Interpreting Earth's top-of-the-atmosphere broadband radiation flux variability using observations and models

Observed broadband radiation fluxes at the top-of-the atmosphere (TOA) and at the Earth’s surface are determined by a complex network of atmospheric and surface processes. It is imperative that climate models are able to accurately simulate these observed variations and relationships in order to provide confidence in projections of our future climate. In this thesis I use a combination of observations, reanalysis fields and output from global circulation models (GCMs) to interpret radiation flux variability with respect to atmospheric properties and processes, in particular clouds, atmospheric water vapour and aerosols. I use observations and models in two ways. In Chapters 3 and 4 I evaluate model output using observations from satellite instruments and surface measurement stations to characterise the model ability to 1) recreate observed variability and 2) contrast TOA and surface radiation flux co-variability with atmospheric properties. In Chapter 5 I use satellite observations of atmospheric temperature and humidity profiles, as well as broadband radiation flux, to assess evidence of physical mechanisms which have recently been hypothesised using output from GCMs. The chapters are based on two regions of the tropics. I focus on the first of these, a region in western Africa, partly due to the presence of aerosols, such as Saharan mineral dust, and also the west African monsoon. Both of these factors have large impacts on the radiation balance and therefore make this region interesting from a radiation perspective. Additionally, west Africa is a region vulnerable to changes in climate, having already suffered from extended droughts in the last decades. My second focus region is the tropical ocean, where changes in tropical low clouds play an important role in the TOA radiation balance, and has therefore been linked to climate model sensitivity. The spatial and temporal scales used in the studies vary dramatically, which determines both the model output evaluated and also the methods I employ. In Chapter 3, I exploit the 2006 high frequency observational data at Niamey, Niger from the Atmospheric Radiation Measurement (ARM) Mobile Facility, the Geostationary Earth Radiation Budget (GERB) and Spinning Enhanced Visible and Infrared Imager (SEVIRI) instruments, and products from the Climate Mon itoring Satellites Applications Facility (CMSAF) to evaluate daily output from the European Centre for Medium-Range Weather Forecasts (ECWMF) Integrated Forecasting System 43r1. The data available include surface, atmospheric pro file and TOA measurements. By constructing multi-variate linear models of each component in the energy budget, I test their sensitivity to changes in atmo spheric properties, including 2m air temperature, aerosol optical depth (AOD), cloud properties and total column water vapour (TCWV). I find that the lack of ice in clouds, manifested as a reduced ice water path (IWP) in 43r1 with respect to the estimate from CMSAF, results in too much shortwave radiation passing through the atmosphere in 43r1, and therefore too much downwelling shortwave radiation (DSR) at the surface and too little reflected shortwave radiation (RSR) at the TOA. I also identify the use of an aerosol climatology in 43r1 as a cause of discrepancy between the observation and the model in the surface fluxes, with the lower aersol loading in the model leading to a reduction in downwelling longwave radiation (DLR) and an increase in DSR. This work is published in Atmospheric Chemistry and Physics as Mackie et al. (2017). In Chapter 4, I examine a wider region in western Africa, which I refer to as ‘west Africa’, which encompasses three distinct sub regions: the Sahel, the Sahara and the south-western coastal region. As observational references, I use a range of radiation data from the TOA and surface from satellite products and surface station measurements to construct mean annual cycles with which to evaluate output from GCMs submitted to the Intergovernmental Panel on Climate Change’s Coupled Model Intercomparison Project Phase 5 (CMIP5). This chapter has two aims: firstly, to compare the reference data and to establish the observational range in the targeted metrics, and secondly to evaluate how the CMIP5 multi-model mean and range fit with this range. By contrasting coupled and atmosphere-only model output, I link differences in radiation at the TOA to the models’ tendency to model the west African monsoon onset too late and to model the limit of its northwards progression to too far south. By contrasting the sensitivity of the models to changes in AOD and TCWV to that of the Clouds and the Earth’s Radiant Energy System Energy Balanced and Filled (CERES EBAF) product, I find some indication that DSR in the CMIP5 models may be too sensitive to changes in water vapour, and not sensitive enough to changes in AOD. This work is under review at the AGU journal Earth and Space Science. In Chapter 5, I evaluate observational evidence for a model-based hypotheses which links tropospheric temperature and humidity changes to patterns in tropical sea surface temperature (SST) warming. The hypothesis states that if SSTs in regions of strong ascent warm relative to the tropical ocean mean, the warming is efficiently lofted to the upper troposphere. In contrast, if warming is concentrated in regions of subsidence, the effects are limited to below the inversion which is characteristic of these regions. The subsequent effects of SST warming patterns are hypothesised to be key in determining the feedbacks from low cloud, and has thus been linked to climate sensitivity. To test this hypothesis I use co located Atmospheric Infrared Sounder (AIRS) temperature and humidity profiles and CERES radiation data, including window region data, and subset these data using vertical velocity at 500 hPa from ECMWF’s ERA-Interim reanalysis. I find some evidence which supports the hypothesised mechanism, specifically that if subsiding regions warm preferentially, there is a strong decrease in low cloud, with associated decrease in reflected shortwave radiation (RSR), and evidence that temperature increases are suppressed above the inversion. I also find small, but statistically significant, increases in humidity above the boundary layer inversion, though the origin of this is not clear. If regions of convection preferentially warm, the observations suggest that changes in relative humidity in the upper troposphere are due to changes in specific humidity rather than temperature, with temperatures in the upper troposphere relatively insensitive to relative warming. The largest changes in TOA radiation are in the longwave, which I hypothesise are linked to the observed increase in high cloud. This work is being prepared for publication

