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This research introduces a novel approach to resampling periodically correlated time series using bandpass filters for frequency separation called the Variable Bandpass Periodic Block Bootstrap and then examines the significant advantages of this new method. While bootstrapping allows estimation of a statistic's sampling distribution by resampling the original data with replacement, and block bootstrapping is a model-free resampling strategy for correlated time series data, both fail to preserve correlations in periodically correlated time series. Existing extensions of the block bootstrap help preserve the correlation structures of periodically correlated processes but suffer from flaws and inefficiencies. Analyses of time series data containing cyclic, seasonal, or periodically correlated principal components often seen in annual, daily, or other cyclostationary processes benefit from separating these components. The Variable Bandpass Periodic Block Bootstrap uses bandpass filters to separate a periodically correlated component from interference such as noise at other uncorrelated frequencies. A simulation study is presented, demonstrating near universal improvements obtained from the Variable Bandpass Periodic Block Bootstrap when compared with prior block bootstrapping methods for periodically correlated time series., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Edward L. Valachovic. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Advancements in sensor technology have brought a revolution in data generation. Therefore, the study variable and several linearly related auxiliary variables are recorded due to cost-effectiveness and ease of recording. These auxiliary variables are commonly observed as quantitative and qualitative (attributes) variables and are jointly used to estimate the study variable's population mean using a mixture estimator. For this purpose, this work proposes a family of generalized mixture estimators under stratified sampling to increase efficiency under symmetrical and asymmetrical distributions and study the estimator's behavior for different sample sizes for its convergence to the Normal distribution. It is found that the proposed estimator estimates the population mean of the study variable with more precision than the competitor estimators under Normal, Uniform, Weibull, and Gamma distributions. It is also revealed that the proposed estimator follows the Cauchy distribution when the sample size is less than 35; otherwise, it converges to normality. Furthermore, the implementation of two real-life datasets related to the health and finance sectors is also presented to support the proposed estimator's significance., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Iqbal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

This paper introduces the modified Kies Topp-Leone (MKTL) distribution for modeling data on the (0, 1) or [0, 1] interval. The shapes of the density and hazard rate functions manifest desirable shapes, making the MKTL distribution suitable for modeling data with different characteristics at the unit interval. Twelve different estimation methods are utilized to estimate the distribution parameters, and Monte Carlo simulation experiments are executed to assess the performance of the methods. The simulation results suggest that the maximum likelihood method is the superior method. The usefulness of the new distribution is illustrated by utilizing three data sets, and its performance is juxtaposed with that of other competing models. The findings affirm the superiority of the MKTL distribution over the other candidate models. Applying the developed quantile regression model using the new distribution disclosed that it offers a competitive fit over other existing regression models., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Alghamdi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

With the rapid development of biotechnology, gene sequencing methods are gradually improved. The structure of gene sequences is also more complex. However, the traditional sequence alignment method is difficult to deal with the complex gene sequence alignment work. In order to improve the efficiency of gene sequence analysis, D2 series method of k-mer statistics is selected to build the model of gene sequence alignment analysis. According to the structure of the foreground sequence, the sequence to be aligned can be cut by different lengths and divided into multiple subsequences. Finally, according to the selected subsequences, the maximum dissimilarity in the alignment results is determined as the statistical result. At the same time, the research also designed an application system for the sequence alignment analysis of the model. The experimental results showed that the statistical power of the sequence alignment analysis model was directly proportional to the sequence coverage and cutting length, and inversely proportional to the K value and module length. At the same time, the model was applied to the system designed in this paper. The maximum storage capacity of the system was 71 GB, the maximum disk capacity was 135 GB, and the running time was less than 2.0s. Therefore, the k-mer statistic sequence alignment model and system proposed in this study have considerable application value in gene alignment analysis., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Dongjie Gao. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Effective analysis of single-cell RNA sequencing (scRNA-seq) data requires a rigorous distinction between technical noise and biological variation. In this work, we propose a simple feature selection model, termed "Differentially Distributed Genes" or DDGs, where a binomial sampling process for each mRNA species produces a null model of technical variation. Using scRNA-seq data where cell identities have been established a priori, we find that the DDG model of biological variation outperforms existing methods. We demonstrate that DDGs distinguish a validated set of real biologically varying genes, minimize neighborhood distortion, and enable accurate partitioning of cells into their established cell-type groups., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Sparta et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging. In this study, we aim to enhance JSDM scalability by leveraging high-performance computing (HPC) resources for an existing fitting method. Our work focuses on the Hmsc R-package, a widely used JSDM framework that supports the integration of various dataset types into a single comprehensive model. We developed a GPU-compatible implementation of its model-fitting algorithm using Python and the TensorFlow library. Despite these changes, our enhanced framework retains the original user interface of the Hmsc R-package. We evaluated the performance of the proposed implementation across various model configurations and dataset sizes. Our results show a significant increase in model fitting speed for most models compared to the baseline Hmsc R-package. For the largest datasets, we achieved speed-ups of over 1000 times, demonstrating the substantial potential of GPU porting for previously CPU-bound JSDM software. This advancement opens promising opportunities for better utilizing the rapidly accumulating new biodiversity data resources for inference and prediction., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Rahman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

An N-of-1 observational design characterizes associations among several variables over time in a single individual. Traditional statistical models recommended for experimental N-of-1 trials may not adequately model these observational relationships. We propose an additive Bayesian network using a generalized linear mixed-effects model for the local mean as a novel method for modeling each of these relationships in a data-driven manner. We validate our approach via simulation studies and apply it to a 12-month observational N-of-1 study exploring the impact of stress on daily exercise engagement. We demonstrate the improved performance of the additive Bayesian network to recover the underlying network structure. From the empirical study, we found statistically discernible associations between reports of stress and physical activity on a population level, but these associations may differ at an individual level., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Pascual et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Recently, it was recommended to omit tied observations before applying the two-sample Wilcoxon-Mann-Whitney test McGee M. et al. (2018). Using a simulation study, we argue for exact tests using all the data (including tied values) as a preferable approach. Exact tests, with tied observations included guarantee the type I error rate with a better exploitation of the significance level and a larger power than the corresponding tests after the omission of tied observations. The omission of ties can produce a considerable change in the shape of the sample, and so can violate underlying test assumptions. Thus, on both theoretical and practical grounds, the recommendation to omit tied values cannot be supported, relative to analysing the whole data set in the same way whether or not ties occur, preferably with an exact permutation test., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Neuhäuser, Ruxton. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

