The Quest for Orthologs orthology benchmark service in 2022

The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.European Molecular Biology Laboratory (EMBL) (core funds to D.J. and M.J.M.); National Institutes of Health [U24HG007822 to D.J. and M.J.M., 75N93019C00077 to D.S.R.]; National Human Genome Research Institute (NHGRI) [U24HG003345 to T.E.M.J, B.Y., E.A.B.]; JSPS KAKENHI [16H06279, 19H05688 to W.I.]; JST CREST [JPMJCR19S2 to W.I.]; MEXT [JPMXD1521474594 to W.I.]; Horizon 2020 [676559 to S.C.-G., 637765] (to D.M.E.), ELIXIR (to S.C.-G.); Wellcome Grant [208349/Z/17/Z to E.A.B.]; National Science Foundation (USA) [1917302 to P.D.T.]; Wellcome Trust [WT-218288, WT-212929 to D.S.R.]; Service and Infrastructure grant from the Swiss Institute of Bioinformatics, Swiss National Science Foundation [186397, 205085 to C.D.]. Funding for open access charge: Swiss National Science Foundation [205085].Peer Reviewed"Article signat per 31 autors/es: Yannis Nevers, Tamsin E M Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codo, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Piližota, Cristina Guijarro-Clarke, the OpenEBench team the Quest for Orthologs Consortium , Wataru Iwasaki, Odile Lecompte, Erik Sonnhammer, David S Roos, Toni Gabaldón, David Thybert, Paul D Thomas, Yanhui Hu, David M Emms, Elspeth Bruford, Salvador Capella-Gutierrez, Maria J Martin, Christophe Dessimoz, Adrian Altenhoff"Postprint (published version

Population neuroimaging:generation of a comprehensive data resource within the ALSPAC pregnancy and birth cohort

Neuroimaging offers a valuable insight into human brain development by allowing in vivo assessment of structure, connectivity and function. Multimodal neuroimaging data have been obtained as part of three sub-studies within the Avon Longitudinal Study of Parents and Children, a prospective multigenerational pregnancy and birth cohort based in the United Kingdom. Brain imaging data were acquired when offspring were between 18 and 24 years of age, and included acquisition of structural, functional and magnetization transfer magnetic resonance, diffusion tensor, and magnetoencephalography imaging. This resource provides a unique opportunity to combine neuroimaging data with extensive phenotypic and genotypic measures from participants, their mothers, and fathers

A longitudinal study of adolescents’ judgments of the attractiveness of facial symmetry, averageness and sexual dimorphism

Adolescents have been found to differ by age in their attraction to facial symmetry, averageness, and sexual dimorphism. However, it has not been demonstrated that attraction to these facial characters changes over time as a consequence of age-linked development. We aimed to extend previous cross-sectional findings by examining whether facial attractiveness judgments change over time during adolescence as a consequence of increasing age, in a within-subjects study of two cohorts of adolescents aged 11–16. Consistent with previous findings, we find that adolescents (often particularly females) judged faces with increased averageness, symmetry and femininity to be more attractive than original, asymmetric and masculine faces, respectively. However, we do not find longitudinal changes in face preference judgments across the course of a year, leading us to question the extent to which some of the previously reported differences in facial attractiveness judgments between younger and older adolescents were due to age-linked changes

Face, body and speech cues independently predict judgments of attractiveness

Research on human attraction frequently makes use of single-modality stimuli such as neutral-expression facial photographs as proxy indicators of an individual’s attractiveness. However, we know little about how judgments of these single-modality stimuli correspond to judgments of stimuli that incorporate multi-modal cues of face, body and speech. In the present study, ratings of attractiveness judged from videos of participants introducing themselves were independently predicted by judgments of the participant’s facial attractiveness (a neutral-expression facial photograph masked to conceal the hairstyle), body attractiveness (a photograph of the upper body), and speech attractiveness (the soundtrack to the video). We also found that ratings of the face, body and speech were positively related to each other. Our results support the assumption that the single-modality stimuli used in much attractiveness research are valid proxy indicators of overall attractiveness in ecologically valid contexts, and complement literature showing cross-modality concordance of trait attractiveness, but also recommend that research relying on assessments of individual attractiveness take account of both visual and vocal attractiveness where possible

