Modeling large scale species abundance with latent spatial processes

Modeling species abundance patterns using local environmental features is an important, current problem in ecology. The Cape Floristic Region (CFR) in South Africa is a global hot spot of diversity and endemism, and provides a rich class of species abundance data for such modeling. Here, we propose a multi-stage Bayesian hierarchical model for explaining species abundance over this region. Our model is specified at areal level, where the CFR is divided into roughly $37{,}000$ one minute grid cells; species abundance is observed at some locations within some cells. The abundance values are ordinally categorized. Environmental and soil-type factors, likely to influence the abundance pattern, are included in the model. We formulate the empirical abundance pattern as a degraded version of the potential pattern, with the degradation effect accomplished in two stages. First, we adjust for land use transformation and then we adjust for measurement error, hence misclassification error, to yield the observed abundance classifications. An important point in this analysis is that only $28$ of the grid cells have been sampled and that, for sampled grid cells, the number of sampled locations ranges from one to more than one hundred. Still, we are able to develop potential and transformed abundance surfaces over the entire region. In the hierarchical framework, categorical abundance classifications are induced by continuous latent surfaces. The degradation model above is built on the latent scale. On this scale, an areal level spatial regression model was used for modeling the dependence of species abundance on the environmental factors.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS335 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Cm-Wavelength Total Flux and Linear Polarization Properties of Radio-Loud BL Lacertae Objects

Results from a long-term program to quantify the range of behavior of the cm-wavelength total flux and linear polarization variability properties of a sample of 41 radio-loud BL Lac objects using weekly to tri-monthly observations with the University of Michigan 26-m telescope operating at 14.5, 8.0, and 4.8 GHz are presented; these observations are used to identify class-dependent differences between these BL Lacs and QSOs in the Pearson-Readhead sample. The BL Lacs are found to be more highly variable in total flux density than the QSOs, exhibiting changes that are often nearly-simultaneous and of comparable amplitude at 14.5 and 4.8 GHz in contrast to the behavior in the QSOs and supporting the existence of class-dependent differences in opacity within the parsec-scale jet flows. Structure function analyses of the flux observations quantify that a characteristic timescale is identifiable in only 1/3 of the BL Lacs. The time-averaged fractional linear polarizations are only on the order of a few percent and are consistent with the presence of tangled magnetic fields within the emitting regions. In many sources a preferred long-term orientation of the EVPA is present; when compared with the VLBI structural axis, no preferred position angle difference is identified. The polarized flux typically exhibits variability with timescales of months to a few years and shows the signature of a propagating shock during several resolved outbursts. The observations indicate that the source emission is predominately due to evolving source components and support the occurrence of more frequent shock formation in BL Lac parsec-scale flows than in QSO jets. The differences in variability behavior and polarization between BL Lacs and QSOs can be explained by differences in jet stability.Comment: 1 LaTex (aastex) file, 21 postscript figure files, 2 external LaTex table files. To appear in the Astrophysical Journa

Semicircular canal shape diversity among modern lepidosaurs: Life habit, size, allometry

Published online: 12 April 2023Background: The shape of the semicircular canals of the inner ear of living squamate reptiles has been used to infer phylogenetic relationships, body size, and life habits. Often these inferences are made without controlling for the effects of the other ones. Here we examine the semicircular canals of 94 species of extant limbed lepidosaurs using three-dimensional landmark-based geometric morphometrics, and analyze them in phylogenetic context to evaluate the relative contributions of life habit, size, and phylogeny on canal shape. Results: Life habit is not a strong predictor of semicircular canal shape across this broad sample. Instead, phylogeny plays a major role in predicting shape, with strong phylogenetic signal in shape as well as size. Allometry has a limited role in canal shape, but inner ear size and body mass are strongly correlated. Conclusions: Our wide sampling across limbed squamates suggests that semicircular canal shape and size are predominantly a factor of phylogenetic relatedness. Given the small proportion of variance in semicircular canal shape explained by life habit, it is unlikely that unknown life habit could be deduced from semicircular canal shape alone. Overall, semicircular canal size is a good estimator of body length and even better for body mass in limbed squamates. Semiaquatic taxa tend to be larger and heavier than non-aquatic taxa, but once body size and phylogeny are accounted for, they are hard to distinguish from their non-aquatic relatives based on bony labyrinth shape and morphology.Ashley E. Latimer, Emma Sherratt, Timothée Bonnet and Torsten M. Scheye

