes not yet described. Copyright 2001 Wiley-Liss, Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andre, J.M.; et al.

The data acquisition system (DAQ) of the CMS experiment at the CERN Large Hadron Collider assembles events at a rate of 100 kHz, transporting event data at an aggregate throughput of to the high-level trigger farm. The DAQ architecture is based on state-of-the-art network technologies for the event building. For the data concentration, 10/40 Gbit/s Ethernet technologies are used together with a reduced TCP/IP protocol implemented in FPGA for a reliable transport between custom electronics and commercial computing hardware. A 56 Gbit/s Infiniband FDR Clos network has been chosen for the event builder. This paper presents the implementation and performancemore » of the event-building system.« less

Using value-based total cost of ownership (TCO) measures to inform subsystem trade-offs

NASA Astrophysics Data System (ADS)

Radziwill, Nicole M.; DuPlain, Ronald F.

2010-07-01

Total Cost of Ownership (TCO) is a metric from management accounting that helps expose both the direct and indirect costs of a business decision. However, TCO can sometimes be too simplistic for "make vs. buy" decisions (or even choosing between competing design alternatives) when value and extensibility are more critical than total cost. A three-dimensional value-based TCO, which was developed to clarify product decisions for an observatory prior to Final Design Review (FDR), will be presented in this session. This value-based approach incorporates priority of requirements, satisfiability of requirements, and cost, and can be easily applied in any environment.

Aberrant Expression of COT Is Related to Recurrence of Papillary Thyroid Cancer

PubMed Central

Lee, Jandee; Jeong, Seonhyang; Park, Jae Hyun; Lee, Cho Rok; Ku, Cheol Ryong; Kang, Sang-Wook; Jeong, Jong Ju; Nam, Kee-Hyun; Shin, Dong Yeob; Lee, Eun Jig; Chung, Woong Youn; Jo, Young Suk

2015-01-01

Abstract Aberrant expression of Cancer Osaka Thyroid Oncogene mitogen-activated protein kinase kinase kinase 8 (COT) (MAP3K8) is a driver of resistance to B-RAF inhibition. However, the de novo expression and clinical implications of COT in papillary thyroid cancer (PTC) have not been investigated. The aim of this study is to investigate the expression of A-, B-, C-RAF, and COT in PTC (n = 167) and analyze the clinical implications of aberrant expression of these genes. Quantitative polymerase chain reaction (qPCR) and immunohistochemical staining (IHC) were performed on primary thyroid cancers. Expression of COT was compared with clinicopathological characteristics including recurrence-free survival. Datasets from public repository (NCBI) were subjected to Gene Set Enrichment Analysis (GSEA). qPCR data showed that the relative mRNA expression of A-, B-, C-RAF and COT of PTC were higher than normal tissues (all P < 0.01). In addition, the expression of COT mRNA in PTC showed positive correlation with A- (r = 0.4083, P < 0.001), B- (r = 0.2773, P = 0.0003), and C-RAF (r = 0.5954, P < 0.001). The mRNA expressions of A-, B,- and C-RAF were also correlated with each other (all P < 0.001). In IHC, the staining intensities of B-RAF and COT were higher in PTC than in normal tissue (P < 0.001). Interestingly, moderate-to-strong staining intensities of B-RAF and COT were more frequent in B-RAFV600E-positive PTC (P < 0.001, P = 0.013, respectively). In addition, aberrant expression of COT was related to old age at initial diagnosis (P = 0.045) and higher recurrence rate (P = 0.025). In multivariate analysis, tumor recurrence was persistently associated with moderate-to-strong staining of COT after adjusting for age, sex, extrathyroidal extension, multifocality, T-stage, N-stage, TNM stage, and B-RAFV600E mutation (odds ratio, 4.662; 95% confidence interval 1.066 − 21.609; P = 0.045). Moreover, moderate-to-strong COT expression in PTC was associated with shorter recurrence-free survival (mean follow-up duration, 14.2 ± 4.1 years; P = 0.0403). GSEA indicated that gene sets related to B-RAF-RAS (P < 0.0001, false discovery rate [FDR] q-value = 0.000) and thyroid differentiation (P = 0.048, FDR q-value = 0.05) scores were enriched in lower COT expression group and gene sets such as T-cell receptor signaling pathway and Toll-like receptor signaling pathway are coordinately upregulated in higher COT expression group (both, P < 0.0001, FDR q-value = 0.000). Aberrant expression of A-, B-, and C-RAF, and COT is frequent in PTC; increased expression of COT is correlated with recurrence of PTC. PMID:25674762

Aberrant expression of COT is related to recurrence of papillary thyroid cancer.

PubMed

Lee, Jandee; Jeong, Seonhyang; Park, Jae Hyun; Lee, Cho Rok; Ku, Cheol Ryong; Kang, Sang-Wook; Jeong, Jong Ju; Nam, Kee-Hyun; Shin, Dong Yeob; Lee, Eun Jig; Chung, Woong Youn; Jo, Young Suk

2015-02-01

Aberrant expression of Cancer Osaka Thyroid Oncogene mitogen-activated protein kinase kinase kinase 8 (COT) (MAP3K8) is a driver of resistance to B-RAF inhibition. However, the de novo expression and clinical implications of COT in papillary thyroid cancer (PTC) have not been investigated.The aim of this study is to investigate the expression of A-, B-, C-RAF, and COT in PTC (n = 167) and analyze the clinical implications of aberrant expression of these genes.Quantitative polymerase chain reaction (qPCR) and immunohistochemical staining (IHC) were performed on primary thyroid cancers. Expression of COT was compared with clinicopathological characteristics including recurrence-free survival. Datasets from public repository (NCBI) were subjected to Gene Set Enrichment Analysis (GSEA).qPCR data showed that the relative mRNA expression of A-, B-, C-RAF and COT of PTC were higher than normal tissues (all P < 0.01). In addition, the expression of COT mRNA in PTC showed positive correlation with A- (r = 0.4083, P < 0.001), B- (r = 0.2773, P = 0.0003), and C-RAF (r = 0.5954, P < 0.001). The mRNA expressions of A-, B,- and C-RAF were also correlated with each other (all P < 0.001). In IHC, the staining intensities of B-RAF and COT were higher in PTC than in normal tissue (P < 0.001). Interestingly, moderate-to-strong staining intensities of B-RAF and COT were more frequent in B-RAF-positive PTC (P < 0.001, P = 0.013, respectively). In addition, aberrant expression of COT was related to old age at initial diagnosis (P = 0.045) and higher recurrence rate (P = 0.025). In multivariate analysis, tumor recurrence was persistently associated with moderate-to-strong staining of COT after adjusting for age, sex, extrathyroidal extension, multifocality, T-stage, N-stage, TNM stage, and B-RAF mutation (odds ratio, 4.662; 95% confidence interval 1.066 - 21.609; P = 0.045). Moreover, moderate-to-strong COT expression in PTC was associated with shorter recurrence-free survival (mean follow-up duration, 14.2 ± 4.1 years; P = 0.0403). GSEA indicated that gene sets related to B-RAF-RAS (P < 0.0001, false discovery rate [FDR] q-value = 0.000) and thyroid differentiation (P = 0.048, FDR q-value = 0.05) scores were enriched in lower COT expression group and gene sets such as T-cell receptor signaling pathway and Toll-like receptor signaling pathway are coordinately upregulated in higher COT expression group (both, P < 0.0001, FDR q-value = 0.000).Aberrant expression of A-, B-, and C-RAF, and COT is frequent in PTC; increased expression of COT is correlated with recurrence of PTC.

Performance of the CMS Event Builder

NASA Astrophysics Data System (ADS)

Andre, J.-M.; Behrens, U.; Branson, J.; Brummer, P.; Chaze, O.; Cittolin, S.; Contescu, C.; Craigs, B. G.; Darlea, G.-L.; Deldicque, C.; Demiragli, Z.; Dobson, M.; Doualot, N.; Erhan, S.; Fulcher, J. F.; Gigi, D.; Gładki, M.; Glege, F.; Gomez-Ceballos, G.; Hegeman, J.; Holzner, A.; Janulis, M.; Jimenez-Estupiñán, R.; Masetti, L.; Meijers, F.; Meschi, E.; Mommsen, R. K.; Morovic, S.; O'Dell, V.; Orsini, L.; Paus, C.; Petrova, P.; Pieri, M.; Racz, A.; Reis, T.; Sakulin, H.; Schwick, C.; Simelevicius, D.; Zejdl, P.

2017-10-01

The data acquisition system (DAQ) of the CMS experiment at the CERN Large Hadron Collider assembles events at a rate of 100 kHz, transporting event data at an aggregate throughput of {\\mathscr{O}}(100 {{GB}}/{{s}}) to the high-level trigger farm. The DAQ architecture is based on state-of-the-art network technologies for the event building. For the data concentration, 10/40 Gbit/s Ethernet technologies are used together with a reduced TCP/IP protocol implemented in FPGA for a reliable transport between custom electronics and commercial computing hardware. A 56 Gbit/s Infiniband FDR Clos network has been chosen for the event builder. This paper presents the implementation and performance of the event-building system.

Blood-Gene Expression Reveals Reduced Circadian Rhythmicity in Individuals Resistant to Sleep Deprivation

PubMed Central

Arnardottir, Erna S.; Nikonova, Elena V.; Shockley, Keith R.; Podtelezhnikov, Alexei A.; Anafi, Ron C.; Tanis, Keith Q.; Maislin, Greg; Stone, David J.; Renger, John J.; Winrow, Christopher J.; Pack, Allan I.

2014-01-01

Study Objectives: To address whether changes in gene expression in blood cells with sleep loss are different in individuals resistant and sensitive to sleep deprivation. Design: Blood draws every 4 h during a 3-day study: 24-h normal baseline, 38 h of continuous wakefulness and subsequent recovery sleep, for a total of 19 time-points per subject, with every 2-h psychomotor vigilance task (PVT) assessment when awake. Setting: Sleep laboratory. Participants: Fourteen subjects who were previously identified as behaviorally resistant (n = 7) or sensitive (n = 7) to sleep deprivation by PVT. Intervention: Thirty-eight hours of continuous wakefulness. Measurements and Results: We found 4,481 unique genes with a significant 24-h diurnal rhythm during a normal sleep-wake cycle in blood (false discovery rate [FDR] < 5%). Biological pathways were enriched for biosynthetic processes during sleep. After accounting for circadian effects, two genes (SREBF1 and CPT1A, both involved in lipid metabolism) exhibited small, but significant, linear changes in expression with the duration of sleep deprivation (FDR < 5%). The main change with sleep deprivation was a reduction in the amplitude of the diurnal rhythm of expression of normally cycling probe sets. This reduction was noticeably higher in behaviorally resistant subjects than sensitive subjects, at any given P value. Furthermore, blood cell type enrichment analysis showed that the expression pattern difference between sensitive and resistant subjects is mainly found in cells of myeloid origin, such as monocytes. Conclusion: Individual differences in behavioral effects of sleep deprivation are associated with differences in diurnal amplitude of gene expression for genes that show circadian rhythmicity. Citation: Arnardottir ES, Nikonova EV, Shockley KR, Podtelezhnikov AA, Anafi RC, Tanis KQ, Maislin G, Stone DJ, Renger JJ, Winrow CJ, Pack AI. Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation. SLEEP 2014;37(10):1589-1600. PMID:25197809

Gene expression profiles in Parkinson disease prefrontal cortex implicate FOXO1 and genes under its transcriptional regulation.

PubMed

Dumitriu, Alexandra; Latourelle, Jeanne C; Hadzi, Tiffany C; Pankratz, Nathan; Garza, Dan; Miller, John P; Vance, Jeffery M; Foroud, Tatiana; Beach, Thomas G; Myers, Richard H

2012-06-01

Parkinson disease (PD) is a complex neurodegenerative disorder with largely unknown genetic mechanisms. While the degeneration of dopaminergic neurons in PD mainly takes place in the substantia nigra pars compacta (SN) region, other brain areas, including the prefrontal cortex, develop Lewy bodies, the neuropathological hallmark of PD. We generated and analyzed expression data from the prefrontal cortex Brodmann Area 9 (BA9) of 27 PD and 26 control samples using the 44K One-Color Agilent 60-mer Whole Human Genome Microarray. All samples were male, without significant Alzheimer disease pathology and with extensive pathological annotation available. 507 of the 39,122 analyzed expression probes were different between PD and control samples at false discovery rate (FDR) of 5%. One of the genes with significantly increased expression in PD was the forkhead box O1 (FOXO1) transcription factor. Notably, genes carrying the FoxO1 binding site were significantly enriched in the FDR-significant group of genes (177 genes covered by 189 probes), suggesting a role for FoxO1 upstream of the observed expression changes. Single-nucleotide polymorphisms (SNPs) selected from a recent meta-analysis of PD genome-wide association studies (GWAS) were successfully genotyped in 50 out of the 53 microarray brains, allowing a targeted expression-SNP (eSNP) analysis for 52 SNPs associated with PD affection at genome-wide significance and the 189 probes from FoxO1 regulated genes. A significant association was observed between a SNP in the cyclin G associated kinase (GAK) gene and a probe in the spermine oxidase (SMOX) gene. Further examination of the FOXO1 region in a meta-analysis of six available GWAS showed two SNPs significantly associated with age at onset of PD. These results implicate FOXO1 as a PD-relevant gene and warrant further functional analyses of its transcriptional regulatory mechanisms.

Expression quantitative trait loci (eQTL) mapping in Puerto Rican children.

PubMed

Chen, Wei; Brehm, John M; Lin, Jerome; Wang, Ting; Forno, Erick; Acosta-Pérez, Edna; Boutaoui, Nadia; Canino, Glorisa; Celedón, Juan C

2015-01-01

Expression quantitative trait loci (eQTL) have been identified using tissue or cell samples from diverse human populations, thus enhancing our understanding of regulation of gene expression. However, few studies have attempted to identify eQTL in racially admixed populations such as Hispanics. We performed a systematic eQTL study to identify regulatory variants of gene expression in whole blood from 121 Puerto Rican children with (n = 63) and without (n = 58) asthma. Genome-wide genotyping was conducted using the Illumina Omni2.5M Bead Chip, and gene expression was assessed using the Illumina HT-12 microarray. After completing quality control, we performed a pair-wise genome analysis of ~15 K transcripts and ~1.3 M SNPs for both local and distal effects. This analysis was conducted under a regression framework adjusting for age, gender and principal components derived from both genotypic and mRNA data. We used a false discovery rate (FDR) approach to identify significant eQTL signals, which were next compared to top eQTL signals from existing eQTL databases. We then performed a pathway analysis for our top genes. We identified 36,720 local pairs in 3,391 unique genes and 1,851 distal pairs in 446 unique genes at FDR <0.05, corresponding to unadjusted P values lower than 1.5x10-4 and 4.5x10-9, respectively. A significant proportion of genes identified in our study overlapped with those identified in previous studies. We also found an enrichment of disease-related genes in our eQTL list. We present results from the first eQTL study in Puerto Rican children, who are members of a unique Hispanic cohort disproportionately affected with asthma, prematurity, obesity and other common diseases. Our study confirmed eQTL signals identified in other ethnic groups, while also detecting additional eQTLs unique to our study population. The identified eQTLs will help prioritize findings from future genome-wide association studies in Puerto Ricans.

Increased odds and predictive rates of MMPI-2-RF scale elevations in patients with psychogenic non-epileptic seizures and observed sex differences.

PubMed

Del Bene, Victor A; Arce Rentería, Miguel; Maiman, Moshe; Slugh, Mitch; Gazzola, Deana M; Nadkarni, Siddhartha S; Barr, William B

2017-07-01

The Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF) is a self-report instrument, previously shown to differentiate patients with epileptic seizures (ES) and psychogenic non-epileptic seizures (PNES). At present, the odds of MMPI-2-RF scale elevations in PNES patients, as well as the diagnostic predictive value of such scale elevations, remain largely unexplored. This can be of clinical utility, particularly when a diagnosis is uncertain. After looking at mean group differences, we applied contingency table derived odds ratios to a sample of ES (n=92) and PNES (n=77) patients from a video EEG (vEEG) monitoring unit. We also looked at the positive and negative predictive values (PPV, NPV), as well as the false discovery rate (FDR) and false omission rate (FOR) for scales found to have increased odds of elevation in PNES patients. This was completed for the overall sample, as well as the sample stratified by sex. The odds of elevations related to somatic concerns, negative mood, and suicidal ideation in the PNES sample ranged from 2 to 5 times more likely. Female PNES patients had 3-6 times greater odds of such scale elevations, while male PNES patients had odds of 5-15 times more likely. PPV rates ranged from 53.66% to 84.62%, while NPV rates ranged from 47.52% to 90.91%. FDR across scales ranged from 15.38% to 50%, while the FOR ranged from 9.09% to 52.47%. Consistent with prior research, PNES patients have greater odds of MMPI-2-RF scale elevations, particularly related to somatic concerns and mood disturbance. Female PNES patients endorsed greater emotional distress, including endorsement of suicide related items. Elevations of these scales could aid in differentiating PNES from ES patients, although caution is warranted due to the possibility of both false positives and the incorrect omissions of PNES cases. Copyright © 2017 Elsevier Inc. All rights reserved.

An extended data mining method for identifying differentially expressed assay-specific signatures in functional genomic studies.

PubMed

Rollins, Derrick K; Teh, Ailing

2010-12-17

Microarray data sets provide relative expression levels for thousands of genes for a small number, in comparison, of different experimental conditions called assays. Data mining techniques are used to extract specific information of genes as they relate to the assays. The multivariate statistical technique of principal component analysis (PCA) has proven useful in providing effective data mining methods. This article extends the PCA approach of Rollins et al. to the development of ranking genes of microarray data sets that express most differently between two biologically different grouping of assays. This method is evaluated on real and simulated data and compared to a current approach on the basis of false discovery rate (FDR) and statistical power (SP) which is the ability to correctly identify important genes. This work developed and evaluated two new test statistics based on PCA and compared them to a popular method that is not PCA based. Both test statistics were found to be effective as evaluated in three case studies: (i) exposing E. coli cells to two different ethanol levels; (ii) application of myostatin to two groups of mice; and (iii) a simulated data study derived from the properties of (ii). The proposed method (PM) effectively identified critical genes in these studies based on comparison with the current method (CM). The simulation study supports higher identification accuracy for PM over CM for both proposed test statistics when the gene variance is constant and for one of the test statistics when the gene variance is non-constant. PM compares quite favorably to CM in terms of lower FDR and much higher SP. Thus, PM can be quite effective in producing accurate signatures from large microarray data sets for differential expression between assays groups identified in a preliminary step of the PCA procedure and is, therefore, recommended for use in these applications.

Localized Glaucomatous Change Detection within the Proper Orthogonal Decomposition Framework

PubMed Central

Balasubramanian, Madhusudhanan; Kriegman, David J.; Bowd, Christopher; Holst, Michael; Weinreb, Robert N.; Sample, Pamela A.; Zangwill, Linda M.

2012-01-01

Purpose. To detect localized glaucomatous structural changes using proper orthogonal decomposition (POD) framework with false-positive control that minimizes confirmatory follow-ups, and to compare the results to topographic change analysis (TCA). Methods. We included 167 participants (246 eyes) with ≥4 Heidelberg Retina Tomograph (HRT)-II exams from the Diagnostic Innovations in Glaucoma Study; 36 eyes progressed by stereo-photographs or visual fields. All other patient eyes (n = 210) were non-progressing. Specificities were evaluated using 21 normal eyes. Significance of change at each HRT superpixel between each follow-up and its nearest baseline (obtained using POD) was estimated using mixed-effects ANOVA. Locations with significant reduction in retinal height (red pixels) were determined using Bonferroni, Lehmann-Romano k-family-wise error rate (k-FWER), and Benjamini-Hochberg false discovery rate (FDR) type I error control procedures. Observed positive rate (OPR) in each follow-up was calculated as a ratio of number of red pixels within disk to disk size. Progression by POD was defined as one or more follow-ups with OPR greater than the anticipated false-positive rate. TCA was evaluated using the recently proposed liberal, moderate, and conservative progression criteria. Results. Sensitivity in progressors, specificity in normals, and specificity in non-progressors, respectively, were POD-Bonferroni = 100%, 0%, and 0%; POD k-FWER = 78%, 86%, and 43%; POD-FDR = 78%, 86%, and 43%; POD k-FWER with retinal height change ≥50 μm = 61%, 95%, and 60%; TCA-liberal = 86%, 62%, and 21%; TCA-moderate = 53%, 100%, and 70%; and TCA-conservative = 17%, 100%, and 84%. Conclusions. With a stronger control of type I errors, k-FWER in POD framework minimized confirmatory follow-ups while providing diagnostic accuracy comparable to TCA. Thus, POD with k-FWER shows promise to reduce the number of confirmatory follow-ups required for clinical care and studies evaluating new glaucoma treatments. (ClinicalTrials.gov number, NCT00221897.) PMID:22491406

Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato

PubMed Central

Li, Li; Paulo, Maria-João; van Eeuwijk, Fred

2010-01-01

Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q ≤ 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q ≤ 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1389-3) contains supplementary material, which is available to authorized users. PMID:20603706

Genome-wide association study of borderline personality disorder reveals genetic overlap with bipolar disorder, major depression and schizophrenia.

PubMed

Witt, S H; Streit, F; Jungkunz, M; Frank, J; Awasthi, S; Reinbold, C S; Treutlein, J; Degenhardt, F; Forstner, A J; Heilmann-Heimbach, S; Dietl, L; Schwarze, C E; Schendel, D; Strohmaier, J; Abdellaoui, A; Adolfsson, R; Air, T M; Akil, H; Alda, M; Alliey-Rodriguez, N; Andreassen, O A; Babadjanova, G; Bass, N J; Bauer, M; Baune, B T; Bellivier, F; Bergen, S; Bethell, A; Biernacka, J M; Blackwood, D H R; Boks, M P; Boomsma, D I; Børglum, A D; Borrmann-Hassenbach, M; Brennan, P; Budde, M; Buttenschøn, H N; Byrne, E M; Cervantes, P; Clarke, T-K; Craddock, N; Cruceanu, C; Curtis, D; Czerski, P M; Dannlowski, U; Davis, T; de Geus, E J C; Di Florio, A; Djurovic, S; Domenici, E; Edenberg, H J; Etain, B; Fischer, S B; Forty, L; Fraser, C; Frye, M A; Fullerton, J M; Gade, K; Gershon, E S; Giegling, I; Gordon, S D; Gordon-Smith, K; Grabe, H J; Green, E K; Greenwood, T A; Grigoroiu-Serbanescu, M; Guzman-Parra, J; Hall, L S; Hamshere, M; Hauser, J; Hautzinger, M; Heilbronner, U; Herms, S; Hitturlingappa, S; Hoffmann, P; Holmans, P; Hottenga, J-J; Jamain, S; Jones, I; Jones, L A; Juréus, A; Kahn, R S; Kammerer-Ciernioch, J; Kirov, G; Kittel-Schneider, S; Kloiber, S; Knott, S V; Kogevinas, M; Landén, M; Leber, M; Leboyer, M; Li, Q S; Lissowska, J; Lucae, S; Martin, N G; Mayoral-Cleries, F; McElroy, S L; McIntosh, A M; McKay, J D; McQuillin, A; Medland, S E; Middeldorp, C M; Milaneschi, Y; Mitchell, P B; Montgomery, G W; Morken, G; Mors, O; Mühleisen, T W; Müller-Myhsok, B; Myers, R M; Nievergelt, C M; Nurnberger, J I; O'Donovan, M C; Loohuis, L M O; Ophoff, R; Oruc, L; Owen, M J; Paciga, S A; Penninx, B W J H; Perry, A; Pfennig, A; Potash, J B; Preisig, M; Reif, A; Rivas, F; Rouleau, G A; Schofield, P R; Schulze, T G; Schwarz, M; Scott, L; Sinnamon, G C B; Stahl, E A; Strauss, J; Turecki, G; Van der Auwera, S; Vedder, H; Vincent, J B; Willemsen, G; Witt, C C; Wray, N R; Xi, H S; Tadic, A; Dahmen, N; Schott, B H; Cichon, S; Nöthen, M M; Ripke, S; Mobascher, A; Rujescu, D; Lieb, K; Roepke, S; Schmahl, C; Bohus, M; Rietschel, M

2017-06-20

Borderline personality disorder (BOR) is determined by environmental and genetic factors, and characterized by affective instability and impulsivity, diagnostic symptoms also observed in manic phases of bipolar disorder (BIP). Up to 20% of BIP patients show comorbidity with BOR. This report describes the first case-control genome-wide association study (GWAS) of BOR, performed in one of the largest BOR patient samples worldwide. The focus of our analysis was (i) to detect genes and gene sets involved in BOR and (ii) to investigate the genetic overlap with BIP. As there is considerable genetic overlap between BIP, major depression (MDD) and schizophrenia (SCZ) and a high comorbidity of BOR and MDD, we also analyzed the genetic overlap of BOR with SCZ and MDD. GWAS, gene-based tests and gene-set analyses were performed in 998 BOR patients and 1545 controls. Linkage disequilibrium score regression was used to detect the genetic overlap between BOR and these disorders. Single marker analysis revealed no significant association after correction for multiple testing. Gene-based analysis yielded two significant genes: DPYD (P=4.42 × 10 -7 ) and PKP4 (P=8.67 × 10 -7 ); and gene-set analysis yielded a significant finding for exocytosis (GO:0006887, P FDR =0.019; FDR, false discovery rate). Prior studies have implicated DPYD, PKP4 and exocytosis in BIP and SCZ. The most notable finding of the present study was the genetic overlap of BOR with BIP (r g =0.28 [P=2.99 × 10 -3 ]), SCZ (r g =0.34 [P=4.37 × 10 -5 ]) and MDD (r g =0.57 [P=1.04 × 10 -3 ]). We believe our study is the first to demonstrate that BOR overlaps with BIP, MDD and SCZ on the genetic level. Whether this is confined to transdiagnostic clinical symptoms should be examined in future studies.

