An Iterative Scale Purification Procedure on lz for the Detection of Aberrant Responses.

Many person-fit statistics have been proposed to detect aberrant response behaviors (e.g., cheating, guessing). Among them, lz is one of the most widely used indices. The computation of lz assumes the item and person parameters are known. In reality, they often have to be estimated from data. The better the estimation, the better lz will perform. When aberrant behaviors occur, the person and item parameter estimations are inaccurate, which in turn degrade the performance of lz. In this study, an iterative procedure was developed to attain more accurate person parameter estimates for improved performance of lz. A series of simulations were conducted to evaluate the iterative procedure under two conditions of item parameters, known and unknown, and three aberrant response styles of difficulty-sharing cheating, random-sharing cheating, and random guessing. The results demonstrated the superiority of the iterative procedure over the non-iterative one in maintaining control of Type-I error rates and improving the power of detecting aberrant responses. The proposed procedure was applied to a high-stake intelligence test.

Inferring circadian gene regulatory relationships from gene expression data with a hybrid framework.

BACKGROUND: The central biological clock governs numerous facets of mammalian physiology, including sleep, metabolism, and immune system regulation. Understanding gene regulatory relationships is crucial for unravelling the mechanisms that underlie various cellular biological processes. While it is possible to infer circadian gene regulatory relationships from time-series gene expression data, relying solely on correlation-based inference may not provide sufficient information about causation. Moreover, gene expression data often have high dimensions but a limited number of observations, posing challenges in their analysis. METHODS: In this paper, we introduce a new hybrid framework, referred to as Circadian Gene Regulatory Framework (CGRF), to infer circadian gene regulatory relationships from gene expression data of rats. The framework addresses the challenges of high-dimensional data by combining the fuzzy C-means clustering algorithm with dynamic time warping distance. Through this approach, we efficiently identify the clusters of genes related to the target gene. To determine the significance of genes within a specific cluster, we employ the Wilcoxon signed-rank test. Subsequently, we use a dynamic vector autoregressive method to analyze the selected significant gene expression profiles and reveal directed causal regulatory relationships based on partial correlation. CONCLUSION: The proposed CGRF framework offers a comprehensive and efficient solution for understanding circadian gene regulation. Circadian gene regulatory relationships are inferred from the gene expression data of rats based on the Aanat target gene. The results show that genes Pde10a, Atp7b, Prok2, Per1, Rhobtb3 and Dclk1 stand out, which have been known to be essential for the regulation of circadian activity. The potential relationships between genes Tspan15, Eprs, Eml5 and Fsbp with a circadian rhythm need further experimental research.

mUSP: a high-accuracy map of the in situ crosstalk of ubiquitylation and SUMOylation proteome predicted via the feature enhancement approach.

Reversible post-translational modification (PTM) orchestrates various biological processes by changing the properties of proteins. Since many proteins are multiply modified by PTMs, identification of PTM crosstalk site has emerged to be an intriguing topic and attracted much attention. In this study, we systematically deciphered the in situ crosstalk of ubiquitylation and SUMOylation that co-occurs on the same lysine residue. We first collected 3363 ubiquitylation-SUMOylation (UBS) crosstalk site on 1302 proteins and then investigated the prime sequence motifs, the local evolutionary degree and the distribution of structural annotations at the residue and sequence levels between the UBS crosstalk and the single modification sites. Given the properties of UBS crosstalk sites, we thus developed the mUSP classifier to predict UBS crosstalk site by integrating different types of features with two-step feature optimization by recursive feature elimination approach. By using various cross-validations, the mUSP model achieved an average area under the curve (AUC) value of 0.8416, indicating its promising accuracy and robustness. By comparison, the mUSP has significantly better performance with the improvement of 38.41 and 51.48% AUC values compared to the cross-results by the previous single predictor. The mUSP was implemented as a web server available at http://bioinfo.ncu.edu.cn/mUSP/index.html to facilitate the query of our high-accuracy UBS crosstalk results for experimental design and validation.

Does one subgenome become dominant in the formation and evolution of a polyploid?

BACKGROUND: Polyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution. SCOPE: In addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered. CONCLUSIONS: Contrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.

Differences between diploid donors are the main contributing factor for subgenome asymmetry measured in either gene ratio or relative diversity in allopolyploids.

