Intermittent fasting and continuous energy restriction result in similar changes in body composition and muscle strength when combined with a 12 week resistance training program.

PURPOSE: The objective of this study was to compare the effects of 12 weeks of resistance training combined with either 5:2 intermittent fasting or continuous energy restriction on body composition, muscle size and quality, and upper and lower body strength. METHODS: Untrained individuals undertook 12 weeks of resistance training plus either continuous energy restriction [20% daily energy restriction (CERT)] or 5:2 intermittent fasting [~ 70% energy restriction 2 days/week, euenergetic consumption 5 days/week (IFT)], with both groups prescribed a mean of ≥ 1.4 g of protein per kilogram of body weight per day. Participants completed 2 supervised resistance and 1 unsupervised aerobic/resistance training combination session per week. Changes in lean body mass (LBM), thigh muscle size and quality, strength and dietary intake were assessed. RESULTS: Thirty-four participants completed the study (CERT = 17, IFT = 17). LBM was significantly increased (+ 3.7%, p < 0.001) and body weight (- 4.6%, p < 0.001) and fat (- 24.1%, p < 0.001) were significantly reduced with no significant difference between groups, though results differed by sex. Both groups showed improvements in thigh muscle size and quality, and reduced intramuscular and subcutaneous fat assessed by ultrasonography and peripheral quantitative computed tomography (pQCT), respectively. The CERT group demonstrated a significant increase in muscle surface area assessed by pQCT compared to the IFT group. Similar gains in upper and lower body strength and muscular endurance were observed between groups. CONCLUSION: When combined with resistance training and moderate protein intake, continuous energy restriction and 5:2 intermittent fasting resulted in similar improvements in body composition, muscle quality, and strength. ACTRN: ACTRN12620000920998, September 2020, retrospectively registered.

Ensembl 2017.

Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.

Ensembl 2016.

The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.

Australian Football Athletes Lack Awareness of Current Sport Nutrition Guidelines.

Sports nutrition is an evolving field, but there is a lack of data on Australian athletes' knowledge of current sports nutrition guidelines. Additionally, several tools used to assess nutrition knowledge (NK) have not undergone adequate validation. The purpose of this study was to assess and compare the sports NK of elite and nonelite Australian football (AF) athletes using a newly validated questionnaire-The Nutrition for Sport Knowledge Questionnaire. Elite AF players (n = 46) were recruited directly from their club dietitian and nonelite AF players (n = 53) were invited to participate via e-mail from their club president or secretary. The mean NK score of elite and nonelite AF players was 46 ± 16% and 51 ± 11%, respectively (p = .041). In both groups, knowledge of macronutrients, weight management, and alcohol was better than knowledge of supplements, micronutrients, and sports nutrition. Nonelite athletes achieved statistically significantly higher scores on the questionnaire subsections testing weight management (elite: 48 ± 18; nonelite: 57 ± 19, p = .019), micronutrients (elite: 39 ± 19; nonelite: 50 ± 16, p = .004), and alcohol (elite: 52 ± 13; nonelite: 71 ± 17, p = .002). While overall NK of Australian athletes was poor, scores varied greatly among individuals (range: 10-70%) and across the six subsections (topics) being assessed. Professionals working with athletes should undertake an assessment of the athletes' NK so that they can provide targeted education programs.

Ensembl 2015.

Ensembl (http://www.ensembl.org) is a genomic interpretation system providing the most up-to-date annotations, querying tools and access methods for chordates and key model organisms. This year we released updated annotation (gene models, comparative genomics, regulatory regions and variation) on the new human assembly, GRCh38, although we continue to support researchers using the GRCh37.p13 assembly through a dedicated site (http://grch37.ensembl.org). Our Regulatory Build has been revamped to identify regulatory regions of interest and to efficiently highlight their activity across disparate epigenetic data sets. A number of new interfaces allow users to perform large-scale comparisons of their data against our annotations. The REST server (http://rest.ensembl.org), which allows programs written in any language to query our databases, has moved to a full service alongside our upgraded website tools. Our online Variant Effect Predictor tool has been updated to process more variants and calculate summary statistics. Lastly, the WiggleTools package enables users to summarize large collections of data sets and view them as single tracks in Ensembl. The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license.

The Ensembl REST API: Ensembl Data for Any Language.

MOTIVATION: We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language. AVAILABILITY AND IMPLEMENTATION: The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest.

Ensembl 2014.

Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.

Ensembl 2013.

The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.

Ensembl 2012.

The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.

Ensembl 2011.

