Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.

Ensembl 2024.

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.

The Effects of Low-Load Squat Jump and Maximal Isometric Priming Exercise on Muscular Performance and Perceptual State.

ABSTRACT: Harrison, PW, James, LP, Jenkins, DG, McGuigan, MR, Holmberg, PM, and Kelly, VG. The effects of low-load squat jump and maximal isometric priming exercise on muscular performance and perceptual state. J Strength Cond Res 38(1): 1-9, 2024-The aim of this study was to examine responses at 3 and 27 hours after low-load jump squat (LL) and maximal isometric half-squat (ISO) priming stimuli. Fifteen resistance-trained males performed LL (4 × 3 at 20% 1 repetition maximum [1RM]), ISO (4 × 3 seconds), and control (CON) activities (standardized warm-up) in a randomized and counterbalanced order. Countermovement jump (CMJ) and isometric midthigh pull tests were conducted to assess performance changes after priming and CON activities. No clear changes in CMJ measures were found after priming activities compared with CON. However, small effect size improvements were found after priming stimuli completed on the same day. A 2.9% decrease in concentric phase duration (CI = 0.3-5.9, p = 0.333, Cliff's delta = -0.156) and a 9.1% increase in RSImod (CI = 0.2-12.3, p = 0.151, Cliff's delta = -0.218) occurred at 3 hours after LL compared with CON. Braking phase duration (CI = 0.8-10.6, p = 0.333, Cliff's delta = -0.213) was 2.9% shorter at 3 hours after ISO compared with CON. No clear changes in isometric peak force occurred after priming activities compared with CON. Additionally, questionnaires were completed to assess perceptual state and perceived effectiveness of the priming stimulus to influence performance. An increase in the "effect of activity" was perceived at 3 hours after LL and ISO (p = 0.013-0.044, Cliff's delta = 0.578-0.6) and at 27 hours after ISO (p = 0.99, Cliff's delta = 0.173) compared with CON. An increase in "muscular heaviness" was also reported at 3 hours after ISO compared with CON (p = 0.199, Cliff's delta = 0.320). The collective findings suggest limited benefits over the day after LL and ISO priming stimuli. However, as there was substantial variation in individual responses, the relative nature of priming responses should be considered when prescribing similar strategies in practical environments.

Effects of Repeated Jump Testing and Diurnal Changes on Subsequent Countermovement Jump and Squat Jump Output and Force-Time Characteristics.

ABSTRACT: Harrison, PW, James, LP, Jenkins, DG, Holmberg, PM, and Kelly, VG. Effects of repeated jump testing and diurnal changes on subsequent countermovement jump and squat jump output and force-time characteristics. J Strength Cond Res 38(1): 174-179, 2024-The aim of this brief study was to investigate the effects of repeated jump testing on performance over 2 consecutive days while considering the possibility of diurnal changes. Fourteen male subjects and 14 recreationally active female subjects completed countermovement jump (CMJ) and squat jump (SJ) testing on 5 occasions (baseline [0,800], 5 minutes [0,820], 8 hours [1,600], 24 hours [0,800], and 32 hours [1,600]) over 32 hours. An additional rested baseline test was conducted on a separate day in the afternoon (1,600) to compare jump performance between morning and afternoon baseline values. Excluding small decreases in CMJ height at 24 hours (p = 0.292, Cliff's delta = -0.225) in male subjects and similar decreases in CMJ height at 5 minutes (p = 0.034, Cliff's delta = -0.245) in addition to SJ height:contraction time at 32 hours (p = 0.126, Cliff's delta = 0.153) in female subjects, findings generally showed no changes in jump performance over multiple assessments. Squat jump metrics may have showed small improvements between morning and afternoon baseline values in male subjects (SJ height:contraction time [p = 0.030, Cliff's delta = 0.225]) and female subjects (SJ height [p = 0.013, Cliff's delta = 0.173] and SJ height:contraction time [p = 0.091, Cliff's delta = 0.163)]. As jump performance was largely unaffected by repeated jump testing, the present findings support the use of monitoring practices and research designs that require multiple jump assessments within acute periods (∼32 hours).

Does Moderate-Load Priming Activity Influence Maximal Upper-Body Performance and Perceptual State?