Subgenome asymmetry (SA) has routinely been attributed to different responses between the subgenomes of a polyploid to various stimuli during evolution. Here, we compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences were not detected between these two types of polyploid genotypes, although they differ in times exposed to evolutionary selection. The estimated ratio of shared genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes than those for the natural genotypes, which is expected as it is now well-known that many genes in a species are not shared among all individuals. As the exact diploid parent for a given subgenome is unknown, the estimated ratios of shared genes for the natural genotypes would also include difference among individual genotypes of the diploid donor species. Further, we detected the presence of SA in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. These results indicate that SA may, to a large degree, reflect differences between its diploid donors or that changes occurred during polyploid evolution are defined by their donor genomes.

Robust approach for variable selection with high dimensional longitudinal data analysis.

This article proposes a new robust smooth-threshold estimating equation to select important variables and automatically estimate parameters for high dimensional longitudinal data. A novel working correlation matrix is proposed to capture correlations within the same subject. The proposed procedure works well when the number of covariates pn increases as the number of subjects n increases. The proposed estimates are competitive with the estimates obtained with the true correlation structure, especially when the data are contaminated. Moreover, the proposed method is robust against outliers in the response variables and/or covariates. Furthermore, the oracle properties for robust smooth-threshold estimating equations under "large n, diverging pn " are established under some regularity conditions. Extensive simulation studies and a yeast cell cycle data are used to evaluate the performance of the proposed method, and results show that the proposed method is competitive with existing robust variable selection procedures.

An efficient Gehan-type estimation for the accelerated failure time model with clustered and censored data.

In medical studies, the collected covariates contain underlying outliers. For clustered/longitudinal data with censored observations, the traditional Gehan-type estimator is robust to outliers in response but sensitive to outliers in the covariate domain, and it also ignores the within-cluster correlations. To take account of within-cluster correlations, varying cluster sizes, and outliers in covariates, we propose weighted Gehan-type estimating functions for parameter estimation in the accelerated failure time model for clustered data. We provide the asymptotic properties of the resulting estimators and carry out simulation studies to evaluate the performance of the proposed method under a variety of realistic settings. The simulation results demonstrate that the proposed method is robust to the outliers existing in the covariate domain and lead to much more efficient estimators when a strong within-cluster correlation exists. Finally, the proposed method is applied to two medical datasets and more reliable and convincing results are hence obtained.

Significance tests for analyzing gene expression data with small sample sizes.

MOTIVATION: Under two biologically different conditions, we are often interested in identifying differentially expressed genes. It is usually the case that the assumption of equal variances on the two groups is violated for many genes where a large number of them are required to be filtered or ranked. In these cases, exact tests are unavailable and the Welch's approximate test is most reliable one. The Welch's test involves two layers of approximations: approximating the distribution of the statistic by a t-distribution, which in turn depends on approximate degrees of freedom. This study attempts to improve upon Welch's approximate test by avoiding one layer of approximation. RESULTS: We introduce a new distribution that generalizes the t-distribution and propose a Monte Carlo based test that uses only one layer of approximation for statistical inferences. Experimental results based on extensive simulation studies show that the Monte Carol based tests enhance the statistical power and performs better than Welch's t-approximation, especially when the equal variance assumption is not met and the sample size of the sample with a larger variance is smaller. We analyzed two gene-expression datasets, namely the childhood acute lymphoblastic leukemia gene-expression dataset with 22 283 genes and Golden Spike dataset produced by a controlled experiment with 13 966 genes. The new test identified additional genes of interest in both datasets. Some of these genes have been proven to play important roles in medical literature. AVAILABILITY AND IMPLEMENTATION: R scripts and the R package mcBFtest is available in CRAN and to reproduce all reported results are available at the GitHub repository, https://github.com/iullah1980/MCTcodes. SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.

Accurate prediction of species-specific 2-hydroxyisobutyrylation sites based on machine learning frameworks.

Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered post-translational modification (PTM) across eukaryotes and prokaryotes in recent years, which plays a significant role in diverse cellular functions. Accurate prediction of Khib sites is a first-crucial step to decipher its molecular mechanism and urgently needed. In this work, based on a large benchmark datasets in multi-species, a novel online species-specific prediction tool, namely KhibPred, was developed to identify Khib sites. Four types of feature strategies, including sequence-based information, physicochemical properties and evolutionary-derived information, were applied to represent a wide range of protein sequences, and the random forest was used to build the optimal feature datasets. Moreover, six representative machine learning (ML) methods were trained and comprehensively discussed and compared for each organism. Data analyses suggested that the unique protein sequence preferences were discovered for each species. When evaluated on independent test datasets, the area under the receiver operating characteristic curves (AUCs) achieved 0.807, 0.781, 0.825 and 0.831 for Saccharomyces cerevisiaes, Physcomitrella patens, Rice Seeds and HeLa cells, respectively. The satisfactory results imply that KhibPred is a promising computational tool. The online predictor can be freely available at: http://bioinfo.ncu.edu.cn/KhibPred.aspx.

Identifying barley pan-genome sequence anchors using genetic mapping and machine learning.

KEY MESSAGE: We identified 1.844 million barley pan-genome sequence anchors from 12,306 genotypes using genetic mapping and machine learning. There is increasing evidence that genes from a given crop genotype are far to cover all genes in that species; thus, building more comprehensive pan-genomes is of great importance in genetic research and breeding. Obtaining a thousand-genotype scale pan-genome using deep-sequencing data is currently impractical for species like barley which has a huge and highly repetitive genome. To this end, we attempted to identify barley pan-genome sequence anchors from a large quantity of genotype-by-sequencing (GBS) datasets by combining genetic mapping and machine learning algorithms. Based on the GBS sequences from 11,166 domesticated and 1140 wild barley genotypes, we identified 1.844 million pan-genome sequence anchors. Of them, 532,253 were identified as presence/absence variation (PAV) tags. Through aligning these PAV tags to the genome of hulless barley genotype Zangqing320, our analysis resulted in a validation of 83.6% of them from the domesticated genotypes and 88.6% from the wild barley genotypes. Association analyses against flowering time, plant height and kernel size showed that the relative importance of the PAV and non-PAV tags varied for different traits. The pan-genome sequence anchors based on GBS tags can facilitate the construction of a comprehensive pan-genome and greatly assist various genetic studies including identification of structural variation, genetic mapping and breeding in barley.

Sweepstakes reproductive success is absent in a New Zealand snapper (Chrysophrus auratus) population protected from fishing despite "tiny" Ne /N ratios elsewhere.

A landmark study published in 2002 estimated a very small Ne /N ratio (around 10-5 ) in a population of pink snapper (Chrysophrys auratus, Forster, 1801) in the Hauraki Gulf in New Zealand. It epitomized the tiny Ne /N ratios (<10-3 ) reported in marine species due to the hypothesized operation of sweepstakes reproductive success (SRS). Here we re-evaluate the occurrence of SRS in marine species and the potential effect of fishing on the Ne /N ratio by studying the same species in the same region, but in a population that has been protected from fishing since 1975. We combine empirical, simulation and model-based approaches to estimate Ne (and Nb ) from genotypes of 1,044 adult fish and estimate N using recapture-probabilities. The estimated Ne /N ratio was much larger (0.33, SE: 0.14) than expected. The magnitude of estimates of population-wide variance in individual lifetime reproductive success (10-18) suggested that the sweepstakes effect was negligible in the study population. After evaluating factors that could explain the contrast between studies - experimental design, life history differences, environmental effects and the influence of exploitation on the Ne /N ratio - we conclude that the low Ne of the Hauraki Gulf population is associated with demographic instability in the harvested compared to the protected population despite circumstantial evidence that the 2002 study may have underestimated Ne . This study has broad implications for the prevailing view that reproductive success in the sea is largely driven by chance, and for genetic monitoring of populations using the Ne /N ratio and Nb .

Selection of working correlation structure in generalized estimating equations.

The well-known generalized estimating equations is a very popular approach for analyzing longitudinal data. Selecting an appropriate correlation structure in the generalized estimating equations framework is a key step for estimating parameters efficiently and deriving reliable statistical inferences. We present two new criteria for selecting the best among the candidates with any arbitrary structures, even for irregularly timed measurements. The simulation results demonstrate that the new criteria perform more similarly to EAIC and EBIC as the sample size becomes large. However, their performance is much enhanced when the sample size is small and the number of measurements is large. Finally, three real datasets are used to illustrate the proposed criteria. Copyright © 2017 John Wiley & Sons, Ltd.

