136986 research outputs found
Sort by
Antisense oligonucleotide treatment in a preterm infant with early-onset SCN2A developmental and epileptic encephalopathy
No full textEarly-onset SCN2A developmental and epileptic encephalopathy is caused by SCN2A gain-of-function variants. Here we describe the clinical experience with intrathecally administered elsunersen, a gapmer antisense oligonucleotide targeting SCN2A, in a female preterm infant with early-onset SCN2A developmental and epileptic encephalopathy, in an expanded access program. Before elsunersen treatement, the patient was in status epilepticus for 7 weeks with a seizure frequency of 20-25 per hour. Voltage-clamp experiments confirmed impaired channel inactivation and increased persistent current consistent with a gain-of-function mechanism. Elsunersen treatment demonstrated a favorable safety profile with no severe or serious adverse events reported after 19 intrathecal administrations over 20 months. After administration in combination with sodium channel blockers, status epilepticus was interrupted intermittently and ultimately ceased after continued dosing. A >60% reduction in seizure frequency corresponding to five to seven seizures per hour was observed, which has been sustained during follow-up until the age of 22 months. These data provide preliminary insights on the safety and efficacy of elsunersen in a preterm infant. Additional investigation on the benefits of elsunersen in clinical trials is warranted.10.1038/s41591-025-03656-
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing
No full textPolyadenylation is a dynamic process that is important in cellular physiology, which has implications in messenger RNA decay rates, translation efficiency, and isoform-specific regulation. Oxford Nanopore Technologies direct RNA sequencing provides a strategy for sequencing the full-length RNA molecule and analysis of the transcriptome. Several tools are currently available for poly(A) tail length estimation, including well-established methods like tailfindr and nanopolish, as well as more recent deep learning models like Dorado. However, there has been limited benchmarking of the accuracy of these tools against gold-standard datasets. In this article, we present our novel deep learning poly(A) estimation tool - BoostNano - and compare with 3 existing tools - tailfindr, nanopolish, and Dorado. We evaluate the 4 poly(A) estimation tools, using 2 sets of synthetic in vitro transcribed RNA standards with known poly(A) tail lengths - Sequin (30 or 60 nucleotides) and enhanced green fluorescent protein (10-150 nucleotides) RNA. Analyzing datasets with known ground-truth values is a valuable approach to measuring the accuracy of poly(A) length estimation. The tools demonstrated length- and sample-dependent performance, and accuracy was enhanced by averaging over multiple reads via estimation of the peak of the density distribution. Overall, Dorado is recommended as the preferred approach due to its relatively fast runtimes, low mean error, and ease of use with integration with base-calling. These results provide a reference for poly(A) tail length estimation analysis, aiding in improving our understanding of the transcriptome and the relationship between poly(A) tail length and other transcriptional mechanisms, including transcript stability or quantification
Pathological contributors to organ damage and mortality in systemic sclerosis: a nationwide matched case-control study
No full textBACKGROUND: Mortality is increased in systemic sclerosis (SSc), including a 10-15-fold increase in sudden cardiac death. Limited histopathology data exist to understand the pathogenesis of this excess. This study aimed to compare heart, lung and renal histopathology at autopsy between SSc and controls. METHODS: A matched case-control study was performed using autopsy data from the Australian National Coronial Information System. SSc cases were selected via keyword search, and age- and sex-matched to controls identified from motor vehicle accidents. Cause of death, antemortem comorbidities and autopsy findings were extracted. Odds ratios were calculated with 95 % confidence intervals (CI). FINDINGS: Fifty-nine SSc cases (64 years, 81 % female) were matched to 59 controls (62 years, 81 % female). Myocardial fibrosis was 11-times more common in SSc (95 %CI 4-29, p < 0.01), inflammation 39-times more common (95 %CI 2-672, p = 0.01) and small vessel vasculopathy 27-times more common (95 %CI 2-485, p = 0.02), despite no difference in epicardial coronary artery disease (p = 0.24). Two-thirds of SSc cases had myocardial fibrosis with no identifiable secondary cause (e.g., coronary/valvular