Persistent Homology in Sparse Regression and its Application to Brain Morphometry

Sparse systems are usually parameterized by a tuning parameter that determines the sparsity of the system. How to choose the right tuning parameter is a fundamental and difficult problem in learning the sparse system. In this paper, by treating the the tuning parameter as an additional dimension, persistent homological structures over the parameter space is introduced and explored. The structures are then further exploited in speeding up the computation using the proposed soft-thresholding technique. The topological structures are further used as multivariate features in the tensor-based morphometry (TBM) in characterizing white matter alterations in children who have experienced severe early life stress and maltreatment. These analyses reveal that stress-exposed children exhibit more diffuse anatomical organization across the whole white matter region.Comment: submitted to IEEE Transactions on Medical Imagin

Hodge-Decomposition of Brain Networks

We analyze brain networks by decomposing them into three orthogonal components: gradient, curl, and harmonic flows, through the Hodge decomposition, a technique advantageous for capturing complex topological features. A Wasserstein distance based topological inference is developed to determine the statistical significance of each component. The Hodge decomposition is applied to human brain networks obtained from a resting-state fMRI study. Our results indicate statistically significant differences in the topological features between male and female brain networks.Comment: Will be published in ISBI 202

Idiosyncratic Drug-Induced Liver Injury (IDILI): Potential Mechanisms and Predictive Assays

Idiosyncratic drug-induced liver injury (IDILI) is a significant source of drug recall and acute liver failure (ALF) in the United States. While current drug development processes emphasize general toxicity and drug metabolizing enzyme- (DME-) mediated toxicity, it has been challenging to develop comprehensive models for assessing complete idiosyncratic potential. In this review, we describe the enzymes and proteins that contain polymorphisms believed to contribute to IDILI, including ones that affect phase I and phase II metabolism, antioxidant enzymes, drug transporters, inflammation, and human leukocyte antigen (HLA). We then describe the various assays that have been developed to detect individual reactions focusing on each of the mechanisms described in the background. Finally, we examine current trends in developing comprehensive models for examining these mechanisms. There is an urgent need to develop a panel of multiparametric assays for diagnosing individual toxicity potential

Topological Data Analysis of Human Brain Networks Through Order Statistics

Understanding the topological characteristics of the brain network across a population is central to understanding brain functions. The abstraction of human connectome as a graph has been pivotal in gaining insights on the topological features of the brain network. The development of group-level statistical inference procedures in brain graphs while accounting for the heterogeneity and randomness still remains a difficult task. In this study, we develop a robust statistical framework based on persistent homology using the order statistics for analyzing brain networks. The use of order statistics greatly simplifies the computation of the persistent barcodes. We validate the proposed methods using comprehensive simulation studies and subsequently apply to the resting-state functional magnetic resonance images. We conclude a statistically significant topological difference between the male and female brain networks

Plug-and-play software for mechanistic modelling of end-to-end continuous manufacturing of monoclonal antibodies

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Health-Promoting Phytochemicals from 11 Mustard Cultivars at Baby Leaf and Mature Stages

Mustard is a Brassica vegetable that provides a number of phytonutrients. However, the phytonutrient profile of mustard has been relatively limited. We analyzed the glucosinolates and their hydrolysis products, carotenoids, total anthocyanin and phenolic contents, and antioxidant capacity of the leaves of 11 mustard cultivars grown in a greenhouse at the baby leaf and mature stages. An aliphatic glucosinolate sinigrin and its hydrolysis products allyl isothiocyanate and 1-cyano-2,3-epithiopropane were the major phytonutrients in the mustard leaves. Carotenoids β-carotene, lutein, violaxanthin, and neoxanthin were detected. We found phytonutrient concentration and their change with plant growth were cultivar-dependent. The %RDA value for vitamin A calculated using β-carotene content and retinol activity equivalents suggests that mustard cultivars used in this study can be a good source of vitamin A. Phenolic contents and antioxidant capacity also varied among cultivars and between physiological stages. Our results suggest that mustard leaves are rich in various phytochemicals and their composition depends on cultivar and the physiological stage. This is the first report on phytochemical composition in various mustard cultivars at different physiological stages

Effects of remote limb ischemic conditioning on muscle strength in healthy young adults: A randomized controlled trial

Remote limb ischemic conditioning (RLIC) is a clinically feasible method in which brief, sub-lethal bouts of ischemia protects remote organs or tissues from subsequent ischemic injury. A single session of RLIC can improve exercise performance and increase muscle activation. The purpose of this study, therefore, was to assess the effects of a brief, two-week protocol of repeated RLIC combined with strength training on strength gain and neural adaptation in healthy young adults. Participants age 18-40 years were randomized to receive either RLIC plus strength training (n = 15) or sham conditioning plus strength training (n = 15). Participants received RLIC or sham conditioning over 8 visits using a blood pressure cuff on the dominant arm with 5 cycles of 5 minutes each alternating inflation and deflation. Visits 3-8 paired conditioning with wrist extensors strength training on the non-dominant (non-conditioned) arm using standard guidelines. Changes in one repetition maximum (1 RM) and electromyography (EMG) amplitude were compared between groups. Both groups were trained at a similar workload. While both groups gained strength over time (P = 0.001), the RLIC group had greater strength gains (9.38 ± 1.01 lbs) than the sham group (6.3 ± 1.08 lbs, P = 0.035). There was not a significant group x time interaction in EMG amplitude (P = 0.231). The RLIC group had larger percent changes in 1 RM (43.8% vs. 26.1%, P = 0.003) and EMG amplitudes (31.0% vs. 8.6%, P = 0.023) compared to sham conditioning. RLIC holds promise for enhancing muscle strength in healthy young and older adults, as well as clinical populations that could benefit from strength training

3D Cultures of Human Liver Cell Lines Encapsulated in PuraMatrix on a Microarray Chip Platform

A high-throughput cell printing technology has developed to simulate the liver tissue environment using a hydrogel-based chip platform that has potential to shift in vivo drug toxicity models towards in vitro tests. However, the hydrophobic nature of polystyrene chips is not promoting direct adhesion of hydrogels, which created a problem with spot attachment. The main goal of this research is to create a surface chemistry that helps to attach a peptide-based hydrogel, including PuraMatrix, to a polystyrenebased micropillar chip. Seven analogs of maleic anhydride co-polymers were used to coat the micropillar chip to create a functional surface. Then, six ionic solutions were tested for inducing gelation of PuraMatrix. Formation of bubbles and spot detachment on the chip platform was quantified. As a result, an optimum polymer, PMA-OD was selected for surface attachment based on its low bubble formation and high spot attachment. This polymer could easily coat the chip for better gel adhesion. In regards to the gelation of PuraMatrix, poly-L-lysine was the most favorable for spot attachment and cell viability on the chip platform. In future research, encapsulated human liver cells expressing drug metabolizing enzymes will be tested with different drugs to determine mechanisms of drug toxicity.https://engagedscholarship.csuohio.edu/u_poster_2014/1019/thumbnail.jp

3DFeat-Net: Weakly Supervised Local 3D Features for Point Cloud Registration

In this paper, we propose the 3DFeat-Net which learns both 3D feature detector and descriptor for point cloud matching using weak supervision. Unlike many existing works, we do not require manual annotation of matching point clusters. Instead, we leverage on alignment and attention mechanisms to learn feature correspondences from GPS/INS tagged 3D point clouds without explicitly specifying them. We create training and benchmark outdoor Lidar datasets, and experiments show that 3DFeat-Net obtains state-of-the-art performance on these gravity-aligned datasets.Comment: 17 pages, 6 figures. Accepted in ECCV 201