An arrayed CRISPR screen is a high-throughput functional genomic screening method, which typically uses 384 well plates and has different gene knockouts in different wells. Despite various computational workflows, there is currently no systematic way to find what is a good workflow for arrayed CRISPR screening data analysis. To guide this choice, we developed a statistical simulation model that mimics the data generating process of arrayed CRISPR screening experiments. Our model is flexible and can simulate effects on phenotypic readouts of various experimental factors, such as the effect size of gene editing, as well as biological and technical variations. With two examples, we showed that the simulation model can assist making principled choice of normalization and hit calling method for the arrayed CRISPR data analysis. This simulation model is implemented in an R package and can be downloaded from Github., Competing Interests: All authors are employees of AstraZeneca and has stock ownership and/or stock options or interests in the company. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Kim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In disciplines from biology to climate science, a routine task is to compute a correlation between a pair of time series and determine whether the correlation is statistically significant (i.e., unlikely under the null hypothesis that the time series are independent). This problem is challenging because time series typically exhibit autocorrelation and thus cannot be properly analyzed with the standard iid-oriented statistical tests. Although there are well-known parametric tests for time series, these are designed for linear correlation statistics and thus not suitable for the increasingly popular nonlinear correlation statistics. There are also nonparametric tests that can be used with any correlation statistic, but for these, the conditions that guarantee correct false positive rates are either restrictive or unclear. Here, we describe the truncated time-shift (TTS) test, a nonparametric procedure to test for dependence between 2 time series. We prove that this test correctly controls the false positive rate as long as one of the time series is stationary, a minimally restrictive requirement among current tests. The TTS test is versatile because it can be used with any correlation statistic. Using synthetic data, we demonstrate that this test performs correctly even while other tests suffer high false positive rates. In simulation examples, simple guidelines for parameter choices allow high statistical power to be achieved with sufficient data. We apply the test to datasets from climatology, animal behavior, and microbiome science, verifying previously discovered dependence relationships and detecting additional relationships., Competing Interests: WS is a member of the PLOS Biology Editorial Board., (Copyright: © 2024 Yuan, Shou. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

This study aims to develop a nonparametric mixed exponentially weighted moving average-moving average (NPEWMA-MA) sign control chart for monitoring shifts in process location, particularly when the distribution of a critical quality characteristic is either unknown or non-normal. In literature, the variance expression of the mixed exponentially weighted moving average-moving average (EWMA-MA) statistic is calculated by allowing sequential moving averages to be independent, and thus the exclusion of covariance terms results in an inaccurate variance expression. Furthermore, the effectiveness of the EWMA-MA control chart deteriorates when the distribution of a critical quality characteristic deviates from normality. The proposed NPEWMA-MA sign control chart addresses these by utilizing the corrected variance of the EWMA-MA statistic and incorporating the nonparametric sign test into the EWMA-MA charting structure. The chart integrates the moving average (MA) statistic into the exponentially weighted moving average (EWMA) statistic. The EWMA-MA charting statistic assigns more weight to recent w samples, with weights for previous observations decling exponentially. Monte Carlo simulations assess the chart's performance using various run length (RL) characteristics such as average run length (ARL), standard deviation of run length (SDRL), and median run length (MRL). Additional measures for overall performance include the average extra quadratic loss (AEQL) and relative mean index (RMI). The proposed NPEWMA-MA sign control chart demonstrates superior performance compared to existing nonparametric control charts across different symmetrical and asymmetric distributions. It efficiently detects process shifts, as validated through both a simulated study and a real-life example from a combined cycle power plant., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Raza et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Accurately estimating the duration of freeway incidents can enhance emergency management practices and reduce the likelihood of secondary incidents. To investigate the mechanisms through which key factors influence incident duration, this study sorted out the characteristics and variables of the incident duration on a special freeway in Zhejiang Province, that is, the ring road, and developed a latent class accelerated hazard model. Heterogeneity was incorporated into the model. Three distributions (Weibull, Log-normal, and Log-logistic) were compared, and the Log-logistic distribution exhibited superior performance. The analysis revealed two distinct latent classes: Latent Class 1 and Class 2, had class membership probability of 0.53 and 0.47, respectively, with a total of 11 variables being statistically significant at the 0.05 significance level. It is worth noting that, some neglected explanatory variables are discussed in depth in this study. For example, the mechanism of which specific lane is closed has an impact on the incident duration, rather than a general discussion of the number of lane closures. Furthermore, the way in which the driver involved in the incident reports to the police has a significant impact on the duration of incidents. Notably, potential heterogeneity and its influencing mechanism are captured in the model. Additionally, by predicting class membership using posterior probabilities, it was determined that most data points were more likely to belong to Class 1, and the incident duration primarily ranged between 0 and 60 minutes. These findings are helpful to reduce the duration of incidents on ring-roads and freeways in China, and provide theoretical support for the formulation of freeway incident management and treatment policies., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Shen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

To understand the transmissibility and spread of infectious diseases, epidemiologists turn to estimates of the instantaneous reproduction number. While many estimation approaches exist, their utility may be limited. Challenges of surveillance data collection, model assumptions that are unverifiable with data alone, and computationally inefficient frameworks are critical limitations for many existing approaches. We propose a discrete spline-based approach that solves a convex optimization problem-Poisson trend filtering-using the proximal Newton method. It produces a locally adaptive estimator for instantaneous reproduction number estimation with heterogeneous smoothness. Our methodology remains accurate even under some process misspecifications and is computationally efficient, even for large-scale data. The implementation is easily accessible in a lightweight R package rtestim., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

