Biology subjects

Green, J.

Publications and source records attributed to Green, J..

4 recordsLinked to original sources

bioRxiv2018

Walking Drosophila aim to maintain a neural heading estimate at an internal goal angle

While navigating their environment, many animals track their angular heading via the activity of heading-sensitive neurons. How internal heading estimates are used to guide navigational behavior, however, remains largely unclear in any species. We found that normal synaptic output from heading neurons in Drosophila is required for flies to stably maintain their trajectory along an arbitrary direction while navigating a simple virtual environment. We further found that if the heading estimate carried by these neurons is experimentally redirected by focal stimulation, the fly typically turns so as to rotate this internal heading estimate back towards the initial angle, while also slowing down until this correction has been made. These experiments argue that flies compare an internal heading estimate with an internal goal angle to guide navigational decisions, highlighting an important computation underlying how a spatial variable in the brain is translated into navigational action.\n\nOne Sentence SummaryFlies compare an internal heading estimate with an internal goal angle to guide navigation.

neuroscience↗

bioRxiv2018

Can we use routinely collected hospital and GP data for epidemiological study of common hand conditions? A UK Biobank based validation project

ObjectiveRoutine health records can be of great value in epidemiological and genetic studies if they are able to reliably identify true disease cases, especially when linked to large cohort studies. Little research has been undertaken into whether coding within UK electronic health records (EHR) is able to accurately identify clinical disease cases of common hand conditions. There is therefore a relative paucity of hand surgical research using EHRs due to concerns that cases cannot be accurately identified.\n\nThe aim of this study was to investigate the accuracy of hospital and primary care coding of routine EHRs for carpal tunnel syndrome (CTS) and base of thumb osteoarthritis (BTOA). Self-reported disease state as recorded in UK Biobank, a large prospective cohort study was also investigated.\n\nMethodsCode lists for each condition were generated by a team of clinicians, clinical coders and epidemiologists. All patients recruited to UK Biobank in one geographical region (Lothian, Scotland) where linked primary and secondary care coded datasets available were included. A decision- making algorithm was designed to define an administratively-confirmed or a clinically confirmed disease case. Patient electronic medical records (EMRs) were independently interrogated by two clinicians and inter-observer reliability calculated.\n\nResultsOf the 17,201 Biobank participants in NHS Lothian, 268 had at least one code for CTS and 82 for BTOA. For CTS, 159 cases were confirmed, 100 cases had insufficient information and 9 cases were refuted. Excluding missing data, the positive predictive value (PPV) for true clinical disease cases was 96% for incident disease (90% for prevalent disease; overall 94%).\n\nFor BTOA, 27 cases were confirmed, 46 cases had insufficient information, and 9 cases were refuted. Excluding missing data, PPV for incident disease was 81% (prevalent disease 56%, overall PPV 75%). Interrogation of the disease cases with insufficient information noted a large proportion arising from primary care and self-report coding systems.\n\nAnalyzing code combinations revealed that secondary care codes had the highest PPV for CTS and BTOA, emphasizing a more robust evaluation of PPV for patients requiring hospital based care. Overall, inter-observer reliability was good, with agreement in 90% of cases (Cohens kappa of 0.79) for clinical disease cases in CTS and agreement of 98%, (kappa 0.96) for BTOA.\n\nConclusionsWe have demonstrated that coding within UK Biobank is of sufficient quality to enable use of the resource for epidemiological and genetic research into common hand conditions, and that EMRs can be used for manual validation of UK health coding systems. Further work is needed to consider potential regional and interdisciplinary differences in coding practice, in strategies for dealing with missing data in EHRs, and to validate coding of common hand conditions in primary care.

epidemiology↗

bioRxiv2017

Folic acid instability and bacterial metabolism combine to impact C. elegans development and ageing

Supplementation with the synthetic oxidised folate, folic acid is used to prevent neural tube defects and other symptoms of folate deficiency. However, several unanswered questions remain over folic acid efficacy, safety and interactions with gut microbes. Prevention of a development defect caused by folate deficiency in the nematode worm Caenorhabditis elegans requires > 10 fold higher concentrations of folic acid compared to folinic acid, a reduced folate. Here we show that the major route for folic acid to restore normal development is indirect via the Escherichia coli used to feed C. elegans. This route occurs mainly via the E. coli transporter AbgT, which takes up the folic acid breakdown product para-aminobenzoate-glutamate (PABA-glu). We found that folic acid preparations, including a commercial supplement, contain 0.3- 4.0 % of this breakdown product. Previously, we have shown that inhibiting bacterial folate synthesis increases C. elegans lifespan by removing a life-shortening bacterial activity. Here, we show that folic acid restores bacterial folate synthesis and reverses this lifespan increase. It is still to be determined whether this bacterial route increases host folate levels in humans and if there are situations where increased bacterial folate synthesis has negative health complications.

microbiology↗

bioRxiv2017

BPG: Seamless, Automated and Interactive Visualization of Scientific Data

We introduce BPG, an easy-to-use framework for generating publication-quality, highly-customizable plots in the R statistical environment. This open-source package includes novel methods of displaying high-dimensional datasets and facilitates generation of complex multi-panel figures, making it ideal for complex datasets. A web-based interactive tool allows online figure customization, from which R code can be downloaded for seamless integration with computational pipelines. BPG is available at http://labs.oicr.on.ca/boutros-lab/software/bpg

bioinformatics↗