Building Leadership through Action Research

In a poem by the Nobel Prize winning Irish poet Seamus Heaney, the narrator remarks, She taught me what her uncle once taught her: how easily the biggest coal block split if you got the grain and the hammer angled right. Getting the grain and the hammer angled right is never an easy task for leaders in any complex organization. However, if the coal block-size dilemmas of education are to be split into problems that are manageable, comprehensible, and mutable, then school leaders will have to work assiduously and persistently to accomplish just this

EcoCyc: fusing model organism databases with systems biology.

EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc

A field and video-annotation guide for baited remote underwater stereo-video surveys of demersal fish assemblages

Researchers TL, BG, JW, NB and JM were supported by the Marine Biodiversity Hub through funding from the Australian Government's National Environmental Science Program. Data validation scripts and GlobalArchive.org were supported by the Australian Research Data Commons, the Gorgon-Barrow Island Gorgon Barrow Island Net Conservation Benefits Fund, administered by the Government of Western Australia and the BHP/UWA Biodiversity and Societal Benefits of Restricted Access Areas collaboration.1. Baited remote underwater stereo-video systems (stereo-BRUVs) are a popular tool to sample demersal fish assemblages and gather data on their relative abundance and body-size structure in a robust, cost-effective, and non-invasive manner. Given the rapid uptake of the method, subtle differences have emerged in the way stereo-BRUVs are deployed and how the resulting imagery are annotated. These disparities limit the interoperability of datasets obtained across studies, preventing broad-scale insights into the dynamics of ecological systems. 2. We provide the first globally accepted guide for using stereo-BRUVs to survey demersal fish assemblages and associated benthic habitats. 3. Information on stereo-BRUV design, camera settings, field operations, and image annotation are outlined. Additionally, we provide links to protocols for data validation, archiving, and sharing. 4. Globally, the use of stereo-BRUVs is spreading rapidly. We provide a standardised protocol that will reduce methodological variation among researchers and encourage the use of Findable, Accessible, Interoperable, and Reproducible (FAIR) workflows to increase the ability to synthesise global datasets and answer a broad suite of ecological questions.Publisher PDFPeer reviewe

Treatment effects may remain the same even when trial participants differed from the target population

Objective RCTs have been criticised for lacking external validity. We assessed whether a trial in people with type I diabetes mellitus (T1DM) mirrored the wider population, and applied sample-weighting methods to assess the impact of differences on our trial's findings. Study design and setting The REPOSE trial was nested within a large UK cohort capturing demographic, clinical and quality of life (QoL) data for people with T1DM undergoing structured diabetes-specific education. We firstly assessed whether our RCT participants were comparable to this cohort using propensity score modelling. Following this we re-weighted the trial population to better match the wider cohort and re-estimated the treatment effect. Results Trial participants differed from the cohort in regards to sex, weight, HbA1c and also QoL and satisfaction with current treatment. Nevertheless, the treatment effects derived from alternative model weightings were similar to that of the original RCT. Conclusions Our RCT participants differed in composition to the wider population but the original findings were unaffected by sampling adjustments. We encourage investigators take steps to address criticisms of generalisability, but doing so is problematic: external data, even if available, may contain limited information and analyses can be susceptible to model misspecification

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

OBJECTIVE: Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS: We have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates. RESULTS: Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets. CONCLUSIONS: We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis

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

KnowOS: The (Re)Birth of the Knowledge Operating System

several real applications, including BioLingua, a knowledge-rich biocomputing workbench, and CACHE, a tool for collaborative information analysis. The KnowOS is essentially a web-based Lisp environment, providing apparent persistence of complex data and processes, internal and external application integration, multi-user management, and user interface tools for dealing with networks of complex objects. We explain the KnowOS vision, how we approached it, the pros and cons of what we did, how the implementation stands up to the vision, and where we are going with this project. The KnowOS Vision and Abstract Architecture Both operating systems and programming languages use abstraction to provide services such as data management, user and process isolation and intercommunication, and interfaces to hardware services and to other software. In historical practice, the broad concepts of operating systems and programming languages overlap with one another in a variety of ways. For example, since one of the most important services provided by operating systems is application integration – the ability to pass the results of on

Including pupils with special educational needs and disability in national assessment : comparison of three country case studies through an inclusive assessment framework

The assessment of educational progress and outcomes of pupils is important to all concerned with education. This includes testing which is undertaken for accountability and award bearing purposes. This article examines how students with special educational needs and disability (SEND) are included in assessment. An “inclusive assessment” framework is outlined based around three core features: (1) all students are included and benefit from assessment; (2) assessments are accessible and appropriate for the diverse range of children in the education system; and (3) the full breadth of the curriculum is assessed (including curriculum areas of particular relevance to students with SEND). Assessment policies and practice in three countries (England, Ireland and the US) are drawn upon to demonstrate how the framework usefully enables between-country comparisons and within-country analysis. This analysis shows that in comparison to Ireland, the US and England have highly developed system-based approaches to assessment which seek to “include all” (feature 1) and be “accessible and appropriate” (feature 2). However, the analysis highlights that a consequence of such assessment approaches is the narrowing of the curriculum around topics that are assessed (most notably literacy and mathematics). Such approaches therefore may be at the expense of wider curriculum areas that have value for all students, but often of particular value for those with SEND (feature 3). It is argued that within such systems there may be a danger of neglecting the third feature of the inclusive assessment framework, i.e. ensuring that the full breadth of the curriculum is assessed. A consequence of such an omission could be a failure to assess and celebrate progress in relation to educational outcomes that are relevant to a diverse range of students