ABSTRACT: Harrison, PW, Kelly, VG, Jenkins, DG, McGuigan, MR, Holmberg, PM, and James, LP. Does moderate-load priming activity influence maximal upper-body performance and perceptual state?. J Strength Cond Res 37(11): e581-e587, 2023-The results of previous research indicate that resistance exercise "priming" may improve strength-power measures within 48 hours after their completion. Although researchers have primarily examined performance responses after lower-body priming stimuli, investigations examining the effects of upper-body resistance priming exercises are presently limited. Therefore, the aim of this study was to examine upper-body pushing and pulling performance in addition to perceptual responses 3 and 27 hours after moderate-load (ML) upper-body resistance priming exercise. Fourteen resistance-trained men were assigned to complete ML priming (4 × 3 bench press and bench pull at 65% 1RM [repetition maximum]) and control (rest) protocols in a randomized and counterbalanced order. Peak velocity during the bench throw and bench pull tests involving different loads (25, 50, and 75% 1RM) showed no practical change at 3 and 27 hours after the priming session (p = 0.216-0.99, Cliff's d = -0.041 to 0.225). Small effect size increases in perceptual measures ("physical feeling," "physical performance," "aggression" [p = 0.400-0.553, Cliff's d = 0.183-0.201], and "muscular heaviness" [p = 0.178, Cliff's d = 0.231]) were found at 3 hours postpriming. A moderate practical increase was observed in perceived "physical feeling" compared with control (p = 0.385, Cliff's d = 0.349) in addition to small effect size increases in perceived "physical performance" and "aggression" (Cliff's d = 0.243-0.290) at 27 hours after priming activities. These results indicate that upper-body strength-power changes within 27 hours after ML upper-body resistance exercise priming are not practically meaningful.

GENCODE: reference annotation for the human and mouse genomes in 2023.

GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

The European Nucleotide Archive in 2021.

The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Here, we outline the major updates to ENA's services and infrastructure that have been delivered over the past year.

The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes.

The Functional Annotation of ANimal Genomes (FAANG) project is a worldwide coordinated action creating high-quality functional annotation of farmed and companion animal genomes. The generation of a rich genome-to-phenome resource and supporting informatic infrastructure advances the scope of comparative genomics and furthers the understanding of functional elements. The project also provides terrestrial and aquatic animal agriculture community powerful resources for supporting improvements to farmed animal production, disease resistance, and genetic diversity. The FAANG Data Portal (https://data.faang.org) ensures Findable, Accessible, Interoperable and Reusable (FAIR) open access to the wealth of sample, sequencing, and analysis data produced by an ever-growing number of FAANG consortia. It is developed and maintained by the FAANG Data Coordination Centre (DCC) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). FAANG projects produce a standardised set of multi-omic assays with resulting data placed into a range of specialised open data archives. To ensure this data is easily findable and accessible by the community, the portal automatically identifies and collates all submitted FAANG data into a single easily searchable resource. The Data Portal supports direct download from the multiple underlying archives to enable seamless access to all FAANG data from within the portal itself. The portal provides a range of predefined filters, powerful predictive search, and a catalogue of sampling and analysis protocols and automatically identifies publications associated with any dataset. To ensure all FAANG data submissions are high-quality, the portal includes powerful contextual metadata validation and data submissions brokering to the underlying EMBL-EBI archives. The portal will incorporate extensive new technical infrastructure to effectively deliver and standardise FAANG's shift to single-cellomics, cell atlases, pangenomes, and novel phenotypic prediction models. The Data Portal plays a key role for FAANG by supporting high-quality functional annotation of animal genomes, through open FAIR sharing of data, complete with standardised rich metadata. Future Data Portal features developed by the DCC will support new technological developments for continued improvement for FAANG projects.

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research.

Time Course of Neuromuscular, Hormonal, and Perceptual Responses Following Moderate- and High-Load Resistance Priming Exercise.

