Curcumin regulates pulmonary extracellular matrix remodeling and mitochondrial function to attenuate pulmonary fibrosis by regulating the miR-29a-3p/DNMT3A axis.

Epigenetic regulation and mitochondrial dysfunction are essential to the progression of idiopathic pulmonary fibrosis (IPF). Curcumin (CCM) in inhibits the progression of pulmonary fibrosis by regulating the expression of specific miRNAs and pulmonary fibroblast mitochondrial function; however, the underlying mechanism is unclear. C57BL/6 mice were intratracheally injected with bleomycin (5 mg/kg) and treated with CCM (25 mg/kg body weight/3 times per week, intraperitoneal injection) for 28 days. Verhoeff-Van Gieson, Picro sirius red, and Masson's trichrome staining were used to examine the expression and distribution of collagen and elastic fibers in the lung tissue. Pulmonary fibrosis was determined using micro-computed tomography and transmission electron microscopy. Human pulmonary fibroblasts were transfected with miR-29a-3p, and RT-qPCR, immunostaining, and western blotting were performed to determine the expression of DNMT3A and extracellular matrix collagen-1 (COL1A1) and fibronectin-1 (FN1) levels. The expression of mitochondrial electron transport chain complex (MRC) and mitochondrial function were detected using western blotting and Seahorse XFp Technology. CCM in increased the expression of miR-29a-3p in the lung tissue and inhibited the DNMT3A to reduce the COL1A1 and FN1 levels leading to pulmonary extracellular matrix remodeling. In addition, CCM inhibited pulmonary fibroblasts MRC and mitochondrial function via the miR-29a-3p/DNMT3A pathway. CCM attenuates pulmonary fibrosis via the miR-29a-3p/DNMT3A axis to regulate extracellular matrix remodeling and mitochondrial function and may provide a new therapeutic intervention for preventing pulmonary fibrosis.

Data-Driven Tool for Cross-Run Ion Selection and Peak-Picking in Quantitative Proteomics with Data-Independent Acquisition LC-MS/MS.

Proteomics provides molecular bases of biology and disease, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a platform widely used for bottom-up proteomics. Data-independent acquisition (DIA) improves the run-to-run reproducibility of LC-MS/MS in proteomics research. However, the existing DIA data processing tools sometimes produce large deviations from true values for the peptides and proteins in quantification. Peak-picking error and incorrect ion selection are the two main causes of the deviations. We present a cross-run ion selection and peak-picking (CRISP) tool that utilizes the important advantage of run-to-run consistency of DIA and simultaneously examines the DIA data from the whole set of runs to filter out the interfering signals, instead of only looking at a single run at a time. Eight datasets acquired by mass spectrometers from different vendors with different types of mass analyzers were used to benchmark our CRISP-DIA against other currently available DIA tools. In the benchmark datasets, for analytes with large content variation among samples, CRISP-DIA generally resulted in 20 to 50% relative decrease in error rates compared to other DIA tools, at both the peptide precursor level and the protein level. CRISP-DIA detected differentially expressed proteins more efficiently, with 3.3 to 90.3% increases in the numbers of true positives and 12.3 to 35.3% decreases in the false positive rates, in some cases. In the real biological datasets, CRISP-DIA showed better consistencies of the quantification results. The advantages of assimilating DIA data in multiple runs for quantitative proteomics were demonstrated, which can significantly improve the quantification accuracy.

Long-term administration of Western diet induced metabolic syndrome in mice and causes cardiac microvascular dysfunction, cardiomyocyte mitochondrial damage, and cardiac remodeling involving caveolae and caveolin-1 expression.

BACKGROUND: Long-term consumption of an excessive fat and sucrose diet (Western diet, WD) has been considered a risk factor for metabolic syndrome (MS) and cardiovascular disease. Caveolae and caveolin-1 (CAV-1) proteins are involved in lipid transport and metabolism. However, studies investigating CAV-1 expression, cardiac remodeling, and dysfunction caused by MS, are limited. This study aimed to investigate the correlation between the expression of CAV-1 and abnormal lipid accumulation in the endothelium and myocardium in WD-induced MS, and the occurrence of myocardial microvascular endothelial cell dysfunction, myocardial mitochondrial remodeling, and damage effects on cardiac remodeling and cardiac function. METHODS: We employed a long-term (7 months) WD feeding mouse model to measure the effect of MS on caveolae/vesiculo-vacuolar organelle (VVO) formation, lipid deposition, and endothelial cell dysfunction in cardiac microvascular using a transmission electron microscopy (TEM) assay. CAV-1 and endothelial nitric oxide synthase (eNOS) expression and interaction were evaluated using real-time polymerase chain reaction, Western blot, and immunostaining. Cardiac mitochondrial shape transition and damage, mitochondria-associated endoplasmic reticulum membrane (MAM) disruption, cardiac function change, caspase-mediated apoptosis pathway activation, and cardiac remodeling were examined using TEM, echocardiography, immunohistochemistry, and Western blot assay. RESULTS: Our study demonstrated that long-term WD feeding caused obesity and MS in mice. In mice, MS increased caveolae and VVO formation in the microvascular system and enhanced CAV-1 and lipid droplet binding affinity. In addition, MS caused a significant decrease in eNOS expression, vascular endothelial cadherin, and ß-catenin interactions in cardiac microvascular endothelial cells, accompanied by impaired vascular integrity. MS-induced endothelial dysfunction caused massive lipid accumulation in the cardiomyocytes, leading to MAM disruption, mitochondrial shape transition, and damage. MS promoted brain natriuretic peptide expression and activated the caspase-dependent apoptosis pathway, leading to cardiac dysfunction in mice. CONCLUSION: MS resulted in cardiac dysfunction, remodeling by regulating caveolae and CAV-1 expression, and endothelial dysfunction. Lipid accumulation and lipotoxicity caused MAM disruption and mitochondrial remodeling in cardiomyocytes, leading to cardiomyocyte apoptosis and cardiac dysfunction and remodeling.

