Bayesian astrostatistics: a backward look to the future

This perspective chapter briefly surveys: (1) past growth in the use of Bayesian methods in astrophysics; (2) current misconceptions about both frequentist and Bayesian statistical inference that hinder wider adoption of Bayesian methods by astronomers; and (3) multilevel (hierarchical) Bayesian modeling as a major future direction for research in Bayesian astrostatistics, exemplified in part by presentations at the first ISI invited session on astrostatistics, commemorated in this volume. It closes with an intentionally provocative recommendation for astronomical survey data reporting, motivated by the multilevel Bayesian perspective on modeling cosmic populations: that astronomers cease producing catalogs of estimated fluxes and other source properties from surveys. Instead, summaries of likelihood functions (or marginal likelihood functions) for source properties should be reported (not posterior probability density functions), including nontrivial summaries (not simply upper limits) for candidate objects that do not pass traditional detection thresholds.Comment: 27 pp, 4 figures. A lightly revised version of a chapter in "Astrostatistical Challenges for the New Astronomy" (Joseph M. Hilbe, ed., Springer, New York, forthcoming in 2012), the inaugural volume for the Springer Series in Astrostatistics. Version 2 has minor clarifications and an additional referenc

The leadership component of Kelly’s Mobilisation Theory : contribution, tensions, limitations and further development

This reassessment of Kelly’s analysis of the relationship of activist leadership to collective action within the overall jigsaw of mobilisation theory draws on social movement literature, studies by industrial relations scholars utilising aspects of Kelly’s approach – including this author’s own work – and related research on union leadership within collective mobilisation. In the process, it identifies and celebrates how Kelly’s work, whilst contributing a distinct and substantive actor-related approach, recognised that leadership is one ingredient amongst other factors, including important structural opportunities and constraints. It considers three potential ambiguities/tensions within Kelly’s conceptualisation of leadership related to the social construction of workers’ interests, spontaneity of workers’ action and the ‘leader/follower’ interplay. The review also identifies two important limitations, related to the union member/bureaucracy dynamic and the role of left-wing political leadership, and concludes by signalling different forms of leadership relationships on which further refinement and development would be fruitful

Empirical study of correlated survival times for recurrent events with proportional hazards margins and the effect of correlation and censoring.

Background: In longitudinal studies where subjects experience recurrent incidents over a period of time, such as respiratory infections, fever or diarrhea, statistical methods are required to take into account the within-subject correlation. Methods: For repeated events data with censored failure, the independent increment (AG), marginal (WLW) and conditional (PWP) models are three multiple failure models that generalize Cox"s proportional hazard model. In this paper, we revise the efficiency, accuracy and robustness of all three models under simulated scenarios with varying degrees of within-subject correlation, censoring levels, maximum number of possible recurrences and sample size. We also study the methods performance on a real dataset from a cohort study with bronchial obstruction. Results: We find substantial differences between methods and there is not an optimal method. AG and PWP seem to be preferable to WLW for low correlation levels but the situation reverts for high correlations. Conclusions: All methods are stable in front of censoring, worsen with increasing recurrence levels and share a bias problem which, among other consequences, makes asymptotic normal confidence intervals not fully reliable, although they are well developed theoretically

The Perceptions on Male Circumcision as a Preventive Measure Against HIV Infection and Considerations in Scaling up of the Services: A Qualitative Study Among Police Officers in Dar es Salaam, Tanzania.

\ud In recent randomized controlled trials, male circumcision has been proven to complement the available biomedical interventions in decreasing HIV transmission from infected women to uninfected men. Consequently, Tanzania is striving to scale-up safe medical male circumcision to reduce HIV transmission. However, there is a need to investigate the perceptions of male circumcision in Tanzania using specific populations. The purpose of the present study was to assess the perceptions of male circumcision in a cohort of police officers that also served as a source of volunteers for a phase I/II HIV vaccine (HIVIS-03) trial in Dar es Salaam, Tanzania. In-depth interviews with 24 men and 10 women were conducted. Content analysis informed by the socio-ecological model was used to analyze the data. Informants perceived male circumcision as a health-promoting practice that may prevent HIV transmission and other sexually transmitted infections. They reported male circumcision promotes sexual pleasure, confidence and hygiene or sexual cleanliness. They added that it is a religious ritual and a cultural practice that enhances the recognition of manhood in the community. However, informants were concerned about the cost involved in male circumcision and cleanliness of instruments used in medical and traditional male circumcision. They also expressed confusion about the shame of undergoing circumcision at an advanced age and pain that could emanate after circumcision. The participants advocated for health policies that promote medical male circumcision at childhood, specifically along with the vaccination program. The perceived benefit of male circumcision as a preventive strategy to HIV and other sexually transmitted infections is important. However, there is a need to ensure that male circumcision is conducted under hygienic conditions. Integrating male circumcision service in the routine childhood vaccination program may increase its coverage at early childhood. The findings from this investigation provide contextual understanding that may assist in scaling-up male circumcision in Tanzania.\u

