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Book ; Online: Truly Bayesian Entropy Estimation

Papageorgiou, Ioannis / Kontoyiannis, Ioannis

2022

Abstract: Estimating the entropy rate of discrete time series is a challenging problem with important applications in numerous areas including neuroscience, genomics, image processing and natural language processing. A number of approaches have been developed for ... ...

Abstract	Estimating the entropy rate of discrete time series is a challenging problem with important applications in numerous areas including neuroscience, genomics, image processing and natural language processing. A number of approaches have been developed for this task, typically based either on universal data compression algorithms, or on statistical estimators of the underlying process distribution. In this work, we propose a fully-Bayesian approach for entropy estimation. Building on the recently introduced Bayesian Context Trees (BCT) framework for modelling discrete time series as variable-memory Markov chains, we show that it is possible to sample directly from the induced posterior on the entropy rate. This can be used to estimate the entire posterior distribution, providing much richer information than point estimates. We develop theoretical results for the posterior distribution of the entropy rate, including proofs of consistency and asymptotic normality. The practical utility of the method is illustrated on both simulated and real-world data, where it is found to outperform state-of-the-art alternatives. Comment: arXiv admin note: substantial text overlap with arXiv:2202.02239
Keywords	Statistics - Methodology ; Computer Science - Information Theory
Subject code	310
Publishing date	2022-12-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Posterior Representations for Bayesian Context Trees

Papageorgiou, Ioannis / Kontoyiannis, Ioannis

Sampling, Estimation and Convergence

2022

Abstract: We revisit the Bayesian Context Trees (BCT) modelling framework for discrete time series, which was recently found to be very effective in numerous tasks including model selection, estimation and prediction. A novel representation of the induced ... ...

Abstract	We revisit the Bayesian Context Trees (BCT) modelling framework for discrete time series, which was recently found to be very effective in numerous tasks including model selection, estimation and prediction. A novel representation of the induced posterior distribution on model space is derived in terms of a simple branching process, and several consequences of this are explored in theory and in practice. First, it is shown that the branching process representation leads to a simple variable-dimensional Monte Carlo sampler for the joint posterior distribution on models and parameters, which can efficiently produce independent samples. This sampler is found to be more efficient than earlier MCMC samplers for the same tasks. Then, the branching process representation is used to establish the asymptotic consistency of the BCT posterior, including the derivation of an almost-sure convergence rate. Finally, an extensive study is carried out on the performance of the induced Bayesian entropy estimator. Its utility is illustrated through both simulation experiments and real-world applications, where it is found to outperform several state-of-the-art methods.
Keywords	Statistics - Methodology ; Computer Science - Information Theory ; Mathematics - Statistics Theory
Subject code	310
Publishing date	2022-02-04
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Two Weeks of Headache and Facial Numbness.

Papageorgiou, Ioannis V

Military medicine

2016 Volume 181, Issue 3, Page(s) 186–188

MeSH term(s)	Brain/diagnostic imaging ; Diagnosis, Differential ; Epidermal Cyst/complications ; Epidermal Cyst/diagnostic imaging ; Face ; Headache/etiology ; Humans ; Hypesthesia/etiology ; Magnetic Resonance Imaging ; Male ; Middle Aged
Language	English
Publishing date	2016-03
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	391061-1
ISSN	1930-613X ; 0026-4075
ISSN (online)	1930-613X
ISSN	0026-4075
DOI	10.7205/MILMED-D-15-00531
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Article ; Online: The Right for Regional Integration Organisations to Protect Democracy

Nyman-Metcalf Katrin / Papageorgiou Ioannis

Baltic Journal of European studies, Vol 6, Iss 1, Pp 28-

Legitimacy at the Regional Level?

2016 Volume 47

Abstract: Recently there have been several examples of different regional integration systems intervening to prevent unconstitutional events. The interventions can be based on explicit powers or be developed in response to events. This happens despite most ... ...

