Fragmentation Analysis Research Articles

Relative performance evaluation of machine learning algorithms for land use classification using multispectral moderate resolution data

Analyses of spatial and temporal patterns of land use and land cover through multi-resolution remote sensing data provide valuable insights into landscape dynamics. Land use changes leading to land degradation and deforestation have been a prime mover for changes in the climate. This necessitates accurately assessing land use dynamics using a machine-learning algorithm’s temporal remote sensing data. The current study investigates land use using the temporal Landsat data from 1973 to 2021 in Chikamagaluru district, Karnataka. The land cover analysis showed 2.77% decrease in vegetation cover. The performance of three supervised learning techniques, namely Random Forest (RF), Support Vector Machine (SVM), and Maximum Likelihood classifier (MLC) were assessed, and results reveal that RF has performed better with an overall accuracy of 90.22% and a kappa value of 0.85. Land use classification has been performed with supervised machine learning classifier Random Forest (RF), which showed a decrease in the forest cover (48.91%) with an increase of agriculture (6.13%), horticulture (43.14%) and built-up cover (2.10%). Forests have been shrinking due to anthropogenic forces, especially forest encroachment for agriculture and industrial development, resulting in forest fragmentation and habitat loss. The fragmentation analysis provided the structural change in the forest cover, where interior forest cover was lost by 27.67% from 1973 to 2021, which highlights intense anthropogenic pressure even in the core Western Ghats regions with dense forests. Temporal details of the extent and condition of land use form an information base for decision-makers.

Multimodal analysis of cell-free DNA whole-methylome sequencing for cancer detection and localization

Multimodal epigenetic characterization of cell-free DNA (cfDNA) could improve the performance of blood-based early cancer detection. However, integrative profiling of cfDNA methylome and fragmentome has been technologically challenging. Here, we adapt an enzyme-mediated methylation sequencing method for comprehensive analysis of genome-wide cfDNA methylation, fragmentation, and copy number alteration (CNA) characteristics for enhanced cancer detection. We apply this method to plasma samples of 497 healthy controls and 780 patients of seven cancer types and develop an ensemble classifier by incorporating methylation, fragmentation, and CNA features. In the test cohort, our approach achieves an area under the curve value of 0.966 for overall cancer detection. Detection sensitivity for early-stage patients achieves 73% at 99% specificity. Finally, we demonstrate the feasibility to accurately localize the origin of cancer signals with combined methylation and fragmentation profiling of tissue-specific accessible chromatin regions. Overall, this proof-of-concept study provides a technical platform to utilize multimodal cfDNA features for improved cancer detection.

Role of TLR4 signaling pathway in the mitigation of damaged lung by low-dose gamma irradiation.

Organisms frequently suffer negative effects from large doses of ionizing radiation. However, radiation is not as hazardous at lower doses as was once believed. The current study aims to evaluate the possible radio-adaptive effect induced by low-dose radiation (LDR) in modulating high-dose radiation (HDR) and N-nitrosodiethylamine (NDEA)-induced lung injury in male albino rats. Sixty-four male rats were randomly divided into four groups: Group 1 (control): normal rats; Group 2 (D): rats given NDEA in drinking water; Group 3 (DR): rats administered with NDEA then exposed to fractionated HDR; and Group 4 (DRL): rats administered with NDEA then exposed to LDR + HDR. In the next stage, malondialdehyde (MDA), glutathione reduced (GSH), catalase (CAT), and superoxide dismutase (SOD) levels in the lung tissues were measured. Furthermore, the enzyme-linked immunoassay analysistechnique was performed to assess the Toll-like receptor 4(TLR4), interleukin-1 receptor-associated kinase 4(IRAK4), and mitogen-activated protein kinases(MAPK) expression levels. Histopathological and DNA fragmentation analyses in lung tissue, in addition to hematological and apoptosis analyses of the blood samples, were also conducted. Results demonstrated a significant increase in antioxidant defense and a reduction in MDA levels were observed in LDR-treated animals compared to the D and DR groups. Additionally, exposure to LDR decreased TLR4, IRAK4, and MAPK levels, decreased apoptosis, and restored all the alterations in the histopathological, hematological parameters, and DNA fragmentation, indicating its protective effects on the lung when compared with untreated rats. Taken together, LDR shows protective action against the negative effects of subsequent HDR and NDEA. This impact may be attributable to the adaptive response induced by LDR, which decreases DNA damage in lung tissue and activates the antioxidative, antiapoptotic, and anti-inflammatory systems in the affected animals, enabling them to withstand the following HDR exposure.