This article suggests a new method to expand a family of life distributions by adding a parameter to the family, increasing its flexibility. It is called the extended Modi-G family of distributions. We derived the general statistical properties of the proposed family. Different methods of estimation were presented to estimate the parameters for the proposed family, such as maximum likelihood, ordinary least square, weighted least square, Anderson Darling, right-tailed Anderson-Darling, Cramér-von Mises, and maximum product of spacing methods. A special sub-model with three parameters called extended Modi exponential distribution was derived along with different shapes of its density and hazard functions. Randomly generated data sets and different estimation methods were used to illustrate the behavior of parameters of the proposal sub-model. To illustrate the importance of the proposed family over the other well-known methods, applications to medicine and geology data sets were analyzed., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Gemeay et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Single-cell ATAC-seq sequencing data (scATAC-seq) has been widely used to investigate chromatin accessibility on the single-cell level. One important application of scATAC-seq data analysis is differential chromatin accessibility (DA) analysis. However, the data characteristics of scATAC-seq such as excessive zeros and large variability of chromatin accessibility across cells impose a unique challenge for DA analysis. Existing statistical methods focus on detecting the mean difference of the chromatin accessible regions while overlooking the distribution difference. Motivated by real data exploration that distribution difference exists among cell types, we introduce a novel composite statistical test named "scaDA", which is based on zero-inflated negative binomial model (ZINB), for performing differential distribution analysis of chromatin accessibility by jointly testing the abundance, prevalence and dispersion simultaneously. Benefiting from both dispersion shrinkage and iterative refinement of mean and prevalence parameter estimates, scaDA demonstrates its superiority to both ZINB-based likelihood ratio tests and published methods by achieving the highest power and best FDR control in a comprehensive simulation study. In addition to demonstrating the highest power in three real sc-multiome data analyses, scaDA successfully identifies differentially accessible regions in microglia from sc-multiome data for an Alzheimer's disease (AD) study that are most enriched in GO terms related to neurogenesis and the clinical phenotype of AD, and AD-associated GWAS SNPs., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Zhao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Neural population responses in sensory systems are driven by external physical stimuli. This stimulus-response relationship is typically characterized by receptive fields, which have been estimated by neural system identification approaches. Such models usually require a large amount of training data, yet, the recording time for animal experiments is limited, giving rise to epistemic uncertainty for the learned neural transfer functions. While deep neural network models have demonstrated excellent power on neural prediction, they usually do not provide the uncertainty of the resulting neural representations and derived statistics, such as most exciting inputs (MEIs), from in silico experiments. Here, we present a Bayesian system identification approach to predict neural responses to visual stimuli, and explore whether explicitly modeling network weight variability can be beneficial for identifying neural response properties. To this end, we use variational inference to estimate the posterior distribution of each model weight given the training data. Tests with different neural datasets demonstrate that this method can achieve higher or comparable performance on neural prediction, with a much higher data efficiency compared to Monte Carlo dropout methods and traditional models using point estimates of the model parameters. At the same time, our variational method provides us with an effectively infinite ensemble, avoiding the idiosyncrasy of any single model, to generate MEIs. This allows us to estimate the uncertainty of stimulus-response function, which we have found to be negatively correlated with the predictive performance at model level and may serve to evaluate models. Furthermore, our approach enables us to identify response properties with credible intervals and to determine whether the inferred features are meaningful by performing statistical tests on MEIs. Finally, in silico experiments show that our model generates stimuli driving neuronal activity significantly better than traditional models in the limited-data regime., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Wu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Like other tropical and subtropical regions, influenza viruses can circulate year-round in Hong Kong. However, during the COVID-19 pandemic, there was a significant decrease in influenza activity. The objective of this study was to retrospectively forecast influenza activity during the year 2020 and assess the impact of COVID-19 public health social measures (PHSMs) on influenza activity and hospital admissions in Hong Kong. Using weekly surveillance data on influenza virus activity in Hong Kong from 2010 to 2019, we developed a statistical modeling framework to forecast influenza virus activity and associated hospital admissions. We conducted short-term forecasts (1-4 weeks ahead) and medium-term forecasts (1-13 weeks ahead) for the year 2020, assuming no PHSMs were implemented against COVID-19. We estimated the reduction in transmissibility, peak magnitude, attack rates, and influenza-associated hospitalization rate resulting from these PHSMs. For short-term forecasts, mean ambient ozone concentration and school holidays were found to contribute to better prediction performance, while absolute humidity and ozone concentration improved the accuracy of medium-term forecasts. We observed a maximum reduction of 44.6% (95% CI: 38.6% - 51.9%) in transmissibility, 75.5% (95% CI: 73.0% - 77.6%) in attack rate, 41.5% (95% CI: 13.9% - 55.7%) in peak magnitude, and 63.1% (95% CI: 59.3% - 66.3%) in cumulative influenza-associated hospitalizations during the winter-spring period of the 2019/2020 season in Hong Kong. The implementation of PHSMs to control COVID-19 had a substantial impact on influenza transmission and associated burden in Hong Kong. Incorporating information on factors influencing influenza transmission improved the accuracy of our predictions., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: BJC received honoraria from AstraZeneca, Fosun Pharma, GSK, Haleon, Moderna, Novavax, Pfizer, Roche, and Sanofi. The authors report no other potential conflicts of interest., (Copyright: © 2024 Lau et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Dynamical system models typically involve numerous input parameters whose "effects" and orthogonality need to be quantified through sensitivity analysis, to identify inputs contributing the greatest uncertainty. Whilst prior art has compared total-order estimators' role in recovering "true" effects, assessing their ability to recover robust parameter orthogonality for use in identifiability metrics has not been investigated. In this paper, we perform: (i) an assessment using a different class of numerical models representing the cardiovascular system, (ii) a wider evaluation of sampling methodologies and their interactions with estimators, (iii) an investigation of the consequences of permuting estimators and sampling methodologies on input parameter orthogonality, (iv) a study of sample convergence through resampling, and (v) an assessment of whether positive outcomes are sustained when model input dimensionality increases. Our results indicate that Jansen or Janon estimators display efficient convergence with minimum uncertainty when coupled with Sobol and the lattice rule sampling methods, making them prime choices for calculating parameter orthogonality and influence. This study reveals that global sensitivity analysis is convergence driven. Unconverged indices are subject to error and therefore the true influence or orthogonality of the input parameters are not recovered. This investigation importantly clarifies the interactions of the estimator and the sampling methodology by reducing the associated ambiguities, defining novel practices for modelling in the life sciences., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Saxton et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Introduction: Estimates for cause-specific mortality for neonates are generally available for all countries for neonates overall (0 to 28 days). However, cause-specific mortality is generally not being estimated at higher age resolution for neonates, despite evidence of heterogeneity in the causes of deaths during this period. We aimed to use the adapted log quadratic model in a setting where verbal autopsy was the primary means of determining cause of death., Methods: We examined the timing and causes of death among a cohort of neonates in rural Nepal followed as part of the Nepal Oil Massage Study (NOMS). We adapted methods defined by Wilmoth et al (2012) and Guillot et al. (2022) to estimate age and cause-specific mortality among neonates. We used cross validation to estimate the accuracy of this model, holding out each three month period. We took the average cross validation across hold out as our measure of model performance and compared to a standard approach which did not account for the heterogeneity in cause-specific mortality rate within this age group., Results: There were 957 neonates in the NOMS cohort with known age and cause of death. We estimated an average cross-validation error of 0.9 per 1000 live births for mortality due to prematurity in the first week, and 1.1 for mortality due to birth asphyxia, compared to the standard approach, having error 7.4 and 7.8 per 1000 live births, respectively. Generally mortality rates for less common causes such as congenital malformations and pneumonia were estimated with higher cross-validation error., Conclusions: The stability