An Information-Theoretic Measure for Balance Assessment in Comparative Clinical Studies

Dalton, Jarrod E.; Benish, William A.; Krieger, Nikolas I.

doi:10.3390/e22020218

Cited by 5 publications

(6 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To further examine the deleterious effect of the identified missense variants on CDH23, and ARSB, several in silico tools, namely, Sorting Intolerant from Tolerant (SIFT) (17), Polymorphism Phenotyping v2 (PolyPhen-2.0) (18), Fathmm (19), and Mutation Taster (20), were used. Multiple sequence alignment (MSA) was performed to determine the conservation of amino acids at the missense position (p. Arg159Cys) in ARSB and (p.Arg1746Gln) in CDH23, and Jensen-Shannon Divergence (JSD) scores were also calculated (21). Amino acid sequences of CDH23, and ARSB protein from Homo sapiens (human), Mus musculus (house mouse), Rattus norvegicus (Norway rat), Callorhinchus milii (elephant shark), Bos taurus (cattle), Danio rerio (zebrafish), Felis catus (domestic cat), Pan troglodytes (chimpanzee), and Vulpes Vulpes (red fox) were retrieved from National Center for Biotechnology Information (NCBI) RefSeq and aligned using Clustal Omega (22).…”

Section: In Silico Analysismentioning

confidence: 99%

Case Report: Reinterpretation and Reclassification of ARSB:p.Arg159Cys Variant Identified in an Emirati Patient With Hearing Loss Caused by a Pathogenic Variant in the CDH23 Gene

et al. 2022

View full text Add to dashboard Cite

Arylsulfatase B is an enzyme present in the lysosomes that involves in the breakdown of large sugar molecules known as glycosaminoglycans (GAGs). Arylsulfatase B chemically modifies two GAGs, namely, dermatan sulfate and chondroitin sulfate, by removing the sulfate group. Mutations in the gene encoding the arylsulfataseB enzyme causes lysosomal storage disorder, mucopolysaccharidosis type VI (MPS VI), or Maroteaux–Lamy syndrome. In this study, we report a case of congenital hearing loss with mild pigmentary changes in the retina, indicative of Usher syndrome, and a missense variant reported as likely pathogenic for MPS VI. Sequencing results identified a pathogenic missense variant p.Arg1746Gln in the CDH23 gene. However, another missense variant ARSB:p.Arg159Cys was reported as likely pathogenic to the treating physician. Mutations in ARSB gene have been associated with MPS VI. Subsequently, ARSB enzyme activity was found low twice in dried blood spot (DBS), suggestive of MPS VI. The patient did not have the clinical features of MPS VI, but considering the wide clinical spectrum, progressive nature of MPS VI, and the fact that a treatment for MPS VI is available to prevent disease progression, further biochemical, enzymatic, and in silico studies were performed to confirm the pathogenicity of this variant. In silico tools predicted this variant to be pathogenic. However, the results of urine and serum GAGs and ARSB enzyme levels measured from patient's fibroblast were found normal. Based on clinical and biochemical findings, ARSB:p.Arg159Cys is likely benign and did not support the diagnosis of MPS VI. However, CDH23:p.Arg1746Gln, a pathogenic variant, supports the underlying cause of hearing loss. This study highlights the importance of a robust correlation between genetic results and clinical presentation, and biochemical and enzymatic studies, to achieve a differential diagnosis.

show abstract

Section: In Silico Analysismentioning

confidence: 99%

Case Report: Reinterpretation and Reclassification of ARSB:p.Arg159Cys Variant Identified in an Emirati Patient With Hearing Loss Caused by a Pathogenic Variant in the CDH23 Gene

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Although this definition is arbitrary, it precisely defines a tight distribution with minimal variation in κ gi that appropriately scales with the magnitude of curvature in a partition. For distributions f 1 (X) and , where is the common distribution and is the relative entropy, which captures the divergence from the given probability distribution f ( X ) t the reference distribution g ( X ) [77, 78]. The discrete form is calculated.…”

Section: Demographic Informationmentioning

confidence: 99%

“…1 g(x) ln g(x) f (x) dx is the relative entropy, which captures the divergence from the given probability distribution f (X) to the reference distribution g(X) [77,78]. The discrete form D(g(X)f (X)) = P x2X g(x) ln g(x) f (x) is calculated.…”