Tailoring Messages to Individual Differences in Monitoring- Blunting Styles to Increase Fruit and Vegetable Intake

Objective To examine whether messages matched to individuals\u27 monitoring-blunting coping styles (MBCS) are more effective in increasing fruit and vegetable intake than mismatched messages. MBCS refers to the tendency to either attend to and amplify, or distract oneself from and minimize threatening information. Design/Setting Randomly assigned messages were tailored to resonate with either monitors or blunters and delivered at baseline, 1 week, 2 months, and 3 months later. Surveys were conducted at baseline and 2 and 4 months later. Participants 531 callers to a cancer information hotline who did not meet the 5 A Day guideline. Intervention A brief telephone-delivered message and 3 mailings of booklets and promotional items encouraging fruit and vegetable intake, tailored for either monitors or blunters. Main Outcome Measure Fruit and vegetable intake 2 and 4 months post-baseline. Analysis Hierarchical regression modeling. Results Messages matched to MBCS were more effective than mismatched messages, particularly for the monitor message, in increasing intake at 2 months but not at 4 months. Conclusions and Implications These minimal interventions influenced fruit and vegetable intake. MBCS may be a promising target for developing tailored messages aimed at increasing intake, although additional research is needed to verify the robustness of these findings

National Geodetic Satellite Program, Part II: Smithsonian Astrophysical Observatory

A sequence of advances in the determination of geodetic parameters presented by the Smithsonian Astrophysical Observatory are described. A Baker-Nunn photographic system was used in addition to a ruby-laser ranging system to obtain data for refinement of geodetic parameters. A summary of the data employed to: (1) derive coordinates for the locations of various tracking stations; and (2) determine the gravitational potential of the earth, is presented

Ten steps or climbing a mountain: A study of Australian health professionals' perceptions of implementing the baby friendly health initiative to protect, promote and support breastfeeding

Background: The Baby Friendly Hospital (Health) Initiative (BFHI) is a global initiative aimed at protecting, promoting and supporting breastfeeding and is based on the ten steps to successful breastfeeding. Worldwide, over 20,000 health facilities have attained BFHI accreditation but only 77 Australian hospitals (approximately 23%) have received accreditation. Few studies have investigated the factors that facilitate or hinder implementation of BFHI but it is acknowledged this is a major undertaking requiring strategic planning and change management throughout an institution. This paper examines the perceptions of BFHI held by midwives and nurses working in one Area Health Service in NSW, Australia. Methods: The study used an interpretive, qualitative approach. A total of 132 health professionals, working across four maternity units, two neonatal intensive care units and related community services, participated in 10 focus groups. Data were analysed using thematic analysis. Results: Three main themes were identified: ‘Belief and Commitment’; ‘Interpreting BFHI’ and ‘Climbing a Mountain’. Participants considered the BFHI implementation a high priority; an essential set of practices that would have positive benefits for babies and mothers both locally and globally as well as for health professionals. It was considered achievable but would take commitment and hard work to overcome the numerous challenges including a number of organisational constraints. There were, however, differing interpretations of what was required to attain BFHI accreditation with the potential that misinterpretation could hinder implementation. A model described by Greenhalgh and colleagues on adoption of innovation is drawn on to interpret the findings. Conclusion: Despite strong support for BFHI, the principles of this global strategy are interpreted differently by health professionals and further education and accurate information is required. It may be that the current processes used to disseminate and implement BFHI need to be reviewed. The findings suggest that there is a contradiction between the broad philosophical stance and best practice approach of this global strategy and the tendency for health professionals to focus on the ten steps as a set of tasks or a checklist to be accomplished. The perceived procedural approach to implementation may be contributing to lower rates of breastfeeding continuation

