Carotid artery wall shear stress is independently correlated with renal function in the elderly.

PubMed

Guo, Yuqi; Wei, Fang; Wang, Juan; Zhao, Yingxin; Sun, Shangwen; Zhang, Hua; Liu, Zhendong

2018-01-12

Hemodynamic has increasingly been regarded as an important factor of renal function. However, the relationship between carotid artery wall shear stress (WSS) and renal function is not clarified. To investigate the relationship between carotid WSS and renal function, we recruited 761 older subjects aged 60 years and over from community-dwelling in the Shandong area, China. Carotid WSS, endothelial function, and estimated glomerular filtration rate (eGFR) were assessed in all subjects. Subjects were grouped by the interquartile of the carotid artery mean WSS. We found that the eGFRs derived from serum creatinine and/or cystatin C using three CKD-EPI equations were significantly higher and albumin/creatinine ratio was lower in the higher interquartile groups than in the lower interquartile groups ( P <0.05). The mean WSS was independently correlated with eGFRs even after adjustment for confounders. Similar findings were found between carotid artery peak WSS and eGFRs and albumin/creatinine ratio. In addition, we found that endothelial function was strongly related to carotid WSS and renal function after adjustment for confounders. In conclusion, there is an independent correlation of carotid WSS with renal function in the elderly. The local rheologic forces may play an important role in renal function changing. The correlation may be mediated by regulation of endothelial function.

Comprehensive Ex Vivo Transposon Mutagenesis Identifies Genes That Promote Growth Factor Independence and Leukemogenesis.

PubMed

Guo, Yabin; Updegraff, Barrett L; Park, Sunho; Durakoglugil, Deniz; Cruz, Victoria H; Maddux, Sarah; Hwang, Tae Hyun; O'Donnell, Kathryn A

2016-02-15

Aberrant signaling through cytokine receptors and their downstream signaling pathways is a major oncogenic mechanism underlying hematopoietic malignancies. To better understand how these pathways become pathologically activated and to potentially identify new drivers of hematopoietic cancers, we developed a high-throughput functional screening approach using ex vivo mutagenesis with the Sleeping Beauty transposon. We analyzed over 1,100 transposon-mutagenized pools of Ba/F3 cells, an IL3-dependent pro-B-cell line, which acquired cytokine independence and tumor-forming ability. Recurrent transposon insertions could be mapped to genes in the JAK/STAT and MAPK pathways, confirming the ability of this strategy to identify known oncogenic components of cytokine signaling pathways. In addition, recurrent insertions were identified in a large set of genes that have been found to be mutated in leukemia or associated with survival, but were not previously linked to the JAK/STAT or MAPK pathways nor shown to functionally contribute to leukemogenesis. Forced expression of these novel genes resulted in IL3-independent growth in vitro and tumorigenesis in vivo, validating this mutagenesis-based approach for identifying new genes that promote cytokine signaling and leukemogenesis. Therefore, our findings provide a broadly applicable approach for classifying functionally relevant genes in diverse malignancies and offer new insights into the impact of cytokine signaling on leukemia development. ©2015 American Association for Cancer Research.

Notch pathway activity identifies cells with cancer stem cell-like properties and correlates with worse survival in lung adenocarcinoma

PubMed Central

Hassan, Khaled A.; Wang, Luo; Korkaya, Hasan; Chen, Guoan; Maillard, Ivan; Beer, David G.; Kalemkerian, Gregory P.; Wicha, Max S.

2013-01-01

Purpose The cancer stem cell theory postulates that tumors contain a subset of cells with stem cell properties of self-renewal, differentiation and tumor-initiation. The purpose of this study is to determine the role of Notch activity in identifying lung cancer stem cells. Experimental Design We investigated the role of Notch activity in lung adenocarcinoma utilizing a Notch GFP-reporter construct and a gamma-secretase inhibitor (GSI), which inhibits Notch pathway activity. Results Transduction of lung cancer cells with Notch GFP-reporter construct identified a subset of cells with high Notch activity (GFP-bright). GFP-bright cells had the ability to form more tumor spheres in serum-free media, and were able to generate both GFP-bright and GFP-dim (lower Notch activity) cell populations. GFP-bright cells were resistant to chemotherapy and were tumorigenic in serial xenotransplantation assays. Tumor xenografts of mice treated with GSI had decreased expression of downstream effectors of Notch pathway and failed to regenerate tumors upon reimplantation in NOD/SCID mice. Using multivariate analysis, we detected a statistically significant correlation between poor clinical outcome and Notch activity (reflected in increased Notch ligand expression or decreased expression of the negative modulators), in a group of 441 lung adenocarcinoma patients. This correlation was further confirmed in an independent group of 89 adenocarcinoma patients where Hes-1 overexpression correlated with poor overall survival. Conclusions Notch activity can identify lung cancer stem cell-like population and its inhibition may be an appropriate target for treating lung adenocarcinoma. PMID:23444212

Self-Care Self-Efficacy Correlates with Independence in Basic Activities of Daily Living in Individuals with Chronic Stroke.

PubMed

Frost, Yael; Weingarden, Harold; Zeilig, Gabi; Nota, Ayala; Rand, Debbie

2015-07-01

(1) To characterize the self-care self-efficacy (SCSE) of community dwelling individuals with chronic stroke and (2) to determine the contribution of SCSE to the independence in basic and instrumental activities of daily living (BADL and IADL) and the participation of individuals with chronic stroke. SCSE is the confidence in one's own ability to perform self-care activities. This cross-sectional study included fifty community-dwelling individuals mean (SD) age 59.8 (9.3) years, mean (SD) 3.1 (1.7) years post-stroke who were able to walk at least 10 meters. SCSE was assessed using the Stroke Self-Efficacy Questionnaire (SSEQ), BADL was assessed by the Functional Independence Measure (FIM) (interview), the IADL questionnaire assessed IADL and the Physical Activity Scale for Individuals with Physical Disabilities (PASIPD) assessed participation. Correlation and regression analyses were performed after controlling for grip strength, executive functions and gait speed, factors known to influence independence in daily living. The mean SCSE level was moderate-high (70%). Significant moderate correlations were found between SCSE to independence in BADL (r = .596, P < .001), IADL (r = .567, P < .001) and participation (r = .340, P < .005). SCSE of our cohort explained 7.4% of the variance of the individual's independence in BADL after controlling for executive functions and gait speed, but did not contribute to their independence in IADL and participation. Higher SCSE of individuals with chronic stroke contributes to more independence in BADL. Additional questionnaires regarding self efficacy for IADL should be developed and investigated. Copyright © 2015 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Multimodal neural correlates of cognitive control in the Human Connectome Project.

PubMed

Lerman-Sinkoff, Dov B; Sui, Jing; Rachakonda, Srinivas; Kandala, Sridhar; Calhoun, Vince D; Barch, Deanna M

2017-12-01

Cognitive control is a construct that refers to the set of functions that enable decision-making and task performance through the representation of task states, goals, and rules. The neural correlates of cognitive control have been studied in humans using a wide variety of neuroimaging modalities, including structural MRI, resting-state fMRI, and task-based fMRI. The results from each of these modalities independently have implicated the involvement of a number of brain regions in cognitive control, including dorsal prefrontal cortex, and frontal parietal and cingulo-opercular brain networks. However, it is not clear how the results from a single modality relate to results in other modalities. Recent developments in multimodal image analysis methods provide an avenue for answering such questions and could yield more integrated models of the neural correlates of cognitive control. In this study, we used multiset canonical correlation analysis with joint independent component analysis (mCCA + jICA) to identify multimodal patterns of variation related to cognitive control. We used two independent cohorts of participants from the Human Connectome Project, each of which had data from four imaging modalities. We replicated the findings from the first cohort in the second cohort using both independent and predictive analyses. The independent analyses identified a component in each cohort that was highly similar to the other and significantly correlated with cognitive control performance. The replication by prediction analyses identified two independent components that were significantly correlated with cognitive control performance in the first cohort and significantly predictive of performance in the second cohort. These components identified positive relationships across the modalities in neural regions related to both dynamic and stable aspects of task control, including regions in both the frontal-parietal and cingulo-opercular networks, as well as regions

Correlation approach to identify coding regions in DNA sequences

NASA Technical Reports Server (NTRS)

Ossadnik, S. M.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

1994-01-01

Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

Ligand-Independent Epidermal Growth Factor Receptor Overexpression Correlates with Poor Prognosis in Colorectal Cancer.

PubMed

Yun, Sumi; Kwak, Yoonjin; Nam, Soo Kyung; Seo, An Na; Oh, Heung-Kwon; Kim, Duck-Woo; Kang, Sung-Bum; Lee, Hye Seung

2018-01-17

Molecular treatments targeting epidermal growth factor receptors (EGFRs) are important strategies for advanced colorectal cancer (CRC). However, clinicopathologic implications of EGFRs and EGFR ligand signaling have not been fully evaluated. We evaluated the expression of EGFR ligands and correlation with their receptors, clinicopathologic factors, and patients' survival with CRC. The expression of EGFR ligands, including heparin binding epidermal growth factor like growth factor (HBEGF), transforming growth factor (TGF), betacellulin, and epidermal growth factor (EGF), were evaluated in 331 consecutive CRC samples using mRNA in situ hybridization (ISH). We also evaluated the expression status of EGFR, human epidermal growth factor receptor 2 (HER2), HER3, and HER4 using immunohistochemistry and/or silver ISH. Unlike low incidences of TGF (38.1%), betacellulin (7.9%), and EGF (2.1%), HBEGF expression was noted in 62.2% of CRC samples. However, the expression of each EGFR ligand did not reveal significant correlations with survival. The combined analyses of EGFR ligands and EGFR expression indicated that the ligands‒/EGFR+ group showed a significant association with the worst disease-free survival (DFS, p=0.018) and overall survival (OS, p=0.005). It was also an independent, unfavorable prognostic factor for DFS (p=0.026) and OS (p=0.007). Additionally, HER4 nuclear expression, regardless of ligand expression, was an independent, favorable prognostic factor for DFS (p=0.034) and OS (p=0.049), by multivariate analysis. Ligand-independent EGFR overexpression was suggested to have a significant prognostic impact; thus, the expression status of EGFR ligands, in addition to EGFR, might be necessary for predicting patients' outcome in CRC.

Gene-based meta-analysis of genome-wide association study data identifies independent single-nucleotide polymorphisms in ANXA6 as being associated with systemic lupus erythematosus in Asian populations.

PubMed

Zhang, Jing; Zhang, Lu; Zhang, Yan; Yang, Jing; Guo, Mengbiao; Sun, Liangdan; Pan, Hai-Feng; Hirankarn, Nattiya; Ying, Dingge; Zeng, Shuai; Lee, Tsz Leung; Lau, Chak Sing; Chan, Tak Mao; Leung, Alexander Moon Ho; Mok, Chi Chiu; Wong, Sik Nin; Lee, Ka Wing; Ho, Marco Hok Kung; Lee, Pamela Pui Wah; Chung, Brian Hon-Yin; Chong, Chun Yin; Wong, Raymond Woon Sing; Mok, Mo Yin; Wong, Wilfred Hing Sang; Tong, Kwok Lung; Tse, Niko Kei Chiu; Li, Xiang-Pei; Avihingsanon, Yingyos; Rianthavorn, Pornpimol; Deekajorndej, Thavatchai; Suphapeetiporn, Kanya; Shotelersuk, Vorasuk; Ying, Shirley King Yee; Fung, Samuel Ka Shun; Lai, Wai Ming; Garcia-Barceló, Maria-Mercè; Cherny, Stacey S; Sham, Pak Chung; Cui, Yong; Yang, Sen; Ye, Dong Qing; Zhang, Xue-Jun; Lau, Yu Lung; Yang, Wanling

2015-11-01

Previous genome-wide association studies (GWAS), which were mainly based on single-variant analysis, have identified many systemic lupus erythematosus (SLE) susceptibility loci. However, the genetic architecture of this complex disease is far from being understood. The aim of this study was to investigate whether using a gene-based analysis may help to identify novel loci, by considering global evidence of association from a gene or a genomic region rather than focusing on evidence for individual variants. Based on the results of a meta-analysis of 2 GWAS of SLE conducted in 2 Asian cohorts, we performed an in-depth gene-based analysis followed by replication in a total of 4,626 patients and 7,466 control subjects of Asian ancestry. Differential allelic expression was measured by pyrosequencing. More than one-half of the reported SLE susceptibility loci showed evidence of independent effects, and this finding is important for understanding the mechanisms of association and explaining disease heritability. ANXA6 was detected as a novel SLE susceptibility gene, with several single-nucleotide polymorphisms (SNPs) contributing independently to the association with disease. The risk allele of rs11960458 correlated significantly with increased expression of ANXA6 in peripheral blood mononuclear cells from heterozygous healthy control subjects. Several other associated SNPs may also regulate ANXA6 expression, according to data obtained from public databases. Higher expression of ANXA6 in patients with SLE was also reported previously. Our study demonstrated the merit of using gene-based analysis to identify novel susceptibility loci, especially those with independent effects, and also demonstrated the widespread presence of loci with independent effects in SLE susceptibility genes. © 2015, American College of Rheumatology.

The Neural Correlates of Driving Performance Identified Using Positron Emission Tomography

ERIC Educational Resources Information Center

Horikawa, E.; Okamura, N.; Tashiro, M.; Sakurada, Y.; Maruyama, M.; Arai, H.; Yamaguchi, K.; Sasaki, H.; Yanai, K.; Itoh, M.

2005-01-01

Driving is a complex behavior involving multiple cognitive domains. To identify neural correlates of driving performance, [^1^5O]H"2O positron emission tomography was performed using a simulated driving task. Compared with the resting condition, simulated driving increased regional cerebral blood flow (rCBF) in the cerebellum, occipital, and…

Hypothesis testing for differentially correlated features.

PubMed

Sheng, Elisa; Witten, Daniela; Zhou, Xiao-Hua

2016-10-01

In a multivariate setting, we consider the task of identifying features whose correlations with the other features differ across conditions. Such correlation shifts may occur independently of mean shifts, or differences in the means of the individual features across conditions. Previous approaches for detecting correlation shifts consider features simultaneously, by computing a correlation-based test statistic for each feature. However, since correlations involve two features, such approaches do not lend themselves to identifying which feature is the culprit. In this article, we instead consider a serial testing approach, by comparing columns of the sample correlation matrix across two conditions, and removing one feature at a time. Our method provides a novel perspective and favorable empirical results compared with competing approaches. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Identifying patients with undetected colorectal cancer: an independent validation of QCancer (Colorectal).

PubMed

Collins, G S; Altman, D G

2012-07-10

Early identification of colorectal cancer is an unresolved challenge and the predictive value of single symptoms is limited. We evaluated the performance of QCancer (Colorectal) prediction model for predicting the absolute risk of colorectal cancer in an independent UK cohort of patients from general practice records. A total of 2.1 million patients registered with a general practice surgery between 01 January 2000 and 30 June 2008, aged 30-84 years (3.7 million person-years) with 3712 colorectal cancer cases were included in the analysis. Colorectal cancer was defined as incident diagnosis of colorectal cancer during the 2 years after study entry. The results from this independent and external validation of QCancer (Colorectal) prediction model demonstrated good performance data on a large cohort of general practice patients. QCancer (Colorectal) had very good discrimination with an area under the ROC curve of 0.92 (women) and 0.91 (men), and explained 68% (women) and 66% (men) of the variation. QCancer (Colorectal) was well calibrated across all tenths of risk and over all age ranges with predicted risks closely matching observed risks. QCancer (Colorectal) appears to be a useful tool for identifying undetected cases of undiagnosed colorectal cancer in primary care in the United Kingdom.

Novel Active Learning Experiences for Students to Identify Barriers to Independent Living for People with Disabilities.

PubMed

McArthur, Polly; Burch, Lillian; Moore, Katherine; Hodges, Mary Sue

2016-07-01

This article describes interactive learning about independent living for people with disabilities and features the partnership of the College of Nursing and a Center for Independent Living (CIL). Using qualitative descriptive approach, students' written reflections were analyzed. Through "Xtreme Challenge," 82 undergraduate nursing students participated in aspects of independent living as well as identifying barriers. Students were engaged and learned to consider the person before the disability. Moreover, students valued the activity leaders' openness, which facilitated understanding the point of view of a person with disability. The value of partnership was evident as it allowed students to participate in active learning, which led to growth in the affective domain. Students became aware of potential education resources through the CIL. This article will guide educators in designing experiences that teach nursing care at the individual, family, and community level for people living with disabilities. © 2015 Association of Rehabilitation Nurses.

Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk.

PubMed

Guo, Xingyi; Long, Jirong; Zeng, Chenjie; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K; Wang, Qin; Milne, Roger L; Shu, Xiao-Ou; Cai, Qiuyin; Beesley, Jonathan; Kar, Siddhartha P; Andrulis, Irene L; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W; Beeghly-Fadiel, Alicia; Benitez, Javier; Blot, William; Bogdanova, Natalia; Bojesen, Stig E; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J; Cox, Angela; Cross, Simon S; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dörk, Thilo; Fasching, Peter A; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G; Grip, Mervi; Guénel, Pascal; Haiman, Christopher A; Hamann, Ute; Hartman, Mikael; Hollestelle, Antoinette; Hopper, John L; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A; Kosma, Veli-Matti; Lambrechts, Diether; Le Marchand, Loic; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona A; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L; Nevanlinna, Heli; Nord, Silje; Olson, Janet E; Orr, Nick; Peterlongo, Paolo; Putti, Thomas Choudary; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J; Schmidt, Marjanka K; Schmutzler, Rita K; Shen, Chen-Yang; Shi, Jiajun; Shrubsole, Martha J; Southey, Melissa C; Swerdlow, Anthony; Teo, Soo Hwang; Thienpont, Bernard; Toland, Amanda Ewart; Tollenaar, Robert A E M; Tomlinson, Ian P M; Truong, Thérèse; Tseng, Chiu-Chen; van den Ouweland, Ans; Wen, Wanqing; Winqvist, Robert; Wu, Anna; Yip, Cheng Har; Zamora, M Pilar; Zheng, Ying; Hall, Per; Pharoah, Paul D P; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M; Easton, Douglas F; Zheng, Wei

2015-11-01

A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10(-4); OR, 1.04; 95% confidence interval (CI), 1.02-1.07] and rs77928427 (P = 1.86 × 10(-4); OR, 1.04; 95% CI, 1.02-1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r(2) ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor-binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk. ©2015 American Association for Cancer Research.

Fine-scale mapping of the 4q24 locus identifies two independent loci associated with breast cancer risk

PubMed Central

Guo, Xingyi; Long, Jirong; Zeng, Chenjie; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K.; Wang, Qin; Milne, Roger L.; Shu, Xiao-Ou; Cai, Qiuyin; Beesley, Jonathan; Kar, Siddhartha P.; Andrulis, Irene L.; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W.; Beeghly-Fadiel, Alicia; Benitez, Javier; Blot, William; Bogdanova, Natalia; Bojesen, Stig E.; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J.; Cox, Angela; Cross, Simon S.; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dörk, Thilo; Fasching, Peter A.; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G.; Grip, Mervi; Guénel, Pascal; Haiman, Christopher A.; Hamann, Ute; Hartman, Mikael; Hollestelle, Antoinette; Hopper, John L.; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A.; Kosma, Veli-Matti; Lambrechts, Diether; Marchand, Loic Le; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona A.; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L.; Nevanlinna, Heli; Nord, Silje; Olson, Janet E.; Orr, Nick; Peterlongo, Paolo; Putti, Thomas Choudary; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J.; Schmidt, Marjanka K.; Schmutzler, Rita K.; Shen, Chen-Yang; Shi, Jiajun; Shrubsole, Martha J; Southey, Melissa C.; Swerdlow, Anthony; Teo, Soo Hwang; Thienpont, Bernard; Toland, Amanda Ewart; Tollenaar, Robert A.E.M.; Tomlinson, Ian P.M.; Truong, Thérèse; Tseng, Chiu-chen; van den Ouweland, Ans; Wen, Wanqing; Winqvist, Robert; Wu, Anna; Yip, Cheng Har; Zamora, M. Pilar; Zheng, Ying; Hall, Per; Pharoah, Paul D.P.; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M.; Easton, Douglas F.; Zheng, Wei

2015-01-01

Background A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. Methods We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Results Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 (conditional p = 2.51 × 10−4; OR = 1.04; 95% CI 1.02–1.07) and rs77928427 (p = 1.86 × 10−4; OR = 1.04; 95% CI 1.02–1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r2 ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Conclusion Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Impact Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk. PMID:26354892

Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.

PubMed

Davies, Gail; Lam, Max; Harris, Sarah E; Trampush, Joey W; Luciano, Michelle; Hill, W David; Hagenaars, Saskia P; Ritchie, Stuart J; Marioni, Riccardo E; Fawns-Ritchie, Chloe; Liewald, David C M; Okely, Judith A; Ahola-Olli, Ari V; Barnes, Catriona L K; Bertram, Lars; Bis, Joshua C; Burdick, Katherine E; Christoforou, Andrea; DeRosse, Pamela; Djurovic, Srdjan; Espeseth, Thomas; Giakoumaki, Stella; Giddaluru, Sudheer; Gustavson, Daniel E; Hayward, Caroline; Hofer, Edith; Ikram, M Arfan; Karlsson, Robert; Knowles, Emma; Lahti, Jari; Leber, Markus; Li, Shuo; Mather, Karen A; Melle, Ingrid; Morris, Derek; Oldmeadow, Christopher; Palviainen, Teemu; Payton, Antony; Pazoki, Raha; Petrovic, Katja; Reynolds, Chandra A; Sargurupremraj, Muralidharan; Scholz, Markus; Smith, Jennifer A; Smith, Albert V; Terzikhan, Natalie; Thalamuthu, Anbupalam; Trompet, Stella; van der Lee, Sven J; Ware, Erin B; Windham, B Gwen; Wright, Margaret J; Yang, Jingyun; Yu, Jin; Ames, David; Amin, Najaf; Amouyel, Philippe; Andreassen, Ole A; Armstrong, Nicola J; Assareh, Amelia A; Attia, John R; Attix, Deborah; Avramopoulos, Dimitrios; Bennett, David A; Böhmer, Anne C; Boyle, Patricia A; Brodaty, Henry; Campbell, Harry; Cannon, Tyrone D; Cirulli, Elizabeth T; Congdon, Eliza; Conley, Emily Drabant; Corley, Janie; Cox, Simon R; Dale, Anders M; Dehghan, Abbas; Dick, Danielle; Dickinson, Dwight; Eriksson, Johan G; Evangelou, Evangelos; Faul, Jessica D; Ford, Ian; Freimer, Nelson A; Gao, He; Giegling, Ina; Gillespie, Nathan A; Gordon, Scott D; Gottesman, Rebecca F; Griswold, Michael E; Gudnason, Vilmundur; Harris, Tamara B; Hartmann, Annette M; Hatzimanolis, Alex; Heiss, Gerardo; Holliday, Elizabeth G; Joshi, Peter K; Kähönen, Mika; Kardia, Sharon L R; Karlsson, Ida; Kleineidam, Luca; Knopman, David S; Kochan, Nicole A; Konte, Bettina; Kwok, John B; Le Hellard, Stephanie; Lee, Teresa; Lehtimäki, Terho; Li, Shu-Chen; Liu, Tian; Koini, Marisa; London, Edythe; Longstreth, Will T; Lopez, Oscar L; Loukola, Anu; Luck, Tobias; Lundervold, Astri J; Lundquist, Anders; Lyytikäinen, Leo-Pekka; Martin, Nicholas G; Montgomery, Grant W; Murray, Alison D; Need, Anna C; Noordam, Raymond; Nyberg, Lars; Ollier, William; Papenberg, Goran; Pattie, Alison; Polasek, Ozren; Poldrack, Russell A; Psaty, Bruce M; Reppermund, Simone; Riedel-Heller, Steffi G; Rose, Richard J; Rotter, Jerome I; Roussos, Panos; Rovio, Suvi P; Saba, Yasaman; Sabb, Fred W; Sachdev, Perminder S; Satizabal, Claudia L; Schmid, Matthias; Scott, Rodney J; Scult, Matthew A; Simino, Jeannette; Slagboom, P Eline; Smyrnis, Nikolaos; Soumaré, Aïcha; Stefanis, Nikos C; Stott, David J; Straub, Richard E; Sundet, Kjetil; Taylor, Adele M; Taylor, Kent D; Tzoulaki, Ioanna; Tzourio, Christophe; Uitterlinden, André; Vitart, Veronique; Voineskos, Aristotle N; Kaprio, Jaakko; Wagner, Michael; Wagner, Holger; Weinhold, Leonie; Wen, K Hoyan; Widen, Elisabeth; Yang, Qiong; Zhao, Wei; Adams, Hieab H H; Arking, Dan E; Bilder, Robert M; Bitsios, Panos; Boerwinkle, Eric; Chiba-Falek, Ornit; Corvin, Aiden; De Jager, Philip L; Debette, Stéphanie; Donohoe, Gary; Elliott, Paul; Fitzpatrick, Annette L; Gill, Michael; Glahn, David C; Hägg, Sara; Hansell, Narelle K; Hariri, Ahmad R; Ikram, M Kamran; Jukema, J Wouter; Vuoksimaa, Eero; Keller, Matthew C; Kremen, William S; Launer, Lenore; Lindenberger, Ulman; Palotie, Aarno; Pedersen, Nancy L; Pendleton, Neil; Porteous, David J; Räikkönen, Katri; Raitakari, Olli T; Ramirez, Alfredo; Reinvang, Ivar; Rudan, Igor; Dan Rujescu; Schmidt, Reinhold; Schmidt, Helena; Schofield, Peter W; Schofield, Peter R; Starr, John M; Steen, Vidar M; Trollor, Julian N; Turner, Steven T; Van Duijn, Cornelia M; Villringer, Arno; Weinberger, Daniel R; Weir, David R; Wilson, James F; Malhotra, Anil; McIntosh, Andrew M; Gale, Catharine R; Seshadri, Sudha; Mosley, Thomas H; Bressler, Jan; Lencz, Todd; Deary, Ian J

2018-05-29

General cognitive function is a prominent and relatively stable human trait that is associated with many important life outcomes. We combine cognitive and genetic data from the CHARGE and COGENT consortia, and UK Biobank (total N = 300,486; age 16-102) and find 148 genome-wide significant independent loci (P < 5 × 10 -8 ) associated with general cognitive function. Within the novel genetic loci are variants associated with neurodegenerative and neurodevelopmental disorders, physical and psychiatric illnesses, and brain structure. Gene-based analyses find 709 genes associated with general cognitive function. Expression levels across the cortex are associated with general cognitive function. Using polygenic scores, up to 4.3% of variance in general cognitive function is predicted in independent samples. We detect significant genetic overlap between general cognitive function, reaction time, and many health variables including eyesight, hypertension, and longevity. In conclusion we identify novel genetic loci and pathways contributing to the heritability of general cognitive function.

Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

NASA Technical Reports Server (NTRS)

Singer, M. S.; Oliveira, L.; Vriend, G.; Shepherd, G. M.

1995-01-01

A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

Overcoming correlation fluctuations in two-photon interference experiments with differently bright and independently blinking remote quantum emitters

NASA Astrophysics Data System (ADS)

Weber, Jonas H.; Kettler, Jan; Vural, Hüseyin; Müller, Markus; Maisch, Julian; Jetter, Michael; Portalupi, Simone L.; Michler, Peter

2018-05-01

As a fundamental building block for quantum computation and communication protocols, the correct verification of the two-photon interference (TPI) contrast between two independent quantum light sources is of utmost importance. Here, we experimentally demonstrate how frequently present blinking dynamics and changes in emitter brightness critically affect the Hong-Ou-Mandel-type (HOM) correlation histograms of remote TPI experiments measured via the commonly utilized setup configuration. We further exploit this qualitative and quantitative explanation of the observed correlation dynamics to establish an alternative interferometer configuration, which is overcoming the discussed temporal fluctuations, giving rise to an error-free determination of the remote TPI visibility. We prove full knowledge of the obtained correlation by reproducing the measured correlation statistics via Monte Carlo simulations. As an exemplary system, we make use of two pairs of remote semiconductor quantum dots; however, the same conclusions apply for TPI experiments with flying qubits from any kind of remote solid-state quantum emitters.

Independence.

ERIC Educational Resources Information Center

Stephenson, Margaret E.

2000-01-01

Discusses the four planes of development and the periods of creation and crystallization within each plane. Identifies the type of independence that should be achieved by the end of the first two planes of development. Maintains that it is through individual work on the environment that one achieves independence. (KB)

Humoral responses to independent vaccinations are correlated in healthy boosted adults

PubMed Central

Garman, Lori; Vineyard, Amanda J.; Crowe, Sherry R.; Harley, John B.; Spooner, Christina E.; Collins, Limone C.; Nelson, Michael R.; Engler, Renata J.M.; James, Judith A.

2015-01-01

Background Roughly half of U.S. adults do not receive recommended booster vaccinations, but protective antibody levels are rarely measured in adults. Demographic factors, vaccination history, and responses to other vaccinations could help identify at-risk individuals. We sought to characterize rates of seroconversion and determine associations of humoral responses to multiple vaccinations in healthy adults. Methods Humoral responses toward measles, mumps, tetanus toxoid, pertussis, hepatitis B surface antigen, and anthrax protective antigen were measured by ELISA in post-immunization samples from 1,465 healthy U.S. military members. We examined the effects of demographic and clinical factors on immunization responses, as well as assessed correlations between vaccination responses. Results Subsets of boosted adults did not have seroprotective levels of antibodies toward measles (10.4%), mumps (9.4%), pertussis (4.7%), hepatitis B (8.6%) or protective antigen (14.4%) detected. Half-lives of antibody responses were generally long (>30 years). Measles and mumps antibody levels were correlated (r=0.31, p<0.001), but not associated with select demographic features or vaccination history. Measles and mumps antibody levels also correlated with tetanus antibody response (r=0.11, p<0.001). Conclusions Vaccination responses are predominantly robust and vaccine specific. However, a small but significant portion of the vaccinated adult population may not have quantitative seroprotective antibody to common vaccine-preventable infections. PMID:25140930

Humoral responses to independent vaccinations are correlated in healthy boosted adults.

PubMed

Garman, Lori; Vineyard, Amanda J; Crowe, Sherry R; Harley, John B; Spooner, Christina E; Collins, Limone C; Nelson, Michael R; Engler, Renata J M; James, Judith A

2014-09-29

Roughly half of U.S. adults do not receive recommended booster vaccinations, but protective antibody levels are rarely measured in adults. Demographic factors, vaccination history, and responses to other vaccinations could help identify at-risk individuals. We sought to characterize rates of seroconversion and determine associations of humoral responses to multiple vaccinations in healthy adults. Humoral responses toward measles, mumps, tetanus toxoid, pertussis, hepatitis B surface antigen, and anthrax protective antigen were measured by ELISA in post-immunization samples from 1465 healthy U.S. military members. We examined the effects of demographic and clinical factors on immunization responses, as well as assessed correlations between vaccination responses. Subsets of boosted adults did not have seroprotective levels of antibodies toward measles (10.4%), mumps (9.4%), pertussis (4.7%), hepatitis B (8.6%) or protective antigen (14.4%) detected. Half-lives of antibody responses were generally long (>30 years). Measles and mumps antibody levels were correlated (r=0.31, p<0.001), but not associated with select demographic features or vaccination history. Measles and mumps antibody levels also correlated with tetanus antibody response (r=0.11, p<0.001). Vaccination responses are predominantly robust and vaccine specific. However, a small but significant portion of the vaccinated adult population may not have quantitative seroprotective antibody to common vaccine-preventable infections. Copyright © 2014 Elsevier Ltd. All rights reserved.

Differential correlation for sequencing data.

PubMed

Siska, Charlotte; Kechris, Katerina

2017-01-19

Several methods have been developed to identify differential correlation (DC) between pairs of molecular features from -omics studies. Most DC methods have only been tested with microarrays and other platforms producing continuous and Gaussian-like data. Sequencing data is in the form of counts, often modeled with a negative binomial distribution making it difficult to apply standard correlation metrics. We have developed an R package for identifying DC called Discordant which uses mixture models for correlations between features and the Expectation Maximization (EM) algorithm for fitting parameters of the mixture model. Several correlation metrics for sequencing data are provided and tested using simulations. Other extensions in the Discordant package include additional modeling for different types of differential correlation, and faster implementation, using a subsampling routine to reduce run-time and address the assumption of independence between molecular feature pairs. With simulations and breast cancer miRNA-Seq and RNA-Seq data, we find that Spearman's correlation has the best performance among the tested correlation methods for identifying differential correlation. Application of Spearman's correlation in the Discordant method demonstrated the most power in ROC curves and sensitivity/specificity plots, and improved ability to identify experimentally validated breast cancer miRNA. We also considered including additional types of differential correlation, which showed a slight reduction in power due to the additional parameters that need to be estimated, but more versatility in applications. Finally, subsampling within the EM algorithm considerably decreased run-time with negligible effect on performance. A new method and R package called Discordant is presented for identifying differential correlation with sequencing data. Based on comparisons with different correlation metrics, this study suggests Spearman's correlation is appropriate for sequencing data

A Trunk Support System to Identify Posture Control Mechanisms in Populations Lacking Independent Sitting

PubMed Central

Goodworth, Adam D.; Wu, Yen-Hsun; Felmlee, Duffy; Dunklebarger, Ellis; Saavedra, Sandra

2016-01-01

Populations with moderate-to-severe motor control impairments often exhibit degraded trunk control and/or lack the ability to sit unassisted. These populations need more research, yet their underdeveloped trunk control complicates identification of neural mechanisms behind their movements. The purpose of this study was to overcome this barrier by developing the first multi-articulated trunk support system to identify visual, vestibular, and proprioception contributions to posture in populations lacking independent sitting. The system provided external stability at a user-specific level on the trunk, so that body segments above the level of support required active posture control. The system included a tilting surface (controlled via servomotor) as a stimulus to investigate sensory contributions to postural responses. Frequency response and coherence functions between the surface tilt and trunk support were used to characterize system dynamics and indicated that surface tilts were accurately transmitted up to 5Hz. Feasibility of collecting kinematic data in participants lacking independent sitting was demonstrated in two populations: two typically developing infants, ~2-8 months, in a longitudinal study (8 sessions each) and four children with moderate-to-severe cerebral palsy (GMFCS III-V). Adaptability in the system was assessed by testing 16 adults (ages 18-63). Kinematic responses to continuous pseudorandom surface tilts were evaluated across 0.046–2Hz and qualitative feedback indicated that the trunk support and stimulus were comfortable for all subjects. Concepts underlying the system enable both research for, and rehabilitation in, populations lacking independent sitting. PMID:27046877

An automated method for identifying artifact in independent component analysis of resting-state FMRI.

PubMed

Bhaganagarapu, Kaushik; Jackson, Graeme D; Abbott, David F

2013-01-01

An enduring issue with data-driven analysis and filtering methods is the interpretation of results. To assist, we present an automatic method for identification of artifact in independent components (ICs) derived from functional MRI (fMRI). The method was designed with the following features: does not require temporal information about an fMRI paradigm; does not require the user to train the algorithm; requires only the fMRI images (additional acquisition of anatomical imaging not required); is able to identify a high proportion of artifact-related ICs without removing components that are likely to be of neuronal origin; can be applied to resting-state fMRI; is automated, requiring minimal or no human intervention. We applied the method to a MELODIC probabilistic ICA of resting-state functional connectivity data acquired in 50 healthy control subjects, and compared the results to a blinded expert manual classification. The method identified between 26 and 72% of the components as artifact (mean 55%). About 0.3% of components identified as artifact were discordant with the manual classification; retrospective examination of these ICs suggested the automated method had correctly identified these as artifact. We have developed an effective automated method which removes a substantial number of unwanted noisy components in ICA analyses of resting-state fMRI data. Source code of our implementation of the method is available.

How Unique is Any Given Seismogram? - Exploring Correlation Methods to Identify Explosions

NASA Astrophysics Data System (ADS)

Walter, W. R.; Dodge, D. A.; Ford, S. R.; Pyle, M. L.; Hauk, T. F.

2015-12-01

As with conventional wisdom about snowflakes, we would expect it unlikely that any two broadband seismograms would ever be exactly identical. However depending upon the resolution of our comparison metric, we do expect, and often find, bandpassed seismograms that correlate to very high levels (>0.99). In fact regional (e.g. Schaff and Richards, 2011) and global investigations (e.g. Dodge and Walter, 2015) find large numbers of highly correlated seismograms. Decreasing computational costs are increasing the tremendous potential for correlation in lowering detection, location and identification thresholds for explosion monitoring (e.g. Schaff et al., 2012, Gibbons and Ringdal, 2012; Zhang and Wen, 2015). We have shown in the case of Source Physics Experiment (SPE) chemical explosions, templates at local and near regional stations can detect, locate and identify very small explosions, which might be applied to monitoring active test sites (Ford and Walter, 2015). In terms of elastic theory, seismograms are the convolution between source and Green function terms. Thus high correlation implies similar sources, closely located. How do we quantify this physically? For example it is well known that as the template event and target events are increasingly separated spatially, their correlation diminishes, as the difference in the Green function between the two events grows larger. This is related to the event separation in terms of wavelength, the heterogeneity of the Earth structure, and the time-bandwidth of the correlation parameters used, but this has not been well quantified. We are using the historic dataset of nuclear explosions in southern Nevada to explore empirically where and how well these events correlate as a function of location, depth, size, time-bandwidth and other parameters. A goal is to develop more meaningful and physical metrics that go beyond the correlation coefficient and can be applied to explosion monitoring problems, particularly event

An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci

PubMed Central

Ju, Jin Hyun; Crystal, Ronald G.

2017-01-01

Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation. The key advance of the CONFETI framework is the use of Independent Component Analysis (ICA) to identify variation likely caused by broad impact eQTL when constructing the sample covariance matrix used for the random effect in a mixed model. We show that CONFETI has better performance than other mixed model confounding factor methods when considering broad impact eQTL recovery from synthetic data. We also used the CONFETI framework and these same confounding factor methods to identify eQTL that replicate between matched twin pair datasets in the Multiple Tissue Human Expression Resource (MuTHER), the Depression Genes Networks study (DGN), the Netherlands Study of Depression and Anxiety (NESDA), and multiple tissue types in the Genotype-Tissue Expression (GTEx) consortium. These analyses identified both cis-eQTL and trans-eQTL impacting individual genes, and CONFETI had better or comparable performance to other mixed model confounding factor analysis methods when identifying such eQTL. In these analyses, we were able to identify and replicate a few broad impact eQTL although the overall number was small even when applying CONFETI. In

An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci.

PubMed

Ju, Jin Hyun; Shenoy, Sushila A; Crystal, Ronald G; Mezey, Jason G

2017-05-01

Genome-wide expression Quantitative Trait Loci (eQTL) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases. While the majority of eQTL identified in genome-wide analyses impact a single gene, eQTL that impact many genes are particularly valuable for network modeling and disease analysis. To enable the identification of such broad impact eQTL, we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis. CONFETI is designed to address two conflicting issues when searching for broad impact eQTL: the need to account for non-genetic confounding factors that can lower the power of the analysis or produce broad impact eQTL false positives, and the tendency of methods that account for confounding factors to model broad impact eQTL as non-genetic variation. The key advance of the CONFETI framework is the use of Independent Component Analysis (ICA) to identify variation likely caused by broad impact eQTL when constructing the sample covariance matrix used for the random effect in a mixed model. We show that CONFETI has better performance than other mixed model confounding factor methods when considering broad impact eQTL recovery from synthetic data. We also used the CONFETI framework and these same confounding factor methods to identify eQTL that replicate between matched twin pair datasets in the Multiple Tissue Human Expression Resource (MuTHER), the Depression Genes Networks study (DGN), the Netherlands Study of Depression and Anxiety (NESDA), and multiple tissue types in the Genotype-Tissue Expression (GTEx) consortium. These analyses identified both cis-eQTL and trans-eQTL impacting individual genes, and CONFETI had better or comparable performance to other mixed model confounding factor analysis methods when identifying such eQTL. In these analyses, we were able to identify and replicate a few broad impact eQTL although the overall number was small even when applying CONFETI. In

Method and apparatus for the simultaneous display and correlation of independently generated images

DOEpatents

Vaitekunas, Jeffrey J.; Roberts, Ronald A.

1991-01-01

An apparatus and method for location by location correlation of multiple images from Non-Destructive Evaluation (NDE) and other sources. Multiple images of a material specimen are displayed on one or more monitors of an interactive graphics system. Specimen landmarks are located in each image and mapping functions from a reference image to each other image are calcuated using the landmark locations. A location selected by positioning a cursor in the reference image is mapped to the other images and location identifiers are simultaneously displayed in those images. Movement of the cursor in the reference image causes simultaneous movement of the location identifiers in the other images to positions corresponding to the location of the reference image cursor.

Graph-theoretic approach to quantum correlations.

PubMed

Cabello, Adán; Severini, Simone; Winter, Andreas

2014-01-31

Correlations in Bell and noncontextuality inequalities can be expressed as a positive linear combination of probabilities of events. Exclusive events can be represented as adjacent vertices of a graph, so correlations can be associated to a subgraph. We show that the maximum value of the correlations for classical, quantum, and more general theories is the independence number, the Lovász number, and the fractional packing number of this subgraph, respectively. We also show that, for any graph, there is always a correlation experiment such that the set of quantum probabilities is exactly the Grötschel-Lovász-Schrijver theta body. This identifies these combinatorial notions as fundamental physical objects and provides a method for singling out experiments with quantum correlations on demand.

Structural and functional correlates of hypnotic depth and suggestibility.

PubMed

McGeown, William Jonathan; Mazzoni, Giuliana; Vannucci, Manila; Venneri, Annalena

2015-02-28

This study explores whether self-reported depth of hypnosis and hypnotic suggestibility are associated with individual differences in neuroanatomy and/or levels of functional connectivity. Twenty-nine people varying in suggestibility were recruited and underwent structural, and after a hypnotic induction, functional magnetic resonance imaging at rest. We used voxel-based morphometry to assess the correlation of grey matter (GM) and white matter (WM) against the independent variables: depth of hypnosis, level of relaxation and hypnotic suggestibility. Functional networks identified with independent components analysis were regressed with the independent variables. Hypnotic depth ratings were positively correlated with GM volume in the frontal cortex and the anterior cingulate cortex (ACC). Hypnotic suggestibility was positively correlated with GM volume in the left temporal-occipital cortex. Relaxation ratings did not correlate significantly with GM volume and none of the independent variables correlated with regional WM volume measures. Self-reported deeper levels of hypnosis were associated with less connectivity within the anterior default mode network. Taken together, the results suggest that the greater GM volume in the medial frontal cortex and ACC, and lower connectivity in the DMN during hypnosis facilitate experiences of greater hypnotic depth. The patterns of results suggest that hypnotic depth and hypnotic suggestibility should not be considered synonyms. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Identifying reliable independent components via split-half comparisons

PubMed Central

Groppe, David M.; Makeig, Scott; Kutas, Marta

2011-01-01

Independent component analysis (ICA) is a family of unsupervised learning algorithms that have proven useful for the analysis of the electroencephalogram (EEG) and magnetoencephalogram (MEG). ICA decomposes an EEG/MEG data set into a basis of maximally temporally independent components (ICs) that are learned from the data. As with any statistic, a concern with using ICA is the degree to which the estimated ICs are reliable. An IC may not be reliable if ICA was trained on insufficient data, if ICA training was stopped prematurely or at a local minimum (for some algorithms), or if multiple global minima were present. Consequently, evidence of ICA reliability is critical for the credibility of ICA results. In this paper, we present a new algorithm for assessing the reliability of ICs based on applying ICA separately to split-halves of a data set. This algorithm improves upon existing methods in that it considers both IC scalp topographies and activations, uses a probabilistically interpretable threshold for accepting ICs as reliable, and requires applying ICA only three times per data set. As evidence of the method’s validity, we show that the method can perform comparably to more time intensive bootstrap resampling and depends in a reasonable manner on the amount of training data. Finally, using the method we illustrate the importance of checking the reliability of ICs by demonstrating that IC reliability is dramatically increased by removing the mean EEG at each channel for each epoch of data rather than the mean EEG in a prestimulus baseline. PMID:19162199

Activation of parallel fiber feedback by spatially diffuse stimuli reduces signal and noise correlations via independent mechanisms in a cerebellum-like structure.

PubMed

Simmonds, Benjamin; Chacron, Maurice J

2015-01-01

Correlations between the activities of neighboring neurons are observed ubiquitously across systems and species and are dynamically regulated by several factors such as the stimulus' spatiotemporal extent as well as by the brain's internal state. Using the electrosensory system of gymnotiform weakly electric fish, we recorded the activities of pyramidal cell pairs within the electrosensory lateral line lobe (ELL) under spatially localized and diffuse stimulation. We found that both signal and noise correlations were markedly reduced (>40%) under the latter stimulation. Through a network model incorporating key anatomical features of the ELL, we reveal how activation of diffuse parallel fiber feedback from granule cells by spatially diffuse stimulation can explain both the reduction in signal as well as the reduction in noise correlations seen experimentally through independent mechanisms. First, we show that burst-timing dependent plasticity, which leads to a negative image of the stimulus and thereby reduces single neuron responses, decreases signal but not noise correlations. Second, we show trial-to-trial variability in the responses of single granule cells to sensory input reduces noise but not signal correlations. Thus, our model predicts that the same feedback pathway can simultaneously reduce both signal and noise correlations through independent mechanisms. To test this prediction experimentally, we pharmacologically inactivated parallel fiber feedback onto ELL pyramidal cells. In agreement with modeling predictions, we found that inactivation increased both signal and noise correlations but that there was no significant relationship between magnitude of the increase in signal correlations and the magnitude of the increase in noise correlations. The mechanisms reported in this study are expected to be generally applicable to the cerebellum as well as other cerebellum-like structures. We further discuss the implications of such decorrelation on the neural

Three-way parallel independent component analysis for imaging genetics using multi-objective optimization.

PubMed

Ulloa, Alvaro; Jingyu Liu; Vergara, Victor; Jiayu Chen; Calhoun, Vince; Pattichis, Marios

2014-01-01

In the biomedical field, current technology allows for the collection of multiple data modalities from the same subject. In consequence, there is an increasing interest for methods to analyze multi-modal data sets. Methods based on independent component analysis have proven to be effective in jointly analyzing multiple modalities, including brain imaging and genetic data. This paper describes a new algorithm, three-way parallel independent component analysis (3pICA), for jointly identifying genomic loci associated with brain function and structure. The proposed algorithm relies on the use of multi-objective optimization methods to identify correlations among the modalities and maximally independent sources within modality. We test the robustness of the proposed approach by varying the effect size, cross-modality correlation, noise level, and dimensionality of the data. Simulation results suggest that 3p-ICA is robust to data with SNR levels from 0 to 10 dB and effect-sizes from 0 to 3, while presenting its best performance with high cross-modality correlations, and more than one subject per 1,000 variables. In an experimental study with 112 human subjects, the method identified links between a genetic component (pointing to brain function and mental disorder associated genes, including PPP3CC, KCNQ5, and CYP7B1), a functional component related to signal decreases in the default mode network during the task, and a brain structure component indicating increases of gray matter in brain regions of the default mode region. Although such findings need further replication, the simulation and in-vivo results validate the three-way parallel ICA algorithm presented here as a useful tool in biomedical data decomposition applications.

Clinical and Electrographic Correlates of Bilateral Independent Periodic Discharges.

PubMed

Freund, Brin; Gugger, James J; Reynolds, Alexandra; Tatum, William O; Claassen, Jan; Kaplan, Peter W

2018-05-01

Periodic discharges (PDs) are EEG patterns denoting brain dysfunction and ictal tendency. Their exact meaning regarding etiology and outcomes is not well known. In particular, bilateral independent PDs (BIPDs) are poorly described. We performed a retrospective, multicenter study evaluating neuroimaging, epileptic, clinical, and EEG correlates of BIPDs. Twenty-five patients studied with a mean Glasgow Coma Scale 6.5 and modified Rankin scale 3.9 who underwent EEG monitoring, mean duration 287 hours (range 0.75-3,216). Most common causes of BIPDs were cardiac arrest, Central Nervous System infections, and acute/chronic ischemic/hemorrhagic stroke. Most had subcortical and cortical injuries on neuroimaging. Most of the PDs ranged from 0.5 to 2 Hz in frequency, were of multiple phase types, and localized to the frontal head regions. Eighteen of 25 patients had clinical or electrographic seizures. There was a trend toward seizures in those with BIPDs with a history of epilepsy (P = 0.08) and acute metabolic dysfunction (P = 0.08), particularly with coincident acute structural lesions (P = 0.05). Seizures were predicted by bilaterally symmetric frequencies (P = 0.02) and trended toward higher likelihood with PD frequency <2 Hz (P = 0.08). Two of 25 patients survived past discharge with modified Rankin scale <3. Cardiac arrest was associated with withdrawal of life-sustaining therapy (P < 0.001). BIPDs arise from acute and chronic neurologic injuries, often associated with metabolic dysfunction. Outcomes are poor in this population. Seizures are common, particularly in patients with PDs that are of a lower frequency or are symmetric in frequency. Further study is warranted to evaluate the association between BIPDs and seizures, as well as functional and longer term outcomes.

Independence and cognition post-stroke and its relationship to burden and quality of life of family caregivers.

PubMed

Caro, Camila Caminha; Mendes, Paulo Vinicius Braga; Costa, Jacqueline Denubila; Nock, Lauren Jane; Cruz, Daniel Marinho Cezar da

2017-04-01

Stroke is a chronic disease responsible for changes in the functional capacity of the patients. Patient care is usually provided by family caregivers, but with great burden and negative impact on their quality of life. (1) To investigate whether a correlation existed between the levels of independence and cognition in stroke patients and the burden and quality of life of their caregivers; (2) to assess whether periods of injury, rehabilitation and care, and age of the stroke patients interfered with these correlations. This was a cross-sectional and correlational study that included 60 participants, of which 30 were post-stroke patients and 30 were their caregivers. The data collection instruments were the Mini Mental State Examination and the Functional Independence Measure for the post-stroke participants, and the Zarit Burden Interview Scale and the World Health Organization Quality of Life-BREF, for the caregivers. The Pearson's product-moment correlation was used for the data analysis. Independence and cognition showed no correlation with the burden and quality of life of the caregivers. We identified a strong positive correlation between independence and cognition (r = 0.882), and a moderate negative correlation between independence and rehabilitation period (r = -0.398) and between burden and quality of life of the caregivers (r = -0.414). Our data suggest the need for health interventions aimed not only at stroke patients, but also at their family caregivers, given the association between the burden and the low levels of quality of life of the caregivers.

Dynamic brain glucose metabolism identifies anti-correlated cortical-cerebellar networks at rest.

PubMed

Tomasi, Dardo G; Shokri-Kojori, Ehsan; Wiers, Corinde E; Kim, Sunny W; Demiral, Şukru B; Cabrera, Elizabeth A; Lindgren, Elsa; Miller, Gregg; Wang, Gene-Jack; Volkow, Nora D

2017-12-01

It remains unclear whether resting state functional magnetic resonance imaging (rfMRI) networks are associated with underlying synchrony in energy demand, as measured by dynamic 2-deoxy-2-[ 18 F]fluoroglucose (FDG) positron emission tomography (PET). We measured absolute glucose metabolism, temporal metabolic connectivity (t-MC) and rfMRI patterns in 53 healthy participants at rest. Twenty-two rfMRI networks emerged from group independent component analysis (gICA). In contrast, only two anti-correlated t-MC emerged from FDG-PET time series using gICA or seed-voxel correlations; one included frontal, parietal and temporal cortices, the other included the cerebellum and medial temporal regions. Whereas cerebellum, thalamus, globus pallidus and calcarine cortex arose as the strongest t-MC hubs, the precuneus and visual cortex arose as the strongest rfMRI hubs. The strength of the t-MC linearly increased with the metabolic rate of glucose suggesting that t-MC measures are strongly associated with the energy demand of the brain tissue, and could reflect regional differences in glucose metabolism, counterbalanced metabolic network demand, and/or differential time-varying delivery of FDG. The mismatch between metabolic and functional connectivity patterns computed as a function of time could reflect differences in the temporal characteristics of glucose metabolism as measured with PET-FDG and brain activation as measured with rfMRI.

Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer

PubMed Central

Zheng, Wei; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Lush, Michael; Milne, Roger L.; Shu, Xiao-Ou; Beesley, Jonathan; Kar, Siddhartha; Andrulis, Irene L.; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W.; Zhao, Zhiguo; Guo, Xingyi; Benitez, Javier; Beeghly-Fadiel, Alicia; Blot, William; Bogdanova, Natalia V.; Bojesen, Stig E.; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J.; Cox, Angela; Cross, Simon S.; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dork, Thilo; Fasching, Peter A.; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G.; Guenel, Pascal; Haiman, Christopher A.; Hamann, Ute; Hartman, Mikael; Miao, Hui; Hollestelle, Antoinette; Hopper, John L.; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Torres, Diana; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A.; Kosma, Veli-Matti; Lambrechts, Diether; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Le Marchand, Loic; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L.; Nevanlinna, Heli; Nord, Silje; Børresen-Dale, Anne-Lise; Olson, Janet E.; Orr, Nick; van den Ouweland, Ans M.W.; Peterlongo, Paolo; Putti, Thomas Choudary; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J.; Schmidt, Marjanka K.; Schmutzler, Rita K.; Shen, Chen-Yang; Hou, Ming-Feng; Shrubsole, Matha J; Southey, Melissa C.; Swerdlow, Anthony; Teo, Soo Hwang; Thienpont, Bernard; Toland, Amanda E.; Tollenaar, Robert A.E.M.; Tomlinson, Ian; Truong, Therese; Tseng, Chiu-chen; Wen, Wanqing; Winqvist, Robert; Wu, Anna H.; Yip, Cheng Har; Zamora, Pilar M.; Zheng, Ying; Floris, Giuseppe; Cheng, Ching-Yu; Hooning, Maartje J.; Martens, John W.M.; Seynaeve, Caroline; Kristensen, Vessela N.; Hall, Per; Pharoah, Paul D.P.; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M.; Antoniou, Antonis C.; Easton, Douglas F.; Cai, Qiuyin; Long, Jirong

2016-01-01

Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. We conducted a fine-mapping study across 2.06 Mb (chr8:127,561,724 −129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium. We found three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional P = 5.8 × 10−6), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional P = 1.1 × 10−6), and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional P = 1.1 × 10−4). Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas, and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r2 = 0.77), were putatively functional variants for two of the five independent association signals. Our results highlight multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry. PMID:27087578

Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer.

PubMed

Shi, Jiajun; Zhang, Yanfeng; Zheng, Wei; Michailidou, Kyriaki; Ghoussaini, Maya; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Lush, Michael; Milne, Roger L; Shu, Xiao-Ou; Beesley, Jonathan; Kar, Siddhartha; Andrulis, Irene L; Anton-Culver, Hoda; Arndt, Volker; Beckmann, Matthias W; Zhao, Zhiguo; Guo, Xingyi; Benitez, Javier; Beeghly-Fadiel, Alicia; Blot, William; Bogdanova, Natalia V; Bojesen, Stig E; Brauch, Hiltrud; Brenner, Hermann; Brinton, Louise; Broeks, Annegien; Brüning, Thomas; Burwinkel, Barbara; Cai, Hui; Canisius, Sander; Chang-Claude, Jenny; Choi, Ji-Yeob; Couch, Fergus J; Cox, Angela; Cross, Simon S; Czene, Kamila; Darabi, Hatef; Devilee, Peter; Droit, Arnaud; Dork, Thilo; Fasching, Peter A; Fletcher, Olivia; Flyger, Henrik; Fostira, Florentia; Gaborieau, Valerie; García-Closas, Montserrat; Giles, Graham G; Guenel, Pascal; Haiman, Christopher A; Hamann, Ute; Hartman, Mikael; Miao, Hui; Hollestelle, Antoinette; Hopper, John L; Hsiung, Chia-Ni; Ito, Hidemi; Jakubowska, Anna; Johnson, Nichola; Torres, Diana; Kabisch, Maria; Kang, Daehee; Khan, Sofia; Knight, Julia A; Kosma, Veli-Matti; Lambrechts, Diether; Li, Jingmei; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mannermaa, Arto; Manoukian, Siranoush; Le Marchand, Loic; Margolin, Sara; Marme, Frederik; Matsuo, Keitaro; McLean, Catriona; Meindl, Alfons; Muir, Kenneth; Neuhausen, Susan L; Nevanlinna, Heli; Nord, Silje; Børresen-Dale, Anne-Lise; Olson, Janet E; Orr, Nick; van den Ouweland, Ans M W; Peterlongo, Paolo; Putti, Thomas Choudary; Rudolph, Anja; Sangrajrang, Suleeporn; Sawyer, Elinor J; Schmidt, Marjanka K; Schmutzler, Rita K; Shen, Chen-Yang; Hou, Ming-Feng; Shrubsole, Matha J; Southey, Melissa C; Swerdlow, Anthony; Teo, Soo Hwang; Thienpont, Bernard; Toland, Amanda E; Tollenaar, Robert A E M; Tomlinson, Ian; Truong, Therese; Tseng, Chiu-Chen; Wen, Wanqing; Winqvist, Robert; Wu, Anna H; Yip, Cheng Har; Zamora, Pilar M; Zheng, Ying; Floris, Giuseppe; Cheng, Ching-Yu; Hooning, Maartje J; Martens, John W M; Seynaeve, Caroline; Kristensen, Vessela N; Hall, Per; Pharoah, Paul D P; Simard, Jacques; Chenevix-Trench, Georgia; Dunning, Alison M; Antoniou, Antonis C; Easton, Douglas F; Cai, Qiuyin; Long, Jirong

2016-09-15

Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2)  = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry. © 2016 UICC.

An Automated Method for Identifying Artifact in Independent Component Analysis of Resting-State fMRI

PubMed Central

Bhaganagarapu, Kaushik; Jackson, Graeme D.; Abbott, David F.

2013-01-01

An enduring issue with data-driven analysis and filtering methods is the interpretation of results. To assist, we present an automatic method for identification of artifact in independent components (ICs) derived from functional MRI (fMRI). The method was designed with the following features: does not require temporal information about an fMRI paradigm; does not require the user to train the algorithm; requires only the fMRI images (additional acquisition of anatomical imaging not required); is able to identify a high proportion of artifact-related ICs without removing components that are likely to be of neuronal origin; can be applied to resting-state fMRI; is automated, requiring minimal or no human intervention. We applied the method to a MELODIC probabilistic ICA of resting-state functional connectivity data acquired in 50 healthy control subjects, and compared the results to a blinded expert manual classification. The method identified between 26 and 72% of the components as artifact (mean 55%). About 0.3% of components identified as artifact were discordant with the manual classification; retrospective examination of these ICs suggested the automated method had correctly identified these as artifact. We have developed an effective automated method which removes a substantial number of unwanted noisy components in ICA analyses of resting-state fMRI data. Source code of our implementation of the method is available. PMID:23847511

Identifying the impact of social determinants of health on disease rates using correlation analysis of area-based summary information.

PubMed

Song, Ruiguang; Hall, H Irene; Harrison, Kathleen McDavid; Sharpe, Tanya Telfair; Lin, Lillian S; Dean, Hazel D

2011-01-01

We developed a statistical tool that brings together standard, accessible, and well-understood analytic approaches and uses area-based information and other publicly available data to identify social determinants of health (SDH) that significantly affect the morbidity of a specific disease. We specified AIDS as the disease of interest and used data from the American Community Survey and the National HIV Surveillance System. Morbidity and socioeconomic variables in the two data systems were linked through geographic areas that can be identified in both systems. Correlation and partial correlation coefficients were used to measure the impact of socioeconomic factors on AIDS diagnosis rates in certain geographic areas. We developed an easily explained approach that can be used by a data analyst with access to publicly available datasets and standard statistical software to identify the impact of SDH. We found that the AIDS diagnosis rate was highly correlated with the distribution of race/ethnicity, population density, and marital status in an area. The impact of poverty, education level, and unemployment depended on other SDH variables. Area-based measures of socioeconomic variables can be used to identify risk factors associated with a disease of interest. When correlation analysis is used to identify risk factors, potential confounding from other variables must be taken into account.

[Poor self-esteem is correlated with suicide intent, independently from the severity of depression].

PubMed

Perrot, C; Vera, L; Gorwood, P

2018-04-01

Suicide is a major Public Health concern, and low self-esteem might represent a major risk factor. Our main objective was to assess the correlation between self-esteem and suicide intent. More specifically, we aimed to examine the relationship between the different dimensions of self-esteem (total, general, familial, professional and social) and suicide intent. We also sought the role of depression in the relationship of self-esteem to suicide intent. This retrospective cross-sectional study was conducted at a suicide prevention department at the CMME (Sainte-Anne Hospital, Paris, France). We included patients aged 15 and older and admitted for suicide attempt over a 3-year period from January 2008 to December 2010. Self-esteem was assessed with the Coopersmith's Self-Esteem Inventory (SEI) scale that takes into account several domains of self-esteem. Subjects scoring over 5 points on the lie scale were excluded. Our primary endpoint was the correlation between self-esteem and suicide intent. Our secondary endpoint was the same correlation adjusted for depression severity (using the Hamilton scale). Suicide intent was estimated using Beck's Suicide Intentionality Scale (SIS). We examined the Pearson's correlation coefficients between self-esteem and suicide intent. These analyses were adjusted for the severity of depressive symptoms assessed with the Hamilton Depression Rating Scale (17 items). Overall, 132 patients were included. Suicide intent was correlated with total self-esteem (r=-0.227, P=0.009), social self-esteem (r=-0.331, P<0.001) and familial self-esteem (r=-0.260, P=0.003). These results remained significant after adjusting for the level of depression for total score (r=-0.181, P=0.038), and the social (r=-0.282, P=0.001) and familial (r=-0.237, P=0.006) dimensions. Self-esteem (and especially social and familial dimensions) is likely to be associated with suicide intent, at least in part independently of the severity of depression, in a population

Multilevel Correlates of Childhood Physical Aggression and Prosocial Behavior

ERIC Educational Resources Information Center

Romano, Elisa; Tremblay, Richard E.; Boulerice, Bernard; Swisher, Raymond

2005-01-01

The study identified independent individual, family, and neighborhood correlates of children's physical aggression and prosocial behavior. Participants were 2,745-11-year olds nested in 1,982 families, which were themselves nested in 96 Canadian neighborhoods. Hierarchical linear modeling showed that the total variation explained by the…

Diffuse myogenin expression by immunohistochemistry is an independent marker of poor survival in pediatric rhabdomyosarcoma: a tissue microarray study of 71 primary tumors including correlation with molecular phenotype.

PubMed

Heerema-McKenney, Amy; Wijnaendts, Liliane C D; Pulliam, Joseph F; Lopez-Terrada, Dolores; McKenney, Jesse K; Zhu, Shirley; Montgomery, Kelli; Mitchell, Janet; Marinelli, Robert J; Hart, Augustinus A M; van de Rijn, Matt; Linn, Sabine C

2008-10-01

The pathologic classification of rhabdomyosarcoma (RMS) into embryonal or alveolar subtype is an important prognostic factor guiding the therapeutic protocol chosen for an individual patient. Unfortunately, this classification is not always straightforward, and the diagnostic criteria are controversial in a subset of cases. Ancillary studies are used to aid in the classification, but their potential use as independent prognostic factors is rarely studied. The aim of this study is to identify immunohistochemical markers of potential prognostic significance in pediatric RMS and to correlate their expression with PAX-3/FKHR and PAX-7/FKHR fusion status. A single tissue microarray containing 71 paraffin-embedded pediatric RMSs was immunostained with antibodies against p53, bcl-2, Ki-67, CD44, myogenin, and MyoD1. The tissue microarray and whole paraffin blocks were studied for PAX-3/FKHR and PAX-7/FKHR gene fusions by fluorescence in situ hybridization and reverse transcription-polymerase chain reaction. Clinical follow-up data were available for each patient. Immunohistochemical staining results and translocation status were correlated with recurrence-free interval (RFI) and overall survival (OS) using the Kaplan-Meier method, the log-rank test, and Cox proportional hazard regression. The minimum clinical follow-up interval was 24 months (median follow-up=57 mo). On univariable analysis, immunohistochemical expression of myogenin, bcl-2, and identification of a gene fusion were associated with decreased 5-year RFI and 10-year OS (myogenin RFI P=0.0028, OS P=0.0021; bcl-2 RFI P=0.037, OS P=0.032; gene fusion RFI P=0.0001, OS P=0.0058). After adjustment for Intergroup Rhabdomyosarcoma Study-TNM stage, tumor site, age, tumor histology, and translocation status by multivariable analysis, only myogenin retained an independent association with RFI (P=0.034) and OS (P=0.0069). In this retrospective analysis, diffuse immunohistochemical reactivity for myogenin in RMS

Self-Identified Goals of Adolescents With Cancer and Healthy Peers: Content, Appraisals, and Correlates

PubMed Central

Schwartz, Lisa A.; Parisi, Michelle L.

2013-01-01

Objective Compare the content, future orientation, and appraisals of self-identified goals of adolescents with cancer and control subjects. Identify correlates of health-related and future-oriented goals of adolescents with cancer. Methods Adolescents with cancer (n = 102) and control subjects (n = 97) self-identified goals, rated appraisals of goals, and completed psychosocial measures. Results Adolescents with cancer identified fewer goals, were more likely to identify a health-related goal, less likely to identify an intrapersonal or leisure goal, and rated their goals as more achievable and supported compared with control subjects. For adolescents with cancer, female gender predicted having a health-related goal. Additionally, age and parent-reported adolescent quality of life predicted having a future-oriented goal. 63 percent of adolescents with cancer reported establishing at least one goal because of cancer. Conclusions Despite similarities between groups, evidence supports that adolescents with cancer made changes to their repertoire of goals, suggesting the need to balance various priorities. PMID:23065108

A combined analysis of genetically correlated traits identifies 187 loci and a role for neurogenesis and myelination in intelligence.

PubMed

Hill, W D; Marioni, R E; Maghzian, O; Ritchie, S J; Hagenaars, S P; McIntosh, A M; Gale, C R; Davies, G; Deary, I J

2018-01-11

Intelligence, or general cognitive function, is phenotypically and genetically correlated with many traits, including a wide range of physical, and mental health variables. Education is strongly genetically correlated with intelligence (r g  = 0.70). We used these findings as foundations for our use of a novel approach-multi-trait analysis of genome-wide association studies (MTAG; Turley et al. 2017)-to combine two large genome-wide association studies (GWASs) of education and intelligence, increasing statistical power and resulting in the largest GWAS of intelligence yet reported. Our study had four goals: first, to facilitate the discovery of new genetic loci associated with intelligence; second, to add to our understanding of the biology of intelligence differences; third, to examine whether combining genetically correlated traits in this way produces results consistent with the primary phenotype of intelligence; and, finally, to test how well this new meta-analytic data sample on intelligence predicts phenotypic intelligence in an independent sample. By combining datasets using MTAG, our functional sample size increased from 199,242 participants to 248,482. We found 187 independent loci associated with intelligence, implicating 538 genes, using both SNP-based and gene-based GWAS. We found evidence that neurogenesis and myelination-as well as genes expressed in the synapse, and those involved in the regulation of the nervous system-may explain some of the biological differences in intelligence. The results of our combined analysis demonstrated the same pattern of genetic correlations as those from previous GWASs of intelligence, providing support for the meta-analysis of these genetically-related phenotypes.

Amyloid-independent functional neural correlates of episodic memory in amnestic mild cognitive impairment.

PubMed

Seo, Eun Hyun; Choo, I L Han

2016-06-01

Although amnestic mild cognitive impairment (aMCI) could have various biological characteristics, little attention has been given to the nature of episodic memory decline in aMCI with pathophysiologies other than Alzheimer's disease (AD), i.e., aMCI with low beta-amyloid (Aβ) burden. This study aimed to identify the functional neural basis of episodic memory impairment in aMCI with Aβ burden negative (aMCI-Aβ-) and to compare these results with aMCI with Aβ burden positive (aMCI-Aβ+). Individuals with aMCI (n = 498) were selected from the Alzheimer's Disease Neuroimaging Initiative database. Based on the mean florbetapir standard uptake value ratio, participants were classified as aMCI-Aβ- or aMCI-Aβ+. Correlations between memory scores and regional cerebral glucose metabolism (rCMglc) were analyzed separately for the two subgroups using a multiple regression model. For aMCI-Aβ-, significant positive correlations between memory and rCMglc were found in the bilateral claustrum, right thalamus, left anterior cingulate cortex, left insula, and right posterior cingulate. For aMCI-Aβ+, significant positive correlations between memory and rCMglc were found in the temporoparietal areas. These correlation patterns remained unchanged when clinical severity was added as a covariate Our findings indicate that memory impairment in aMCI-Aβ- is related to multimodal integrative processing and the attentional control system, whereas memory impairment in aMCI-Aβ+ is related to the typical brain memory systems and AD signature. These results suggest that although the two subgroups are clinically in the same category as aMCI, the memory impairment process depends on completely different functional brain regions according to their Aβ burden level.

Analytic uncertainty and sensitivity analysis of models with input correlations

NASA Astrophysics Data System (ADS)

Zhu, Yueying; Wang, Qiuping A.; Li, Wei; Cai, Xu

2018-03-01

Probabilistic uncertainty analysis is a common means of evaluating mathematical models. In mathematical modeling, the uncertainty in input variables is specified through distribution laws. Its contribution to the uncertainty in model response is usually analyzed by assuming that input variables are independent of each other. However, correlated parameters are often happened in practical applications. In the present paper, an analytic method is built for the uncertainty and sensitivity analysis of models in the presence of input correlations. With the method, it is straightforward to identify the importance of the independence and correlations of input variables in determining the model response. This allows one to decide whether or not the input correlations should be considered in practice. Numerical examples suggest the effectiveness and validation of our analytic method in the analysis of general models. A practical application of the method is also proposed to the uncertainty and sensitivity analysis of a deterministic HIV model.

An in-depth analysis identifies two new independent signals in 11q23.3 associated with vitiligo in the Chinese Han population.

