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Article ; Online: Reduced athletic performance post-COVID-19 is associated with reduced anaerobic threshold.

Barker-Davies, Robert M / Ladlow, Peter / Chamley, Rebecca / Nicol, Edward / Holdsworth, David A

BMJ case reports

2023 Volume 16, Issue 2

Abstract: Detailed characterisation of cardiopulmonary limitations in patients post-COVID-19 is currently limited, particularly in elite athletes. A male elite distance runner in his late 30s experienced chest pain following confirmed COVID-19. He underwent ... ...

Abstract	Detailed characterisation of cardiopulmonary limitations in patients post-COVID-19 is currently limited, particularly in elite athletes. A male elite distance runner in his late 30s experienced chest pain following confirmed COVID-19. He underwent cardiopulmonary exercise testing (CPET) at 5 months postacute illness. Subjective exercise tolerance was reduced compared with normal, he described inability to 'kick' (rapidly accelerate). His CPET was compared with an identical protocol 15 months prior to COVID-19. While supranormal maximal oxygen uptake was maintained (155% of peak predicted V̇O
MeSH term(s)	Humans ; Male ; Anaerobic Threshold ; COVID-19 ; Athletic Performance ; Chest Pain ; Exercise Test
Language	English
Publishing date	2023-02-17
Publishing country	England
Document type	Case Reports ; Journal Article
ISSN	1757-790X
ISSN (online)	1757-790X
DOI	10.1136/bcr-2022-250191
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Article ; Online: Biomechanical differences between military patients with patellar tendinopathy and asymptomatic controls during single-leg squatting and gait - A statistical parametric mapping study.

Houston, Andrew / Fong, Daniel T P / Bennett, Alexander N / Walters, Vanessa / Barker-Davies, Robert M

Clinical biomechanics (Bristol, Avon)

2021 Volume 90, Page(s) 105514

Abstract: Background: Prior identification of biomechanical differences between patients with patellar tendinopathy and healthy controls has utilised time-discrete analysis which is susceptible to type I error when multiple comparisons are uncorrected. We employ ... ...

Abstract	Background: Prior identification of biomechanical differences between patients with patellar tendinopathy and healthy controls has utilised time-discrete analysis which is susceptible to type I error when multiple comparisons are uncorrected. We employ statistical parametric mapping to minimise the risk of such error, enabling more appropriate clinical decision-making. Methods: Lower-limb biomechanics of 21 patients with patellar tendinopathy and 22 controls were captured during walking and three types of squats. A statistical parametric mapping two-sample t-test was used to identify kinematic and kinetic differences between groups for each joint. Paired t-tests were used to compare pain before and after tasks, in patients with patellar tendinopathy. Findings: During walking, cases demonstrated reduced knee joint power during initial contact and hip joint power during terminal stance. In squatting, cases demonstrated increased knee abduction angles at various time points of the small knee bend and single-leg squat. Cases demonstrated reduced knee internal rotation moment during the deepest portion of the single-leg squat and single-leg decline squat. Interpretation: Gait appears unaffected by patellar tendinopathy, likely due to low task difficulty. Elevated knee abductions angles during squatting were confirmed as a key difference in patients with patellar tendinopathy. Reduced knee internal rotation moments in patients were attributed to a potential reduction in hip external rotator strength and possible pain avoidance strategy; however further evidence is required to substantiate these claims. Findings provide a clear rationale for rehabilitation programs to focus on knee stabilisation and strengthening of the muscles surrounding the hip.
MeSH term(s)	Biomechanical Phenomena ; Gait ; Humans ; Knee Joint ; Leg ; Military Personnel ; Range of Motion, Articular ; Tendinopathy
Language	English
Publishing date	2021-10-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	632747-3
ISSN	1879-1271 ; 0268-0033
ISSN (online)	1879-1271
ISSN	0268-0033
DOI	10.1016/j.clinbiomech.2021.105514
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Article ; Online: How long is Long-COVID? Symptomatic improvement between 12 and 18 months in a prospective cohort study.