lesions). Pulmonary fibrosis, inflammation and vasculopathy ranged from 23 to 100-times more common in SSc. Renal fibrosis/scarring, inflammation/infiltrates and vasculopathy were 3-6-times more common in SSc. Among SSc cases, combined pathologies (≥2 of fibrosis, inflammation or vasculopathy) were seen concurrently in 31 % of hearts, 41 % of lungs and 45 % of kidneys. INTERPRETATION: The high frequency of unexplained myocardial fibrosis in SSc provides insights into the mechanism of excess mortality and sudden cardiac death observed in SSc. This matched autopsy study demonstrates the mechanisms and complexity of organ damage in SSc, with 30-45 % of organs displaying multiple concurrent pathologies
Bicarbonate-buffered solution versus Plasma-Lyte™ in orthotopic adult liver transplantation: a pilot open-label, randomized, non-inferiority trial
No full textBACKGROUND: The ideal intravenous maintenance and resuscitation fluid for patients undergoing orthotopic liver transplantation (OLT) remains unknown. We aimed to determine whether bicarbonate-buffered solution was non-inferior to Plasma-LyteTM in preventing metabolic acidosis during OLT. METHODS: We conducted a pilot single-center, open-label, randomized trial to compare the physiological effects of intravascular volume maintenance with a bicarbonate-buffered solution vs. Plasma-LyteTM in adults undergoing OLT. Non-inferiority was defined as a median difference in the standard base excess (SBE) of less than -2.5 mEq/L. The primary endpoint was the SBE at 5 minutes post-reperfusion. Quantile regression analysis was applied to confirm non-inferiority. Secondary endpoints included other forms of acid-base and electrolyte imbalances at pre-specified time points and postoperative complications. RESULTS: We randomized 52 adults undergoing OLT. The median (Q1, Q3) volume infused was 5 000 (3 125, 7 000) ml in the bicarbonate-buffered solution group and 5 500 (4 000, 10 500) ml in the Plasma-LyteTM group (P = 0.37). The median (Q1, Q3) SBE at 5 minutes post-reperfusion was -4.857 (-6.231, -3.565) mEq/L in patients receiving bicarbonate-buffered solution and -4.749 (-7.574, -2.963) mEq/L amongst those in the Plasma-LyteTM group. The estimated median difference by quantile regression was -0.043 mEq/L (95% CI [-1.988 to 1.902] mEq/L; one-sided P = 0.015). There were no significant differences in the acid-base secondary outcomes, number of complications, or patient mortality. There were no reported adverse events or safety concerns associated with the use of either solution. CONCLUSIONS: A bicarbonate-buffered solution was non-inferior to Plasma-LyteTM for maintaining acid-base homeostasis post-reperfusion in OLT patients
Immunotherapy with low-dose IL-2 attenuates vascular injury in mice with diabetic and neovascular retinopathy by restoring the balance between Foxp3+ Tregs and CD8+ T cells
No full textAIMS/HYPOTHESIS: Diabetic retinopathy features damage to the retinal microvasculature that causes vessels to leak and proliferate and can lead to vision loss and blindness. Inflammation contributes to the development of diabetic retinopathy, but little is known about the role of the adaptive immune system, including the benefits of augmenting the Forkhead box protein P3 (Foxp3) regulatory T cell (Treg) compartment. We aimed to determine whether treatment with low-dose IL-2 expands and activates Tregs and reduces CD8+ T cells in the retina, and attenuates retinal inflammation and vasculopathy in murine models of diabetic retinopathy and neovascular retinopathy. METHODS: Mouse models of streptozocin-induced diabetes and oxygen-induced retinopathy (OIR) were administered low-dose IL-2 (25,000 U) or vehicle (sterile water) by i.p. injection. Reporter mice expressing Foxp3 as a red fluorescent protein (RFP) conjugate or CD8 as a green fluorescent protein (GFP) conjugate were used to evaluate Foxp3+ Tregs and CD8+ T cells, respectively, in blood, lymphoid organs and retina using flow cytometry or confocal microscopy. Vasculopathy and the expression of angiogenic and inflammatory factors were assessed in the retina. RESULTS: Low-dose IL-2 significantly expanded CD4+CD25+Foxp3+ Tregs in the blood and spleen of mouse models of OIR and diabetes (1.4- to 1.9-fold increase, p<0.01). This expansion enhanced Treg functionality, increasing the expression of cytotoxic T-lymphocyte-associated protein4 (CTLA4), programmed cell death protein1 (PD1) and T-cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibitory motif (ITIM) domain (TIGIT), and increased the ratio of Tregs to CD8+ T cells. This was accompanied in the retina by a twofold increase in Foxp3+ Tregs (diabetes: 3.01 ± 0.41 vs 5.90 ± 1.25 