Whole-genome transcriptional analysis of Escherichia coli during heat inactivation processes related to industrial cooking.

PubMed

Guernec, A; Robichaud-Rincon, P; Saucier, L

2013-08-01

Escherichia coli K-12 was grown to the stationary phase, for maximum physiological resistance, in brain heart infusion (BHI) broth at 37°C. Cells were then heated at 58°C or 60°C to reach a process lethality value \\[\\mathbf{\\left(}{{\\mathit{F}}^{\\mathit{o}}}_{\\mathbf{70}}^{\\mathbf{10}}\\mathbf{\\right)} \\] of 2 or 3 or to a core temperature of 71°C (control industrial cooking temperature). Growth recovery and cell membrane integrity were evaluated immediately after heating, and a global transcription analysis was performed using gene expression microarrays. Only cells heated at 58°C with F(o) = 2 were still able to grow on liquid or solid BHI broth after heat treatment. However, their transcriptome did not differ from that of bacteria heated at 58°C with F(o) = 3 (P value for the false discovery rate [P-FDR] > 0.01), where no growth recovery was observed posttreatment. Genome-wide transcriptomic data obtained at 71°C were distinct from those of the other treatments without growth recovery. Quantification of heat shock gene expression by real-time PCR revealed that dnaK and groEL mRNA levels decreased significantly above 60°C to reach levels similar to those of control cells at 37°C (P < 0.0001). Furthermore, despite similar levels of cell inactivation measured by growth on BHI media after heating, 132 and 8 genes were differentially expressed at 71°C compared to 58°C and 60°C at F(o) = 3, respectively (P-FDR < 0.01). Among them, genes such as aroA, citE, glyS, oppB, and asd, whose expression was upregulated at 71°C, may be worth investigating as good biomarkers for accurately determining the efficiency of heat treatments, especially when cells are too injured to be enumerated using growth media.

Transcriptomic Identification of ADH1B as a Novel Candidate Gene for Obesity and Insulin Resistance in Human Adipose Tissue in Mexican Americans from the Veterans Administration Genetic Epidemiology Study (VAGES)

PubMed Central

Winnier, Deidre A.; Fourcaudot, Marcel; Norton, Luke; Abdul-Ghani, Muhammad A.; Hu, Shirley L.; Farook, Vidya S.; Coletta, Dawn K.; Kumar, Satish; Puppala, Sobha; Chittoor, Geetha; Dyer, Thomas D.; Arya, Rector; Carless, Melanie; Lehman, Donna M.; Curran, Joanne E.; Cromack, Douglas T.; Tripathy, Devjit; Blangero, John; Duggirala, Ravindranath; Göring, Harald H. H.; DeFronzo, Ralph A.; Jenkinson, Christopher P.

2015-01-01

Type 2 diabetes (T2D) is a complex metabolic disease that is more prevalent in ethnic groups such as Mexican Americans, and is strongly associated with the risk factors obesity and insulin resistance. The goal of this study was to perform whole genome gene expression profiling in adipose tissue to detect common patterns of gene regulation associated with obesity and insulin resistance. We used phenotypic and genotypic data from 308 Mexican American participants from the Veterans Administration Genetic Epidemiology Study (VAGES). Basal fasting RNA was extracted from adipose tissue biopsies from a subset of 75 unrelated individuals, and gene expression data generated on the Illumina BeadArray platform. The number of gene probes with significant expression above baseline was approximately 31,000. We performed multiple regression analysis of all probes with 15 metabolic traits. Adipose tissue had 3,012 genes significantly associated with the traits of interest (false discovery rate, FDR ≤ 0.05). The significance of gene expression changes was used to select 52 genes with significant (FDR ≤ 10-4) gene expression changes across multiple traits. Gene sets/Pathways analysis identified one gene, alcohol dehydrogenase 1B (ADH1B) that was significantly enriched (P < 10-60) as a prime candidate for involvement in multiple relevant metabolic pathways. Illumina BeadChip derived ADH1B expression data was consistent with quantitative real time PCR data. We observed significant inverse correlations with waist circumference (2.8 x 10-9), BMI (5.4 x 10-6), and fasting plasma insulin (P < 0.001). These findings are consistent with a central role for ADH1B in obesity and insulin resistance and provide evidence for a novel genetic regulatory mechanism for human metabolic diseases related to these traits. PMID:25830378

A co-expression gene network associated with developmental regulation of apple fruit acidity.

PubMed

Bai, Yang; Dougherty, Laura; Cheng, Lailiang; Xu, Kenong

2015-08-01

Apple fruit acidity, which affects the fruit's overall taste and flavor to a large extent, is primarily determined by the concentration of malic acid. Previous studies demonstrated that the major QTL malic acid (Ma) on chromosome 16 is largely responsible for fruit acidity variations in apple. Recent advances suggested that a natural mutation that gives rise to a premature stop codon in one of the two aluminum-activated malate transporter (ALMT)-like genes (called Ma1) is the genetic causal element underlying Ma. However, the natural mutation does not explain the developmental changes of fruit malate levels in a given genotype. Using RNA-seq data from the fruit of 'Golden Delicious' taken at 14 developmental stages from 1 week after full-bloom (WAF01) to harvest (WAF20), we characterized their transcriptomes in groups of high (12.2 ± 1.6 mg/g fw, WAF03-WAF08), mid (7.4 ± 0.5 mg/g fw, WAF01-WAF02 and WAF10-WAF14) and low (5.4 ± 0.4 mg/g fw, WAF16-WAF20) malate concentrations. Detailed analyses showed that a set of 3,066 genes (including Ma1) were expressed not only differentially (P FDR < 0.05) between the high and low malate groups (or between the early and late developmental stages) but also in significant (P < 0.05) correlation with malate concentrations. The 3,066 genes fell in 648 MapMan (sub-) bins or functional classes, and 19 of them were significantly (P FDR < 0.05) co-enriched or co-suppressed in a malate dependent manner. Network inferring using the 363 genes encompassed in the 19 (sub-) bins, identified a major co-expression network of 239 genes. Since the 239 genes were also differentially expressed between the early (WAF03-WAF08) and late (WAF16-WAF20) developmental stages, the major network was considered to be associated with developmental regulation of apple fruit acidity in 'Golden Delicious'.

Alterations in Bronchial Airway miRNA Expression for Lung Cancer Detection.

PubMed

Pavel, Ana B; Campbell, Joshua D; Liu, Gang; Elashoff, David; Dubinett, Steven; Smith, Kate; Whitney, Duncan; Lenburg, Marc E; Spira, Avrum

2017-11-01

We have previously shown that gene expression alterations in normal-appearing bronchial epithelial cells can serve as a lung cancer detection biomarker in smokers. Given that miRNAs regulate airway gene expression responses to smoking, we evaluated whether miRNA expression is also altered in the bronchial epithelium of smokers with lung cancer. Using epithelial brushings from the mainstem bronchus of patients undergoing bronchoscopy for suspected lung cancer (as part of the AEGIS-1/2 clinical trials), we profiled miRNA expression via small-RNA sequencing from 347 current and former smokers for which gene expression data were also available. Patients were followed for one year postbronchoscopy until a final diagnosis of lung cancer ( n = 194) or benign disease ( n = 153) was made. Following removal of 6 low-quality samples, we used 138 patients (AEGIS-1) as a discovery set to identify four miRNAs (miR-146a-5p, miR-324-5p, miR-223-3p, and miR-223-5p) that were downregulated in the bronchial airway of lung cancer patients (ANOVA P < 0.002, FDR < 0.2). The expression of these miRNAs is significantly more negatively correlated with the expression of their mRNA targets than with the expression of other nontarget genes (K-S P < 0.05). Furthermore, these mRNA targets are enriched among genes whose expression is elevated in cancer patients (GSEA FDR < 0.001). Finally, we found that the addition of miR-146a-5p to an existing mRNA biomarker for lung cancer significantly improves its performance (AUC) in the 203 samples (AEGIS-1/2) serving an independent test set (DeLong P < 0.05). Our findings suggest that there are miRNAs whose expression is altered in the cytologically normal bronchial epithelium of smokers with lung cancer, and that they may regulate cancer-associated gene expression differences. Cancer Prev Res; 10(11); 651-9. ©2017 AACR . ©2017 American Association for Cancer Research.

TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer

PubMed Central

Fagerholm, Rainer; Khan, Sofia; Schmidt, Marjanka K.; GarcClosas, Montserrat; Heikkilä, Päivi; Saarela, Jani; Beesley, Jonathan; Jamshidi, Maral; Aittomäki, Kristiina; Liu, Jianjun; Raza Ali, H.; Andrulis, Irene L.; Beckmann, Matthias W.; Behrens, Sabine; Blows, Fiona M.; Brenner, Hermann; Chang-Claude, Jenny; Couch, Fergus J.; Czene, Kamila; Fasching, Peter A.; Figueroa, Jonine; Floris, Giuseppe; Glendon, Gord; Guo, Qi; Hall, Per; Hallberg, Emily; Hamann, Ute; Holleczek, Bernd; Hooning, Maartje J.; Hopper, John L.; Jager, Agnes; Kabisch, Maria; Investigators, kConFab/AOCS; Keeman, Renske; Kosma, Veli-Matti; Lambrechts, Diether; Lindblom, Annika; Mannermaa, Arto; Margolin, Sara; Provenzano, Elena; Shah, Mitul; Southey, Melissa C.; Dennis, Joe; Lush, Michael; Michailidou, Kyriaki; Wang, Qin; Bolla, Manjeet K.; Dunning, Alison M.; Easton, Douglas F.; Pharoah, Paul D.P .; Chenevix-Trench, Georgia; Blomqvist, Carl; Nevanlinna, Heli

2017-01-01

TP53 overexpression is indicative of somatic TP53 mutations and associates with aggressive tumors and poor prognosis in breast cancer. We utilized a two-stage SNP association study to detect variants associated with breast cancer survival in a TP53-dependent manner. Initially, a genome-wide study (n = 575 cases) was conducted to discover candidate SNPs for genotyping and validation in the Breast Cancer Association Consortium (BCAC). The SNPs were then tested for interaction with tumor TP53 status (n = 4,610) and anthracycline treatment (n = 17,828). For SNPs interacting with anthracycline treatment, siRNA knockdown experiments were carried out to validate candidate genes. In the test for interaction between SNP genotype and TP53 status, we identified one locus, represented by rs10916264 (p(interaction) = 3.44 05E010-5; FDR-adjusted p = 0.0011) in estrogen receptor (ER) positive cases. The rs10916264 AA genotype associated with worse survival among cases with ER-positive, TP53-positive tumors (hazard ratio [HR] 2.36, 95% confidence interval [C.I] 1.45 - 3.82). This is a cis-eQTL locus for FBXO28 and TP53BP2; expression levels of these genes were associated with patient survival specifically in ER-positive, TP53-mutated tumors. Additionally, the SNP rs798755 was associated with survival in interaction with anthracycline treatment (p(interaction) = 9.57 05E010-5, FDR-adjusted p = 0.0130). RNAi-based depletion of a predicted regulatory target gene, FAM53A, indicated that this gene can modulate doxorubicin sensitivity in breast cancer cell lines. If confirmed in independent data sets, these results may be of clinical relevance in the development of prognostic and predictive marker panels for breast cancer. PMID:28179588

Associations between cruciferous vegetable intake and selected biomarkers among women scheduled for breast biopsies.

PubMed

Zhang, Zhenzhen; Atwell, Lauren L; Farris, Paige E; Ho, Emily; Shannon, Jackilen

2016-05-01

To examine the relationship between dietary cruciferous vegetable intake and selected tumour biomarkers for histone acetylation (H3K9ac, H3K18ac, HDAC3 and HDAC6), proliferation (Ki-67) and cell-cycle regulation (p21) from breast tissue. The study used baseline data of women recruited to participate in a clinical trial of sulforaphane supplement. Dietary cruciferous vegetable intake was collected through a validated Arizona Cruciferous Vegetable Intake Questionnaire. Breast tissue was obtained from biopsy samples. Spearman correlations were calculated between intake of specific cruciferous vegetables and biomarkers. Tissue biomarkers were log2-transformed to obtain approximate normality. Linear regression analyses were conducted to examine associations between cruciferous vegetable intake and biomarkers adjusting for age and use of non-steroidal anti-inflammatory drugs. False discovery rate (FDR) was used to account for multiple comparisons. Clinical trial baseline. Fifty-four women who had abnormal mammogram findings and were scheduled for breast biopsy. Mean intake of total cruciferous vegetables from all food sources was 81·7 (sd 57·3) g/d. Mean urinary total sulforaphane metabolites was 0·08 (sd 0·07) µm/mm creatinine. Total cruciferous vegetable intake was inversely associated with Ki-67 protein expression in breast ductal carcinoma in situ (DCIS) tissue (β=-0·004; se=0·001; FDR q value=0·03), but not in benign or invasive ductal carcinoma (IDC) tissue. No association was found for other biomarkers measured (HDAC3, HDAC6, H3K9, H3K18 and p21) in all tissues examined (benign, DCIS and IDC). The present study sought to provide additional evidence for the potential role of sulforaphane in histone acetylation and cell proliferation. Here, we report that total cruciferous vegetable intake is associated with decreased cell proliferation in breast DCIS tissue.

A method to identify differential expression profiles of time-course gene data with Fourier transformation.

PubMed

Kim, Jaehee; Ogden, Robert Todd; Kim, Haseong

2013-10-18

Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization.The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics.

SLOPE—ADAPTIVE VARIABLE SELECTION VIA CONVEX OPTIMIZATION

PubMed Central

Bogdan, Małgorzata; van den Berg, Ewout; Sabatti, Chiara; Su, Weijie; Candès, Emmanuel J.

2015-01-01

We introduce a new estimator for the vector of coefficients β in the linear model y = Xβ + z, where X has dimensions n × p with p possibly larger than n. SLOPE, short for Sorted L-One Penalized Estimation, is the solution to minb∈ℝp12‖y−Xb‖ℓ22+λ1|b|(1)+λ2|b|(2)+⋯+λp|b|(p),where λ1 ≥ λ2 ≥ … ≥ λp ≥ 0 and |b|(1)≥|b|(2)≥⋯≥|b|(p) are the decreasing absolute values of the entries of b. This is a convex program and we demonstrate a solution algorithm whose computational complexity is roughly comparable to that of classical ℓ1 procedures such as the Lasso. Here, the regularizer is a sorted ℓ1 norm, which penalizes the regression coefficients according to their rank: the higher the rank—that is, stronger the signal—the larger the penalty. This is similar to the Benjamini and Hochberg [J. Roy. Statist. Soc. Ser. B 57 (1995) 289–300] procedure (BH) which compares more significant p-values with more stringent thresholds. One notable choice of the sequence {λi} is given by the BH critical values λBH(i)=z(1−i⋅q/2p), where q ∈ (0, 1) and z(α) is the quantile of a standard normal distribution. SLOPE aims to provide finite sample guarantees on the selected model; of special interest is the false discovery rate (FDR), defined as the expected proportion of irrelevant regressors among all selected predictors. Under orthogonal designs, SLOPE with λBH provably controls FDR at level q. Moreover, it also appears to have appreciable inferential properties under more general designs X while having substantial power, as demonstrated in a series of experiments running on both simulated and real data. PMID:26709357

Brain Gray Matter Deficits at 33-Year Follow-Up in Adults with Attention-Deficit/Hyperactivity Disorder Established in Childhood

PubMed Central

Proal, Erika; Reiss, Philip T.; Klein, Rachel G.; Mannuzza, Salvatore; Gotimer, Kristin; Ramos-Olazagasti, Maria A.; Lerch, Jason P.; He, Yong; Zijdenbos, Alex; Kelly, Clare; Milham, Michael P.; Castellanos, F. Xavier

2013-01-01

Context Volumetric studies have reported relatively decreased cortical thickness and gray matter volumes in adults with Attention-Deficit/Hyperactivity Disorder (ADHD) whose childhood status was retrospectively recalled. We present the first prospective study combining cortical thickness and voxel-based morphometry (VBM) in adults diagnosed with ADHD in childhood. Objective In adults who had Combined Type ADHD in childhood, to 1) test whether they exhibit cortical thinning and decreased gray matter in regions hypothesized related to ADHD, and 2) test whether anatomic differences are associated with current ADHD diagnosis, including persistence versus remission. Design Cross-sectional analysis embedded in a 33-year prospective follow-up at mean age 41. Setting Research outpatient center. Participants ADHD probands were from a cohort of 207 6–12 year old Caucasian boys; male comparison subjects (n=178) had been free of ADHD in childhood. We obtained MRI scans in 59 probands and 80 comparisons (28% and 45% of original samples, respectively). Main Outcome Measure Whole-brain VBM and vertex-wise cortical thickness analyses. Results Cortex was significantly thinner in ADHD probands than comparisons in the dorsal attentional network and limbic areas (FDR<0.05, corrected). Additionally, gray matter was significantly decreased in probands in right caudate, right thalamus and bilateral cerebellar hemispheres. Probands with persistent ADHD (n=17) did not differ significantly from remitters (n=26) at FDR<0.05. At uncorrected p<0.05, remitters had thicker cortex relative to those with persistent ADHD in medial occipital cortex, insula, parahippocampus, and prefrontal regions. Conclusions We observed anatomic gray matter reductions in adults with childhood ADHD, regardless of current diagnosis. The most affected regions underpin top-down control of attention and regulation of emotion and motivation. Exploratory analyses suggest that diagnostic remission may result from compensatory maturation of prefrontal, cerebellar, and thalamic circuitry. PMID:22065528

Screening for Pancreatic Adenocarcinoma in BRCA2 Mutation Carriers: Results of a Disease Simulation Model.

PubMed

Pandharipande, Pari V; Jeon, Alvin; Heberle, Curtis R; Dowling, Emily C; Kong, Chung Yin; Chung, Daniel C; Brugge, William R; Hur, Chin

2015-12-01

BRCA2 mutation carriers are at increased risk for multiple cancers including pancreatic adenocarcinoma (PAC). Our goal was to compare the effectiveness of different PAC screening strategies in BRCA2 mutation carriers, from the standpoint of life expectancy. A previously published Markov model of PAC was updated and extended to incorporate key aspects of BRCA2 mutation carrier status, including competing risks of breast- and ovarian-cancer specific mortality. BRCA2 mutation carriers were modeled and analyzed as the primary cohort for the analysis. Additional higher risk BRCA2 cohorts that were stratified according to the number of first-degree relatives (FDRs) with PAC were also analyzed. For each cohort, one-time screening and annual screening were evaluated, with screening starting at age 50 in both strategies. The primary outcome was net gain in life expectancy (LE) compared to no screening. Sensitivity analysis was performed on key model parameters, including surgical mortality and MRI test performance. One-time screening at age 50 resulted in a LE gain of 3.9 days for the primary BRCA2 cohort, and a gain of 5.8 days for those with BRCA2 and one FDR. Annual screening resulted in LE loss of 12.9 days for the primary cohort and 1.3 days for BRCA2 carriers with 1 FDR, but resulted in 20.6 days gained for carriers with 2 FDRs and 260 days gained for those with 3 FDRs. For patients with ≥ 3 FDRs, annual screening starting at an earlier age (i.e. 35-40) was optimal. Among BRCA2 mutation carriers, aggressive screening regimens may be ineffective unless additional indicators of elevated risk (e.g., 2 or more FDRs) are present. More clinical studies are needed to confirm these findings. American Cancer Society - New England Division - Ellison Foundation Research Scholar Grant (RSG-15-129-01-CPHPS).

Brain grey and white matter predictors of verbal ability traits in older age: The Lothian Birth Cohort 1936.

PubMed

Hoffman, Paul; Cox, Simon R; Dykiert, Dominika; Muñoz Maniega, Susana; Valdés Hernández, Maria C; Bastin, Mark E; Wardlaw, Joanna M; Deary, Ian J

2017-08-01

Cerebral grey and white matter MRI parameters are related to general intelligence and some specific cognitive abilities. Less is known about how structural brain measures relate specifically to verbal processing abilities. We used multi-modal structural MRI to investigate the grey matter (GM) and white matter (WM) correlates of verbal ability in 556 healthy older adults (mean age = 72.68 years, s.d. = .72 years). Structural equation modelling was used to decompose verbal performance into two latent factors: a storage factor that indexed participants' ability to store representations of verbal knowledge and an executive factor that measured their ability to regulate their access to this information in a flexible and task-appropriate manner. GM volumes and WM fractional anisotropy (FA) for components of the language/semantic network were used as predictors of these verbal ability factors. Volume of the ventral temporal cortices predicted participants' storage scores (β = .12, FDR-adjusted p = .04), consistent with the theory that this region acts as a key substrate of semantic knowledge. This effect was mediated by childhood IQ, suggesting a lifelong association between ventral temporal volume and verbal knowledge, rather than an effect of cognitive decline in later life. Executive ability was predicted by FA fractional anisotropy of the arcuate fasciculus (β = .19, FDR-adjusted p = .001), a major language-related tract implicated in speech production. This result suggests that this tract plays a role in the controlled retrieval of word knowledge during speech. At a more general level, these data highlight a basic distinction between information representation, which relies on the accumulation of tissue in specialised GM regions, and executive control, which depends on long-range WM pathways for efficient communication across distributed cortical networks. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Temporal analysis of reciprocal miRNA-mRNA expression patterns predicts regulatory networks during differentiation in human skeletal muscle cells

PubMed Central

Sjögren, Rasmus J. O.; Egan, Brendan; Katayama, Mutsumi; Zierath, Juleen R.

2014-01-01

microRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through posttranscriptional repression of target genes. miRNAs exert a fundamental level of control over many developmental processes, but their role in the differentiation and development of skeletal muscle from myogenic progenitor cells in humans remains incompletely understood. Using primary cultures established from human skeletal muscle satellite cells, we performed microarray profiling of miRNA expression during differentiation of myoblasts (day 0) into myotubes at 48 h intervals (day 2, 4, 6, 8, and 10). Based on a time-course analysis, we identified 44 miRNAs with altered expression [false discovery rate (FDR) < 5%, fold change > ±1.2] during differentiation, including the marked upregulation of the canonical myogenic miRNAs miR-1, miR-133a, miR-133b, and miR-206. Microarray profiling of mRNA expression at day 0, 4, and 10 identified 842 and 949 genes differentially expressed (FDR < 10%) at day 4 and 10, respectively. At day 10, 42% of altered transcripts demonstrated reciprocal expression patterns in relation to the directional change of their in silico predicted regulatory miRNAs based on analysis using Ingenuity Pathway Analysis microRNA Target Filter. Bioinformatic analysis predicted networks of regulation during differentiation including myomiRs miR-1/206 and miR-133a/b, miRNAs previously established in differentiation including miR-26 and miR-30, and novel miRNAs regulated during differentiation of human skeletal muscle cells such as miR-138-5p and miR-20a. These reciprocal expression patterns may represent new regulatory nodes in human skeletal muscle cell differentiation. This analysis serves as a reference point for future studies of human skeletal muscle differentiation and development in healthy and disease states. PMID:25547110

Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes.