Evaluating the effects of landscape fragmentation on ecosystem services: A three-decade perspective

Landscape fragmentation and structure play a crucial role in determining the provision of ecosystem services. Although there has been extensive research on the impact of shifting land use and land cover on ecosystem services, the specific effect of landscape fragmentation on the value of these services has not yet been quantified. This study aims to address this gap by examining the relationship between landscape fragmentation and Ecosystem service value (ESV). The findings indicate that ESV is negatively associated with the increasing conversion of landscapes into smaller patches. To conduct this analysis, a mapping methodology was employed using Landsat images from four different time periods (1990, 2000, 2010, and 2020). The fragmentation analysis resulted in the identification of six hierarchical landscape parts: patch, edge, perforated, small core, medium core, and large core. ESV for a typical land use and land cover was calculated using a weighted Coefficient value (CV) based on the Analytic Hierarchy Process (AHP), while ESV for fragmented landscapes was estimated using Costanza's Coefficient Value from the years 1997 and 2014. The deterioration of eco-regions in terms of quality can be attributed to fragmented vegetation and water bodies. This degradation has resulted in a decrease in the ecosystem service value (ESV) of specific areas from 62.07 million USD/year to 50.56 million USD/year between 1990 and 2020. In 1990, the ESV of agricultural land was 381.04 USD/year, while that of built-up areas was 15.83 USD/year. However, by 2020, these values had increased to 431.05 USD/year and 105.33 USD/year, respectively. Furthermore, in the fractured landscape of 2020, the service values of water bodies were significantly lower compared to the past. It is important to note that anthropogenic influences play a significant role in driving land use changes and causing the transformation and fragmentation of ecosystem services in naturally occurring landscapes.

Comparative metabolomic profiling of Cupriavidus necator B-4383 revealed production of cupriachelin siderophores, one with activity against Cryptococcus neoformans.

Cupriavidus necator H16 is known to be a rich source of linear lipopeptide siderophores when grown under iron-depleted conditions; prior literature termed these compounds cupriachelins. These small molecules bear β-hydroxyaspartate moieties that contribute to a photoreduction of iron when bound as ferric cupriachelin. Here, we present structural assignment of cupriachelins from C. necator B-4383 grown under iron limitation. The characterization of B-4383 cupriachelins is based on MS/MS fragmentation analysis, which was confirmed by 1D- and 2D-NMR for the most abundant analog (1). The cupriachelin congeners distinguish these two strains with differences in the preferred lipid tail; however, our rigorous metabolomic investigation also revealed minor analogs with changes in the peptide core, hinting at a potential mechanism by which these siderophores may reduce biologically unavailable ferric iron (4-6). Antifungal screening of the C. necator B-4383 supernatant extract and the isolated cupriachelin analog (1) revealed inhibitory activity against Cryptococcus neoformans, with IC50 values of 16.6 and 3.2μg/mL, respectively. This antifungal activity could be explained by the critical role of the iron acquisition pathway in the growth and pathogenesis of the C. neoformans fungal pathogen.

