bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational approaches for identifying bioactive compounds inhibiting SARS-CoV-2 main protease
Authors:   , Pojtanadithee Piyatida 
Published: September 2023

The infectious disease caused by the novel coronavirus 2019 has devastatingly affected the global economy and society. However, the drug discovery process from concept to approval requires a significant investment of time and resources. To address these challenges, we employed structure-based virtual screening techniques, including drug-likeness screening, pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and fragment molecular orbital calculation. The protein target of this investigation was the main protease or 3-chymotrypsin-like-protease (3CLpro) of the coronavirus, given its pivotal role in the viral replication process. Using our in-house database of natural products and their derivatives, we aimed to identify potent compounds with the potential for further development as anti-SARS-CoV-2 medications. Notably, the derivatives of sulfonamide chalcone (SWC422, SWC423, and SWC424) and ester derivatives of caffeic acid (4k and 4l) exhibited exceptional binding energy and substantial interactions with the 3CLpro binding pocket compared to peptidomimetic inhibitors (11a, 13b, and N3) and an FDA-approved drug (nirmatrelvir). While our findings show that in-silico strategies have the potential to identify new potent compounds that inhibit the 3CLpro activity of coronavirus, further studies such as enzyme inhibition assay and cell-based assay are necessary to ensure their effectiveness from these virtual screenings.
The effect of histone methylation in trained innate immunity of cord blood monocytes in newborn infants of chronic HBV-infected mothers
Authors:   , Plypongsa Pennapa 
Published: September 2023

Newborns contract Hepatitis B virus (HBV) through exposure in utero from mothers who are infected with HBV. In newborn infant from chronic HBV-infected mothers, the immune system displays innate immune cell maturation and enhances immune response upon restimulation with unrelated pathogens such as bacteria. This pattern is called “trained immunity” or “innate immune memory”. Trained immunity is regulated by epigenetic programming, especially histone modification. To date, there is not report on the epigenetics to regulate trained immunity in HBV. Therefore, this study investigated the cytokines levels and expression levels of histone modification enzyme genes in HBV-exposed cord blood monocytes. Moreover, we demonstrated histone modifications at position H3K4me3 that regulated IL-12p40, IL-6, IL-10, TNF-a, and IL-1b genes in monocytes from HBV-exposed cord blood. The expression of IL-12p40 was significantly higher in HBV-exposed cord blood monocytes than healthy cord blood monocytes after restimulation with TLR8 agonist. In addition, mRNA expression of histone modification enzymes was not significantly different between HBV-exposed cord blood monocytes and cord blood monocytes. Moreover, the level of histone methylation at position H3K4me3 of cytokine genes did not support trained immunity in this study. It is likely to be that epigenetic programming through histone modification at position H3K4me3 might be not involved in HBV-trained immunity.
The role of b1 methylation, physiologic replication independent endogenous dna double strand breaks (phy-rind-edsb) and laminin 511 e8 proteins in rat second degree burn wound healing
Authors:   , Meevassana Jiraroch 
Published: September 2023

Background: DNA methylation via short interspersed nuclear element (SINE) small interfering (si)RNA prevents DNA damage and promotes cell proliferation. Furthermore, laminin α5 β1 γ1(LM511) is an extracellular structural protein that can support epithelial cell adhesion and migration. Box A of high-mobility group box 1 protein (Box A of HMGB1) is a common nuclear protein in eukaryotic cells that can reduce DNA damage response toward burn injury.

Objective: To investigate whether treatment of burn wounds using B1 siRNA, Box A of HMGB1 and LM511-E8 fragment improved wound closure in a rat second-degree burn wound model.

Methods: I performed a cross-sectional analytical study using tissue and blood samples from post-burn and healthy patients (n = 23 each) to measure Alu methylation levels and patterns. In in vivo experiments, second-degree burn wounds were introduced on the backs of rats. The rats were then divided into control and experiment groups: a B1 siRNA-treated, Box A of HMGB1 protein and LM511-E8, saline-treated control, and calcium phosphate-nanoparticle-treated control group (n = 15–20/group). The wounds were imaged on days 0, 7, 14, 21, and 28 post-injuries. The tissue sections were processed for methylation and histological and immunohistochemical examination and scored based on the overall expression of histone H2AX phosphorylated on serine 139 (γH2AX), 8-hydroxy-2′-deoxyguanosine (8-OHdG), and presence of cytokeratin 10 and 14.

