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Article ; Online: Sensory representation of surface reflectances: assessments with hyperspectral images.

Karimipour, Hamed / O'Regan, J Kevin / Witzel, Christoph

Journal of the Optical Society of America. A, Optics, image science, and vision

2023 Volume 40, Issue 3, Page(s) A183–A189

Abstract: Specifying surface reflectances in a simple and perceptually informative way would be beneficial for many areas of research and application. We assessed whether a 3×3 matrix may be used to approximate how a surface reflectance modulates the sensory color ...

Abstract	Specifying surface reflectances in a simple and perceptually informative way would be beneficial for many areas of research and application. We assessed whether a 3×3 matrix may be used to approximate how a surface reflectance modulates the sensory color signal across illuminants. We tested whether observers could discriminate between the model's approximate and accurate spectral renderings of hyperspectral images under narrowband and naturalistic, broadband illuminants for eight hue directions. Discriminating the approximate from the spectral rendering was possible with narrowband, but almost never with broadband illuminants. These results suggest that our model specifies the sensory information of reflectances across naturalistic illuminants with high fidelity, and with lower computational cost than spectral rendering.
Language	English
Publishing date	2023-05-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	283633-6
ISSN	1520-8532 ; 1084-7529 ; 0740-3232
ISSN (online)	1520-8532
ISSN	1084-7529 ; 0740-3232
DOI	10.1364/JOSAA.477276
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Article ; Online: Monolayer Capping Provides Close to Optimal Resistance to Laser Dewetting of Au Films.

Murray, Christopher P / Mamyraimov, Daniyar / Ali, Mugahid / Downing, Clive / Povey, Ian M / McCloskey, David / O'Regan, David D / Donegan, John F

ACS applied electronic materials

2023 Volume 5, Issue 8, Page(s) 4080–4093

Abstract: Next-generation heat-assisted magnetic recording (HAMR) relies on fast, localized heating of the magnetic medium during the write process. Au plasmonic near-field transducers are an attractive solution to this challenge, but increased thermal stability ... ...

Abstract	Next-generation heat-assisted magnetic recording (HAMR) relies on fast, localized heating of the magnetic medium during the write process. Au plasmonic near-field transducers are an attractive solution to this challenge, but increased thermal stability of Au films is required to improve long-term reliability. This work compares the effect of nanoscale Al, AlO
Language	English
Publishing date	2023-08-04
Publishing country	United States
Document type	Journal Article
ISSN	2637-6113
ISSN (online)	2637-6113
DOI	10.1021/acsaelm.3c00052
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Article ; Online: Digital ECMT Cancer Trial Matching Tool: an Open Source Research Application to Support Oncologists in the Identification of Precision Medicine Clinical Trials.

O'Regan, Paul / Hoskins, Richard / Grave, Christopher / Stevenson, Julie-Anne / Frost, Hannah / Graham, Donna M / Krebs, Matthew G / Freitas, Andre / Landers, Dónal

JCO clinical cancer informatics

2023 Volume 7, Page(s) e2200137

Abstract: Purpose: Matching patients with cancer to precision medicine clinical trials on the basis of their tumor genotype has the potential to improve outcomes for patients who have exhausted standard-of-care treatment options. However, the matching process ... ...

Abstract	Purpose: Matching patients with cancer to precision medicine clinical trials on the basis of their tumor genotype has the potential to improve outcomes for patients who have exhausted standard-of-care treatment options. However, the matching process presents a substantial challenge because of the number of clinical trials available. We describe a free, open source research tool designed to extract relevant trial information to support oncologists in the matching process, and we illustrate its utility with recent case studies of patients who were matched to trials using this tool. Methods: Trial records are sourced from ClinicalTrials.gov and indexed using natural language processing techniques, including named entity recognition, term normalization, and relationship extraction. Relationships between trials and genetic alterations are assigned scores on the basis of a rule-based system. All data are updated daily. A user interface is provided via R Shiny app. Results: An instance of the trial match tool, configured for UK clinical trials, is hosted by the digital Experimental Cancer Medicine Team (see link in Data Sharing Statement). Users select the relevant cancer type and genetic alteration(s). Matching studies are ranked according to the score assigned for the selected genetic alterations. Results may be downloaded and attached to the patient's health record if desired. The tool is currently being used to support the ongoing TARGET National study, which aims to match up to 6,000 patients to early phase clinical trials. We present three case studies that exemplify relationships between genetic alterations and studies. Conclusion: With increasing numbers of precision medicine treatments and as comprehensive molecular profiling of tumor samples becomes more common, decision support tools are likely to become increasingly important. This work represents an important step toward the development and wider implementation of such systems.
MeSH term(s)	Humans ; Mutation ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/therapy ; Oncologists ; Precision Medicine ; Clinical Trials as Topic
Language	English
Publishing date	2023-01-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2473-4276
ISSN (online)	2473-4276
DOI	10.1200/CCI.22.00137
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Article ; Online: Errors noted in: re: Migliore A, Bizzi E, Broccoli S Laganà (2011). Indirect comparison of etanercept, infliximab, and adalumimab for psoriatic arthritis: mixed treatment comparison using placebo as common comparator. Published on line June 21st 2011.

O'Regan, Christopher

Clinical rheumatology

2011 Volume 30, Issue 12, Page(s) 1647–1648

MeSH term(s)	Adalimumab ; Anti-Inflammatory Agents/therapeutic use ; Anti-Inflammatory Agents, Non-Steroidal/therapeutic use ; Antibodies, Monoclonal/therapeutic use ; Antibodies, Monoclonal, Humanized/therapeutic use ; Antirheumatic Agents/therapeutic use ; Arthritis, Psoriatic/drug therapy ; Arthritis, Psoriatic/physiopathology ; Comparative Effectiveness Research/methods ; Etanercept ; Humans ; Immunoglobulin G/therapeutic use ; Infliximab ; Randomized Controlled Trials as Topic ; Receptors, Tumor Necrosis Factor/therapeutic use ; Research Design ; Treatment Outcome
Chemical Substances	Anti-Inflammatory Agents ; Anti-Inflammatory Agents, Non-Steroidal ; Antibodies, Monoclonal ; Antibodies, Monoclonal, Humanized ; Antirheumatic Agents ; Immunoglobulin G ; Receptors, Tumor Necrosis Factor ; Infliximab (B72HH48FLU) ; Adalimumab (FYS6T7F842) ; Etanercept (OP401G7OJC)
Language	English
Publishing date	2011-09-22
Publishing country	Germany
Document type	Comparative Study ; Letter
ZDB-ID	604755-5
ISSN	1434-9949 ; 0770-3198
ISSN (online)	1434-9949
ISSN	0770-3198
DOI	10.1007/s10067-011-1850-y
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Article: 'Remote' behavioural ecology: do megaherbivores consume vegetation in proportion to its presence in the landscape?

Marston, Christopher G / Wilkinson, David M / Sponheimer, Matt / Codron, Daryl / Codron, Jacqui / O'Regan, Hannah J

PeerJ

2020 Volume 8, Page(s) e8622

Abstract: Examination of the feeding habits of mammalian species such as the African elephant ( ...

Abstract	Examination of the feeding habits of mammalian species such as the African elephant (
Language	English
Publishing date	2020-02-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.8622
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Article ; Online: Reduction of multiple reaction monitoring protein target list using correlation analysisa.

Ebhardt, Holger A / Ponchon, Pierre / Theodosiadis, Konstantinos / Fuerer, Christophe / Courtet-Compondu, Marie-Claude / O'Regan, Jonathan / Affolter, Michael / Joubran, Yousef

Journal of dairy science

2022 Volume 105, Issue 9, Page(s) 7216–7229

Abstract: High mass resolution mass spectrometry provides hundreds to thousands of protein identifications per sample, and quantification is typically performed using label-free quantification. However, the gold standard of quantitative proteomics is multiple ... ...

Abstract	High mass resolution mass spectrometry provides hundreds to thousands of protein identifications per sample, and quantification is typically performed using label-free quantification. However, the gold standard of quantitative proteomics is multiple reaction monitoring (MRM) using triple quadrupole mass spectrometers and stable isotope reference peptides. This raises the question how to reduce a large data set to a small one without losing essential information. Here we present the reduction of such a data set using correlation analysis of bovine dairy ingredients and derived products. We were able to explain the variance in the proteomics data set using only 9 proteins across all major dairy protein classes: caseins, whey, and milk fat globule membrane proteins. We term this method Trinity-MRM. The reproducibility of the protein extraction and Trinity-MRM methods was shown to be below 5% in independent experiments (multi-day single-user and single-day multi-user) using double cream. Further application of this reductionist approach might include screening of large sample cohorts for biologically interesting samples before analysis by high-resolution mass spectrometry or other omics methodologies.
MeSH term(s)	Animals ; Cattle ; Mass Spectrometry/methods ; Mass Spectrometry/veterinary ; Peptides/analysis ; Proteomics/methods ; Reproducibility of Results ; Whey Proteins/analysis
Chemical Substances	Peptides ; Whey Proteins
Language	English
Publishing date	2022-07-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	242499-x
ISSN	1525-3198 ; 0022-0302
ISSN (online)	1525-3198
ISSN	0022-0302
DOI	10.3168/jds.2021-21647
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Article ; Online: Mineral and isotopic (Nd, Sr) signature of fine-grained deglacial and Holocene sediments from the Mackenzie Trough, Arctic Canada

