Smoothing and mean-covariance estimation of functional data with a Bayesian hierarchical model

Functional data, with basic observational units being functions (e.g., curves, surfaces) varying over a continuum, are frequently encountered in various applications. While many statistical tools have been developed for functional data analysis, the issue of smoothing all functional observations simultaneously is less studied. Existing methods often focus on smoothing each individual function separately, at the risk of removing important systematic patterns common across functions. We propose a nonparametric Bayesian approach to smooth all functional observations simultaneously and nonparametrically. In the proposed approach, we assume that the functional observations are independent Gaussian processes subject to a common level of measurement errors, enabling the borrowing of strength across all observations. Unlike most Gaussian process regression models that rely on pre-specified structures for the covariance kernel, we adopt a hierarchical framework by assuming a Gaussian process prior for the mean function and an Inverse-Wishart process prior for the covariance function. These prior assumptions induce an automatic mean-covariance estimation in the posterior inference in addition to the simultaneous smoothing of all observations. Such a hierarchical framework is flexible enough to incorporate functional data with different characteristics, including data measured on either common or uncommon grids, and data with either stationary or nonstationary covariance structures. Simulations and real data analysis demonstrate that, in comparison with alternative methods, the proposed Bayesian approach achieves better smoothing accuracy and comparable mean-covariance estimation results. Furthermore, it can successfully retain the systematic patterns in the functional observations that are usually neglected by the existing functional data analyses based on individual-curve smoothing.Comment: Submitted to Bayesian Analysi

Semi-automatic selection of summary statistics for ABC model choice

A central statistical goal is to choose between alternative explanatory models of data. In many modern applications, such as population genetics, it is not possible to apply standard methods based on evaluating the likelihood functions of the models, as these are numerically intractable. Approximate Bayesian computation (ABC) is a commonly used alternative for such situations. ABC simulates data x for many parameter values under each model, which is compared to the observed data xobs. More weight is placed on models under which S(x) is close to S(xobs), where S maps data to a vector of summary statistics. Previous work has shown the choice of S is crucial to the efficiency and accuracy of ABC. This paper provides a method to select good summary statistics for model choice. It uses a preliminary step, simulating many x values from all models and fitting regressions to this with the model as response. The resulting model weight estimators are used as S in an ABC analysis. Theoretical results are given to justify this as approximating low dimensional sufficient statistics. A substantive application is presented: choosing between competing coalescent models of demographic growth for Campylobacter jejuni in New Zealand using multi-locus sequence typing data

Using retracted journal articles in psychology to understand research misconduct in the social sciences: What is to be done?

This paper explores the nature and impact of research misconduct in psychology by analyzing 160 articles that were retracted from prominent scholarly journals between 1998 and 2017. We compare findings with recent studies of retracted papers in economics, and business and management, to profile practices that are likely to be problematic in cognate social science disciplines. In psychology, the principal reason for retraction was data fabrication. Retractions took longer to make, and generally were from higher ranked and more prestigious journals, than in the two cognate disciplines. We recommend that journal editors should be more forthcoming in the reasons they provide for article retractions. We also recommend that the discipline of psychology gives a greater priority to the publication of replication studies; initiates a debate about how to respond to failed replications; adopts a more critical attitude to the importance of attaining statistical significance; discourages p-hacking and Hypothesizing After Results are Known (HARKing); assesses the long-term effects of pre-registering research; and supports stronger procedures to attest to the authenticity of data in research papers. Our contribution locates these issues in the context of a growing crisis of confidence in the value of social science research. We also challenge individual researchers to reassert the primacy of disinterested academic inquiry above pressures that can lead to an erosion of scholarly integrity

Effect of dusts on tomato production

The phytotoxicity of bauxite, cement flue, mud lake, alumina and kaolin dusts were examined on tomatoes. Mud lake white dust caused severe leaf scorch, affected plant growth and resulted in no harvestable yield. Flue dust applied daily depressed market yield of fruit from 64 t ha to 42 t ha. Flue dust applied at 3.1 t ha had no effect. There was no phytotoxic effect from bauxite, alumina or kaolin

A BAC transgenic analysis of the Mrf4/Myf5 locus reveals interdigitated elements that control activation and maintenance of gene expression during muscle development