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

Mutations in SLC29A3, encoding an equilibrative nucleoside transporter ENT3, cause a familial histiocytosis syndrome (Faisalabad histiocytosis) and familial Rosai-Dorfman disease.

The histiocytoses are a heterogeneous group of disorders characterised by an excessive number of histiocytes. In most cases the pathophysiology is unclear and treatment is nonspecific. Faisalabad histiocytosis (FHC) (MIM 602782) has been classed as an autosomal recessively inherited form of histiocytosis with similarities to Rosai-Dorfman disease (RDD) (also known as sinus histiocytosis with massive lymphadenopathy (SHML)). To elucidate the molecular basis of FHC, we performed autozygosity mapping studies in a large consanguineous family and identified a novel locus at chromosome 10q22.1. Mutation analysis of candidate genes within the target interval identified biallelic germline mutations in SLC29A3 in the FHC kindred and in two families reported to have familial RDD. Analysis of SLC29A3 expression during mouse embryogenesis revealed widespread expression by e14.5 with prominent expression in the central nervous system, eye, inner ear, and epithelial tissues including the gastrointestinal tract. SLC29A3 encodes an intracellular equilibrative nucleoside transporter (hENT3) with affinity for adenosine. Recently germline mutations in SLC29A3 were also described in two rare autosomal recessive disorders with overlapping phenotypes: (a) H syndrome (MIM 612391) that is characterised by cutaneous hyperpigmentation and hypertrichosis, hepatomegaly, heart anomalies, hearing loss, and hypogonadism; and (b) PHID (pigmented hypertrichosis with insulin-dependent diabetes mellitus) syndrome. Our findings suggest that a variety of clinical diagnoses (H and PHID syndromes, FHC, and familial RDD) can be included in a new diagnostic category of SLC29A3 spectrum disorder.

Patient Mealtime Experience: Capturing Patient Perceptions Using a Novel Patient Mealtime Experience Tool.

INTRODUCTION: The aim of this study is to describe the mealtime experience using the qualitative components of the Austin Health Patient Mealtime Experience Tool (AHPMET) to complement the quantitative findings of this tool. METHODS: A multiphase, cross-sectional study was undertaken across all sites of Austin Health (Victoria, Australia) between March 2020 and November 2021. Patient mealtime experience was measured using the AHPMET. Descriptive statistics and a deductive thematic analysis approach described the patients' mealtime experiences. RESULTS: Questionnaire data were collected from 149 participants. Patients were most satisfied with staff interactions, and least satisfied with dimensions of food quality, specifically, flavour, presentation, and menu variety. Clinical symptoms, nutrition impact symptoms and the patient's position were barriers to consumption. DISCUSSION: Food quality was perceived as the poorest aspect of patient satisfaction with the hospital foodservice, particularly flavour, presentation, and menu variety. Future foodservice quality improvements must prioritise improving food quality to have the greatest impact on patient satisfaction. While clinical and organisational systems have a role in improving mealtime experience and oral intake, communicating patient perceptions of the mealtime experience is critical for responding to current perceptions of hospital food quality. CONCLUSION: Mealtime experience in the hospital has a significant impact on oral intake and patients' wider perception of hospital services. Questionnaires have been used to capture patient satisfaction with foodservice in the hospital; however, no comprehensive questionnaires including qualitative questions that capture the broader mealtime experience have been validated across different hospital settings. The tool developed through this study can be implemented in any acute and subacute health service to provide feedback and improve the mealtime experience of patients. This has the capacity to improve mealtime intake, mitigate malnutrition, and improve quality of life and patient outcomes.

Ensembl's 10th year.

Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.

The Effects of Intermittent Fasting and Continuous Energy Restriction with Exercise on Cardiometabolic Biomarkers, Dietary Compliance, and Perceived Hunger and Mood: Secondary Outcomes of a Randomised, Controlled Trial.

