Informing the design of a randomised controlled trial of an exercise-based programme for long term stroke survivors: lessons from a before-and-after case series study

Background: To inform the design of a randomised controlled trial (RCT) of an exercise-based programme for long term stroke survivors, we conducted a mixed methods before-and-after case series with assessment at three time points. We evaluated Action for Rehabilitation from Neurological Injury (ARNI), a personalised, functionally-focussed programme. It was delivered through 24 hours of one-to-one training by an Exercise Professional (EP), plus at least 2 hours weekly unsupervised exercise, over 12- 14 weeks. Assessment was by patient-rated questionnaires addressing function, physical activity, confidence, fatigue and health-related quality of life; objective assessment of gait quality and speed; qualitative individual interviews conducted with participants. Data were collected at baseline, 3 months and 6 months. Fidelity and acceptability was assessed by participant interviews, audit of participant and EP records, and observation of training. Findings: Four of six enrolled participants completed the exercise programme. Quantitative data demonstrated little change across the sample, but marked changes on some measures for some individuals. Qualitative interviews suggested that small benefits in physical outcomes could be of great psychological significance to participants. Participant-reported fatigue levels commonly increased, and non-completers said they found the programme too demanding. Most key components of the intervention were delivered, but there were several potentially important departures from intervention fidelity. Discussion: The study provided data and experience that are helping to inform the design of an RCT of this intervention. It suggested the need for a broader recruitment strategy; indicated areas that could be explored in more depth in the qualitative component of the trial; and highlighted issues that should be addressed to enhance and evaluate fidelity, particularly in the preparation and monitoring of intervention providers. The experience illustrates the value of even small sample before-and-after studies in the development of trials of complex interventions.PenCLAHRC; NIH

Target prediction for small, noncoding RNAs in bacteria

Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a limited number of the corresponding mRNA targets have been identified. Here we present a program, TargetRNA, that predicts the targets of these bacterial RNA regulators. The program was evaluated by assessing whether previously known targets could be identified. The program was then used to predict targets for the Escherichia coli RNAs RyhB, OmrA, OmrB and OxyS, and the predictions were compared with changes in whole genome expression patterns observed upon expression of the sRNAs. Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs

The SAMI Galaxy Survey: mass-kinematics scaling relations

We use data from the Sydney-AAO Multi-object Integral-field spectroscopy (SAMI) Galaxy Survey to study the dynamical scaling relation between galaxy stellar mass $M_*$ and the general kinematic parameter $S_K = \sqrt{K V_{rot}^2 + \sigma^2}$ that combines rotation velocity $V_{rot}$ and velocity dispersion $\sigma$. We show that the $\log M_* - \log S_K$ relation: (1)~is linear above limits set by properties of the samples and observations; (2)~has slightly different slope when derived from stellar or gas kinematic measurements; (3)~applies to both early-type and late-type galaxies and has smaller scatter than either the Tully-Fisher relation ($\log M_* - \log V_{rot}$) for late types or the Faber-Jackson relation ($\log M_* - \log\sigma$) for early types; and (4)~has scatter that is only weakly sensitive to the value of $K$, with minimum scatter for $K$ in the range 0.4 and 0.7. We compare $S_K$ to the aperture second moment (the `aperture velocity dispersion') measured from the integrated spectrum within a 3-arcsecond radius aperture ($\sigma_{3^{\prime\prime}}$). We find that while $S_{K}$ and $\sigma_{3^{\prime\prime}}$ are in general tightly correlated, the $\log M_* - \log S_K$ relation has less scatter than the $\log M_* - \log \sigma_{3^{\prime\prime}}$ relation.Comment: 14 pages, 8 figures, Accepted 2019 May 22. Received 2019 May 18; in original form 2019 January

The SAMI Galaxy Survey: Revising the Fraction of Slow Rotators in IFS Galaxy Surveys

The fraction of galaxies supported by internal rotation compared to galaxies stabilized by internal pressure provides a strong constraint on galaxy formation models. In integral field spectroscopy surveys, this fraction is biased because survey instruments typically only trace the inner parts of the most massive galaxies. We present aperture corrections for the two most widely used stellar kinematic quantities $V/\sigma$ and $\lambda_{R}$. Our demonstration involves integral field data from the SAMI Galaxy Survey and the ATLAS$^{\rm{3D}}$ Survey. We find a tight relation for both $V/\sigma$ and $\lambda_{R}$ when measured in different apertures that can be used as a linear transformation as a function of radius, i.e., a first-order aperture correction. We find that $V/\sigma$ and $\lambda_{R}$ radial growth curves are well approximated by second order polynomials. By only fitting the inner profile (0.5$R_{\rm{e}}$), we successfully recover the profile out to one $R_{\rm{e}}$ if a constraint between the linear and quadratic parameter in the fit is applied. However, the aperture corrections for $V/\sigma$ and $\lambda_{R}$ derived by extrapolating the profiles perform as well as applying a first-order correction. With our aperture-corrected $\lambda_{R}$ measurements, we find that the fraction of slow rotating galaxies increases with stellar mass. For galaxies with $\log M_{*}/M_{\odot}>$ 11, the fraction of slow rotators is $35.9\pm4.3$ percent, but is underestimated if galaxies without coverage beyond one $R_{\rm{e}}$ are not included in the sample ($24.2\pm5.3$ percent). With measurements out to the largest aperture radius the slow rotator fraction is similar as compared to using aperture corrected values ($38.3\pm4.4$ percent). Thus, aperture effects can significantly bias stellar kinematic IFS studies, but this bias can now be removed with the method outlined here.Comment: Accepted for Publication in the Monthly Notices of the Royal Astronomical Society. 16 pages and 11 figures. The key figures of the paper are: 1, 4, 9, and 1