Additive and multiplicative hazards modeling for recurrent event data analysis

<p>Abstract</p> <p>Background</p> <p>Sequentially ordered multivariate failure time or recurrent event duration data are commonly observed in biomedical longitudinal studies. In general, standard hazard regression methods cannot be applied because of correlation between recurrent failure times within a subject and induced dependent censoring. Multiplicative and additive hazards models provide the two principal frameworks for studying the association between risk factors and recurrent event durations for the analysis of multivariate failure time data.</p> <p>Methods</p> <p>Using emergency department visits data, we illustrated and compared the additive and multiplicative hazards models for analysis of recurrent event durations under (i) a varying baseline with a common coefficient effect and (ii) a varying baseline with an order-specific coefficient effect.</p> <p>Results</p> <p>The analysis showed that both additive and multiplicative hazards models, with varying baseline and common coefficient effects, gave similar results with regard to covariates selected to remain in the model of our real dataset. The confidence intervals of the multiplicative hazards model were wider than the additive hazards model for each of the recurrent events. In addition, in both models, the confidence interval gets wider as the revisit order increased because the risk set decreased as the order of visit increased.</p> <p>Conclusions</p> <p>Due to the frequency of multiple failure times or recurrent event duration data in clinical and epidemiologic studies, the multiplicative and additive hazards models are widely applicable and present different information. Hence, it seems desirable to use them, not as alternatives to each other, but together as complementary methods, to provide a more comprehensive understanding of data.</p

Prediction of peptide and protein propensity for amyloid formation

Understanding which peptides and proteins have the potential to undergo amyloid formation and what driving forces are responsible for amyloid-like fiber formation and stabilization remains limited. This is mainly because proteins that can undergo structural changes, which lead to amyloid formation, are quite diverse and share no obvious sequence or structural homology, despite the structural similarity found in the fibrils. To address these issues, a novel approach based on recursive feature selection and feed-forward neural networks was undertaken to identify key features highly correlated with the self-assembly problem. This approach allowed the identification of seven physicochemical and biochemical properties of the amino acids highly associated with the self-assembly of peptides and proteins into amyloid-like fibrils (normalized frequency of β-sheet, normalized frequency of β-sheet from LG, weights for β-sheet at the window position of 1, isoelectric point, atom-based hydrophobic moment, helix termination parameter at position j+1 and ΔGº values for peptides extrapolated in 0 M urea). Moreover, these features enabled the development of a new predictor (available at http://cran.r-project.org/web/packages/appnn/index.html) capable of accurately and reliably predicting the amyloidogenic propensity from the polypeptide sequence alone with a prediction accuracy of 84.9 % against an external validation dataset of sequences with experimental in vitro, evidence of amyloid formation

Multiscale Systems, Homogenization, and Rough Paths:VAR75 2016: Probability and Analysis in Interacting Physical Systems

In recent years, substantial progress was made towards understanding convergence of fast-slow deterministic systems to stochastic differential equations. In contrast to more classical approaches, the assumptions on the fast flow are very mild. We survey the origins of this theory and then revisit and improve the analysis of Kelly-Melbourne [Ann. Probab. Volume 44, Number 1 (2016), 479-520], taking into account recent progress in $p$-variation and c\`adl\`ag rough path theory.Comment: 27 pages. Minor corrections. To appear in Proceedings of the Conference in Honor of the 75th Birthday of S.R.S. Varadha

A typhoid fever outbreak in a slum of South Dumdum municipality, West Bengal, India, 2007: Evidence for foodborne and waterborne transmission

<p>Abstract</p> <p>Background</p> <p>In April 2007, a slum of South Dumdum municipality, West Bengal reported an increase in fever cases. We investigated to identify the agent, the source and to propose recommendations.</p> <p>Methods</p> <p>We defined a suspected case of typhoid fever as occurrence of fever for ≥ one week among residents of ward 1 of South Dumdum during February – May 2007. We searched for suspected cases in health care facilities and collected blood specimens. We described the outbreak by time, place and person. We compared probable cases (Widal positive >= 1:80) with neighbourhood-matched controls. We assessed the environment and collected water specimens.</p> <p>Results</p> <p>We identified 103 suspected cases (Attack rate: 74/10,000, highest among 5–14 years old group, no deaths). Salmonella (enterica) Typhi was isolated from one of four blood specimens and 65 of 103 sera were >= 1:80 Widal positive. The outbreak started on 13 February, peaked twice during the last week of March and second week of April and lasted till 27 April. Suspected cases clustered around three public taps. Among 65 probable cases and 65 controls, eating milk products from a sweet shop (Matched odds ratio [MOR]: 6.2, 95% confidence interval [CI]: 2.4–16, population attributable fraction [PAF]: 53%) and drinking piped water (MOR: 7.3, 95% CI: 2.5–21, PAF-52%) were associated with illness. The sweet shop food handler suffered from typhoid in January. The pipelines of intermittent non-chlorinated water supply ran next to an open drain connected with sewerage system and water specimens showed faecal contamination.</p> <p>Conclusion</p> <p>The investigation suggested that an initial foodborne outbreak of typhoid led to the contamination of the water supply resulting in a secondary, waterborne wave. We educated the food handler, repaired the pipelines and ensured chlorination of the water.</p

Exploring the relationship between environmental enteric dysfunction and oral vaccine responses.

Oral vaccines significantly underperform in low-income countries. One possible contributory factor is environmental enteric dysfunction (EED), a subclinical disorder of small intestinal structure and function among children living in poverty. Here, we review studies describing oral vaccine responses and EED. We identified eight studies evaluating EED and oral vaccine responses. There was substantial heterogeneity in study design and few consistent trends emerged. Four studies reported a negative association between EED and oral vaccine responses; two showed no significant association; and two described a positive correlation. Current evidence is therefore insufficient to determine whether EED contributes to oral vaccine underperformance. We identify roadblocks in the field and future research needs, including carefully designed studies those can investigate this hypothesis further.JAC (Grant 201293/Z/16/Z) and AJP (Grant 108065/Z/15/Z) are funded by the Wellcome Trust. JAC and AJP also received funding from DfID via the Sanitation & Hygiene Applied Research for Equity (SHARE) Consortium