BIEMS: A Fortran 90 Program for Calculating Bayes Factors for Inequality and Equality Constrained Models

This paper discusses a Fortran 90 program referred to as BIEMS (Bayesian inequality and equality constrained model selection) that can be used for calculating Bayes factors of multivariate normal linear models with equality and/or inequality constraints between the model parameters versus a model containing no constraints, which is referred to as the unconstrained model. The prior that is used under the unconstrained model is the conjugate expected-constrained posterior prior and the prior under the constrained model is proportional to the unconstrained prior truncated in the constrained space. This results in Bayes factors that appropriately balance between model fit and complexity for a broad class of constrained models. When the set of equality and/or inequality constraints in the model represents a hypothesis that applied researchers have in, for instance, (M)AN(C)OVA, (multivariate) regression, or repeated measurements, the obtained Bayes factor can be used to determine how much evidence is provided by the data in favor of the hypothesis in comparison to the unconstrained model. If several hypotheses are under investigation, the Bayes factors between the constrained models can be calculated using the obtained Bayes factors from BIEMS. Furthermore, posterior model probabilities of constrained models are provided which allows the user to compare the models directly with each other

Maternal attitudes and child-feeding practices: relationship with the BMI of Chilean children

<p>Abstract</p> <p>Background</p> <p>Chile has experienced the nutritional transition due to both social and economic progress. As a consequence, higher rates of overweight and obesity have been observed in children. In western countries, researchers have tried to determine pathways by which parents influence their children's eating behavior; up to now findings have been inconsistent. The objective of this study was to evaluate the cross-sectional and retrospective relationship between maternal attitudes and child-feeding practices and children's weight status in children who had been subject of an obesity prevention intervention for two years.</p> <p>Methods</p> <p>In 2006, for a cross-sectional study, a random sample of 232 children (125 girls, mean age 11.91 ± 1.56 y and 107 boys mean age 11.98 ± 1.51 y) was selected from three primary schools from a small city called Casablanca. Weight and height were determined to assess their nutritional status, using body mass index (BMI) <it>z </it>scores. Child-feeding practices and attitudes were determined cross-sectionally in 2006, using the Child Feeding Questionnaire (CFQ). To analyze the relationship between trends in weight change and child-feeding practices and attitudes, BMI <it>z </it>scores of all the 232 children in 2003 were used.</p> <p>Results</p> <p>Cross-sectionally, mothers of overweight children were significantly more concerned (P < 0.01) about their child's weight. Mothers of normal weight sons used significantly more pressure to eat (P < 0.05). Only in boys, the BMI <it>z </it>score was positively correlated with concern for child's weight (r = 0.28, P < 0.05) and negatively with pressure to eat (r = -0.21, P < 0.05). Retrospectively, the change in BMI <it>z </it>score between age 9 and 12 was positively correlated with concern for child's weight, but only in boys (r = 0.21, P < 0.05). Perceived child weight and concern for child's weight, explained 37% in boys and 45% in girls of the variance in BMI <it>z </it>score at age 12.</p> <p>Conclusion</p> <p>Mothers of overweight children were more concerned with their children's weight; this indicated the Western negative attitude towards childhood overweight. None of the child-feeding practices were significantly correlated with a change in BMI <it>z </it>score.</p

A review of readiness assessments for mining projects

The objective of this paper is to describe the research followed in creating a generalized, readiness assessment tool for mining projects. We start by highlighting the need for the assessment tool and then progress towards explaining the methodology followed during the study. The selection and finalization of the list of elements, sections, and categories that make up the unweighted values are described, followed by a summary of the weighting process applied. The outcome of this process is a weighted readiness assessment tool for mining project studies. The main benefits of the tool are that it will guide decision-makers and project managers through the definition phases of the project and improve the likelihood of project success.https://journals.co.za/journal/saimmam2023Graduate School of Technology Management (GSTM

Towards a generalizable project readiness assessment methodology for the mining industry

The principal objective of this investigation was to conduct a thorough literature review on the status of project readiness mechanisms, tools, techniques, and frameworks for mining projects. The review aimed at identifying common readiness evaluation criteria as well as potential shortcomings that prevent the establishment of a generalizable project readiness index. The literature review included a general overview of capital project performances and the importance of project readiness assessments to improve project delivery success. The study then progressed towards literature involving mining projects and how this differs from infrastructure and industrial project assessments. The paper concludes by summarizing the current state of mining project readiness assessments, the unique and differentiating factors to be considered, and suggests recommendations towards the development of generalizable readiness assessment criteria for mining projects.https://journals.co.za/journal/saimmam2023Mining Engineerin