Magnolol regulates miR-200c-3p to inhibit epithelial-mesenchymal transition and retinoblastoma progression by modulating the ZEB1/E-cadherin axis in vitro and in vivo.

BACKGROUND: Retinoblastoma, the most common pediatric intraocular malignancy, can develop during embryogenesis, with most children being diagnosed at 3-4 years of age. Multimodal therapies are typically associated with high levels of cytotoxicity and side effects. Therefore, the development of novel treatments with minimal side effects is crucial. Magnolol has a significant anti-tumor effect on various cancers. However, its antitumor effect on retinoblastoma remains unclear. PURPOSE: The study aimed to determine the effects of magnolol on the regulation of EMT, migration, invasion, and cancer progression in retinoblastoma and the modulation of miR-200c-3p expression and the Wnt/ zinc finger E-box binding homeobox 1 (ZEB1)/E-cadherin axis in vivo and in vitro. METHODS: The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) (MTT) assay was used to evaluate magnolol-induced cell toxicity in the Y79 retinoblastoma cell line. Flow cytometry and immunostaining assays were performed to investigate the magnolol-regulated mitochondrial membrane potential and the intracellular and mitochondrial reactive oxygen species levels in Y79 retinoblastoma cells. Orthotopic and subcutaneous xenograft experiments were performed in eight-week-old male null mice to study retinoblastoma progression and metastasis. In situ hybridization and quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays were performed to evaluate the level of the anti-cancer miRNA miR-200c-3p. The mRNA and protein levels of E-cadherin, ß-catenin, α-smooth muscle actin (α-SMA), fibronectin-1, and ZEB1 were analyzed using RT-qPCR, immunoblot, immunocytochemistry, and immunohistochemistry assays in vitro and in vivo. RESULTS: Magnolol increased E-cadherin levels and reduced the activation of the EMT signaling pathway, EMT, tumor growth, metastasis, and cancer progression in the Y79 retinoblastoma cell line as well as in the orthotopic and subcutaneous xenograft animal models. Furthermore, magnolol increased the expression of miR-200c-3p. Our results demonstrate that miRNA-200c-3p inhibits EMT progression through the Wnt16/ß-catenin/ZEB1/E-cadherin axis, and the ZEB1 silencing response shows that miR-200c-3p regulates ZEB1-mediated EMT in retinoblastoma. CONCLUSION: Magnolol has an antitumor effect by increasing E-cadherin and miRNA-200c-3p expression to regulate ZEB1-mediated EMT and cancer progression in retinoblastoma. The anti-tumor effect of magnolol by increasing E-cadherin and miRNA-200c-3p expression to regulate ZEB1-mediated EMT and cancer progression in retinoblastoma has been elucidated for the first time.

miR-29a-3p/THBS2 Axis Regulates PAH-Induced Cardiac Fibrosis.

Pulmonary artery hypertension (PAH) pathology involves extracellular matrix (ECM) remodeling in cardiac tissues, thus promoting cardiac fibrosis progression. miR-29a-3p reportedly inhibits lung progression and liver fibrosis by regulating ECM protein expression; however, its role in PAH-induced fibrosis remains unclear. In this study, we aimed to investigate the role of miR-29a-3p in cardiac fibrosis progression in PAH and its influence on ECM protein thrombospondin-2 (THBS2) expression. The diagnostic and prognostic values of miR-29a-3p and THBS2 in PAH were evaluated. The expressions and effects of miR-29a-3p and THBS2 were assessed in cell culture, monocrotaline-induced PAH mouse model, and patients with PAH. The levels of circulating miR-29a-3p and THBS2 in patients and mice with PAH decreased and increased, respectively. miR-29a-3p directly targets THBS2 and regulates THBS2 expression via a direct anti-fibrotic effect on PAH-induced cardiac fibrosis. The circulating levels of miR-29a-3p and THBS2 were correlated with PAH diagnostic parameters, suggesting their independent prognostic value. miR-29a-3p targeted THBS2 expression via a direct anti-fibrotic effect on PAH-induced cardiac fibrosis, indicating miR-29a-3p acts as a messenger with promising therapeutic effects.

Endocardial Endothelial Dysfunction and Unknown Polymorphic Composite Accumulation in Heart Failure.