Mixture of time-dependent growth models with an application to blue swimmer crab length-frequency data.

Understanding how aquatic species grow is fundamental in fisheries because stock assessment often relies on growth dependent statistical models. Length-frequency-based methods become important when more applicable data for growth model estimation are either not available or very expensive. In this article, we develop a new framework for growth estimation from length-frequency data using a generalized von Bertalanffy growth model (VBGM) framework that allows for time-dependent covariates to be incorporated. A finite mixture of normal distributions is used to model the length-frequency cohorts of each month with the means constrained to follow a VBGM. The variances of the finite mixture components are constrained to be a function of mean length, reducing the number of parameters and allowing for an estimate of the variance at any length. To optimize the likelihood, we use a minorization-maximization (MM) algorithm with a Nelder-Mead sub-step. This work was motivated by the decline in catches of the blue swimmer crab (BSC) (Portunus armatus) off the east coast of Queensland, Australia. We test the method with a simulation study and then apply it to the BSC fishery data.

Optimization of suspended particulate transport parameters from measured concentration profiles with a new analytical model.

The water body's suspended concentration reflects many coastal environmental indicators, which is important for predicting ecological hazards. The modeling of any concentration in water requires solving the settling-diffusion equation (SDE), and the values of several key input parameters therein (settling velocity ws, eddy diffusivity Ds, and erosion rates p(t)) directly determine the prediction performance. The time-consuming large-scale simulations would benefit if the parameter values could be estimated through available observations in the target sea area. The present work proposes a new optimization method for synchronously estimating the three parameters from limited concentration observations. First, an analytical solution to the one-dimensional vertical (1DV) SDE for suspended concentrations in an unsteady scenario is derived. Second, the near bottom suspended sediment concentration (SSC) profiles are measured with high-resolution observation. Third, the key parameters are optimized through the best fit of the measured SSC profiles and those modeled with the unsteady solution. Nonlinear least square fitting (NLSF) is introduced to judge the best fits automatically. The high-resolution concentration measurements in a specially-designed cylindrical tank experiment using the Yellow River Delta sediments test the proposed method. The method performs well in the initial period of turbulence generation when sediment resuspension is significant. It optimizes p(t), ws, and Ds with reasonable values and uniqueness of their combination. The proposed theory is a practical tool for quickly estimating key substance transport parameters from limited observations; it also has the potential to construct local parametric models to benefit the 3D modeling of coastal substance transport. Although the present work takes SSC as an example, it can be extended to any suspended particulate concentration in the water.

Assessing and predicting water quality index with key water parameters by machine learning models in coastal cities, China.

The water quality index (WQI) is a widely used tool for comprehensive assessment of river environments. However, its calculation involves numerous water quality parameters, making sample collection and laboratory analysis time-consuming and costly. This study aimed to identify key water parameters and the most reliable prediction models that could provide maximum accuracy using minimal indicators. Water quality from 2020 to 2023 were collected including nine biophysical and chemical indicators in seventeen rivers in Yancheng and Nantong, two coastal cities in Jiangsu Province, China, adjacent to the Yellow Sea. Linear regression and seven machine learning models (Artificial Neural Network (ANN), Self-Organizing Maps (SOM), K-Nearest Neighbor (KNN), Support Vector Machines (SVM), Random Forest (RF), Extreme Gradient Boosting (XGB) and Stochastic Gradient Boosting (SGB)) were developed to predict WQI using different groups of input variables based on correlation analysis. The results indicated that water quality improved from 2020 to 2022 but deteriorated in 2023, with inland stations exhibiting better conditions than coastal ones, particularly in terms of turbidity and nutrients. The water environment was comparatively better in Nantong than in Yancheng, with mean WQI values of approximately 55.3-72.0 and 56.4-67.3, respectively. The classifications "Good" and "Medium" accounted for 80 % of the records, with no instances of "Excellent" and 2 % classified as "Bad". The performance of all prediction models, except for SOM, improved with the addition of input variables, achieving R2 values higher than 0.99 in models such as SVM, RF, XGB, and SGB. The most reliable models were RF and XGB with key parameters of total phosphorus (TP), ammonia nitrogen (AN), and dissolved oxygen (DO) (R2 = 0.98 and 0.91 for training and testing phase) for predicting WQI values, and RF using TP and AN (accuracy higher than 85 %) for WQI grades. The prediction accuracy for "Medium" and "Low" water quality grades was highest at 90 %, followed by the "Good" level at 70 %. The model results could contribute to efficient water quality evaluation by identifying key water parameters and facilitating effective water quality management in river basins.

Optimising the sampling effort in riparian surveys.

Riparian condition is commonly measured as part of stream health monitoring programs as riparian vegetation provides an intricate linkage between the terrestrial and aquatic ecosystems. Field surveys of a riparian zone provide comprehensive riparian attribute data but can be considerably intensive and onerous on resources and workers. Our objective was to assess the impact of reducing the sampling effort on the variation in key riparian health indicators. Subsequently, we developed a non-parametric approach to calculate an information retained (IR) statistic for comparing several constrained systematic sampling schemes to the original survey. The IR statistic is used to select a scheme that reduces the time taken to undertake riparian surveys (and thus potentially the costs) whilst maximising the IR from the original survey. Approximate bootstrap confidence intervals were calculated to improve the inferential capability of the IR statistic. The approach is demonstrated using riparian vegetation indicators collected as part of an aquatic ecosystem health monitoring program in Queensland, Australia. Of the nine alternative sampling designs considered, the sampling design that reduced the sampling intensity per site by sixfold without significantly comprising the quality of the IR, results in halving the time taken to complete a riparian survey at a site. This approach could also be applied to reducing sampling effort involved in monitoring other ecosystem health indicators, where an intensive systematic sampling scheme was initially employed.

A hybrid deep learning framework for air quality prediction with spatial autocorrelation during the COVID-19 pandemic.

China implemented a strict lockdown policy to prevent the spread of COVID-19 in the worst-affected regions, including Wuhan and Shanghai. This study aims to investigate impact of these lockdowns on air quality index (AQI) using a deep learning framework. In addition to historical pollutant concentrations and meteorological factors, we incorporate social and spatio-temporal influences in the framework. In particular, spatial autocorrelation (SAC), which combines temporal autocorrelation with spatial correlation, is adopted to reflect the influence of neighbouring cities and historical data. Our deep learning analysis obtained the estimates of the lockdown effects as - 25.88 in Wuhan and - 20.47 in Shanghai. The corresponding prediction errors are reduced by about 47% for Wuhan and by 67% for Shanghai, which enables much more reliable AQI forecasts for both cities.

Synthesis of cationic polymer decorated with halogen for highly efficient trapping 99TcO4-/ReO4.

The elimination of anion is of great importance from radioactive nuclear waste containing 99TcO4- by rationally designing anion-scavenging materials with high density of charge and more accessible adsorption sites. Herein, a tailor-made cationic organic polymer with donor-acceptor (D-A) structure, namely TrDCPN, was successfully synthesized by rationally modifying the benzimidazole unit for efficient trapping the perrhenate (ReO4-) as a 99Tc surrogate. Systematic control of the skeleton affect enables the material to integrate a variety of features, surmounting the long-term challenge of 99TcO4-/ReO4- remediation under extreme conditions of high acid/base and high ionic strength. Furthermore, the TrDCPN shows excellent affinity toward ReO4- in the existence of large excess of competitive anions (SO42-, NO3- and PO43-etc.) as well as promising reusability for trapping ReO4-. The excellent stability and separation were derived from the introduction of large conjugated modules, triazine core and hydrophobic. More importantly, the synthetic cationic organic polymer with D-A feature was first proved that the introduction of halogen can effectively enhance the backbone charge, and increase the adsorption capacity by synergy of ion exchange, electrostatic interaction and δ hole-anion interaction. The adsorption capacity of TrDCPN can be up to 420.3 mg/g and reach equilibrium within 20 min. It is noteworthy that TrDCPN successfully immobilizes ReO4- from simulated Hanford waste with a high separation efficiency of 93 %, providing a new paradigm for material design to dispose of the problem of radioactive pollutants in the environment.