Results: Alu methylation levels were lower in hypertrophic scar tissues than in normal skin (29.4 ± 2.5% vs. 35.6± 3.2%, P = 0.0002). Burn wound closure improved in the B1 siRNA-treated group compared to that in the control group, especially from days 14 to 28 post-injury (P < 0.001). The overall pathological score and degree of B1 methylation in the B1 siRNA-treated group improved at days 14–28 days post-injury. The Box A of HMGB1 protein group demonstrated improvement in burn wound closure, starting from day 7th until day 28th after injury (P < 0.001). Furthermore, γH2AX and 8-OHdG expression in the HMGB1 plasmid-treated group was lower than that in the control group (P < 0.05). The re-epithelialisation in the LM511-E8-treated group was quicker than that of the control group at 7–28 days post-injury, with the largest improvement observed on days 7 and 14 (P < 0.001). The pathological score of the LM511-E8-treated group was higher than that of the control group at 14–28 days post-injury.

Conclusion: These results imply that LM511-E8 fragment, B1 siRNA, and Box A of High-mobility group box 1 protein (Box A of HMGB1) are promising therapeutic options for managing second-degree burns.
Accuracy in classification of liver lesion ultrasound using artificial intelligence
Authors:   , Tangruangkiat Sutthirak 
Published: September 2023

B-mode ultrasound imaging is the standard method for hepatocellular carcinoma (HCC) screening. If a lesion has a unique appearance, a conventional detector can be applied. However, if the lesion shares its appearance with other lesion, a large training dataset is required, which may be unavailable. Therefore, a two-stage method is proposed. In the first stage, lesions are detected but not differentiated into any particular class. The detected lesions are then classified in the second stage using a conventional convolutional neural network (CNN).

The aims of the dissertation are to design an artificial intelligent system model and to investigate the most accurate deep learning structure for hepatic lesion classification using two-stage model.

Even though the cysts and hepatic vessels are both anechoic pattern and present black oval in ultrasound images, cysts have unique artifacts that present posterior acoustic enhancement. By including the artifacts in the detection, conventional detectors can be applied. In the study, Region-based convolutional neural networks, R-CNN, with Residual Network-50, ResNet-50, as the backbone was applied for the detection of 615 hepatic cysts. The system was evaluated by five-fold cross validation. The result indicated that the addition of artifacts led to better detection in term of accuracy, reduction of false positives and false negatives.

Hemangioma (HEM) and HCC share lots of sonographic appearance. There is no unique artifact to differentiate these two lesions. A two-stage method is applied. In the first stage, the detector is trained to identify HEM and HCC like lesions. In the second stage, the classifier is applied to differentiate lesions into typical HEM, atypical HEM and HCC. Since atypical HEM and HCC display the same sonographic appearance, both lesions cannot be differentiated solely by B-mode ultrasound images. They require further CT or MR investigation, so it is unnecessary to accurately differentiate these two lesions during screening. The study showed that grouping HCC and atypical HEM into the same one led to the increase of HCC recall of the detector from 0.64 to 0.68. The application of the two-stage method in place of detector only method improved the recall from 0.68 to 0.72. The recall rate was comparable to the detector only method that was trained by a much larger database and used more relax criterion (0.5 and 0.2 intersection over union (IoU) for the correct detection in the proposed two-stage and the detector only methods, respectively).
Analysis of VOCs from exhaled breath for the diagnosis of hepatocellular carcinoma
Authors:   , Suk-aram Thanikarn 
Published: September 2023

Background: Volatile organic compounds (VOCs) were shown as promising biomarkers for hepatocellular carcinoma (HCC) diagnosis. We aimed to investigate the performance of VOCs for diagnosing early-stage HCC in patients at-risk for HCC.

Methods: VOCs were identified in exhaled breath samples collected from 90 early-stage HCC patients, 90 cirrhotic patients, 91 HBV-infected patients, and 95 healthy volunteers using thermal desorption-gas chromatography/field-asymmetric ion mobility spectrometry. The VOC levels were compared between the four groups. An association between VOCs and HCC was determined using logistic regression analysis. Diagnostic performance of VOCs was estimated using the AUROC and compared to serum alpha-fetoprotein (AFP).

