An empirical study of software ecosystem related tweets by npm maintainers.

The npm ecosystem is crucial for the JavaScript community and its development is significantly influenced by the opinions and feedback of npm maintainers. Many software ecosystem maintainers have utilized social media, such as Twitter, to share community-related information and their views. However, the communication between npm maintainers via Twitter in terms of topics, nature, and sentiment have not been analyzed. This study conducts an empirical analysis of tweets by npm maintainers related to the software ecosystem to understand their perceptions and opinions better. A dataset of tweets was collected and analyzed using qualitative analysis techniques to identify the topic of tweets, nature, and their sentiments. Our study demonstrates that most tweets belong to the package management category, followed by notifications and community-related information. The most frequently discussed topics among npm maintainers in the package management category are usage scenarios. It appears that the nature of tweets mostly shared by npm maintainers is information, followed by question and answer, respectively. Additionally, the sentiment analysis reveals that npm maintainers express more positive sentiments towards notification and community-related discussion while expressing more neutral opinions towards the package management related discussion. This case study provides valuable insights into the perceptions and opinions of the npm maintainers regarding the software ecosystem and can inform future development and decision making.

Understanding the biodegradation pathways of azo dyes by immobilized white-rot fungus, Trametes hirsuta D7, using UPLC-PDA-FTICR MS supported by in silico simulations and toxicity assessment.

No biodegradation methods are absolute in the treatment of all textile dyes, which leads to structure-dependent degradation. In this study, biodegradation of three azo dyes, reactive black 5 (RB5), acid blue 113 (AB113), and acid orange 7 (AO7), was investigated using an immobilized fungus, Trametes hirsuta D7. The degraded metabolites were identified using UPLC-PDA-FTICR MS and the biodegradation pathway followed was proposed. RB5 (92%) and AB113 (97%) were effectively degraded, whereas only 30% of AO7 was degraded. Molecular docking simulations were performed to determine the reason behind the poor degradation of AO7. Weak binding affinity, deficiency in H-bonding interactions, and the absence of interactions between the azo (-NN-) group and active residues of the model laccase enzyme were responsible for the low degradation efficiency of AO7. Furthermore, cytotoxicity and genotoxicity assays confirmed that the fungus-treated dye produced non-toxic metabolites. The observations of this study will be useful for understanding and further improving enzymatic dye biodegradation.

Metabolite profiling of Nymphaea rubra (Burm. f.) flower extracts using cyclic ion mobility-mass spectrometry and their associated biological activities.

Nymphaea rubra flowers (NRF) are widely used as a food and in folk medicine throughout the subtropical regions due to their health-promoting characteristics. This study characterized the phytochemical composition of various extracts/fractions of NRF by establishing a quadrupole-cyclic ion mobility-time-of-flight (Q-cIM-TOF) mass spectrometry method in both positive and negative electrospray ionization modes. Over 100 phytoconstituents were tentatively identified, among which 53 phytochemicals belonging to phenolic acids, tannins, flavonoids, terpenoids, alkaloids, xanthones, and naphthopyrones have never been documented in NRF before. Moreover, the ethyl acetate fraction of NRF demonstrated strong antioxidant potential (IC50: 9.21 ± 0.47 µg/mL in DPPH assay and 13.65 ± 0.03 µg/mL in ABTS assay) and tyrosinase, α-glucosidase, and elastase inhibition (IC50: 10.58 ± 0.20, 2.48 ± 0.02, and 38.15 ± 0.25 µg/mL, respectively). The findings highlight the value of NRF as a source of functional components and broaden its potential applications in the food and nutraceutical industries.

Dataset of network simulator related-question posts in stack overflow.

Although the use of network simulator (NS) in predicting the behavior of computer networks has increased, the users often face a variety of challenges and share them on Stack Overflow (SO). However, the challenges that users deal with have not been studied. This paper presents an NS discussion dataset extracted from SOTorrent, which consists of 2,322 NS-related question posts spanning 17 features. The process of data collection was conducted in five steps, including filtering initial post dataset using simulator tags, discovering NS-related tags, collecting the tagged posts, extracting the posts title and preprocessing for LDA (Latent Dirichlet Allocation), and finally applying the LDA topic modeling to obtain the NS posts clustered into eight different topic names. We believe that this dataset will help research community in highlighting issues faced by NS users.