PURPOSE: The aim of this study was to map responses over 32 hours following high-load (HL) and moderate-load (ML) half-squat priming. METHODS: Fifteen participants completed control, HL (87% 1RM), and ML (65% 1RM) activities in randomized, counterbalanced order. Countermovement jump (CMJ), squat jump (SJ), saliva testosterone, saliva cortisol, and perceptual measures were assessed before and 5 minutes, 8 hours, 24 hours, and 32 hours after each activity. Results are presented as percentage change from baseline and 95% confidence interval (CI). Cliff delta was used to determine threshold for group changes. RESULTS: SJ height increased by 4.5% (CI = 2.2-6.8, Cliff delta = 0.20) 8 hours following HL. CMJ and SJ improved by 6.1% (CI = 2.1-7.8, Cliff delta = 0.27) and 6.5% (CI = 1.2-11.8, Cliff delta = 0.30), respectively, 32 hours after ML. No clear diurnal changes in CMJ or SJ occurred 8 hours following control; however, increases of 3.9% (CI = 2.9-9.2, Cliff delta = 0.26) and 4.5% (CI = 0.9-8.1, Cliff delta = 0.24), respectively, were observed after 32 hours. Although diurnal changes in saliva hormone concentration occurred (Cliff delta = 0.37-0.92), the influence of priming was unclear. Perceived "physical feeling" was greater 8 hours following HL (Cliff delta = 0.36) and 32 hours after ML and control (Cliff delta = 0.17-0.34). CONCLUSIONS: HL priming in the morning may result in small improvements in jump output and psychophysiological state in the afternoon. Similar improvements were observed in the afternoon the day after ML priming.

The European Nucleotide Archive in 2020.

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present the world's public sequencing data for the benefit of the entire scientific community and for the acceleration of the global research effort. Here we highlight the major developments to ENA services and content in 2020, focussing in particular on the recently released updated ENA browser, modernisation of our release process and our data coordination collaborations with specific research communities.

Prevalence and application of priming exercise in high performance sport.

OBJECTIVES: Recent research has revealed that low volume resistance 'priming' exercise may improve neuromuscular performance when completed within 48h before competition. The aim of this study was to investigate the current prevalence and application of this strategy by practitioners in sport. DESIGN: This study surveyed practitioners who were currently programming and/or prescribing resistance training programs for high performance athletes. METHODS: Sixty-nine practitioners completed the online survey relating to their perceptions of resistance priming exercise strategies and the training methods prescribed in the days prior to competition. RESULTS: Fifty-one percent of respondents currently prescribed priming exercise. Of the practitioners who prescribed this strategy, most respondents (59%) prescribed this session within 8h of competition. Sessions typically included 2-3 upper body and lower body exercises (mean=2.5±0.7 and 2.1±0.6 respectively), usually involving both loaded and unloaded activities. Large variations in exercise selection were reported, however, unloaded jumps (87%), loaded jumps (60%) and bench press (56%) were commonly prescribed. A low volume of sets (mean=2.8±0.9) and repetitions (mean=3.8±1.3) were used during these sessions. Lastly, various resistance loading strategies were prescribed, ranging from unloaded activities to heavy loaded exercises performed at ≥85% 1RM. CONCLUSIONS: Priming exercise is currently prescribed by many practitioners to prepare athletes for competition. A wide range of priming exercise methods are used, despite limited evidence supporting these methods. Future research should examine the effects of the various priming methods which are currently applied in practice.

The European Nucleotide Archive in 2019.

The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) at the European Molecular Biology Laboratory's European Bioinformatics Institute provides open and freely available data deposition and access services across the spectrum of nucleotide sequence data types. Making the world's public sequencing datasets available to the scientific community, the ENA represents a globally comprehensive nucleotide sequence resource. Here, we outline ENA services and content in 2019 and provide an insight into selected key areas of development in this period.

The COMPARE Data Hubs.

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders.

Resistance Priming to Enhance Neuromuscular Performance in Sport: Evidence, Potential Mechanisms and Directions for Future Research.