(1) Background: Excess weight in the form of adiposity plays a key role in the pathogenesis of cardiometabolic diseases. Lifestyle modifications that incorporate continuous energy restriction (CER) are effective at inducing weight loss and reductions in adiposity; however, prescribing daily CER results in poor long-term adherence. Over the past decade, intermittent fasting (IF) has emerged as a promising alternative to CER that may promote increased compliance and/or improvements in cardiometabolic health parameters independent of weight loss. (2) Methods: This paper presents a secondary analysis of data from a 12-week intervention investigating the effects of a twice-weekly fast (5:2 IF; IFT group) and CER (CERT group) when combined with resistance exercise in 34 healthy participants (17 males and 17 females, mean BMI: 27.0 kg/m2, mean age: 23.9 years). Specifically, changes in cardiometabolic blood markers and ratings of hunger, mood, energy and compliance within and between groups were analysed. Dietary prescriptions were hypoenergetic and matched for energy and protein intake. (3) Results: Both dietary groups experienced reductions in total cholesterol (TC; mean reduction, 7.8%; p < 0.001), low-density lipoprotein cholesterol (LDL-C; mean reduction, 11.1%; p < 0.001) and high-density lipoprotein cholesterol (mean reduction 2.6%, p = 0.049) over the 12 weeks. Reductions in TC and LDL-C were greater in the IFT group after adjustment for baseline levels and change in weight. No significant changes in markers of glucose regulation were observed. Both groups maintained high levels of dietary compliance (~80%) and reported low levels of hunger over the course of the intervention period. (4) Conclusions: Secondary data analysis revealed that when combined with resistance training, both dietary patterns improved blood lipids, with greater reductions observed in the IFT group. High levels of compliance and low reported levels of hunger throughout the intervention period suggest both diets are well tolerated in the short-to-medium term.

The Effects of Intermittent Fasting Combined with Resistance Training on Lean Body Mass: A Systematic Review of Human Studies.

Diets utilising intermittent fasting (IF) as a strategic method to manipulate body composition have recently grown in popularity, however, dietary practices involving fasting have also been followed for centuries for religious reasons (i.e., Ramadan). Regardless of the reasons for engaging in IF, the impacts on lean body mass (LBM) may be detrimental. Previous research has demonstrated that resistance training promotes LBM accrual, however, whether this still occurs during IF is unclear. Therefore, the objective of this review is to systematically analyse human studies investigating the effects of variations of IF combined with resistance training on changes in LBM in previously sedentary or trained (non-elite) individuals. Changes in body weight and fat mass, and protocol adherence were assessed as a secondary objective. This review followed the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. MEDLINE, CINAHL, PubMed and SportDiscus databases were searched for articles investigating IF, combined with resistance training that reported measures of body composition. Eight studies met the eligibility criteria. LBM was generally maintained, while one study reported a significant increase in LBM. Body fat mass or percentage was significantly reduced in five of eight studies. Results suggest that IF paired with resistance training generally maintains LBM, and can also promote fat loss. Future research should examine longer-term effects of various forms of IF combined with resistance training compared to traditional forms of energy restriction. Prospero registration CRD42018103867.

Publisher Correction: Federated discovery and sharing of genomic data using Beacons.

In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, Toronto, Ontario, Canada. The error has been corrected in the HTML and PDF versions of the article.

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). Database URL: http://www.ensembl.org.

The impact of coaches providing healthy snacks at junior sport training.

OBJECTIVE: Sports clubs provide an opportunity to tackle childhood obesity rates through targeted interventions. Our study aimed to investigate if coaches providing healthy snacks to participants before junior netball sessions at five clubs in Melbourne, Australia, increased consumption of healthy foods and influenced coach perceptions of participants' attention/participation levels. METHODS: Coaches provided healthy snacks to participants before each netball session for one school term. Children's food consumption was observed at one session before, during and after the intervention. Parents attending the observed session completed pre- and post-intervention questionnaires. Coaches rated participants' attention/participation at the observed sessions before and during the intervention, and completed a questionnaire post-intervention. RESULTS: Baseline: Ice cream and cake were the most frequently consumed snacks. During intervention: Fruit, cheese and crackers and vegetables were the most frequently consumed snacks. Coaches ratings of participants' attention/participation increased significantly (baseline: 6.4 ± 0.17, intervention: 7.5 ± 0.36; p=0.02) where the same coach undertook ratings at both time points. CONCLUSIONS: Coaches providing healthy snacks before sessions at sports clubs increased consumption of nutrient-dense foods at the session, and may have positively affected participants' attention/participation. Implications for public health: This study highlights how a simple intervention could improve the diet of Australian children.

The Ensembl analysis pipeline.

The Ensembl pipeline is an extension to the Ensembl system which allows automated annotation of genomic sequence. The software comprises two parts. First, there is a set of Perl modules ("Runnables" and "RunnableDBs") which are 'wrappers' for a variety of commonly used analysis tools. These retrieve sequence data from a relational database, run the analysis, and write the results back to the database. They inherit from a common interface, which simplifies the writing of new wrapper modules. On top of this sits a job submission system (the "RuleManager") which allows efficient and reliable submission of large numbers of jobs to a compute farm. Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis.