P137 Supporting patients to get the best from their osteoporosis treatment; what works for whom, why and in what circumstance: a rapid realist review

Abstract Background/Aims For two decades, clinicians and academics have been writing about the problem of poor adherence in osteoporosis, while people with osteoporosis have identified a need for more follow up and information about medicines. We aimed to understand what works in supporting people with osteoporosis to get the best from their medicines, and specifically, to understand what mechanisms enable components of interventions to support osteoporosis medication optimisation and the underlying contextual conditions that enabled these mechanisms. Methods We conducted a Rapid Realist Review. The scope was informed by a workshop of the Effectiveness Working Group of the Royal Osteoporosis Society Osteoporosis and Bone Research Academy and the approach informed by background syntheses of qualitative literature and the Perceptions and Practicalities Approach as an underpinning conceptual framework. A primary search identified observational or interventional studies which aimed to improve medicines adherence or optimisation. Included studies were assessed for quality and data extracted relating to context, mechanism and outcomes. A supplementary second search was conducted to gain additional insight on included key papers and emerging mechanisms. Extracted data were interrogated by authors independently for patterns of context-mechanism-outcome configurations and further discussed in weekly team meetings. Recommendations for research and clinical practice were co-developed with clinical and lay stakeholders. Results 41 papers were included. We identified five contextual timepoints for the person with osteoporosis (identifying a problem; starting medicine; continuing medicine) and the practitioner and healthcare system (making a diagnosis and giving a treatment recommendation; reviewing medicine) and mechanisms relating to patient informed decision making, treatment burden, supporting routinisation and memory, supporting clinical decision making, targeting support, and approaches which were integrated and sustainable. Interventions which support patient informed decision making, improve patient knowledge and understanding, have potential to influence long-term commitment to treatment, although few studies explicitly addressed patients’ perceptions of illness and treatment as recommended in NICE guidelines. During treatment, targeting additional consultations to those most in need may be a cost and clinically effective approach to enable this. Supporting primary care clinician decision making and integration of primary and secondary care services also appears to be important, in improving rates of treatment initiation and adherence. Supporting patients’ ability to adhere (eg by lowering treatment burden and issuing reminders) may be helpful to address practical difficulties but there is little evidence to support the use of reminders alone. Conclusion For medicines optimisation for people with osteoporosis, we suggest a need for more patient-centred interventions to address patients’ perceptions of illness and treatment, and reduce treatment burden. Specialist services should consider the extent to which they integrate with, and support primary care clinical decision-making, in order to impact long-term clinical outcomes. Specific research recommendations have been co-developed, to address these knowledge gaps. Disclosure Z. Paskins: Grants/research support; NIHR, Versus Arthritis, Royal Osteoporosis Society. O. Babatunde: None. A. Sturrock: None. L. Toh: None. R. Horne: None. I. Maidment: None. </jats:sec

Inference of population splits and mixtures from genome-wide allele frequency data

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.comComment: 28 pages, 6 figures in main text. Attached supplement is 22 pages, 15 figures. This is an updated version of the preprint available at http://precedings.nature.com/documents/6956/version/

Exploring the current and future role of the pharmacists in osteoporosis screening and management in Malaysia

Background Several studies have found that pharmacists can assist in screening and prevention of osteoporosis by referring patients for bone mineral density scans and counselling on lifestyle changes. In Malaysia, screening osteoporosis in all elderly women is not mandatory due to its cost. One approach to address this gap is to develop a pharmacist-led osteoporosis screening and prevention program. However, there is a paucity of data on the perspectives of Malaysian pharmacists in this area. Objective To explore the perspective of stakeholders (policy makers, doctors, pharmacists, nurses and patients) towards the role of pharmacists in osteoporosis screening and management. Setting A primary care clinic located within a teaching hospital in Kuala Lumpur, Malaysia. Method Patients (n = 20), nurses (n = 10), pharmacists (n = 11), doctors (n = 10) and policy makers (n = 5) were individually interviewed using a semi-structured topic guide. Purposive sampling was used. Interviews were transcribed verbatim and analysed using thematic analysis. Main outcome measure Perspective of stakeholders on the current and future role of pharmacists. Results All participants perceived pharmacists to be suppliers of medication, although there was some recognition of roles in providing medication advice. Nonetheless, these stakeholders were eager for pharmacists to expand their non-dispensing roles towards counselling, creating awareness and screening of osteoporosis. Interviewed pharmacists referred to their current role as ‘robotic dispensers’ and unanimously agreed to spread out to osteoporosis management role. Conclusion Under stakeholders there is a willingness to expand the role of pharmacists in Malaysia to non-dispensing roles, particularly in osteoporosis screening and management

