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Article ; Online: A year in our understanding of COVID-19.

Thwaites, R S

2020 Volume 202, Issue 2, Page(s) 146–148

MeSH term(s)	Antibodies, Monoclonal, Humanized/therapeutic use ; Betacoronavirus/physiology ; Blood Coagulation ; COVID-19 ; COVID-19 Vaccines ; Complement System Proteins/metabolism ; Coronavirus Infections/immunology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/therapy ; Humans ; Immunotherapy/methods ; Interferon Type I/immunology ; Pandemics/prevention & control ; Pneumonia, Viral/immunology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/therapy ; Receptors, Interleukin-6/immunology ; SARS-CoV-2 ; Viral Vaccines/immunology
Chemical Substances	Antibodies, Monoclonal, Humanized ; COVID-19 Vaccines ; Interferon Type I ; Receptors, Interleukin-6 ; Viral Vaccines ; Complement System Proteins (9007-36-7) ; tocilizumab (I031V2H011)
Keywords	covid19
Language	English
Publishing date	2020-09-30
Publishing country	England
Document type	Editorial
ZDB-ID	218531-3
ISSN	1365-2249 ; 0009-9104 ; 0964-2536
ISSN (online)	1365-2249
ISSN	0009-9104 ; 0964-2536
DOI	10.1111/cei.13538
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Article: A year in our understanding of COVID-19

Thwaites, R S

Clin Exp Immunol

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #894736
Database	COVID19

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Article ; Online: Dosimetric Impact of Delineation and Motion Uncertainties on the Heart and Substructures in Lung Cancer Radiotherapy.

Chin, V / Finnegan, R N / Chlap, P / Holloway, L / Thwaites, D I / Otton, J / Delaney, G P / Vinod, S K

Clinical oncology (Royal College of Radiologists (Great Britain))

2024

Abstract: Aims: Delineation variations and organ motion produce difficult-to-quantify uncertainties in planned radiation doses to targets and organs at risk. Similar to manual contouring, most automatic segmentation tools generate single delineations per ... ...

Abstract	Aims: Delineation variations and organ motion produce difficult-to-quantify uncertainties in planned radiation doses to targets and organs at risk. Similar to manual contouring, most automatic segmentation tools generate single delineations per structure; however, this does not indicate the range of clinically acceptable delineations. This study develops a method to generate a range of automatic cardiac structure segmentations, incorporating motion and delineation uncertainty, and evaluates the dosimetric impact in lung cancer. Materials and methods: Eighteen cardiac structures were delineated using a locally developed auto-segmentation tool. It was applied to lung cancer planning CTs for 27 curative (planned dose ≥50 Gy) cases, and delineation variations were estimated by using ten mapping-atlases to provide separate substructure segmentations. Motion-related cardiac segmentation variations were estimated by auto-contouring structures on ten respiratory phases for 9/27 cases that had 4D-planning CTs. Dose volume histograms (DVHs) incorporating these variations were generated for comparison. Results: Variations in mean doses (Dmean), defined as the range in values across ten feasible auto-segmentations, were calculated for each cardiac substructure. Over the study cohort the median variations for delineation uncertainty and motion were 2.20-11.09 Gy and 0.72-4.06 Gy, respectively. As relative values, variations in Dmean were between 18.7%-65.3% and 7.8%-32.5% for delineation uncertainty and motion, respectively. Doses vary depending on the individual planned dose distribution, not simply on segmentation differences, with larger dose variations to cardiac structures lying within areas of steep dose gradient. Conclusion: Radiotherapy dose uncertainties from delineation variations and respiratory-related heart motion were quantified using a cardiac substructure automatic segmentation tool. This predicts the 'dose range' where doses to structures are most likely to fall, rather than single DVH curves. This enables consideration of these uncertainties in cardiotoxicity research and for future plan optimisation. The tool was designed for cardiac structures, but similar methods are potentially applicable to other OARs.
Language	English
Publishing date	2024-04-04
Publishing country	England
Document type	Journal Article
ZDB-ID	1036844-9
ISSN	1433-2981 ; 0936-6555
ISSN (online)	1433-2981
ISSN	0936-6555
DOI	10.1016/j.clon.2024.04.002
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Article ; Online: Bridging the gap between primary and secondary care: a utilisation evaluation of an otolaryngology GPwSI programme.