PubMed

Zhao, Suli; Fang, Fang; Tang, Xianfa; Dou, Jinfa; Wang, Wenjun; Zheng, Xiaodong; Sun, Liangdan; Zhang, Anping

2017-10-01

Vitiligo is an autoimmune disease, characterized by progressive loss of skin pigmentation, which is caused by the interactions of multiple factors, such as heredity, immunity and environment. Recently, a single nucleotide polymorphism (SNP) rs638893 at 11q23.3 region was identified as a risk factor for vitiligo in genome-wide association studies and multiple SNPs in this region have been associated with other autoimmune diseases. This study aims to identify additional susceptibility variants associated with vitiligo at 11q23.3 in the Chinese Han population. We selected and genotyped 26 SNPs at 11q23.3 in an independent cohort including 2924 cases and 4048 controls using the Sequenom MassArray iPLEX ® system. Bonferroni adjustment was used for multiple comparisons and P value <1.92×10 -3 (0.05/26) was considered statistically significant. The A allele of rs613791 and G allele of rs523604 located in CXCR5 were observed to be significantly associated with vitiligo (OR=1.21, 95% CI: 1.11-1.31, P=1.20×10 -5 ; OR=1.14, 95% CI: 1.07-1.23, P=1.90×10 -4 , respectively). The C allele of rs638893 (a previously reported one) located upstream of DDX6 was also significantly associated with vitiligo (OR=1.25, 95% CI: 1.12-1.38, P=3.04×10 -5 ). The genotypes distribution of 3 SNPs also showed significant differences between case and control (rs613791: P=7.00×10 -6 , rs523604: P=4.00×10 -3 , rs638893: P=1.20×10 -5 , respectively). The two newly identified SNPs (rs613791 and rs523604) showed independent associations with vitiligo by linkage disequilibrium analysis and conditional logistic regression. The study identified two new independent signals in the associated locus 11q23.3 for vitiligo. The presence of multiple independent variants emphasizes an important role of this region in disease susceptibility. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

Search for Cross-Correlations of Ultrahigh-Energy Cosmic Rays with BL Lacertae Objects

NASA Astrophysics Data System (ADS)

Abbasi, R. U.; Abu-Zayyad, T.; Amann, J. F.; Archbold, G.; Belov, K.; Belz, J. W.; BenZvi, S.; Bergman, D. R.; Blake, S. A.; Boyer, J. H.; Burt, G. W.; Cao, Z.; Connolly, B. M.; Deng, W.; Fedorova, Y.; Findlay, J.; Finley, C. B.; Hanlon, W. F.; Hoffman, C. M.; Holzscheiter, M. H.; Hughes, G. A.; Hüntemeyer, P.; Jui, C. C. H.; Kim, K.; Kirn, M. A.; Knapp, B. C.; Loh, E. C.; Maestas, M. M.; Manago, N.; Mannel, E. J.; Marek, L. J.; Martens, K.; Matthews, J. A. J.; Matthews, J. N.; O'Neill, A.; Painter, C. A.; Perera, L.; Reil, K.; Riehle, R.; Roberts, M. D.; Rodriguez, D.; Sasaki, M.; Schnetzer, S. R.; Seman, M.; Sinnis, G.; Smith, J. D.; Snow, R.; Sokolsky, P.; Springer, R. W.; Stokes, B. T.; Thomas, J. R.; Thomas, S. B.; Thomson, G. B.; Tupa, D.; Westerhoff, S.; Wiencke, L. R.; Zech, A.; HIRES Collaboration

2006-01-01

Data taken in stereo mode by the High Resolution Fly's Eye (HiRes) air fluorescence experiment are analyzed to search for correlations between the arrival directions of ultrahigh-energy cosmic rays with the positions of BL Lacertae objects. Several previous claims of significant correlations between BL Lac objects and cosmic rays observed by other experiments are tested. These claims are not supported by the HiRes data. However, we verify a recent analysis of correlations between HiRes events and a subset of confirmed BL Lac objects from the 10th Veron Catalog, and we study this correlation in detail. Due to the a posteriori nature of the search, the significance level cannot be reliably estimated and the correlation must be tested independently before any claim can be made. We identify the precise hypotheses that will be tested with statistically independent data.

Correlational analysis for identifying genes whose regulation contributes to chronic neuropathic pain

PubMed Central

Persson, Anna-Karin; Gebauer, Mathias; Jordan, Suzana; Metz-Weidmann, Christiane; Schulte, Anke M; Schneider, Hans-Christoph; Ding-Pfennigdorff, Danping; Thun, Jonas; Xu, Xiao-Jun; Wiesenfeld-Hallin, Zsuzsanna; Darvasi, Ariel; Fried, Kaj; Devor, Marshall

2009-01-01

Background Nerve injury-triggered hyperexcitability in primary sensory neurons is considered a major source of chronic neuropathic pain. The hyperexcitability, in turn, is thought to be related to transcriptional switching in afferent cell somata. Analysis using expression microarrays has revealed that many genes are regulated in the dorsal root ganglion (DRG) following axotomy. But which contribute to pain phenotype versus other nerve injury-evoked processes such as nerve regeneration? Using the L5 spinal nerve ligation model of neuropathy we examined differential changes in gene expression in the L5 (and L4) DRGs in five mouse strains with contrasting susceptibility to neuropathic pain. We sought genes for which the degree of regulation correlates with strain-specific pain phenotype. Results In an initial experiment six candidate genes previously identified as important in pain physiology were selected for in situ hybridization to DRG sections. Among these, regulation of the Na+ channel α subunit Scn11a correlated with levels of spontaneous pain behavior, and regulation of the cool receptor Trpm8 correlated with heat hypersensibility. In a larger scale experiment, mRNA extracted from individual mouse DRGs was processed on Affymetrix whole-genome expression microarrays. Overall, 2552 ± 477 transcripts were significantly regulated in the axotomized L5DRG 3 days postoperatively. However, in only a small fraction of these was the degree of regulation correlated with pain behavior across strains. Very few genes in the "uninjured" L4DRG showed altered expression (24 ± 28). Conclusion Correlational analysis based on in situ hybridization provided evidence that differential regulation of Scn11a and Trpm8 contributes to across-strain variability in pain phenotype. This does not, of course, constitute evidence that the others are unrelated to pain. Correlational analysis based on microarray data yielded a larger "look-up table" of genes whose regulation likely

A simple method for identifying parameter correlations in partially observed linear dynamic models.

PubMed

Li, Pu; Vu, Quoc Dong

2015-12-14

Parameter estimation represents one of the most significant challenges in systems biology. This is because biological models commonly contain a large number of parameters among which there may be functional interrelationships, thus leading to the problem of non-identifiability. Although identifiability analysis has been extensively studied by analytical as well as numerical approaches, systematic methods for remedying practically non-identifiable models have rarely been investigated. We propose a simple method for identifying pairwise correlations and higher order interrelationships of parameters in partially observed linear dynamic models. This is made by derivation of the output sensitivity matrix and analysis of the linear dependencies of its columns. Consequently, analytical relations between the identifiability of the model parameters and the initial conditions as well as the input functions can be achieved. In the case of structural non-identifiability, identifiable combinations can be obtained by solving the resulting homogenous linear equations. In the case of practical non-identifiability, experiment conditions (i.e. initial condition and constant control signals) can be provided which are necessary for remedying the non-identifiability and unique parameter estimation. It is noted that the approach does not consider noisy data. In this way, the practical non-identifiability issue, which is popular for linear biological models, can be remedied. Several linear compartment models including an insulin receptor dynamics model are taken to illustrate the application of the proposed approach. Both structural and practical identifiability of partially observed linear dynamic models can be clarified by the proposed method. The result of this method provides important information for experimental design to remedy the practical non-identifiability if applicable. The derivation of the method is straightforward and thus the algorithm can be easily implemented into a

Identifying module biomarkers from gastric cancer by differential correlation network

PubMed Central

Liu, Xiaoping; Chang, Xiao

2016-01-01

Gastric cancer (stomach cancer) is a severe disease caused by dysregulation of many functionally correlated genes or pathways instead of the mutation of individual genes. Systematic identification of gastric cancer biomarkers can provide insights into the mechanisms underlying this deadly disease and help in the development of new drugs. In this paper, we present a novel network-based approach to predict module biomarkers of gastric cancer that can effectively distinguish the disease from normal samples. Specifically, by assuming that gastric cancer has mainly resulted from dysfunction of biomolecular networks rather than individual genes in an organism, the genes in the module biomarkers are potentially related to gastric cancer. Finally, we identified a module biomarker with 27 genes, and by comparing the module biomarker with known gastric cancer biomarkers, we found that our module biomarker exhibited a greater ability to diagnose the samples with gastric cancer. PMID:27703371

Single-leg squats identify independent stair negotiation ability in older adults referred for a physiotherapy mobility assessment at a rural hospital.

PubMed

Hockings, Rowena L; Schmidt, David D; Cheung, Christopher W

2013-07-01

To determine whether single-leg squats identify ability to negotiate stairs in older adults at a rural hospital. Cross-sectional analytical study. Acute wards and emergency department of a rural hospital in Australia. A systematic sample of 143 older adults (72 men, 71 women, 80.0 ± 6.8 years) from the emergency department or acute wards of Shoalhaven Hospital referred for a physiotherapy mobility assessment. Ability to complete up to three single-leg squats and negotiate up to three steps were measured. Covariates and demographic variables were collected. The squat test had 86% sensitivity, 100% specificity, 100% positive predictive value, and 49% negative predictive value in correctly identifying stair negotiation ability. Participants who could complete single-leg squats were 57 times more likely to be able to independently negotiate stairs than participants who could not complete squats. Multivariate regression analysis indicated that walker use, pain severity and whether participants lived alone were significant and independent predictors of ability to negotiate stairs independently. Single-leg squats may be an accurate identifier of stair negotiation ability in older adults admitted to the hospital for an acute illness or injury. A traditional stairs assessment would be required if older adults were unable to complete the squat test or had moderate to severe pain, used a walker to ambulate, or did not live alone. The squat test is a potentially more-efficient assessment tool than traditional stair assessments in determining an individual's ability to negotiate stairs and suitability for discharge where poor mobility is a problem. © 2013, Copyright the Authors Journal compilation © 2013, The American Geriatrics Society.

Rapid independent trait evolution despite a strong pleiotropic genetic correlation.

PubMed

Conner, Jeffrey K; Karoly, Keith; Stewart, Christy; Koelling, Vanessa A; Sahli, Heather F; Shaw, Frank H

2011-10-01

Genetic correlations are the most commonly studied of all potential constraints on adaptive evolution. We present a comprehensive test of constraints caused by genetic correlation, comparing empirical results to predictions from theory. The additive genetic correlation between the filament and the corolla tube in wild radish flowers is very high in magnitude, is estimated with good precision (0.85 ± 0.06), and is caused by pleiotropy. Thus, evolutionary changes in the relative lengths of these two traits should be constrained. Still, artificial selection produced rapid evolution of these traits in opposite directions, so that in one replicate relative to controls, the difference between them increased by six standard deviations in only nine generations. This would result in a 54% increase in relative fitness on the basis of a previous estimate of natural selection in this population, and it would produce the phenotypes found in the most extreme species in the family Brassicaceae in less than 100 generations. These responses were within theoretical expectations and were much slower than if the genetic correlation was zero; thus, there was evidence for constraint. These results, coupled with comparable results from other species, show that evolution can be rapid despite the constraints caused by genetic correlations.

Correlates of dietary behavior in adults: an umbrella review

PubMed Central

Kroeze, Willemieke; Kohl, Leonie F.M.; Bolten, Laura M.; Velema, Elizabeth; Kaspers, Pam; Kremers, Stef P.J.; Brug, Johannes

2015-01-01

Context: Multiple studies have been conducted on correlates of dietary behavior in adults, but a clear overview is currently lacking. Objective: An umbrella review, or review-of-reviews, was conducted to summarize and synthesize the scientific evidence on correlates and determinants of dietary behavior in adults. Data Sources: Eligible systematic reviews were identified in four databases: PubMed, PsycINFO, The Cochrane Library, and Web of Science. Only reviews published between January 1990 and May 2014 were included. Study Selection: Systematic reviews of observable food and dietary behavior that describe potential behavioral determinants of dietary behavior in adults were included. After independent selection of potentially relevant reviews by two authors, a total of 14 reviews were considered eligible. Data Extraction: For data extraction, the importance of determinants, the strength of the evidence, and the methodological quality of the eligible reviews were evaluated. Multiple observers conducted the data extraction independently. Data Synthesis: Social-cognitive determinants and environmental determinants (mainly the social-cultural environment) were included most often in the available reviews. Sedentary behavior and habit strength were consistently identified as important correlates of dietary behavior. Other correlates and potential determinants of dietary behavior, such as motivational regulation, shift work, and the political environment, have been studied in relatively few studies, but results are promising. Conclusions: The multitude of studies conducted on correlates of dietary behavior provides mixed, but sometimes quite convincing, evidence. However, because of the generally weak research design of the studies covered in the available reviews, the evidence for true determinants is suggestive, at best. PMID:26106126

Unexpected flood loss correlations across Europe

NASA Astrophysics Data System (ADS)

Booth, Naomi; Boyd, Jessica

2017-04-01

Floods don't observe country borders, as highlighted by major events across Europe that resulted in heavy economic and insured losses in 1999, 2002, 2009 and 2013. Flood loss correlations between some countries occur along multi-country river systems or between neighbouring nations affected by the same weather systems. However, correlations are not so obvious and whilst flooding in multiple locations across Europe may appear independent, for a re/insurer providing cover across the continent, these unexpected correlations can lead to high loss accumulations. A consistent, continental-scale method that allows quantification and comparison of losses, and identifies correlations in loss between European countries is therefore essential. A probabilistic model for European river flooding was developed that allows estimation of potential losses to pan-European property portfolios. By combining flood hazard and exposure information in a catastrophe modelling platform, we can consider correlations between river basins across Europe rather than being restricted to country boundaries. A key feature of the model is its statistical event set based on extreme value theory. Using historical river flow data, the event set captures spatial and temporal patterns of flooding across Europe and simulates thousands of events representing a full range of possible scenarios. Some known correlations were identified, such as between neighbouring Belgium and Luxembourg where 28% of events that affect either country produce a loss in both. However, our model identified some unexpected correlations including between Austria and Poland, and Poland and France, which are geographically distant. These correlations in flood loss may be missed by traditional methods and are key for re/insurers with risks in multiple countries. The model also identified that 46% of European river flood events affect more than one country. For more extreme events with a return period higher than 200 years, all events

Fine mapping in TERT-CLPTM1L region identified three independent lung cancer susceptibility signals: a large-scale multi-ethnic population study.

PubMed

Li, Zhihua; Fan, Jingyi; Li, Ni; Zhu, Meng; Zhang, Jiahui; Wang, Yuzhuo; Geng, Liguo; Cheng, Yang; Ma, Hongxia; Jin, Guangfu; Dai, Juncheng; Hu, Zhibin; Shen, Hongbing

2018-05-29

Genome-wide association studies (GWAS) and fine mapping studies have identified multiple lung cancer susceptibility variants in TERT-CLPTM1L region. However, it is still unclear about the relationship between these risk variants and the independent lung cancer risk signals in this region. Therefore, we evaluated the independent susceptibility signals for lung cancer and explored the potential functional variants in this region. Sequential conditional analysis was used to detect the independent susceptibility loci based on four lung cancer GWAS datasets with 12,843 lung cases and 12,639 controls. Comprehensively functional annotations were performed for each independent signal. Three independent susceptibility signals were identified in multi-ethnic population. For the first signal, rs2736100 showed the most significant association with lung cancer risk (C > A, OR = 0.82, 95%CI: 0.79-0.85, P = 1.98 × 10 -25 ). Rs36019446 was the top-ranked site (A > G, OR = 0.88, 95%CI: 0.84-0.92, P = 1.74 × 10 -9 ) in the second signal. For the third signal, rs326048 was the leading SNP (A > G, OR = 0.91, 95%CI: 0.87-0.95, P = 1.38 × 10 -5 ). The following subgroup analysis found the same three loci among Asian population. Further, we compared the difference between various subgroup populations. Functional annotations revealed that rs2736100, rs27996 (r 2  = 0.85 with rs36019446) and rs326049 (r 2  = 0.73 with rs326048) could be potential functional variants in these three risk signals, respectively. In conclusion, although multiple variants have been found associated with lung cancer risk in TERT-CLPTM1L region, our findings indicated that there are three independent lung cancer susceptibility signals in this region. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Failure criterion for materials with spatially correlated mechanical properties

NASA Astrophysics Data System (ADS)

Faillettaz, J.; Or, D.

2015-03-01

The role of spatially correlated mechanical elements in the failure behavior of heterogeneous materials represented by fiber bundle models (FBMs) was evaluated systematically for different load redistribution rules. Increasing the range of spatial correlation for FBMs with local load sharing is marked by a transition from ductilelike failure characteristics into brittlelike failure. The study identified a global failure criterion based on macroscopic properties (external load and cumulative damage) that is independent of spatial correlation or load redistribution rules. This general metric could be applied to assess the mechanical stability of complex and heterogeneous systems and thus provide an important component for early warning of a class of geophysical ruptures.

Hyperirisinemia is independently associated with subclinical hypothyroidism: correlations with cardiometabolic biomarkers and risk factors.

PubMed

Stratigou, Theodora; Dalamaga, Maria; Antonakos, Georgios; Marinou, Ioanna; Vogiatzakis, Evaggelos; Christodoulatos, Gerasimos Socrates; Karampela, Irene; Papavassiliou, Athanasios G

2018-02-17

Irisin, a newly discovered adipo-myokine, is implicated in the modulation of the adipose phenotype, increasing energy expenditure and ameliorating systemic metabolism. Our aim was to investigate circulating irisin in subclinical hypothyroidism (SH) and study its associations with cardiometabolic risk factors. In a large case-control study, serum irisin, insulin resistance and lipid parameters, classic adipokines, inflammatory and hepatic biomarkers, and cardiovascular risk factors were determined in 120 consecutive patients with SH and 120 healthy controls matched on age, gender, and date of blood draw. Sixteen patients with SH received L-T4 treatment and, after 6 months, serum irisin and other biomarkers were assessed. SH cases exhibited significantly higher circulating irisin than controls (p < 0.001). In all participants, irisin was positively associated with TSH, anti-TG, HOMA-IR, C-peptide, lipid and inflammatory biomarkers, leptin, and cardiovascular risk factors, including Framigham score and apolipoprotein B/apolipoprotein A-I. Irisin was negatively correlated with adiponectin, HDL-C, and thyroid hormones. Serum irisin was independently associated with SH, above and beyond body mass index and cardiometabolic factors (p = 0.02). TSH was an independent predictor of circulating irisin (p = 0.003). L-T4 therapy did not reverse considerably the hyperirisinemic status in treated SH patients (p = 0.09). Irisin may represent an adipo-myokine counterbalancing a potential, gradual deterioration of lipid metabolism and insulin sensitivity in SH as well as reflecting a protective compensatory mechanism against oxidative muscle and thyroid cell stress. More mechanistic and prospective studies shedding light on the pathogenetic role of irisin in SH are needed to confirm and extend these data.

DAPK1 as an independent prognostic marker in liver cancer.

PubMed

Li, Ling; Guo, Libin; Wang, Qingshui; Liu, Xiaolong; Zeng, Yongyi; Wen, Qing; Zhang, Shudong; Kwok, Hang Fai; Lin, Yao; Liu, Jingfeng

2017-01-01

The death-associated protein kinase 1 (DAPK1) can act as an oncogene or a tumor suppressor gene depending on the cellular context as well as external stimuli. Our study aims to investigate the prognostic significance of DAPK1 in liver cancer in both mRNA and protein levels. The mRNA expression of DAPK1 was extracted from the Gene Expression Omnibus database in three independent liver cancer datasets while protein expression of DAPK1 was detected by immunohistochemistry in our Chinese liver cancer patient cohort. The associations between DAPK1 expression and clinical characteristics were tested. DAPK1 mRNA expression was down-regulated in liver cancer. Low levels of DAPK1 mRNA were associated with shorter survival in a liver cancer patient cohort ( n  = 115;  p  = 0.041), while negative staining of DAPK1 protein was significantly correlated with shorter time to progression ( p  = 0.002) and overall survival ( p  = 0.02). DAPK1 was an independent prognostic marker for both time to progression and overall survival by multivariate analysis. Liver cancer with the b-catenin mutation has a lower DAPK1 expression, suggesting that DAPK1 may be regulated under the b-catenin pathway. In addition, we also identified genes that are co-regulated with DAPK1. DAPK1 expression was positively correlated with IRF2, IL7R, PCOLCE and ZBTB16, and negatively correlated with SLC16A3 in both liver cancer datasets. Among these genes, PCOLCE and ZBTB16 were significantly down-regulated, while SLC16A3 was significantly upregulated in liver cancer. By using connectivity mapping of these co-regulated genes, we have identified amcinonide and sulpiride as potential small molecules that could potentially reverse DAPK1/PCOLCE/ZBTB16/SLC16A3 expression. Our study demonstrated for the first time that both DAPK1 mRNA and protein expression levels are important prognostic markers in liver cancer, and have identified genes that may contribute to DAPK1-mediated liver carcinogenesis.

Applicant Characteristics Associated With Selection for Ranking at Independent Surgery Residency Programs.

PubMed

Dort, Jonathan M; Trickey, Amber W; Kallies, Kara J; Joshi, Amit R T; Sidwell, Richard A; Jarman, Benjamin T

2015-01-01

This study evaluated characteristics of applicants selected for interview and ranked by independent general surgery residency programs and assessed independent program application volumes, interview selection, rank list formation, and match success. Demographic and academic information was analyzed for 2014-2015 applicants. Applicant characteristics were compared by ranking status using univariate and multivariable statistical techniques. Characteristics independently associated with whether or not an applicant was ranked were identified using multivariable logistic regression modeling with backward stepwise variable selection and cluster-correlated robust variance estimates to account for correlations among individuals who applied to multiple programs. The Electronic Residency Application Service was used to obtain applicant data and program match outcomes at 33 independent surgery programs. All applicants selected to interview at 33 participating independent general surgery residency programs were included in the study. Applicants were 60% male with median age of 26 years. Birthplace was well distributed. Most applicants (73%) had ≥1 academic publication. Median United States Medical Licensing Exams (USMLE) Step 1 score was 228 (interquartile range: 218-240), and median USMLE Step 2 clinical knowledge score was 241 (interquartile range: 231-250). Residency programs in some regions more often ranked applicants who attended medical school within the same region. On multivariable analysis, significant predictors of ranking by an independent residency program were: USMLE scores, medical school region, and birth region. Independent programs received an average of 764 applications (range: 307-1704). On average, 12% interviews, and 81% of interviewed applicants were ranked. Most programs (84%) matched at least 1 applicant ranked in their top 10. Participating independent programs attract a large volume of applicants and have high standards in the selection process

Greater than the sum of its parts: single-nucleus sequencing identifies convergent evolution of independent EGFR mutants in GBM.

PubMed

Gini, Beatrice; Mischel, Paul S

2014-08-01

Single-cell sequencing approaches are needed to characterize the genomic diversity of complex tumors, shedding light on their evolutionary paths and potentially suggesting more effective therapies. In this issue of Cancer Discovery, Francis and colleagues develop a novel integrative approach to identify distinct tumor subpopulations based on joint detection of clonal and subclonal events from bulk tumor and single-nucleus whole-genome sequencing, allowing them to infer a subclonal architecture. Surprisingly, the authors identify convergent evolution of multiple, mutually exclusive, independent EGFR gain-of-function variants in a single tumor. This study demonstrates the value of integrative single-cell genomics and highlights the biologic primacy of EGFR as an actionable target in glioblastoma. ©2014 American Association for Cancer Research.

Application of wide selected-ion monitoring data-independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor

USDA-ARS?s Scientific Manuscript database

We describe here the use of label-free wide selected-ion monitoring data-independent acquisition (WiSIM-DIA) to identify proteins that are involved in the formation of tomato (Solanum lycopersicum) fruit cuticles and that are regulated by the transcription factor CUTIN DEFICIENT2 (CD2). A spectral l...

From micro-correlations to macro-correlations

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

Eliazar, Iddo, E-mail: iddo.eliazar@intel.com

2016-11-15

Random vectors with a symmetric correlation structure share a common value of pair-wise correlation between their different components. The symmetric correlation structure appears in a multitude of settings, e.g. mixture models. In a mixture model the components of the random vector are drawn independently from a general probability distribution that is determined by an underlying parameter, and the parameter itself is randomized. In this paper we study the overall correlation of high-dimensional random vectors with a symmetric correlation structure. Considering such a random vector, and terming its pair-wise correlation “micro-correlation”, we use an asymptotic analysis to derive the random vector’smore » “macro-correlation” : a score that takes values in the unit interval, and that quantifies the random vector’s overall correlation. The method of obtaining macro-correlations from micro-correlations is then applied to a diverse collection of frameworks that demonstrate the method’s wide applicability.« less

Identifying compromised systems through correlation of suspicious traffic from malware behavioral analysis

NASA Astrophysics Data System (ADS)

Camilo, Ana E. F.; Grégio, André; Santos, Rafael D. C.

2016-05-01

Malware detection may be accomplished through the analysis of their infection behavior. To do so, dynamic analysis systems run malware samples and extract their operating system activities and network traffic. This traffic may represent malware accessing external systems, either to steal sensitive data from victims or to fetch other malicious artifacts (configuration files, additional modules, commands). In this work, we propose the use of visualization as a tool to identify compromised systems based on correlating malware communications in the form of graphs and finding isomorphisms between them. We produced graphs from over 6 thousand distinct network traffic files captured during malware execution and analyzed the existing relationships among malware samples and IP addresses.

Statistical Analyses of Scatterplots to Identify Important Factors in Large-Scale Simulations

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

Kleijnen, J.P.C.; Helton, J.C.

1999-04-01

The robustness of procedures for identifying patterns in scatterplots generated in Monte Carlo sensitivity analyses is investigated. These procedures are based on attempts to detect increasingly complex patterns in the scatterplots under consideration and involve the identification of (1) linear relationships with correlation coefficients, (2) monotonic relationships with rank correlation coefficients, (3) trends in central tendency as defined by means, medians and the Kruskal-Wallis statistic, (4) trends in variability as defined by variances and interquartile ranges, and (5) deviations from randomness as defined by the chi-square statistic. The following two topics related to the robustness of these procedures are consideredmore » for a sequence of example analyses with a large model for two-phase fluid flow: the presence of Type I and Type II errors, and the stability of results obtained with independent Latin hypercube samples. Observations from analysis include: (1) Type I errors are unavoidable, (2) Type II errors can occur when inappropriate analysis procedures are used, (3) physical explanations should always be sought for why statistical procedures identify variables as being important, and (4) the identification of important variables tends to be stable for independent Latin hypercube samples.« less

Energy normalization of TV viewed optical correlation (automated correlation plane analyzer for an optical processor)

NASA Technical Reports Server (NTRS)

Grumet, A.

1981-01-01

An automatic correlation plane processor that can rapidly acquire, identify, and locate the autocorrelation outputs of a bank of multiple optical matched filters is described. The read-only memory (ROM) stored digital silhouette of each image associated with each matched filter allows TV video to be used to collect image energy to provide accurate normalization of autocorrelations. The resulting normalized autocorrelations are independent of the illumination of the matched input. Deviation from unity of a normalized correlation can be used as a confidence measure of correct image identification. Analog preprocessing circuits permit digital conversion and random access memory (RAM) storage of those video signals with the correct amplitude, pulse width, rising slope, and falling slope. TV synchronized addressing of 3 RAMs permits on-line storage of: (1) the maximum unnormalized amplitude, (2) the image x location, and (3) the image y location of the output of each of up to 99 matched filters. A fourth RAM stores all normalized correlations. A normalization approach, normalization for cross correlations, a system's description with block diagrams, and system's applications are discussed.

Sustained State-Independent Quantum Contextual Correlations from a Single Ion

NASA Astrophysics Data System (ADS)

Leupold, F. M.; Malinowski, M.; Zhang, C.; Negnevitsky, V.; Alonso, J.; Home, J. P.; Cabello, A.

2018-05-01

We use a single trapped-ion qutrit to demonstrate the quantum-state-independent violation of noncontextuality inequalities using a sequence of randomly chosen quantum nondemolition projective measurements. We concatenate 53 ×106 sequential measurements of 13 observables, and unambiguously violate an optimal noncontextual bound. We use the same data set to characterize imperfections including signaling and repeatability of the measurements. The experimental sequence was generated in real time with a quantum random number generator integrated into our control system to select the subsequent observable with a latency below 50 μ s , which can be used to constrain contextual hidden-variable models that might describe our results. The state-recycling experimental procedure is resilient to noise and independent of the qutrit state, substantiating the fact that the contextual nature of quantum physics is connected to measurements and not necessarily to designated states. The use of extended sequences of quantum nondemolition measurements finds applications in the fields of sensing and quantum information.

Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.

PubMed

Misic, Ana M; Miedel, Emily L; Brice, Angela K; Cole, Stephen; Zhang, Grace F; Dyer, Cecilia D; Secreto, Anthony; Smith, Abigail L; Danet-Desnoyers, Gwenn; Beiting, Daniel P

2018-06-13

Immunocompromised mice are used frequently in biomedical research, in part because they accommodate the engraftmentandstudy of primary human cells within a mouse model; however, these animals are susceptible to opportunistic infectionsand require special husbandry considerations. In 2015, an outbreak marked by high morbidity but low mortality swept througha colony of immunocompromised mice; this outbreak rapidly affected 75% of the colony and ultimately required completedepopulation of the barrier suite. Conventional microbiologic and molecular diagnostics were unsuccessful in determiningthe cause; therefore, we explored culture-independent methods to broadly profile the microbial community in the feces of affected animals. This approach identified 4 bacterial taxa-Candidatus Arthromitus, Clostridium celatum, Clostridiales bacterium VE202-01, and Bifidobacterium pseudolongum strain PV8-2- that were significantly enriched in the affected mice. Based on these results, specific changes were made to the animal husbandry procedures for immunocompromised mice. This case report highlights the utility of culture-independent methods in laboratory animal diagnostics.

Independent Orbiter Assessment (IOA): Analysis of the instrumentation subsystem

NASA Technical Reports Server (NTRS)

Howard, B. S.

1986-01-01

The results of the Independent Orbiter Assessment (IOA) of the Failure Modes and Effects Analysis (FMEA) and Critical Items List (CIL) are presented. The IOA approach features a top-down analysis of the hardware to determine failure modes, criticality, and potential critical items. To preserve independence, this analysis was accomplished without reliance upon the results contained within the NASA FMEA/CIL documentation. The independent analysis results for the Instrumentation Subsystem are documented. The Instrumentation Subsystem (SS) consists of transducers, signal conditioning equipment, pulse code modulation (PCM) encoding equipment, tape recorders, frequency division multiplexers, and timing equipment. For this analysis, the SS is broken into two major groupings: Operational Instrumentation (OI) equipment and Modular Auxiliary Data System (MADS) equipment. The OI equipment is required to acquire, condition, scale, digitize, interleave/multiplex, format, and distribute operational Orbiter and payload data and voice for display, recording, telemetry, and checkout. It also must provide accurate timing for time critical functions for crew and payload specialist use. The MADS provides additional instrumentation to measure and record selected pressure, temperature, strain, vibration, and event data for post-flight playback and analysis. MADS data is used to assess vehicle responses to the flight environment and to permit correlation of such data from flight to flight. The IOA analysis utilized available SS hardware drawings and schematics for identifying hardware assemblies and components and their interfaces. Criticality for each item was assigned on the basis of the worst-case effect of the failure modes identified.

Correlates of meeting the combined and independent aerobic and strength exercise guidelines in hematologic cancer survivors.

PubMed

Vallerand, James R; Rhodes, Ryan E; Walker, Gordon J; Courneya, Kerry S

2017-03-28

Most previous research on the correlates of physical activity has examined the aerobic or strength exercise guidelines separately. Such an approach does not allow an examination of the correlates of meeting the combined guidelines versus a single guideline, or one guideline versus the other. Here, we report the prevalence and correlates of meeting the combined and independent exercise guidelines in hematologic cancer survivors (HCS). In a population-based, cross-sectional survey of 606 HCS from Alberta, Canada using a mailed questionnaire, we obtained separate assessments of aerobic and strength exercise behaviors, as well as separate assessments for motivations, regulations, and reflective processes using the multi-process action control framework (M-PAC). Overall, 22% of HCS met the combined exercise guideline, 22% met aerobic-only, 10% met strength-only, and 46% met neither exercise guideline. HCS were more likely to meet the combined guideline over the aerobic-only guideline if they had no children living at home, and over both the aerobic and strength-only guidelines if they had completed university. As hypothesized, those meeting the combined guideline also had a more favorable strength-specific M-PAC profile (i.e., motivations, regulations, and reflective processes) than those meeting the aerobic-only guideline, and a more favorable aerobic-specific M-PAC profile than those meeting the strength-only guideline. Interestingly and unexpectedly, HCS meeting the combined guidelines also reported significantly greater aerobic-specific perceived control, planning, and obligation/regret than those meeting the aerobic-only guideline, and greater strength-specific perceived control, planning, and obligation/regret than those meeting the strength-only guideline. Few HCS are meeting the combined exercise guidelines. M-PAC based variables are strong correlates of meeting the combined guidelines compared to aerobic or strength only guidelines. Strategies to help HCS meet

Analysis of Culture-Dependent versus Culture-Independent Techniques for Identification of Bacteria in Clinically Obtained Bronchoalveolar Lavage Fluid

PubMed Central

Dickson, Robert P.; Erb-Downward, John R.; Prescott, Hallie C.; Martinez, Fernando J.; Curtis, Jeffrey L.; Lama, Vibha N.

2014-01-01

The diagnosis and management of pneumonia are limited by the use of culture-based techniques of microbial identification, which may fail to identify unculturable, fastidious, and metabolically active viable but unculturable bacteria. Novel high-throughput culture-independent techniques hold promise but have not been systematically compared to conventional culture. We analyzed 46 clinically obtained bronchoalveolar lavage (BAL) fluid specimens from symptomatic and asymptomatic lung transplant recipients both by culture (using a clinical microbiology laboratory protocol) and by bacterial 16S rRNA gene pyrosequencing. Bacteria were identified in 44 of 46 (95.7%) BAL fluid specimens by culture-independent sequencing, significantly more than the number of specimens in which bacteria were detected (37 of 46, 80.4%, P ≤ 0.05) or “pathogen” species reported (18 of 46, 39.1%, P ≤ 0.0001) via culture. Identification of bacteria by culture was positively associated with culture-independent indices of infection (total bacterial DNA burden and low bacterial community diversity) (P ≤ 0.01). In BAL fluid specimens with no culture growth, the amount of bacterial DNA was greater than that in reagent and rinse controls, and communities were markedly dominated by select Gammaproteobacteria, notably Escherichia species and Pseudomonas fluorescens. Culture growth above the threshold of 104 CFU/ml was correlated with increased bacterial DNA burden (P < 0.01), decreased community diversity (P < 0.05), and increased relative abundance of Pseudomonas aeruginosa (P < 0.001). We present two case studies in which culture-independent techniques identified a respiratory pathogen missed by culture and clarified whether a cultured “oral flora” species represented a state of acute infection. In summary, we found that bacterial culture of BAL fluid is largely effective in discriminating acute infection from its absence and identified some specific limitations of BAL fluid culture in

Analysis of culture-dependent versus culture-independent techniques for identification of bacteria in clinically obtained bronchoalveolar lavage fluid.

PubMed

Dickson, Robert P; Erb-Downward, John R; Prescott, Hallie C; Martinez, Fernando J; Curtis, Jeffrey L; Lama, Vibha N; Huffnagle, Gary B

2014-10-01

The diagnosis and management of pneumonia are limited by the use of culture-based techniques of microbial identification, which may fail to identify unculturable, fastidious, and metabolically active viable but unculturable bacteria. Novel high-throughput culture-independent techniques hold promise but have not been systematically compared to conventional culture. We analyzed 46 clinically obtained bronchoalveolar lavage (BAL) fluid specimens from symptomatic and asymptomatic lung transplant recipients both by culture (using a clinical microbiology laboratory protocol) and by bacterial 16S rRNA gene pyrosequencing. Bacteria were identified in 44 of 46 (95.7%) BAL fluid specimens by culture-independent sequencing, significantly more than the number of specimens in which bacteria were detected (37 of 46, 80.4%, P ≤ 0.05) or "pathogen" species reported (18 of 46, 39.1%, P ≤ 0.0001) via culture. Identification of bacteria by culture was positively associated with culture-independent indices of infection (total bacterial DNA burden and low bacterial community diversity) (P ≤ 0.01). In BAL fluid specimens with no culture growth, the amount of bacterial DNA was greater than that in reagent and rinse controls, and communities were markedly dominated by select Gammaproteobacteria, notably Escherichia species and Pseudomonas fluorescens. Culture growth above the threshold of 10(4) CFU/ml was correlated with increased bacterial DNA burden (P < 0.01), decreased community diversity (P < 0.05), and increased relative abundance of Pseudomonas aeruginosa (P < 0.001). We present two case studies in which culture-independent techniques identified a respiratory pathogen missed by culture and clarified whether a cultured "oral flora" species represented a state of acute infection. In summary, we found that bacterial culture of BAL fluid is largely effective in discriminating acute infection from its absence and identified some specific limitations of BAL fluid culture in the

Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome.

PubMed

Morine, Melissa J; McMonagle, Jolene; Toomey, Sinead; Reynolds, Clare M; Moloney, Aidan P; Gormley, Isobel C; Gaora, Peadar O; Roche, Helen M

2010-10-07

constituent genes, as well as strong correlations between gene expression and plasma markers of metabolic syndrome independent of the dietary effect. Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of analysis has the potential to generate novel transcriptome-based biomarkers of disease.

Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome

PubMed Central

2010-01-01

-sensitive changes in constituent genes, as well as strong correlations between gene expression and plasma markers of metabolic syndrome independent of the dietary effect. Conclusion Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of analysis has the potential to generate novel transcriptome-based biomarkers of disease. PMID:20929581

Genome-wide analysis in UK Biobank identifies four loci associated with mood instability and genetic correlation with major depressive disorder, anxiety disorder and schizophrenia.

PubMed

Ward, Joey; Strawbridge, Rona J; Bailey, Mark E S; Graham, Nicholas; Ferguson, Amy; Lyall, Donald M; Cullen, Breda; Pidgeon, Laura M; Cavanagh, Jonathan; Mackay, Daniel F; Pell, Jill P; O'Donovan, Michael; Escott-Price, Valentina; Smith, Daniel J

2017-11-30

Mood instability is a core clinical feature of affective and psychotic disorders. In keeping with the Research Domain Criteria approach, it may be a useful construct for identifying biology that cuts across psychiatric categories. We aimed to investigate the biological validity of a simple measure of mood instability and evaluate its genetic relationship with several psychiatric disorders, including major depressive disorder (MDD), bipolar disorder (BD), schizophrenia, attention deficit hyperactivity disorder (ADHD), anxiety disorder and post-traumatic stress disorder (PTSD). We conducted a genome-wide association study (GWAS) of mood instability in 53,525 cases and 60,443 controls from UK Biobank, identifying four independently associated loci (on chromosomes 8, 9, 14 and 18), and a common single-nucleotide polymorphism (SNP)-based heritability estimate of ~8%. We found a strong genetic correlation between mood instability and MDD (r g  = 0.60, SE = 0.07, p = 8.95 × 10 -17 ) and a small but significant genetic correlation with both schizophrenia (r g  = 0.11, SE = 0.04, p = 0.01) and anxiety disorders (r g  = 0.28, SE = 0.14, p = 0.04), although no genetic correlation with BD, ADHD or PTSD was observed. Several genes at the associated loci may have a role in mood instability, including the DCC netrin 1 receptor (DCC) gene, eukaryotic translation initiation factor 2B subunit beta (eIF2B2), placental growth factor (PGF) and protein tyrosine phosphatase, receptor type D (PTPRD). Strengths of this study include the very large sample size, but our measure of mood instability may be limited by the use of a single question. Overall, this work suggests a polygenic basis for mood instability. This simple measure can be obtained in very large samples; our findings suggest that doing so may offer the opportunity to illuminate the fundamental biology of mood regulation.

Device-independent point estimation from finite data and its application to device-independent property estimation

NASA Astrophysics Data System (ADS)

Lin, Pei-Sheng; Rosset, Denis; Zhang, Yanbao; Bancal, Jean-Daniel; Liang, Yeong-Cherng

2018-03-01

The device-independent approach to physics is one where conclusions are drawn directly from the observed correlations between measurement outcomes. In quantum information, this approach allows one to make strong statements about the properties of the underlying systems or devices solely via the observation of Bell-inequality-violating correlations. However, since one can only perform a finite number of experimental trials, statistical fluctuations necessarily accompany any estimation of these correlations. Consequently, an important gap remains between the many theoretical tools developed for the asymptotic scenario and the experimentally obtained raw data. In particular, a physical and concurrently practical way to estimate the underlying quantum distribution has so far remained elusive. Here, we show that the natural analogs of the maximum-likelihood estimation technique and the least-square-error estimation technique in the device-independent context result in point estimates of the true distribution that are physical, unique, computationally tractable, and consistent. They thus serve as sound algorithmic tools allowing one to bridge the aforementioned gap. As an application, we demonstrate how such estimates of the underlying quantum distribution can be used to provide, in certain cases, trustworthy estimates of the amount of entanglement present in the measured system. In stark contrast to existing approaches to device-independent parameter estimations, our estimation does not require the prior knowledge of any Bell inequality tailored for the specific property and the specific distribution of interest.

SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data.

PubMed

Li, Jun; Roebuck, Paul; Grünewald, Stefan; Liang, Han

2012-07-01

An important task in biomedical research is identifying biomarkers that correlate with patient clinical data, and these biomarkers then provide a critical foundation for the diagnosis and treatment of disease. Conventionally, such an analysis is based on individual genes, but the results are often noisy and difficult to interpret. Using a biological network as the searching platform, network-based biomarkers are expected to be more robust and provide deep insights into the molecular mechanisms of disease. We have developed a novel bioinformatics web server for identifying network-based biomarkers that most correlate with patient survival data, SurvNet. The web server takes three input files: one biological network file, representing a gene regulatory or protein interaction network; one molecular profiling file, containing any type of gene- or protein-centred high-throughput biological data (e.g. microarray expression data or DNA methylation data); and one patient survival data file (e.g. patients' progression-free survival data). Given user-defined parameters, SurvNet will automatically search for subnetworks that most correlate with the observed patient survival data. As the output, SurvNet will generate a list of network biomarkers and display them through a user-friendly interface. SurvNet can be accessed at http://bioinformatics.mdanderson.org/main/SurvNet.

Projection correlation between two random vectors.

PubMed

Zhu, Liping; Xu, Kai; Li, Runze; Zhong, Wei

2017-12-01

We propose the use of projection correlation to characterize dependence between two random vectors. Projection correlation has several appealing properties. It equals zero if and only if the two random vectors are independent, it is not sensitive to the dimensions of the two random vectors, it is invariant with respect to the group of orthogonal transformations, and its estimation is free of tuning parameters and does not require moment conditions on the random vectors. We show that the sample estimate of the projection correction is [Formula: see text]-consistent if the two random vectors are independent and root-[Formula: see text]-consistent otherwise. Monte Carlo simulation studies indicate that the projection correlation has higher power than the distance correlation and the ranks of distances in tests of independence, especially when the dimensions are relatively large or the moment conditions required by the distance correlation are violated.

Endothelial dysfunction in patients with obstructive sleep apnoea independent of metabolic syndrome.

PubMed

Amra, Babak; Karbasi, Elaheh; Hashemi, Mohammad; Hoffmann-Castendiek, Birgit; Golshan, Mohammad

2009-05-01

Obstructive sleep apnoea syndrome (OSAS), characterised by intermittent hypoxia/re-oxygenation, has been identified as an independent risk factor for cardiovascular diseases and endothelial dysfunction. Our aim was to investigate flow-mediated dilatation (FMD) in patients with obstructive sleep apnoea with and without metabolic syndrome. Fifty-two subjects with OSAS diagnosed by polysomnography were classified into 2 groups according to the presence and absence of the metabolic syndrome and also according to the severity: mild to moderate OSAS group and severe OSAS group. Endothelial function of the brachial artery was evaluated by using high-resolution vascular ultrasound. Endothelial-dependent dilatation (EDD) was assessed by establishing reactive hyperaemia and endothelial-independent dilatation (EID) was determined by using sublingual isosorbide dinitrate. Spearman correlation and regression analysis were performed. EDD was not significantly different in patients with OSAS and metabolic syndrome as compared with OSAS without metabolic syndrome (4.62 +/- 0.69 versus 4.49 +/- 0.93, P >0.05). Endothelial dysfunction in OSA may be independent of metabolic syndrome.

Fuzzy inference enhanced information recovery from digital PIV using cross-correlation combined with particle tracking

NASA Technical Reports Server (NTRS)

Wernet, Mark P.

1995-01-01

Particle Image Velocimetry provides a means of measuring the instantaneous 2-component velocity field across a planar region of a seeded flowfield. In this work only two camera, single exposure images are considered where both cameras have the same view of the illumination plane. Two competing techniques which yield unambiguous velocity vector direction information have been widely used for reducing the single exposure, multiple image data: cross-correlation and particle tracking. Correlation techniques yield averaged velocity estimates over subregions of the flow, whereas particle tracking techniques give individual particle velocity estimates. The correlation technique requires identification of the correlation peak on the correlation plane corresponding to the average displacement of particles across the subregion. Noise on the images and particle dropout contribute to spurious peaks on the correlation plane, leading to misidentification of the true correlation peak. The subsequent velocity vector maps contain spurious vectors where the displacement peaks have been improperly identified. Typically these spurious vectors are replaced by a weighted average of the neighboring vectors, thereby decreasing the independence of the measurements. In this work fuzzy logic techniques are used to determine the true correlation displacement peak even when it is not the maximum peak on the correlation plane, hence maximizing the information recovery from the correlation operation, maintaining the number of independent measurements and minimizing the number of spurious velocity vectors. Correlation peaks are correctly identified in both high and low seed density cases. The correlation velocity vector map can then be used as a guide for the particle tracking operation. Again fuzzy logic techniques are used, this time to identify the correct particle image pairings between exposures to determine particle displacements, and thus velocity. The advantage of this technique is the

Identifying Dental Anxiety in Children's Drawings and correlating It with Frankl's Behavior Rating Scale.

PubMed

Mathur, Jyoti; Diwanji, Amish; Sarvaiya, Bhumi; Sharma, Dipal

2017-01-01

To develop a simple method to assess the level of anxiety by using children's drawings and correlating them with Frankl's behavior rating scale. A total of 178 patients aged of 3 to 14 years were handed out two-page forms which contained three sections on coloring and drawing, along with general information, and Frankl's behavior rating scale for the visit. The three types of drawing exercises given to the patients were geometric copy drawings, coloring a nonthreatening figure, and an empty sheet for freehand drawing. Out of 178 patients, 60 showed definitely positive behavior, 73 exhibited positive behavior, 37 showed negative behavior, and 8 were definitely negative on Frankl's behavior rating scale; 133 children had none or, 1 stress marker and 45 exhibited 2 or 3 stress markers in their drawings. Chi-square (χ 2 ) analysis was done with a 2 × 2 contingency table. Observed χ 2 value was 46.166, which at 1 degree of freedom was much greater than that at 0.995 percentile. Therefore, the result was highly significant. Children requiring specialized behavioral techniques can be identified by the presence of stress markers in their drawings. This nonverbal activity by itself can have an overall positive effect on the behavior displayed in the dental clinic. Mathur J, Diwanji A, Sarvaiya B, Sharma D. Identifying Dental Anxiety in Children's Drawings and correlating It with Frankl's Behavior Rating Scale. Int J Clin Pediatr Dent 2017;10(1):24-28.

Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach.

PubMed

Núñez-Vivanco, Gabriel; Valdés-Jiménez, Alejandro; Besoaín, Felipe; Reyes-Parada, Miguel

2016-01-01

Since the structure of proteins is more conserved than the sequence, the identification of conserved three-dimensional (3D) patterns among a set of proteins, can be important for protein function prediction, protein clustering, drug discovery and the establishment of evolutionary relationships. Thus, several computational applications to identify, describe and compare 3D patterns (or motifs) have been developed. Often, these tools consider a 3D pattern as that described by the residues surrounding co-crystallized/docked ligands available from X-ray crystal structures or homology models. Nevertheless, many of the protein structures stored in public databases do not provide information about the location and characteristics of ligand binding sites and/or other important 3D patterns such as allosteric sites, enzyme-cofactor interaction motifs, etc. This makes necessary the development of new ligand-independent methods to search and compare 3D patterns in all available protein structures. Here we introduce Geomfinder, an intuitive, flexible, alignment-free and ligand-independent web server for detailed estimation of similarities between all pairs of 3D patterns detected in any two given protein structures. We used around 1100 protein structures to form pairs of proteins which were assessed with Geomfinder. In these analyses each protein was considered in only one pair (e.g. in a subset of 100 different proteins, 50 pairs of proteins can be defined). Thus: (a) Geomfinder detected identical pairs of 3D patterns in a series of monoamine oxidase-B structures, which corresponded to the effectively similar ligand binding sites at these proteins; (b) we identified structural similarities among pairs of protein structures which are targets of compounds such as acarbose, benzamidine, adenosine triphosphate and pyridoxal phosphate; these similar 3D patterns are not detected using sequence-based methods; (c) the detailed evaluation of three specific cases showed the versatility

Identifying Key Networks Linked to Light-Independent Photoreceptor Degeneration in Visual Arrestin 1 Knockout Mice.

PubMed

Kim, Hwa Sun; Huang, Shun-Ping; Lee, Eun-Jin; Craft, Cheryl Mae

2018-01-01

When visual arrestin 1 (ARR1, S-antigen, 48 KDa protein) was genetically knocked out in mice (original Arr1 -/- , designated Arr1 -/-A ), rod photoreceptors degenerated in a light-dependent manner. Subsequently, a light-independent cone dystrophy was identified with minimal rod death in ARR1 knockout mice (Arr1 -/-A Arr4 +/+ , designated Arr1 -/-B ), which were F2 littermates from breeding the original Arr1 -/-A and cone arrestin knockout 4 (Arr4 -/- ) mice. To resolve the genetic and phenotypic differences between the two ARR1 knockouts, we performed Affymetrix™ exon array analysis to focus on the potential differential gene expression profile and to explore the molecular and cellular pathways leading to this observed susceptibility to cone dystrophy in Arr1 -/-B compared to Arr1 -/-A or control Arr1 +/+ Arr4 +/+ (wild type [WT]). Only in the Arr1 -/-B retina did we observe an up-regulation of retinal transcripts involved in the immune response, inflammatory response and JAK-STAT signaling molecules, OSMRβ and phosphorylation of STAT3. Of these responses, the complement system was significantly higher, and a variety of inflammatory responses by complement regulation and anti-inflammatory cytokine or factors were identified in Arr1 -/-B retinal transcripts. This discovery supports that Arr1 -/-B has a distinct genetic background from Arr1 -/-A that results in alterations in its retinal phenotype leading to susceptibility to cone degeneration induced by inappropriate inflammatory and immune responses.

Identifying the Correlates and Barriers of Future Planning among Parents of Individuals with Intellectual and Developmental Disabilities

ERIC Educational Resources Information Center

Burke, Meghan; Arnold, Catherine; Owen, Aleksa

2018-01-01

Although individuals with intellectual and developmental disabilities (IDD) are living longer lives, fewer than half of parents of individuals with IDD conduct future planning. The correlates and barriers to future planning must be identified to develop targeted interventions to facilitate future planning. In this study, 388 parents of individuals…

Identifying the Critical Links in Road Transportation Networks: Centrality-based approach utilizing structural properties

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

Chinthavali, Supriya

Surface transportation road networks share structural properties similar to other complex networks (e.g., social networks, information networks, biological networks, and so on). This research investigates the structural properties of road networks for any possible correlation with the traffic characteristics such as link flows those determined independently. Additionally, we define a criticality index for the links of the road network that identifies the relative importance in the network. We tested our hypotheses with two sample road networks. Results show that, correlation exists between the link flows and centrality measures of a link of the road (dual graph approach is followed) andmore » the criticality index is found to be effective for one test network to identify the vulnerable nodes.« less

Correlation between electrical conductivity and apparent diffusion coefficient in breast cancer: effect of necrosis on magnetic resonance imaging.

PubMed

Kim, Soo-Yeon; Shin, Jaewook; Kim, Dong-Hyun; Kim, Eun-Kyung; Moon, Hee Jung; Yoon, Jung Hyun; You, Jai Kyung; Kim, Min Jung

2018-03-06

To investigate the correlation between conductivity and ADC in invasive ductal carcinoma according to the presence of necrosis on MRI. Eighty-one women with invasive ductal carcinoma ≥1 cm on T2-weighted fast spin echo sequence of preoperative MRI were included. Phase-based MR electric properties tomography was used to reconstruct conductivity. Mean ADC was measured. Necrosis was defined as an area with very high T2 signal intensity. The relationship between conductivity and ADC was examined using Spearman's correlation coefficient (r). Multiple linear regression analysis was performed to identify factors associated with conductivity or ADC. In the total group, conductivity showed negative correlation with ADC (r = -0.357, p = 0.001). This correlation was maintained in the subgroup without necrosis (n = 53, r = -0.455, p = 0.001), but not in the subgroup with necrosis (n = 28, r = -0.080, p = 0.687). The correlation between the two parameters was different according to necrosis (r = -0.455 vs -0.080, p = 0.047). HER2 enriched subtype was independently associated with conductivity (p = 0.029). Necrosis on MRI was independently associated with ADC (p = 0.027). Conductivity shows negative correlation with ADC that is abolished by the presence of necrosis on MRI. • Electric conductivity showed negative correlation with ADC • However, the correlation was abolished by the presence of necrosis on MRI • HER2-enriched subtype was independently associated with conductivity • Necrosis on MRI was independently associated with ADC.

Quest for Correlates of Protection against Tuberculosis

PubMed Central

Bhatt, Kamlesh; Verma, Sheetal; Ellner, Jerrold J.

2015-01-01

A major impediment to tuberculosis (TB) vaccine development is the lack of reliable correlates of immune protection or biomarkers that would predict vaccine efficacy. Gamma interferon (IFN-γ) produced by CD4+ T cells and, recently, multifunctional CD4+ T cells secreting IFN-γ, tumor necrosis factor (TNF), and interleukin-2 (IL-2) have been used in vaccine studies as a measurable immune parameter, reflecting activity of a vaccine and potentially predicting protection. However, accumulating experimental evidence suggests that host resistance against Mycobacterium tuberculosis infection is independent of IFN-γ and TNF secretion from CD4+ T cells. Furthermore, the booster vaccine MVA85A, despite generating a high level of multifunctional CD4+ T cell response in the host, failed to confer enhanced protection in vaccinated subjects. These findings suggest the need for identifying reliable correlates of protection to determine the efficacy of TB vaccine candidates. This article focuses on alternative pathways that mediate M. tuberculosis control and their potential for serving as markers of protection. The review also discusses the significance of investigating the natural human immune response to M. tuberculosis to identify the correlates of protection in vaccination. PMID:25589549

Identifying the structure of group correlation in the Korean financial market

NASA Astrophysics Data System (ADS)

Ahn, Sanghyun; Choi, Jaewon; Lim, Gyuchang; Cha, Kil Young; Kim, Sooyong; Kim, Kyungsik

2011-06-01

We investigate the structure of the cross-correlation in the Korean stock market. We analyze daily cross-correlations between price fluctuations of 586 different Korean stock entities for the 6-year time period from 2003 to 2008. The main purpose is to investigate the structure of group correlation and its stability by undressing the market-wide effect using the Markowitz multi-factor model and the network-based approach. We find the explicit list of significant firms in the few largest eigenvectors from the undressed correlation matrix. We also observe that each contributor is involved in the same business sectors. The structure of group correlation can not remain constant during each 1-year time period with different starting points, whereas only two largest eigenvectors are stable for 6 years 8-9 eigenvectors remain stable for half-year. The structure of group correlation in the Korean financial market is disturbed during a sufficiently short time period even though the group correlation exists as an ensemble for the 6-year time period in the evolution of the system. We verify the structure of group correlation by applying a network-based approach. In addition, we examine relations between market capitalization and businesses. The Korean stock market shows a different behavior compared to mature markets, implying that the KOSPI is a target for short-positioned investors.

Towards a Healthy High Street: Identifying Skill Needs in Small Independent Retailers.

ERIC Educational Resources Information Center

Byrom, John; Parker, Cathy; Harris, John

2002-01-01

Secondary analysis of data from a study of skill needs in the British independent retail sector suggests there is justification for focusing on higher-level training in three areas: building and sustaining competitive advantage, e-commerce, and retail operations. These areas are the core modules in a distance learning initiative that resulted from…

Detection of periodicity based on independence tests - III. Phase distance correlation periodogram

NASA Astrophysics Data System (ADS)

Zucker, Shay

2018-02-01

I present the Phase Distance Correlation (PDC) periodogram - a new periodicity metric, based on the Distance Correlation concept of Gábor Székely. For each trial period, PDC calculates the distance correlation between the data samples and their phases. PDC requires adaptation of the Székely's distance correlation to circular variables (phases). The resulting periodicity metric is best suited to sparse data sets, and it performs better than other methods for sawtooth-like periodicities. These include Cepheid and RR-Lyrae light curves, as well as radial velocity curves of eccentric spectroscopic binaries. The performance of the PDC periodogram in other contexts is almost as good as that of the Generalized Lomb-Scargle periodogram. The concept of phase distance correlation can be adapted also to astrometric data, and it has the potential to be suitable also for large evenly spaced data sets, after some algorithmic perfection.

Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape.

PubMed

Baker, Robert L; Leong, Wen Fung; Brock, Marcus T; Markelz, R J Cody; Covington, Michael F; Devisetty, Upendra K; Edwards, Christine E; Maloof, Julin; Welch, Stephen; Weinig, Cynthia

2015-10-01

Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point (STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement. We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL). We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development. Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Nonclassicality of Temporal Correlations.

PubMed

Brierley, Stephen; Kosowski, Adrian; Markiewicz, Marcin; Paterek, Tomasz; Przysiężna, Anna

2015-09-18

The results of spacelike separated measurements are independent of distant measurement settings, a property one might call two-way no-signaling. In contrast, timelike separated measurements are only one-way no-signaling since the past is independent of the future but not vice versa. For this reason some temporal correlations that are formally identical to nonclassical spatial correlations can still be modeled classically. We propose a new formulation of Bell's theorem for temporal correlations; namely, we define nonclassical temporal correlations as the ones which cannot be simulated by propagating in time the classical information content of a quantum system given by the Holevo bound. We first show that temporal correlations between results of any projective quantum measurements on a qubit can be simulated classically. Then we present a sequence of general measurements on a single m-level quantum system that cannot be explained by propagating in time an m-level classical system and using classical computers with unlimited memory.

Motivated independence? Implicit party identity predicts political judgments among self-proclaimed Independents.

PubMed

Hawkins, Carlee Beth; Nosek, Brian A

2012-11-01

Reporting an Independent political identity does not guarantee the absence of partisanship. Independents demonstrated considerable variability in relative identification with Republicans versus Democrats as measured by an Implicit Association Test (IAT; M = 0.10, SD = 0.47). To test whether this variation predicted political judgment, participants read a newspaper article describing two competing welfare (Study 1) or special education (Study 2) policies. The authors manipulated which policy was proposed by which party. Among self-proclaimed Independents, those who were implicitly Democratic preferred the liberal welfare plan, and those who were implicitly Republican preferred the conservative welfare plan. Regardless of the policy details, these implicit partisans preferred the policy proposed by "their" party, and this effect occurred more strongly for implicit than explicit plan preference. The authors suggest that implicitly partisan Independents may consciously override some partisan influence when making explicit political judgments, and Independents may identify as such to appear objective even when they are not.

Accurate Structural Correlations from Maximum Likelihood Superpositions

PubMed Central

Theobald, Douglas L; Wuttke, Deborah S

2008-01-01

The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

Quasi-independence, fitness, and advantageousness.

PubMed

Brosnan, Kevin

2009-09-01

I argue that the idea of 'quasi-independence' [Lewontin, R. C. (1978). Adaptation. Scientific American, 239(3), 212-230] cannot be understood without attending to the distinction between fitness and advantageousness [Sober, E. (1993). Philosophy of biology. Boulder: Westview Press]. Natural selection increases the frequency of fitter traits, not necessarily of advantageous ones. A positive correlation between an advantageous trait and a disadvantageous one may prevent the advantageous trait from evolving. The quasi-independence criterion is aimed at specifying the conditions under which advantageous traits will evolve by natural selection in this type of situation. Contrary to what others have argued [Sterelny, K. (1992). Evolutionary explanations of human behavior. Australian Journal of Philosophy, 70(2), 156-172, and Sterelny, K., & Griffiths, P. (1999). Sex and death. Chicago: University of Chicago Press], these conditions must involve a precise quantitative measure of (a) the extent to which advantageous traits are beneficial, and (b) the degree to which they are correlated with other traits. Driscoll (2004) [Driscoll, C. (2004). Can behaviors be adaptations? Philosophy of Science, 71, 16-35] recognizes the need for such a measure, but I argue that she does not provide the correct formulation. The account of quasi-independence that I offer clarifies this point.

Student Orientations to Independent Learning.

ERIC Educational Resources Information Center

Jones, Alice; Jones, Douglas

1996-01-01

A study investigated the relationship of 46 college students' preferred teaching method (conventional lecture versus independent study package) and their own approaches to study (surface, deep, achieving). Results indicated that while students preferred the conventional lecture method, preference did not correlate with their study approach and…

Development and Validation of a Novel Platform-Independent Metastasis Signature in Human Breast Cancer

PubMed Central

Speers, Corey; Liu, Meilan; Wilder-Romans, Kari; Lawrence, Theodore S.; Pierce, Lori J.; Feng, Felix Y.

2015-01-01

Purpose The molecular drivers of metastasis in breast cancer are not well understood. Therefore, we sought to identify the biological processes underlying distant progression and define a prognostic signature for metastatic potential in breast cancer. Experimental design In vivo screening for metastases was performed using Chick Chorioallantoic Membrane assays in 21 preclinical breast cancer models. Expressed genes associated with metastatic potential were identified using high-throughput analysis. Correlations with biological function were determined using the Database for Annotation, Visualization and Integrated Discovery. Results We identified a broad range of metastatic potential that was independent of intrinsic breast cancer subtypes. 146 genes were significantly associated with metastasis progression and were linked to cancer-related biological functions, including cell migration/adhesion, Jak-STAT, TGF-beta, and Wnt signaling. These genes were used to develop a platform-independent gene expression signature (M-Sig), which was trained and subsequently validated on 5 independent cohorts totaling nearly 1800 breast cancer patients with all p-values < 0.005 and hazard ratios ranging from approximately 2.5 to 3. On multivariate analysis accounting for standard clinicopathologic prognostic variables, M-Sig remained the strongest prognostic factor for metastatic progression, with p-values < 0.001 and hazard ratios > 2 in three different cohorts. Conclusion M-Sig is strongly prognostic for metastatic progression, and may provide clinical utility in combination with treatment prediction tools to better guide patient care. In addition, the platform-independent nature of the signature makes it an excellent research tool as it can be directly applied onto existing, and future, datasets. PMID:25974184

A combinatorial extracellular matrix platform identifies cell-extracellular matrix interactions that correlate with metastasis

PubMed Central

Reticker-Flynn, Nathan E.; Braga Malta, David F.; Winslow, Monte M.; Lamar, John M.; Xu, Mary J.; Underhill, Gregory H.; Hynes, Richard O.; Jacks, Tyler E.; Bhatia, Sangeeta N.

2013-01-01

Extracellular matrix interactions play essential roles in normal physiology and many pathological processes. While the importance of ECM interactions in metastasis is well documented, systematic approaches to identify their roles in distinct stages of tumorigenesis have not been described. Here we report a novel screening platform capable of measuring phenotypic responses to combinations of ECM molecules. Using a genetic mouse model of lung adenocarcinoma, we measure the ECM-dependent adhesion of tumor-derived cells. Hierarchical clustering of the adhesion profiles differentiates metastatic cell lines from primary tumor lines. Furthermore, we uncovered that metastatic cells selectively associate with fibronectin when in combination with galectin-3, galectin-8, or laminin. We show that these molecules correlate with human disease and that their interactions are mediated in part by α3β1 integrin. Thus, our platform allowed us to interrogate interactions between metastatic cells and their microenvironments, and identified ECM and integrin interactions that could serve as therapeutic targets. PMID:23047680

On the background independence of two-dimensional topological gravity

NASA Astrophysics Data System (ADS)

Imbimbo, Camillo

1995-04-01

We formulate two-dimensional topological gravity in a background covariant Lagrangian framework. We derive the Ward identities which characterize the dependence of physical correlators on the background world-sheet metric defining the gauge-slice. We point out the existence of an "anomaly" in Ward identitites involving correlators of observables with higher ghost number. This "anomaly" represents an obstruction for physical correlators to be globally defined forms on moduli space which could be integrated in a background independent way. Starting from the anomalous Ward identities, we derive "descent" equations whose solutions are cocycles of the Lie algebra of the diffeomorphism group with values in the space of local forms on the moduli space. We solve the descent equations and provide explicit formulas for the cocycles, which allow for the definition of background independent integrals of physical correlators on the moduli space.

The Geriatric Hand: Correlation of Hand-Muscle Function and Activity Restriction in Elderly

ERIC Educational Resources Information Center

Incel, Nurgul Arinci; Sezgin, Melek; As, Ismet; Cimen, Ozlem Bolgen; Sahin, Gunsah

2009-01-01

On the basis of the importance of hand manipulation in activities of daily living (ADL), deterioration of hand function because of various factors reduces quality and independence of life of the geriatric population. The aim of this study was to identify age-induced changes in manual function and to quantify the correlations between hand-muscle…

Device-independent characterizations of a shared quantum state independent of any Bell inequalities

NASA Astrophysics Data System (ADS)

Wei, Zhaohui; Sikora, Jamie

2017-03-01

In a Bell experiment two parties share a quantum state and perform local measurements on their subsystems separately, and the statistics of the measurement outcomes are recorded as a Bell correlation. For any Bell correlation, it turns out that a quantum state with minimal size that is able to produce this correlation can always be pure. In this work, we first exhibit two device-independent characterizations for the pure state that Alice and Bob share using only the correlation data. Specifically, we give two conditions that the Schmidt coefficients must satisfy, which can be tight, and have various applications in quantum tasks. First, one of the characterizations allows us to bound the entanglement between Alice and Bob using Renyi entropies and also to bound the underlying Hilbert space dimension. Second, when the Hilbert space dimension bound is tight, the shared pure quantum state has to be maximally entangled. Third, the second characterization gives a sufficient condition that a Bell correlation cannot be generated by particular quantum states. We also show that our results can be generalized to the case of shared mixed states.

Reduction of novel circulating long-chain fatty acids in colorectal cancer patients is independent of tumor burden and correlates with age

PubMed Central

2010-01-01

Background Serum levels of novel hydroxy polyunsaturated ultra long-chain fatty acids (hPULCFAs) have been previously shown to be reduced in pre-treatment CRC patients compared to disease-free subjects, independent of disease stage. However, whether reduced levels of hPULCFAs result from the presence of cancer is currently unknown, as is the distribution of hPULCFAs in the general population. The following studies were carried out to assess whether conventional therapy would result in restoration of systemic hPULCFAs in CRC patients, and to investigate the relationship between hPULCFA levels and age. Methods Tandem mass spectrometry was used to determine serum levels of the 28 carbon-containing hPULCFA C28H46O4 (CRC-446) in the following cohorts: two independent Japanese CRC populations following surgical tumor removal (n = 86), a North American Caucasian CRC cohort (n = 150) following post-surgery combination chemo/radiation therapy, 990 randomly selected anonymized serum samples from subjects ranging between 11 and 99 years of age, as well as longitudinally collected serum samples from healthy normals (n = 8, up to 90 weeks) and stage IV CRC subjects on combination therapy (n = 12, up to 63 weeks). Results Serum CRC-446 levels in CRC subjects were significantly lower than controls (mean of 0.297 ± 0.07 ug/ml in controls versus 0.092 ± 0.03 in CRCs, p < 0.001), and were unaffected by surgical tumor removal or by chemo/radiation treatment (p > 0.05 between pre vs post surgery). CRC-446 levels showed a strong inverse association with age (p < E-11) across the randomly-selected cohort of 990 subjects, with no correlation observed in the CRC-positive subjects. Longitudinal intra-subject results, however, showed relatively stable CRC-446 levels over the short term of up to 90 weeks in both disease-free subjects and late-stage CRC patients. Conclusions Our findings show that CRC-446 levels are not affected by conventional CRC treatment and inversely correlate with age

Phanerozoic marine diversity: rock record modelling provides an independent test of large-scale trends.

PubMed

Smith, Andrew B; Lloyd, Graeme T; McGowan, Alistair J

2012-11-07

Sampling bias created by a heterogeneous rock record can seriously distort estimates of marine diversity and makes a direct reading of the fossil record unreliable. Here we compare two independent estimates of Phanerozoic marine diversity that explicitly take account of variation in sampling-a subsampling approach that standardizes for differences in fossil collection intensity, and a rock area modelling approach that takes account of differences in rock availability. Using the fossil records of North America and Western Europe, we demonstrate that a modelling approach applied to the combined data produces results that are significantly correlated with those derived from subsampling. This concordance between independent approaches argues strongly for the reality of the large-scale trends in diversity we identify from both approaches.

Modified Regression Correlation Coefficient for Poisson Regression Model

NASA Astrophysics Data System (ADS)

Kaengthong, Nattacha; Domthong, Uthumporn

2017-09-01

This study gives attention to indicators in predictive power of the Generalized Linear Model (GLM) which are widely used; however, often having some restrictions. We are interested in regression correlation coefficient for a Poisson regression model. This is a measure of predictive power, and defined by the relationship between the dependent variable (Y) and the expected value of the dependent variable given the independent variables [E(Y|X)] for the Poisson regression model. The dependent variable is distributed as Poisson. The purpose of this research was modifying regression correlation coefficient for Poisson regression model. We also compare the proposed modified regression correlation coefficient with the traditional regression correlation coefficient in the case of two or more independent variables, and having multicollinearity in independent variables. The result shows that the proposed regression correlation coefficient is better than the traditional regression correlation coefficient based on Bias and the Root Mean Square Error (RMSE).

Acceptance of Tinnitus As an Independent Correlate of Tinnitus Severity.