Insights into the binding of half-sandwich phosphino Ir(III) and Ru(II) complexes to deoxyribonucleic acid, albumin and apo-transferrin: Experimental and theoretical investigation

A group of cytotoxic half-sandwich iridium(III) (Ir(η5-Cp*)Cl2PPh2CH2OH (IrPOH)), (Ir(η5-Cp*)Cl2P(p-OCH3Ph)2CH2OH (IrMPOH)), and ruthenium(II) (Ru(η6-p-cymene)Cl2PPh2CH2OH (RuPOH), Ru(η6-p-cymene)Cl2P(p-OCH3Ph)2CH2OH (RuMPOH)) complexes with phosphine ligands exhibit the ability to (i) slow hydrolysis which is reversed by adding a high NaCl concentration; (ii) oxidation of NADH to NAD+; (iii) induction of cytotoxicity towards various cancer cell lines. Furthermore, we found that RuPOH and RuMPOH selectively inhibit the proliferation of skin cancer cells (WM266-4) while Ir(III) complexes were found to be moderate against prostate cancer cells (DU-145). Herein, to elucidate the cytotoxic effects, we investigated the interaction of these complexes with DNA and serum proteins by gel electrophoresis, fluorescence spectroscopy, and molecular docking studies. Fluorescence spectroscopic data (calf thymus DNA: CT-DNA titration), together with analysis of DNA fragmentation (gel electrophoresis) and molecular docking provided evidence for the multimodal interaction of Ir(III) and Ru(III) complexes with DNA with predominance of intercalation and minor groove binding. All examined complexes caused single-stranded cleavage of the sugar–phosphate backbone of plasmid DNA. The affinity of the complexes for apo-transferrin (apo-Tf) and human serum albumin (HSA) was evaluated by fluorescence emission spectroscopy to calculate the binding constants which suggested a tight and reversible binding. Moreover, ruthenium complexes can mimic the binding of iron compounds to specific biomolecules such as albumin and transferrin better than iridium complexes. In silico study indicate that complexes mostly bind to (i) apo-Tf with a preference for a single binding site and/or (ii) to dock within all the four predicted binding sites of HSA with the predominance of site I which include tryptophan residues of HSA. This class of ruthenium(II) and iridium(III) complexes has unusual features worthy of further exploration in the design of novel anticancer drugs.

Social Fragmentation in Achebe’s Things Fall Apart and Head’s Maru: A Comparative Study

This qualitative research sought to do a comparative analysis of social fragmentation in Things Fall Apart and Maru. Textual analysis was employed to analyse, interpret and evaluate the two novels in the light of postcolonial criticism, focusing on otherness. The researchers engaged the texts in multiple readings to gain a descriptive understanding of them and take descriptive notes at every stage of reading. Excerpts were purposefully sampled from the novels and analysed thematically. The study revealed that in pre-colonial Africa, social fragmentation resulted from classism, patriarchy and bad tradition; hence, the society operates in a binary relationship. In colonial Africa, social fragmentation resulted from religion and racism. However, post-colonial Africa experienced the deepest form of social fragmentation; spiced by tribalism and other pre-colonial factors. The study concluded that both novels confirm the concept of ‘otherness’. So, future research can focus on emotional and structural fragmentations.

Analysis of the vegetation fragments connectivity

The habitat fragmentation is one of the most cited causes of species extinction and loss of biological diversity and it is defined as the process by a continuous area is reduced in size and divided into two or more fragments separated by an environment or matrix, different from the original. The analysis of landscape fragmentation is done through land use mapping, where it is possible to identify different spots and determine the degree of fragmentation or connectivity. This work aims to analyze the connectivity of the landscape fragments present in the Tietê-Jacaré Hydrographic Basin - SP, through the application of the metric indices of Connectivity and Fragmentation, with the purpose of evaluating the dynamic and temporal process in 2007 and 2017, through the use of Geographic Information Systems (GIS). Considering the interval of 10 years, there was an expansion of agricultural activities with an increase of 24,507.53ha of cultivated areas and a vegetation loss of 32,149ha. It was also evidenced the decrease in the number of fragments, as well as the increase in the average size of the fragments, derived from the growth of the agricultural matrix with consequent reduction of the fragment’s diversification. The vegetation configuration of the region has undergone few structural changes, the main connections are related to the end of each sub-basin and consequently the hydrographic basin as a whole. The fragmentation indexes, when expressing the state of configuration of the landscapes, were presented as important tools in the diagnosis aimed at the conservation of ecosystems. These indices allowed the comparison not only of natural fragments but of all classes of land use and land cover, which is essential in regional planning.

