The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.

For multivariate non-Gaussian involving copulas, likelihood inference is dominated by the data in the middle, and fitted models might not be very good for joint tail inference, such as assessing the strength of tail dependence. When preliminary data and likelihood analysis suggest asymmetric tail dependence, a method is proposed to improve extreme value inferences based on the joint lower and upper tails. A prior that uses previous information on tail dependence can be used in combination with the likelihood. With the combination of the prior and the likelihood (which in practice has some degree of misspecification) to obtain a tilted log-likelihood, inferences with suitably transformed parameters can be based on Bayesian computing methods or with numerical optimization of the tilted log-likelihood to obtain the posterior mode and Hessian at this mode.

The landscape of survival analysis is constantly being revolutionized to answer biomedical challenges, most recently the statistical challenge of censored covariates rather than outcomes. There are many promising strategies to tackle censored covariates, including weighting, imputation, maximum likelihood, and Bayesian methods. Still, this is a relatively fresh area of research, different from the areas of censored outcomes (i.e., survival analysis) or missing covariates. In this review, we discuss the unique statistical challenges encountered when handling censored covariates and provide an in-depth review of existing methods designed to address those challenges. We emphasize each method\'s relative strengths and weaknesses, providing recommendations to help investigators pinpoint the best approach to handling censored covariates in their data.

Mathematical models that accurately simulate the physiological systems of the human body serve as cornerstone instruments for advancing medical science and facilitating innovative clinical interventions. One application is the modeling of the subglottal tract and neck skin properties for its use in the ambulatory assessment of vocal function, by enabling non-invasive monitoring of glottal airflow via a neck surface accelerometer. For the technique to be effective, the development of an accurate building block model for the subglottal tract is required. Such a model is expected to utilize glottal volume velocity as the input parameter and yield neck skin acceleration as the corresponding output. In contrast to preceding efforts that employed frequency-domain methods, the present paper leverages system identification techniques to derive a parsimonious continuous-time model of the subglottal tract using time-domain data samples. Additionally, an examination of the model order is conducted through the application of various information criteria. Once a low-order model is successfully fitted, an inverse filter based on a Kalman smoother is utilized for the estimation of glottal volume velocity and related aerodynamic metrics, thereby constituting the most efficient execution of these estimates thus far. Anticipated reductions in computational time and complexity due to the lower order of the subglottal model hold particular relevance for real-time monitoring. Simultaneously, the methodology proves efficient in generating a spectrum of aerodynamic features essential for ambulatory vocal function assessment.

Categorical data analysis of 2 × 2 contingency tables is extremely common, not least because they provide risk difference, risk ratio, odds ratio, and log odds statistics in medical research. A χ2 test analysis is most often used, although some researchers use likelihood ratio test (LRT) analysis. Does it matter which test is used? A review of the literature, examination of the theoretical foundations, and analyses of simulations and empirical data are used by this paper to argue that only the LRT should be used when we are interested in testing whether the binomial proportions are equal. This so-called test of independence is by far the most popular, meaning the χ2 test is widely misused. By contrast, the χ2 test should be reserved for where the data appear to match too closely a particular hypothesis (e.g., the null hypothesis), where the variance is of interest, and is less than expected. Low variance can be of interest in various scenarios, particularly in investigations of data integrity. Finally, it is argued that the evidential approach provides a consistent and coherent method that avoids the difficulties posed by significance testing. The approach facilitates the calculation of appropriate log likelihood ratios to suit our research aims, whether this is to test the proportions or to test the variance. The conclusions from this paper apply to larger contingency tables, including multi-way tables.

A general consensus persists that sensory-perceptual differences in autism, such as hypersensitivities to light or sound, result from an overreliance on new (rather than prior) sensory observations. However, conflicting Bayesian accounts of autism remain unresolved as to whether such alterations are caused by more precise sensory observations (precise likelihood model) or by forming a less precise model of the sensory context (hypo-priors model). We used a decision-under-uncertainty paradigm that manipulated uncertainty in both likelihoods and priors. Contrary to model predictions we found no differences in reliance on likelihood in autistic group (AS) compared to neurotypicals (NT) and found no differences in subjective prior variance between groups. However, we found reduced context adjustment in the AS group compared to NT. Further, the AS group showed heightened variability in their relative weighting of sensory information (vs. prior) on a trial-by-trial basis. When participants were aligned on a continuum of autistic traits, we found no associations with likelihood reliance or prior variance but found an increase in likelihood precision with autistic traits. These findings together provide empirical evidence for intact priors, precise likelihood, reduced context updating and heightened variability during sensory learning in autism.