Results: The levels of dimethyl sulfide, 1,4-pentadiene, isopropyl alcohol, and acetone were significantly different between the four groups. After adjusting for liver function test and AFP, acetone was significantly associated with HCC. Acetone significantly outperformed AFP, with 88.9% vs. 68.2% sensitivity, 87.3% vs. 63.6% specificity, 87.7% vs. 65.2% for accuracy, and AUROC of 0.932 vs. 0.725, p=0.017, 0.001, <0.001, and 0.001, respectively, for differentiating between HCC and non-HCC group.

Conclusion: Acetone has a better performance than AFP for diagnosing early HCC in high-risk patients. Further studies to validate the utility of VOCs as a HCC surveillance tool are needed.
Comparing the Success Rate of Pleurodesis with Thoracoscopic Talc Poudrage Combined with Indwelling Pleural Catheter versus Thoracoscopic Talc Poudrage in Patient with Malignant Pleural Effusion, A Randomized, Non-inferiority Clinical Trial
Authors:   , Sootlek Jitanong 
Published: September 2023

Background: Malignant pleural effusion (MPE) can cause dyspnea symptoms that greatly impact a patient's quality of life. Talc pleurodesis or indwelling pleural catheter (IPC) insertion are two treatment options that can prevent recurrent MPE, alleviate dyspnea, and improve quality of life. However, talc pleurodesis requires a lengthy hospital stay, while IPC insertion is associated with lower pleurodesis success rates. Due to limited hospital bed capacity, we have devised a practical approach to managing MPE by combining TTP and IPC.

Objective: This study aims to evaluate the efficacy of combined Thoracoscopic talc poudrage (TTP) and IPC compared to TTP alone in patients with symptomatic MPE.
Methods: The study was conducted as a randomized non-inferiority trial at a single center. Patients were randomly allocated to receive either TTP and IPC or TTP alone. The study collected demographic data, hospital length of stay (LOS), symptoms, and pleurodesis success rates. The primary outcome of the study was the success rate of pleurodesis at 12 weeks post-procedure.
Results: Preliminary data analysis from 26 patients with a mean age of 61 years showed that the baseline characteristics were similar between the two groups, except for the baseline mean VAS dyspnea score, which was significantly higher in the TTP+IPC group. Successful pleurodesis at 12 weeks was achieved in 88.89% of the TTP+IPC group and 64.29% of the TTP alone group, with a difference of 24.6% [95% CI, -7.83% to 57.03%]. Additionally, the TTP+IPC group showed a greater reduction in dyspnea, less pain following the procedure, and less analgesic medication use. The hospital LOS was also shorter, and the overall quality of life was significantly better. Furthermore, there was no difference in the incidence of complications between the two groups.
Conclusion: Combining thoracoscopic talc pleurodesis and IPC is both effective and safe for treating symptomatic MPE patients.
Job satisfaction, grit and associated factors of job satisfaction among Thai working adults who are currently undertaking their graduate studies in Thailand
Authors:   , Visitchaichan Somchat 
Published: September 2023

Whether in health care or business organizations, most individuals spend a large part of their lives at work attempting to be successful therefore an understanding of factors involved in job satisfaction is relevant to improving the well - being of a large number of individuals in an important aspect of their lives. The basic premises underlying the study of job satisfaction, grit, and associated factors of job satisfaction among Thai working adults who are currently undertaking their graduate studies in Thailand is the belief that increasing job satisfaction will improve well-being of individuals, increase productivity and thus the effectiveness of organizations. Objectives of this study are therefore two-folds; to study the level of job satisfaction and association between job satisfaction and grit among Thai working adults who are currently undertaking their graduate studies in Thailand. A sample size of 294 full - time working adults who are currently undertaking postgraduate degrees is selected randomly from four universities in Thailand: National institute of development administration (NIDA), Naresuan University, Assumption University and Bangkok University. The 12-item Grit Scale (GRIT-S) which was developed by Angela Duckworth and her associates and questions to measure the level of job satisfaction and job autonomy which were formulated from the underlying concepts critically examined and discussed from the review of literature and research section by the researcher were used in this study. Research findings reveal that the majority of respondents tend to have moderate levels of job satisfaction (52.79%), followed by 24.08% of high level of job satisfaction and 23.13% of low level of job satisfaction with the mean score of 3.75. In addition to this, there is a low positive relationship between grit and job satisfaction (r = 0.13, P = 0.01). This suggests that as the level of grit increases, we can predict slightly higher levels of job satisfaction.
A new spinel high-entropy oxides nanoparticles (FeCoNiMnZn)3O4 as anode materials for lithium-ion batteries
Authors:   , Aida Maha 
Published: September 2023

