N1-Src kinase is required for primary neurogenesis in Xenopus tropicalis

The presence of the neuronal-specific N1-Src splice variant of the C-Src tyrosine kinase is conserved through vertebrate evolution, suggesting an important role in complex nervous systems. Alternative splicing involving a N1-Src specific microexon leads to a five or six amino acid insertion into the SH3 domain of Src. A prevailing model suggests that N1-Src regulates neuronal differentiation via cytoskeletal dynamics in the growth cone. Here we have investigated the role of n1-src in the early development of the amphibian Xenopus tropicalis, and find that n1-src expression is regulated in embryogenesis, with highest levels detected during the phases of primary and secondary neurogenesis. In situ hybridisation analysis, using locked nucleic acid (LNA) oligo probes complementary to the n1-src microexon indicate that n1-src expression is highly enriched in the open neural plate during neurula stages and in the neural tissue of adult frogs. Given the n1-src expression pattern, we investigated a possible role for n1-src in neurogenesis. Using splice site-specific antisense morpholino oligos, we are able to inhibit n1-src splicing, whilst preserving c-src expression. Differentiation of neurons in the primary nervous system is reduced in n1-src knockdown embryos, accompanied by a severely impaired touch response in later development. These data reveal an essential role for n1-src in amphibian neural development and suggest that alternative splicing of C-Src in the developing vertebrate nervous system evolved to regulate neurogenesis

N1-Src kinase is required for primary neurogenesis in Xenopus tropicalis

The presence of the neuronal-specific N1-Src splice variant of the C-Src tyrosine kinase is conserved through vertebrate evolution, suggesting an important role in complex nervous systems. Alternative splicing involving a N1-Src specific microexon leads to a five or six amino acid insertion into the SH3 domain of Src. A prevailing model suggests that N1-Src regulates neuronal differentiation via cytoskeletal dynamics in the growth cone. Here we have investigated the role of n1-src in the early development of the amphibian Xenopus tropicalis, and find that n1-src expression is regulated in embryogenesis, with highest levels detected during the phases of primary and secondary neurogenesis. In situ hybridisation analysis, using locked nucleic acid (LNA) oligo probes complementary to the n1-src microexon indicate that n1-src expression is highly enriched in the open neural plate during neurula stages and in the neural tissue of adult frogs. Given the n1-src expression pattern, we investigated a possible role for n1-src in neurogenesis. Using splice site-specific antisense morpholino oligos, we are able to inhibit n1-src splicing, whilst preserving c-src expression. Differentiation of neurons in the primary nervous system is reduced in n1-src knockdown embryos, accompanied by a severely impaired touch response in later development. These data reveal an essential role for n1-src in amphibian neural development and suggest that alternative splicing of C-Src in the developing vertebrate nervous system evolved to regulate neurogenesis

Differentially Testing Soundness and Precision of Program Analyzers

In the last decades, numerous program analyzers have been developed both by academia and industry. Despite their abundance however, there is currently no systematic way of comparing the effectiveness of different analyzers on arbitrary code. In this paper, we present the first automated technique for differentially testing soundness and precision of program analyzers. We used our technique to compare six mature, state-of-the art analyzers on tens of thousands of automatically generated benchmarks. Our technique detected soundness and precision issues in most analyzers, and we evaluated the implications of these issues to both designers and users of program analyzers

18F-FDG PET/CT assessment of histopathologically confirmed mediastinal lymph nodes in non-small cell lung cancer using a penalised likelihood reconstruction

Purpose To investigate whether using a Bayesian penalised likelihood reconstruction (BPL) improves signal-to-background (SBR), signal-to-noise (SNR) and SUVmax when evaluating mediastinal nodal disease in non-small cell lung cancer (NSCLC) compared to ordered subset expectation maximum (OSEM) reconstruction. Materials and methods 18F-FDG PET/CT scans for NSCLC staging in 47 patients (112 nodal stations with histopathological confirmation) were reconstructed using BPL and compared to OSEM. Node and multiple background SUV parameters were analysed semi-quantitatively and visually. Results Comparing BPL to OSEM, there were significant increases in SUVmax (mean 3.2–4.0, p<0.0001), SBR (mean 2.2–2.6, p<0.0001) and SNR (mean 27.7–40.9, p<0.0001). Mean background SNR on OSEM was 10.4 (range 7.6–14.0), increasing to 12.4 (range 8.2–16.7, p<0.0001). Changes in background SUVs were minimal (largest mean difference 0.17 for liver SUVmean, p<0.001). There was no significant difference between either algorithm on receiver operating characteristic analysis (p=0.26), although on visual analysis, there was an increase in sensitivity and small decrease in specificity and accuracy on BPL. Conclusion BPL increases SBR, SNR and SUVmax of mediastinal nodes in NSCLC compared to OSEM, but did not improve the accuracy for determining nodal involvement

