RedRibbon: A new rank-rank hypergeometric overlap for gene and transcript expression signatures

High-throughput omics technologies have generated a wealth of large protein, gene, and transcript datasets that have exacerbated the need for new methods to analyse and compare big datasets. Rank-rank hypergeometric overlap is an important threshold-free method to combine and visualize two ranked lists of P-values or fold-changes, usually from differential gene expression analyses. Here, we introduce a new rank-rank hypergeometric overlap-based method aimed at gene level and alternative splicing analyses at transcript or exon level, hitherto unreachable as transcript numbers are an order of magnitude larger than gene numbers. We tested the tool on synthetic and real datasets at gene and transcript levels to detect correlation and anticorrelation patterns and found it to be fast and accurate, even on very large datasets thanks to an evolutionary algorithm-based minimal P-value search. The tool comes with a ready-to-use permutation scheme allowing the computation of adjusted P-values at low time cost. The package compatibility mode is a drop-in replacement to previous packages. RedRibbon holds the promise to accurately extricate detailed information from large comparative analyses.

Global Alliance for the Promotion of Physical Activity: the Hamburg Declaration

Non-communicable diseases (NCDs), including coronary heart disease, stroke, hypertension, type 2 diabetes, dementia, depression and cancers, are on the rise worldwide and are often associated with a lack of physical activity (PA). Globally, the levels of PA among individuals are below WHO recommendations. A lack of PA can increase morbidity and mortality, worsen the quality of life and increase the economic burden on individuals and society. In response to this trend, numerous organisations came together under one umbrella in Hamburg, Germany, in April 2021 and signed the 'Hamburg Declaration'. This represented an international commitment to take all necessary actions to increase PA and improve the health of individuals to entire communities. Individuals and organisations are working together as the 'Global Alliance for the Promotion of Physical Activity' to drive long-term individual and population-wide behaviour change by collaborating with all stakeholders in the community: active hospitals, physical activity specialists, community services and healthcare providers, all achieving sustainable health goals for their patients/clients. The 'Hamburg Declaration' calls on national and international policymakers to take concrete action to promote daily PA and exercise at a population level and in healthcare settings.

Joint position statement of the International Federation of Sports Medicine (FIMS) and European Federation of Sports Medicine Associations (EFSMA) on the IOC framework on fairness, inclusion and non-discrimination based on gender identity and sex variations

The IOC recently published its framework on fairness, inclusion and non-discrimination based on gender identity and sex variations. This framework is drafted mainly from a human rights perspective, with less consideration for medical/scientific issues. The framework places the onus for gender eligibility and classification entirely on the International Federations (IFs), even though most will not have the capacity to implement the framework. The position of no presumption of advantage is contrary to the 2015 IOC consensus. Implementation of the 2021 framework will be a major challenge for IFs that have already recognised the inclusion of trans and women athletes with differences of sexual development (DSD) using a scientific/medical solution. The potential consequences for sports that need to prioritise fairness or safety could be one of two extremes (1) exclusion of all transgender or DSD athletes on the grounds of advantage or (2) self-identification that essentially equates to no eligibility rules. Exclusion of all transgender or DSD athletes is contrary to the Olympic charter and unlawful in many countries. While having no gender eligibility rules, sport loses its meaning and near-universal support. Athletes should not be under pressure to undergo medical procedures or treatment to meet eligibility criteria. However, if an athlete is fully informed and consents, then it is their free choice to undergo carefully considered or necessary interventions for gender classification for sport to compete fairly and safely in their chosen gender. Free choice is a fundamental human right, but so is the right to fair and safe competition.

Preparticipation medical evaluation for elite athletes: EFSMA recommendations on standardised preparticipation evaluation form in European countries

Sports medicine is a medical specialty that supports the performance of professional and amateur athletes while maintaining their health. Sports medicine professionals need to ensure the safe participation of athletes in sports activities achieved through a periodical preparticipation evaluation (PPE) and a regular medical monitoring of the athletes’ health in accordance with the latest recommendations regarding health condition and medical history, physical working capacity, training period and programme, recovery, nutrition, use of supplements, injuries prevention and safe return to play.

In order to harmonise these national variations in the content and application of the PPE, the EFSMA Scientific and Educational Commission proposes a ‘gold standard’ for elite athletes across Europe.

Important objectives of PPE are early detection and prevention of severe complications during sports activities both in leisure time and competitive sports. The PPE should entail the following diagnostic components: health status, anthropometry, functional and exercise capacity.