Henrik Swärd / Per Andersson / Robert Hilton / Christoph Vogt / Matt O’Regan

Arctic, Antarctic, and Alpine Research, Vol 54, Iss 1, Pp 346-

2022 Volume 367

Abstract: Dolomites in Arctic Ocean sediments are widely attributed to erosion and transport of sediments from northern Canada and Greenland. Coarse-grained dolomite-rich ice-rafted debris is often linked to iceberg transport, but the origin of fine-grained ... ...

Abstract	Dolomites in Arctic Ocean sediments are widely attributed to erosion and transport of sediments from northern Canada and Greenland. Coarse-grained dolomite-rich ice-rafted debris is often linked to iceberg transport, but the origin of fine-grained dolomite is less well constrained. A presumed source is the Mackenzie River. In this article, we fingerprint the minerogenic and isotopic (Nd and Sr) composition of deglacial and Holocene fine-grained sediments (<38 μm) from the shallow Mackenzie Trough. Sediments from an 81.5-m borehole (MTW01) were analyzed. The borehole is composed of a progradational (deltaic), transitional (transgressive), and marine unit (<9.4 cal. ka BP). The average dolomite content (~7 percent) and ɛNd signals (−13.3) are surprisingly constant in the progradational and marine units. The isotopic signature is inherited from the Interior Platform, the major underlying bedrock region of the Mackenzie River mainstream. The transitional unit contains fluctuations in ɛNd (−11.0 and −14.6), reflecting enhanced input from the North American Cordillera and Canadian Shield that are not associated with elevated amounts of dolomite. Additional studies combining minerogenic and detrital ɛNd analyses from sites proximal to the paleo-icestreams draining the Canadian Arctic are required to ascertain the origin of dolomite enrichment in central Arctic Ocean sediments.
Keywords	Arctic Ocean ; Mackenzie River ; Canadian Beaufort Sea ; dolomite ; neodynium ; strontium ; Environmental sciences ; GE1-350 ; Ecology ; QH540-549.5
Subject code	550
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Taylor & Francis Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The most reasonable explanation of "the dress": Implicit assumptions about illumination.

Witzel, Christoph / Racey, Chris / O'Regan, J Kevin

Journal of vision

2017 Volume 17, Issue 2, Page(s) 1

Abstract: Millions of Internet users around the world challenged science by asking why a certain photo of a dress led different observers to have surprisingly different judgments about the color of the dress. The reason this particular photo produces so diverse a ... ...

Abstract	Millions of Internet users around the world challenged science by asking why a certain photo of a dress led different observers to have surprisingly different judgments about the color of the dress. The reason this particular photo produces so diverse a variety of judgments presumably is that the photo allows a variety of interpretations about the illumination of the dress. The most obvious explanation from color science should be that observers have different implicit assumptions about the illumination in the photo. We show that the perceived color of the dress is negatively correlated with the assumed illumination along the daylight locus. Moreover, by manipulating the observers' assumptions prior to seeing the photo, we can steer how observers will see the colors of the dress. These findings confirm the idea that the perceived colors of the dress depend on the assumptions about the illumination. The phenomenon illustrates the power of unconscious inferences and implicit assumptions in perception.
MeSH term(s)	Adult ; Clothing ; Color Perception/physiology ; Color Vision/physiology ; Female ; Humans ; Judgment ; Lighting ; Male ; Photic Stimulation ; Photography ; Vision, Ocular ; Young Adult
Language	English
Publishing date	2017-01-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2106064-2
ISSN	1534-7362 ; 1534-7362
ISSN (online)	1534-7362
ISSN	1534-7362
DOI	10.1167/17.2.1
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Article: Fully automatic cardiac four chamber and great vessel segmentation on CT pulmonary angiography using deep learning.

Sharkey, Michael J / Taylor, Jonathan C / Alabed, Samer / Dwivedi, Krit / Karunasaagarar, Kavitasagary / Johns, Christopher S / Rajaram, Smitha / Garg, Pankaj / Alkhanfar, Dheyaa / Metherall, Peter / O'Regan, Declan P / van der Geest, Rob J / Condliffe, Robin / Kiely, David G / Mamalakis, Michail / Swift, Andrew J

Frontiers in cardiovascular medicine

2022 Volume 9, Page(s) 983859

Abstract: Introduction: Computed tomography pulmonary angiography (CTPA) is an essential test in the work-up of suspected pulmonary vascular disease including pulmonary hypertension and pulmonary embolism. Cardiac and great vessel assessments on CTPA are based on ...