Fidelity protocol for the Action Success Knowledge (ASK) trial: A psychosocial intervention administered by speech and language therapists to prevent depression in people with post-stroke aphasia

Introduction: Treatment fidelity is a complex, multifaceted evaluative process which refers to whether a studied intervention was delivered as intended. Monitoring and enhancing fidelity is one recommendation of the TiDIER (Template for Intervention Description and Replication) checklist, as fidelity can inform interpretation and conclusions drawn about treatment effects. Despite the methodological and translational benefits, fidelity strategies have been used inconsistently within health behaviour intervention studies; in particular, within aphasia intervention studies, reporting of fidelity remains relatively rare. This paper describes the development of a fidelity protocol for the Action Success Knowledge (ASK) study, a current cluster randomised trial investigating an early mood intervention for people with aphasia (a language disability caused by stroke). Methods and analysis: A novel fidelity protocol and tool was developed to monitor and enhance fidelity within the two arms (experimental treatment and attention control) of the ASK study. The ASK fidelity protocol was developed based on the National Institutes of Health Behaviour Change Consortium fidelity framework. Ethics and dissemination: The study protocol was approved by the Darling Downs Hospital and Health Service Human Research Ethics Committee in Queensland, Australia under the National Mutual Acceptance scheme of multicentre human research projects. Specific ethics approval was obtained for those participating sites who were not under the National Mutual Agreement at the time of application. The monitoring and ongoing conduct of the research project is in line with requirements under the National Mutual Acceptance. On completion of the trial, findings from the fidelity reviews will be disseminated via publications and conference presentations. Trial registration number ACTRN12614000979651

Reducing the psychosocial impact of aphasia on mood and quality of life in people with aphasia and the impact of caregiving in family members through the Aphasia Action Success Knowledge (Aphasia ASK) program: Study protocol for a randomized controlled trial

© 2016 Worrall et al. Background: People with aphasia and their family members are at high risk of experiencing post stroke depression. The impact of early interventions on mood and quality of life for people with aphasia is unknown. Methods/design: This study will determine whether an early intervention for both the person with aphasia after stroke and their family members leads to better mood and quality of life outcomes for people with aphasia, and less caregiver burden and better mental health for their family members. This is a multicenter, cluster-randomized controlled trial. Clusters, which are represented by Health Service Districts, will be randomized to the experimental intervention (Aphasia Action Success Knowledge Program) or an attention control (Secondary Stroke Prevention Information Program). People with aphasia and their family members will be blinded to the study design and treatment allocation (that is, will not know there are two arms to the study). Both arms of the study will receive usual care in addition to either the experimental or the attention control intervention. A total of 344 people with aphasia and their family members will be recruited. Considering a cluster size of 20, the required sample size can be achieved from 18 clusters. However, 20 clusters will be recruited to account for the potential of cluster attrition during the study. Primary outcome measures will be mood and quality of life of people with aphasia at 12 months post stroke. Secondary measures will be family member outcomes assessing the impact of caregiving and mental health, and self-reported stroke risk-related behaviors of people with aphasia. Discussion: This is the first known program tailored for people with aphasia and their family members that aims to prevent depression in people with aphasia by providing intervention early after the stroke. Trial registration: This trial is registered in the Australian New Zealand Clinical Trials Registry (ANZCTR) as ACTRN12614000979651. Date registered: 11 September 2014