It is of utmost importance to develop and implement preventive strategies such as the PPE. Besides monitoring the health status of athletes, the PPE plays an important role in the selection process, bringing valuable information for coaches and supporting a personalised treatment approach. Screening of athletes through a standardised digital PPE could be beneficial for a better understanding of the impact of long-term physical activity. Furthermore, PPE leads the scientific community to a way of working closer together in the interest of the athletes.

Use of an isometric mid-thigh pull test during musculoskeletal rehabilitation: can the criterion values from the updated British Army physical employment standards be used to inform UK Defence Rehabilitation practice?

INTRODUCTION

Objective outcome measures that can quantify the force generating capacity of the lower limb are required to allow clinicians to accurately measure functional status and treatment adaptations over time. The aim of this prospective observational cohort study is to: (1) evaluate the acceptability of the isometric mid-thigh pull (IMTP) test as a measure of functional strength with military personnel undergoing residential hip pain rehabilitation; (2) compare the peak force values recorded against the updated Army physical employment standards (PES) assessment criteria and (3) assess if the minimum PES required of military personnel has the potential to inform clinical decision making and return to duty criteria within UK Defence Rehabilitation.

METHODS

Acceptability was assessed against patient's adherence to the testing procedures and test burden. Clinician acceptability was assessed against ease of administration and safety of test procedure. Hip pain was recorded before, immediately following and 1 hour after testing. Net peak force was recorded using portable force plates.

RESULTS

Full patient and clinician acceptability to IMTP testing procedures were demonstrated. Minimal changes in visual analogue scale (VAS) pain scores were demonstrated between baseline values at rest and follow-up. Despite being medically downgraded and functionally compromised due to chronic hip pain, 100% of patients met the PES expected on entry to the British Army and 79% met the PES expected at the end of basic training.

CONCLUSION

The IMTP provides rehabilitation clinicians with an objective quantifiable measure of maximum muscle strength that can be used early in the rehabilitation care pathway. Based on our finding, it is unclear if the current British Army PES can be used as a criterion standard in Defence Rehabilitation. Therefore, further research focused on generating clinically relevant patient-specific IMTP score criteria, with a larger sample of diverse diagnostic sub-groups is required.

Integrating Transwomen and Female Athletes with Differences of Sex Development (DSD) into Elite Competition: The FIMS 2021 Consensus Statement

Sport is historically designated by the binary categorization of male and female that conflicts with modern society. Sport’s governing bodies should consider reviewing rules determining the eligibility of athletes in the female category as there may be lasting advantages of previously high testosterone concentrations for transwomen athletes and currently high testosterone concentrations in differences in sex development (DSD) athletes. The use of serum testosterone concentrations to regulate the inclusion of such athletes into the elite female category is currently the objective biomarker that is supported by most available scientific literature, but it has limitations due to the lack of sports performance data before, during or after testosterone suppression. Innovative research studies are needed to identify other biomarkers of testosterone sensitivity/responsiveness, including molecular tools to determine the functional status of androgen receptors. The scientific community also needs to conduct longitudinal studies with specific control groups to generate the biological and sports performance data for individual sports to inform the fair inclusion or exclusion of these athletes. Eligibility of each athlete to a sport-specific policy needs to be based on peer-reviewed scientific evidence made available to policymakers from all scientific communities. However, even the most evidence-based regulations are unlikely to eliminate all differences in performance between cisgender women with and without DSD and transwomen athletes. Any remaining advantage held by transwomen or DSD women could be considered as part of the athlete’s unique makeup.

Recommendations for Face Coverings While Exercising During the COVID-19 Pandemic

In an effort to reduce transmission and number of infections of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or COVID-19) virus, governments and official bodies around the world have produced guidelines on the use of face masks and face coverings. While there is a growing body of recommendations for healthcare professionals and the wider population to use facial protection in "enclosed spaces" where minimal distancing from other individuals is not possible, there is a dearth of clear guidelines for individuals undertaking exercise and sporting activity. The present viewpoint aims to propose recommendations for face coverings while exercising during the COVID-19 pandemic that consider physical distancing, the environment, the density of active cases associated with the specific sports activity, and the practical use of face coverings in order to reduce potential viral transmission. Recommendations are provided on the basis of very limited available evidence in conjunction with the extensive collective clinical experience of the authors and acknowledging the need to consider the likelihood of the presence of the SARS-CoV-2 in the general population. We recommend that face coverings should be used in any environment considered to be of a high or moderate transmission risk, where tolerated and after individual risk assessment. In addition, as national caseloads fluctuate, individual sporting bodies should consider up to date guidance on the use of face coverings during sport and exercise, alongside other preventative measures.

