bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome sequencing, de novo assembly, and comparative analysis of varanus salvator and megaustenia siamensis
Authors:   , Chetruengchai Wanna 
Published: September 2023

Background: Understanding the animal genome structure and function is pivotal for expanding our current knowledge of evolution, biodiversity, cosmeceutical and medical applications. Each species has a unique characteristic feature. Varanus salvator is a reptile (vertebrate) prevalent in Thailand. It has evolved over millions of years to adapt and survive in urban environments, polluted canals, and garbage dumps. It still survives without noticeable effects. Megaustenia siamensis, an invertebrate, is famous for its ability to produce biological adhesive substances enabling it to stick to trees’ leaves even in heavy rain. However, there is very little genomics or transcriptomics data for V. salvator and M. siamensis. Herein, High-throughput whole-genome assembly would serve as a genomic reference of V. salvator and M. siamensis. The transcriptomics would lead to the discovery of proteins involving in bioactive compound syntheses, which may have high potential in cosmeceutical and medical applications. Method: We generated reference genomes using a hybrid approach of short-read and long-read sequencing platforms. Performing comparative genomics within and between species to understand the evolution and adaptation. We also studied positively selected genes which were associated with V.salvator-specific traits and M.siamensis-specific traits. Furthermore, we sought for potential bioactive compounds, antimicrobial peptides, and differential expression between foot and mantle from transcriptomic data. Result: The final size of the reference genome assembly of V. salvator was 1.7 Gb with an N50 scaffold size of 71Mb featuring 87.5% completeness of the genome assembly. Our comparative genomic analysis revealed that V. salvator is closely related to V. komodoensis. We also found a positive selection in V. salvator genome within the genes controlling blood clotting and innate immunity genes. The final size of the reference genome assembly of M. siamensis was 2.59 Gb with an N50 scaffold size of 84.3Mb featuring 85.9% completeness of the genome assembly. The phylogenetic tree showed that M. siamensis was most closely to A. vulgaris, which is a group of land snails. Positive selection was found in pathways related to ubiquitin-proteasome. Moreover, RNA from foot and mantle tissues suggested the major components of the glue, which comprised lectin-like proteins (C-lectin, H-lectin, and C1q) and matrilin-like proteins (VWA and EGF). The result also reveals 44 potential antimicrobial peptides (AMPs). Conclusion: The draft genome data are expected to provide useful information for future studies and contribute significantly to understanding the biological insight. Furthermore, the transcriptome data reveal the highest protein composition and bioactive compounds, which might be useful for medical applications.
Macrophage depletion enhances gut dysbiosis and severity in sepsis mouse model
Authors:   , Hiengrach Pratsanee 
Published: September 2023

Macrophage is vital players in the responsiveness of the innate immune system against injury or infection. Although macrophage depletion is well-known for some emerging therapies, such as osteoporosis, osteopenia, and decreasing tumor-associated macrophages in melanoma, dysfunction of macrophages leads to an inability of an appropriate immune response and implicated in various disease processes, especially intestinal macrophages that play a key role in the gut immune system and the regulation of gastrointestinal physiology. To obtain an understanding of the role of sepsis-associated macrophages, clodronate was used for the dysfunction of mouse macrophages with and without cecal ligation and puncture (CLP) sepsis. Macrophage depletion significantly increased fecal Ascomycota, with a slight growth of bacterial microbiota which might be enhanced gut-barrier damage as Candida pintolopesii, Klebsiella pneumoniae, Acinetobacter radioresistens, and Enterococcus faecalis that were identified from mouse blood. In addition, increased mortality, cytokine overproduction, organ damage (liver and kidney), gut leakage (FITC-dextran), imbalance of fecal fungi and pathogenic bacteria, as well as fungemia and bacteremia in sepsis with macrophage-depleted animals was more severe than sepsis in control mice (fungemia and bacteremia). To determine the interaction between fungal molecules and bacterial abundance, each heat-kill lysate of C. pintolopesii, C. albicans ATCC90028, C. albicans (isolated from human blood), and purified (1→3)-β-D-Glucan (BG), a major component of the fungal cell wall was co-cultured with each pathogenic bacterium, including K. pneumoniae, E. faecalis, and A. radioresistens, indicating that the enhanced growth of bacteria that were isolated from the blood implying a direct enhancer to some bacterial species. Furthermore, the additive effect of heat-kill lysate Candida yeast cells or their components together with heat-kill lysate of isolated bacteria on enterocytes (Caco-2) also supported an influence of gut fungi in worsening sepsis. In conclusion, macrophage depletion enhanced fecal Candida and fecal pathogenic bacteria overgrowth, intestinal barrier damage, and gut translocation of bacteria and fungi that additively worsened sepsis severity. These findings suggested that fecal fungus could spontaneously elevate in response to macrophage-depleted therapy, increasing the severity of sepsis.
Epigenetic regulation in trained and tolerized macrophages
Authors:   , Benjaskulluecha Salisa 
Published: September 2023