The accumulation of unknown polymorphic composites in the endocardium damages the endocardial endothelium (EE). However, the composition and role of unknown polymorphic composites in heart failure (HF) progression remain unclear. Here, we aimed to explore composite deposition during endocardium damage and HF progression. Adult male Sprague-Dawley rats were divided into two HF groups-angiotensin II-induced HF and left anterior descending artery ligation-induced HF. Heart tissues from patients who had undergone coronary artery bypass graft surgery (non-HF) and those with dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM) were collected. EE damage, polymorphic unknown composite accumulation, and elements in deposits were examined. HF progression reduced the expression of CD31 in the endocardium, impaired endocardial integrity, and exposed the myofibrils and mitochondria. The damaged endocardial surface showed the accumulation of unknown polymorphic composites. In the animal HF model, especially HF caused by myocardial infarction, the weight and atomic percentages of O, Na, and N in the deposited composites were significantly higher than those of the other groups. The deposited composites in the human HF heart section (DCM) had a significantly higher percentage of Na and S than the other groups, whereas the percentage of C and Na in the DCM and ICM groups was significantly higher than those of the control group. HF causes widespread EE dysfunction, and EndMT was accompanied by polymorphic composites of different shapes and elemental compositions, which further damage and deteriorate heart function.

Mitigating Biases in CORD-19 for Analyzing COVID-19 Literature.

On the behest of the Office of Science and Technology Policy in the White House, six institutions, including ours, have created an open research dataset called COVID-19 Research Dataset (CORD-19) to facilitate the development of question-answering systems that can assist researchers in finding relevant research on COVID-19. As of May 27, 2020, CORD-19 includes more than 100,000 open access publications from major publishers and PubMed as well as preprint articles deposited into medRxiv, bioRxiv, and arXiv. Recent years, however, have also seen question-answering and other machine learning systems exhibit harmful behaviors to humans due to biases in the training data. It is imperative and only ethical for modern scientists to be vigilant in inspecting and be prepared to mitigate the potential biases when working with any datasets. This article describes a framework to examine biases in scientific document collections like CORD-19 by comparing their properties with those derived from the citation behaviors of the entire scientific community. In total, three expanded sets are created for the analyses: 1) the enclosure set CORD-19E composed of CORD-19 articles and their references and citations, mirroring the methodology used in the renowned "A Century of Physics" analysis; 2) the full closure graph CORD-19C that recursively includes references starting with CORD-19; and 3) the inflection closure CORD-19I, that is, a much smaller subset of CORD-19C but already appropriate for statistical analysis based on the theory of the scale-free nature of the citation network. Taken together, all these expanded datasets show much smoother trends when used to analyze global COVID-19 research. The results suggest that while CORD-19 exhibits a strong tilt toward recent and topically focused articles, the knowledge being explored to attack the pandemic encompasses a much longer time span and is very interdisciplinary. A question-answering system with such expanded scope of knowledge may perform better in understanding the literature and answering related questions. However, while CORD-19 appears to have topical coverage biases compared to the expanded sets, the collaboration patterns, especially in terms of team sizes and geographical distributions, are captured very well already in CORD-19 as the raw statistics and trends agree with those from larger datasets.

A Review of Microsoft Academic Services for Science of Science Studies.

Since the relaunch of Microsoft Academic Services (MAS) 4 years ago, scholarly communications have undergone dramatic changes: more ideas are being exchanged online, more authors are sharing their data, and more software tools used to make discoveries and reproduce the results are being distributed openly. The sheer amount of information available is overwhelming for individual humans to keep up and digest. In the meantime, artificial intelligence (AI) technologies have made great strides and the cost of computing has plummeted to the extent that it has become practical to employ intelligent agents to comprehensively collect and analyze scholarly communications. MAS is one such effort and this paper describes its recent progresses since the last disclosure. As there are plenty of independent studies affirming the effectiveness of MAS, this paper focuses on the use of three key AI technologies that underlies its prowess in capturing scholarly communications with adequate quality and broad coverage: (1) natural language understanding in extracting factoids from individual articles at the web scale, (2) knowledge assisted inference and reasoning in assembling the factoids into a knowledge graph, and (3) a reinforcement learning approach to assessing scholarly importance for entities participating in scholarly communications, called the saliency, that serves both as an analytic and a predictive metric in MAS. These elements enhance the capabilities of MAS in supporting the studies of science of science based on the GOTO principle, i.e., good and open data with transparent and objective methodologies. The current direction of development and how to access the regularly updated data and tools from MAS, including the knowledge graph, a REST API and a website, are also described.

Phase shifting interferometry of cold atoms.

We propose a scheme to engage phase shifting interferometry on cold atomic samples and present the simulation results under several experimentally achievable conditions nowadays. This method allows far-detuning, low power probing, and is intrinsically nondestructive. This novel detection means yields image quality superior to the conventional phase contrast imaging at certain conditions and could be experimentally realized. Furthermore, the longitudinal resolution of imaging by this manner is mainly set by optical interference and can be better than the diffraction limit. This scheme also provides special advantages to diagnose the surface-trapped clouds, with which phase imaging on the fabricated wires and atoms altogether is possible as well.