cells per field, p<0.001; OIR: 4.41 ± 1.48 vs 10.05 ± 2.91 cells per field, p<0.001) and a reduction in CD8+ T cells (diabetes: 4.65 ± 0.58 vs 3.00 ± 0.81 cells per field, p<0.01; OIR: 5.51 ± 1.33 vs 3.17 ± 1.14 cells per field, p<0.01). Low-dose IL-2 reduced the levels of the potent inflammatory factors intercellular adhesion protein1 and TNF and the chemokine IFNγ-inducible protein10 (IP-10) in the retina. Importantly, low-dose IL-2 treatment effectively attenuated retinal vasculopathy, with marked reductions in acellular capillaries (diabetes: 0.48-fold decrease, p<0.001), neovascularisation (OIR: 0.68-fold decrease, p<0.01) and vascular leakage, and expression of vascular endothelial growth factor. CONCLUSIONS/INTERPRETATION: This study highlights the therapeutic potential of low-dose IL-2 to reduce retinal inflammation and severe vascular injury by boosting Tregs and reducing CD8+ T cells and inflammatory factors
Exploration of Li-decorated g-C2O monolayer for enhancing hydrogen storage via first-principles calculations
No full textThe g-C2O monolayer, notable for its electron-rich oxygen atoms and pronounced van der Waals (vdW) forces, presents itself as a viable candidate for hydrogen storage. Through first-principles based calculations, we explore a novel composite, Li@g-C2O, tailored for physical hydrogen adsorption. Lithium (Li) atoms are stably anchored onto the g-C2O surface with a binding energy of −1.747 eV, ensuring thermal stability at 300 K. The system can accommodate up to eight H2 molecules per unit cell, resulting in a total hydrogen storage capacity that exceeds the DOE target (2025). The desorption process occurs within a temperature range of 253 K–384 K, corresponding to average adsorption energy ranging from −0.152 eV/H2 to −0.101 eV/H2, highlighting its favorable kinetic properties for hydrogen release. The hydrogen adsorption mechanism leverages both vdW interactions and electrostatic effects, with the oxygen atoms acting as active sites. These results offer critical theoretical insights into designing high-performance hydrogen storage materials for energy applications, including sustainable transportation
The ultraviolet spectra of 2003fg-like Type Ia supernovae
No full textABSTRACT
2003fg-like Type Ia supernovae (03fg-like SNe Ia) are rare sub-type of SNe Ia, photometrically characterized by broader optical light curves and bluer ultraviolet (UV) colours compared to normal SNe Ia. In this work, we study four 03fg-like SNe Ia using Swift UltraViolet and Optical Telescope (UVOT) grism observations to understand their unique UV properties and progenitor scenario(s). We report 03fg-like SNe Ia to have similar UV features and elemental compositions as normal SNe Ia, but with higher UV flux relative to optical. Previous studies have suggested that the UV flux levels of normal SNe Ia could be influenced by their progenitor properties, such as metallicity, with metal-poor progenitors producing higher UV flux levels. While 03fg-like SNe were previously reported to occur in low-mass and metal-poor host environments, our analysis indicates that their UV excess cannot be explained by their host-galaxy parameters. Instead, we demonstrate that the addition of a hot blackbody component, likely arising from the interaction with the circumstellar material (CSM), to the normal SN Ia spectrum, can reproduce their distinctive UV excess. This supports the hypothesis that 03fg-like SNe Ia could explode in a CSM-rich environment
Glycoproteomics and Its Role in Understanding Bacterial O-Linked Glycosylation
No full textProtein glycosylation is now recognized as a ubiquitous process observed in all domains of life. Within bacterial species, carbohydrates can be attached to multiple residues with glycosylation of serine, threonine, or tyrosine residues via their hydroxyl side chains referred to as O-linked glycosylation. To date, multiple bacterial enzymes have been identified that mediate O-linked glycosylation targeting either surface or periplasmic bacterial proteins, and in the case of toxin/effectors, host proteins. Within this review, we discuss the current understanding of common bacterial O-linked glycosylation systems and the glycoproteomic approaches which have been used to characterize these events. Focusing on O-oligosaccharyltransferases (O-OTases), flagellin-specific glycosylation systems, and glycosyltransferase toxin/effectors, we discuss the characteristics of known glycosylation systems. For the general O-linked systems mediated by the PglL oligosaccharyltransferases, we outline the key considerations when assessing glycosylation events across the Burkholderia, Neisseria, and Acinetobacter genera. In addition, we highlight the technologies and advancements in glycoproteomic techniques, as well as the bioinformatic tools that now facilitate high throughput studies of O-linked glycosylation within bacterial species. Combined, this review outlines our current understanding of O-linked glycosylation within well characterized Gram-negative genera and the current technologies available for exploring bacterial O-glycoproteomes