Innate immune memory is the phenomenon that can either enhance (trained) or suppress (tolerized) immune response by innate immune cells during the second encounter of the stimuli such as pathogens. Previous studies reported that epigenetic regulations critically regulate both types of innate immune memory. However, a complete understanding of the underlying mechanisms is still lacking. In this study, we performed a screening of an epigenetics compound library to identify inhibitors that affect ß-glucan (BG)-trained or LPS-tolerized macrophages. Among 181 compounds tested, various inhibitors targeting Aurora kinase, histone methyltransferase PRMT and EZH2, histone demethylase LSD1 and JMJD2, histone deacetylase 6 and sirtuin-1, and PARP showed inhibitory activity against LPS tolerance by promoting effects on TNFα production. The effect of LSD1 in LPS tolerance was validated in this study. Inhibition or silencing of LSD1 results in suppressed LPS tolerance by enhance cytokines production. However, no change was observed in H3K4me3 level associated with the Tnf promoter upon LSD1 inhibition. In trained immunity, we identified an inhibitor of O6-methylguanine DNA methyltransferase (MGMT), a DNA repair enzyme of the lesion triggered by alkylating agent, as a novel regulator of trained immunity in macrophages. MGMT expression significantly increased after the priming with BG, and inhibition or silencing of MGMT expression during the priming resulted in increased trained immunity. To further investigate the role of MGMT in trained immunity, mice with myeloid specific deletion of MGMT were generated (LysM-crecre/+; MGMTfl/fl mice). However, targeted deletion of MGMT expression resulted in a decrease in proinflammatory cytokines production in trained immunity both in vitro and in vivo. Depletion of MGMT in trained macrophages resulted in decrease downstream signaling molecules of TLR4 receptor, such as p38 and SAPK/JNK. In addition, signaling downstream of dectin-1 receptor, such as mTOR, and glycolytic function was also damped. These results highlight the unexpected role of MGMT in regulation of trained immunity beyond its role in DNA repair. Based on transcriptomic data, MGMT may regulate trained immunity through farnesoid X receptor (Nr1h4) and PR domain zinc figure protein 5 (Prdm5). Taken together, this screening approach indicates that innate immune memory is regulated by numerous mechanisms and the novel target proteins identified from this research has the potential to regulate innate immune memory, which could be used as a target of therapeutic agents for several diseases.
Genetic analysis of focal segmental glomerulosclerosis in Thailand
Authors:   , Isaranuwatchai Suramath 
Published: September 2023

Background: The genetic variants spectra of focal segmental glomerulosclerosis (FSGS) vary among different populations. Here we described the clinical and genetic characteristics of biopsy-proven FSGS patients in Thailand. We also used special staining in renal biopsy tissue to describe protein expression related to the variants found by whole-exome sequencing (WES). Also, a functional study in cells was studied to investigate the etiologic evidence of the variants found by WES.

Methods: Fifty-three unrelated FSGS patients without secondary causes were included in our study. Whole-exome sequencing (WES) was subsequently performed. Immunohistochemistry (IHC) staining method was used to characterize the morphology of renal pathology for clinical and genomic correlation. Cell-based split-luciferase-based trimer formation assay was used to investigate whether the variances found by WES related to clinical, pathology, and genomic findings.