and precision of these estimates compare favorably with similar estimates developed with higher quality cause-specific mortality surveillance from China, demonstrating that reliably estimating causes of mortality at high resolution is possible for neonates in low resources areas., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Perin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Schistosomiasis is a neglected disease prevalent in tropical and sub-tropical areas of the world, especially in Africa. Detecting the presence of the disease is based on the detection of the parasites in the stool or urine of children and adults. In such studies, typically, data collected on schistosomiasis infection includes information on many negative individuals leading to a high zero inflation. Thus, in practice, counts data with excessive zeros are common. However, the purpose of this analysis is to apply statistical models to the count data and evaluate their performance and results., Methods: This is a secondary analysis of previously collected data. As part of a modelling process, a comparison of the Poisson regression, negative binomial regression and their associated zero inflated and hurdle models were used to determine which offered the best fit to the count data., Results: Overall, 94.1% of the study participants did not have any schistosomiasis eggs out of 1345 people tested, resulting in a high zero inflation. The performance of the negative binomial regression models (hurdle negative binomial (HNB), zero inflated negative binomial (ZINB) and the standard negative binomial) were better than the Poisson-based regression models (Poisson, zero inflated Poisson, hurdle Poisson). The best models were the ZINB and HNB and their performances were indistinguishable according to information-based criteria test values., Conclusion: The zero-inflated negative binomial and hurdle negative binomial models were found to be the most satisfactory fit for modelling the over-dispersed zero inflated count data and are recommended for use in future statistical modelling analyses., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Nketia, de Souza. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Boolean networks are largely employed to model the qualitative dynamics of cell fate processes by describing the change of binary activation states of genes and transcription factors with time. Being able to bridge such qualitative states with quantitative measurements of gene expression in cells, as scRNA-seq, is a cornerstone for data-driven model construction and validation. On one hand, scRNA-seq binarisation is a key step for inferring and validating Boolean models. On the other hand, the generation of synthetic scRNA-seq data from baseline Boolean models provides an important asset to benchmark inference methods. However, linking characteristics of scRNA-seq datasets, including dropout events, with Boolean states is a challenging task. We present scBoolSeq, a method for the bidirectional linking of scRNA-seq data and Boolean activation state of genes. Given a reference scRNA-seq dataset, scBoolSeq computes statistical criteria to classify the empirical gene pseudocount distributions as either unimodal, bimodal, or zero-inflated, and fit a probabilistic model of dropouts, with gene-dependent parameters. From these learnt distributions, scBoolSeq can perform both binarisation of scRNA-seq datasets, and generate synthetic scRNA-seq datasets from Boolean traces, as issued from Boolean networks, using biased sampling and dropout simulation. We present a case study demonstrating the application of scBoolSeq's binarisation scheme in data-driven model inference. Furthermore, we compare synthetic scRNA-seq data generated by scBoolSeq with BoolODE's, data for the same Boolean Network model. The comparison shows that our method better reproduces the statistics of real scRNA-seq datasets, such as the mean-variance and mean-dropout relationships while exhibiting clearly defined trajectories in two-dimensional projections of the data., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Magaña-López et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Importance: Sleep is critical to a person's physical and mental health and there is a need to create high performing machine learning models and critically understand how models rank covariates., Objective: The study aimed to compare how different model metrics rank the importance of various covariates., Design, Setting, and Participants: A cross-sectional cohort study was conducted retrospectively using the National Health and Nutrition Examination Survey (NHANES), which is publicly available., Methods: This study employed univariate logistic models to filter out strong, independent covariates associated with sleep disorder outcome, which were then used in machine-learning models, of which, the most optimal was chosen. The machine-learning model was used to rank model covariates based on gain, cover, and frequency to identify risk factors for sleep disorder and feature importance was evaluated using both univariable and multivariable t-statistics. A correlation matrix was created to determine the similarity of the importance of variables ranked by different model metrics., Results: The XGBoost model had the highest mean AUROC of 0.865 (SD = 0.010) with Accuracy of 0.762 (SD = 0.019), F1 of 0.875 (SD = 0.766), Sensitivity of 0.768 (SD = 0.023), Specificity of 0.782 (SD = 0.025), Positive Predictive Value of 0.806 (SD = 0.025), and Negative Predictive Value of 0.737 (SD = 0.034). The model metrics from the machine learning of gain and cover were strongly positively correlated with one another (r > 0.70). Model metrics from the multivariable model and univariable model were weakly negatively correlated with machine learning model metrics (R between -0.3 and 0)., Conclusion: The ranking of important variables associated with sleep disorder in this cohort from the machine learning models were not related to those from regression models., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Huang, Huang. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Spatial interaction models with spatial origin-destination (OD) filters are powerful tools to characterize trip flows in space, which is a classic and important problem in regional science. To the authors' knowledge, existing studies adopting OD filters mostly specify the spatial dependence as an autoregressive process, which may not be the full picture of spatial effects. To examine the problem, this paper proposes the hypotheses that 1) spatial OD dependences can take place in both the spatial autoregressive term and the spatial error term in a spatial interaction model. 2) Estimating a spatial autoregressive model with spatial autoregressive disturbances (SARAR) model with OD filters would disentangle where the spatial dependence exists and by how much. 3) The marginal effects obtained from SARAR models would be preferred to analysts when SARAR models outperform spatial autoregressive (SAR) models and spatial error models (SEM) from the statistical point of view. To assess these hypotheses, this paper specifies, estimates, and applies SARAR models with OD filters to investigate trip distributions. By comparing against alternative models, this paper investigates the estimation results in SAR, SEM and SARAR models using an empirical data collected from Hangzhou, China. The contribution of this paper is to be the first in developing an SARAR model with OD filters for trip distribution analyses and examining its performance., Competing Interests: he authors have declared that no competing interests exist., (Copyright: © 2024 Ni, Zhang. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In almost every country, patents need to be renewed multiple times after they are granted. A patentee assesses the value of the patent and then pays a renewal fee to keep it active for another stipulated period. The factors that characterize the value of a patent is subjective. This paper aims to address the research gap of building an accurate model for predicting the renewal life (often considered as a substitute for the patent value) of Indian patents, and identification of significant factors that influence the renewal life. This study uses an extensive data set collected from the Indian Patent Office for all granted patents filed between 1995 and 2005. The popular statistical and machine learning algorithms do not result in accurate predictive models, because the patent renewal life distribution (at least for the Indian patents) shows unusual spikes at the two extreme values, which makes the modeling task more challenging. We propose a new two-stage hybrid model by combining an efficient multi-class classifier and a binomial regression model for predicting the complex renewal data distribution. We conducted a comparative analysis of the proposed model with several state-of-the-art machine learning and statistical models. The results show that the proposed hybrid model gives 90% accuracy as compared to the best competitor which gives only 40% accuracy., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Kumar