Abstract	Recently there have been several examples of different regional integration systems intervening to prevent unconstitutional events. The interventions can be based on explicit powers or be developed in response to events. This happens despite most regional integration systems having economic cooperation rather than explicit democratisation aims. Organs that issue laws or take constraining decisions must have a clear right to do this and a basis for exercising power-in other words, be legitimate. Where legitimacy comes from is debated, but as most countries today are democracies or purport to be, it somehow emanates from the people. National governments have a higher degree of legitimacy than regional integration organisations, possibly except the European Union. Regional integration organisations have to prove their legitimacy. The article examines if, to what extent, and on what basis regional integration systems have the right to exercise an independent role on the global stage. Legitimacy is a precondition for effective application of decisions of the organisation. Given the frequent lack of strong enforcement mechanisms, the question of legitimacy becomes even more important. With strong legitimacy, decisions taken by the regional integration organisation will be followed to a large extent even despite absence of effective enforcement mechanisms.
Keywords	african union ; asean ; democracy ; enforcement ; european union ; legitimacy ; political community ; regional institutions ; regional integration ; regional courts of justice ; the americas ; Political science ; J ; International relations ; JZ2-6530
Language	English
Publishing date	2016-02-01T00:00:00Z
Publisher	Sciendo
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Segmented 3D Echo Planar Acquisition for Rapid Susceptibility-Weighted Imaging: Application to Microhemorrhage Detection in Traumatic Brain Injury.

Wang, Wen-Tung / Li, Ningzhi / Papageorgiou, Ioannis / Chan, Leighton / Pham, Dzung L / Butman, John A

Journal of magnetic resonance imaging : JMRI

2022 Volume 56, Issue 5, Page(s) 1529–1535

Abstract: Background: Susceptibility-weighted imaging (SWI) provides superior image contrast of cerebral microhemorrhages (CMBs). It is based on a three-dimensional (3D) gradient echo (GRE) sequence with a relatively long imaging time.: Purpose: To evaluate ... ...

Abstract	Background: Susceptibility-weighted imaging (SWI) provides superior image contrast of cerebral microhemorrhages (CMBs). It is based on a three-dimensional (3D) gradient echo (GRE) sequence with a relatively long imaging time. Purpose: To evaluate whether an accelerated 3D segmented echo planar imaging SWI is comparable to GRE SWI in detecting CMBs in traumatic brain injury (TBI). Study type: Prospective. Subjects: Four healthy volunteers and 46 consecutive subjects (38.0 ± 14.4 years, 16 females; 12 mild, 13 moderate, and 7 severe TBI). Field strength/sequence: A 3 T scanner/3D gradient echo and 3D segmented echo planar imaging (segEPI). Assessment: Brain images were acquired using GRE and segEPI in a single session (imaging time = 9 minutes 47 seconds and 1 minute 30 seconds, respectively). The signal-to-noise ratio (SNR) calculated from healthy volunteer thalamus and centrum semiovale were compared. CMBs were counted by three raters blinded to diagnostic information. Statistical tests: A t-test was used to assess SNR difference. Pearson correlation and Wilcoxon signed-rank test were performed using CMB counts. The intermethod agreement was evaluated using Bland-Altman method. Intermethod and interrater reliabilities of image-based diffuse axonal injury (DAI) diagnoses were evaluated using Cohen's kappa and percent agreement. P ≤ 0.05 was considered statistically significant. Results: Thalamus SNRs were 16.9 ± 2.2 and 16.5 ± 3 for GRE and segEPI (P = 0.84), respectively. Centrum semiovale SNRs were 25.8 ± 4.6 and 21.1 ± 2.7 (P = 0.13). The correlation coefficient of CMBs was 0.93, and differences were not significant (P = 0.56-0.85). For DAI diagnoses, Cohen's kappa was 0.62-0.84 and percent agreement was 85%-94%. Data conclusion: CMB counts on segEPI and GRE were highly correlated, and DAI diagnosis was made equally effectively. segEPI SWI can potentially replace GRE SWI in detecting TBI CMBs, especially when time constraints are critical. Evidence level: 1 TECHNICAL EFFICACY: Stage 2.
MeSH term(s)	Brain Injuries, Traumatic/complications ; Brain Injuries, Traumatic/diagnostic imaging ; Diffuse Axonal Injury ; Echo-Planar Imaging/methods ; Female ; Humans ; Magnetic Resonance Imaging/methods ; Prospective Studies
Language	English
Publishing date	2022-07-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1146614-5
ISSN	1522-2586 ; 1053-1807
ISSN (online)	1522-2586
ISSN	1053-1807
DOI	10.1002/jmri.28326
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Zs.A 3648: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: The European Union Digital Single Market—Challenges and Impact for the EU Neighbourhood States

Nyman-Metcalf Katrin / Papageorgiou Ioannis F.

Baltic Journal of European studies, Vol 8, Iss 2, Pp 7-

2018 Volume 23

Abstract: The digital single market is one of the most important objectives and challenges for the European Union. However, given that digitalisation implies a borderless world it requires a different form of governance and has distinctive features from other ... ...

