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{userid:"satra", "refid":"4","repocollections":"","attachment":"","_thumb":"","articletype":"article","sectionheading":"","title":"Evaluation of volume-based and surface-based brain image registration methods.","year":"2010","author":"Arno Klein, Satrajit S Ghosh, Brian Avants, B T T Yeo, Bruce Fischl, Babak Ardekani, James C Gee, J J Mann, Ramin V Parsey","journal":"Neuroimage","volume":"51","number":"1","pages":"214-220","month":"May","doi":"10.1016\/j.neuroimage.2010.01.091","pubmed":"20123029","pdflink":"http:\/\/www.mendeley.com\/download\/public\/1121631\/4366884125\/6a27fb3d80567e44cd35e6d935d163850e04bd53\/dl.pdf","urllink":"","abstract":"Establishing correspondences across brains for the purposes of comparison and group analysis is almost universally done by registering images to one another either directly or via a template. However, there are many registration algorithms to choose from. A recent evaluation of fully automated nonlinear deformation methods applied to brain image registration was restricted to volume-based methods. The present study is the first that directly compares some of the most accurate of these volume registration methods with surface registration methods, as well as the first study to compare registrations of whole-head and brain-only (de-skulled) images. We used permutation tests to compare the overlap or Hausdorff distance performance for more than 16,000 registrations between 80 manually labeled brain images. We compared every combination of volume-based and surface-based labels, registration, and evaluation. Our primary findings are the following: 1. de-skulling aids volume registration methods; 2. custom-made optimal average templates improve registration over direct pairwise registration; and 3. resampling volume labels on surfaces or converting surface labels to volumes introduces distortions that preclude a fair comparison between the highest ranking volume and surface registration methods using present resampling methods. From the results of this study, we recommend constructing a custom template from a limited sample drawn from the same or a similar representative population, using the same algorithm used for registering brains to the template.","note":"","tags":"Adult,Algorithms,Brain,Female,Head,Humans,Image Processing, Computer-Assisted,Imaging, Three-Dimensional,Magnetic Resonance Imaging,Male,Organ Size,Software,Young Adult","publisher":"","booktitle":"","editor":"","address":"","school":"","issn":"1095-9572","isi":"","key":"Klein2010","howpublished":""}
,

{userid:"carmenjeronimo", "articletype":"article","pages":"2612-2624","author":"F R Talukdar, S C Soares Lima, R Khoueiry, R S Laskar, C Cuenin, B P Sorroche, A C Boisson, B Abedi-Ardekani, C Carreira, D Menya, C P Dzamalala, M Assefa, A Aseffa, V Miranda-Gon\u00e7alves, C Jer\u00f3nimo, R M Henrique, R Shakeri, R Malekzadeh, N Gasmelseed, M Ellaithi, N Gangane, D R S Middleton, F Le Calvez-Kelm, A Ghantous, M L Roux, J Sch\u00fcz, V McCormack, M I Parker, L F R Pinto, Z Herceg","year":"2021","title":"Genome-Wide DNA Methylation Profiling of Esophageal Squamous Cell Carcinoma from Global High-Incidence Regions Identifies Crucial Genes and Potential Cancer Markers","month":"","journal":"Cancer Res","publisher":"","volume":"81","number":"10","note":"1538-7445 xD;Talukdar, Fazlur Rahman xD;Orcid: 0000-0002-6558-5543 xD;Soares Lima, Sheila C xD;Orcid: 0000-0002-6742-3708 xD;Khoueiry, Rita xD;Laskar, Ruhina Shirin xD;Orcid: 0000-0001-6455-094x xD;Cuenin, Cyrille xD;Sorroche, Bruna Pereira xD;Orcid: 0000-0001-9802-8236 xD;Boisson, Anne-Claire xD;Abedi-Ardekani, Behnoush xD;Carreira, Christine xD;Menya, Diana xD;Dzamalala, Charles P xD;Assefa, Mathewos