The role of medical diagnosis is essential in patient care and healthcare. Established diagnostic practices typically rely on predetermined clinical criteria and numerical thresholds. In contrast, Bayesian inference provides an advanced framework that supports diagnosis via in-depth probabilistic analysis. This study\'s aim is to introduce a software tool dedicated to the quantification of uncertainty in Bayesian diagnosis, a field that has seen minimal exploration to date. The presented tool, a freely available specialized software program, utilizes uncertainty propagation techniques to estimate the sampling, measurement, and combined uncertainty of the posterior probability for disease. It features two primary modules and fifteen submodules, all designed to facilitate the estimation and graphical representation of the standard uncertainty of the posterior probability estimates for diseased and non-diseased population samples, incorporating parameters such as the mean and standard deviation of the test measurand, the size of the samples, and the standard measurement uncertainty inherent in screening and diagnostic tests. Our study showcases the practical application of the program by examining the fasting plasma glucose data sourced from the National Health and Nutrition Examination Survey. Parametric distribution models are explored to assess the uncertainty of Bayesian posterior probability for diabetes mellitus, using the oral glucose tolerance test as the reference diagnostic method.

Bayesian decision theory suggests that optimal decision-making should use and weigh prior beliefs with current information, according to their relative uncertainties. However, some characteristics of borderline personality disorder (BPD) patients, such as fast, drastic changes in the overall perception of themselves and others, suggest they may be underrelying on priors. Here, we investigated if BPD patients have a general deficit in relying on or combining prior with current information. We analyzed this by having BPD patients (n = 23) and healthy controls (n = 18) perform a coin-catching sensorimotor task with varying levels of prior and current information uncertainty. Our results indicate that BPD patients learned and used prior information and combined it with current information in a qualitatively Bayesian-like way. Our results show that, at least in a lower-level, nonsocial sensorimotor task, BPD patients can appropriately use both prior and current information, illustrating that potential deficits using priors may not be widespread or domain-general.

UNASSIGNED: Injuries during elite level competition like the Canada Games, occur frequently and injury history is one of the strongest predictors of future injury; however, this association is unknown in the Canada Games.
UNASSIGNED: To determine the association between injury history and incidence of lower extremity joint injury during Canada Games competition.
UNASSIGNED: Data from the 2009 - 2019 Canada Games (8710 male and 8391 female athletes) competitions were de-identified by the Canada Games Council for analysis. Injury data were cleaned and categorized for previous injury and injury type and location. Injury history was self-reported and included concussion, major surgical procedure, neck and back, trauma to joint or bone, and trauma to ligament or tendon. Injury from the Canada Games competitions were categorized to include ankle, knee, hip, and patellofemoral joint injuries. Chi-Square (χ2 ) test of independence determined association between injury history and incidence of lower extremity joint injury during Canada Games competition. IBM SPSS (Version 26) was used for statistical analysis (p-value < 0.05).
UNASSIGNED: Four hundred and seventy-five ankle, 503 knee, 253 hip, and 106 patellofemoral joint injuries were reported during 10 years of Canada Games competitions. There were significant associations between history of neck and back injuries with ankle injuries and knee injuries, history of trauma and overuse of ligament or tendon with hip injuries and history of trauma or overuse of joint or bone with patellofemoral joint injuries.
UNASSIGNED: These findings support previous literature suggesting that injury history is associated with future injury.
UNASSIGNED: 3.

Medical diagnosis is the basis for treatment and management decisions in healthcare. Conventional methods for medical diagnosis commonly use established clinical criteria and fixed numerical thresholds. The limitations of such an approach may result in a failure to capture the intricate relations between diagnostic tests and the varying prevalence of diseases. To explore this further, we have developed a freely available specialized computational tool that employs Bayesian inference to calculate the posterior probability of disease diagnosis. This novel software comprises of three distinct modules, each designed to allow users to define and compare parametric and nonparametric distributions effectively. The tool is equipped to analyze datasets generated from two separate diagnostic tests, each performed on both diseased and nondiseased populations. We demonstrate the utility of this software by analyzing fasting plasma glucose, and glycated hemoglobin A1c data from the National Health and Nutrition Examination Survey. Our results are validated using the oral glucose tolerance test as a reference standard, and we explore both parametric and nonparametric distribution models for the Bayesian diagnosis of diabetes mellitus.