Results: Of 53 FSGS patients, 35 patients were adults (66.0%), and 51 patients were sporadic cases (96.2%). Clinical diagnosis before kidney biopsy was steroid-resistant nephrotic syndrome (SRNS) in 58.5%, and proteinuric chronic kidney disease in 32.1%. Using WES, disease-associated pathogenic/likely pathogenic (P/LP) variants could be identified in six patients including the two familial cases, making the P/LP detection rate of 11.3% (6/53). Of these six patients, two patients harbored novel variants with one in the COL4A4 gene and one in the MAFB gene. Four other patients carried previously reported variants in the CLCN5, LMX1B and COL4A4 genes. Protein expression study with IHC staining of α5(IV) collagen in kidney tissues were positive in kidney tissues of both P/LP variants and benign variants; therefore, IHC staining did not correlated with pathogenicity of variants classified. However, cell-based split-luciferase-based trimer formation assay of α345(IV) collagen showed decreased in protein expression of α345(IV) collagen in the cells with P/LP variants; hence, predicted that these P/LP variants were the cause of FSGS in the respective patients.

Conclusions: The overall P/LP variant detection rate by WES in biopsy-proven FSGS patients was 11.3%. The most identified variants were in COL4A4. IHC staining of α5(IV) collagen was not associated with pathogenicity of variants, but cell-based study can successfully demonstrated the etiologic evidence of COL4A4 variants found by WES.
Effect of thiosulfate on the passivation of zinc-alloyed anodes, (Z32120 and Z13000) at 80°C after 288h immersion in 3.5% NaCl solution
Authors:   , Zaw Thwelt 
Published: September 2023

In this research, the inhibition of passivation on Zn alloys (Z32120 with Al) and Z13000 without Al) in artificial seawater (3.5% NaCl) mixing with different thiosulfate concentrations (100ppm, 150ppm, 200ppm) were investigated electrochemically after 288h immersion at 80°C and compared the results with that of testing without thiosulfate in the environment. According to the Potentiodynamic polarization test results, it is found that the presence of thiosulfate (S2O32-) in the solution hinders the passivation that was formed during the immersion of Zn alloys between 120h and 288h at 80°C in the absence of thiosulfate. Thiosulfate effect promotes Cl- penetration for not only hinderance of the passivation but also generating the depassivation of passive films resulting in retarding repassivation. It is confirmed by the comparison between polarization test results of testing without thiosulfate and with thiosulfate in the solution. However, although all thiosulfate concentrations used in the study impedes the passivation, the different thiosulfate concentration gives the different effectiveness depending on the immersion time and temperature. Also, Al presence in the Zn alloys supports the different effectiveness. The lower thiosulfate concentration (100ppm) exhibits the decrease of current density at longer immersion for Z32120 whilst Z13000 exhibits the decrease of the current density at higher thiosulfate concentration (200ppm). Regarding the results investigated in this study, Z32120 is effective with 150ppm and 200ppm thiosulfate meanwhile Z13000 is better result with 100ppm and 150ppm. Therefore, 150ppm is considered to be the proper and average value for both Zn alloys. The effect of thiosulfate on passivation of both Zn alloys was discussed based on immersion time, temperature, pH, and the ratio of Cl- and S2O32-.
Effect of normal saline in different concentration on soft tissue healing of extraction wound: a clinical study
Authors:   , Kunthikarn Walailuk 
Published: September 2023

Sodium chloride solution (NaCl) is regarded as the most suitable and recommended medical irrigation, because of the nontoxic and isotonic properties. The previous in vitro study showed that NaCl solution induced migration and extracellular matrix excretion from human gingival fibroblast. However, there is no report concerning the effect of rinsing extraction wound with NaCl solution in clinical trial study. This research study is split mouth single-blind randomized controlled clinical trial to investigate if rinsing with 0.9% and 1.8% NaCl solution on extraction wound can promote soft tissue healing. The operation was performed in 60 socket sites. The patients, who had been planned for bilateral premolar extraction, were randomly divided into 3 groups with different solutions used including sterile water solution (control), 0.9% NaCl solution, and 1.8% NaCl solution, respectively. Mesio-distal dimension, bucco-lingual dimension and the depth of sockets were evaluated to determine the socket wound healing property on day 0 (immediate post-operation), 7 and 21, respectively. The results showed that there was a significant reduction in Mesio-Distal dimension of the sterile water and 1.8% NaCl group in the first week, but not in the third week. The Bucco-Lingual dimension did not show a significant difference in the results. And the socket depth, there was a significant difference in the percentage reduction in socket depth in the 0.9% NaCl group in the third week. The result of this study may be helpful in term of the acceleration of the healing period in the complicated case or in immunocompromised patients.
Prediction of future caries in toddlers via salivary microbiome: A 1-year longitudinal study
Authors:   , Raksakmanut Ratcha 
Published: September 2023

