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Article ; Online: RefMet: a reference nomenclature for metabolomics.

Fahy, Eoin / Subramaniam, Shankar

2020 Volume 17, Issue 12, Page(s) 1173–1174

MeSH term(s)	Databases, Chemical ; Humans ; Metabolome ; Metabolomics ; Molecular Sequence Annotation ; Terminology as Topic
Language	English
Publishing date	2020-11-16
Publishing country	United States
Document type	Letter ; Research Support, N.I.H., Extramural
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-020-01009-y
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Article ; Online: MetGENE: gene-centric metabolomics information retrieval tool.

Srinivasan, Sumana / Maurya, Mano R / Ramachandran, Srinivasan / Fahy, Eoin / Subramaniam, Shankar

GigaScience

2023 Volume 12

Abstract: Background: Biomedical research often involves contextual integration of multimodal and multiomic data in search of mechanisms for improved diagnosis, treatment, and monitoring. Researchers need to access information from diverse sources, comprising ... ...

Abstract	Background: Biomedical research often involves contextual integration of multimodal and multiomic data in search of mechanisms for improved diagnosis, treatment, and monitoring. Researchers need to access information from diverse sources, comprising data in various and sometimes incongruent formats. The downstream processing of the data to decipher mechanisms by reconstructing networks and developing quantitative models warrants considerable effort. Results: MetGENE is a knowledge-based, gene-centric data aggregator that hierarchically retrieves information about the gene(s), their related pathway(s), reaction(s), metabolite(s), and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. We note that MetGENE focuses only on those genes that encode for proteins directly associated with metabolites. All other gene-metabolite associations are beyond the current scope of MetGENE. Further, the information can be contextualized by filtering by species, anatomy (tissue), and condition (disease or phenotype). Conclusions: MetGENE is an open-source tool that aggregates metabolite information for a given gene(s) and presents them in different computable formats (e.g., JSON) for further integration with other omics studies. MetGENE is available at https://bdcw.org/MetGENE/index.php.
MeSH term(s)	Metabolomics ; Phenotype ; Proteins ; Information Storage and Retrieval
Chemical Substances	Proteins
Language	English
Publishing date	2023-11-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giad089
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Article ; Online: ADAP-KDB: A Spectral Knowledgebase for Tracking and Prioritizing Unknown GC-MS Spectra in the NIH's Metabolomics Data Repository.

Smirnov, Aleksandr / Liao, Yunfei / Fahy, Eoin / Subramaniam, Shankar / Du, Xiuxia

Analytical chemistry

2021 Volume 93, Issue 36, Page(s) 12213–12220

Abstract: We report the development of a spectral knowledgebase named ADAP-KDB for tracking and prioritizing unknown gas chromatography-mass spectrometry (GC-MS) spectra in the NIH's Metabolomics Data Repository-a national and international repository for ... ...

Abstract	We report the development of a spectral knowledgebase named ADAP-KDB for tracking and prioritizing unknown gas chromatography-mass spectrometry (GC-MS) spectra in the NIH's Metabolomics Data Repository-a national and international repository for metabolomics data. ADAP-KDB consists of two parts. One part is a computational workflow that preprocesses raw mass spectrometry data and derives consensus mass spectra. The other part is a web portal for users to browse the consensus spectra and match query spectra against them. For each consensus spectrum, the Gini-Simpson diversity index and the
MeSH term(s)	Gas Chromatography-Mass Spectrometry ; Knowledge Bases ; Mass Spectrometry ; Metabolomics ; Software
Language	English
Publishing date	2021-08-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00355
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Article: ADAP-KDB: A Spectral Knowledgebase for Tracking and Prioritizing Unknown GC–MS Spectra in the NIH’s Metabolomics Data Repository

Smirnov, Aleksandr / Liao, Yunfei / Fahy, Eoin / Subramaniam, Shankar / Du, Xiuxia

Analytical chemistry. 2021 Aug. 29, v. 93, no. 36

2021

Abstract: We report the development of a spectral knowledgebase named ADAP-KDB for tracking and prioritizing unknown gas chromatography–mass spectrometry (GC–MS) spectra in the NIH’s Metabolomics Data Repository—a national and international repository for ... ...

Abstract	We report the development of a spectral knowledgebase named ADAP-KDB for tracking and prioritizing unknown gas chromatography–mass spectrometry (GC–MS) spectra in the NIH’s Metabolomics Data Repository—a national and international repository for metabolomics data. ADAP-KDB consists of two parts. One part is a computational workflow that preprocesses raw mass spectrometry data and derives consensus mass spectra. The other part is a web portal for users to browse the consensus spectra and match query spectra against them. For each consensus spectrum, the Gini-Simpson diversity index and the p-value from χ² goodness-of-fit test are calculated to measure its statistical significance, which enables prioritization of unknown mass spectra for subsequent costly compound identification.
Keywords	Internet ; analytical chemistry ; gas chromatography-mass spectrometry ; metabolomics ; prioritization
Language	English
Dates of publication	2021-0829
Size	p. 12213-12220.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.1c00355
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Article ; Online: Intravascular imaging-guided intracoronary lithotripsy: First real-world experience.

Sinclair, Hannah / Fan, Lampson / Fahy, Eoin / Shahid, Farhan / Ratib, Karim / Nolan, James / Mamas, Mamas / Zaman, Azfar / Ahmed, Javed

Health science reports

2021 Volume 4, Issue 3, Page(s) e307

Abstract: Background and aims: Coronary calcification remains a significant challenge for the contemporary interventional cardiologist. We aim to describe the use of intravascular lithotripsy (IVL) in a range of real-world settings.: Methods: A retrospective ... ...

Abstract	Background and aims: Coronary calcification remains a significant challenge for the contemporary interventional cardiologist. We aim to describe the use of intravascular lithotripsy (IVL) in a range of real-world settings. Methods: A retrospective two-center analysis of patients treated with IVL between June 2018 and November 2019. Technical and procedural success, as well as procedural complications and 30-day outcomes (death, myocardial infarction, or repeat target vessel revascularization), was recorded. Results: Sixty-five patients underwent IVL: 80% were male and the mean age was 70.1 ± 12.0 years. 54% of patients presented with acute coronary syndrome (ACS) and 68% of patients had intracoronary imaging. Twelve patients required IVL within pre-existing stents, and 12 underwent IVL in the left main stem. All balloons were successfully delivered with 98.5% procedural success. There was a significant gain in MLA post PCI of 261.9 ± 100% following IVL. There were two procedural complications. At 30-day follow-up, there was one death, and one patient required a repeat procedure due to stent underexpansion. Conclusions: In this largest real-world series of imaging-guided IVL for calcified lesions to date, we demonstrate that IVL is deliverable, safe, and effective at calcium modification especially when intracoronary imaging is used.
Language	English
Publishing date	2021-08-09
Publishing country	United States
Document type	Journal Article
ISSN	2398-8835
ISSN (online)	2398-8835
DOI	10.1002/hsr2.307
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Article ; Online: LIPID MAPS: update to databases and tools for the lipidomics community.

Conroy, Matthew J / Andrews, Robert M / Andrews, Simon / Cockayne, Lauren / Dennis, Edward A / Fahy, Eoin / Gaud, Caroline / Griffiths, William J / Jukes, Geoff / Kolchin, Maksim / Mendivelso, Karla / Lopez-Clavijo, Andrea F / Ready, Caroline / Subramaniam, Shankar / O'Donnell, Valerie B

Nucleic acids research

2023 Volume 52, Issue D1, Page(s) D1677–D1682

Abstract: LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become ... ...

Abstract	LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school.
MeSH term(s)	Databases, Factual ; Lipid Metabolism ; Lipidomics ; Lipids/chemistry ; Software
Chemical Substances	Lipids
Language	English
Publishing date	2023-10-19
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad896
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Article ; Online: Intravascular imaging–guided intracoronary lithotripsy

Hannah Sinclair / Lampson Fan / Eoin Fahy / Farhan Shahid / Karim Ratib / James Nolan / Mamas Mamas / Azfar Zaman / Javed Ahmed

Health Science Reports, Vol 4, Iss 3, Pp n/a-n/a (2021)

First real‐world experience

2021

Abstract: Abstract Background and Aims Coronary calcification remains a significant challenge for the contemporary interventional cardiologist. We aim to describe the use of intravascular lithotripsy (IVL) in a range of real‐world settings. Methods A retrospective ...

Abstract	Abstract Background and Aims Coronary calcification remains a significant challenge for the contemporary interventional cardiologist. We aim to describe the use of intravascular lithotripsy (IVL) in a range of real‐world settings. Methods A retrospective two‐center analysis of patients treated with IVL between June 2018 and November 2019. Technical and procedural success, as well as procedural complications and 30‐day outcomes (death, myocardial infarction, or repeat target vessel revascularization), was recorded. Results Sixty‐five patients underwent IVL: 80% were male and the mean age was 70.1 ± 12.0 years. 54% of patients presented with acute coronary syndrome (ACS) and 68% of patients had intracoronary imaging. Twelve patients required IVL within pre‐existing stents, and 12 underwent IVL in the left main stem. All balloons were successfully delivered with 98.5% procedural success. There was a significant gain in MLA post PCI of 261.9 ± 100% following IVL. There were two procedural complications. At 30‐day follow‐up, there was one death, and one patient required a repeat procedure due to stent underexpansion. Conclusions In this largest real‐world series of imaging‐guided IVL for calcified lesions to date, we demonstrate that IVL is deliverable, safe, and effective at calcium modification especially when intracoronary imaging is used.
Keywords	coronary artery disease ; lithotripsy ; optical coherence tomography ; percutaneous coronary intervention ; Medicine ; R
Subject code	610 ; 616
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
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Article ; Online: Isoprostane nomenclature: more suggestions.

