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Niraula NB, Dulal S, Koirala D. Linguistic Taboos and Euphemisms in Nepali. ACM T ASIAN LOW-RESO 2022. [DOI: 10.1145/3524111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Languages across the world have words, phrases, and behaviors - the taboos - that are avoided in public communication considering them as obscene or disturbing to the social, religious, and ethical values of society. However, people deliberately use these linguistic taboos and other language constructs to make hurtful, derogatory, and obscene comments. It is nearly impossible to construct a universal set of offensive or taboo terms because offensiveness is determined entirely by different factors such as socio–physical setting, speaker-listener relationship, and word choices. In this paper, we present a detailed corpus-based study of offensive language in Nepali. We identify and describe more than 18 different categories of linguistic offenses including politics, religion, race, and sex. We discuss 12 common euphemisms such as synonym, metaphor and circumlocution. In addition, we introduce a manually constructed data set of over 1000 offensive and taboo terms popular among contemporary speakers. We describe the first experiments that provide baseline results in detecting offensive language in Nepali. This in-depth study of offensive language and resource will provide a foundation for several downstream tasks such as offensive language detection and language learning.
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Koirala D, Beranova-Giorgianni S, Giorgianni F. Early Transcriptomic Response to OxLDL in Human Retinal Pigment Epithelial Cells. Int J Mol Sci 2020; 21:ijms21228818. [PMID: 33233417 PMCID: PMC7700619 DOI: 10.3390/ijms21228818] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
In the sub-retinal pigment epithelium (sub-RPE) space of the aging macula, deposits of oxidized phospholipids, oxidized derivatives of cholesterol and associated oxidized low-density lipoproteins (OxLDL) are considered contributors to the onset and development of age-related macular degeneration (AMD). We investigated the gene expression response of a human-derived RPE cell line exposed for short periods of time to non-cytotoxic levels of OxLDL or LDL. In our cell model, treatment with OxLDL, but not LDL, generated an early gene expression response which affected more than 400 genes. Gene pathway analysis unveiled gene networks involved in the regulation of various cellular functions, including acute response to oxidative stress via up-regulation of antioxidative gene transcripts controlled by nuclear factor erythroid-2 related factor 2 (NRF2), and up-regulation of aryl hydrocarbon receptor-controlled detoxifying gene transcripts. In contrast, circadian rhythm-controlling genes and genes involved in lipid metabolism were strongly down-regulated. Treatment with low-density lipoprotein (LDL) did not induce the regulation of these pathways. These findings show that RPE cells are able to selectively respond to the oxidized forms of LDL via the up-regulation of gene pathways involved in molecular mechanisms that minimize cellular oxidative damage, and the down-regulation of the expression of genes that regulate the intracellular levels of lipids and lipid derivatives. The effect on genes that control the cellular circadian rhythm suggests that OxLDL might also disrupt the circadian clock-dependent phagocytic activity of the RPE. The data reveal a complex cellular response to a highly heterogeneous oxidative stress-causing agent such as OxLDL commonly present in drusen formations.