PubMed

Hesser, Hugo; Bånkestad, Ellinor; Andersson, Gerhard

2015-01-01

Tinnitus is the experience of sounds without an identified external source, and for some the experience is associated with significant severity (i.e., perceived negative affect, activity limitation, and participation restriction due to tinnitus). Acceptance of tinnitus has recently been proposed to play an important role in explaining heterogeneity in tinnitus severity. The purpose of the present study was to extend previous investigations of acceptance in relation to tinnitus by examining the unique contribution of acceptance in accounting for tinnitus severity, beyond anxiety and depression symptoms. In a cross-sectional study, 362 participants with tinnitus attending an ENT clinic in Sweden completed a standard set of psychometrically examined measures of acceptance of tinnitus, tinnitus severity, and anxiety and depression symptoms. Participants also completed a background form on which they provided information about the experience of tinnitus (loudness, localization, sound characteristics), other auditory-related problems (hearing problems and sound sensitivity), and personal characteristics. Correlational analyses showed that acceptance was strongly and inversely related to tinnitus severity and anxiety and depression symptoms. Multivariate regression analysis, in which relevant patient characteristics were controlled, revealed that acceptance accounted for unique variance beyond anxiety and depression symptoms. Acceptance accounted for more of the variance than anxiety and depression symptoms combined. In addition, mediation analysis revealed that acceptance of tinnitus mediated the direct association between self-rated loudness and tinnitus severity, even after anxiety and depression symptoms were taken into account. Findings add to the growing body of work, supporting the unique and important role of acceptance in tinnitus severity. The utility of the concept is discussed in relation to the development of new psychological models and interventions for

c-Met in esophageal squamous cell carcinoma: an independent prognostic factor and potential therapeutic target.

PubMed

Ozawa, Yohei; Nakamura, Yasuhiro; Fujishima, Fumiyoshi; Felizola, Saulo J A; Takeda, Kenichiro; Okamoto, Hiroshi; Ito, Ken; Ishida, Hirotaka; Konno, Takuro; Kamei, Takashi; Miyata, Go; Ohuchi, Noriaki; Sasano, Hironobu

2015-06-03

c-Met is widely known as a poor prognostic factor in various human malignancies. Previous studies have suggested the involvement of c-Met and/or its ligand, hepatocyte growth factor (HGF), in esophageal squamous cell carcinoma (ESCC), but the correlation between c-Met status and clinical outcome remains unclear. Furthermore, the identification of a novel molecular therapeutic target might potentially help improve the clinical outcome of ESCC patients. The expression of c-Met and HGF was immunohistochemically assessed in 104 surgically obtained tissue specimens. The correlation between c-Met/HGF expression and patients' clinicopathological features, including survival, was evaluated. We also investigated changes in cell functions and protein expression of c-Met and its downstream signaling pathway components under treatments with HGF and/or c-Met inhibitor in ESCC cell lines. Elevated expression of c-Met was significantly correlated with tumor depth and pathological stage. Patients with high c-Met expression had significantly worse survival. In addition, multivariate analysis identified the high expression of c-Met as an independent prognostic factor. Treatment with c-Met inhibitor under HGF stimulation significantly inhibited the invasive capacity of an ESCC cell line with elevated c-Met mRNA expression. Moreover, c-Met and its downstream signaling inactivation was also detected after treatment with c-Met inhibitor. The results of our study identified c-Met expression as an independent prognostic factor in ESCC patients and demonstrated that c-Met could be a potential molecular therapeutic target for the treatment of ESCC with elevated c-Met expression.

Identification of Correlated GRACE Monthly Harmonic Coefficients Using Pattern Recognition and Neural Networks

NASA Astrophysics Data System (ADS)

Piretzidis, D.; Sra, G.; Sideris, M. G.

2016-12-01

This study explores new methods for identifying correlation errors in harmonic coefficients derived from monthly solutions of the Gravity Recovery and Climate Experiment (GRACE) satellite mission using pattern recognition and neural network algorithms. These correlation errors are evidenced in the differences between monthly solutions and can be suppressed using a de-correlation filter. In all studies so far, the implementation of the de-correlation filter starts from a specific minimum order (i.e., 11 for RL04 and 38 for RL05) until the maximum order of the monthly solution examined. This implementation method has two disadvantages, namely, the omission of filtering correlated coefficients of order less than the minimum order and the filtering of uncorrelated coefficients of order higher than the minimum order. In the first case, the filtered solution is not completely free of correlated errors, whereas the second case results in a monthly solution that suffers from loss of geophysical signal. In the present study, a new method of implementing the de-correlation filter is suggested, by identifying and filtering only the coefficients that show indications of high correlation. Several numerical and geometric properties of the harmonic coefficient series of all orders are examined. Extreme cases of both correlated and uncorrelated coefficients are selected, and their corresponding properties are used to train a two-layer feed-forward neural network. The objective of the neural network is to identify and quantify the correlation by providing the probability of an order of coefficients to be correlated. Results show good performance of the neural network, both in the validation stage of the training procedure and in the subsequent use of the trained network to classify independent coefficients. The neural network is also capable of identifying correlated coefficients even when a small number of training samples and neurons are used (e.g.,100 and 10, respectively).

A correlational and predictive study of creativity and personality of college students.

PubMed

Sanz de Acedo Baquedano, María Teresa; Sanz de Acedo Lizarraga, María Luisa

2012-11-01

The goals of this study were to examine the relationship between creativity and personality, to identify what personality variables better predict creativity, and to determine whether significant differences exist among them in relation to gender. The research was conducted with a sample of 87 students at the Universidad Pública de Navarra, Spain. We administered the Creative Intelligence Test (CREA), which provides a cognitive measure for creativity and the Situational Personality Questionnaire (SPQ), which is composed of 15 personality features. Positive and significant correlations between creativity and independence, cognitive control, and tolerance personality scales were found. Negative and significant correlations between creativity and anxious, dominant, and aggressive personalities were also found. Moreover, four personality variables that positively predicted creativity (efficacy, independence, cognitive control, and integrity-honesty) and another four that negatively predicted creativity (emotional stability, anxiety, dominance, and leadership) were identified. The results did not show significant differences in creativity and personality in relation to gender, except in self-concept and in social adjustment. In conclusion, the results from this study can potentially be used to expand the types of features that support creative personalities.

Foxp3 and IL17 expression in tumor infiltrating lymphocytes (TIL) and tumor cells - correlated or independent factors?

PubMed

Vasilescu, Florina; Arsene, D; Cionca, Florina; Comănescu, Maria; Enache, V; Iosif, Cristina; Alexandru, D O; Georgescu, D; Dobrea, Camelia; Bălan, Adina; Ardeleanu, Carmen

2013-01-01

Tumor infiltrating lymphocytes (TIL), as a microenvironment component were studied in various epithelial tumors, with contradictory results. Recent data about regulatory T-cells (Treg) revealed new explanations for pro- and anti-tumor implications of TIL. Tregs immunoprofile was recently completed with Foxp3 expression. A T-cell fraction (Th) is producing cytokine IL17 and is now considered acting in tumor progression. Our study aimed to analyze immunohistochemically (IHC) Foxp3+ and IL17 expression in resected lung adenocarcinomas, since they could become possible targets in the antitumor immunotherapy. The studied material was represented by paraffin-embedded tumor fragments from 59 patients with TIL identified on HE staining. The antibodies used were Foxp3 and IL17. The statistical analysis used logistical regression on SPSS19 software (Chicago, IL, USA). TIL was usually mild or scarce. A positive statistic correlation resulted between the amounts of TIL in peritumoral and intratumoral location but without correlation to histopathological grading. Foxp3 and IL17 were present in TIL lymphocytes, tumor cells and fibroblasts; IL17 was expressed also in periendothelial cells (PEC). Foxp3 positivity was significantly correlated for lymphocytes÷tumor cells, lymphocytes÷fibroblasts and tumor cells÷fibroblasts, suggesting their concerted action. Tumor cells and lymphocytes Foxp3 expression was inversely correlated with the amount of TIL. Between lymphocytic Foxp3 and PEC IL17, we found a weak negative correlation. The TIL had a quite positive correlation with PEC IL17. In these conditions, Foxp3 could be a mediator of the tumor cells inhibitory aggression upon the immune system and could be used as a molecular target for biological antitumor therapy.

Neural correlates of efficacy of voice therapy in Parkinson's disease identified by performance-correlation analysis.

PubMed

Narayana, Shalini; Fox, Peter T; Zhang, Wei; Franklin, Crystal; Robin, Donald A; Vogel, Deanie; Ramig, Lorraine O

2010-02-01

LSVT LOUD (Lee Silverman Voice Treatment) is efficacious in the treatment of speech disorders in idiopathic Parkinson's disease (IPD), particularly hypophonia. Functional imaging in patients with IPD has shown abnormalities in several speech regions and changes in these areas immediately following treatment. This study serves to extend the analysis by correlating changes of regional neural activity with the main behavioral change following treatment, namely, increased vocal intensity. Ten IPD participants with hypophonia were studied before and after LSVT LOUD. Cerebral blood flow during rest and reading conditions were measured by H(2)(15)O-positron emission tomography. Z-score images were generated by contrasting reading with rest conditions for pre- and post-LSVT LOUD sessions. Neuronal activity during reading in the pre- versus post-LSVT LOUD contrast was correlated with corresponding change in vocal intensity to generate correlation images. Behaviorally, vocal intensity for speech tasks increased significantly after LSVT LOUD. The contrast and correlation analyses indicate a treatment-dependent shift to the right hemisphere with modification in the speech motor regions as well as in prefrontal and temporal areas. We interpret the modification of activity in these regions to be a top-down effect of LSVT LOUD. The absence of an effect of LSVT LOUD on the basal ganglion supports this argument. Our findings indicate that the therapeutic effect of LSVT LOUD in IPD hypophonia results from a shift in cortical activity to the right hemisphere. These findings demonstrate that the short-term changes in the speech motor and multimodal integration areas can occur in a top-down manner. (c) 2009 Wiley-Liss, Inc.

Experimental demonstration of nonbilocal quantum correlations

PubMed Central

Saunders, Dylan J.; Bennet, Adam J.; Branciard, Cyril; Pryde, Geoff J.

2017-01-01

Quantum mechanics admits correlations that cannot be explained by local realistic models. The most studied models are the standard local hidden variable models, which satisfy the well-known Bell inequalities. To date, most works have focused on bipartite entangled systems. We consider correlations between three parties connected via two independent entangled states. We investigate the new type of so-called “bilocal” models, which correspondingly involve two independent hidden variables. These models describe scenarios that naturally arise in quantum networks, where several independent entanglement sources are used. Using photonic qubits, we build such a linear three-node quantum network and demonstrate nonbilocal correlations by violating a Bell-like inequality tailored for bilocal models. Furthermore, we show that the demonstration of nonbilocality is more noise-tolerant than that of standard Bell nonlocality in our three-party quantum network. PMID:28508045

Experimental demonstration of nonbilocal quantum correlations.

PubMed

Saunders, Dylan J; Bennet, Adam J; Branciard, Cyril; Pryde, Geoff J

2017-04-01

Quantum mechanics admits correlations that cannot be explained by local realistic models. The most studied models are the standard local hidden variable models, which satisfy the well-known Bell inequalities. To date, most works have focused on bipartite entangled systems. We consider correlations between three parties connected via two independent entangled states. We investigate the new type of so-called "bilocal" models, which correspondingly involve two independent hidden variables. These models describe scenarios that naturally arise in quantum networks, where several independent entanglement sources are used. Using photonic qubits, we build such a linear three-node quantum network and demonstrate nonbilocal correlations by violating a Bell-like inequality tailored for bilocal models. Furthermore, we show that the demonstration of nonbilocality is more noise-tolerant than that of standard Bell nonlocality in our three-party quantum network.

Device-independent tests of quantum channels

NASA Astrophysics Data System (ADS)

Dall'Arno, Michele; Brandsen, Sarah; Buscemi, Francesco

2017-03-01

We develop a device-independent framework for testing quantum channels. That is, we falsify a hypothesis about a quantum channel based only on an observed set of input-output correlations. Formally, the problem consists of characterizing the set of input-output correlations compatible with any arbitrary given quantum channel. For binary (i.e. two input symbols, two output symbols) correlations, we show that extremal correlations are always achieved by orthogonal encodings and measurements, irrespective of whether or not the channel preserves commutativity. We further provide a full, closed-form characterization of the sets of binary correlations in the case of: (i) any dihedrally covariant qubit channel (such as any Pauli and amplitude-damping channels) and (ii) any universally-covariant commutativity-preserving channel in an arbitrary dimension (such as any erasure, depolarizing, universal cloning and universal transposition channels).

Device-independent tests of quantum channels.

PubMed

Dall'Arno, Michele; Brandsen, Sarah; Buscemi, Francesco

2017-03-01

We develop a device-independent framework for testing quantum channels. That is, we falsify a hypothesis about a quantum channel based only on an observed set of input-output correlations. Formally, the problem consists of characterizing the set of input-output correlations compatible with any arbitrary given quantum channel. For binary (i.e. two input symbols, two output symbols) correlations, we show that extremal correlations are always achieved by orthogonal encodings and measurements, irrespective of whether or not the channel preserves commutativity. We further provide a full, closed-form characterization of the sets of binary correlations in the case of: (i) any dihedrally covariant qubit channel (such as any Pauli and amplitude-damping channels) and (ii) any universally-covariant commutativity-preserving channel in an arbitrary dimension (such as any erasure, depolarizing, universal cloning and universal transposition channels).

Regional Differences in Correlates of Daily Walking among Middle Age and Older Australian Rural Adults: Implications for Health Promotion

PubMed Central

Dollman, James; Hull, Melissa; Lewis, Nicole; Carroll, Suzanne; Zarnowiecki, Dorota

2016-01-01

Rural Australians are less physically active than their metropolitan counterparts, and yet very little is known of the candidate intervention targets for promoting physical activity in rural populations. As rural regions are economically, socially and environmentally diverse, drivers of regular physical activity are likely to vary between regions. This study explored the region-specific correlates of daily walking among middle age and older adults in rural regions with contrasting dominant primary industries. Participants were recruited through print and electronic media, primary care settings and community organisations. Pedometers were worn by 153 adults for at least four days, including a weekend day. A questionnaire identified potential intra-personal, social and environmental correlates of physical activity, according to a social ecological framework. Regression modelling identified independent correlates of daily walking separately in the two study regions. In one region, there were independent correlates of walking from all levels of the social ecological framework. In the other region, significant correlates of daily walking were almost all demographic (age, education and marital status). Participants living alone were less likely to be physically active regardless of region. This study highlights the importance of considering region-specific factors when designing strategies for promoting regular walking among rural adults. PMID:26761020

How device-independent approaches change the meaning of physical theory

NASA Astrophysics Data System (ADS)

Grinbaum, Alexei

2017-05-01

Dirac sought an interpretation of mathematical formalism in terms of physical entities and Einstein insisted that physics should describe ;the real states of the real systems;. While Bell inequalities put into question the reality of states, modern device-independent approaches do away with the idea of entities: physical theory may contain no physical systems. Focusing on the correlations between operationally defined inputs and outputs, device-independent methods promote a view more distant from the conventional one than Einstein's 'principle theories' were from 'constructive theories'. On the examples of indefinite causal orders and almost quantum correlations, we ask a puzzling question: if physical theory is not about systems, then what is it about? Device-independent models suggest that physical theory can be 'about' languages.

An attempt to determine the effect of increase of observation correlations on detectability and identifiability of a single gross error

NASA Astrophysics Data System (ADS)

Prószyński, Witold; Kwaśniak, Mieczysław

2016-12-01

The paper presents the results of investigating the effect of increase of observation correlations on detectability and identifiability of a single gross error, the outlier test sensitivity and also the response-based measures of internal reliability of networks. To reduce in a research a practically incomputable number of possible test options when considering all the non-diagonal elements of the correlation matrix as variables, its simplest representation was used being a matrix with all non-diagonal elements of equal values, termed uniform correlation. By raising the common correlation value incrementally, a sequence of matrix configurations could be obtained corresponding to the increasing level of observation correlations. For each of the measures characterizing the above mentioned features of network reliability the effect is presented in a diagram form as a function of the increasing level of observation correlations. The influence of observation correlations on sensitivity of the w-test for correlated observations (Förstner 1983, Teunissen 2006) is investigated in comparison with the original Baarda's w-test designated for uncorrelated observations, to determine the character of expected sensitivity degradation of the latter when used for correlated observations. The correlation effects obtained for different reliability measures exhibit mutual consistency in a satisfactory extent. As a by-product of the analyses, a simple formula valid for any arbitrary correlation matrix is proposed for transforming the Baarda's w-test statistics into the w-test statistics for correlated observations.

Identifying Wave-Particle Interactions in the Solar Wind using Statistical Correlations

NASA Astrophysics Data System (ADS)

Broiles, T. W.; Jian, L. K.; Gary, S. P.; Lepri, S. T.; Stevens, M. L.

2017-12-01

Heavy ions are a trace component of the solar wind, which can resonate with plasma waves, causing heating and acceleration relative to the bulk plasma. While wave-particle interactions are generally accepted as the cause of heavy ion heating and acceleration, observations to constrain the physics are lacking. In this work, we statistically link specific wave modes to heavy ion heating and acceleration. We have computed the Fast Fourier Transform (FFT) of transverse and compressional magnetic waves between 0 and 5.5 Hz using 9 days of ACE and Wind Magnetometer data. The FFTs are averaged over plasma measurement cycles to compute statistical correlations between magnetic wave power at each discrete frequency, and ion kinetic properties measured by ACE/SWICS and Wind/SWE. The results show that lower frequency transverse oscillations (< 0.2 Hz) and higher frequency compressional oscillations (> 0.4 Hz) are positively correlated with enhancements in the heavy ion thermal and drift speeds. Moreover, the correlation results for the He2+ and O6+ were similar on most days. The correlations were often weak, but most days had some frequencies that correlated with statistical significance. This work suggests that the solar wind heavy ions are possibly being heated and accelerated by both transverse and compressional waves at different frequencies.

Neuroimaging and Neuromodulation: Complementary Approaches for Identifying the Neuronal Correlates of Tinnitus

PubMed Central

Langguth, Berthold; Schecklmann, Martin; Lehner, Astrid; Landgrebe, Michael; Poeppl, Timm Benjamin; Kreuzer, Peter Michal; Schlee, Winfried; Weisz, Nathan; Vanneste, Sven; De Ridder, Dirk

2012-01-01

An inherent limitation of functional imaging studies is their correlational approach. More information about critical contributions of specific brain regions can be gained by focal transient perturbation of neural activity in specific regions with non-invasive focal brain stimulation methods. Functional imaging studies have revealed that tinnitus is related to alterations in neuronal activity of central auditory pathways. Modulation of neuronal activity in auditory cortical areas by repetitive transcranial magnetic stimulation (rTMS) can reduce tinnitus loudness and, if applied repeatedly, exerts therapeutic effects, confirming the relevance of auditory cortex activation for tinnitus generation and persistence. Measurements of oscillatory brain activity before and after rTMS demonstrate that the same stimulation protocol has different effects on brain activity in different patients, presumably related to interindividual differences in baseline activity in the clinically heterogeneous study cohort. In addition to alterations in auditory pathways, imaging techniques also indicate the involvement of non-auditory brain areas, such as the fronto-parietal “awareness” network and the non-tinnitus-specific distress network consisting of the anterior cingulate cortex, anterior insula, and amygdale. Involvement of the hippocampus and the parahippocampal region putatively reflects the relevance of memory mechanisms in the persistence of the phantom percept and the associated distress. Preliminary studies targeting the dorsolateral prefrontal cortex, the dorsal anterior cingulate cortex, and the parietal cortex with rTMS and with transcranial direct current stimulation confirm the relevance of the mentioned non-auditory networks. Available data indicate the important value added by brain stimulation as a complementary approach to neuroimaging for identifying the neuronal correlates of the various clinical aspects of tinnitus. PMID:22509155

Postural transitions during activities of daily living could identify frailty status – Application of wearable technology to identify frailty during unsupervised condition

PubMed Central

Parvaneh, Saman; Mohler, Jane; Toosizadeh, Nima; Grewal, Gurtej Singh; Najafi, Bijan

2017-01-01

Background Impairment of physical function is a major indicator of frailty. Functional performance tests have been shown to be useful for identification of frailty in older adults. However, these tests are often not translatable into unsupervised and remote monitoring of frailty status at home and/or community settings. Objective In this study, we explored daily postural transition quantified using a chest-worn wearable technology to identify frailty in community-dwelling older adults. Methods Spontaneous daily physical activity was monitored over 24 hours in 120 community dwelling (age: 78±8 years) using an unobtrusive wearable sensor (PAMSys™, Biosensics LLC). Participants were classified as non-frail and pre-frail/frail using Fried’s criteria. A validated software was used to identify body postures and postural transition between each independent postural activities such as sit-to-stand, stand-to-sit, stand-to-walk, and walk-to-stand. Transition from walking to sitting was further classified as quick-sitting and cautious-sitting based on presence/absence of a standing-posture pause between sitting and walking. General linear model univariate test was used for between groups comparison. Pearson’s correlation was used to determine the association between sensor-derived parameters with age. Logistic regression model was used to identify independent predictors of frailty. Results According to Fried’s criteria, 63% of participants were pre-frail/frail. The total number of postural transitions, stand-to-walk, and walk-to-stand were, respectively, 25.2%, 30.2%, and 30.6% lower in the pre-frail/frail group when compared to non-frails (p<0.05, Cohen’s d=0.73–0.79). Furthermore, ratio of cautious-sitting was significantly higher by 6.2% in pre-frail/frail compared to non-frail (p=0.025, Cohen’s d=0.22). Total number of postural transitions and ratio of cautious-sitting also showed significant negative and positive correlations with age, respectively (r=-0

Analysis of 320 gastroenteropancreatic neuroendocrine tumors identifies TS expression as independent biomarker for survival.

PubMed

Lee, Hye Seung; Chen, Min; Kim, Ji Hun; Kim, Woo Ho; Ahn, Soyeon; Maeng, Kyungah; Allegra, Carmen J; Kaye, Frederic J; Hochwald, Steven N; Zajac-Kaye, Maria

2014-07-01

Thymidylate synthase (TS), a critical enzyme for DNA synthesis and repair, is both a potential tumor prognostic biomarker as well as a tumorigenic oncogene in animal models. We have now studied the clinical implications of TS expression in gastroenteropancreatic (GEP) neuroendocrine tumors (NETs) and compared these results to other cell cycle biomarker genes. Protein tissue arrays were used to study TS, Ki-67, Rb, pRb, E2F1, p18, p21, p27 and menin expression in 320 human GEP-NETs samples. Immunohistochemical expression was correlated with univariate and multivariate predictors of survival utilizing Kaplan Meier and Cox proportional hazards models. Real time RT-PCR was used to validate these findings. We found that 78 of 320 GEP-NETs (24.4%) expressed TS. NETs arising in the colon, stomach and pancreas showed the highest expression of TS (47.4%, 42.6% and 37.3%, respectively), whereas NETs of the appendix, rectum and duodenum displayed low TS expression (3.3%, 12.9% and 15.4%, respectively). TS expression in GEP-NETs was associated with poorly differentiated endocrine carcinoma, angiolymphatic invasion, lymph node metastasis and distant metastasis (p < 0.05). Patients with TS-positive NETs had markedly worse outcomes than TS-negative NETs as shown by univariate (p < 0.001) and multivariate (p = 0.01) survival analyses. Expression of p18 predicted survival in TS-positive patients that received chemotherapy (p = 0.015). In conclusion, TS protein expression was an independent prognostic biomarker for GEP-NETs. The strong association of increased TS expression with aggressive disease and early death supports the role of TS as a cancer promoting agent in these tumors. © 2013 UICC.

Two speed factors of visual recognition independently correlated with fluid intelligence.

PubMed

Tachibana, Ryosuke; Namba, Yuri; Noguchi, Yasuki

2014-01-01

Growing evidence indicates a moderate but significant relationship between processing speed in visuo-cognitive tasks and general intelligence. On the other hand, findings from neuroscience proposed that the primate visual system consists of two major pathways, the ventral pathway for objects recognition and the dorsal pathway for spatial processing and attentive analysis. Previous studies seeking for visuo-cognitive factors of human intelligence indicated a significant correlation between fluid intelligence and the inspection time (IT), an index for a speed of object recognition performed in the ventral pathway. We thus presently examined a possibility that neural processing speed in the dorsal pathway also represented a factor of intelligence. Specifically, we used the mental rotation (MR) task, a popular psychometric measure for mental speed of spatial processing in the dorsal pathway. We found that the speed of MR was significantly correlated with intelligence scores, while it had no correlation with one's IT (recognition speed of visual objects). Our results support the new possibility that intelligence could be explained by two types of mental speed, one related to object recognition (IT) and another for manipulation of mental images (MR).

Two Speed Factors of Visual Recognition Independently Correlated with Fluid Intelligence

PubMed Central

Tachibana, Ryosuke; Namba, Yuri; Noguchi, Yasuki

2014-01-01

Growing evidence indicates a moderate but significant relationship between processing speed in visuo-cognitive tasks and general intelligence. On the other hand, findings from neuroscience proposed that the primate visual system consists of two major pathways, the ventral pathway for objects recognition and the dorsal pathway for spatial processing and attentive analysis. Previous studies seeking for visuo-cognitive factors of human intelligence indicated a significant correlation between fluid intelligence and the inspection time (IT), an index for a speed of object recognition performed in the ventral pathway. We thus presently examined a possibility that neural processing speed in the dorsal pathway also represented a factor of intelligence. Specifically, we used the mental rotation (MR) task, a popular psychometric measure for mental speed of spatial processing in the dorsal pathway. We found that the speed of MR was significantly correlated with intelligence scores, while it had no correlation with one’s IT (recognition speed of visual objects). Our results support the new possibility that intelligence could be explained by two types of mental speed, one related to object recognition (IT) and another for manipulation of mental images (MR). PMID:24825574

Scale-dependence of transverse momentum correlations in PbAu collisions at 158A GeV/c

NASA Astrophysics Data System (ADS)

Ceres Collaboration; Adamová, D.; Agakichiev, G.; Antończyk, D.; Appelshäuser, H.; Belaga, V.; Bielcikova, S.; Braun-Munzinger, P.; Busch, O.; Cherlin, A.; Damjanović, S.; Dietel, T.; Dietrich, L.; Drees, A.; Dubitzky, W.; Esumi, S. I.; Filimonov, K.; Fomenko, K.; Fraenkel, Z.; Garabatos, C.; Glässel, P.; Holeczek, J.; Kushpil, V.; Maas, A.; Marín, A.; Milošević, J.; Milov, A.; Miśkowiec, D.; Panebrattsev, Yu.; Petchenova, O.; Petráček, V.; Pfeiffer, A.; Płoskoń, M.; Radomski, S.; Rak, J.; Ravinovich, I.; Rehak, P.; Sako, H.; Schmitz, W.; Sedykh, S.; Shimansky, S.; Stachel, J.; Šumbera, M.; Tilsner, H.; Tserruya, I.; Tsiledakis, G.; Wessels, J. P.; Wienold, T.; Wurm, J. P.; Xie, W.; Yurevich, S.; Yurevich, V.

2008-10-01

We present results on transverse momentum correlations of charged particle pairs produced in PbAu collisions at 158A GeV/c at the Super Proton Synchrotron. The transverse momentum correlations have been studied as a function of collision centrality, angular separation of the particle pairs, transverse momentum and charge sign. We demonstrate that the results are in agreement with previous findings in scale-independent analyses at the same beam energy. Employing the two-particle momentum correlator <Δp,Δp> and the cumulative p variable x(p), we identify, using the scale-dependent approach presented in this paper, different sources contributing to the measured correlations, such as quantum and Coulomb correlations, elliptic flow and mini-jet fragmentation.

Boosting Orthographic Learning during Independent Reading

ERIC Educational Resources Information Center

Nielsen, Anne-Mette Veber

2016-01-01

Research has shown that phonological decoding is critical for orthographic learning of new words during independent reading. Moreover, correlational studies have demonstrated that the strength of orthographic learning is related to the orthographic knowledge with which readers approach a text. The present training study was conducted to assess…

Plasma MIC-1 correlates with systemic inflammation but is not an independent determinant of nutritional status or survival in oesophago-gastric cancer.

PubMed

Skipworth, R J E; Deans, D A C; Tan, B H L; Sangster, K; Paterson-Brown, S; Brown, D A; Hunter, M; Breit, S N; Ross, J A; Fearon, K C H

2010-02-16

Macrophage inhibitory cytokine-1(MIC-1) is a potential modulator of systemic inflammation and nutritional depletion, both of which are adverse prognostic factors in oesophago-gastric cancer (OGC). Plasma MIC-1, systemic inflammation (defined as plasma C-reactive protein (CRP) of > or =10 mg l(-1) or modified Glasgow prognostic score (mGPS) of > or =1), and nutritional status were assessed in newly diagnosed OGC patients (n=293). Healthy volunteers (n=35) served as controls. MIC-1 was elevated in patients (median=1371 pg ml(-1); range 141-39 053) when compared with controls (median=377 pg ml(-1); range 141-3786; P<0.001). Patients with gastric tumours (median=1592 pg ml(-1); range 141-12 643) showed higher MIC-1 concentrations than patients with junctional (median=1337 pg ml(-1); range 383-39 053) and oesophageal tumours (median=1180 pg ml(-1); range 258-31 184; P=0.015). Patients showed a median weight loss of 6.4% (range 0.0-33.4%), and 42% of patients had an mGPS of > or =1 or plasma CRP of > or =10 mg l(-1) (median=9 mg l(-1); range 1-200). MIC-1 correlated positively with disease stage (r(2)=0.217; P<0.001), age (r(2)=0.332; P<0.001), CRP (r(2)=0.314; P<0.001), and mGPS (r(2)=0.336; P<0.001), and negatively with Karnofsky Performance Score (r(2)=-0.269; P<0.001). However, although MIC-1 correlated weakly with dietary intake (r(2)=0.157; P=0.031), it did not correlate with weight loss, BMI, or anthropometry. Patients with MIC-1 levels in the upper quartile showed reduced survival (median=204 days; 95% CI 157-251) when compared with patients with MIC-1 levels in the lower three quartiles (median=316 days; 95% CI 259-373; P=0.036), but MIC-1 was not an independent prognostic indicator. There is no independent link between plasma MIC-1 levels and depleted nutritional status or survival in OGC.

Overcoming multicollinearity in multiple regression using correlation coefficient

NASA Astrophysics Data System (ADS)

Zainodin, H. J.; Yap, S. J.

2013-09-01

Multicollinearity happens when there are high correlations among independent variables. In this case, it would be difficult to distinguish between the contributions of these independent variables to that of the dependent variable as they may compete to explain much of the similar variance. Besides, the problem of multicollinearity also violates the assumption of multiple regression: that there is no collinearity among the possible independent variables. Thus, an alternative approach is introduced in overcoming the multicollinearity problem in achieving a well represented model eventually. This approach is accomplished by removing the multicollinearity source variables on the basis of the correlation coefficient values based on full correlation matrix. Using the full correlation matrix can facilitate the implementation of Excel function in removing the multicollinearity source variables. It is found that this procedure is easier and time-saving especially when dealing with greater number of independent variables in a model and a large number of all possible models. Hence, in this paper detailed insight of the procedure is shown, compared and implemented.

Initial 12-h operative fluid volume is an independent risk factor for pleural effusion after hepatectomy.

PubMed

Cheng, Xiang; Wu, Jia-Wei; Sun, Ping; Song, Zi-Fang; Zheng, Qi-Chang

2016-12-01

Pleural effusion after hepatectomy is associated with significant morbidity and prolonged hospital stays. Several studies have addressed the risk factors for postoperative pleural effusion. However, there are no researches concerning the role of the initial 12-h operative fluid volume. The aim of this study was to evaluate whether the initial 12-h operative fluid volume during liver resection is an independent risk factor for pleural effusion after hepatectomy. In this study, we retrospectively analyzed clinical data of 470 patients consecutively undergoing elective hepatectomy between January 2011 and December 2012. We prospectively collected and retrospectively analyzed baseline and clinical data, including preoperative, intraoperative, and postoperative variables. Univariate and multivariate analyses were carried out to identify whether the initial 12-h operative fluid volume was an independent risk factor for pleural effusion after hepatectomy. The multivariate analysis identified 2 independent risk factors for pleural effusion: operative time [odds ratio (OR)=10.2] and initial 12-h operative fluid volume (OR=1.0003). Threshold effect analyses revealed that the initial 12 h operative fluid volume was positively correlated with the incidence of pleural effusion when the initial 12-h operative fluid volume exceeded 4636 mL. We conclude that the initial 12-h operative fluid volume during liver resection and operative time are independent risk factors for pleural effusion after hepatectomy. Perioperative intravenous fluids should be restricted properly.

76 FR 16735 - Federal Acquisition Regulation; Information Collection; Certification of Independent Price...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-25

...; Information Collection; Certification of Independent Price Determination and Parent Company and Identifying... requirement concerning certification of independent price determination and parent company and identifying.... Please cite OMB Control No. 9000-0018, Certification of Independent Price Determination and Parent...

76 FR 37353 - Federal Acquisition Regulation; Information Collection; Certification of Independent Price...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-27

...; Information Collection; Certification of Independent Price Determination and Parent Company and Identifying... requirement concerning certification of independent price determination and parent company and identifying.... Please cite OMB Control No. 9000-0018, Certification of Independent Price Determination and Parent...

Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis

PubMed Central

Kümpers, Britta M. C.; Smith-Unna, Richard D.; Hibberd, Julian M.

2014-01-01

With at least 60 independent origins spanning monocotyledons and dicotyledons, the C4 photosynthetic pathway represents one of the most remarkable examples of convergent evolution. The recurrent evolution of this highly complex trait involving alterations to leaf anatomy, cell biology and biochemistry allows an increase in productivity by ∼50% in tropical and subtropical areas. The extent to which separate lineages of C4 plants use the same genetic networks to maintain C4 photosynthesis is unknown. We developed a new informatics framework to enable deep evolutionary comparison of gene expression in species lacking reference genomes. We exploited this to compare gene expression in species representing two independent C4 lineages (Cleome gynandra and Zea mays) whose last common ancestor diverged ∼140 million years ago. We define a cohort of 3,335 genes that represent conserved components of leaf and photosynthetic development in these species. Furthermore, we show that genes encoding proteins of the C4 cycle are recruited into networks defined by photosynthesis-related genes. Despite the wide evolutionary separation and independent origins of the C4 phenotype, we report that these species use homologous transcription factors to both induce C4 photosynthesis and to maintain the cell specific gene expression required for the pathway to operate. We define a core molecular signature associated with leaf and photosynthetic maturation that is likely shared by angiosperm species derived from the last common ancestor of the monocotyledons and dicotyledons. We show that deep evolutionary comparisons of gene expression can reveal novel insight into the molecular convergence of highly complex phenotypes and that parallel evolution of trans-factors underpins the repeated appearance of C4 photosynthesis. Thus, exploitation of extant natural variation associated with complex traits can be used to identify regulators. Moreover, the transcription factors that are shared by

Identifying a correlated spin fluctuation in an entangled spin chain subject to a quantum phase transition.

PubMed

Shimizu, Kaoru; Tokura, Yasuhiro

2015-12-01

This paper presents a theoretical framework for analyzing the quantum fluctuation properties of a quantum spin chain subject to a quantum phase transition. We can quantify the fluctuation properties by examining the correlation between the fluctuations of two neighboring spins subject to the quantum uncertainty. To do this, we first compute the reduced density matrix ρ of the spin pair from the ground state |Ψ⟩ of a spin chain, and then identify the quantum correlation part ρ(q) embedded in ρ. If the spin chain is translationally symmetric and characterized by a nearest-neighbor two-body spin interaction, we can determine uniquely the form of ρ(q) as W|Φ〉〈Φ| with the weight W ≤1, and quantify the fluctuation properties using the two-spin entangled state |Φ〉. We demonstrate the framework for a transverse-field quantum Ising spin chain and indicate its validity for more general spin chain models.

CD25 expression status improves prognostic risk classification in AML independent of established biomarkers: ECOG phase 3 trial, E1900

PubMed Central

Gönen, Mithat; Sun, Zhuoxin; Figueroa, Maria E.; Patel, Jay P.; Abdel-Wahab, Omar; Racevskis, Janis; Ketterling, Rhett P.; Fernandez, Hugo; Rowe, Jacob M.; Tallman, Martin S.; Melnick, Ari; Levine, Ross L.

2012-01-01

We determined the prognostic relevance of CD25 (IL-2 receptor-α) expression in 657 patients (≤ 60 years) with de novo acute myeloid leukemia (AML) treated in the Eastern Cooperative Oncology Group trial, E1900. We identified CD25POS myeloblasts in 87 patients (13%), of whom 92% had intermediate-risk cytogenetics. CD25 expression correlated with expression of stem cell antigen CD123. In multivariate analysis, controlled for prognostic baseline characteristics and daunorubicin dose, CD25POS patients had inferior complete remission rates (P = .0005) and overall survival (P < .0001) compared with CD25NEG cases. In a subset of 396 patients, we integrated CD25 expression with somatic mutation status to determine whether CD25 impacted outcome independent of prognostic mutations. CD25 was positively correlated with internal tandem duplications in FLT3 (FLT3-ITD), DNMT3A, and NPM1 mutations. The adverse prognostic impact of FLT3-ITDPOS AML was restricted to CD25POS patients. CD25 expression improved AML prognostication independent of integrated, cytogenetic and mutational data, such that it reallocated 11% of patients with intermediate-risk disease to the unfavorable-risk group. Gene expression analysis revealed that CD25POS status correlated with the expression of previously reported leukemia stem cell signatures. We conclude that CD25POS status provides prognostic relevance in AML independent of known biomarkers and is correlated with stem cell gene-expression signatures associated with adverse outcome in AML. PMID:22855599

Carrier density independent scattering rate in SrTiO₃-based electron liquids

DOE PAGES

Mikheev, Evgeny; Raghavan, Santosh; Zhang, Jack Y.; ...

2016-02-10

We examine the carrier density dependence of the scattering rate in two- and three-dimensional electron liquids in SrTiO 3 in the regime where it scales with T n (T is the temperature and n ≤ 2) in the cases when it is varied by electrostatic control and chemical doping, respectively. It is shown that the scattering rate is independent of the carrier density. This is contrary to the expectations from Landau Fermi liquid theory, where the scattering rate scales inversely with the Fermi energy (E F). We discuss that the behavior is very similar to systems traditionally identified as non-Fermimore » liquids (n < 2). This includes the cuprates and other transition metal oxide perovskites, where strikingly similar density independent scattering rates have been observed. Ultimately, the results indicate that the applicability of Fermi liquid theory should be questioned for a much broader range of correlated materials and point to the need for a unified theory.« less

Correlation between automatic detection of malaria on thin film and experts' parasitaemia scores

NASA Astrophysics Data System (ADS)

Sunarko, Budi; Williams, Simon; Prescott, William R.; Byker, Scott M.; Bottema, Murk J.

2017-03-01

An algorithm was developed to diagnose the presence of malaria and to estimate the depth of infection by automatically counting individual normal and infected erythrocytes in images of thin blood smears. During the training stage, the parameters of the algorithm were optimized to maximize correlation with estimates of parasitaemia from expert human observers. The correlation was tested on a set of 1590 images from seven thin film blood smears. The correlation between the results from the algorithm and expert human readers was r = 0.836. Results indicate that reliable estimates of parasitaemia may be achieved by computational image analysis methods applied to images of thin film smears. Meanwhile, compared to biological experiments, the algorithm fitted well the three high parasitaemia slides and a mid-level parasitaemia slide, and overestimated the three low parasitaemia slides. To improve the parasitaemia estimation, the sources of the overestimation were identified. Emphasis is laid on the importance of further research in order to identify parasites independently of their erythrocyte hosts

Effects of isoflurane anesthesia on ensemble patterns of Ca2+ activity in mouse v1: reduced direction selectivity independent of increased correlations in cellular activity.

PubMed

Goltstein, Pieter M; Montijn, Jorrit S; Pennartz, Cyriel M A

2015-01-01

Anesthesia affects brain activity at the molecular, neuronal and network level, but it is not well-understood how tuning properties of sensory neurons and network connectivity change under its influence. Using in vivo two-photon calcium imaging we matched neuron identity across episodes of wakefulness and anesthesia in the same mouse and recorded spontaneous and visually evoked activity patterns of neuronal ensembles in these two states. Correlations in spontaneous patterns of calcium activity between pairs of neurons were increased under anesthesia. While orientation selectivity remained unaffected by anesthesia, this treatment reduced direction selectivity, which was attributable to an increased response to the null-direction. As compared to anesthesia, populations of V1 neurons coded more mutual information on opposite stimulus directions during wakefulness, whereas information on stimulus orientation differences was lower. Increases in correlations of calcium activity during visual stimulation were correlated with poorer population coding, which raised the hypothesis that the anesthesia-induced increase in correlations may be causal to degrading directional coding. Visual stimulation under anesthesia, however, decorrelated ongoing activity patterns to a level comparable to wakefulness. Because visual stimulation thus appears to 'break' the strength of pairwise correlations normally found in spontaneous activity under anesthesia, the changes in correlational structure cannot explain the awake-anesthesia difference in direction coding. The population-wide decrease in coding for stimulus direction thus occurs independently of anesthesia-induced increments in correlations of spontaneous activity.

Effects of Isoflurane Anesthesia on Ensemble Patterns of Ca2+ Activity in Mouse V1: Reduced Direction Selectivity Independent of Increased Correlations in Cellular Activity

PubMed Central

Goltstein, Pieter M.; Montijn, Jorrit S.; Pennartz, Cyriel M. A.

2015-01-01

Anesthesia affects brain activity at the molecular, neuronal and network level, but it is not well-understood how tuning properties of sensory neurons and network connectivity change under its influence. Using in vivo two-photon calcium imaging we matched neuron identity across episodes of wakefulness and anesthesia in the same mouse and recorded spontaneous and visually evoked activity patterns of neuronal ensembles in these two states. Correlations in spontaneous patterns of calcium activity between pairs of neurons were increased under anesthesia. While orientation selectivity remained unaffected by anesthesia, this treatment reduced direction selectivity, which was attributable to an increased response to the null-direction. As compared to anesthesia, populations of V1 neurons coded more mutual information on opposite stimulus directions during wakefulness, whereas information on stimulus orientation differences was lower. Increases in correlations of calcium activity during visual stimulation were correlated with poorer population coding, which raised the hypothesis that the anesthesia-induced increase in correlations may be causal to degrading directional coding. Visual stimulation under anesthesia, however, decorrelated ongoing activity patterns to a level comparable to wakefulness. Because visual stimulation thus appears to ‘break’ the strength of pairwise correlations normally found in spontaneous activity under anesthesia, the changes in correlational structure cannot explain the awake-anesthesia difference in direction coding. The population-wide decrease in coding for stimulus direction thus occurs independently of anesthesia-induced increments in correlations of spontaneous activity. PMID:25706867

Neural Correlates of Efficacy of Voice Therapy in Parkinson’s Disease Identified by Performance–Correlation Analysis

PubMed Central

Narayana, Shalini; Fox, Peter T.; Zhang, Wei; Franklin, Crystal; Robin, Donald A.; Vogel, Deanie; Ramig, Lorraine O.

2009-01-01

LSVT® LOUD (Lee Silverman Voice Treatment) is efficacious in the treatment of speech disorders in idiopathic Parkinson’s disease (IPD), particularly hypophonia. Functional imaging in patients with IPD has shown abnormalities in several speech regions and changes in these areas immediately following treatment. This study serves to extend the analysis by correlating changes of regional neural activity with the main behavioral change following treatment, namely, increased vocal intensity. Ten IPD participants with hypophonia were studied before and after LSVT LOUD. Cerebral blood flow during rest and reading conditions were measured by H215O-positron emission tomography. Z-score images were generated by contrasting reading with rest conditions for pre- and post-LSVT LOUD sessions. Neuronal activity during reading in the pre- versus post-LSVT LOUD contrast was correlated with corresponding change in vocal intensity to generate correlation images. Behaviorally, vocal intensity for speech tasks increased significantly after LSVT LOUD. The contrast and correlation analyses indicate a treatment-dependent shift to the right hemisphere with modification in the speech motor regions as well as in prefrontal and temporal areas. We interpret the modification of activity in these regions to be a top–down effect of LSVT LOUD. The absence of an effect of LSVT LOUD on the basal ganglion supports this argument. Our findings indicate that the therapeutic effect of LSVT LOUD in IPD hypophonia results from a shift in cortical activity to the right hemisphere. These findings demonstrate that the short-term changes in the speech motor and multimodal integration areas can occur in a top–down manner. PMID:19639554

Correlation of Higher Levels of Soluble TNF-R1 with a Shorter Survival, Independent of Age, in Recurrent Glioblastoma

PubMed Central

Ahluwalia, Manmeet S.; Bou-Anak, Stephanie; Burgett, Monica E.; Sarmey, Nehaw; Khosla, Divya; Dahiya, Saurabh; Weil, Robert J.; Bae, Eunnyung; Huang, Ping; McGraw, Mary; Grove, Lisa M.; Olman, Mitchell A.; Prayson, Richard A.; Suh, John H.; Gillespie, G. Yancey; Barnholtz-Sloan, Jill; Nowacki, Amy S.; Barnett, Gene H.; Gladson, Candece L.

2016-01-01

The circulating levels of soluble tumor necrosis factor receptor-1 (sTNF-R1) and sTNF-R2 are altered in numerous diseases, including several types of cancer. Correlations with the risk of progression in some cancers, as well as systemic manifestations of the disease and therapeutic side-effects, have been described. However, there is very little information on the levels of these soluble receptors in glioblastoma (GBM). Here, we report on an exploratory retrospective study of the levels of sTNF-Rs in the vascular circulation of patients with GBM. Banked samples were obtained from 112 GBM patients (66 untreated, newly-diagnosed patients and 46 with recurrent disease) from two institutions. The levels of sTNF-R1 in the plasma were significantly lower in patients with newly-diagnosed or recurrent GBM than apparently healthy individuals and correlated with the intensity of expression of TNF-R1 on the tumor-associated endothelial cells (ECs) in the corresponding biopsies. Elevated levels of sTNF-R1 in patients with recurrent, but not newly-diagnosed GBM, were significantly associated with a shorter survival, independent of age (p=0.02) or steroid medication. In contrast, the levels of circulating sTNF-R2 were significantly higher in recurrent GBM than healthy individuals and there was no significant correlation with expression of TNF-R2 on the tumor-associated ECs or survival time. The results indicate that larger, prospective studies are warranted to determine the predictive value of the levels of sTNF-R1 in patients with recurrent GBM and the factors that regulate the levels of sTNF-Rs in the circulation in GBM patients. PMID:27858267

Scale-dependence of transverse momentum correlations in Pb sbnd Au collisions at 158A GeV/c

NASA Astrophysics Data System (ADS)

Adamová, D.; Agakichiev, G.; Antończyk, D.; Appelshäuser, H.; Belaga, V.; Bielcikova, S.; Braun-Munzinger, P.; Busch, O.; Cherlin, A.; Damjanović, S.; Dietel, T.; Dietrich, L.; Drees, A.; Dubitzky, W.; Esumi, S. I.; Filimonov, K.; Fomenko, K.; Fraenkel, Z.; Garabatos, C.; Glässel, P.; Holeczek, J.; Kushpil, V.; Maas, A.; Marín, A.; Milošević, J.; Milov, A.; Miśkowiec, D.; Panebrattsev, Yu.; Petchenova, O.; Petráček, V.; Pfeiffer, A.; Płoskoń, M.; Radomski, S.; Rak, J.; Ravinovich, I.; Rehak, P.; Sako, H.; Schmitz, W.; Sedykh, S.; Shimansky, S.; Stachel, J.; Šumbera, M.; Tilsner, H.; Tserruya, I.; Tsiledakis, G.; Wessels, J. P.; Wienold, T.; Wurm, J. P.; Xie, W.; Yurevich, S.; Yurevich, V.; Ceres Collaboration

2008-10-01

We present results on transverse momentum correlations of charged particle pairs produced in Pb sbnd Au collisions at 158A GeV/c at the Super Proton Synchrotron. The transverse momentum correlations have been studied as a function of collision centrality, angular separation of the particle pairs, transverse momentum and charge sign. We demonstrate that the results are in agreement with previous findings in scale-independent analyses at the same beam energy. Employing the two-particle momentum correlator <Δp,Δp> and the cumulative p variable x(p), we identify, using the scale-dependent approach presented in this paper, different sources contributing to the measured correlations, such as quantum and Coulomb correlations, elliptic flow and mini-jet fragmentation.

Common neural correlates of intertemporal choices and intelligence in adolescents.

PubMed

Ripke, Stephan; Hübner, Thomas; Mennigen, Eva; Müller, Kathrin U; Li, Shu-Chen; Smolka, Michael N

2015-02-01

Converging behavioral evidence indicates that temporal discounting, measured by intertemporal choice tasks, is inversely related to intelligence. At the neural level, the parieto-frontal network is pivotal for complex, higher-order cognitive processes. Relatedly, underrecruitment of the pFC during a working memory task has been found to be associated with steeper temporal discounting. Furthermore, this network has also been shown to be related to the consistency of intertemporal choices. Here we report an fMRI study that directly investigated the association of neural correlates of intertemporal choice behavior with intelligence in an adolescent sample (n = 206; age 13.7-15.5 years). After identifying brain regions where the BOLD response during intertemporal choice was correlated with individual differences in intelligence, we further tested whether BOLD responses in these areas would mediate the associations between intelligence, the discounting rate, and choice consistency. We found positive correlations between BOLD response in a value-independent decision network (i.e., dorsolateral pFC, precuneus, and occipital areas) and intelligence. Furthermore, BOLD response in a value-dependent decision network (i.e., perigenual ACC, inferior frontal gyrus, ventromedial pFC, ventral striatum) was positively correlated with intelligence. The mediation analysis revealed that BOLD responses in the value-independent network mediated the association between intelligence and choice consistency, whereas BOLD responses in the value-dependent network mediated the association between intelligence and the discounting rate. In summary, our findings provide evidence for common neural correlates of intertemporal choice and intelligence, possibly linked by valuation as well as executive functions.

The nutrient transceptor/PKA pathway functions independently of TOR and responds to leucine and Gcn2 in a TOR-independent manner.

PubMed

Conrad, Michaela; Kankipati, Harish Nag; Kimpe, Marlies; Van Zeebroeck, Griet; Zhang, Zhiqiang; Thevelein, Johan M

2017-08-01

Two nutrient-controlled signalling pathways, the PKA and TOR pathway, play a major role in nutrient regulation of growth as well as growth-correlated properties in yeast. The relationship between the two pathways is not well understood. We have used Gap1 and Pho84 transceptor-mediated activation of trehalase and phosphorylation of fragmented Sch9 as a read-out for rapid nutrient activation of PKA or TORC1, respectively. We have identified conditions in which L-citrulline-induced activation of Sch9 phosphorylation is compromised, but not activation of trehalase: addition of the TORC1 inhibitor, rapamycin and low levels of L-citrulline. The same disconnection was observed for phosphate activation in phosphate-starved cells. The leu2 auxotrophic mutation reduces amino acid activation of trehalase, which is counteracted by deletion of GCN2. Both effects were also independent of TORC1. Our results show that rapid activation of the TOR pathway by amino acids is not involved in rapid activation of the PKA pathway and that effects of Gcn2 inactivation as well as leu2 auxotrophy all act independently of the TOR pathway. Hence, rapid nutrient signalling to PKA and TOR in cells arrested by nutrient starvation acts through parallel pathways. © FEMS 2017.

High-frequency electrical stimulation reveals a p38-mTOR signaling module correlated with force-time integral.

PubMed

Rahnert, Jill A; Burkholder, Thomas J

2013-07-15

High-frequency electrical stimulation (HFES) leads to muscle hypertrophy, and attention has been drawn to the high forces involved. However, both mechanical and metabolic stresses occur simultaneously, and both stimuli influence signaling cascades related to protein synthesis. This study aimed to identify the immediate signaling correlates of contraction-induced force and metabolic stresses under the hypothesis that HFES induces growth-related signaling through mechanical stimulation. Force-time integral (FTI) signaling in mouse tibialis anterior muscle was examined by separately manipulating the time of contraction to emphasize the metabolic aspect or the force of contraction to emphasize the mechanical aspect. When FTI was manipulated by changing the total time of activation, phosphorylation of p54 JNK, ERK and p70S6k(T421/S424) was independent of FTI, while phosphorylation of acetyl-CoA carboxylase and p38 correlated with FTI. When FTI was manipulated by changing the force of contraction, p54 JNK, ERK and p70S6k(T421/S424) were again independent of FTI, while phosphorylation of p38 and FAK correlated with FTI. Factor analysis identified a p38-mTOR signaling module that correlated with FTI in both experiments. The consistent link among p38, mTOR and FTI suggests that they form a connected signaling module sensitive to the mechanical aspects of FTI, separate from markers of metabolic load.

Measuring Frailty Can Help Emergency Departments Identify Independent Seniors at Risk of Functional Decline After Minor Injuries

PubMed Central

Griffith, Lauren; Perry, Jeffrey; Daoust, Raoul; Veillette, Nathalie; Lee, Jacques; Pelletier, Mathieu; Wilding, Laura; Émond, Marcel

2017-01-01

Background. This study aims to (i) describe frailty in the subgroup of independent community-dwelling seniors consulting emergency departments (EDs) for minor injuries, (ii) examine the association between frailty and functional decline 3 months postinjury, (iii) ascertain the predictive accuracy of frailty measures and emergency physicians’ for functional decline. Method. Prospective cohort in 2011–2013 among 1,072 seniors aged 65 years or older, independent in basic daily activities, evaluated in Canadian EDs for minor injuries. Frailty was assessed at EDs using the Canadian Study of Health and Aging-Clinical Frailty scale (CSHA-CFS) and the Study of Osteoporotic Fracture frailty index (SOF). Functional decline was defined as a loss ≥2/28 on the Older American Resources Services scale 3 months postinjury. Generalized mixed models were used to explore differences in functional decline across frailty levels. Areas under the receiver operating characteristic curve were used to ascertain the predictive accuracy of frailty measures and emergency physicians’ clinical judgment. Results. The SOF and CSHA-CFS were available in 342 and 1,058 participants, respectively. The SOF identified 55.6%, 32.7%, 11.7% patients as robust, prefrail, and frail. These CSHA-CFS (n = 1,058) proportions were 51.9%, 38.3%, and 9.9%. The 3-month incidence of functional decline was 12.1% (10.0%−14.6%). The Areas under the receiver operating characteristic curves of the CSHA-CFS and the emergency physicians’ were similar (0.548–0.777), while the SOF was somewhat higher (0.704–0.859). Conclusion. Measuring frailty in community-dwelling seniors with minor injuries in EDs may enhance current risk screening for functional decline. However, before implementation in usual care, feasibility issues such as inter-rater reliability and acceptability of frailty tools in the EDs have to be addressed. PMID:26400735

Segment-Wise Genome-Wide Association Analysis Identifies a Candidate Region Associated with Schizophrenia in Three Independent Samples

PubMed Central

Rietschel, Marcella; Mattheisen, Manuel; Breuer, René; Schulze, Thomas G.; Nöthen, Markus M.; Levinson, Douglas; Shi, Jianxin; Gejman, Pablo V.; Cichon, Sven; Ophoff, Roel A.

2012-01-01

Recent studies suggest that variation in complex disorders (e.g., schizophrenia) is explained by a large number of genetic variants with small effect size (Odds Ratio∼1.05–1.1). The statistical power to detect these genetic variants in Genome Wide Association (GWA) studies with large numbers of cases and controls (∼15,000) is still low. As it will be difficult to further increase sample size, we decided to explore an alternative method for analyzing GWA data in a study of schizophrenia, dramatically reducing the number of statistical tests. The underlying hypothesis was that at least some of the genetic variants related to a common outcome are collocated in segments of chromosomes at a wider scale than single genes. Our approach was therefore to study the association between relatively large segments of DNA and disease status. An association test was performed for each SNP and the number of nominally significant tests in a segment was counted. We then performed a permutation-based binomial test to determine whether this region contained significantly more nominally significant SNPs than expected under the null hypothesis of no association, taking linkage into account. Genome Wide Association data of three independent schizophrenia case/control cohorts with European ancestry (Dutch, German, and US) using segments of DNA with variable length (2 to 32 Mbp) was analyzed. Using this approach we identified a region at chromosome 5q23.3-q31.3 (128–160 Mbp) that was significantly enriched with nominally associated SNPs in three independent case-control samples. We conclude that considering relatively wide segments of chromosomes may reveal reliable relationships between the genome and schizophrenia, suggesting novel methodological possibilities as well as raising theoretical questions. PMID:22723893

Sound Sources Identified in High-Speed Jets by Correlating Flow Density Fluctuations With Far-Field Noise

NASA Technical Reports Server (NTRS)

Panda, Jayanta; Seasholtz, Richard G.

2003-01-01

Noise sources in high-speed jets were identified by directly correlating flow density fluctuation (cause) to far-field sound pressure fluctuation (effect). The experimental study was performed in a nozzle facility at the NASA Glenn Research Center in support of NASA s initiative to reduce the noise emitted by commercial airplanes. Previous efforts to use this correlation method have failed because the tools for measuring jet turbulence were intrusive. In the present experiment, a molecular Rayleigh-scattering technique was used that depended on laser light scattering by gas molecules in air. The technique allowed accurate measurement of air density fluctuations from different points in the plume. The study was conducted in shock-free, unheated jets of Mach numbers 0.95, 1.4, and 1.8. The turbulent motion, as evident from density fluctuation spectra was remarkably similar in all three jets, whereas the noise sources were significantly different. The correlation study was conducted by keeping a microphone at a fixed location (at the peak noise emission angle of 30 to the jet axis and 50 nozzle diameters away) while moving the laser probe volume from point to point in the flow. The following figure shows maps of the nondimensional coherence value measured at different Strouhal frequencies ([frequency diameter]/jet speed) in the supersonic Mach 1.8 and subsonic Mach 0.95 jets. The higher the coherence, the stronger the source was.

Evaluation of bus management options for Independence National Historical Site

DOT National Transportation Integrated Search

2000-07-06

This project analyzes options and identifies preferred designs for a new transportation center in Independence National Historical Park. The Independence Transportation Center will be part of a planned National Constitution Center at Independence Mal...

Sca-1 Identifies a Distinct Androgen-Independent Murine Prostatic Luminal Cell Lineage with Bipotent Potential

PubMed Central

Kwon, Oh-Joon; Zhang, Li; Xin, Li

2016-01-01

Recent lineage tracing studies support the existence of prostate luminal progenitors that possess extensive regenerative capacity, but their identity remains unknown. We show that Sca-1 (Stem Cell Antigen-1) identifies a small population of murine prostate luminal cells that reside in the proximal prostatic ducts adjacent to the urethra. Sca-1+ luminal cells do not express Nkx3.1. They do not carry the secretory function, although they express the androgen receptor. These cells are enriched in the prostates of castrated mice. In the in vitro prostate organoid assay, a small fraction of the Sca-1+ luminal cells are capable of generating budding organoids that are morphologically distinct from those derived from other cell lineages. Histologically, this type of organoid is composed of multiple inner layers of luminal cells surrounded by multiple outer layers of basal cells. When passaged, these organoids retain their morphological and histological features. Finally, the Sca-1+ luminal cells are capable of forming small prostate glands containing both basal and luminal cells in an in vivo prostate regeneration assay. Collectively, our study establishes the androgen-independent and bipotent organoid-forming Sca-1+ luminal cells as a functionally distinct cellular entity. These cells may represent a putative luminal progenitor population and serve as a cellular origin for castration resistant prostate cancer. PMID:26418304

Fully device-independent quantum key distribution.

PubMed

Vazirani, Umesh; Vidick, Thomas

2014-10-03

Quantum cryptography promises levels of security that are impossible to replicate in a classical world. Can this security be guaranteed even when the quantum devices on which the protocol relies are untrusted? This central question dates back to the early 1990s when the challenge of achieving device-independent quantum key distribution was first formulated. We answer this challenge by rigorously proving the device-independent security of a slight variant of Ekert's original entanglement-based protocol against the most general (coherent) attacks. The resulting protocol is robust: While assuming only that the devices can be modeled by the laws of quantum mechanics and are spatially isolated from each other and from any adversary's laboratory, it achieves a linear key rate and tolerates a constant noise rate in the devices. In particular, the devices may have quantum memory and share arbitrary quantum correlations with the eavesdropper. The proof of security is based on a new quantitative understanding of the monogamous nature of quantum correlations in the context of a multiparty protocol.

Fully Device-Independent Quantum Key Distribution

NASA Astrophysics Data System (ADS)

Vazirani, Umesh; Vidick, Thomas

2014-10-01

Quantum cryptography promises levels of security that are impossible to replicate in a classical world. Can this security be guaranteed even when the quantum devices on which the protocol relies are untrusted? This central question dates back to the early 1990s when the challenge of achieving device-independent quantum key distribution was first formulated. We answer this challenge by rigorously proving the device-independent security of a slight variant of Ekert's original entanglement-based protocol against the most general (coherent) attacks. The resulting protocol is robust: While assuming only that the devices can be modeled by the laws of quantum mechanics and are spatially isolated from each other and from any adversary's laboratory, it achieves a linear key rate and tolerates a constant noise rate in the devices. In particular, the devices may have quantum memory and share arbitrary quantum correlations with the eavesdropper. The proof of security is based on a new quantitative understanding of the monogamous nature of quantum correlations in the context of a multiparty protocol.

Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency.

PubMed

Yeh, Hsiang-Yuan; Cheng, Shih-Wu; Lin, Yu-Chun; Yeh, Cheng-Yu; Lin, Shih-Fang; Soo, Von-Wun

2009-12-21

Prostate cancer is a world wide leading cancer and it is characterized by its aggressive metastasis. According to the clinical heterogeneity, prostate cancer displays different stages and grades related to the aggressive metastasis disease. Although numerous studies used microarray analysis and traditional clustering method to identify the individual genes during the disease processes, the important gene regulations remain unclear. We present a computational method for inferring genetic regulatory networks from micorarray data automatically with transcription factor analysis and conditional independence testing to explore the potential significant gene regulatory networks that are correlated with cancer, tumor grade and stage in the prostate cancer. To deal with missing values in microarray data, we used a K-nearest-neighbors (KNN) algorithm to determine the precise expression values. We applied web services technology to wrap the bioinformatics toolkits and databases to automatically extract the promoter regions of DNA sequences and predicted the transcription factors that regulate the gene expressions. We adopt the microarray datasets consists of 62 primary tumors, 41 normal prostate tissues from Stanford Microarray Database (SMD) as a target dataset to evaluate our method. The predicted results showed that the possible biomarker genes related to cancer and denoted the androgen functions and processes may be in the development of the prostate cancer and promote the cell death in cell cycle. Our predicted results showed that sub-networks of genes SREBF1, STAT6 and PBX1 are strongly related to a high extent while ETS transcription factors ELK1, JUN and EGR2 are related to a low extent. Gene SLC22A3 may explain clinically the differentiation associated with the high grade cancer compared with low grade cancer. Enhancer of Zeste Homolg 2 (EZH2) regulated by RUNX1 and STAT3 is correlated to the pathological stage. We provide a computational framework to reconstruct

Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency

PubMed Central

2009-01-01

Background Prostate cancer is a world wide leading cancer and it is characterized by its aggressive metastasis. According to the clinical heterogeneity, prostate cancer displays different stages and grades related to the aggressive metastasis disease. Although numerous studies used microarray analysis and traditional clustering method to identify the individual genes during the disease processes, the important gene regulations remain unclear. We present a computational method for inferring genetic regulatory networks from micorarray data automatically with transcription factor analysis and conditional independence testing to explore the potential significant gene regulatory networks that are correlated with cancer, tumor grade and stage in the prostate cancer. Results To deal with missing values in microarray data, we used a K-nearest-neighbors (KNN) algorithm to determine the precise expression values. We applied web services technology to wrap the bioinformatics toolkits and databases to automatically extract the promoter regions of DNA sequences and predicted the transcription factors that regulate the gene expressions. We adopt the microarray datasets consists of 62 primary tumors, 41 normal prostate tissues from Stanford Microarray Database (SMD) as a target dataset to evaluate our method. The predicted results showed that the possible biomarker genes related to cancer and denoted the androgen functions and processes may be in the development of the prostate cancer and promote the cell death in cell cycle. Our predicted results showed that sub-networks of genes SREBF1, STAT6 and PBX1 are strongly related to a high extent while ETS transcription factors ELK1, JUN and EGR2 are related to a low extent. Gene SLC22A3 may explain clinically the differentiation associated with the high grade cancer compared with low grade cancer. Enhancer of Zeste Homolg 2 (EZH2) regulated by RUNX1 and STAT3 is correlated to the pathological stage. Conclusions We provide a

Linear Least Squares for Correlated Data

NASA Technical Reports Server (NTRS)

Dean, Edwin B.

1988-01-01

Throughout the literature authors have consistently discussed the suspicion that regression results were less than satisfactory when the independent variables were correlated. Camm, Gulledge, and Womer, and Womer and Marcotte provide excellent applied examples of these concerns. Many authors have obtained partial solutions for this problem as discussed by Womer and Marcotte and Wonnacott and Wonnacott, which result in generalized least squares algorithms to solve restrictive cases. This paper presents a simple but relatively general multivariate method for obtaining linear least squares coefficients which are free of the statistical distortion created by correlated independent variables.

Necessary and sufficient criterion for extremal quantum correlations in the simplest Bell scenario

NASA Astrophysics Data System (ADS)

Ishizaka, Satoshi

2018-05-01

In the study of quantum nonlocality, one obstacle is that the analytical criterion for identifying the boundaries between quantum and postquantum correlations has not yet been given, even in the simplest Bell scenario. We propose a plausible, analytical, necessary and sufficient condition ensuring that a nonlocal quantum correlation in the simplest scenario is an extremal boundary point. Our extremality condition amounts to certifying an information-theoretical quantity; the probability of guessing a measurement outcome of a distant party optimized using any quantum instrument. We show that this quantity can be upper and lower bounded from any correlation in a device-independent way, and we use numerical calculations to confirm that coincidence of the upper and lower bounds appears to be necessary and sufficient for the extremality.

Depression correlates with quality of life in people with epilepsy independent of the measures used.

PubMed

Agrawal, Niruj; Bird, Jacob S; von Oertzen, Tim J; Cock, Hannah; Mitchell, Alex J; Mula, Marco

2016-09-01

A number of studies have suggested that depressed mood is one of the most important predictors of quality of life (QoL) in patients with epilepsy. However, the QoL measure used in previous studies was limited to the Quality of Life in Epilepsy (QOLIE) scales. It could be questioned whether correlation of QOLIE with measures of depression is influenced by the properties of the instruments used rather than being a valid effect. By using visual analogue scales, the current study aimed to clarify whether depression and QoL are truly correlated in patients with epilepsy. Data from a sample of 261 outpatients with epilepsy attending the Epilepsy Clinics of the Atkinson Morley Outpatient Department, St George's Hospital in London, were analyzed. Patients were screened using the European Quality-of-Life scale (EQ-5D-3L) which includes an overall visual analogue score (EQ-VAS), the Emotional Thermometer (ET7), the Beck Depression inventory-II (BDI-II), the Hospital Anxiety and Depression scale (HADS), and the Major Depression inventory (MDI). Depression was found to significantly correlate with EQ-VAS score with r coefficient ranging from 0.42 to 0.51 and r(2) coefficients ranging between 0.18 and 0.26. In addition, we identified patients who were depressed according to DSM-IV criteria (MD) and those with atypical forms of depression (AD). The EQ-5D-3L scores in these subjects compared with those without depression (ND) showed a different impact of AD and MD on QoL. The relationship between depression and QoL in people with epilepsy has been demonstrated to be a robust and valid effect, not a result of potential bias of the specific measures used. However, the strength of the association is influenced by the individual instrument. Atypical or subsyndromic forms of depression are as relevant as DSM-based depression in terms of impact on QoL. Copyright © 2016 Elsevier Inc. All rights reserved.

Optical Correlation

NASA Technical Reports Server (NTRS)

Cotariu, Steven S.

1991-01-01

Pattern recognition may supplement or replace certain navigational aids on spacecraft in docking or landing activities. The need to correctly identify terrain features remains critical in preparation of autonomous planetary landing. One technique that may solve this problem is optical correlation. Correlation has been successfully demonstrated under ideal conditions; however, noise significantly affects the ability of the correlator to accurately identify input signals. Optical correlation in the presence of noise must be successfully demonstrated before this technology can be incorporated into system design. An optical correlator is designed and constructed using a modified 2f configuration. Liquid crystal televisions (LCTV) are used as the spatial light modulators (SLM) for both the input and filter devices. The filter LCTV is characterized and an operating curve is developed. Determination of this operating curve is critical for reduction of input noise. Correlation of live input with a programmable filter is demonstrated.

Optical correlation

NASA Astrophysics Data System (ADS)

Cotariu, Steven S.

1991-12-01

Pattern recognition may supplement or replace certain navigational aids on spacecraft in docking or landing activities. The need to correctly identify terrain features remains critical in preparation of autonomous planetary landing. One technique that may solve this problem is optical correlation. Correlation has been successfully demonstrated under ideal conditions; however, noise significantly affects the ability of the correlator to accurately identify input signals. Optical correlation in the presence of noise must be successfully demonstrated before this technology can be incorporated into system design. An optical correlator is designed and constructed using a modified 2f configuration. Liquid crystal televisions (LCTV) are used as the spatial light modulators (SLM) for both the input and filter devices. The filter LCTV is characterized and an operating curve is developed. Determination of this operating curve is critical for reduction of input noise. Correlation of live input with a programmable filter is demonstrated.

A provisional effective evaluation when errors are present in independent variables

NASA Technical Reports Server (NTRS)

Gurin, L. S.

1983-01-01

Algorithms are examined for evaluating the parameters of a regression model when there are errors in the independent variables. The algorithms are fast and the estimates they yield are stable with respect to the correlation of errors and measurements of both the dependent variable and the independent variables.

