BACKGROUND AND OBJECTIVE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of COVID-19 has significantly challenged the public health landscape in late 2019. After almost 3 years of the first ever SARS-CoV-2 case, the World Health Organization (WHO) declared the end of this global health emergency in May 2023. Although, despite the subsequent drop of COVID-19 cases, the SARS-CoV-2 infection still exhibited multiple waves of infection, primarily attributed to the appearance of new variants. Five of these variants have been classified as Variants of Concern (VOC): Alpha, Beta, Gamma, Delta, and the most recent, Omicron. Therefore, the development of methods for the timely and accurate detection of viral variants remains fundamental, ensuring an ongoing and effective response to the disease. This study aims to evaluate the feasibility of the application of an in-house approach in genomic surveillance for the detection of SARS-CoV-2 variants using in silico designed primers.

METHODS

The primers used for the study were particularly designed based on conserved regions of certain genes in the virus, targeting distinct mutations found in known variants of SARS-CoV-2. Viral RNA extracts from nasopharyngeal samples (n=14) were subjected to quantitative and qualitative tests (Nanodrop and AGE). Selected samples were then analyzed by RT-PCR and amplicons were submitted for sequencing. Sequence alignment analysis was carried out to identify the prevailing COVID-19 variant present in the sample population.

RESULTS

The study findings demonstrated that the in-house method was able to successfully amplify conserved sequences (spike, envelope, membrane, ORF1ab) and enabled identification of the circulating SARS-CoV-2 variant among the samples. Majority of the samples were identified as Omicron variant. Three out of four designed primers effectively bound into the conserved sequence of target genes present in the sample, revealing the specific SARSCoV-2 variant. The detected mutations characterized for Omicron found in the identified lineages included K417N, S477N, and P681H which were also identified as mutations of interest. Furthermore, identification of the B.1.448 lineage which was not classified in any known variant also provided the potential of the developed in-house method in detecting unknown variants of COVID-19.

CONCLUSION

Among the five VOCs, Omicron is the most prevalent and dominant variant. The in-house direct PCR product sequencing surveillance (DPPSS) method provided an alternative platform for SAR-CoV-2 variant analysis which is accessible and affordable than the conventional diagnostic surveillance methods and the whole genome sequencing. Further evaluation and improvements on the oligonucleotide primers may offer significant contribution to the development of a specific and direct PCRbased detection of new emerging COVID-19 variants.

Sars-cov-2 ; Polymerase Chain Reaction ; Dna Primers ; Oligonucleotide Primers ; Computer Simulation ; Conserved Sequence ; Coronavirus ; Covid-19 ; Disease ; Emergencies ; Evaluation Studies As Topic ; Genes ; Genome ; Global Health ; Health ; Identification (psychology) ; Infection ; Infections ; Membranes ; Methods ; Mutation ; Oligonucleotides ; Organizations ; Population ; Public Health ; Rna ; Rna, Viral ; Sars Virus ; Sequence Alignment ; Severe Acute Respiratory Syndrome ; Syndrome ; Viruses ; Whole Genome Sequencing ; World Health Organization

Objective: This study aimed to compare aneuploidy rates and clinical outcomes between trophectoderm biopsy at fresh blastocyst (biopsy-fresh) followed by vitrification and biopsy at vitrified-warmed blastocyst (biopsy-vitri) followed by next day transfer (without re-vitrification). Methods: This retrospective study included 844 patients undergoing 844 cycles conducted from August 2019 to December 2023. Preimplantation genetic testing for aneuploidy (PGT-A) was performed via trophectoderm biopsy using array comparative genomic hybridization or next-generation sequencing for comprehensive 24-chromosome screening. Patients were divided into two groups based on the blastocyst status at the time of biopsy: the biopsy-fresh group (531 patients) and the biopsy-vitri group (313 patients). Results: The clinical pregnancy rate was significantly higher in the biopsy-fresh group compared to the biopsy-vitri group (58.7% vs. 45.6%; odds ratio [OR], 1.695; 95% confidence interval [CI], 1.215 to 2.364; p=0.002). Furthermore, the biopsy-fresh group showed higher implantation rates (45.6% vs. 32.1%; OR, 1.767; 95% CI, 1.274 to 2.451; p=0.002), ongoing pregnancy or live birth rates per cycle (48.0% vs. 35.8%; OR, 1.652; 95% CI, 1.177 to 2.319; p=0.004), and rates of good-quality blastocysts (57.1% vs. 32.1%, p<0.001) compared with the biopsy-vitri group. Miscarriage rates did not differ significantly between the groups (18.2% vs. 21.4%; OR, 0.818; 95% CI, 0.457 to 1.465; p=0.501). Conclusion Biopsy at fresh blastocyst demonstrated superior clinical outcomes compared with biopsy at vitrified-warmed blastocyst, likely due to better embryo quality. Both biopsy at fresh blastocyst and vitrified-warmed blastocyst remain viable options for PGT-A, with biopsy at vitrified-warmed blastocyst serving as a practical alternative. Embryo quality and euploid status continue to be critical considerations for embryo transfer selection.

Objective: The aims of this study were to assess embryonic development using a time-lapse monitoring system based on cleavage timing and the use of vitrification and to investigate the correlation between miRNA-429 expression and embryonic development in both fresh and vitrified-thawed embryos. Methods: Mouse embryos at the 1-cell stage were collected and randomly divided into fresh and vitrified-thawed groups. The embryos were monitored and further subdivided into early and delayed cleavage based on the timing of the third cleavage event at 55 hours after human chorionic gonadotropin injection. miRNA-429 extracted from spent media or embryos cultured in vitro was analyzed by quantitative reverse transcription-polymerase chain reaction. Results: Early cleavage was associated with a significantly higher blastulation rate, regardless of cryopreservation status. Notably, among vitrified-thawed embryos, outgrowth was greater in those exhibiting early cleavage compared to those with delayed cleavage. Furthermore, miRNA-429 expression was elevated in embryos exhibiting delayed cleavage, but only within the cryopreserved group. Conclusion Based on these findings, we suggest that the timing of the third cleavage event may be more critical than the vitrification process itself, and evaluating miRNA-429 expression could serve as an alternative non-invasive selection tool for vitrified surplus embryos.

Objective: Lipopolysaccharide (LPS), derived from various infectious bacteria in the uterus, interferes with communication between embryonic trophoblasts and endometrial cells, thereby inhibiting successful embryo implantation. This study aimed to investigate the effects of LPS and the anti-inflammatory compound nicotinamide (NAM) on early embryo implantation processes, focusing on the adhesion and outgrowth between trophoblast spheroids and endometrial cells. Methods: We used JAr mixed JEG-3 (JmJ) spheroids, prepared by combining JAr and JEG-3 cells in a 1:1 ratio. Following treatment with LPS with or without NAM, the attachment and outgrowth of JmJ spheroids on endometrial epithelial cells (ECC-1) were assessed. Additionally, changes in the gene expression of inflammatory cytokines (chemokine (C-X-C motif) ligand 1 [CXCL1], interleukin 8 [IL-8], and IL-33) and cell adhesion molecules (integrin alpha-V [ITGαV], integrin beta 3 [ITGβ3], and integrin beta 5 [ITGβ5]) in ECC-1 cells following LPS and/or NAM treatment were evaluated using quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blot analysis. Results: Decreased attachment rates and reduced outgrowth areas caused by LPS treatment were significantly restored by NAM. These restorative effects of NAM were associated with the modulation of inflammatory cytokines—specifically CXCL1 and IL-33, as shown by qRT-PCR—and expression of the cell adhesion molecule ITGβ3, as indicated by Western blot analysis. Conclusion Our study confirmed that LPS-induced endometrial infection may inhibit embryo implantation. NAM treatment ameliorated the detrimental effects of LPS by modulating the expression of inflammatory cytokines and adhesion molecules. Further studies are needed to explore the potential use of NAM as an effective additive to improve embryo implantation rates in human in vitro fertilization-embryo transfer programs.

Background: The conventional magnetic resonance imaging (MRI) grading system for foraminal stenosis (FS), known as the Lee classification, was introduced in 2010 and is widely utilized in clinical practice. Previous studies have reported that the conventional grading system for FS lacks prediction ability for surgical treatment. The purpose of this study was to develop a novel MRI grading system for lumbar FS with improved prediction ability for surgical treatment by incorporating facet effusion to indicate segmental instability. Methods: We retrospectively reviewed patients diagnosed with lumbar FS between 2011 and 2017 who had a follow-up period of at least 5 years. The FS severity was assessed using a conventional MRI grading system developed by Lee et al. We recorded whether the patient underwent surgical treatment for FS during the follow-up period and the time from the initial diagnosis to surgery. Survival analysis using a Kaplan-Meier curve and log-rank test was performed to verify the impact of FS severity on the surgical treatment. We performed additional survival analysis after modifying the grading system by incorporating the presence of excessive facet joint effusion assessed using axial MRI. We also compared the discrimination ability of the modified and conventional grading systems using Uno’s concordance index (C-index). Results: In total, 235 patients with a mean age of 63.7 years were included in this study. During the mean follow-up period of 8.1 years, 63 patients underwent surgical treatment for FS. The conventional grading system revealed no significant difference in survival between the grade 2 and 3 groups (p = 0.104). Conversely, the modified grading system revealed a significant difference in survival between the new grade 2 and 3 groups (p < 0.001). After modification, the discrimination ability, assessed using Uno’s Cindex, significantly improved from 0.69 to 0.73. Conclusions The Facet Effusion-Incorporating Grading System, which adds excessive facet joint effusion to the conventional MRI grading framework, demonstrated improved predictive value for surgical treatment and better discriminatory ability compared with the original system.

Background: Vascular smooth muscle cells (VSMCs) play a crucial role in the development of occlusive vascular diseases through abnormal proliferation and migration. This pathological behavior is closely associated with mitochondrial reactive oxygen species (ROS)-mediated mitochondrial DNA (mtDNA) damage. The mitochondrial carrier protein solute carrier family 25 member 33 (SLC25A33), essential for nucleoside transport, is integral to mtDNA production. This study aimed to investigate the effects of SLC25A33 inhibition on the proliferation and migration of VSMCs, as well as its impact on neointima formation. Methods: VSMCs were isolated from the thoracic aorta of 4-week-old Sprague-Dawley rats. The effects of small interfering RNAinduced silencing of SLC25A33 mRNA on platelet-derived growth factor (PDGF)-induced proliferation and migration of VSMCs were analyzed. The in vivo effects of targeting the SLC25A33 gene on neointima formation were evaluated using a murine carotid artery ligation model by perivascularly applying Lenti-shSLC25A33 with Pluronic F-127 gel. Results: First, we observed an upregulation of the SLC25A33 protein in the carotid artery ligation-induced neointima in mice. Silencing of SLC25A33 suppressed the PDGF-stimulated proliferation and migration of VSMCs and cell cycle progression. Knockdown of SLC25A33 inhibited PDGF-induced production of mtDNA and ROS, consequently inactivating the cyclic GMP-AMP synthesis (cGAS)-stimulator of interferon genes (STING)-TANK-binding kinase 1 (TBK1)-nuclear factor kappa B (NF-κB) pathway. Furthermore, the downregulation of SLC25A33 reduced carotid artery ligation-induced neointima in mice. Conclusion This study suggests that targeting SLC25A33 in VSMCs could be a novel therapeutic strategy to prevent occlusive vascular diseases.

Background/Aims: Helicobacter pylori is a pathogen that causes chronic gastritis and peptic ulcer diseases and is a carcinogen responsible for the development of malignancies, including gastric cancer. In the current era of high antimicrobial resistance, rifabutin-based triple therapy is recommended as a salvage therapy. Bismuth has not only a strong bacteriostatic effect but also a synergic effect when combined with antibiotics. Our study aimed to compare and evaluate the eradication rates between rifabutin-based triple therapy and rifabutin with bismuth-containing quadruple therapy as salvage treatments. Methods: In this single-center study, patients who received rifabutin-based triple therapy and rifabutin with bismuth-containing quadruple therapy after failure of conventional therapy, including first- and second-line treatment, between January 2016 and July 2024, were retrospectively investigated. A total of 53 patients who received rifabutin-based triple therapy and 50 who received bismuth-containing quadruple therapy were included. Results: In the rifabutin-based triple therapy group, eradication was achieved in 32 out of 53 patients (60.4%; 95% confidence interval [CI], 46.8% to 74.0%). In the bismuth-containing quadruple therapy group, eradication was achieved in 40 out of 50 patients (80.0%; 95% CI, 68.5% to 91.5%), demonstrating significant therapeutic benefit (p=0.030). Adverse events, including nausea, epigastric discomfort, and lethargy, were significantly more frequent in the bismuth-containing quadruple therapy group (p=0.007), but they were mild and tolerable enough not to affect compliance (p=0.329). Conclusions Rifabutin with bismuth-containing quadruple regimen as a salvage treatment achieved significantly superior eradication efficacy over the rifabutin-based triple regimen. Further multicenter prospective studies are needed to provide additional supporting evidence.