Recent scientific evidence supports the use of a low-volume strength-power 'resistance priming' session prior to sporting competition in an effort to enhance neuromuscular performance. Though research evidence relating to this strategy is presently limited, it has been shown to be effective in improving various measures of neuromuscular performance within 48 h. Post-activation potentiation strategies have previously been shown to enhance strength-power performance within 20 min of completing maximal or near-maximal resistance exercise. Comparably, a delayed potentiation effect has been demonstrated following 'resistance priming' at various times between 1 and 48 h in upper- and lower-body performance measures. This may have significant implications for a range of athletes when preparing for competition. Various exercise protocols have been shown to improve upper- and lower-body neuromuscular performance measures in this period. In particular, high-intensity resistance exercise through high loading (≥ 85% 1 repetition maximum) or ballistic exercise at lower loads appears to be an effective stimulus for this strategy. Although current research has identified the benefits of resistance priming to some physical qualities, many questions remain over the application of this type of session, as well as the effects that it may have on a range of specific sporting activities. The aims of this brief review are to assess the current literature examining the acute effects (1-48 h) of resistance exercise on neuromuscular performance and discuss potential mechanisms of action as well as provide directions for future research.

A Report from a Workshop of the International Stem Cell Banking Initiative, Held in Collaboration of Global Alliance for iPSC Therapies and the Harvard Stem Cell Institute, Boston, 2017.

This report summarizes the recent activity of the International Stem Cell Banking Initiative held at Harvard Stem Cell Institute, Boston, MA, USA, on June 18, 2017. In this meeting, we aimed to find consensus on ongoing issues of quality control (QC), safety, and efficacy of human pluripotent stem cell banks and their derivative cell therapy products for the global harmonization. In particular, assays for the QC testing such as pluripotency assays test and general QC testing criteria were intensively discussed. Moreover, the recent activities of global stem cell banking centers and the regulatory bodies were briefly summarized to provide an overview on global developments and issues. Stem Cells 2019;37:1130-1135.

The European Nucleotide Archive in 2018.

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided from EMBL-EBI, has for more than three decades been responsible for archiving the world's public sequencing data and presenting this important resource to the scientific community to support and accelerate the global research effort. Here, we outline ENA services and content in 2018 and provide an overview of a selection of focus areas of development work: extending data coordination services around ENA, sequence submissions through template expansion, early pre-submission validation tools and our move towards a new browser and retrieval infrastructure.

Applied Sport Science of Australian Football: A Systematic Review.

BACKGROUND: In recent years, there has been a large expansion in literature pertaining to the game of Australian football (AF). Furthermore, there have been a number of rule changes that are likely to have changed the demands of the game. Based on these advances and changes, it seemed important to conduct a review assessing the scientific literature surrounding the sport. OBJECTIVE: The review evaluates the match demands of AF, the qualities required for success, and the impact training and competition have on adaptation, injury and fatigue. METHODS: A systematic search of PubMed, CINAHL, SPORTDiscus, Web of Science and Scopus for AF literature was conducted; studies investigating match demands, physical qualities, training practices and injury were included. Weighted means and standard deviations were calculated for match demands and physical and anthropometric profiles across playing standards. RESULTS: A total of 1830 articles were retrieved in the initial search, with 888 removed as duplicates, 626 removed for being non-relevant and a further 152 removed for being AF papers but not relevant to the review. As such, 164 AF papers were included in the review. Due to the intermittent high-intensity nature of match-play, players need a wide range of physical and technical qualities to excel, with speed, aerobic fitness, reactive agility and well-developed lean mass being central to success. Training for AF at the elite level is associated with high workloads, with players engaging in numerous training modalities; even altitude and heat training camps have been utilised by Australian Football League (AFL) teams to further augment fitness improvements. While high chronic workloads can be tolerated and are needed for improving physical qualities, careful planning and monitoring of internal and external workloads is required to minimise sharp spikes in load that are associated with injury. CONCLUSIONS: There is a complex interaction between numerous contextual factors that influence the match demands that are discussed in this review. Whilst players must have the physical capacities to cope with the intense physical demands of AF matches, the successful execution of technical skills during match-play is central to success. To develop these skills and attributes, specific and carefully planned and monitored training must be performed over a number of years.

The European Nucleotide Archive in 2017.

For 35 years the European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) has been responsible for making the world's public sequencing data available to the scientific community. Advances in sequencing technology have driven exponential growth in the volume of data to be processed and stored and a substantial broadening of the user community. Here, we outline ENA services and content in 2017 and provide insight into a selection of current key areas of development in ENA driven by challenges arising from the above growth.