Carrier density independent scattering rate in SrTiO3-based electron liquids

PubMed Central

Mikheev, Evgeny; Raghavan, Santosh; Zhang, Jack Y.; Marshall, Patrick B.; Kajdos, Adam P.; Balents, Leon; Stemmer, Susanne

2016-01-01

We examine the carrier density dependence of the scattering rate in two- and three-dimensional electron liquids in SrTiO3 in the regime where it scales with Tn (T is the temperature and n ≤ 2) in the cases when it is varied by electrostatic control and chemical doping, respectively. It is shown that the scattering rate is independent of the carrier density. This is contrary to the expectations from Landau Fermi liquid theory, where the scattering rate scales inversely with the Fermi energy (EF). We discuss that the behavior is very similar to systems traditionally identified as non-Fermi liquids (n < 2). This includes the cuprates and other transition metal oxide perovskites, where strikingly similar density-independent scattering rates have been observed. The results indicate that the applicability of Fermi liquid theory should be questioned for a much broader range of correlated materials and point to the need for a unified theory. PMID:26861764

Plasma MIC-1 correlates with systemic inflammation but is not an independent determinant of nutritional status or survival in oesophago-gastric cancer

PubMed Central

Skipworth, R J E; Deans, D A C; Tan, B H L; Sangster, K; Paterson-Brown, S; Brown, D A; Hunter, M; Breit, S N; Ross, J A; Fearon, K C H

2010-01-01

Background: Macrophage inhibitory cytokine-1(MIC-1) is a potential modulator of systemic inflammation and nutritional depletion, both of which are adverse prognostic factors in oesophago-gastric cancer (OGC). Methods: Plasma MIC-1, systemic inflammation (defined as plasma C-reactive protein (CRP) of ⩾10 mg l–1 or modified Glasgow prognostic score (mGPS) of ⩾1), and nutritional status were assessed in newly diagnosed OGC patients (n=293). Healthy volunteers (n=35) served as controls. Results: MIC-1 was elevated in patients (median=1371 pg ml–1; range 141–39 053) when compared with controls (median=377 pg ml–1; range 141–3786; P<0.001). Patients with gastric tumours (median=1592 pg ml–1; range 141–12 643) showed higher MIC-1 concentrations than patients with junctional (median=1337 pg ml–1; range 383–39 053) and oesophageal tumours (median=1180 pg ml–1; range 258–31 184; P=0.015). Patients showed a median weight loss of 6.4% (range 0.0–33.4%), and 42% of patients had an mGPS of ⩾1 or plasma CRP of ⩾10 mg l–1 (median=9 mg l–1; range 1–200). MIC-1 correlated positively with disease stage (r2=0.217; P<0.001), age (r2=0.332; P<0.001), CRP (r2=0.314; P<0.001), and mGPS (r2=0.336; P<0.001), and negatively with Karnofsky Performance Score (r2=−0.269; P<0.001). However, although MIC-1 correlated weakly with dietary intake (r2=0.157; P=0.031), it did not correlate with weight loss, BMI, or anthropometry. Patients with MIC-1 levels in the upper quartile showed reduced survival (median=204 days; 95% CI 157–251) when compared with patients with MIC-1 levels in the lower three quartiles (median=316 days; 95% CI 259–373; P=0.036), but MIC-1 was not an independent prognostic indicator. Conclusions: There is no independent link between plasma MIC-1 levels and depleted nutritional status or survival in OGC. PMID:20104227

Nutritional status deteriorates as the severity of diabetic foot ulcers increases and independently associates with prognosis.

PubMed

Zhang, Shan-Shan; Tang, Zheng-Yi; Fang, Ping; Qian, Hong-Jie; Xu, Lei; Ning, Guang

2013-01-01

The prognosis for diabetic foot ulcers (DFUs) remains poor. Nutritional status has not been identified as one of the factors affecting the outcome of DFUs. Therefore, indicators correlated with nutritional status and outcome were analyzed to investigate their relationship. A total of 192 hospitalized patients with Wagner grade 1-5 ulcers and 60 patients with Wagner grade 0 ulcers (all had type 2 diabetes) were assessed by the following: subjective global assessment (SGA), anthropometric measurements, biochemical indicators and physical examinations to evaluate nutritional status, severity of infection and complications. Patient outcome was recorded as healing of the ulcer and the patients were followed up for 6 months or until the wound was healed. The percentage of malnutrition was 62.0% in the DFU patients. The SGA was closely correlated with infection (r=0.64), outcome (r=0.37) and BMI (r=-0.36), all P<0.001. The risk of poor outcome increased with malnutrition [odds ratio (OR), 10.6, P<0.001]. The nutritional status of the DFU patients was independently correlated with the severity of infection and outcome (both P<0.001) and Wagner grades and nutritional status (SGA) were independent risk factors for patient outcome (both P<0.001). Nutritional status deteriorated as the severity of the DFU increased, and malnutrition was a predictor of poor prognosis.

Naive Bayes Bearing Fault Diagnosis Based on Enhanced Independence of Data

PubMed Central

Zhang, Nannan; Wu, Lifeng; Yang, Jing; Guan, Yong

2018-01-01

The bearing is the key component of rotating machinery, and its performance directly determines the reliability and safety of the system. Data-based bearing fault diagnosis has become a research hotspot. Naive Bayes (NB), which is based on independent presumption, is widely used in fault diagnosis. However, the bearing data are not completely independent, which reduces the performance of NB algorithms. In order to solve this problem, we propose a NB bearing fault diagnosis method based on enhanced independence of data. The method deals with data vector from two aspects: the attribute feature and the sample dimension. After processing, the classification limitation of NB is reduced by the independence hypothesis. First, we extract the statistical characteristics of the original signal of the bearings effectively. Then, the Decision Tree algorithm is used to select the important features of the time domain signal, and the low correlation features is selected. Next, the Selective Support Vector Machine (SSVM) is used to prune the dimension data and remove redundant vectors. Finally, we use NB to diagnose the fault with the low correlation data. The experimental results show that the independent enhancement of data is effective for bearing fault diagnosis. PMID:29401730

A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants

PubMed Central

2011-01-01

Background The numerous diverse metabolic pathways by which plant compounds can be produced make it difficult to predict how colour pigmentation is lost for different tissues and plants. This study employs mathematical and in silico methods to identify correlated gene targets for the loss of colour pigmentation in plants from a whole cell perspective based on the full metabolic network of Arabidopsis. This involves extracting a self-contained flavonoid subnetwork from the AraCyc database and calculating feasible metabolic routes or elementary modes (EMs) for it. Those EMs leading to anthocyanin compounds are taken to constitute the anthocyanin biosynthetic pathway (ABP) and their interplay with the rest of the EMs is used to study the minimal cut sets (MCSs), which are different combinations of reactions to block for eliminating colour pigmentation. By relating the reactions to their corresponding genes, the MCSs are used to explore the phenotypic roles of the ABP genes, their relevance to the ABP and the impact their eliminations would have on other processes in the cell. Results Simulation and prediction results of the effect of different MCSs for eliminating colour pigmentation correspond with existing experimental observations. Two examples are: i) two MCSs which require the simultaneous suppression of genes DFR and ANS to eliminate colour pigmentation, correspond to observational results of the same genes being co-regulated for eliminating floral pigmentation in Aquilegia and; ii) the impact of another MCS requiring CHS suppression, corresponds to findings where the suppression of the early gene CHS eliminated nearly all flavonoids but did not affect the production of volatile benzenoids responsible for floral scent. Conclusions From the various MCSs identified for eliminating colour pigmentation, several correlate to existing experimental observations, indicating that different MCSs are suitable for different plants, different cells, and different conditions

Independent Prognostic Factors for Acute Organophosphorus Pesticide Poisoning.

PubMed

Tang, Weidong; Ruan, Feng; Chen, Qi; Chen, Suping; Shao, Xuebo; Gao, Jianbo; Zhang, Mao

2016-07-01

Acute organophosphorus pesticide poisoning (AOPP) is becoming a significant problem and a potential cause of human mortality because of the abuse of organophosphate compounds. This study aims to determine the independent prognostic factors of AOPP by using multivariate logistic regression analysis. The clinical data for 71 subjects with AOPP admitted to our hospital were retrospectively analyzed. This information included the Acute Physiology and Chronic Health Evaluation II (APACHE II) scores, 6-h post-admission blood lactate levels, post-admission 6-h lactate clearance rates, admission blood cholinesterase levels, 6-h post-admission blood cholinesterase levels, cholinesterase activity, blood pH, and other factors. Univariate analysis and multivariate logistic regression analyses were conducted to identify all prognostic factors and independent prognostic factors, respectively. A receiver operating characteristic curve was plotted to analyze the testing power of independent prognostic factors. Twelve of 71 subjects died. Admission blood lactate levels, 6-h post-admission blood lactate levels, post-admission 6-h lactate clearance rates, blood pH, and APACHE II scores were identified as prognostic factors for AOPP according to the univariate analysis, whereas only 6-h post-admission blood lactate levels, post-admission 6-h lactate clearance rates, and blood pH were independent prognostic factors identified by multivariate logistic regression analysis. The receiver operating characteristic analysis suggested that post-admission 6-h lactate clearance rates were of moderate diagnostic value. High 6-h post-admission blood lactate levels, low blood pH, and low post-admission 6-h lactate clearance rates were independent prognostic factors identified by multivariate logistic regression analysis. Copyright © 2016 by Daedalus Enterprises.

Device-Independent Certification of a Nonprojective Qubit Measurement

NASA Astrophysics Data System (ADS)

Gómez, Esteban S.; Gómez, Santiago; González, Pablo; Cañas, Gustavo; Barra, Johanna F.; Delgado, Aldo; Xavier, Guilherme B.; Cabello, Adán; Kleinmann, Matthias; Vértesi, Tamás; Lima, Gustavo

2016-12-01

Quantum measurements on a two-level system can have more than two independent outcomes, and in this case, the measurement cannot be projective. Measurements of this general type are essential to an operational approach to quantum theory, but so far, the nonprojective character of a measurement can only be verified experimentally by already assuming a specific quantum model of parts of the experimental setup. Here, we overcome this restriction by using a device-independent approach. In an experiment on pairs of polarization-entangled photonic qubits we violate by more than 8 standard deviations a Bell-like correlation inequality that is valid for all sets of two-outcome measurements in any dimension. We combine this with a device-independent verification that the system is best described by two qubits, which therefore constitutes the first device-independent certification of a nonprojective quantum measurement.

Paternal education status significantly influences infants' measles vaccination uptake, independent of maternal education status.

PubMed

Rammohan, Anu; Awofeso, Niyi; Fernandez, Renae C

2012-05-08

Despite increased funding of measles vaccination programs by national governments and international aid agencies, structural factors encumber attainment of childhood measles immunisation to levels which may guarantee herd immunity. One of such factors is parental education status. Research on the links between parental education and vaccination has typically focused on the influence of maternal education status. This study aims to demonstrate the independent influence of paternal education status on measles immunisation. Comparable nationally representative survey data were obtained from six countries with the highest numbers of children missing the measles vaccine in 2008. Logistic regression analysis was applied to examine the influence of paternal education on uptake of the first dose of measles vaccination, independent of maternal education, whilst controlling for confounding factors such as respondent's age, urban/rural residence, province/state of residence, religion, wealth and occupation. The results of the analysis show that even if a mother is illiterate, having a father with an education of Secondary (high school) schooling and above is statistically significant and positively correlated with the likelihood of a child being vaccinated for measles, in the six countries analysed. Paternal education of secondary or higher level was significantly and independently correlated with measles immunisation uptake after controlling for all potential confounders. The influence of paternal education status on measles immunisation uptake was investigated and found to be statistically significant in six nations with the biggest gaps in measles immunisation coverage in 2008. This study underscores the imperative of utilising both maternal and paternal education as screening variables to identify children at risk of missing measles vaccination prospectively.

The relationship between motor function, cognition, independence and quality of life in myelomeningocele patients.

PubMed

Luz, Carolina Lundberg; Moura, Maria Clara Drummond Soares de; Becker, Karine Kyomi; Teixeira, Rosani Aparecida Antunes; Voos, Mariana Callil; Hasue, Renata Hydee

2017-08-01

Motor function, cognition, functional independence and quality of life have been described in myelomeningocele patients, but no study has investigated their relationships. We aimed to investigate the relationships between motor function, cognition, functional independence, quality of life, age, and lesion level in myelomeningocele patients, and investigate the influence of hydrocephalus on these variables. We assessed 47 patients with the Gross Motor Function Measure (motor function), Raven's Colored Progressive Matrices (cognition), Pediatric Evaluation of Disability Inventory (functional independence) and the Autoquestionnaire Qualité de vie Enfant Imagé (quality of life). Spearman's correlation tests determined relationships between the variables. The Friedman ANOVAs determined the influence of hydrocephalus. Motor function was strongly related to mobility and lesion level, and moderately related to cognition, self-care and social function. Cognition and quality of life were moderately related to functional independence. Age correlated moderately with functional independence and quality of life. Hydrocephalus resulted in poorer motor/cognitive outcomes and lower functional independence.

Are Independent Probes Truly Independent?

ERIC Educational Resources Information Center

Camp, Gino; Pecher, Diane; Schmidt, Henk G.; Zeelenberg, Rene

2009-01-01

The independent cue technique has been developed to test traditional interference theories against inhibition theories of forgetting. In the present study, the authors tested the critical criterion for the independence of independent cues: Studied cues not presented during test (and unrelated to test cues) should not contribute to the retrieval…

Accuracy Evaluation of the Unified P-Value from Combining Correlated P-Values

PubMed Central

Alves, Gelio; Yu, Yi-Kuo

2014-01-01

Meta-analysis methods that combine -values into a single unified -value are frequently employed to improve confidence in hypothesis testing. An assumption made by most meta-analysis methods is that the -values to be combined are independent, which may not always be true. To investigate the accuracy of the unified -value from combining correlated -values, we have evaluated a family of statistical methods that combine: independent, weighted independent, correlated, and weighted correlated -values. Statistical accuracy evaluation by combining simulated correlated -values showed that correlation among -values can have a significant effect on the accuracy of the combined -value obtained. Among the statistical methods evaluated those that weight -values compute more accurate combined -values than those that do not. Also, statistical methods that utilize the correlation information have the best performance, producing significantly more accurate combined -values. In our study we have demonstrated that statistical methods that combine -values based on the assumption of independence can produce inaccurate -values when combining correlated -values, even when the -values are only weakly correlated. Therefore, to prevent from drawing false conclusions during hypothesis testing, our study advises caution be used when interpreting the -value obtained from combining -values of unknown correlation. However, when the correlation information is available, the weighting-capable statistical method, first introduced by Brown and recently modified by Hou, seems to perform the best amongst the methods investigated. PMID:24663491

Seed germination strategies: an evolutionary trajectory independent of vegetative functional traits

PubMed Central

Hoyle, Gemma L.; Steadman, Kathryn J.; Good, Roger B.; McIntosh, Emma J.; Galea, Lucy M. E.; Nicotra, Adrienne B.

2015-01-01

Seed germination strategies vary dramatically among species but relatively little is known about how germination traits correlate with other elements of plant strategy systems. Understanding drivers of germination strategy is critical to our understanding of the evolutionary biology of plant reproduction.We present a novel assessment of seed germination strategies focussing on Australian alpine species as a case study. We describe the distribution of germination strategies and ask whether these are correlated with, or form an independent axis to, other plant functional traits. Our approach to describing germination strategy mimicked realistic temperatures that seeds experience in situ following dispersal. Strategies were subsequently assigned using an objective clustering approach. We hypothesized that two main strategies would emerge, involving dormant or non-dormant seeds, and that while these strategies would be correlated with seed traits (e.g., mass or endospermy) they would be largely independent of vegetative traits when analysed in a phylogenetically structured manner.Across all species, three germination strategies emerged. The majority of species postponed germination until after a period of cold, winter-like temperatures indicating physiological and/or morphological dormancy mechanisms. Other species exhibited immediate germination at temperatures representative of those at dispersal. Interestingly, seeds of an additional 13 species “staggered” germination over time. Germination strategies were generally conserved within families. Across a broad range of ecological traits only seed mass and endospermy showed any correlation with germination strategy when phylogenetic relatedness was accounted for; vegetative traits showed no significant correlations with germination strategy. The results indicate that germination traits correlate with other aspects of seed ecology but form an independent axis relative to vegetative traits. PMID:26528294

COPD-related bronchiectasis; independent impact on disease course and outcomes.

PubMed

Gatheral, Timothy; Kumar, Neelam; Sansom, Ben; Lai, Dilys; Nair, Arjun; Vlahos, Ioannis; Baker, Emma H

2014-12-01

COPD and radiographic bronchiectasis frequently coexist but the effect of this on the clinical course of COPD is not fully understood. We determined the impact of bronchiectasis on clinical outcomes in COPD patients, independent of coexisting emphysema and bronchial wall thickening (BWT). COPD patients admitted with first exacerbation 1998-2008 were identified retrospectively using ICD10 codes J44.0,1,8,9. Patients with suitable CT scans were graded for severity of bronchiectasis, emphysema and BWT on a 5 point scale (0-absent, 1-minor, 2-mild, 3-moderate, 4-severe). 406 patients (71 ± 11 years, 56% male, FEV1 52 ± 23% predicted) were included; 278 (69%) patients had bronchiectasis: minor, 112 (40%); mild, 81 (29%); moderate, 62 (22%); severe 23 (8%). Bronchiectasis severity correlated with severity of BWT (p < 0.001) but not emphysema (p = 0.090). Bronchiectasis independently determined sputum isolation of Pseudomonas aeruginosa (Odds ratio (OR) 1.39 (95% CI 1.07 to 1.80), p = 0.013) and atypical mycobacteria (OR 2.44 (95% CI 1.04 to 5.69), p = 0.040), annual respiratory admissions (p = 0.044) and inpatient days (p < 0.001), but did not predict survival (p = 0.256). Radiographic bronchiectasis in COPD patients is associated with increased respiratory infection and hospitalisation, independent of coexisting emphysema and BWT. COPD-related bronchiectasis is therefore an important diagnosis with potential implications for treatment.

Transcriptomic correlates of neuron electrophysiological diversity

PubMed Central

Li, Brenna; Crichlow, Cindy-Lee; Mancarci, B. Ogan; Pavlidis, Paul

2017-01-01

How neuronal diversity emerges from complex patterns of gene expression remains poorly understood. Here we present an approach to understand electrophysiological diversity through gene expression by integrating pooled- and single-cell transcriptomics with intracellular electrophysiology. Using neuroinformatics methods, we compiled a brain-wide dataset of 34 neuron types with paired gene expression and intrinsic electrophysiological features from publically accessible sources, the largest such collection to date. We identified 420 genes whose expression levels significantly correlated with variability in one or more of 11 physiological parameters. We next trained statistical models to infer cellular features from multivariate gene expression patterns. Such models were predictive of gene-electrophysiological relationships in an independent collection of 12 visual cortex cell types from the Allen Institute, suggesting that these correlations might reflect general principles relating expression patterns to phenotypic diversity across very different cell types. Many associations reported here have the potential to provide new insights into how neurons generate functional diversity, and correlations of ion channel genes like Gabrd and Scn1a (Nav1.1) with resting potential and spiking frequency are consistent with known causal mechanisms. Our work highlights the promise and inherent challenges in using cell type-specific transcriptomics to understand the mechanistic origins of neuronal diversity. PMID:29069078

Identifying environmental correlates of intraspecific genetic variation.

PubMed

Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

2016-09-01

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

Correlation, Cost Risk, and Geometry

NASA Technical Reports Server (NTRS)

Dean, Edwin B.

1992-01-01

The geometric viewpoint identifies the choice of a correlation matrix for the simulation of cost risk with the pairwise choice of data vectors corresponding to the parameters used to obtain cost risk. The correlation coefficient is the cosine of the angle between the data vectors after translation to an origin at the mean and normalization for magnitude. Thus correlation is equivalent to expressing the data in terms of a non orthogonal basis. To understand the many resulting phenomena requires the use of the tensor concept of raising the index to transform the measured and observed covariant components into contravariant components before vector addition can be applied. The geometric viewpoint also demonstrates that correlation and covariance are geometric properties, as opposed to purely statistical properties, of the variates. Thus, variates from different distributions may be correlated, as desired, after selection from independent distributions. By determining the principal components of the correlation matrix, variates with the desired mean, magnitude, and correlation can be generated through linear transforms which include the eigenvalues and the eigenvectors of the correlation matrix. The conversion of the data to a non orthogonal basis uses a compound linear transformation which distorts or stretches the data space. Hence, the correlated data does not have the same properties as the uncorrelated data used to generate it. This phenomena is responsible for seemingly strange observations such as the fact that the marginal distributions of the correlated data can be quite different from the distributions used to generate the data. The joint effect of statistical distributions and correlation remains a fertile area for further research. In terms of application to cost estimating, the geometric approach demonstrates that the estimator must have data and must understand that data in order to properly choose the correlation matrix appropriate for a given estimate

Experimental assessment of the importance of amino acid positions identified by an entropy-based correlation analysis of multiple-sequence alignments.

PubMed

Dietrich, Susanne; Borst, Nadine; Schlee, Sandra; Schneider, Daniel; Janda, Jan-Oliver; Sterner, Reinhard; Merkl, Rainer

2012-07-17

The analysis of a multiple-sequence alignment (MSA) with correlation methods identifies pairs of residue positions whose occupation with amino acids changes in a concerted manner. It is plausible to assume that positions that are part of many such correlation pairs are important for protein function or stability. We have used the algorithm H2r to identify positions k in the MSAs of the enzymes anthranilate phosphoribosyl transferase (AnPRT) and indole-3-glycerol phosphate synthase (IGPS) that show a high conn(k) value, i.e., a large number of significant correlations in which k is involved. The importance of the identified residues was experimentally validated by performing mutagenesis studies with sAnPRT and sIGPS from the archaeon Sulfolobus solfataricus. For sAnPRT, five H2r mutant proteins were generated by replacing nonconserved residues with alanine or the prevalent residue of the MSA. As a control, five residues with conn(k) values of zero were chosen randomly and replaced with alanine. The catalytic activities and conformational stabilities of the H2r and control mutant proteins were analyzed by steady-state enzyme kinetics and thermal unfolding studies. Compared to wild-type sAnPRT, the catalytic efficiencies (k(cat)/K(M)) were largely unaltered. In contrast, the apparent thermal unfolding temperature (T(M)(app)) was lowered in most proteins. Remarkably, the strongest observed destabilization (ΔT(M)(app) = 14 °C) was caused by the V284A exchange, which pertains to the position with the highest correlation signal [conn(k) = 11]. For sIGPS, six H2r mutant and four control proteins with alanine exchanges were generated and characterized. The k(cat)/K(M) values of four H2r mutant proteins were reduced between 13- and 120-fold, and their T(M)(app) values were decreased by up to 5 °C. For the sIGPS control proteins, the observed activity and stability decreases were much less severe. Our findings demonstrate that positions with high conn(k) values have an

Measuring Frailty Can Help Emergency Departments Identify Independent Seniors at Risk of Functional Decline After Minor Injuries.

PubMed

Sirois, Marie-Josée; Griffith, Lauren; Perry, Jeffrey; Daoust, Raoul; Veillette, Nathalie; Lee, Jacques; Pelletier, Mathieu; Wilding, Laura; Émond, Marcel

2017-01-01

This study aims to (i) describe frailty in the subgroup of independent community-dwelling seniors consulting emergency departments (EDs) for minor injuries, (ii) examine the association between frailty and functional decline 3 months postinjury, (iii) ascertain the predictive accuracy of frailty measures and emergency physicians' for functional decline. Prospective cohort in 2011-2013 among 1,072 seniors aged 65 years or older, independent in basic daily activities, evaluated in Canadian EDs for minor injuries.Frailty was assessed at EDs using the Canadian Study of Health and Aging-Clinical Frailty scale (CSHA-CFS) and the Study of Osteoporotic Fracture frailty index (SOF). Functional decline was defined as a loss ≥2/28 on the Older American Resources Services scale 3 months postinjury. Generalized mixed models were used to explore differences in functional decline across frailty levels. Areas under the receiver operating characteristic curve were used to ascertain the predictive accuracy of frailty measures and emergency physicians' clinical judgment. The SOF and CSHA-CFS were available in 342 and 1,058 participants, respectively. The SOF identified 55.6%, 32.7%, 11.7% patients as robust, prefrail, and frail. These CSHA-CFS (n = 1,058) proportions were 51.9%, 38.3%, and 9.9%. The 3-month incidence of functional decline was 12.1% (10.0%-14.6%). The Areas under the receiver operating characteristic curves of the CSHA-CFS and the emergency physicians' were similar (0.548-0.777), while the SOF was somewhat higher (0.704-0.859). Measuring frailty in community-dwelling seniors with minor injuries in EDs may enhance current risk screening for functional decline. However, before implementation in usual care, feasibility issues such as inter-rater reliability and acceptability of frailty tools in the EDs have to be addressed. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions

Genetic variants associated with subjective well-being, depressive symptoms and neuroticism identified through genome-wide analyses

PubMed Central

Derringer, Jaime; Gratten, Jacob; Lee, James J; Liu, Jimmy Z; de Vlaming, Ronald; Ahluwalia, Tarunveer S; Buchwald, Jadwiga; Cavadino, Alana; Frazier-Wood, Alexis C; Davies, Gail; Furlotte, Nicholas A; Garfield, Victoria; Geisel, Marie Henrike; Gonzalez, Juan R; Haitjema, Saskia; Karlsson, Robert; van der Laan, Sander W; Ladwig, Karl-Heinz; Lahti, Jari; van der Lee, Sven J; Miller, Michael B; Lind, Penelope A; Liu, Tian; Matteson, Lindsay; Mihailov, Evelin; Minica, Camelia C; Nolte, Ilja M; Mook-Kanamori, Dennis O; van der Most, Peter J; Oldmeadow, Christopher; Qian, Yong; Raitakari, Olli; Rawal, Rajesh; Realo, Anu; Rueedi, Rico; Schmidt, Börge; Smith, Albert V; Stergiakouli, Evie; Tanaka, Toshiko; Taylor, Kent; Thorleifsson, Gudmar; Wedenoja, Juho; Wellmann, Juergen; Westra, Harm-Jan; Willems, Sara M; Zhao, Wei; Amin, Najaf; Bakshi, Andrew; Bergmann, Sven; Bjornsdottir, Gyda; Boyle, Patricia A; Cherney, Samantha; Cox, Simon R; Davis, Oliver S P; Ding, Jun; Direk, Nese; Eibich, Peter; Emeny, Rebecca T; Fatemifar, Ghazaleh; Faul, Jessica D; Ferrucci, Luigi; Forstner, Andreas J; Gieger, Christian; Gupta, Richa; Harris, Tamara B; Harris, Juliette M; Holliday, Elizabeth G; Hottenga, Jouke-Jan; De Jager, Philip L; Kaakinen, Marika A; Kajantie, Eero; Karhunen, Ville; Kolcic, Ivana; Kumari, Meena; Launer, Lenore J; Franke, Lude; Li-Gao, Ruifang; Liewald, David C; Koini, Marisa; Loukola, Anu; Marques-Vidal, Pedro; Montgomery, Grant W; Mosing, Miriam A; Paternoster, Lavinia; Pattie, Alison; Petrovic, Katja E; Pulkki-Råback, Laura; Quaye, Lydia; Räikkönen, Katri; Rudan, Igor; Scott, Rodney J; Smith, Jennifer A; Sutin, Angelina R; Trzaskowski, Maciej; Vinkhuyzen, Anna E; Yu, Lei; Zabaneh, Delilah; Attia, John R; Bennett, David A; Berger, Klaus; Bertram, Lars; Boomsma, Dorret I; Snieder, Harold; Chang, Shun-Chiao; Cucca, Francesco; Deary, Ian J; van Duijn, Cornelia M; Eriksson, Johan G; Bültmann, Ute; de Geus, Eco J C; Groenen, Patrick J F; Gudnason, Vilmundur; Hansen, Torben; Hartman, Catharine A; Haworth, Claire M A; Hayward, Caroline; Heath, Andrew C; Hinds, David A; Hyppönen, Elina; Iacono, William G; Järvelin, Marjo-Riitta; Jöckel, Karl-Heinz; Kaprio, Jaakko; Kardia, Sharon L R; Keltikangas-Järvinen, Liisa; Kraft, Peter; Kubzansky, Laura D; Lehtimäki, Terho; Magnusson, Patrik K E; Martin, Nicholas G; McGue, Matt; Metspalu, Andres; Mills, Melinda; de Mutsert, Renée; Oldehinkel, Albertine J; Pasterkamp, Gerard; Pedersen, Nancy L; Plomin, Robert; Polasek, Ozren; Power, Christine; Rich, Stephen S; Rosendaal, Frits R; den Ruijter, Hester M; Schlessinger, David; Schmidt, Helena; Svento, Rauli; Schmidt, Reinhold; Alizadeh, Behrooz Z; Sørensen, Thorkild I A; Spector, Tim D; Starr, John M; Stefansson, Kari; Steptoe, Andrew; Terracciano, Antonio; Thorsteinsdottir, Unnur; Thurik, A Roy; Timpson, Nicholas J; Tiemeier, Henning; Uitterlinden, André G; Vollenweider, Peter; Wagner, Gert G; Weir, David R; Yang, Jian; Conley, Dalton C; Smith, George Davey; Hofman, Albert; Johannesson, Magnus; Laibson, David I; Medland, Sarah E; Meyer, Michelle N; Pickrell, Joseph K; Esko, Tõnu; Krueger, Robert F; Beauchamp, Jonathan P; Koellinger, Philipp D; Benjamin, Daniel J; Bartels, Meike; Cesarini, David

2016-01-01

We conducted genome-wide association studies of three phenotypes: subjective well-being (N = 298,420), depressive symptoms (N = 161,460), and neuroticism (N = 170,910). We identified three variants associated with subjective well-being, two with depressive symptoms, and eleven with neuroticism, including two inversion polymorphisms. The two depressive symptoms loci replicate in an independent depression sample. Joint analyses that exploit the high genetic correlations between the phenotypes (|ρ^| ≈ 0.8) strengthen the overall credibility of the findings, and allow us to identify additional variants. Across our phenotypes, loci regulating expression in central nervous system and adrenal/pancreas tissues are strongly enriched for association. PMID:27089181

Correlational structure of 'frontal' tests and intelligence tests indicates two components with asymmetrical neurostructural correlates in old age.

PubMed

Cox, Simon R; MacPherson, Sarah E; Ferguson, Karen J; Nissan, Jack; Royle, Natalie A; MacLullich, Alasdair M J; Wardlaw, Joanna M; Deary, Ian J

2014-09-01

Both general fluid intelligence ( g f ) and performance on some 'frontal tests' of cognition decline with age. Both types of ability are at least partially dependent on the integrity of the frontal lobes, which also deteriorate with age. Overlap between these two methods of assessing complex cognition in older age remains unclear. Such overlap could be investigated using inter-test correlations alone, as in previous studies, but this would be enhanced by ascertaining whether frontal test performance and g f share neurobiological variance. To this end, we examined relationships between g f and 6 frontal tests (Tower, Self-Ordered Pointing, Simon, Moral Dilemmas, Reversal Learning and Faux Pas tests) in 90 healthy males, aged ~ 73 years. We interpreted their correlational structure using principal component analysis, and in relation to MRI-derived regional frontal lobe volumes (relative to maximal healthy brain size). g f correlated significantly and positively (.24 ≤  r  ≤ .53) with the majority of frontal test scores. Some frontal test scores also exhibited shared variance after controlling for g f . Principal component analysis of test scores identified units of g f -common and g f -independent variance. The former was associated with variance in the left dorsolateral (DL) and anterior cingulate (AC) regions, and the latter with variance in the right DL and AC regions. Thus, we identify two biologically-meaningful components of variance in complex cognitive performance in older age and suggest that age-related changes to DL and AC have the greatest cognitive impact.

The Skill of Identifying Argumentation.

ERIC Educational Resources Information Center

van Eemeren, Frans H.; And Others

1989-01-01

Investigates 14-year-old students' ability to recognize argumentation without having systematic instruction; and whether the identification of argumentation is an independent skill. Finds that after a 20-minute explanation, a large proportion of 14-year-olds could not identify simple argumentation. Concludes that identifying argumentation is a…

Early Origins of Autism Comorbidity: Neuropsychiatric Traits Correlated in Childhood Are Independent in Infancy.

PubMed

Hawks, Zoë W; Marrus, Natasha; Glowinski, Anne L; Constantino, John N

2018-03-16

Previous research has suggested that behavioral comorbidity is the rule rather than the exception in autism. The present study aimed to trace the respective origins of autistic and general psychopathologic traits-and their association-to infancy. Measurements of autistic traits and early liability for general psychopathology were assessed in 314 twins at 18 months, ascertained from the general population using birth records. 222 twins were re-evaluated at 36 months. Standardized ratings of variation in social communication at 18 months were highly heritable and strongly predicted autistic trait scores at 36 months. These early indices of autistic liability were independent from contemporaneous ratings of behavior problems on the Brief Infant-Toddler Social and Emotional Assessment (which were substantially environmentally-influenced), and did not meaningfully predict internalizing or externalizing scores on the Achenbach Scales of Empirically Based Assessment at 36 months. In this general population infant twin study, variation in social communication was independent from variation in other domains of general psychopathology, and exhibited a distinct genetic structure. The commonly-observed comorbidity of specific psychiatric syndromes with autism may arise from subsequent interactions between autistic liability and independent susceptibilities to other psychopathologic traits, suggesting opportunities for preventive amelioration of outcomes of these interactions over the course of development.

Independence as a practice issue in occupational therapy: the safety clause.

PubMed

Russell, Cherry; Fitzgerald, Maureen H; Williamson, Peter; Manor, Debra; Whybrow, Samantha

2002-01-01

This article reports findings from interviews that explored the meanings occupational therapists attach to independence as a value and a therapeutic goal in interactions with elderly clients. Through a historical review of the literature, we trace the changing use of this term and identify two analytically distinct concepts associated with it: independence as self-reliance in activity and independence as autonomy, self-determination, or choice. We show how the latter has emerged in contemporary service contexts to represent an ideal of client-centered practice for persons with chronic disabilities, such as frail elderly clients. Using a "critical incident" interview approach with 12 Australian occupational therapists, we identified the therapists' explicit and implicit understandings of independence as a value concept and practice issue. Our findings suggest that a mismatch often exists between idealized and practice-based talk about independence and that therapists narrativize this opposition around what we call "the safety clause." That is, therapists invoke concerns about safety and duty of care as a caveat to implementing their independence ideals and justifying the retention of professional control. We identify key issues that therapists need to address if the rhetoric of independence-related client-centered practice is to be achieved in reality.

Harnessing pain heterogeneity and RNA transcriptome to identify blood–based pain biomarkers: a novel correlational study design and bioinformatics approach in a graded chronic constriction injury model

PubMed Central

Grace, Peter M.; Hurley, Daniel; Barratt, Daniel T.; Tsykin, Anna; Watkins, Linda R.; Rolan, Paul E.; Hutchinson, Mark R.

2017-01-01

A quantitative, peripherally accessible biomarker for neuropathic pain has great potential to improve clinical outcomes. Based on the premise that peripheral and central immunity contribute to neuropathic pain mechanisms, we hypothesized that biomarkers could be identified from the whole blood of adult male rats, by integrating graded chronic constriction injury (CCI), ipsilateral lumbar dorsal quadrant (iLDQ) and whole blood transcriptomes, and pathway analysis with pain behavior. Correlational bioinformatics identified a range of putative biomarker genes for allodynia intensity, many encoding for proteins with a recognized role in immune/nociceptive mechanisms. A selection of these genes was validated in a separate replication study. Pathway analysis of the iLDQ transcriptome identified Fcγ and Fcε signaling pathways, among others. This study is the first to employ the whole blood transcriptome to identify pain biomarker panels. The novel correlational bioinformatics, developed here, selected such putative biomarkers based on a correlation with pain behavior and formation of signaling pathways with iLDQ genes. Future studies may demonstrate the predictive ability of these biomarker genes across other models and additional variables. PMID:22697386

Di-hadron correlations with identified leading hadrons in 200 GeV Au + Au and d + Au collisions at STAR

NASA Astrophysics Data System (ADS)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Alekseev, I.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Averichev, G. S.; Bai, X.; Bairathi, V.; Banerjee, A.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Bouchet, J.; Brandenburg, D.; Brandin, A. V.; Bunzarov, I.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Campbell, J. M.; Cebra, D.; Cervantes, M. C.; Chakaberia, I.; Chaloupka, P.; Chang, Z.; Chattopadhyay, S.; Chen, X.; Chen, J. H.; Cheng, J.; Cherney, M.; Christie, W.; Contin, G.; Crawford, H. J.; Das, S.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; di Ruzza, B.; Didenko, L.; Dilks, C.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Du, C. M.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Engelage, J.; Eppley, G.; Esha, R.; Evdokimov, O.; Eyser, O.; Fatemi, R.; Fazio, S.; Federic, P.; Fedorisin, J.; Feng, Z.; Filip, P.; Fisyak, Y.; Flores, C. E.; Fulek, L.; Gagliardi, C. A.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Greiner, L.; Grosnick, D.; Gunarathne, D. S.; Guo, Y.; Gupta, S.; Gupta, A.; Guryn, W.; Hamad, A.; Hamed, A.; Haque, R.; Harris, J. W.; He, L.; Heppelmann, S.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Hofman, D. J.; Horvat, S.; Huang, T.; Huang, B.; Huang, H. Z.; Huang, X.; Huck, P.; Humanic, T. J.; Igo, G.; Jacobs, W. W.; Jang, H.; Jia, J.; Jiang, K.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Khan, Z. H.; Kikoła, D. P.; Kisiel, A.; Kochenda, L.; Koetke, D. D.; Kosarzewski, L. K.; Kraishan, A. F.; Kravtsov, P.; Krueger, K.; Kumar, L.; Lamont, M. A. C.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Li, X.; Li, W.; Li, Z. M.; Li, Y.; Li, C.; Li, X.; Lisa, M. A.; Liu, F.; Ljubicic, T.; Llope, W. J.; Lomnitz, M.; Longacre, R. S.; Luo, X.; Ma, G. L.; Ma, Y. G.; Ma, R.; Ma, L.; Magdy, N.; Majka, R.; Manion, A.; Margetis, S.; Markert, C.; Masui, H.; Matis, H. S.; McDonald, D.; Meehan, K.; Mei, J. C.; Minaev, N. G.; Mioduszewski, S.; Mishra, D.; Mohanty, B.; Mondal, M. M.; Morozov, D. A.; Mustafa, M. K.; Nandi, B. K.; Nasim, Md.; Nayak, T. K.; Nigmatkulov, G.; Niida, T.; Nogach, L. V.; Noh, S. Y.; Novak, J.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Okorokov, V.; Olvitt, D.; Page, B. S.; Pak, R.; Pan, Y. X.; Pandit, Y.; Panebratsev, Y.; Pawlik, B.; Pei, H.; Perkins, C.; Peterson, A.; Pile, P.; Pluta, J.; Poniatowska, K.; Porter, J.; Posik, M.; Poskanzer, A. M.; Pruthi, N. K.; Putschke, J.; Qiu, H.; Quintero, A.; Ramachandran, S.; Raniwala, R.; Raniwala, S.; Ray, R. L.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Roy, A.; Ruan, L.; Rusnak, J.; Rusnakova, O.; Sahoo, N. R.; Sahu, P. K.; Sakrejda, I.; Salur, S.; Sandweiss, J.; Sarkar, A.; Schambach, J.; Scharenberg, R. P.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Seger, J.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, B.; Sharma, M. K.; Shen, W. Q.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Sikora, R.; Simko, M.; Singha, S.; Skoby, M. J.; Smirnov, N.; Smirnov, D.; Song, L.; Sorensen, P.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Stepanov, M.; Strikhanov, M.; Stringfellow, B.; Sumbera, M.; Summa, B.; Sun, Y.; Sun, Z.; Sun, X. M.; Sun, X.; Surrow, B.; Svirida, D. N.; Szelezniak, M. A.; Tang, A. H.; Tang, Z.; Tarnowsky, T.; Tawfik, A.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Todoroki, T.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Tripathy, S. K.; Tsai, O. D.; Ullrich, T.; Underwood, D. G.; Upsal, I.; Van Buren, G.; van Nieuwenhuizen, G.; Vandenbroucke, M.; Varma, R.; Vasiliev, A. N.; Vertesi, R.; Videbæk, F.; Viyogi, Y. P.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wang, J. S.; Wang, F.; Wang, H.; Wang, G.; Wang, Y.; Wang, Y.; Webb, G.; Webb, J. C.; Wen, L.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y. F.; Wu; Xiao, Z. G.; Xie, W.; Xin, K.; Xu, H.; Xu, Z.; Xu, Q. H.; Xu, Y. F.; Xu, N.; Yang, S.; Yang, Y.; Yang, Q.; Yang, Y.; Yang, C.; Yang, Y.; Ye, Z.; Ye, Z.; Yepes, P.; Yi, L.; Yip, K.; Yoo, I.-K.; Yu, N.; Zbroszczyk, H.; Zha, W.; Zhang, Y.; Zhang, Z.; Zhang, J. B.; Zhang, J.; Zhang, X. P.; Zhang, S.; Zhang, J.; Zhao, J.; Zhong, C.; Zhou, L.; Zhu, X.; Zoulkarneeva, Y.

2015-12-01

The STAR Collaboration presents for the first time two-dimensional di-hadron correlations with identified leading hadrons in 200 GeV central Au + Au and minimum-bias d + Au collisions to explore hadronization mechanisms in the quark gluon plasma. The enhancement of the jet-like yield for leading pions in Au + Au data with respect to the d + Au reference and the absence of such an enhancement for leading non-pions (protons and kaons) are discussed within the context of a quark recombination scenario. The correlated yield at large angles, specifically in the ridge region, is found to be significantly higher for leading non-pions than pions. The consistencies of the constituent quark scaling, azimuthal harmonic model and a mini-jet modification model description of the data are tested, providing further constraints on hadronization.

Loss of consciousness is related to hyper-correlated gamma-band activity in anesthetized macaques and sleeping humans.

PubMed

Bola, Michał; Barrett, Adam B; Pigorini, Andrea; Nobili, Lino; Seth, Anil K; Marchewka, Artur

2018-02-15

Loss of consciousness can result from a wide range of causes, including natural sleep and pharmacologically induced anesthesia. Important insights might thus come from identifying neuronal mechanisms of loss and re-emergence of consciousness independent of a specific manipulation. Therefore, to seek neuronal signatures of loss of consciousness common to sleep and anesthesia we analyzed spontaneous electrophysiological activity recorded in two experiments. First, electrocorticography (ECoG) acquired from 4 macaque monkeys anesthetized with different anesthetic agents (ketamine, medetomidine, propofol) and, second, stereo-electroencephalography (sEEG) from 10 epilepsy patients in different wake-sleep stages (wakefulness, NREM, REM). Specifically, we investigated co-activation patterns among brain areas, defined as correlations between local amplitudes of gamma-band activity. We found that resting wakefulness was associated with intermediate levels of gamma-band coupling, indicating neither complete dependence, nor full independence among brain regions. In contrast, loss of consciousness during NREM sleep and propofol anesthesia was associated with excessively correlated brain activity, as indicated by a robust increase of number and strength of positive correlations. However, such excessively correlated brain signals were not observed during REM sleep, and were present only to a limited extent during ketamine anesthesia. This might be related to the fact that, despite suppression of behavioral responsiveness, REM sleep and ketamine anesthesia often involve presence of dream-like conscious experiences. We conclude that hyper-correlated gamma-band activity might be a signature of loss of consciousness common across various manipulations and independent of behavioral responsiveness. Copyright © 2017 Elsevier Inc. All rights reserved.

The Role of Independent Assessment in the International Space Station Program

NASA Technical Reports Server (NTRS)

Strachan, Russell L.; Cook, David B.; Baker, Hugh A.

1999-01-01

This paper presents the role of Independent Assessment in the International Space Station (ISS) Program. Independent Assessment is responsible for identifying and specifying technical and programmatic risks that may impact development, launch, and on-orbit assembly and operations of the ISS. The various phases of the assessment process are identified and explained. This paper also outlines current and future participation by Independent Assessment in Human Exploration and Development of Space projects including the X-38 Space Plane, Mars mission scenarios, and applications of Nanotechnology. This paper describes how Independent Assessment helps the shuttle, ISS, and other programs to safely achieve mission goals now and into the next century.

High-frequency electrical stimulation reveals a p38–mTOR signaling module correlated with force–time integral

PubMed Central

Rahnert, Jill A.; Burkholder, Thomas J.

2013-01-01

SUMMARY High-frequency electrical stimulation (HFES) leads to muscle hypertrophy, and attention has been drawn to the high forces involved. However, both mechanical and metabolic stresses occur simultaneously, and both stimuli influence signaling cascades related to protein synthesis. This study aimed to identify the immediate signaling correlates of contraction-induced force and metabolic stresses under the hypothesis that HFES induces growth-related signaling through mechanical stimulation. Force–time integral (FTI) signaling in mouse tibialis anterior muscle was examined by separately manipulating the time of contraction to emphasize the metabolic aspect or the force of contraction to emphasize the mechanical aspect. When FTI was manipulated by changing the total time of activation, phosphorylation of p54 JNK, ERK and p70S6kT421/S424 was independent of FTI, while phosphorylation of acetyl-CoA carboxylase and p38 correlated with FTI. When FTI was manipulated by changing the force of contraction, p54 JNK, ERK and p70S6kT421/S424 were again independent of FTI, while phosphorylation of p38 and FAK correlated with FTI. Factor analysis identified a p38–mTOR signaling module that correlated with FTI in both experiments. The consistent link among p38, mTOR and FTI suggests that they form a connected signaling module sensitive to the mechanical aspects of FTI, separate from markers of metabolic load. PMID:23531822

Independent data validation of an in vitro method for ...

EPA Pesticide Factsheets

In vitro bioaccessibility assays (IVBA) estimate arsenic (As) relative bioavailability (RBA) in contaminated soils to improve the accuracy of site-specific human exposure assessments and risk calculations. For an IVBA assay to gain acceptance for use in risk assessment, it must be shown to reliably predict in vivo RBA that is determined in an established animal model. Previous studies correlating soil As IVBA with RBA have been limited by the use of few soil types as the source of As. Furthermore, the predictive value of As IVBA assays has not been validated using an independent set of As-contaminated soils. Therefore, the current study was undertaken to develop a robust linear model to predict As RBA in mice using an IVBA assay and to independently validate the predictive capability of this assay using a unique set of As-contaminated soils. Thirty-six As-contaminated soils varying in soil type, As contaminant source, and As concentration were included in this study, with 27 soils used for initial model development and nine soils used for independent model validation. The initial model reliably predicted As RBA values in the independent data set, with a mean As RBA prediction error of 5.3% (range 2.4 to 8.4%). Following validation, all 36 soils were used for final model development, resulting in a linear model with the equation: RBA = 0.59 * IVBA + 9.8 and R2 of 0.78. The in vivo-in vitro correlation and independent data validation presented here provide

Correlation between Mitochondrial Reactive Oxygen and Severity of Atherosclerosis.

PubMed

Dorighello, Gabriel G; Paim, Bruno A; Kiihl, Samara F; Ferreira, Mônica S; Catharino, Rodrigo R; Vercesi, Anibal E; Oliveira, Helena C F

2016-01-01

Atherosclerosis has been associated with mitochondria dysfunction and damage. Our group demonstrated previously that hypercholesterolemic mice present increased mitochondrial reactive oxygen (mtROS) generation in several tissues and low NADPH/NADP+ ratio. Here, we investigated whether spontaneous atherosclerosis in these mice could be modulated by treatments that replenish or spare mitochondrial NADPH, named citrate supplementation, cholesterol synthesis inhibition, or both treatments simultaneously. Robust statistical analyses in pooled group data were performed in order to explain the variation of atherosclerosis lesion areas as related to the classic atherosclerosis risk factors such as plasma lipids, obesity, and oxidative stress, including liver mtROS. Using three distinct statistical tools (univariate correlation, adjusted correlation, and multiple regression) with increasing levels of stringency, we identified a novel significant association and a model that reliably predicts the extent of atherosclerosis due to variations in mtROS. Thus, results show that atherosclerosis lesion area is positively and independently correlated with liver mtROS production rates. Based on these findings, we propose that modulation of mitochondrial redox state influences the atherosclerosis extent.

Exploiting jet binning to identify the initial state of high-mass resonances

NASA Astrophysics Data System (ADS)

Ebert, Markus A.; Liebler, Stefan; Moult, Ian; Stewart, Iain W.; Tackmann, Frank J.; Tackmann, Kerstin; Zeune, Lisa

2016-09-01

If a new high-mass resonance is discovered at the Large Hadron Collider, model-independent techniques to identify the production mechanism will be crucial to understand its nature and effective couplings to Standard Model particles. We present a powerful and model-independent method to infer the initial state in the production of any high-mass color-singlet system by using a tight veto on accompanying hadronic jets to divide the data into two mutually exclusive event samples (jet bins). For a resonance of several hundred GeV, the jet binning cut needed to discriminate quark and gluon initial states is in the experimentally accessible range of several tens of GeV. It also yields comparable cross sections for both bins, making this method viable already with the small event samples available shortly after a discovery. Theoretically, the method is made feasible by utilizing an effective field theory setup to compute the jet cut dependence precisely and model independently and to systematically control all sources of theoretical uncertainties in the jet binning, as well as their correlations. We use a 750 GeV scalar resonance as an example to demonstrate the viability of our method.

Expression of pyruvate dehydrogenase is an independent prognostic marker in gastric cancer

PubMed Central

Sun, Xu-Ren; Sun, Zhe; Zhu, Zhi; Guan, Hai-Xia; Li, Chen-Yan; Zhang, Jun-Yan; Zhang, Yi-Ning; Zhou, Huan; Zhang, Hui-Jing; Xu, Hui-Mian; Sun, Ming-Jun

2015-01-01

AIM: To investigate the expression and prognostic role of pyruvate dehydrogenase (PDH) in gastric cancer (GC). METHODS: This study included 265 patients (194 male, 71 female, mean age 59 years (range, 29-81 years) with GC who underwent curative surgery at the First Affiliated Hospital of China Medical University from January 2006 to May 2007. All patients were followed up for more than 5 years. Patient-derived paraffin embedded GC specimens were collected for tissue microarrays (TMAs). We examined PDH expression by immunohistochemistry in TMAs containing tumor tissue and matched non-neoplastic mucosa. Immunoreactivity was evaluated independently by two researchers. Overall survival (OS) rates were determined using the Kaplan-Meier estimator. Correlations with other clinicopathologic factors were evaluated by two-tailed χ2 tests or a two-tailed t-test. The Cox proportional-hazard model was used in univariate analysis and multivariate analysis to identify factors significantly correlated with prognosis. RESULTS: Immunohistochemistry showed that 35.47% of total cancer tissue specimens had cytoplasmic PDH staining. PDH expression was much higher in normal mucosa specimens (75.09%; P = 0.001). PDH expression was correlated with Lauren grade (70.77% in intestinal type vs 40.0% in diffuse type; P = 0.001), lymph node metastasis (65.43% with no metastasis vs 51.09% with metastasis; P = 0.033), lymphatic invasion (61.62% with no invasion vs 38.81% with invasion; P = 0.002), histologic subtypes (70.77% in intestinal type vs 40.0% in diffuse type; P = 0.001) and tumor-node-metastasis (TNM) stage (39% in poorly differentiated vs 65.91% in well differentiated and 67.11% in moderately differentiated; P = 0.001) in GC. PDH expression in cancer tissue was significantly associated with higher OS (P < 0.001). The multivariate analysis adjusted for age, Lauren classification, TNM stage, lymph node metastasis, histological type, tumor size, depth of invasion and lymphatic invasion

Prevalence and correlates of human immunodeficiency virus testing and posttest counseling among outpatients with serious mental illness.

PubMed

Desai, Mayur M; Rosenheck, Robert A; Desai, Rani A

2007-09-01

This study examined the prevalence and correlates of receipt of human immunodeficiency virus (HIV) testing, test results, and posttest counseling among outpatients with serious mental illness at 3 public-sector facilities in Connecticut (N = 487). A substantial proportion (41.9%) reported never having been tested for HIV, including fully one-third of those who were "very afraid" of getting acquired immune deficiency syndrome. Independent correlates of HIV testing included younger age, felony criminal history, stronger therapeutic alliance with one's primary clinician, and increased drug problems and psychological distress. Of those tested, nearly all (96.5%) reported receiving the test results; however, only half (50.5%) reported receiving any posttest counseling. Independent correlates of posttest counseling included higher educational level, felony criminal history, and receipt of community-based case management services. Greater efforts are needed to increase HIV testing and counseling among persons with serious mental illness to better identify and care for HIV-positive individuals and potentially reduce future transmission of the virus in this vulnerable, at-risk population.

Novel Sensor Technology To Assess Independence and Limb-Use Laterality in Cervical Spinal Cord Injury.

PubMed

Brogioli, Michael; Popp, Werner L; Albisser, Urs; Brust, Anne K; Frotzler, Angela; Gassert, Roger; Curt, Armin; Starkey, Michelle L

2016-11-01

After spinal cord injury (SCI), levels of independence are commonly assessed with standardized clinical assessments. However, such tests do not provide information about the actual extent of upper limb activities or the impact on independence of bi- versus unilateral usage throughout daily life following cervical SCI. The objective of this study was to correlate activity intensity and laterality of upper extremity activity measured by body-fixed inertial measurement units (IMUs) with clinical assessment scores of independence. Limb-use intensity and laterality of activities performed by the upper extremities was measured in 12 subjects with cervical SCI using four IMUs (positioned on both wrists, on the chest, and on one wheel of the wheelchair). Algorithms capable of reliably detecting self-propulsion and arm activity in a clinical environment were applied to rate functional outcome levels, and were related to clinical independence measures during inpatient rehabilitation. Measures of intensity of upper extremity activity during self-propulsion positively correlated (p < 0.05, r = 0.643) with independence measures related to mobility. Clinical measures of laterality were positively correlated (p < 0.01, r = 0.900) with laterality as measured by IMUs during "daily life," and increased laterality was negatively correlated (p < 0.01, r = -0.739) with independence. IMU sensor technology is sensitive in assessing and quantifying upper limb-use intensity and laterality in human cervical SCI. Continuous and objective movement data of distinct daily activities (i.e., mobility and day-to-day activities) can be related to levels of independence. Therefore, IMU sensor technology is suitable not only for monitoring activity levels during rehabilitation (including during clinical trials) but could also be used to assess levels of participation after discharge.

Correlational structure of ‘frontal’ tests and intelligence tests indicates two components with asymmetrical neurostructural correlates in old age

PubMed Central

Cox, Simon R.; MacPherson, Sarah E.; Ferguson, Karen J.; Nissan, Jack; Royle, Natalie A.; MacLullich, Alasdair M.J.; Wardlaw, Joanna M.; Deary, Ian J.

2014-01-01

Both general fluid intelligence (gf) and performance on some ‘frontal tests’ of cognition decline with age. Both types of ability are at least partially dependent on the integrity of the frontal lobes, which also deteriorate with age. Overlap between these two methods of assessing complex cognition in older age remains unclear. Such overlap could be investigated using inter-test correlations alone, as in previous studies, but this would be enhanced by ascertaining whether frontal test performance and gf share neurobiological variance. To this end, we examined relationships between gf and 6 frontal tests (Tower, Self-Ordered Pointing, Simon, Moral Dilemmas, Reversal Learning and Faux Pas tests) in 90 healthy males, aged ~ 73 years. We interpreted their correlational structure using principal component analysis, and in relation to MRI-derived regional frontal lobe volumes (relative to maximal healthy brain size). gf correlated significantly and positively (.24 ≤ r ≤ .53) with the majority of frontal test scores. Some frontal test scores also exhibited shared variance after controlling for gf. Principal component analysis of test scores identified units of gf-common and gf-independent variance. The former was associated with variance in the left dorsolateral (DL) and anterior cingulate (AC) regions, and the latter with variance in the right DL and AC regions. Thus, we identify two biologically-meaningful components of variance in complex cognitive performance in older age and suggest that age-related changes to DL and AC have the greatest cognitive impact. PMID:25278641

Correlates of strength training in older rural African American and Caucasian women.

PubMed

Bopp, Melissa; Wilcox, Sara; Oberrecht, Larissa; Kammermann, Sandra; McElmurray, Charles T

2004-01-01

This study examined factors influencing strength training (ST) in two convenience samples of older rural women. Focus group (FG) participants were 23 Caucasian and 16 African American women aged 67.5 +/- 9.2 years. Survey participants were 60 Caucasian and 42 African American women, aged 70.59 +/- 9.21 years. FG participants answered questions about the risks, benefits, and barriers to ST. Survey participants completed measures of demographics, physical activity (including ST), depression and stress, decisional balance for exercise (DBE), barriers to PA, and social support (SS). Regression modeling examined correlates of ST. FG participants identified physical health gains and improved appearance as ST benefits. African American women also included mental health benefits and "feeling good". Both Caucasian and African American groups named physical health problems as risks of ST. Caucasian women identified time constraints, lack of ST knowledge, physical health problems, lack of exercise facilities, and the cost of ST as barriers. African American women cited being "too tired", physical health problems, lack of support, and other family and work responsibilities. The linear regression model explained 23.2% of the variance in hours per week of ST; DBE and family SS were independent positive correlates. This study identified correlates to participation in ST in older rural women and provides a basis for developing ST interventions in this population.

Paternal education status significantly influences infants’ measles vaccination uptake, independent of maternal education status

PubMed Central

2012-01-01

Background Despite increased funding of measles vaccination programs by national governments and international aid agencies, structural factors encumber attainment of childhood measles immunisation to levels which may guarantee herd immunity. One of such factors is parental education status. Research on the links between parental education and vaccination has typically focused on the influence of maternal education status. This study aims to demonstrate the independent influence of paternal education status on measles immunisation. Methods Comparable nationally representative survey data were obtained from six countries with the highest numbers of children missing the measles vaccine in 2008. Logistic regression analysis was applied to examine the influence of paternal education on uptake of the first dose of measles vaccination, independent of maternal education, whilst controlling for confounding factors such as respondent’s age, urban/rural residence, province/state of residence, religion, wealth and occupation. Results The results of the analysis show that even if a mother is illiterate, having a father with an education of Secondary (high school) schooling and above is statistically significant and positively correlated with the likelihood of a child being vaccinated for measles, in the six countries analysed. Paternal education of secondary or higher level was significantly and independently correlated with measles immunisation uptake after controlling for all potential confounders. Conclusions The influence of paternal education status on measles immunisation uptake was investigated and found to be statistically significant in six nations with the biggest gaps in measles immunisation coverage in 2008. This study underscores the imperative of utilising both maternal and paternal education as screening variables to identify children at risk of missing measles vaccination prospectively. PMID:22568861

SO2 photoexcitation mechanism links mass-independent sulfur isotopic fractionation in cryospheric sulfate to climate impacting volcanism

PubMed Central

Hattori, Shohei; Schmidt, Johan A.; Johnson, Matthew S.; Danielache, Sebastian O.; Yamada, Akinori; Ueno, Yuichiro; Yoshida, Naohiro

2013-01-01

Natural climate variation, such as that caused by volcanoes, is the basis for identifying anthropogenic climate change. However, knowledge of the history of volcanic activity is inadequate, particularly concerning the explosivity of specific events. Some material is deposited in ice cores, but the concentration of glacial sulfate does not distinguish between tropospheric and stratospheric eruptions. Stable sulfur isotope abundances contain additional information, and recent studies show a correlation between volcanic plumes that reach the stratosphere and mass-independent anomalies in sulfur isotopes in glacial sulfate. We describe a mechanism, photoexcitation of SO2, that links the two, yielding a useful metric of the explosivity of historic volcanic events. A plume model of S(IV) to S(VI) conversion was constructed including photochemistry, entrainment of background air, and sulfate deposition. Isotopologue-specific photoexcitation rates were calculated based on the UV absorption cross-sections of 32SO2, 33SO2, 34SO2, and 36SO2 from 250 to 320 nm. The model shows that UV photoexcitation is enhanced with altitude, whereas mass-dependent oxidation, such as SO2 + OH, is suppressed by in situ plume chemistry, allowing the production and preservation of a mass-independent sulfur isotope anomaly in the sulfate product. The model accounts for the amplitude, phases, and time development of Δ33S/δ34S and Δ36S/Δ33S found in glacial samples. We are able to identify the process controlling mass-independent sulfur isotope anomalies in the modern atmosphere. This mechanism is the basis of identifying the magnitude of historic volcanic events. PMID:23417298

N400 Event-Related Potential and Standardized Measures of Reading in Late Elementary School Children: Correlated or Independent?

PubMed Central

Coch, Donna; Benoit, Clarisse

2015-01-01

We investigated whether and how standardized behavioral measures of reading and electrophysiological measures of reading were related in 72 typically developing, late elementary school children. Behavioral measures included standardized tests of spelling, phonological processing, vocabulary, comprehension, naming speed, and memory. Electrophysiological measures were composed of the amplitude of the N400 component of the event-related potential waveform elicited by real words, pseudowords, nonpronounceable letter strings, and strings of letter-like symbols (false fonts). The only significant brain-behavior correlations were between standard scores on the vocabulary test and N400 mean amplitude to real words (r = −.272) and pseudowords (r = −.235). We conclude that, while these specific sets of standardized behavioral and electrophysiological measures both provide an index of reading, for the most part, they are independent and draw upon different underlying processing resources. [T]o completely analyze what we do when we read… would be to describe very many of the most intricate workings of the human mind, as well as to unravel the tangled story of the most remarkable specific performance that civilization has learned in all its history(Huey, 1908/1968, p. 3). PMID:26346715

Vectorized data acquisition and fast triple-correlation integrals for Fluorescence Triple Correlation Spectroscopy

NASA Astrophysics Data System (ADS)

Ridgeway, William K.; Millar, David P.; Williamson, James R.

2013-04-01

Fluorescence Correlation Spectroscopy (FCS) is widely used to quantify reaction rates and concentrations of molecules in vitro and in vivo. We recently reported Fluorescence Triple Correlation Spectroscopy (F3CS), which correlates three signals together instead of two. F3CS can analyze the stoichiometries of complex mixtures and detect irreversible processes by identifying time-reversal asymmetries. Here we report the computational developments that were required for the realization of F3CS and present the results as the Triple Correlation Toolbox suite of programs. Triple Correlation Toolbox is a complete data analysis pipeline capable of acquiring, correlating and fitting large data sets. Each segment of the pipeline handles error estimates for accurate error-weighted global fitting. Data acquisition was accelerated with a combination of off-the-shelf counter-timer chips and vectorized operations on 128-bit registers. This allows desktop computers with inexpensive data acquisition cards to acquire hours of multiple-channel data with sub-microsecond time resolution. Off-line correlation integrals were implemented as a two delay time multiple-tau scheme that scales efficiently with multiple processors and provides an unprecedented view of linked dynamics. Global fitting routines are provided to fit FCS and F3CS data to models containing up to ten species. Triple Correlation Toolbox is a complete package that enables F3CS to be performed on existing microscopes. Catalogue identifier: AEOP_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOP_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 50189 No. of bytes in distributed program, including test data, etc.: 6135283 Distribution format: tar.gz Programming language: C/Assembly. Computer: Any with GCC and

Di-hadron correlations with identified leading hadrons in 200 GeV Au + Au and d + Au collisions at STAR

DOE PAGES

Adamczyk, L.

2015-10-23

The STAR Collaboration presents for the first time two-dimensional di-hadron correlations with identified leading hadrons in 200 GeV central Au + Au and minimum-bias d + Au collisions to explore hadronization mechanisms in the quark gluon plasma. The enhancement of the jet-like yield for leading pions in Au + Au data with respect to the d + Au reference and the absence of such an enhancement for leading non-pions (protons and kaons) are discussed within the context of a quark recombination scenario. The correlated yield at large angles, specifically in the ridge region, is found to be significantly higher formore » leading non-pions than pions. As a result, the consistencies of the constituent quark scaling, azimuthal harmonic model and a mini-jet modification model description of the data are tested, providing further constraints on hadronization.« less

Functional independence of Taiwanese children with Prader-Willi syndrome.

PubMed

Lee, Chung-Lin; Lin, Hsiang-Yu; Tsai, Li-Ping; Chiu, Huei-Ching; Tu, Ru-Yi; Huang, You-Hsin; Chien, Yin-Hsiu; Lee, Ni-Chung; Niu, Dau-Ming; Chao, Mei-Chyn; Tsai, Fuu-Jen; Chou, Yen-Yin; Chuang, Chih-Kuang; Lin, Shuan-Pei

2018-06-01

Prader-Willi syndrome (PWS) is a genetic disorder with obesity, developmental delay, short stature, and behavioral abnormalities. The study aimed to assess the functional independence in children with PWS. The Functional Independence Measure for Children (WeeFIM) was used to evaluate 81 children with PWS (44 boys and 37 girls) with a median age of 11 years 1 month (range 2 years 8 months to 20 years 2 months) were recruited between January 2013 and December 2016. The mean total WeeFIM score was 103.8 (maximum 126). Sixty-five patients (80%) had deletion type PWS, 16 (20.0%) had nondeletion type. The scores were 103.6 ± 18.5 for deletion and 104.8 ± 18.3 for nondeletion type (p = .405), 104.8 ± 19.3 in boys and 102.6 ± 17.3 in girls (p = .293). The mean self-care, mobility, and cognition scores were 47 (maximum 56), 33 (maximum 35), and 24 (maximum 35), respectively. All total scores and 18 subscores in the three functional domains were positively correlated with age (p < .05). Most children required assistance in problem-solving, comprehension, and expression. The WeeFIM identified the strengths and limitations of children with PWS and confirmed that support and supervision were needed in cognitive and self-care tasks. © 2018 Wiley Periodicals, Inc.

Using background air pollutants levels correlation analysis to identify periods of long-range transport of anthropogenic pollution

NASA Astrophysics Data System (ADS)

Konkova, Elizaveta S.; Burtseva, Larisa V.; Gromov, Sergey A.; Gromov, Sergey S.

2017-04-01

Increasing trends of airborne lead and cadmium at background station within the central region of European Russia have been identified previously (e.g., Gromov & Konkova, 2016). In order to reveal the possible drivers of these trends, a deeper investigation of correlation among these heavy metals (HM) and other co-measured pollutants is done in this study. Based on the data for the 2001-2012 period, calculations have been carried out for the period from 2006 onwards, when the growth of HM concentrations is observed. Pairwise correlations of individual species abundances were derived for the entire time series and subsets for each calendar year, including warm (April to September) and cold seasons (October to March). The calculated values for the seasons and the whole years vary substantially, suggesting that that variable ratios of atmospheric HM emission sources could affect the final air concentrations at measurement site in these periods. To distinguish the events of predominant influence of natural and anthropogenic sources, we assume that correlation between lead and cadmium levels must be greater in the case of natural sources being in effect. High values of the correlation coefficient are expected in cases when HM air abundances are induced by the long-range transport from the regions of anthropogenic sources (co-emission of these metals results from a number of same sources, and both of them are also present on same matrix aerosols). The results demonstrate a substantial correlation between Pb and Cd, with higher values for individual seasons (70% of 0.5 and higher) than for whole years. Higher mass concentrations of airborne dust (TSP) in remote areas are to large extent promoted by large particles blown away from the surface at local surroundings. Captured better by filters, such events could be a particular indicator of local (mostly natural) sources. Low or insignificant correlation with HM indicates prevalence of long-range transport of them and could

Tissue microstructural changes are independently associated with cognitive impairment in cerebral amyloid angiopathy.

PubMed

Viswanathan, Anand; Patel, Pratik; Rahman, Rosanna; Nandigam, R N Kaveer; Kinnecom, Catherine; Bracoud, Luc; Rosand, Jonathan; Chabriat, Hugues; Greenberg, Steven M; Smith, Eric E

2008-07-01

Cerebral amyloid angiopathy (CAA) is a major cause of lobar intracerebral hemorrhage and cognitive impairment and is associated with white matter hyperintensities and cerebral microbleeds. MRI diffusion tensor imaging detects microstructural tissue damage in advanced CAA even in areas that appear normal on conventional MRI. We hypothesized that higher global mean apparent diffusion coefficient (mean ADC), reflecting a higher amount of chronic tissue disruption caused by CAA, would be independently associated with CAA-related cognitive impairment. Preintracerebral hemorrhage cognitive impairment was systematically assessed using a standardized questionnaire (IQCODE) in 49 patients. Volume of white matter hyperintensities, number of microbleeds, and mean ADC were determined from MRIs obtained within 14.0+/-22.5 days of intracerebral hemorrhage cognitive impairment. White matter hyperintensities and mean ADC were measured in the hemisphere uninvolved by intracerebral hemorrhage to avoid confounding. Preintracerebral hemorrhage cognitive impairment was identified in 10 of 49 subjects. Mean ADC was the only variable associated with preintracerebral hemorrhage cognitive impairment and was elevated in those with preintracerebral hemorrhage cognitive impairment compared with those without (12.4x10(-4) versus 11.7x10(-4) mm(2)/s; P=0.03). Mean ADC positively correlated with age but not white matter hyperintensities or number of microbleeds. In logistic regression controlling for age and visible cerebral atrophy, mean ADC was independently associated with preintracerebral hemorrhage cognitive impairment (OR per 1x10(-4) mm(2)/s increase=2.45, 95% CI 1.11 to 5.40, P=0.04). Mean ADC is independently associated with preintracerebral hemorrhage cognitive impairment in CAA. The lack of correlation with other MRI markers of CAA suggests that mean ADC may be sensitive to distinct aspects of CAA pathology and its tissue consequences. These results suggest that global MRI diffusion

A method for functional network connectivity among spatially independent resting-state components in schizophrenia.

PubMed

Jafri, Madiha J; Pearlson, Godfrey D; Stevens, Michael; Calhoun, Vince D

2008-02-15

Functional connectivity of the brain has been studied by analyzing correlation differences in time courses among seed voxels or regions with other voxels of the brain in healthy individuals as well as in patients with brain disorders. The spatial extent of strongly temporally coherent brain regions co-activated during rest has also been examined using independent component analysis (ICA). However, the weaker temporal relationships among ICA component time courses, which we operationally define as a measure of functional network connectivity (FNC), have not yet been studied. In this study, we propose an approach for evaluating FNC and apply it to functional magnetic resonance imaging (fMRI) data collected from persons with schizophrenia and healthy controls. We examined the connectivity and latency among ICA component time courses to test the hypothesis that patients with schizophrenia would show increased functional connectivity and increased lag among resting state networks compared to controls. Resting state fMRI data were collected and the inter-relationships among seven selected resting state networks (identified using group ICA) were evaluated by correlating each subject's ICA time courses with one another. Patients showed higher correlation than controls among most of the dominant resting state networks. Patients also had slightly more variability in functional connectivity than controls. We present a novel approach for quantifying functional connectivity among brain networks identified with spatial ICA. Significant differences between patient and control connectivity in different networks were revealed possibly reflecting deficiencies in cortical processing in patients.

A Method for Functional Network Connectivity Among Spatially Independent Resting-State Components in Schizophrenia

PubMed Central

Jafri, Madiha J; Pearlson, Godfrey D; Stevens, Michael; Calhoun, Vince D

2011-01-01

Functional connectivity of the brain has been studied by analyzing correlation differences in time courses among seed voxels or regions with other voxels of the brain in patients versus controls. The spatial extent of strongly temporally coherent brain regions co-activated during rest has also been examined using independent component analysis (ICA). However, the weaker temporal relationships among ICA component time courses, which we operationally define as a measure of functional network connectivity (FNC), have not yet been studied. In this study, we propose an approach for evaluating FNC and apply it to functional magnetic resonance imaging (fMRI) data collected from persons with schizophrenia and healthy controls. We examined the connectivity and latency among ICA component time courses to test the hypothesis that patients with schizophrenia would show increased functional connectivity and increased lag among resting state networks compared to controls. Resting state fMRI data were collected and the inter-relationships among seven selected resting state networks (identified using group ICA) were evaluated by correlating each subject’s ICA time courses with one another. Patients showed higher correlation than controls among most of the dominant resting state networks. Patients also had slightly more variability in functional connectivity than controls. We present a novel approach for quantifying functional connectivity among brain networks identified with spatial ICA. Significant differences between patient and control connectivity in different networks were revealed possibly reflecting deficiencies in cortical processing in patients. PMID:18082428

Correlates of weight stigma in adults with overweight and obesity: A systematic literature review.

PubMed

Papadopoulos, Stephanie; Brennan, Leah

2015-09-01

While evidence regarding associations between weight stigma and biopsychosocial outcomes is accumulating, outcomes are considered in isolation. Thus, little is known about their complex relationships. This article extends existing work by systematically reviewing the biopsychosocial consequences of stigma in adults with overweight/obesity. Articles were identified through Medline, CINAHL, PsycINFO, Embase, Web of Science, and Cochrane databases. Independent extraction of articles was conducted using predefined data fields, including data on biopsychosocial correlates in each study. Twenty-three studies published from 2001 and addressing correlates of stigma in adults with overweight/obesity (body mass index ≥25 kg m(-2); 18-65 years) were identified. Numerous biopsychosocial correlates of weight stigma were studied, particularly in treatment-seeking individuals. Available research shows that weight stigma is consistently associated with medication non-adherence, mental health, anxiety, perceived stress, antisocial behavior, substance use, coping strategies, and social support. Biopsychosocial correlates were not considered in combination in research. Psychological correlates were well documented in comparison to biological and social correlates for each weight stigma type. There were some indications that associations are stronger once stigma is internalized. While there is evidence for biopsychosocial correlates of weight stigma, these are not considered in combination in research; thus their inter-relationships are unknown. Conclusions from the review are limited by this and the small number of studies, types of designs, and variables considered. © 2015 The Obesity Society.

TP53 mutation-correlated genes predict the risk of tumor relapse and identify MPS1 as a potential therapeutic kinase in TP53-mutated breast cancers.

PubMed

Győrffy, Balázs; Bottai, Giulia; Lehmann-Che, Jacqueline; Kéri, György; Orfi, László; Iwamoto, Takayuki; Desmedt, Christine; Bianchini, Giampaolo; Turner, Nicholas C; de Thè, Hugues; André, Fabrice; Sotiriou, Christos; Hortobagyi, Gabriel N; Di Leo, Angelo; Pusztai, Lajos; Santarpia, Libero

2014-05-01

Breast cancers (BC) carry a complex set of gene mutations that can influence their gene expression and clinical behavior. We aimed to identify genes driven by the TP53 mutation status and assess their clinical relevance in estrogen receptor (ER)-positive and ER-negative BC, and their potential as targets for patients with TP53 mutated tumors. Separate ROC analyses of each gene expression according to TP53 mutation status were performed. The prognostic value of genes with the highest AUC were assessed in a large dataset of untreated, and neoadjuvant chemotherapy treated patients. The mitotic checkpoint gene MPS1 was the most significant gene correlated with TP53 status, and the most significant prognostic marker in all ER-positive BC datasets. MPS1 retained its prognostic value independently from the type of treatment administered. The biological functions of MPS1 were investigated in different BC cell lines. We also assessed the effects of a potent small molecule inhibitor of MPS1, SP600125, alone and in combination with chemotherapy. Consistent with the gene expression profiling and siRNA assays, the inhibition of MPS1 by SP600125 led to a reduction in cell viability and a significant increase in cell death, selectively in TP53-mutated BC cells. Furthermore, the chemical inhibition of MPS1 sensitized BC cells to conventional chemotherapy, particularly taxanes. Our results collectively demonstrate that TP53-correlated kinase MPS1, is a potential therapeutic target in BC patients with TP53 mutated tumors, and that SP600125 warrant further development in future clinical trials. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Harnessing pain heterogeneity and RNA transcriptome to identify blood-based pain biomarkers: a novel correlational study design and bioinformatics approach in a graded chronic constriction injury model.

PubMed

Grace, Peter M; Hurley, Daniel; Barratt, Daniel T; Tsykin, Anna; Watkins, Linda R; Rolan, Paul E; Hutchinson, Mark R

2012-09-01

A quantitative, peripherally accessible biomarker for neuropathic pain has great potential to improve clinical outcomes. Based on the premise that peripheral and central immunity contribute to neuropathic pain mechanisms, we hypothesized that biomarkers could be identified from the whole blood of adult male rats, by integrating graded chronic constriction injury (CCI), ipsilateral lumbar dorsal quadrant (iLDQ) and whole blood transcriptomes, and pathway analysis with pain behavior. Correlational bioinformatics identified a range of putative biomarker genes for allodynia intensity, many encoding for proteins with a recognized role in immune/nociceptive mechanisms. A selection of these genes was validated in a separate replication study. Pathway analysis of the iLDQ transcriptome identified Fcγ and Fcε signaling pathways, among others. This study is the first to employ the whole blood transcriptome to identify pain biomarker panels. The novel correlational bioinformatics, developed here, selected such putative biomarkers based on a correlation with pain behavior and formation of signaling pathways with iLDQ genes. Future studies may demonstrate the predictive ability of these biomarker genes across other models and additional variables. © 2012 The Authors. Journal of Neurochemistry © 2012 International Society for Neurochemistry.

Localization of spontaneous magnetoencephalographic activity of neonates and fetuses using independent component and Hilbert phase analysis.

PubMed

Vairavan, Srinivasan; Eswaran, Hari; Preissl, Hubert; Wilson, James D; Haddad, Naim; Lowery, Curtis L; Govindan, Rathinaswamy B

2010-01-01

The fetal magnetoencephalogram (fMEG) is measured in the presence of large interference from maternal and fetal magnetocardiograms (mMCG and fMCG). These cardiac interferences can be attenuated by orthogonal projection (OP) technique of the corresponding spatial vectors. However, the OP technique redistributes the fMEG signal among the channels and also leaves some cardiac residuals (partially attenuated mMCG and fMCG) due to loss of stationarity in the signal. In this paper, we propose a novel way to extract and localize the neonatal and fetal spontaneous brain activity by using independent component analysis (ICA) technique. In this approach, we perform ICA on a small subset of sensors for 1-min duration. The independent components obtained are further investigated for the presence of discontinuous patterns as identified by the Hilbert phase analysis and are used as decision criteria for localizing the spontaneous brain activity. In order to locate the region of highest spontaneous brain activity content, this analysis is performed on the sensor subsets, which are traversed across the entire sensor space. The region of the spontaneous brain activity as identified by the proposed approach correlated well with the neonatal and fetal head location. In addition, the burst duration and the inter-burst interval computed for the identified discontinuous brain patterns are in agreement with the reported values.

Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production

PubMed Central

Xiang, Ruidong; McNally, Jody; Rowe, Suzanne; Jonker, Arjan; Pinares-Patino, Cesar S.; Oddy, V. Hutton; Vercoe, Phil E.; McEwan, John C.; Dalrymple, Brian P.

2016-01-01

Ruminants obtain nutrients from microbial fermentation of plant material, primarily in their rumen, a multilayered forestomach. How the different layers of the rumen wall respond to diet and influence microbial fermentation, and how these process are regulated, is not well understood. Gene expression correlation networks were constructed from full thickness rumen wall transcriptomes of 24 sheep fed two different amounts and qualities of a forage and measured for methane production. The network contained two major negatively correlated gene sub-networks predominantly representing the epithelial and muscle layers of the rumen wall. Within the epithelium sub-network gene clusters representing lipid/oxo-acid metabolism, general metabolism and proliferating and differentiating cells were identified. The expression of cell cycle and metabolic genes was positively correlated with dry matter intake, ruminal short chain fatty acid concentrations and methane production. A weak correlation between lipid/oxo-acid metabolism genes and methane yield was observed. Feed consumption level explained the majority of gene expression variation, particularly for the cell cycle genes. Many known stratified epithelium transcription factors had significantly enriched targets in the epithelial gene clusters. The expression patterns of the transcription factors and their targets in proliferating and differentiating skin is mirrored in the rumen, suggesting conservation of regulatory systems. PMID:27966600

Identifying Rodent Resting-State Brain Networks with Independent Component Analysis

PubMed Central

Bajic, Dusica; Craig, Michael M.; Mongerson, Chandler R. L.; Borsook, David; Becerra, Lino

2017-01-01

Rodent models have opened the door to a better understanding of the neurobiology of brain disorders and increased our ability to evaluate novel treatments. Resting-state functional magnetic resonance imaging (rs-fMRI) allows for in vivo exploration of large-scale brain networks with high spatial resolution. Its application in rodents affords researchers a powerful translational tool to directly assess/explore the effects of various pharmacological, lesion, and/or disease states on known neural circuits within highly controlled settings. Integration of animal and human research at the molecular-, systems-, and behavioral-levels using diverse neuroimaging techniques empowers more robust interrogations of abnormal/ pathological processes, critical for evolving our understanding of neuroscience. We present a comprehensive protocol to evaluate resting-state brain networks using Independent Component Analysis (ICA) in rodent model. Specifically, we begin with a brief review of the physiological basis for rs-fMRI technique and overview of rs-fMRI studies in rodents to date, following which we provide a robust step-by-step approach for rs-fMRI investigation including data collection, computational preprocessing, and brain network analysis. Pipelines are interwoven with underlying theory behind each step and summarized methodological considerations, such as alternative methods available and current consensus in the literature for optimal results. The presented protocol is designed in such a way that investigators without previous knowledge in the field can implement the analysis and obtain viable results that reliably detect significant differences in functional connectivity between experimental groups. Our goal is to empower researchers to implement rs-fMRI in their respective fields by incorporating technical considerations to date into a workable methodological framework. PMID:29311770

Identifying strongly correlated elements of a moderately correlated wavefunction in URu2Si2 with resonant inelastic X-ray scattering

NASA Astrophysics Data System (ADS)

Wray, L. Andrew; He, Haowei; Miao, Lin; Denlinger, Jonathan; Chuang, Yi-De; Yang, Wanli; Butch, Nicholas; Maple, Brian; Gray, Alexander; Dürr, Herman

The RIXS technique is best known for significant breakthroughs in the investigation of strongly correlated materials such as cuprates. However, the rapid advancement of RIXS spectrographs has made it increasingly attractive to apply the technique to a broad range of quantum materials outside of this comfort zone. This talk will review lessons learned from our recent measurements on material systems that feature a balance of correlated and itinerant physics, focusing on the hidden order compound URu2Si2, and touching on VO2 and Prussian blue analogue battery electrodes. RIXS spectra are found to reveal essential features defining low energy degrees of freedom in these moderately correlated wavefunctions. In the case of URu2Si2, we show that a principal energy gap defining strong correlations is fragile, and can be melted via modest chemical doping. Work at NYU was supported by the MRSEC Program of the National Science Foundation under Award Number DMR-1420073.

Parallel evolution of serotonergic neuromodulation underlies independent evolution of rhythmic motor behavior.

PubMed

Lillvis, Joshua L; Katz, Paul S

2013-02-06

Neuromodulation can dynamically alter neuronal and synaptic properties, thereby changing the behavioral output of a neural circuit. It is therefore conceivable that natural selection might act upon neuromodulation as a mechanism for sculpting the behavioral repertoire of a species. Here we report that the presence of neuromodulation is correlated with the production of a behavior that most likely evolved independently in two species: Tritonia diomedea and Pleurobranchaea californica (Mollusca, Gastropoda, Opisthobranchia, Nudipleura). Individuals of both species exhibit escape swimming behaviors consisting of repeated dorsal-ventral whole-body flexions. The central pattern generator (CPG) circuits underlying these behaviors contain homologous identified neurons: DSI and C2 in Tritonia and As and A1 in Pleurobranchaea. Homologs of these neurons also can be found in Hermissenda crassicornis where they are named CPT and C2, respectively. However, members of this species do not exhibit an analogous swimming behavior. In Tritonia and Pleurobranchaea, but not in Hermissenda, the serotonergic DSI homologs modulated the strength of synapses made by C2 homologs. Furthermore, the serotonin receptor antagonist methysergide blocked this neuromodulation and the swimming behavior. Additionally, in Pleurobranchaea, the robustness of swimming correlated with the extent of the synaptic modulation. Finally, injection of serotonin induced the swimming behavior in Tritonia and Pleurobranchaea, but not in Hermissenda. This suggests that the analogous swimming behaviors of Tritonia and Pleurobranchaea share a common dependence on serotonergic neuromodulation. Thus, neuromodulation may provide a mechanism that enables species to acquire analogous behaviors independently using homologous neural circuit components.

Correlations of Platooning Track Test and Wind Tunnel Data

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

Lammert, Michael P.; Kelly, Kenneth J.; Yanowitz, Janet

In this report, the National Renewable Energy Laboratory analyzed results from multiple, independent truck platooning projects to compare and contrast track test results with wind tunnel test results conducted by Lawrence Livermore National Laboratory (LLNL). Some highlights from the report include compiled data, and results from four independent SAE J1321 full-size track test campaigns that were compared to LLNL wind tunnel testing results. All platooning scenarios tested demonstrated significant fuel savings with good correlation relative to following distances, but there are still unanswered questions and clear opportunities for system optimization. NOx emissions showed improvements from NREL tests in 2014 tomore » Auburn tests in 2015 with respect to J1321 platooning track testing of Peloton system. NREL evaluated data from Volpe's Naturalistic Study of Truck Following Behavior, which showed minimal impact of naturalistic background platooning. We found significant correlation between multiple track studies, wind tunnel tests, and computational fluid dynamics, but also showed that there is more to learn regarding close formation and longer-distance effects. We also identified potential areas for further research and development, including development of advanced aerodynamic designs optimized for platooning, measurement of platoon system performance in traffic conditions, impact of vehicle lateral offsets on platooning performance, and characterization of the national potential for platooning based on fleet operational characteristics.« less

A novel approach to analyzing fMRI and SNP data via parallel independent component analysis

NASA Astrophysics Data System (ADS)

Liu, Jingyu; Pearlson, Godfrey; Calhoun, Vince; Windemuth, Andreas

2007-03-01

There is current interest in understanding genetic influences on brain function in both the healthy and the disordered brain. Parallel independent component analysis, a new method for analyzing multimodal data, is proposed in this paper and applied to functional magnetic resonance imaging (fMRI) and a single nucleotide polymorphism (SNP) array. The method aims to identify the independent components of each modality and the relationship between the two modalities. We analyzed 92 participants, including 29 schizophrenia (SZ) patients, 13 unaffected SZ relatives, and 50 healthy controls. We found a correlation of 0.79 between one fMRI component and one SNP component. The fMRI component consists of activations in cingulate gyrus, multiple frontal gyri, and superior temporal gyrus. The related SNP component is contributed to significantly by 9 SNPs located in sets of genes, including those coding for apolipoprotein A-I, and C-III, malate dehydrogenase 1 and the gamma-aminobutyric acid alpha-2 receptor. A significant difference in the presences of this SNP component is found between the SZ group (SZ patients and their relatives) and the control group. In summary, we constructed a framework to identify the interactions between brain functional and genetic information; our findings provide new insight into understanding genetic influences on brain function in a common mental disorder.

Improving consensus contact prediction via server correlation reduction.

PubMed

Gao, Xin; Bu, Dongbo; Xu, Jinbo; Li, Ming

2009-05-06

Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although template-based consensus methods outperform sequence-based methods on targets with typical templates, such consensus methods perform poorly on new fold targets. However, we find out that even for new fold targets, the models generated by threading programs can contain many true contacts. The challenge is how to identify them. In this paper, we develop an integer linear programming model for consensus contact prediction. In contrast to the simple majority voting method assuming that all the individual servers are equally important and independent, the newly developed method evaluates their correlation by using maximum likelihood estimation and extracts independent latent servers from them by using principal component analysis. An integer linear programming method is then applied to assign a weight to each latent server to maximize the difference between true contacts and false ones. The proposed method is tested on the CASP7 data set. If the top L/5 predicted contacts are evaluated where L is the protein size, the average accuracy is 73%, which is much higher than that of any previously reported study. Moreover, if only the 15 new fold CASP7 targets are considered, our method achieves an average accuracy of 37%, which is much better than that of the majority voting method, SVM-LOMETS, SVM-SEQ, and SAM-T06. These methods demonstrate an average accuracy of 13.0%, 10.8%, 25.8% and 21.2%, respectively. Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use.

Multifractal analysis of managed and independent float exchange rates

NASA Astrophysics Data System (ADS)

Stošić, Darko; Stošić, Dusan; Stošić, Tatijana; Stanley, H. Eugene

2015-06-01

We investigate multifractal properties of daily price changes in currency rates using the multifractal detrended fluctuation analysis (MF-DFA). We analyze managed and independent floating currency rates in eight countries, and determine the changes in multifractal spectrum when transitioning between the two regimes. We find that after the transition from managed to independent float regime the changes in multifractal spectrum (position of maximum and width) indicate an increase in market efficiency. The observed changes are more pronounced for developed countries that have a well established trading market. After shuffling the series, we find that the multifractality is due to both probability density function and long term correlations for managed float regime, while for independent float regime multifractality is in most cases caused by broad probability density function.

Diffusion Tensor Fractional Anisotropy in the Superior Longitudinal Fasciculus Correlates with Functional Independence Measure Cognition Scores in Patients with Cerebral Infarction.

PubMed

Koyama, Tetsuo; Domen, Kazuhisa

2017-08-01

This study aimed to determine the relationship between fiber tract degeneration measured by diffusion-tensor imaging (DTI) and outcome of patients after cerebral infarction. Fractional anisotropy (FA) maps were generated by DTI in patients 14-21 days after the first infarction and were analyzed by tract-based spatial statistics (TBSS). Mean FA values within the corticospinal tract (CST) and the superior longitudinal fasciculus (SLF) were extracted from individual TBSS data. Relationships between FA ratios (rFAs, lesioned to non-lesioned hemisphere) and outcomes assessed by Brunnstrom stage (BRS) and Functional Independence Measure (FIM) motor and cognition scores were examined using Spearman's rank correlation test. Forty patients (21 left and 19 right hemisphere lesions) were entered into an analytical database. BRS ranged from 1 to 6 (median, 5) for shoulder, elbow, or forearm; from 2 to 6 (median, 4.5) for hand or finger; and from 3 to 6 (median, 5) for lower extremity. FIM motor ranged from 51 to 91 (median, 79.5), and FIM cognition ranged from 16 to 35 (median, 29). rFA values in the CST ranged from .692 to 1.053 (median, .933), and those in the SLF ranged from .778 to 1.076 (median, .965). Mann-Whitney U test (P <.05) revealed no significant differences between the left and the right hemisphere lesion groups. Individual rFA values in the CST correlated with BRS scores (r = .585-0.654), whereas those in the SLF correlated with FIM cognition scores (r = .409, P <.05). DTI-FA values in the SLF and CST may be useful for outcome prediction of cognitive function and extremity function, respectively. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation

PubMed Central

Khatri, Purvesh; Roedder, Silke; Kimura, Naoyuki; De Vusser, Katrien; Morgan, Alexander A.; Gong, Yongquan; Fischbein, Michael P.; Robbins, Robert C.; Naesens, Maarten

2013-01-01

Using meta-analysis of eight independent transplant datasets (236 graft biopsy samples) from four organs, we identified a common rejection module (CRM) consisting of 11 genes that were significantly overexpressed in acute rejection (AR) across all transplanted organs. The CRM genes could diagnose AR with high specificity and sensitivity in three additional independent cohorts (794 samples). In another two independent cohorts (151 renal transplant biopsies), the CRM genes correlated with the extent of graft injury and predicted future injury to a graft using protocol biopsies. Inferred drug mechanisms from the literature suggested that two FDA-approved drugs (atorvastatin and dasatinib), approved for nontransplant indications, could regulate specific CRM genes and reduce the number of graft-infiltrating cells during AR. We treated mice with HLA-mismatched mouse cardiac transplant with atorvastatin and dasatinib and showed reduction of the CRM genes, significant reduction of graft-infiltrating cells, and extended graft survival. We further validated the beneficial effect of atorvastatin on graft survival by retrospective analysis of electronic medical records of a single-center cohort of 2,515 renal transplant patients followed for up to 22 yr. In conclusion, we identified a CRM in transplantation that provides new opportunities for diagnosis, drug repositioning, and rational drug design. PMID:24127489

A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation.

PubMed

Khatri, Purvesh; Roedder, Silke; Kimura, Naoyuki; De Vusser, Katrien; Morgan, Alexander A; Gong, Yongquan; Fischbein, Michael P; Robbins, Robert C; Naesens, Maarten; Butte, Atul J; Sarwal, Minnie M

2013-10-21

Using meta-analysis of eight independent transplant datasets (236 graft biopsy samples) from four organs, we identified a common rejection module (CRM) consisting of 11 genes that were significantly overexpressed in acute rejection (AR) across all transplanted organs. The CRM genes could diagnose AR with high specificity and sensitivity in three additional independent cohorts (794 samples). In another two independent cohorts (151 renal transplant biopsies), the CRM genes correlated with the extent of graft injury and predicted future injury to a graft using protocol biopsies. Inferred drug mechanisms from the literature suggested that two FDA-approved drugs (atorvastatin and dasatinib), approved for nontransplant indications, could regulate specific CRM genes and reduce the number of graft-infiltrating cells during AR. We treated mice with HLA-mismatched mouse cardiac transplant with atorvastatin and dasatinib and showed reduction of the CRM genes, significant reduction of graft-infiltrating cells, and extended graft survival. We further validated the beneficial effect of atorvastatin on graft survival by retrospective analysis of electronic medical records of a single-center cohort of 2,515 renal transplant patients followed for up to 22 yr. In conclusion, we identified a CRM in transplantation that provides new opportunities for diagnosis, drug repositioning, and rational drug design.

Detecting independent and recurrent copy number aberrations using interval graphs.

PubMed

Wu, Hsin-Ta; Hajirasouliha, Iman; Raphael, Benjamin J

2014-06-15

Somatic copy number aberrations SCNAS: are frequent in cancer genomes, but many of these are random, passenger events. A common strategy to distinguish functional aberrations from passengers is to identify those aberrations that are recurrent across multiple samples. However, the extensive variability in the length and position of SCNA: s makes the problem of identifying recurrent aberrations notoriously difficult. We introduce a combinatorial approach to the problem of identifying independent and recurrent SCNA: s, focusing on the key challenging of separating the overlaps in aberrations across individuals into independent events. We derive independent and recurrent SCNA: s as maximal cliques in an interval graph constructed from overlaps between aberrations. We efficiently enumerate all such cliques, and derive a dynamic programming algorithm to find an optimal selection of non-overlapping cliques, resulting in a very fast algorithm, which we call RAIG (Recurrent Aberrations from Interval Graphs). We show that RAIG outperforms other methods on simulated data and also performs well on data from three cancer types from The Cancer Genome Atlas (TCGA). In contrast to existing approaches that employ various heuristics to select independent aberrations, RAIG optimizes a well-defined objective function. We show that this allows RAIG to identify rare aberrations that are likely functional, but are obscured by overlaps with larger passenger aberrations. http://compbio.cs.brown.edu/software. © The Author 2014. Published by Oxford University Press.

Ranking and averaging independent component analysis by reproducibility (RAICAR).

PubMed

Yang, Zhi; LaConte, Stephen; Weng, Xuchu; Hu, Xiaoping

2008-06-01

Independent component analysis (ICA) is a data-driven approach that has exhibited great utility for functional magnetic resonance imaging (fMRI). Standard ICA implementations, however, do not provide the number and relative importance of the resulting components. In addition, ICA algorithms utilizing gradient-based optimization give decompositions that are dependent on initialization values, which can lead to dramatically different results. In this work, a new method, RAICAR (Ranking and Averaging Independent Component Analysis by Reproducibility), is introduced to address these issues for spatial ICA applied to fMRI. RAICAR utilizes repeated ICA realizations and relies on the reproducibility between them to rank and select components. Different realizations are aligned based on correlations, leading to aligned components. Each component is ranked and thresholded based on between-realization correlations. Furthermore, different realizations of each aligned component are selectively averaged to generate the final estimate of the given component. Reliability and accuracy of this method are demonstrated with both simulated and experimental fMRI data. Copyright 2007 Wiley-Liss, Inc.

Identifying the Correlation between Professional Learning Communities and Collective Teacher Efficacy for Math Data Teams in Kaua'i Complex Area Secondary Schools

ERIC Educational Resources Information Center

Ellwood, Cheryl Kathryn

2013-01-01

Professional learning communities and teacher efficacy are at the core of many of the current educational reform models. The intention of this dissertation was to identify the correlation between professional learning communities and collective teacher efficacy for math data teams in the six Kaua'i Complex Area secondary schools, as measured by…

Exchange-Correlation Effects for Noncovalent Interactions in Density Functional Theory.

PubMed

Otero-de-la-Roza, A; DiLabio, Gino A; Johnson, Erin R

2016-07-12

In this article, we develop an understanding of how errors from exchange-correlation functionals affect the modeling of noncovalent interactions in dispersion-corrected density-functional theory. Computed CCSD(T) reference binding energies for a collection of small-molecule clusters are decomposed via a molecular many-body expansion and are used to benchmark density-functional approximations, including the effect of semilocal approximation, exact-exchange admixture, and range separation. Three sources of error are identified. Repulsion error arises from the choice of semilocal functional approximation. This error affects intermolecular repulsions and is present in all n-body exchange-repulsion energies with a sign that alternates with the order n of the interaction. Delocalization error is independent of the choice of semilocal functional but does depend on the exact exchange fraction. Delocalization error misrepresents the induction energies, leading to overbinding in all induction n-body terms, and underestimates the electrostatic contribution to the 2-body energies. Deformation error affects only monomer relaxation (deformation) energies and behaves similarly to bond-dissociation energy errors. Delocalization and deformation errors affect systems with significant intermolecular orbital interactions (e.g., hydrogen- and halogen-bonded systems), whereas repulsion error is ubiquitous. Many-body errors from the underlying exchange-correlation functional greatly exceed in general the magnitude of the many-body dispersion energy term. A functional built to accurately model noncovalent interactions must contain a dispersion correction, semilocal exchange, and correlation components that minimize the repulsion error independently and must also incorporate exact exchange in such a way that delocalization error is absent.

Quantitative gene expression deregulation in mantle-cell lymphoma: correlation with clinical and biologic factors.

PubMed

Kienle, Dirk; Katzenberger, Tiemo; Ott, German; Saupe, Doreen; Benner, Axel; Kohlhammer, Holger; Barth, Thomas F E; Höller, Sylvia; Kalla, Jörg; Rosenwald, Andreas; Müller-Hermelink, Hans Konrad; Möller, Peter; Lichter, Peter; Döhner, Hartmut; Stilgenbauer, Stephan

2007-07-01

There is evidence for a direct role of quantitative gene expression deregulation in mantle-cell lymphoma (MCL) pathogenesis. Our aim was to investigate gene expression associations with other pathogenic factors and the significance of gene expression in a multivariate survival analysis. Quantitative expression of 20 genes of potential relevance for MCL prognosis and pathogenesis were analyzed using real-time reverse transcriptase polymerase chain reaction and correlated with clinical and genetic factors, tumor morphology, and Ki-67 index in 65 MCL samples. Genomic losses at the loci of TP53, RB1, and P16 were associated with reduced transcript levels of the respective genes, indicating a gene-dosage effect as the pathomechanism. Analysis of gene expression correlations between the candidate genes revealed a separation into two clusters, one dominated by proliferation activators, another by proliferation inhibitors and regulators of apoptosis. Whereas only weak associations were identified between gene expression and clinical parameters or blastoid morphology, several genes were correlated closely with the Ki-67 index, including the short CCND1 variant (positive correlation) and RB1, ATM, P27, and BMI (negative correlation). In multivariate survival analysis, expression levels of MYC, MDM2, EZH2, and CCND1 were the strongest prognostic factors independently of tumor proliferation and clinical factors. These results indicate a pathogenic contribution of several gene transcript levels to the biology and clinical course of MCL. Genes can be differentiated into factors contributing to proliferation deregulation, either by enhancement or loss of inhibition, and proliferation-independent factors potentially contributing to MCL pathogenesis by apoptosis impairment.

Multivariate analysis identifies the estradiol level at ovulation triggering as an independent predictor of the first trimester pregnancy-associated plasma protein-A level in IVF/ICSI pregnancies.

PubMed

Giorgetti, C; Vanden Meerschaut, F; De Roo, C; Saunier, O; Quarello, E; Hairion, D; Penaranda, G; Chabert-Orsini, V; De Sutter, P

2013-10-01

Can independent predictors of pregnancy-associated plasma protein-A (PAPP-A) levels be identified in a group of women who conceived following IVF/ICSI? The significantly decreased PAPP-A level in IVF and ICSI pregnancies compared with non-IVF/ICSI pregnancies was correlated strongly with the serum estradiol (E2) level at ovulation triggering. The first trimester prenatal combined screening test for fetal aneuploidies in pregnancies conceived following assisted reproduction techniques (ART) is complicated by an alteration of the maternal biomarkers free β-hCG and PAPP-A, causing a higher false-positive rate compared with pregnancies which are conceived naturally. The use of controlled ovarian stimulation prior to IVF/ICSI is suggested to be the principle reason for these alterations of biomarkers in ART pregnancies. Between January 2010 and December 2011, 1474 women who conceived naturally and 374 women who conceived following IVF (n = 89), ICSI (n = 204) or intrauterine insemination (IUI, n = 81) were included in this retrospective study. Only singleton pregnancies were eligible for this study. For all women, serum analysis was performed in the same clinical laboratory. Measurement of nuchal translucency (NT) thickness was performed by four physicians belonging to the same infertility centre. First-trimester combined screening test of aneuploidy parameters (maternal age, PAPP-A and free β-hCG, NT thickness) were compared between non-ART and ART (IVF, ICSI and IUI) singleton pregnancies. Next, a minimal threshold E2 level at ovulation triggering was suggested for IVF/ICSI pregnancies above which the PAPP-A levels were significantly decreased compared with non-ART pregnancies. Finally, a multivariate analysis was performed to reveal independent predictors of PAPP-A level in IVF/ICSI pregnancies. We showed a decrease of the multiple of the median (MoM) PAPP-A level in IVF and ICSI singleton pregnancies compared with non-ART singleton pregnancies (P < 0.001), with Mo

Are independent probes truly independent?

PubMed

Camp, Gino; Pecher, Diane; Schmidt, Henk G; Zeelenberg, René

2009-07-01

The independent cue technique has been developed to test traditional interference theories against inhibition theories of forgetting. In the present study, the authors tested the critical criterion for the independence of independent cues: Studied cues not presented during test (and unrelated to test cues) should not contribute to the retrieval process. Participants first studied a subset of cues (e.g., rope) that were subsequently studied together with a target in a 2nd study phase (e.g., rope-sailing, sunflower-yellow). In the test phase, an extralist category cue (e.g., sports, color) was presented, and participants were instructed to recall an item from the study list that was a member of the category (e.g., sailing, yellow). The experiments showed that previous study of the paired-associate word (e.g., rope) enhanced category cued recall even though this word was not presented at test. This experimental demonstration of covert cuing has important implications for the effectiveness of the independent cue technique.

Distance correlation methods for discovering associations in large astrophysical databases

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

Martínez-Gómez, Elizabeth; Richards, Mercedes T.; Richards, Donald St. P., E-mail: elizabeth.martinez@itam.mx, E-mail: mrichards@astro.psu.edu, E-mail: richards@stat.psu.edu

2014-01-20

High-dimensional, large-sample astrophysical databases of galaxy clusters, such as the Chandra Deep Field South COMBO-17 database, provide measurements on many variables for thousands of galaxies and a range of redshifts. Current understanding of galaxy formation and evolution rests sensitively on relationships between different astrophysical variables; hence an ability to detect and verify associations or correlations between variables is important in astrophysical research. In this paper, we apply a recently defined statistical measure called the distance correlation coefficient, which can be used to identify new associations and correlations between astrophysical variables. The distance correlation coefficient applies to variables of any dimension,more » can be used to determine smaller sets of variables that provide equivalent astrophysical information, is zero only when variables are independent, and is capable of detecting nonlinear associations that are undetectable by the classical Pearson correlation coefficient. Hence, the distance correlation coefficient provides more information than the Pearson coefficient. We analyze numerous pairs of variables in the COMBO-17 database with the distance correlation method and with the maximal information coefficient. We show that the Pearson coefficient can be estimated with higher accuracy from the corresponding distance correlation coefficient than from the maximal information coefficient. For given values of the Pearson coefficient, the distance correlation method has a greater ability than the maximal information coefficient to resolve astrophysical data into highly concentrated horseshoe- or V-shapes, which enhances classification and pattern identification. These results are observed over a range of redshifts beyond the local universe and for galaxies from elliptical to spiral.« less

Spatial correlated games

PubMed Central

2017-01-01

This article studies correlated two-person games constructed from games with independent players as proposed in Iqbal et al. (2016 R. Soc. open sci. 3, 150477. (doi:10.1098/rsos.150477)). The games are played in a collective manner, both in a two-dimensional lattice where the players interact with their neighbours, and with players interacting at random. Four game types are scrutinized in iterated games where the players are allowed to change their strategies, adopting that of their best paid mate neighbour. Particular attention is paid in the study to the effect of a variable degree of correlation on Nash equilibrium strategy pairs. PMID:29291120

Partner's influences and other correlates of prenatal alcohol use.

PubMed

van der Wulp, Nickie Y; Hoving, Ciska; de Vries, Hein

2015-04-01

To investigate the influence of partners on alcohol consumption in pregnant women within the context of other factors. A Dutch nationwide online cross-sectional study among 158 pregnant women and their partners was conducted. To identify correlates of prenatal alcohol use, including perceived and reported partner norm (i.e. partner's belief regarding acceptability of prenatal alcohol use), partner modeling (i.e. partner's alcohol use during the woman's pregnancy) and partner support (i.e. partner's help in abstaining from alcohol during pregnancy), independent sample T-tests and Chi square tests were conducted. Correlation analyses tested the relationship between perceived and reported partner influence. Multivariate logistic hierarchical regression analyses tested the independent impact of partner's perceived and reported influence next to other correlates from the I-Change Model. Pregnant women who consumed alcohol perceived a weaker partner norm (p < 0.001) and less partner modeling (p < 0.05), with the partner reporting a weaker norm (p < 0.001), more drinking days per week (p < 0.05) and weaker support (p < 0.05). Perceived and reported partner norm, modeling and support were positively related (respectively p < 0.01, p < 0.01 and p < 0.05). The multivariate analyses demonstrated that pregnant women with a higher education who perceived lower severity of harm due to prenatal alcohol use and a weaker partner norm were more likely to use alcohol (R(2) = 0.42). This study demonstrated that perceived partner norm was the most critical of the constructs of perceived and reported partner influences in explaining prenatal alcohol use.

Multiple brain networks underpinning word learning from fluent speech revealed by independent component analysis.

PubMed

López-Barroso, Diana; Ripollés, Pablo; Marco-Pallarés, Josep; Mohammadi, Bahram; Münte, Thomas F; Bachoud-Lévi, Anne-Catherine; Rodriguez-Fornells, Antoni; de Diego-Balaguer, Ruth

2015-04-15

Although neuroimaging studies using standard subtraction-based analysis from functional magnetic resonance imaging (fMRI) have suggested that frontal and temporal regions are involved in word learning from fluent speech, the possible contribution of different brain networks during this type of learning is still largely unknown. Indeed, univariate fMRI analyses cannot identify the full extent of distributed networks that are engaged by a complex task such as word learning. Here we used Independent Component Analysis (ICA) to characterize the different brain networks subserving word learning from an artificial language speech stream. Results were replicated in a second cohort of participants with a different linguistic background. Four spatially independent networks were associated with the task in both cohorts: (i) a dorsal Auditory-Premotor network; (ii) a dorsal Sensory-Motor network; (iii) a dorsal Fronto-Parietal network; and (iv) a ventral Fronto-Temporal network. The level of engagement of these networks varied through the learning period with only the dorsal Auditory-Premotor network being engaged across all blocks. In addition, the connectivity strength of this network in the second block of the learning phase correlated with the individual variability in word learning performance. These findings suggest that: (i) word learning relies on segregated connectivity patterns involving dorsal and ventral networks; and (ii) specifically, the dorsal auditory-premotor network connectivity strength is directly correlated with word learning performance. Copyright © 2015 Elsevier Inc. All rights reserved.

Patterns of glaucomatous visual field loss in sita fields automatically identified using independent component analysis.

PubMed

Goldbaum, Michael H; Jang, Gil-Jin; Bowd, Chris; Hao, Jiucang; Zangwill, Linda M; Liebmann, Jeffrey; Girkin, Christopher; Jung, Tzyy-Ping; Weinreb, Robert N; Sample, Pamela A

2009-12-01

To determine if the patterns uncovered with variational Bayesian-independent component analysis-mixture model (VIM) applied to a large set of normal and glaucomatous fields obtained with the Swedish Interactive Thresholding Algorithm (SITA) are distinct, recognizable, and useful for modeling the severity of the field loss. SITA fields were obtained with the Humphrey Visual Field Analyzer (Carl Zeiss Meditec, Inc, Dublin, California) on 1,146 normal eyes and 939 glaucoma eyes from subjects followed by the Diagnostic Innovations in Glaucoma Study and the African Descent and Glaucoma Evaluation Study. VIM modifies independent component analysis (ICA) to develop separate sets of ICA axes in the cluster of normal fields and the 2 clusters of abnormal fields. Of 360 models, the model with the best separation of normal and glaucomatous fields was chosen for creating the maximally independent axes. Grayscale displays of fields generated by VIM on each axis were compared. SITA fields most closely associated with each axis and displayed in grayscale were evaluated for consistency of pattern at all severities. The best VIM model had 3 clusters. Cluster 1 (1,193) was mostly normal (1,089, 95% specificity) and had 2 axes. Cluster 2 (596) contained mildly abnormal fields (513) and 2 axes; cluster 3 (323) held mostly moderately to severely abnormal fields (322) and 5 axes. Sensitivity for clusters 2 and 3 combined was 88.9%. The VIM-generated field patterns differed from each other and resembled glaucomatous defects (eg, nasal step, arcuate, temporal wedge). SITA fields assigned to an axis resembled each other and the VIM-generated patterns for that axis. Pattern severity increased in the positive direction of each axis by expansion or deepening of the axis pattern. VIM worked well on SITA fields, separating them into distinctly different yet recognizable patterns of glaucomatous field defects. The axis and pattern properties make VIM a good candidate as a preliminary process for

Sourcing faecal pollution: a combination of library-dependent and library-independent methods to identify human faecal pollution in non-sewered catchments.

PubMed

Ahmed, W; Stewart, J; Gardner, T; Powell, D; Brooks, P; Sullivan, D; Tindale, N

2007-08-01

Library-dependent (LD) (biochemical fingerprinting of Escherichia coli and enterococci) and library-independent (LI) (PCR detection of human-specific biomarkers) methods were used to detect human faecal pollution in three non-sewered catchments. In all, 550 E. coli isolates and 700 enterococci isolates were biochemically fingerprinted from 18 water samples and compared with metabolic fingerprint libraries of 4508 E. coli and 4833 enterococci isolates. E. coli fingerprints identified human unique biochemical phenotypes (BPTs) in nine out of 18 water samples; similarly, enterococci fingerprints identified human faecal pollution in 10 water samples. Seven samples were tested by PCR for the detection of biomarkers. Human-specific HF134 Bacteroides and enterococci surface protein (esp) biomarkers were detected in five samples. Four samples were also positive for HF183 Bacteroides biomarker. The combination of biomarkers detected human faecal pollution in six out of seven water samples. Of the seven samples analysed for both the indicators/markers, at least one indicator/marker was detected in every sample. Four of the seven PCR-positive samples were also positive for one of the human-specific E. coli or enterococci BPTs. The results indicated human faecal pollution in the studied sub-catchments after storm events. LD and LI methods used in this study complimented each other and provided additional information regarding the polluting sources when one method failed to detect human faecal pollution. Therefore, it is recommended that a combination of methods should be used to identify the source(s) of faecal pollution where possible.

In Nonobese Children, Fitness and BMI are Independent Predictors of Fasting Insulin.

PubMed

Watson, Andrew M; Eickhoff, Jens; Nemeth, Blaise A; Carrel, Aaron L

2015-05-01

Although fitness and obesity have been shown to be independent predictors of cardiometabolic disease risk in obese children, this interaction is not well defined in nonobese children. The purpose of this study was to define the relationships between peak aerobic capacity, body composition, and fasting insulin levels in nonobese middle school children. 148 middle school children (mean age 11.0 ± 2.1 years, 49% male) underwent determination of body mass index (BMI) z-score, fasting glucose, fasting insulin, body composition by DXA scan (lean body mass and body fat percentage), and peak oxygen uptake per kg of lean body mass (VO2peak). Univariate correlations and multivariate regression analysis were used to identify independent predictors of fasting insulin using age, sex, percent body fat, body mass index z-score, and VO2peak. fasting insulin was significantly related to VO2peak (r =-0.37, p < .001), percent body fat (r = .27, p < .001), and BMI z-score (r = .33, p = .002). After inclusion in the multivariate model, VO2peak (p = .018) and body mass index z-score (p = .043) remained significant predictors of fasting insulin, while age (p = .39), sex (p = .49), and percent body fat (p = .72) did not. Among nonobese middle school children, fasting insulin is independently related to aerobic fitness after accounting for age, sex, and body composition. Public health efforts to reduce cardiometabolic disease risk among all adolescents should include exercise programs to increase cardiovascular fitness.

Rapidity dependence of proton cumulants and correlation functions

DOE PAGES

Bzdak, Adam; Koch, Volker

2017-11-13

The dependence of multiproton correlation functions and cumulants on the acceptance in rapidity and transverse momentum is studied. Here, we found that the preliminary data of various cumulant ratios are consistent, within errors, with rapidity and transverse momentum-independent correlation functions. But, rapidity correlations which moderately increase with rapidity separation between protons are slightly favored. We propose to further explore the rapidity dependence of multiparticle correlation functions by measuring the dependence of the integrated reduced correlation functions as a function of the size of the rapidity window.

Rapidity dependence of proton cumulants and correlation functions

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

Bzdak, Adam; Koch, Volker

The dependence of multiproton correlation functions and cumulants on the acceptance in rapidity and transverse momentum is studied. Here, we found that the preliminary data of various cumulant ratios are consistent, within errors, with rapidity and transverse momentum-independent correlation functions. But, rapidity correlations which moderately increase with rapidity separation between protons are slightly favored. We propose to further explore the rapidity dependence of multiparticle correlation functions by measuring the dependence of the integrated reduced correlation functions as a function of the size of the rapidity window.

Universal freezing of quantum correlations within the geometric approach

PubMed Central

Cianciaruso, Marco; Bromley, Thomas R.; Roga, Wojciech; Lo Franco, Rosario; Adesso, Gerardo

2015-01-01

Quantum correlations in a composite system can be measured by resorting to a geometric approach, according to which the distance from the state of the system to a suitable set of classically correlated states is considered. Here we show that all distance functions, which respect natural assumptions of invariance under transposition, convexity, and contractivity under quantum channels, give rise to geometric quantifiers of quantum correlations which exhibit the peculiar freezing phenomenon, i.e., remain constant during the evolution of a paradigmatic class of states of two qubits each independently interacting with a non-dissipative decohering environment. Our results demonstrate from first principles that freezing of geometric quantum correlations is independent of the adopted distance and therefore universal. This finding paves the way to a deeper physical interpretation and future practical exploitation of the phenomenon for noisy quantum technologies. PMID:26053239

Teachers' Experiences with Multiple Victimization: Identifying Demographic, Cognitive, and Contextual Correlates

ERIC Educational Resources Information Center

Martinez, Andrew; McMahon, Susan D.; Espelage, Dorothy; Anderman, Eric M.; Reddy, Linda A.; Sanchez, Bernadette

2016-01-01

Extant scholarship has primarily examined demographic predictors of teacher victimization. Teacher multiple victimization, or the extent to which teachers experience multiple types of violence, has not been examined. Using social-ecological theory, we examine correlates of violence among 2,324 teachers who reported having been victimized at least…

Fruit and Juice Epigenetic Signatures Are Associated with Independent Immunoregulatory Pathways.

PubMed

Nicodemus-Johnson, Jessie; Sinnott, Robert A

2017-07-14

Epidemiological evidence strongly suggests that fruit consumption promotes many health benefits. Despite the general consensus that fruit and juice are nutritionally similar, epidemiological results for juice consumption are conflicting. Our objective was to use DNA methylation marks to characterize fruit and juice epigenetic signatures within PBMCs and identify shared and independent signatures associated with these groups. Genome-wide DNA methylation marks (Illumina Human Methylation 450k chip) for 2,148 individuals that participated in the Framingham Offspring exam 8 were analyzed for correlations between fruit or juice consumption using standard linear regression. CpG sites with low P -values ( P < 0.01) were characterized using Gene Set Enrichment Analysis (GSEA), Ingenuity Pathway Analysis (IPA), and epigenetic Functional element Overlap analysis of the Results of Genome Wide Association Study Experiments (eFORGE). Fruit and juice-specific low P -value epigenetic signatures were largely independent. Genes near the fruit-specific epigenetic signature were enriched among pathways associated with antigen presentation and chromosome or telomere maintenance, while the juice-specific epigenetic signature was enriched for proinflammatory pathways. IPA and eFORGE analyses implicate fruit and juice-specific epigenetic signatures in the modulation of macrophage (fruit) and B or T cell (juice) activities. These data suggest a role for epigenetic regulation in fruit and juice-specific health benefits and demonstrate independent associations with distinct immune functions and cell types, suggesting that these groups may not confer the same health benefits. Identification of such differences between foods is the first step toward personalized nutrition and ultimately the improvement of human health and longevity.

Fruit and Juice Epigenetic Signatures Are Associated with Independent Immunoregulatory Pathways

PubMed Central

Nicodemus-Johnson, Jessie; Sinnott, Robert A.

2017-01-01

Epidemiological evidence strongly suggests that fruit consumption promotes many health benefits. Despite the general consensus that fruit and juice are nutritionally similar, epidemiological results for juice consumption are conflicting. Our objective was to use DNA methylation marks to characterize fruit and juice epigenetic signatures within PBMCs and identify shared and independent signatures associated with these groups. Genome-wide DNA methylation marks (Illumina Human Methylation 450k chip) for 2,148 individuals that participated in the Framingham Offspring exam 8 were analyzed for correlations between fruit or juice consumption using standard linear regression. CpG sites with low P-values (P < 0.01) were characterized using Gene Set Enrichment Analysis (GSEA), Ingenuity Pathway Analysis (IPA), and epigenetic Functional element Overlap analysis of the Results of Genome Wide Association Study Experiments (eFORGE). Fruit and juice-specific low P-value epigenetic signatures were largely independent. Genes near the fruit-specific epigenetic signature were enriched among pathways associated with antigen presentation and chromosome or telomere maintenance, while the juice-specific epigenetic signature was enriched for proinflammatory pathways. IPA and eFORGE analyses implicate fruit and juice-specific epigenetic signatures in the modulation of macrophage (fruit) and B or T cell (juice) activities. These data suggest a role for epigenetic regulation in fruit and juice-specific health benefits and demonstrate independent associations with distinct immune functions and cell types, suggesting that these groups may not confer the same health benefits. Identification of such differences between foods is the first step toward personalized nutrition and ultimately the improvement of human health and longevity. PMID:28708104

The Process of Curriculum Development and the Use of Assessments in Independent Schools

ERIC Educational Resources Information Center

Young, JoAnn P.

2012-01-01

This qualitative study was designed to examine and identify the site-based process that two elementary, independent schools, accredited by the Southern Association of Independent Schools use for curriculum and instructional development. Also, the study examined and identified the development and use of assessments to support each school's…

Initial state q q g correlations as a background for the chiral magnetic effect in collision of small systems

NASA Astrophysics Data System (ADS)

Kovner, Alex; Lublinsky, Michael; Skokov, Vladimir

2017-11-01

Motivated by understanding the background to chiral magnetic effect in proton-nucleus collisions from first principles, we compute the three particle correlation in the projectile wave function. We extract the correlations between two quarks and one gluon in the framework of the color glass condensate. This is related to the same-charge correlation of the conventional observable for the chiral magnetic effect. We show that there are two different contributions to this correlation function. One contribution is rapidity-independent and as such can be identified with the pedestal; while the other displays rather strong rapidity dependence. The pedestal contribution and the rapidity-dependent contribution at large rapidity separation between the two quarks result in the negative same charge correlations, while at small rapidity separation the second contribution changes sign. We argue that the computed initial state correlations might be partially responsible for the experimentally observed signal in proton-nucleus collisions.

MicroRNA-Related DNA Repair/Cell-Cycle Genes Independently Associated With Relapse After Radiation Therapy for Early Breast Cancer

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

Gee, Harriet E., E-mail: harriet.gee@sydney.edu.au; The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW; Central Clinical School, Sydney Medical School, University of Sydney, NSW

Purpose: Local recurrence and distant failure after adjuvant radiation therapy for breast cancer remain significant clinical problems, incompletely predicted by conventional clinicopathologic markers. We had previously identified microRNA-139-5p and microRNA-1274a as key regulators of breast cancer radiation response in vitro. The purpose of this study was to investigate standard clinicopathologic markers of local recurrence in a contemporary series and to establish whether putative target genes of microRNAs involved in DNA repair and cell cycle control could better predict radiation therapy response in vivo. Methods and Materials: With institutional ethics board approval, local recurrence was measured in a contemporary, prospectively collected series ofmore » 458 patients treated with radiation therapy after breast-conserving surgery. Additionally, independent publicly available mRNA/microRNA microarray expression datasets totaling >1000 early-stage breast cancer patients, treated with adjuvant radiation therapy, with >10 years of follow-up, were analyzed. The expression of putative microRNA target biomarkers—TOP2A, POLQ, RAD54L, SKP2, PLK2, and RAG1—were correlated with standard clinicopathologic variables using 2-sided nonparametric tests, and to local/distant relapse and survival using Kaplan-Meier and Cox regression analysis. Results: We found a low rate of isolated local recurrence (1.95%) in our modern series, and that few clinicopathologic variables (such as lymphovascular invasion) were significantly predictive. In multiple independent datasets (n>1000), however, high expression of RAD54L, TOP2A, POLQ, and SKP2 significantly correlated with local recurrence, survival, or both in univariate and multivariate analyses (P<.001). Low RAG1 expression significantly correlated with local recurrence (multivariate, P=.008). Additionally, RAD54L, SKP2, and PLK2 may be predictive, being prognostic in radiation therapy–treated patients but not in untreated

The correlation between highly sensitive C-reactive protein levels and erectile function among men with late-onset hypogonadism.

PubMed

Shigehara, Kazuyoshi; Konaka, Hiroyuki; Ijima, Masashi; Nohara, Takahiro; Narimoto, Kazutaka; Izumi, Koji; Kadono, Yoshifumi; Kitagawa, Yasuhide; Mizokami, Atsushi; Namiki, Mikio

2016-12-01

We investigated the correlation between highly sensitive C-reactive protein (hs-CRP) levels and erectile function, and assessed the clinical role of hs-CRP levels in men with late-onset hypogonadism (LOH) syndrome. For 77 participants, we assessed Sexual Health Inventory for men (SHIM) score, Aging Male Symptoms (AMS) score and International Prostate Symptom Score (IPSS). We also evaluated free testosterone (FT), hs-CRP, total cholesterol, triglyceride levels, high density lipoprotein cholesterol, hemoglobin A1c, body mass index, waist size and blood pressure. We attempted to identify parameters correlated with SHIM score and to determine the factors affecting cardiovascular risk based on hs-CRP levels. A Spearman rank correlation test revealed that age, AMS score, IPSS and hs-CRP levels were significantly correlated with SHIM score. Age-adjusted analysis revealed that hs-CRP and IPSS were the independent factors affecting SHIM score (r= -0.304 and -0.322, respectively). Seventeen patients belonged to the moderate to high risk group for cardiovascular disease, whereas the remaining 60 belonged to the low risk group. Age, FT value and SHIM score showed significant differences between the two groups. A multivariate regression analysis demonstrated that SHIM score was an independent factor affecting cardiovascular risk (OR: 0.796; 95%CI: 0.637-0.995).

Prognostic breast cancer signature identified from 3D culture model accurately predicts clinical outcome across independent datasets

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

Martin, Katherine J.; Patrick, Denis R.; Bissell, Mina J.

2008-10-20

One of the major tenets in breast cancer research is that early detection is vital for patient survival by increasing treatment options. To that end, we have previously used a novel unsupervised approach to identify a set of genes whose expression predicts prognosis of breast cancer patients. The predictive genes were selected in a well-defined three dimensional (3D) cell culture model of non-malignant human mammary epithelial cell morphogenesis as down-regulated during breast epithelial cell acinar formation and cell cycle arrest. Here we examine the ability of this gene signature (3D-signature) to predict prognosis in three independent breast cancer microarray datasetsmore » having 295, 286, and 118 samples, respectively. Our results show that the 3D-signature accurately predicts prognosis in three unrelated patient datasets. At 10 years, the probability of positive outcome was 52, 51, and 47 percent in the group with a poor-prognosis signature and 91, 75, and 71 percent in the group with a good-prognosis signature for the three datasets, respectively (Kaplan-Meier survival analysis, p<0.05). Hazard ratios for poor outcome were 5.5 (95% CI 3.0 to 12.2, p<0.0001), 2.4 (95% CI 1.6 to 3.6, p<0.0001) and 1.9 (95% CI 1.1 to 3.2, p = 0.016) and remained significant for the two larger datasets when corrected for estrogen receptor (ER) status. Hence the 3D-signature accurately predicts breast cancer outcome in both ER-positive and ER-negative tumors, though individual genes differed in their prognostic ability in the two subtypes. Genes that were prognostic in ER+ patients are AURKA, CEP55, RRM2, EPHA2, FGFBP1, and VRK1, while genes prognostic in ER patients include ACTB, FOXM1 and SERPINE2 (Kaplan-Meier p<0.05). Multivariable Cox regression analysis in the largest dataset showed that the 3D-signature was a strong independent factor in predicting breast cancer outcome. The 3D-signature accurately predicts breast cancer outcome across multiple datasets and holds

Freezing of Gait Detection in Parkinson's Disease: A Subject-Independent Detector Using Anomaly Scores.

PubMed

Pham, Thuy T; Moore, Steven T; Lewis, Simon John Geoffrey; Nguyen, Diep N; Dutkiewicz, Eryk; Fuglevand, Andrew J; McEwan, Alistair L; Leong, Philip H W

2017-11-01

Freezing of gait (FoG) is common in Parkinsonian gait and strongly relates to falls. Current clinical FoG assessments are patients' self-report diaries and experts' manual video analysis. Both are subjective and yield moderate reliability. Existing detection algorithms have been predominantly designed in subject-dependent settings. In this paper, we aim to develop an automated FoG detector for subject independent. After extracting highly relevant features, we apply anomaly detection techniques to detect FoG events. Specifically, feature selection is performed using correlation and clusterability metrics. From a list of 244 feature candidates, 36 candidates were selected using saliency and robustness criteria. We develop an anomaly score detector with adaptive thresholding to identify FoG events. Then, using accuracy metrics, we reduce the feature list to seven candidates. Our novel multichannel freezing index was the most selective across all window sizes, achieving sensitivity (specificity) of (). On the other hand, freezing index from the vertical axis was the best choice for a single input, achieving sensitivity (specificity) of () for ankle and () for back sensors. Our subject-independent method is not only significantly more accurate than those previously reported, but also uses a much smaller window (e.g., versus ) and/or lower tolerance (e.g., versus ).Freezing of gait (FoG) is common in Parkinsonian gait and strongly relates to falls. Current clinical FoG assessments are patients' self-report diaries and experts' manual video analysis. Both are subjective and yield moderate reliability. Existing detection algorithms have been predominantly designed in subject-dependent settings. In this paper, we aim to develop an automated FoG detector for subject independent. After extracting highly relevant features, we apply anomaly detection techniques to detect FoG events. Specifically, feature selection is performed using correlation and clusterability metrics. From

A new interpretation and validation of variance based importance measures for models with correlated inputs

NASA Astrophysics Data System (ADS)

Hao, Wenrui; Lu, Zhenzhou; Li, Luyi

2013-05-01

In order to explore the contributions by correlated input variables to the variance of the output, a novel interpretation framework of importance measure indices is proposed for a model with correlated inputs, which includes the indices of the total correlated contribution and the total uncorrelated contribution. The proposed indices accurately describe the connotations of the contributions by the correlated input to the variance of output, and they can be viewed as the complement and correction of the interpretation about the contributions by the correlated inputs presented in "Estimation of global sensitivity indices for models with dependent variables, Computer Physics Communications, 183 (2012) 937-946". Both of them contain the independent contribution by an individual input. Taking the general form of quadratic polynomial as an illustration, the total correlated contribution and the independent contribution by an individual input are derived analytically, from which the components and their origins of both contributions of correlated input can be clarified without any ambiguity. In the special case that no square term is included in the quadratic polynomial model, the total correlated contribution by the input can be further decomposed into the variance contribution related to the correlation of the input with other inputs and the independent contribution by the input itself, and the total uncorrelated contribution can be further decomposed into the independent part by interaction between the input and others and the independent part by the input itself. Numerical examples are employed and their results demonstrate that the derived analytical expressions of the variance-based importance measure are correct, and the clarification of the correlated input contribution to model output by the analytical derivation is very important for expanding the theory and solutions of uncorrelated input to those of the correlated one.

Comment on atomic independent-particle models

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

Doda, D.D.; Gravey, R.H.; Green, A.E.S.

1975-08-01

The Hartree-Fock-Slater (HFS) independent-particle model in the form developed by Hermann and Skillman (HS) and the Green, Sellin, and Zachor (GSZ) analytic independent-particle model are being used for many types of applications of atomic theory to avoid cumbersome, albeit more rigorous, many-body calculations. The single-electron eigenvalues obtained with these models are examined and it is found that the GSZ model is capable of yielding energy eigenvalues for valence electrons which are substantially closer to experimental values than are the results of HS-HFS calculations. With the aid of an analytic representation of the equivalent HS-HFS screening function, the difficulty with thismore » model is identified as a weakness of the potential in the neighborhood of the valence shell. Accurate representations of valence states are important in most atomic applications of the independent-particle model. (auth)« less

Genetic correlations between wellbeing, depression and anxiety symptoms and behavioral responses to the emotional faces task in healthy twins.

PubMed

Routledge, Kylie M; Williams, Leanne M; Harris, Anthony W F; Schofield, Peter R; Clark, C Richard; Gatt, Justine M

2018-06-01

Currently there is a very limited understanding of how mental wellbeing versus anxiety and depression symptoms are associated with emotion processing behaviour. For the first time, we examined these associations using a behavioural emotion task of positive and negative facial expressions in 1668 healthy adult twins. Linear mixed model results suggested faster reaction times to happy facial expressions was associated with higher wellbeing scores, and slower reaction times with higher depression and anxiety scores. Multivariate twin modelling identified a significant genetic correlation between depression and anxiety symptoms and reaction time to happy facial expressions, in the absence of any significant correlations with wellbeing. We also found a significant negative phenotypic relationship between depression and anxiety symptoms and accuracy for identifying neutral emotions, although the genetic or environment correlations were not significant in the multivariate model. Overall, the phenotypic relationships between speed of identifying happy facial expressions and wellbeing on the one hand, versus depression and anxiety symptoms on the other, were in opposing directions. Twin modelling revealed a small common genetic correlation between response to happy faces and depression and anxiety symptoms alone, suggesting that wellbeing and depression and anxiety symptoms show largely independent relationships with emotion processing at the behavioral level. Copyright © 2018 Elsevier B.V. All rights reserved.

Cop9/signalosome subunits and Pcu4 regulate ribonucleotide reductase by both checkpoint-dependent and -independent mechanisms

PubMed Central

Liu, Cong; Powell, Kelly A.; Mundt, Kirsten; Wu, LeJung; Carr, Antony M.; Caspari, Thomas

2003-01-01

The signalosome is implicated in regulating cullin-dependent ubiquitin ligases. We find that two signalosome subunits, Csn1 and Csn2, are required to regulate ribonucleotide reductase (RNR) through the degradation of a small protein, Spd1, that acts to anchor the small RNR subunit in the nucleus. Spd1 destruction correlates with the nuclear export of the small RNR subunit, which, in turn, correlates with a requirement for RNR in replication and repair. Spd1 degradation is promoted by two separate CSN-dependent mechanisms. During unperturbed S phase, Spd1 degradation is independent of checkpoint proteins. In irradiated G2 cells, Spd1 degradation requires the DNA damage checkpoint. The signalosome copurifies with Pcu4 (cullin 4). Pcu4, Csn1, and Csn2 promote the degradation of Spd1, identifying a new function for the signalosome as a regulator of Pcu4-containing E3 ubiquitin ligase. PMID:12695334

Factors associated with independent pharmacy owners' satisfaction with Medicare Part D contracts.

PubMed

Zhang, Su; Doucette, William R; Urmie, Julie M; Xie, Yang; Brooks, John M

2010-06-01

As Medicare Part D contracts apply pressure on the profitability of independent pharmacies, there is concern about their owners' willingness to sign such contracts. Identifying factors affecting independent pharmacy owners' satisfaction with Medicare Part D contracts could inform policy makers in managing Medicare Part D. (1) To identify influences on independent pharmacy owners' satisfaction with Medicare Part D contracts and (2) to characterize comments made by independent pharmacy owners about Medicare Part D. This cross-sectional study used a mail survey of independent pharmacy owners in 15 states comprising 6 Medicare regions to collect information on their most- and least-favorable Medicare Part D contracts, including satisfaction, contract management activities, market position, pharmacy operation, and specific payment levels on brand and generic drugs. Of the 1649 surveys mailed, 296 surveys were analyzed. The regression models for satisfaction with both the least and the most-favorable Part D contracts were significant (P<0.05). A different set of significant influences on satisfaction was identified for each regression model. For the most-favorable contract, influences were contending and equity. For the least-favorable contract, influences were negotiation, equity, generic rate bonus, and medication therapy management (MTM) payment. About one-third of the survey respondents made at least 1 comment. The most frequent themes in the comments were that Medicare Part D reimbursement rate is too low (28%) and that contracts are offered without negotiation in a "take it or leave it" manner (20%). Equity, contending, negotiation, generic rate bonus, and MTM payments were identified as the influences of independent pharmacy owners' satisfaction toward Medicare Part D contracts. Generic rate bonus and MTM payment provide additional financial incentives to less financially favorable contracts and, in turn, contribute to independent pharmacy owner's satisfaction

Genomic ancestry and education level independently influence abdominal fat distributions in a Brazilian admixed population.

PubMed

França, Giovanny Vinícius Araújo de; De Lucia Rolfe, Emanuella; Horta, Bernardo Lessa; Gigante, Denise Petrucci; Yudkin, John S; Ong, Ken K; Victora, Cesar Gomes

2017-01-01

We aimed to identify the independent associations of genomic ancestry and education level with abdominal fat distributions in the 1982 Pelotas birth cohort study, Brazil. In 2,890 participants (1,409 men and 1,481 women), genomic ancestry was assessed using genotype data on 370,539 genome-wide variants to quantify ancestral proportions in each individual. Years of completed education was used to indicate socio-economic position. Visceral fat depth and subcutaneous abdominal fat thickness were measured by ultrasound at age 29-31y; these measures were adjusted for BMI to indicate abdominal fat distributions. Linear regression models were performed, separately by sex. Admixture was observed between European (median proportion 85.3), African (6.6), and Native American (6.3) ancestries, with a strong inverse correlation between the African and European ancestry scores (ρ = -0.93; p<0.001). Independent of education level, African ancestry was inversely associated with both visceral and subcutaneous abdominal fat distributions in men (both P = 0.001), and inversely associated with subcutaneous abdominal fat distribution in women (p = 0.009). Independent of genomic ancestry, higher education level was associated with lower visceral fat, but higher subcutaneous fat, in both men and women (all p<0.001). Our findings, from an admixed population, indicate that both genomic ancestry and education level were independently associated with abdominal fat distribution in adults. African ancestry appeared to lower abdominal fat distributions, particularly in men.

Genomic ancestry and education level independently influence abdominal fat distributions in a Brazilian admixed population

PubMed Central

De Lucia Rolfe, Emanuella; Horta, Bernardo Lessa; Gigante, Denise Petrucci; Yudkin, John S.; Ong, Ken K.; Victora, Cesar Gomes

2017-01-01

We aimed to identify the independent associations of genomic ancestry and education level with abdominal fat distributions in the 1982 Pelotas birth cohort study, Brazil. In 2,890 participants (1,409 men and 1,481 women), genomic ancestry was assessed using genotype data on 370,539 genome-wide variants to quantify ancestral proportions in each individual. Years of completed education was used to indicate socio-economic position. Visceral fat depth and subcutaneous abdominal fat thickness were measured by ultrasound at age 29–31y; these measures were adjusted for BMI to indicate abdominal fat distributions. Linear regression models were performed, separately by sex. Admixture was observed between European (median proportion 85.3), African (6.6), and Native American (6.3) ancestries, with a strong inverse correlation between the African and European ancestry scores (ρ = -0.93; p<0.001). Independent of education level, African ancestry was inversely associated with both visceral and subcutaneous abdominal fat distributions in men (both P = 0.001), and inversely associated with subcutaneous abdominal fat distribution in women (p = 0.009). Independent of genomic ancestry, higher education level was associated with lower visceral fat, but higher subcutaneous fat, in both men and women (all p<0.001). Our findings, from an admixed population, indicate that both genomic ancestry and education level were independently associated with abdominal fat distribution in adults. African ancestry appeared to lower abdominal fat distributions, particularly in men. PMID:28582437

Spatio-Chromatic Adaptation via Higher-Order Canonical Correlation Analysis of Natural Images

PubMed Central

Gutmann, Michael U.; Laparra, Valero; Hyvärinen, Aapo; Malo, Jesús

2014-01-01

Independent component and canonical correlation analysis are two general-purpose statistical methods with wide applicability. In neuroscience, independent component analysis of chromatic natural images explains the spatio-chromatic structure of primary cortical receptive fields in terms of properties of the visual environment. Canonical correlation analysis explains similarly chromatic adaptation to different illuminations. But, as we show in this paper, neither of the two methods generalizes well to explain both spatio-chromatic processing and adaptation at the same time. We propose a statistical method which combines the desirable properties of independent component and canonical correlation analysis: It finds independent components in each data set which, across the two data sets, are related to each other via linear or higher-order correlations. The new method is as widely applicable as canonical correlation analysis, and also to more than two data sets. We call it higher-order canonical correlation analysis. When applied to chromatic natural images, we found that it provides a single (unified) statistical framework which accounts for both spatio-chromatic processing and adaptation. Filters with spatio-chromatic tuning properties as in the primary visual cortex emerged and corresponding-colors psychophysics was reproduced reasonably well. We used the new method to make a theory-driven testable prediction on how the neural response to colored patterns should change when the illumination changes. We predict shifts in the responses which are comparable to the shifts reported for chromatic contrast habituation. PMID:24533049

Spatio-chromatic adaptation via higher-order canonical correlation analysis of natural images.

PubMed

Gutmann, Michael U; Laparra, Valero; Hyvärinen, Aapo; Malo, Jesús

2014-01-01

Independent component and canonical correlation analysis are two general-purpose statistical methods with wide applicability. In neuroscience, independent component analysis of chromatic natural images explains the spatio-chromatic structure of primary cortical receptive fields in terms of properties of the visual environment. Canonical correlation analysis explains similarly chromatic adaptation to different illuminations. But, as we show in this paper, neither of the two methods generalizes well to explain both spatio-chromatic processing and adaptation at the same time. We propose a statistical method which combines the desirable properties of independent component and canonical correlation analysis: It finds independent components in each data set which, across the two data sets, are related to each other via linear or higher-order correlations. The new method is as widely applicable as canonical correlation analysis, and also to more than two data sets. We call it higher-order canonical correlation analysis. When applied to chromatic natural images, we found that it provides a single (unified) statistical framework which accounts for both spatio-chromatic processing and adaptation. Filters with spatio-chromatic tuning properties as in the primary visual cortex emerged and corresponding-colors psychophysics was reproduced reasonably well. We used the new method to make a theory-driven testable prediction on how the neural response to colored patterns should change when the illumination changes. We predict shifts in the responses which are comparable to the shifts reported for chromatic contrast habituation.

Accounting for non-independent detection when estimating abundance of organisms with a Bayesian approach

USGS Publications Warehouse

Martin, Julien; Royle, J. Andrew; MacKenzie, Darryl I.; Edwards, Holly H.; Kery, Marc; Gardner, Beth

2011-01-01

Summary 1. Binomial mixture models use repeated count data to estimate abundance. They are becoming increasingly popular because they provide a simple and cost-effective way to account for imperfect detection. However, these models assume that individuals are detected independently of each other. This assumption may often be violated in the field. For instance, manatees (Trichechus manatus latirostris) may surface in turbid water (i.e. become available for detection during aerial surveys) in a correlated manner (i.e. in groups). However, correlated behaviour, affecting the non-independence of individual detections, may also be relevant in other systems (e.g. correlated patterns of singing in birds and amphibians). 2. We extend binomial mixture models to account for correlated behaviour and therefore to account for non-independent detection of individuals. We simulated correlated behaviour using beta-binomial random variables. Our approach can be used to simultaneously estimate abundance, detection probability and a correlation parameter. 3. Fitting binomial mixture models to data that followed a beta-binomial distribution resulted in an overestimation of abundance even for moderate levels of correlation. In contrast, the beta-binomial mixture model performed considerably better in our simulation scenarios. We also present a goodness-of-fit procedure to evaluate the fit of beta-binomial mixture models. 4. We illustrate our approach by fitting both binomial and beta-binomial mixture models to aerial survey data of manatees in Florida. We found that the binomial mixture model did not fit the data, whereas there was no evidence of lack of fit for the beta-binomial mixture model. This example helps illustrate the importance of using simulations and assessing goodness-of-fit when analysing ecological data with N-mixture models. Indeed, both the simulations and the goodness-of-fit procedure highlighted the limitations of the standard binomial mixture model for aerial

ICA-Derived EEG Correlates to Mental Fatigue, Effort, and Workload in a Realistically Simulated Air Traffic Control Task.