Barker-Davies, Robert M / O'Sullivan, O / Holdsworth, D A / Ladlow, P / Houston, A / Chamley, R / Greenhalgh, A / Nicol, E D / Bennett, A N

BMJ military health

2023

Abstract: Introduction: COVID-19 infection can precede, in a proportion of patients, a prolonged syndrome including fatigue, exercise intolerance, mood and cognitive problems. This study aimed to describe the profile of fatigue-related, exercise-related, mood- ... ...

Abstract	Introduction: COVID-19 infection can precede, in a proportion of patients, a prolonged syndrome including fatigue, exercise intolerance, mood and cognitive problems. This study aimed to describe the profile of fatigue-related, exercise-related, mood-related and cognitive-related outcomes in a COVID-19-exposed group compared with controls. Methods: 113 serving UK Armed Forces participants were followed up at 5, 12 (n=88) and 18 months (n=70) following COVID-19. At 18 months, 56 were in the COVID-19-exposed group with 14 matched controls. Exposed participants included hospitalised (n=25) and community (n=31) managed participants. 43 described at least one of the six most frequent symptoms at 5 months: fatigue, shortness of breath, chest pain, joint pain, exercise intolerance and anosmia. Participants completed a symptom checklist, patient-reported outcome measures (PROMs), the National Institute for Health cognitive battery and a 6-minute walk test (6MWT). PROMs included the Fatigue Assessment Scale (FAS), Generalised Anxiety Disorder-7 (GAD-7), Patient Health Questionnaire-9 (PHQ-9) and Patient Checklist-5 (PCL-5) for post-traumatic stress. Results: At 5 and 12 months, exposed participants presented with higher PHQ-9, PCL-5 and FAS scores than controls (ES (effect size) ≥0.25, p≤0.04). By 12 months, GAD-7 was not significantly different to controls (ES <0.13, p=0.292). Remaining PROMs lost significant difference by 18 months (ES ≤0.11, p≥0.28). No significant differences in the cognitive scales were observed at any time point (F=1.96, p=0.167). At 5 and 12 months, exposed participants recorded significantly lower distances on the 6MWT (η Conclusions: This prospective cohort-controlled study observed adverse outcomes in depression, post-traumatic stress, fatigue and submaximal exercise performance up to 12 months but improved by 18-month follow-up, in participants exposed to COVID-19 compared with a matched control group.
Language	English
Publishing date	2023-10-03
Publishing country	England
Document type	Journal Article
ZDB-ID	3011686-7
ISSN	2633-3775 ; 2633-3767
ISSN (online)	2633-3775
ISSN	2633-3767
DOI	10.1136/military-2023-002500
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Article ; Online: HTSlib: C library for reading/writing high-throughput sequencing data.

Bonfield, James K / Marshall, John / Danecek, Petr / Li, Heng / Ohan, Valeriu / Whitwham, Andrew / Keane, Thomas / Davies, Robert M

GigaScience

2021 Volume 10, Issue 2

Abstract: Background: Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on ... ...

Abstract	Background: Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health. Findings: We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and iterators, and better use of threading. Conclusion: Since the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded >1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.
MeSH term(s)	High-Throughput Nucleotide Sequencing ; Reading ; Sequence Alignment ; Software ; Writing
Language	English
Publishing date	2021-02-02
Publishing country	United States
Document type	Journal Article ; Legal Case ; Research Support, Non-U.S. Gov't
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giab007
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Article ; Online: Exercise tolerance, fatigue, mental health, and employment status at 5 and 12 months following COVID-19 illness in a physically trained population.

Ladlow, Peter / Holdsworth, David A / O'Sullivan, Oliver / Barker-Davies, Robert M / Houston, Andrew / Chamley, Rebecca / Rogers-Smith, Kasha / Kinkaid, Victoria / Kedzierski, Adam / Naylor, Jon / Mulae, Joseph / Cranley, Mark / Nicol, Edward D / Bennett, Alexander N

Journal of applied physiology (Bethesda, Md. : 1985)

2023 Volume 134, Issue 3, Page(s) 622–637

Abstract: Failure to recover following severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) may have a profound impact on individuals who participate in high-intensity/volume exercise as part of their occupation/recreation. The aim of this study was to ... ...