A novel (FeCoNiMnZn)3O4 HEO as an anode in lithium-ion batteries (LIBs) was developed for the first time. High-entropy oxide (HEO) of (FeCoNiMnZn)3O4 was synthesized using a hydrothermal technique to control size and crystallinity. We also synthesized oxides of each element (Fe, Co, Ni, Mn, Zn) from HEO composition under similar condition for comparison. The samples were then analyzed using XRD, SEM, TEM, EDS elemental mapping, surface area analysis, ICP-OES, and XPS. Cyclic voltammetry, galvanostatic charge-discharge, electrochemical impedance spectroscopy, and associated coulombic efficiencies were also used to study the electrochemical performance of (FeCoNiMnZn)3O4. Three samples with different preparation conditions, HEO-3, HEO-6, and HEO-9, were selected for investigation. HEO-3 particles are the smallest, 2.95 ± 0.29 nm, and have an irregular shape, making them difficult to measure. In contrast, HEO-6 and HEO-9 particles have diameters between 23.16 ± 7.56 nm and 90.42 ± 3.27 nm, respectively. The HEO-9 performs exceptionally well electrochemically. It exhibits excellent performance of 625.5 mA h g-1 at 1000 mA g-1 and a large capacity of 1333.54 mA h g-1 at 50 mA g-1. After cycling, we also investigated the physical and chemical characterization to identify the change. HEO-9 still has a more stable performance and the least volume change. From these results, developing an anode for lithium-ion batteries (LIBs) in the future looks promising.
Application of core annular flow for oil transportation in different pipe configurations using computational fluid dynamics
Authors:   , Dianita Cindy 
Published: September 2023

The application of Core Annular Flow (CAF) has become an interesting solution in transporting heavy oil through pipeline because of its energy reduction and cost efficiency. Current study conducted a 3D computational fluid dynamic (CFD) to simulate CAF of oil-water in horizontal T- and Y-pipe junctions with two types of oil characteristic i.e., oil as Newtonian fluid and oil as non-Newtonian Carreau Fluid. The 2k factorial statistical experimental design was applied to investigate the effect of geometry on the flow performance. Eight cases were run with different diameter combinations and junction angle. The most attractive design was measured by the high value of oil holdup with small average values of pressure gradient and pressure standard deviation. The simulation result showed the stable CAF along the upstream region but then broke up when passing the intersection. A strategy to recover the stability of CAF after passing the intersection area of a T-pipe without interrupting the flow process was also proposed specifically for T50-50 (T-pipe with inlet and outlet diameter of 50 mm) as the most desired design for water-oil as non-Newtonian Carreau Fluid case. An additional water insertion was introduced at the intersection point to support the recovery of CAF structure by suppressing fouling. The proposed design showed significant improvement of CAF consistency for downstream region until pipe outlets. Energy evaluation was also has been conducted and it was estimated that CAF in T50-50 was able to reduce the pressure drop to more than 90% compared to transportation without lubrication. In addition, the cost of power consumption can be saved to more than 80% than single phase oil transportation. A scaled-up pipe size simulation was also completed to 10 times bigger dimension. More consistence result of lubricated flow was shown by bigger dimension pipe.
Screening of Clostridium sp. for butanol production from Sato (Thai rice wine) factory wastewater
Authors:   , Buranaprasopchai Julalak 
Published: September 2023