Structure and expression of GSL1 and GSL2 genes encoding gibberellin stimulated-like proteins in diploid and highly heterozygous tetraploid potato reveals their highly conserved and essential status

Background: GSL1 and GSL2, Gibberellin Stimulated-Like proteins (also known as Snakin-1 and Snakin-2), are cysteine-rich peptides from potato (Solanum tuberosum L.) with antimicrobial properties. Similar peptides in other species have been implicated in diverse biological processes and are hypothesised to play a role in several aspects of plant development, plant responses to biotic or abiotic stress through their participation in hormone crosstalk, and redox homeostasis. To help resolve the biological roles of GSL1 and GSL2 peptides we have undertaken an in depth analysis of the structure and expression of these genes in potato. Results: We have characterised the full length genes for both GSL1 (chromosome 4) and GSL2 (chromosome 1) from diploid and tetraploid potato using the reference genome sequence of potato, coupled with further next generation sequencing of four highly heterozygous tetraploid cultivars. The frequency of SNPs in GSL1 and GSL2 were very low with only one SNP every 67 and 53 nucleotides in exon regions of GSL1 and GSL2, respectively. Analysis of comprehensive RNA-seq data substantiated the role of specific promoter motifs in transcriptional control of gene expression. Expression analysis based on the frequency of next generation sequence reads established that GSL2 was expressed at a higher level than GSL1 in 30 out of 32 tissue and treatment libraries. Furthermore, both the GSL1 and GSL2 genes exhibited constitutive expression that was not up regulated in response to biotic or abiotic stresses, hormone treatments or wounding. Potato transformation with antisense knock-down expression cassettes failed to recover viable plants. Conclusions: The potato GSL1 and GSL2 genes are very highly conserved suggesting they contribute to an important biological function. The known antimicrobial activity of the GSL proteins, coupled with the FPKM analysis from RNA-seq data, implies that both genes contribute to the constitutive defence barriers in potatoes. The lethality of antisense knock-down expression of GSL1 and GSL2, coupled with the rare incidence of SNPs in these genes, suggests an essential role for this gene family. These features are consistent with the GSL protein family playing a role in several aspects of plant development in addition to plant defence against biotic stresses. © 2014 Meiyalaghan et al.; licensee BioMed Central Ltd

Repelling neoliberal world-making? How the ageing–dementia relation is reassembling the social

Growing old ‘badly’ is stigmatizing, a truism that is enrolled into contemporary agendas for the biomedicalization of ageing. Among the many discourses that emphasize ageing as the root cause of later life illnesses, dementia is currently promoted as an epidemic and such hyperbole serves to legitimate its increasing biomedicalization. The new stigma however is no longer contained to simply having dementia, it is failing to prevent it. Anti-ageing cultures of consumption, alongside a proliferation of cultural depictions of the ageing–dementia relation, seem to be refiguring dementia as a future to be worked on to eliminate it from our everyday life. The article unpacks this complexity for how the ageing–dementia relation is being reassembled in biopolitics in ways that enact it as something that can be transformed and managed. Bringing together Bauman’s theories of how cultural communities cope with the otherness of the other with theories of the rationale for the making of monsters – such as the figure of the abject older person with dementia – the article suggests that those older body-persons that personify the ageing–dementia relation, depicted in film and television for example, threaten the modes of ordering underpinning contemporary lives. This is not just because they intimate loss of mind, or because they are disruptive, but because they do not perform what it is to be ‘response-able’ and postpone frailty through managing self and risk

Computerised speech and language therapy or attention control added to usual care for people with long-term post-stroke aphasia : the Big CACTUS three-arm RCT