PubMed

Dasari, Deepika; Shou, Guofa; Ding, Lei

2017-01-01

Electroencephalograph (EEG) has been increasingly studied to identify distinct mental factors when persons perform cognitively demanding tasks. However, most of these studies examined EEG correlates at channel domain, which suffers the limitation that EEG signals are the mixture of multiple underlying neuronal sources due to the volume conduction effect. Moreover, few studies have been conducted in real-world tasks. To precisely probe EEG correlates with specific neural substrates to mental factors in real-world tasks, the present study examined EEG correlates to three mental factors, i.e., mental fatigue [also known as time-on-task (TOT) effect], workload and effort, in EEG component signals, which were obtained using an independent component analysis (ICA) on high-density EEG data. EEG data were recorded when subjects performed a realistically simulated air traffic control (ATC) task for 2 h. Five EEG independent component (IC) signals that were associated with specific neural substrates (i.e., the frontal, central medial, motor, parietal, occipital areas) were identified. Their spectral powers at their corresponding dominant bands, i.e., the theta power of the frontal IC and the alpha power of the other four ICs, were detected to be correlated to mental workload and effort levels, measured by behavioral metrics. Meanwhile, a linear regression analysis indicated that spectral powers at five ICs significantly increased with TOT. These findings indicated that different levels of mental factors can be sensitively reflected in EEG signals associated with various brain functions, including visual perception, cognitive processing, and motor outputs, in real-world tasks. These results can potentially aid in the development of efficient operational interfaces to ensure productivity and safety in ATC and beyond.

Life-history correlates of extinction risk and recovery potential.

PubMed

Hutchings, Jeffrey A; Myers, Ransom A; García, Verónica B; Lucifora, Luis O; Kuparinen, Anna

2012-06-01

Extinction risk is inversely associated with maximum per capita population growth rate (r(max)). However, this parameter is not known for most threatened species, underscoring the value in identifying correlates of r(max) that, in the absence of demographic data, would indirectly allow one to identify species and populations at elevated risk of extinction and their associated recovery potential. We undertook a comparative life-history analysis of 199 species from three taxonomic classes: Chondrichthyes (e.g., sharks; n = 82), Actinopterygii (teleost or bony fishes; n = 47), and Mammalia (n = 70, including 16 marine species). Median r(max) was highest for (and similar between) terrestrial mammals (0.71) and teleosts (0.43), significantly lower among chondrichthyans (0.26), and lower still in marine mammals (0.07). Age at maturity was the primary (and negative) correlate of r(max). In contrast, although body size was negatively correlated with r(max) in chondrichthyans and mammals, evidence of an association in teleosts was equivocal, and fecundity was not related to r(max) in fishes, despite recurring assertions to the contrary. Our analyses suggest that age at maturity can serve as a universal predictor of extinction risk in fishes and mammals when r(max) itself is unknown. Moreover, in contrast to what is generally expected, the recovery potential of teleost fishes does not differ from that of terrestrial mammals. Our findings are supportive of the application of extinction-risk criteria that are based on generation time and that are independent of taxonomic affinity.

Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels

PubMed Central

Patel, Chirag J; Cullen, Mark R; Ioannidis, John PA; Butte, Atul J

2012-01-01

Background Both genetic and environmental factors contribute to triglyceride, low-density lipoprotein-cholesterol (LDL-C), and high-density lipoprotein-cholesterol (HDL-C) levels. Although genome-wide association studies are currently testing the genetic factors systematically, testing and reporting one or a few factors at a time can lead to fragmented literature for environmental chemical factors. We screened for correlation between environmental factors and lipid levels, utilizing four independent surveys with information on 188 environmental factors from the Centers of Disease Control, National Health and Nutrition Examination Survey, collected between 1999 and 2006. Methods We used linear regression to correlate each environmental chemical factor to triglycerides, LDL-C and HDL-C adjusting for age, age2, sex, ethnicity, socio-economic status and body mass index. Final estimates were adjusted for waist circumference, diabetes status, blood pressure and survey. Multiple comparisons were controlled for by estimating the false discovery rate and significant findings were tentatively validated in an independent survey. Results We identified and validated 29, 9 and 17 environmental factors correlated with triglycerides, LDL-C and HDL-C levels, respectively. Findings include hydrocarbons and nicotine associated with lower HDL-C and vitamin E (γ-tocopherol) associated with unfavourable lipid levels. Higher triglycerides and lower HDL-C were correlated with higher levels of fat-soluble contaminants (e.g. polychlorinated biphenyls and dibenzofurans). Nutrients and vitamin markers (e.g. vitamins B, D and carotenes), were associated with favourable triglyceride and HDL-C levels. Conclusions Our systematic association study has enabled us to postulate about broad environmental correlation to lipid levels. Although subject to confounding and reverse causality bias, these findings merit evaluation in additional cohorts. PMID:22421054

Military and mental health correlates of unemployment in a national sample of women veterans.

PubMed

Hamilton, Alison B; Williams, Lindsay; Washington, Donna L

2015-04-01

The unemployment rate is currently higher among women Veterans than among male Veterans and civilian women. Employment is a key social determinant of health, with unemployment being strongly associated with adverse health. To identify military-related and health-related characteristics associated with unemployment in women Veterans. Secondary analysis of workforce participants (n=1605) in the National Survey of Women Veterans telephone survey. Demographics, mental health conditions, health care utilization, and military experiences and effects. Unemployment was defined as being in the labor force but unemployed and looking for work. The χ analyses to identify characteristics of unemployed women Veterans; logistic regression to identify independent factors associated with unemployment. Ten percent of women Veterans were unemployed. Independent correlates of unemployment were screening positive for depression [odds ratio (OR)=4.7; 95% confidence interval [CI], 1.8-12.4], military service during wartime (OR=2.9; 95%, CI 1.1-7.3), and service in the regular military (vs. in the National Guards/Reserves only) (OR=6.8; 95% CI, 2.2-20.5). Two postactive duty perceptions related to not being respected and understood as a Veteran were each independently associated with unemployment. Whether depression underlies unemployment, is exacerbated by unemployment, or both, it is critical to identify and treat depression among women Veterans, and also to investigate women Veterans' experiences and identities in civilian life. Community-based employers may need education regarding women Veterans' unique histories and strengths. Women who served in the regular military and during wartime may benefit from job assistance before and after they leave the military. Gender-specific adaptation of employment services may be warranted.

Tissue Microstructural Changes Are Independently Associated With Cognitive Impairment in Cerebral Amyloid Angiopathy

PubMed Central

Viswanathan, Anand; Patel, Pratik; Rahman, Rosanna; Nandigam, R.N. Kaveer; Kinnecom, Catherine; Bracoud, Luc; Rosand, Jonathan; Chabriat, Hugues; Greenberg, Steven M.; Smith, Eric E.

2009-01-01

Background and Purpose Cerebral amyloid angiopathy (CAA) is a major cause of lobar intracerebral hemorrhage and cognitive impairment and is associated with white matter hyperintensities and cerebral microbleeds. MRI diffusion tensor imaging detects microstructural tissue damage in advanced CAA even in areas that appear normal on conventional MRI. We hypothesized that higher global mean apparent diffusion coefficient (mean ADC), reflecting a higher amount of chronic tissue disruption caused by CAA, would be independently associated with CAA-related cognitive impairment. Methods Preintracerebral hemorrhage cognitive impairment was systematically assessed using a standardized questionnaire (IQCODE) in 49 patients. Volume of white matter hyperintensities, number of microbleeds, and mean ADC were determined from MRIs obtained within 14.0±22.5 days of intracerebral hemorrhage cognitive impairment. White matter hyperintensities and mean ADC were measured in the hemisphere uninvolved by intracerebral hemorrhage to avoid confounding. Results Preintracerebral hemorrhage cognitive impairment was identified in 10 of 49 subjects. Mean ADC was the only variable associated with preintracerebral hemorrhage cognitive impairment and was elevated in those with preintracerebral hemorrhage cognitive impairment compared with those without (12.4×10-4 versus 11.7×10-4 mm2/s; P=0.03). Mean ADC positively correlated with age but not white matter hyperintensities or number of microbleeds. In logistic regression controlling for age and visible cerebral atrophy, mean ADC was independently associated with preintracerebral hemorrhage cognitive impairment (OR per 1×10-4 mm2/s increase=2.45, 95% CI 1.11 to 5.40, P=0.04). Conclusions Mean ADC is independently associated with preintracerebral hemorrhage cognitive impairment in CAA. The lack of correlation with other MRI markers of CAA suggests that mean ADC may be sensitive to distinct aspects of CAA pathology and its tissue consequences. These

Initial state q q g correlations as a background for the chiral magnetic effect in collision of small systems

DOE PAGES

Kovner, Alex; Lublinsky, Michael; Skokov, Vladimir

2017-11-13

Motivated by understanding the background to chiral magnetic effect in proton-nucleus collisions from first principles, we compute the three particle correlation in the projectile wave function. We extract the correlations between two quarks and one gluon in the framework of the color glass condensate. This is related to the same-charge correlation of the conventional observable for the chiral magnetic effect. We show that there are two different contributions to this correlation function. One contribution is rapidity-independent and as such can be identified with the pedestal; while the other displays rather strong rapidity dependence. The pedestal contribution and the rapidity-dependent contributionmore » at large rapidity separation between the two quarks result in the negative same charge correlations, while at small rapidity separation the second contribution changes sign. We argue that the computed initial state correlations might be partially responsible for the experimentally observed signal in proton-nucleus collisions.« less

Initial state q q g correlations as a background for the chiral magnetic effect in collision of small systems

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

Kovner, Alex; Lublinsky, Michael; Skokov, Vladimir

Motivated by understanding the background to chiral magnetic effect in proton-nucleus collisions from first principles, we compute the three particle correlation in the projectile wave function. We extract the correlations between two quarks and one gluon in the framework of the color glass condensate. This is related to the same-charge correlation of the conventional observable for the chiral magnetic effect. We show that there are two different contributions to this correlation function. One contribution is rapidity-independent and as such can be identified with the pedestal; while the other displays rather strong rapidity dependence. The pedestal contribution and the rapidity-dependent contributionmore » at large rapidity separation between the two quarks result in the negative same charge correlations, while at small rapidity separation the second contribution changes sign. We argue that the computed initial state correlations might be partially responsible for the experimentally observed signal in proton-nucleus collisions.« less

Short-Range Nucleon-Nucleon Correlations

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

Douglas Higinbotham

2011-10-01

Valence-shell nucleon knock-out experiments, such as 12C(e,e'p)11B, measure less strength then is predicted by independent particle shell model calculations. The theoretical solution to this problem is to include the correlations between the nucleons in the nucleus in the calculations. Motivated by these results, many electron scattering experiments have tried to directly observe these correlations in order to gain new insight into the short-range part of the nucleon-nucleon potential. Unfortunately, many competing mechanisms can cause the same observable final-state as an initial-state correlation, making truly isolating the signal extremely challenging. This paper reviews the recent experimental evidence for short-range correlations, asmore » well as explores the possibility that such correlations are responsible for the EMC effect in the 0.3 < xB < 0.7 deep inelastic scattering ratios.« less

“High On My Own Supply”: Correlates of Drug Dealing among Heterosexually-identified Methamphetamine Users

PubMed Central

Semple, Shirley J.; Strathdee, Steffanie A.; Volkmann, Tyson; Zians, Jim; Patterson, Thomas L.

2011-01-01

Although rates of methamphetamine use continue to increase throughout the United States, little is known about the individuals who sell methamphetamine at the street level. This exploratory study examined the prevalence and correlates of drug-dealing behavior in a sample of 404 heterosexually-identified methamphetamine users who were participants in a sexual risk reduction intervention in San Diego, CA. Twenty-nine percent of participants (N = 116) reported “dealing” methamphetamine in the past two months. In a multivariate logistic regression, methamphetamine dealing was associated with being male (OR = 1.99; 95% CI 1.16 – 3.39), younger age (OR = 1.87 per year; 95% CI 1.10 – 3.17), more frequent use of methamphetamine (OR = 2.69; 95% CI 1.59 – 4.57), injecting methamphetamine (OR = 3.10; 95% CI 1.79 – 5.37), and higher hostility scores (OR = 1.07 per unit increase; 95% CI 1.01 – 1.13). These characteristics, particularly intensity of drug use and hostility, may be associated with greater resistance to drug treatment and lower success in treatment programs. PMID:21999496

Cultural relativism: occupation and independence reconsidered.

PubMed

Whiteford, G E; Wilcock, A A

2000-12-01

In this article, findings from a qualitative study of a cohort of occupational therapy students in Auckland, New Zealand are presented. The study focussed on the experiences of students as they learned to work with people from different social and cultural backgrounds over a 3-year period. As well as identifying curriculum and teaching/learning processes that enhance intercultural competence development, the data that emerged from the study also highlight important issues about how occupation and independence are conceptualised across cultures. A review of the trans-disciplinary and occupational therapy literature dealing with theoretical, conceptual and educational issues relating to cross-cultural practice is followed by a presentation of narrative extracts that address the key concepts of occupation and independence. These are then discussed with reference to relevant occupational therapy literature. In conclusion, implications for future research and practice are explored focussing on a need for occupation and independence to be reconsidered as culturally relative constructions.

Independent community care gerontological nursing: becoming an entrepreneur.

PubMed

Caffrey, Rosalie A

2005-08-01

Few nurses have the experience of developing an independent practice. This ethnographic study explores the process and challenges of becoming an entrepreneur as described by nurses developing independent practices in community care gerontologic nursing. The process included developing a legal contract, marketing strategies, and reimbursement amounts and strategies. Major barriers to implementing this role identified by the nurses included ignorance and confusion by others about their role, financial issues related to an uncertain income, time management, and legal concerns especially around delegation. These were experienced and dedicated nurses who were also risk-takers and enjoyed the independence of practicing nursing because they believed it was meant to be practiced. Suggestions for research, education, and practice are included.

Neural correlates of frog calling: production by two semi-independent generators.

PubMed

Schmidt, R S

1992-09-28

The anterior preoptic nuclei of the isolated brainstem of male, Northern leopard frogs (Rana p. pipiens) were stimulated electrically and neural correlates of mating calling recorded from the rhombencephalic mating calling pattern generator. Lesions of discrete areas of the brainstem showed that the mating calling generator is separable into two generators, the pretrigeminal nucleus and the classical pulmonary respiration generator (which is approximately co-extensive with the motor nuclei IX-X). Each of these still can produce pulses when isolated from the other. Their interaction changes the expiratory phase of breathing into the vocal phase of calling. All stages of intermediates between these phases could be seen. An updated and simplified model of call production and evolution is presented.

Higher ambulatory systolic blood pressure independently associated with enlarged perivascular spaces in basal ganglia.

PubMed

Yang, Shuna; Yuan, Junliang; Zhang, Xiaoyu; Fan, Huimin; Li, Yue; Yin, Jiangmei; Hu, Wenli

2017-09-01

Enlarged perivascular spaces (EPVS) have been identified as a marker of cerebral small vessel diseases (CSVD). Ambulatory blood pressure (ABP) is the strongest predictor of hypertension-related brain damage. However, the relationship between ABP levels and EPVS is unclear. This study aimed to investigate the association between ABP levels and EPVS by 24-hour ambulatory blood pressure monitoring (ABPM). We prospectively recruited inpatients for physical examinations in our hospital from May 2013 to Jun 2016. 24-hour ABPM data and cranial magnetic resonance imaging information were collected. EPVS in basal ganglia (BG) and centrum semiovale (CSO) were identified and classified into three categories by the severity. White matter hyperintensities were scored by Fazekas scale. Spearman correlation analysis and multiple logistic regression analysis were used to determine the relationship between ABP levels and EPVS. A total of 573 subjects were enrolled in this study. 24-hour, day and night systolic blood pressure (SBP) levels were positively related to higher numbers of EPVS in BG (24-hour SBP: r = 0.23, p < 0.01; day SBP: r = 0.25, p < 0.01; night SBP: r = 0.30, p < 0.01). The association was unchanged after controlling for confounders by multiple logistic regression analysis. 24-hour and day diastolic blood pressure (DBP) levels increased with an increasing degree of EPVS in CSO (p = 0.04 and 0.049, respectively). But the association disappeared after adjusting for confounders. Spearman correlation analysis indicated that ABP levels were not associated with higher numbers of EPVS in CSO (p > 0.05). DBP levels were not independently associated with the severity of EPVS in BG and CSO. Higher SBP levels were independently associated with EPVS in BG, but not in CSO, which supported EPVS in BG to be a marker of CSVD. Pathogenesis of EPVS in BG and CSO might be different.

Microwave moisture sensing through use of a piecewise density-independent function

USDA-ARS?s Scientific Manuscript database

Microwave moisture sensing provides a means to determine nondestructively the amount of water in materials. This is accomplished through the correlation of dielectric properties with moisture in the material. In this study, linear relationships between a density-independent function of the dielectri...

Testing of the coalescence mechanism in high energy heavy ion collisions using two-particle correlations with identified particle trigger

NASA Astrophysics Data System (ADS)

Choudhury, Subikash; Sarkar, Debojit; Chattopadhyay, Subhasis

2016-05-01

In central Au-Au collisions at top RHIC energy, two-particle correlation measurements with identified hadron trigger have shown attenuation of near-side proton triggered jetlike yield at intermediate transverse momentum (p T ),2

correlations at LHC energy within the framework of a multiphase transport (AMPT) model that implements quark coalescence as a mode of hadronization. In this paper we have calculated the proton over pion ratio and the near side per trigger yield associated with pion and proton triggers at intermediate p T from the string melting (SM) version of AMPT. Results obtained are contrasted with the AMPT default (Def.) which does not include coalescence. Baryon enhancement was observed in AMPT SM at intermediate p T . Near-side jetlike correlated yield associated with baryon (proton) trigger in the momentum region where baryon generation is enhanced is found to be suppressed as compared to the corresponding yields for the meson (pion) trigger in most central Pb-Pb events. No such effect was found in the default version of AMPT.

Identifying States along the Hematopoietic Stem Cell Differentiation Hierarchy with Single Cell Specificity via Raman Spectroscopy.

PubMed

Ilin, Yelena; Choi, Ji Sun; Harley, Brendan A C; Kraft, Mary L

2015-11-17

A major challenge for expanding specific types of hematopoietic cells ex vivo for the treatment of blood cell pathologies is identifying the combinations of cellular and matrix cues that direct hematopoietic stem cells (HSC) to self-renew or differentiate into cell populations ex vivo. Microscale screening platforms enable minimizing the number of rare HSCs required to screen the effects of numerous cues on HSC fate decisions. These platforms create a strong demand for label-free methods that accurately identify the fate decisions of individual hematopoietic cells at specific locations on the platform. We demonstrate the capacity to identify discrete cells along the HSC differentiation hierarchy via multivariate analysis of Raman spectra. Notably, cell state identification is accurate for individual cells and independent of the biophysical properties of the functionalized polyacrylamide gels upon which these cells are cultured. We report partial least-squares discriminant analysis (PLS-DA) models of single cell Raman spectra enable identifying four dissimilar hematopoietic cell populations across the HSC lineage specification. Successful discrimination was obtained for a population enriched for long-term repopulating HSCs (LT-HSCs) versus their more differentiated progeny, including closely related short-term repopulating HSCs (ST-HSCs) and fully differentiated lymphoid (B cells) and myeloid (granulocytes) cells. The lineage-specific differentiation states of cells from these four subpopulations were accurately identified independent of the stiffness of the underlying biomaterial substrate, indicating subtle spectral variations that discriminated these populations were not masked by features from the culture substrate. This approach enables identifying the lineage-specific differentiation stages of hematopoietic cells on biomaterial substrates of differing composition and may facilitate correlating hematopoietic cell fate decisions with the extrinsic cues that

Reading Cooperatively or Independently? Study on ELL Student Reading Development

ERIC Educational Resources Information Center

Liu, Siping; Wang, Jian

2015-01-01

This study examines the effectiveness of cooperative reading teaching activities and independent reading activities for English language learner (ELL) students at 4th grade level. Based on simple linear regression and correlational analyses of data collected from two large data bases, PIRLS and NAEP, the study found that cooperative reading…

The Formation of Students' Creative Independence at the English Language Classes

ERIC Educational Resources Information Center

Shangaraeva, Liya F.; Yarkhamova, Alfiya A.; Biktagirova, Zubayda A.; Agol, Dorice

2016-01-01

The article is devoted to the formation of students' creative independence. The aim of the article is to identify and test pedagogical conditions of formation students' creative independence studying the English language. The leading methods are analyses of scientific works and practice, empirical and experimental data, method of involved…

Inter-correlations between Cloninger's temperament dimensions-- a meta-analysis.

PubMed

Miettunen, Jouko; Lauronen, Erika; Kantojärvi, Liisa; Veijola, Juha; Joukamaa, Matti

2008-07-15

The Temperament and Character Inventory (TCI) was developed to measure the following temperament dimensions: novelty seeking (NS), harm avoidance (HA), reward dependence (RD) and persistence (P). These four dimensions of temperament were originally proposed to be independent of one another. In this study the inter-relationships between the dimensions were studied with meta-analytic techniques. We also studied the effects of sociodemographic factors (location of the study, mean age and gender distribution) on correlations between temperament dimensions. We searched studies on healthy (non-clinical) populations that used the TCI (version 9), and that had a required sample size of at least 100. The search resulted in 16 articles. The resulted pooled correlation coefficient was medium level between NS and HA (-0.27). Correlations were small for HA-P (-0.20), NS-P (-0.14), NS-RD (0.10), RD-P (0.05) and HA-RD (0.04). In meta-regression, the correlation NS-P was significantly affected by the location of the study (Asian/other) and by the gender distribution of the sample. In the HA-P correlation, the mean age of the sample affected the correlation. In conclusion, we found a medium level negative correlation between NS and HA; other correlations between the dimensions were small. These findings mainly support Cloninger's theory of independent dimensions.

Independent component analysis applied to long bunch beams in the Los Alamos Proton Storage Ring

NASA Astrophysics Data System (ADS)

Kolski, Jeffrey S.; Macek, Robert J.; McCrady, Rodney C.; Pang, Xiaoying

2012-11-01

Independent component analysis (ICA) is a powerful blind source separation (BSS) method. Compared to the typical BSS method, principal component analysis, ICA is more robust to noise, coupling, and nonlinearity. The conventional ICA application to turn-by-turn position data from multiple beam position monitors (BPMs) yields information about cross-BPM correlations. With this scheme, multi-BPM ICA has been used to measure the transverse betatron phase and amplitude functions, dispersion function, linear coupling, sextupole strength, and nonlinear beam dynamics. We apply ICA in a new way to slices along the bunch revealing correlations of particle motion within the beam bunch. We digitize beam signals of the long bunch at the Los Alamos Proton Storage Ring with a single device (BPM or fast current monitor) for an entire injection-extraction cycle. ICA of the digitized beam signals results in source signals, which we identify to describe varying betatron motion along the bunch, locations of transverse resonances along the bunch, measurement noise, characteristic frequencies of the digitizing oscilloscopes, and longitudinal beam structure.

Classification of independent components of EEG into multiple artifact classes.

PubMed

Frølich, Laura; Andersen, Tobias S; Mørup, Morten

2015-01-01

In this study, we aim to automatically identify multiple artifact types in EEG. We used multinomial regression to classify independent components of EEG data, selecting from 65 spatial, spectral, and temporal features of independent components using forward selection. The classifier identified neural and five nonneural types of components. Between subjects within studies, high classification performances were obtained. Between studies, however, classification was more difficult. For neural versus nonneural classifications, performance was on par with previous results obtained by others. We found that automatic separation of multiple artifact classes is possible with a small feature set. Our method can reduce manual workload and allow for the selective removal of artifact classes. Identifying artifacts during EEG recording may be used to instruct subjects to refrain from activity causing them. Copyright © 2014 Society for Psychophysiological Research.

Memory attacks on device-independent quantum cryptography.

PubMed

Barrett, Jonathan; Colbeck, Roger; Kent, Adrian

2013-01-04

Device-independent quantum cryptographic schemes aim to guarantee security to users based only on the output statistics of any components used, and without the need to verify their internal functionality. Since this would protect users against untrustworthy or incompetent manufacturers, sabotage, or device degradation, this idea has excited much interest, and many device-independent schemes have been proposed. Here we identify a critical weakness of device-independent protocols that rely on public communication between secure laboratories. Untrusted devices may record their inputs and outputs and reveal information about them via publicly discussed outputs during later runs. Reusing devices thus compromises the security of a protocol and risks leaking secret data. Possible defenses include securely destroying or isolating used devices. However, these are costly and often impractical. We propose other more practical partial defenses as well as a new protocol structure for device-independent quantum key distribution that aims to achieve composable security in the case of two parties using a small number of devices to repeatedly share keys with each other (and no other party).

Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators.

PubMed

Clarke, Luka A; Botelho, Hugo M; Sousa, Lisete; Falcao, Andre O; Amaral, Margarida D

2015-11-01

A meta-analysis of 13 independent microarray data sets was performed and gene expression profiles from cystic fibrosis (CF), similar disorders (COPD: chronic obstructive pulmonary disease, IPF: idiopathic pulmonary fibrosis, asthma), environmental conditions (smoking, epithelial injury), related cellular processes (epithelial differentiation/regeneration), and non-respiratory "control" conditions (schizophrenia, dieting), were compared. Similarity among differentially expressed (DE) gene lists was assessed using a permutation test, and a clustergram was constructed, identifying common gene markers. Global gene expression values were standardized using a novel approach, revealing that similarities between independent data sets run deeper than shared DE genes. Correlation of gene expression values identified putative gene regulators of the CF transmembrane conductance regulator (CFTR) gene, of potential therapeutic significance. Our study provides a novel perspective on CF epithelial gene expression in the context of other lung disorders and conditions, and highlights the contribution of differentiation/EMT and injury to gene signatures of respiratory disease. Copyright © 2015 Elsevier Inc. All rights reserved.

The Culture of the Independent Progressive School

ERIC Educational Resources Information Center

Kloss, Dean

2018-01-01

Even in this "Age of Data," independent progressive schools have shown a remarkable persistence in offering an alternative educational model. As Traditional Public Schools (TPS) become even more committed to a testing model of achievement, there are schools that continue to operate on identified progressive educational principles. This…

5 Tips for Creating Independent Activities Aligned with the Common Core State Standards

ERIC Educational Resources Information Center

Fraser, Dawn W.

2013-01-01

Promoting independence in all students is one important part of education. It can be difficult for educators to identify meaningful tasks that students with severe disabilities can complete with full independence. By incorporating visual supports into a student's independent work, the teacher is providing the student with an opportunity to…

Identifying the Correlates and Barriers of Future Planning Among Parents of Individuals With Intellectual and Developmental Disabilities.

PubMed

Burke, Meghan; Arnold, Catherine; Owen, Aleksa

2018-04-01

Although individuals with intellectual and developmental disabilities (IDD) are living longer lives, fewer than half of parents of individuals with IDD conduct future planning. The correlates and barriers to future planning must be identified to develop targeted interventions to facilitate future planning. In this study, 388 parents of individuals with IDD responded to a national, web-based survey. Participants who were older, more educated, attended more parent training and support activities, and had children with fewer functional abilities, were more likely to engage in future planning. Reported barriers to future planning included: (a) lack of available services, (b) financial challenges, (c) reluctance of family members, (d) lack of time, (e) the emotional nature of future planning, (f) inertia, and (g) a lack of family members to be caregivers. Implications for policy, practice, and future research are discussed.

Statistical image reconstruction from correlated data with applications to PET

PubMed Central

Alessio, Adam; Sauer, Ken; Kinahan, Paul

2008-01-01

Most statistical reconstruction methods for emission tomography are designed for data modeled as conditionally independent Poisson variates. In reality, due to scanner detectors, electronics and data processing, correlations are introduced into the data resulting in dependent variates. In general, these correlations are ignored because they are difficult to measure and lead to computationally challenging statistical reconstruction algorithms. This work addresses the second concern, seeking to simplify the reconstruction of correlated data and provide a more precise image estimate than the conventional independent methods. In general, correlated variates have a large non-diagonal covariance matrix that is computationally challenging to use as a weighting term in a reconstruction algorithm. This work proposes two methods to simplify the use of a non-diagonal covariance matrix as the weighting term by (a) limiting the number of dimensions in which the correlations are modeled and (b) adopting flexible, yet computationally tractable, models for correlation structure. We apply and test these methods with simple simulated PET data and data processed with the Fourier rebinning algorithm which include the one-dimensional correlations in the axial direction and the two-dimensional correlations in the transaxial directions. The methods are incorporated into a penalized weighted least-squares 2D reconstruction and compared with a conventional maximum a posteriori approach. PMID:17921576

Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.

PubMed

de Menezes, Alexandre B; Prendergast-Miller, Miranda T; Richardson, Alan E; Toscas, Peter; Farrell, Mark; Macdonald, Lynne M; Baker, Geoff; Wark, Tim; Thrall, Peter H

2015-08-01

Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Electroencephalographic dynamics of musical emotion perception revealed by independent spectral components.

PubMed

Lin, Yuan-Pin; Duann, Jeng-Ren; Chen, Jyh-Horng; Jung, Tzyy-Ping

2010-04-21

This study explores the electroencephalographic (EEG) correlates of emotional experience during music listening. Independent component analysis and analysis of variance were used to separate statistically independent spectral changes of the EEG in response to music-induced emotional processes. An independent brain process with equivalent dipole located in the fronto-central region exhibited distinct δ-band and θ-band power changes associated with self-reported emotional states. Specifically, the emotional valence was associated with δ-power decreases and θ-power increases in the frontal-central area, whereas the emotional arousal was accompanied by increases in both δ and θ powers. The resultant emotion-related component activations that were less interfered by the activities from other brain processes complement previous EEG studies of emotion perception to music.

Genome-wide association study identifies novel breast cancer susceptibility loci

PubMed Central

Easton, Douglas F.; Pooley, Karen A.; Dunning, Alison M.; Pharoah, Paul D. P.; Thompson, Deborah; Ballinger, Dennis G.; Struewing, Jeffery P.; Morrison, Jonathan; Field, Helen; Luben, Robert; Wareham, Nicholas; Ahmed, Shahana; Healey, Catherine S.; Bowman, Richard; Meyer, Kerstin B.; Haiman, Christopher A.; Kolonel, Laurence K.; Henderson, Brian E.; Marchand, Loic Le; Brennan, Paul; Sangrajrang, Suleeporn; Gaborieau, Valerie; Odefrey, Fabrice; Shen, Chen-Yang; Wu, Pei-Ei; Wang, Hui-Chun; Eccles, Diana; Evans, D. Gareth; Peto, Julian; Fletcher, Olivia; Johnson, Nichola; Seal, Sheila; Stratton, Michael R.; Rahman, Nazneen; Chenevix-Trench, Georgia; Bojesen, Stig E.; Nordestgaard, Børge G.; Axelsson, Christen K.; Garcia-Closas, Montserrat; Brinton, Louise; Chanock, Stephen; Lissowska, Jolanta; Peplonska, Beata; Nevanlinna, Heli; Fagerholm, Rainer; Eerola, Hannaleena; Kang, Daehee; Yoo, Keun-Young; Noh, Dong-Young; Ahn, Sei-Hyun; Hunter, David J.; Hankinson, Susan E.; Cox, David G.; Hall, Per; Wedren, Sara; Liu, Jianjun; Low, Yen-Ling; Bogdanova, Natalia; Schürmann, Peter; Dörk, Thilo; Tollenaar, Rob A. E. M.; Jacobi, Catharina E.; Devilee, Peter; Klijn, Jan G. M.; Sigurdson, Alice J.; Doody, Michele M.; Alexander, Bruce H.; Zhang, Jinghui; Cox, Angela; Brock, Ian W.; MacPherson, Gordon; Reed, Malcolm W. R.; Couch, Fergus J.; Goode, Ellen L.; Olson, Janet E.; Meijers-Heijboer, Hanne; van den Ouweland, Ans; Uitterlinden, André; Rivadeneira, Fernando; Milne, Roger L.; Ribas, Gloria; Gonzalez-Neira, Anna; Benitez, Javier; Hopper, John L.; McCredie, Margaret; Southey, Melissa; Giles, Graham G.; Schroen, Chris; Justenhoven, Christina; Brauch, Hiltrud; Hamann, Ute; Ko, Yon-Dschun; Spurdle, Amanda B.; Beesley, Jonathan; Chen, Xiaoqing; Mannermaa, Arto; Kosma, Veli-Matti; Kataja, Vesa; Hartikainen, Jaana; Day, Nicholas E.; Cox, David R.; Ponder, Bruce A. J.; Luccarini, Craig; Conroy, Don; Shah, Mitul; Munday, Hannah; Jordan, Clare; Perkins, Barbara; West, Judy; Redman, Karen; Driver, Kristy; Aghmesheh, Morteza; Amor, David; Andrews, Lesley; Antill, Yoland; Armes, Jane; Armitage, Shane; Arnold, Leanne; Balleine, Rosemary; Begley, Glenn; Beilby, John; Bennett, Ian; Bennett, Barbara; Berry, Geoffrey; Blackburn, Anneke; Brennan, Meagan; Brown, Melissa; Buckley, Michael; Burke, Jo; Butow, Phyllis; Byron, Keith; Callen, David; Campbell, Ian; Chenevix-Trench, Georgia; Clarke, Christine; Colley, Alison; Cotton, Dick; Cui, Jisheng; Culling, Bronwyn; Cummings, Margaret; Dawson, Sarah-Jane; Dixon, Joanne; Dobrovic, Alexander; Dudding, Tracy; Edkins, Ted; Eisenbruch, Maurice; Farshid, Gelareh; Fawcett, Susan; Field, Michael; Firgaira, Frank; Fleming, Jean; Forbes, John; Friedlander, Michael; Gaff, Clara; Gardner, Mac; Gattas, Mike; George, Peter; Giles, Graham; Gill, Grantley; Goldblatt, Jack; Greening, Sian; Grist, Scott; Haan, Eric; Harris, Marion; Hart, Stewart; Hayward, Nick; Hopper, John; Humphrey, Evelyn; Jenkins, Mark; Jones, Alison; Kefford, Rick; Kirk, Judy; Kollias, James; Kovalenko, Sergey; Lakhani, Sunil; Leary, Jennifer; Lim, Jacqueline; Lindeman, Geoff; Lipton, Lara; Lobb, Liz; Maclurcan, Mariette; Mann, Graham; Marsh, Deborah; McCredie, Margaret; McKay, Michael; McLachlan, Sue Anne; Meiser, Bettina; Milne, Roger; Mitchell, Gillian; Newman, Beth; O'Loughlin, Imelda; Osborne, Richard; Peters, Lester; Phillips, Kelly; Price, Melanie; Reeve, Jeanne; Reeve, Tony; Richards, Robert; Rinehart, Gina; Robinson, Bridget; Rudzki, Barney; Salisbury, Elizabeth; Sambrook, Joe; Saunders, Christobel; Scott, Clare; Scott, Elizabeth; Scott, Rodney; Seshadri, Ram; Shelling, Andrew; Southey, Melissa; Spurdle, Amanda; Suthers, Graeme; Taylor, Donna; Tennant, Christopher; Thorne, Heather; Townshend, Sharron; Tucker, Kathy; Tyler, Janet; Venter, Deon; Visvader, Jane; Walpole, Ian; Ward, Robin; Waring, Paul; Warner, Bev; Warren, Graham; Watson, Elizabeth; Williams, Rachael; Wilson, Judy; Winship, Ingrid; Young, Mary Ann; Bowtell, David; Green, Adele; deFazio, Anna; Chenevix-Trench, Georgia; Gertig, Dorota; Webb, Penny

2009-01-01

Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r2>0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P<10−7). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P<0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach. PMID:17529967

Germ-line mutations in the neurofibromatosis 2 gene: Correlations with disease severity and retinal abnormalities

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

Parry, D.M.; Kaiser-Kupfer, M.; Eldridge, R.

Neurofibromatosis 2 (NF2) features bilateral vestibular schwannomas, other benign neural tumors, and cataracts. Patients in some families develop many tumors at an early age and have rapid clinical progression, whereas in other families, patients may not have symptoms until much later and vestibular schwannomas may be the only tumors. The NF2 gene has been cloned from chromosome 22q; most identified germ-line mutations result in a truncated protein and severe NF2. To look for additional mutations and clinical correlations, we used SSCP analysis to screen DNA from 32 unrelated patients. We identified 20 different mutations in 21 patients (66%): 10 nonsensemore » mutations, 2 frameshifts, 7 splice-site mutations, and 1 large in-frame deletion. Clinical information on 47 patients from the 21 families included ages at onset and at diagnosis, numbers of meningiomas, spinal and skin tumors, and presence of cataracts and retinal abnormalities. We compared clinical findings in patients with nonsense or frameshift mutations to those with splice-site mutations. When each patient was considered as an independent random event, the two groups differed (P {le} .05) for nearly every variable. Patients with nonsense or frameshift mutations were younger at onset and at diagnosis and had a higher frequency and mean number of tumors, supporting the correlation between nonsense and frameshift mutations and severe NF2. When each family was considered as an independent random event, statistically significant differences between the two groups were observed only for mean ages at onset and at diagnosis. A larger data set is needed to resolve these discrepancies. We observed retinal hamartomas and/or epiretinal membranes in nine patients from five families with four different nonsense mutations. This finding, which may represent a new genotype-phenotype correlation, merits further study. 58 refs., 2 tabs.« less

A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data

PubMed Central

Zhu, Yun; Fan, Ruzong; Xiong, Momiao

2017-01-01

Investigating the pleiotropic effects of genetic variants can increase statistical power, provide important information to achieve deep understanding of the complex genetic structures of disease, and offer powerful tools for designing effective treatments with fewer side effects. However, the current multiple phenotype association analysis paradigm lacks breadth (number of phenotypes and genetic variants jointly analyzed at the same time) and depth (hierarchical structure of phenotype and genotypes). A key issue for high dimensional pleiotropic analysis is to effectively extract informative internal representation and features from high dimensional genotype and phenotype data. To explore correlation information of genetic variants, effectively reduce data dimensions, and overcome critical barriers in advancing the development of novel statistical methods and computational algorithms for genetic pleiotropic analysis, we proposed a new statistic method referred to as a quadratically regularized functional CCA (QRFCCA) for association analysis which combines three approaches: (1) quadratically regularized matrix factorization, (2) functional data analysis and (3) canonical correlation analysis (CCA). Large-scale simulations show that the QRFCCA has a much higher power than that of the ten competing statistics while retaining the appropriate type 1 errors. To further evaluate performance, the QRFCCA and ten other statistics are applied to the whole genome sequencing dataset from the TwinsUK study. We identify a total of 79 genes with rare variants and 67 genes with common variants significantly associated with the 46 traits using QRFCCA. The results show that the QRFCCA substantially outperforms the ten other statistics. PMID:29040274

The correlation of urban heat island in tropical middle-class housing

NASA Astrophysics Data System (ADS)

Wazir, Zuber Angkasa

2017-11-01

A very limited number of green and sustainable construction studies have explored factors related to Urban Heat Island (UHI) in tropical middle-class housing. This paper aimed to investigate the correlation of Urban Heat Island in tropical middle-class housing in three urban housing for middle-class residents of Palembang, which were Taman Sari Kenten, TOP Jakabaring, and Talang Kelapa. Samples consisted of 125 Taman Sari Kenten housing, 27 Talang Kelapa housing, and 12 TOP Jakabaring housing. Independent variables were the resident density, socioeconomic status, house location, roof type, green area ratio, weather, time, air conditioner, pro-environment institution, and NEP scale. The Analytic method included correlation and regression. We identified that all housing had different UHI profiles where Taman Sari Kenten had the highest UHI (4.17 K), followed by Talang Kelapa (2.66 K) and TOP Jakabaring (0.66 K) against temperature in measuring station nearby, owned by BMKG (National Meteorological Station). UHI correlated with the resident density, roof type, green area ratio, weather, time, and air conditioner. The results should add to the design of ideal housing in the tropical climate for middle-class residents, focusing on its ability to mitigate Urban Heat Island.

Fitness and Adiposity Are Independently Associated with Cardiometabolic Risk in Youth

PubMed Central

Buchan, Duncan S.; Young, John D.; Boddy, Lynne M.; Malina, Robert M.; Baker, Julien S.

2013-01-01

Purpose. The purpose of the study was to examine the independent associations of adiposity and cardiorespiratory fitness with clustered cardiometabolic risk. Methods. A cross-sectional sample of 192 adolescents (118 boys), aged 14–16 years, was recruited from a South Lanarkshire school in the West of Scotland. Anthropometry and blood pressure were measured, and blood samples were taken. The 20 m multistage fitness test was the indicator of cardiorespiratory fitness (CRF). A clustered cardiometabolic risk score was constructed from HDL-C (inverted), LDL-C, HOMA, systolic blood pressure, and triglycerides. Interleukin-6, C-reactive protein, and adiponectin were also measured and examined relative to the clustered cardiometabolic risk score, CRF, and adiposity. Results. Although significant, partial correlations between BMI and waist circumference (WC) and both CRF and adiponectin were negative and weak to moderate, while correlations between the BMI and WC and CRP were positive but weak to moderate. Weak to moderate negative associations were also evident for adiponectin with CRP, IL-6, and clustered cardiometabolic risk. WC was positively associated while CRF was negatively associated with clustered cardiometabolic risk. With the additional adjustment for either WC or CRF, the independent associations with cardiometabolic risk persisted. Conclusion. WC and CRF are independently associated with clustered cardiometabolic risk in Scottish adolescents. PMID:23984329

Genome-Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content.

PubMed

Rabbi, Ismail Y; Udoh, Lovina I; Wolfe, Marnin; Parkes, Elizabeth Y; Gedil, Melaku A; Dixon, Alfred; Ramu, Punna; Jannink, Jean-Luc; Kulakow, Peter

2017-11-01

Cassava is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Primary selection objectives in cassava breeding include dry matter content and micronutrient density, particularly provitamin A carotenoids. These traits are negatively correlated in the African germplasm. This study aimed at identifying genetic markers associated with these traits and uncovering whether linkage and/or pleiotropy were responsible for observed negative correlation. A genome-wide association mapping using 672 clones genotyped at 72,279 single nucleotide polymorphism (SNP) loci was performed. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness were identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that colocated with the 24.1 Mbp peak for carotenoids was identified. Haplotypes at these loci explained 70 and 37% of the phenotypic variability for root yellowness and dry matter content, respectively. Evidence of megabase-scale linkage disequilibrium (LD) around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white- and yellow-root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid () and starch biosynthesis ( and ) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate the genetic architecture of carotenoids and dry matter in cassava and provide an opportunity to accelerate breeding of these traits. Copyright © 2017 Crop Science Society of America.

Bose-Einstein condensation and independent production of pions

NASA Astrophysics Data System (ADS)

Bialas, A.; Zalewski, K.

1998-09-01

The influence of the HBT effect on the momentum spectra of independently produced pions is studied using the method developed earlier for discussion of multiplicity distributions. It is shown that in this case all the spectra and multiparticle correlation functions are expressible in terms of one function of two momenta. It is also shown that at the critical point all pions are attracted into one quantum state and thus form a Bose-Einstein condensate.

Interactome disassembly during apoptosis occurs independent of caspase cleavage.

PubMed

Scott, Nichollas E; Rogers, Lindsay D; Prudova, Anna; Brown, Nat F; Fortelny, Nikolaus; Overall, Christopher M; Foster, Leonard J

2017-01-12

Protein-protein interaction networks (interactomes) define the functionality of all biological systems. In apoptosis, proteolysis by caspases is thought to initiate disassembly of protein complexes and cell death. Here we used a quantitative proteomics approach, protein correlation profiling (PCP), to explore changes in cytoplasmic and mitochondrial interactomes in response to apoptosis initiation as a function of caspase activity. We measured the response to initiation of Fas-mediated apoptosis in 17,991 interactions among 2,779 proteins, comprising the largest dynamic interactome to date. The majority of interactions were unaffected early in apoptosis, but multiple complexes containing known caspase targets were disassembled. Nonetheless, proteome-wide analysis of proteolytic processing by terminal amine isotopic labeling of substrates (TAILS) revealed little correlation between proteolytic and interactome changes. Our findings show that, in apoptosis, significant interactome alterations occur before and independently of caspase activity. Thus, apoptosis initiation includes a tight program of interactome rearrangement, leading to disassembly of relatively few, select complexes. These early interactome alterations occur independently of cleavage of these protein by caspases. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Independent predictors of delay in emergence from general anesthesia.

PubMed

Maeda, Shigeru; Tomoyasu, Yumiko; Higuchi, Hitoshi; Ishii-Maruhama, Minako; Egusa, Masahiko; Miyawaki, Takuya

2015-01-01

Some patients with intellectual disabilities spend longer than others in emergence from ambulatory general anesthesia for dental treatment. Although antiepileptic drugs and anesthetics might be involved, an independent predictor for delay of the emergence remains unclear. Thus, a purpose of this study is to identify independent factors affecting the delay of emergence from general anesthesia. This was a retrospective cohort study in dental patients with intellectual disabilities. Patients in need of sedative premedication were removed from participants. The outcome was time until emergence from general anesthesia. Stepwise multivariate regression analysis was used to extract independent factors affecting the outcome. Antiepileptic drugs and anesthetic parameters were included as predictor variables. The study included 102 cases. Clobazam, clonazepam, and phenobarbital were shown to be independent determinants of emergence time. Parameters relating to anesthetics, patients' backgrounds, and dental treatment were not independent factors. Delay in emergence time in ambulatory general anesthesia is likely to be related to the antiepileptic drugs of benzodiazepine or barbiturates in patients with intellectual disability.

Application of wide selected-ion monitoring data-independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor.

PubMed

Martin, Laetitia B B; Sherwood, Robert W; Nicklay, Joshua J; Yang, Yong; Muratore-Schroeder, Tara L; Anderson, Elizabeth T; Thannhauser, Theodore W; Rose, Jocelyn K C; Zhang, Sheng

2016-08-01

We describe here the use of label-free wide selected-ion monitoring data-independent acquisition (WiSIM-DIA) to identify proteins that are involved in the formation of tomato (Solanum lycopersicum) fruit cuticles and that are regulated by the transcription factor CUTIN DEFICIENT2 (CD2). A spectral library consisting of 11 753 unique peptides, corresponding to 2338 tomato protein groups, was used and the DIA analysis was performed at the MS1 level utilizing narrow mass windows for extraction with Skyline 2.6 software. We identified a total of 1140 proteins, 67 of which had expression levels that differed significantly between the cd2 tomato mutant and the wild-type cultivar M82. Differentially expressed proteins including a key protein involved in cutin biosynthesis, were selected for validation by target SRM/MRM and by Western blot analysis. In addition to confirming a role for CD2 in regulating cuticle formation, the results also revealed that CD2 influences pathways associated with cell wall biology, anthocyanin biosynthesis, plant development, and responses to stress, which complements findings of earlier RNA-Seq experiments. Our results provide new insights into molecular processes and aspects of fruit biology associated with CD2 function, and demonstrate that the WiSIM-DIA is an effective quantitative approach for global protein identifications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of wide selected-ion monitoring data-independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor

PubMed Central

Martin, Laetitia B. B.; Sherwood, Robert W.; Nicklay, Joshua J.; Yang, Yong; Muratore-Schroeder, Tara L.; Anderson, Elizabeth T.; Thannhauser, Theodore W.; Rose, Jocelyn K. C.; Zhang, Sheng

2017-01-01

We describe here the use of label-free wide selected-ion monitoring data-independent acquisition (WiSIM-DIA) to identify proteins that are involved in the formation of tomato (Solanum lycopersicum) fruit cuticles and that are regulated by the transcription factor CUTIN DEFICIENT2 (CD2). A spectral library consisting of 11 753 unique peptides, corresponding to 2338 tomato protein groups, was used and the DIA analysis was performed at the MS1 level utilizing narrow mass windows for extraction with Skyline 2.6 software. We identified a total of 1140 proteins, 67 of which had expression levels that differed significantly between the cd2 tomato mutant and the wild-type cultivar M82. Differentially expressed proteins including a key protein involved in cutin biosynthesis, were selected for validation by target SRM/MRM and by Western blot analysis. In addition to confirming a role for CD2 in regulating cuticle formation, the results also revealed that CD2 influences pathways associated with cell wall biology, anthocyanin biosynthesis, plant development, and responses to stress, which complements findings of earlier RNA-Seq experiments. Our results provide new insights into molecular processes and aspects of fruit biology associated with CD2 function, and demonstrate that the WiSIM-DIA is an effective quantitative approach for global protein identifications. PMID:27089858

On an additive partial correlation operator and nonparametric estimation of graphical models.

PubMed

Lee, Kuang-Yao; Li, Bing; Zhao, Hongyu

2016-09-01

We introduce an additive partial correlation operator as an extension of partial correlation to the nonlinear setting, and use it to develop a new estimator for nonparametric graphical models. Our graphical models are based on additive conditional independence, a statistical relation that captures the spirit of conditional independence without having to resort to high-dimensional kernels for its estimation. The additive partial correlation operator completely characterizes additive conditional independence, and has the additional advantage of putting marginal variation on appropriate scales when evaluating interdependence, which leads to more accurate statistical inference. We establish the consistency of the proposed estimator. Through simulation experiments and analysis of the DREAM4 Challenge dataset, we demonstrate that our method performs better than existing methods in cases where the Gaussian or copula Gaussian assumption does not hold, and that a more appropriate scaling for our method further enhances its performance.

On an additive partial correlation operator and nonparametric estimation of graphical models

PubMed Central

Li, Bing; Zhao, Hongyu

2016-01-01

Abstract We introduce an additive partial correlation operator as an extension of partial correlation to the nonlinear setting, and use it to develop a new estimator for nonparametric graphical models. Our graphical models are based on additive conditional independence, a statistical relation that captures the spirit of conditional independence without having to resort to high-dimensional kernels for its estimation. The additive partial correlation operator completely characterizes additive conditional independence, and has the additional advantage of putting marginal variation on appropriate scales when evaluating interdependence, which leads to more accurate statistical inference. We establish the consistency of the proposed estimator. Through simulation experiments and analysis of the DREAM4 Challenge dataset, we demonstrate that our method performs better than existing methods in cases where the Gaussian or copula Gaussian assumption does not hold, and that a more appropriate scaling for our method further enhances its performance. PMID:29422689

Large-scale fluctuations in the number density of galaxies in independent surveys of deep fields

NASA Astrophysics Data System (ADS)

Shirokov, S. I.; Lovyagin, N. Yu.; Baryshev, Yu. V.; Gorokhov, V. L.

2016-06-01

New arguments supporting the reality of large-scale fluctuations in the density of the visible matter in deep galaxy surveys are presented. A statistical analysis of the radial distributions of galaxies in the COSMOS and HDF-N deep fields is presented. Independent spectral and photometric surveys exist for each field, carried out in different wavelength ranges and using different observing methods. Catalogs of photometric redshifts in the optical (COSMOS-Zphot) and infrared (UltraVISTA) were used for the COSMOS field in the redshift interval 0.1 < z < 3.5, as well as the zCOSMOS (10kZ) spectroscopic survey and the XMM-COSMOS and ALHAMBRA-F4 photometric redshift surveys. The HDFN-Zphot and ALHAMBRA-F5 catalogs of photometric redshifts were used for the HDF-N field. The Pearson correlation coefficient for the fluctuations in the numbers of galaxies obtained for independent surveys of the same deep field reaches R = 0.70 ± 0.16. The presence of this positive correlation supports the reality of fluctuations in the density of visible matter with sizes of up to 1000 Mpc and amplitudes of up to 20% at redshifts z ~ 2. The absence of correlations between the fluctuations in different fields (the correlation coefficient between COSMOS and HDF-N is R = -0.20 ± 0.31) testifies to the independence of structures visible in different directions on the celestial sphere. This also indicates an absence of any influence from universal systematic errors (such as "spectral voids"), which could imitate the detection of correlated structures.

Overexpression of c-kit(CD117), relevant with microvessel density, is an independent survival prognostic factor for patients with HBV-related hepatocellular carcinoma.

PubMed

Yan, Weiwei; Zhu, Zhenyu; Pan, Fei; Huang, Ang; Dai, Guang-Hai

2018-01-01

To explore new biomarkers for indicating the recurrence and prognosis in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) patients after tumor resection, we investigated the expression and prognostic value of c-kit(CD117) in HBV-related HCC. Immunohistochemistry was used to estimate the expression of c-kit(CD117) and CD34 in the liver cancer tissues. The correlations between the expression of these biomarkers and the clinicopathologic characteristics were analyzed. The positive rate of c-kit(CD117) expression in 206 HCC cases was 48.1%, and c-kit expression was significantly related with CD34-positive microvessel density. CD34-microvessel density numbers were much higher in c-kit(+) HCC tissues than in c-kit(-) HCC tissues (44.13±17.01 vs 26.87±13.16, P =0.003). The expression of c-kit was significantly higher in patients with Edmondson grade III-IV ( P <0.001) and TNM stage III ( P <0.001). Moreover, Kaplan-Meier survival analysis showed that c-kit ( P <0.001) expression was correlated with reduced disease-free survival (DFS). Multivariate analysis identified c-kit as an independent poor prognostic factor of DFS in HCC patients ( P <0.001). Increased c-kit expression could be considered as an independent unfavorable prognostic factor for predicting DFS in HBV-related HCC patients after surgery. These results could be used to identify patients at a higher risk of early tumor recurrence and poor prognosis.

Development of the upper-body dressing scale for a buttoned shirt: a preliminary correlational study.

PubMed

Suzuki, Makoto; Yamada, Sumio; Omori, Mikayo; Hatakeyama, Mayumi; Sugimura, Yuko; Matsushita, Kazuhiko; Tagawa, Yoshikatsu

2008-09-01

A patient with poststroke hemiparesis learns to use the nonparetic arm to compensate for the weakness of the paretic arm to achieve independence in dressing. This is the learning process of new component actions on dressing. The purpose of this study was to develop the Upper-Body Dressing Scale (UBDS) for buttoned shirt dressing, which evaluates the component actions of upper-body dressing, and to provide preliminary data on internal consistency of the UBDS, as well as its reproducibility, validity, and sensitivity to clinical change. Correlational study of concurrent validity and reliability in which 63 consecutive stroke patients were enrolled in the study and were assessed repeatedly by the UBDS and the dressing item of Functional Independent Measure (FIM). Fifty-one patients completed the 3-wk study. The Cronbach's coefficient alpha of UBDS was 0.88. The principal component analysis extracted two components, which explained 62.3% of total variance. All items of the scale had high loading on the first component (0.65-0.83). Actions on the paralytic side were the positive loadings and actions on the healthy side were the negative loadings on the second component. Intraclass correlation coefficient was 0.87. The level of correlation between UBDS score and FIM dressing item scores was -0.72. Logistic regression analysis showed that only the score of UBDS on the first day of evaluation was a significant independent predictor of dressing ability (odds ratio, 0.82; 95% confidence interval, 0.71-0.95). The UBDS scores for paralytic hand passed into the sleeve, sleeve pulled up beyond the elbow joint, and sleeve pulled up beyond the shoulder joint were worse than the score for the other components of the task. These component actions had positive loading on the second component, which was identified by the principal component analysis. The UBDS has good internal consistency, reproducibility, validity, and sensitivity to clinical changes of patients with poststroke

Hidden asymmetry and forward-backward correlations

NASA Astrophysics Data System (ADS)

Bialas, A.; Zalewski, K.

2010-09-01

A model-independent method of studying the forward-backward correlations in symmetric high-energy processes is developed. The method allows a systematic study of the properties of various particle sources and allows one to uncover asymmetric structures hidden in symmetric hadron-hadron and nucleus-nucleus inelastic reactions.

HbA1c Variability as an Independent Correlate of Nephropathy, but Not Retinopathy, in Patients With Type 2 Diabetes

PubMed Central

Penno, Giuseppe; Solini, Anna; Bonora, Enzo; Fondelli, Cecilia; Orsi, Emanuela; Zerbini, Gianpaolo; Morano, Susanna; Cavalot, Franco; Lamacchia, Olga; Laviola, Luigi; Nicolucci, Antonio; Pugliese, Giuseppe

2013-01-01

OBJECTIVE To examine the association of hemoglobin (Hb) A1c variability with microvascular complications in the large cohort of subjects with type 2 diabetes from the Renal Insufficiency And Cardiovascular Events (RIACE) Italian Multicenter Study. RESEARCH DESIGN AND METHODS Serial (3–5) HbA1c values collected in a 2-year period before enrollment were available from 8,260 subjects from 9 centers (of 15,773 patients from 19 centers). HbA1c variability was measured as the intraindividual SD of 4.52 ± 0.76 values. Diabetic retinopathy (DR) was assessed by dilated funduscopy. Chronic kidney disease (CKD) was defined based on albuminuria, as measured by immunonephelometry or immunoturbidimetry, and estimated glomerular filtration rate (eGFR) was calculated from serum creatinine. RESULTS Median and interquartile range of average HbA1c (HbA1c-MEAN) and HbA1c-SD were 7.57% (6.86–8.38) and 0.46% (0.29–0.74), respectively. The highest prevalence of microalbuminuria, macroalbuminuria, reduced eGFR, albuminuric CKD phenotypes, and advanced DR was observed when both HbA1c parameters were above the median and the lowest when both were below the median. Logistic regression analyses showed that HbA1c-SD adds to HbA1c-MEAN as an independent correlate of microalbuminuria and stages 1–2 CKD and is an independent predictor of macroalbuminuria, reduced eGFR, and stages 3–5 albuminuric CKD, whereas HbA1c-MEAN is not. The opposite was found for DR, whereas neither HbA1c-MEAN nor HbA1c-SD affected nonalbuminuric CKD. CONCLUSIONS In patients with type 2 diabetes, HbA1c variability affects (albuminuric) CKD more than average HbA1c, whereas only the latter parameter affects DR, thus suggesting a variable effect of these measures on microvascular complications. PMID:23491522

Unidimensional factor models imply weaker partial correlations than zero-order correlations.

PubMed

van Bork, Riet; Grasman, Raoul P P P; Waldorp, Lourens J

2018-06-01

In this paper we present a new implication of the unidimensional factor model. We prove that the partial correlation between two observed variables that load on one factor given any subset of other observed variables that load on this factor lies between zero and the zero-order correlation between these two observed variables. We implement this result in an empirical bootstrap test that rejects the unidimensional factor model when partial correlations are identified that are either stronger than the zero-order correlation or have a different sign than the zero-order correlation. We demonstrate the use of the test in an empirical data example with data consisting of fourteen items that measure extraversion.

Multiplicity evolution of identified particle charge-dependent correlations in Pb-Pb, p-Pb and pp collisions at the LHC with ALICE

NASA Astrophysics Data System (ADS)

Pan, Jinjin; Alice Collaboration

2017-09-01

The charge pair creation and transport processes in heavy-ion collisions are investigated experimentally by measurements of charge-dependent correlations of identified particle pairs, related to the Balance Function. The produced pair separation in rapidity is expected to be larger for hadrons arising from quark-antiquark pair creation in the early stages of the collision than for hadrons emerging from the later hadronization stage. Correlations are reported for charged-pion pairs in Pb-Pb, p-Pb and pp collisions at √{sNN } = 2.76, 5.02 and 7 TeV, respectively; and for charged-kaon pairs in Pb-Pb collisions at √{sNN } = 2.76 TeV. The correlations are measured as a function of relative rapidity Δy and azimuthal angle Δϕ , and are dominated by a peak centered at Δy = Δϕ = 0. We observe that the peak widths in Δy and Δϕ are narrower in higher multiplicity events in Pb-Pb, p-Pb, and pp collisions, which is consistent with the effects of radial flow, as well as the two-wave quark production mechanism. We investigate the charge transport and system evolution further by studying the Δϕ width of the peak as a function of Δy. Funded by the US Department of Energy.

Spatio-Temporal Trends and Identification of Correlated Variables with Water Quality for Drinking-Water Reservoirs

PubMed Central

Gu, Qing; Wang, Ke; Li, Jiadan; Ma, Ligang; Deng, Jinsong; Zheng, Kefeng; Zhang, Xiaobin; Sheng, Li

2015-01-01

It is widely accepted that characterizing the spatio-temporal trends of water quality parameters and identifying correlated variables with water quality are indispensable for the management and protection of water resources. In this study, cluster analysis was used to classify 56 typical drinking water reservoirs in Zhejiang Province into three groups representing different water quality levels, using data of four water quality parameters for the period 2006–2010. Then, the spatio-temporal trends in water quality were analyzed, assisted by geographic information systems (GIS) technology and statistical analysis. The results indicated that the water quality showed a trend of degradation from southwest to northeast, and the overall water quality level was exacerbated during the study period. Correlation analysis was used to evaluate the relationships between water quality parameters and ten independent variables grouped into four categories (land use, socio-economic factors, geographical features, and reservoir attributes). According to the correlation coefficients, land use and socio-economic indicators were identified as the most significant factors related to reservoir water quality. The results offer insights into the spatio-temporal variations of water quality parameters and factors impacting the water quality of drinking water reservoirs in Zhejiang Province, and they could assist managers in making effective strategies to better protect water resources. PMID:26492263

Spatio-Temporal Trends and Identification of Correlated Variables with Water Quality for Drinking-Water Reservoirs.

PubMed

Gu, Qing; Wang, Ke; Li, Jiadan; Ma, Ligang; Deng, Jinsong; Zheng, Kefeng; Zhang, Xiaobin; Sheng, Li

2015-10-20

It is widely accepted that characterizing the spatio-temporal trends of water quality parameters and identifying correlated variables with water quality are indispensable for the management and protection of water resources. In this study, cluster analysis was used to classify 56 typical drinking water reservoirs in Zhejiang Province into three groups representing different water quality levels, using data of four water quality parameters for the period 2006-2010. Then, the spatio-temporal trends in water quality were analyzed, assisted by geographic information systems (GIS) technology and statistical analysis. The results indicated that the water quality showed a trend of degradation from southwest to northeast, and the overall water quality level was exacerbated during the study period. Correlation analysis was used to evaluate the relationships between water quality parameters and ten independent variables grouped into four categories (land use, socio-economic factors, geographical features, and reservoir attributes). According to the correlation coefficients, land use and socio-economic indicators were identified as the most significant factors related to reservoir water quality. The results offer insights into the spatio-temporal variations of water quality parameters and factors impacting the water quality of drinking water reservoirs in Zhejiang Province, and they could assist managers in making effective strategies to better protect water resources.

More Polarized but More Independent: Political Party Identification and Ideological Self-Categorization Among U.S. Adults, College Students, and Late Adolescents, 1970-2015.

PubMed

Twenge, Jean M; Honeycutt, Nathan; Prislin, Radmila; Sherman, Ryne A

2016-10-01

In three nationally representative surveys of U.S. residents (N = 10 million) from 1970 to 2015, more Americans in the early 2010s (vs. previous decades) identified as Independent, including when age effects were controlled. More in the early 2010s (vs. previous decades) expressed polarized political views, including stronger political party affiliation or more extreme ideological self-categorization (liberal vs. conservative) with fewer identifying as moderate. The correlation between party affiliation and ideological views grew stronger over time. The overall trend since the 1970s was toward more Americans identifying as Republican or conservative. Older adults were more likely to identify as conservative and Republican. More Millennials (born 1980-1994) identify as conservative than either GenXers or Boomers did at the same age, and fewer are Democrats compared with Boomers. These trends are discussed in the context of social identification processes and their implications for the political dynamics in the United States. © 2016 by the Society for Personality and Social Psychology, Inc.

The Comparative Performance of Conditional Independence Indices

ERIC Educational Resources Information Center

Kim, Doyoung; De Ayala, R. J.; Ferdous, Abdullah A.; Nering, Michael L.

2011-01-01

To realize the benefits of item response theory (IRT), one must have model-data fit. One facet of a model-data fit investigation involves assessing the tenability of the conditional item independence (CII) assumption. In this Monte Carlo study, the comparative performance of 10 indices for identifying conditional item dependence is assessed. The…

Identify super quality markers from prototype-based pharmacokinetic markers of Tangzhiqing tablet (TZQ) based on in vitro dissolution/ permeation and in vivo absorption correlations.

PubMed

Li, Ziqiang; Liu, Jia; Li, Yazhuo; Du, Xi; Li, Yanfen; Wang, Ruihua; Lv, Chunxiao; He, Xin; Wang, Baohe; Huang, Yuhong; Zhang, Deqin

2018-06-01

A quality marker (Q-marker) is defined as an inherent chemical compound that is used for the quality control of a drug. Its biological activities are closely related to safety and therapeutic effects. Generally, a multiple-component herbal medicine may have many Q-markers. We therefore proposed a concept of "super Q-marker" satisfying both the criterion of Q-markers and PK-markers to be used in more effective quality control of herbal medicine. The first aim was to find suitable prototype-based PK-markers from Tangzhiqing tablets (TZQ), a Chinese patent medicine. Then super Q-markers were expected to be identified from the prototype-based PK-markers based on an in vitro-in vivo correlation study. Potentially eligible prototype-based PK-markers were identified in a single- and multiple-dose pharmacokinetic study on TZQ in 30 healthy volunteers. The in vitro dissolution and permeation profiles of the prototype-based PK-markers of TZQ were evaluated by the physiologically-based drug dissolution/absorption simulating system (DDASS). An in vitro-in vivo correlation analysis was conducted between the dissolution/permeation behaviors in DDASS and the actual absorption profiles in human to test the transferability and traceability of the promising super Q-markers for TZQ. In human, plasma paeoniflorin and nuciferine as prototype-based PK-markers exhibited the appropriate pharmacokinetic properties, including dose-dependent systemic exposure (AUC, C max ) and a proper elimination half-life (1∼3h). In DDASS, it was predicted that paeoniflorin and nuciferine are highly permeable but the absorption rates are primarily limited by the dissolution rates. Moreover, the established in vitro-in vivo correlations of paeoniflorin and nuciferine were in support of the super Q-markers features. Paeoniflorin and nuciferine are identified as the super Q-markers from the prototype-based PK-markers of TZQ based on findings from a combination of in vitro, in vivo, and in vitro-in vivo

CULTURE-INDEPENDENT MOLECULAR METHODS FOR FECAL SOURCE IDENTIFICATION

EPA Science Inventory

Fecal contamination is widespread in the waterways of the United States. Both to correct the problem, and to estimate public health risk, it is necessary to identify the source of the contamination. Several culture-independent molecular methods for fecal source identification hav...

Independent component analysis decomposition of hospital emergency department throughput measures

NASA Astrophysics Data System (ADS)

He, Qiang; Chu, Henry

2016-05-01

We present a method adapted from medical sensor data analysis, viz. independent component analysis of electroencephalography data, to health system analysis. Timely and effective care in a hospital emergency department is measured by throughput measures such as median times patients spent before they were admitted as an inpatient, before they were sent home, before they were seen by a healthcare professional. We consider a set of five such measures collected at 3,086 hospitals distributed across the U.S. One model of the performance of an emergency department is that these correlated throughput measures are linear combinations of some underlying sources. The independent component analysis decomposition of the data set can thus be viewed as transforming a set of performance measures collected at a site to a collection of outputs of spatial filters applied to the whole multi-measure data. We compare the independent component sources with the output of the conventional principal component analysis to show that the independent components are more suitable for understanding the data sets through visualizations.

Python Waveform Cross-Correlation

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

Templeton, Dennise

PyWCC is a tool to compute seismic waveform cross-correlation coefficients on single-component or multiple-component seismic data across a network of seismic sensors. PyWCC compares waveform data templates with continuous seismic data, associates the resulting detections, identifies the template with the highest cross-correlation coefficient, and outputs a catalog of detections above a user-defined absolute cross-correlation threshold value.

Progressive Disintegration of Brain Networking from Normal Aging to Alzheimer Disease: Analysis of Independent Components of 18F-FDG PET Data.

PubMed

Pagani, Marco; Giuliani, Alessandro; Öberg, Johanna; De Carli, Fabrizio; Morbelli, Silvia; Girtler, Nicola; Arnaldi, Dario; Accardo, Jennifer; Bauckneht, Matteo; Bongioanni, Francesca; Chincarini, Andrea; Sambuceti, Gianmario; Jonsson, Cathrine; Nobili, Flavio

2017-07-01

Brain connectivity has been assessed in several neurodegenerative disorders investigating the mutual correlations between predetermined regions or nodes. Selective breakdown of brain networks during progression from normal aging to Alzheimer disease dementia (AD) has also been observed. Methods: We implemented independent-component analysis of 18 F-FDG PET data in 5 groups of subjects with cognitive states ranging from normal aging to AD-including mild cognitive impairment (MCI) not converting or converting to AD-to disclose the spatial distribution of the independent components in each cognitive state and their accuracy in discriminating the groups. Results: We could identify spatially distinct independent components in each group, with generation of local circuits increasing proportionally to the severity of the disease. AD-specific independent components first appeared in the late-MCI stage and could discriminate converting MCI and AD from nonconverting MCI with an accuracy of 83.5%. Progressive disintegration of the intrinsic networks from normal aging to MCI to AD was inversely proportional to the conversion time. Conclusion: Independent-component analysis of 18 F-FDG PET data showed a gradual disruption of functional brain connectivity with progression of cognitive decline in AD. This information might be useful as a prognostic aid for individual patients and as a surrogate biomarker in intervention trials. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Clathrin-independent internalization and recycling

PubMed Central

Gong, Qiang; Huntsman, Christopher; Ma, Dzwokai

2008-01-01

Abstract The functionality of receptor and channel proteins depends directly upon their expression level on the plasma membrane. Therefore, the ability to selectively adjust the surface level of a particular receptor or channel protein is pivotal to many cellular signalling events. The internalization and recycling pathway plays a major role in the regulation of protein surface level, and thus has been a focus of research for many years. Although several endocytic pathways have been identified, most of our knowledge has come from the clathrin-dependent pathway, while the other pathways remain much less well defined. Considering that clathrin-independent internalization may account for as much as 50% of the total endocytic activity in the cell, the lack of such knowledge constitutes a major gap in our efforts to understand how different internalization pathways are utilized and co-ordinated. Recent studies have provided valuable insights into this area, yet many more questions still remain. In this review, we will give a panoramic introduction to the current knowledge of various internalization and recycling pathways, with an emphasis on the latest findings that have broadened our view of the clathrin-independent pathways. We will also dedicate one section to the emerging studies of the clathrin-independent internalization pathways in neuronal cells. PMID:18039352

Selection of early-occurring mutations dictates hormone-independent progression in mouse mammary tumor lines.