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Donato L, Bramanti P, Scimone C, Rinaldi C, Giorgianni F, Beranova-Giorgianni S, Koirala D, D'Angelo R, Sidoti A. Corrigendum to: miRNA expression profile of retinal pigment epithelial cells under oxidative stress conditions. FEBS Open Bio 2018; 8:1884. [PMID: 30410868 PMCID: PMC6212636 DOI: 10.1002/2211-5463.12526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Luigi Donato
- Division of Medical Biotechnologies and Preventive Medicine Department of Biomedical and Dental Sciences and Morphofunctional Imaging University of Messina Italy.,Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience Section of Neuroscience-Applied, Molecular Genetics and Predictive Medicine I.E.ME.S.T. Palermo Italy
| | | | - Concetta Scimone
- Division of Medical Biotechnologies and Preventive Medicine Department of Biomedical and Dental Sciences and Morphofunctional Imaging University of Messina Italy.,Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience Section of Neuroscience-Applied, Molecular Genetics and Predictive Medicine I.E.ME.S.T. Palermo Italy
| | - Carmela Rinaldi
- Division of Medical Biotechnologies and Preventive Medicine Department of Biomedical and Dental Sciences and Morphofunctional Imaging University of Messina Italy
| | - Francesco Giorgianni
- Department of Pharmaceutical Sciences University of Tennessee Health Science Center Memphis TN USA
| | | | - Diwa Koirala
- Department of Pharmaceutical Sciences University of Tennessee Health Science Center Memphis TN USA
| | - Rosalia D'Angelo
- Division of Medical Biotechnologies and Preventive Medicine Department of Biomedical and Dental Sciences and Morphofunctional Imaging University of Messina Italy
| | - Antonina Sidoti
- Division of Medical Biotechnologies and Preventive Medicine Department of Biomedical and Dental Sciences and Morphofunctional Imaging University of Messina Italy.,Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience Section of Neuroscience-Applied, Molecular Genetics and Predictive Medicine I.E.ME.S.T. Palermo Italy
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Koirala D, Beranova-Giorgianni S, Giorgianni F. Data-independent proteome analysis of ARPE-19 cells. Data Brief 2018; 20:333-336. [PMID: 30167441 PMCID: PMC6111057 DOI: 10.1016/j.dib.2018.06.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/14/2018] [Accepted: 06/27/2018] [Indexed: 11/24/2022] Open
Abstract
We have performed a proteomics analysis of a human retinal pigment epithelial cell line (ARPE-19), which represents a widely used model for in vitro studies of cellular and molecular mechanisms related to human RPE cells (Dunn et al., 1996; Weigel et al., 2002) [1], [2]. Whole cell protein extracts were separated in four gel fractions via short (10 min) SDS-PAGE runs. Following fractionation and trypsin digestion, the resulting peptides were separated on a nano UPLC LC system and analyzed on-line with a QTof-IMS instrument: a tandem mass spectrometer with ion mobility separation (Synapt G2-Si). Data were acquired in data-independent mode (UDMSE), which allows for absolute and/or relative post-acquisition protein quantification (Silva et al., 2006) [3]. The proteome profile data obtained from this study can be used as a protein reference database with qualitative and quantitative protein information related to ARPE-19 cells under normal growth conditions.
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Affiliation(s)
- Diwa Koirala
- University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, 881 Madison Av., Pharmacy Bldg., Memphis, TN 38163, United States
| | - Sarka Beranova-Giorgianni
- University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, 881 Madison Av., Pharmacy Bldg., Memphis, TN 38163, United States
| | - Francesco Giorgianni
- University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, 881 Madison Av., Pharmacy Bldg., Memphis, TN 38163, United States
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Donato L, Bramanti P, Scimone C, Rinaldi C, Giorgianni F, Beranova-Giorgianni S, Koirala D, D'Angelo R, Sidoti A. miRNAexpression profile of retinal pigment epithelial cells under oxidative stress conditions. FEBS Open Bio 2018; 8:219-233. [PMID: 29435412 PMCID: PMC5794457 DOI: 10.1002/2211-5463.12360] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 11/03/2017] [Accepted: 11/24/2017] [Indexed: 12/22/2022] Open
Abstract
Deep analysis of regulative mechanisms of transcription and translation in eukaryotes could improve knowledge of many genetic pathologies such as retinitis pigmentosa (RP). New layers of complexity have recently emerged with the discovery that ‘junk’ DNA is transcribed and, among these, miRNAs have assumed a preponderant role. We compared changes in the expression of miRNAs obtained from whole transcriptome analyses, between two groups of retinal pigment epithelium (RPE) cells, one untreated and the other exposed to the oxidant agent oxidized low‐density lipoprotein (oxLDL), examining four time points (1, 2, 4 and 6 h). We found that 23 miRNAs exhibited altered expression in the treated samples, targeting genes involved in several biochemical pathways, many of them associated to RP for the first time, such as those mediated by insulin receptor signaling and son of sevenless. Moreover, five RP causative genes (KLHL7, RDH11,CERKL, AIPL1 and USH1G) emerged as already validated targets of five altered miRNAs (hsa‐miR‐1307, hsa‐miR‐3064, hsa‐miR‐4709, hsa‐miR‐3615 and hsa‐miR‐637), suggesting a tight connection between induced oxidative stress and RP development and progression. This miRNA expression analysis of oxidative stress‐induced RPE cells has discovered new regulative functions of miRNAs in RP that should lead to the discovery of new ways to regulate the etiopathogenesis of RP.