Abstract	Failure to recover following severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) may have a profound impact on individuals who participate in high-intensity/volume exercise as part of their occupation/recreation. The aim of this study was to describe the longitudinal cardiopulmonary exercise function, fatigue, and mental health status of military-trained individuals (up to 12-mo postinfection) who feel recovered, and those with persistent symptoms from two acute disease severity groups (hospitalized and community-managed), compared with an age-, sex-, and job role-matched control. Eighty-eight participants underwent cardiopulmonary functional tests at baseline (5 mo following acute illness) and 12 mo; 25 hospitalized with persistent symptoms (hospitalized-symptomatic), 6 hospitalized and recovered (hospitalized-recovered); 28 community-managed with persistent symptoms (community-symptomatic); 12 community-managed, now recovered (community-recovered), and 17 controls. Cardiopulmonary exercise function and mental health status were comparable between the 5 and 12-mo follow-up. At 12 mo, symptoms of fatigue (48% and 46%) and shortness of breath (SoB; 52% and 43%) remain high in hospitalized-symptomatic and community-symptomatic groups, respectively. At 12 mo, COVID-19-exposed participants had a reduced capacity for work at anaerobic threshold and at peak exercise levels of deconditioning persist, with many individuals struggling to return to strenuous activity. The prevalence considered "fully fit" at 12 mo was lowest in symptomatic groups (hospitalized-symptomatic, 4%; hospitalized-recovered, 50%; community-symptomatic, 18%; community-recovered, 82%; control, 82%) and 49% of COVID-19-exposed participants remained medically nondeployable within the British Armed Forces. For hospitalized and symptomatic individuals, cardiopulmonary exercise profiles are consistent with impaired metabolic efficiency and deconditioning at 12 mo postacute illness. The long-term deployability status of COVID-19-exposed military personnel is uncertain.
MeSH term(s)	Humans ; COVID-19 ; Exercise Tolerance ; SARS-CoV-2 ; Fatigue ; Dyspnea ; Employment ; Mental Fatigue
Language	English
Publishing date	2023-02-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219139-8
ISSN	1522-1601 ; 0021-8987 ; 0161-7567 ; 8750-7587
ISSN (online)	1522-1601
ISSN	0021-8987 ; 0161-7567 ; 8750-7587
DOI	10.1152/japplphysiol.00370.2022
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Article: High-Volume Image-Guided Injections in Achilles and Patellar Tendinopathy in a Young Active Military Population: A Double-Blind Randomized Controlled Trial.

Barker-Davies, Robert M / Baker, Polly / Watson, James / Goodall, Duncan / Wheeler, Patrick C / Nicol, Alastair M / Fong, Daniel T P / Lewis, Mark P / Bennett, Alexander N

Orthopaedic journal of sports medicine

2022 Volume 10, Issue 4, Page(s) 23259671221088326

Abstract: Background: Chronic Achilles and patellar tendinopathy are a significant burden in physically active populations. High-volume image-guided injection (HVIGI) proposes to strip away associated neovascularity, disrupt painful nerve ingrowth, and facilitate ...

