Biostatistic

A large-scale outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) occurred in Shanghai, China, in early December 2022. To study the incidence and characteristics of otitis media with effusion (OME) complicating SARS-CoV-2, we collected 267 middle ear effusion (MEE) samples and 172 nasopharyngeal (NP) swabs from patients. The SARS-CoV-2 virus was detected by RT-PCR targeting. The SARS-CoV-2 virus, angiotensin-converting enzyme 2 (ACE2), and transmembrane serine protease 2 (TMPRSS2) expression in human samples was examined via immunofluorescence...

A genome, composed of a precisely ordered sequence of four nucleotides (ATCG), encompasses a multitude of specific genome features like AAA motif. Mutations occurring within a genome disrupt the sequential order and composition of these features, thereby influencing the evolutionary trajectories and yielding variants. The evolutionary relatedness between a variant and its ancestor can be estimated by assessing evolutionary distances across a spectrum of genome features. This study develops a novel, alignment-free algorithm that considers both the sequential order and composition of genome features, enabling computation of the Fréchet distance (Fr) across multiple genome features to quantify the evolutionary status of a variant...

BACKGROUND: Doctoral recipients of public health play pivotal roles in the support and leadership of the public health industry and academic research. We conducted this study to assess and track the long-term career outcomes of public health PhDs (PHPhD). METHODS: We linked data from the Survey of Doctorate Recipients to the Survey of Earned Doctorates and tracked the long-term career outcomes and job placements of PHPhD from 2001 to 2017. Logistic regression and ordinary least squares regression models were used to model career outcomes and behavioral characteristics...

Genetic association studies for brain connectivity phenotypes have gained prominence due to advances in noninvasive imaging techniques and quantitative genetics. Brain connectivity traits, characterized by network configurations and unique biological structures, present distinct challenges compared to other quantitative phenotypes. Furthermore, the presence of sample relatedness in the most imaging genetics studies limits the feasibility of adopting existing network-response modeling. In this article, we fill this gap by proposing a Bayesian network-response mixed-effect model that considers a network-variate phenotype and incorporates population structures including pedigrees and unknown sample relatedness...

Biostatistics is foundational to public health research and Canada has a history of high impact contributions both in seminal methodological advances and in the rigorous application of methods for the design or analysis of public health studies. In this article, we provide a brief and personal review of selected contributions from Canadian biostatisticians to fields such as survival and life history analysis, sampling, clinical trial methodology, environmental risk assessment, infectious disease epidemiology, and early work on prediction...

Linear and generalized linear scalar-on-function modeling have been commonly used to understand the relationship between a scalar response variable (e.g. continuous, binary outcomes) and functional predictors. Such techniques are sensitive to model misspecification when the relationship between the response variable and the functional predictors is complex. On the other hand, support vector machines (SVMs) are among the most robust prediction models but do not take account of the high correlations between repeated measurements and cannot be used for irregular data...

INTRODUCTION: Skills in critical appraisal of medical literature are compulsory to achieve in medical practice. This step is the third step of the evidence-based medicine process whose main role is to bridge a gap between scientific evidence and practice. Acquiring skills in critical appraisal of the literature has been reported to be challenging for the trainees with different limits according to their levels, backgrounds or specialties. AIM: To assess the limits and factors influencing the practice of appraising literature of different students from the same faculty...

We are currently experiencing a period of rapid advancement in various areas of science and technology. The integration of high throughput 'omics' techniques with advanced biostatistics, and the help of artificial intelligence, is significantly impacting our understanding of sperm biology. These advances will have an appreciable impact on the practice of reproductive medicine in horses. This article provides a brief overview of recent advances in the field of spermatology and how they are changing assessment of sperm quality...

Mendelian randomization (MR) analysis is increasingly popular for testing the causal effect of exposures on disease outcomes using data from genome-wide association studies. In some settings, the underlying exposure, such as systematic inflammation, may not be directly observable, but measurements can be available on multiple biomarkers or other types of traits that are co-regulated by the exposure. We propose a method for MR analysis on latent exposures (MRLE), which tests the significance for, and the direction of, the effect of a latent exposure by leveraging information from multiple related traits...

Observational studies have determined numerous correlations between sequence-based gut microbiota data and human mental traits. However, these associations are often inconsistent across studies. This inconsistency is one of the reasons that mechanistic validation studies of the observed correlations are lagging, making it difficult to establish causal associations. The absence of consistent study findings may partially be due to the lack of clear guidelines for identifying confounders of relations between complex microbial communities and mental conditions...

BACKGROUND: Complementary to traditional biostatistics, the integration of untargeted urine metabolomic profiling with Machine Learning (ML) has the potential to unveil metabolic profiles crucial for understanding diseases. However, the application of this approach in autism remains underexplored. Our objective was to delve into the metabolic profiles of autism utilizing a comprehensive untargeted metabolomics platform coupled with ML. METHODS: Untargeted metabolomics quantification (UHPLC/Q-TOF-MS) was performed for urine analysis...

Over 400 different types of post-translational modifications (PTMs) have been reported and over 200 various types of PTMs have been discovered using mass spectrometry (MS)-based proteomics. MS-based proteomics has proven to be a powerful method capable of global PTM mapping with the identification of modified proteins/peptides, the localization of PTM sites and PTM quantitation. PTMs play regulatory roles in protein functions, activities and interactions in various heart related diseases, such as ischemia/reperfusion injury, cardiomyopathy and heart failure...

Breath analysis offers tremendous potential for diagnostic approaches, since it allows for easy and non-invasive sample collection. "Breathomics" as one major research field comprehensively analyses the metabolomic profile of exhaled breath providing insights into various (patho)physiological processes. Recent research, however, primarily focuses on volatile compounds. This is the first study that evaluates the non-volatile organic compounds (nVOCs) in breath following an untargeted metabolomic approach. Herein, we developed an innovative method utilizing a filter-based device for metabolite extraction...

Objectives: Regulatory bodies, health technology assessment agencies, payers, physicians, and other decision-makers increasingly recognize the importance of real-world evidence (RWE) to provide important and relevant insights on treatment patterns, burden/cost of illness, product safety, and long-term and comparative effectiveness. However, RWE generation requires a careful approach to ensure rigorous analysis and interpretation. There are limited examples of comprehensive methodology for the generation of RWE on patients who have undergone neuromodulation for drug-resistant epilepsy (DRE)...

Dynamic models have been successfully used in producing estimates of HIV epidemics at the national level due to their epidemiological nature and their ability to estimate prevalence, incidence, and mortality rates simultaneously. Recently, HIV interventions and policies have required more information at sub-national levels to support local planning, decision-making and resource allocation. Unfortunately, many areas lack sufficient data for deriving stable and reliable results, and this is a critical technical barrier to more stratified estimates...

OBJECTIVES: Intraoperative fluorescence imaging (FI) of head and neck squamous cell carcinoma (HNSCC) is performed to identify tumour-positive surgical margins, currently using epidermal growth factor receptor (EGFR) as imaging target. EGFR, not exclusively present in HNSCC, may result in non-specific tracer accumulation in normal tissues. We aimed to identify new potential HNSCC FI targets. MATERIALS AND METHODS: Publicly available transcriptomic data were collected, and a biostatistical method (Transcriptional Adaptation to Copy Number Alterations (TACNA)-profiling) was applied...

BACKGROUND: Completing internal medicine specialty training in Israel involves passing the Israel National Internal Medicine Exam (Shlav Aleph), a challenging multiple-choice test. multiple-choice test. Chat generative pre-trained transformer (ChatGPT) 3.5, a language model, is increasingly used for exam preparation. OBJECTIVES: To assess the ability of ChatGPT 3.5 to pass the Israel National Internal Medicine Exam in Hebrew. METHODS: Using the 2023 Shlav Aleph exam questions, ChatGPT received prompts in Hebrew...

Elselijn Kingma argues that Christopher Boorse's biostatistical theory (the BST) does not show how the reference classes it uses are objective and naturalistic. Recently, philosophers of medicine have attempted to rebut Kingma's concerns. I argue that these rebuttals are theoretically unconvincing, and that there are clear examples of physicians adjusting their reference classes according to their prior knowledge of health and disease. I focus on the use of age-adjusted reference classes to diagnose low bone mineral density in children...

Modern longitudinal studies collect multiple outcomes as the primary endpoints to understand the complex dynamics of the diseases. Oftentimes, especially in clinical trials, the joint variation among the multidimensional responses plays a significant role in assessing the differential characteristics between two or more groups, rather than drawing inferences based on a single outcome. We develop a projection-based two-sample significance test to identify the population-level difference between the multivariate profiles observed under a sparse longitudinal design...

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