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Affiliation(s)
- Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging Division of Medical Biotechnologies and Preventive Medicine University of Messina Italy.,Department of Cutting-Edge Medicine and Therapies Biomolecular Strategies and Neuroscience Section of Neuroscience-applied, Molecular Genetics and Predictive MedicineI.E.M E.S.T. Palermo Italy
| | | | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging Division of Medical Biotechnologies and Preventive Medicine University of Messina Italy.,Department of Cutting-Edge Medicine and Therapies Biomolecular Strategies and Neuroscience Section of Neuroscience-applied, Molecular Genetics and Predictive MedicineI.E.M E.S.T. Palermo Italy
| | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging Division of Medical Biotechnologies and Preventive Medicine University of Messina Italy
| | | | | | | | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging Division of Medical Biotechnologies and Preventive Medicine University of Messina Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging Division of Medical Biotechnologies and Preventive Medicine University of Messina Italy.,Department of Cutting-Edge Medicine and Therapies Biomolecular Strategies and Neuroscience Section of Neuroscience-applied, Molecular Genetics and Predictive MedicineI.E.M E.S.T. Palermo Italy
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Iannaccone A, Hollingsworth TJ, Koirala D, New DD, Lenchik NI, Beranova-Giorgianni S, Gerling IC, Radic MZ, Giorgianni F. Retinal pigment epithelium and microglia express the CD5 antigen-like protein, a novel autoantigen in age-related macular degeneration. Exp Eye Res 2016; 155:64-74. [PMID: 27989757 DOI: 10.1016/j.exer.2016.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 11/19/2022]
Abstract
We report on a novel autoantigen expressed in human macular tissues, identified following an initial Western blot (WB)-based screening of sera from subjects with age-related macular degeneration (AMD) for circulating auto-antibodies (AAbs) recognizing macular antigens. Immunoprecipitation, 2D-gel electrophoresis (2D-GE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), direct enzyme-linked immunosorbent assays (ELISA), WBs, immunohistochemistry (IHC), human primary and ARPE-19 immortalized cell cultures were used to characterize this novel antigen. An approximately 40-kDa autoantigen in AMD was identified as the scavenger receptor CD5 antigen-like protein (CD5L), also known as apoptosis inhibitor of macrophage (AIM). CD5L/AIM was localized to human RPE by IHC and WB methods and to retinal microglial cells by IHC. ELISAs with recombinant CD5L/AIM on a subset of AMD sera showed a nearly 2-fold higher anti-CD5L/AIM reactivity in AMD vs. Control sera (p = 0.000007). Reactivity ≥0.4 was associated with 18-fold higher odds of having AMD (χ2 = 21.42, p = 0.00063). Circulating CD5L/AIM levels were also nearly 2-fold higher in AMD sera compared to controls (p = 0.0052). The discovery of CD5L/AIM expression in the RPE and in retinal microglial cells adds to the known immunomodulatory roles of these cells in the retina. The discovery of AAbs recognizing CD5L/AIM identifies a possible novel disease biomarker and suggest a potential role for CD5L/AIM in the pathogenesis of AMD in situ. The possible mechanisms via which anti-CD5L/AIM AAbs may contribute to AMD pathogenesis are discussed. In particular, since CD5L is known to stimulate autophagy and to participate in oxidized LDL uptake in macrophages, we propose that anti-CD5L/AIM auto-antibodies may play a role in drusen biogenesis and inflammatory RPE damage in AMD.