xD;Aseffa, Abraham xD;Orcid: 0000-0002-8028-1150 xD;Miranda-Gon\u00e7alves, Vera xD;Jer\u00f3nimo, Carmen xD;Orcid: 0000-0003-4186-5345 xD;Henrique, Rui M xD;Orcid: 0000-0003-3171-4666 xD;Shakeri, Ramin xD;Malekzadeh, Reza xD;Orcid: 0000-0002-9820-6335 xD;Gasmelseed, Nagla xD;Ellaithi, Mona xD;Orcid: 0000-0002-8380-0227 xD;Gangane, Nitin xD;Orcid: 0000-0003-0190-4215 xD;Middleton, Daniel R S xD;Orcid: 0000-0003-2450-8610 xD;Le Calvez-Kelm, Florence xD;Ghantous, Akram xD;Orcid: 0000-0002-2582-6402 xD;Roux, Maria Leon xD;Sch\u00fcz, Joachim xD;Orcid: 0000-0001-9687-2134 xD;McCormack, Valerie xD;Orcid: 0000-0001-7397-3442 xD;Parker, M Iqbal xD;Orcid: 0000-0001-7087-3825 xD;Pinto, Luis Felipe Ribeiro xD;Herceg, Zdenko xD;MC_PC_16097\/MRC_\/Medical Research Council\/United Kingdom xD;R21 CA191965\/CA\/NCI NIH HHS\/United States xD;Journal Article xD;Research Support, N.I.H., Extramural xD;Research Support, Non-U.S. Gov't xD;United States xD;2021\/03\/21 xD;Cancer Res. 2021 May 15;81(10):2612-2624. doi: 10.1158\/0008-5472.CAN-20-3445. Epub 2021 Mar 19.","tags":"Adult,Aged,Aged, 80 and over,Biomarkers, Tumor\/*genetics,Case-Control Studies,*DNA Methylation,DNA, Neoplasm\/analysis\/*genetics,*Epigenesis, Genetic,Esophageal Neoplasms\/epidemiology\/genetics\/*pathology,Esophageal Squamous Cell Carcinoma\/epidemiology\/genetics\/*pathology,Female,Follow-Up Studies,Gene Expression Regulation, Neoplastic,*Genome, Human,Global Health,Humans,Incidence,Male,Middle Aged,Prognosis","booktitle":"","editor":"","abstract":"Epigenetic mechanisms such as aberrant DNA methylation (DNAme) are known to drive esophageal squamous cell carcinoma (ESCC), yet they remain poorly understood. Here, we studied tumor-specific DNAme in ESCC cases from nine high-incidence countries of Africa, Asia, and South America. Infinium MethylationEPIC array was performed on 108 tumors and 51 normal tissues adjacent to the tumors (NAT) in the discovery phase, and targeted pyrosequencing was performed on 132 tumors and 36 NAT in the replication phase. Top genes for replication were prioritized by weighting methylation results using RNA-sequencing data from The Cancer Genome Atlas and GTEx and validated by qPCR. Methylome analysis comparing tumor and NAT identified 6,796 differentially methylated positions (DMP) and 866 differential methylated regions (DMR), with a 30% methylation (\u0394\u03b2) difference. The majority of identified DMPs and DMRs were hypermethylated in tumors, particularly in promoters and gene-body regions of genes involved in transcription activation. The top three prioritized genes for replication, PAX9, SIM2, and THSD4, had similar methylation differences in the discovery and replication sets. These genes were exclusively expressed in normal esophageal tissues in GTEx and downregulated in tumors. The specificity and sensitivity of these DNAme events in discriminating tumors from NAT were assessed. Our study identified novel, robust, and crucial tumor-specific DNAme events in ESCC tumors across several high-incidence populations of the world. Methylome changes identified in this study may serve as potential targets for biomarker discovery and warrant further functional characterization. SIGNIFICANCE: This largest genome-wide DNA methylation study on ESCC from high-incidence populations of the world identifies functionally relevant and robust DNAme events that could serve as potential tumor-specific markers. GRAPHICAL ABSTRACT: http:\/\/cancerres.aacrjournals.org\/content\/canres\/81\/10\/2612\/F1.large.jpg.","address":"","school":"","issn":"0008-5472","doi":"10.1158\/0008-5472.Can-20-3445","isi":"","pubmed":"","key":"Talukdar2021","howpublished":"","urllink":"","refid":304,"weight":304}
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