Enabling general practice research in singapore: A qualitative exploration of barriers, facilitators and solutions
No full textBACKGROUND: The importance of primary care research in informing clinical practice and policy is well demonstrated. In the Singapore setting, the majority of research occurs in public institutions called polyclinics as opposed to the private general practice setting where approximately 80% of primary care clinical service provision takes place. There is a need to increase research in the private general practice setting to ensure that findings are relevant to this setting. This study aimed to explore the barriers, facilitators and motivations impacting on Singaporean GP's involvement in research with a view to optimising the structure and supports offered by SPARK, a practice-based research network (PBRN). METHODS: GPs were recruited from SPARK network, research collaborators and networks of the researchers. Semi-structured interviews were conducted face to face or via zoom and audio recorded. Interviews were transcribed and then thematic analysis was conducted using a deductive and inductive approach. RESULTS: Fifteen GPs participated in the study. Four major themes (motivators, barriers, facilitators, PBRN) and 14 subthemes were identified from the interviews. Whilst there were barriers at the GP, practice, system and individual research project levels, there were strong intrinsic (altruism, alignment with personal interest) and extrinsic (better patient care, job enrichment, enhancing primary care) motivators. Important facilitators included practice support, funding, streamlining of research practices, collaboration and acknowledgement of the contribution of GPs. PBRNs could support this through providing research infrastructure underpinned by communication and relationships and the sharing of research outcomes. CONCLUSIONS: There is acknowledgement that research conducted in the Singapore general practice environment is important, but barriers such as time, financial support and lack of systemic structures exist which limit participation. PBRNs, such as SPARK, can play a role in bridging the existing gap between clinical experience and academic expertise. The findings of this study will inform future SPARK activities to build a dynamic general practice research environment in Singapore
The simulation of large-sized pathogen-laden respiratory droplet spread inside a passenger ferry
No full textThis paper presents computational fluid dynamics (CFD) of Reynolds-Averaged Navier Stokes (RANS) simulations to analyse the flow movement of pathogen-laden particles/droplets with relatively large diameter range of 50 − 150 μ m inside an air-conditioned ferry cabin. Three major cases are investigated, the first cases is when one infected passenger sits on a passenger chair that is located close to the edge of the cabin in the centre row; the second case is when the infected passenger is standing in the middle of the cabin; and the third case is for a passenger who sits on the opposite edge of the cabin, and located at the front row. For each of these three positions, three air conditioner velocities were investigated. The results indicate that as the air conditioner velocities velocity increases, the spread of the particles is also getting wider and they are elevated further from the floor. The simulation results also indicate that passenger location is also an important aspect in influencing the spread of the particles, particularly for those who are directly blown by the air conditioner’s airflow. Our results also show the effectiveness of 1.5-meter (minimum 1-meter) social distancing rule by the WHO (World Health Organisation) for particles with diameter range of 50 − 150 μ m, however there are certain cases in which this separation distance may be insufficient. Such as in which the infected patient is directly blown by the air conditioner or when the particle diameters are smaller than 50 μ m in which it could be suspended in the air longer. Finally, this report also discuss RANS validation technique with respect to experiment and the weakness of RANS in simulating the movement of particles inside a room. Hence the result of the simulation should be treated as an approximation only