Search Results (32)

Basal cell carcinoma (BCC), the most common skin cancer, is primarily driven by Hedgehog (Hh) and TP53 pathway alterations. Although additional pathways were implicated, the mutational landscape in Asian populations, particularly Koreans, remains underexplored. We performed whole-exome sequencing of BCC tumor tissues from Korean patients and analyzed mutations in 11 established BCC driver genes (PTCH1, SMO, GLI1, TP53, CSMD1/2, NOTCH1/2, ITIH2, DPP10, and STEAP4). Mutational profiles were compared with Caucasian cohort profiles to identify ethnicity-specific variants. Ultraviolet (UV)-exposed and non-UV-exposed tumor sites were compared; genes unique to non-UV-exposed tumors were further analyzed with protein–protein interaction analysis. BCCs in Koreans exhibited distinct features, including fewer truncating and more intronic variants compared to Caucasians. Korean-specific mutations in SMO, PTCH1, TP53, and NOTCH2 overlapped with oncogenic gain-of-function/loss-of-function (GOF/LOF) variants annotated in OncoKB, with some occurring at hotspot sites. BCCs in non-exposed areas showed recurrent mutations in CSMD1, PTCH1, and NOTCH1, suggesting a UV-independent mechanism. Novel mutations in TAS1R2 and ADCY10 were exclusive to non-exposed BCCs, with protein–protein interaction analysis linking them to TP53 and NOTCH2. We found unique ethnic-specific and UV-independent mutational profiles of BCCs in Koreans. TAS1R2 and ADCY10 may contribute to tumorigenesis of BCC in non-exposed areas, supporting the need for population-specific precision oncology. Full article

Objectives: The accurate prediction of lymph node metastasis (LNM) and lymphovascular invasion (LVI) is crucial for determining treatment strategies for early gastric cancer (EGC). This study aimed to develop and validate a deep learning-based clinical decision support system (CDSS) to predict LNM including LVI in EGC using real-world data. Methods: A deep learning-based CDSS was developed by integrating endoscopic images, demographic data, biopsy pathology, and CT findings from the data of 2927 patients with EGC across five institutions. We compared a transformer-based model to an image-only (basic convolutional neural network (CNN)) model and a multimodal classification (CNN with random forest) model. Internal testing was conducted on 449 patients from the five institutions, and external validation was performed on 766 patients from two other institutions. Model performance was assessed using the area under the receiver operating characteristic curve (AUC), probability density function, and clinical utility curve. Results: In the training, internal, and external validation cohorts, LNM/LVI was observed in 379 (12.95%), 49 (10.91%), 15 (9.09%), and 41 (6.82%) patients, respectively. The transformer-based model achieved an AUC of 0.9083, sensitivity of 85.71%, and specificity of 90.75%, outperforming the CNN (AUC 0.5937) and CNN with random forest (AUC 0.7548). High sensitivity and specificity were maintained in internal and external validations. The transformer model distinguished 91.8% of patients with LNM in the internal validation dataset, and 94.0% and 89.1% in the two different external datasets. Conclusions: We propose a deep learning-based CDSS for predicting LNM/LVI in EGC by integrating real-world data, potentially guiding treatment strategies in clinical settings. Full article

Bolting time is a critical trait that affects crop yield, adaptability, and overall productivity, making its regulation vital for agricultural success. In this study, we explored the genetic mechanisms controlling flowering time in radish (Raphanus sativus) via a combination of quantitative trait locus (QTL) analysis and genome-wide association study (GWAS). By developing an F₂ population from a cross between the relatively late-bolting variety ‘L432’ and the early-bolting variety ‘L285’, we identified 12 QTLs associated with bolting time. Furthermore, a GWAS performed on 60 East Asian radish accessions revealed 14 candidate genes potentially involved in flowering and bolting regulation. FLOWERING LOCUS C (FLC2) was the major candidate gene explaining the early and late bolting types. One locus was commonly detected from QTL and GWAS on chromosome 4, where CONSTANS-like (COL4) is located. To validate these findings, SNP markers were designed and applied to F₂ populations, revealing a correlation between marker presence and bolting phenotypes. These results offer valuable insights into the molecular control of bolting time in radish and identify candidate genes for use in marker-assisted breeding. These findings could enhance breeding efforts for optimizing bolting time in various radish markets. Full article