Abstract	Background: Chronic Achilles and patellar tendinopathy are a significant burden in physically active populations. High-volume image-guided injection (HVIGI) proposes to strip away associated neovascularity, disrupt painful nerve ingrowth, and facilitate rehabilitation. Purpose: To investigate the efficacy of HVIGI with and without steroid relative to placebo. Study design: Randomized controlled trial; Level of evidence, 1. Methods: A total of 62 participants were recruited between May 25, 2016, and March 5, 2020. Participants were men aged 18 to 55 years with Achilles or patellar tendinopathy of at least 6-month chronicity that had not improved with nonoperative management (including physical therapy and shockwave therapy), with ultrasound evidence of neovascularization, tendon thickening, and echogenic changes. They were assigned to the following groups: control (3 mL of subcutaneous 0.5% bupivacaine), HVIGI (10 mL of 0.5% bupivacaine and 30 mL of normal saline, ultrasound-guided between tendon and underlying fat pad), or HVIGI with steroid (HVIGIwSteroid; 0.25 mL of 100 mg/mL hydrocortisone). Clinicians and assessors were blinded. All participants were supervised through a pain-guided progressive loading program for 6 months postinjection. The main outcome measures were the Victoria Institute of Sport Assessments (VISA) for Achilles and patellar tendinopathy and the visual analog scale (VAS) for pain at 6 months postinjection. Results: The VISA score improved by a mean of 22.8 points (95% CI, 10.4-35.3 points; effect size [ES], 1.51) in the control group (n = 21), 18.6 points (95% CI, 9.1-28.0 points; ES, 1.31) in the HVIGI group (n = 21), and 18.5 points (95% CI, 3.4-33.6 points; ES, 0.88) in the HVIGIwSteroid group (n = 20). VAS pain improved by a mean of 15 points (interquartile range [IQR], -38.75, 8 points; ES, 0.39) in controls, 13 points (IQR,-34.0, 3.75 points; ES, 0.47) in the HVIGI group, and 27 points (IQR,-38.0, -1.0 points; ES, 0.54) in the HVIGIwSteroid group. The main effects were significant for time ( Conclusion: Study findings did not demonstrate superiority of HVIGI over control injection. Registration: EU Clinical Trials Register (EudraCT: 2015-003587-36).
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2706251-X
ISSN	2325-9671
ISSN	2325-9671
DOI	10.1177/23259671221088326
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Article ; Online: Twelve years of SAMtools and BCFtools.

Danecek, Petr / Bonfield, James K / Liddle, Jennifer / Marshall, John / Ohan, Valeriu / Pollard, Martin O / Whitwham, Andrew / Keane, Thomas / McCarthy, Shane A / Davies, Robert M / Li, Heng

GigaScience

2021 Volume 10, Issue 2

Abstract: Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis ... ...

Abstract	Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.
MeSH term(s)	Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; Software
Language	English
Publishing date	2021-02-15
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giab008
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Article ; Online: Refget: standardized access to reference sequences.

Yates, Andrew D / Adams, Jeremy / Chaturvedi, Somesh / Davies, Robert M / Laird, Matthew / Leinonen, Rasko / Nag, Rishi / Sheffield, Nathan C / Hofmann, Oliver / Keane, Thomas M

Bioinformatics (Oxford, England)

2021 Volume 38, Issue 1, Page(s) 299–300

Abstract: Motivation: Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing.: Results: We have created refget, a Global Alliance for Genomics and Health API ... ...

Abstract	Motivation: Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. Results: We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself. We present four reference implementations across in-house and cloud infrastructure, a compliance suite and a web report used to ensure specification conformity across implementations. Availability and implementation: The refget specification can be found at: https://w3id.org/ga4gh/refget. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Software ; Genomics
Language	English
Publishing date	2021-07-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab524
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Article ; Online: Kinematic and kinetic differences between military patients with patellar tendinopathy and asymptomatic controls during single leg squats.

Barker-Davies, Robert M / Roberts, Andrew / Watson, James / Baker, Polly / Bennett, Alexander N / Fong, Daniel T P / Wheeler, Patrick / Lewis, Mark P

Clinical biomechanics (Bristol, Avon)

2019 Volume 62, Page(s) 127–135

Abstract: Background: Knee valgus alignment has been associated with lower-limb musculoskeletal injury. This case-control study aims to: assess biomechanical differences between patients with patellar tendinopathy and healthy controls.: Methods: 43 military ... ...

