Introduction

Bowman, Judith

doi:10.1093/oso/9780197547366.003.0001

Cited by 2 publications

(2 citation statements)

References 16 publications

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“…PsiPartition is implemented within Python 3.12.1. To perform the Bayesian optimization, wandb package (version 0.16.1) [52] are also used [53]. It employed normalized Gaussian process model with Matern kernel [54] and parameter 𝛼 = 10 −7 .…”

Section: Resultsmentioning

confidence: 99%

PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization

Xu,

Onoda

2024

Preprint

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Phylogenetics has been widely used in molecular biology to infer the evolutionary relationships among species. With the rapid development of sequencing technology, genomic data with thousands of sites becomes increasingly common in phylogenetic analysis, while heterogeneity among sites arises as one of the major challenges. A single homogeneous model is not sufficient to describe the evolution of all sites and partitioned models are often employed to model the evolution of heterogeneous sites by partitioning them into distinct groups and utilizing distinct evolutionary models for each group. It is crucial to determine the best partitioning, which greatly affects the reconstruction correctness of phylogeny. However, the best partitioning is usually intractable to obtain in practice. Traditional partitioning methods rely on heuristic algorithms or greedy search to determine the best ones in their solution space, are usually time-consuming, and with no guarantee of optimality. In this study, we propose a novel partitioning approach, termed PsiPartition, based on the parameterized sorting indices of sites and Bayesian optimization. We apply our method to empirical data sets and it performs significantly better compared to existing methods, in terms of Bayesian information criterion (BIC) and the corrected Akaike information criterion (AICc). We test PsiPartition on the simulated data sets with different site heterogeneity, alignment lengths, and number of loci. It is demonstrated that PsiPartition evidently and stably outperforms other methods in terms of the Robinson-Foulds (RF) distance between the true simulated trees and the reconstructed trees, especially on the data with more site heterogeneity. More importantly, our proposed Bayesian optimization-based method, for the first time, provides a new general framework to efficiently determine the optimal number of partitions. The corresponding reproducible source code and data are available athttp://github.com/xu-shi-jie/PsiPartition.

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Section: Resultsmentioning

confidence: 99%

PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization

Xu,

Onoda

2024

Preprint

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“…Oral symptoms in children due to B6 deficiency encompass angular cheilitis, glossitis, RAS, and halitosis (Figure 7). Immune system decline may also precipitate fungal infections in the oral cavity, akin to those seen with vitamin A shortages [91,92]. Biotin (vitamin H or B7) serves as a vital coenzyme for the metabolism of fats, carbohydrates, and amino acids, supporting cellular proliferation and the health of hair and nails [21,93].…”

Section: Oral Manifestations Of B-complex Vitamin Deficiencymentioning

confidence: 99%

The Impact of Vitamin Deficiencies on Oral Manifestations in Children

Lešić,

Ivanišević,

Špiljak

et al. 2024

Dentistry Journal

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Vitamins play a vital role in human health, particularly in the development and maintenance of oral health in children. These nutrients are broadly categorized into fat-soluble and water-soluble types, crucial for children’s well-being. The objective of this study is to investigate the impact of vitamin deficiencies on the oral health of children, focusing on how these deficiencies contribute to various oral health issues and determining the relationship between specific vitamin shortages and oral diseases. Findings indicate that shortages in vitamins A and D lead to enamel issues and a higher susceptibility to dental diseases, vitamin E assists in treating oral mucositis, and vitamin K is essential for blood clotting in dental surgeries. Deficits in B-complex and vitamin C result in enamel hypomineralization and soft tissue ailments, including aphthous stomatitis and gingival petechiae. Additionally, a lack of vitamin B7 compromises the immune response, increasing oral candidiasis risk. Therefore, vitamin deficiencies markedly affect children’s oral health, highlighting the need for joint efforts between dental professionals and caregivers for effective pediatric care. Addressing vitamin deficiencies through supplementation and tailored dental care emphasizes the significance of nutritional health in children’s overall and dental well-being, advocating for a collaborative approach to achieve optimal health outcomes.

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Introduction

Cited by 2 publications

References 16 publications

PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization

PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization

The Impact of Vitamin Deficiencies on Oral Manifestations in Children

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