FEELnc : a tool for long non-coding RNA annotation and its application to the dog transcriptome

Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc.Peer reviewe

Spaceflight Induces Strength Decline in Caenorhabditis elegans

This is the final version. Available on open access from MDPI via the DOI in this recordData Availability Statement: Raw RNA sequencing data are deposited in the NCBI Sequence Read Archive with links to BioProject ID PRJNA1026503 (https://www.ncbi.nlm.nih.gov/bioproject/).Background: Understanding and countering the well-established negative health consequences of spaceflight remains a primary challenge preventing safe deep space exploration. Targeted/personalized therapeutics are at the forefront of space medicine strategies, and cross-species molecular signatures now define the 'typical' spaceflight response. However, a lack of direct genotype-phenotype associations currently limits the robustness and, therefore, the therapeutic utility of putative mechanisms underpinning pathological changes in flight. Methods: We employed the worm Caenorhabditis elegans as a validated model of space biology, combined with 'NemaFlex-S' microfluidic devices for assessing animal strength production as one of the most reproducible physiological responses to spaceflight. Wild-type and dys-1 (BZ33) strains (a Duchenne muscular dystrophy (DMD) model for comparing predisposed muscle weak animals) were cultured on the International Space Station in chemically defined media before loading second-generation gravid adults into NemaFlex-S devices to assess individual animal strength. These same cultures were then frozen on orbit before returning to Earth for next-generation sequencing transcriptomic analysis. Results: Neuromuscular strength was lower in flight versus ground controls (16.6% decline, p < 0.05), with dys-1 significantly more (23% less strength, p < 0.01) affected than wild types. The transcriptional gene ontology signatures characterizing both strains of weaker animals in flight strongly corroborate previous results across species, enriched for upregulated stress response pathways and downregulated mitochondrial and cytoskeletal processes. Functional gene cluster analysis extended this to implicate decreased neuronal function, including abnormal calcium handling and acetylcholine signaling, in space-induced strength declines under the predicted control of UNC-89 and DAF-19 transcription factors. Finally, gene modules specifically altered in dys-1 animals in flight again cluster to neuronal/neuromuscular pathways, suggesting strength loss in DMD comprises a strong neuronal component that predisposes these animals to exacerbated strength loss in space. Conclusions: Highly reproducible gene signatures are strongly associated with space-induced neuromuscular strength loss across species and neuronal changes in calcium/acetylcholine signaling require further study. These results promote targeted medical efforts towards and provide an in vivo model for safely sending animals and people into deep space in the near future.NASABiotechnology and Biological Sciences Research Council (BBSRC)Engineering and Physical Sciences Research Council (EPSRC)Osteopathic Heritage Foundatio

Identification of Nucleases and Phosphatases by Direct Biochemical Screen of the Saccharomyces cerevisiae Proteome

The availability of yeast strain collections expressing individually tagged proteins to facilitate one-step purification provides a powerful approach to identify proteins with particular biochemical activities. To identify novel exo- and endo-nucleases that might function in DNA repair, we undertook a proteomic screen making use of the movable ORF (MORF) library of yeast expression plasmids. This library consists of 5,854 yeast strains each expressing a unique yeast ORF fused to a tripartite tag consisting of His6, an HA epitope, a protease 3C cleavage site, and the IgG-binding domain (ZZ) from protein A, under the control of the GAL1 promoter for inducible expression. Pools of proteins were partially purified on IgG sepharose and tested for nuclease activity using three different radiolabeled DNA substrates. Several known nucleases and phosphatases were identified, as well as two new members of the histidine phosphatase superfamily, which includes phosphoglycerate mutases and phosphatases. Subsequent characterization revealed YDR051c/Det1 to be an acid phosphatase with broad substrate specificity, whereas YOR283w has a broad pH range and hydrolyzes hydrophilic phosphorylated substrates. Although no new nuclease activities were identified from this screen, we did find phosphatase activity associated with a protein of unknown function, YOR283w, and with the recently characterized protein Det1. This knowledge should guide further genetic and biochemical characterization of these proteins

An improved microRNA annotation of the canine genome

The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions

Minimal information for studies of extracellular vesicles 2018 (MISEV2018):a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles (“MISEV”) guidelines for the field in 2014. We now update these “MISEV2014” guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

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