PubMed

Gattelli, Albana; Zimberlin, María N; Meiss, Roberto P; Castilla, Lucio H; Kordon, Edith C

2006-11-01

Mice harboring three mouse mammary tumor virus (MMTV) variants develop pregnancy-dependent (PD) tumors that progress to pregnancy-independent (PI) behavior through successive passages. Herein, we identified 10 predominant insertions in PI transplants from 8 independent tumor lines. These mutations were also detected in small cell populations in the early PD passages. In addition, we identified a new viral insertion upstream of the gene Rspo3, which is overexpressed in three of the eight independent tumor lines and codes for a protein very similar to the recently described protein encoded by Int7. This study suggests that during progression towards hormone independence, clonal expansion of cells with specific mutations might be more relevant than the occurrence of new MMTV insertions.

Selection of Early-Occurring Mutations Dictates Hormone-Independent Progression in Mouse Mammary Tumor Lines▿

PubMed Central

Gattelli, Albana; Zimberlin, María N.; Meiss, Roberto P.; Castilla, Lucio H.; Kordon, Edith C.

2006-01-01

Mice harboring three mouse mammary tumor virus (MMTV) variants develop pregnancy-dependent (PD) tumors that progress to pregnancy-independent (PI) behavior through successive passages. Herein, we identified 10 predominant insertions in PI transplants from 8 independent tumor lines. These mutations were also detected in small cell populations in the early PD passages. In addition, we identified a new viral insertion upstream of the gene Rspo3, which is overexpressed in three of the eight independent tumor lines and codes for a protein very similar to the recently described protein encoded by Int7. This study suggests that during progression towards hormone independence, clonal expansion of cells with specific mutations might be more relevant than the occurrence of new MMTV insertions. PMID:16971449

Development and Validation of a Chronic Pancreatitis Prognosis Score in 2 Independent Cohorts.

PubMed

Beyer, Georg; Mahajan, Ujjwal M; Budde, Christoph; Bulla, Thomas J; Kohlmann, Thomas; Kuhlmann, Louise; Schütte, Kerstin; Aghdassi, Ali A; Weber, Eckhard; Weiss, F Ulrich; Drewes, Asbjørn M; Olesen, Søren S; Lerch, Markus M; Mayerle, Julia

2017-12-01

The clinical course of chronic pancreatitis is unpredictable. There is no model to assess disease severity or progression or predict patient outcomes. We performed a prospective study of 91 patients with chronic pancreatitis; data were collected from patients seen at academic centers in Europe from January 2011 through April 2014. We analyzed correlations between clinical, laboratory, and imaging data with number of hospital readmissions and in-hospital days over the next 12 months; the parameters with the highest degree of correlation were used to develop a 3-stage chronic pancreatitis prognosis score (COPPS). The predictive strength was validated in 129 independent subjects identified from 2 prospective databases. The mean number of hospital admissions was 1.9 (95% confidence interval [CI], 1.39-2.44) and 15.2 for hospital days (95% CI, 10.76-19.71) for the development cohort and 10.9 for the validation cohort (95% CI, 7.54-14.30) (P = .08). Based on bivariate correlations, pain (numeric rating scale), level of glycated hemoglobin A1c, level of C-reactive protein, body mass index, and platelet count were used to develop the COPPS system. The patients' median COPPS was 8.9 points (range, 5-14). The system accurately discriminated stages of disease severity (low to high): A (5-6 points), B (7-9), and C (10-15). In Pearson correlation analysis of the development cohort, the COPPS correlated with hospital admissions (0.39; P < .01) and number of hospital days (0.33; P < .01). The correlation was validated in the validation set (Pearson correlation values of 0.36 and 0.44; P < .01). COPPS did not correlate with results from the Cambridge classification system. We developed and validated an easy to use dynamic multivariate scoring system, similar to the Child-Pugh-Score for liver cirrhosis. The COPPS allows objective monitoring of patients with chronic pancreatitis, determining risk for readmission to hospital and potential length of hospital stay. Copyright �

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting.

PubMed

Aguirre, Andrew J; Meyers, Robin M; Weir, Barbara A; Vazquez, Francisca; Zhang, Cheng-Zhong; Ben-David, Uri; Cook, April; Ha, Gavin; Harrington, William F; Doshi, Mihir B; Kost-Alimova, Maria; Gill, Stanley; Xu, Han; Ali, Levi D; Jiang, Guozhi; Pantel, Sasha; Lee, Yenarae; Goodale, Amy; Cherniack, Andrew D; Oh, Coyin; Kryukov, Gregory; Cowley, Glenn S; Garraway, Levi A; Stegmaier, Kimberly; Roberts, Charles W; Golub, Todd R; Meyerson, Matthew; Root, David E; Tsherniak, Aviad; Hahn, William C

2016-08-01

The CRISPR/Cas9 system enables genome editing and somatic cell genetic screens in mammalian cells. We performed genome-scale loss-of-function screens in 33 cancer cell lines to identify genes essential for proliferation/survival and found a strong correlation between increased gene copy number and decreased cell viability after genome editing. Within regions of copy-number gain, CRISPR/Cas9 targeting of both expressed and unexpressed genes, as well as intergenic loci, led to significantly decreased cell proliferation through induction of a G2 cell-cycle arrest. By examining single-guide RNAs that map to multiple genomic sites, we found that this cell response to CRISPR/Cas9 editing correlated strongly with the number of target loci. These observations indicate that genome targeting by CRISPR/Cas9 elicits a gene-independent antiproliferative cell response. This effect has important practical implications for the interpretation of CRISPR/Cas9 screening data and confounds the use of this technology for the identification of essential genes in amplified regions. We found that the number of CRISPR/Cas9-induced DNA breaks dictates a gene-independent antiproliferative response in cells. These observations have practical implications for using CRISPR/Cas9 to interrogate cancer gene function and illustrate that cancer cells are highly sensitive to site-specific DNA damage, which may provide a path to novel therapeutic strategies. Cancer Discov; 6(8); 914-29. ©2016 AACR.See related commentary by Sheel and Xue, p. 824See related article by Munoz et al., p. 900This article is highlighted in the In This Issue feature, p. 803. 2016 American Association for Cancer Research.

Ataxia-telangiectasia mutated (ATM) silencing promotes neuroblastoma progression through a MYCN independent mechanism

PubMed Central

Mandriota, Stefano J.; Valentijn, Linda J.; Lesne, Laurence; Betts, David R.; Marino, Denis; Boudal-Khoshbeen, Mary; London, Wendy B.; Rougemont, Anne-Laure; Attiyeh, Edward F.; Maris, John M.; Hogarty, Michael D.; Koster, Jan; Molenaar, Jan J.; Versteeg, Rogier

2015-01-01

Neuroblastoma, a childhood cancer with highly heterogeneous biology and clinical behavior, is characterized by genomic aberrations including amplification of MYCN. Hemizygous deletion of chromosome 11q is a well-established, independent marker of poor prognosis. While 11q22-q23 is the most frequently deleted region, the neuroblastoma tumor suppressor in this region remains to be identified. Chromosome bands 11q22-q23 contain ATM, a cell cycle checkpoint kinase and tumor suppressor playing a pivotal role in the DNA damage response. Here, we report that haploinsufficiency of ATM in neuroblastoma correlates with lower ATM expression, event-free survival, and overall survival. ATM loss occurs in high stage neuroblastoma without MYCN amplification. In SK-N-SH, CLB-Ga and GI-ME-N human neuroblastoma cells, stable ATM silencing promotes neuroblastoma progression in soft agar assays, and in subcutaneous xenografts in nude mice. This effect is dependent on the extent of ATM silencing and does not appear to involve MYCN. Our findings identify ATM as a potential haploinsufficient neuroblastoma tumor suppressor, whose inactivation mirrors the increased aggressiveness associated with 11q deletion in neuroblastoma. PMID:26053094

Experimental investigation of correlation between fading and glint for aircraft targets

NASA Astrophysics Data System (ADS)

Wallin, C. M.; Aas, B.

The correlation between the fading and glint of aircraft targets is investigated experimentally using a conventional amplitude comparison three-channel monopulse radar operating in the Ku-band. A significant correlation is found between the RCS and the variance of the angle error signals; this correlation seems to be independent of the aspect angle. The correlation between the RCS and the angle error signals themselves, however, is found to be very small.

Independent Research (IR) and Independent Exploratory Development (IED)

DTIC Science & Technology

1994-08-01

in the Workplace . Independent research/independent exploratory development, IR/IED...Exclusion Rate differences Over a Cut Score Domain, An Examination of Cognitive and Motivational Effects of Employee Interventions, and Cultural Diversity

Transition-Independent Decentralized Markov Decision Processes

NASA Technical Reports Server (NTRS)

Becker, Raphen; Silberstein, Shlomo; Lesser, Victor; Goldman, Claudia V.; Morris, Robert (Technical Monitor)

2003-01-01

There has been substantial progress with formal models for sequential decision making by individual agents using the Markov decision process (MDP). However, similar treatment of multi-agent systems is lacking. A recent complexity result, showing that solving decentralized MDPs is NEXP-hard, provides a partial explanation. To overcome this complexity barrier, we identify a general class of transition-independent decentralized MDPs that is widely applicable. The class consists of independent collaborating agents that are tied up by a global reward function that depends on both of their histories. We present a novel algorithm for solving this class of problems and examine its properties. The result is the first effective technique to solve optimally a class of decentralized MDPs. This lays the foundation for further work in this area on both exact and approximate solutions.

Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders

PubMed Central

Lo, Min-Tzu; Hinds, David A.; Tung, Joyce Y.; Franz, Carol; Fan, Chun-Chieh; Wang, Yunpeng; Smeland, Olav B.; Schork, Andrew; Holland, Dominic; Kauppi, Karolina; Sanyal, Nilotpal; Escott-Price, Valentina; Smith, Daniel J.; O'Donovan, Michael; Stefansson, Hreinn; Bjornsdottir, Gyda; Thorgeirsson, Thorgeir E.; Stefansson, Kari; McEvoy, Linda K.; Dale, Anders M.; Andreassen, Ole A.; Chen, Chi-Hua

2017-01-01

Summary Personality is influenced by genetic and environmental factors1, and associated with mental health. However, the underlying genetic determinants are largely unknown. We identified six genetic loci, including five novel loci2,3, significantly associated with personality traits in a meta-analysis of genome-wide association studies (N=123,132–260,861). Of these genome-wide significant loci, extraversion was associated with variants in WSCD2 and near PCDH15, and neuroticism with variants on chromosome 8p23.1 and in L3MBTL2. We performed a principal component analysis to extract major dimensions underlying genetic variations among five personality traits and six psychiatric disorders (N=5,422–18,759). The first genetic dimension separated personality traits and psychiatric disorders, except that neuroticism and openness to experience were clustered with the disorders. High genetic correlations were found between extraversion and attention-deficit/hyperactivity disorder (ADHD), and between openness and schizophrenia/bipolar disorder. The second genetic dimension was closely aligned with extraversion-introversion and grouped neuroticism with internalizing psychopathology (e.g., depression/anxiety). PMID:27918536

Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders.

PubMed

Lo, Min-Tzu; Hinds, David A; Tung, Joyce Y; Franz, Carol; Fan, Chun-Chieh; Wang, Yunpeng; Smeland, Olav B; Schork, Andrew; Holland, Dominic; Kauppi, Karolina; Sanyal, Nilotpal; Escott-Price, Valentina; Smith, Daniel J; O'Donovan, Michael; Stefansson, Hreinn; Bjornsdottir, Gyda; Thorgeirsson, Thorgeir E; Stefansson, Kari; McEvoy, Linda K; Dale, Anders M; Andreassen, Ole A; Chen, Chi-Hua

2017-01-01

Personality is influenced by genetic and environmental factors and associated with mental health. However, the underlying genetic determinants are largely unknown. We identified six genetic loci, including five novel loci, significantly associated with personality traits in a meta-analysis of genome-wide association studies (N = 123,132-260,861). Of these genome-wide significant loci, extraversion was associated with variants in WSCD2 and near PCDH15, and neuroticism with variants on chromosome 8p23.1 and in L3MBTL2. We performed a principal component analysis to extract major dimensions underlying genetic variations among five personality traits and six psychiatric disorders (N = 5,422-18,759). The first genetic dimension separated personality traits and psychiatric disorders, except that neuroticism and openness to experience were clustered with the disorders. High genetic correlations were found between extraversion and attention-deficit-hyperactivity disorder (ADHD) and between openness and schizophrenia and bipolar disorder. The second genetic dimension was closely aligned with extraversion-introversion and grouped neuroticism with internalizing psychopathology (e.g., depression or anxiety).

Identifying Affective Domains That Correlate and Predict Mathematics Performance in High-Performing Students in Singapore

ERIC Educational Resources Information Center

Lim, Siew Yee; Chapman, Elaine

2015-01-01

Past studies have shown that distinct yet highly correlated sub-constructs of three broad mathematics affective variables: (a) motivation, (b) attitudes and (c) anxiety, have varying degree of correlation with mathematics achievement. The sub-constructs of these three affective constructs are as follows: (a) (i) amotivation, (ii) external…

Assessment of canine BEST1 variations identifies new mutations and establishes an independent bestrophinopathy model (cmr3)

PubMed Central

Wickström, Kaisa; Slavik, Julianna; Lindauer, Sarah J.; Ahonen, Saija; Schelling, Claude; Lohi, Hannes; Guziewicz, Karina E.; Aguirre, Gustavo D.

2010-01-01

Purpose Mutations in bestrophin 1 (BEST1) are associated with a group of retinal disorders known as bestrophinopathies in man and canine multifocal retinopathies (cmr) in the dog. To date, the dog is the only large animal model suitable for the complex characterization and in-depth studies of Best-related disorders. In the first report of cmr, the disease was described in a group of mastiff-related breeds (cmr1) and the Coton de Tulear (cmr2). Additional breeds, e.g., the Lapponian herder (LH) and others, subsequently were recognized with similar phenotypes, but linked loci are unknown. Analysis of the BEST1 gene aimed to identify mutations in these additional populations and extend our understanding of genotype–phenotype associations. Methods Animals were subjected to routine eye exams, phenotypically characterized, and samples were collected for molecular studies. Known BEST1 mutations were assessed, and the canine BEST1 coding exons were amplified and sequenced in selected individuals that exhibited a cmr compatible phenotype but that did not carry known mutations. Resulting sequence changes were genotyped in several different breeds and evaluated in the context of the phenotype. Results Seven novel coding variants were identified in exon 10 of cBEST1. Two linked mutations were associated with cmr exclusive to the LH breed (cmr3). Two individuals of Jämthund and Norfolk terrier breeds were heterozygous for two conservative changes, but these were unlikely to have disease-causing potential. Another three substitutions were found in the Bernese mountain dog that were predicted to have a deleterious effect on protein function. Previously reported mutations were excluded from segregation in these populations, but cmr1 was confirmed in another mastiff-related breed, the Italian cane corso. Conclusions A third independent canine model for human bestrophinopathies has been established in the LH breed. While exhibiting a phenotype comparable to cmr1 and cmr2, the

Cap-independent translation of plant viral RNAs

PubMed Central

Pettit Kneller, Elizabeth L.; Rakotondrafara, Aurélie M.; Miller, W. Allen

2007-01-01

The RNAs of many plant viruses lack a 5′ cap and must be translated by a cap-independent mechanism. Here, we discuss the remarkably diverse cap-independent translation elements that have been identified in members of the Potyviridae, Luteoviridae, and Tombusviridae families, and genus Tobamovirus. Many other plant viruses have uncapped RNAs but their translation control elements are uncharacterized. Cap-independent translation elements of plant viruses differ strikingly from those of animal viruses: they are smaller (<200 nt), some are located in the 3′ untranslated region, some require ribosome scanning from the 5′ end of the mRNA, and the 5′ UTR elements are much less structured than those of animal viruses. We discuss how these elements may interact with host translation factors, and speculate on their mechanism of action and their roles in the virus replication cycle. Much remains to be learned about how these elements enable plant viruses to usurp the host translational machinery. PMID:16360925

A correlational study of illness knowledge, self-care behaviors, and quality of life in elderly patients with heart failure.

PubMed

Liu, Min-Hui; Wang, Chao-Hung; Huang, Yu-Yen; Cherng, Wen-Jin; Wang, Kai-Wei Katherine

2014-06-01

Patients with heart failure experience adverse physical symptoms that affect quality of life. The number of patients with heart failure in Taiwan has been growing in recent years. This article examines correlations among illness knowledge, self-care behaviors, and quality of life in elderly patients with heart failure. A cross-sectional research design using three questionnaires was adopted. The study was undertaken in an outpatient department of a teaching hospital in Taiwan from January to June 2008. Potential participants aged 65 years or older were selected by a physician based on several diagnostic findings of heart failure that included an International Classification of Diseases' code 4280 or 4289. Patients who were bedridden or had a prognosis of less than 6 months were excluded from consideration. One hundred forty-one patients with heart failure were recruited. Most participants were men (51.8%), older adults (49.6% older than 71 years old), and either educated to an elementary school level or illiterate (69.5%) and have New York Heart Association class II (61.0%). Participants had an average left ventricular ejection fraction of 41.1%. The illness knowledge of participants was poor (accuracy rate: 29.3%), and most were unaware of the significance of self-care. Illness knowledge correlated with both self-care behaviors (r = -.42, p < .01) and quality of life (r = -.22, p < .01). Illness knowledge and age were identified as significant correlated factors of self-care behaviors (R = .22); and functional class, living independently, and age were identified as significant correlated factors of quality of life (R = .41). Participants in this study with higher self-reported self-care behaviors and quality of life were younger in age and had better illness knowledge. Furthermore, physical function and independence in daily living significantly affected quality of life. Care for patients with heart failure, particularly older adults, should focus on teaching

Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants

PubMed Central

Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J.; Carlson, Christopher S.; Casey, Graham; Chang-Claude, Jenny; Conti, David V.; Curtis, Keith R.; Duggan, David; Gallinger, Steven; Haile, Robert W.; Harrison, Tabitha A.; Hayes, Richard B.; Hoffmeister, Michael; Hopper, John L.; Hudson, Thomas J.; Jenkins, Mark A.; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M.; Newcomb, Polly A.; Nickerson, Deborah A.; Potter, John D.; Schoen, Robert E.; Schumacher, Fredrick R.; Seminara, Daniela; Slattery, Martha L.; Hsu, Li; Chan, Andrew T.; White, Emily; Berndt, Sonja I.; Peters, Ulrike

2016-01-01

Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s). PMID:27379672

SIMBAD : a sequence-independent molecular-replacement pipeline

DOE PAGES

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.; ...

2018-06-08

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two

SIMBAD : a sequence-independent molecular-replacement pipeline

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

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two

Computing physical properties with quantum Monte Carlo methods with statistical fluctuations independent of system size.

PubMed

Assaraf, Roland

2014-12-01

We show that the recently proposed correlated sampling without reweighting procedure extends the locality (asymptotic independence of the system size) of a physical property to the statistical fluctuations of its estimator. This makes the approach potentially vastly more efficient for computing space-localized properties in large systems compared with standard correlated methods. A proof is given for a large collection of noninteracting fragments. Calculations on hydrogen chains suggest that this behavior holds not only for systems displaying short-range correlations, but also for systems with long-range correlations.

Mutation-Independent Activation of the Anaplastic Lymphoma Kinase in Neuroblastoma.

PubMed

Regairaz, Marie; Munier, Fabienne; Sartelet, Hervé; Castaing, Marine; Marty, Virginie; Renauleaud, Céline; Doux, Camille; Delbé, Jean; Courty, José; Fabre, Monique; Ohta, Shigeru; Vielh, Philippe; Michiels, Stefan; Valteau-Couanet, Dominique; Vassal, Gilles

2016-02-01

Activating mutations of anaplastic lymphoma kinase (ALK) have been identified as important players in neuroblastoma development. Our goal was to evaluate the significance of overall ALK activation in neuroblastoma. Expression of phosphorylated ALK, ALK, and its putative ligands, pleiotrophin and midkine, was screened in 289 neuroblastomas and 56 paired normal tissues. ALK was expressed in 99% of tumors and phosphorylated in 48% of cases. Pleiotrophin and midkine were expressed in 58% and 79% of tumors, respectively. ALK activation was significantly higher in tumors than in paired normal tissues, together with ALK and midkine expression. ALK activation was largely independent of mutations and correlated with midkine expression in tumors. ALK activation in tumors was associated with favorable features, including a younger age at diagnosis, hyperdiploidy, and detection by mass screening. Antitumor activity of the ALK inhibitor TAE684 was evaluated in wild-type or mutated ALK neuroblastoma cell lines and xenografts. TAE684 was cytotoxic in vitro in all cell lines, especially those harboring an ALK mutation. TAE684 efficiently inhibited ALK phosphorylation in vivo in both F1174I and R1275Q xenografts but demonstrated antitumor activity only against the R1275Q xenograft. In conclusion, ALK activation occurs frequently during neuroblastoma oncogenesis, mainly through mutation-independent mechanisms. However, ALK activation is not associated with a poor outcome and is not always a driver of cell proliferation and/or survival in neuroblastoma. Copyright © 2016 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

The difficulty with correlations: Energy expenditure and brain mass in bats.

PubMed

McNab, Brian K; Köhler, Meike

2017-10-01

Brain mass has been suggested to determine a mammal's energy expenditure. This potential dependence is examined in 48 species of bats. A correlation between characters may be direct or derived from shared correlations with intervening factors without a direct interaction. Basal rate of metabolism in these bats increases with brain mass: large brains are more expensive than small brains, and both brain mass and basal rate increase with body mass. Basal rate and brain mass also correlate with food habits in bats. Mass-independent basal rate weakly correlates with mass-independent brain mass, the correlation only accounting for 12% of the variation in basal rate, which disappears when the combined effects of body mass and food habits are deleted. The correlation between basal rate and brain mass seen in this and other studies usually accounts for <10% of the variation in basal rate and often <4%, even when statistically significant, a minimalist explanation for the level the basal rate. This correlation probably reflects the intermediacy of secondary factors, as occurred with food habits in bats. Most biological correlations are complicated and must be examined in detail before assurance can be given as to their bases. Copyright © 2017 Elsevier Inc. All rights reserved.

Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term.

PubMed

Romero, Roberto; Tarca, Adi L; Chaemsaithong, Piya; Miranda, Jezid; Chaiworapongsa, Tinnakorn; Jia, Hui; Hassan, Sonia S; Kalita, Cynthia A; Cai, Juan; Yeo, Lami; Lipovich, Leonard

2014-09-01

To identify differentially expressed long non-coding RNA (lncRNA) genes in human myometrium in women with spontaneous labor at term. Myometrium was obtained from women undergoing cesarean deliveries who were not in labor (n = 19) and women in spontaneous labor at term (n = 20). RNA was extracted and profiled using an Illumina® microarray platform. We have used computational approaches to bound the extent of long non-coding RNA representation on this platform, and to identify co-differentially expressed and correlated pairs of long non-coding RNA genes and protein-coding genes sharing the same genomic loci. We identified co-differential expression and correlation at two genomic loci that contain coding-lncRNA gene pairs: SOCS2-AK054607 and LMCD1-NR_024065 in women in spontaneous labor at term. This co-differential expression and correlation was validated by qRT-PCR, an experimental method completely independent of the microarray analysis. Intriguingly, one of the two lncRNA genes differentially expressed in term labor had a key genomic structure element, a splice site, that lacked evolutionary conservation beyond primates. We provide, for the first time, evidence for coordinated differential expression and correlation of cis-encoded antisense lncRNAs and protein-coding genes with known as well as novel roles in pregnancy in the myometrium of women in spontaneous labor at term.

Modifiable correlates of illness perceptions in adults with chronic somatic conditions: A systematic review.

PubMed

Arat, Seher; De Cock, Diederik; Moons, Philip; Vandenberghe, Joris; Westhovens, René

2018-04-01

When individuals become ill, they want to understand and give meaning to their illness. The interpretation of this illness experience, or illness perception, is influenced by a range of individual, contextual, and cultural factors. Some of these factors may be modifiable by nursing interventions. The purpose of this systematic review was to investigate which modifiable factors were correlated with illness perceptions across studies of adults with different chronic somatic diseases. Using search terms tailored to each of four electronic databases, studies retrieved were reviewed by two independent evaluators, and each relevant article was assessed for methodological quality. Results were standardized by calculating correlation coefficients. Fifteen papers on illness perceptions in a variety of chronic diseases met the inclusion criteria. All used standardized measures of illness perceptions. We identified five groups of modifiable correlates of illness perceptions: illness-related factors, psychosocial factors, medication beliefs, information provision and satisfaction with information received, and quality of care. Our findings add to the knowledge of modifiable factors correlated with illness perceptions, including the importance of illness-related factors and psychosocial factors such as anxiety and depression. Knowledge of these correlates can facilitate understanding of patients' illness perceptions and might be useful in tailoring patient education programs. © 2018 Wiley Periodicals, Inc.

Phenotype/genotype correlation in a case series of Stargardt's patients identifies novel mutations in the ABCA4 gene.

PubMed

Gemenetzi, M; Lotery, A J

2013-11-01

To investigate phenotypic variability in terms of best-corrected visual acuity (BCVA) in patients with Stargardt disease (STGD) and confirmed ABCA4 mutations. Entire coding region analysis of the ABCA4 gene by direct sequencing of seven patients with clinical findings of STGD seen in the Retina Clinics of Southampton Eye Unit between 2002 and 2011.Phenotypic variables recorded were BCVA, fluorescein angiographic appearance, electrophysiology, and visual fields. All patients had heterozygous amino acid-changing variants (missense mutations) in the ABCA4 gene. A splice sequence change was found in a 30-year-old patient with severly affected vision. Two novel sequence changes were identified: a missense mutation in a mildly affected 44-year-old patient and a frameshift mutation in a severly affected 34-year-old patient. The identified ABCA4 mutations were compatible with the resulting phenotypes in terms of BCVA. Higher BCVAs were recorded in patients with missense mutations. Sequence changes, predicted to have more deleterious effect on protein function, resulted in a more severe phenotype. This case series of STGD patients demonstrates novel genotype/phenotype correlations, which may be useful to counselling of patients. This information may prove useful in selection of candidates for clinical trials in ABCA4 disease.

Canonical correlation analysis to identify the semen characteristics used to forecast the freeze survival of Curimba (Prochilodus lineatus) spermatozoa.

PubMed

Carvalho, A F S; Murgas, L D S; Ferreira-Machad, M R; Andrade, E S; Felizardo, V O; Allaman, I B; de Paula, F G

　　OBJECTIVE: To identify which sperm characteristics were able to predict more accurately the quality of curimba (Prochilodus lineatus) semen upon freezing using canonical correlation analysis. Eleven fish breeders with initial mean weight of 705.21 ± 111 g were used. For cryopreservation, 200 µL of semen were taken from each animal and diluted in the cryoprotectant solution (10% dimethyl sulfoxide and 5% Beltsville Thawing Solution Minitub) in a 1:4 ratio and placed into 0.5-mL straws. Sperm characteristics (motility, sperm abnormalities, total antioxidant activity and lipid peroxidation) were evaluated. A randomized block design with duplicate samples per treatment (fresh and frozen semen) was used. The block factor was the animals, and the experimental unit the ejaculates. Canonical correlation was used to evaluate the association between sperm characteristics of fresh semen and thawed semen. There was a significant association (P = 0.10) among the variables measured in fresh semen with the variables measured in thawed semen, and 78.6% of the difference observed in the thawed semen can be attributed to variation of variables measured in fresh semen. Sperm motility, motility duration and antioxidant activity of the thawed semen showed an inverse relationship with those of the fresh semen; whereas the minor sperm abnormalities, major sperm abnormalities and lipid peroxidation showed a direct relationship with those of the fresh semen. Only the rate and motility duration of the thawed semen presented high correlation (-0.63 and -0.73, respectively) with the canonical variable represented by the sperm characteristics of fresh semen. The rate and motility duration of fresh semen may be used to predict the quality of the thawed sperm in Prochilodus lineatus.

Prevalence and clinical correlates of sarcopenia in community-dwelling older people: application of the EWGSOP definition and diagnostic algorithm.

PubMed

Volpato, Stefano; Bianchi, Lara; Cherubini, Antonio; Landi, Francesco; Maggio, Marcello; Savino, Elisabetta; Bandinelli, Stefania; Ceda, Gian Paolo; Guralnik, Jack M; Zuliani, Giovanni; Ferrucci, Luigi

2014-04-01

Muscle impairment is a common condition in older people and a powerful risk factor for disability and mortality. The aim of this study was to apply the European Working Group on Sarcopenia in Older People criteria to estimate the prevalence and investigate the clinical correlates of sarcopenia, in a sample of Italian community-dwelling older people. Cross-sectional analysis of 730 participants (74% aged 65 years and older) enrolled in the InCHIANTI study. Sarcopenia was defined according to the European Working Group on Sarcopenia in Older People criteria using bioimpedance analysis for muscle mass assessment. Logistic regression analysis was used to identify the factors independently associated with sarcopenia. Sarcopenia defined by the European Working Group on Sarcopenia in Older People criteria increased steeply with age (p < .001), with 31.6% of women and 17.4% of men aged 80 years or older being affected by this condition. Higher education (odds ratio: 0.85; 95% CI: 0.74-0.98), lower insulin-like growth factor I (lowest vs highest tertile, odds ratio: 3.89; 95% CI: 1.03-14.1), and low bioavailable testosterone (odds ratio: 2.67; 95% CI: 1.31-5.44) were independently associated with the likelihood of being sarcopenic. Nutritional intake, physical activity, and level of comorbidity were not associated with sarcopenia. Sarcopenia identified by the European Working Group on Sarcopenia in Older People criteria is a relatively common condition in Italian octogenarians, and its prevalence increases with aging. Correlates of sarcopenia identified in this study might suggest new approaches for prevention and treatment of sarcopenia.

Identifying nursing home residents at risk for falling.

PubMed

Kiely, D K; Kiel, D P; Burrows, A B; Lipsitz, L A

1998-05-01

To develop a fall risk model that can be used to identify prospectively nursing home residents at risk for falling. The secondary objective was to determine whether the nursing home environment independently influenced the development of falls. A prospective study involving 1 year of follow-up. Two hundred seventy-two nursing homes in the state of Washington. A total of 18,855 residents who had a baseline assessment in 1991 and a follow-up assessment within the subsequent year. Baseline Minimum Data Set items that could be potential risk factors for falling were considered as independent variables. The dependent variable was whether the resident fell as reported at the follow-up assessment. We estimated the extrinsic risk attributable to particular nursing home environments by calculating the annual fall rate in each nursing home and grouping them into tertiles of fall risk according to these rates. Factors associated independently with falling were fall history, wandering behavior, use of a cane or walker, deterioration of activities of daily living performance, age greater than 87 years, unsteady gait, transfer independence, wheelchair independence, and male gender. Nursing home residents with a fall history were more than three times as likely to fall during the follow-up period than residents without a fall history. Residents in homes with the highest tertile of fall rates were more than twice as likely to fall compared with residents of homes in the lowest tertile, independent of resident-specific risk factors. Fall history was identified as the strongest risk factor associated with subsequent falls and accounted for the vast majority of the predictive strength of the model. We recommend that fall history be used as an initial screener for determining eligibility for fall intervention efforts. Studies are needed to determine the facility characteristics that contribute to fall risk, independent of resident-specific risk factors.

Canonical correlation analysis of infant's size at birth and maternal factors: a study in rural northwest Bangladesh.

PubMed

Kabir, Alamgir; Merrill, Rebecca D; Shamim, Abu Ahmed; Klemn, Rolf D W; Labrique, Alain B; Christian, Parul; West, Keith P; Nasser, Mohammed

2014-01-01

This analysis was conducted to explore the association between 5 birth size measurements (weight, length and head, chest and mid-upper arm [MUAC] circumferences) as dependent variables and 10 maternal factors as independent variables using canonical correlation analysis (CCA). CCA considers simultaneously sets of dependent and independent variables and, thus, generates a substantially reduced type 1 error. Data were from women delivering a singleton live birth (n = 14,506) while participating in a double-masked, cluster-randomized, placebo-controlled maternal vitamin A or β-carotene supplementation trial in rural Bangladesh. The first canonical correlation was 0.42 (P<0.001), demonstrating a moderate positive correlation mainly between the 5 birth size measurements and 5 maternal factors (preterm delivery, early pregnancy MUAC, infant sex, age and parity). A significant interaction between infant sex and preterm delivery on birth size was also revealed from the score plot. Thirteen percent of birth size variability was explained by the composite score of the maternal factors (Redundancy, RY/X = 0.131). Given an ability to accommodate numerous relationships and reduce complexities of multiple comparisons, CCA identified the 5 maternal variables able to predict birth size in this rural Bangladesh setting. CCA may offer an efficient, practical and inclusive approach to assessing the association between two sets of variables, addressing the innate complexity of interactions.

Independent Predictors of Delay in Emergence From General Anesthesia

PubMed Central

Maeda, Shigeru; Tomoyasu, Yumiko; Higuchi, Hitoshi; Ishii-Maruhama, Minako; Egusa, Masahiko; Miyawaki, Takuya

2015-01-01

Some patients with intellectual disabilities spend longer than others in emergence from ambulatory general anesthesia for dental treatment. Although antiepileptic drugs and anesthetics might be involved, an independent predictor for delay of the emergence remains unclear. Thus, a purpose of this study is to identify independent factors affecting the delay of emergence from general anesthesia. This was a retrospective cohort study in dental patients with intellectual disabilities. Patients in need of sedative premedication were removed from participants. The outcome was time until emergence from general anesthesia. Stepwise multivariate regression analysis was used to extract independent factors affecting the outcome. Antiepileptic drugs and anesthetic parameters were included as predictor variables. The study included 102 cases. Clobazam, clonazepam, and phenobarbital were shown to be independent determinants of emergence time. Parameters relating to anesthetics, patients' backgrounds, and dental treatment were not independent factors. Delay in emergence time in ambulatory general anesthesia is likely to be related to the antiepileptic drugs of benzodiazepine or barbiturates in patients with intellectual disability. PMID:25849468

Statistical measures of Planck scale signal correlations in interferometers

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

Hogan, Craig J.; Kwon, Ohkyung

2015-06-22

A model-independent statistical framework is presented to interpret data from systems where the mean time derivative of positional cross correlation between world lines, a measure of spreading in a quantum geometrical wave function, is measured with a precision smaller than the Planck time. The framework provides a general way to constrain possible departures from perfect independence of classical world lines, associated with Planck scale bounds on positional information. A parametrized candidate set of possible correlation functions is shown to be consistent with the known causal structure of the classical geometry measured by an apparatus, and the holographic scaling of informationmore » suggested by gravity. Frequency-domain power spectra are derived that can be compared with interferometer data. As a result, simple projections of sensitivity for specific experimental set-ups suggests that measurements will directly yield constraints on a universal time derivative of the correlation function, and thereby confirm or rule out a class of Planck scale departures from classical geometry.« less

Mitochondrial assembly receptor expression is an independent prognosticator for patients with oral tongue squamous cell carcinoma.

PubMed

Su, Yan-Ye; Chen, Chang-Han; Chien, Chih-Yen; Lin, Wei-Che; Huang, Wan-Ting; Li, Shau-Hsuan

2017-01-01

Recent evidence suggests that the local renin-angiotensin system has been implicated in various malignancies. The mitochondrial assembly receptor is a newly identified receptor for angiotensin peptides, angiotensin-(1-7), and has an important role in the renin-angiotensin system. However, the role of the mitochondrial assembly receptor in the prognosis of cancer patients remains unclear. The aim of this study was to evaluate the significance of mitochondrial assembly receptor signaling in the prognosis of oral tongue squamous cell carcinoma. Mitochondrial assembly receptor immunohistochemistry was examined in 151 oral tongue squamous cell carcinoma patients and was correlated with treatment outcome. The functional relevance of the mitochondrial assembly receptor in oral tongue squamous cell carcinoma cell lines was evaluated by 3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyltetrazolium bromide reduction and bromodeoxyuridine incorporation assays. Mitochondrial assembly receptor overexpression was significantly correlated with early pathological T classification ( p=0.029) and the absence of extracapsular spread ( p=0.039). Univariate analyses demonstrated that mitochondrial assembly receptor overexpression was significantly associated with superior overall survival ( p=0.012). In multivariate comparison, mitochondrial assembly receptor overexpression remained independently associated with superior overall survival ( p=0.008, hazard ratio=1.862). In vitro, angiotensin-(1-7) suppressed the cell growth in oral tongue squamous cell carcinoma cells, and this response was reversed by the mitochondrial assembly receptor antagonist, A779. Mitochondrial assembly receptor expression is independently associated with the prognosis of oral tongue squamous cell carcinoma patients. These findings suggest that mitochondrial assembly receptor signaling may be a promising novel target for oral tongue squamous cell carcinoma.

Evaluation of Two Library-Independent Microbial Source Tracking Methods To Identify Sources of Fecal Contamination in French Estuaries▿

PubMed Central

Gourmelon, Michèle; Caprais, Marie Paule; Ségura, Raphaël; Le Mennec, Cécile; Lozach, Solen; Piriou, Jean Yves; Rincé, Alain

2007-01-01

In order to identify the origin of the fecal contamination observed in French estuaries, two library-independent microbial source tracking (MST) methods were selected: (i) Bacteroidales host-specific 16S rRNA gene markers and (ii) F-specific RNA bacteriophage genotyping. The specificity of the Bacteroidales markers was evaluated on human and animal (bovine, pig, sheep, and bird) feces. Two human-specific markers (HF183 and HF134), one ruminant-specific marker (CF193′), and one pig-specific marker (PF163) showed a high level of specificity (>90%). However, the data suggest that the proposed ruminant-specific CF128 marker would be better described as an animal marker, as it was observed in all bovine and sheep feces and 96% of pig feces. F RNA bacteriophages were detected in only 21% of individual fecal samples tested, in 60% of pig slurries, but in all sewage samples. Most detected F RNA bacteriophages were from genotypes II and III in sewage samples and from genotypes I and IV in bovine, pig, and bird feces and from pig slurries. Both MST methods were applied to 28 water samples collected from three watersheds at different times. Classification of water samples as subject to human, animal, or mixed fecal contamination was more frequent when using Bacteroidales markers (82.1% of water samples) than by bacteriophage genotyping (50%). The ability to classify a water sample increased with increasing Escherichia coli or enterococcus concentration. For the samples that could be classified by bacteriophage genotyping, 78% agreed with the classification obtained from Bacteroidales markers. PMID:17557850

Comparative genome analysis of a large Dutch Legionella pneumophila strain collection identifies five markers highly correlated with clinical strains

PubMed Central

2010-01-01

Background Discrimination between clinical and environmental strains within many bacterial species is currently underexplored. Genomic analyses have clearly shown the enormous variability in genome composition between different strains of a bacterial species. In this study we have used Legionella pneumophila, the causative agent of Legionnaire's disease, to search for genomic markers related to pathogenicity. During a large surveillance study in The Netherlands well-characterized patient-derived strains and environmental strains were collected. We have used a mixed-genome microarray to perform comparative-genome analysis of 257 strains from this collection. Results Microarray analysis indicated that 480 DNA markers (out of in total 3360 markers) showed clear variation in presence between individual strains and these were therefore selected for further analysis. Unsupervised statistical analysis of these markers showed the enormous genomic variation within the species but did not show any correlation with a pathogenic phenotype. We therefore used supervised statistical analysis to identify discriminating markers. Genetic programming was used both to identify predictive markers and to define their interrelationships. A model consisting of five markers was developed that together correctly predicted 100% of the clinical strains and 69% of the environmental strains. Conclusions A novel approach for identifying predictive markers enabling discrimination between clinical and environmental isolates of L. pneumophila is presented. Out of over 3000 possible markers, five were selected that together enabled correct prediction of all the clinical strains included in this study. This novel approach for identifying predictive markers can be applied to all bacterial species, allowing for better discrimination between strains well equipped to cause human disease and relatively harmless strains. PMID:20630115

Positive selection moments identify potential functional residues in human olfactory receptors

NASA Technical Reports Server (NTRS)

Singer, M. S.; Weisinger-Lewin, Y.; Lancet, D.; Shepherd, G. M.

1996-01-01

Correlated mutation analysis and molecular models of olfactory receptors have provided evidence that residues in the transmembrane domains form a binding pocket for odor ligands. As an independent test of these results, we have calculated positive selection moments for the alpha-helical sixth transmembrane domain (TM6) of human olfactory receptors. The moments can be used to identify residues that have been preferentially affected by positive selection and are thus likely to interact with odor ligands. The results suggest that residue 622, which is commonly a serine or threonine, could form critical H-bonds. In some receptors a dual-serine subsite, formed by residues 622 and 625, could bind hydroxyl determinants on odor ligands. The potential importance of these residues is further supported by site-directed mutagenesis in the beta-adrenergic receptor. The findings should be of practical value for future physiological studies, binding assays, and site-directed mutagenesis.

Multiple independent identification decisions: a method of calibrating eyewitness identifications.

PubMed

Pryke, Sean; Lindsay, R C L; Dysart, Jennifer E; Dupuis, Paul

2004-02-01

Two experiments (N = 147 and N = 90) explored the use of multiple independent lineups to identify a target seen live. In Experiment 1, simultaneous face, body, and sequential voice lineups were used. In Experiment 2, sequential face, body, voice, and clothing lineups were used. Both studies demonstrated that multiple identifications (by the same witness) from independent lineups of different features are highly diagnostic of suspect guilt (G. L. Wells & R. C. L. Lindsay, 1980). The number of suspect and foil selections from multiple independent lineups provides a powerful method of calibrating the accuracy of eyewitness identification. Implications for use of current methods are discussed. ((c) 2004 APA, all rights reserved)

Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment

USDA-ARS?s Scientific Manuscript database

Interindividual epigenetic variation that occurs systemically must be established prior to gastrulation in the very early embryo and, because it is systemic, can be assessed in easily biopsiable tissues. We employ two independent genome-wide approaches to search for such variants. First, we screen f...

Radiogenomics analysis identifies correlations of digital mammography with clinical molecular signatures in breast cancer.

PubMed

Tamez-Peña, Jose-Gerardo; Rodriguez-Rojas, Juan-Andrés; Gomez-Rueda, Hugo; Celaya-Padilla, Jose-Maria; Rivera-Prieto, Roxana-Alicia; Palacios-Corona, Rebeca; Garza-Montemayor, Margarita; Cardona-Huerta, Servando; Treviño, Victor

2018-01-01

In breast cancer, well-known gene expression subtypes have been related to a specific clinical outcome. However, their impact on the breast tissue phenotype has been poorly studied. Here, we investigate the association of imaging data of tumors to gene expression signatures from 71 patients with breast cancer that underwent pre-treatment digital mammograms and tumor biopsies. From digital mammograms, a semi-automated radiogenomics analysis generated 1,078 features describing the shape, signal distribution, and texture of tumors along their contralateral image used as control. From tumor biopsy, we estimated the OncotypeDX and PAM50 recurrence scores using gene expression microarrays. Then, we used multivariate analysis under stringent cross-validation to train models predicting recurrence scores. Few univariate features reached Spearman correlation coefficients above 0.4. Nevertheless, multivariate analysis yielded significantly correlated models for both signatures (correlation of OncotypeDX = 0.49 ± 0.07 and PAM50 = 0.32 ± 0.10 in stringent cross-validation and OncotypeDX = 0.83 and PAM50 = 0.78 for a unique model). Equivalent models trained from the unaffected contralateral breast were not correlated suggesting that the image signatures were tumor-specific and that overfitting was not a considerable issue. We also noted that models were improved by combining clinical information (triple negative status and progesterone receptor). The models used mostly wavelets and fractal features suggesting their importance to capture tumor information. Our results suggest that molecular-based recurrence risk and breast cancer subtypes have observable radiographic phenotypes. To our knowledge, this is the first study associating mammographic information to gene expression recurrence signatures.

Phase correlated adequate afferent action potentials as a drive of human spinal oscillators.

PubMed

Schalow, G

1993-12-01

1. By recording, with 2 pairs of wire electrodes, single-fibre action potentials (APs) from lower sacral nerve roots of a brain-dead human and a patient with spinal cord lesion, impulse patterns of afferent APs and impulse trains of oscillatory firing motoneurons could be identified and correlated. 2. Two highly activated secondary muscle spindle afferents increased and decreased their activity at about 0.3 Hz. The duration of the doublet interspike interval of a secondary spindle afferent fibre showed no correlation to the oscillation period of the motoneuron. 3. A continuously oscillatory firing motoneuron innervating the external and sphincter showed more transient breaks with the reduction of the number of phase correlated APs from 2 spindle afferents, indicating a looser oscillation. A transient brake of a 157 msec period alpha 2-oscillation could be correlated to the shift of a interspike interval distribution peak from 150 to 180 msec of the adequate afferent input, which suggests a transient loss of the necessary phase relation. 4. Oscillatory firing alpha 2-motoneurons innervating the external bladder and anal sphincters fired independently according to their phase correlated APs from the urinary bladder stretch receptor and muscle spindle afferents respectively; the bladder motoneuron slightly inhibited the anal motoneuron. 5. Receptors of the afferents and innervation sites of oscillatory firing motoneurons could be located within the urinary tract and the anal canal.

Analysis of Aircraft Clusters to Measure Sector-Independent Airspace Congestion

NASA Technical Reports Server (NTRS)

Bilimoria, Karl D.; Lee, Hilda Q.

2005-01-01

boundaries. Figure 1 , reproduced from Ref. 1, depicts an example traffic situation. When the situation is analyzed by sector boundaries (left side of figure), a Dynamic Density metric would identify excessive congestion in the central sector. When the same traffic situation is analyzed independent of sector boundaries (right side of figure), a Gaggle Density metric would identify congestion in two dynamically defined areas covering portions of several sectors. The first step towards measuring airspace-independent congestion is to identify aircraft clusters, i.e., groups of closely spaced aircraft. The objective of this work is to develop techniques to detect and classify clusters of aircraft.

Correlation of breast tissue histology and optical signatures to improve margin assessment techniques

NASA Astrophysics Data System (ADS)

Kennedy, Stephanie; Caldwell, Matthew; Bydlon, Torre; Mulvey, Christine; Mueller, Jenna; Wilke, Lee; Barry, William; Ramanujam, Nimmi; Geradts, Joseph

2016-06-01

Optical spectroscopy is sensitive to morphological composition and has potential applications in intraoperative margin assessment. Here, we evaluate ex vivo breast tissue and corresponding quantified hematoxylin & eosin images to correlate optical scattering signatures to tissue composition stratified by patient characteristics. Adipose sites (213) were characterized by their cell area and density. All other benign and malignant sites (181) were quantified using a grid method to determine composition. The relationships between mean reduced scattering coefficient (<μs‧>), and % adipose, % collagen, % glands, adipocyte cell area, and adipocyte density were investigated. These relationships were further stratified by age, menopausal status, body mass index (BMI), and breast density. We identified a positive correlation between <μs‧> and % collagen and a negative correlation between <μs‧> and age and BMI. Increased collagen corresponded to increased <μs‧> variability. In postmenopausal women, <μs‧> was similar regardless of fibroglandular content. Contributions from collagen and glands to <μs‧> were independent and equivalent in benign sites; glands showed a stronger positive correlation than collagen to <μs‧> in malignant sites. Our data suggest that scattering could differentiate highly scattering malignant from benign tissues in postmenopausal women. The relationship between scattering and tissue composition will support improved scattering models and technologies to enhance intraoperative optical margin assessment.

Pediatric Eosinophilic Esophagitis Symptom Scores (PEESS® v2.0) identify histologic and molecular correlates of the key clinical features of disease

PubMed Central

Martin, Lisa J.; Franciosi, James P.; Collins, Margaret H.; Abonia, J. Pablo; Lee, James J.; Hommel, Kevin A.; Varni, James W.; Grotjan, J. Tommie; Eby, Michael; He, Hua; Marsolo, Keith; Putnam, Philip E.; Garza, Jose M.; Kaul, Ajay; Wen, Ting; Rothenberg, Marc E.

2015-01-01

Background The Pediatric Eosinophilic Esophagitis Symptom Score (PEESS® v2.0) measures patient-relevant outcomes. However, whether patient-identified domains (dysphagia, gastrointestinal reflux disease (GERD), nausea/vomiting, and pain) align with clinical symptomology and histopathologic and molecular features of eosinophilic esophagitis (EoE) is unclear. Objective The purpose of this study was to determine if clinical features of EoE, measured through the PEESS® v2.0, associate with histopathologic and molecular features of EoE. This represents a novel approach for analysis of allergic diseases, given the availability of allergic tissue biopsy specimens. Methods We systematically recruited treated and untreated, pediatric patients with EoE (aged 2–18 years) and examined parent proxy–reported symptoms using the PEESS® v2.0. Clinical symptomology was collected by questionnaire. Esophageal biopsy samples were quantified for levels of eosinophils, eosinophil peroxidase (EPX) immunohistochemical staining, and mast cells. Molecular features were assessed by the EoE Diagnostic Panel (94 EoE-related gene transcripts). Associations between domain scores and clinical symptoms and biologic features were analyzed using Wilcoxon Rank Sum and Spearman correlation. Results The PEESS® v2.0 domains correlated to specific parent-reported symptoms: dysphagia (p = 0.0012), GERD (p = 0.0001), and nausea/vomiting (p < 0.0001). Pain correlated with multiple symptoms (p < 0.0005). Dysphagia correlated most strongly with overall histopathology, particularly in the proximal esophagus (p ≤ 0.0049). Markers of esophageal activity (EPX) were significantly associated with dysphagia (strongest r = .37; p = 0.02). Eosinophil levels were more associated with pain (r = 0.27; p=0.06) than for dysphagia (r = 0.24; p = 0.13). The dysphagia domain correlated the most with esophageal gene transcript levels, predominantly with mast cell–specific genes. Conclusion We have 1) established a

k-Space Image Correlation Spectroscopy: A Method for Accurate Transport Measurements Independent of Fluorophore Photophysics

PubMed Central

Kolin, David L.; Ronis, David; Wiseman, Paul W.

2006-01-01

We present the theory and application of reciprocal space image correlation spectroscopy (kICS). This technique measures the number density, diffusion coefficient, and velocity of fluorescently labeled macromolecules in a cell membrane imaged on a confocal, two-photon, or total internal reflection fluorescence microscope. In contrast to r-space correlation techniques, we show kICS can recover accurate dynamics even in the presence of complex fluorophore photobleaching and/or “blinking”. Furthermore, these quantities can be calculated without nonlinear curve fitting, or any knowledge of the beam radius of the exciting laser. The number densities calculated by kICS are less sensitive to spatial inhomogeneity of the fluorophore distribution than densities measured using image correlation spectroscopy. We use simulations as a proof-of-principle to show that number densities and transport coefficients can be extracted using this technique. We present calibration measurements with fluorescent microspheres imaged on a confocal microscope, which recover Stokes-Einstein diffusion coefficients, and flow velocities that agree with single particle tracking measurements. We also show the application of kICS to measurements of the transport dynamics of α5-integrin/enhanced green fluorescent protein constructs in a transfected CHO cell imaged on a total internal reflection fluorescence microscope using charge-coupled device area detection. PMID:16861272

Brief Report: An Independent Replication and Extension of Psychometric Evidence Supporting the Theory of Mind Inventory.

PubMed

Greenslade, Kathryn J; Coggins, Truman E

2016-08-01

This study presents an independent replication and extension of psychometric evidence supporting the Theory of Mind Inventory (ToMI). Parents of 20 children with ASD (4; 1-6; 7 years; months) and 20 with typical development (3; 1-6; 5), rated their child's theory of mind abilities in everyday situations. Other parent report and child behavioral assessments included the Social Responsiveness Scale-2, Vineland Adaptive Behavior Scales-2, Peabody Picture Vocabulary Test-4, and Clinical Evaluation of Language Fundamentals-Preschool, 2. Results revealed high internal consistency, expected developmental changes in children with typical development, expected group differences between children with and without ASD, and strong correlations with other measures of social and communication abilities. The ToMI demonstrates strong psychometrics, suggesting considerable utility in identifying theory of mind deficits in children with ASD.

The Audio-Visual Marketing Handbook for Independent Schools.

ERIC Educational Resources Information Center

Griffith, Tom

This how-to booklet offers specific advice on producing video or slide/tape programs for marketing independent schools. Five chapters present guidelines for various stages in the process: (1) Audio-Visual Marketing in Context (aesthetics and economics of audiovisual marketing); (2) A Question of Identity (identifying the audience and deciding on…

Independent School Leadership: Heads, Boards, and Strategic Thinking

ERIC Educational Resources Information Center

Baker, Troy; Campbell, Stephen; Ostroff, David

2016-01-01

This study seeks to identify and assess factors that contribute to effective independent school governance at the board of trustees level. A review of extant literature reveals two major challenges: (a) definitions and standards of board effectiveness are inconsistent, and (b) there is very little empirical evidence to support existing definitions…

Genome-wide screen identifies a novel prognostic signature for breast cancer survival

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

Mao, Xuan Y.; Lee, Matthew J.; Zhu, Jeffrey

Large genomic datasets in combination with clinical data can be used as an unbiased tool to identify genes important in patient survival and discover potential therapeutic targets. We used a genome-wide screen to identify 587 genes significantly and robustly deregulated across four independent breast cancer (BC) datasets compared to normal breast tissue. Gene expression of 381 genes was significantly associated with relapse-free survival (RFS) in BC patients. We used a gene co-expression network approach to visualize the genetic architecture in normal breast and BCs. In normal breast tissue, co-expression cliques were identified enriched for cell cycle, gene transcription, cell adhesion,more » cytoskeletal organization and metabolism. In contrast, in BC, only two major co-expression cliques were identified enriched for cell cycle-related processes or blood vessel development, cell adhesion and mammary gland development processes. Interestingly, gene expression levels of 7 genes were found to be negatively correlated with many cell cycle related genes, highlighting these genes as potential tumor suppressors and novel therapeutic targets. A forward-conditional Cox regression analysis was used to identify a 12-gene signature associated with RFS. A prognostic scoring system was created based on the 12-gene signature. This scoring system robustly predicted BC patient RFS in 60 sampling test sets and was further validated in TCGA and METABRIC BC data. Our integrated study identified a 12-gene prognostic signature that could guide adjuvant therapy for BC patients and includes novel potential molecular targets for therapy.« less

Genome-wide screen identifies a novel prognostic signature for breast cancer survival

DOE PAGES

Mao, Xuan Y.; Lee, Matthew J.; Zhu, Jeffrey; ...

2017-01-21

Large genomic datasets in combination with clinical data can be used as an unbiased tool to identify genes important in patient survival and discover potential therapeutic targets. We used a genome-wide screen to identify 587 genes significantly and robustly deregulated across four independent breast cancer (BC) datasets compared to normal breast tissue. Gene expression of 381 genes was significantly associated with relapse-free survival (RFS) in BC patients. We used a gene co-expression network approach to visualize the genetic architecture in normal breast and BCs. In normal breast tissue, co-expression cliques were identified enriched for cell cycle, gene transcription, cell adhesion,more » cytoskeletal organization and metabolism. In contrast, in BC, only two major co-expression cliques were identified enriched for cell cycle-related processes or blood vessel development, cell adhesion and mammary gland development processes. Interestingly, gene expression levels of 7 genes were found to be negatively correlated with many cell cycle related genes, highlighting these genes as potential tumor suppressors and novel therapeutic targets. A forward-conditional Cox regression analysis was used to identify a 12-gene signature associated with RFS. A prognostic scoring system was created based on the 12-gene signature. This scoring system robustly predicted BC patient RFS in 60 sampling test sets and was further validated in TCGA and METABRIC BC data. Our integrated study identified a 12-gene prognostic signature that could guide adjuvant therapy for BC patients and includes novel potential molecular targets for therapy.« less

Decay of random correlation functions for unimodal maps

NASA Astrophysics Data System (ADS)

Baladi, Viviane; Benedicks, Michael; Maume-Deschamps, Véronique

2000-10-01

Since the pioneering results of Jakobson and subsequent work by Benedicks-Carleson and others, it is known that quadratic maps tfa( χ) = a - χ2 admit a unique absolutely continuous invariant measure for a positive measure set of parameters a. For topologically mixing tfa, Young and Keller-Nowicki independently proved exponential decay of correlation functions for this a.c.i.m. and smooth observables. We consider random compositions of small perturbations tf + ωt, with tf = tfa or another unimodal map satisfying certain nonuniform hyperbolicity axioms, and ωt chosen independently and identically in [-ɛ, ɛ]. Baladi-Viana showed exponential mixing of the associated Markov chain, i.e., averaging over all random itineraries. We obtain stretched exponential bounds for the random correlation functions of Lipschitz observables for the sample measure μωof almost every itinerary.

Elevated serum progastrin-releasing peptide (31-98) in metastatic and androgen-independent prostate cancer patients.

PubMed

Yashi, Masahiro; Muraishi, Osamu; Kobayashi, Yutaka; Tokue, Akihiko; Nanjo, Hiroshi

2002-05-01

Increases in neuroendocrine phenotype and secretory products are closely correlated with tumor progression and androgen independence in prostate cancer. In this study, we explored this correlation using serum progastrin-releasing peptide (ProGRP), a carboxy-terminal region common to three subtypes of precursors for gastrin-releasing peptide (GRP), which is released from the neuroendocrine phenotype to act as a growth factor. In 60 patients with benign prostatic hyperplasia (BPH) and 200 with prostate cancer, serum ProGRP levels were determined with an enzyme-linked immunosorbent assay (ELISA) kit and evaluated in relation to clinical stage, hormonal treatment, and prostate-specific antigen (PSA) values. Fourteen randomly selected patients were entered in the follow-up study. Additionally, expression of ProGRP as determined by immunohistochemical analysis was compared to that of chromogranin-A (CgA) in tissue samples from several subjects. We found a positive correlation between PSA and ProGRP in patients with untreated prostate cancer; no correlation was found in the treated groups. The increases in the ProGRP value and in the percentage of patients with higher than normal values were significant (P < 0.0001), especially in the androgen-independent group (P < 0.0001). A longitudinal study showed that, in a subset of patients, the ProGRP values tended to increase transiently when the cancer became androgen independent, but remained unchanged or decreased at the androgen-dependent stage. Positive staining for ProGRP occurred in a different distribution in neuroendocrine tissues than that of staining for CgA. The clinical results demonstrated the existence of a regulatory mechanism for GRP, which to date had only been observed in cell lines. These findings suggest that GRP is a growth factor potentially upregulated by androgen but that does not rely principally on androgen modulation. The large overlap in levels of ProGRP among the groups limits the use of this value

Functional mental capacity is not independent of the severity of psychosis.

PubMed

Rutledge, Emer; Kennedy, Miriam; O'Neill, Helen; Kennedy, Harry G

2008-01-01

Function-specific mental capacities are the legal criteria for competence. These are regarded as superior to clinical assessments of mental state and general function. To determine whether tests of fitness to plead and capacity to consent are independent of each other and independent of mental state and global function in psychosis. The MacCAT-T and MacCAT-FP, PANSS and GAF were administered to 102 compulsorily detained forensic patients with psychosis. Criteria for incompetence were inability to express a preference concerning treatment, and independent rating as unfit to plead. MacCAT-T, MacCAT-FP totals and sub-scales correlated with each other and with PANSS and GAF. Those independently rated unfit to plead or who were incapable of making a treatment choice scored significantly worse on all rating scales. No test had satisfactory sensitivity or specificity. Legal definitions of mind and of functional capacity offer a basis for structured clinical judgement regarding decision-making capacity. However, function-specific measures of understanding, reasoning and appreciation generate much the same results as measures of mental state and global functioning.

Cthrc1 overexpression is an independent prognostic marker in gastric cancer.

PubMed

Gu, Lina; Liu, Lei; Zhong, Lili; Bai, Yuxian; Sui, Hong; Wei, Xiaoli; Zhang, Wenjie; Huang, Peng; Gao, Dandan; Kong, Ying; Lou, Ge

2014-05-01

Collagen triple helix repeat containing 1 (CTHRC1) was identified as a novel gene expressed in the adventitia and neointima on arterial injury and was found to be overexpressed in several malignant tumors, such as breast cancer and malignant melanoma. However, the expression of Cthrc1 and its role in gastric cancer progression remain unknown. We investigated the expression of the Cthrc1 protein by immunohistochemistry in 30 normal tissues from the control subjects and 166 gastric carcinomas and analyzed its correlation with various clinicopathological features, including patient outcome. Cthrc1 immunoreactivity was overexpressed in gastric carcinoma cases compared with normal tissues (P < .001). High Cthrc1 expression was found in 108 (65.06%) of these 166 carcinomas and was positively correlated with the American Joint Committee on Cancer stage classification, depth of gastric wall invasion, lymph node metastasis, lymphovascular space involvement, and recurrence but not with age, tumor site, and carcinoembryonic antigen level. Patients with high Cthrc1 expression had significantly poorer overall survival and disease-free survival compared with patients with low expression of Cthrc1 (P = .001 and P = .002, respectively). Multivariate analysis showed that high Cthrc1 expression was an independent prognostic factor for both overall survival and disease-free survival of patients with gastric carcinoma (both P = .005). These results showed that high Cthrc1 expression was associated with progression and prognosis of gastric carcinoma. Copyright © 2014 Elsevier Inc. All rights reserved.

Recent mathematical developments in 2D correlation spectroscopy

NASA Astrophysics Data System (ADS)

Noda, I.

2000-03-01

Recent mathematical developments in the field of 2D correlation spectroscopy, especially those related to the statistical theory, are reported. The notion of correlation phase angle is introduced. The significance of correlation phase angle between dynamic fluctuations of signals measured at two different spectral variables may be linked to more commonly known statistical concepts, such as coherence and correlation coefficient. This treatment provides the direct mathematical connection between the synchronous 2D correlation spectrum with a continuous form of the variance-covariance matrix. Moreover, it gives the background for the formal definition of the disrelation spectrum, which may be used as a heuristic substitution for the asynchronous 2D spectrum. The 2D correlation intensity may be separated into two independent factors representing the normalized extent of signal fluctuation coherence (i.e., correlation coefficient) and the magnitude of spectral intensity changes (i.e., variance). Such separation offers a convenient way to artificially enhance the discriminating power of 2D correlation spectra.

Origins of correlated activity in an olfactory circuit.

PubMed

Kazama, Hokto; Wilson, Rachel I

2009-09-01

Multineuronal recordings often reveal synchronized spikes in different neurons. The manner in which correlated spike timing affects neural codes depends on the statistics of correlations, which in turn reflects the connectivity that gives rise to correlations. However, determining the connectivity of neurons recorded in vivo can be difficult. We investigated the origins of correlated activity in genetically labeled neurons of the Drosophila antennal lobe. Dual recordings showed synchronized spontaneous spikes in projection neurons (PNs) postsynaptic to the same type of olfactory receptor neuron (ORN). Odors increased these correlations. The primary origin of correlations lies in the divergence of each ORN onto every PN in its glomerulus. Reciprocal PN-PN connections make a smaller contribution to correlations and PN spike trains in different glomeruli were only weakly correlated. PN axons from the same glomerulus reconverge in the lateral horn, where pooling redundant signals may allow lateral horn neurons to average out noise that arises independently in these PNs.

Radiogenomics analysis identifies correlations of digital mammography with clinical molecular signatures in breast cancer

PubMed Central

Tamez-Peña, Jose-Gerardo; Rodriguez-Rojas, Juan-Andrés; Gomez-Rueda, Hugo; Celaya-Padilla, Jose-Maria; Rivera-Prieto, Roxana-Alicia; Palacios-Corona, Rebeca; Garza-Montemayor, Margarita; Cardona-Huerta, Servando

2018-01-01

In breast cancer, well-known gene expression subtypes have been related to a specific clinical outcome. However, their impact on the breast tissue phenotype has been poorly studied. Here, we investigate the association of imaging data of tumors to gene expression signatures from 71 patients with breast cancer that underwent pre-treatment digital mammograms and tumor biopsies. From digital mammograms, a semi-automated radiogenomics analysis generated 1,078 features describing the shape, signal distribution, and texture of tumors along their contralateral image used as control. From tumor biopsy, we estimated the OncotypeDX and PAM50 recurrence scores using gene expression microarrays. Then, we used multivariate analysis under stringent cross-validation to train models predicting recurrence scores. Few univariate features reached Spearman correlation coefficients above 0.4. Nevertheless, multivariate analysis yielded significantly correlated models for both signatures (correlation of OncotypeDX = 0.49 ± 0.07 and PAM50 = 0.32 ± 0.10 in stringent cross-validation and OncotypeDX = 0.83 and PAM50 = 0.78 for a unique model). Equivalent models trained from the unaffected contralateral breast were not correlated suggesting that the image signatures were tumor-specific and that overfitting was not a considerable issue. We also noted that models were improved by combining clinical information (triple negative status and progesterone receptor). The models used mostly wavelets and fractal features suggesting their importance to capture tumor information. Our results suggest that molecular-based recurrence risk and breast cancer subtypes have observable radiographic phenotypes. To our knowledge, this is the first study associating mammographic information to gene expression recurrence signatures. PMID:29596496

Parcellating an Individual Subject's Cortical and Subcortical Brain Structures Using Snowball Sampling of Resting-State Correlations

PubMed Central

Wig, Gagan S.; Laumann, Timothy O.; Cohen, Alexander L.; Power, Jonathan D.; Nelson, Steven M.; Glasser, Matthew F.; Miezin, Francis M.; Snyder, Abraham Z.; Schlaggar, Bradley L.; Petersen, Steven E.

2014-01-01

We describe methods for parcellating an individual subject's cortical and subcortical brain structures using resting-state functional correlations (RSFCs). Inspired by approaches from social network analysis, we first describe the application of snowball sampling on RSFC data (RSFC-Snowballing) to identify the centers of cortical areas, subdivisions of subcortical nuclei, and the cerebellum. RSFC-Snowballing parcellation is then compared with parcellation derived from identifying locations where RSFC maps exhibit abrupt transitions (RSFC-Boundary Mapping). RSFC-Snowballing and RSFC-Boundary Mapping largely complement one another, but also provide unique parcellation information; together, the methods identify independent entities with distinct functional correlations across many cortical and subcortical locations in the brain. RSFC parcellation is relatively reliable within a subject scanned across multiple days, and while the locations of many area centers and boundaries appear to exhibit considerable overlap across subjects, there is also cross-subject variability—reinforcing the motivation to parcellate brains at the level of individuals. Finally, examination of a large meta-analysis of task-evoked functional magnetic resonance imaging data reveals that area centers defined by task-evoked activity exhibit correspondence with area centers defined by RSFC-Snowballing. This observation provides important evidence for the ability of RSFC to parcellate broad expanses of an individual's brain into functionally meaningful units. PMID:23476025

Loss of cell invasiveness through PKC-mediated syndecan-1 downregulation in melanoma cells under anchorage independency.

PubMed

Wang, ChiaChen; Tseng, TingTing; Jhang, Yaoyun; Tseng, JenChih; Hsieh, ChiaoHui; Wu, Wen-guey; Lee, ShaoChen

2014-11-01

Anchorage-independent survival is one of the key features for malignant tumor cells. Whether specific gene alterations contributed by anchorage independency would further affect metastatic phenotypes of melanoma cells was unclear. We adapted suspension culture of melanoma cells to establish anchorage independency. The suspended melanoma cells lost their invasive abilities in vitro. Specific loss of laminin-binding ability in suspended melanoma cells was observed, which was correlated with downregulation of syndecan-1 as revealed by microarray and validated by qPCR and Western blot. Modulation of syndecan-1 expression level affected laminin binding, transwell migration and matrix metalloproteinase-2 secretion in melanoma cells. SDC1 expression and transwell migration were correlated with activity or level of protein kinase Cδ as evidence by specific inhibitors and shRNA transfection. In this study, we compared metastatic phenotypes and gene expressions of adherent and suspended melanoma cells. The anchorage independency led to protein kinase Cδ-mediated syndecan-1 downregulation, which contributed to loss of laminin-binding ability, reduced metalloproteinase-2 secretion and loss of invasiveness. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Field dependence-independence as related to young women's participation in sports activity.

PubMed

Lambrecht, Jeanne L; Cuevas, Jacqueline L

2007-06-01

To estimate association between field dependence-independence measured by scores on the Group Embedded Figures Test and young women's participation in sports activity. Participants were 37 undergraduate college women between the ages of 18 and 25 years (M=21). Participants were categorized into two groups, one high in participation in sports activity and one low. A one-tailed independent samples t test yielded no significant difference. Correlations of .36 and .18 were significant but account for little common variance. An ad hoc analysis performed without participants who reported softball activity but who were highly involved in sport activities was significant.

Microbial composition during Chinese soy sauce koji-making based on culture dependent and independent methods.

PubMed

Yan, Yin-zhuo; Qian, Yu-lin; Ji, Feng-di; Chen, Jing-yu; Han, Bei-zhong

2013-05-01

Koji-making is a key process for production of high quality soy sauce. The microbial composition during koji-making was investigated by culture-dependent and culture-independent methods to determine predominant bacterial and fungal populations. The culture-dependent methods used were direct culture and colony morphology observation, and PCR amplification of 16S/26S rDNA fragments followed by sequencing analysis. The culture-independent method was based on the analysis of 16S/26S rDNA clone libraries. There were differences between the results obtained by different methods. However, sufficient overlap existed between the different methods to identify potentially significant microbial groups. 16 and 20 different bacterial species were identified using culture-dependent and culture-independent methods, respectively. 7 species could be identified by both methods. The most predominant bacterial genera were Weissella and Staphylococcus. Both 6 different fungal species were identified using culture-dependent and culture-independent methods, respectively. Only 3 species could be identified by both sets of methods. The most predominant fungi were Aspergillus and Candida species. This work illustrated the importance of a comprehensive polyphasic approach in the analysis of microbial composition during soy sauce koji-making, the knowledge of which will enable further optimization of microbial composition and quality control of koji to upgrade Chinese traditional soy sauce product. Copyright © 2013 Elsevier Ltd. All rights reserved.

Individual, network, and neighborhood correlates of exchange sex among female non-injection drug users in Baltimore, MD (2005–2007)

PubMed Central

Rudolph, Abby E; Linton, Sabriya; Dyer, Typhanye Penniman; Latkin, Carl

2012-01-01

The “HIV risk environment” has been characterized as a dynamic interplay between structural and network factors. However, most HIV prevention research has not examined the independent and combined impact of network and structural factors. We aimed to identify individual, network, and neighborhood correlates of exchange sex (≥1 exchange sex partner, past 90 days) among female non-injection drug users (NIDUs). We used baseline data from 417 NIDUs enrolled in a randomized HIV prevention trial in Baltimore (2005–2007). Surveys ascertained demographic variables, drug/sex risk behaviors, neighborhood perceptions, and social/sexual network characteristics. Correlates of exchange sex were identified with descriptive statistics and log-binomial regression. Our findings suggest that sex and drug relationships among female NIDUs are interlinked and may be difficult to modify without altering social norms. Strengthening ties that provide social support but not drug support and reducing ties that provide both drug and social support may facilitate reductions in individual-level HIV-risk behaviors. PMID:22983502

Identifying tectonic parameters that affect tsunamigenesis

NASA Astrophysics Data System (ADS)

van Zelst, I.; Brizzi, S.; Heuret, A.; Funiciello, F.; van Dinther, Y.

