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Introduction: The advent of RNA sequencing (RNA-Seq) has significantly advanced our understanding of the transcriptomic landscape, revealing intricate gene expression patterns across biological states and conditions. However, the complexity and volume of RNA-Seq data pose challenges in identifying differentially expressed genes (DEGs), critical for understanding the molecular basis of diseases like cancer. Methods: We introduce a novel Machine Learning-Enhanced Genomic Data Analysis Pipeline (ML-GAP) that incorporates autoencoders and innovative data augmentation strategies, notably the MixUp method, to overcome these challenges. By creating synthetic training examples through a linear combination of input pairs and their labels, MixUp significantly enhances the model's ability to generalize from the training data to unseen examples. Results: Our results demonstrate the ML-GAP's superiority in accuracy, efficiency, and insights, particularly crediting the MixUp method for its substantial contribution to the pipeline's effectiveness, advancing greatly genomic data analysis and setting a new standard in the field. Discussion: This, in turn, suggests that ML-GAP has the potential to perform more accurate detection of DEGs but also offers new avenues for therapeutic intervention and research. By integrating explainable artificial intelligence (XAI) techniques, ML-GAP ensures a transparent and interpretable analysis, highlighting the significance of identified genetic markers. [ABSTRACT FROM AUTHOR]

Reduced exercise capacity in pulmonary hypertension (PH) significantly impacts quality of life. However, the cause of reduced exercise capacity in PH remains unclear. The objective of this study was to investigate whether intrinsic skeletal muscle changes are causative in reduced exercise capacity in PH using preclinical PH rat models with different PH severity. PH was induced in adult Sprague–Dawley (SD) or Fischer (CDF) rats with one dose of SU5416 (20 mg/kg) injection, followed by 3 weeks of hypoxia and additional 0–4 weeks of normoxia exposure. Control rats were injected with vehicle and housed in normoxia. Echocardiography was performed to assess cardiac function. Exercise capacity was assessed by VO2 max. Skeletal muscle structural changes (atrophy, fiber type switching, and capillary density), mitochondrial function, isometric force, and fatigue profile were assessed. In SD rats, right ventricular systolic dysfunction is associated with reduced exercise capacity in PH rats at 7‐week timepoint in comparison to control rats, while no changes were observed in skeletal muscle structure, mitochondrial function, isometric force, or fatigue profile. CDF rats at 4‐week timepoint developed a more severe PH and, in addition to right ventricular dysfunction, the reduced exercise capacity in these rats is associated with skeletal muscle atrophy; however, mitochondrial function, isometric force, and fatigue profile in skeletal muscle remain unchanged. Our data suggest that cardiopulmonary impairments in PH are the primary cause of reduced exercise capacity, which occurs before intrinsic skeletal muscle dysfunction. [ABSTRACT FROM AUTHOR]

Coronary artery disease (CAD) is the leading cause of mortality in diabetic patients. Because of the diffuse nature of their disease, diabetic patients may be at risk for incomplete revascularization, highlighting a potential role for proangiogenic therapy in this group. This study investigates molecular mechanisms of angiogenesis in diabetic patients. Myocardial tissue was harvested from patients undergoing coronary artery bypass grafting [nondiabetic (ND) 11, type 2 diabetic (DM) 10]. Expression of angiostatin, endostatin, their precursors (plasminogen and collagen XVIII, respectively), enzymes leading to their production [matrix metalloprotease (MMP)-2 and -9, cathepsin L], and an inhibitor of MMPs (tissue inhibitor of metalloproteinase) was assessed with Western blotting. MMP activity was assessed. Coronary collateralization was graded by Rentrop scoring of angiograms. Plasminogen and collagen XVIII expression were similar between groups. Angiostatin expression trended to increase 1.24-fold (P = 0.07), and endostatin expression increased 2.02-fold in DM patients relative to ND (P = 0.02). MMP-9 expression was no different between groups, whereas MMP-2 expression decreased 1.8-fold in diabetics (P = 0.003). MMP-2 and -9 activity decreased 1.33-fold (P = 0.03) and 1.57-fold (P = 0.04), respectively, in diabetic patients. Cathepsin L expression was 1.38-fold higher in diabetic patients (P = 0.02). Coronary collateralization scores were ND 2.1 [+ or -] 0.37 vs. DM 1.0 [+ or -] 0.4 (P = 0.05). Myocardial endostatin expression correlated strongly with the percentage of hemoglobin [A.sub.1c] (r = 0.742, P = 0.0001). Myocardial expression of angiostatin and endostatin demonstrated significant negative linear correlations with coronary collateralization (angiostatin r = -0.531, P = 0.035, endostatin r = -0.794, P = 0.0002). Diabetic patients with CAD exhibit increased levels of the antiangiogenie proteins angiostatin and endostatin and differential regulation of the enzymes governing their production relative to ND patients. Myocardial levels of these proteins show significant correlation to coronary collateralization. These findings offer potential new therapeutic targets for enhancing proangiogenic therapy and insight into the angiogenic impairments seen in diabetes. matrix metalloprotease; tissue inhibitor of metalloprotease