Technology Enhanced Writing Therapy for People with Aphasia: Results of a Quasi-Randomised Waitlist Controlled Study

Background: Acquired writing impairment, or dysgraphia, is common in aphasia. It affects both handwriting and typing, and may recover less well than other aphasic symptoms. Dysgraphia is an increasing priority for intervention, particularly for those wishing to participate in online written communication. Effective dysgraphia treatment studies have been reported, but many did not target, or did not achieve, improvements in functional writing. Functional outcomes might be promoted by therapies that exploit digital technologies, such as voice recognition and word prediction software. Aims: This study evaluated the benefits of technology enhanced writing therapy for people with acquired dysgraphia. It aimed to explore the impact of therapy on a functional writing activity, and to examine whether treatment remediated or compensated for the writing impairment. The primary question was: Does therapy improve performance on a functional assessment of writing; and, if so, do gains occur only when writing is assisted by technology? Secondary measures examined whether therapy improved unassisted written naming, functional communication, mood and quality of life. Methods & Procedures: The study employed a quasi randomised waitlist controlled design. 21 people with dysgraphia received 12 hours of writing therapy, either immediately, or after a 6 week delay. The primary outcome measure was a functional assessment of writing, which was administered in handwriting and on a computer with assistive technology enabled. Secondary measures were: The Boston Naming Test (written version), Communication Activities of Daily Living - 2, Visual Analogue Mood Scales (Sad question), and the Assessment of Living with Aphasia. ANOVA analyses were used to examine change on the outcome measures over two time points, between which the immediate group had received therapy, but the delayed group had not. Pre therapy, post therapy and follow up scores on the measures were also examined for all participants. Outcomes & Results: Time x group interactions in the ANOVA analyses showed that therapy improved performance on the functional writing assessment. Further interactions with condition showed that gains occurred only when writing was assisted by technology. There were no significant interactions in the analyses of the secondary outcome measures. A treatment effect on these measures was therefore unconfirmed. Conclusions & Implications. This study showed that 21 people with dysgraphia improved on a functional writing measure following therapy using assistive technology. The results suggest that treatment compensated for, rather than remediated the impairment, given that unassisted writing did not change. Further studies of technology enhanced writing therapy are warranted. What this paper adds What is known already: Writing abilities are typically impaired in aphasia, and may recover less well than other language modalities. Many previous writing therapy studies did not achieve functional gains on everyday writing tasks. What this study adds: This study shows that mainstream digital technologies, such as speech to text software, can be used in therapy to help compensate for writing impairments. Gains were shown on a functional task (writing emails) after 12 hours of treatment. Clinical implications: With specific training, people with aphasia can learn to use mainstream technologies in order to support writing. Greater use of such technologies could be made in practice

Which outcomes are most important to people with aphasia and their families? an international nominal group technique study framed within the ICF

PURPOSE: To identify important treatment outcomes from the perspective of people with aphasia and their families using the ICF as a frame of reference. METHODS: The nominal group technique was used with people with aphasia and their family members in seven countries to identify and rank important treatment outcomes from aphasia rehabilitation. People with aphasia identified outcomes for themselves; and family members identified outcomes for themselves and for the person with aphasia. Outcomes were analysed using qualitative content analysis and ICF linking. RESULTS: A total of 39 people with aphasia and 29 family members participated in one of 16 nominal groups. Inductive qualitative content analysis revealed the following six themes: (1) Improved communication; (2) Increased life participation; (3) Changed attitudes through increased awareness and education about aphasia; (4) Recovered normality; (5) Improved physical and emotional well-being; and (6) Improved health (and support) services. Prioritized outcomes for both participant groups linked to all ICF components; primary activity/participation (39%) and body functions (36%) for people with aphasia, and activity/participation (49%) and environmental factors (28%) for family members. Outcomes prioritized by family members relating to the person with aphasia, primarily linked to body functions (60%). CONCLUSIONS: People with aphasia and their families identified treatment outcomes which span all components of the ICF. This has implications for research outcome measurement and clinical service provision which currently focuses on the measurement of body function outcomes. The wide range of desired outcomes generated by both people with aphasia and their family members, highlights the importance of collaborative goal setting within a family-centred approach to rehabilitation. These results will be combined with other stakeholder perspectives to establish a core outcome set for aphasia treatment research. Implications for Rehabilitation Important outcomes for people with aphasia and their families span all components of the ICF. The relevancy and translation of research findings may be increased by measuring and reporting research outcomes which are important to people living with aphasia. The results of this study indicate that important treatment outcomes for people living with aphasia most frequently link to the activity/participation and body function components of the ICF. The outcomes identified in this study suggest a broad role for clinicians working in aphasia rehabilitation. The categories of identified outcomes may be used clinically as a starting point in goal-setting discussions with clients and their families