The muscle-specific transcription factors Myf5 and Mrf4 are two of the four myogenic regulatory factors involved in the transcriptional cascade responsible for skeletal myogenesis in the vertebrate embryo. Myf5 is the first of these four genes to be expressed in the mouse. We have previously described discrete enhancers that drive Myf5 expression in epaxial and hypaxial somites, branchial arches and central nervous system, and argued that additional elements are required for proper expression (Summerbell, D., Ashby, P.R., Coutelle, O., Cox, D., Yee, S.P. and Rigby, P.W.J. (2000) Development 127, 3745-3757). We have now investigated the transcriptional regulation of both Myf5 and Mrf4 using bacterial artificial chromosome transgenesis. We show that a clone containing Myf5 and 140 kb of upstream sequences is sufficient to recapitulate the known expression patterns of both genes. Our results confirm and reinforce the conclusion of our earlier studies, that Myf5 expression is regulated differently in each of a considerable number of populations of muscle progenitors, and they begin to illuminate the evolutionary origins of this complex regulation. We further show that separate elements are involved in the activation and maintenance of expression in the various precursor populations, reflecting the diversity of the signals that control myogenesis. Mrf4 expression requires at least four elements, one of which may be shared with Myf5, providing a possible explanation for the linkage of these genes throughout vertebrate phylogeny. Further complexity is revealed by the demonstration that elements which control Mrf4 and Myf5 are embedded in an unrelated neighbouring gene.J. J. C. was supported by a Research Training Fellowship from the Medical Research Council (UK), which also paid for this work.Peer reviewe

Light-Directed Ranging System Implementing Single Camera System for Telerobotics Applications

A laser-directed ranging system has utility for use in various fields, such as telerobotics applications and other applications involving physically handicapped individuals. The ranging system includes a single video camera and a directional light source such as a laser mounted on a camera platform, and a remotely positioned operator. In one embodiment, the position of the camera platform is controlled by three servo motors to orient the roll axis, pitch axis and yaw axis of the video cameras, based upon an operator input such as head motion. The laser is offset vertically and horizontally from the camera, and the laser/camera platform is directed by the user to point the laser and the camera toward a target device. The image produced by the video camera is processed to eliminate all background images except for the spot created by the laser. This processing is performed by creating a digital image of the target prior to illumination by the laser, and then eliminating common pixels from the subsequent digital image which includes the laser spot. A reference point is defined at a point in the video frame, which may be located outside of the image area of the camera. The disparity between the digital image of the laser spot and the reference point is calculated for use in a ranging analysis to determine range to the target

Vaginal Microbicide Preferences Among Midwestern Urban Adolescent Women

Purpose The purpose of this study was to assess adolescent women's preferences for specific microbicide characteristics including pregnancy prevention, timing of application, potential for side effects, and whether it targeted human immunodeficiency virus (HIV) or other sexually transmitted infections (STI). Potential differences in microbicide preferences by adolescent age group and behavioral patterns including engaging in sexual intercourse and use of hormonal contraception were examined, as it was hypothesized that as adolescents progress into adulthood and gain sexual experience their preferences in microbicide characteristics may shift. Method Adolescent and young women (N = 405, 56.0% African American; 24.0% Euro-American) between the ages of 14 and 20 (mean = 17.0, SD = 1.8) were recruited from urban community-based clinics. Video-Audio Computer-Assisted Self-Interviews were conducted with the young women, during which they were asked about their preferences regarding the characteristics of hypothetical vaginal microbicides. Conjoint analysis was utilized to determine adolescent women's relative preferences for each microbicide characteristic and intent-to-purchase microbicides based upon a combination of the selected properties. Results Overall, the results suggest adolescent and young women had an ordered preference for a microbicide with (1) no side effects, (2) pregnancy prevention, (3) postcoital application, and (4) protection against HIV. Age and behavioral group conjoint analyses resulted in the same pattern of preferences as those reported for the entire group. However, women having sex and not using hormonal contraception had a stronger preference for postcoital application. Conclusion The findings suggest that young women's ratings of microbicides were sensitive to characteristics such as side effects, pregnancy prevention, and timing of application and should be considered in microbicide development. The conjoint analysis approach is useful in understanding microbicide preferences, and should be utilized with other populations to assess preferences for specific microbicide characteristics

Standard methods for Apis mellifera anatomy and dissection

An understanding of the anatomy and functions of internal and external structures is fundamental to many studies on the honey bee Apis mellifera. Similarly, proficiency in dissection techniques is vital for many more complex procedures. In this paper, which is a prelude to the other papers of the COLOSS BEEBOOK, we outline basic honey bee anatomy and basic dissection techniques