Academic Articles & Research Papers

Pairwise Performance Comparison of Docking Scoring Functions: Computational Approach Using InterCriteria Analysis

Scoring functions are key elements in docking protocols as they approximate the binding affinity of a ligand (usually a small bioactive molecule) by calculating its interaction energy with a biomacromolecule (usually a protein). In this stu...

FAM83A as a Potential Biological Marker Is Regulated by miR-206 to Promote Cervical Cancer Progression Through PI3K/AKT/mTOR Pathway

Background and Objective: Chemotherapy and radiotherapy are effective treatment options for cervical cancer (CC), but their efficacy is limited by short survival rate of about 5 years particularly for advance stage CC. Bioinformatics analys...

Comparative Analysis of Tools and Approaches for Source Tracking Listeria monocytogenes in a Food Facility Using Whole-Genome Sequence Data

As WGS is increasingly used by food industry to characterize pathogen isolates, users are challenged by the variety of analysis approaches available, ranging from methods that require extensive bioinformatics expertise to commercial softwar...

An integrated analysis of multiple datasets reveals novel gene signatures in human granulosa cells

Abstract Granulosa cells (GCs) play crucial roles in oocyte maturation. Through gap junctions and extracellular vesicles, they mediate the exchange of molecules such as microRNAs and messenger RNAs. Different ovarian cell types exhibit uniq...

Identification of functional pathways for regenerative bioactivity of selected renal cells

Abstract Background Selected renal cells (SRC) are in Phase II clinical trials as a kidney-sourced, autologous, tubular epithelial cell-enriched cell-based therapy for chronic kidney disease (CKD). In preclinical studies with rodent models ...

Can Bacillus paranthracis cause bacteremia in a T-ALL patient? WGS-based diagnosis

Introduction: Most of Bacillus spp. generally avirulent species in healthy patients, but if there is a fragile in the patient, especially their immune system, Bacillus spp. can be an agent for infections. Case Report: In this case, we rep...

Proteomic analysis of synergetic neuroprotective effect of adenosine, thiamine, niacin and cyanocobalamin in pathophysiology of diabetic polyneuropathy

Background. Neurotransmitter adenosine and B-group vitamins have neuroprotective, remyelinizing and anti-neuroinflammatory properties. Despite the studies of these molecules for decades, the molecular mechanisms of their synergistic effect ...

Cranial ultrasonographic findings in newborns exposed to SARS-CoV-2: a single-centre cross-sectional analysis

Abstract Background SARS-CoV-2’s potential consequences on the developing brain are still unknown. The aim of this study was to describe cranial ultrasonographic (cUS) findings in a population of newborns exposed to SARS-CoV-2 born at San M...

Effects of Luteolin on Human Breast Cancer Using Gene Expression Array: Inferring Novel Genes

Taraxacum officinale (dandelion) is often used in traditional Chinese medicine for the treatment of cancer; however, the downstream regulatory genes and signaling pathways mediating its effects on breast cancer remain unclear. The present s...

Dysregulation of Angiogenesis and Inflammatory Genes in Endometrial Mesenchymal Stem Cells and Their Contribution to Endometriosis

Endometriosis is a common, chronic, inflammatory disorder in women, characterized by the presence of endometrial tissue outside the uterus cavity. The disease affects ~10% of women during their reproductive age. There is some debates on the...

Assessment of Safety and Probiotic Traits of Enterococcus durans OSY-EGY, Isolated From Egyptian Artisanal Cheese, Using Comparative Genomics and Phenotypic Analyses

An Enterococcus durans strain, designated OSY-EGY, was previously isolated from artisanal cheese. In this work, comparative genomic and phenotypic analyses were utilized to assess the safety characteristics and probiotic traits of the bacte...

Correcting palindromes in long reads after whole-genome amplification

Abstract Background Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments...

miR-130a-3p Exacerbates Sepsis-Induced Cardiac Dysfunction by Promoting Inflammation and Targeting PDK4

Background Sepsis is frequently complicated by systemic inflammatory injury and cardiac dysfunction, which serve as risk factors of adverse clinical outcomes and increased mortality risk. To clarify the function of miR-130a-3p in sepsis dia...

RNA-seq analysis of gene expression profiles in isolated stria vascularis from wild-type and Alport mice reveals key pathways underling Alport strial pathogenesis.

Previous work demonstrates that the hearing loss in Alport mice is caused by defects in the stria vascularis. As the animals age, progressive thickening of strial capillary basement membranes (SCBMs) occurs associated with elevated levels o...

CD56-Negative Extranodal Natural Killer/T-Cell Lymphoma: A Retrospective Study in 443 Patients Treated by Chemotherapy With or Without Asparaginase

ObjectiveExtranodal natural killer/T cell lymphoma (NKTCL) is an aggressive EBV-related lymphoma, originating from NK cells or T cells. Previous study demonstrated that CD56 negative NKTCL should be recognized as a distinct subtype. In this...

Research software: A key (neglected) component of the digital research infrastructure ecosystem

Multi-Cohort Transcriptomics Combined with Mendelian Randomization Identifies PPARGC1A, NAAA and GIPC2 as NLRP3 Inflammasome-Related Key Genes in Ulcerative Colitis

Jian Cheng, Yangfeng Huang Department of Traditional Chinese Medicine, Sichuan Provincial People’s Hospital, School of Medicine,University of Electronic Science and Technology of China, Chengdu, Sichuan, People’s Republic of ChinaCorrespond...

Mouse hippocampal CA1 VIP interneurons detect novelty in the environment and support recognition memory

Summary: In the CA1 hippocampus, vasoactive intestinal polypeptide-expressing interneurons (VIP-INs) play a prominent role in disinhibitory circuit motifs. However, the specific behavioral conditions that lead to circuit disinhibition remai...

Atorvastatin suppresses high-risk colorectal adenomas via reprogramming of lipid metabolism and Inhibition of stemness

Abstract As critical precursors to colorectal cancer (CRC), high-risk colorectal adenomas (HR-CRAs) lack effective chemopreventive strategies beyond endoscopic resection. We previously established a standardized protocol for culturing patie...

Constraining PERMANOVA and LDM to within-set comparisons by projection improves the efficiency of analyses of matched sets of microbiome data

Abstract Background Matched-set data arise frequently in microbiome studies. For example, we may collect pre- and post-treatment samples from a set of individuals, or use important confounding variables to match data from case participants ...