et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The Latent Dirichlet Allocation (LDA) model is used to extract the text themes of newspaper news and construct the Chinese Economic Policy Uncertainty (EPU) Index. On this basis, based on the relevant data of Chinese A-share listed companies from 2008 to 2020, this paper empirically analyzes the impact of EPU on peer effects of firms R&D investment, and finds that EPU will aggravate the peer effects of firms R&D investment. Furthermore, the moderating effect of manager's motivation to maintain reputation on the process of EPU influencing the peer effects of firms R&D investment was tested, and the mechanism of EPU influencing the peer effects of firms R&D investment through financial frictions was verified., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The one-sample log-rank test is the preferred method for analysing the outcome of single-arm survival trials. It compares the survival distribution of patients with a prefixed reference survival curve that usually represents the expected outcome under standard of care. However, classical one-sample log-rank tests assume that the reference curve is known, ignoring that it is frequently estimated from historical data and therefore susceptible to sampling error. Neglecting the variability of the reference curve can lead to an inflated type I error rate, as shown in a previous paper. Here, we propose a new survival test that allows to account for the sampling error of the reference curve without knowledge of the full underlying historical survival time data. Our new test allows to perform a valid historical comparison of patient survival times when only a historical survival curve rather than the full historic data is available. It thus applies in settings where the two-sample log-rank test is not applicable as method of choice due to non-availability of historic individual patient survival time data. We develop sample size calculation formulas, give an example application and study the performance of the new test in a simulation study., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Feld et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The primary focus of all sample surveys is on providing point estimates for the parameters of primary interest, and also estimating the variance associated with those point estimates to quantify the uncertainty. Larger samples and important measurement tools can help to reduce the point estimates' uncertainty. Numerous effective stratification criteria may be used in survey to reduce variance within stratum. In fine stratification design, the population is divided into numerous small strata, each containing a relatively small number of sampling units as one or two. This is done to ensure that certain characteristics or subgroups of the population are well-represented in the sample. But with many strata, the sample size within each stratum can become small, potentially resulting in higher errors and less stable estimates. The variance estimation process becomes difficult when we only have one unit per stratum. In that case, the collapsed stratum technique is the classical methods for estimating variance. This method, however, is biased and results in an overestimation of the variance. This paper proposes a bootstrap-based variance estimator for the total population under fine stratification, which overcomes the drawbacks of the previously explored estimation approach. Also, the estimator's properties were investigated. A simulation study and practical application on survey of mental health organizations data were done to investigate properties of the proposed estimators. The results show that the proposed estimator performs well., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Habineza et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Research has substantiated that the presence of outliers in data usually introduces additional errors and biases, which typically leads to a degradation in the precision of volatility forecasts. However, correcting outliers can mitigate these adverse effects. This study corrects the additive outliers through a weighting method and let these corrected values to replace the original outliers. Then, the model parameters are re-estimated based on this new return series. This approach reduces the extent to which outliers distort volatility estimates, allowing the model to better adapt to market conditions and improving the accuracy of volatility forecasts. This study introduces this approach for the first time to generalized autoregressive conditional heteroskedasticity mixed data sampling (GARCH-MIDAS) models, so as to establish an additional outliers corrected GARCH-MIDAS model (AO-GARCH-MIDAS). This pioneering approach marks a unique innovation. The research employs a diverse array of evaluation methods to validate the model's robustness and consistently demonstrates its dependable performance. Findings unequivocally reveal the substantial influence of outliers on the model's predictive capacity, with the AO-GARCH-MIDAS model exhibiting consistent superiority across all evaluation criteria. Additionally, while the GARCH model showcases stronger estimation capabilities compared to the GARCH-MIDAS model, the latter demonstrates heightened predictive prowess. Notably, regarding variable selection, the results underscore the greater predictive informational value inherent in realized volatility over other low-frequency factors., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Ebolavirus disease (EVD) outbreaks have intermittently occurred since the first documented case in the 1970s. Due to its transmission characteristics, large outbreaks have not been observed outside Africa. However, within the continent, significant outbreaks have been attributed to factors such as endemic diseases with similar symptoms and inadequate medical infrastructure, which complicate timely diagnosis. In this study, we employed a stochastic modeling approach to analyze the spread of EVD during the early stages of an outbreak, with an emphasis on inherent risks. We developed a model that considers healthcare workers and unreported cases, and assessed the effect of non-pharmaceutical interventions (NPIs) using actual data. Our results indicate that the implementation of NPIs led to a decrease in the transmission rate and infectious period by 30% and 40% respectively, following the declaration of the outbreak. We also investigated the risks associated with delayed outbreak recognition. Our simulations suggest that, when accounting for NPIs and recognition delays, prompt detection could have resulted in a similar outbreak scale, with approximately 50% of the baseline NPIs effect. Finally, we discussed the potential effects of a vaccination strategy as a follow-up measure after the outbreak declaration. Our findings suggest that a vaccination strategy can reduce both the burden of NPIs and the scale of the outbreak., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Ko et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

For the purpose of this study, A statistical test of Biblical books was conducted using the recently discovered probability models for text homogeneity and text change point detection. Accordingly, translations of Biblical books of Tigrigna and Amharic (major languages spoken in Eritrea and Ethiopia) and English were studied. A Zipf-Mandelbrot distribution with a parameter range of 0.55 to 0.88 was obtained in these three Bibles. According to the statistical analysis of the texts' homogeneity, the translation of Bible in each of these three languages was a heterogeneous concatenation of different books or genres. Furthermore, an in-depth examination of the text segmentation of prat of a single genre-the English Bible letters revealed that the Pauline letters are heterogeneous concatenations of two homogeneous segments., Competing Interests: The author have declared that no competing interests exist., (Copyright: © 2024 Berhane Abebe. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

