The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi

Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or “SNP chips”, enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species

Patterns of analgesic use, pain and self-efficacy: a cross-sectional study of patients attending a hospital rheumatology clinic

Background: Many people attending rheumatology clinics use analgesics and non-steroidal anti-inflammatories for persistent musculoskeletal pain. Guidelines for pain management recommend regular and pre-emptive use of analgesics to reduce the impact of pain. Clinical experience indicates that analgesics are often not used in this way. Studies exploring use of analgesics in arthritis have historically measured adherence to such medication. Here we examine patterns of analgesic use and their relationships to pain, self-efficacy and demographic factors. Methods: Consecutive patients were approached in a hospital rheumatology out-patient clinic. Pattern of analgesic use was assessed by response to statements such as 'I always take my tablets every day.' Pain and self-efficacy (SE) were measured using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and Arthritis Self-Efficacy Scale (ASES). Influence of factors on pain level and regularity of analgesic use were investigated using linear regression. Differences in pain between those agreeing and disagreeing with statements regarding analgesic use were assessed using t-tests. Results: 218 patients (85% of attendees) completed the study. Six (2.8%) patients reported no current pain, 26 (12.3%) slight, 100 (47.4%) moderate, 62 (29.4%) severe and 17 (8.1%) extreme pain. In multiple linear regression self efficacy and regularity of analgesic use were significant (p < 0.01) with lower self efficacy and more regular use of analgesics associated with more pain. Low SE was associated with greater pain: 40 (41.7%) people with low SE reported severe pain versus 22 (18.3%) people with high SE, p < 0.001. Patients in greater pain were significantly more likely to take analgesics regularly; 13 (77%) of those in extreme pain reported always taking their analgesics every day, versus 9 (35%) in slight pain. Many patients, including 46% of those in severe pain, adjusted analgesic use to current pain level. In simple linear regression, pain was the only variable significantly associated with regularity of analgesic use: higher levels of pain corresponded to more regular analgesic use (p = 0.003). Conclusion: Our study confirms that there is a strong inverse relationship between self-efficacy and pain severity. Analgesics are often used irregularly by people with arthritis, including some reporting severe pain

Scanning the European Ecosystem of Distributed Ledger Technologies for Social and Public Good: What, Why, Where, How, and Ways to Move Forward

Distributed Ledger Technologies (DLTs), such as blockchains, are primarily tamper-resistant and time-stamped databases. They allow multiple parties to record, verify and share data on a peer-to-peer basis across a network, in decentralised, synchronised and transparent ways, with limited human intervention and reduced intermediate steps. These technologies are mostly known for business use cases, from cryptocurrencies to asset track and tracing. But there are numerous organisations nowadays searching for alternative ways to harness the potential of DLTs in the pursuit of public and social good, from local to global challenges, and towards more inclusive, cooperative, sustainable, ethical or accountable digital and physical worlds. This Science for Policy report explores the current status of this particular field both theoretically and empirically, in the framework of the project #DLT4Good: Co-creating a European Ecosystem of DLTs for Social and Public Good. Part I offers a conceptual overview of the connections between main features of DLTs and their potential for social and public good goals. Emphasis is placed on different approaches to decentralisation, and on core building blocks of DLTs linked with values such as trust, privacy, self-sovereignty, autonomy, inclusiveness, transparency, openness, or the commons. Part II comprises a scanning of the current European ecosystem of DLT projects with activities in this field. It contains a summarized version of a database published online with 131 projects, and a quantitative review of main trends. It also includes a qualitative assessment of 10 projects selected from the larger sample to showcase this field and its diversity. Part III concludes with six independent position papers and recommendations from experts and advisors of the #DLT4Good project. The main topics addressed range from decentralized governance to collaborative economies, with highlights on issues such as trust, verifiability, transparency, privacy or bottom-up coordination.JRC.I.2-Foresight, Modelling, Behavioural Insights & Design for Polic

Scanning the European Ecosystem of Distributed Ledger Technologies for Social and Public Good: What, Why, Where, How, and Ways to Move Forward

Distributed Ledger Technologies (DLTs), such as blockchains, are primarily tamper-resistant and time-stamped databases. They allow multiple parties to record, verify and share data on a peer-to-peer basis across a network, in decentralised, synchronised and transparent ways, with limited human intervention and reduced intermediate steps. These technologies are mostly known for business use cases, from cryptocurrencies to asset track and tracing. But there are numerous organisations nowadays searching for alternative ways to harness the potential of DLTs in the pursuit of public and social good, from local to global challenges, and towards more inclusive, cooperative, sustainable, ethical or accountable digital and physical worlds. This Science for Policy report explores the current status of this particular field both theoretically and empirically, in the framework of the project #DLT4Good: Co-creating a European Ecosystem of DLTs for Social and Public Good. Part One offers a conceptual overview of the connections between main features of DLTs and their potential for social and public good goals. Emphasis is placed on different approaches to decentralisation, and on core building blocks of DLTs linked with values such as trust, privacy, self-sovereignty, autonomy, inclusiveness, transparency, openness, or the commons. Part Two comprises a scanning of the current European ecosystem of DLT projects with activities in this field. It contains a summarized version of a database published online with 131 projects, and a quantitative review of main trends. It also includes a qualitative assessment of 10 projects selected from the larger sample to showcase this field and its diversity. Part Three concludes with six independent position papers and recommendations from experts and advisors of the #DLT4Good project. The main topics addressed range from decentralized governance to collaborative economies, with highlights on issues such as trust, verifiability, transparency, privacy or bottom-up coordination

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Polygenic basis for adaptive morphological variation in a threatened Aotearoa | New Zealand bird, the hihi ( Notiomystis cincta )

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