The SAMI Galaxy Survey: gravitational potential and surface density drive stellar populations -- I. early-type galaxies

The well-established correlations between the mass of a galaxy and the properties of its stars are considered evidence for mass driving the evolution of the stellar population. However, for early-type galaxies (ETGs), we find that $g-i$ color and stellar metallicity [Z/H] correlate more strongly with gravitational potential $\Phi$ than with mass $M$, whereas stellar population age correlates best with surface density $\Sigma$. Specifically, for our sample of 625 ETGs with integral-field spectroscopy from the SAMI Galaxy Survey, compared to correlations with mass, the color--$\Phi$, [Z/H]--$\Phi$, and age--$\Sigma$ relations show both smaller scatter and less residual trend with galaxy size. For the star formation duration proxy [$\alpha$/Fe], we find comparable results for trends with $\Phi$ and $\Sigma$, with both being significantly stronger than the [$\alpha$/Fe]-$M$ relation. In determining the strength of a trend, we analyze both the overall scatter, and the observational uncertainty on the parameters, in order to compare the intrinsic scatter in each correlation. These results lead us to the following inferences and interpretations: (1) the color--$\Phi$ diagram is a more precise tool for determining the developmental stage of the stellar population than the conventional color--mass diagram; and (2) gravitational potential is the primary regulator of global stellar metallicity, via its relation to the gas escape velocity. Furthermore, we propose the following two mechanisms for the age and [$\alpha$/Fe] relations with $\Sigma$: (a) the age--$\Sigma$ and [$\alpha$/Fe]--$\Sigma$ correlations arise as results of compactness driven quenching mechanisms; and/or (b) as fossil records of the $\Sigma_{SFR}\propto\Sigma_{gas}$ relation in their disk-dominated progenitors.Comment: 9 pages, 4 figures, 1 table Accepted to Ap

The Sydney-AAO Multi-object Integral field spectrograph (SAMI)

We demonstrate a novel technology that combines the power of the multi-object spectrograph with the spatial multiplex advantage of an integral field spectrograph (IFS). The Sydney-AAO Multi-object IFS (SAMI) is a prototype wide-field system at the Anglo-Australian Telescope (AAT) that allows 13 imaging fibre bundles ("hexabundles") to be deployed over a 1-degree diameter field of view. Each hexabundle comprises 61 lightly-fused multimode fibres with reduced cladding and yields a 75 percent filling factor. Each fibre core diameter subtends 1.6 arcseconds on the sky and each hexabundle has a field of view of 15 arcseconds diameter. The fibres are fed to the flexible AAOmega double-beam spectrograph, which can be used at a range of spectral resolutions (R=lambda/delta(lambda) ~ 1700-13000) over the optical spectrum (3700-9500A). We present the first spectroscopic results obtained with SAMI for a sample of galaxies at z~0.05. We discuss the prospects of implementing hexabundles at a much higher multiplex over wider fields of view in order to carry out spatially--resolved spectroscopic surveys of 10^4 to 10^5 galaxies.Comment: 24 pages, 16 figures. Accepted by MNRA

A Video-based End-to-end Pipeline for Non-nutritive Sucking Action Recognition and Segmentation in Young Infants

We present an end-to-end computer vision pipeline to detect non-nutritive sucking (NNS) -- an infant sucking pattern with no nutrition delivered -- as a potential biomarker for developmental delays, using off-the-shelf baby monitor video footage. One barrier to clinical (or algorithmic) assessment of NNS stems from its sparsity, requiring experts to wade through hours of footage to find minutes of relevant activity. Our NNS activity segmentation algorithm solves this problem by identifying periods of NNS with high certainty -- up to 94.0\% average precision and 84.9\% average recall across 30 heterogeneous 60 s clips, drawn from our manually annotated NNS clinical in-crib dataset of 183 hours of overnight baby monitor footage from 19 infants. Our method is based on an underlying NNS action recognition algorithm, which uses spatiotemporal deep learning networks and infant-specific pose estimation, achieving 94.9\% accuracy in binary classification of 960 2.5 s balanced NNS vs. non-NNS clips. Tested on our second, independent, and public NNS in-the-wild dataset, NNS recognition classification reaches 92.3\% accuracy, and NNS segmentation achieves 90.8\% precision and 84.2\% recall

'Keeping busy' as agency in early desistance

Agency in desistance research has often been understood as deliberate action undertaken in pursuit of a desisting identity. Through a micro-longitudinal approach, this research focuses on the early desistance experiences of a number of mainly white British female participants. Agency was exhibited not with a new identity in mind, but instead through 'keeping busy'. The surprising lack of identity concerns may be due to the early stages of the participants' desistance experiences, with new identities emerging later in the process. Alternatively, it may indicate a fundamental difference to the classic desistance narrative, linked to the differences between this sample and the frequently researched, Western, male, high-frequency offender. Finally, important aspects of the cultures surrounding desistance research may have shaped the narratives of desisters and the biases of researchers towards finding a concern for identity when this is not necessarily experienced in the everyday lives of desisters