Improved coverage of plant metabolites using powder laser desorption/ionization coupled with Fourier-transform ion cyclotron mass spectrometry.

In this study, the effectiveness of powder laser desorption/ionization (LDI) coupled with Fourier-transform ion cyclotron mass spectrometry (FT-ICR MS) was evaluated for the improved coverage of plant metabolites. Ground plant (powder) was fixed on a metal plate using double-sided tape. Compared with the conventional approach involving liquid extraction, which is followed by electrospray ionization MS analysis, a smaller amount of sample (∼200 µg) was required in the proposed method. Additionally, the laborious steps of liquid extraction, concentration, and solid-phase extraction were avoided. Employing the proposed method in Centella asiatica leaves analysis, higher number of reproducible molecular formulas (>5000) and metabolites (>650) were obtained than the conventional methods. Flavonoids, phenolic acids, xanthones, lipids, carbohydrates, terpenoids, and alkaloids compounds were detected from leaves, stems, and roots of C. asiatica. This study indicates that LDI FT-ICR MS is a quick and effective tool for enhanced plant metabolite profiling in the solid phase.

Meta-analysis of single-cell RNA-seq data reveals phenotypic switching of immune cells in severe COVID-19 patients.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the global coronavirus disease 2019 (COVID-19) pandemic. Despite several single-cell RNA sequencing (RNA-seq) studies, conclusions cannot be reached owing to the small number of available samples and the differences in technology and tissue types used in the studies. To better understand the cellular landscape and disease severity in COVID-19, we performed a meta-analysis of publicly available single-cell RNA-seq data from peripheral blood and lung samples of COVID-19 patients with varying degrees of severity. Patients with severe disease showed increased numbers of M1 macrophages in lung tissue, while the number of M2 macrophages was depleted. Cellular profiling of the peripheral blood showed a marked increase of CD14+, CD16+ monocytes and a concomitant depletion of overall B cells and CD4+, CD8+ T cells in severe patients when compared with moderate patients. Our analysis indicates the presence of faulty innate-to-adaptive switching, marked by a prolonged innate immune response and a dysregulated adaptive immune response in severe COVID-19 patients. Furthermore, we identified cell types with a transcriptome signature that can be used as a prognostic biomarker for disease state prediction and the effective therapeutic management of COVID-19 patients.

SARS-CoV-2 infection initiates interleukin-17-enriched transcriptional response in different cells from multiple organs.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has emerged as a pandemic. Paucity of information concerning the virus and therapeutic interventions have made SARS-CoV-2 infection a genuine threat to global public health. Therefore, there is a growing need for understanding the molecular mechanism of SARS-CoV-2 infection at cellular level. To address this, we undertook a systems biology approach by analyzing publicly available RNA-seq datasets of SARS-CoV-2 infection of different cells and compared with other lung pathogenic infections. Our study identified several key genes and pathways uniquely associated with SARS-CoV-2 infection. Genes such as interleukin (IL)-6, CXCL8, CCL20, CXCL1 and CXCL3 were upregulated, which in particular regulate the cytokine storm and IL-17 signaling pathway. Of note, SARS-CoV-2 infection strongly activated IL-17 signaling pathway compared with other respiratory viruses. Additionally, this transcriptomic signature was also analyzed to predict potential drug repurposing and small molecule inhibitors. In conclusion, our comprehensive data analysis identifies key molecular pathways to reveal underlying pathological etiology and potential therapeutic targets in SARS-CoV-2 infection.

High Resolution Mass Spectroscopy-Based Secondary Metabolite Profiling of Nymphaea nouchali (Burm. f) Stem Attenuates Oxidative Stress via Regulation of MAPK/Nrf2/HO-1/ROS Pathway.