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

8 Pág.Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.This work was supported in part by NSF Expeditions in Computing Program Award No. 1522074 as part of the Living Computing Project and by the Defense Advanced Research Projects Agency under Contract No. W911NF-17-2-0098. The views, opinions, and/or findings expressed are of the author(s) and should not be interpreted as representing official views or policies of the Department of Defense or the U.S. Government. A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (No.EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU Grant No. 820699)Peer reviewe

Integrating personality research and animal contest theory: aggressiveness in the green swordtail <i>Xiphophorus helleri</i>

&lt;p&gt;Aggression occurs when individuals compete over limiting resources. While theoretical studies have long placed a strong emphasis on context-specificity of aggression, there is increasing recognition that consistent behavioural differences exist among individuals, and that aggressiveness may be an important component of individual personality. Though empirical studies tend to focus on one aspect or the other, we suggest there is merit in modelling both within-and among-individual variation in agonistic behaviour simultaneously. Here, we demonstrate how this can be achieved using multivariate linear mixed effect models. Using data from repeated mirror trials and dyadic interactions of male green swordtails, &lt;i&gt;Xiphophorus helleri&lt;/i&gt;, we show repeatable components of (co)variation in a suite of agonistic behaviour that is broadly consistent with a major axis of variation in aggressiveness. We also show that observed focal behaviour is dependent on opponent effects, which can themselves be repeatable but were more generally found to be context specific. In particular, our models show that within-individual variation in agonistic behaviour is explained, at least in part, by the relative size of a live opponent as predicted by contest theory. Finally, we suggest several additional applications of the multivariate models demonstrated here. These include testing the recently queried functional equivalence of alternative experimental approaches, (e. g., mirror trials, dyadic interaction tests) for assaying individual aggressiveness.&lt;/p&gt

Emergency Department Escalation in Theory and Practice: A Mixed-Methods Study Using a Model of Organizational Resilience

Study objective Escalation policies are used by emergency departments (EDs) when responding to an increase in demand (eg, a sudden inflow of patients) or a reduction in capacity (eg, a lack of beds to admit patients). The policies aim to maintain the ability to deliver patient care, without compromising safety, by modifying “normal” processes. The study objective is to examine escalation policies in theory and practice. Methods This was a mixed-method study involving a conceptual analysis of National Health Service escalation policies (n=12) and associated escalation actions (n=92), as well as a detailed ethnographic study of escalation in situ during a 16-month period in a large UK ED (n=30 observations). Results The conceptual analysis of National Health Service escalation policies found that their use requires the ability to dynamically reconfigure resources (staff and equipment), change work flow, and relocate patients. In practice, it was discovered that when the ED is under pressure, these prerequisites cannot always be attained. Instead, escalation processes were adapted to manage pressures informally. This adaptive need (“work as done”) was found to be incompletely specified in policies (“work as imagined”). Conclusion Formal escalation actions and their implementation in practice differed and varied in their effectiveness. Monitoring how escalation works in practice is essential in understanding whether and how escalation policies help to manage workload

A 'combined framework' approach to developing a patient decision aid: the PANDAs model

Background There is a lack of practical research frameworks to guide the development of patient decision aids [PtDAs]. This paper described how a PtDA was developed using the International Patient Decision Aids (IPDAS) guideline and UK Medical Research Council (UKMRC) frameworks to support patients when making treatment decisions in type 2 diabetes mellitus. Methods This study used mixed methods to develop a PtDA for use in a UK general practice setting. A 10-member expert panel was convened to guide development and patients and clinicians were also interviewed individually using semi-structured interview guides to identify their decisional needs. Current literature was reviewed systematically to determine the best available evidence. The Ottawa Decision Support Framework was used to guide the presentation of the information and value clarification exercise. An iterative draft-review-revise process by the research team and review panel was conducted until the PtDA reached content and format `saturation’. The PtDA was then pilot-tested by users in actual consultations to assess its acceptability and feasibility. The IPDAS and UKMRC frameworks were used throughout to inform the development process. Results The PANDAs PtDA was developed systematically and iteratively. Patients and clinicians highlighted the needs for information, decisional, emotional and social support, which were incorporated into the PtDA. The literature review identified gaps in high quality evidence and variations in patient outcome reporting. The PtDA comprised five components: background of the treatment options; pros and cons of each treatment option; value clarification exercise; support needs; and readiness to decide. Conclusions This study has demonstrated the feasibility of combining the IPDAS and the UKMRC frameworks for the development and evaluation of a PtDA. Future studies should test this model for developing PtDAs across different decisions and healthcare contexts