PubMed

Wada, Masayoshi; Takahashi, Hiroki; Altaf-Ul-Amin, Md; Nakamura, Kensuke; Hirai, Masami Y; Ohta, Daisaku; Kanaya, Shigehiko

2012-07-15

Operon-like arrangements of genes occur in eukaryotes ranging from yeasts and filamentous fungi to nematodes, plants, and mammals. In plants, several examples of operon-like gene clusters involved in metabolic pathways have recently been characterized, e.g. the cyclic hydroxamic acid pathways in maize, the avenacin biosynthesis gene clusters in oat, the thalianol pathway in Arabidopsis thaliana, and the diterpenoid momilactone cluster in rice. Such operon-like gene clusters are defined by their co-regulation or neighboring positions within immediate vicinity of chromosomal regions. A comprehensive analysis of the expression of neighboring genes therefore accounts a crucial step to reveal the complete set of operon-like gene clusters within a genome. Genome-wide prediction of operon-like gene clusters should contribute to functional annotation efforts and provide novel insight into evolutionary aspects acquiring certain biological functions as well. We predicted co-expressed gene clusters by comparing the Pearson correlation coefficient of neighboring genes and randomly selected gene pairs, based on a statistical method that takes false discovery rate (FDR) into consideration for 1469 microarray gene expression datasets of A. thaliana. We estimated that A. thaliana contains 100 operon-like gene clusters in total. We predicted 34 statistically significant gene clusters consisting of 3 to 22 genes each, based on a stringent FDR threshold of 0.1. Functional relationships among genes in individual clusters were estimated by sequence similarity and functional annotation of genes. Duplicated gene pairs (determined based on BLAST with a cutoff of E<10(-5)) are included in 27 clusters. Five clusters are associated with metabolism, containing P450 genes restricted to the Brassica family and predicted to be involved in secondary metabolism. Operon-like clusters tend to include genes encoding bio-machinery associated with ribosomes, the ubiquitin/proteasome system, secondary metabolic pathways, lipid and fatty-acid metabolism, and the lipid transfer system. Copyright © 2012 Elsevier B.V. All rights reserved.

Integrative analysis of copy number alteration and gene expression profiling in ovarian clear cell adenocarcinoma.

PubMed

Sung, Chang Ohk; Choi, Chel Hun; Ko, Young-Hyeh; Ju, Hyunjeong; Choi, Yoon-La; Kim, Nyunsu; Kang, So Young; Ha, Sang Yun; Choi, Kyusam; Bae, Duk-Soo; Lee, Jeong-Won; Kim, Tae-Joong; Song, Sang Yong; Kim, Byoung-Gie

2013-05-01

Ovarian clear cell adenocarcinoma (Ov-CCA) is a distinctive subtype of ovarian epithelial carcinoma. In this study, we performed array comparative genomic hybridization (aCGH) and paired gene expression microarray of 19 fresh-frozen samples and conducted integrative analysis. For the copy number alterations, significantly amplified regions (false discovery rate [FDR] q <0.05) were 1q21.3 and 8q24.3, and significantly deleted regions were 3p21.31, 4q12, 5q13.2, 5q23.2, 5q31.1, 7p22.1, 7q11.23, 8p12, 9p22.1, 11p15.1, 12p13.31, 15q11.2, 15q21.2, 18p11.31, and 22q11.21 using the Genomic Identification of Significant Targets in Cancer (GISTIC) analysis. Integrative analysis revealed 94 genes demonstrating frequent copy number alterations (>25% of samples) that correlated with gene expression (FDR <0.05). These genes were mainly located on 8p11.21, 8p21.2-p21.3, 8q22.1, 8q24.3, 17q23.2-q23.3, 19p13.3, and 19p13.11. Among the regions, 8q24.3 was found to contain the most genes (30 of 94 genes) including PTK2. The 8q24.3 region was indicated as the most significant region, as supported by copy number, GISTIC, and integrative analysis. Pathway analysis using differentially expressed genes on 8q24.3 revealed several major nodes, including PTK2. In conclusion, we identified a set of 94 candidate genes with frequent copy number alterations that correlated with gene expression. Specific chromosomal alterations, such as the 8q24.3 gain containing PTK2, could be a therapeutic target in a subset of Ov-CCAs. Copyright © 2013. Published by Elsevier Inc.

Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma.

PubMed

Dai, Wei; Cheung, Arthur Kwok Leung; Ko, Josephine Mun Yee; Cheng, Yue; Zheng, Hong; Ngan, Roger Kai Cheong; Ng, Wai Tong; Lee, Anne Wing Mui; Yau, Chun Chung; Lee, Victor Ho Fu; Lung, Maria Li

2015-07-01

Altered patterns of DNA methylation are key features of cancer. Nasopharyngeal carcinoma (NPC) has the highest incidence in Southern China. Aberrant methylation at the promoter region of tumor suppressors is frequently reported in NPC; however, genome-wide methylation changes have not been comprehensively investigated. Therefore, we systematically analyzed methylome data in 25 primary NPC tumors and nontumor counterparts using a high-throughput approach with the Illumina HumanMethylation450 BeadChip. Comparatively, we examined the methylome data of 11 types of solid tumors collected by The Cancer Genome Atlas (TCGA). In NPC, the hypermethylation pattern was more dominant than hypomethylation and the majority of de novo methylated loci were within or close to CpG islands in tumors. The comparative methylome analysis reveals hypermethylation at chromosome 6p21.3 frequently occurred in NPC (false discovery rate; FDR=1.33 × 10(-9) ), but was less obvious in other types of solid tumors except for prostate and Epstein-Barr virus (EBV)-positive gastric cancer (FDR<10(-3) ). Bisulfite pyrosequencing results further confirmed the aberrant methylation at 6p in an additional patient cohort. Evident enrichment of the repressive mark H3K27me3 and active mark H3K4me3 derived from human embryonic stem cells were found at these regions, indicating both DNA methylation and histone modification function together, leading to epigenetic deregulation in NPC. Our study highlights the importance of epigenetic deregulation in NPC. Polycomb Complex 2 (PRC2), responsible for H3K27 trimethylation, is a promising therapeutic target. A key genomic region on 6p with aberrant methylation was identified. This region contains several important genes having potential use as biomarkers for NPC detection. © 2015 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

The impact of a moderate chronic temperature increase on spleen immune-relevant gene transcription depends on whether Atlantic cod (Gadus morhua) are stimulated with bacterial versus viral antigens.

PubMed

Hori, Tiago S; Gamperl, A Kurt; Nash, Gord; Booman, Marije; Barat, Ashoktaru; Rise, Matthew L

2013-10-01

Exposure to elevated temperature is an inherent feature of Atlantic cod (Gadus morhua) sea-cage culture in some regions (e.g., Newfoundland) and may also become an increasingly prevalent challenge for wild fish populations because of accelerated climate change. Therefore, understanding how elevated temperatures impacts the immune response of this commercially important species may help to reduce the potential negative impacts of such challenges. Previously, we investigated the impacts of moderately elevated temperature on the antiviral responses of Atlantic cod (Hori et al. 2012) and reported that elevated temperature modulated the spleen transcriptome response to polyriboinosinic polyribocytidylic acid (pIC, a viral mimic). Herein, we report a complementary microarray study that investigated the impact of the same elevated temperature regime on the Atlantic cod spleen transcriptome response to intraperitoneal (IP) injection of formalin-killed Aeromonas salmonicida (ASAL). Fish were held at two different temperatures (10 °C and 16 °C) prior to immune stimulation and sampled 6 and 24 h post-injection (HPI). In this experiment, we identified 711 and 666 nonredundant ASAL-responsive genes at 6HPI and 24HPI, respectively. These included several known antibacterial genes, including hepcidin, cathelicidin, ferritin heavy subunit, and interleukin 8. However, we only identified 15 differentially expressed genes at 6HPI and 2 at 24HPI (FDR 1%) when comparing ASAL-injected fish held at 10 °C versus 16 °C. In contrast, the same comparisons with pIC-injected fish yielded 290 and 339 differentially expressed genes (FDR 1%) at 6HPI and 24HPI, respectively. These results suggest that moderately elevated temperature has a lesser effect on the Atlantic cod spleen transcriptome response to ASAL (i.e., the antibacterial response) than to pIC (i.e., antiviral response). Thus, the impacts of high temperatures on the cod's immune response may be pathogen dependent.

Crescendo: A Protein Sequence Database Search Engine for Tandem Mass Spectra.

PubMed

Wang, Jianqi; Zhang, Yajie; Yu, Yonghao

2015-07-01

A search engine that discovers more peptides reliably is essential to the progress of the computational proteomics. We propose two new scoring functions (L- and P-scores), which aim to capture similar characteristics of a peptide-spectrum match (PSM) as Sequest and Comet do. Crescendo, introduced here, is a software program that implements these two scores for peptide identification. We applied Crescendo to test datasets and compared its performance with widely used search engines, including Mascot, Sequest, and Comet. The results indicate that Crescendo identifies a similar or larger number of peptides at various predefined false discovery rates (FDR). Importantly, it also provides a better separation between the true and decoy PSMs, warranting the future development of a companion post-processing filtering algorithm.

Remote Strain Sensing of CFRP Using Microwave Frequency Domain Reflectometry

NASA Technical Reports Server (NTRS)

Wilson, William C.; Moore, Jason P.; Juarez, Peter D.

2016-01-01

NASA's Advanced Composites Project is investigating technologies that increase automated remote inspection of aircraft composite structures. Therefore, microwave Frequency Domain Reflectometry (FDR) is being investigated as a method of enabling rapid remote measurement of strain occurring at the first ply of a composite fiber reinforced polymer (CFRP) structure using Radio Frequency (RF) Electro-Magnetic (EM) radiation. While microwave reflectometry has been used to detect disbonds in CFRP structures, its use in detecting strain has been limited. This work will present data demonstrating the measurement of the reactance changes due to loading conditions that are indicative of strain in a CFRP structure. In addition, the basic EM signature will be presented along with an analysis of temperature and humidity effects.

DNA methylation levels at chromosome 8q24 in peripheral blood are associated with 8q24 cancer susceptibility loci.

PubMed

Barry, Kathryn Hughes; Moore, Lee E; Sampson, Joshua; Yan, Liying; Meyer, Ann; Oler, Andrew J; Chung, Charles C; Wang, Zhaoming; Yeager, Meredith; Amundadottir, Laufey; Berndt, Sonja I

2014-12-01

Chromosome 8q24 has emerged as an important region for genetic susceptibility to various cancers, but little is known about the contribution of DNA methylation at 8q24. To evaluate variability in DNA methylation levels at 8q24 and the relationship with cancer susceptibility single nucleotide polymorphisms (SNPs) in this region, we quantified DNA methylation levels in peripheral blood at 145 CpG sites nearby 8q24 cancer susceptibility SNPs or MYC using pyrosequencing among 80 Caucasian men in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. For the 60 CpG sites meeting quality control, which also demonstrated temporal stability over a 5-year period, we calculated pairwise Spearman correlations for DNA methylation levels at each CpG site with 42 8q24 cancer susceptibility SNPs. To account for multiple testing, we adjusted P values into q values reflecting the false discovery rate (FDR). In contrast to the MYC CpG sites, most sites nearby the SNPs demonstrated good reproducibility, high methylation levels, and moderate-high between-individual variation. We observed 10 statistically significant (FDR < 0.05) CpG site-SNP correlations. These included correlations between an intergenic CpG site at Chr8:128393157 and the prostate cancer SNP rs16902094 (ρ = -0.54; P = 9.7 × 10(-7); q = 0.002), a PRNCR1 CpG site at Chr8:128167809 and the prostate cancer SNP rs1456315 (ρ = 0.52; P = 1.4 × 10(-6); q = 0.002), and two POU5F1B CpG sites and several prostate/colorectal cancer SNPs (for Chr8:128498051 and rs6983267, ρ = 0.46; P = 2.0 × 10(-5); q = 0.01). This is the first report of correlations between blood DNA methylation levels and cancer susceptibility SNPs at 8q24, suggesting that DNA methylation at this important susceptibility locus may contribute to cancer risk. ©2014 American Association for Cancer Research.

Ground Albedo Neutron Sensing (GANS) method for measurements of soil moisture in cropped fields

NASA Astrophysics Data System (ADS)

Andres Rivera Villarreyes, Carlos; Baroni, Gabriele; Oswald, Sascha E.

2013-04-01

Measurement of soil moisture at the plot or hill-slope scale is an important link between local vadose zone hydrology and catchment hydrology. However, so far only few methods are on the way to close this gap between point measurements and remote sensing. This study evaluates the applicability of the Ground Albedo Neutron Sensing (GANS) for integral quantification of seasonal soil moisture in the root zone at the scale of a field or small watershed, making use of the crucial role of hydrogen as neutron moderator relative to other landscape materials. GANS measurements were performed at two locations in Germany under different vegetative situations and seasonal conditions. Ground albedo neutrons were measured at (i) a lowland Bornim farmland (Brandenburg) cropped with sunflower in 2011 and winter rye in 2012, and (ii) a mountainous farmland catchment (Schaefertal, Harz Mountains) since middle 2011. At both sites depth profiles of soil moisture were measured at several locations in parallel by frequency domain reflectometry (FDR) for comparison and calibration. Initially, calibration parameters derived from a previous study with corn cover were tested under sunflower and winter rye periods at the same farmland. GANS soil moisture based on these parameters showed a large discrepancy compared to classical soil moisture measurements. Therefore, two new calibration approaches and four different ways of integration the soil moisture profile to an integral value for GANS were evaluated in this study. This included different sets of calibration parameters based on different growing periods of sunflower. New calibration parameters showed a good agreement with FDR network during sunflower period (RMSE = 0.023 m3 m-3), but they underestimated soil moisture in the winter rye period. The GANS approach resulted to be highly affected by temporal changes of biomass and crop types which suggest the need of neutron corrections for long-term observations with crop rotation. Finally, Bornim sunflower parameters were transferred to Schaefertal catchment for further evaluation. This study proves GANS potential to close the measurement gap between point scale and remote sensing scale; however, its calibration needs to be adapted for vegetation in cropped fields.

Discovery biology of neuropsychiatric syndromes (DBNS): a center for integrating clinical medicine and basic science.

PubMed

Viswanath, Biju; Rao, Naren P; Narayanaswamy, Janardhanan C; Sivakumar, Palanimuthu T; Kandasamy, Arun; Kesavan, Muralidharan; Mehta, Urvakhsh Meherwan; Venkatasubramanian, Ganesan; John, John P; Mukherjee, Odity; Purushottam, Meera; Kannan, Ramakrishnan; Mehta, Bhupesh; Kandavel, Thennarasu; Binukumar, B; Saini, Jitender; Jayarajan, Deepak; Shyamsundar, A; Moirangthem, Sydney; Vijay Kumar, K G; Thirthalli, Jagadisha; Chandra, Prabha S; Gangadhar, Bangalore N; Murthy, Pratima; Panicker, Mitradas M; Bhalla, Upinder S; Chattarji, Sumantra; Benegal, Vivek; Varghese, Mathew; Reddy, Janardhan Y C; Raghu, Padinjat; Rao, Mahendra; Jain, Sanjeev

2018-04-18

There is emerging evidence that there are shared genetic, environmental and developmental risk factors in psychiatry, that cut across traditional diagnostic boundaries. With this background, the Discovery biology of neuropsychiatric syndromes (DBNS) proposes to recruit patients from five different syndromes (schizophrenia, bipolar disorder, obsessive compulsive disorder, Alzheimer's dementia and substance use disorders), identify those with multiple affected relatives, and invite these families to participate in this study. The families will be assessed: 1) To compare neuro-endophenotype measures between patients, first degree relatives (FDR) and healthy controls., 2) To identify cellular phenotypes which differentiate the groups., 3) To examine the longitudinal course of neuro-endophenotype measures., 4) To identify measures which correlate with outcome, and 5) To create a unified digital database and biorepository. The identification of the index participants will occur at well-established specialty clinics. The selected individuals will have a strong family history (with at least another affected FDR) of mental illness. We will also recruit healthy controls without family history of such illness. All recruited individuals (N = 4500) will undergo brief clinical assessments and a blood sample will be drawn for isolation of DNA and peripheral blood mononuclear cells (PBMCs). From among this set, a subset of 1500 individuals (300 families and 300 controls) will be assessed on several additional assessments [detailed clinical assessments, endophenotype measures (neuroimaging- structural and functional, neuropsychology, psychophysics-electroencephalography, functional near infrared spectroscopy, eye movement tracking)], with the intention of conducting repeated measurements every alternate year. PBMCs from this set will be used to generate lymphoblastoid cell lines, and a subset of these would be converted to induced pluripotent stem cell lines and also undergo whole exome sequencing. We hope to identify unique and overlapping brain endophenotypes for major psychiatric syndromes. In a proportion of subjects, we expect these neuro-endophenotypes to progress over time and to predict treatment outcome. Similarly, cellular assays could differentiate cell lines derived from such groups. The repository of biomaterials as well as digital datasets of clinical parameters, will serve as a valuable resource for the broader scientific community who wish to address research questions in the area.

Actinomyces spp. gene expression in root caries lesions

PubMed Central

Dame-Teixeira, Naile; Parolo, Clarissa Cavalcanti Fatturi; Maltz, Marisa; Tugnait, Aradhna; Devine, Deirdre; Do, Thuy

2016-01-01

Background The studies of the distribution of Actinomyces spp. on carious and non-carious root surfaces have not been able to confirm the association of these bacteria with root caries, although they were extensively implicated as a prime suspect in root caries. Objective The aim of this study was to observe the gene expression of Actinomyces spp. in the microbiota of root surfaces with and without caries. Design The oral biofilms from exposed sound root surface (SRS; n=10) and active root caries (RC; n=30) samples were collected. The total bacterial RNA was extracted, and the mRNA was isolated. Samples with low RNA concentration were pooled, yielding a final sample size of SRS=10 and RC=9. Complementary DNA (cDNA) libraries were prepared and sequenced on an Illumina® HiSeq 2500 system. Sequence reads were mapped to eight Actinomyces genomes. Count data were normalized using DESeq2 to analyse differential gene expression applying the Benjamini-Hochberg correction (false discovery rate [FDR]<0.001). Results Actinomyces spp. had similar numbers of reads (Mann-Whitney U-test; p>0.05), except for Actinomyces OT178 (p=0.001) and Actinomyces gerencseriae (p=0.004), which had higher read counts in the SRS. Genes that code for stress proteins (clp, dnaK, and groEL), enzymes of glycolysis pathways (including enolase and phosphoenolpyruvate carboxykinase), adhesion (Type-2 fimbrial and collagen-binding protein), and cell growth (EF-Tu) were highly – but not differentially (p>0.001) – expressed in both groups. Genes with the most significant upregulation in RC were those coding for hypothetical proteins and uracil DNA glycosylase (p=2.61E-17). The gene with the most significant upregulation in SRS was a peptide ABC transporter substrate-binding protein (log2FC=−6.00, FDR=2.37E-05). Conclusion There were similar levels of Actinomyces gene expression in both sound and carious root biofilms. These bacteria can be commensal in root surface sites but may be cariogenic due to survival mechanisms that allow them to exist in acid environments and to metabolize sugars, saving energy. PMID:27640531

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.

PubMed

Knoll, Rebecca L; Forslund, Kristoffer; Kultima, Jens Roat; Meyer, Claudius U; Kullmer, Ulrike; Sunagawa, Shinichi; Bork, Peer; Gehring, Stephan

2017-04-01

Current treatment for pediatric inflammatory bowel disease (IBD) patients is often ineffective, with serious side effects. Manipulating the gut microbiota via fecal microbiota transplantation (FMT) is an emerging treatment approach but remains controversial. We aimed to assess the composition of the fecal microbiome through a comparison of pediatric IBD patients to their healthy siblings, evaluating risks and prospects for FMT in this setting. A case-control (sibling) study was conducted analyzing fecal samples of six children with Crohn's disease (CD), six children with ulcerative colitis (UC) and 12 healthy siblings by metagenomic sequencing. In addition, lifetime antibiotic intake was retrospectively determined. Species richness and diversity were significantly reduced in UC patients compared with control [Mann-Whitney U -test false discovery rate (MWU FDR) = 0.011]. In UC, bacteria positively influencing gut homeostasis, e.g., Eubacterium rectale and Faecalibacterium prausnitzii , were significantly reduced in abundance (MWU FDR = 0.05). Known pathobionts like Escherichia coli were enriched in UC patients (MWU FDR = 0.084). Moreover, E. coli abundance correlated positively with that of several virulence genes (SCC > 0.65, FDR < 0.1). A shift toward antibiotic-resistant taxa in both IBD groups distinguished them from controls [MWU Benjamini-Hochberg-Yekutieli procedure (BY) FDR = 0.062 in UC, MWU BY FDR = 0.019 in CD). The collected results confirm a microbial dysbiosis in pediatric UC, and to a lesser extent in CD patients, replicating associations found previously using different methods. Taken together, these observations suggest microbiotal remodeling therapy from family donors, at least for children with UC, as a viable option. NEW & NOTEWORTHY In this sibling study, prior reports of microbial dysbiosis in IBD patients from 16S rRNA sequencing was verified using deep shotgun sequencing and augmented with insights into the abundance of bacterial virulence genes and bacterial antibiotic resistance determinants, seen against the background of data on the specific antibiotic intake of each of the study participants. The observed dysbiosis, which distinguishes patients from siblings, highlights such siblings as potential donors for microbiotal remodeling therapy in IBD. Copyright © 2017 the American Physiological Society.

Crossbred steer temperament as yearlings and whole genome association of steer temperament as yearlings and calf temperament post-weaning.

PubMed

Riley, D G; Gill, C A; Boldt, C R; Funkhouser, R R; Herring, A D; Riggs, P K; Sawyer, J E; Lunt, D K; Sanders, J O

2016-04-01

cattle often have the reputation for a poor or dangerous temperament. Identification of genomic regions that associate with temperament of such cattle may be useful for genetic improvement strategies. The objectives of this study were to evaluate subjective temperament scores (1 to 9; higher scores indicated more unfavorable temperament) for aggressiveness, nervousness, flightiness, gregariousness, and overall temperament of one-half steers in feedlot conditions at 1 yr of age and compare those scores of those steers when evaluated approximately 1 mo postweaning, and conduct whole genome association analyses using SNP markers and the temperament traits of those steers at 1 yr of age and for temperament traits of all calves at weaning. Contemporary groups ( < 0.001) were steers born in the same year and season, and fed in the same feedlot pen. Aggressiveness of steers at 1 yr of age was not associated with aggressiveness at weaning (linear regression coefficient did not differ from 0; = 0.96), but regressions of all other yearling scores of steers on the scores at weaning were positive (coefficients ranged from 0.26 ± 0.04 to 0.32 ± 0.04; < 0.001). Estimates of Pearson correlation coefficients (using unadjusted values and residual values) of the different traits measured at 1 yr of age were large ( > 0.63; < 0.008) except for aggressiveness with nervousness, flightiness, or gregariousness, which did not differ from 0 ( > 0.1). Five SNP on BTA 1, 24, and 29 had suggestive associations (0.17 < [adjusted for FDR] < 0.24) with aggressiveness, nervousness, or flightiness at evaluation postweaning and 13 SNP on 11 chromosomes had suggestive associations (0.07 < [adjusted for FDR] < 0.24) with aggressiveness, nervousness, flightiness, or overall temperament score of steers at 1 yr of age. Genes close to these loci with roles in neural systems of various organisms included synaptotagmin 4 (BTA 24), FAT atypical cadhedrin 3 (BTA 29), tubulin tyrosine ligase-like 1 (BTA 5), spermatogenesis associated 17 (BTA 16), stanniocalcin 2 (BTA 20), and GABA receptor γ 3 (BTA 21).