Abstract	The digital single market is one of the most important objectives and challenges for the European Union. However, given that digitalisation implies a borderless world it requires a different form of governance and has distinctive features from other aspects of the single market. In addition, it raises a number of practical and political issues for countries outside the EU, but which maintain close economic and trade relations with the latter. The article examines the regulatory implications of the digital world from the point of view of states involved in the European Neighbourhood Policy, in particular Georgia, and looks into the future challenges in this process.
Keywords	digitalisation ; eu single market ; georgia ; neighbourhood policy ; Political science ; J ; International relations ; JZ2-6530
Language	English
Publishing date	2018-09-01T00:00:00Z
Publisher	Sciendo
Document type	Article ; Online
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Article ; Online: Identification and validation of microRNAs directly regulating the UDP-glucuronosyltransferase 1A subfamily enzymes by a functional genomics approach.

Papageorgiou, Ioannis / Court, Michael H

Biochemical pharmacology

2017 Volume 137, Page(s) 93–106

Abstract: Posttranscriptional repression of UDP-glucuronosyltransferase (UGT) 1A expression by microRNAs (miRNAs) may be an important mechanism underlying interindividual variability in drug glucuronidation. Furthermore, the UGT1A 3'-UTR shared by all UGT1A ... ...

Abstract	Posttranscriptional repression of UDP-glucuronosyltransferase (UGT) 1A expression by microRNAs (miRNAs) may be an important mechanism underlying interindividual variability in drug glucuronidation. Furthermore, the UGT1A 3'-UTR shared by all UGT1A enzymes is polymorphic, containing three linked SNPs (rs10929303, rs1042640, and rs8330) that could influence miRNA binding. The aim of this study was to identify the complete complement of miRNAs that could regulate UGT1A expression through binding to the reference and/or common variant UGT1A 3'-UTR. Luciferase reporter plasmids containing either the reference or variant UGT1A 3'-UTR were screened against a 2048 human miRNA library to identify those miRNAs that decrease luciferase activity by at least 30% when co-transfected into HEK293 cells. Four novel miRNAs (miR-103b, miR-141-3p, miR-200a-3p, and miR-376b-3p) were identified that repressed both reference and variant UGT1A 3'-UTR, while two other miRNAs selectively repressed the reference (miR-1286) or variant (miR-21-3p) 3'-UTR. Deletion and mutagenesis studies confirmed the binding site location for each miRNA. rs8330 disrupted miR-1286 binding to the reference UGT1A 3'-UTR, while rs10929303 enhanced miR-21-3p binding to the variant 3'-UTR. Transfection of miR-21-3p, miR-103b, miR-141-3p, miR-200a-3p, and miR-376b-3p mimics into LS180 human intestinal cells showed repression of UGT1A1 and UGT1A6 mediated glucuronidation and mRNA without affecting UGT2B7 activity or mRNA. Furthermore, transfection of miR-21-3p, miR-141-3p, and miR-200a-3p into primary human hepatocytes, repressed UGT1A1 activity and mRNA without affecting CYP3A activity. Finally, miR-21-3p and miR-200a-3p expression were negatively correlated with UGT1A6 activity and mRNA in human liver samples. Thus, UGT1A is regulated by multiple miRNAs with some showing allele-dependent effects.
MeSH term(s)	Adult ; Aged ; Child ; Child, Preschool ; Female ; Genomics/methods ; Glucuronosyltransferase/genetics ; Glucuronosyltransferase/metabolism ; HEK293 Cells ; Hepatocytes/physiology ; Humans ; Male ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Middle Aged ; Young Adult
Chemical Substances	MicroRNAs ; UGT1A1 enzyme (EC 2.4.1.-) ; Glucuronosyltransferase (EC 2.4.1.17)
Language	English
Publishing date	2017-04-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	208787-x
ISSN	1873-2968 ; 0006-2952
ISSN (online)	1873-2968
ISSN	0006-2952
DOI	10.1016/j.bcp.2017.04.017
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Article ; Online: Identification and validation of the microRNA response elements in the 3'-untranslated region of the UDP glucuronosyltransferase (UGT) 2B7 and 2B15 genes by a functional genomics approach.

Papageorgiou, Ioannis / Court, Michael H

Biochemical pharmacology

2017 Volume 146, Page(s) 199–213

Abstract: Posttranscriptional repression of UDP-glucuronosyltransferase (UGT) 2B7 and 2B15 expression by microRNAs (miRNAs) may be an important mechanism underlying inter-individual variability in drug glucuronidation. Furthermore, the UGT2B15 3'-UTR contains a ... ...