Background: People with aphasia may improve their communication with speech and language therapy many months/years after stroke. However, NHS speech and language therapy reduces in availability over time post stroke. Objective: This trial evaluated the clinical effectiveness and cost-effectiveness of self-managed computerised speech and language therapy to provide additional therapy. Design: A pragmatic, superiority, single-blind, parallel-group, individually randomised (stratified block randomisation, stratified by word-finding severity and site) adjunct trial. Setting: Twenty-one UK NHS speech and language therapy departments. Participants: People with post-stroke aphasia (diagnosed by a speech and language therapist) with long-standing (> 4 months) word-finding difficulties. Interventions: The groups were (1) usual care; (2) daily self-managed computerised word-finding therapy tailored by speech and language therapists and supported by volunteers/speech and language therapy assistants for 6 months plus usual care (computerised speech and language therapy); and (3) activity/attention control (completion of puzzles and receipt of telephone calls from a researcher for 6 months) plus usual care. Main outcome measures: Co-primary outcomes – change in ability to find treated words of personal relevance in a bespoke naming test (impairment) and change in functional communication in conversation rated on the activity scale of the Therapy Outcome Measures (activity) 6 months after randomisation. A key secondary outcome was participant-rated perception of communication and quality of life using the Communication Outcomes After Stroke questionnaire at 6 months. Outcomes were assessed by speech and language therapists using standardised procedures. Cost-effectiveness was estimated using treatment costs and an accessible EuroQol-5 Dimensions, five-level version, measuring quality-adjusted life-years. Results: A total of 818 patients were assessed for eligibility and 278 participants were randomised between October 2014 and August 2016. A total of 240 participants (86 usual care, 83 computerised speech and language therapy, 71 attention control) contributed to modified intention-to-treat analysis at 6 months. The mean improvements in word-finding were 1.1% (standard deviation 11.2%) for usual care, 16.4% (standard deviation 15.3%) for computerised speech and language therapy and 2.4% (standard deviation 8.8%) for attention control. Computerised speech and language therapy improved word-finding 16.2% more than usual care did (95% confidence interval 12.7% to 19.6%; p < 0.0001) and 14.4% more than attention control did (95% confidence interval 10.8% to 18.1%). Most of this effect was maintained at 12 months (n = 219); the mean differences in change in word-finding score were 12.7% (95% confidence interval 8.7% to 16.7%) higher in the computerised speech and language therapy group (n = 74) than in the usual-care group (n = 84) and 9.3% (95% confidence interval 4.8% to 13.7%) higher in the computerised speech and language therapy group than in the attention control group (n = 61). Computerised speech and language therapy did not show significant improvements on the Therapy Outcome Measures or Communication Outcomes After Stroke scale compared with usual care or attention control. Primary cost-effectiveness analysis estimated an incremental cost per participant of £732.73 (95% credible interval £674.23 to £798.05). The incremental quality-adjusted life-year gain was 0.017 for computerised speech and language therapy compared with usual care, but its direction was uncertain (95% credible interval –0.05 to 0.10), resulting in an incremental cost-effectiveness ratio of £42,686 per quality-adjusted life-year gained. For mild and moderate word-finding difficulty subgroups, incremental cost-effectiveness ratios were £22,371 and £28,898 per quality-adjusted life-year gained, respectively, for computerised speech and language therapy compared with usual care. Limitations: This trial excluded non-English-language speakers, the accessible EuroQol-5 Dimensions, five-level version, was not validated and the measurement of attention control fidelity was limited. Conclusions: Computerised speech and language therapy enabled additional self-managed speech and language therapy, contributing to significant improvement in finding personally relevant words (as specifically targeted by computerised speech and language therapy) long term post stroke. Gains did not lead to improvements in conversation or quality of life. Cost-effectiveness is uncertain owing to uncertainty around the quality-adjusted life-year gain, but computerised speech and language therapy may be more cost-effective for participants with mild and moderate word-finding difficulties. Exploring ways of helping people with aphasia to use new words in functional communication contexts is a priority. Trial registration: Current Controlled Trials ISRCTN68798818