Proposed minimum information guideline for kidney disease—research and clinical data reporting: a cross-sectional study

Objective This project aimed to develop and propose a standardised reporting guideline for kidney disease research and clinical data reporting, in order to improve kidney disease data quality and integrity, and combat challenges associated with the management and challenges of ‘Big Data’. Methods A list of recommendations was proposed for the reporting guideline based on the systematic review and consolidation of previously published data collection and reporting standards, including PhenX measures and Minimal Information about a Proteomics Experiment (MIAPE). Thereafter, these recommendations were reviewed by domain-specialists using an online survey, developed in Research Electronic Data Capture (REDCap). Following interpretation and consolidation of the survey results, the recommendations were mapped to existing ontologies using Zooma, Ontology Lookup Service and the Bioportal search engine. Additionally, an associated eXtensible Markup Language schema was created for the REDCap implementation to increase user friendliness and adoption. Results The online survey was completed by 53 respondents; the majority of respondents were dual clinician-researchers (57%), based in Australia (35%), Africa (33%) and North America (22%). Data elements within the reporting standard were identified as participant-level, study-level and experiment-level information, further subdivided into essential or optional information. Conclusion The reporting guideline is readily employable for kidney disease research projects, and also adaptable for clinical utility. The adoption of the reporting guideline in kidney disease research can increase data quality and the value for long-term preservation, ensuring researchers gain the maximum benefit from their collected and generated data. This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial

Predicted Pharmacokinetic Interactions Between Hormonal Contraception and Single or Intermittently Dosed Rifampicin

The scale-up of rifampicin-based prevention regimens is an essential part of the global leprosy strategy. Daily rifampicin may reduce the effectiveness of the oral contraceptive pill (OCP), but little is known about the effects of rifampicin at the less frequent dosing intervals used for leprosy prophylaxis. As many women of reproductive age rely on OCP for family planning, evaluating the interaction with less-than-daily rifampicin regimens would enhance the scalability and acceptability of leprosy prophylaxis. Using a semi-mechanistic pharmacokinetic model of rifampicin induction, we simulated predicted changes in OCP clearance when coadministered with varying rifampicin dosing schedules. Rifampicin given as a single dose (600 or 1200 mg) or 600 mg every 4 weeks was not predicted to result in a clinically relevant interaction with OCP, defined as a &gt;25% increase in clearance. Simulations of daily rifampicin were predicted to increase OCP clearance within the range of observed changes previously reported in the literature. Therefore, our findings suggest that OCP efficacy will be maintained when coadministered with rifampicin-based leprosy prophylaxis regimens of 600 mg once, 1200 mg once, and 600 mg every 4 weeks. This work provides reassurance to stakeholders that leprosy prophylaxis can be used with OCP without any additional recommendations for contraception prevention.</p

Self-Reported Systemic Sclerosis-Related Symptoms Are More Prevalent in Subjects with Raynaud's Phenomenon in the Lifelines Population:Focus on Pulmonary Complications

Puffy fingers and Raynaud's phenomenon (RP) are important clinical predictors of the development of systemic sclerosis (SSc). We aim to assess the prevalence of SSc-related symptoms, explore pulmonary symptoms, and test the usefulness of skin autofluorescence (SAF) as a non-invasive marker for Advanced Glycation Endproducts (AGEs). Subjects from the Lifelines Cohort Study with known connective tissue disease (CTD) were excluded. Patient characteristics, SAF, self-reported pulmonary symptoms, and spirometry were obtained. Subjects ( n = 73,948) were categorized into definite RP (5.3%) with and without SSc-related symptoms and non-RP. Prevalence of at least one potential SSc-related symptom (other than RP) was 8.7%; 23.5% in subjects with RP and 7.1% without RP ( p &lt; 0.001). Subjects with RP and additional SSc-related symptoms more frequently reported dyspnea at rest, dyspnea after exertion, and self-reported pulmonary fibrosis, and had the lowest mean forced vital capacity compared to the other groups (RP without SSc-related symptoms and no RP, both p &lt; 0.001). In multivariate regression, dyspnea at rest/on exertion remained associated with an increased risk of SSc-related symptoms in subjects with RP (both p &lt; 0.001). SAF was higher in subjects with RP and SSc-related symptoms compared to the other groups ( p &lt; 0.001), but this difference was not significant after correction for potential confounders. The prevalence of SSc-related symptoms was approximately three-fold higher in subjects with RP. Pulmonary symptoms are more prevalent in subjects with RP who also reported additional potential SSc-related symptoms. This might suggest that (suspected) early SSc develops more insidiously than acknowledged. According to this study, SAF is no marker for early detection of SSc. </p