Abstract	Posttranscriptional repression of UDP-glucuronosyltransferase (UGT) 2B7 and 2B15 expression by microRNAs (miRNAs) may be an important mechanism underlying inter-individual variability in drug glucuronidation. Furthermore, the UGT2B15 3'-UTR contains a common SNP (rs3100) that could influence miRNA binding. The aim of this study was to identify the complete complement of miRNAs that could regulate UGT2B7 and UGT2B15 expression through binding to the reference and/or variant 3'-UTRs. Luciferase reporter plasmids containing either the reference or variant 3'-UTRs were screened against a 2,048 human miRNA library to identify those miRNAs that decrease luciferase activity by at least 30% when co-transfected into HEK293 cells. Six novel miRNAs (miR-1293, miR-3664-3p, miR-4317, miR-513c-3p, miR-4483, and miR-142-3p) were identified that repressed the reference UGT2B7 3'-UTR, while twelve novel miRNAs (miR-770-5p, miR-103b, miR-3924, miR-376b-3p, miR-455-5p, miR-605, miR-624-3p, miR-4712-5p, miR-3675-3p, miR-6500-5p, miR-548as-3p, and miR-4292) repressed both the reference and rs3100 variant UGT2B15 3'-UTR. Deletion and mutagenesis studies confirmed the binding site location of each miRNA. Although the UGT2B15 rs3100 SNP was located within the miR-376c-3p response element, there was no effect on miRNA binding. miR-142-3p, miR-3664-3p, miR-4317, miR-455-5p, miR-376c-3p, miR-770-5p, miR-3675-3p, miR-331-5p, miR-605, and miR-376b-3p transcript levels were measured by quantitative PCR and correlated with UGT2B7 and UGT2B15 enzyme activities in 27 human liver samples. A significant negative correlation (R
MeSH term(s)	3' Untranslated Regions/genetics ; Adult ; Aged ; Child ; Child, Preschool ; Female ; Gene Expression Regulation, Enzymologic ; Genomics ; Glucuronosyltransferase/genetics ; Glucuronosyltransferase/metabolism ; Humans ; Liver/metabolism ; Male ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Middle Aged ; Reproducibility of Results ; Response Elements/genetics ; Young Adult
Chemical Substances	3' Untranslated Regions ; MicroRNAs ; UGT2B7 protein, human (EC 2.4.1.-) ; Glucuronosyltransferase (EC 2.4.1.17) ; UDP-glucuronosyltransferase 2B15, human (EC 2.4.1.17)
Language	English
Publishing date	2017-09-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	208787-x
ISSN	1873-2968 ; 0006-2952
ISSN (online)	1873-2968
ISSN	0006-2952
DOI	10.1016/j.bcp.2017.09.013
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Article: Lung-Targeted Delivery of Dimethyl Fumarate Promotes the Reversal of Age-Dependent Established Lung Fibrosis

Kato, Kosuke / Papageorgiou, Ioannis / Shin, Yoon-Joo / Kleinhenz, Jennifer M. / Palumbo, Sunny / Hahn, Seongmin / Irish, Joseph D. / Rounseville, Skye P. / Knox, Kenneth S. / Hecker, Louise

Antioxidants. 2022 Feb. 28, v. 11, no. 3

2022

Abstract: Idiopathic pulmonary fibrosis (IPF), a severe and deadly form of lung fibrosis, is widely regarded as a disease of aging. We previously demonstrated that aged mice with persistent lung fibrosis and IPF lung myofibroblasts exhibit deficient Nrf2-mediated ... ...