Biomechanical and clinical outcomes in response to inpatient multidisciplinary hip and groin rehabilitation in UK military personnel

INTRODUCTION

Hip and groin related pain is a common complaint among the military population across UK Defence Rehabilitation and addressing associated biomechanical dysfunction is a key treatment goal. Personnel are exposed to complex occupational loads, therefore assessing movement during demanding tasks may expose biomechanical deficits. Observing biomechanical and clinical outcomes in response to treatment is therefore an important consideration. The aims were to examine clinical and biomechanical outcomes prior to (T₁) and 12 weeks post (T₂) inpatient rehabilitation and explore the influence of pathological subgroup.

METHODS

Prospective cohort study as part of a clinical service evaluation of 25 patients undergoing treatment for hip and groin related pain. Three-dimensional motion capture (3DM) during a single-leg squat, hip strength and patient-reported outcome measures were collected at T₁ and T₂.

RESULTS

Increased abductor and external rotator strength with reductions in contralateral pelvic drop (1.9°; p=0.041) at T₂ on the injured side. Pain reduced by 9.6 mm (p=0.017) but no differences were found for Non-Arthritic Hip Score (NAHS). No statistically significant differences were found between pathological subgroups. Kinematic profiles display variation between diagnostic subgroups and response to treatment.

CONCLUSION

Strength and pain improved with treatment in this service evaluation although biomechanical adaptation and NAHS remain inconclusive. Small and uneven sample size prevents a firm conclusion regarding the effect of pathological subgroupings, however, the data can be considered hypothesis generating for future, larger studies to integrate 3DM for monitoring response to rehabilitation in pathological subgroups to support clinical decision making.

Sport and exercise genomics: the FIMS 2019 consensus statement update

Rapid advances in technologies in the field of genomics such as high throughput DNA sequencing, big data processing by machine learning algorithms and gene-editing techniques are expected to make precision medicine and gene-therapy a greater reality. However, this development will raise many important new issues, including ethical, moral, social and privacy issues. The field of exercise genomics has also advanced by incorporating these innovative technologies. There is therefore an urgent need for guiding references for sport and exercise genomics to allow the necessary advancements in this field of sport and exercise medicine, while protecting athletes from any invasion of privacy and misuse of their genomic information. Here, we update a previous consensus and develop a guiding reference for sport and exercise genomics based on a SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis. This SWOT analysis and the developed guiding reference highlight the need for scientists/clinicians to be well-versed in ethics and data protection policy to advance sport and exercise genomics without compromising the privacy of athletes and the efforts of international sports federations. Conducting research based on the present guiding reference will mitigate to a great extent the risks brought about by inappropriate use of genomic information and allow further development of sport and exercise genomics in accordance with best ethical standards and international data protection principles and policies. This guiding reference should regularly be updated on the basis of new information emerging from the area of sport and exercise medicine as well as from the developments and challenges in genomics of health and disease in general in order to best protect the athletes, patients and all other relevant stakeholders.

The Stanford Hall consensus statement for post-COVID-19 rehabilitation

The highly infectious and pathogenic novel coronavirus (CoV), severe acute respiratory syndrome (SARS)-CoV-2, has emerged causing a global pandemic. Although COVID-19 predominantly affects the respiratory system, evidence indicates a multisystem disease which is frequently severe and often results in death. Long-term sequelae of COVID-19 are unknown, but evidence from previous CoV outbreaks demonstrates impaired pulmonary and physical function, reduced quality of life and emotional distress. Many COVID-19 survivors who require critical care may develop psychological, physical and cognitive impairments. There is a clear need for guidance on the rehabilitation of COVID-19 survivors. This consensus statement was developed by an expert panel in the fields of rehabilitation, sport and exercise medicine (SEM), rheumatology, psychiatry, general practice, psychology and specialist pain, working at the Defence Medical Rehabilitation Centre, Stanford Hall, UK. Seven teams appraised evidence for the following domains relating to COVID-19 rehabilitation requirements: pulmonary, cardiac, SEM, psychological, musculoskeletal, neurorehabilitation and general medical. A chair combined recommendations generated within teams. A writing committee prepared the consensus statement in accordance with the appraisal of guidelines research and evaluation criteria, grading all recommendations with levels of evidence. Authors scored their level of agreement with each recommendation on a scale of 0-10. Substantial agreement (range 7.5-10) was reached for 36 recommendations following a chaired agreement meeting that was attended by all authors. This consensus statement provides an overarching framework assimilating evidence and likely requirements of multidisciplinary rehabilitation post COVID-19 illness, for a target population of active individuals, including military personnel and athletes.

