Optimizing astrophotonic spatial reformatters using simulated on-sky performance

One of the most useful techniques in astronomical instrumentation is image slicing. It enables a spectrograph to have a more compact angular slit, whilst retaining throughput and increasing resolving power. Astrophotonic components like the photonic lanterns and photonic reformatters can be used to replace bulk optics used so far. This study investigates the performance of such devices using end-to-end simulations to approximate realistic on-sky conditions. It investigates existing components, tries to optimize their performance and aims to understand better how best to design instruments to maximize their performance. This work complements the recent work in the field and provides an estimation for the performance of the new components.Comment: Conference proceedings in SPIE 2018 Austin Texa

Observational study of the effects of traumatic injury, haemorrhagic shock and resuscitation on the microcirculation: a protocol for the MICROSHOCK study

Introduction: The microcirculation is the physiological site of oxygen and substrate exchange. Its effectiveness during circulatory shock is vital for the perfusion of tissues, and has a bearing on subsequent organ function and prognosis. Microcirculatory dysfunction following traumatic haemorrhagic shock (THS) has been understudied compared with other pathologies such as sepsis. The aim of the MICROSHOCK study is to investigate changes seen in the microcirculation of patients following THS, and to assess its response to resuscitation. A greater understanding of the behaviour and mechanisms of microcirculatory dysfunction in this context may direct future avenues of goal-directed resuscitation for these patients. Methods and analysis: This multicentre prospective longitudinal observational study includes patients who present as an emergency with THS. Microcirculatory parameters are recorded using sublingual incident dark field microscopy alongside measurements of global flow (oesophageal Doppler and transthoracic echocardiography). Patients are enrolled into the study as soon as feasible after they arrive in hospital, and then at subsequent daily time points. Blood samples are taken for investigation into the mechanisms of microcirculatory dysfunction. Sequential Organ Failure Assessment scores will be analysed with microcirculatory parameters to determine whether they correlate with greater fidelity than more conventional, global circulatory parameters. Ethics and dissemination: Research Ethics Committee approval has been granted for this study (Reference: 14/YH/0078). Owing to the nature of THS, capacity for informed consent will be absent on patient enrolment. This will be addressed according to the Mental Health Capacity Act 2005. The physician in charge of the patient's care (nominated consultee) may consent on behalf of the patient. Consent will also be sought from a personal consultee (close relative or friend). After capacity is regained, the participant will be asked for their consent. Results will be submitted for publication in peer-reviewed journal format and presented at relevant academic meetings

All-fibre wavefront sensor

We report on a tapered three-core optical fibre that can be used as a tip-tilt wavefront sensor. In this device, a coupled region of a few millimetres at the sensing tip of the fibre converts fragile phase information from an incoming wavefront into robust intensity information within each of the cores. The intensity information can be easily converted to linear wavefront error over small ranges, making it ideal for closed loop systems. The sensor uses minimal information to infer tip-tilt and is compatible with remote detector arrays. We explore its application within adaptive optics and present a validation case to show its applicability to astronomy.Comment: 7 pages, 6 figure

Clinical deployment environments: Five pillars of translational machine learning for health

Machine Learning for Health (ML4H) has demonstrated efficacy in computer imaging and other self-contained digital workflows, but has failed to substantially impact routine clinical care. This is no longer because of poor adoption of Electronic Health Records Systems (EHRS), but because ML4H needs an infrastructure for development, deployment and evaluation within the healthcare institution. In this paper, we propose a design pattern called a Clinical Deployment Environment (CDE). We sketch the five pillars of the CDE: (1) real world development supported by live data where ML4H teams can iteratively build and test at the bedside (2) an ML-Ops platform that brings the rigour and standards of continuous deployment to ML4H (3) design and supervision by those with expertise in AI safety (4) the methods of implementation science that enable the algorithmic insights to influence the behaviour of clinicians and patients and (5) continuous evaluation that uses randomisation to avoid bias but in an agile manner. The CDE is intended to answer the same requirements that bio-medicine articulated in establishing the translational medicine domain. It envisions a transition from "real-world" data to "real-world" development

Properties of the mechanosensitive channel MscS pore revealed by tryptophan scanning mutagenesis

Funding This work was supported by a Wellcome Trust Programme grant [092552/A/10/Z awarded to I.R.B., S.M., J. H. Naismith (University of St Andrews, St Andrews, U.K.), and S. J. Conway (University of Oxford, Oxford, U.K.)] (T.R. and M.D.E.), by a BBSRC grant (A.R.) [BB/H017917/1 awarded to I.R.B., J. H. Naismith, and O. Schiemann (University of St Andrews)], by a Leverhulme Emeritus Fellowship (EM-2012-060\2), and by a CEMI grant to I.R.B. from the California Institute of Technology. The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013 FP7/2007-2011) under Grant PITN-GA-2011-289384 (FP7-PEOPLE-2011-ITN NICHE) (H.G.) (awarded to S.M.).Peer reviewedPublisher PD

Estimating the prevalence of problem drug use from drug-related mortality data.