Abstract	Introduction: Computed tomography pulmonary angiography (CTPA) is an essential test in the work-up of suspected pulmonary vascular disease including pulmonary hypertension and pulmonary embolism. Cardiac and great vessel assessments on CTPA are based on visual assessment and manual measurements which are known to have poor reproducibility. The primary aim of this study was to develop an automated whole heart segmentation (four chamber and great vessels) model for CTPA. Methods: A nine structure semantic segmentation model of the heart and great vessels was developed using 200 patients (80/20/100 training/validation/internal testing) with testing in 20 external patients. Ground truth segmentations were performed by consultant cardiothoracic radiologists. Failure analysis was conducted in 1,333 patients with mixed pulmonary vascular disease. Segmentation was achieved using deep learning Results: Dice similarity coefficients (DSC) for segmented structures were in the range 0.58-0.93 for both the internal and external test cohorts. The left and right ventricle myocardium segmentations had lower DSC of 0.83 and 0.58 respectively while all other structures had DSC >0.89 in the internal test cohort and >0.87 in the external test cohort. Interobserver comparison found that the left and right ventricle myocardium segmentations showed the most variation between observers: mean DSC (range) of 0.795 (0.785-0.801) and 0.520 (0.482-0.542) respectively. Right ventricle myocardial volume had strong correlation with mean pulmonary artery pressure (Spearman's correlation coefficient = 0.7). The volume of segmented cardiac structures by deep learning had higher or equivalent correlation with invasive haemodynamics than by manual segmentations. The model demonstrated good generalisability to different vendors and hospitals with similar performance in the external test cohort. The failure rates in mixed pulmonary vascular disease were low (<3.9%) indicating good generalisability of the model to different diseases. Conclusion: Fully automated segmentation of the four cardiac chambers and great vessels has been achieved in CTPA with high accuracy and low rates of failure. DL volumetric biomarkers can potentially improve CTPA cardiac assessment and invasive haemodynamic prediction.
Language	English
Publishing date	2022-09-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2781496-8
ISSN	2297-055X
ISSN	2297-055X
DOI	10.3389/fcvm.2022.983859
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Article ; Online: Mineral and isotopic (Nd, Sr) signature of fine-grained deglacial and Holocene sediments from the Mackenzie Trough, Arctic Canada

Swärd, Henrik / Andersson, Per / Hilton, Robert / Vogt, Christoph / O’Regan, Matt

Arctic, Antarctic, and Alpine Research. 2022 Dec. 31, v. 54, no. 1 p.346-367

2022

Abstract	Dolomites in Arctic Ocean sediments are widely attributed to erosion and transport of sediments from northern Canada and Greenland. Coarse-grained dolomite-rich ice-rafted debris is often linked to iceberg transport, but the origin of fine-grained dolomite is less well constrained. A presumed source is the Mackenzie River. In this article, we fingerprint the minerogenic and isotopic (Nd and Sr) composition of deglacial and Holocene fine-grained sediments (<38 μm) from the shallow Mackenzie Trough. Sediments from an 81.5-m borehole (MTW01) were analyzed. The borehole is composed of a progradational (deltaic), transitional (transgressive), and marine unit (<9.4 cal. ka BP). The average dolomite content (~7 percent) and ɛNd signals (−13.3) are surprisingly constant in the progradational and marine units. The isotopic signature is inherited from the Interior Platform, the major underlying bedrock region of the Mackenzie River mainstream. The transitional unit contains fluctuations in ɛNd (−11.0 and −14.6), reflecting enhanced input from the North American Cordillera and Canadian Shield that are not associated with elevated amounts of dolomite. Additional studies combining minerogenic and detrital ɛNd analyses from sites proximal to the paleo-icestreams draining the Canadian Arctic are required to ascertain the origin of dolomite enrichment in central Arctic Ocean sediments.
Keywords	Canadian Shield ; Holocene epoch ; bedrock ; dolomite ; glaciation ; research ; rivers ; Antarctic region ; Arctic Ocean ; Arctic region ; Canada ; Greenland ; Mackenzie River ; Canadian Beaufort Sea ; neodynium ; strontium
Language	English
Dates of publication	2022-1231
Size	p. 346-367.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	2045941-5
ISSN	1938-4246 ; 1523-0430
ISSN (online)	1938-4246
ISSN	1523-0430
DOI	10.1080/15230430.2022.2096425
Database	NAL-Catalogue (AGRICOLA)

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