2016-12-01

The role of tectonics in tsunami generation is at present poorly understood. However, the fact thatsome regions produce more tsunamis than others indicates that tectonics could influencetsunamigenesis. Here, we complement a global earthquake database that contains geometrical,mechanical, and seismicity parameters of subduction zones with tsunami data. We statisticallyanalyse the database to identify the tectonic parameters that affect tsunamigenesis. The Pearson'sproduct-moment correlation coefficients reveal high positive correlations of 0.65 between,amongst others, the maximum water height of tsunamis and the seismic coupling in a subductionzone. However, these correlations are mainly caused by outliers. The Spearman's rank correlationcoefficient results in statistically significant correlations of 0.60 between the number of tsunamisin a subduction zone and subduction velocity (positive correlation) and the sediment thickness atthe trench (negative correlation). Interestingly, there is a positive correlation between the latter andtsunami magnitude. These bivariate statistical methods are extended to a binary decision tree(BDT) and multivariate analysis. Using the BDT, the tectonic parameters that distinguish betweensubduction zones with tsunamigenic and non-tsunamigenic earthquakes are identified. To assessphysical causality of the tectonic parameters with regard to tsunamigenesis, we complement ouranalysis by a numerical study of the most promising parameters using a geodynamic seismic cyclemodel. We show that the inclusion of sediments on the subducting plate results in an increase insplay fault activity, which could lead to larger vertical seafloor displacements due to their steeperdips and hence a larger tsunamigenic potential. We also show that the splay fault is the preferredrupture path for a strongly velocity strengthening friction regime in the shallow part of thesubduction zone, which again increases the tsunamigenic potential.

Correlates of sedentary time in different age groups: results from a large cross sectional Dutch survey.

PubMed

Bernaards, Claire M; Hildebrandt, Vincent H; Hendriksen, Ingrid J M

2016-10-26

Evidence shows that prolonged sitting is associated with an increased risk of mortality, independent of physical activity (PA). The aim of the study was to identify correlates of sedentary time (ST) in different age groups and day types (i.e. school-/work day versus non-school-/non-work day). The study sample consisted of 1895 Dutch children (4-11 years), 1131 adolescents (12-17 years), 8003 adults (18-64 years) and 1569 elderly (65 years and older) who enrolled in the Dutch continuous national survey 'Injuries and Physical Activity in the Netherlands' between 2006 and 2011. Respondents estimated the number of sitting hours during a regular school-/workday and a regular non-school/non-work day. Multiple linear regression analyses on cross-sectional data were used to identify correlates of ST. Significant positive associations with ST were observed for: higher age (4-to-17-year-olds and elderly), male gender (adults), overweight (children), higher education (adults ≥ 30 years), urban environment (adults), chronic disease (adults ≥ 30 years), sedentary work (adults), not meeting the moderate to vigorous PA (MVPA) guideline (children and adults ≥ 30 years) and not meeting the vigorous PA (VPA) guideline (4-to-17-year-olds). Correlates of ST that significantly differed between day types were working hours and meeting the VPA guideline. More working hours were associated with more ST on school-/work days. In children and adolescents, meeting the VPA guideline was associated with less ST on non-school/non-working days only. This study provides new insights in the correlates of ST in different age groups and thus possibilities for interventions in these groups. Correlates of ST appear to differ between age groups and to a lesser degree between day types. This implies that interventions to reduce ST should be age specific. Longitudinal studies are needed to draw conclusions on causality of the relationship between identified correlates and ST.

Identifying prognostic signature in ovarian cancer using DirGenerank

PubMed Central

Wang, Jian-Yong; Chen, Ling-Ling; Zhou, Xiong-Hui

2017-01-01

Identifying the prognostic genes in cancer is essential not only for the treatment of cancer patients, but also for drug discovery. However, it's still a big challenge to select the prognostic genes that can distinguish the risk of cancer patients across various data sets because of tumor heterogeneity. In this situation, the selected genes whose expression levels are statistically related to prognostic risks may be passengers. In this paper, based on gene expression data and prognostic data of ovarian cancer patients, we used conditional mutual information to construct gene dependency network in which the nodes (genes) with more out-degrees have more chances to be the modulators of cancer prognosis. After that, we proposed DirGenerank (Generank in direct netowrk) algorithm, which concerns both the gene dependency network and genes’ correlations to prognostic risks, to identify the gene signature that can predict the prognostic risks of ovarian cancer patients. Using ovarian cancer data set from TCGA (The Cancer Genome Atlas) as training data set, 40 genes with the highest importance were selected as prognostic signature. Survival analysis of these patients divided by the prognostic signature in testing data set and four independent data sets showed the signature can distinguish the prognostic risks of cancer patients significantly. Enrichment analysis of the signature with curated cancer genes and the drugs selected by CMAP showed the genes in the signature may be drug targets for therapy. In summary, we have proposed a useful pipeline to identify prognostic genes of cancer patients. PMID:28615526

Independent Demographic Responses to Climate Change among Temperate and Tropical Milksnakes (Colubridae: Genus Lampropeltis)

PubMed Central

Ruane, Sara; Torres-Carvajal, Omar; Burbrink, Frank T.

2015-01-01

The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as coalescent-based methods. In addition, we determine whether range sizes are correlated with effective population sizes for milksnakes. Results indicate that there are no identifiable trends with respect to demographic response based on location, and that species responded to changing climates independently, with tropical taxa showing greater instability. There is also no correlation between range size and effective population size, with the largest population size belonging to the species with the smallest geographic distribution. Our study highlights the importance of not generalizing the demographic histories of taxa by region and further illustrates that the New World tropics may not have been a stable refuge during the Pleistocene. PMID:26083467

Independent Demographic Responses to Climate Change among Temperate and Tropical Milksnakes (Colubridae: Genus Lampropeltis).

PubMed

Ruane, Sara; Torres-Carvajal, Omar; Burbrink, Frank T

2015-01-01

The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as coalescent-based methods. In addition, we determine whether range sizes are correlated with effective population sizes for milksnakes. Results indicate that there are no identifiable trends with respect to demographic response based on location, and that species responded to changing climates independently, with tropical taxa showing greater instability. There is also no correlation between range size and effective population size, with the largest population size belonging to the species with the smallest geographic distribution. Our study highlights the importance of not generalizing the demographic histories of taxa by region and further illustrates that the New World tropics may not have been a stable refuge during the Pleistocene.

Correlates of individual, and age-related, differences in short-term learning.

PubMed

Zhang, Zhiyong; Davis, Hasker P; Salthouse, Timothy A; Tucker-Drob, Elliot M

2007-07-01

Latent growth models were applied to data on multitrial verbal and spatial learning tasks from two independent studies. Although significant individual differences in both initial level of performance and subsequent learning were found in both tasks, age differences were found only in mean initial level, and not in mean learning. In neither task was fluid or crystallized intelligence associated with learning. Although there were moderate correlations among the level parameters across the verbal and spatial tasks, the learning parameters were not significantly correlated with one another across task modalities. These results are inconsistent with the existence of a general (e.g., material-independent) learning ability.

Evidence supporting oral sensitivity to complex carbohydrates independent of sweet taste sensitivity in humans.

PubMed

Low, Julia Y Q; Lacy, Kathleen E; McBride, Robert L; Keast, Russell S J

2017-01-01

Compared to simple sugars, complex carbohydrates have been assumed invisible to taste. However, two recent studies proposed that there may be a perceivable taste quality elicited by complex carbohydrates independent of sweet taste. There is precedent with behavioural studies demonstrating that rats are very attracted to complex carbohydrates, and that complex carbohydrates are preferred to simple sugars at low concentrations. This suggests that rats may have independent taste sensors for simple sugars and complex carbohydrates. The aim of this paper is to investigate oral sensitivities of two different classes of complex carbohydrates (a soluble digestible and a soluble non-digestible complex carbohydrate), and to compare these to other caloric and non-nutritive sweeteners in addition to the prototypical tastes using two commonly used psychophysical measures. There were strong correlations between the detection thresholds and mean intensity ratings for complex carbohydrates (maltodextrin, oligofructose) (r = 0.94, P < 0.001). There were no significant correlations between the detection thresholds of the complex carbohydrates (maltodextrin, oligofructose) and the sweeteners (glucose, fructose, sucralose, Rebaudioside A, erythritol) (all P > 0.05). However, moderate correlations were observed between perceived intensities of complex carbohydrates and sweeteners (r = 0.48-0.61, P < 0.05). These data provide evidence that complex carbohydrates can be sensed in the oral cavity over a range of concentrations independent of sweet taste sensitivity at low concentrations, but with partial overlap with sweet taste intensity at higher concentrations.

Evidence supporting oral sensitivity to complex carbohydrates independent of sweet taste sensitivity in humans

PubMed Central

Lacy, Kathleen E.; Keast, Russell S. J.

2017-01-01

Compared to simple sugars, complex carbohydrates have been assumed invisible to taste. However, two recent studies proposed that there may be a perceivable taste quality elicited by complex carbohydrates independent of sweet taste. There is precedent with behavioural studies demonstrating that rats are very attracted to complex carbohydrates, and that complex carbohydrates are preferred to simple sugars at low concentrations. This suggests that rats may have independent taste sensors for simple sugars and complex carbohydrates. The aim of this paper is to investigate oral sensitivities of two different classes of complex carbohydrates (a soluble digestible and a soluble non-digestible complex carbohydrate), and to compare these to other caloric and non-nutritive sweeteners in addition to the prototypical tastes using two commonly used psychophysical measures. There were strong correlations between the detection thresholds and mean intensity ratings for complex carbohydrates (maltodextrin, oligofructose) (r = 0.94, P < 0.001). There were no significant correlations between the detection thresholds of the complex carbohydrates (maltodextrin, oligofructose) and the sweeteners (glucose, fructose, sucralose, Rebaudioside A, erythritol) (all P > 0.05). However, moderate correlations were observed between perceived intensities of complex carbohydrates and sweeteners (r = 0.48–0.61, P < 0.05). These data provide evidence that complex carbohydrates can be sensed in the oral cavity over a range of concentrations independent of sweet taste sensitivity at low concentrations, but with partial overlap with sweet taste intensity at higher concentrations. PMID:29281655

The relationship of community activities with cognitive impairment and depressive mood independent of mobility disorder in Japanese older adults.

PubMed

Okura, Mika; Ogita, Mihoko; Yamamoto, Miki; Nakai, Toshimi; Numata, Tomoko; Arai, Hidenori

This study aimed to examine the relationship of participating in community activities (CA) with cognitive impairment and depressive mood independent of mobility disorder (MD) among older Japanese people. Elderly residents in institutions or those requiring long-term care insurance services were excluded; questionnaires were mailed to 5401 older adults in 2013. The response rate was 94.3% (n=5094). We used multiple imputation to manage missing data. The questionnaire addressed physical fitness, memory, mood, and CA. Participants were divided into two groups (good and bad) based on the median scores for physical fitness, memory, and mood. We identified items related to periodically performed CA, cognitive impairment, and depressive mood, and examined correlations between scores on these sets of items. The mean age was 75.9 years; 58.4% of participants were women. The following CA significantly predicted reduced cognitive impairment and depressive mood independent of MD: volunteer activity, community activity, visiting friends at home, pursuing hobbies, paid work, farm work, and daily shopping. These results were corrected for age, sex, and response method (mail or home-visit). Higher CA scores were associated with lower cognitive impairment and lower depressive mood independent of MD. CA is negatively associated with cognitive impairment and depressive mood among community-dwelling elderly independent of MD; promoting CA may protect against cognitive impairment and depressive mood in this population. However, MD, cognitive impairment, and depressive mood may lead to reduced CA. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Making and Executing Decisions for Safe and Independent Living (MED-SAIL): development and validation of a brief screening tool.

PubMed

Mills, Whitney L; Regev, Tziona; Kunik, Mark E; Wilson, Nancy L; Moye, Jennifer; McCullough, Laurence B; Naik, Aanand D

2014-03-01

Older adults prefer to remain in their own homes for as long as possible. The purpose of this article is to describe the development and preliminary validation of Making and Executing Decisions for Safe and Independent Living (MED-SAIL), a brief screening tool for capacity to live safely and independently in the community. Prospective preliminary validation study. Outpatient geriatrics clinic located in a community-based hospital. Forty-nine community-dwelling older adults referred to the clinic for a comprehensive capacity assessment. We examined internal consistency, criterion-based validity, concurrent validity, and accuracy of classification for MED-SAIL. The items included in MED-SAIL demonstrated internal consistency (5 items; α = 0.85). MED-SAIL was significantly correlated with the Independent Living Scales (r = 0.573, p ≤0.001) and instrumental activities of daily living (r = 0.440, p ≤0.01). The Mann-Whitney U test revealed significant differences between the no capacity and partial/full capacity classifications on MED-SAIL (U(48) = 60.5, Z = -0.38, p <0.0001). The area under the curve was 0.864 (95% confidence interval: 0.84-0.99). This study demonstrated the validity of MED-SAIL as a brief screening tool to identify older adults with impaired capacity for remaining safe and independent in their current living environment. MED-SAIL is useful tool for health and social service providers in the community for the purpose of referral for definitive capacity evaluation. Published by Elsevier Inc.

Sensorimotor and neuropsychological correlates of force perturbations that induce stepping in older adults.

PubMed

Sturnieks, Daina L; Menant, Jasmine; Vanrenterghem, Jos; Delbaere, Kim; Fitzpatrick, Richard C; Lord, Stephen R

2012-07-01

Inappropriate stepping in response to unexpected balance perturbations is more prevalent in older people and in those at risk of falling. This study examined responses to force-controlled waist pulls in young and older people, and sought to identify physiological and cognitive correlates of the force threshold for stepping. 242 older (79.7±4.2 years) and 15 young (29.5±5.3 years) adults underwent waist pull perturbations and assessments of physiological and neuropsychological functioning, general health and falls efficacy. Perturbation force that induced stepping, stepping strategy and number of steps were measured. The older group withstood less forceful perturbations with a feet-in-place strategy, compared to young. Likewise, older adults with high falls risk withstood less force than those with low risk. After controlling for body weight and gender, sway and lower limb strength were independent predictors of anterior stepping thresholds, reaction time was an independent predictor of posterior thresholds, and executive functioning and lower limb strength were independent predictors of the lateral thresholds. These results suggest that balance, strength and agility training, in addition to cognitive exercises may enhance the ability to withstand unexpected balance perturbations and reduce the risk of falls in older people. Copyright © 2012 Elsevier B.V. All rights reserved.

A scoping review of anorexia of aging correlates and their relevance to population health interventions.

PubMed

Roy, Mathieu; Gaudreau, Pierrette; Payette, Hélène

2016-10-01

Anorexia of aging (AA, i.e., loss of appetite and/or reduction of food intake with aging) is an important public health issue. It leads to unintentional weight loss, which is an independent risk factor for morbidity and mortality among seniors. AA has mainly been studied from a biological perspective and regarded as a normal physiological consequence of aging, rather than a negative health outcome with underlying determinants. Some potentially modifiable correlates have however been found to be associated with this geriatric condition. Here, we conducted a scoping review of the literature to: 1) identify AA correlates, and 2) discuss their relevance to population health interventions. Our results indicate two main categories of AA correlates, namely, physiopathological and non-physiopathological. The first category relates to physiological dysfunctions, pathologies involving (or culminating in) biomarker dysregulation, and polypharmacy. These correlates are difficult to modify, especially through population health interventions. The second category, which contains fewer correlates, includes potentially modifiable public health targets, such as food-related properties, psychological, sociocultural, and environmental issues. We conclude that there are several AA correlates. Some of them are modifiable and could be targeted for development and implementation as appropriate population health interventions to prevent appetite loss and promote maintenance of adequate food intake in aging. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantifying colocalization by correlation: the Pearson correlation coefficient is superior to the Mander's overlap coefficient.

PubMed

Adler, Jeremy; Parmryd, Ingela

2010-08-01

The Pearson correlation coefficient (PCC) and the Mander's overlap coefficient (MOC) are used to quantify the degree of colocalization between fluorophores. The MOC was introduced to overcome perceived problems with the PCC. The two coefficients are mathematically similar, differing in the use of either the absolute intensities (MOC) or of the deviation from the mean (PCC). A range of correlated datasets, which extend to the limits of the PCC, only evoked a limited response from the MOC. The PCC is unaffected by changes to the offset while the MOC increases when the offset is positive. Both coefficients are independent of gain. The MOC is a confusing hybrid measurement, that combines correlation with a heavily weighted form of co-occurrence, favors high intensity combinations, downplays combinations in which either or both intensities are low and ignores blank pixels. The PCC only measures correlation. A surprising finding was that the addition of a second uncorrelated population can substantially increase the measured correlation, demonstrating the importance of excluding background pixels. Overall, since the MOC is unresponsive to substantial changes in the data and is hard to interpret, it is neither an alternative to nor a useful substitute for the PCC. The MOC is not suitable for making measurements of colocalization either by correlation or co-occurrence.

Plasma kisspeptin and ghrelin levels are independently correlated with physical activity in patients with anorexia nervosa.

PubMed

Hofmann, Tobias; Elbelt, Ulf; Haas, Verena; Ahnis, Anne; Klapp, Burghard F; Rose, Matthias; Stengel, Andreas

2017-01-01

While physical hyperactivity represents a frequent symptom of anorexia nervosa and may have a deleterious impact on the course of the disease, the underlying mechanisms are poorly understood. Since several food intake-regulatory hormones affect physical activity, the aim of the study was to investigate the association of physical activity with novel candidate hormones (kisspeptin, ghrelin, oxyntomodulin, orexin-A, FGF-21, R-spondin-1) possibly involved in patients with anorexia nervosa. Associations with psychometric parameters and body composition were also assessed. We included 38 female anorexia nervosa inpatients (body mass index, BMI, mean ± SD: 14.8 ± 1.7 kg/m 2 ). Physical activity was evaluated using portable armband devices, body composition by bioelectrical impedance analysis. Blood withdrawal (hormones measured by ELISA) and psychometric assessment of depressiveness (PHQ-9), anxiety (GAD-7), perceived stress (PSQ-20) and disordered eating (EDI-2) were performed at the same time. Patients displayed a broad spectrum of physical activity (2479-26,047 steps/day) which showed a negative correlation with kisspeptin (r = -0.41, p = 0.01) and a positive association with ghrelin (r = 0.42, p = 0.01). The negative correlation with oxyntomodulin (r = -0.37, p = 0.03) was lost after consideration of potential confounders by regression analysis. No correlations were observed between physical activity and orexin-A, FGF-21 and R-spondin-1 (p > 0.05). Kisspeptin was positively correlated with BMI and body fat mass and negatively associated with the interpersonal distrust subscale of the EDI-2 (p < 0.01). Depressiveness, anxiety, and perceived stress did not correlate with kisspeptin or any other of the investigated hormones (p > 0.05). In conclusion, kisspeptin is inversely and ghrelin positively associated with physical activity as measured by daily step counts in anorexia nervosa patients suggesting an implication of these peptide hormones in

Patterns of Dupuytren disease in fingers: studying correlations with a multivariate ordinal logit model.

PubMed

Lanting, Rosanne; Nooraee, Nazanin; Werker, Paul M N; van den Heuvel, Edwin R

2014-09-01

Dupuytren disease affects fingers in a variable fashion. Knowledge about specific disease patterns (phenotype) based on location and severity of the disease is lacking. In this cross-sectional study, 344 primary affected hands with Dupuytren disease were physically examined. The Pearson correlation coefficient between the coexistence of Dupuytren disease in pairs of fingers was calculated, and agglomerative hierarchical clustering was applied to identify possible clusters of affected fingers. With a multivariate ordinal logit model, the authors studied the correlation on severity, taking into account age and sex, and tested hypotheses on independence between groups of fingers. The ring finger was most frequently affected by Dupuytren disease, and contractures were seen in 15.1 percent of affected rays. The severity of thumb and index finger, middle and ring fingers, and middle and little fingers was significantly correlated. Occurrences in pairs of fingers were highest in the middle and ring fingers and lowest in the thumb and index finger. Correlation between the ring and little fingers and a correlation between fingers from the ulnar and radial sides could not be demonstrated. Rays on the ulnar side of the hand are predominantly affected. The middle finger is substantially correlated with other fingers on the ulnar side, and the thumb and index finger are correlated; however, there was no evidence that the ulnar side and the radial side were correlated in any way, which suggests that occurrence on one side of the hand does not predict Dupuytren disease on the other side of the hand. Risk, III.

Crossed versus conventional pseudophakic monovision: Patient satisfaction, visual function, and spectacle independence.

PubMed

Zhang, Fuxiang; Sugar, Alan; Arbisser, Lisa; Jacobsen, Gordon; Artico, Jessica

2015-09-01

To compare patient satisfaction, visual function, and spectacle independence in patients with crossed or conventional pseudophakic monovision. Department of Ophthalmology, Henry Ford Health System, Taylor, Michigan, USA. Retrospective comparative cohort study. Cataract surgery patient records from June 1999 to December 2013 were reviewed. Crossed monovision patients were identified. Control conventional monovision cases were matched for age, sex, general health, personal lifestyle/main hobbies, preoperative refractive status, postoperative refractive status, uncorrected distance visual acuity, uncorrected near visual acuity, astigmatism level, and anisometropia level. A survey was mailed to participants, and results were independently analyzed. The review comprised 7311 patient records. Forty-four crossed monovision patients were identified, and 30 of them were enrolled. Thirty matched pairs were surveyed. The mean anisometropia was 1.19 diopters (D) in the conventional and 1.12 D in the crossed monovision groups. No significant difference was identified for eye-hand coordination, eye-foot coordination, or sport-related depth perception, but satisfaction was slightly better in the crossed monovision group (P = .028). No significant difference was identified for 6 of 8 spectacle independence measures, but nighttime driving was a little easier for the crossed monovision group (P = .025). Seventy-seven percent of crossed and 50% of conventional monovision patients did not use glasses for intermediate distance activities (P = .037). Crossed pseudophakic monovision appears to work as well as conventional pseudophakic monovision in terms of patient satisfaction and spectacle independence in patients with a mild degree of anisometropic pseudophakia. No author has a financial or proprietary interest in any material or method mentioned. Copyright © 2015 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Correlations in star networks: from Bell inequalities to network inequalities

NASA Astrophysics Data System (ADS)

Tavakoli, Armin; Olivier Renou, Marc; Gisin, Nicolas; Brunner, Nicolas

2017-07-01

The problem of characterizing classical and quantum correlations in networks is considered. Contrary to the usual Bell scenario, where distant observers share a physical system emitted by one common source, a network features several independent sources, each distributing a physical system to a subset of observers. In the quantum setting, the observers can perform joint measurements on initially independent systems, which may lead to strong correlations across the whole network. In this work, we introduce a technique to systematically map a Bell inequality to a family of Bell-type inequalities bounding classical correlations on networks in a star-configuration. Also, we show that whenever a given Bell inequality can be violated by some entangled state ρ, then all the corresponding network inequalities can be violated by considering many copies of ρ distributed in the star network. The relevance of these ideas is illustrated by applying our method to a specific multi-setting Bell inequality. We derive the corresponding network inequalities, and study their quantum violations.

Comparative Analyses of Data Independent Acquisition Mass Spectrometric Approaches: DIA, WiSIM‐DIA, and Untargeted DIA

PubMed Central

Ho, Jenny T. C.; Smit, August B.; Li, Ka Wan

2018-01-01

Abstract Data‐independent acquisition (DIA) is an emerging technology for quantitative proteomics. Current DIA focusses on the identification and quantitation of fragment ions that are generated from multiple peptides contained in the same selection window of several to tens of m/z. An alternative approach is WiSIM‐DIA, which combines conventional DIA with wide‐SIM (wide selected‐ion monitoring) windows to partition the precursor m/z space to produce high‐quality precursor ion chromatograms. However, WiSIM‐DIA has been underexplored; it remains unclear if it is a viable alternative to DIA. We demonstrate that WiSIM‐DIA quantified more than 24 000 unique peptides over five orders of magnitude in a single 2 h analysis of a neuronal synapse‐enriched fraction, compared to 31 000 in DIA. There is a strong correlation between abundance values of peptides quantified in both the DIA and WiSIM‐DIA datasets. Interestingly, the S/N ratio of these peptides is not correlated. We further show that peptide identification directly from DIA spectra identified >2000 proteins, which included unique peptides not found in spectral libraries generated by DDA. PMID:29134766

An early-stage epidemic: a systematic review of correlates of smoking among Chinese women.

PubMed

Ding, Ding; Gebel, Klaus; Oldenburg, Brian F; Wan, Xia; Zhong, Xuefeng; Novotny, Thomas E

2014-08-01

Despite the historically low smoking prevalence among Chinese women, there is a trend of future increase. We systematically reviewed the correlates of smoking among Chinese girls and women. We conducted a systematic review of literature on correlates of smoking among Chinese women using Medline and China Academic Journals databases. Following the PRISMA statement, two investigators independently searched for literature, identified and reviewed papers, assessed the quality of the papers, and extracted information. The characteristics of studies and correlates of smoking were synthesized separately for youth and adults. A total of 15 articles (11 on adults, 4 on youth) met the inclusion criteria. Based on these studies, peer smoking was the most consistent correlate of smoking among Chinese girls. Among Chinese women, partner smoking, job-related stress, and exposure to cigarettes made for women were consistent correlates of smoking. Knowledge of harms and negative attitudes towards smoking were found to be negatively associated with smoking. Overall, the evidence base for smoking among Chinese women is limited. Although smoking among Chinese women is still at an early stage, it is becoming more prevalent among specific population subgroups, such as rural-to-urban migrant workers. Although further research is needed, findings from the current study provide a roadmap for research and policy on prevention of smoking among Chinese girls and women.

An asymptotic theory for cross-correlation between auto-correlated sequences and its application on neuroimaging data.

PubMed

Zhou, Yunyi; Tao, Chenyang; Lu, Wenlian; Feng, Jianfeng

2018-04-20

Functional connectivity is among the most important tools to study brain. The correlation coefficient, between time series of different brain areas, is the most popular method to quantify functional connectivity. Correlation coefficient in practical use assumes the data to be temporally independent. However, the time series data of brain can manifest significant temporal auto-correlation. A widely applicable method is proposed for correcting temporal auto-correlation. We considered two types of time series models: (1) auto-regressive-moving-average model, (2) nonlinear dynamical system model with noisy fluctuations, and derived their respective asymptotic distributions of correlation coefficient. These two types of models are most commonly used in neuroscience studies. We show the respective asymptotic distributions share a unified expression. We have verified the validity of our method, and shown our method exhibited sufficient statistical power for detecting true correlation on numerical experiments. Employing our method on real dataset yields more robust functional network and higher classification accuracy than conventional methods. Our method robustly controls the type I error while maintaining sufficient statistical power for detecting true correlation in numerical experiments, where existing methods measuring association (linear and nonlinear) fail. In this work, we proposed a widely applicable approach for correcting the effect of temporal auto-correlation on functional connectivity. Empirical results favor the use of our method in functional network analysis. Copyright © 2018. Published by Elsevier B.V.

Neuropsychological and Early Maturational Correlates of Intelligence.

ERIC Educational Resources Information Center

Denno, Deborah J.

A study designed to examine biological, sociological, and early maturational correlates of intelligence collected data prospectively, from birth to 15 years of age, on a sample of 987 black children. Multiple indicators of eight independent and three dependent variables were tested in a structural equation model. Altogether, clear sex differences…

Prevalence and Clinical Correlates of Sarcopenia in Community-Dwelling Older People: Application of the EWGSOP Definition and Diagnostic Algorithm

PubMed Central

2014-01-01

Background. Muscle impairment is a common condition in older people and a powerful risk factor for disability and mortality. The aim of this study was to apply the European Working Group on Sarcopenia in Older People criteria to estimate the prevalence and investigate the clinical correlates of sarcopenia, in a sample of Italian community-dwelling older people. Methods. Cross-sectional analysis of 730 participants (74% aged 65 years and older) enrolled in the InCHIANTI study. Sarcopenia was defined according to the European Working Group on Sarcopenia in Older People criteria using bioimpedance analysis for muscle mass assessment. Logistic regression analysis was used to identify the factors independently associated with sarcopenia. Results. Sarcopenia defined by the European Working Group on Sarcopenia in Older People criteria increased steeply with age (p < .001), with 31.6% of women and 17.4% of men aged 80 years or older being affected by this condition. Higher education (odds ratio: 0.85; 95% CI: 0.74–0.98), lower insulin-like growth factor I (lowest vs highest tertile, odds ratio: 3.89; 95% CI: 1.03–14.1), and low bioavailable testosterone (odds ratio: 2.67; 95% CI: 1.31–5.44) were independently associated with the likelihood of being sarcopenic. Nutritional intake, physical activity, and level of comorbidity were not associated with sarcopenia. Conclusions. Sarcopenia identified by the European Working Group on Sarcopenia in Older People criteria is a relatively common condition in Italian octogenarians, and its prevalence increases with aging. Correlates of sarcopenia identified in this study might suggest new approaches for prevention and treatment of sarcopenia. PMID:24085400

Dysphagic Independent Feeders' Justifications for Noncompliance with Recommendations by a Speech-Language Pathologist

ERIC Educational Resources Information Center

Colodny, Nancy

2005-01-01

The purpose of this study was to examine the various ways in which independent-feeding patients with dysphagia justified their noncompliance with swallowing recommendations suggested by a speech-language pathologist (SLP). Sixty-three independent-feeding dysphagia patients between the ages of 65 and 100 years who had been identified by the SLP or…

Identifying in vivo DCE MRI markers associated with microvessel architecture and gleason grades of prostate cancer.

PubMed

Singanamalli, Asha; Rusu, Mirabela; Sparks, Rachel E; Shih, Natalie N C; Ziober, Amy; Wang, Li-Ping; Tomaszewski, John; Rosen, Mark; Feldman, Michael; Madabhushi, Anant

2016-01-01

To identify computer extracted in vivo dynamic contrast enhanced (DCE) MRI markers associated with quantitative histomorphometric (QH) characteristics of microvessels and Gleason scores (GS) in prostate cancer. This study considered retrospective data from 23 biopsy confirmed prostate cancer patients who underwent 3 Tesla multiparametric MRI before radical prostatectomy (RP). Representative slices from RP specimens were stained with vascular marker CD31. Tumor extent was mapped from RP sections onto DCE MRI using nonlinear registration methods. Seventy-seven microvessel QH features and 18 DCE MRI kinetic features were extracted and evaluated for their ability to distinguish low from intermediate and high GS. The effect of temporal sampling on kinetic features was assessed and correlations between those robust to temporal resolution and microvessel features discriminative of GS were examined. A total of 12 microvessel architectural features were discriminative of low and intermediate/high grade tumors with area under the receiver operating characteristic curve (AUC) > 0.7. These features were most highly correlated with mean washout gradient (WG) (max rho = -0.62). Independent analysis revealed WG to be moderately robust to temporal resolution (intraclass correlation coefficient [ICC] = 0.63) and WG variance, which was poorly correlated with microvessel features, to be predictive of low grade tumors (AUC = 0.77). Enhancement ratio was the most robust (ICC = 0.96) and discriminative (AUC = 0.78) kinetic feature but was moderately correlated with microvessel features (max rho = -0.52). Computer extracted features of prostate DCE MRI appear to be correlated with microvessel architecture and may be discriminative of low versus intermediate and high GS. © 2015 Wiley Periodicals, Inc.

Learning Bayesian Networks from Correlated Data

NASA Astrophysics Data System (ADS)

Bae, Harold; Monti, Stefano; Montano, Monty; Steinberg, Martin H.; Perls, Thomas T.; Sebastiani, Paola

2016-05-01

Bayesian networks are probabilistic models that represent complex distributions in a modular way and have become very popular in many fields. There are many methods to build Bayesian networks from a random sample of independent and identically distributed observations. However, many observational studies are designed using some form of clustered sampling that introduces correlations between observations within the same cluster and ignoring this correlation typically inflates the rate of false positive associations. We describe a novel parameterization of Bayesian networks that uses random effects to model the correlation within sample units and can be used for structure and parameter learning from correlated data without inflating the Type I error rate. We compare different learning metrics using simulations and illustrate the method in two real examples: an analysis of genetic and non-genetic factors associated with human longevity from a family-based study, and an example of risk factors for complications of sickle cell anemia from a longitudinal study with repeated measures.

Electroencephalographic correlates of states of concentrative meditation.

PubMed

DeLosAngeles, Dylan; Williams, Graham; Burston, John; Fitzgibbon, Sean P; Lewis, Trent W; Grummett, Tyler S; Clark, C Richard; Pope, Kenneth J; Willoughby, John O

2016-12-01

Meditative techniques aim for and meditators report states of mental alertness and focus, concurrent with physical and emotional calm. We aimed to determine the electroencephalographic (EEG) correlates of five states of Buddhist concentrative meditation, particularly addressing a correlation with meditative level. We studied 12 meditators and 12 pair-matched meditation-naïve participants using high-resolution scalp-recorded EEG. To maximise reduction of EMG, data were pre-processed using independent component analysis and surface Laplacian transformed data. Two non-meditative and five meditative states were used: resting baseline, mind-wandering, absorptions 1, 2, 3, 4 and 5 (corresponding to four levels of absorption and an absorption with a different object of focus, otherwise equivalent to level 4; these five meditative states produce repeatable, distinctly different experiences for experienced meditators). The experimental protocol required participants to experience the states in the order listed above, followed immediately by the reverse. We then calculated EEG power in standard frequency bands from 1 to 80Hz. We observed decreases of central scalp beta (13-25Hz), and central low gamma (25-48Hz) power in meditators during deeper absorptions. In contrast, we identified increases in frontal midline and temporo-parietal theta power in meditators, again, during deeper absorptions. Alpha activity was increased over all meditative states, not depth-related. This study demonstrates that the subjective experiences of deepening meditation partially correspond to measures of EEG. Our results are in accord with prior studies on non-graded meditative states. These results are also consistent with increased theta correlating with tightness of focus, and reduced beta/gamma with the desynchronization associated with enhanced alertness. Copyright © 2016. Published by Elsevier B.V.

The meaning of "independence" for older people in different residential settings.

PubMed

Hillcoat-Nallétamby, Sarah

2014-05-01

Drawing on older people's understandings of "independence" and Collopy's work on autonomy, the article elaborates an interpretive framework of the concept in relation to 3 residential settings-the private dwelling-home, the extra-care, and the residential-care settings. Data include 91 qualitative interviews with frail, older people living in each setting, collected as part of a larger Welsh study. Thematic analysis techniques were employed to identify patterns in meanings of independence across settings and then interpreted using Collopy's conceptualizations of autonomy, as well as notions of space and interdependencies. Independence has multiple meanings for older people, but certain meanings are common to all settings: Accepting help at hand; doing things alone; having family, friends, and money as resources; and preserving physical and mental capacities. Concepts of delegated, executional, authentic, decisional, and consumer autonomy, as well as social interdependencies and spatial and social independence, do provide appropriate higher order interpretive constructs of these meanings across settings. A broader interpretive framework of "independence" should encompass concepts of relative independence, autonomy(ies), as well as spatial and social independence, and can provide more nuanced interpretations of structured dependency and institutionalization theories when applied to different residential settings.

Regularized Generalized Canonical Correlation Analysis

ERIC Educational Resources Information Center

Tenenhaus, Arthur; Tenenhaus, Michel

2011-01-01

Regularized generalized canonical correlation analysis (RGCCA) is a generalization of regularized canonical correlation analysis to three or more sets of variables. It constitutes a general framework for many multi-block data analysis methods. It combines the power of multi-block data analysis methods (maximization of well identified criteria) and…

Pathologic features of metastatic lymph nodes identified from prophylactic central neck dissection in patients with papillary thyroid carcinoma.

PubMed

Lee, Hyoung Shin; Park, Chanwoo; Kim, Sung Won; Noh, Woong Jae; Lim, Soo Jin; Chun, Bong Kwon; Kim, Beom Su; Hong, Jong Chul; Lee, Kang Dae

2016-10-01

The importance of pathologic features of metastatic lymph nodes (LNs), such as size, number, and extranodal extension, has been recently emphasized in patients with papillary thyroid carcinoma (PTC). We evaluated the characteristics of metastatic LNs identified after prophylactic central neck dissection (CND) in patients with PTC. We performed a retrospective review of 1,046 patients who underwent unilateral or bilateral thyroidectomy with ipsilateral prophylactic CND. We reviewed the characteristics of the metastatic LNs and analyzed their correlation to the clinicopathologic characteristics of the primary tumor. Cervical LN metastasis after prophylactic CND was identified in 280 out of 1046 patients (26.8 %). The size of metastatic foci (≥2 mm) was independently correlated with primary tumor size (≥1 cm) (p = 0.016, OR = 1.88). Primary tumor size (≥1 cm) was also correlated to the number of metastatic LNs (≥5) (p = 0.004, OR = 3.14) and extranodal extension (p = 0.021, OR = 2.41) in univariate analysis. The size of the primary tumor affects pathologic features of subclinical LN metastasis in patients with PTC. Patients with primary tumors ≥1 cm have an increased risk of larger LN metastases (≥2 mm), an increased number of LN metastases (≥5), and a higher incidence of ENE, which should be considered in decision for prophylactic CND.

Using Correlation to Compute Better Probability Estimates in Plan Graphs

NASA Technical Reports Server (NTRS)

Bryce, Daniel; Smith, David E.

2006-01-01

Plan graphs are commonly used in planning to help compute heuristic "distance" estimates between states and goals. A few authors have also attempted to use plan graphs in probabilistic planning to compute estimates of the probability that propositions can be achieved and actions can be performed. This is done by propagating probability information forward through the plan graph from the initial conditions through each possible action to the action effects, and hence to the propositions at the next layer of the plan graph. The problem with these calculations is that they make very strong independence assumptions - in particular, they usually assume that the preconditions for each action are independent of each other. This can lead to gross overestimates in probability when the plans for those preconditions interfere with each other. It can also lead to gross underestimates of probability when there is synergy between the plans for two or more preconditions. In this paper we introduce a notion of the binary correlation between two propositions and actions within a plan graph, show how to propagate this information within a plan graph, and show how this improves probability estimates for planning. This notion of correlation can be thought of as a continuous generalization of the notion of mutual exclusion (mutex) often used in plan graphs. At one extreme (correlation=0) two propositions or actions are completely mutex. With correlation = 1, two propositions or actions are independent, and with correlation > 1, two propositions or actions are synergistic. Intermediate values can and do occur indicating different degrees to which propositions and action interfere or are synergistic. We compare this approach with another recent approach by Bryce that computes probability estimates using Monte Carlo simulation of possible worlds in plan graphs.

Does anxiety sensitivity correlate with startle habituation? An examination in two independent samples.

PubMed

Campbell, Miranda L; Gorka, Stephanie M; McGowan, Sarah K; Nelson, Brady D; Sarapas, Casey; Katz, Andrea C; Robison-Andrew, E Jenna; Shankman, Stewart A

2014-01-01

Individuals with anxiety disorders have previously demonstrated abnormal habituation to aversiveness over time. As anxiety sensitivity (AS), or an individuals' propensity to fear of anxiety-related sensations, has been shown to be a risk factor for anxiety disorders (particularly panic disorder), the present study examined whether AS was also associated with abnormal habituation. This association was examined in two independent samples of undergraduates (Ntotal=178). Habituation was operationalised as the reduction in startle response to multiple startle probes presented over 2.5 minutes and three definitions of this reduction were employed. Results indicated that individuals with higher levels of AS evidenced deficits in startle habituation, but the strength of this relationship was somewhat dependent on the definition of startle habituation, with the most robust definition being an analysis of participants' individual slopes across all nine blinks. The present findings suggest that startle habituation is a key mechanism underlying AS, and may help elucidate the role this risk factor plays in the pathogenesis of anxiety disorders.

Long-range correlations and burstiness in written texts: Universal and language-specific aspects

NASA Astrophysics Data System (ADS)

Constantoudis, Vassilios; Kalimeri, Maria; Diakonos, Fotis; Karamanos, Konstantinos; Papadimitriou, Constantinos; Chatzigeorgiou, Manolis; Papageorgiou, Harris

2016-08-01

Recently, methods from the statistical physics of complex systems have been applied successfully to identify universal features in the long-range correlations (LRCs) of written texts. However, in real texts, these universal features are being intermingled with language-specific influences. This paper aims at the characterization and further understanding of the interplay between universal and language-specific effects on the LRCs in texts. To this end, we apply the language-sensitive mapping of written texts to word-length series (wls) and analyse large parallel (of same content) corpora from 10 languages classified to four families (Romanic, Germanic, Greek and Uralic). The autocorrelation functions of the wls reveal tiny but persistent LRCs decaying at large scales following a power-law with a language-independent exponent ˜0.60-0.65. The impact of language is displayed in the amplitude of correlations where a relative standard deviation >40% among the analyzed languages is observed. The classification to language families seems to play a significant role since, the Finnish and Germanic languages exhibit more correlations than the Greek and Roman families. To reveal the origins of the LRCs, we focus on the long words and perform burst and correlation analysis in their positions along the corpora. We find that the universal features are linked more to the correlations of the inter-long word distances while the language-specific aspects are related more to their distributions.

Three field tests of a gas filter correlation radiometer

NASA Technical Reports Server (NTRS)

Campbell, S. A.; Casas, J. C.; Condon, E. P.

1977-01-01

Test flights to remotely measure nonurban carbon monoxide (CO) concentrations by gas filter correlation radiometry are discussed. The inferred CO concentrations obtained through use of the Gas Filter Correlation Radiometer (GFCR) agreed with independent measurements obtained by gas chromatography air sample bottle analysis to within 20 percent. The equipment flown on board the aircraft, the flight test procedure, the gas chromatograph direct air sampling procedure, and the GFCR data analysis procedure are reported.

Adipocyte Triglyceride Turnover Is Independently Associated With Atherogenic Dyslipidemia

PubMed Central

Frayn, Keith; Bernard, Samuel; Spalding, Kirsty; Arner, Peter

2012-01-01

Background Inappropriate storage of fatty acids as triglycerides in adipocytes and their removal from adipocytes through lipolysis and subsequent oxidation may cause the atherogenic dyslipidemia phenotype of elevated apolipoprotein B levels and subsequent hypertriglyceridemia. We tested whether turnover of triglycerides in fat cells was related to dyslipidemia. Methods and Results The age of triglycerides (reflecting removal) and triglyceride storage in adipocytes was determined under free living conditions by measuring incorporation of atmospheric 14C into these lipids within the adipocytes in 47 women and 26 men with a large interindividual variability in body mass index. Because limited 14C data were available, triglyceride age was also determined in 97 men and 233 women by using an algorithm based on adipocyte lipolysis, body fat content, waist‐to‐hip ratio, and insulin sensitivity. This cohort consisted of nonobese subjects since obesity per se is related to all components in the algorithm. Triglyceride turnover (age and storage) was compared with plasma levels of apolipoproteins and lipids. Plasma levels of apolipoprotein B and triglycerides were positively related to triglyceride age in adipocytes, when measured directly using radiocarbon analyses (r=0.45 to 0.47; P<0.0001). This effect was independent of subject age, waist circumference measures, and insulin sensitivity (partial r=0.29 to 0.45; P from 0.03 to <0.0001). Triglyceride storage showed no independent correlation (partial r=0.02 to 0.11; P=0.42 to 0.91). Algorithm‐based values for adipocyte removal of triglycerides were positively associated with plasma triglycerides and apolipoprotein B (r=0.44 to 0.45; P<0.0001) and (also positively) with the inflammation status of adipose tissue (r=0.39 to 0.47; P<0.05). These correlations were statistically independent of subject age and observed in men and women as well as in lean and overweight subjects when subgroups were examined separately

Complexity of intracranial pressure correlates with outcome after traumatic brain injury

PubMed Central

Lu, Cheng-Wei; Czosnyka, Marek; Shieh, Jiann-Shing; Smielewska, Anna; Pickard, John D.

2012-01-01

This study applied multiscale entropy analysis to investigate the correlation between the complexity of intracranial pressure waveform and outcome after traumatic brain injury. Intracranial pressure and arterial blood pressure waveforms were low-pass filtered to remove the respiratory and pulse components and then processed using a multiscale entropy algorithm to produce a complexity index. We identified significant differences across groups classified by the Glasgow Outcome Scale in intracranial pressure, pressure-reactivity index and complexity index of intracranial pressure (P < 0.0001; P = 0.001; P < 0.0001, respectively). Outcome was dichotomized as survival/death and also as favourable/unfavourable. The complexity index of intracranial pressure achieved the strongest statistical significance (F = 28.7; P < 0.0001 and F = 17.21; P < 0.0001, respectively) and was identified as a significant independent predictor of mortality and favourable outcome in a multivariable logistic regression model (P < 0.0001). The results of this study suggest that complexity of intracranial pressure assessed by multiscale entropy was significantly associated with outcome in patients with brain injury. PMID:22734128

Scalar rate correlation at a turbulent liquid free surface - A two-regime correlation for high Schmidt numbers

NASA Technical Reports Server (NTRS)

Khoo, Boo-Cheong; Sonin, Ain A.

1992-01-01

An experimental correlation is derived for gas absorption at a turbulent, shear-free liquid interface. The correlation is expressed in terms of the liquid-side turbulence intensity, liquid-side macroscale, and the properties of the diffusing gas and solvent. The transfer coefficient increases linearly with rms velocity up to a point where the eddy Reynolds number reaches a critical (Schmidt number dependent) value. At higher velocities, there is a more rapid linear rise. The slope of the lower Reynolds number region is proportional to the square root of the diffusivity; at Reynolds numbers much higher than that of the break point, the slope becomes independent of diffusivity.

Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

PubMed Central

Orr, Nick; Dudbridge, Frank; Dryden, Nicola; Maguire, Sarah; Novo, Daniela; Perrakis, Eleni; Johnson, Nichola; Ghoussaini, Maya; Hopper, John L.; Southey, Melissa C.; Apicella, Carmel; Stone, Jennifer; Schmidt, Marjanka K.; Broeks, Annegien; Van't Veer, Laura J.; Hogervorst, Frans B.; Fasching, Peter A.; Haeberle, Lothar; Ekici, Arif B.; Beckmann, Matthias W.; Gibson, Lorna; Aitken, Zoe; Warren, Helen; Sawyer, Elinor; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Schneeweiss, Andreas; Sohn, Chistof; Guénel, Pascal; Truong, Thérèse; Cordina-Duverger, Emilie; Sanchez, Marie; Bojesen, Stig E.; Nordestgaard, Børge G.; Nielsen, Sune F.; Flyger, Henrik; Benitez, Javier; Zamora, Maria Pilar; Arias Perez, Jose Ignacio; Menéndez, Primitiva; Anton-Culver, Hoda; Neuhausen, Susan L.; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Hamann, Ute; Brauch, Hiltrud; Justenhoven, Christina; Brüning, Thomas; Ko, Yon-Dschun; Nevanlinna, Heli; Aittomäki, Kristiina; Blomqvist, Carl; Khan, Sofia; Bogdanova, Natalia; Dörk, Thilo; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Chenevix-Trench, Georgia; Beesley, Jonathan; Lambrechts, Diether; Moisse, Matthieu; Floris, Guiseppe; Beuselinck, Benoit; Chang-Claude, Jenny; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Radice, Paolo; Peterlongo, Paolo; Peissel, Bernard; Pensotti, Valeria; Couch, Fergus J.; Olson, Janet E.; Slettedahl, Seth; Vachon, Celine; Giles, Graham G.; Milne, Roger L.; McLean, Catriona; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S.; Labrèche, France; Dumont, Martine; Kristensen, Vessela; Alnæs, Grethe Grenaker; Nord, Silje; Borresen-Dale, Anne-Lise; Zheng, Wei; Deming-Halverson, Sandra; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Andrulis, Irene L.; Knight, Julia A.; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robertus A. E. M.; Seynaeve, Caroline M.; Van Asperen, Christi J.; Garcia-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J.; Lissowska, Jolanta; Czene, Kamila; Darabi, Hatef; Eriksson, Mikael; Klevebring, Daniel; Hooning, Maartje J.; Hollestelle, Antoinette; van Deurzen, Carolien H. M.; Kriege, Mieke; Hall, Per; Li, Jingmei; Liu, Jianjun; Humphreys, Keith; Cox, Angela; Cross, Simon S.; Reed, Malcolm W. R.; Pharoah, Paul D. P.; Dunning, Alison M.; Shah, Mitul; Perkins, Barbara J.; Jakubowska, Anna; Lubinski, Jan; Jaworska-Bieniek, Katarzyna; Durda, Katarzyna; Ashworth, Alan; Swerdlow, Anthony; Jones, Michael; Schoemaker, Minouk J.; Meindl, Alfons; Schmutzler, Rita K.; Olswold, Curtis; Slager, Susan; Toland, Amanda E.; Yannoukakos, Drakoulis; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Matsuo, Keitaro; Ito, Hidema; Iwata, Hiroji; Ishiguro, Junko; Wu, Anna H.; Tseng, Chiu-chen; Van Den Berg, David; Stram, Daniel O.; Teo, Soo Hwang; Yip, Cheng Har; Kang, Peter; Ikram, Mohammad Kamran; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K.; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Lee, Soo Chin; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; Mckay, James; Wu, Pei-Ei; Hou, Ming-Feng; Yu, Jyh-Cherng; Shen, Chen-Yang; Blot, William; Cai, Qiuyin; Signorello, Lisa B.; Luccarini, Craig; Bayes, Caroline; Ahmed, Shahana; Maranian, Mel; Healey, Catherine S.; González-Neira, Anna; Pita, Guillermo; Alonso, M. Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C.; Vincent, Daniel; Bacot, Francois; Hunter, David J.; Lindstrom, Sara; Dennis, Joe; Michailidou, Kyriaki; Bolla, Manjeet K.; Easton, Douglas F.; dos Santos Silva, Isabel; Fletcher, Olivia; Peto, Julian

2015-01-01

We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88–0.92]; P-value = 1.58 × 10−25). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08–1.17]; P-value = 7.89 × 10−09) and rs13294895 (OR = 1.09 [1.06–1.12]; P-value = 2.97 × 10−11). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06–1.18]; P-value = 2.77 × 10−05). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis. PMID:25652398

Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2.

PubMed

Orr, Nick; Dudbridge, Frank; Dryden, Nicola; Maguire, Sarah; Novo, Daniela; Perrakis, Eleni; Johnson, Nichola; Ghoussaini, Maya; Hopper, John L; Southey, Melissa C; Apicella, Carmel; Stone, Jennifer; Schmidt, Marjanka K; Broeks, Annegien; Van't Veer, Laura J; Hogervorst, Frans B; Fasching, Peter A; Haeberle, Lothar; Ekici, Arif B; Beckmann, Matthias W; Gibson, Lorna; Aitken, Zoe; Warren, Helen; Sawyer, Elinor; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Schneeweiss, Andreas; Sohn, Chistof; Guénel, Pascal; Truong, Thérèse; Cordina-Duverger, Emilie; Sanchez, Marie; Bojesen, Stig E; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Benitez, Javier; Zamora, Maria Pilar; Arias Perez, Jose Ignacio; Menéndez, Primitiva; Anton-Culver, Hoda; Neuhausen, Susan L; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Hamann, Ute; Brauch, Hiltrud; Justenhoven, Christina; Brüning, Thomas; Ko, Yon-Dschun; Nevanlinna, Heli; Aittomäki, Kristiina; Blomqvist, Carl; Khan, Sofia; Bogdanova, Natalia; Dörk, Thilo; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Chenevix-Trench, Georgia; Beesley, Jonathan; Lambrechts, Diether; Moisse, Matthieu; Floris, Guiseppe; Beuselinck, Benoit; Chang-Claude, Jenny; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Radice, Paolo; Peterlongo, Paolo; Peissel, Bernard; Pensotti, Valeria; Couch, Fergus J; Olson, Janet E; Slettedahl, Seth; Vachon, Celine; Giles, Graham G; Milne, Roger L; McLean, Catriona; Haiman, Christopher A; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S; Labrèche, France; Dumont, Martine; Kristensen, Vessela; Alnæs, Grethe Grenaker; Nord, Silje; Borresen-Dale, Anne-Lise; Zheng, Wei; Deming-Halverson, Sandra; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Andrulis, Irene L; Knight, Julia A; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robertus A E M; Seynaeve, Caroline M; Van Asperen, Christi J; Garcia-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J; Lissowska, Jolanta; Czene, Kamila; Darabi, Hatef; Eriksson, Mikael; Klevebring, Daniel; Hooning, Maartje J; Hollestelle, Antoinette; van Deurzen, Carolien H M; Kriege, Mieke; Hall, Per; Li, Jingmei; Liu, Jianjun; Humphreys, Keith; Cox, Angela; Cross, Simon S; Reed, Malcolm W R; Pharoah, Paul D P; Dunning, Alison M; Shah, Mitul; Perkins, Barbara J; Jakubowska, Anna; Lubinski, Jan; Jaworska-Bieniek, Katarzyna; Durda, Katarzyna; Ashworth, Alan; Swerdlow, Anthony; Jones, Michael; Schoemaker, Minouk J; Meindl, Alfons; Schmutzler, Rita K; Olswold, Curtis; Slager, Susan; Toland, Amanda E; Yannoukakos, Drakoulis; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Matsuo, Keitaro; Ito, Hidema; Iwata, Hiroji; Ishiguro, Junko; Wu, Anna H; Tseng, Chiu-Chen; Van Den Berg, David; Stram, Daniel O; Teo, Soo Hwang; Yip, Cheng Har; Kang, Peter; Ikram, Mohammad Kamran; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Lee, Soo Chin; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; Mckay, James; Wu, Pei-Ei; Hou, Ming-Feng; Yu, Jyh-Cherng; Shen, Chen-Yang; Blot, William; Cai, Qiuyin; Signorello, Lisa B; Luccarini, Craig; Bayes, Caroline; Ahmed, Shahana; Maranian, Mel; Healey, Catherine S; González-Neira, Anna; Pita, Guillermo; Alonso, M Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C; Vincent, Daniel; Bacot, Francois; Hunter, David J; Lindstrom, Sara; Dennis, Joe; Michailidou, Kyriaki; Bolla, Manjeet K; Easton, Douglas F; dos Santos Silva, Isabel; Fletcher, Olivia; Peto, Julian

2015-05-15

We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88-0.92]; P-value = 1.58 × 10(-25)). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08-1.17]; P-value = 7.89 × 10(-09)) and rs13294895 (OR = 1.09 [1.06-1.12]; P-value = 2.97 × 10(-11)). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06-1.18]; P-value = 2.77 × 10(-05)). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis. © The Author 2015. Published by Oxford University Press.

High-Content Screening Identifies Src Family Kinases as Potential Regulators of AR-V7 Expression and Androgen-Independent Cell Growth.

PubMed

Szafran, Adam T; Stephan, Cliff; Bolt, Michael; Mancini, Maureen G; Marcelli, Marco; Mancini, Michael A

2017-01-01

AR-V7 is an androgen receptor (AR) splice variant that lacks the ligand-binding domain and is isolated from prostate cancer cell lines. Increased expression of AR-V7 is associated with the transition from hormone-sensitive prostate cancer to more advanced castration-resistant prostate cancer (CRPC). Due to the loss of the ligand-binding domain, AR-V7 is not responsive to traditional AR-targeted therapies, and the mechanisms that regulate AR-V7 are still incompletely understood. Therefore, we aimed to explore existing classes of small molecules that may regulate AR-V7 expression and intracellular localization and their potential therapeutic role in CRPC. We used AR high-content analysis (AR-HCA) to characterize the effects of a focused library of well-characterized clinical compounds on AR-V7 expression at the single-cell level in PC3 prostate cancer cells stably expressing green fluorescent protein (GFP)-AR-V7 (GFP-AR-V7:PC3). In parallel, an orthogonal AR-HCA screen of a small interfering (si)RNA library targeting 635 protein kinases was performed in GFP-AR-V7:PC3. The effect of the Src-Abl inhibitor PD 180970 was further characterized using cell-proliferation assays, quantitative PCR, and western blot analysis in multiple hormone-sensitive and CRPC cell lines. Compounds that tended to target Akt, Abl, and Src family kinases (SFKs) decreased overall AR-V7 expression, nuclear translocation, absolute nuclear level, and/or altered nuclear distribution. We identified 20 protein kinases that, when knocked down, either decreased nuclear GFP-AR-V7 levels or altered AR-V7 nuclear distribution, a set that included the SFKs Src and Fyn. The Src-Abl dual kinase inhibitor PD180970 decreased expression of AR-V7 by greater than 46% and decreased ligand-independent transcription of AR target genes in the 22RV1 human prostate carcinoma cell line. Further, PD180970 inhibited androgen-independent cell proliferation in endogenous-AR-V7-expressing prostate cancer cell lines and also

High-content screening identifies Src family kinases as potential regulators of AR-V7 expression and androgen-independent cell growth

PubMed Central

Szafran, Adam T.; Stephan, Cliff; Bolt, Michael; Mancini, Maureen G.; Marcelli, Marco; Mancini, Michael A.

2018-01-01

Background AR-V7 is an androgen receptor (AR) splice variant that lacks the ligand-binding domain and is isolated from prostate cancer cell lines. Increased expression of AR-V7 is associated with the transition from hormone-sensitive prostate cancer to more advanced castration-resistant prostate cancer (CRPC). Due to the loss of the ligand-binding domain, AR-V7 is not responsive to traditional AR-targeted therapies, and the mechanisms that regulate AR-V7 are still incompletely understood. Therefore, we aimed to explore existing classes of small molecules that may regulate AR-V7 expression and intracellular localization and their potential therapeutic role in CRPC. Methods We used AR high-content analysis (AR-HCA) to characterize the effects of a focused library of well-characterized clinical compounds on AR-V7 expression at the single-cell level in PC3 prostate cancer cells stably expressing green fluorescent protein (GFP)-AR-V7 (GFP-AR-V7:PC3). In parallel, an orthogonal AR-HCA screen of a small interfering (si)RNA library targeting 635 protein kinases was performed in GFP-AR-V7:PC3. The effect of the Src-Abl inhibitor PD 180970 was further characterized using cell-proliferation assays, quantitative PCR, and western blot analysis in multiple hormone-sensitive and CRPC cell lines. Results Compounds that tended to target Akt, Abl, and Src family kinases (SFKs) decreased overall AR-V7 expression, nuclear translocation, absolute nuclear level, and/or altered nuclear distribution. We identified 20 protein kinases that, when knocked down, either decreased nuclear GFP-AR-V7 levels or altered AR-V7 nuclear distribution, a set that included the SFKs Src and Fyn. The Src-Abl dual kinase inhibitor PD180970 decreased expression of AR-V7 by greater than 46% and decreased ligand-independent transcription of AR target genes in the 22RV1 human prostate carcinoma cell line. Further, PD180970 inhibited androgen-independent cell proliferation in endogenous–AR-V7�

The Health Informatics Trial Enhancement Project (HITE): Using routinely collected primary care data to identify potential participants for a depression trial

PubMed Central

2010-01-01

Background Recruitment to clinical trials can be challenging. We identified anonymous potential participants to an existing pragmatic randomised controlled depression trial to assess the feasibility of using routinely collected data to identify potential trial participants. We discuss the strengths and limitations of this approach, assess its potential value, report challenges and ethical issues encountered. Methods Swansea University's Health Information Research Unit's Secure Anonymised Information Linkage (SAIL) database of routinely collected health records was interrogated, using Structured Query Language (SQL). Read codes were used to create an algorithm of inclusion/exclusion criteria with which to identify suitable anonymous participants. Two independent clinicians rated the eligibility of the potential participants' identified. Inter-rater reliability was assessed using the kappa statistic and inter-class correlation. Results The study population (N = 37263) comprised all adults registered at five general practices in Swansea UK. Using the algorithm 867 anonymous potential participants were identified. The sensitivity and specificity results > 0.9 suggested a high degree of accuracy from the algorithm. The inter-rater reliability results indicated strong agreement between the confirming raters. The Intra Class Correlation Coefficient (Cronbach's Alpha) > 0.9, suggested excellent agreement and Kappa coefficient > 0.8; almost perfect agreement. Conclusions This proof of concept study showed that routinely collected primary care data can be used to identify potential participants for a pragmatic randomised controlled trial of folate augmentation of antidepressant therapy for the treatment of depression. Further work will be needed to assess generalisability to other conditions and settings and the inclusion of this approach to support Electronic Enhanced Recruitment (EER). PMID:20398303

Quantum walks of correlated photon pairs in two-dimensional waveguide arrays.

PubMed

Poulios, Konstantinos; Keil, Robert; Fry, Daniel; Meinecke, Jasmin D A; Matthews, Jonathan C F; Politi, Alberto; Lobino, Mirko; Gräfe, Markus; Heinrich, Matthias; Nolte, Stefan; Szameit, Alexander; O'Brien, Jeremy L

2014-04-11

We demonstrate quantum walks of correlated photons in a two-dimensional network of directly laser written waveguides coupled in a "swiss cross" arrangement. The correlated detection events show high-visibility quantum interference and unique composite behavior: strong correlation and independence of the quantum walkers, between and within the planes of the cross. Violations of a classically defined inequality, for photons injected in the same plane and in orthogonal planes, reveal nonclassical behavior in a nonplanar structure.

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici.

PubMed

Xia, Chongjing; Wang, Meinan; Cornejo, Omar E; Jiwan, Derick A; See, Deven R; Chen, Xianming

2017-01-01

Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is one of the most destructive diseases of wheat worldwide. Planting resistant cultivars is an effective way to control this disease, but race-specific resistance can be overcome quickly due to the rapid evolving Pst population. Studying the pathogenicity mechanisms is critical for understanding how Pst virulence changes and how to develop wheat cultivars with durable resistance to stripe rust. We re-sequenced 7 Pst isolates and included additional 7 previously sequenced isolates to represent balanced virulence/avirulence profiles for several avirulence loci in seretome analyses. We observed an uneven distribution of heterozygosity among the isolates. Secretome comparison of Pst with other rust fungi identified a large portion of species-specific secreted proteins, suggesting that they may have specific roles when interacting with the wheat host. Thirty-two effectors of Pst were identified from its secretome. We identified candidates for Avr genes corresponding to six Yr genes by correlating polymorphisms for effector genes to the virulence/avirulence profiles of the 14 Pst isolates. The putative AvYr76 was present in the avirulent isolates, but absent in the virulent isolates, suggesting that deleting the coding region of the candidate avirulence gene has produced races virulent to resistance gene Yr76 . We conclude that incorporating avirulence/virulence phenotypes into correlation analysis with variations in genomic structure and secretome, particularly presence/absence polymorphisms of effectors, is an efficient way to identify candidate Avr genes in Pst . The candidate effector genes provide a rich resource for further studies to determine the evolutionary history of Pst populations and the co-evolutionary arms race between Pst and wheat. The Avr candidates identified in this study will lead to cloning avirulence genes in Pst , which will enable us to understand molecular mechanisms

Communication: importance sampling including path correlation in semiclassical initial value representation calculations for time correlation functions.

PubMed

Pan, Feng; Tao, Guohua

2013-03-07

Full semiclassical (SC) initial value representation (IVR) for time correlation functions involves a double phase space average over a set of two phase points, each of which evolves along a classical path. Conventionally, the two initial phase points are sampled independently for all degrees of freedom (DOF) in the Monte Carlo procedure. Here, we present an efficient importance sampling scheme by including the path correlation between the two initial phase points for the bath DOF, which greatly improves the performance of the SC-IVR calculations for large molecular systems. Satisfactory convergence in the study of quantum coherence in vibrational relaxation has been achieved for a benchmark system-bath model with up to 21 DOF.

Kolmogorov-Smirnov test for spatially correlated data

USGS Publications Warehouse

Olea, R.A.; Pawlowsky-Glahn, V.

2009-01-01

The Kolmogorov-Smirnov test is a convenient method for investigating whether two underlying univariate probability distributions can be regarded as undistinguishable from each other or whether an underlying probability distribution differs from a hypothesized distribution. Application of the test requires that the sample be unbiased and the outcomes be independent and identically distributed, conditions that are violated in several degrees by spatially continuous attributes, such as topographical elevation. A generalized form of the bootstrap method is used here for the purpose of modeling the distribution of the statistic D of the Kolmogorov-Smirnov test. The innovation is in the resampling, which in the traditional formulation of bootstrap is done by drawing from the empirical sample with replacement presuming independence. The generalization consists of preparing resamplings with the same spatial correlation as the empirical sample. This is accomplished by reading the value of unconditional stochastic realizations at the sampling locations, realizations that are generated by simulated annealing. The new approach was tested by two empirical samples taken from an exhaustive sample closely following a lognormal distribution. One sample was a regular, unbiased sample while the other one was a clustered, preferential sample that had to be preprocessed. Our results show that the p-value for the spatially correlated case is always larger that the p-value of the statistic in the absence of spatial correlation, which is in agreement with the fact that the information content of an uncorrelated sample is larger than the one for a spatially correlated sample of the same size. ?? Springer-Verlag 2008.

Temporal evolution of financial-market correlations.

PubMed

Fenn, Daniel J; Porter, Mason A; Williams, Stacy; McDonald, Mark; Johnson, Neil F; Jones, Nick S

2011-08-01

We investigate financial market correlations using random matrix theory and principal component analysis. We use random matrix theory to demonstrate that correlation matrices of asset price changes contain structure that is incompatible with uncorrelated random price changes. We then identify the principal components of these correlation matrices and demonstrate that a small number of components accounts for a large proportion of the variability of the markets that we consider. We characterize the time-evolving relationships between the different assets by investigating the correlations between the asset price time series and principal components. Using this approach, we uncover notable changes that occurred in financial markets and identify the assets that were significantly affected by these changes. We show in particular that there was an increase in the strength of the relationships between several different markets following the 2007-2008 credit and liquidity crisis.

Temporal evolution of financial-market correlations

NASA Astrophysics Data System (ADS)

Fenn, Daniel J.; Porter, Mason A.; Williams, Stacy; McDonald, Mark; Johnson, Neil F.; Jones, Nick S.

2011-08-01

We investigate financial market correlations using random matrix theory and principal component analysis. We use random matrix theory to demonstrate that correlation matrices of asset price changes contain structure that is incompatible with uncorrelated random price changes. We then identify the principal components of these correlation matrices and demonstrate that a small number of components accounts for a large proportion of the variability of the markets that we consider. We characterize the time-evolving relationships between the different assets by investigating the correlations between the asset price time series and principal components. Using this approach, we uncover notable changes that occurred in financial markets and identify the assets that were significantly affected by these changes. We show in particular that there was an increase in the strength of the relationships between several different markets following the 2007-2008 credit and liquidity crisis.

Probing the independence of formant control using altered auditory feedback

PubMed Central

MacDonald, Ewen N.; Purcell, David W.; Munhall, Kevin G.

2011-01-01

Two auditory feedback perturbation experiments were conducted to examine the nature of control of the first two formants in vowels. In the first experiment, talkers heard their auditory feedback with either F1 or F2 shifted in frequency. Talkers altered production of the perturbed formant by changing its frequency in the opposite direction to the perturbation but did not produce a correlated alteration of the unperturbed formant. Thus, the motor control system is capable of fine-grained independent control of F1 and F2. In the second experiment, a large meta-analysis was conducted on data from talkers who received feedback where both F1 and F2 had been perturbed. A moderate correlation was found between individual compensations in F1 and F2 suggesting that the control of F1 and F2 is processed in a common manner at some level. While a wide range of individual compensation magnitudes were observed, no significant correlations were found between individuals’ compensations and vowel space differences. Similarly, no significant correlations were found between individuals’ compensations and variability in normal vowel production. Further, when receiving normal auditory feedback, most of the population exhibited no significant correlation between the natural variation in production of F1 and F2. PMID:21361452

Health-related quality of life of people living with HIV followed up in hospitals in France: comparing trends and correlates between 2003 and 2011 (ANRS-VESPA and VESPA2 national surveys).

PubMed

Douab, Taoufiq; Marcellin, Fabienne; Vilotitch, Antoine; Protopopescu, Camelia; Préau, Marie; Suzan-Monti, Marie; Sagaon-Teyssier, Luis; Lert, France; Carrieri, Maria Patrizia; Dray-Spira, Rosemary; Spire, Bruno

2014-01-01

In recent years, France has witnessed both structural changes in the population of people living with HIV and a relative improvement in the social representation of HIV infection. However, potential changes in people's day-to-day experience with HIV have not been documented. We used data from the national surveys ANRS-VESPA (2003) and VESPA2 (2011) to compare the levels and patterns of correlates of health-related quality of life (HRQL) in adult HIV-infected patients followed up in French hospitals over a period of eight years. Mean physical and mental SF-12 scores were compared (VESPA, n = 2072; and VESPA2, n = 2267) using analysis of variance (ANOVA) F tests. Heckman regression models were then used to identify independent correlates of physical and mental quality of life in the two surveys, while accounting for possible bias due to missing score values. A common set of potential socio-demographic, clinical, behavioral, and psychosocial correlates was tested. Individuals reported a decrease in physical quality of life in VESPA2 compared with VESPA (mean score (standard error): 47.5 (0.2) versus 49.6 (0.2), p < .0001), and better mental HRQL (44.3 (0.3) versus 42.3 (0.3), p < 0.0001). In both surveys, financial difficulties and patient-perceived experience of rejection behaviors by medical staff were independently associated with impaired physical and mental quality of life. Older age and unemployment were independently associated with impaired physical quality of life. Immigrants from Sub-Saharan Africa reported better mental quality of life. Findings show that quality of life levels in adult HIV-infected patients followed up at hospital in France has significantly, yet modestly, changed in recent years. However, the pattern of quality of life correlates has remained relatively stable. The impact of patient-provider relationships on self-reported outcomes is confirmed. Further research is needed to identify potential differences in quality of life correlates in

Identifying microRNA/mRNA dysregulations in ovarian cancer

PubMed Central

2012-01-01

Background MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC), revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA). Methods TCGA Microarray data was normalized and samples whose class labels (tumour or normal) were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. Results We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from indirect regulatory

Identifying microRNA/mRNA dysregulations in ovarian cancer.

PubMed

Miles, Gregory D; Seiler, Michael; Rodriguez, Lorna; Rajagopal, Gunaretnam; Bhanot, Gyan

2012-03-27

MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC), revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA). TCGA Microarray data was normalized and samples whose class labels (tumour or normal) were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from indirect regulatory mechanisms. Our findings identify