Fecal microbiome profiles in infants with biliary atresia versus nonbiliary atresia cholestasis: a pilot study.

Background: Cholestasis is characterized by disrupted bile flow and can lead to severe liver disease in newborns, of which biliary atresia (BA) is a common cause. The gut microbiome plays a crucial role in aggravating liver injury in BA and non-BA cholestasis. However, information is lacking regarding the differences in gut microbiome composition between patients with BA and non-BA cholestasis.

Caffeine Modulates Cell Death and Telomerase Activity in Triple-negative Breast Cancer Cells.

Triple-negative breast cancer (TNBC) is an aggressive subtype defined by the lack of estrogen receptors (ER), progesterone receptors (PR), and HER2 expression, resulting in limited therapeutic options. Given this challenge, this study explores caffeine, a widely consumed stimulant, as a potential anticancer agent, particularly for TNBC. Although caffeine has demonstrated stimulatory and inhibitory effects on telomerase in other cancer types, its influence on telomerase activity in TNBC remains uncharacterized.

Impact of semen insemination on the vaginal microbiome profile of candidiasis rat model: A preliminary forensic study on sexual violence evidence.

Sexual violence, including sexual intercourse, can occur in women experiencing vaginal discharge, particularly in cases of vaginal candidiasis. In candidiasis, the vaginal microbiome undergoes changes that could serve as a diagnostic indicator or as evidence of sexual activity. The aim of this study was to assess the effects of semen insemination on the vaginal microbiome profile of candidiasis rats and to determine its forensic investigations in cases of sexual violence.

DNA methylation profiles for breast cancer subtype classifications: A translational study from microarray to methylation-specific PCR (MSP).

Breast cancer subtypes can be categorized based on their gene expression profiles using immunohistochemistry into Luminal A, Luminal B, human epidermal growth factor receptor 2-positive (HER), and triple-negative breast cancer (TNBC) subtypes. However, immunohistochemistry has certain limitations that can lead to misclassification. DNA methylation is an epigenetic modification, and changes in the promoter region can alter gene expression and the quantity of functional protein synthesized, disrupting gene function.

Colcemid duration effects on extrachromosomal DNA analysis in breast cancer cell line.

Extrachromosomal DNA (ecDNA) is a circular form of genetic material that exists outside the chromosomes and plays a significant role in tumour heterogeneity and drug resistance. In this preliminary study, we aimed to optimize the visualization of ecDNA by investigating the effects of varying colcemid treatment durations on metaphase arrest in MDA-MB-231 breast cancer cells. We tested four durations of colcemid treatment: 20 hours, 3 hours, 1 hour, and 30 minutes.

SNP-array profiling data from breast cancer patients and healthy women's blood DNA samples.

Breast cancer is commonly acknowledged as the primary type of cancer on a global scale, exerting a substantial influence on death rates, particularly in developing countries. The aforementioned discovery provides evidence in favor of the concept that genetic factors may contribute to the onset of breast cancer. This paper presents the unprocessed idat data containing single nucleotide polymorphisms (SNPs) acquired from breast cancer patients and a control group comprising of healthy women.

An insight of Streptococcus pneumoniae serotype 3 genomic profile in Indonesia.

Background: Streptococcus pneumoniae Serotype 3 (SPN3) remains a significant cause of morbidity and mortality worldwide despite of pneumococcal conjugate vaccine (PCV) implementation. We explored genomic profile of SPN3 from children and adult groups to understand population structure and evolution dynamics of SPN3 in Indonesia.

Methods: We undertook whole genome sequencing (WGS) from 19 isolates of SPN3 in Indonesia between 2017 and 2021 prior to PCV introduction.

Association of Prepregnancy Body Mass Index with Gut Microbiota Diversity and Abundance in Pregnant Women.

Background: Understanding the link between prepregnancy nutritional status and gut microbiota during pregnancy may lead to novel maternal and child health interventions.

Objective: To explore the association of prepregnancy body mass index (BMI) status with gut microbiota diversity and abundance during pregnancy.

Methods: A cross-sectional study was conducted on 90 pregnant women from primary health centers in Jakarta, Indonesia.

Clinical phenotype and trio whole exome sequencing data from a patient with glycogen storage disease IV in Indonesia.

Glycogen storage disease type IV (GSD IV) is a rare disease caused by a defect in glycogen branching enzyme 1 (GBE1), which played a crucial role in glycogen branching. GSD IV occurs once in approximately 1 in every 760,000 to 960,000 live births and is inherited in an autosomal recessive pattern. Early diagnosis of GSD IV is challenging due to non-specific symptoms, such as liver and spleen enlargement, which can overlap with other hematologic and hepatobiliary disorders.

Extrachromosomal DNA in Breast Cancer Cell Lines: Detection and Characterization.

This study delves into the intriguing world of extrachromosomal DNA (ecDNA) in breast cancer, uncovering its pivotal role in cancer's aggressiveness and genetic variability. ecDNA, a form of circular DNA found outside chromosomes, is known to play a significant role in cancer progression by increasing oncogene expression. Focusing on two contrasting cell lines, MDA-MB-231 (triple-negative) and MCF-7 (Luminal-A), we utilized advanced microscopy and fluorescence techniques to detect and characterize ecDNA.

Dynamics of SARS-CoV-2 Spike RBD Protein Mutation and Pathogenicity Consequences in Indonesian Circulating Variants in 2020-2022.

Background: Since the beginning of the coronavirus disease 2019 (COVID-19) outbreak, dynamic mutations in the receptor-binding domain (RBD) in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have altered the pathogenicity of the variants of the virus circulating in Indonesia. This research analyzes the mutation trend in various RBD samples from Indonesia published in the Global Initiative on Sharing All Influenza Data (GISAID) database using genomic profiling.

Method: Patients in Indonesia infected with SARS-CoV-2, whose samples have been published in genomic databases, were selected for this research.

Association of Gut Microbiota Composition with Stunting Incidence in Children under Five in Jakarta Slums.

Background: Stunting can be linked to various factors, one of which is dysbiosis. This study aims to analyze the microbiota composition and related contributing factors of stunted and non-stunted children in the slum areas of Jakarta.

Methods: The subjects in this study included 21 stunted (HAZ ≤ -2SD) and 21 non-stunted children (-2SD ≤ HAZ ≤ 3SD) aged 2-5 years.

Forecasting the Effects of Platelet-Rich Plasma on Follicle Development Following Premature Ovarian Insufficiency by Network Interaction Analysis.

<b>Background and Objective:</b> Platelet-Rich Plasma (PRP) is proposed to have a potential regenerative effect on the ovaries following premature ovarian insufficiency (POI), however, the main impact on the process of follicle development (folliculogenesis) remains unclear. Protein-protein interaction (PPI) or network interaction analysis enables us to predict the targets of PRP's biomolecules using biological data through public databases and platforms. Therefore, this method is more efficient in time and cost than traditional laboratory procedures.

Profibrotic Inflammatory Cytokines and Growth Factors Are Predicted as the Key Targets of (Hunter) Roxb. in Keloids: An Epistatic and Molecular Simulation Approach.

Keloid is characterized as the fibrotic tissue resulting from the increase of fibroblast activity. (Hunter) Roxb. possesses bioactive compounds that have potential as antifibrotic agents, while the mechanism of action in keloid has not yet been elucidated.

IDeRare: a lightweight and extensible open-source phenotype and exome analysis pipeline for germline rare disease diagnosis.

Objectives: Diagnosing rare diseases is an arduous and challenging process in clinical settings, resulting in the late discovery of novel variants and referral loops. To help clinicians, we built IDeRare pipelines to accelerate phenotype-genotype analysis for patients with suspected rare diseases.

Materials And Methods: IDeRare pipeline is separated into phenotype and genotype parts.

A narrative review of genomic characteristics, serotype, immunogenicity, and vaccine development of capsular polysaccharide.

This narrative review describes genomic characteristic, serotyping, immunogenicity, and vaccine development of capsular polysaccharide (CPS). CPS is a primary virulence factor of . The genomic characteristics of CPS, including the role of biosynthetic gene and genetic variation within (capsule polysaccharide) locus which may lead to serotype replacement are still being investigated.

The Antifungal Activities of Syzygium aromaticum and Alpinia purpurata Extracts Against Candida krusei: Bioactivity Tests, Molecular Modeling, and Toxicity Tests.

Background: Candida krusei is the cause of the fungal infection candidiasis, which has a high mortality rate. Intrinsic resistance to fluconazole can cause the failure of Krusei candidiasis treatment. Therefore, it is necessary to find alternative drugs to eliminate the fungus.

Exploration of the main active metabolites from Tinospora crispa (L.) Hook. f. & Thomson stem as insulin sensitizer in L6.C11 skeletal muscle cell by integrating in vitro, metabolomics, and molecular docking.

Ethnopharmacological Relevance: Tinospora crispa (L.) Hook. f.

Synthesis and in vitro Activity of Eugenyl Benzoate Derivatives as BCL-2 Inhibitor in Colorectal Cancer with QSAR and Molecular Docking Approach.

Objective: This study is aimed to acquiring new compounds of Eugenyl benzoate (2-methoxy-4-(prop-2-en-1-yl)phenyl benzoate) derivatives that can inhibit HT29 colorectal cancer cells.

Methods: In this research, we used several chemical reactions to synthesize novel compounds, such as Esterification, Demethylation, Halohydrin, and Sharpless reaction. Cytotoxicity assays were performed to test the inhibitory activity of compounds against HT29 colon cancer cells.

Linn. Extract Increases the mRNA Expression of the Arcuate Nucleus Leptin Receptor and is Predicted as an Anti-obesity Agent.

Background: Leptin is predominant in regulating body weight by stimulating energy expenditure through its neuronal action in the brain. Moreover, it is projected to adipose tissue and induces adipocyte browning by activating the β3-adrenergic receptor (β3AR). However, the expression of leptin receptor (Lep-R) and β3AR in people with obesity is downregulated.

Prediction of Translational Regulation by Network Interaction in Synaptic Plasticity Induced with .

Background: Recently, human life expectancy, aging, and age-related health disorders, especially neurodegenerative diseases such as Alzheimer's disease (AD), have increased. The increasing number of AD patients causes a heavy social and economic burden on society. Since there is no treatment for AD, utilization of natural products is currently accepted as an alternative or integrative treatment agent against AD.