Dental caries in children is the most common chronic oral disease that could disturb their quality of life including their development. Early prevention is a key approach to reducing the prevalence of early childhood caries. However, a reliable caries predictor, as an essential tool for targeted prevention that is important to this approach, is still lacking for infants before caries onset. Therefore, we aimed to develop the caries risk prediction model based on the salivary microbiome of caries-free 1-year-old children to predict caries onset at 1-year follow-up. Using a nested case-control design within a prospective cohort study, 30 saliva samples, collected at a baseline time point, were selected based on sufficient sample quantity and caries status when children were 2-year-old: 10 children who developed non-cavitated caries lesions, 10 who developed cavitated caries lesions, and 10 who remained caries-free then 16S rRNA gene sequencing was performed. The salivary microbiota of the children who remained caries-free was significantly different when compared with those who developed cavitated caries lesions (unweighted UniFrac, ANOSIM, Benjamini-Hochberg corrected, P = 0.042). The relative abundance of Prevotella nanceiensis, Leptotrichia sp. HMT 215, Prevotella melaninogenica, and Campylobacter concisus were significantly higher in the children who remained caries-free compared with those who developed cavitated caries lesions (Wilcoxon rank-sum test, P = 0.024, 0.040, 0.049, and 0.049, respectively) and were identified as biomarkers for the children who remained caries-free (LEfSe, LDA score = 3.69, 3.74, 3.52, and 3.46, respectively). Caries prediction model generated by machine learning based on these 4 biomarkers differentiated the 1-year-old children between those who did and did not develop cavitated caries lesion at 2-year-old with an accuracy of 80%, sensitivity of 80%, and specificity of 80% (AUC, 0.8; 95% CI, 44.4-97.5). These findings suggest that the salivary microbiome of caries-free 1-year-old children could predict future caries onset in infants that could further develop into a promising caries predictor for targeted prevention.
Anti-inflammatory compounds in human peripheral blood mononuclear cells from dendrobium species
Authors:   , Kongkatitham Virunh 
Published: September 2023

In these studies, four new compounds including three phenanthrene derivatives (dendrocrumenols A, B and D) and one fluorenone (dendrocrumenol C) and four known compounds including gigantol, 3,7-dihydroxy-2,4,8-trimethoxyphenanthrene, densiflorol B and cypripedin were isolated from Dendrobium crumenatum Sw. Each structure of isolated compounds from D. crumenatum was elucidated by spectroscopic data. These isolated compounds were then evaluated for anti-inflammatory effects in human peripheral blood mononuclear cells (PBMCs). Among the tested compounds, dendrocrumenols B and D showed the most promising anti-inflammatory effects through inhibition of tumor necrosis factor tumor (TNF) and interleukin-2 (IL-2) in monocytes and T cells. The deep immune profiling using high-dimensional single-cell mass cytometry (CyTOF) could confirm the anti-inflammatory effects based on immunomodulation of dendrocrumenol D through the decreasing of activated T cell population in phorbol-12-myristate-13-acetate and ionomycin (PMA/Iono) stimulation in human PBMCs. Next, the seven known bibenzyls isolated from Dendrobium plants were investigated the immunomodulatory effects in lipopolysaccharide (LPS)-induced human PBMCs. Two bibenzyls, moscatilin and crepidatin, exhibited the strongest inhibitory effect of TNF-expressed monocytes. The deep immune profiling using CyTOF could confirm the anti-inflammatory activity based on immunomodulation effect of crepidatin through reduction of NK cells, pSTAT5+ non-classical monocytes and monocytes expressing co-stimulatory molecule CD86.
Digital nomadism in Southeast Asia: its cultural identities and the new labor model
Authors:   , Zhong Wenjue 
Published: September 2023

This thesis examines the cultural identity of digital nomads in Southeast Asia and its impact on their evolving labor model. Employing qualitative interviews and document research, the study investigates the lifestyles of these contemporary nomads.