A method to identify differential expression profiles of time-course gene data with Fourier transformation

PubMed Central

2013-01-01

Background Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. Results This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization. The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Conclusions Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics. PMID:24134721

Transcriptional profiling identifies differentially expressed genes in developing turkey skeletal muscle

PubMed Central

2011-01-01

Background Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. Understanding these developmental changes in agriculturally important species is essential to the production of high quality meat products. For example, consumer demand for lean, inexpensive meat products has driven the turkey industry to unprecedented production through intensive genetic selection. However, achievements of increased body weight and muscle mass have been countered by an increased incidence of myopathies and meat quality defects. In a previous study, we developed and validated a turkey skeletal muscle-specific microarray as a tool for functional genomics studies. The goals of the current study were to utilize this microarray to elucidate functional pathways of genes responsible for key events in turkey skeletal muscle development and to compare differences in gene expression between two genetic lines of turkeys. To achieve these goals, skeletal muscle samples were collected at three critical stages in muscle development: 18d embryo (hyperplasia), 1d post-hatch (shift from myoblast-mediated growth to satellite cell-modulated growth by hypertrophy), and 16wk (market age) from two genetic lines: a randombred control line (RBC2) maintained without selection pressure, and a line (F) selected from the RBC2 line for increased 16wk body weight. Array hybridizations were performed in two experiments: Experiment 1 directly compared the developmental stages within genetic line, while Experiment 2 directly compared the two lines within each developmental stage. Results A total of 3474 genes were differentially expressed (false discovery rate; FDR < 0.001) by overall effect of development, while 16 genes were differentially expressed (FDR < 0.10) by overall effect of genetic line. Ingenuity Pathways Analysis was used to group annotated genes into networks, functions, and canonical pathways. The expression of 28 genes involved in extracellular matrix regulation, cell death/apoptosis, and calcium signaling/muscle function, as well as genes with miscellaneous function was confirmed by qPCR. Conclusions The current study identified gene pathways and uncovered novel genes important in turkey muscle growth and development. Future experiments will focus further on several of these candidate genes and the expression and mechanism of action of their protein products. PMID:21385442

Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures

PubMed Central

2012-01-01

Background Biological systems respond to changes in both the Earth's magnetic and gravitational fields, but as experiments in space are expensive and infrequent, Earth-based simulation techniques are required. A high gradient magnetic field can be used to levitate biological material, thereby simulating microgravity and can also create environments with a reduced or an enhanced level of gravity (g), although special attention should be paid to the possible effects of the magnetic field (B) itself. Results Using diamagnetic levitation, we exposed Arabidopsis thaliana in vitro callus cultures to five environments with different levels of effective gravity and magnetic field strengths. The environments included levitation, i.e. simulated μg* (close to 0 g* at B = 10.1 T), intermediate g* (0.1 g* at B = 14.7 T) and enhanced gravity levels (1.9 g* at B = 14.7 T and 2 g* at B = 10.1 T) plus an internal 1 g* control (B = 16.5 T). The asterisk denotes the presence of the background magnetic field, as opposed to the effective gravity environments in the absence of an applied magnetic field, created using a Random Position Machine (simulated μg) and a Large Diameter Centrifuge (2 g). Microarray analysis indicates that changes in the overall gene expression of cultured cells exposed to these unusual environments barely reach significance using an FDR algorithm. However, it was found that gravitational and magnetic fields produce synergistic variations in the steady state of the transcriptional profile of plants. Transcriptomic results confirm that high gradient magnetic fields (i.e. to create μg* and 2 g* conditions) have a significant effect, mainly on structural, abiotic stress genes and secondary metabolism genes, but these subtle gravitational effects are only observable using clustering methodologies. Conclusions A detailed microarray dataset analysis, based on clustering of similarly expressed genes (GEDI software), can detect underlying global-scale responses, which cannot be detected by means of individual gene expression techniques using raw or corrected p values (FDR). A subtle, but consistent, genome-scale response to hypogravity environments was found, which was opposite to the response in a hypergravity environment. PMID:22435851

Analysis of Sex Hormone Genes Reveals Gender Differences in the Genetic Etiology of Blood Pressure Salt Sensitivity: The GenSalt Study

PubMed Central

2013-01-01

BACKGROUND We examined the association between 799 single-nucleotide polymorphisms in 39 sex hormone genes and blood pressure (BP) responses to a dietary-sodium intervention. METHODS A 7-day low-sodium feeding study (51.3 mmol sodium/day) followed by a 7-day high-sodium feeding study (307.8 mmol sodium/day) was conducted among 1,906 Han Chinese participants. Nine BP measurements were obtained at baseline and the end of each intervention period using a random-zero sphygmomanometer. RESULTS Among men, absolute BP responses to sodium interventions decreased with the number of minor alleles of estrogen receptor 1 (ESR1) markers rs9340844, rs9397453, rs9371562, rs9397459, and rs9383951. For example, mean diastolic blood pressure (DBP) responses to low-sodium intervention (95% confidence interval) were –2.67 (–3.13, –2.22) mm Hg among those with the rs9397453 C/C genotype, –1.23 (–1.98, –0.48) mm Hg among those with the C/T genotype, and 0.08 (–2.31, 2.47) mm Hg among those with the T/T genotype (P = 1×10–4; false discovery rate (FDR)-q = 0.04). Mean DBP responses to high sodium according to the rs9397453 genotypes were 1.46 (1.03, 1.89) mm Hg among those with C/C, 0.19 (–0.54, 0.91) mm Hg among those with C/T, and –1.10 (–2.82, 0.61) mm Hg among those with T/T (P = 2×10–4; FDR-q = 0.04). Similar trends were noted for the association between these ESR1 variants and SBP responses to the dietary intervention. There were no significant associations between sex hormone gene variants and salt sensitivity in women, with genotype-gender interactions noted for the ESR1 markers that achieved significance in men. CONCLUSIONS We identified strong, consistent associations between ESR1 gene variants and salt sensitivity in men. Our results support a gender-specific role for ESR1 in the etiology of this complex trait. PMID:23382403

An epigenome-wide study of body mass index and DNA methylation in blood using participants from the Sister Study cohort.

PubMed

Wilson, L E; Harlid, S; Xu, Z; Sandler, D P; Taylor, J A

2017-01-01

The relationship between obesity and chronic disease risk is well-established; the underlying biological mechanisms driving this risk increase may include obesity-related epigenetic modifications. To explore this hypothesis, we conducted a genome-wide analysis of DNA methylation and body mass index (BMI) using data from a subset of women in the Sister Study. The Sister Study is a cohort of 50 884 US women who had a sister with breast cancer but were free of breast cancer themselves at enrollment. Study participants completed examinations which included measurements of height and weight, and provided blood samples. Blood DNA methylation data generated with the Illumina Infinium HumanMethylation27 BeadChip array covering 27,589 CpG sites was available for 871 women from a prior study of breast cancer and DNA methylation. To identify differentially methylated CpG sites associated with BMI, we analyzed this methylation data using robust linear regression with adjustment for age and case status. For those CpGs passing the false discovery rate significance level, we examined the association in a replication set comprised of a non-overlapping group of 187 women from the Sister Study who had DNA methylation data generated using the Infinium HumanMethylation450 BeadChip array. Analysis of this expanded 450 K array identified additional BMI-associated sites which were investigated with targeted pyrosequencing. Four CpG sites reached genome-wide significance (false discovery rate (FDR) q<0.05) in the discovery set and associations for all four were significant at strict Bonferroni correction in the replication set. An additional 23 sites passed FDR in the replication set and five were replicated by pyrosequencing in the discovery set. Several of the genes identified including ANGPT4, RORC, SOCS3, FSD2, XYLT1, ABCG1, STK39, ASB2 and CRHR2 have been linked to obesity and obesity-related chronic diseases. Our findings support the hypothesis that obesity-related epigenetic differences are detectable in blood and may be related to risk of chronic disease.

A more randomly organized grey matter network is associated with deteriorating language and global cognition in individuals with subjective cognitive decline.

PubMed

Verfaillie, Sander C J; Slot, Rosalinde E R; Dicks, Ellen; Prins, Niels D; Overbeek, Jozefien M; Teunissen, Charlotte E; Scheltens, Philip; Barkhof, Frederik; van der Flier, Wiesje M; Tijms, Betty M

2018-03-30

Grey matter network disruptions in Alzheimer's disease (AD) are associated with worse cognitive impairment cross-sectionally. Our aim was to investigate whether indications of a more random network organization are associated with longitudinal decline in specific cognitive functions in individuals with subjective cognitive decline (SCD). We included 231 individuals with SCD who had annually repeated neuropsychological assessment (3 ± 1 years; n = 646 neuropsychological investigations) available from the Amsterdam Dementia Cohort (54% male, age: 63 ± 9, MMSE: 28 ± 2). Single-subject grey matter networks were extracted from baseline 3D-T1 MRI scans and we computed basic network (size, degree, connectivity density) and higher-order (path length, clustering, betweenness centrality, normalized path length [lambda] and normalized clustering [gamma]) parameters at whole brain and/or regional levels. We tested associations of network parameters with baseline and annual cognition (memory, attention, executive functioning, language composite scores, and global cognition [all domains with MMSE]) using linear mixed models, adjusted for age, sex, education, scanner and total gray matter volume. Lower network size was associated with steeper decline in language (β ± SE = 0.12 ± 0.05, p < 0.05FDR). Higher-order network parameters showed no cross-sectional associations. Lower gamma and lambda values were associated with steeper decline in global cognition (gamma: β ± SE = 0.06 ± 0.02); lambda: β ± SE = 0.06 ± 0.02), language (gamma: β ± SE = 0.11 ± 0.04; lambda: β ± SE = 0.12 ± 0.05; all p < 0.05FDR). Lower path length values in precuneus and fronto-temporo-occipital cortices were associated with a steeper decline in global cognition. A more randomly organized grey matter network was associated with a steeper decline of cognitive functioning, possibly indicating the start of cognitive impairment. © 2018 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Health status monitoring for ICU patients based on locally weighted principal component analysis.

PubMed

Ding, Yangyang; Ma, Xin; Wang, Youqing

2018-03-01

Intelligent status monitoring for critically ill patients can help medical stuff quickly discover and assess the changes of disease and then make appropriate treatment strategy. However, general-type monitoring model now widely used is difficult to adapt the changes of intensive care unit (ICU) patients' status due to its fixed pattern, and a more robust, efficient and fast monitoring model should be developed to the individual. A data-driven learning approach combining locally weighted projection regression (LWPR) and principal component analysis (PCA) is firstly proposed and applied to monitor the nonlinear process of patients' health status in ICU. LWPR is used to approximate the complex nonlinear process with local linear models, in which PCA could be further applied to status monitoring, and finally a global weighted statistic will be acquired for detecting the possible abnormalities. Moreover, some improved versions are developed, such as LWPR-MPCA and LWPR-JPCA, which also have superior performance. Eighteen subjects were selected from the Physiobank's Multi-parameter Intelligent Monitoring for Intensive Care II (MIMIC II) database, and two vital signs of each subject were chosen for online monitoring. The proposed method was compared with several existing methods including traditional PCA, Partial least squares (PLS), just in time learning combined with modified PCA (L-PCA), and Kernel PCA (KPCA). The experimental results demonstrated that the mean fault detection rate (FDR) of PCA can be improved by 41.7% after adding LWPR. The mean FDR of LWPR-MPCA was increased by 8.3%, compared with the latest reported method L-PCA. Meanwhile, LWPR spent less training time than others, especially KPCA. LWPR is first introduced into ICU patients monitoring and achieves the best monitoring performance including adaptability to changes in patient status, sensitivity for abnormality detection as well as its fast learning speed and low computational complexity. The algorithm is an excellent approach to establishing a personalized model for patients, which is the mainstream direction of modern medicine in the following development, as well as improving the global monitoring performance. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Associations between STAT3 rs744166 Polymorphisms and Susceptibility to Ulcerative Colitis and Crohn's Disease: A Meta-Analysis

PubMed Central

Peng, Xiulan; Song, Jia; Wang, Jun; Dong, Weiguo

2014-01-01

Background Many studies have investigated the associations between the signal transducer and activator of transcription 3 (STAT3) in the susceptibility to ulcerative colitis (UC) and Crohn's disease (CD). However, the results remain inconsistent. This meta-analysis determined the risk of STAT3 rs744166 polymorphism-conferred UC and CD susceptibility. Materials and Methods Electronic databases, including PubMed, EMBASE and the Cochrane Library, were searched for all eligible studies that evaluated the association between STAT3 rs744166 polymorphisms with UC and CD risk up to August 21, 2014. The pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated using fixed- or random-effects models. Results Twelve studies containing 10298 patients with CD, 4244 patients with UC and 11191 controls were included in this meta-analysis. The results indicated that the STAT3 rs744166 polymorphism was associated with CD and UC susceptibility (CD: GA+AA vs. GG, OR = 1.20, 95%CI, 1.11–1.30, I 2 = 0%, P unadjusted<0.00001, P Bonferroni<0.00005, P FDR<0.00001; UC: GA+AA vs. GG, OR = 1.21, 95%CI, 1.08–1.36, I 2 = 1%, P unadjusted = 0.001, P Bonferroni = 0.005, P FDR = 0.00125). In subgroup analyses by ethnicity, the significant association was found only among Caucasians. However, when grouped by age of onset, positive associations were found both among adults and children. In addition, when stratified by study design and genotyping methods, the risk of CD was significantly associated with the STAT3 rs744166 polymorphism in hospital-based and population-based groups and in SNP Array and SNPlex groups. For UC, significant associations were also found in population-based, PCR-RFLP and SNPlex groups. Moreover, these findings were sufficiently robust to withstand the Bonferroni correction and false discovery rate (FDR). Conclusion This meta-analysis indicates that carriers of the STAT3 rs744166 ‘A’ allele have a significantly greater risk of CD and UC, especially among Caucasians. PMID:25286337

Comparing performances of a CdTe X-ray spectroscopic detector and an X-ray dual-energy sandwich detector

NASA Astrophysics Data System (ADS)

Gorecki, A.; Brambilla, A.; Moulin, V.; Gaborieau, E.; Radisson, P.; Verger, L.

2013-11-01

Multi-energy (ME) detectors are becoming a serious alternative to classical dual-energy sandwich (DE-S) detectors for X-ray applications such as medical imaging or explosive detection. They can use the full X-ray spectrum of irradiated materials, rather than disposing only of low and high energy measurements, which may be mixed. In this article, we intend to compare both simulated and real industrial detection systems, operating at a high count rate, independently of the dimensions of the measurements and independently of any signal processing methods. Simulations or prototypes of similar detectors have already been compared (see [1] for instance), but never independently of estimation methods and never with real detectors. We have simulated both an ME detector made of CdTe - based on the characteristics of the MultiX ME100 and - a DE-S detector - based on the characteristics of the Detection Technology's X-Card 1.5-64DE model. These detectors were compared to a perfect spectroscopic detector and an optimal DE-S detector. For comparison purposes, two approaches were investigated. The first approach addresses how to distinguise signals, while the second relates to identifying materials. Performance criteria were defined and comparisons were made over a range of material thicknesses and with different photon statistics. Experimental measurements in a specific configuration were acquired to checks simulations. Results showed good agreement between the ME simulation and the ME100 detector. Both criteria seem to be equivalent, and the ME detector performs 3.5 times better than the DE-S detector with same photon statistics based on simulations and experimental measurements. Regardless of the photon statistics ME detectors appeared more efficient than DE-S detectors for all material thicknesses between 1 and 9 cm when measuring plastics with an attenuation signature close that of explosive materials. This translates into an improved false detection rate (FDR): DE-S detectors have an FDR 2.87±0.03-fold higher than ME detectors for 4 cm of POM with 20 000 incident photons, when identifications are screened against a two-material base.

Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: applications to differential gene expression.

PubMed

Montazeri, Zahra; Yanofsky, Corey M; Bickel, David R

2010-01-01

Research on analyzing microarray data has focused on the problem of identifying differentially expressed genes to the neglect of the problem of how to integrate evidence that a gene is differentially expressed with information on the extent of its differential expression. Consequently, researchers currently prioritize genes for further study either on the basis of volcano plots or, more commonly, according to simple estimates of the fold change after filtering the genes with an arbitrary statistical significance threshold. While the subjective and informal nature of the former practice precludes quantification of its reliability, the latter practice is equivalent to using a hard-threshold estimator of the expression ratio that is not known to perform well in terms of mean-squared error, the sum of estimator variance and squared estimator bias. On the basis of two distinct simulation studies and data from different microarray studies, we systematically compared the performance of several estimators representing both current practice and shrinkage. We find that the threshold-based estimators usually perform worse than the maximum-likelihood estimator (MLE) and they often perform far worse as quantified by estimated mean-squared risk. By contrast, the shrinkage estimators tend to perform as well as or better than the MLE and never much worse than the MLE, as expected from what is known about shrinkage. However, a Bayesian measure of performance based on the prior information that few genes are differentially expressed indicates that hard-threshold estimators perform about as well as the local false discovery rate (FDR), the best of the shrinkage estimators studied. Based on the ability of the latter to leverage information across genes, we conclude that the use of the local-FDR estimator of the fold change instead of informal or threshold-based combinations of statistical tests and non-shrinkage estimators can be expected to substantially improve the reliability of gene prioritization at very little risk of doing so less reliably. Since the proposed replacement of post-selection estimates with shrunken estimates applies as well to other types of high-dimensional data, it could also improve the analysis of SNP data from genome-wide association studies.

JPRS Report, Science & Technology, China: Energy.

DTIC Science & Technology

1992-03-30

breeder reactors should become...the primary type of reactors . In developing breeder reactors , we should follow the path of using metal fuel. Breeder reactors give us more time to...first reactor used for power generation was a fast reactor : the " Breeder 1" reactor at the Idaho National Reactor Test Center which was used to

Biofilm reactors for industrial bioconversion processes: employing potential of enhanced reaction rates

PubMed Central

Qureshi, Nasib; Annous, Bassam A; Ezeji, Thaddeus C; Karcher, Patrick; Maddox, Ian S

2005-01-01

This article describes the use of biofilm reactors for the production of various chemicals by fermentation and wastewater treatment. Biofilm formation is a natural process where microbial cells attach to the support (adsorbent) or form flocs/aggregates (also called granules) without use of chemicals and form thick layers of cells known as "biofilms." As a result of biofilm formation, cell densities in the reactor increase and cell concentrations as high as 74 gL-1 can be achieved. The reactor configurations can be as simple as a batch reactor, continuous stirred tank reactor (CSTR), packed bed reactor (PBR), fluidized bed reactor (FBR), airlift reactor (ALR), upflow anaerobic sludge blanket (UASB) reactor, or any other suitable configuration. In UASB granular biofilm particles are used. This article demonstrates that reactor productivities in these reactors have been superior to any other reactor types. This article describes production of ethanol, butanol, lactic acid, acetic acid/vinegar, succinic acid, and fumaric acid in addition to wastewater treatment in the biofilm reactors. As the title suggests, biofilm reactors have high potential to be employed in biotechnology/bioconversion industry for viable economic reasons. In this article, various reactor types have been compared for the above bioconversion processes. PMID:16122390

Control of reactor coolant flow path during reactor decay heat removal

DOEpatents

Hunsbedt, Anstein N.

1988-01-01

An improved reactor vessel auxiliary cooling system for a sodium cooled nuclear reactor is disclosed. The sodium cooled nuclear reactor is of the type having a reactor vessel liner separating the reactor hot pool on the upstream side of an intermediate heat exchanger and the reactor cold pool on the downstream side of the intermediate heat exchanger. The improvement includes a flow path across the reactor vessel liner flow gap which dissipates core heat across the reactor vessel and containment vessel responsive to a casualty including the loss of normal heat removal paths and associated shutdown of the main coolant liquid sodium pumps. In normal operation, the reactor vessel cold pool is inlet to the suction side of coolant liquid sodium pumps, these pumps being of the electromagnetic variety. The pumps discharge through the core into the reactor hot pool and then through an intermediate heat exchanger where the heat generated in the reactor core is discharged. Upon outlet from the heat exchanger, the sodium is returned to the reactor cold pool. The improvement includes placing a jet pump across the reactor vessel liner flow gap, pumping a small flow of liquid sodium from the lower pressure cold pool into the hot pool. The jet pump has a small high pressure driving stream diverted from the high pressure side of the reactor pumps. During normal operation, the jet pumps supplement the normal reactor pressure differential from the lower pressure cold pool to the hot pool. Upon the occurrence of a casualty involving loss of coolant pump pressure, and immediate cooling circuit is established by the back flow of sodium through the jet pumps from the reactor vessel hot pool to the reactor vessel cold pool. The cooling circuit includes flow into the reactor vessel liner flow gap immediate the reactor vessel wall and containment vessel where optimum and immediate discharge of residual reactor heat occurs.

Neutron fluxes in test reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Youinou, Gilles Jean-Michel

Communicate the fact that high-power water-cooled test reactors such as the Advanced Test Reactor (ATR), the High Flux Isotope Reactor (HFIR) or the Jules Horowitz Reactor (JHR) cannot provide fast flux levels as high as sodium-cooled fast test reactors. The memo first presents some basics physics considerations about neutron fluxes in test reactors and then uses ATR, HFIR and JHR as an illustration of the performance of modern high-power water-cooled test reactors.

A note on the false discovery rate of novel peptides in proteogenomics.

PubMed

Zhang, Kun; Fu, Yan; Zeng, Wen-Feng; He, Kun; Chi, Hao; Liu, Chao; Li, Yan-Chang; Gao, Yuan; Xu, Ping; He, Si-Min

2015-10-15

Proteogenomics has been well accepted as a tool to discover novel genes. In most conventional proteogenomic studies, a global false discovery rate is used to filter out false positives for identifying credible novel peptides. However, it has been found that the actual level of false positives in novel peptides is often out of control and behaves differently for different genomes. To quantitatively model this problem, we theoretically analyze the subgroup false discovery rates of annotated and novel peptides. Our analysis shows that the annotation completeness ratio of a genome is the dominant factor influencing the subgroup FDR of novel peptides. Experimental results on two real datasets of Escherichia coli and Mycobacterium tuberculosis support our conjecture. yfu@amss.ac.cn or xupingghy@gmail.com or smhe@ict.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Entorhinal cortex receptive fields are modulated by spatial attention, even without movement

PubMed Central

König, Peter; König, Seth; Buffalo, Elizabeth A

2018-01-01

Grid cells in the entorhinal cortex allow for the precise decoding of position in space. Along with potentially playing an important role in navigation, grid cells have recently been hypothesized to make a general contribution to mental operations. A prerequisite for this hypothesis is that grid cell activity does not critically depend on physical movement. Here, we show that movement of covert attention, without any physical movement, also elicits spatial receptive fields with a triangular tiling of space. In monkeys trained to maintain central fixation while covertly attending to a stimulus moving in the periphery we identified a significant population (20/141, 14% neurons at a FDR <5%) of entorhinal cells with spatially structured receptive fields. This contrasts with recordings obtained in the hippocampus, where grid-like representations were not observed. Our results provide evidence that neurons in macaque entorhinal cortex do not rely on physical movement. PMID:29537964

Characterization of the human plasma phosphoproteome using linear ion trap mass spectrometry and multiple search engines.

PubMed

Carrascal, Montserrat; Gay, Marina; Ovelleiro, David; Casas, Vanessa; Gelpí, Emilio; Abian, Joaquin

2010-02-05

Major plasma protein families play different roles in blood physiology and hemostasis and in immunodefense. Other proteins in plasma can be involved in signaling as chemical messengers or constitute biological markers of the status of distant tissues. In this respect, the plasma phosphoproteome holds potentially relevant information on the mechanisms modulating these processes through the regulation of protein activity. In this work we describe for the first time a collection of phosphopeptides identified in human plasma using immunoaffinity separation of the seven major serum protein families from other plasma proteins, SCX fractionation, and TiO(2) purification prior to LC-MS/MS analysis. One-hundred and twenty-seven phosphosites in 138 phosphopeptides mapping 70 phosphoproteins were identified with FDR < 1%. A high-confidence collection of phosphosites was obtained using a combined search with the OMSSA, SEQUEST, and Phenyx search engines.

A New Event Builder for CMS Run II

NASA Astrophysics Data System (ADS)

Albertsson, K.; Andre, J.-M.; Andronidis, A.; Behrens, U.; Branson, J.; Chaze, O.; Cittolin, S.; Darlea, G.-L.; Deldicque, C.; Dobson, M.; Dupont, A.; Erhan, S.; Gigi, D.; Glege, F.; Gomez-Ceballos, G.; Hegeman, J.; Holzner, A.; Jimenez-Estupiñán, R.; Masetti, L.; Meijers, F.; Meschi, E.; Mommsen, R. K.; Morovic, S.; Nunez-Barranco-Fernandez, C.; O'Dell, V.; Orsini, L.; Paus, C.; Petrucci, A.; Pieri, M.; Racz, A.; Roberts, P.; Sakulin, H.; Schwick, C.; Stieger, B.; Sumorok, K.; Veverka, J.; Zaza, S.; Zejdl, P.