Brundell, William / Thwaites, Nadina / Arrol, Sharon / Arroll, Bruce / Coomarasamy, Christin / Morton, Randall

Journal of primary health care

2023 Volume 15, Issue 1, Page(s) 67–70

Abstract: Introduction Counties Manukau Health Otolaryngology programme for general practitioners with special interest (GPwSI) was developed to provide a group of GPs with tools to manage low complexity, secondary otolaryngology (ORL) problems in their local ... ...

Abstract	Introduction Counties Manukau Health Otolaryngology programme for general practitioners with special interest (GPwSI) was developed to provide a group of GPs with tools to manage low complexity, secondary otolaryngology (ORL) problems in their local communities. After clinical triaging, the medical records were retrieved to assess patient outcomes from community (GPwSI) review. This programme provides an example of how the aims of the Health NZ reforms may work in practice, by bridging primary and secondary services. Aim To assess whether the GPwSI programme provides patients with suitable specialty care in the community, compared to a specialised, hospital outpatient otolaryngology clinic (OPC). Methods This is a retrospective study of patients with an assigned priority of three (non-urgent) referred to Middlemore Hospital for a first specialist assessment (FSA) during 2018-19. Results Of the 6231 patients referred, one-fifth (22%) were directed to the GPwSI service, and the remainder (78%) were arranged to be seen in the OPC. GPwSI patients were more likely to be seen for their FSA earlier than OPC patients (RR 1.55, 95% CI 1.46-1.64, P Discussion Patients being seen through the GPwSI programme are suitably managed in the community, more efficiently than if they were to be seen in an outpatient specialist clinic.
MeSH term(s)	Humans ; General Practitioners ; Secondary Care ; Retrospective Studies ; Hospitals ; Otolaryngology ; Referral and Consultation
Language	English
Publishing date	2023-03-31
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2572943-3
ISSN	1172-6156 ; 1172-6156
ISSN (online)	1172-6156
ISSN	1172-6156
DOI	10.1071/HC22113
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Article ; Online: Treatment of tuberculous meningitis: Overdue for concerted action.

Wilkinson, Robert J / Donovan, Joseph / Thwaites, Guy E / van Crevel, Reinout / Wasserman, Sean

Tuberculosis (Edinburgh, Scotland)

2023 Volume 142, Page(s) 102361

MeSH term(s)	Humans ; Tuberculosis, Meningeal/diagnosis ; Tuberculosis, Meningeal/drug therapy ; Mycobacterium tuberculosis ; Antitubercular Agents/therapeutic use
Chemical Substances	Antitubercular Agents
Language	English
Publishing date	2023-06-30
Publishing country	Scotland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2046804-0
ISSN	1873-281X ; 1472-9792
ISSN (online)	1873-281X
ISSN	1472-9792
DOI	10.1016/j.tube.2023.102361
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Article ; Online: Detection of changes in regional colonic fermentation in response to supplementing a low FODMAP diet with dietary fibres by hydrogen concentrations, but not by luminal pH.

So, Daniel / Yao, Chu K / Gill, Paul A / Thwaites, Phoebe A / Ardalan, Zaid S / McSweeney, Chris S / Denman, Stuart E / Chrimes, Adam F / Muir, Jane G / Berean, Kyle J / Kalantar-Zadeh, Kourosh / Gibson, Peter R

Alimentary pharmacology & therapeutics

2023 Volume 58, Issue 4, Page(s) 417–428

Abstract: Background: Carbohydrate fermentation plays a pivotal role in maintaining colonic health with excessive proximal and deficient distal fermentation being detrimental.: Aims: To utilise telemetric gas- and pH-sensing capsule technologies for defining ... ...

