Bias and information in biological records

Biological recording is in essence a very simple concept in which a record is the report of a species at a physical location at a certain time. The collation of these records into a dataset is a powerful approach to addressing large-scale questions about biodiversity change. Records are collected by volunteers at times and places that suit them, leading to a variety of biases: uneven sampling over space and time, uneven sampling effort per visit and uneven detectability. These need to be controlled for in statistical analyses that use biological records. In particular, the data are ‘presence-only’, and lack information on the sampling protocol or intensity. Submitting ‘complete lists’ of all the species seen is one potential solution because the data can be treated as ‘presence–absence’ and detectability of each species can be statistically modelled. The corollary of bias is that records vary in their ‘information content’. The information content is a measure of how much an individual record, or collection of records, contributes to reducing uncertainty in a parameter of interest. The information content of biological records varies, depending on the question to which the data are being applied. We consider a set of hypothetical ‘syndromes’ of recording behaviour, each of which is characterized by different information content. We demonstrate how these concepts can be used to support the growth of a particular type of recording behaviour. Approaches to recording are rapidly changing, especially with the growth of mass participation citizen science. We discuss how these developments present a range of challenges and opportunities for biological recording in the future

BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology

BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism

Evaluation of Biodiversity 2020. Evaluation report [Final report]

In the 25 Year Environment Plan, published in 2018, the Government committed to publishing a new strategy for nature to take forward international commitments on biodiversity and build upon the current Strategy, ‘Biodiversity 2020: a Strategy for England’s wildlife and ecosystem services’. This report provides an evaluation of the outcomes and actions under Biodiversity 2020 to provide an evidence base for ensuring any new strategy is targeted and effective. The evaluation aimed to: 1. assess progress towards the Outcomes set out in Biodiversity 2020 (relating to land and freshwater only); 2. evaluate what worked well and why, and the factors that have influenced progress; 3. identify lessons and opportunities to improve delivery in the future (i.e. under a new strategy). The evaluation was carried out at a Theme level. Evaluation was based on: (i) a synthesis of existing quantitative indicators, (ii) evidence from evaluations and reports of activities undertaken since 2011, and (iii) expert opinions drawn from questionnaires, interviews, and four workshops with stakeholders. The workshops were a key component of the evaluation, and comprised participants from the project team, Defra, other government agencies (usually involved in delivery of activities directly supporting the Strategy), NGOs, businesses (Theme 2) and research and academia. Facilitated discussions amongst workshop participants provided further insight into progress and the factors that have influenced progress, drawing on participants’ experiences and knowledge

Estimation of the direct health and indirect societal costs of diabetes in the UK using a cost of illness model

AimsThe direct cost of diabetes to the UK health system was estimated at around £10 billion in 2012. This analysis updates that estimate using more recent and accurate data sources.MethodsA pragmatic review of relevant data sources for UK nations was conducted, including population-level datasets and published literature, to generate estimates of costs separately for Type 1, Type 2 and gestational diabetes. A comprehensive cost framework, developed in collaboration with experts, was used to create a population-based cost of illness model. The key driver of the analysis was prevalence of diabetes and its complications. Estimates were made of the excess costs of diagnosis, treatment and diabetes-related complications compared with the general UK population. Estimates of the indirect costs of diabetes focused on productivity losses due to absenteeism and premature mortality.ResultsThe direct costs of diabetes in 2021/22 for the UK were estimated at £10.6 billion, of which just over 40% related to diagnosis and treatment, with the rest relating to the excess costs of complications. Indirect costs were estimated at £3.3 billion.Conclusions Diabetes remains a considerable cost burden in the UK and the majority of those costs are still spent on potentially preventable complications. Although rates of some complications are reducing, prevalence continues to increase and effective approaches to primary and secondary prevention continue to be needed. Improvements in data capture, data quality and reporting, and further research on the human and financial implications of increasing incidence of Type 2 diabetes in younger people are recommended.<br/

Guidelines for the management of postmenopausal osteoporosis for GPs

Copyright © 2004 Royal Australian College of General Practitioners Copyright to Australian Family Physician. Reproduced with permission. Permission to reproduce must be sought from the publisher, The Royal Australian College of General Practitioners.Background: Since the last series of guidelines on the management of osteoporosis from Osteoporosis Australia was published in Australian Family Physician (October 2002), there have been further advances in our understanding of the treatment involved in both the prevention of bone loss and the management of established osteoporosis. Objective: This article provides updated guidelines for the management of postmenopausal osteoporosis to assist general practitioners identify those women at risk, and reviews current treatment strategies. DISCUSSION: Osteoporosis and its associated problems are major health concerns in Australia, especially with an aging population. While important principles of management are still considered to be maximising peak bone mass and preventing postmenopausal bone loss, new clinical trial data about drugs such as the bisphosphonates, raloxifene and oestrogen have recently become available and the relative role of various agents is gradually becoming clearer. The use of long term hormone therapy has mixed risks and benefits that requires individual patient counselling.O'Neill S; MacLennan A; Bass S; Diamond T; Ebeling P; Findlay D; Flicker L; Markwell A; Nowson C; Pocock N; Sambrook P; Singh M