2015-12-01

The data acquisition system (DAQ) of the CMS experiment at the CERN Large Hadron Collider (LHC) assembles events at a rate of 100 kHz, transporting event data at an aggregate throughput of 100GB/s to the high-level trigger (HLT) farm. The DAQ system has been redesigned during the LHC shutdown in 2013/14. The new DAQ architecture is based on state-of-the-art network technologies for the event building. For the data concentration, 10/40 Gbps Ethernet technologies are used together with a reduced TCP/IP protocol implemented in FPGA for a reliable transport between custom electronics and commercial computing hardware. A 56 Gbps Infiniband FDR CLOS network has been chosen for the event builder. This paper discusses the software design, protocols, and optimizations for exploiting the hardware capabilities. We present performance measurements from small-scale prototypes and from the full-scale production system.

Bayesian models based on test statistics for multiple hypothesis testing problems.

PubMed

Ji, Yuan; Lu, Yiling; Mills, Gordon B

2008-04-01

We propose a Bayesian method for the problem of multiple hypothesis testing that is routinely encountered in bioinformatics research, such as the differential gene expression analysis. Our algorithm is based on modeling the distributions of test statistics under both null and alternative hypotheses. We substantially reduce the complexity of the process of defining posterior model probabilities by modeling the test statistics directly instead of modeling the full data. Computationally, we apply a Bayesian FDR approach to control the number of rejections of null hypotheses. To check if our model assumptions for the test statistics are valid for various bioinformatics experiments, we also propose a simple graphical model-assessment tool. Using extensive simulations, we demonstrate the performance of our models and the utility of the model-assessment tool. In the end, we apply the proposed methodology to an siRNA screening and a gene expression experiment.

Cloud-based solution to identify statistically significant MS peaks differentiating sample categories.

PubMed

Ji, Jun; Ling, Jeffrey; Jiang, Helen; Wen, Qiaojun; Whitin, John C; Tian, Lu; Cohen, Harvey J; Ling, Xuefeng B

2013-03-23

Mass spectrometry (MS) has evolved to become the primary high throughput tool for proteomics based biomarker discovery. Until now, multiple challenges in protein MS data analysis remain: large-scale and complex data set management; MS peak identification, indexing; and high dimensional peak differential analysis with the concurrent statistical tests based false discovery rate (FDR). "Turnkey" solutions are needed for biomarker investigations to rapidly process MS data sets to identify statistically significant peaks for subsequent validation. Here we present an efficient and effective solution, which provides experimental biologists easy access to "cloud" computing capabilities to analyze MS data. The web portal can be accessed at http://transmed.stanford.edu/ssa/. Presented web application supplies large scale MS data online uploading and analysis with a simple user interface. This bioinformatic tool will facilitate the discovery of the potential protein biomarkers using MS.

A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics

PubMed Central

Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W.; Monroe, Matthew E.; Purvine, Samuel O.; Karpievitch, Yuliya V.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

2011-01-01

Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, as this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referred to as Statistical Tools for AMT tag Confidence (STAC). STAC additionally provides a Uniqueness Probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download as both a command line and a Windows graphical application. PMID:21692516

Dragon Stream Cipher for Secure Blackbox Cockpit Voice Recorder

NASA Astrophysics Data System (ADS)

Akmal, Fadira; Michrandi Nasution, Surya; Azmi, Fairuz

2017-11-01

Aircraft blackbox is a device used to record all aircraft information, which consists of Flight Data Recorder (FDR) and Cockpit Voice Recorder (CVR). Cockpit Voice Recorder contains conversations in the aircraft during the flight.Investigations on aircraft crashes usually take a long time, because it is difficult to find the aircraft blackbox. Then blackbox should have the ability to send information to other places. Aircraft blackbox must have a data security system, data security is a very important part at the time of information exchange process. The system in this research is to perform the encryption and decryption process on Cockpit Voice Recorder by people who are entitled by using Dragon Stream Cipher algorithm. The tests performed are time of data encryption and decryption, and avalanche effect. Result in this paper show us time encryption and decryption are 0,85 seconds and 1,84 second for 30 seconds Cockpit Voice Recorder data witn an avalanche effect 48,67 %.

Assessing differential gene expression with small sample sizes in oligonucleotide arrays using a mean-variance model.

PubMed

Hu, Jianhua; Wright, Fred A

2007-03-01

The identification of the genes that are differentially expressed in two-sample microarray experiments remains a difficult problem when the number of arrays is very small. We discuss the implications of using ordinary t-statistics and examine other commonly used variants. For oligonucleotide arrays with multiple probes per gene, we introduce a simple model relating the mean and variance of expression, possibly with gene-specific random effects. Parameter estimates from the model have natural shrinkage properties that guard against inappropriately small variance estimates, and the model is used to obtain a differential expression statistic. A limiting value to the positive false discovery rate (pFDR) for ordinary t-tests provides motivation for our use of the data structure to improve variance estimates. Our approach performs well compared to other proposed approaches in terms of the false discovery rate.

A new event builder for CMS Run II

DOE PAGES

Albertsson, K.; Andre, J-M; Andronidis, A.; ...

2015-12-23

The data acquisition system (DAQ) of the CMS experiment at the CERN Large Hadron Collider (LHC) assembles events at a rate of 100 kHz, transporting event data at an aggregate throughput of 100 GB/s to the high-level trigger (HLT) farm. The DAQ system has been redesigned during the LHC shutdown in 2013/14. The new DAQ architecture is based on state-of-the-art network technologies for the event building. For the data concentration, 10/40 Gbps Ethernet technologies are used together with a reduced TCP/IP protocol implemented in FPGA for a reliable transport between custom electronics and commercial computing hardware. A 56 Gbps Innibandmore » FDR CLOS network has been chosen for the event builder. This paper discusses the software design, protocols, and optimizations for exploiting the hardware capabilities. In conclusion, ee present performance measurements from small-scale prototypes and from the full-scale production system.« less

FINAL DESIGN REVIEW REPORT Subcritical Experiments Gen 2, 3-ft Confinement Vessel Weldment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Romero, Christopher

A Final Design Review (FDR) of the Subcritical Experiments (SCE) Gen 2, 3-ft. Confinement Vessel Weldment was held at Los Alamos National Laboratory (LANL) on September 14, 2017. The review was a focused review on changes only to the confinement vessel weldment (versus a system design review). The changes resulted from lessons-learned in fabricating and inspecting the current set of confinement vessels used for the SCE Program. The baseline 3-ft. confinement vessel weldment design has successfully been used (to date) for three (3) high explosive (HE) over-tests, two (2) fragment tests, and five (5) integral HE experiments. The design teammore » applied lessons learned from fabrication and inspection of these vessel weldments to enhance fit-up, weldability, inspection, and fitness for service evaluations. The review team consisted of five (5) independent subject matter experts with engineering design, analysis, testing, fabrication, and inspection experience. The« less

Study of flight data recorder, underwater locator beacon, data logger and flarm collision avoidance system

NASA Astrophysics Data System (ADS)

Timi, Purnota Hannan; Shermin, Saima; Rahman, Asifur

2017-06-01

Flight data recorder is one of the most important sources of flight data in event of aviation disaster which records a wide range of flight parameters including altitude, airspeed, heading etc. and also helps monitoring and analyzing aircraft performance. Cockpit voice recorder records radio microphone transmissions and sounds in the cockpit. These devices help to find out and understand the root causes of aircraft crashes and help building better aircraft systems and technical solutions to prevent similar type of crashes in future, which lead to improvement in safety of aircrafts and passengers. There are other devices also which enhance the aircraft safety and assists in emergency or catastrophic situations. This paper discusses the concept of Flight Data Recorder (FDR), Cockpit Voice Recorder (CVR), Underwater Locator Beacon (ULB), Data logger and flarm-collision avoidance system for aircraft and their applications in aviation.

Doubling down on phosphorylation as a variable peptide modification.

PubMed

Cooper, Bret

2016-09-01

Some mass spectrometrists believe that searching for variable PTMs like phosphorylation of serine or threonine when using database-search algorithms to interpret peptide tandem mass spectra will increase false-positive matching. The basis for this is the premise that the algorithm compares a spectrum to both a nonphosphorylated peptide candidate and a phosphorylated candidate, which is double the number of candidates compared to a search with no possible phosphorylation. Hence, if the search space doubles, false-positive matching could increase accordingly as the algorithm considers more candidates to which false matches could be made. In this study, it is shown that the search for variable phosphoserine and phosphothreonine modifications does not always double the search space or unduly impinge upon the FDR. A breakdown of how one popular database-search algorithm deals with variable phosphorylation is presented. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry.

PubMed

Swaney, Danielle L; Wenger, Craig D; Thomson, James A; Coon, Joshua J

2009-01-27

Protein phosphorylation is central to the understanding of cellular signaling, and cellular signaling is suggested to play a major role in the regulation of human embryonic stem (ES) cell pluripotency. Here, we describe the use of conventional tandem mass spectrometry-based sequencing technology--collision-activated dissociation (CAD)--and the more recently developed method electron transfer dissociation (ETD) to characterize the human ES cell phosphoproteome. In total, these experiments resulted in the identification of 11,995 unique phosphopeptides, corresponding to 10,844 nonredundant phosphorylation sites, at a 1% false discovery rate (FDR). Among these phosphorylation sites are 5 localized to 2 pluripotency critical transcription factors--OCT4 and SOX2. From these experiments, we conclude that ETD identifies a larger number of unique phosphopeptides than CAD (8,087 to 3,868), more frequently localizes the phosphorylation site to a specific residue (49.8% compared with 29.6%), and sequences whole classes of phosphopeptides previously unobserved.

Reactor engineering support of operations at the Davis-Besse nuclear power station

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelley, D.B.

1995-12-31

Reactor engineering functions differ greatly from unit to unit; however, direct support of the reactor operators during reactor startups and operational transients is common to all units. This paper summarizes the support the reactor engineers provide the reactor operators during reactor startups and power changes through the use of automated computer programs at the Davis-Besse nuclear power station.

10 CFR 2.337 - Evidence at a hearing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... chapter by the Director, Office of Nuclear Reactor Regulation, Director, Office of New Reactors, or... the Director, Office of Nuclear Reactor Regulation, Director, Office of New Reactors, or Director... the Director, Office of Nuclear Reactor Regulation, Director, Office of New Reactors, or Director...

Nuclear Reactors. Revised.

ERIC Educational Resources Information Center

Hogerton, John F.

This publication is one of a series of information booklets for the general public published by the United States Atomic Energy Commission. Among the topics discussed are: How Reactors Work; Reactor Design; Research, Teaching, and Materials Testing; Reactors (Research, Teaching and Materials); Production Reactors; Reactors for Electric Power…

10 CFR 2.337 - Evidence at a hearing.

Code of Federal Regulations, 2012 CFR

2012-01-01

... chapter by the Director, Office of Nuclear Reactor Regulation, Director, Office of New Reactors, or... the Director, Office of Nuclear Reactor Regulation, Director, Office of New Reactors, or Director... the Director, Office of Nuclear Reactor Regulation, Director, Office of New Reactors, or Director...

Nuclear reactor construction with bottom supported reactor vessel

DOEpatents

Sharbaugh, John E.

1987-01-01

An improved liquid metal nuclear reactor construction has a reactor core and a generally cylindrical reactor vessel for holding a large pool of low pressure liquid metal coolant and housing the core within the pool. The reactor vessel has an open top end, a closed flat bottom end wall and a continuous cylindrical closed side wall interconnecting the top end and bottom end wall. The reactor also has a generally cylindrical concrete containment structure surrounding the reactor vessel and being formed by a cylindrical side wall spaced outwardly from the reactor vessel side wall and a flat base mat spaced below the reactor vessel bottom end wall. A central support pedestal is anchored to the containment structure base mat and extends upwardly therefrom to the reactor vessel and upwardly therefrom to the reactor core so as to support the bottom end wall of the reactor vessel and the lower end of the reactor core in spaced apart relationship above the containment structure base mat. Also, an annular reinforced support structure is disposed in the reactor vessel on the bottom end wall thereof and extends about the lower end of the core so as to support the periphery thereof. In addition, an annular support ring having a plurality of inward radially extending linear members is disposed between the containment structure base mat and the bottom end of the reactor vessel wall and is connected to and supports the reactor vessel at its bottom end on the containment structure base mat so as to allow the reactor vessel to expand radially but substantially prevent any lateral motions that might be imposed by the occurrence of a seismic event. The reactor construction also includes a bed of insulating material in sand-like granular form, preferably being high density magnesium oxide particles, disposed between the containment structure base mat and the bottom end wall of the reactor vessel and uniformly supporting the reactor vessel at its bottom end wall on the containment structure base mat so as to insulate the reactor vessel bottom end wall from the containment structure base mat and allow the reactor vessel bottom end wall to freely expand as it heats up while providing continuous support thereof. Further, a deck is supported upon the side wall of the containment structure above the top open end of the reactor vessel, and a plurality of serially connected extendible and retractable annular bellows extend between the deck and the top open end of the reactor vessel and flexibly and sealably interconnect the reactor vessel at its top end to the deck. An annular guide ring is disposed on the containment structure and extends between its side wall and the top open end of the reactor vessel for providing lateral support of the reactor vessel top open end by limiting imposition of lateral loads on the annular bellows by the occurrence of a lateral seismic event.

Request for Naval Reactors Comment on Proposed Prometheus Space Flight Nuclear Reactor High Tier Reactor Safety Requirements and for Naval Reactors Approval to Transmit These Requirements to JPL

DOE Office of Scientific and Technical Information (OSTI.GOV)

D. Kokkinos

2005-04-28

The purpose of this letter is to request Naval Reactors comments on the nuclear reactor high tier requirements for the PROMETHEUS space flight reactor design, pre-launch operations, launch, ascent, operation, and disposal, and to request Naval Reactors approval to transmit these requirements to Jet Propulsion Laboratory to ensure consistency between the reactor safety requirements and the spacecraft safety requirements. The proposed PROMETHEUS nuclear reactor high tier safety requirements are consistent with the long standing safety culture of the Naval Reactors Program and its commitment to protecting the health and safety of the public and the environment. In addition, the philosophymore » on which these requirements are based is consistent with the Nuclear Safety Policy Working Group recommendations on space nuclear propulsion safety (Reference 1), DOE Nuclear Safety Criteria and Specifications for Space Nuclear Reactors (Reference 2), the Nuclear Space Power Safety and Facility Guidelines Study of the Applied Physics Laboratory.« less

Heat transfer analysis of cylindrical anaerobic reactors with different sizes: a heat transfer model.

PubMed

Liu, Jiawei; Zhou, Xingqiu; Wu, Jiangdong; Gao, Wen; Qian, Xu

2017-10-01

The temperature is the essential factor that influences the efficiency of anaerobic reactors. During the operation of the anaerobic reactor, the fluctuations of ambient temperature can cause a change in the internal temperature of the reactor. Therefore, insulation and heating measures are often used to maintain anaerobic reactor's internal temperature. In this paper, a simplified heat transfer model was developed to study heat transfer between cylindrical anaerobic reactors and their surroundings. Three cylindrical reactors of different sizes were studied, and the internal relations between ambient temperature, thickness of insulation, and temperature fluctuations of the reactors were obtained at different reactor sizes. The model was calibrated by a sensitivity analysis, and the calibrated model was well able to predict reactor temperature. The Nash-Sutcliffe model efficiency coefficient was used to assess the predictive power of heat transfer models. The Nash coefficients of the three reactors were 0.76, 0.60, and 0.45, respectively. The model can provide reference for the thermal insulation design of cylindrical anaerobic reactors.

Solvent refined coal reactor quench system

DOEpatents

Thorogood, Robert M.

1983-01-01

There is described an improved SRC reactor quench system using a condensed product which is recycled to the reactor and provides cooling by evaporation. In the process, the second and subsequent reactors of a series of reactors are cooled by the addition of a light oil fraction which provides cooling by evaporation in the reactor. The vaporized quench liquid is recondensed from the reactor outlet vapor stream.

Solvent refined coal reactor quench system

DOEpatents

Thorogood, R.M.

1983-11-08

There is described an improved SRC reactor quench system using a condensed product which is recycled to the reactor and provides cooling by evaporation. In the process, the second and subsequent reactors of a series of reactors are cooled by the addition of a light oil fraction which provides cooling by evaporation in the reactor. The vaporized quench liquid is recondensed from the reactor outlet vapor stream. 1 fig.

Nuclear reactor neutron shielding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Speaker, Daniel P; Neeley, Gary W; Inman, James B

A nuclear reactor includes a reactor pressure vessel and a nuclear reactor core comprising fissile material disposed in a lower portion of the reactor pressure vessel. The lower portion of the reactor pressure vessel is disposed in a reactor cavity. An annular neutron stop is located at an elevation above the uppermost elevation of the nuclear reactor core. The annular neutron stop comprises neutron absorbing material filling an annular gap between the reactor pressure vessel and the wall of the reactor cavity. The annular neutron stop may comprise an outer neutron stop ring attached to the wall of the reactormore » cavity, and an inner neutron stop ring attached to the reactor pressure vessel. An excore instrument guide tube penetrates through the annular neutron stop, and a neutron plug comprising neutron absorbing material is disposed in the tube at the penetration through the neutron stop.« less

Reactor pressure vessel head vents and methods of using the same

DOEpatents

Gels, John L; Keck, David J; Deaver, Gerald A

2014-10-28

Internal head vents are usable in nuclear reactors and include piping inside of the reactor pressure vessel with a vent in the reactor upper head. Piping extends downward from the upper head and passes outside of the reactor to permit the gas to escape or be forcibly vented outside of the reactor without external piping on the upper head. The piping may include upper and lowers section that removably mate where the upper head joins to the reactor pressure vessel. The removable mating may include a compressible bellows and corresponding funnel. The piping is fabricated of nuclear-reactor-safe materials, including carbon steel, stainless steel, and/or a Ni--Cr--Fe alloy. Methods install an internal head vent in a nuclear reactor by securing piping to an internal surface of an upper head of the nuclear reactor and/or securing piping to an internal surface of a reactor pressure vessel.

Proposed Advanced Reactor Adaptation of the Standard Review Plan NUREG-0800 Chapter 4 (Reactor) for Sodium-Cooled Fast Reactors and Modular High-Temperature Gas-Cooled Reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belles, Randy; Poore, III, Willis P.; Brown, Nicholas R.

2017-03-01

This report proposes adaptation of the previous regulatory gap analysis in Chapter 4 (Reactor) of NUREG 0800, Standard Review Plan (SRP) for the Review of Safety Analysis Reports for Nuclear Power Plants: LWR [Light Water Reactor] Edition. The proposed adaptation would result in a Chapter 4 review plan applicable to certain advanced reactors. This report addresses two technologies: the sodium-cooled fast reactor (SFR) and the modular high temperature gas-cooled reactor (mHTGR). SRP Chapter 4, which addresses reactor components, was selected for adaptation because of the possible significant differences in advanced non-light water reactor (non-LWR) technologies compared with the current LWR-basedmore » description in Chapter 4. SFR and mHTGR technologies were chosen for this gap analysis because of their diverse designs and the availability of significant historical design detail.« less

10 CFR 52.167 - Issuance of manufacturing license.

Code of Federal Regulations, 2010 CFR

2010-01-01

... proposed reactor(s) can be incorporated into a nuclear power plant and operated at sites having... design and manufacture the proposed nuclear power reactor(s); (5) The proposed inspections, tests... the construction of a nuclear power facility using the manufactured reactor(s). (2) A holder of a...

A novel plant protection strategy for transient reactors

NASA Astrophysics Data System (ADS)

Bhattacharyya, Samit K.; Lipinski, Walter C.; Hanan, Nelson A.

A novel plant protection system designed for use in the TREAT Upgrade (TU) reactor is described. The TU reactor is designed for controlled transient operation in the testing of reactor fuel behavior under simulated reactor accident conditions. Safe operation of the reactor is of paramount importance and the Plant Protection System (PPS) had to be designed to exacting requirements. Researchers believe that the strategy developed for the TU has potential application to the multimegawatt space reactors and represents the state of the art in terrestrial transient reactor protection systems.

Process and apparatus for adding and removing particles from pressurized reactors

DOEpatents

Milligan, John D.

1983-01-01

A method for adding and removing fine particles from a pressurized reactor is provided, which comprises connecting the reactor to a container, sealing the container from the reactor, filling the container with particles and a liquid material compatible with the reactants, pressurizing the container to substantially the reactor pressure, removing the seal between the reactor and the container, permitting particles to fall into or out of the reactor, and resealing the container from the reactor. An apparatus for adding and removing particles is also disclosed.

Effects of imperfect mixing on low-density polyethylene reactor dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Villa, C.M.; Dihora, J.O.; Ray, W.H.

1998-07-01

Earlier work considered the effect of feed conditions and controller configuration on the runaway behavior of LDPE autoclave reactors assuming a perfectly mixed reactor. This study provides additional insight on the dynamics of such reactors by using an imperfectly mixed reactor model and bifurcation analysis to show the changes in the stability region when there is imperfect macroscale mixing. The presence of imperfect mixing substantially increases the range of stable operation of the reactor and makes the process much easier to control than for a perfectly mixed reactor. The results of model analysis and simulations are used to identify somemore » of the conditions that lead to unstable reactor behavior and to suggest ways to avoid reactor runaway or reactor extinction during grade transitions and other process operation disturbances.« less

Startup of reactors for anoxic ammonium oxidation: experiences from the first full-scale anammox reactor in Rotterdam.

PubMed

van der Star, Wouter R L; Abma, Wiebe R; Blommers, Dennis; Mulder, Jan-Willem; Tokutomi, Takaaki; Strous, Marc; Picioreanu, Cristian; van Loosdrecht, Mark C M

2007-10-01

The first full-scale anammox reactor in the world was started in Rotterdam (NL). The reactor was scaled-up directly from laboratory-scale to full-scale and treats up to 750 kg-N/d. In the initial phase of the startup, anammox conversions could not be identified by traditional methods, but quantitative PCR proved to be a reliable indicator for growth of the anammox population, indicating an anammox doubling time of 10-12 days. The experience gained during this first startup in combination with the availability of seed sludge from this reactor, will lead to a faster startup of anammox reactors in the future. The anammox reactor type employed in Rotterdam was compared to other reactor types for the anammox process. Reactors with a high specific surface area like the granular sludge reactor employed in Rotterdam provide the highest volumetric loading rates. Mass transfer of nitrite into the biofilm is limiting the conversion of those reactor types that have a lower specific surface area. Now the first full-scale commercial anammox reactor is in operation, a consistent and descriptive nomenclature is suggested for reactors in which the anammox process is employed.

A small, 1400 K, reactor for Brayton space power systems.

NASA Technical Reports Server (NTRS)

Lantz, E.; Mayo, W.

1972-01-01

An investigation was conducted to determine minimum dimensions and minimum weight obtainable in a design for a reactor using uranium-233 nitride or plutonium-239 nitride as fuel. Such a reactor had been considered by Krasner et al. (1971). Present space power status is discussed, together with questions of reactor design and power distribution in the reactor. The characteristics of various reactor types are compared, giving attention also to a zirconium hydride reactor.

Alternative approaches to fusion. [reactor design and reactor physics for Tokamak fusion reactors

NASA Technical Reports Server (NTRS)

Roth, R. J.

1976-01-01

The limitations of the Tokamak fusion reactor concept are discussed and various other fusion reactor concepts are considered that employ the containment of thermonuclear plasmas by magnetic fields (i.e., stellarators). Progress made in the containment of plasmas in toroidal devices is reported. Reactor design concepts are illustrated. The possibility of using fusion reactors as a power source in interplanetary space travel and electric power plants is briefly examined.

10 CFR 50.46a - Acceptance criteria for reactor coolant system venting systems.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Acceptance criteria for reactor coolant system venting... criteria for reactor coolant system venting systems. Each nuclear power reactor must be provided with high point vents for the reactor coolant system, for the reactor vessel head, and for other systems required...

10 CFR 50.46a - Acceptance criteria for reactor coolant system venting systems.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Acceptance criteria for reactor coolant system venting... criteria for reactor coolant system venting systems. Each nuclear power reactor must be provided with high point vents for the reactor coolant system, for the reactor vessel head, and for other systems required...

KINETICS OF TREAT USED AS A TEST REACTOR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dickerman, C.E.; Johnson, R.D.; Gasidlo, J.

1962-05-01

An analysis is presented concerning the reactor kinetics of TREAT used as a pulsed, engineering test reactor for fast reactor fuel element studies. A description of the reactor performance is given for a wide range of conditions associated with its use as a test reactor. Supplemental information on meltdown experimentation is included. (J.R.D.)

Generating unstructured nuclear reactor core meshes in parallel

DOE PAGES

Jain, Rajeev; Tautges, Timothy J.

2014-10-24

Recent advances in supercomputers and parallel solver techniques have enabled users to run large simulations problems using millions of processors. Techniques for multiphysics nuclear reactor core simulations are under active development in several countries. Most of these techniques require large unstructured meshes that can be hard to generate in a standalone desktop computers because of high memory requirements, limited processing power, and other complexities. We have previously reported on a hierarchical lattice-based approach for generating reactor core meshes. Here, we describe efforts to exploit coarse-grained parallelism during reactor assembly and reactor core mesh generation processes. We highlight several reactor coremore » examples including a very high temperature reactor, a full-core model of the Korean MONJU reactor, a ¼ pressurized water reactor core, the fast reactor Experimental Breeder Reactor-II core with a XX09 assembly, and an advanced breeder test reactor core. The times required to generate large mesh models, along with speedups obtained from running these problems in parallel, are reported. A graphical user interface to the tools described here has also been developed.« less

Nuclear reactor having a polyhedral primary shield and removable vessel insulation

DOEpatents

Ekeroth, Douglas E.; Orr, Richard

1993-01-01

A nuclear reactor is provided having a generally cylindrical reactor vessel disposed within an opening in a primary shield. The opening in the primary shield is defined by a plurality of generally planar side walls forming a generally polyhedral-shaped opening. The reactor vessel is supported within the opening in the primary shield by reactor vessel supports which are in communication and aligned with central portions of some of the side walls. The reactor vessel is connected to the central portions of the reactor vessel supports. A thermal insulation polyhedron formed from a plurality of slidably insertable and removable generally planar insulation panels substantially surrounds at least a portion of the reactor vessel and is disposed between the reactor vessel and the side walls of the primary shield. The shape of the insulation polyhedron generally corresponds to the shape of the opening in the primary shield. Reactor monitoring instrumentation may be mounted in the corners of the opening in the primary shield between the side walls and the reactor vessel such that insulation is not disposed between the instrumentation and the reactor vessel.

Nuclear reactor having a polyhedral primary shield and removable vessel insulation

DOEpatents

Ekeroth, D.E.; Orr, R.

1993-12-07

A nuclear reactor is provided having a generally cylindrical reactor vessel disposed within an opening in a primary shield. The opening in the primary shield is defined by a plurality of generally planar side walls forming a generally polyhedral-shaped opening. The reactor vessel is supported within the opening in the primary shield by reactor vessel supports which are in communication and aligned with central portions of some of the side walls. The reactor vessel is connected to the central portions of the reactor vessel supports. A thermal insulation polyhedron formed from a plurality of slidably insertable and removable generally planar insulation panels substantially surrounds at least a portion of the reactor vessel and is disposed between the reactor vessel and the side walls of the primary shield. The shape of the insulation polyhedron generally corresponds to the shape of the opening in the primary shield. Reactor monitoring instrumentation may be mounted in the corners of the opening in the primary shield between the side walls and the reactor vessel such that insulation is not disposed between the instrumentation and the reactor vessel. 5 figures.

Boiling water neutronic reactor incorporating a process inherent safety design

DOEpatents

Forsberg, C.W.

1985-02-19

A boiling-water reactor core is positioned within a prestressed concrete reactor vessel of a size which will hold a supply of coolant water sufficient to submerge and cool the reactor core by boiling for a period of at least one week after shutdown. Separate volumes of hot, clean (nonborated) water for cooling during normal operation and cool highly borated water for emergency cooling and reactor shutdown are separated by an insulated wall during normal reactor operation with contact between the two water volumes being maintained at interfaces near the top and bottom ends of the reactor vessel. Means are provided for balancing the pressure of the two water volumes at the lower interface zone during normal operation to prevent entry of the cool borated water into the reactor core region, for detecting the onset of excessive power to coolant flow conditions in the reactor core and for detecting low water levels of reactor coolant. Cool borated water is permitted to flow into the reactor core when low reactor coolant levels or excessive power to coolant flow conditions are encountered.

Boiling water neutronic reactor incorporating a process inherent safety design

DOEpatents

Forsberg, Charles W.

1987-01-01

A boiling-water reactor core is positioned within a prestressed concrete reactor vessel of a size which will hold a supply of coolant water sufficient to submerge and cool the reactor core by boiling for a period of at least one week after shutdown. Separate volumes of hot, clean (non-borated) water for cooling during normal operation and cool highly borated water for emergency cooling and reactor shutdown are separated by an insulated wall during normal reactor operation with contact between the two water volumes being maintained at interfaces near the top and bottom ends of the reactor vessel. Means are provided for balancing the pressure of the two volumes at the lower interface zone during normal operation to prevent entry of the cool borated water into the reactor core region, for detecting the onset of excessive power to coolant flow conditions in the reactor core and for detecting low water levels of reactor coolant. Cool borated water is permitted to flow into the reactor core when low reactor coolant levels or excessive power to coolant flow conditions are encountered.

Summary of NR Program Prometheus Efforts

DOE Office of Scientific and Technical Information (OSTI.GOV)

J Ashcroft; C Eshelman

2006-02-08

The Naval Reactors Program led work on the development of a reactor plant system for the Prometheus space reactor program. The work centered on a 200 kWe electric reactor plant with a 15-20 year mission applicable to nuclear electric propulsion (NEP). After a review of all reactor and energy conversion alternatives, a direct gas Brayton reactor plant was selected for further development. The work performed subsequent to this selection included preliminary nuclear reactor and reactor plant design, development of instrumentation and control techniques, modeling reactor plant operational features, development and testing of core and plant material options, and development ofmore » an overall project plan. Prior to restructuring of the program, substantial progress had been made on defining reference plant operating conditions, defining reactor mechanical, thermal and nuclear performance, understanding the capabilities and uncertainties provided by material alternatives, and planning non-nuclear and nuclear system testing. The mission requirements for the envisioned NEP missions cannot be accommodated with existing reactor technologies. Therefore concurrent design, development and testing would be needed to deliver a functional reactor system. Fuel and material performance beyond the current state of the art is needed. There is very little national infrastructure available for fast reactor nuclear testing and associated materials development and testing. Surface mission requirements may be different enough to warrant different reactor design approaches and development of a generic multi-purpose reactor requires substantial sacrifice in performance capability for each mission.« less

Transcriptome difference and potential crosstalk between liver and mammary tissue in mid-lactation primiparous dairy cows.

PubMed

Bu, Dengpan; Bionaz, Massimo; Wang, Mengzhi; Nan, Xuemei; Ma, Lu; Wang, Jiaqi

2017-01-01

Liver and mammary gland are among the most important organs during lactation in dairy cows. With the purpose of understanding both the different and the complementary roles and the crosstalk of those two organs during lactation, a transcriptome analysis was performed on liver and mammary tissues of 10 primiparous dairy cows in mid-lactation. The analysis was performed using a 4×44K Bovine Agilent microarray chip. The transcriptome difference between the two tissues was analyzed using SAS JMP Genomics using ANOVA with a false discovery rate correction (FDR). The analysis uncovered >9,000 genes differentially expressed (DEG) between the two tissues with a FDR<0.001. The functional analysis of the DEG uncovered a larger metabolic (especially related to lipid) and inflammatory response capacity in liver compared with mammary tissue while the mammary tissue had a larger protein synthesis and secretion, proliferation/differentiation, signaling, and innate immune system capacity compared with the liver. A plethora of endogenous compounds, cytokines, and transcription factors were estimated to control the DEG between the two tissues. Compared with mammary tissue, the liver transcriptome appeared to be under control of a large array of ligand-dependent nuclear receptors and, among endogenous chemical, fatty acids and bacteria-derived compounds. Compared with liver, the transcriptome of the mammary tissue was potentially under control of a large number of growth factors and miRNA. The in silico crosstalk analysis between the two tissues revealed an overall large communication with a reciprocal control of lipid metabolism, innate immune system adaptation, and proliferation/differentiation. In summary the transcriptome analysis confirmed prior known differences between liver and mammary tissue, especially considering the indication of a larger metabolic activity in liver compared with the mammary tissue and the larger protein synthesis, communication, and proliferative capacity in mammary tissue compared with the liver. Relatively novel is the indication by the data that the transcriptome of the liver is highly regulated by dietary and bacteria-related compounds while the mammary transcriptome is more under control of hormones, growth factors, and miRNA. A large crosstalk between the two tissues with a reciprocal control of metabolism and innate immune-adaptation was indicated by the network analysis that allowed uncovering previously unknown crosstalk between liver and mammary tissue for several signaling molecules.

Exposure to Low Levels of Lead in Utero and Umbilical Cord Blood DNA Methylation in Project Viva: An Epigenome-Wide Association Study

PubMed Central

Hivert, Marie-France; Cardenas, Andres; Zhong, Jia; Rifas-Shiman, Sheryl L.; Agha, Golareh; Colicino, Elena; Just, Allan C.; Amarasiriwardena, Chitra; Lin, Xihong; Litonjua, Augusto A.; DeMeo, Dawn L.; Gillman, Matthew W.; Wright, Robert O.; Oken, Emily

2017-01-01

Background: Early-life exposure to lead is associated with deficits in neurodevelopment and with hematopoietic system toxicity. DNA methylation may be one of the underlying mechanisms for the adverse effects of prenatal lead on the offspring, but epigenome-wide methylation data for low levels of prenatal lead exposure are lacking. Objectives: We investigated the association between prenatal maternal lead exposure and epigenome-wide DNA methylation in umbilical cord blood nucleated cells in Project Viva, a prospective U.S.-based prebirth cohort with relatively low levels of lead exposure. Methods: Among 268 mother–infant pairs, we measured lead concentrations in red blood cells (RBC) from prenatal maternal blood samples, and using HumanMethylation450 Bead Chips, we measured genome-wide methylation levels at 482,397 CpG loci in umbilical cord blood and retained 394,460 loci after quality control. After adjustment for batch effects, cell types, and covariates, we used robust linear regression models to examine associations of prenatal lead exposure with DNA methylation in cord blood at epigenome-wide significance level [false discovery rate (FDR)<0.05]. Results: The mean [standard deviation (SD)] maternal RBC lead level was 1.22 (0.63) μg/dL. CpG cg10773601 showed an epigenome-wide significant negative association with prenatal lead exposure (−1.4% per doubling increase in lead exposure; p=2.3×10−7) and was annotated to C-Type Lectin Domain Family 11, Member A (CLEC11A), which functions as a growth factor for primitive hematopoietic progenitor cells. In sex-specific analyses, we identified more CpGs with FDR<0.05 among female infants (n=38) than among male infants (n=2). One CpG (cg24637308), which showed a strong negative association with prenatal lead exposure among female infants (−4.3% per doubling increase in lead exposure; p=1.1×10−06), was annotated to Dynein Heavy Chain Domain 1 gene (DNHD1) which is highly expressed in human brain. Interestingly, there were strong correlations between blood and brain methylation for CpG (cg24637308) based on another independent set of samples with a high proportion of female participants. Conclusion: Prenatal low-level lead exposure was associated with newborn DNA methylation, particularly in female infants. https://doi.org/10.1289/EHP1246 PMID:28858830

Exposure to Low Levels of Lead in Utero and Umbilical Cord Blood DNA Methylation in Project Viva: An Epigenome-Wide Association Study.

PubMed

Wu, Shaowei; Hivert, Marie-France; Cardenas, Andres; Zhong, Jia; Rifas-Shiman, Sheryl L; Agha, Golareh; Colicino, Elena; Just, Allan C; Amarasiriwardena, Chitra; Lin, Xihong; Litonjua, Augusto A; DeMeo, Dawn L; Gillman, Matthew W; Wright, Robert O; Oken, Emily; Baccarelli, Andrea A

2017-08-25

Early-life exposure to lead is associated with deficits in neurodevelopment and with hematopoietic system toxicity. DNA methylation may be one of the underlying mechanisms for the adverse effects of prenatal lead on the offspring, but epigenome-wide methylation data for low levels of prenatal lead exposure are lacking. We investigated the association between prenatal maternal lead exposure and epigenome-wide DNA methylation in umbilical cord blood nucleated cells in Project Viva, a prospective U.S.-based prebirth cohort with relatively low levels of lead exposure. Among 268 mother-infant pairs, we measured lead concentrations in red blood cells (RBC) from prenatal maternal blood samples, and using HumanMethylation450 Bead Chips, we measured genome-wide methylation levels at 482,397 CpG loci in umbilical cord blood and retained 394,460 loci after quality control. After adjustment for batch effects, cell types, and covariates, we used robust linear regression models to examine associations of prenatal lead exposure with DNA methylation in cord blood at epigenome-wide significance level [false discovery rate (FDR)<0.05]. The mean [standard deviation (SD)] maternal RBC lead level was 1.22 (0.63) μg/dL. CpG cg10773601 showed an epigenome-wide significant negative association with prenatal lead exposure (-1.4% per doubling increase in lead exposure; p=2.3×10-7) and was annotated to C-Type Lectin Domain Family 11, Member A ( CLEC11A ), which functions as a growth factor for primitive hematopoietic progenitor cells. In sex-specific analyses, we identified more CpGs with FDR<0.05 among female infants (n=38) than among male infants (n=2). One CpG (cg24637308), which showed a strong negative association with prenatal lead exposure among female infants (-4.3% per doubling increase in lead exposure; p=1.1×10-06), was annotated to Dynein Heavy Chain Domain 1 gene ( DNHD1 ) which is highly expressed in human brain. Interestingly, there were strong correlations between blood and brain methylation for CpG (cg24637308) based on another independent set of samples with a high proportion of female participants. Prenatal low-level lead exposure was associated with newborn DNA methylation, particularly in female infants. https://doi.org/10.1289/EHP1246.

P17.04 Radiomics analysis of primary central nervous system lymphoma (PCNSL) - A LOC network study

PubMed Central

Royer-Perron, L.; Bruno, A.; Daniau, M.; Labrèche, K.; Mokhtari, K.; Nguyen Them, L.; Houillier, C.; Soussain, C.; Hoang-Xuan, K.; Alentorn, A.

2016-01-01

Abstract Background: PCNSL are rare extranodal, malignant non-Hodgkin lymphomas of diffuse large B-cell type confined to the CNS. In the last years, several recurrent molecular genetic alterations have been described in PCNSL but whether they are correlated with the tumor anatomical localization has never been investigated. Objectives: We sought to analyze a genotype (molecular alterations) - phenotype (MRI data) in PCNSL. Material and methods: 50 PCNSL MR images of treatment-naïve patients were correlated with molecular alterations (i.e. MYD88 L265P, CD79B and TERT promoter mutations as well as a novel chimeric transcript that our laboratory has recently identified in PCNSL) obtained by Sanger sequencing. MRI data was analyzed as follows: (i) NIfTI data were registered to a 1.0 mm isotropic, high-resolution T1-weighted brain atlas provided by the Montreal Neurological Institute (MNI152) using a mutual information algorithm with a 12-degree of freedom transformation with FSL-FLIRT; (ii) gadolinium-enhancing lesions were manually segmented and saved as voxels-of-interest (VOIs); (iii) A heat-map for the frequency of lesion occurrence was reconstructed and superimposed on the reference MNI152; (iv) Structure probability maps (brain regions) were defined according to Talairach MRI Atlas and (v) genotype - phenotype correlation was performed using voxel-based lesion-symptom mapping (VLSM) using FDR < 0.05 after 4000 permutations. Results: We found mutations of MYD88 in 18 patients, of CD79B in 15 patients and of TERT promoter in 6 patients. The novel chimeric transcript was identified in 11 patients. PCNSL harboring TERT promoter mutations and the chimeric transcript were more frequently found in the corpus callosum (FDR < 0.05). Conversely, we did not find a specific genotype-phenotype correlation with the rest of molecular alterations. Conclusion: We provide a MRI probabilistic atlas linking genotype to phenotype in PCNSL. These results need further investigation. Acknowledgements: Association pour la Recherche sur les Tumeurs Cérébrales (ARTC), Ligue contre le Cancer, Fondation pour la recherche médicale, Institut National du Cancer (INCa), Cancéropôle Île-de-France, Département de la Recherche Clinique de l’APHP, CRC de l’APHP, réseau Lymphomes Oculo-Cérébraux (LOC).

MOST: most-similar ligand based approach to target prediction.

PubMed

Huang, Tao; Mi, Hong; Lin, Cheng-Yuan; Zhao, Ling; Zhong, Linda L D; Liu, Feng-Bin; Zhang, Ge; Lu, Ai-Ping; Bian, Zhao-Xiang

2017-03-11

Many computational approaches have been used for target prediction, including machine learning, reverse docking, bioactivity spectra analysis, and chemical similarity searching. Recent studies have suggested that chemical similarity searching may be driven by the most-similar ligand. However, the extent of bioactivity of most-similar ligands has been oversimplified or even neglected in these studies, and this has impaired the prediction power. Here we propose the MOst-Similar ligand-based Target inference approach, namely MOST, which uses fingerprint similarity and explicit bioactivity of the most-similar ligands to predict targets of the query compound. Performance of MOST was evaluated by using combinations of different fingerprint schemes, machine learning methods, and bioactivity representations. In sevenfold cross-validation with a benchmark Ki dataset from CHEMBL release 19 containing 61,937 bioactivity data of 173 human targets, MOST achieved high average prediction accuracy (0.95 for pKi ≥ 5, and 0.87 for pKi ≥ 6). Morgan fingerprint was shown to be slightly better than FP2. Logistic Regression and Random Forest methods performed better than Naïve Bayes. In a temporal validation, the Ki dataset from CHEMBL19 were used to train models and predict the bioactivity of newly deposited ligands in CHEMBL20. MOST also performed well with high accuracy (0.90 for pKi ≥ 5, and 0.76 for pKi ≥ 6), when Logistic Regression and Morgan fingerprint were employed. Furthermore, the p values associated with explicit bioactivity were found be a robust index for removing false positive predictions. Implicit bioactivity did not offer this capability. Finally, p values generated with Logistic Regression, Morgan fingerprint and explicit activity were integrated with a false discovery rate (FDR) control procedure to reduce false positives in multiple-target prediction scenario, and the success of this strategy it was demonstrated with a case of fluanisone. In the case of aloe-emodin's laxative effect, MOST predicted that acetylcholinesterase was the mechanism-of-action target; in vivo studies validated this prediction. Using the MOST approach can result in highly accurate and robust target prediction. Integrated with a FDR control procedure, MOST provides a reliable framework for multiple-target inference. It has prospective applications in drug repurposing and mechanism-of-action target prediction.

Transcriptome difference and potential crosstalk between liver and mammary tissue in mid-lactation primiparous dairy cows

PubMed Central

Bu, Dengpan; Bionaz, Massimo; Wang, Mengzhi; Nan, Xuemei; Ma, Lu; Wang, Jiaqi

2017-01-01

Liver and mammary gland are among the most important organs during lactation in dairy cows. With the purpose of understanding both the different and the complementary roles and the crosstalk of those two organs during lactation, a transcriptome analysis was performed on liver and mammary tissues of 10 primiparous dairy cows in mid-lactation. The analysis was performed using a 4×44K Bovine Agilent microarray chip. The transcriptome difference between the two tissues was analyzed using SAS JMP Genomics using ANOVA with a false discovery rate correction (FDR). The analysis uncovered >9,000 genes differentially expressed (DEG) between the two tissues with a FDR<0.001. The functional analysis of the DEG uncovered a larger metabolic (especially related to lipid) and inflammatory response capacity in liver compared with mammary tissue while the mammary tissue had a larger protein synthesis and secretion, proliferation/differentiation, signaling, and innate immune system capacity compared with the liver. A plethora of endogenous compounds, cytokines, and transcription factors were estimated to control the DEG between the two tissues. Compared with mammary tissue, the liver transcriptome appeared to be under control of a large array of ligand-dependent nuclear receptors and, among endogenous chemical, fatty acids and bacteria-derived compounds. Compared with liver, the transcriptome of the mammary tissue was potentially under control of a large number of growth factors and miRNA. The in silico crosstalk analysis between the two tissues revealed an overall large communication with a reciprocal control of lipid metabolism, innate immune system adaptation, and proliferation/differentiation. In summary the transcriptome analysis confirmed prior known differences between liver and mammary tissue, especially considering the indication of a larger metabolic activity in liver compared with the mammary tissue and the larger protein synthesis, communication, and proliferative capacity in mammary tissue compared with the liver. Relatively novel is the indication by the data that the transcriptome of the liver is highly regulated by dietary and bacteria-related compounds while the mammary transcriptome is more under control of hormones, growth factors, and miRNA. A large crosstalk between the two tissues with a reciprocal control of metabolism and innate immune-adaptation was indicated by the network analysis that allowed uncovering previously unknown crosstalk between liver and mammary tissue for several signaling molecules. PMID:28291785

Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations

PubMed Central

2013-01-01

Background Intronic and intergenic long noncoding RNAs (lncRNAs) are emerging gene expression regulators. The molecular pathogenesis of renal cell carcinoma (RCC) is still poorly understood, and in particular, limited studies are available for intronic lncRNAs expressed in RCC. Methods Microarray experiments were performed with custom-designed arrays enriched with probes for lncRNAs mapping to intronic genomic regions. Samples from 18 primary RCC tumors and 11 nontumor adjacent matched tissues were analyzed. Meta-analyses were performed with microarray expression data from three additional human tissues (normal liver, prostate tumor and kidney nontumor samples), and with large-scale public data for epigenetic regulatory marks and for evolutionarily conserved sequences. Results A signature of 29 intronic lncRNAs differentially expressed between RCC and nontumor samples was obtained (false discovery rate (FDR) <5%). A signature of 26 intronic lncRNAs significantly correlated with the RCC five-year patient survival outcome was identified (FDR <5%, p-value ≤0.01). We identified 4303 intronic antisense lncRNAs expressed in RCC, of which 22% were significantly (p <0.05) cis correlated with the expression of the mRNA in the same locus across RCC and three other human tissues. Gene Ontology (GO) analysis of those loci pointed to 'regulation of biological processes’ as the main enriched category. A module map analysis of the protein-coding genes significantly (p <0.05) trans correlated with the 20% most abundant lncRNAs, identified 51 enriched GO terms (p <0.05). We determined that 60% of the expressed lncRNAs are evolutionarily conserved. At the genomic loci containing the intronic RCC-expressed lncRNAs, a strong association (p <0.001) was found between their transcription start sites and genomic marks such as CpG islands, RNA Pol II binding and histones methylation and acetylation. Conclusion Intronic antisense lncRNAs are widely expressed in RCC tumors. Some of them are significantly altered in RCC in comparison with nontumor samples. The majority of these lncRNAs is evolutionarily conserved and possibly modulated by epigenetic modifications. Our data suggest that these RCC lncRNAs may contribute to the complex network of regulatory RNAs playing a role in renal cell malignant transformation. PMID:24238219

Integrated monitoring technologies for the management of a Soil-Aquifer-Treatment (SAT) system.

NASA Astrophysics Data System (ADS)

Papadopoulos, Alexandros; Kallioras, Andreas; Kofakis, Petros; Bumberger, Jan; Schmidt, Felix; Athanasiou, Georgios; Uzunoglou, Nikolaos; Amditis, Angelos; Dietrich, Peter

2016-04-01

Artificial recharge of groundwater has an important role to play in water reuse as treated wastewater effluent can be infiltrated into the ground for aquifer recharge. As the effluent moves through the soil and the aquifer, it undergoes significant quality improvements through physical, chemical, and biological processes in the underground environment. Collectively, these processes and the water quality improvement obtained are called soil-aquifer-treatment (SAT) or geopurification. The pilot site of Lavrion Technological & Cultural Park (LTCP) of the National Technical University of Athens (NTUA), involves the employment of plot infiltration basins at experimental scale, which will be using waters of impaired quality as a recharge source, and hence acting as a Soil-Aquifer-Treatment, SAT, system. Τhe LTCP site will be employed as a pilot SAT system complemented by new technological developments, which will be providing continuous monitoring of the quantitative and qualitative characteristics of infiltrating groundwater through all hydrologic zones (i.e. surface, unsaturated and saturated zone). This will be achieved by the development and installation of an integrated system of prototype sensing technologies, installed on-site, and offering a continuous evaluation of the performance of the SAT system. An integrated approach of the performance evaluation of any operating SAT system should aim at parallel monitoring of all hydrologic zones, proving the sustainability of all involved water quality treatment processes within unsaturated and saturated zone. Hence a prototype system of Time and Frequency Domain Reflectometry (TDR & FDR) sensors is developed and will be installed, in order to achieve continuous quantitative monitoring of the unsaturated zone through the entire soil column down to significant depths below the SAT basin. Additionally, the system contains two different radar-based sensing systems that will be offering (i) identification of preferential flow effects of the TDR/FDR sensors and (ii) monitoring of the water table within the shallow karst aquifer layer. The above technique will offer continuous monitoring of infiltration rates and identify possible mechanical or biological clogging effects. The monitoring system will be connected to an ad-hoc wireless network for continuous data transfer within the SAT facilities. It is envisaged that the development and combined application of all the above technologies will provide an integrated monitoring platform for the evaluation of SAT system performance.