Abstract	Background: Carbohydrate fermentation plays a pivotal role in maintaining colonic health with excessive proximal and deficient distal fermentation being detrimental. Aims: To utilise telemetric gas- and pH-sensing capsule technologies for defining patterns of regional fermentation following dietary manipulations, alongside conventional techniques of measuring fermentation. Methods: In a double-blind crossover trial, 20 patients with irritable bowel syndrome were fed low FODMAP diets that included no extra fibre (total fibre content 24 g/day), or additional poorly fermented fibre, alone (33 g/day) or with fermentable fibre (45 g/day) for 2 weeks. Plasma and faecal biochemistry, luminal profiles defined by tandem gas- and pH-sensing capsules, and faecal microbiota were assessed. Results: Plasma short-chain fatty acid (SCFA) concentrations (μmol/L) were median (IQR) 121 (100-222) with fibre combination compared with 66 (44-120) with poorly fermented fibre alone (p = 0.028) and 74 (55-125) control (p = 0.069), but no differences in faecal content were observed. Luminal hydrogen concentrations (%), but not pH, were higher in distal colon (mean 4.9 [95% CI: 2.2-7.5]) with fibre combination compared with 1.8 (0.8-2.8) with poorly fermented fibre alone (p = 0.003) and 1.9 (0.7-3.1) control (p = 0.003). Relative abundances of saccharolytic fermentative bacteria were generally higher in association with supplementation with the fibre combination. Conclusions: A modest increase in fermentable plus poorly fermented fibres had minor effects on faecal measures of fermentation, despite increases in plasma SCFA and abundance of fermentative bacteria, but the gas-sensing capsule, not pH-sensing capsule, detected the anticipated propagation of fermentation distally in the colon. The gas-sensing capsule technology provides unique insights into localisation of colonic fermentation. Trial registration: ACTRN12619000691145.
MeSH term(s)	Humans ; Hydrogen/analysis ; Fermentation ; FODMAP Diet ; Colon/metabolism ; Dietary Fiber/metabolism ; Fatty Acids, Volatile ; Feces/microbiology ; Diet
Chemical Substances	Hydrogen (7YNJ3PO35Z) ; Dietary Fiber ; Fatty Acids, Volatile
Language	English
Publishing date	2023-06-30
Publishing country	England
Document type	Randomized Controlled Trial ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	639012-2
ISSN	1365-2036 ; 0269-2813 ; 0953-0673
ISSN (online)	1365-2036
ISSN	0269-2813 ; 0953-0673
DOI	10.1111/apt.17629
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Article ; Online: Validation of a Fully Automated Hybrid Deep Learning Cardiac Substructure Segmentation Tool for Contouring and Dose Evaluation in Lung Cancer Radiotherapy.

Chin, V / Finnegan, R N / Chlap, P / Otton, J / Haidar, A / Holloway, L / Thwaites, D I / Dowling, J / Delaney, G P / Vinod, S K

Clinical oncology (Royal College of Radiologists (Great Britain))

2023 Volume 35, Issue 6, Page(s) 370–381

Abstract: Background and purpose: Accurate and consistent delineation of cardiac substructures is challenging. The aim of this work was to validate a novel segmentation tool for automatic delineation of cardiac structures and subsequent dose evaluation, with ... ...