COVID-19 prediction has been essential in the aid of prevention and control of the disease. The motivation of this case study is to develop predictive models for COVID-19 cases and deaths based on a cross-sectional data set with a total of 28,955 observations and 18 variables, which is compiled from 5 data sources from Kaggle. A two-part modeling framework, in which the first part is a logistic classifier and the second part includes machine learning or statistical smoothing methods, is introduced to model the highly skewed distribution of COVID-19 cases and deaths. We also aim to understand what factors are most relevant to COVID-19's occurrence and fatality. Evaluation criteria such as root mean squared error (RMSE) and mean absolute error (MAE) are used. We find that the two-part XGBoost model perform best with predicting the entire distribution of COVID-19 cases and deaths. The most important factors relevant to either COVID-19 cases or deaths include population and the rate of primary care physicians., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Le, Liao. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In this paper we consider a special kind of semicontinous distribution. We try to concern with the situation where the probability of zero observation is associated with the location and scale parameters in lognormal distribution. We first propose a goodness-of-fit test to ensure that the data can be fit by the associated delta-lognormal distribution. Then we define the updated fiducial distributions of the parameters and establish the results that the confidence interval has asymtotically correct level while the significance level of the hypothesis testing is also asymtotically correct. We propose an exact sampling method to sample from the updated fiducial distribution. It can be seen in our simulation study that the inference on the parameters is largely improved. A real data example is also used to illustrate our method., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Wang, Xu. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Spatial complexity is always associated with spatial autocorrelation. Spatial autocorrelation coefficients including Moran's index proved to be an eigenvalue of the spatial correlation matrixes. An eigenvalue represents a kind of characteristic length for quantitative analysis. However, if a spatial correlation process is based on self-organized evolution, complex structure, and the distributions without characteristic scale, the eigenvalue will be ineffective. In this case, a scaling exponent such as fractal dimension can be used to compensate for the shortcoming of characteristic length parameters such as Moran's index., Method: This paper is devoted to finding an intrinsic relationship between Moran's index and fractal dimension by means of spatial correlation modeling. Using relative step function as spatial contiguity function, we can convert spatial autocorrelation coefficients into spatial autocorrelation functions., Result: By decomposition of spatial autocorrelation functions, we can derive the relation between spatial correlation dimension and spatial autocorrelation functions. As results, a series of useful mathematical models are constructed, including the functional relation between Moran's index and fractal parameters. Correlation dimension proved to be a scaling exponent in the spatial correlation equation based on Moran's index. As for empirical analysis, the scaling exponent of spatial autocorrelation of Chinese cities is Dc = 1.3623±0.0358, which is equal to the spatial correlation dimension of the same urban system, D2. The goodness of fit is about R2 = 0.9965. This fractal parameter value suggests weak spatial autocorrelation of Chinese cities., Conclusion: A conclusion can be drawn that we can utilize spatial correlation dimension to make deep spatial autocorrelation analysis, and employ spatial autocorrelation functions to make complex spatial autocorrelation analysis. This study reveals the inherent association of fractal patterns with spatial autocorrelation processes. The work may inspire new ideas for spatial modeling and exploration of complex systems such as cities., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Yanguang Chen. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In this paper, the fused graphical lasso (FGL) method is used to estimate multiple precision matrices from multiple populations simultaneously. The lasso penalty in the FGL model is a restraint on sparsity of precision matrices, and a moderate penalty on the two precision matrices from distinct groups restrains the similar structure across multiple groups. In high-dimensional settings, an oracle inequality is provided for FGL estimators, which is necessary to establish the central limit law. We not only focus on point estimation of a precision matrix, but also work on hypothesis testing for a linear combination of the entries of multiple precision matrices. We apply a de-biasing technology, which is used to obtain a new consistent estimator with known distribution for implementing the statistical inference, and extend the statistical inference problem to multiple populations. The corresponding de-biasing FGL estimator and its asymptotic theory are provided. A simulation study and an application of the diffuse large B-cell lymphoma data show that the proposed test works well in high-dimensional situation., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Statistical quality control is concerned with the analysis of production and manufacturing processes. Control charts are process control techniques, commonly applied to observe and control deviations. Shewhart control charts are very sensitive and used for large shifts based on the basic assumption of normality. Cumulative Sum (CUSUM) control charts are effective for identifying that may have special causes, such as outliers or excessive variability in subgroup means. This study uses a CUSUM control chart problems structure to evaluate the performance of robust dispersion parameters. We investigated the design structure features of various control charts, based on currently defined estimators and some new robust scale estimators using trimming and winsorization in different scenarios. The Median Absolute Deviation based on trimming and winsorization is introduced. The effectiveness of CUSUM control charts based on these estimators is evaluated in terms of average run length (ARL) and Standard Deviation of the Run Length (SDRL) using a simulation study. The results show the robustness of the CUSUM chart in observing small changes in magnitude for both normal and contaminated data. In general, robust estimators MADTM and MADWM based on CUSUM charts outperform in all environments., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Khalil et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Ukraine's tug-of-war between Russia and the West has had significant and lasting consequences for the country. In 2013, Viktor Yanukovych, the Ukrainian president aligned with Russia, opted against signing an association agreement with the European Union. This agreement aimed to facilitate trade and travel between the EU and Ukraine. This decision sparked widespread protests that coalesced in Kyiv's Maidan Square, eventually becoming known as the Euromaidan protests. In this study, we analyze the protest data from 2013, sourced from Ukraine's Center for Social and Labor Research. Despite the dataset's limitations and occasional inconsistencies, we demonstrate the extraction of valuable insights and the construction of a descriptive model from such data. Our investigation reveals a pre-existing state of self-excitation within the system even before the onset of the Euromaidan protests. This self-excitation intensified during the Euromaidan protests. A statistical analysis indicates that the government's utilization of force correlates with increased future protests, exacerbating rather than quelling the protest movement. Furthermore, we introduce the implementation of Hawkes process models to comprehend the spatiotemporal dynamics of the protest activity. Our findings highlight that, while protest activities spread across the entire country, the driving force behind the dynamics of these protests was the level of activity in Kyiv. Furthermore, in contrast to prior research that emphasized geographical proximity as a key predictor of event propagation, our study illustrates that the political alignment among oblasts, which are the distinct municipalities comprising Ukraine, had a more profound impact than mere geographic distance. This underscores the significance of social and cultural factors in molding the trajectory of political movements., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Bahid et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Considerable spatial heterogeneity has been observed in COVID-19 transmission across administrative areas of England throughout the pandemic. This study investigates what drives these differences. We constructed a probabilistic case count model for 306 administrative areas of England across 95 weeks, fit using a Bayesian evidence synthesis framework. We incorporate the impact of acquired immunity, of spatial exportation of cases, and 16 spatially-varying socio-economic, socio-demographic, health, and mobility variables. Model comparison assesses the relative contributions of these respective mechanisms. We find that spatially-varying and time-varying differences in week-to-week transmission were definitively associated with differences in: time spent at home, variant-of-concern proportion, and adult social care funding. However, model comparison demonstrates that the impact of these terms is negligible compared to the role of spatial exportation between administrative areas. While these results confirm the impact of some, but not all, static measures of spatially-varying inequity in England, our work corroborates the finding that observed differences in disease transmission during the pandemic were predominantly driven by underlying epidemiological factors rather than aggregated metrics of demography and health inequity between areas. Further work is required to assess how health inequity more broadly contributes to these epidemiological factors., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: AC has received payment from Pfizer for teaching of mathematical modelling of infectious diseases. All other authors declare no competing interests., (Copyright: © 2024 Rawson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Black ice, a phenomenon that occurs abruptly owing to freezing rain, is difficult for drivers to identify because it mirrors the color of the road. Effectively managing the occurrence of unforeseen accidents caused by black ice requires predicting their probability using spatial, weather, and traffic factors and formulating appropriate countermeasures. Among these factors, weather and traffic exhibit the highest levels of uncertainty. To address these uncertainties, a study was conducted using a Monte Carlo simulation based on random values to predict the probability of black ice accidents at individual road points and analyze their trigger factors. We numerically modeled black ice accidents and visualized the simulation results in a geographical information system (GIS) by employing a sensitivity analysis, another feature of Monte Carlo simulations, to analyze the factors that trigger black ice accidents. The Monte Carlo simulation allowed us to map black ice accident occurrences at each road point on the GIS. The average black ice accident probability was found to be 0.0058, with a standard deviation of 0.001. Sensitivity analysis using Monte Carlo simulations identified wind speed, air temperature, and angle as significant triggers of black ice accidents, with sensitivities of 0.354, 0.270, and 0.203, respectively. We predicted the probability of black ice accidents per road section and analyzed the primary triggers of black ice accidents. The scientific contribution of this study lies in the development of a method beyond simple road temperature predictions for evaluating the risk of black ice occurrences and subsequent accidents. By employing Monte Carlo simulations, the probability of black ice accidents can be predicted more accurately through decoupling meteorological and traffic factors over time. The results can serve as a reference for government agencies, including road traffic authorities, to identify accident-prone spots and devise strategies focused on the primary triggers of black ice accidents., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Hong, Yun. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In the field of financial risk management, the accuracy of portfolio Value-at-Risk (VaR) forecasts is of critical importance to both practitioners and academics. This study pioneers a comprehensive evaluation of a univariate model that leverages high-frequency intraday data to improve portfolio VaR forecasts, providing a novel contrast to both univariate and multivariate models based on daily data. Existing research has used such high-frequency-based univariate models for index portfolios, it has not adequately studied their robustness for portfolios with diverse risk profiles, particularly under changing market conditions, such as during crises. Our research fills this gap by proposing a refined univariate long-memory realized volatility model that incorporates realized variance and covariance metrics, eliminating the necessity for a parametric covariance matrix. This model captures the long-run dependencies inherent in the volatility process and provides a flexible alternative that can be paired with appropriate return innovation distributions for VaR estimation. Empirical analyses show that our methodology significantly outperforms traditional univariate and multivariate Generalized AutoRegressive Conditional Heteroskedasticity (GARCH) models in terms of forecasting accuracy while maintaining computational simplicity and ease of implementation. In particular, the inclusion of high-frequency data in univariate volatility models not only improves forecasting accuracy but also streamlines the complexity of portfolio risk assessment. This research extends the discourse between academic research and financial practice, highlighting the transformative impact of high-frequency data on risk management strategies within the financial sector., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Wei Kuang. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Choudhery et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In the last few years, Micro-C has shown itself as an improved alternative to Hi-C. It replaced the restriction enzymes in Hi-C assays with micrococcal nuclease (MNase), resulting in capturing nucleosome resolution chromatin interactions. The signal-to-noise improvement of Micro-C allows it to detect more chromatin loops than high-resolution Hi-C. However, compared with massive Hi-C datasets available in the literature, there are only a limited number of Micro-C datasets. To take full advantage of these Hi-C datasets, we present HiC2MicroC, a computational method learning and then predicting Micro-C from Hi-C based on the denoising diffusion probabilistic models (DDPM). We trained our DDPM and other regression models in human foreskin fibroblast (HFFc6) cell line and evaluated these methods in six different cell types at 5-kb and 1-kb resolution. Our evaluations demonstrate that both HiC2MicroC and regression methods can markedly improve Hi-C towards Micro-C, and our DDPM-based HiC2MicroC outperforms regression in various terms. First, HiC2MicroC successfully recovers most of the Micro-C loops even those not detected in Hi-C maps. Second, a majority of the HiC2MicroC-recovered loops anchor CTCF binding sites in a convergent orientation. Third, HiC2MicroC loops share genomic and epigenetic properties with Micro-C loops, including linking promoters and enhancers, and their anchors are enriched for structural proteins (CTCF and cohesin) and histone modifications. Lastly, we find our recovered loops are also consistent with the loops identified from promoter capture Micro-C (PCMicro-C) and Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET). Overall, HiC2MicroC is an effective tool for further studying Hi-C data with Micro-C as a template. HiC2MicroC is publicly available at https://github.com/zwang-bioinformatics/HiC2MicroC/., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Projects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes. We present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three baselines derived from standard statistical forecasting methods (a naive model, auto-regression, and an ensemble of exponential smoothing and ARIMA). In terms of median absolute error for forecasting critical care unit occupancy at the two-week horizon, our model only outperformed the naive baseline for 4 out of 14 geographical units and underperformed compared to the ensemble baseline for 5 of them at the 90% confidence level (n = 38). However, for the same level at the 4 week horizon, our model was never statistically outperformed for any unit despite outperforming the baselines 10 times spanning 7 out of 14 geographical units. This implies modest forecasting utility for longer horizons which may justify the application of non-Markovian compartmental models in the context of hospital-strain surveillance for future pandemics., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Massey et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In recent years, concern has grown about the inappropriate application and interpretation of P values, especially the use of P<0.05 to denote "statistical significance" and the practice of P-hacking to produce results below this threshold and selectively reporting these in publications. Such behavior is said to be a major contributor to the large number of false and non-reproducible discoveries found in academic journals. In response, it has been proposed that the threshold for statistical significance be changed from 0.05 to 0.005. The aim of the current study was to use an evolutionary agent-based model comprised of researchers who test hypotheses and strive to increase their publication rates in order to explore the impact of a 0.005 P value threshold on P-hacking and published false positive rates. Three scenarios were examined, one in which researchers tested a single hypothesis, one in which they tested multiple hypotheses using a P<0.05 threshold, and one in which they tested multiple hypotheses using a P<0.005 threshold. Effects sizes were varied across models and output assessed in terms of researcher effort, number of hypotheses tested and number of publications, and the published false positive rate. The results supported the view that a more stringent P value threshold can serve to reduce the rate of published false positive results. Researchers still engaged in P-hacking with the new threshold, but the effort they expended increased substantially and their overall productivity was reduced, resulting in a decline in the published false positive rate. Compared to other proposed interventions to improve the academic publishing system, changing the P value threshold has the advantage of being relatively easy to implement and could be monitored and enforced with minimal effort by journal editors and peer reviewers., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Fitzpatrick