Pragmatic cluster-randomized trial of home-based preventive treatment for TB in Ethiopia and South Africa (CHIP-TB)

Background Each year, 1 million children develop TB resulting in over 200,000 child deaths. TB preventive treatment (TPT) is highly effective in preventing TB but remains poorly implemented for household child contacts. Home-based child contact management and TPT services may improve access to care. In this study, we aim to evaluate the effectiveness and cost-effectiveness of home-based contact management with TPT initiation in two TB high-burden African countries, Ethiopia and South Africa. Methods This pragmatic cluster randomized trial compares home-based versus facility-based care delivery models for contact management. Thirty-six clinics with decentralized TB services (18 in Ethiopia and 18 in South Africa) were randomized in a 1:1 ratio to conduct either home-based or facility-based contact management. The study will attempt to enroll all eligible close child contacts of infectious drug-sensitive TB index patients diagnosed and treated for TB by one of the study clinics. Child TB contact management, including contact tracing, child evaluation, and TPT initiation and follow-up, will take place in the childs home for the intervention arm and at the clinic for the control arm. The primary outcome is the cluster-level ratio of the number of household child contacts less than 15 years of age in Ethiopia and less than 5 years of age in South Africa initiated on TPT per index patient, comparing the intervention to the control arm. Secondary outcomes include child contact identification and the TB prevention continuum of care. Other implementation outcomes include acceptability, feasibility, fidelity, cost, and cost-effectiveness of the intervention. Discussion This implementation research trial will determine whether home-based contact management identifies and initiates more household child contacts on TPT than facility-based contact management.This project is funded by UNITAID and IMPAACT4TB. NSA salary is supported by the National Institutes of Health (K23HD096973). The Aurum Institute, 29 Queens Rd, Parktown, Johannesburg, 2194, South Africa is the sponsor of the trial. The funder had no role in the writing of this manuscript after concept approva

Quantifying Vegetation Biophysical Variables from Imaging Spectroscopy Data: A Review on Retrieval Methods

An unprecedented spectroscopic data stream will soon become available with forthcoming Earth-observing satellite missions equipped with imaging spectroradiometers. This data stream will open up a vast array of opportunities to quantify a diversity of biochemical and structural vegetation properties. The processing requirements for such large data streams require reliable retrieval techniques enabling the spatiotemporally explicit quantification of biophysical variables. With the aim of preparing for this new era of Earth observation, this review summarizes the state-of-the-art retrieval methods that have been applied in experimental imaging spectroscopy studies inferring all kinds of vegetation biophysical variables. Identified retrieval methods are categorized into: (1) parametric regression, including vegetation indices, shape indices and spectral transformations; (2) nonparametric regression, including linear and nonlinear machine learning regression algorithms; (3) physically based, including inversion of radiative transfer models (RTMs) using numerical optimization and look-up table approaches; and (4) hybrid regression methods, which combine RTM simulations with machine learning regression methods. For each of these categories, an overview of widely applied methods with application to mapping vegetation properties is given. In view of processing imaging spectroscopy data, a critical aspect involves the challenge of dealing with spectral multicollinearity. The ability to provide robust estimates, retrieval uncertainties and acceptable retrieval processing speed are other important aspects in view of operational processing. Recommendations towards new-generation spectroscopy-based processing chains for operational production of biophysical variables are given

Tuberculosis control among immigrants

The results in this thesis suggest a revision of the Dutch immigrant TB screening program. LTBI screening at entry rather than screening for TB only is expected to improve the cost-effectiveness. We provided evidence that the QFT-GIT could be a useful tool in this respect, but also the TST could perform well. An implementation study is needed to gain more insight in the preferred screening and preventive treatment strategy. The effectiveness of contact investigations involving immigrant contacts should be improved by updating guidelines with explicit recommendations and a comprehensive dissemination strategy, and by training PHNs. Future developments could further target these TB control activities and could contribute to a decline in TB incidence among immigrants