The secondary metabolites profiling of Nymphaea nouchali stem (NNSE) extract was carried out using a high-resolution mass spectroscopic technique. The antioxidant effects of NNSE, as well as the underlying mechanisms, were also investigated in tert-butyl hydroperoxide (t-BHP)-stimulated oxidative stress in RAW264.7 cells. Tandem mass spectroscopy with (-) negative mode tentatively revealed the presence of 54 secondary metabolites in NNSE. Among them, phenolic acids and flavonoids were predominant. Phenolic acids (brevifolincarboxylic acid, p-coumaroyltartaric acid, niazinin B, lalioside, 3-feruloylquinic acid, and gallic acid-O-rutinoside), flavonoids (elephantorrhizol, apigenin-6-C-galactoside 8-C-arabinoside, and vicenin-2), sialic acid (2-deoxy-2,3-dehydro-N-acetylneuraminic acid), and terpenoid (α-γ-onoceradienedione) were identified in NNSE for the first time. Unbridled reactive oxygen species/nitrogen species (ROS/RNS) and redox imbalances participate in the induction and development of many oxidative stress-linked diseases. The NNSE exhibited significant free radical scavenging capabilities and was also able to reduce t-BHP-induced cellular generation in RAW264.7 cells. The NNSE prevented oxidative stress by inducing the endogenous antioxidant system and the levels of heme oxygenase-1 (HO-1) by upregulating Nrf2 through the modulation of mitogen-activated protein kinases (MAPK), such as phosphorylated p38 and c-Jun N terminal kinase. Collectively, these results indicate that the NNSE exhibits potent effects in preventing oxidative stress-stimulated diseases and disorders through the modulation of the MAPK/Nrf2/HO-1 signaling pathway. Our findings provide new insights into the cytoprotective effects and mechanisms of Nymphaea nouchali stem extract against oxidative stress, which may be a useful remedy for oxidative stress-induced disorders.

Effect of Copresence of Zerovalent Iron and Sulfate Reducing Bacteria on Reductive Dechlorination of Trichloroethylene.

Sulfur amendment of zerovalent iron (ZVI) materials has been shown to improve the reactivity and selectivity of ZVI toward a select group of organohalide contaminants in groundwater, most notably trichloroethene (TCE). In previous studies, chemical or mechanochemical sulfidation methods were used; however, the potential of using sulfate-reducing bacteria (SRB) to enable sulfur amendment has not been closely examined. In this study, lab-synthesized nanoscale ZVI (nZVI) and Peerless iron particles (ZVIPLS) were treated in a sulfate-reducing monoculture (D. desulfuricans) and an enrichment culture derived from freshwater sediments (AMR-1) prior to reactivity assessments with TCE as the model contaminant. ZVI conditioned in both cultures exhibited higher dechlorination efficiencies compared to unamended ZVIs. Remarkably, nZVI and ZVIPLS exposed to AMR-1 attained similar TCE dechlorination rates as their counterparts receiving chemical sulfidation (i.e., S-nZVI) using previously reported method. Product distribution data show that, in the SRB-ZVI system, abiotic dechlorination is the dominant TCE reduction pathway. In addition to dissolved sulfide, biogenic or synthesized FeS particles can enhance nZVI reactivity even as nZVI and FeS were not in direct contact, implying that SRB may influence the reactivity of ZVI via multiple mechanisms in different remediation situations. A shift in Archaea abundance in AMR-1 with nZVI amendment was observed but not with ZVIPLS. Overall, the synergy exhibited in the SRB-ZVI system may offer a valuable remediation strategy to overcome limitations of standalone biological or abiotic dechlorination approaches for chlorinated solvent abatement.

Metabolite Profiling of Manilkara zapota L. Leaves by High-Resolution Mass Spectrometry Coupled with ESI and APCI and In Vitro Antioxidant Activity, α-Glucosidase, and Elastase Inhibition Assays.

High-resolution mass spectrometry equipped with electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources was used to enhance the characterization of phytochemicals of ethanol extracts of Manilkara zapota L. leaves (ZLE). Sugar compounds, dicarboxylic acids, compounds of phenolic acids and flavonoids groups, and other phytochemicals were detected from the leaves. Antioxidant activity and inhibition potentiality of ZLE against α-glucosidase enzyme, and elastase enzyme activities were evaluated in in vitro analysis. ZLE significantly inhibited activities of α-glucosidase enzyme at a lower concentration (IC50 2.51 ± 0.15 µg/mL). Glucose uptake in C2C12 cells was significantly enhanced by 42.13 ± 0.15% following the treatment with ZLE at 30 µg/mL. It also exhibited potential antioxidant activities and elastase enzyme inhibition activity (IC50 27.51 ± 1.70 µg/mL). Atmospheric pressure chemical ionization mass spectrometry (APCI-MS) detected more m/z peaks than electrospray ionization mass spectrometry (ESI-MS), and both ionization techniques illustrated the biological activities of the detected compounds more thoroughly compared to single-mode analysis. Our findings suggest that APCI along with ESI is a potential ionization technique for metabolite profiling, and ZLE has the potential in managing diabetes by inhibiting α-glucosidase activity and enhancing glucose uptake.