Transforming growth factor (TGF)-[beta] is a potent inflammatory mediator involved in acute lung injury. TGF-[beta] directly increases pulmonary endothelial myosin light chain (MLC) phosphorylation, which is associated with increased endothelial stress fiber formation, gap formation, and protein permeability, all hallmarks of pulmonary endothelial responses during acute lung injury. We performed the following experiments in pulmonary endothelial monolayers to determine whether RhoA and Rho-kinase mediate these TGF-[beta]-induced responses. TGF-[beta] caused the sustained activation of RhoA 2 h post-treatment associated with increased MLC phosphorylation. Inhibition of either RhoA or Rho-kinase with either C3 exoenzyme or Y-27632 blocked MLC phosphorylation. In addition, both C3 and Y-27632 partially attenuated the maximal TGF-[beta]-induced increase in permeability but did not affect the initial phase of compromised barrier integrity. Inhibition of Rho-kinase completely blocked the TGF-[beta]-induced increase in the content of filamentous actin (F-actin) but only partially inhibited TGF-[beta]-induced changes in actin reorganization. To assess the contribution of Rho-kinase in RhoA-mediated responses independent of additional TGF-[beta]-induced signals, cells were infected with a constitutively active RhoA adenovirus (RhoAQ63L) with or without Y-27632. RhoAQ63L increased MLC phosphorylation, Factin content, and permeability. Treatment with Y-27632 blocked these responses, suggesting that Rho-kinase mediates these RhoA-induced effects. Collectively, these data suggest the following: 1) the RhoA/Rho-kinase pathway is an important component of TGF-[beta]-induced effects on endothelial MLC phosphorylation, cytoskeletal reorganization, and barrier integrity; and 2) additional signaling mechanisms independent of the RhoA/Rho-kinase signaling cascade contribute to TGF-[beta]-induced changes in cytoskeletal organization and permeability. myosin light chain; actin; stress fiber; transforming growth factor-[beta]

p38 MAPK activation by TGF-[beta]1 increases MLC phosphorylation and endothelial monolayer permeability. Am J Physiol Lung Cell Mol Physiol 282: L146-L154, 2002.--Transforming growth factor (TGF)-[beta]1 increases endothelial monolayer permeability and myosin light chain phosphorylation (MLC-P) beginning 1-2 h posttreatment, suggesting that changes in gene expression may be required for these responses. The role of extracellular signal-regulated kinase (ERK)1/2 and p38 mitogen-activated protein kinase (p38 MAPK) was investigated because both kinases have been implicated in regulating gene expression after TGF-[beta]1. ERK1/2 phosphorylation increased threefold above the control level, and the increase was temporally associated with the increase in MLC-P. Inhibition of ERK1/2 phosphorylation with the MAPK kinase inhibitor U-0126 did not prevent the increase in either monolayer permeability or MLC-P. p38 MAPK phosphorylation increased fourfold above the control level, but unlike ERK1/2, this increase peaked 30 min and i h post-TGF-[beta]1 treatment. Inhibition of p38 MAPK activity with SB-203580 prevented the increases in both monolayer permeability and MLC-P. Treatment of the monolayers with cycloheximide in conjunction with TGF-[beta]1-inhibited MLC-P, showing a requirement for protein synthesis. These studies demonstrate that p38 MAPK activation and subsequent protein synthesis are part of the signal transduction pathway leading to the TGF-[betal]1-induced increases in monolayer permeability and MLC-P. transforming growth factor-[beta]1; myosin light chain phosphorylation; endothelial cells; cycloheximide; mitogen-activated protein kinase