Abstract	Idiopathic pulmonary fibrosis (IPF), a severe and deadly form of lung fibrosis, is widely regarded as a disease of aging. We previously demonstrated that aged mice with persistent lung fibrosis and IPF lung myofibroblasts exhibit deficient Nrf2-mediated antioxidant responses. Tecfidera is an orally administered FDA-approved drug for the treatment of multiple sclerosis, where the active pharmaceutical ingredient is dimethyl fumarate (DMF), an active Nrf2 activator. However, no studies have evaluated the efficacy of DMF for age-associated persistent lung fibrosis. Here, we demonstrate that in IPF lung fibroblasts, DMF treatment inhibited both TGF-β-mediated pro-fibrotic phenotypes and led to a reversal of established pro-fibrotic phenotypes. We also evaluated the pre-clinical efficacy of lung-targeted (inhaled) vs. systemic (oral) delivery of DMF in an aging murine model of bleomycin-induced persistent lung fibrosis. DMF or vehicle was administered daily to aged mice by oral gavage or intranasal delivery from 3–6 weeks post-injury when mice exhibited non-resolving lung fibrosis. In contrast to systemic (oral) delivery, only lung-targeted (inhaled) delivery of DMF restored lung Nrf2 expression levels, reduced lung oxidative stress, and promoted the resolution of age-dependent established fibrosis. This is the first study to demonstrate the efficacy of lung-targeted DMF delivery to promote the resolution of age-dependent established lung fibrosis.
Keywords	active pharmaceutical ingredients ; animal models ; antioxidants ; dimethyl fumarate ; drugs ; fibroblasts ; fibrosis ; lungs ; oxidative stress ; pulmonary fibrosis ; sclerosis
Language	English
Dates of publication	2022-0228
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2704216-9
ISSN	2076-3921
ISSN	2076-3921
DOI	10.3390/antiox11030492
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Pharmacogenomics of poor drug metabolism in Greyhounds: Cytochrome P450 (CYP) 2B11 genetic variation, breed distribution, and functional characterization.

Martinez, Stephanie E / Andresen, Marie C / Zhu, Zhaohui / Papageorgiou, Ioannis / Court, Michael H

Scientific reports

2020 Volume 10, Issue 1, Page(s) 69

Abstract: Greyhounds recover more slowly from certain injectable anesthetics than other dog breeds. Previous studies implicate cytochrome P450 (CYP) 2B11 as an important clearance mechanism for these drugs and suggest Greyhounds are deficient in CYP2B11. However, ... ...

Abstract	Greyhounds recover more slowly from certain injectable anesthetics than other dog breeds. Previous studies implicate cytochrome P450 (CYP) 2B11 as an important clearance mechanism for these drugs and suggest Greyhounds are deficient in CYP2B11. However, no CYP2B11 gene mutations have been identified that explain this deficiency in Greyhounds. The objectives of this study were to provide additional evidence for CYP2B11 deficiency in Greyhounds, determine the mechanisms underlying this deficiency, and identify CYP2B11 mutations that contribute to this phenotype in Greyhounds. Greyhound livers metabolized CYP2B11 substrates slower, possessed lower CYP2B11 protein abundance, but had similar or higher mRNA expression than other breeds. Gene resequencing identified three CYP2B11 haplotypes, H1 (reference), H2, and H3 that were differentiated by mutations in the gene 3'-untranslated region (3'-UTR). Compared with 63 other dog breeds, Greyhounds had the highest CYP2B11-H3 allele frequency, while CYP2B11-H2 was widely distributed across most breeds. Using 3'-UTR luciferase reporter constructs, CYP2B11-H3 showed markedly lower gene expression (over 70%) compared to CYP2B11-H1 while CYP2B11-H2 expression was intermediate. Truncated mRNA transcripts were observed in CYP2B11-H2 and CYP2B11-H3 but not CYP2B11-H1 transfected cells. Our results implicate CYP2B11 3'-UTR mutations as a cause of decreased CYP2B11 enzyme expression in Greyhounds through reduced translational efficiency.
MeSH term(s)	3' Untranslated Regions ; Alleles ; Anesthetics, Intravenous/metabolism ; Animals ; Aryl Hydrocarbon Hydroxylases/genetics ; Aryl Hydrocarbon Hydroxylases/metabolism ; Breeding ; Cytochrome P450 Family 2/genetics ; Cytochrome P450 Family 2/metabolism ; Dogs ; Gene Frequency ; Genetic Variation ; Haplotypes ; Linkage Disequilibrium ; Liver/enzymology ; Liver/metabolism ; Microsomes, Liver/metabolism ; Pharmacogenetics/methods ; Propofol/metabolism ; RNA Splicing ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/isolation & purification ; Steroid Hydroxylases/genetics ; Steroid Hydroxylases/metabolism
Chemical Substances	3' Untranslated Regions ; Anesthetics, Intravenous ; Recombinant Proteins ; Steroid Hydroxylases (EC 1.14.-) ; Aryl Hydrocarbon Hydroxylases (EC 1.14.14.1) ; Cytochrome P450 Family 2 (EC 1.14.14.1) ; cytochrome P-450 CYP2B11 (dog) (EC 1.14.14.1) ; Propofol (YI7VU623SF)
Language	English
Publishing date	2020-01-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-56660-z
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