Evaluation of Sperm DNA Fragmentation Using Two Different Methods: TUNEL via Fluorescence Microscopy, and Flow Cytometry.

Background and Objectives: Sperm DNA fragmentation refers to any break in one or both of the strands of DNA in the head of a sperm. The most widely used methodologies for assessing sperm DNA fragmentation are the sperm chromatin structure assay (SCSA), the sperm chromatin dispersion assay (SCD), the single-cell gel electrophoresis assay (SCGE-comet), and the terminal-deoxynucleotidyl-transferase (TdT)-mediated dUTP nick end labelling (TUNEL) assay. The aim of this study was to compare the efficiency and sensitivity of the analysis of sperm DNA fragmentation using TUNEL via fluorescence microscopy, and flow cytometry. Materials and Methods: Semen samples were collected and analyzed for standard characteristics using light microscopy, and for sperm DNA fragmentation using both TUNEL via fluorescence microscopy, and flow cytometry. Results: There were no significant differences in the values of the sperm DNA fragmentation index (DFI) obtained when the analysis was performed using TUNEL or flow cytometry (p = 0.543). Spearman's correlation analysis revealed a significant negative correlation between sperm motility (%) and sperm DNA fragmentation (p < 0.01), as well as between sperm concentration and sperm DNA fragmentation (p < 0.05). The Mann-Whitney U test showed no significant difference in the DFI among couples with repeated implantation failure (RIF) and miscarriages (p = 0.352). Conclusions: Both methods (TUNEL via fluorescence microscopy, and flow cytometry) have a high efficiency and sensitivity in accurately detecting sperm DNA fragmentation, and can be effectively used to assess male fertility.

6-Oxofurostane and (iso)Spirostane Types of Saponins in Smilax sieboldii: UHPLC-QToF-MS/MS and GNPS-Molecular Networking Approach for the Rapid Dereplication and Biodistribution of Specialized Metabolites.

Identifying novel phytochemical secondary metabolites following classical pharmacognostic investigations is tedious and often involves repetitive chromatographic efforts. During the past decade, Ultra-High Performance Liquid Chromatography-Quadrupole Time of Flight-Tandem Mass Spectrometry (UHPLC-QToF-MS/MS), in combination with molecular networking, has been successfully demonstrated for the rapid dereplication of novel natural products in complex mixtures. As a logical application of such innovative tools in botanical research, more than 40 unique 3-oxy-, 3, 6-dioxy-, and 3, 6, 27-trioxy-steroidal saponins were identified in aerial parts and rhizomes of botanically verified Smilax sieboldii. Tandem mass diagnostic fragmentation patterns of aglycones, diosgenin, sarsasapogenin/tigogenin, or laxogenin were critical to establishing the unique nodes belonging to six groups of nineteen unknown steroidal saponins identified in S. sieboldii. Mass fragmentation analysis resulted in the identification of 6-hydroxy sapogenins, believed to be key precursors in the biogenesis of characteristic smilaxins and sieboldins, along with other saponins identified within S. sieboldii. These analytes' relative biodistribution and characteristic molecular networking profiles were established by analyzing the leaf, stem, and root/rhizome of S. sieboldii. Deducing such profiles is anticipated to aid the overall product integrity of botanical dietary supplements while avoiding tedious pharmacognostic investigations and helping identify exogenous components within the finished products.

Identification, Chemical Synthesis, and Sweetness Evaluation of Rhamnose or Xylose Containing Steviol Glycosides of Stevia (Stevia rebaudiana) Leaves.