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Affiliation(s)
- Alessandro Iannaccone
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA; Department of Ophthalmology, Duke Eye Center, Duke University School of Medicine, Durham, NC, USA.
| | - T J Hollingsworth
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA
| | - Diwa Koirala
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA; University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, Memphis, TN, USA
| | - David D New
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA
| | - Nataliya I Lenchik
- University of Tennessee Health Science Center, Department of Ophthalmology, Hamilton Eye Institute, Memphis, TN, USA; University of Tennessee Health Science Center, Department of Medicine, Division of Endocrinology, Memphis, TN, USA
| | - Sarka Beranova-Giorgianni
- University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, Memphis, TN, USA
| | - Ivan C Gerling
- University of Tennessee Health Science Center, Department of Medicine, Division of Endocrinology, Memphis, TN, USA
| | - Marko Z Radic
- University of Tennessee Health Science Center, Department of Microbiology, Immunology and Biochemistry, Memphis, TN, USA
| | - Francesco Giorgianni
- University of Tennessee Health Science Center, Department of Pharmaceutical Sciences, Memphis, TN, USA
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Wang X, Sun R, Huang Y, Yan Y, Gao M, Wang DN, Koirala D, Li DW, Hu C. Development of Thieno[3`,2`:5,6]thiopyrano[4,3-c]pyrazole-3-carboxamide Derivatives as the Estrogen Receptor Ligands: Synthesis, Characterization and Biological Activity. Med Chem 2014; 10:836-42. [DOI: 10.2174/1573406410666140428145753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 04/20/2014] [Accepted: 04/24/2014] [Indexed: 11/22/2022]
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Giorgianni F, Koirala D, Weber KT, Beranova-Giorgianni S. Proteome analysis of subsarcolemmal cardiomyocyte mitochondria: a comparison of different analytical platforms. Int J Mol Sci 2014; 15:9285-301. [PMID: 24865490 PMCID: PMC4100094 DOI: 10.3390/ijms15069285] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/05/2023] Open
Abstract
Mitochondria are complex organelles that play critical roles in diverse aspects of cellular function. Heart disease and a number of other pathologies are associated with perturbations in the molecular machinery of the mitochondria. Therefore, comprehensive, unbiased examination of the mitochondrial proteome represents a powerful approach toward system-level insights into disease mechanisms. A crucial aspect in proteomics studies is design of bioanalytical strategies that maximize coverage of the complex repertoire of mitochondrial proteins. In this study, we evaluated the performance of gel-based and gel-free multidimensional platforms for profiling of the proteome in subsarcolemmal mitochondria harvested from rat heart. We compared three different multidimensional proteome fractionation platforms: polymeric reversed-phase liquid chromatography at high pH (PLRP), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and isoelectric focusing (IEF) separations combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS), and bioinformatics for protein identification. Across all three platforms, a total of 1043 proteins were identified. Among the three bioanalytical strategies, SDS-PAGE followed by LC-MS/MS provided the best coverage of the mitochondrial proteome. With this platform, 890 proteins with diverse physicochemical characteristics were identified; the mitochondrial protein panel encompassed proteins with various functional roles including bioenergetics, protein import, and mitochondrial fusion. Taken together, results of this study provide a large-scale view of the proteome in subsarcolemmal mitochondria from the rat heart, and aid in the selection of optimal bioanalytical platforms for differential protein expression profiling of mitochondria in health and disease.
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Affiliation(s)
- Francesco Giorgianni
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Diwa Koirala
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Karl T Weber
- Division of Cardiology, Department of Medicine, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, the University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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Abstract
Unilateral or bilateral hypoplasia or agenesis of one or both thyroid lobes, with or without isthmic agenesis, is a rare developmental anomaly. Hemiagenesis of the left lobe is far commoner than of the right. Clinically, these patients may be euthyroid, hyperthyroid, or hypothyroid. Ultrasonography is usually able to diagnose this condition easily, as we demonstrate in this case report of a 37-year-old lady with an incidentally detected thyroid nodule who was found to have hemiagenesis of the right lobe and isthmus.
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Hu C, Wang SH, Wang Y, Zhu YY, Han J, Zhou YF, Koirala D, Li DW. Synthesis, characterization, crystal structure and cytotoxicity of 2-aroyl-3-aryl-5H-furo[3,2-g]chromen derivatives. ARKIVOC 2010. [DOI: 10.3998/ark.5550190.0011.b17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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