Recommendations for return to sport during the SARS-CoV-2 pandemic

In this viewpoint we make specific recommendations that can assist and make the return to sport/exercise as safe as possible for all those impacted - from the recreational athlete to the elite athlete. We acknowledge that there are varying rules and regulations around the world, not to mention the varying philosophies and numerous schools of thought as it relates to return to sport/exercise and we have been cognisant of this in our recommendations. Despite the varying rules and circumstances around the world, we believe it is essential to provide some helpful and consistent guidance for return to training and sport for sport and exercise physicians around the world at this most difficult time. The present viewpoint provides practical and medical recommendations on the resumption to sport process.

The test-retest reliability of the Military Physical Loading Questionnaire (MPLQ)

INTRODUCTION

Despite the high prevalence of musculoskeletal injuries, there is a shortage of data quantifying the risk factors attributable to cumulative occupational demands among UK Military personnel. We developed a new comprehensive questionnaire that examines occupational and operational physical loading during military service. The aim of this study was to examine the test-retest reliability of the Military Physical Loading Questionnaire (MPLQ).

METHODS

Intraclass correlation coefficients (ICC) were used to evaluate the test-retest reliability (4-week interval) of the MPLQ on 18 occupational and 18 operational items in 50 male (mean age: 36 years; SD ±7.9) UK military personnel. A stratified analysis based on duration of Service (0-10 years, 11-20 years and ≥21 years) was conducted to assess whether stability of task items was dependent on participant length of recall. Internal consistency was assessed by Cronbach's alpha (α) coefficients.

RESULTS

Reliability of individual operational items ranged from fair to almost perfect agreement (ICC range: 0.37-0.89; α range: 0.53-0.94) with most items demonstrating moderate to substantial reliability. Overall scores related to occupational items showed substantial to almost perfect agreement between administrations (ICC range: 0.73-0.94; α range: 0.84-0.96). Stratifying by duration of Service showed similar within group reliability to the entire sample and no pattern of decreasing or increasing reliability with length of recall period was observed.

CONCLUSIONS

It is essential that data used in planning UK military policy and health services are as accurate as possible. This study provides preliminary support for the MPLQ as a reliable self-report instrument for assessing the cumulative lifelong effects of occupational loading in UK military personnel. Further validation studies using larger and more demographically diverse military populations will support its interpretation in future epidemiological research.

The Fluidity of Gender and Implications for the Biology of Inclusion for Transgender and Intersex Athletes

One of the most contentious issues in modern day sport arises when sports are divided into male and female categories. The International Association of Athletics Federations' (IAAF) previous policy regulating intersex athletes was suspended by the Court of Arbitration for Sport (CAS), resulting in a new policy. The challenge faced by the governing body of athletics is to formulate a policy that upholds both international law and the Olympic charter that stipulates athletes compete without discrimination of any kind. Implementation of the policy has been delayed until after a verdict, expected no later than March 26, 2019, in the Semenya versus IAAF trial in the Court of Arbitration for Sport. If the policy is enacted, it will restrict athletes from competing in the female athletics category with specific differences of sex development (DSD) in races from 400 m up to the mile in international level competitions unless they lower their natural testosterone (T) levels below 5 nmol·L. To thoroughly assess this new IAAF policy, one needs to appreciate its legal, sociological, and scientific underpinnings but also the history of previous policies attempting to define precisely how athletes should be divided into male and female categories. We previously proposed a system to deal with gender variant athletes that relied on a determination of an "athlete/athletic gender." The concept of "athlete gender" was presented to multiple audiences, and the resulting survey is included. A large majority of participants (71% of 153) who answered the survey agreed with the idea of an athlete gender. This position also was accompanied by the request for more studies (20% of those who agreed) and concern over the process of hormone monitoring (32% of those who agreed) to avoid doping misuse. The primary argument of those participating in the survey that disagreed with the position (23% of 153) was that biological differences between males and females remained even after the transition (47% of opposing comments). Mixed gender/sex competitions provide unique opportunities for athletes to compete against one another outside of the traditional male/female divide and pave the way for a more flexible approach for dealing with gender variant athletes.