GPR55 is a receptor for lysophosphatidylinositols (LPIs) in digestive metabolites. Overnutrition leads to obesity, insulin resistance, and increased LPI levels in the plasma. The involvement of LPIs and GPR55 in adiposity, hepatic steatosis, and atherosclerosis has been previously elucidated. However, the therapeutic efficacy of GPR55 antagonists against obesity-induced airway inflammation has not been studied. The present study investigated whether CID16020046, a selective antagonist of GPR55, could modulate obesity-induced airway inflammation caused by a high-fat diet (HFD) in C57BL/6 mice. Administration of CID16020046 (1 mg/kg) inhibits HFD-induced adiposity and glucose intolerance. Analysis of immune cells in BALF showed that CID16020046 inhibited HFD-induced increase in immune cell infiltration. Histological analysis revealed the HFD induced hypersecretion of mucus and extensive fibrosis in the lungs. CID16020046 inhibited these HFD-induced pathological features. qRT-PCR revealed the HFD-induced increase in the expression of Ifn-γ, Tnf-α, Il-6, Il-13, Il-17A, Il-1β, Nlrp3, and Mpo mRNAs in the lungs. CID16020046 inhibited the HFD-induced increases in these genes. The expression levels of adipokines were regulated by the HFD and CID16020046. AdipoQ in the lungs and gonadal white adipose tissue was decreased by the HFD and reversed by CID16020046. In contrast, Lep was increased by the HFD and suppressed by CID16020046. The findings suggest the potential application of the GPR55 antagonist CID16020046 in obesity-induced airway inflammation. Full article

Although the pathogenesis of solar lentigo (SL) involves chronic ultraviolet (UV) exposure, cellular senescence, and upregulated melanogenesis, underlying molecular-level mechanisms associated with SL remain unclear. The aim of this study was to investigate the gene regulatory mechanisms intimately linked to inflammation in SL. Skin samples from patients with SL with or without histological inflammatory features were obtained. RNA-seq data from the samples were analyzed via multiple analysis approaches, including exploration of core inflammatory gene alterations, identifying functional pathways at both transcription and protein levels, comparison of inflammatory module (gene clusters) activation levels, and analyzing correlations between modules. These analyses disclosed specific core genes implicated in oxidative stress, especially the upregulation of nuclear factor kappa B in the inflammatory SLs, while genes associated with protective mechanisms, such as SLC6A9, were highly expressed in the non-inflammatory SLs. For inflammatory modules, Extracellular Immunity and Mitochondrial Innate Immunity were exclusively upregulated in the inflammatory SL. Analysis of protein–protein interactions revealed the significance of CXCR3 upregulation in the pathogenesis of inflammatory SL. In conclusion, the upregulation of stress response-associated genes and inflammatory pathways in response to UV-induced oxidative stress implies their involvement in the pathogenesis of inflammatory SL. Full article

Infectious bronchitis virus (IBV) causes a highly contagious respiratory disease in chickens, leading to significant economic losses in the poultry industry worldwide. IBV exhibits a high mutation rate, resulting in the continuous emergence of new variants and strains. A complete genome analysis of IBV is crucial for understanding its characteristics. However, it is challenging to obtain whole-genome sequences from IBV-infected clinical samples due to the low abundance of IBV relative to the host genome. Here, we present a novel approach employing next-generation sequencing (NGS) to directly sequence the complete genome of IBV. Through in silico analysis, six primer pairs were designed to match various genotypes, including the GI-19 lineage of IBV. The primer sets successfully amplified six overlapping fragments by long-range PCR and the size of the amplicons ranged from 3.7 to 6.4 kb, resulting in full coverage of the IBV genome. Furthermore, utilizing Illumina sequencing, we obtained the complete genome sequences of two strains belonging to the GI-19 lineage (QX genotype) from clinical samples, with 100% coverage rates, over 1000 × mean depth coverage, and a high percentage of mapped reads to the reference genomes (96.63% and 97.66%). The reported method significantly improves the whole-genome sequencing of IBVs from clinical samples; thus, it can improve understanding of the epidemiology and evolution of IBVs. Full article

Most anesthetics reduce cardiac functions and lower blood pressure (BP), potentially causing excessive BP reduction in dehydrated patients or those with heart conditions, such as coronary artery disease (CAD). Considering the increased prevalence of cardiovascular disease with age, anesthesiologists must be cautious about BP reduction during general anesthesia in older adults. In the present case, a 76-year-old male patient with undiagnosed CAD in a hypovolemic state experienced a significant drop in systolic BP to the fifties during propofol and sevoflurane anesthesia. Despite the use of vasopressors, excessive hypotension persisted, leading to anesthesia suspension. Subsequent cardiac examinations, including computed tomography heart angio and calcium score, and coronary angiogram, revealed a near total occlusion of the proximal left anterior descending coronary artery (pLAD) and the formation of collateral circulation. After 5 days of hydration and anticoagulation medications and confirmation of normovolemic state, general anesthesia was attempted again and successfully induced; a normal BP was maintained throughout the surgery. Thus, it is important to conduct a thorough cardiac evaluation and maintain normovolemia for general anesthesia in older adults. Full article

Smoking cigarettes is known to lower the risk of preeclampsia. The objective of this study is to evaluate the effect of smoking on the expression of soluble FMS-like tyrosine kinase-1 (sFlt-1), vascular endothelial growth factor (VEGF), and endoglin (sEng)-1 and the role of the aryl hydrocarbon receptor (AhR) in pregnant mice. We developed a smoking mouse model using a gas-filling system. One or two cigarettes per day were exposed to each of the five pregnant mice for five days a week throughout pregnancy. AhR agonist and antagonist were injected. Serum levels and expression in the placenta of sFlt-1, VEGF, and sEng-1 were analyzed and compared among the cigarette smoke and no-exposure groups after delivery. Compared to the no-smoke exposure group, the serum level of sFlt-1 was significantly decreased in the two-cigarette-exposed group (p < 0.001). When the AhR antagonist was added to the two-cigarette-exposed group, sFlt-1 levels were significantly increased compared to the two-cigarette group (p = 0.002). The levels of sFlt-1 in the AhR antagonist group did not change regardless of two-cigarette exposure (p = 0.064). With the AhR agonist, sFlt-1 decreased significantly compared to the control (p = 0.001) and AhR antagonist group (p = 0.002). The sFlt-1 level was significantly decreased after the injection of the AhR agonist compared to the control group (p = 0.001). Serum levels of VEGF were significantly decreased in the one-cigarette-exposed group compared to the control group; however, there was no difference between the control and the two-cigarette-exposed groups. The placental expression of sFlt-1, VEGF, and sEng were inconsistent. This study offers insights into the potential role of AhR on antiangiogenic sFlt-1 associated with preeclampsia. It may support the invention of a new treatment strategy for preeclampsia using AhR activation. Full article

The occurrence of antimicrobial-resistant bacteria in companion animals poses public health hazards globally. This study aimed to evaluate the antimicrobial resistance profiles and patterns of commensal E. coli strains obtained from fecal samples of healthy dogs and cats in South Korea between 2020 and 2022. In total, 843 E. coli isolates (dogs, n = 637, and cats, n = 206) were assessed for susceptibility to 20 antimicrobials. The resistance rates of the most tested antimicrobials were significantly higher in dog than in cat isolates. Cefalexin (68.9%) demonstrated the highest resistance rates, followed by ampicillin (38.3%), tetracycline (23.1%), and cefazolin (18.7%). However, no or very low resistance (0–0.6%) to amikacin, imipenem, piperacillin, and colistin was found in both dog and cat isolates. Overall, 42.3% of the isolates exhibited multidrug resistance (MDR). MDR in isolates from dogs (34.9%) was significantly higher than in those from cats (20.9%). The main components of the resistance patterns were cefalexin and ampicillin in both dog and cat isolates. Additionally, MDR patterns in isolates from dogs (29.2%) and cats (16%) were shown to encompass five or more antimicrobials. Multidrug-resistant commensal E. coli could potentially be spread to humans or other animals through clonal or zoonotic transmission. Therefore, the incidence of antimicrobial resistance in companion animals highlights the urgent need to restrict antimicrobial resistance and ensure the prudent use of antimicrobials in Korea. Full article

Enterococcus spp. are typically found in the gastrointestinal tracts of humans and animals. However, they have the potential to produce opportunistic infections that can be transmitted to humans or other animals, along with acquired antibiotic resistance. In this study, we aimed to investigate the antimicrobial resistance profiles of Enterococcus faecium and Enterococcus faecalis isolates obtained from companion animal dogs and cats in Korea during 2020–2022. The resistance rates in E. faecalis towards most of the tested antimicrobials were relatively higher than those in E. faecium isolated from dogs and cats. We found relatively higher resistance rates to tetracycline (65.2% vs. 75.2%) and erythromycin (39.5% vs. 49.6%) in E. faecalis isolated from cats compared to those from dogs. However, in E. faecium, the resistance rates towards tetracycline (35.6% vs. 31.5%) and erythromycin (40.3% vs. 35.2%) were comparatively higher for dog isolates than cats. No or very few E. faecium and E. faecalis isolates were found to be resistant to daptomycin, florfenicol, tigecycline, and quinupristin/dalfopristin. Multidrug resistance (MDR) was higher in E. faecalis recovered from cats (44%) and dogs (33.9%) than in E. faecium isolated from cats (24.1%) and dogs (20.5%). Moreover, MDR patterns in E. faecalis isolates from dogs (27.2%) and cats (35.2%) were shown to encompass five or more antimicrobials. However, E. faecium isolates from dogs (at 13.4%) and cats (at 14.8%) were resistant to five or more antimicrobials. Taken together, the prevalence of antimicrobial-resistant enterococci in companion animals presents a potential public health concern. Full article

The concentration of phenolic compounds in rapeseed is important because they are either anti-nutritional compounds or directly related to antioxidant activity. In this study, single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing (GBS), and an association study was conducted to investigate phenolic content in 95 rapeseed mutant lines derived from gamma rays and their original cultivar. A total of 3,196,318 SNPs were detected, resulting in the identification of a set of 70,208 union SNPs used to perform association studies. Seven compounds were identified, sinapine being the major phenolic compound (91.2–99.2%) in all genotypes. An association study was conducted for seven compounds and total phenolic content (TPC). It identified 241 SNPs that were significantly associated with these compounds, total sinapine content (TSC), and TPC. Based on the SNP markers detected, BnaC02g20420D was associated with dihexose, BnaC08g30570D with progoitrin, BnaA01g06890D with methyl sinapate, BnaA09g16810D with sinapine(4-O-8′)guaiacyl, BnaCnng39930D with trans-sinapine 1, BnaA07g31720D with trans-sinapine 2, BnaC03g31950D with sinapoyl malate, and BnaAnng27700D with TPC. These were selected as candidate genes that may play a key role in rapeseed. The SNP markers associated with these key phenolic compounds can be used as targets in breeding programs to reduce anti-nutritional components. Full article

Newcastle disease (ND) is a highly pathogenic viral infection of poultry with significant economic impacts worldwide. Despite the widespread use of vaccines, ND outbreaks continue to occur even within vaccinated poultry farms. Furthermore, novel Newcastle disease virus (NDV) genotypes are emerging in poultry, increasing the need for the development of rapid, accurate, and simple diagnostic methods. We therefore developed two novel sets of visual reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays based on highly conserved regions of the HN and F genes. The limits of detection of the NDV-Common-LAMP assay, for all the NDV strains, were 10^3.0 EID₅₀/0.1 mL for Kr005 and 10^2.0 EID₅₀/0.1 mL for Lasota within 35 min. The sensitivity of the NDV-Patho-LAMP assay, used for the strain differentiation of virulent NDV, was 10^2.0 EID₅₀/0.1 mL for Kr005. No amplification was detected for the non-NDV templates. Next, we probed 95 clinical strains and 7 reference strains with the RT-LAMP assays to assess the feasibility of their use in diagnostics. We observed no cross-reactivity across the 102 strains. Furthermore, there was 100% congruence between the RT-LAMP assays and full-length sequencing of the target genes, indicating the potential for visual RT-LAMP in the identification and differentiation of NDV. These novel RT-LAMP assays are ideally suited for the field or resource-limited environments to facilitate the faster detection and differentiation of NDV, which can reduce or avoid further spread. Full article

Sorghum (Sorghum bicolor L.) is a promising biomass crop with high yields of cellulose, hemicellulose, and lignin. Sorghum biomass has emerged as an eco-friendly industrial material useful for producing biofuels and bioplastics. This study conducted genotyping-by-sequencing (GBS)-based genome-wide association studies (GWAS) to establish the genetic basis of traits associated with biomass. Specifically, the researchers evaluated agronomic traits and phenolic compounds using 96 sorghum genotypes. Six phenolic compounds, luteolinidin diglucoside, luteolin glucoside, apigeninidin glucoside, luteolinidin, apigeninidin, and 5-O-Me luteolinidin, were found to be the major phenolic compounds in all genotypes. Out of our six detected phenolic compounds (luteolinidin diglucoside, luteolin glucoside, apigeninidin glucoside, luteolinidin, apigeninidin, and 5-O-Me luteolinidin), luteolinidin was the major phenolic compound in all genotypes. Next, a GWAS analysis was performed to confirm significant associations between 192,040 filtered single-nucleotide polymorphisms (SNPs) and biomass-related traits. The study identified 40 SNPs on 10 chromosomes that were significantly associated with heading date (4 SNPs), plant height (3 SNPs), dry yield (2 SNPs), and phenolic compounds (31 SNPs). The GWAS analysis showed that SbRio.10G099600 (FUT1) was associated with heading date, SbRio.09G149200 with plant height, SbRio.06G211400 (MAFB) with dry yield, SbRio.04G259800 (PDHA1) with total phenolic content and luteolinidin diglucoside, and SbRio.02G343600 (LeETR4) with total phenolic content and luteolinidin, suggesting that these genes could play key roles in sorghum. These findings demonstrate the potential value of sorghum as a biomass resource and the potential for selecting sorghum genotypes with reduced phenolic contents for use in the bioindustry. Full article

The purpose of this study is to analyze the cognitive characteristics that can be induced by vibration stimuli at two intensities, three frequencies, and five presentation periods. The experiment was conducted on 20 right-handed adult males, and a subjective evaluation was performed using a questionnaire. Regression analysis was performed to observe the parameters affecting cognitive characteristics according to changes in intensity, frequency, and stimulation duration. The regression analysis results showed that the cognitive characteristics affected by changes in intensity, frequency, and stimulation duration were “heavy”, “bold”, “thick”, and “light”. The cognitive characteristics affected by two-variable combinations were “deep”, “clear”, “vibrating”, “dense”, “numb”, “blunt”, “shallow”, “fuzzy”, and “soft”. Cognitive characteristics affected by either intensity, frequency, or stimulation duration were “fast”, “pungent”, “skinny”, “thin”, “slow”, “ticklish”, “tingling”, “prickling”, “tap”, and “rugged”. By observing the cognitive characteristics that can be induced by the combination of intensity, frequency, and stimulation duration, we confirmed that in addition to intensity and frequency, the stimulation duration is an important factor that influences the induction of various cognitive characteristics. The results presented in the study can be used to enhance the utility of haptic surfaces for extended reality applications. Full article

Glycine max Merr. (GM) is a functional food that provides many beneficial phytochemicals. However, scientific evidence of its antidepressive and sedative activities is scarce. The present study was designed to investigate the antidepressive and calmative effects of GM and its biologically active compound, genistein (GE), using electroencephalography (EEG) analysis in an electric foot shock (EFS)-stressed rat. The underlying neural mechanisms of their beneficial effects were determined by assessing corticotropin-releasing factor (CRF), serotonin (5-HT), and c-Fos immunoreactivity in the brain using immunohistochemical methods. In addition, the 5-HT2C receptor binding assay was performed because it is considered a major target of antidepressants and sleep aids. In the binding assay, GM displayed binding affinity to the 5-HT2C receptor (IC50 value of 14.25 ± 11.02 µg/mL). GE exhibited concentration-dependent binding affinity, resulting in the binding of GE to the 5-HT_2C receptor (IC50, 77.28 ± 26.57 mg/mL). Administration of GM (400 mg/kg) increased non-rapid eye movement (NREM) sleep time. Administration of GE (30 mg/kg) decreased wake time and increased rapid eye movement (REM) and NREM sleep in EPS-stressed rats. In addition, treatment with GM and GE significantly decreased c-Fos and CRF expression in the paraventricular nucleus (PVN) and increased 5-HT levels in the dorsal raphe in the brain. Overall, these results suggest that GM and GE have antidepressant-like effects and are effective in sleep maintenance. These results will benefit researchers in developing alternatives to decrease depression and prevent sleep disorders. Full article