Inducible nitric oxide synthase gene polymorphisms are associated with a risk of nephritis in Henoch-Schönlein purpura children.

PubMed

Jiang, Jue; Duan, Wuqiong; Shang, Xu; Wang, Hua; Gao, Ya; Tian, Peijun; Zhou, Qi

2017-08-01

Henoch-Schönlein purpura (HSP) is the most common form of systemic small-vessel vasculitis in children, and HSP nephritis (HSPN) is a major complication of HSP and is the primary cause of morbidity and mortality. Previous studies have suggested that inducible nitric oxide synthase (iNOS) may play an important role in the pathogenesis of HSP. In this study, we performed a detailed analysis to investigate the potential association between iNOS polymorphisms and the risk of HSP and the tendency for children with HSP to develop HSPN in a Chinese Han population. A promoter pentanucleotide repeat (CCTTT)n and 10 functional single-nucleotide polymorphisms (SNPs) from 532 healthy controls and 513 children with HSP were genotyped using the MassARRAY system and GeneScan. The results suggested that the allelic and genotypic frequencies of the rs3729508 polymorphism were nominally associated with susceptibility to HSP. In addition, there was a significant difference in the allelic distribution of the (CCTTT)12 repeats and rs2297518 between the HSP children with and without nephritis; the HSP children with nephritis exhibited a significantly higher frequency of the (CCTTT)12 repeats and A allele of rs2297518 than the HSP children without nephritis (P FDR  = 0.033, OR = 1.624, 95% CI = 1.177-2.241 and P FDR  = 0.030, OR = 1.660, 95% CI = 1.187-2.321, respectively). Our results support that iNOS polymorphisms are associated with the risk of HSP and may strongly contribute to the genetic basis of individual differences in the progression to nephritis among children with HSP in the Chinese Han population. What is Known: • The etiology of HSP is unknown, but the genetic factors may play an important role in the pathogenesis of HSP. • iNOS could contribute to the development and clinical manifestations of HSP, and this has not been studied extensively so far. What is New: • Our results support that iNOS polymorphisms not only are associated with HSP risk but also strongly contribute to the genetic basis of individual differences in the progression of HSP to nephritis among Chinese Han children.

First-line erlotinib and fixed dose-rate gemcitabine for advanced pancreatic cancer.

PubMed

Vaccaro, Vanja; Bria, Emilio; Sperduti, Isabella; Gelibter, Alain; Moscetti, Luca; Mansueto, Giovanni; Ruggeri, Enzo Maria; Gamucci, Teresa; Cognetti, Francesco; Milella, Michele

2013-07-28

To investigate activity, toxicity, and prognostic factors for survival of erlotinib and fixed dose-rate gemcitabine (FDR-Gem) in advanced pancreatic cancer. We designed a single-arm prospective, multicentre, open-label phase II study to evaluate the combination of erlotinib (100 mg/d, orally) and weekly FDR-Gem (1000 mg/m(2), infused at 10 mg/m(2) per minute) in a population of previously untreated patients with locally advanced, inoperable, or metastatic pancreatic cancer. Primary endpoint was the rate of progression-free survival at 6 mo (PFS-6); secondary endpoints were overall response rate (ORR), response duration, tolerability, overall survival (OS), and clinical benefit. Treatment was not considered to be of further interest if the PFS-6 was < 20% (p0 = 20%), while a PFS-6 > 40% would be of considerable interest (p1 = 40%); with a 5% rejection error (α = 5%) and a power of 80%, 35 fully evaluable patients with metastatic disease were required to be enrolled in order to complete the study. Analysis of prognostic factors for survival was also carried out. From May 2007 to September 2009, 46 patients were enrolled (male/female: 25/21; median age: 64 years; median baseline carbohydrate antigen 19-9 (CA 19-9): 897 U/mL; locally advanced/metastatic disease: 5/41). PFS-6 and median PFS were 30.4% and 14 wk (95%CI: 10-19), respectively; 1-year and median OS were 20.2% and 26 wk (95%CI: 8-43). Five patients achieved an objective response (ORR: 10.9%, 95%CI: 1.9-19.9); disease control rate was 56.5% (95%CI: 42.2-70.8); clinical benefit rate was 43.5% (95%CI: 29.1-57.8). CA 19-9 serum levels were decreased by > 25% as compared to baseline in 14/23 evaluable patients (63.6%). Treatment was well-tolerated, with skin rash being the most powerful predictor of both longer PFS (P < 0.0001) and OS (P = 0.01) at multivariate analysis (median OS for patients with or without rash: 42 wk vs 15 wk, respectively, Log-rank P = 0.03). Additional predictors of better outcome were: CA 19-9 reduction, female sex (for PFS), and good performance status (for OS). Primary study endpoint was not met. However, skin rash strongly predicted erlotinib efficacy, suggesting that a pharmacodynamic-based strategy for patient selection deserves further investigation.

Transcriptional signature associated with early rheumatoid arthritis and healthy individuals at high risk to develop the disease

PubMed Central

Macías-Segura, N.; Bastian, Y.; Santiago-Algarra, D.; Castillo-Ortiz, J. D.; Alemán-Navarro, A. L.; Jaime-Sánchez, E.; Gomez-Moreno, M.; Saucedo-Toral, C. A.; Lara-Ramírez, Edgar E.; Zapata-Zuñiga, M.; Enciso-Moreno, L.; González-Amaro, R.; Ramos-Remus, C.; Enciso-Moreno, J. A.

2018-01-01

Background Little is known regarding the mechanisms underlying the loss of tolerance in the early and preclinical stages of autoimmune diseases. The aim of this work was to identify the transcriptional profile and signaling pathways associated to non-treated early rheumatoid arthritis (RA) and subjects at high risk. Several biomarker candidates for early RA are proposed. Methods Whole blood total RNA was obtained from non-treated early RA patients with <1 year of evolution as well as from healthy first-degree relatives of patients with RA (FDR) classified as ACCP+ and ACCP- according to their antibodies serum levels against cyclic citrullinated peptides. Complementary RNA (cRNA) was synthetized and hybridized to high-density microarrays. Data was analyzed in Genespring Software and functional categories were assigned to a specific transcriptome identified in subjects with RA and FDR ACCP positive. Specific signaling pathways for genes associated to RA were identified. Gene expression was evaluated by qPCR. Receiver operating characteristic (ROC) analysis was used to evaluate these genes as biomarkers. Results A characteristic transcriptome of 551 induced genes and 4,402 repressed genes were identified in early RA patients. Bioinformatics analysis of the data identified a specific transcriptome in RA patients. Moreover, some overlapped transcriptional profiles between patients with RA and ACCP+ were identified, suggesting an up-regulated distinctive transcriptome from the preclinical stages up to progression to an early RA state. A total of 203 pathways have up-regulated genes that are shared between RA and ACCP+. Some of these genes show potential to be used as progression biomarkers for early RA with area under the curve of ROC > 0.92. These genes come from several functional categories associated to inflammation, Wnt signaling and type I interferon pathways. Conclusion The presence of a specific transcriptome in whole blood of RA patients suggests the activation of a specific inflammatory transcriptional signature in early RA development. The set of overexpressed genes in early RA patients that are shared with ACCP+ subjects but not with ACCP- subjects, can represent a transcriptional signature involved with the transition of a preclinical to a clinical RA stage. Some of these particular up-regulated and down-regulated genes are related to inflammatory processes and could be considered as biomarker candidates for disease progression in subjects at risk to develop RA. PMID:29584756

Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions.

PubMed

Muleta, Kebede T; Rouse, Matthew N; Rynearson, Sheri; Chen, Xianming; Buta, Bedada G; Pumphrey, Michael O

2017-08-04

The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments. A total of 24,281 single nucleotide polymorphism (SNP) markers filtered from the wheat 90 K iSelect genotyping assay was used to survey Ethiopian germplasm for population structure, genetic diversity and marker-trait associations. Upon screening for field resistance to stripe rust in the Pacific Northwest of the United States and Ethiopia over multiple growing seasons, and against multiple races of stripe rust and stem rust at seedling stage, eight accessions displayed resistance to all tested races of stem rust and field resistance to stripe rust in all environments. Our GWAS results show 15 loci were significantly associated with seedling and adult plant resistance to stripe rust at false discovery rate (FDR)-adjusted probability (P) <0.10. GWAS also detected 9 additional genomic regions significantly associated (FDR-adjusted P < 0.10) with seedling resistance to stem rust in the Ethiopian wheat accessions. Many of the identified resistance loci were mapped close to previously identified rust resistance genes; however, three loci on the short arms of chromosomes 5A and 7B for stripe rust resistance and two on chromosomes 3B and 7B for stem rust resistance may be novel. Our results demonstrate that considerable genetic variation resides within the landrace accessions that can be utilized to broaden the genetic base of rust resistance in wheat breeding germplasm. The molecular markers identified in this study should be useful in efficiently targeting the associated resistance loci in marker-assisted breeding for rust resistance in Ethiopia and other countries.

TU-CD-BRB-07: Identification of Associations Between Radiologist-Annotated Imaging Features and Genomic Alterations in Breast Invasive Carcinoma, a TCGA Phenotype Research Group Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, A; Net, J; Brandt, K

2015-06-15

Purpose: To determine associations between radiologist-annotated MRI features and genomic measurements in breast invasive carcinoma (BRCA) from the Cancer Genome Atlas (TCGA). Methods: 98 TCGA patients with BRCA were assessed by a panel of radiologists (TCGA Breast Phenotype Research Group) based on a variety of mass and non-mass features according to the Breast Imaging Reporting and Data System (BI-RADS). Batch corrected gene expression data was obtained from the TCGA Data Portal. The Kruskal-Wallis test was used to assess correlations between categorical image features and tumor-derived genomic features (such as gene pathway activity, copy number and mutation characteristics). Image-derived features weremore » also correlated with estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2/neu) status. Multiple hypothesis correction was done using Benjamini-Hochberg FDR. Associations at an FDR of 0.1 were selected for interpretation. Results: ER status was associated with rim enhancement and peritumoral edema. PR status was associated with internal enhancement. Several components of the PI3K/Akt pathway were associated with rim enhancement as well as heterogeneity. In addition, several components of cell cycle regulation and cell division were associated with imaging characteristics.TP53 and GATA3 mutations were associated with lesion size. MRI features associated with TP53 mutation status were rim enhancement and peritumoral edema. Rim enhancement was associated with activity of RB1, PIK3R1, MAP3K1, AKT1,PI3K, and PIK3CA. Margin status was associated with HIF1A/ARNT, Ras/ GTP/PI3K, KRAS, and GADD45A. Axillary lymphadenopathy was associated with RB1 and BCL2L1. Peritumoral edema was associated with Aurora A/GADD45A, BCL2L1, CCNE1, and FOXA1. Heterogeneous internal nonmass enhancement was associated with EGFR, PI3K, AKT1, HF/MET, and EGFR/Erbb4/neuregulin 1. Diffuse nonmass enhancement was associated with HGF/MET/MUC20/SHIP, and HGF/MET/RANBP9. Linear nonmass enhancement was associated with PIK3R1 and AKT activity. Conclusion: MRI-genomic association analysis revealed that several BRCA-associated gene features were associated with radiologist-annotated image features.« less

METHOD AND APPARATUS FOR CONTROLLING DIRECT-CYCLE NEUTRONIC REACTORS

DOEpatents

Reed, G.A.

1961-01-10

A control arrangement is offered for a boiling-water reactor. Boric acid is maintained in the water in the reactor and the amount in the reactor is controlled by continuously removing a portion of the water from the reactor, concentrating the boric acid by evaporating the water therefrom, returning a controlled amount of the acid to the reactor, and simultaneously controlling the water level by varying the rate of spent steam return to the reactor.

Control Means for Reactor

DOEpatents

Manley, J. H.

1961-06-27

An apparatus for controlling a nuclear reactor includes a tank just below the reactor, tubes extending from the tank into the reactor, and a thermally expansible liquid neutron absorbent material in the tank. The liquid in the tank is exposed to a beam of neutrons from the reactor which heats the liquid causing it to expand into the reactor when the neutron flux in the reactor rises above a predetermincd danger point. Boron triamine may be used for this purpose.

10 CFR 2.621 - Acceptance and docketing of application for early review of site suitability issues in a combined...

Code of Federal Regulations, 2014 CFR

2014-01-01

... Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, will inform the... Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, will accept for... New Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, that they...

10 CFR 2.621 - Acceptance and docketing of application for early review of site suitability issues in a combined...

Code of Federal Regulations, 2013 CFR

2013-01-01

... Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, will inform the... Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, will accept for... New Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, that they...

Low temperature pre-treatment of domestic sewage in an anaerobic hybrid or an anaerobic filter reactor.

PubMed

Elmitwalli, Tarek A; Sklyar, Vladimir; Zeeman, Grietje; Lettinga, Gatze

2002-05-01

The pre-treatment of domestic sewage for removal of suspended solids (SS) at a process temperature of 13 degrees C and an hydraulic retention time (HRT) of 4 h was investigated in an anaerobic filter (AF) and anaerobic hybrid (AH) reactor. The AF and the top of the AH reactor consisted of vertical sheets of reticulated polyurethane foam (RPF) with knobs. All biomass in the AF was only in attached form to avoid clogging and sludge washout. The AF reactor showed a significantly higher removal of total and suspended chemical oxygen demand (COD) than the AH reactor, respectively, 55% and 82% in the AF reactor and 34% and 53% in the AH reactor. Because the reactors were operated at a short HRT and low temperature, the hydrolysis, acidification and methanogenesis based on the influent COD were limited to, respectively, 12%, 21% and 23% for the AF reactor and 12%, 17% and 16% for the AH reactor. The excess sludge from the AH reactor was more stabilised and had a better settling capacity and dewaterability. However, the excess sludge from both the AH and AF reactors needed stabilisation. Therefore, the AF reactor is recommended for the pretreatment of domestic sewage at low temperatures.

Nuclear reactor cavity floor passive heat removal system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edwards, Tyler A.; Neeley, Gary W.; Inman, James B.

A nuclear reactor includes a reactor core disposed in a reactor pressure vessel. A radiological containment contains the nuclear reactor and includes a concrete floor located underneath the nuclear reactor. An ex vessel corium retention system includes flow channels embedded in the concrete floor located underneath the nuclear reactor, an inlet in fluid communication with first ends of the flow channels, and an outlet in fluid communication with second ends of the flow channels. In some embodiments the inlet is in fluid communication with the interior of the radiological containment at a first elevation and the outlet is in fluidmore » communication with the interior of the radiological containment at a second elevation higher than the first elevation. The radiological containment may include a reactor cavity containing a lower portion of the pressure vessel, wherein the concrete floor located underneath the nuclear reactor is the reactor cavity floor.« less

Methods and apparatuses for deoxygenating pyrolysis oil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baird, Lance Awender; Brandvold, Timothy A.; Frey, Stanley Joseph

Methods and apparatuses are provided for deoxygenating pyrolysis oil. A method includes contacting a pyrolysis oil with a deoxygenation catalyst in a first reactor at deoxygenation conditions to produce a first reactor effluent. The first reactor effluent has a first oxygen concentration and a first hydrogen concentration, based on hydrocarbons in the first reactor effluent, and the first reactor effluent includes an aromatic compound. The first reactor effluent is contacted with a dehydrogenation catalyst in a second reactor at conditions that deoxygenate the first reactor effluent while preserving the aromatic compound to produce a second reactor effluent. The second reactormore » effluent has a second oxygen concentration lower than the first oxygen concentration and a second hydrogen concentration that is equal to or lower than the first hydrogen concentration, where the second oxygen concentration and the second hydrogen concentration are based on the hydrocarbons in the second reactor effluent.« less

Methanation assembly using multiple reactors

DOEpatents

Jahnke, Fred C.; Parab, Sanjay C.

2007-07-24

A methanation assembly for use with a water supply and a gas supply containing gas to be methanated in which a reactor assembly has a plurality of methanation reactors each for methanating gas input to the assembly and a gas delivery and cooling assembly adapted to deliver gas from the gas supply to each of said methanation reactors and to combine water from the water supply with the output of each methanation reactor being conveyed to a next methanation reactor and carry the mixture to such next methanation reactor.

When Do Commercial Reactors Permanently Shut Down?

EIA Publications

2011-01-01

For those wishing to obtain current data, the following resources are available: U.S. reactors, go to the Energy Information Administration's nuclear reactor shutdown list. (Note: As of April 30, 2010, the last U.S. reactor to permanently shut down was Big Rock Point in 1997.) Foreign Reactors, go to the Power Reactor Information System (PRIS) on the International Atomic Energy Agency's website.

10 CFR 140.11 - Amounts of financial protection for certain reactors.

Code of Federal Regulations, 2014 CFR

2014-01-01

...,000,000 for each nuclear reactor he is authorized to operate at a thermal power level not exceeding ten kilowatts; (2) In the amount of $1,500,000 for each nuclear reactor he is authorized to operate at... amount of $2,500,000 for each nuclear reactor other than a testing reactor or a reactor licensed under...

10 CFR 2.603 - Acceptance and docketing of application for early review of site suitability issues in a...

Code of Federal Regulations, 2013 CFR

2013-01-01

... Office of New Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, will... Office of New Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, will... Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, that they are...

10 CFR 140.11 - Amounts of financial protection for certain reactors.

Code of Federal Regulations, 2012 CFR

2012-01-01

...,000,000 for each nuclear reactor he is authorized to operate at a thermal power level not exceeding ten kilowatts; (2) In the amount of $1,500,000 for each nuclear reactor he is authorized to operate at... amount of $2,500,000 for each nuclear reactor other than a testing reactor or a reactor licensed under...

10 CFR 2.603 - Acceptance and docketing of application for early review of site suitability issues in a...

Code of Federal Regulations, 2014 CFR

2014-01-01

... Office of New Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, will... Office of New Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, will... Reactors or the Director of the Office of Nuclear Reactor Regulation, as appropriate, that they are...

10 CFR 140.11 - Amounts of financial protection for certain reactors.

Code of Federal Regulations, 2013 CFR

2013-01-01

...,000,000 for each nuclear reactor he is authorized to operate at a thermal power level not exceeding ten kilowatts; (2) In the amount of $1,500,000 for each nuclear reactor he is authorized to operate at... amount of $2,500,000 for each nuclear reactor other than a testing reactor or a reactor licensed under...

Determination of the Sensitivity of the Antineutrino Probe for Reactor Core Monitoring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cormon, S.; Fallot, M., E-mail: fallot@subatech.in2p3.fr; Bui, V.-M.

This paper presents a feasibility study of the use of the detection of reactor-antineutrinos (ν{sup ¯}{sub e}) for non proliferation purpose. To proceed, we have started to study different reactor designs with our simulation tools. We use a package called MCNP Utility for Reactor Evolution (MURE), initially developed by CNRS/IN2P3 labs to study Generation IV reactors. The MURE package has been coupled to fission product beta decay nuclear databases for studying reactor antineutrino emission. This method is the only one able to predict the antineutrino emission from future reactor cores, which don't use the thermal fission of {sup 235}U, {supmore » 239}Pu and {sup 241}Pu. It is also the only way to include off-equilibrium effects, due to neutron captures and time evolution of the fission product concentrations during a reactor cycle. We will present here the first predictions of antineutrino energy spectra from innovative reactor designs (Generation IV reactors). We will then discuss a summary of our results of non-proliferation scenarios involving the latter reactor designs, taking into account reactor physics constraints.« less

Bioaugmentation of activated sludge towards 3-chloroaniline removal with a mixed bacterial population carrying a degradative plasmid.

PubMed

Bathe, Stephan; Schwarzenbeck, Norbert; Hausner, Martina

2009-06-01

A bioaugmentation approach combining several strategies was applied to achieve degradation of 3-chloroaniline (3CA) in semicontinuous activated sludge reactors. In a first step, a 3CA-degrading Comamonas testosteroni strain carrying the degradative plasmid pNB2 was added to a biofilm reactor, and complete 3CA degradation together with spread of the plasmid within the indigenous biofilm population was achieved. A second set of reactors was then bioaugmented with either a suspension of biofilm cells removed from the carrier material or with biofilm-containing carrier material. 3CA degradation was established rapidly in all bioaugmented reactors, followed by a slow adaptation of the non-bioaugmented control reactors. In response to variations in 3CA concentration, all reactors exhibited temporary performance breakdowns. Whereas duplicates of the control reactors deviated in their behaviour, the bioaugmented reactors appeared more reproducible in their performance and population dynamics. Finally, the carrier-bioaugmented reactors showed an improved performance in the presence of high 3CA influent concentrations over the suspension-bioaugmented reactors. In contrast, degradation in one control reactor failed completely, but was rapidly established in the remaining control reactor.

A comparative study of thermophilic and mesophilic anaerobic co-digestion of food waste and wheat straw: Process stability and microbial community structure shifts.

PubMed

Shi, Xuchuan; Guo, Xianglin; Zuo, Jiane; Wang, Yajiao; Zhang, Mengyu

2018-05-01

Renewable energy recovery from organic solid waste via anaerobic digestion is a promising way to provide sustainable energy supply and eliminate environmental pollution. However, poor efficiency and operational problems hinder its wide application of anaerobic digestion. The effects of two key parameters, i.e. temperature and substrate characteristics on process stability and microbial community structure were studied using two lab-scale anaerobic reactors under thermophilic and mesophilic conditions. Both the reactors were fed with food waste (FW) and wheat straw (WS). The organic loading rates (OLRs) were maintained at a constant level of 3 kg VS/(m 3 ·d). Five different FW:WS substrate ratios were utilized in different operational phases. The synergetic effects of co-digestion improved the stability and performance of the reactors. When FW was mono-digested, both reactors were unstable. The mesophilic reactor eventually failed due to volatile fatty acid accumulation. The thermophilic reactor had better performance compared to mesophilic one. The biogas production rate of the thermophilic reactor was 4.9-14.8% higher than that of mesophilic reactor throughout the experiment. The shifts in microbial community structures throughout the experiment in both thermophilic and mesophilic reactors were investigated. With increasing FW proportions, bacteria belonging to the phylum Thermotogae became predominant in the thermophilic reactor, while the phylum Bacteroidetes was predominant in the mesophilic reactor. The genus Methanosarcina was the predominant methanogen in the thermophilic reactor, while the genus Methanothrix remained predominant in the mesophilic reactor. The methanogenesis pathway shifted from acetoclastic to hydrogenotrophic when the mesophilic reactor experienced perturbations. Moreover, the population of lignocellulose-degrading microorganisms in the thermophilic reactor was higher than those in mesophilic reactor, which explained the better performance of the thermophilic reactor. Copyright © 2018. Published by Elsevier Ltd.

Coupled reactor kinetics and heat transfer model for heat pipe cooled reactors

NASA Astrophysics Data System (ADS)

Wright, Steven A.; Houts, Michael

2001-02-01

Heat pipes are often proposed as cooling system components for small fission reactors. SAFE-300 and STAR-C are two reactor concepts that use heat pipes as an integral part of the cooling system. Heat pipes have been used in reactors to cool components within radiation tests (Deverall, 1973); however, no reactor has been built or tested that uses heat pipes solely as the primary cooling system. Heat pipe cooled reactors will likely require the development of a test reactor to determine the main differences in operational behavior from forced cooled reactors. The purpose of this paper is to describe the results of a systems code capable of modeling the coupling between the reactor kinetics and heat pipe controlled heat transport. Heat transport in heat pipe reactors is complex and highly system dependent. Nevertheless, in general terms it relies on heat flowing from the fuel pins through the heat pipe, to the heat exchanger, and then ultimately into the power conversion system and heat sink. A system model is described that is capable of modeling coupled reactor kinetics phenomena, heat transfer dynamics within the fuel pins, and the transient behavior of heat pipes (including the melting of the working fluid). This paper focuses primarily on the coupling effects caused by reactor feedback and compares the observations with forced cooled reactors. A number of reactor startup transients have been modeled, and issues such as power peaking, and power-to-flow mismatches, and loading transients were examined, including the possibility of heat flow from the heat exchanger back into the reactor. This system model is envisioned as a tool to be used for screening various heat pipe cooled reactor concepts, for designing and developing test facility requirements, for use in safety evaluations, and for developing test criteria for in-pile and out-of-pile test facilities. .