Murphy, Robert C / Fahy, Eoin

Prostaglandins, leukotrienes, and essential fatty acids

2010 Volume 82, Issue 2-3, Page(s) 69–70

MeSH term(s)	Isoprostanes/classification ; Terminology as Topic
Chemical Substances	Isoprostanes
Language	English
Publishing date	2010-01-22
Publishing country	Scotland
Document type	Editorial ; Introductory Journal Article
ZDB-ID	286714-x
ISSN	1532-2823 ; 0952-3278
ISSN (online)	1532-2823
ISSN	0952-3278
DOI	10.1016/j.plefa.2010.01.001
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Article ; Online: Revascularisation therapies improve the outcomes of ischemic stroke patients with atrial fibrillation and heart failure.

Pana, Tiberiu A / Mohamed, Mohamed O / Clark, Allan B / Fahy, Eoin / Mamas, Mamas A / Myint, Phyo K

International journal of cardiology

2020 Volume 324, Page(s) 205–213

Abstract: Background: Atrial fibrillation (AF) and heart failure (HF) carry a poor prognosis in acute ischaemic stroke (AIS). The impact of revascularisation therapies on outcomes in these patients is not fully understood.: Method: National Inpatient Sample ( ... ...

Abstract	Background: Atrial fibrillation (AF) and heart failure (HF) carry a poor prognosis in acute ischaemic stroke (AIS). The impact of revascularisation therapies on outcomes in these patients is not fully understood. Method: National Inpatient Sample (NIS) AIS admissions (January 2004-September 2015) were included (n = 4,597,428). Logistic regressions analysed the relationship between exposures (neither AF nor HF-reference, AF-only, HF-only, AF + HF) and outcomes (in-hospital mortality, length-of-stay >median and moderate-to-severe disability on discharge), stratifying by receipt of intravenous thrombolysis (IVT) or endovascular thrombectomy (ET). Results: 69.2% patients had neither AF nor HF, 16.5% had AF-only, 7.5% had HF-only and 6.7% had AF + HF. 5.04% and 0.72% patients underwent IVT and/or ET, respectively. AF-only and HF-only were each associated with 75-85% increase in the odds of in-hospital mortality. AF + HF was associated with greater than two-fold increase in mortality. Patients with AF-only, HF-only or AF + HF undergoing IVT had better or at least similar in-hospital outcomes compared to their counterparts not undergoing IVT, except for prolonged hospitalisation. Patients undergoing ET with AF-only, HF-only or AF + HF had better (in-hospital mortality, discharge disability, all-cause bleeding) or at least similar (length-of-stay) outcomes to their counterparts not undergoing ET. Compared to AIS patients without AF, AF patients had approximately 50% and more than two-fold increases in the likelihood of receiving IVT or ET, respectively. Conclusions: We confirmed the combined and individual impact of co-existing AF or HF on important patient-related outcomes. Revascularisation therapies improve these outcomes significantly in patients with these comorbidities.
MeSH term(s)	Atrial Fibrillation/diagnosis ; Atrial Fibrillation/epidemiology ; Atrial Fibrillation/therapy ; Brain Ischemia/diagnosis ; Brain Ischemia/epidemiology ; Brain Ischemia/therapy ; Heart Failure/diagnosis ; Heart Failure/epidemiology ; Heart Failure/therapy ; Humans ; Ischemic Stroke ; Stroke/diagnosis ; Stroke/epidemiology ; Stroke/therapy
Language	English
Publishing date	2020-10-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	779519-1
ISSN	1874-1754 ; 0167-5273
ISSN (online)	1874-1754
ISSN	0167-5273
DOI	10.1016/j.ijcard.2020.09.076
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Article ; Online: Self-consistent Green's function method for dilute nitride conduction band structure.

Seifikar, Masoud / O'Reilly, Eoin P / Fahy, Stephen

Journal of physics. Condensed matter : an Institute of Physics journal

2014 Volume 26, Issue 36, Page(s) 365502

Abstract: We present a self-consistent Green's function (SCGF) approach for the Anderson many-impurity model to calculate the band dispersion and density of states near the conduction band edge in GaN(x)As(1-x) dilute nitride alloys. Two different models of the N ... ...

Abstract	We present a self-consistent Green's function (SCGF) approach for the Anderson many-impurity model to calculate the band dispersion and density of states near the conduction band edge in GaN(x)As(1-x) dilute nitride alloys. Two different models of the N states have been studied to investigate the band structure of these materials: (1) the two-band model, which assumes all N states have the same energy, EN; (2) a model which includes a full distribution of N states obtained by allowing for direct interaction between N sites. The density of states, projected onto extended and localised states, calculated by the SCGF two-band model, are in excellent agreement with those previously obtained in supercell calculations and reveal a gap in the density of states just above E(N), in contrast with the results of previous non-self-consistent Green's function calculations. However, including the full distribution of N states in a SCGF calculation removes this gap, in agreement with experiment.
Language	English
Publishing date	2014-09-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1472968-4
ISSN	1361-648X ; 0953-8984
ISSN (online)	1361-648X
ISSN	0953-8984
DOI	10.1088/0953-8984/26/36/365502
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