Steviol glycosides obtained from Stevia rebaudiana leaves are increasingly used in the food industry as natural low-calorie sweeteners. Among them, the sweetness of major glycosides composed of glucose residues (e.g., stevioside and rebaudioside A) has been widely studied. However, the properties of minor natural products containing rhamnose or xylose residues are poorly investigated. In this study, five unreported steviol glycosides containing rhamnose or xylose were extracted from our developing stevia leaves, and their sweetness was evaluated. The highly glycosylated steviol glycosides were identified, and their structures were examined by fragmentation analysis using mass spectrometry. Chemical synthesis of these glycosides confirmed their structures and allowed sensory evaluation of minor steviol glycosides. Our study revealed that a xylose-containing glycoside, rebaudioside FX1, exhibits a well-balanced sweetness, and thus, it is a promising candidate for natural sweeteners used in the food industry.

Development and testing of self-swelling cartridge for use as stemming material in open-pit blasting —A quarry case study

This paper examines the problems of low explosive energy utilization rate and poor blasting efficiency due to the use of unsuitable stemming materials in open-pit blasting. A self-swelling cartridge stemming plug is developed for use in quarry and open pit blast hole stemming. The self-swelling cartridge stemming development and testing procedures are presented in the paper. Various amounts of magnesium-aluminum mix activator are added to a self-swelling agent to determine the optimum amount of activator that results in the quick initiation of hydration reaction of the self-swelling agent to achieve complete reaction within acceptable field production stemming time. The laboratory test results show that the reaction time of the self-swelling cartridge increases with activator content. The expansion pressure of the self-swelling cartridge and the shear force at its interface with the blasthole wall for different diameters of cartridges increase with the increase of the cartridge diameter. Thus, from the indoor test results, the self-swelling cartridge in a saturated state effectively sealed the simulated blast hole within about 1 h, with an expansion pressure of 26.3–49.8 MPa and a shear force of 113.4 kN. Field tests were conducted to compare the effects of the self-swelling cartridge and drill cuttings as stemming materials in a limestone quarry using high-speed photography and fragmentation analysis. The results show that the self-swelling cartridge stemming can effectively prevent blast hole blowout compared to the drill cuttings stemming. This is shown in the field fragmentation analysis comparing from zones using the self-swelling cartridge to the drill cutting stemming zone fragmentation. It is concluded that use of self-swelling cartridge stemming results in better blast fragmentation at lower cost and higher safety than drill cuttings stemming in open pit blasting.

Effect Of Land-Use Changes On Landscape Fragmentation: The Case Of Ramallah Area In Central Palestine

The urban sprawl of cities periphery is one of such changes that has led to drastic land-use changes, which resulted in landscape fragmentation. The objective of this study is to understand the process of landscape fragmentation because of urban expansion; identifying the most influential drivers that have changed the land-use. To achieve the objectives due to changes in land use, a study had conducted in Ramallah area of Palestine. The study utilized Fragstat software to quantify the landscape changes with regard to its pattern and structure through a number of indices, also using Geographic Information System tool to draw up different landscape parcels spatially with its characteristics. The spatial analysis carried out on the land-use change used the 1997 and 2017 aerial photos to quantify the landscape fragmentation, which included a variety of land-uses. Over 52% of the study area underwent noticeable urbanization process, resulting in appreciable landscape changes to the area, especially after 1993. The statistical analysis of the landscape fragmentation revealed significant changes in land-use during the period from 1997 to 2017; the green landscape has been fragmented at a large scale by increasing the number of landscape patches (from 71 to 148 patches). As a result, there was an obvious reduction in agricultural lands, such as olive groves and grassland. At the same time, the urban surface areas increased from 654 patches in 1997 to 2019 patches in 2017. These results indicate that the landscape has become more fragmented due to geopolitical and socio-economic drivers since mid-1995 after Oslo accord.

Predicting lethal ventricular arrhythmias in hypertrophic cardiomyopathy using non-electrophysiologic methods: Invasive EGM vs. non-invasive ECG analysis of fragmentation.

Predicting lethal ventricular arrhythmias in hypertrophic cardiomyopathy using non-electrophysiologic methods: Invasive EGM vs. non-invasive ECG analysis of fragmentation.

Antiproliferative Potential of Olneya tesota PF2 Lectin in Human Acute Monocytic Leukemia Cells.