Technical Application of Nuclear Fission

NASA Astrophysics Data System (ADS)

Denschlag, J. O.

The chapter is devoted to the practical application of the fission process, mainly in nuclear reactors. After a historical discussion covering the natural reactors at Oklo and the first attempts to build artificial reactors, the fundamental principles of chain reactions are discussed. In this context chain reactions with fast and thermal neutrons are covered as well as the process of neutron moderation. Criticality concepts (fission factor η, criticality factor k) are discussed as well as reactor kinetics and the role of delayed neutrons. Examples of specific nuclear reactor types are presented briefly: research reactors (TRIGA and ILL High Flux Reactor), and some reactor types used to drive nuclear power stations (pressurized water reactor [PWR], boiling water reactor [BWR], Reaktor Bolshoi Moshchnosti Kanalny [RBMK], fast breeder reactor [FBR]). The new concept of the accelerator-driven systems (ADS) is presented. The principle of fission weapons is outlined. Finally, the nuclear fuel cycle is briefly covered from mining, chemical isolation of the fuel and preparation of the fuel elements to reprocessing the spent fuel and conditioning for deposit in a final repository.

Optimally moderated nuclear fission reactor and fuel source therefor

DOEpatents

Ougouag, Abderrafi M [Idaho Falls, ID; Terry, William K [Shelley, ID; Gougar, Hans D [Idaho Falls, ID

2008-07-22

An improved nuclear fission reactor of the continuous fueling type involves determining an asymptotic equilibrium state for the nuclear fission reactor and providing the reactor with a moderator-to-fuel ratio that is optimally moderated for the asymptotic equilibrium state of the nuclear fission reactor; the fuel-to-moderator ratio allowing the nuclear fission reactor to be substantially continuously operated in an optimally moderated state.

Flow rate analysis of wastewater inside reactor tanks on tofu wastewater treatment plant

NASA Astrophysics Data System (ADS)

Mamat; Sintawardani, N.; Astuti, J. T.; Nilawati, D.; Wulan, D. R.; Muchlis; Sriwuryandari, L.; Sembiring, T.; Jern, N. W.

2017-03-01

The research aimed to analyse the flow rate of the wastewater inside reactor tanks which were placed a number of bamboo cutting. The resistance of wastewater flow inside reactor tanks might not be occurred and produce biogas fuel optimally. Wastewater from eleven tofu factories was treated by multi-stages anaerobic process to reduce its organic pollutant and produce biogas. Biogas plant has six reactor tanks of which its capacity for waste water and gas dome was 18 m3 and 4.5 m3, respectively. Wastewater was pumped from collecting ponds to reactors by either serial or parallel way. Maximum pump capacity, head, and electrical motor power was 5m3/h, 50m, and 0.75HP, consecutively. Maximum pressure of biogas inside the reactor tanks was 55 mbar higher than atmosphere pressure. A number of 1,400 pieces of cutting bamboo at 50-60 mm diameter and 100 mm length were used as bacteria growth media inside each reactor tank, covering around 14,287 m2 bamboo area, and cross section area of inner reactor was 4,9 m2. In each reactor, a 6 inches PVC pipe was installed vertically as channel. When channels inside reactor were opened, flow rate of wastewater was 6x10-1 L.sec-1. Contrary, when channels were closed on the upper part, wastewater flow inside the first reactor affected and increased gas dome. Initially, wastewater flowed into each reactor by a gravity mode with head difference between the second and third reactor was 15x10-2m. However, head loss at the second reactor was equal to the third reactor by 8,422 x 10-4m. As result, wastewater flow at the second and third reactors were stagnant. To overcome the problem pump in each reactor should be installed in serial mode. In order to reach the output from the first reactor and the others would be equal, and biogas space was not filled by wastewater, therefore biogas production will be optimum.

Operators in the Plum Brook Reactor Facility Control Room

NASA Image and Video Library

1970-03-21

Donald Rhodes, left, and Clyde Greer, right, monitor the operation of the National Aeronautics and Space Administration’s (NASA) Plum Brook Reactor Facility from the control room. The 60-megawatt test reactor, NASA’s only reactor, was the eighth largest test reactor in the world. The facility was built by the Lewis Research Center in the late 1950s to study the effects of radiation on different materials that could be used to construct nuclear propulsion systems for aircraft or rockets. The reactor went critical for the first time in 1961. For the next two years, two operators were on duty 24 hours per day working on the fission process until the reactor reached its full-power level in 1963. Reactor Operators were responsible for monitoring and controlling the reactor systems. Once the reactor was running under normal operating conditions, the work was relatively uneventful. Normally the reactor was kept at a designated power level within certain limits. Occasionally the operators had to increase the power for a certain test. The shift supervisor and several different people would get together and discuss the change before boosting the power. All operators were required to maintain a Reactor Operator License from the Atomic Energy Commission. The license included six months of training, an eight-hour written exam, a four-hour walkaround, and testing on the reactor controls.

10 CFR 50.70 - Inspections.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Director, Office of Nuclear Reactor Regulation or Director, Office of New Reactors, as appropriate, provide... New Reactors, or the Director, Office of Nuclear Reactor Regulation. All furniture, supplies and... construction permit holder (nuclear power reactor only) shall ensure that the arrival and presence of an NRC...

10 CFR 50.70 - Inspections.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Director, Office of Nuclear Reactor Regulation or Director, Office of New Reactors, as appropriate, provide... New Reactors, or the Director, Office of Nuclear Reactor Regulation. All furniture, supplies and... construction permit holder (nuclear power reactor only) shall ensure that the arrival and presence of an NRC...

10 CFR 50.70 - Inspections.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Director, Office of Nuclear Reactor Regulation or Director, Office of New Reactors, as appropriate, provide... New Reactors, or the Director, Office of Nuclear Reactor Regulation. All furniture, supplies and... construction permit holder (nuclear power reactor only) shall ensure that the arrival and presence of an NRC...

10 CFR 50.70 - Inspections.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Director, Office of Nuclear Reactor Regulation or Director, Office of New Reactors, as appropriate, provide... New Reactors, or the Director, Office of Nuclear Reactor Regulation. All furniture, supplies and... construction permit holder (nuclear power reactor only) shall ensure that the arrival and presence of an NRC...

10 CFR 50.70 - Inspections.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Director, Office of Nuclear Reactor Regulation or Director, Office of New Reactors, as appropriate, provide... New Reactors, or the Director, Office of Nuclear Reactor Regulation. All furniture, supplies and... construction permit holder (nuclear power reactor only) shall ensure that the arrival and presence of an NRC...

10 CFR 2.101 - Filing of application.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Reactors, the Director, Office of Nuclear Reactor Regulation, the Director, Office of Nuclear Material... Nuclear Reactor Regulation, Director, Office of New Reactors, Director, Office of Federal and State... be requested to: (i) Submit to the Director, Office of Nuclear Reactor Regulation, Director, Office...

10 CFR 2.101 - Filing of application.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Reactors, the Director, Office of Nuclear Reactor Regulation, the Director, Office of Nuclear Material... Nuclear Reactor Regulation, Director, Office of New Reactors, Director, Office of Federal and State... be requested to: (i) Submit to the Director, Office of Nuclear Reactor Regulation, Director, Office...

Weld monitor and failure detector for nuclear reactor system

DOEpatents

Sutton, Jr., Harry G.

1987-01-01

Critical but inaccessible welds in a nuclear reactor system are monitored throughout the life of the reactor by providing small aperture means projecting completely through the reactor vessel wall and also through the weld or welds to be monitored. The aperture means is normally sealed from the atmosphere within the reactor. Any incipient failure or cracking of the weld will cause the environment contained within the reactor to pass into the aperture means and thence to the outer surface of the reactor vessel where its presence is readily detected.

Demonstration of Robustness and Integrated Operation of a Series-Bosch System

NASA Technical Reports Server (NTRS)

Abney, Morgan B.; Mansell, Matthew J.; Stanley, Christine; Barnett, Bill; Junaedi, Christian; Vilekar, Saurabh A.; Ryan, Kent

2016-01-01

Manned missions beyond low Earth orbit will require highly robust, reliable, and maintainable life support systems that maximize recycling of water and oxygen. Bosch technology is one option to maximize oxygen recovery, in the form of water, from metabolically-produced carbon dioxide (CO2). A two stage approach to Bosch, called Series-Bosch, reduces metabolic CO2 with hydrogen (H2) to produce water and solid carbon using two reactors: a Reverse Water-Gas Shift (RWGS) reactor and a carbon formation (CF) reactor. Previous development efforts demonstrated the stand-alone performance of a NASA-designed RWGS reactor designed for robustness against carbon formation, two membrane separators intended to maximize single pass conversion of reactants, and a batch CF reactor with both transit and surface catalysts. In the past year, Precision Combustion, Inc. (PCI) developed and delivered a RWGS reactor for testing at NASA. The reactor design was based on their patented Microlith® technology and was first evaluated under a Phase I Small Business Innovative Research (SBIR) effort in 2010. The RWGS reactor was recently evaluated at NASA to compare its performance and operating conditions with NASA's RWGS reactor. The test results will be provided in this paper. Separately, in 2015, a semi-continuous CF reactor was designed and fabricated at NASA based on the results from batch CF reactor testing. The batch CF reactor and the semi-continuous CF reactor were individually integrated with an upstream RWGS reactor to demonstrate the system operation and to evaluate performance. Here, we compare the performance and robustness to carbon formation of both RWGS reactors. We report the results of the integrated operation of a Series-Bosch system and we discuss the technology readiness level.

Reactor water cleanup system

DOEpatents

Gluntz, Douglas M.; Taft, William E.

1994-01-01

A reactor water cleanup system includes a reactor pressure vessel containing a reactor core submerged in reactor water. First and second parallel cleanup trains are provided for extracting portions of the reactor water from the pressure vessel, cleaning the extracted water, and returning the cleaned water to the pressure vessel. Each of the cleanup trains includes a heat exchanger for cooling the reactor water, and a cleaner for cleaning the cooled reactor water. A return line is disposed between the cleaner and the pressure vessel for channeling the cleaned water thereto in a first mode of operation. A portion of the cooled water is bypassed around the cleaner during a second mode of operation and returned through the pressure vessel for shutdown cooling.

The role of nuclear reactors in space exploration and development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lipinski, R.J.

2000-07-01

The United States has launched more than 20 radioisotopic thermoelectric generators (RTGs) into space over the past 30 yr but has launched only one nuclear reactor, and that was in 1965. Russia has launched more than 30 reactors. The RTGs use the heat of alpha decay of {sup 238}Pu for power and typically generate <1 kW of electricity. Apollo, Pioneer, Voyager, Viking, Galileo, Ulysses, and Cassini all used RTGs. Space reactors use the fission energy of {sup 235}U; typical designs are for 100 to 1000 kW of electricity. The only US space reactor launch (SNAP-10A) was a demonstration mission. Onemore » reason for the lack of space reactor use by the United States was the lack of space missions that required high power. But, another was the assumed negative publicity that would accompany a reactor launch. The net result is that all space reactor programs after 1970 were terminated before an operating space reactor could be developed, and they are now many years from recovering the ability to build them. Two major near-term needs for space reactors are the human exploration of Mars and advanced missions to and beyond the orbit of Jupiter. To help obtain public acceptance of space reactors, one must correct some of the misconceptions concerning space reactors and convey the following facts to the public and to decision makers: Space reactors are 1000 times smaller in power and size than a commercial power reactor. A space reactor at launch is only as radioactive as a pile of dirt 60 m (200 ft) across. A space reactor contains no plutonium at launch. It does not become significantly radioactive until it is turned on, and it will be engineered so that no launch accident can turn it on, even if that means fueling it after launch. The reactor will not be turned on until it is in a high stable orbit or even on an earth-escape trajectory for some missions. The benefits of space reactors are that they give humanity a stairway to the planets and perhaps the stars. They open a new frontier for their children and their grandchildren. They pave the way for all life on earth to move out into the solar system. At one time, humans built and flew space reactors; it is time to do so again.« less

Degradation of Acid Orange 7 Dye in Two Hybrid Plasma Discharge Reactors

NASA Astrophysics Data System (ADS)

Shen, Yongjun; Lei, Lecheng; Zhang, Xingwang; Ding, Jiandong

2014-11-01

To get an optimized pulsed electrical plasma discharge reactor and to increase the energy utilization efficiency in the removal of pollutants, two hybrid plasma discharge reactors were designed and optimized. The reactors were compared via the discharge characteristics, energy transfer efficiency, the yields of the active species and the energy utilization in dye wastewater degradation. The results showed that under the same AC input power, the characteristics of the discharge waveform of the point-to-plate reactor were better. Under the same AC input power, the two reactors both had almost the same peak voltage of 22 kV. The peak current of the point-to-plate reactor was 146 A, while that of the wire-to-cylinder reactor was only 48.8 A. The peak powers of the point-to-plate reactor and the wire-to-cylinder reactor were 1.38 MW and 1.01 MW, respectively. The energy per pulse of the point-to-plate reactor was 0.2221 J, which was about 29.4% higher than that of the wire-to-cylinder reactor (0.1716 J). To remove 50% Acid Orange 7 (AO7), the energy utilizations of the point-to-plate reactor and the wire-to-cylinder reactor were 1.02 × 10-9 mol/L and 0.61 × 10-9 mol/L, respectively. In the point-to-plate reactor, the concentration of hydrogen peroxide in pure water was 3.6 mmol/L after 40 min of discharge, which was higher than that of the wire-to-cylinder reactor (2.5 mmol/L). The concentration of liquid phase ozone in the point-to-plate reactor (5.7 × 10-2 mmol/L) was about 26.7% higher than that in the wire-to-cylinder reactor (4.5 × 10-2 mmol/L). The analysis results of the variance showed that the type of reactor and reaction time had significant impacts on the yields of the hydrogen peroxide and ozone. The main degradation intermediates of AO7 identified by gas chromatography and mass spectrometry (GCMS) were acetic acid, maleic anhydride, p-benzoquinone, phenol, benzoic acid, phthalic anhydride, coumarin and 2-naphthol. Proposed degradation pathways were elucidated in light of the analyzed degradation products.

10 CFR 72.1 - Purpose.

Code of Federal Regulations, 2011 CFR

2011-01-01

... RADIOACTIVE WASTE, AND REACTOR-RELATED GREATER THAN CLASS C WASTE General Provisions § 72.1 Purpose. The... receive, transfer, and possess power reactor spent fuel, power reactor-related Greater than Class C (GTCC... reactor spent fuel, high-level radioactive waste, power reactor-related GTCC waste, and other radioactive...

10 CFR 72.1 - Purpose.

Code of Federal Regulations, 2010 CFR

2010-01-01

... RADIOACTIVE WASTE, AND REACTOR-RELATED GREATER THAN CLASS C WASTE General Provisions § 72.1 Purpose. The... receive, transfer, and possess power reactor spent fuel, power reactor-related Greater than Class C (GTCC... reactor spent fuel, high-level radioactive waste, power reactor-related GTCC waste, and other radioactive...

Unmixed fuel processors and methods for using the same

DOEpatents

Kulkarni, Parag Prakash; Cui, Zhe

2010-08-24

Disclosed herein are unmixed fuel processors and methods for using the same. In one embodiment, an unmixed fuel processor comprises: an oxidation reactor comprising an oxidation portion and a gasifier, a CO.sub.2 acceptor reactor, and a regeneration reactor. The oxidation portion comprises an air inlet, effluent outlet, and an oxygen transfer material. The gasifier comprises a solid hydrocarbon fuel inlet, a solids outlet, and a syngas outlet. The CO.sub.2 acceptor reactor comprises a water inlet, a hydrogen outlet, and a CO.sub.2 sorbent, and is configured to receive syngas from the gasifier. The regeneration reactor comprises a water inlet and a CO.sub.2 stream outlet. The regeneration reactor is configured to receive spent CO.sub.2 adsorption material from the gasification reactor and to return regenerated CO.sub.2 adsorption material to the gasification reactor, and configured to receive oxidized oxygen transfer material from the oxidation reactor and to return reduced oxygen transfer material to the oxidation reactor.

Thermionic switched self-actuating reactor shutdown system

DOEpatents

Barrus, Donald M.; Shires, Charles D.; Brummond, William A.

1989-01-01

A self-actuating reactor shutdown system incorporating a thermionic switched electromagnetic latch arrangement which is responsive to reactor neutron flux changes and to reactor coolant temperature changes. The system is self-actuating in that the sensing thermionic device acts directly to release (scram) the control rod (absorber) without reference or signal from the main reactor plant protective and control systems. To be responsive to both temperature and neutron flux effects, two detectors are used, one responsive to reactor coolant temperatures, and the other responsive to reactor neutron flux increase. The detectors are incorporated into a thermionic diode connected electrically with an electromagnetic mechanism which under normal reactor operating conditions holds the the control rod in its ready position (exterior of the reactor core). Upon reaching either a specified temperature or neutron flux, the thermionic diode functions to short-circuit the electromagnetic mechanism causing same to lose its holding power and release the control rod, which drops into the reactor core region under gravitational force.

Thermal insulating barrier and neutron shield providing integrated protection for a nuclear reactor vessel

DOEpatents

Schreiber, R.B.; Fero, A.H.; Sejvar, J.

1997-12-16

The reactor vessel of a nuclear reactor installation which is suspended from the cold leg nozzles in a reactor cavity is provided with a lower thermal insulating barrier spaced from the reactor vessel to form a chamber which can be flooded with cooling water through passive valving to directly cool the reactor vessel in the event of a severe accident. The passive valving also includes bistable vents at the upper end of the thermal insulating barrier for releasing steam. A removable, modular neutron shield extending around the upper end of the reactor cavity below the nozzles forms with the upwardly and outwardly tapered transition on the outer surface of the reactor vessel, a labyrinthine channel which reduces neutron streaming while providing a passage for the escape of steam during a severe accident, and for the cooling air which is circulated along the reactor cavity walls outside the thermal insulating barrier during normal operation of the reactor. 8 figs.

Thermal insulating barrier and neutron shield providing integrated protection for a nuclear reactor vessel

DOEpatents

Schreiber, Roger B.; Fero, Arnold H.; Sejvar, James

1997-01-01

The reactor vessel of a nuclear reactor installation which is suspended from the cold leg nozzles in a reactor cavity is provided with a lower thermal insulating barrier spaced from the reactor vessel to form a chamber which can be flooded with cooling water through passive valving to directly cool the reactor vessel in the event of a severe accident. The passive valving also includes bistable vents at the upper end of the thermal insulating barrier for releasing steam. A removable, modular neutron shield extending around the upper end of the reactor cavity below the nozzles forms with the upwardly and outwardly tapered transition on the outer surface of the reactor vessel, a labyrinthine channel which reduces neutron streaming while providing a passage for the escape of steam during a severe accident, and for the cooling air which is circulated along the reactor cavity walls outside the thermal insulating barrier during normal operation of the reactor.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Soldevilla, M.; Salmons, S.; Espinosa, B.

The new application BDDR (Reactor database) has been developed at CEA in order to manage nuclear reactors technological and operating data. This application is a knowledge management tool which meets several internal needs: -) to facilitate scenario studies for any set of reactors, e.g. non-proliferation assessments; -) to make core physics studies easier, whatever the reactor design (PWR-Pressurized Water Reactor-, BWR-Boiling Water Reactor-, MAGNOX- Magnesium Oxide reactor-, CANDU - CANada Deuterium Uranium-, FBR - Fast Breeder Reactor -, etc.); -) to preserve the technological data of all reactors (past and present, power generating or experimental, naval propulsion,...) in a uniquemore » repository. Within the application database are enclosed location data and operating history data as well as a tree-like structure containing numerous technological data. These data address all kinds of reactors features and components. A few neutronics data are also included (neutrons fluxes). The BDDR application is based on open-source technologies and thin client/server architecture. The software architecture has been made flexible enough to allow for any change. (authors)« less

Propellant actuated nuclear reactor steam depressurization valve

DOEpatents

Ehrke, Alan C.; Knepp, John B.; Skoda, George I.

1992-01-01

A nuclear fission reactor combined with a propellant actuated depressurization and/or water injection valve is disclosed. The depressurization valve releases pressure from a water cooled, steam producing nuclear reactor when required to insure the safety of the reactor. Depressurization of the reactor pressure vessel enables gravity feeding of supplementary coolant water through the water injection valve to the reactor pressure vessel to prevent damage to the fuel core.

NEUTRONIC REACTOR CONSTRUCTION AND OPERATION

DOEpatents

West, J.M.; Weills, J.T.

1960-03-15

A method is given for operating a nuclear reactor having a negative coefficient of reactivity to compensate for the change in reactor reactivity due to the burn-up of the xenon peak following start-up of the reactor. When it is desired to start up the reactor within less than 72 hours after shutdown, the temperature of the reactor is lowered prior to start-up, and then gradually raised after start-up.

Thermal-hydraulic interfacing code modules for CANDU reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, W.S.; Gold, M.; Sills, H.

1997-07-01

The approach for CANDU reactor safety analysis in Ontario Hydro Nuclear (OHN) and Atomic Energy of Canada Limited (AECL) is presented. Reflecting the unique characteristics of CANDU reactors, the procedure of coupling the thermal-hydraulics, reactor physics and fuel channel/element codes in the safety analysis is described. The experience generated in the Canadian nuclear industry may be useful to other types of reactors in the areas of reactor safety analysis.

97. ARAIII. ML1 reactor has been moved into GCRE reactor ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

97. ARA-III. ML-1 reactor has been moved into GCRE reactor building (ARA-608) for examination of corrosion on its underside and repair. May 24, 1963. Ineel photo no. 63-3485. - Idaho National Engineering Laboratory, Army Reactors Experimental Area, Scoville, Butte County, ID

NEUTRONIC REACTOR MANIPULATING DEVICE

DOEpatents

Ohlinger, L.A.

1962-08-01

A cable connecting a control rod in a reactor with a motor outside the reactor for moving the rod, and a helical conduit in the reactor wall, through which the cable passes are described. The helical shape of the conduit prevents the escape of certain harmful radiations from the reactor. (AEC)

40 CFR 63.1406 - Reactor batch process vent provisions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 11 2011-07-01 2011-07-01 false Reactor batch process vent provisions... § 63.1406 Reactor batch process vent provisions. (a) Emission standards. Owners or operators of reactor... reactor batch process vent located at a new affected source shall control organic HAP emissions by...

78 FR 73898 - Operator Licensing Examination Standards for Power Reactors

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-09

... Reactors AGENCY: Nuclear Regulatory Commission. ACTION: Draft NUREG; request for comment. SUMMARY: The U.S..., Revision 10, ``Operator Licensing Examination Standards for Power Reactors.'' DATES: Submit comments [email protected] . Both of the Office of New Reactors; or Timothy Kolb, Office of Nuclear Reactor Regulation, U...

76 FR 55718 - Advisory Committee on Reactor Safeguards (ACRS); Meeting of the ACRS Subcommittee on Materials...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-08

... NUCLEAR REGULATORY COMMISSION Advisory Committee on Reactor Safeguards (ACRS); Meeting of the ACRS Subcommittee on Materials, Metallurgy & Reactor Fuels The ACRS Subcommittee on Materials, Metallurgy & Reactor...'' for reactor coolant system (RCS) components, as mentioned in 10 CFR 50 Appendix A, GDC-4. The...

40 CFR 63.1406 - Reactor batch process vent provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 11 2010-07-01 2010-07-01 true Reactor batch process vent provisions... § 63.1406 Reactor batch process vent provisions. (a) Emission standards. Owners or operators of reactor... reactor batch process vent located at a new affected source shall control organic HAP emissions by...

75 FR 58449 - Advisory Committee on Reactor Safeguards (ACRS); Meeting of the ACRS Subcommittee on Materials...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-24

... NUCLEAR REGULATORY COMMISSION Advisory Committee on Reactor Safeguards (ACRS); Meeting of the ACRS Subcommittee on Materials, Metallurgy & Reactor Fuels The ACRS Subcommittee on Materials, Metallurgy & Reactor... would result in a major inconvenience. Dated: September 17, 2010. Antonio Dias, Chief, Reactor Safety...