OAR@UM Community:

Validation of autosomal dominant polycystic kidney disease variants using long-range pcr and third generation sequencing

2026-05-22T07:00:08Z

Title: Validation of autosomal dominant polycystic kidney disease variants using long-range pcr and third generation sequencing Abstract: Autosomal dominant polycystic kidney disease (ADPKD) is a hereditary disorder which is characterized by the formation and progressive enlargement of multiple bilateral kidney cysts with an estimated prevalence of 1 in 1000 to 1 in 2500 individuals. ADPKD is also associated with a high phenotypic variability even between affected members of the same family such that the age of onset and the severity of the disease differ significantly between affected individuals. With molecular testing, it is known that 80-85 % of the affected individuals possess a pathogenic variant in PKD1 and almost all the rest are characterized by a pathogenic variant in PKD2. This study involved 3 objectives. The first objective was to confirm the presence, location and pathogenicity of the PKD1 p.C508R variant. Long range (LR) PCR followed by long-read 3rd generation amplicon sequencing were performed which successfully determined that the p.C508R variant is present on PKD1P3 in both ADPKD patients and in non-PKD individuals and thus should be reclassified as a likely benign polymorphism. The second objective was to confirm previously identified variants which were shortlisted by 2nd generation high-throughput sequencing (HTS) in the Malta NGS Project. LR-PCR and/or nested PCR followed by Sanger sequencing were used, which successfully confirmed 7 out of 11 potential causative variants. These variants were re-evaluated to determine pathogenicity. The third and final objective of this project was to carry out further testing on the patients from the 2 pedigrees (P12 and P13) in which no potential causative variant had been identified. PacBio whole genome sequencing (WGS) was performed on a single Sequel IIe SMRT flowcell however, unsatisfactory results were obtained, with insufficient coverage across several parts of the genome and almost no coverage across PKD1. Additional sequencing runs on other Sequel IIe SMRT flowcells per genome or higher throughput HiFi systems such as Revio or Vega are necessary. This study highlights the differences between short-read and long-read sequencing techniques and encourages the integration of LR-PCR with long-read 3rd generation sequencing especially for complex genomic regions or genes with homologous pseudogenes such as PKD1. Description: M.Sc.(Melit.)

Deciphering the compartmentalized host response in sepsis secondary to community-acquired pneumonia

2026-05-21T13:20:09Z

Title: Deciphering the compartmentalized host response in sepsis secondary to community-acquired pneumonia Abstract: Sepsis, currently defined as a complex condition resulting from a dysregulated host response to infection leading to lethal organ dysfunction, is a major global health concern and a leading cause of both morbidity and mortality worldwide. Emerging evidence suggests that immune compartmentalization, variation in the immune response between the circulation and the tissue microenvironment, plays a vital role in the clinical trajectory of sepsis. In sepsis secondary to community-acquired pneumonia (CAP), distinct immune cell distribution and localization of cytokine production may contribute to divergent inflammatory signatures between bronchoalveolar lavage fluid (BALF) and plasma. This project aims to identify compartment-specific immune responses which would aid in further uncovering the pathophysiology of pneumosepsis. This project was a prospective observational single-center study in the intensive care unit (ICU) within Mater Dei Hospital, Malta, forming part of the Molecular Endotype-Specific Dynamics of Lung Endothelial Barrier Integrity in Sepsis (MENDSEP) study. Peripheral blood and BALF samples were obtained from 29 consenting critically ill patients diagnosed with sepsis secondary to CAP (pneumosepsis) between 2023 and 2025. In addition, 16 age, sex, and co-morbidity-matched controls were recruited from the community and from St Vincent de Paul Residence (SVPR). The levels of various cytokines and markers in blood and BALF of septic samples were quantified using multiplex immunoassays. Cytokine analysis revealed marked immune compartmentalization in pneumosepsis. Pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), anti-inflammatory cytokines (IL-10) and anti-viral interferons (IFN-α, IFN-β, IFN-γ) were all found to be significantly enriched in BALF relative to plasma (p<0.001), indicating localized inflammatory and antiviral activity. Conversely, angiopoietin-2 (Ang-2) and the Ang-2:Ang-1 ratio were elevated in the circulation, representing systemic endothelial dysfunction. These findings underscore the compartmentalized nature of the immune response in sepsis, with localized pulmonary inflammation alongside systemic endothelial dysfunction. This study lays the groundwork to further elucidate the complex pathophysiology of sepsis, in improving early diagnosis, and the development of compartment-specific therapeutic targets. Description: M.Sc.(Melit.)

Beyond 42 days : a national cohort study of maternal and late maternal deaths in Brazil from 2010 to 2023

2026-05-21T07:45:37Z

Title: Beyond 42 days : a national cohort study of maternal and late maternal deaths in Brazil from 2010 to 2023 Abstract: Background/Objectives: Maternal mortality is a serious public health problem and reflects social, ethnic, racial, and regional inequalities in access to and quality of obstetric care. Despite advances in the surveillance and investigation of maternal deaths in Brazil, late maternal deaths (occurring between 43 days and 1 year after birth) are still underestimated and underexplored. Therefore, the objective of this study was to analyze the distribution and factors associated with maternal deaths and late maternal deaths in Brazil between 2010 and 2023. Methods: This was a population-based, retrospective cohort study with a quantitative approach, using secondary data from the Mortality �� System. All maternal deaths (Chapter XV of ICD-10) and late deaths recorded during the period were included. Sociodemographic, clinical, and administrative variables were analyzed. Statistical tests of association (chi-square, test of proportions, and 95% CI) were used, with a significance level of 5%. Results: A total of 26,953 deaths were identified, of which 24,387 were maternal and 2,566 were late deaths. Most deaths occurred among single, mixed-race women with 8 to 11 years of schooling, and residing in the Southeast region. Late deaths were more frequent in the South and among women aged 40 to 49. The main causes were direct obstetric conditions. A statistically significant association was observed between the type of death and sociodemographic variables. Conclusions: The results highlight structural inequalities in maternal mortality in Brazil and reinforce the importance of expanding postpartum surveillance beyond 42 days, with a focus on equity and continuity of care.

Exploring nurses’ knowledge, attitudes, and perceptions of medication errors in a general hospital in Malta – a cross-sectional survey

2026-05-20T12:12:46Z

Title: Exploring nurses’ knowledge, attitudes, and perceptions of medication errors in a general hospital in Malta – a cross-sectional survey Authors: Schiavone, Natalya; Scicluna Ward, Corinne Abstract: Background: Medication errors (MEs) continue to pose a significant risk to patient safety despite established safety measures. Nurses are central to administering medications, and their knowledge, experience, and work environment influence both the likelihood of errors and whether they are reported. This study explored nurses’ perspectives on MEs, reporting practices, and barriers to reporting in a general hospital in Malta. Methods: A quantitative cross-sectional study was conducted using an anonymous online questionnaire informed by the Theory of Planned Behaviour. Of the 429 nurses invited, 301 completed the survey (response rate 70.2%). The questionnaire addressed the prevalence of MEs, reporting behaviours, knowledge of medications, perceived contributing factors, and attitudes towards reporting. Descriptive and inferential statistics were used to analyse the data. Results: Most nurses (88%, n = 265/301) reported having made at least one medication error. Reporting was inconsistent: 54% (n = 163/301) had never reported an error, 35% (n = 105/301) reported some, and only 11.6% (n = 35/301) reported all incidents. The area of work was significantly linked to perceived barriers and reporting behaviour. Nurses in reliever pools (92.6%), medical wards (89.9%), and surgical wards (79.7%) were more likely to feel concerns or barriers about reporting. Reporting practices also varied by area, with lower reporting in paediatric (36.8%) and orthopaedic wards (44.0%) and higher reporting in reliever pools (67.9%). While most nurses valued reporting (89%, n = 268/301), only 34% (n = 102/301) would report errors causing no harm, and 78% (n = 235/301) were reluctant to report colleagues. Conclusions: The findings reveal that MEs are common and underreported. Knowledge gaps, communication challenges, and systemic issues such as staffing shortages create barriers to safe medication management. Fear of repercussions further discourages reporting, highlighting the need for supportive, transparent practices. Hospitals should foster a non-punitive reporting culture, strengthen training, and improve interprofessional communication. Addressing these challenges can reduce medication errors and enhance patient safety and care quality.