et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Improved adaptive type-II progressive censoring schemes (IAT-II PCS) are increasingly being used to estimate parameters and reliability characteristics of lifetime distributions, leading to more accurate and reliable estimates. The logistic exponential distribution (LED), a flexible distribution with five hazard rate forms, is employed in several fields, including lifetime, financial, and environmental data. This research aims to enhance the accuracy and reliability estimation capabilities for the logistic exponential distribution under IAT-II PCS. By developing novel statistical inference methods, we can better understand the behavior of failure times, allow for more accurate decision-making, and improve the overall reliability of the model. In this research, we consider both classical and Bayesian techniques. The classical technique involves constructing maximum likelihood estimators of the model parameters and their asymptotic covariance matrix, followed by estimating the distribution's reliability using survival and hazard functions. The delta approach is used to create estimated confidence intervals for the model parameters. In the Bayesian technique, prior information about the LED parameters is used to estimate the posterior distribution of the parameters, which is derived using Bayes' theorem. The model's reliability is determined by computing the posterior predictive distribution of the survival or hazard functions. Extensive simulation studies and real-data applications assess the effectiveness of the proposed methods and evaluate their performance against existing methods., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Dutta et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Intuitively, combining multiple sources of evidence should lead to more accurate decisions than considering single sources of evidence individually. In practice, however, the proper computation may be difficult, or may require additional data that are inaccessible. Here, based on the concept of conditional independence, we consider expressions that can serve either as recipes for integrating evidence based on limited data, or as statistical benchmarks for characterizing evidence integration processes. Consider three events, A, B, and C. We find that, if A and B are conditionally independent with respect to C, then the probability that C occurs given that both A and B are known, P(C|A, B), can be easily calculated without the need to measure the full three-way dependency between A, B, and C. This simplified approach can be used in two general ways: to generate predictions by combining multiple (conditionally independent) sources of evidence, or to test whether separate sources of evidence are functionally independent of each other. These applications are demonstrated with four computer-simulated examples, which include detecting a disease based on repeated diagnostic testing, inferring biological age based on multiple biomarkers of aging, discriminating two spatial locations based on multiple cue stimuli (multisensory integration), and examining how behavioral performance in a visual search task depends on selection histories. Besides providing a sound prescription for predicting outcomes, this methodology may be useful for analyzing experimental data of many types., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Salinas, Stanford. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Despite the huge importance that the centrality metrics have in understanding the topology of a network, too little is known about the effects that small alterations in the topology of the input graph induce in the norm of the vector that stores the node centralities. If so, then it could be possible to avoid re-calculating the vector of centrality metrics if some minimal changes occur in the network topology, which would allow for significant computational savings. Hence, after formalising the notion of centrality, three of the most basic metrics were herein considered (i.e., Degree, Eigenvector, and Katz centrality). To perform the simulations, two probabilistic failure models were used to describe alterations in network topology: Uniform (i.e., all nodes can be independently deleted from the network with a fixed probability) and Best Connected (i.e., the probability a node is removed depends on its degree). Our analysis suggests that, in the case of degree, small variations in the topology of the input graph determine small variations in Degree centrality, independently of the topological features of the input graph; conversely, both Eigenvector and Katz centralities can be extremely sensitive to changes in the topology of the input graph. In other words, if the input graph has some specific features, even small changes in the topology of the input graph can have catastrophic effects on the Eigenvector or Katz centrality., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Cavallaro et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Cell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method's robustness is investigated using various synthetic datasets and a biological dataset of 18 cells., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Koptagel et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

One of the key tools to understand and reduce the spread of the SARS-CoV-2 virus is testing. The total number of tests, the number of positive tests, the number of negative tests, and the positivity rate are interconnected indicators and vary with time. To better understand the relationship between these indicators, against the background of an evolving pandemic, the association between the number of positive tests and the number of negative tests is studied using a joint modeling approach. All countries in the European Union, Switzerland, the United Kingdom, and Norway are included in the analysis. We propose a joint penalized spline model in which the penalized spline is reparameterized as a linear mixed model. The model allows for flexible trajectories by smoothing the country-specific deviations from the overall penalized spline and accounts for heteroscedasticity by allowing the autocorrelation parameters and residual variances to vary among countries. The association between the number of positive tests and the number of negative tests is derived from the joint distribution for the random intercepts and slopes. The correlation between the random intercepts and the correlation between the random slopes were both positive. This suggests that, when countries increase their testing capacity, both the number of positive tests and negative tests will increase. A significant correlation was found between the random intercepts, but the correlation between the random slopes was not significant due to a wide credible interval., Competing Interests: The authors declare that no competing interests exist., (Copyright: © 2024 De Witte et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub (https://covid19forecasthub.org). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1-4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: APP report grants from Metabiota Inc outside the submitted work. J.S. and Columbia University declare partial ownership of SK Analytics. No other authors have competing interests to declare., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Bayesian Control charts are emerging as the most efficient statistical tools for monitoring manufacturing processes and providing effective control over process variability. The Bayesian approach is particularly suitable for addressing parametric uncertainty in the manufacturing industry. In this study, we determine the monitoring threshold for the shape parameter of the Inverse Gaussian distribution (IGD) and design different exponentially-weighted-moving-average (EWMA) control charts based on different loss functions (LFs). The impact of hyperparameters is investigated on Bayes estimates (BEs) and posterior risks (PRs). The performance measures such as average run length (ARL), standard deviation of run length (SDRL), and median of run length (MRL) are employed to evaluate the suggested approach. The designed Bayesian charts are evaluated for different settings of smoothing constant of the EWMA chart, different sample sizes, and pre-specified false alarm rates. The simulative study demonstrates the effectiveness of the suggested Bayesian method-based EWMA charts as compared to the conventional classical setup-based EWMA charts. The proposed techniques of EWMA charts are highly efficient in detecting shifts in the shape parameter and outperform their classical counterpart in detecting faults quickly. The proposed technique is also applied to real-data case studies from the aerospace manufacturing industry. The quality characteristic of interest was selected as the monthly industrial production index of aircraft from January 1980 to December 2022. The real-data-based findings also validate the conclusions based on the simulative results., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Javed et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)