Section: A5 Jensen-shannon Divergence Of Within-partition Gaussian Cu...mentioning

confidence: 99%

The Geometric Evolution of Aortic Dissections: Predicting Surgical Success using Fluctuations in Integrated Gaussian Curvature

Khabaz

Sankary

Yuan

et al. 2022

Preprint

View full text Add to dashboard Cite

Cross-sectional imaging, such as computed tomography (CTA) scans, provide unparalleled visualization of aortic anatomy. However, despite the immense geometric and anatomic detail provided by CTA imaging, surgeons continue to interact with this data in a linear and dimensionally reduced feature space. Aortic pathologies such as aneurysms and dissections are clinically quantified using a single scalar: maximum aortic diameter. To date, not feature of aortic shape has reproducibly captured what surgeons often describe qualitatively when looking at CT scans or when in the operating room observing the physical anatomy. Shape along with size plays a central role in differentiating normal from diseased aortas. We defined a geometric feature space using tools of modern differential geometry that incorporate shape and size. We show that size can be parameterized by l, the radial aortic extent commonly taken as aortic diameter. Size invariant shape is quantified by performing a Gauss map of local regions on the aortic surface and calculating the variance of the total integrated curvature (δK) across each aorta. While we do not inherently study aortic stability as it relates to clinical rupture in this paper, aortas appearing at high δK are clinically classified by size and qualitative appearance as high risk. It is therefor interesting to conjecture that divergence in the (δK,l)-space is a sign of aortic topologic instability. Projection into (δK, l)-space provides two independent variables that show a natural division of the data as it transitions from size to shape dominated behavior, an indictor of aortic fragility.

show abstract

“…where I represent Kullback-Leibler (KL), information divergence against independence, and is a measure of the likely dependence between the component variables [38], [39].The joint distribution of the random variables to the product of their marginal distribution is the major contrast base on the hypothesis that they are distributed independently to the level that the joint distribution significantly varies from the distribution of the random variable base on the theory of dependency. Hence, this is known as measure of multicollinearity or interdependence between variables.…”

Section: Information Measure Of Dependence In High-dimensionsmentioning

confidence: 99%

Maximal Covariance Complexity-Based Penalized Likelihood Method in High Dimensional Data

Kargi¹,

Ismail²,

Mohamad³

2020

IJMH

View full text Add to dashboard Cite

Classification of cancer and selection of genes is one of the most important application of DNA microarray data. As a result of the higher dimensionality of microarray data, classification and selection of gene techniques are frequently employed to support the professional systems in the diagnosing ability of cancer with higher precision in classification. Least absolute shrinkage and selection operator (LASSO) is one of the most popular method for cancer classification and gene selection in high dimensional data. However, Lasso has limitations of being biased and cannot select variables more than the sample size (n) in gene selection and classification of high dimensional microarray data. To address this problems, LASSO-C1F was proposed using scale invariant measure of maximal information complexity of covariance matrix denoted with weight modifications as data-adaptive alternative to the fairly arbitrary choice of the regularization term in the least absolute shrinkage and selection operator (LASSO). The results indicated the effectiveness of the proposed method LASSO-C1F over the classical LASSO. The evaluation criteria result shows that the proposed method, LASSO-C1F has a better performance in terms of AUC and number of genes selected

show abstract

An Information-Theoretic Measure for Balance Assessment in Comparative Clinical Studies

Cited by 5 publications

References 8 publications

Case Report: Reinterpretation and Reclassification of ARSB:p.Arg159Cys Variant Identified in an Emirati Patient With Hearing Loss Caused by a Pathogenic Variant in the CDH23 Gene

Case Report: Reinterpretation and Reclassification of ARSB:p.Arg159Cys Variant Identified in an Emirati Patient With Hearing Loss Caused by a Pathogenic Variant in the CDH23 Gene

The Geometric Evolution of Aortic Dissections: Predicting Surgical Success using Fluctuations in Integrated Gaussian Curvature

Maximal Covariance Complexity-Based Penalized Likelihood Method in High Dimensional Data

Contact Info

Product

Resources

About