A novel enrichment-free, low-volume filtration and rapid lysis (ELR) method in combination with real-time PCR for detection of Shiga toxin-producing Escherichia coli (STEC) in water

Consequences of Shiga toxin-producing Escherichia coli (STEC) infection can range in severity from asymptomatic infection to haemolytic uraemic syndrome, renal failure and death. Groundwater-derived drinking water is an important route for STEC transmission. Detection of STEC in water is crucial for timely response and public health interventions; however, currently used culture-based methods are time-consuming and laborious. Therefore, there is a need for rapid methods that maintain high sensitivity and specificity [1]. We describe a novel, sensitive, enrichment-free water filtration method using a convenient sample volume (100 ml) to detect DNA markers of STEC serogroups and virulence factors within 6 h. Quantitative real-time PCR (qPCR) was used to detect and quantify the most common STEC infection-associated serogroups globally, O157 and O26. Real-time PCR was used to detect genetic determinants of STEC virulence (stx1, stx2 and eae genes) and specific marker genes for the clinically relevant serogroups O111, O103, O145 and O104. Results showed that the novel method can detect as low as 5 c.f.u. ml−1 of STEC in water. The limit of detection for O157 and O26 qPCR assays was two and six copies, respectively. Groundwater and surface water samples (n=28) were collected and processed using the novel method. STEC O157 and O26 serogroups were detected in 23 out of 28 (82.1%) samples (mean 5.2×104 copies/reaction) and 19 out of 28 (67.9%) samples (mean 7.83×104 copies/reaction), respectively. Shiga toxin genes stx1 or stx2 were detected in 15 out of 28 (53.6%) and 9 out of 28 (32.1%) samples, respectively. The virulence factor intimin gene eae was detected in 24 out of 28 (85.7%) samples. STEC serogroups O111, O103, O145 and O104 were detected in 15 out of 28 (53.6%), 10 out of 28 (35.7%), 11 out of 28 (39.3%) and 15 out of 28 (53.6%) samples, respectively. This novel method reproducibly detects low copies of STEC in low-volume fresh water and has the potential to be used for the detection and quantification of waterborne bacterial pathogens.This work was supported by the Environmental Protection Agency (EPA) of Ireland, project reference 2021-HE-1033. The EPA Research Programme is a Government of Ireland initiative funded by the Department of Communications, Climate Action and Environment. It is administered by the Environmental Protection Agency, which has the statutory function of coordinating and promoting environmental research

Shining a light on solar chemicals and fuels: Findings from a SWOT-led (Strengths, Weaknesses, Opportunities, and Threats) literature review and workshop

Solar chemicals and fuels (SCF) show enormous potential and can offer solutions to renewable energy intermittency and storage while reducing industrial CO2 emissions. Yet many challenges remain. SCF advocates face formidable obstacles, which include coordination across the different technological pathways and information dissemination, prohibitive costs, raw materials scarcity, or lengthy development timelines. Our study, then, offers a deeper and more critical understanding of these challenges through a systematic review that discusses the key Strengths, Weaknesses, Opportunities, and Threats threatening or supporting the development of a SCF market. NVivo software was employed to produce this comprehensive SWOT analysis, which was further complemented with a workshop that validated the data and offers a valuable resource for future strategic planning. Results indicate that while technological immaturity remains a major obstacle, a primary strength lies in SCF technologies' suitability for decentralized deployment and specialized applications. Insights from the literature and our workshop participants highlight SCF's potential for energy integration, alongside the critical need for targeted regulation, education, and training within a cohesive policy framework. Our conclusions also emphasize the value of SWOT analysis and workshops in generating insights to help stakeholders address research gaps, foster collaboration, and secure funding to drive future developments.This research, including the workshop featured in this paper, received support from H2020 Marie Skłodowska-Curie Action

Macromolecular crowding in animal component-free and/or xeno-free media for human mesenchymal stromal cell cultures: In vitro and preliminary in vivo studies

Mesenchymal stromal cells (MSCs) present great potential for therapeutic and reparative use in tissue engineering due to their self-renewal, multi-lineage differentiation and immunomodulatory properties. In the last twenty years, different strategies to expand the therapeutic potential of MSCs have been developed, however manufacturing and handling of these cells for their use as advanced therapy medicinal products remains insufficiently studied and available data are mainly related to non-industrial processes. Cell culture media containing undefined animal-derived components and prolonged in vitro culture periods in the absence of native extracellular matrix result in phenotypic drift of MSCs. Another limiting factor in the development of tissue engineered medicines is the prolonged in vitro expansion times required to reach the high cell numbers needed for therapeutic effects which is associated with loss of phenotype and immunomodulatory capability. Herein, we assessed whether animal component-free (ACF) or xeno-free (XF) media formulations maintain human bone marrow MSC (hBM-MSC) phenotypic characteristics more effectively than foetal bovine serum (FBS)-based media. In addition, we assessed whether tissue-specific extracellular matrix, induced via macromolecular crowding (MMC) during expansion and / or differentiation, can more tightly control hBMSC fate. Then, the effect of carrageenan in a xeno-free media on human umbilical cord derived MSCs (hUC-MSCs) was studied and in vitro and in vivo assessment of a non-animal sourced chitosan scaffold loaded with xeno-free umbilical cord mesenchymal stromal cells cultured under macromolecular crowding conditions was conducted. hBM-MSCs expanded in animal component-free media showed overall the highest phenotype maintenance, as judged by cluster of differentiation expression analysis. Contrary to FBS media, ACF and XF media increased cellularity over time in culture, as measured by total DNA concentration. While MMC with Ficoll™ increased collagen deposition of cells in FBS media, FBS media induced significantly lower collagen synthesis and/or deposition than the ACF and XF media. Cells expanded in FBS media showed higher adipogenic differentiation than ACF and XF media, which was augmented by MMC with Ficoll™ during expansion. Similarly, Ficoll™ crowding also increased chondrogenic differentiation. Of note, donor-to-donor variability was observed for collagen type I deposition and trilineage differentiation capacity of hBM-MSCs. Collectively, our data indicate that appropriate screening of donors, media and supplements, in this case MMC agent, should be conducted for the development of clinically relevant MSC medicines. Following appropriate in vitro experimentation, a splinted nude mouse wound healing model was used to assess wound closure and epidermal thickness of non-treated control, non-animal sourced chitosan scaffold, non-animal sourced chitosan scaffold loaded with xeno-free human umbilical cord mesenchymal stromal cells and non-animal sourced chitosan scaffold loaded with xeno-free human umbilical cord mesenchymal stromal cells cultured under macromolecular crowding conditions groups. Across all three donors, carrageenan supplementation significantly increased collagen deposition at day 5, day 8 and day 11 without affecting cell morphology, viability, DNA concentration and metabolic activity. Through freeze drying, a non-animal sourced chitosan sponge was developed with appropriate structural and mechanical properties for wound healing applications. In vitro biological analysis made apparent that neither the scaffold nor macromolecular crowding negatively impacted xeno-free human umbilical cord mesenchymal stromal cell metabolic activity and proliferation. In vivo biological analysis revealed no significant differences between the groups in wound closure and epidermal thickness, raising question about the suitability of the model. In any case, this work sets the foundations for the development of completely xeno-free tissue engineered medicines

Mobile privatization and the COVID-19 pandemic: Charting the interregnum

Rather than reaffirming technological determinist predictions of a total movement toward the domestication of labor and the full enclosure of the commons, the COVID-19 pandemic has thrown preexisting shifts in societal relations into high relief, demonstrating how technological change operates in conjunction with the larger political economy to structure class formation. This essay puts these developments in historical perspective through the lens of Raymond Williams’s notion of “mobile privatization.”3 Mobile privatization has not been a linear process; rather, it has been dialectical, contradictory, and experienced differently among different social groups at different times. While mobility and privacy are generally seen as marks of privilege, COVID-19 inverted that in significant ways.4 Making sense of these inversions is critical to mapping the terrain on which we now struggle to build a new social order amid deep crisis

KpSC-ID: a multiplex real-time PCR assay for the simultaneous detection of the Klebsiella pneumoniae species complex and specific identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae and Klebsiella variicola

The Klebsiella pneumoniae species complex (KpSC) comprises five closely related bacterial species, namely Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola, Klebsiella quasivariicola and Klebsiella africana. The KpSC is ubiquitous in the environment and is also an important human pathogen, particularly associated with healthcare-associated infections. The accurate detection and differentiation of the KpSC is challenging owing to the close phenotypic and genotypic identity (93–95% average nucleotide identity) shared between these members. Current diagnostic assays either fail to detect and identify all KpSC members or misidentify some KpSC members as K. pneumoniae sensu stricto. It is currently estimated that ~20% of human infections are caused by members of the KpSC other than K. pneumoniae. This leads to underreporting of some KpSC members in both clinical and environmental settings, which impacts our understanding of the importance of each species. Furthermore, it limits our understanding of the global and local epidemiological impact of some members of the KpSC. In this study, a rapid multiplex real-time PCR assay (KpSC-ID) was designed and developed to detect all KpSC members while simultaneously identifying the predominant human pathogens K. pneumoniae, K. quasipneumoniae and K. variicola. Assay performance was verified in silico using a panel of over 1,000 publicly available genome sequences and experimentally validated using a panel of genomic DNA extracted from 54 Enterobacteriaceae. The assay displayed excellent specificity against over 1,000 genome sequences tested in silico. During in vitro validation, the pan-KpSC assay detected each (29/29) KpSC species and strains tested. For the species-specific assays, 100% specificity was demonstrated in the K. pneumoniae, K. quasipneumoniae and K. variicola assays, respectively. Sensitivity of 10 genomic equivalents was demonstrated for each assay. Ultimately, the diagnostic assay developed in this study can improve our understanding of the significance of KpSC members, which is important when investigating their routes of transmission and epidemiology.We wish to acknowledge the College of Science and Engineering at University of Galway which has funded GMA’s postgraduate scholarship. This work was supported financially by the MedVetKlebs project from the European Joint Programme One Health, which has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no. 773830

Open-source Raman spectra of chemical compounds for active pharmaceutical ingredient development

Raman spectroscopy is utilised extensively in pharmaceutical analysis for tasks such as drug discovery, quality control and active pharmaceutical ingredient (API) development. Despite this, access to open-source Raman spectral datasets for modelling and analysis is often a challenge. In laboratory settings, small spectral libraries are typically compiled for one-shot identification of intermediates or unknown chemicals, which restricts availability to comprehensive and high-quality reference data. In this work, we introduce a new open-source Raman dataset consisting of pure chemical compounds commonly employed in the development of APIs. By curating and publishing this dataset, we aim to provide the scientific community with access to high-quality, reusable data. Containing 3,510 samples spanning 32 compounds, this data can be utilised for referencing and can potentially facilitate in the development of more accurate and generalisable calibration models when access to reference data is limited.This publication has emanated from research conducted with the financial support of Taighde Éireann - Research Ireland Centre’s for Research Training in Artificial Intelligence under grant number 18/CRT/6223 and the University of Galway. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The authors would like to express their sincere gratitude to Matthew Webberley and SK Pharmteco for providing the necessary facilities and supporting the data acquisition

Social capital in large-scale agile software product management: A multi-case study

Context Large fintech organizations are increasingly adopting agile methodologies to enhance product development capabilities. However, implementing agile at scale presents unique challenges, particularly related to collaboration essential for successful software product management (SPM). Social capital, comprising structural, cognitive, and relational dimensions, may play a crucial role in facilitating the collaboration needed to overcome these challenges. Objectives We examine the role of social capital in large-scale agile SPM, focusing on how it facilitates coordination, collaboration, and, ultimately, success, in complex, product-focused environments. Methods We employ a multi-case study approach, comprising 33 interviews, observations, and document analysis, analyzing two Scandinavian fintech companies that have adopted large-scale agile practices organized around product areas. Results Our findings, viewed through the lens of social capital theory, show that its three dimensions help explain how large-scale organizations adopting SPM manage dependencies and enable product-focused coordination. Specifically, the structural dimension helps illuminate how networks are formed; the cognitive dimension clarifies how shared understanding of product visions and development practices emerges; and the relational dimension highlights how trust is cultivated among product development actors across multiple operational levels (i.e., product team, product area, organizational, and external levels). Together, these dimensions offer insight into how agile practices are effectively implemented at scale. Conclusion Our study finds that social capital is a critical enabler of effective SPM in large-scale agile contexts. Its three dimensions support the collaboration and relational networks necessary for agility at scale. These insights suggest that fostering social capital should be prioritized in agile transformations to address the sociotechnical complexities inherent in large-scale SPM.The Research Council of Norway supported the work through the projects 10xTeams (grant 309344) and Transformit (grant 321477). The contribution by Astri Barbala was supported, in part, by Taighde Éireann – Research Ireland under Grant number 13/RC/2094_2. Co-funded by the European Union under the Systems, Methods and Context (SyMeCo) programme grant agreement number 101081459

High-latitude cabbeling observations along the east Greenland polar front

Cabbeling is the process where water parcels of the same density but different temperatures/salinities combine to form a new parcel of higher density. This can result in a statically stable profile becoming unstable after mixing has occurred. High-latitude cold, fresh, and shallow ocean waters exhibit greater nonlinearity in density dependence on temperature and are prone to cabbeling along fronts. While modeling shows there are important implications of high-latitude cabbeling, harsh polar conditions and the evanescent nature of cabbeling events make direct observations of the small-scale and shifting vertical structure difficult and rare. The East Greenland Polar Front (EGPF), where mixing of cold-fresh Arctic water and warmer-saltier Atlantic water occurs, is a location which has a high potential for cabbeling. Cabbeling-induced density anomalies of up to 0.05 kg m−3 within the upper 40 m were observed along the EGPF in 2023. Shallow stratification shows staircase structures within a strong halocline overlaying warm water intrusions, displaying a characteristic “jagged” shape in TS space. Enhanced turbulence was identified in regions where cabbeling instabilities occurred. These observations offer new insight into the vertical and temporal structure of cabbeling in high-latitude environments via rapidly repeated profiling. The observed anomalies align in magnitude and character with previously documented studies, extended here to include shallower observations coupled with shear measurements within frontal zones as identified by sea surface temperature. These findings suggest that cabbeling-induced mixing moderates locally enhanced heat flux, with implications for ice-ocean interaction and the broader high-latitude climate system.The author acknowledges the support from the Irish Center for Research in Applied Geosciences iCRAG, part of the Research Ireland Centre for conducting this research funded by a research Grant from Research Ireland under Grant 13/RC/2092_2. Additional funding was provided from the European Union's Horizon 2020 Research and Innovation Programme under Grant agreement 821001 awarded to BW. AM acknowledges Grant in Aid funding from the Marine Institute for research expedition CE23011 on the RV Celtic Explorer with special thanks to the captain and crew. In addition, AM acknowledges the financial support of Research Ireland and the Geological Survey of Ireland under the Frontiers for the Future Programme 21/FFP-P/10261

Counter-speech generation for homophobic and transphobic social media content in Malayalam

The growing prevalence of hate speech online has amplified acts of discrimination against marginalized populations, with the LGBTQIA+ community being particularly affected. In areas where under-resourced languages such as Malayalam are used, the issue grows more complex because of the absence of localized resources. This research offers an in-depth analysis of the production of counter-speech to address transphobia and homophobia in Malayalam. Our work incorporates both native Malayalam script and Malayalam written in Latin script, addressing the diverse linguistic practices of online users in Kerala. This paper introduces a two-stage pipeline to counter such online abuse. The first stage focuses on dataset creation through a human-in-the-loop process, beginning with 100 seed pairs of hate speech and their corresponding counter-speech manually curated. This set is expanded iteratively using language models culminating in 5,000 validated pairs. In the second stage, we propose a method to generate counter speech in Malayalam that leverages the Retrieval-Augmented Generation framework enhanced by REFINE (Retrieval Evaluation via Fluency, Inversion, and NEarness) for knowledge retrieval and constrained decoding. Evaluation metrics for both dataset quality and model performance demonstrate the effectiveness of this approach in producing diverse, fluent, and target-specific counter-speech. This research provides a foundational resource and scalable strategy for countering hate in low-resource regional languages. GitHub Link: https://github.com/Bharathi-AI-for-Social-Good/CN-Malayalam.Open Access funding provided by the IReL Consortium. This research has not been funded by any company or organization

Evaluation of the potential for genomic selection in an Irish breeding population of sitka spruce (Picea sitchensis (Bong.) Carr))

Genomic selection is a form of breeding predicting for phenotypic traits within a population, using allelic data drawn from individuals within this population as the explanatory variable. Genomic selection has been widely evaluated within livestock and crop species, and is now an established part of breeding endeavours within such species. In the era of increasingly cheaper whole-genomic sequencing strategies, the potential for genomic selection is increasingly being investigated in more niche species with features that otherwise discourage evaluation such as long generational intervals or particularly large genomes. Sitka spruce (Picea sitchensis) is one such species, yet equally is also one of great importance to Irish forestry. Efforts to breed Sitka spruce in Ireland have been have resulted in a national breeding program, but have not yet attempted to incorporate any of the recent advances regarding genetic and genomic breeding. In this thesis, I investigated the the potential for genomic selection among the Irish breeding population of Sitka spruce. I evaluated the suitability of phenotypic data generated from the breeding program for the used as traits of interest within a genomic selection model. Comparing the historical data of the program to contemporary data, I investigated the assumptions of correlation of the genetic control of a traits across different ages which underpins breeding in many long-lived species. Combining the available phenotypic data of the breeding program, derived from families of half-siblings, with genomic data generated from their maternal parent through Genotype-by-Sequencing, I explored the potential for genomic selection in Irish Sitka spruce with respect to the nature of these data. Finally, using a sub-population of full-siblings derived from the breeding program's genotypes, I examined the effectiveness of genomic selection against more conventional breeding methods such pedigree-based breeding. In totality, this thesis demonstrates a clear potential for viable genomic selection in the Irish Sitka spruce breeding population as is, and highlights opportunities for changes to current practices which would further improve genomic selection within this population