Objectives: Large language models (LLMs) demonstrate remarkable potential in healthcare communication. However, whether they can process complex, high-volume medical information, such as stroke-related content, remains insufficiently validated. This study aimed to evaluate the natural language processing capabilities of LLMs in handling such content and to develop an evaluation instrument. Methods: A survey compared educational materials generated by two LLMs (ChatGPT 4.0 and Claude 3) with neurologist-authored content on stroke. The materials were based on two clinical scenarios representing distinct stroke etiologies: cardioembolism and large-artery atherosclerosis. They were evaluated in terms of accuracy, legality, ethics, comprehensiveness, and information delivery. Scores for comprehensiveness and information delivery were compared according to participants’ agreement with the use of LLMs in healthcare. Results: ChatGPT received the highest scores across all domains, except for legality in Scenario 2. In Scenario 1, the ranking for accuracy and summarization of clinical information was, from highest to lowest, ChatGPT, Claude, and the neurologist (η2 = 0.140, p < 0.001; η2 = 0.175, p < 0.001). The same hierarchy was observed in Scenario 2 for accuracy (η2 = 0.077, p < 0.001) and summarization (η2 = 0.194, p < 0.001). Participants who agreed with the use of LLMs in healthcare assigned higher scores for the comprehensiveness (Scenario 1, p = 0.005; Scenario 2, p = 0.007) and information delivery (Scenario 1, p = 0.003; Scenario 2, p = 0.026) of ChatGPT-generated materials than participants who did not agree. Conclusions LLMs demonstrated adequate capability to convey complex content, such as stroke-related information, in an accessible and understandable manner for non-experts.

Objectives: Large language models (LLMs) are increasingly being used for medical question-answering (QA) tasks. However, most models are trained primarily on English-language data, which limits their effectiveness in non-English clinical contexts. In healthcare settings such as Korea, LLMs adapted to both the local language and the medical domain are needed. This study aimed to evaluate the performance of Korean-native and multilingual LLMs fine-tuned on Korean arthritis-related medical QA data and to examine the impact of language and domain adaptation. Methods: A dataset of 5,451 Korean QA pairs related to arthritis was constructed from a public medical corpus (AI Hub). Five LLMs (Mi:dm, EXAONE, Kanana, HyperCLOVAX, and LLaMA) were fine-tuned under identical conditions using Low-Rank Adaptation with 4-bit quantization. Model performance was evaluated on 597 validation samples using BERTScore-F1 and SBERT similarity, along with a qualitative evaluation of clinical correctness, safety, and response completeness. Results: EXAONE and HyperCLOVAX showed comparable quantitative performance in semantic accuracy and contextual consistency. Mi:dm achieved lower similarity-based scores than EXAONE and HyperCLOVAX but showed the highest performance in the qualitative evaluation, particularly for clinical correctness. Kanana exhibited moderate performance with limited domain adaptability. LLaMA showed the lowest performance in Korean medical QA, although it achieved the largest relative improvement, indicating challenges in adaptation to Korean clinical contexts. Conclusions Domain-specific fine-tuning and Korean-oriented model design improved performance in Korean arthritis medical QA. EXAONE and HyperCLOVAX achieved the highest semantic similarity, whereas Mi:dm demonstrated superior clinical correctness and safety in the qualitative evaluation. General multilingual LLaMA remained limited despite substantial gains, supporting the development of disease-specific Korean medical LLMs.

Janus kinase (JAK) inhibitors are an important treatment option for ulcerative colitis, providing rapid onset of action, oral administration, and efficacy even after biologic failure. The 3 approved agents—tofacitinib, filgotinib, and upadacitinib—differ in JAK isoform selectivity, leading to clinically meaningful differences in efficacy and safety. Evidence from network meta-analyses, clinical trials, and real-world studies consistently shows that upadacitinib provides the highest efficacy for induction and maintenance of remission, whereas filgotinib demonstrates the most favorable safety profile. The strong efficacy of upadacitinib and tofacitinib is particularly relevant in patients with severe disease, including acute severe ulcerative colitis, and upadacitinib maintains high efficacy regardless of prior advanced therapy exposure. JAK inhibitors also benefit extraintestinal manifestations. Although risks such as herpes zoster, serious infection, thromboembolism, and major cardiovascular events differ among agents, long-term data suggest generally acceptable safety when used appropriately. Intraclass JAK-to-JAK cycling is feasible, with about half of patients achieving steroid-free clinical remission in retrospective cohorts. Based on mechanistic, clinical, and real-world evidence, filgotinib may be a first-line option for patients with lower disease activity or when safety is a priority, whereas upadacitinib or tofacitinib may be preferred in higher disease activity. Strategically selecting agents may improve durability and outcomes.