Abstract	Background and purpose: Accurate and consistent delineation of cardiac substructures is challenging. The aim of this work was to validate a novel segmentation tool for automatic delineation of cardiac structures and subsequent dose evaluation, with potential application in clinical settings and large-scale radiation-related cardiotoxicity studies. Materials and methods: A recently developed hybrid method for automatic segmentation of 18 cardiac structures, combining deep learning, multi-atlas mapping and geometric segmentation of small challenging substructures, was independently validated on 30 lung cancer cases. These included anatomical and imaging variations, such as tumour abutting heart, lung collapse and metal artefacts. Automatic segmentations were compared with manual contours of the 18 structures using quantitative metrics, including Dice similarity coefficient (DSC), mean distance to agreement (MDA) and dose comparisons. Results: A comparison of manual and automatic contours across all cases showed a median DSC of 0.75-0.93 and a median MDA of 2.09-3.34 mm for whole heart and chambers. The median MDA for great vessels, coronary arteries, cardiac valves, sinoatrial and atrioventricular conduction nodes was 3.01-8.54 mm. For the 27 cases treated with curative intent (planned target volume dose ≥50 Gy), the median dose difference was -1.12 to 0.57 Gy (absolute difference of 1.13-3.25%) for the mean dose to heart and chambers; and -2.25 to 4.45 Gy (absolute difference of 0.94-6.79%) for the mean dose to substructures. Conclusion: The novel hybrid automatic segmentation tool reported high accuracy and consistency over a validation set with challenging anatomical and imaging variations. This has promising applications in substructure dose calculations of large-scale datasets and for future studies on long-term cardiac toxicity.
MeSH term(s)	Humans ; Deep Learning ; Tomography, X-Ray Computed/methods ; Image Processing, Computer-Assisted/methods ; Heart/diagnostic imaging ; Lung Neoplasms/diagnostic imaging ; Lung Neoplasms/radiotherapy ; Radiotherapy Planning, Computer-Assisted/methods ; Organs at Risk
Language	English
Publishing date	2023-03-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1036844-9
ISSN	1433-2981 ; 0936-6555
ISSN (online)	1433-2981
ISSN	0936-6555
DOI	10.1016/j.clon.2023.03.005
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Article ; Online: Mucosal and systemic immune correlates of viral control after SARS-CoV-2 infection challenge in seronegative adults.

Wagstaffe, Helen R / Thwaites, Ryan S / Reynaldi, Arnold / Sidhu, Jasmin K / McKendry, Richard / Ascough, Stephanie / Papargyris, Loukas / Collins, Ashley M / Xu, Jiayun / Lemm, Nana-Marie / Siggins, Matthew K / Chain, Benny M / Killingley, Ben / Kalinova, Mariya / Mann, Alex / Catchpole, Andrew / Davenport, Miles P / Openshaw, Peter J M / Chiu, Christopher

Science immunology

2024 Volume 9, Issue 92, Page(s) eadj9285

Abstract: Human infection challenge permits in-depth, early, and pre-symptomatic characterization of the immune response, enabling the identification of factors that are important for viral clearance. Here, we performed intranasal inoculation of 34 young adult, ... ...

Abstract	Human infection challenge permits in-depth, early, and pre-symptomatic characterization of the immune response, enabling the identification of factors that are important for viral clearance. Here, we performed intranasal inoculation of 34 young adult, seronegative volunteers with a pre-Alpha severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain. Of these participants, 18 (53%) became infected and showed an interferon-dominated mediator response with divergent kinetics between nasal and systemic sites. Peripheral CD4
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Vaccination ; CD8-Positive T-Lymphocytes ; Nasal Mucosa
Language	English
Publishing date	2024-02-09
Publishing country	United States
Document type	Journal Article
ISSN	2470-9468
ISSN (online)	2470-9468
DOI	10.1126/sciimmunol.adj9285
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Article ; Online: The Reproducibility of Bio-Acoustic Features is Associated With Sample Duration, Speech Task, and Gender.

Almaghrabi, Shaykhah A / Thewlis, Dominic / Thwaites, Simon / Rogasch, Nigel C / Lau, Stephan / Clark, Scott R / Baumert, Mathias

IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society

2022 Volume 30, Page(s) 167–175

Abstract: Bio-acoustic properties of speech show evolving value in analyzing psychiatric illnesses. Obtaining a sufficient speech sample length to quantify these properties is essential, but the impact of sample duration on the stability of bio-acoustic features ... ...

Abstract	Bio-acoustic properties of speech show evolving value in analyzing psychiatric illnesses. Obtaining a sufficient speech sample length to quantify these properties is essential, but the impact of sample duration on the stability of bio-acoustic features has not been systematically explored. We aimed to evaluate bio-acoustic features' reproducibility against changes in speech durations and tasks. We extracted source, spectral, formant, and prosodic features in 185 English-speaking adults (98 w, 87 m) for reading-a-story and counting tasks. We compared features at 25% of the total sample duration of the reading task to those obtained from non-overlapping randomly selected sub-samples shortened to 75%, 50%, and 25% of total duration using intraclass correlation coefficients. We also compared the features extracted from entire recordings to those measured at 25% of the duration and features obtained from 50% of the duration. Further, we compared features extracted from reading-a-story to counting tasks. Our results show that the number of reproducible features (out of 125) decreased stepwise with duration reduction. Spectral shape, pitch, and formants reached excellent reproducibility. Mel-frequency cepstral coefficients (MFCCs), loudness, and zero-crossing rate achieved excellent reproducibility only at a longer duration. Reproducibility of source, MFCC derivatives, and voicing probability (VP) was poor. Significant gender differences existed in jitter, MFCC first-derivative, spectral skewness, pitch, VP, and formants. Around 97% of features in both genders were not reproducible across speech tasks, in part due to the short counting task duration. In conclusion, bio-acoustic features are less reproducible in shorter samples and are affected by gender.
MeSH term(s)	Acoustics ; Adult ; Female ; Humans ; Male ; Reproducibility of Results ; Speech ; Speech Acoustics ; Voice
Language	English
Publishing date	2022-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1166307-8
ISSN	1558-0210 ; 1063-6528 ; 1534-4320
ISSN (online)	1558-0210
ISSN	1063-6528 ; 1534-4320
DOI	10.1109/TNSRE.2022.3143117
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Article ; Online: Preventing hospital falls: feasibility of care workforce redesign to optimise patient falls education.

Morris, Meg E / Thwaites, Claire / Lui, Rosalie / McPhail, Steven M / Haines, Terry / Kiegaldie, Debra / Heng, Hazel / Shaw, Louise / Hammond, Susan / McKercher, Jonathan P / Knight, Matthew / Carey, Leeanne M / Gray, Richard / Shorr, Ron / Hill, Anne-Marie

Age and ageing

2024 Volume 53, Issue 1

Abstract: Objective: To examine the feasibility of using allied health assistants to deliver patient falls prevention education within 48 h after hospital admission.: Design and setting: Feasibility study with hospital patients randomly allocated to usual care ...

Abstract	Objective: To examine the feasibility of using allied health assistants to deliver patient falls prevention education within 48 h after hospital admission. Design and setting: Feasibility study with hospital patients randomly allocated to usual care or usual care plus additional patient falls prevention education delivered by supervised allied health assistants using an evidence-based scripted conversation and educational pamphlet. Participants: (i) allied health assistants and (ii) patients admitted to participating hospital wards over a 20-week period. Outcomes: (i) feasibility of allied health assistant delivery of patient education; (ii) hospital falls per 1,000 bed days; (iii) injurious falls; (iv) number of falls requiring transfer to an acute medical facility. Results: 541 patients participated (median age 81 years); 270 control group and 271 experimental group. Allied health assistants (n = 12) delivered scripted education sessions to 254 patients in the experimental group, 97% within 24 h after admission. There were 32 falls in the control group and 22 in the experimental group. The falls rate was 8.07 falls per 1,000 bed days in the control group and 5.69 falls per 1,000 bed days for the experimental group (incidence rate ratio = 0.66 (95% CI 0.32, 1.36; P = 0.26)). There were 2.02 injurious falls per 1,000 bed days for the control group and 1.03 for the experimental group. Nine falls (7 control, 2 experimental) required transfer to an acute facility. No adverse events were attributable to the experimental group intervention. Conclusions: It is feasible and of benefit to supplement usual care with patient education delivered by allied health assistants.
MeSH term(s)	Aged, 80 and over ; Humans ; Feasibility Studies ; Hospitalization ; Hospitals ; Workforce
Language	English
Publishing date	2024-01-11
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial
ZDB-ID	186788-x
ISSN	1468-2834 ; 0002-0729
ISSN (online)	1468-2834
ISSN	0002-0729
DOI	10.1093/ageing/afad250
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