BACKGROUND AND AIMS: Indirect estimation methods are required for estimating the size of populations where only a proportion of individuals are observed directly, such as problem drug users (PDUs). Capture-recapture and multiplier methods are widely used, but have been criticized as subject to bias. We propose a new approach to estimating prevalence of PDU from numbers of fatal drug-related poisonings (fDRPs) using linked databases, addressing the key limitations of simplistic 'mortality multipliers'. METHODS: Our approach requires linkage of data on a large cohort of known PDUs to mortality registers and summary information concerning additional fDRPs observed outside this cohort. We model fDRP rates among the cohort and assume that rates in unobserved PDUs are equal to rates in the cohort during periods out of treatment. Prevalence is estimated in a Bayesian statistical framework, in which we simultaneously fit regression models to fDRP rates and prevalence, allowing both to vary by demographic factors and the former also by treatment status. RESULTS: We report a case study analysis, estimating the prevalence of opioid dependence in England in 2008/09, by gender, age group and geographical region. Overall prevalence was estimated as 0.82% (95% credible interval = 0.74-0.94%) of 15-64-year-olds, which is similar to a published estimate based on capture-recapture analysis. CONCLUSIONS: Our modelling approach estimates prevalence from drug-related mortality data, while addressing the main limitations of simplistic multipliers. This offers an alternative approach for the common situation where available data sources do not meet the strong assumptions required for valid capture-recapture estimation. In a case study analysis, prevalence estimates based on our approach were surprisingly similar to existing capture-recapture estimates but, we argue, are based on a much more objective and justifiable modelling approach

Mouse H6 Homeobox 1 (Hmx1) mutations cause cranial abnormalities and reduced body mass

<p>Abstract</p> <p>Background</p> <p>The H6 homeobox genes <it>Hmx1</it>, <it>Hmx2</it>, and <it>Hmx3 </it>(also known as <it>Nkx5-3</it>; <it>Nkx5-2 </it>and <it>Nkx5-1</it>, respectively), compose a family within the NKL subclass of the ANTP class of homeobox genes. Hmx gene family expression is mostly limited to sensory organs, branchial (pharyngeal) arches, and the rostral part of the central nervous system. Targeted mutation of either <it>Hmx2 </it>or <it>Hmx3 </it>in mice disrupts the vestibular system. These tandemly duplicated genes have functional overlap as indicated by the loss of the entire vestibular system in double mutants. Mutants have not been described for <it>Hmx1</it>, the most divergent of the family.</p> <p>Results</p> <p>Dumbo (<it>dmbo</it>) is a semi-lethal mouse mutation that was recovered in a forward genetic mutagenesis screen. Mutants exhibit enlarged ear pinnae with a distinctive ventrolateral shift. Here, we report on the basis of this phenotype and other abnormalities in the mutant, and identify the causative mutation as being an allele of <it>Hmx1</it>. Examination of dumbo skulls revealed only subtle changes in cranial bone morphology, namely hyperplasia of the gonial bone and irregularities along the caudal border of the squamous temporal bone. Other nearby otic structures were unaffected. The semilethality of <it>dmbo/dmbo </it>mice was found to be ~40%, occured perinatally, and was associated with exencephaly. Surviving mutants of both sexes exhibited reduced body mass from ~3 days postpartum onwards. Most dumbo adults were microphthalmic. Recombinant animals and specific deletion-bearing mice were used to map the <it>dumbo </it>mutation to a 1.8 Mb region on Chromosome 5. DNA sequencing of genes in this region revealed a nonsense mutation in the first exon of H6 Homeobox 1 (<it>Hmx1</it>; also <it>Nkx5-3</it>). An independent spontaneous allele called misplaced ears (<it>mpe</it>) was also identified, confirming <it>Hmx1 </it>as the responsible mutant gene.</p> <p>Conclusion</p> <p>The divergence of <it>Hmx1 </it>from its paralogs is reflected by different and diverse developmental roles exclusive of vestibular involvement. Additionally, these mutant <it>Hmx1 </it>alleles represent the first mouse models of a recently-discovered Oculo-Auricular syndrome caused by mutation of the orthologous human gene.</p