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2011
Nature Genetics
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1,4 , Johan T den Dunnen 1 , Gertjan van Ommen 1,4 , Erik van Mulligen 3,4 , Bharat Singh 2,3 , Rob Hooft 2,4 , Marco Roos 1,2,4 , Joel Hammond 5 , Bruce Kiesel 5 , Belinda Giardine 6 , Jan Velterop 4,7 ...
, Paul Groth 4,8 & Erik Schultes 1,4
Figure 2 2 A proposal for the future of scholarly communication. ...
doi:10.1038/ng0411-281
pmid:21445068
fatcat:ffxifjtm4vcr3jw3mcjxaclqq4
Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood
2015
European Journal of Human Genetics
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Asterisks represent statistical significance from a Student's t-test (*Po0.05, **Po0.01). Error bars represent SEM values. ...
Canonical pathway analysis using IPA further confirmed our initial Global test results, as common pathways reported were those of diabetes mellitus, Toll-like receptor and T-cell receptor signaling. ...
doi:10.1038/ejhg.2014.281
pmid:25626709
pmcid:PMC4592077
fatcat:lp6prx7ynjhnjay77jud46mv3m
Promoter DNA Methylation Pattern Identifies Prognostic Subgroups in Childhood T-Cell Acute Lymphoblastic Leukemia
2013
PLoS ONE
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Treatment of pediatric T-cell acute lymphoblastic leukemia (T-ALL) has improved, but there is a considerable fraction of patients experiencing a poor outcome. ...
CIMP2 T-ALL patients had significantly worse overall and event free survival (p = 0.02 and p = 0.001, respectively) compared to CIMP+ cases. ...
However, about 15% derive from the T-cell lineage (T-ALL). ...
doi:10.1371/journal.pone.0065373
pmid:23762353
pmcid:PMC3675104
fatcat:n3cytc5cezfk3kfldbecju2e3e
Acute stress impairs inhibitory control based on individual differences in parasympathetic nervous system activity
2017
Biological Psychology
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Roos received support from HHS-2014-ACF-ACYF-CA-0803. Elliot Berkman received support from NIH grants R01 AG048840, R21 CA175241 and P50 DA035763. Philip A. ...
doi:10.1016/j.biopsycho.2017.03.004
pmid:28268165
pmcid:PMC5448703
fatcat:jwwj3tasljdx5crf6ora6kopc4
Immortalization of T-Cells Is Accompanied by Gradual Changes in CpG Methylation Resulting in a Profile Resembling a Subset of T-Cell Leukemias
2014
Neoplasia: An International Journal for Oncology Research
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Interestingly, the pattern of CpG site methylation observed in immortal T-cell cultures was similar to clinical T-cell acute lymphoblastic leukemia (T-ALL) samples classified as CpG island methylator phenotype ...
The presence of non-random methylation events in in vitro immortalized T-cell cultures and diagnostic T-ALL samples indicates altered methylation of CpG sites with a possible role in malignant hematopoiesis ...
cultures and in relation to diagnostic T-cell acute lymphoblastic leukemia (T-ALL) samples. ...
doi:10.1016/j.neo.2014.07.001
pmid:25065939
pmcid:PMC4198827
fatcat:lhbcvy7grfhu3bcoax2lrdh2hi
Conceptual precision is key in acute stress research: A commentary on Shields, Sazma, & Yonelinas, 2016
2017
Neuroscience and Biobehavioral Reviews
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., 2008) , so acute stressors might have greater effects on Stop Signal (consistent with a recent finding by our research group; Roos et al., 2017) , compared with Go/No-Go inhibition performance. ...
Similarly, our own research examining the effects of acute stress on stop-signal inhibition found that parasympathetic augmentation to the TSST predicted individual differences in EF impairment (Roos ...
doi:10.1016/j.neubiorev.2017.10.005
pmid:28988779
pmcid:PMC5840802
fatcat:qm557bpumnatbl2jetfetznhyy
A putative role for genome-wide epigenetic regulatory mechanisms in Huntington's disease: A computational assessment
2017
F1000Research
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Differential expression was computed using moderated t statistics with the package limma 35 (version 3.14.1), which is provided by the bioconductor project 36 , R version https://www.bioconductor. org/ ...
doi:10.12688/f1000research.9703.1
fatcat:cn4drsedardsdgk6fxwqjb2yh4
DNA Methylation Adds Prognostic Value to Minimal Residual Disease Status in Pediatric T-Cell Acute Lymphoblastic Leukemia
2016
Pediatric Blood & Cancer
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INTRODUCTION T-cell acute lymphoblastic leukemia (T-ALL) accounts for 10-15% of childhood ALL, but is more common among adolescents and adults. ...
[8, 22, 23] The prognostic relevance of CIMP classification in pediatric T-ALL shown in this paper confirms our previous finding in a separate T-ALL cohort. ...
doi:10.1002/pbc.25958
pmid:26928953
fatcat:dzn7majbwrb5lkk74veqyeprhm
T helper 17.1 cells associate with multiple sclerosis disease activity: perspectives for early intervention
2018
Brain
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Across all pro-inflammatory T helper cells analysed in relapsing-remitting multiple sclerosis blood, Th1-like Th17 subpopulation T helper 17.1 (Th17.1; CCR6 + CXCR3 + CCR4 À ) expressed the highest very ...
Interleukin-17-expressing CD4 + T helper 17 (Th17) cells are considered as critical regulators of multiple sclerosis disease activity. ...
staining of the T helper subsets of interest. ...
doi:10.1093/brain/awy069
pmid:29659729
fatcat:4oblt2djnvdf7c2rluca3g3lm4
Common disease signatures from gene expression analysis in Huntington's disease human blood and brain
2016
Orphanet Journal of Rare Diseases
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Common annotations included major histocompatibility complex location, lymphocyte activation, cytokine activity, T cell activation and adaptive immune response. ...
doi:10.1186/s13023-016-0475-2
pmid:27476530
pmcid:PMC4968014
fatcat:kietohcjxvfixdv2sc7qxjdmge
Drug prioritization using the semantic properties of a knowledge graph
2019
Scientific Reports
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Based on the extracted features, the classifier is trained/cross-validated to classify the status of each drug-disease combination as "Approved" (A) or "Terminated" (T). www.nature.com/scientificreports ...
doi:10.1038/s41598-019-42806-6
pmid:31000794
pmcid:PMC6472420
fatcat:oytdymtcqjgxxel2h7f45rf3oy
The Implicitome: A Resource for Rationalizing Gene-Disease Associations
2016
PLoS ONE
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High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations.
doi:10.1371/journal.pone.0149621
pmid:26919047
pmcid:PMC4769089
fatcat:dru6ynlspfaf7dsrfj6ojiqg74
Supplemental material for Clinical prediction of thrombectomy eligibility: A systematic review and 4-item decision tree
2018
Figshare
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Supplemental material for Clinical prediction of thrombectomy eligibility: A systematic review and 4-item decision tree by Gaia T Koster, T Truc My Nguyen, Erik W van Zwet, Bjarty L Garcia, Hannah R Rowling ...
, J Bosch, Wouter J Schonewille, Birgitta K Velthuis, Ido R van der Wijngaard, Heleen M den Hertog, Yvo BWEM Roos, Marianne AA van Walderveen, Marieke JH Wermer and Nyika D Kruyt in International Journal ...
doi:10.25384/sage.7087637.v1
fatcat:eoo5nf2zzrbflp2clx7kzfscsm
Clinical prediction of thrombectomy eligibility: A systematic review and 4-item decision tree
2018
International Journal of Stroke
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Continuous variables are compared using the t test or Mann-Whitney U test, and are presented as mean AE standard deviation or median (interquartile range, IQR) if appropriate. ...
Koster http://orcid.org/0000-0001-7138-5313 T Truc My Nguyen http://orcid.org/0000-0003-3545-3053 ...
Funding The author(s) disclosed receipt of the following financial support for the research, authorship and/or publication of this article: This work was supported by The Netherlands Brain
ORCID iD Gaia T ...
doi:10.1177/1747493018801225
pmid:30209989
fatcat:3mtkjtuznjgotinowlpnddtqbe
Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington's disease peripheral blood samples
2016
Metabolomics
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Introduction Metabolic changes have been frequently associated with Huntington's disease (HD). At the same time peripheral blood represents a minimally invasive sampling avenue with little distress to Huntington's disease patients especially when brain or other tissue samples are difficult to collect. Objectives We investigated the levels of 163 metabolites in HD patient and control serum samples in order to identify disease related changes. Additionally, we integrated the metabolomics data
doi:10.1007/s11306-016-1084-8
pmid:27524956
pmcid:PMC4963448
fatcat:2iog33cdyncsldoaustht5xfm4
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... our previously published next generation sequencing-based gene expression data from the same patients in order to interconnect the metabolomics changes with transcriptional alterations. Methods This analysis was performed using targeted metabolomics and flow injection electrospray ionization tandem mass spectrometry in 133 serum samples from 97 Huntington's disease patients (29 pre-symptomatic and 68 symptomatic) and 36 controls. Results By comparing HD mutation carriers with controls we identified 3 metabolites significantly changed in HD (serine and threonine and one phosphatidylcholine-PC ae C36:0) and an additional 8 phosphatidylcholines (PC aa C38:6, PC aa C36:0, PC ae C38:0, PC aa C38:0, PC ae C38:6, PC ae C42:0, PC aa C36:5 and PC ae C36:0) that exhibited a significant association with disease severity. Using workflow based exploitation of pathway databases and by integrating our metabolomics data with our gene expression data from the same patients we identified 4 deregulated phosphatidylcholine metabolism related genes (ALDH1B1, MBOAT1, MTRR and PLB1) that showed significant association with the changes in metabolite concentrations. Conclusion Our results support the notion that phosphatidylcholine metabolism is deregulated in HD blood and that these metabolite alterations are associated with specific gene expression changes.
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