Guidelines for the management of postmenopausal osteoporosis for GPs

BACKGROUND : Since the last series of guidelines on the management of osteoporosis from Osteoporosis Australia was published in Australian Family Physician (October 2002), there have been further advances in our understanding of the treatment involved in both the prevention of bone loss and the management of established osteoporosis.OBJECTIVE : This article provides updated guidelines for the management of postmenopausal osteoporosis to assist general practitioners identify those women at risk, and reviews current treatment strategies.DISCUSSION : Osteoporosis and its associated problems are major health concerns in Australia, especially with an aging population. While important principles of management are still considered to be maximising peak bone mass and preventing postmenopausal bone loss, new clinical trial data about drugs such as the bisphosphonatesr raloxifene and oestrogen have recently become available and the relative role of various agents is gradually becoming clearer. The use of long term hormone therapy has mixed risks and benefits that requires individual patient counselling.<br /

Efficacy and safety assessment of prolonged maintenance with subcutaneous rituximab in patients with relapsed or refractory indolent non-Hodgkin lymphoma: results of the phase III MabCute study

Rituximab plus chemotherapy induction followed by rituximab maintenance for up to 2 years confers a long-term benefit in terms of progression-free survival in patients with indolent non-Hodgkin lymphoma. It is not known whether further prolonged maintenance with rituximab provides additional benefit. The phase III MabCute study enrolled 692 patients with relapsed or refractory indolent non-Hodgkin lymphoma. Patients who responded to induction with rituximab plus chemotherapy and were still responding after up to 2 years’ initial maintenance with subcutaneous rituximab were randomized to extended maintenance with subcutaneous rituximab (n=138) or observation only (n=138). The primary endpoint of investigator-assessed progression-free survival in the randomized population was un-addressed by the end of study because of an insufficient number of events (129 events were needed for 80% power at 5% significance if approximately 330 patients were randomized). In total, there were 46 progression-free survival events, 19 and 27 in the rituximab and observation arms, respectively (P=0.410 by stratified log-rank test; hazard ratio 0.76 [95% confidence interval: 0.37– 1.53]). The median progression-free survival was not reached in either randomized arm. There were no new safety signals; however, adverse events were seen slightly more frequently with rituximab than with observation during extended maintenance. Maintenance for up to 2 years with rituximab after response to initial induction therefore remains the standard of care in patients with relapsed or refractory indolent non- Hodgkin lymphoma. (Clinicaltrials.gov identifier: NCT01461928).</jats:p

Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway

The clinical course and eventual outcome, or prognosis, of complex diseases varies enormously between affected individuals. This variability critically determines the impact a disease has on a patient’s life but is very poorly understood. Here, we exploit existing genome-wide association study data to gain insight into the role of genetics in prognosis. We identify a noncoding polymorphism in FOXO3A (rs12212067: T > G) at which the minor (G) allele, despite not being associated with disease susceptibility, is associated with a milder course of Crohn’s disease and rheumatoid arthritis and with increased risk of severe malaria. Minor allele carriage is shown to limit inflammatory responses in monocytes via a FOXO3-driven pathway, which through TGFβ1 reduces production of proinflammatory cytokines, including TNFα, and increases production of anti-inflammatory cytokines, including IL-10. Thus, we uncover a shared genetic contribution to prognosis in distinct diseases that operates via a FOXO3-driven pathway modulating inflammatory responses. PAPERCLIP

The efficacy of indwelling pleural catheter placement versus placement plus talc sclerosant in patients with malignant pleural effusions managed exclusively as outpatients (IPC-PLUS): study protocol for a randomised controlled trial

BACKGROUND: Malignant pleural effusions (MPEs) remain a common problem, with 40,000 new cases in the United Kingdom each year and up to 250,000 in the United States. Traditional management of MPE usually involves an inpatient stay with placement of a chest drain, followed by the instillation of a pleural sclerosing agent such as talc, which aims to minimise further fluid build-up. Despite a good success rate in studies, this approach can be expensive, time-consuming and inconvenient for patients. More recently, an alternative method has become available in the form of indwelling pleural catheters (IPCs), which can be inserted and managed in an outpatient setting. It is currently unknown whether combining talc pleurodesis with IPCs will provide improved pleural symphysis rates over those of IPCs alone. METHODS/DESIGN: IPC-PLUS is a patient-blind, multicentre randomised controlled trial (RCT) comparing the combination of talc with an IPC to the use of an IPC alone for inducing pleurodesis in MPEs. The primary outcome is successful pleurodesis at five weeks post-randomisation. This study will recruit 154 patients, with an interim analysis for efficacy after 100 patients, and aims to help to define the future gold standard for outpatient management of patients with symptomatic MPEs. DISCUSSION: IPC-PLUS is the first RCT to examine the practicality and utility of talc administered via an IPC. The study remains in active recruitment and has the potential to significantly alter how patients requiring pleurodesis for MPE are approached in the future. TRIAL REGISTRATION: This trial was registered with Current Controlled Trials (identifier: ISRCTN73255764) on 23 August 2012

STrengthening the REporting of Genetic Association Studies (STREGA)— An Extension of the STROBE Statement

Julian Little and colleagues present the STREGA recommendations, which are aimed at improving the reporting of genetic association studies