Abstract	Background: Knee valgus alignment has been associated with lower-limb musculoskeletal injury. This case-control study aims to: assess biomechanical differences between patients with patellar tendinopathy and healthy controls. Methods: 43 military participants (21 cases, 22 controls) were recorded using 3D-motion capture performing progressively demanding, small knee bend, single leg and single leg decline squats. Planned a priori analysis of peak: hip adduction, knee flexion, pelvic tilt, pelvic obliquity and trunk flexion was conducted using MANOVA. Kinematic and kinetic data were graphed with bootstrapped t-tests and 95% CI's normalised to the squat cycle. ANOVA and correlations in SPSS were used for exploratory analysis. Findings: On their symptomatic side cases squatted to less depth (-6.62°, p < 0.05) than controls with exploratory curve analysis revealing a pattern of increased knee valgus collapse throughout the squatting movement (p < 0.05). Greater patella tendon force was generated by: the eccentric than concentric phase of squatting (+30-43%, ES 0.52-1.32, p < 0.01), declined (plantarflexed) compared to horizontal surface (+36-51%, ES 1.19-1.68, p < 0.01) and deeper knee flexion angles (F ≥ 658.3, p < 0.01) with no difference between groups (F ≤ 1.380, p > 0.05). Cases experienced more pain on testing on decline board (ES = 0.69, p < 0.01). For symptomatic limbs pain (r Interpretation: Knee valgus alignment is a plausible risk factor for patellar tendinopathy. Conclusions relating to causation are limited by the cross-sectional study design. Increasing squat depth, use of a declined surface and isolating the eccentric phase enable progression of loading prescription guided by pain.
MeSH term(s)	Adolescent ; Adult ; Analysis of Variance ; Biomechanical Phenomena ; Case-Control Studies ; Cross-Sectional Studies ; Exercise/physiology ; Humans ; Kinetics ; Knee Joint/physiology ; Male ; Middle Aged ; Military Personnel ; Patellar Ligament/physiopathology ; Posture/physiology ; Range of Motion, Articular ; Tendinopathy/physiopathology ; Young Adult
Language	English
Publishing date	2019-02-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	632747-3
ISSN	1879-1271 ; 0268-0033
ISSN (online)	1879-1271
ISSN	0268-0033
DOI	10.1016/j.clinbiomech.2019.02.001
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Article: Cardiopulmonary, Functional, Cognitive and Mental Health Outcomes Post-COVID-19, Across the Range of Severity of Acute Illness, in a Physically Active, Working-Age Population.

Sports medicine - open

2023 Volume 9, Issue 1, Page(s) 7

Abstract: Background: The COVID-19 pandemic has led to significant morbidity and mortality, with the former impacting and limiting individuals requiring high physical fitness, including sportspeople and emergency services.: Methods: Observational cohort study ... ...

Abstract	Background: The COVID-19 pandemic has led to significant morbidity and mortality, with the former impacting and limiting individuals requiring high physical fitness, including sportspeople and emergency services. Methods: Observational cohort study of 4 groups: hospitalised, community illness with on-going symptoms (community-symptomatic), community illness now recovered (community-recovered) and comparison. A total of 113 participants (aged 39 ± 9, 86% male) were recruited: hospitalised (n = 35), community-symptomatic (n = 34), community-recovered (n = 18) and comparison (n = 26), approximately five months following acute illness. Participant outcome measures included cardiopulmonary imaging, submaximal and maximal exercise testing, pulmonary function, cognitive assessment, blood tests and questionnaires on mental health and function. Results: Hospitalised and community-symptomatic groups were older (43 ± 9 and 37 ± 10, P = 0.003), with a higher body mass index (31 ± 4 and 29 ± 4, P < 0.001), and had worse mental health (anxiety, depression and post-traumatic stress), fatigue and quality of life scores. Hospitalised and community-symptomatic participants performed less well on sub-maximal and maximal exercise testing. Hospitalised individuals had impaired ventilatory efficiency (higher VE/V̇CO Conclusion: Symptomatically recovered individuals who suffered mild-moderate acute COVID-19 do not differ from an age-, sex- and job-role-matched comparison population five months post-illness. Individuals who were hospitalised or continue to suffer symptoms may require a specific comprehensive assessment prior to return to full physical activity.
Language	English
Publishing date	2023-02-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2809942-4
ISSN	2198-9761 ; 2199-1170
ISSN (online)	2198-9761
ISSN	2199-1170
DOI	10.1186/s40798-023-00552-0
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