The production of Sato, a Thai traditional beverage, yields Sato wastewater (STW), which contains residual rice constituents with high chemical and biological oxygen demands and so forms an environmental problem. In addition, STW often smells rotten from the formation of hydrogen sulfide. To solve this problem, the composition of STW was analyzed for its physiological and chemical characteristics to evaluate its potential as a substrate for ABE fermentation using Clostridium spp., which has never been reported for use in acetone-butanol-ethanol (ABE) fermentation before. Solvent-producing Clostridium isolates were obtained from environmental sources in Thailand, and that producing the highest butanol level (isolate CUEA02 from the sludge of a biodiesel plant) was selected. The butanol production was 8.32 ± 0.08 g/L in flask fermentation under an initial pH of 6.5, 35 ˚C, 10% (v/v) inoculum size, and 50 g/L of glucose. Whole-genome sequencing analysis was used to identify this strain and its ability to use different carbon sources for ABE fermentation was evaluated. Isolate CUEA02 was closely related to Clostridium beijerinckii with an average nucleotide identity of 95.14% and could grow and produce butanol in various carbon sources, especially starch and carboxymethyl cellulose. The STW was diluted 1:10, 1:20, 1:30, and 1:40 for ABE production by CUEA02, where the obtained butanol yield (0.23 g/g) under an anaerobic condition was highest with the 1:10 diluted STW. To improve the butanol production, the initial pH was adjusted from 4.75 to 6.5, resulting in a 2.13-fold enhanced butanol yield (0.49 g/g). Furthermore, adding yeast extract at 2 g/L enhanced butanol production in STW utilizing C. beijerinckii CUEA02 by up to 29%.
Identification of potential drug targets for COVID 19 patients with cytokine storm
Authors:   , Buana Bayu 
Published: September 2023

The outcome of SARS-CoV-2 infection may vary depending on gender, lifestyle, and age. The elderly is more likely to have the severe condition than the younger population. However, several young people suffer from severe lung diseases caused by cytokine dysregulation, also known as a "cytokine storm." Cytokine storms are associated with Covid-19 severity and mortality. Identification of potential cytokine storm targets is critical for improving patient survival. Transcriptomic analysis of expression data from publicly available databases could be used to identify differentially expressed genes and pathways. The list of both results was used to narrow down the potential candidates in the co-expression network and immune cell fraction analysis. In addition, the drug-gene interaction database was queried for information on the candidate's draggability. According to the findings, AMHR2 is a potential drug target. AMHR2 overexpression may cause the TGF beta signaling pathway to becoming overactive, resulting in the activation of pro-inflammatory macrophages and a delay in the adaptive immune response. This systemic effect may initiate the cytokine storm that the infection has started in the lung, activating pro-inflammatory macrophages and T gamma delta cells that secrete cytokines excessively. Furthermore, AMHR2 has evidence of drug modulation and demonstrates pathway regulatory importance. Therefore, inhibiting the TGF beta signaling pathway via AMHR2 may be beneficial in relieving cytokine storms in Covid 19 patients.
Renieramycin t derivative dh_22 induces apoptosis in lung cancer cells by downregulation of C-Myc protein
Authors:   , Anggraeni Indiana 
Published: September 2023

Lung cancer is a prevalent cause of death, indicated by an elevated c-Myc level. We synthesized a new derivative of renieramycin T (RT), named DH_22, and tested it for anti-cancer activities in human lung cancer cells. In the cell viability and nuclear staining tests, DH_22 was discovered to be cytotoxic, with an IC50 of around 13 μM; and found to mediate apoptosis in the lung cancer cells. Meanwhile, in a mechanistic sense, DH_22 contributed to the activation of p53-dependent apoptosis and decreased the cellular level of c-Myc. The p53-dependent mechanism was indicated by an increase of p53, an induction of the pro-apoptotic Bax protein, and a decrease of the anti-apoptotic B-cell lymphoma 2 (Bcl-2) protein. The fluorescence intensity of Akt, p-Akt, and c-Myc also declined significantly. Akt and p-Akt were detected in the cytoplasm and nucleus, while most of c-Myc was located in the nucleus of the untreated control cells. These results demonstrated that DH_22 could reduce c-Myc, supported by molecular docking. The mechanism of action of renieramycin T derivative DH_22 starts with the inhibition of mTOR, which reduces the phosphorylation of Akt, which then reduces the phosphorylation of GSK3b and accelerates the degradation of c-Myc. In addition, DH_22 itself could inhibit Akt via allosteric inhibition, which could disrupt the c-Myc stabilization.