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.This work was supported by the following grants: NHGRIU54HG003273 to R.A.G; EU Marie Curie ITN #215781 “Evonet” to M.A.; a Wellcome Trust Value in People (VIP) award to C.B. and Wellcome Trust graduate studentship WT089615MA to J.E.G; Marine rhythms of Life” of the University of Vienna, an FWF (http://www.fwf.ac.at/) START award (#AY0041321) and HFSP (http://www.hfsp.org/) research grant (#RGY0082/2010) to KT-­‐R; MFPL Vienna International PostDoctoral Program for Molecular Life Sciences (funded by Austrian Ministry of Science and Research and City of Vienna, Cultural Department -­‐Science and Research to T.K; Direct Grant (4053034) of the Chinese University of Hong Kong to J.H.L.H.; NHGRI HG004164 to G.M.; Danish Research Agency (FNU), Carlsberg Foundation, and Lundbeck Foundation to C.J.P.G.; U.S. National Institutes of Health R01AI55624 to J.H.W.; Royal Society University Research fellowship to F.M.J.; P.D.E. was supported by the BBSRC via the Babraham Institute;This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pbio.100200

The social life of measurement:How methods have shaped the idea of culture in urban regeneration

Although ‘culture-led regeneration’ has been critiqued as both a concept and practice, it is clear that policy-makers continue to make efforts to use cultural activity of varying forms to achieve ends which could be (and are) described in terms of urban ‘regeneration’. Whilst the idea of culture-led urban regeneration had gained considerable prominence in a range of policy by the early twenty-first century, many questions have remained over how exactly such ‘regenerative’ outcomes could be convincingly demonstrated, despite much activity to attempt such demonstration over the course of preceding years. The desire for convincing evidence can be seen in a continued, and increasing, focus on evaluation, and methods aimed at providing evidence of impact and outcomes. In light of the renewed political focus in recent years on ‘proving’ the effects and value of cultural activity, this paper considers the continuation of practice in this area, and asks what lessons, if any, have been learned in evaluative practice which seeks to demonstrate the regenerative effects of culture. In light of the continuation of apparently problematic practices, the paper seeks to delineate and account for what has been learned, and what has not

The UK stand together trial: protocol for a multicentre cluster randomised controlled trial to evaluate the effectiveness and cost-effectiveness of KiVa to reduce bullying in primary schools

Background Reducing bullying is a public health priority. KiVa, a school-based anti-bullying programme, is effective in reducing bullying in Finland and requires rigorous testing in other countries, including the UK. This trial aims to test the effectiveness and cost-effectiveness of KiVa in reducing child reported bullying in UK schools compared to usual practice. The trial is currently on-going. Recruitment commenced in October 2019, however due to COVID-19 pandemic and resulting school closures was re-started in October 2020. Methods Design: Two-arm pragmatic multicentre cluster randomised controlled trial with an embedded process and cost-effectiveness evaluation. Participants: 116 primary schools from four areas; North Wales, West Midlands, South East and South West England. Outcomes will be assessed at student level (ages 7–11 years; n = approximately 13,000 students). Intervention: KiVa is a whole school programme with universal actions that places a strong emphasis on changing bystander behaviour alongside indicated actions that provide consistent strategies for dealing with incidents of bullying. KiVa will be implemented over one academic year. Comparator: Usual practice. Primary outcome: Student-level bullying-victimisation assessed through self-report using the extensively used and validated Olweus Bully/Victim questionnaire at baseline and 12-month follow-up. Secondary outcomes: student-level bullying-perpetration; student mental health and emotional well-being; student level of, and roles in, bullying; school related well-being; school attendance and academic attainment; and teachers’ self-efficacy in dealing with bullying, mental well-being, and burnout. Sample size: 116 schools (58 per arm) with an assumed ICC of 0.02 will provide 90% power to identify a relative reduction of 22% with a 5% significance level. Randomisation: recruited schools will be randomised on 1:1 basis stratified by Key-Stage 2 size and free school meal status. Process evaluation: assess implementation fidelity, identify influences on KiVa implementation, and examine intervention mechanisms. Economic evaluation: Self-reported victimisation, Child Health Utility 9D, Client Service Receipt Inventory, frequency of services used, and intervention costs. The health economic analysis will be conducted from a schools and societal perspective. Discussion This two-arm pragmatic multicentre cluster randomised controlled trial will evaluate the KiVa anti-bullying intervention to generate evidence of the effectiveness, cost-effectiveness and scalability of the programme in the UK. Our integrated process evaluation will assess implementation fidelity, identify influences on KiVa implementation across England and Wales and examine intervention mechanisms. The integrated health economic analysis will be conducted from a schools and societal perspective. Our trial will also provide evidence regarding the programme impact on inequalities by testing whether KiVa is effective across the socio-economic gradient

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead