SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics.

Background: Ireland's COVID-19 response combined extensive SARS-CoV-2 testing to estimate incidence, with whole genome sequencing (WGS) for genome surveillance. As an island with two political jurisdictions-Northern Ireland (NI) and Republic of Ireland (RoI)-and access to detailed passenger travel data, Ireland provides a unique setting to study virus introductions and evaluate public health measures. Using a substantial Irish genomic dataset alongside global data from GISAID, this study aimed to trace the introduction and spread of SARS-CoV-2 across the island.

Regulation of human interferon signaling by transposon exonization.

Innate immune signaling is essential for clearing pathogens and damaged cells and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2.

Does strain-level persistence of lactobacilli in long-term back-slopped sourdoughs inform on domestication of food-fermenting lactic acid bacteria?

Sourdoughs are maintained by back-slopping over long time periods. To determine strain-level persistence of bacteria, we characterized four sourdoughs from bakeries over a period of 3.3, 11.

Massively parallel sequencing of mitochondrial genome in primary open angle glaucoma identifies somatically acquired mitochondrial mutations in ocular tissue.

Glaucoma is a sight threatening neurodegenerative condition of the optic nerve head associated with ageing and marked by the loss of retinal ganglion cells. Mitochondrial dysfunction plays a crucial role in the pathogenesis of neurodegeneration in the most prevalent type of glaucoma: primary open angle glaucoma (POAG). All previous mitochondrial genome sequencing studies in POAG analyzed mitochondrial DNA (mtDNA) isolated from peripheral blood leukocytes and have not evaluated cells derived from ocular tissue, which better represent the glaucomatous disease context.

Automated wave labelling of the auditory brainstem response using machine learning.

Objective: To compare the performance of a selection of machine learning algorithms, trained to label peaks I, III, and V of the auditory brainstem response (ABR) waveform. An additional algorithm was trained to provide a confidence measure related to the ABR wave latency estimates.

Design: Secondary data analysis of a previously published ABR dataset.

Optical Tweezers Assembled Nanodiamond Quantum Sensors.

Here we show that gradient force optical tweezers can be used to mediate the self-assembly of nanodiamonds into superstructures, which can serve as optically trapped nanoscale quantum probes with superior magnetic resonance sensing capabilities. Enhanced fluorescence rates from nitrogen-vacancy NV defect centers enable rapid acquisition of optically detected magnetic resonance (ODMR), and shape-induced forces can improve both positioning accuracy and orientation control. The use of confocal imaging can isolate the signal from individual nanodiamonds within the assembly, thereby retaining the desirable properties of a single crystal probe.

Audiogram Estimation Performance Using Auditory Evoked Potentials and Gaussian Processes.

Objectives: Auditory evoked potentials (AEPs) play an important role in evaluating hearing in infants and others who are unable to participate reliably in behavioral testing. Discriminating the AEP from the much larger background activity, however, can be challenging and time-consuming, especially when several AEP measurements are needed, as is the case for audiogram estimation. This task is usually entrusted to clinicians, who visually inspect the AEP waveforms to determine if a response is present or absent.

Integrin beta-like 1 is regulated by DNA methylation and increased in heart failure patients.

Aims: Dynamic alterations in cardiac DNA methylation have been implicated in the development of heart failure (HF) with evidence of ischaemic heart disease (IHD); however, there is limited research into cell specific, DNA methylation sensitive genes that are affected by dysregulated DNA methylation patterns. In this study, we aimed to identify DNA methylation sensitive genes in the ischaemic heart and elucidate their role in cardiac fibrosis.

Methods: A multi-omics integrative analysis was carried out on RNA sequencing and methylation sequencing on HF with IHD (n = 9) versus non-failing (n = 9) left ventricular tissue, which identified Integrin beta-like 1 (ITGBL1) as a gene of interest.

Neural rhythms of narcissism: Facets of narcissism are associated with different neural sources in resting-state EEG.

Trait narcissism is characterized by significant heterogeneity across individuals. Despite advances in the conceptualization of narcissism, including the increasing recognition that narcissism is a multidimensional construct, the sources of this heterogeneity remain poorly understood. Here, we used a neural trait approach to help better understand "how," and shed light on "why," individuals vary in facets of trait narcissism.

Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.

Cancer cells exhibit rewired transcriptional regulatory networks that promote tumor growth and survival. However, the mechanisms underlying the formation of these pathological networks remain poorly understood. Through a pan-cancer epigenomic analysis, we found that primate-specific endogenous retroviruses (ERVs) are a rich source of enhancers displaying cancer-specific activity.

Incobotulinum Toxin-A in Professional Musicians with Focal Task-Specific Dystonia: A Double Blind, Placebo Controlled, Cross-Over Study.

Background: Musician's focal task-specific dystonia is a complex disorder of fine motor control, with incomplete understanding of its etiology. There have been relatively few trials of botulinum toxin in upper limb task-specific dystonia, and prior studies have yielded variable results, leading to skepticism regarding the utility of this approach in elite performers.

Methods: We conducted a double-blind, placebo-controlled, randomized, cross-over study of incobotulinum toxin-A in 21 professional musicians with focal upper extremity task-specific dystonia affecting performance on their instrument, using a novel paradigm of initial injections followed by booster injections at two- and four-week intervals.

The TGFβ Induced MicroRNAome of the Trabecular Meshwork.

Primary open-angle glaucoma (POAG) is a progressive optic neuropathy with a complex, multifactorial aetiology. Raised intraocular pressure (IOP) is the most important clinically modifiable risk factor for POAG. All current pharmacological agents target aqueous humour dynamics to lower IOP.

Optimization of microbial fuel cell performance application to high sulfide industrial wastewater treatment by modulating microbial function.

Microbial fuel cells (MFCs) are innovative eco-friendly technologies that advance a circular economy by enabling the conversion of both organic and inorganic substances in wastewater to electricity. While conceptually promising, there are lingering questions regarding the performance and stability of MFCs in real industrial settings. To address this research gap, we investigated the influence of specific operational settings, regarding the hydraulic retention time (HRT) and organic loading rate (OLR) on the performance of MFCs used for treating sulfide-rich wastewater from a canned pineapple factory.

Is the persistence of in food processing facilities and its resistance to pathogen intervention linked to its phylogeny?

The foodborne pathogen is differentiated into four distinct lineages which differ in their virulence. It remains unknown, however, whether the four lineages also differ with respect to their ability to persist in food processing facilities, their resistance to high pressure, a preservation method that is used commercially for control on ready-to-eat meats, and their ability to form biofilms. This study aimed to determine differences in the pressure resistance and biofilm formation of 59 isolates of representing lineages I and II.

Single-Cell RNA Sequencing Reveals Cardiac Fibroblast-Specific Transcriptomic Changes in Dilated Cardiomyopathy.

Dilated cardiomyopathy (DCM) is the most common cause of heart failure, with a complex aetiology involving multiple cell types. We aimed to detect cell-specific transcriptomic alterations in DCM through analysis that leveraged recent advancements in single-cell analytical tools. Single-cell RNA sequencing (scRNA-seq) data from human DCM cardiac tissue were subjected to an updated bioinformatic workflow in which unsupervised clustering was paired with reference label transfer to more comprehensively annotate the dataset.

Individual Patient Data Meta-Analysis of Dynamic Cerebral Autoregulation and Functional Outcome After Ischemic Stroke.

Background: The relationship between dynamic cerebral autoregulation (dCA) and functional outcome after acute ischemic stroke (AIS) is unclear. Previous studies are limited by small sample sizes and heterogeneity.

Methods: We performed a 1-stage individual patient data meta-analysis to investigate associations between dCA and functional outcome after AIS.

The effect of seed germination and spp. on the ripening of plant cheese analogs.

Unlabelled: Consumer demand for plant cheeses is increasing, but challenges of improving both flavor and quality remain. This study investigated the microbiological and physicochemical impact of seed germination and fermentation with and on the ripening of plant cheese analogs. Chlorine treatment or addition of and controlled microbial growth during seed germination.

Mapping the daily rhythmic transcriptome in the diabetic retina.

Retinal function changes dramatically from day to night, yet clinical diagnosis, treatments, and experimental sampling occur during the day. To begin to address this gap in our understanding of disease pathobiology, this study investigates whether diabetes affects the retina's daily rhythm of gene expression. Diabetic, Ins2 mice, and non-diabetic littermates were kept under a 12 h:12 h light/dark cycle until 4 months of age.

Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats.

Poales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test six hypotheses regarding the evolution and assembly of Poales in open and closed habitats throughout the world, and examine whether diversification patterns demonstrate parallel evolution. We sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts.