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Common Gene Variants in the Tumor Necrosis Factor (TNF) and TNF Receptor Superfamilies and NF-kB Transcription Factors and Non-Hodgkin Lymphoma Risk

Sophia S. Wang, Mark P. Purdue, James R. Cerhan, Tongzhang Zheng, Idan Menashe, Bruce K. Armstrong, Qing Lan, Patricia Hartge, Anne Kricker, Yawei Zhang, Lindsay M. Morton, Claire M. Vajdic (+11 others)
2009 PLoS ONE  
the NF-kB and related transcription factors, in 1946 NHL cases and 1808 controls pooled from three independent population-based case-control studies.  ...  Conclusions/Significance: Our results provide consistent evidence that variation in the TNF superfamily of genes and specifically within chromosome 6p21.3 impacts lymphomagenesis.  ...  The NSW study was made possible by access to new notifications to the NSW Central Cancer Registry, which is funded by the NSW Health Department.  ... 
doi:10.1371/journal.pone.0005360 pmid:19390683 pmcid:PMC2669130 fatcat:zbyu3t2445h2deii5c7bu42kim

Page 1709 of Mathematical Reviews Vol. , Issue 84e [page]

1984 Mathematical Reviews  
These permutation models have been used by Scott and others in obtaining independence results for Quine’s set theory “New Foundations”.  ...  {In the corrections and additions, it is noted that two of the lemmas used for the consistency results are false, so that a few of the latter are in doubt.  ... 

Page 3956 of Mathematical Reviews Vol. , Issue 84j [page]

1984 Mathematical Reviews  
E. 84j:03101 Further consistency and independence results in NF obtained by the permutation method. J. Symbolic Logic 48 (1983), no. 2, 236-238.  ...  Con(NF) > Con(NF + Vx3y(x EE y=yE€x)). (3) Con(NF)- not all instances of (p=@) are provable in NF, where } is obtained from @ by replacing each atomic subformula y of p by ~y.  ... 

Variational Bayesian Matching

Arto Klami
2012 Journal of machine learning research  
We approximate the posterior over the permutations, and demonstrate that the resulting matching algorithm clearly outperforms all of the earlier solutions.  ...  In this work we present an variational Bayesian solution for the problem, learning a Bayesian canonical correlation analysis model with a permutation parameter for re-ordering the samples in one of the  ...  Matej Orešič for providing the data used in the metabolomics experiment.  ... 
dblp:journals/jmlr/Klami12 fatcat:2rujkrccbfd6tpor4t6hger3cu

Inferring Network Structure from Co-Occurrences

Michael G. Rabbat, Mário A. T. Figueiredo, Robert D. Nowak
2006 Neural Information Processing Systems  
This problem is motivated by network inference problems arising in computational biology and communication systems, in which it is difficult or impossible to obtain precise time ordering information.  ...  Without order information, every permutation of the activated nodes leads to a different feasible solution, resulting in combinatorial explosion of the feasible set.  ...  This work was supported in part by the Portuguese Foundation for Science and Technology grant POSC/EEA-SRI/61924/2004, the Directorate of National Intelligence, and National Science Foundation grants CCF  ... 
dblp:conf/nips/RabbatFN06 fatcat:cvicesgr6rcfvpgjnycfgl3cv4

Identifying Novel Candidate Genes Related to Apoptosis from a Protein-Protein Interaction Network

Baoman Wang, Fei Yuan, Xiangyin Kong, Lan-Dian Hu, Yu-Dong Cai
2015 Computational and Mathematical Methods in Medicine  
Second, a shortest path algorithm was applied to the graph to search for new candidate genes. Finally, the obtained genes were filtered by a permutation test.  ...  As a result, 26 genes were obtained, and we discuss their likelihood of being novel apoptosis-related genes by collecting evidence from published literature.  ...  The analyses of the obtained genes further suggest that they are related to apoptosis. Figure 1 : 1 The procedure and result of each step in our method. 3.2.17. PTPN1 (PTP1B).  ... 
doi:10.1155/2015/715639 pmid:26543496 pmcid:PMC4620916 fatcat:lbfvcbctkva6dmwjnlzjs2p77y

Estimating Times of Surgeries with Two Component Procedures

David P. Strum, Jerrold H. May, Allan R. Sampson, Luis G. Vargas, William E. Spangler
2003 Anesthesiology  
Variability inherent in the duration of surgical procedures complicates surgical scheduling. Modeling the duration and variability of surgeries might improve time estimates.  ...  Methods: The authors studied, retrospectively, 10,740 surgeries each with exactly two CPTs and 46,322 surgical cases with only one CPT from a large teaching hospital to determine if the distribution of  ...  The authors thank Gerard Bashein, M.D. (Professor of Anesthesiology, University of Washington, Seattle, Washington), for his assistance.  ... 
doi:10.1097/00000542-200301000-00035 pmid:12503002 fatcat:b2us7hw7ezeireei4pt37mr5x4

Page 7804 of Mathematical Reviews Vol. , Issue 2002K [page]

2002 Mathematical Reviews  
This paper discusses the extension of permutation methods first applied to Quine’s NF by Scott to Jensen’s system NFU (NF with extensionality weakened to allow urelements).  ...  There follow further independence results and variants of the principles BR and BR”, in particular, as to their relation to various choice principles.  ... 

Association Testing of the Mitochondrial Genome Using Pedigree Data

Chunyu Liu, Josée Dupuis, Martin G. Larson, Daniel Levy
2013 Genetic Epidemiology  
In addition, we proposed two permutation tests to obtain empirical p-values for these strategies.  ...  In this report, we sought to identify the best strategy for association testing of mitochondrial variants when genotype and phenotype data are available in pedigrees.  ...  The Center for Population Studies is supported by the Division of Intramural Research of the National Heart, Lung, and Blood Institute (Daniel Levy). We thank Dr.  ... 
doi:10.1002/gepi.21706 pmid:23319385 pmcid:PMC4171957 fatcat:7mv256p54rf4pkdxrwiwcpmjmm

Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostate Cancer

S. R. Setlur, T. E. Royce, A. Sboner, J.-M. Mosquera, F. Demichelis, M. D. Hofer, K. D. Mertz, M. Gerstein, M. A. Rubin
2007 Cancer Research  
Validation by unsupervised analysis on an independent data set using the gene expression signature from the HIV-I NEF pathway verified the accuracy of our method.  ...  The pathway that showed the most significant dysregulation, HIV-I NEF, was validated at both the transcript level and the protein level by quantitative PCR and immunohistochemical analysis, respectively  ...  The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C.  ... 
doi:10.1158/0008-5472.can-07-2173 pmid:17974971 fatcat:y3nkkuk6xzczfgcs4zw65uwx5q

Mutual enrichment in aggregated ranked lists with applications to gene expression regulation

Dalia Cohn-Alperovich, Alona Rabner, Ilona Kifer, Yael Mandel-Gutfreund, Zohar Yakhini
2016 Bioinformatics  
For example, a scenario in which genes targeted by multiple miRNAs play a central role in the DE signal but the effect of each single miRNA is too subtle to be detected, as shown in our results.  ...  Motivation: It is often the case in biological measurement data that results are given as a ranked list of quantities-for example, differential expression (DE) of genes as inferred from microarrays or  ...  Acknowledgements We thank Israel Steinfeld, from Agilent Laboratories, for useful comments and Shlomi Dvir for advice and help in the DE analysis.  ... 
doi:10.1093/bioinformatics/btw727 pmid:28011778 pmcid:PMC6041743 fatcat:nue26dkktfbnplwktkhm35msbi

Covert neurofeedback without awareness shapes cortical network spontaneous connectivity

Michal Ramot, Shany Grossman, Doron Friedman, Rafael Malach
2016 Proceedings of the National Academy of Sciences of the United States of America  
Results Implicit NF. A total of 18 participants was enrolled in this study. Two were removed from the experiment after the first day of scanning, due to excessive movement (Methods).  ...  Recent advances in functional MRI (fMRI) techniques and hardware have made real-time fMRI (rtfMRI) a viable method for NF (14).  ...  We thank the participants for volunteering to take part in the study.  ... 
doi:10.1073/pnas.1516857113 pmid:27071084 pmcid:PMC4855583 fatcat:nxjj7tyiozcanprplb4d4dgg3u

Differentiable DAG Sampling [article]

Bertrand Charpentier, Simon Kibler, Stephan Günnemann
2022 arXiv   pre-print
To this end, DP-DAG samples a DAG by successively (1) sampling a linear ordering of the node and (2) sampling edges consistent with the sampled linear ordering.  ...  We further propose VI-DP-DAG, a new method for DAG learning from observational data which combines DP-DAG with variational inference.  ...  Given the aforementioned methods for differentiable edge and permutation sampling, we propose a new simple and valid sampling procedure for DAG sampling which consists in three steps (see Fig. 1): (1  ... 
arXiv:2203.08509v1 fatcat:xw5fyrfcvzhhrhrlpvk45qau5q

Trajectory Splitting by Restricted Replication

Alexander Keller
2004 Monte Carlo Methods and Applications  
By derandomizing these techniques that are derived from randomized quasi-Monte Carlo integration, trajectory splitting for the quasi-Monte Carlo method becomes available.  ...  Acknowledgements The author is especially thankful to Thomas Kollig for his comments, and to Peter Schröder and Rolf Herken for supporting this research.  ...  The quasi-Monte Carlo method applies deterministic points that expose better uniformity properties than random numbers can obtain resulting in a much faster convergence on certain function dasses.  ... 
doi:10.1515/mcma.2004.10.3-4.321 fatcat:r5toyaizr5dofapm5z5agkvqvu

DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds

Diana M. Hendrickx, Terezinha Souza, Danyel G. J. Jennen, Jos C. S. Kleinjans
2016 Archives of Toxicology  
Applying DTNI on experimental data from TG-GATEs, we demonstrate that DTNI provides indepth information on the mode of action of compounds, in particular key events and potential molecular initiating events  ...  induced by a group of compounds influencing a common biological process.  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s00204-016-1922-5 pmid:28032149 pmcid:PMC5429357 fatcat:wjhrpan2zfdjxdz4ws4jvqzshm
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