Conversation therapy with people with aphasia and conversation partners using video feedback: a group and case series investigation of changes in interaction

Conversation therapies employing video for feedback and to facilitate outcome measurement are increasingly used with people with post-stroke aphasia and their conversation partners; however the evidence base for change in everyday interaction remains limited. We investigated the effect of Better Conversations with Aphasia (BCA), an intervention that is freely available online at https://extend.ucl.ac.uk/. Eight people with chronic agrammatic aphasia, and their regular conversation partners participated in the tailored 8 week program involving significant video feedback. We explored changes in: (i) conversation facilitators (such as multi-modal turns by people with aphasia); and (ii) conversation barriers (such as use of test questions by conversation partners). The outcome of intervention was evaluated directly by measuring change in video-recorded everyday conversations. The study employed a pre-post design with multiple 5 minute samples of conversation before and after intervention, scored by trained raters blind to the point of data collection. Group level analysis showed no significant increase in conversation facilitators. There was, however, a significant reduction in the number of conversation barriers. The case series data revealed variability in conversation behaviors across occasions for the same dyad and between different dyads. Specifically, post-intervention there was a significant increase in facilitator behaviors for two dyads, a decrease for one and no significant change for five dyads. There was a significant decrease in barrier behaviors for five dyads and no significant change for three dyads. The reduction in barrier behaviors was considerable; on average change from over eight to fewer than three barrier behaviors in 5 minutes of conversation. The pre-post design has the limitation of no comparison group. However, change occurs in targeted conversational behaviors and in people with chronic aphasia and their partners. The findings suggest change can occur after eight therapy sessions and have implications for clinical practice. A reduction in barrier behaviors may be easier to obtain, although the controlled case series results demonstrate a significant increase in conversation facilitators is also possible. The rehabilitation tool is available online and video technology was central to delivering intervention and evaluating change

Glycerol treatment as recovery procedure for cryopreserved human skin allografts positive for bacteria and fungi

Human donor skin allografts are suitable and much used temporary biological (burn) wound dressings. They prepare the excised wound bed for final autografting and form an excellent substrate for revascularisation and for the formation of granulation tissue. Two preservation methods, glycerol preservation and cryopreservation, are commonly used by tissue banks for the long-term storage of skin grafts. The burn surgeons of the Queen Astrid Military Hospital preferentially use partly viable cryopreserved skin allografts. After mandatory 14-day bacterial and mycological culture, however, approximately 15% of the cryopreserved skin allografts cannot be released from quarantine because of positive culture. To maximize the use of our scarce and precious donor skin, we developed a glycerolisation-based recovery method for these culture positive cryopreserved allografts. The inactivation and preservation method, described in this paper, allowed for an efficient inactivation of the colonising bacteria and fungi, with the exception of spore-formers, and did not influence the structural and functional aspects of the skin allografts

MeCP2 binds to nucleosome free (linker DNA) regions and to H3K9/H3K27 methylated nucleosomes in the brain

Methyl-CpG-binding protein 2 (MeCP2) is a chromatin-binding protein that mediates transcriptional regulation, and is highly abundant in brain. The nature of its binding to reconstituted templates has been well characterized in vitro. However, its interactions with native chromatin are less understood. Here we show that MeCP2 displays a distinct distribution within fractionated chromatin from various tissues and cell types. Artificially induced global changes in DNA methylation by 3-aminobenzamide or 5-aza-2′-deoxycytidine, do not significantly affect the distribution or amount of MeCP2 in HeLa S3 or 3T3 cells. Most MeCP2 in brain is chromatin-bound and localized within highly nuclease-accessible regions. We also show that, while in most tissues and cell lines, MeCP2 forms stable complexes with nucleosome, in brain, a fraction of it is loosely bound to chromatin, likely to nucleosome-depleted regions. Finally, we provide evidence for novel associations of MeCP2 with mononucleosomes containing histone H2A.X, H3K9me2 and H3K27me3 in different chromatin fractions from brain cortex and in vitro. We postulate that the functional compartmentalization and tissue-specific distribution of MeCP2 within different chromatin types may be directed by its association with nucleosomes containing specific histone variants, and post-translational modifications