Acute monocytic leukemia is a type of myeloid leukemia that develops in monocytes. The current clinical therapies for leukemia are unsatisfactory due to their side effects and nonspecificity toward target cells. Some lectins display antitumor activity and may specifically recognize cancer cells by binding to carbohydrate structures on their surface. Therefore, this study evaluated the response of the human monocytic leukemia cell lines THP-1 to the Olneya tesota PF2 lectin. The induction of apoptosis and reactive oxygen species production in PF2-treated cells was evaluated by flow cytometry, and the lectin-THP-1 cell interaction and mitochondrial membrane potential were evaluated by confocal fluorescence microscopy. PF2 genotoxicity was evaluated by DNA fragmentation analysis via gel electrophoresis. The results showed that PF2 binds to THP-1 cells, triggers apoptosis and DNA degradation, changes the mitochondrial membrane potential, and increases reactive oxygen species levels in PF2-treated THP-1 cells. These results suggest the potential use of PF2 for developing alternative anticancer treatments with enhanced specificity.

Spatial correlation and impact mechanism analysis of cultivated land fragmentation and quality in the Central Plain of Liaoning Province, Northeast China

AbstractFurther exploration of the spatial correlation and mechanism of action between cultivated land fragmentation (CLF) and quality, which have guiding roles in improving cultivated land quality, is needed. However, the mechanism that determines how CLF affects quality has not yet been thoroughly investigated. The Central Plain of Liaoning Province was utilized as the research's study area, and the spatial autocorrelation analysis method was used to investigate the correlations between CLF and quality. The precise effects of different CLF indices on cultivated land quality have been specifically examined using the spatial error model (SEM). According to the findings, there is a “low in the west and high in the east” distribution tendency for CLF in the Central Plain area, and “high in the middle and low on both sides” for cultivated land quality. Furthermore, CLF and quality have a significant negative spatial link, with a correlation coefficient of −0.186. A rise in some CLF indices may enhance the difficulty of improving land quality. The quality of cultivated land declines by 0.275, 1.306, and 1.085 units for each unit rise in the number of patches (NP), edge density (ED), and aggregation index (AI) values, respectively. Therefore, it is possible to improve the degree of fragmentation of cultivated land according to local conditions, thereby improving the quality of cultivated land. The research results can provide a reference for achieving the trinity protection of cultivated land, in order to better improve the sustainability of cultivated land.

Blasting Fragmentation Study Using 3D Image Analysis of a Hard Rock Mine

Rock blasting with explosives is the first stage of rock fragmentation and plays a key role in the results of the mining chain. Fragmentation optimization is achieved by considering the energy efficiency of the explosive, the optimal distribution of explosive energy in the rocky mass, and the programmed and controlled release of explosive energy during blasting. The quality of fragmentation is usually performed using tools that estimate the sizes of fragments via the analysis of two- or three-dimensional images. This article presents a study of the rock fragmentation optimization of very compact itabirites, based on four blasting tests, performed in a different way from the conventional blasting design. The fragmentation analysis was performed using the PortaMetricsTM tool, and compared with the Kuznetsov and Rosin–Rammler particle size distribution model, to compare the reliability of this tool. Finally, the mine productivity after blasting was estimated from the particle size distribution obtained in the tests. The model presented idealistic results considering the technical parameters used in the equations. However, the PortaMetricsTM tool suggests good performance for the preliminary evaluation of blast design.

Real-world performance of a multi-cancer early detection test based on integrative analysis of cell-free DNA whole-methylome sequencing.

10521 Background: Early detection and diagnosis is key to reducing cancer-related mortality. We developed a blood-based multi-cancer early detection test, called THEMIS, using multimodal analysis of plasma cell-free DNA (cfDNA) methylation, fragmentation, and copy number alteration features by whole-methylome sequencing (WMS). The real-world performance of THEMIS was investigated with a prospective cohort of high-risk populations and the preliminary results were reported here. Methods: A total of 1,374 adults over 65 y with additional cancer risk factors for five common cancers (colorectal, esophageal, liver, lung, or stomach cancer) were recruited in the city of Wuxi, Jiangsu province, China. Additional risk factors included fecal occult blood, smoking history, H. pylori infection, HBV infection, and serum protein biomarkers. Participants had no known cancer diagnosis at the time of administration. Blood samples were collected and subject to low-pass WMS assay (~2X) and cancer probability was predicted by the THEMIS model, which was developed and locked in previous studies. Participants predicted as cancer positive by THEMIS were followed up until positive cancer diagnosis in a clinic or one year after receiving the test report, whichever was earlier. Results: At a fixed cutoff rendering 99% training specificity, THEMIS predicted 58 (4.15%) positive cases, among whom 19 participants consented to and completed follow-up. Ten participants received confirmed cancer diagnosis within the follow-up period, including five lung cancers, three liver cancers, one esophageal cancer, and one colorectal cancer. These results yielded a positive predictive value (PPV) of 52.6%. Those who declined follow-up upon a positive THEMIS report were predicted with digestive tract cancers, which need gastrointestinal endoscope for diagnostic confirmation. Conclusions: The nonivasive blood-based THEMIS test demonstrated promising performance and patient compliance for clinical utility to detect cancer early and improve patient outcome. Given that clinical follow-ups were only conducted with a subset of participants, future investigations of the precise real-world performance of THEMIS are needed with more complete patient follow-up.

Comprehensive metabolomic analysis of Mangifera indica leaves using UPLC-ESI-Q-TOF-MSE for cell differentiation: An in vitro and in vivo study

The comprehensive metabolic profiling was performed in the leaf extracts of Mangifera indica and assessed for their significant therapeutic application in tissue engineering and regenerative medicine in both in vitro and in vivo studies. About 147 compounds were identified in the ethyl acetate and methanol extracts of M. indica using MS/MS fragmentation analysis and the selected compounds were quantified using LC-QqQ-MS analysis. The in vitro cytotoxic activity showed that the M. indica extracts enhance the proliferation of mouse myoblast cells in concentration-dependent manner. As well, the extracts of M. indica induce the myotube formation by generating oxidative stress in the C2C12 cells was confirmed. The western blot analysis clearly showed that the M. indica induce myogenic differentiation by upregulating the myogenic marker proteins such as PI3K, Akt, mTOR, MyoG, and MyoD. The in vivo studies showed that the extracts expedites the acute wound repair by formation of crust, wound closure and improves the blood perfusion towards the wound area. Together, the leaves of M. indica can be used as excellent therapeutic agent for tissue repair and wound healing applications.

Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection.

Generating top-down tandem mass spectra (MS/MS) from complex mixtures of proteoforms benefits from improvements in fractionation, separation, fragmentation, and mass analysis. The algorithms to match MS/MS to sequences have undergone a parallel evolution, with both spectral alignment and match-counting approaches producing high-quality proteoform-spectrum matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification (ProSight PD, TopPIC, MSPathFinderT, and pTop) in their yield of PrSMs while controlling false discovery rate. We evaluated deconvolution engines (ThermoFisher Xtract, Bruker AutoMSn, Matrix Science Mascot Distiller, TopFD, and FLASHDeconv) in both ThermoFisher Orbitrap-class and Bruker maXis Q-TOF data (PXD033208) to produce consistent precursor charges and mass determinations. Finally, we sought post-translational modifications (PTMs) in proteoforms from bovine milk (PXD031744) and human ovarian tissue. Contemporary identification workflows produce excellent PrSM yields, although approximately half of all identified proteoforms from these four pipelines were specific to only one workflow. Deconvolution algorithms disagree on precursor masses and charges, contributing to identification variability. Detection of PTMs is inconsistent among algorithms. In bovine milk, 18% of PrSMs produced by pTop and TopMG were singly phosphorylated, but this percentage fell to 1% for one algorithm. Applying multiple search engines produces more comprehensive assessments of experiments. Top-down algorithms would benefit from greater interoperability.