The research reveals a finding: despite roaming abroad, digital nomads maintain a strong connection to their national identity. This intriguing phenomenon demonstrates the persistence of cultural heritage in shaping their self-identity.

Unlike traditional global nomads, digital nomads display a more utility-oriented approach, where their nomadic lifestyle is deeply interwoven with their work status. Consequently, digital nomadism emerges as a unique labor model, reflecting the transformative nature of work in the digital era.

The study also highlights the pursuit of mental fulfillment as a prominent theme among digital nomads. This aligns with the prevailing post-modern and individualist trends, as individuals seek meaning and personal growth in their nomadic journey.
A comparison of imbalanced data handling methods for pre-trained model in multi-label classification of stack overflow
Authors:   , Umparat Arisa 
Published: September 2023

Tag classification is essential in Stack Overflow. Instead of combining through pages or replies of irrelevant information, users can easily and quickly pinpoint relevant posts and answers using tags. Since User-submitted posts can have multiple tags, classifying tags in Stack Overflow can be challenging. This results in an imbalance problem between labels in the whole labelset. Pretrained deep learning models with small datasets can improve tag classification accuracy. Common multi-label resampling techniques with machine learning classifiers can also fix this issue. Still, few studies have explored which resampling technique can improve the performance of pre-trained deep models for predicting tags. To address this gap, we experimented to evaluate the effectiveness of ELECTRA, a powerful deep learning pre-trained model, with various multi-label resampling techniques in decreasing the imbalance that induces mislabeling in Stack Overflow's tagging posts. We compared six resampling techniques, such as ML-ROS, MLSMOTE, MLeNN, MLTL, ML-SOL, and REMEDIAL, to find the best method to mitigate the imbalance and improve tag prediction accuracy. Our results show that MLTL is the most effective selection to tackle the inequality in multi-label classification for our Stack Overflow data with deep learning scenarios. MLTL achieved 0.517, 0.804, 0.467, and 0.98 from the metrics Precision@1, Recall@5, F1-score@1, and AUC, respectively. Conversely, MLeNN gained only 0.323, 0.648, 0.277, and 0.95 from the same metrics.
Metaproteomic analysis of gut resistome in the cecal microbiota of fattening pigs raised without antibiotics
Authors:   , Buthasane Pamornya 
Published: September 2023

Improper use of antibiotics in swine could reduce commensal bacteria and possibly increase pathogen infections via the gut resistome. This study aimed to compare the metaproteomic profiles of gut resistome and related metabolism in the cecal microbiota of fattening pigs raised under antibiotic-free (ABF) conditions with those of ordinary industrial pigs (controls, CTRL). The top three relative abundant microbials in both groups were Escherichia coli, Ruminococcus and Lactobacillus, followed by Bacteroides and Bifidobacterium. E. coli, Lactobacillus and Bacteroides were found to be increased in the CTRL group, whereas Ruminococcus and Clostridium were greater in the ABF group. The highest abundance of antibiotic resistance proteins (>10 log2 expression levels, ELs) was tetracycline resistance (TetR) and aminoglycoside resistance (AMGR) proteins found in Bacteroides with a significant increase in the CTRL group. High TetR (5.32 ELs) was found in Ruminococcus in the CTRL group although pigs in both groups have never received tetracycline, possibly reflecting the influence of environments in farms. In E. coli, AMGR and β-Lactamase family were observed in both groups (3-6 ELs), whereas multidrug resistance proteins were significantly expressed in the CTRL group (~3 ELs). In the ABF group, CRISPR-associated endonucleases Cas1 and Cas9, functioned to defend against viruses, were markedly observed in Ruminococcus and Lactobacillus, respectively, with 8.6 and 4.15 ELs, respectively. In conclusion, this study demonstrated that CRISPR-associated endonucleases were markedly observed in the ABF group, whereas higher levels of TetR, AMGR and multidrug resistance proteins were markedly observed in dominant bacterial species in the CTRL group.