Phytochemical Characterization of Dillenia indica L. Bark by Paper Spray Ionization-Mass Spectrometry and Evaluation of Its Antioxidant Potential Against t-BHP-Induced Oxidative Stress in RAW 264.7 Cells.

The antioxidant effects of the ethyl acetate fraction of Dillenia indica bark (DIBEt) and the underlying mechanisms were investigated in tert-butyl hydroperoxide (t-BHP)-stimulated oxidative stress in RAW 264.7 cells. Paper spray ionization-mass spectroscopy with positive-ion mode tentatively revealed 27 secondary metabolites in D. indica bark extract; predominant among them were alkaloids, phenolic acids, and flavonoids. A new triterpenoid (nutriacholic acid) was confirmed in DIBEt for the first time. DIBEt had strong free radical-scavenging capabilities and was also able to reduce t-BHP-induced cellular reactive oxygen species (ROS) generation in RAW 264.7 cells. DIBEt was found to prevent oxidative stress by boosting the levels of heme oxygenase-1 (HO-1) through the up-regulation of nuclear factor erythroid 2-related factor 2 (Nrf2) via the regulation of extracellular signal-regulated kinase (ERK) phosphorylation in RAW 264.7 cells. These results support the potential of DIBEt for defense against oxidative stress-stimulated diseases.

Identification of secondary metabolites in Averrhoa carambola L. bark by high-resolution mass spectrometry and evaluation for α-glucosidase, tyrosinase, elastase, and antioxidant potential.

In this study, paper spray ionization (PSI) coupled to high-resolution mass spectrometry has been used to identify secondary metabolites from ethanol extracts of Averrhoa carambola L. bark (ABE). Various phytoconstituents including phenolic acids, flavonoids, xanthones and terpenoids were identified from the bark. ABE shows potential antioxidant activity as well as markedly inhibited α-glucosidase, elastase, and tyrosinase enzyme activities in a concentration-dependent fashion, respectively. ABE significantly inhibited α-glucosidase at lower concentration (IC50: 7.15 ± 0.06 µg/mL). Identified compounds were tested to understand the biological activity of ABE. Experimental results suggest that norathyriol, one of the identified compounds, has significant α-glucosidase (IC50: 0.81 ± 0.01 µg/mL) inhibition and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activities (IC50: 4.90 ± 0.09 µg/mL). At a dose of 100 mg/kg, ABE significantly decreased the postprandial blood glucose level in oral glucose tolerance test (OGTT). This study shows that carambola bark can be a potential source of bioactive compounds.

Reactions of chlorinated ethenes with surface-sulfidated iron materials: reactivity enhancement and inhibition effects.

Recent studies on the use of controlled sulfur amendment to improve the reactivity and selectivity of zerovalent iron (ZVI) in reductive dechlorination reactions have generated renewed interest in ZVI-based remediation materials. However, existing studies have focused on the reactions between trichloroethene (TCE) and lab-synthesized ZVI, and the applicability of sulfidation to ZVIs with different material characteristics for reductive dechlorination of chloroethenes such as tetrachloroethene (PCE) and cis-dichloroethene (cis-DCE) has not been systematically examined. In this study, four ZVI materials from commercial sources having different sizes and morphological and compositional characteristics were subjected to various sulfidation treatments and were assessed in batch reactions with PCE, TCE, or cis-DCE. Sulfur amendment induces modest increases in PCE degradation rates and steers reactions towards a cleaner pathway that has minimum accumulation of partially dechlorinated intermediates. In the case of cis-DCE, bifurcating outcomes were observed that include enhancement effects for two high-purity ZVIs and inhibitory effects for two ZVIs possessing low levels of metal impurities. Further investigations based on controlled metal dosing reveal that the trace metals commonly present in cast iron or recycled metal scraps, such as Cu and Ni, can act as adventitious catalysts for cis-DCE reduction. Sulfidation results in poisoning of these catalytic ingredients and accounts for the adverse effect observed with a subset of ZVIs. Collectively, this study confirms enhanced degradation of highly chlorinated ethenes (PCE and TCE) by sulfidation of ZVIs from diverse origins; nonetheless, the effects of sulfidation can be highly variable for the less chlorinated ethenes due to differences in the material characteristics of ZVI and the predominant dechlorination pathways.