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Microbial Signatures in Oil Reservoirs: Biomarker Stability and Their Role in Subsurface Fluid Monitoring
Get PDFSustainable energy solutions such as carbon capture, utilization, and storage (CCUS), geothermal energy, and hydrogen storage are vital for achieving low-carbon energy goals. However, these technologies face significant challenges, including gas leakage and the need for reliable monitoring systems within subsurface geological formations. Indigenous microorganisms, naturally widespread in these formations, offer a novel approach for dynamic monitoring over time through DNA sequencing analysis. Yet, critical questions remain: Can ground-level samples accurately represent geological information? How stable is the microbial DNA under surface conditions and for how long? This study investigates the stability of microbial community structures from deep subsurface oil reservoir samples during degradation at room temperature over 120 h. Samples were analyzed at 24 h intervals using DNA extraction, concentration measurements, and sequencing. Microbial diversity was assessed via α and β diversity indexes, while Venn analysis compared community structures to identify formation-specific genera. Findings reveal that microbial profiles from subsurface samples remain largely reflective of their original environments despite surface degradation. This highlights the feasibility of using subsurface microbial biosensing for dynamic environmental monitoring. By addressing the stability of microbial data, this research enhances the potential of DNA-based tools to support CCUS, geothermal energy, and hydrogen storage. It underscores the role of microbial biosensing in advancing sustainable energy practices, offering a robust framework for tackling challenges in subsurface monitoring, while contributing to the transition toward a low-carbon future
Development and validation of an epigenetic signature of allostatic load
Get PDFThe allostatic load (AL) concept measures physiological dysregulation in response to internal and external stressors that accumulate across the life course. AL has been consistently linked to chronic disease risk across studies. However, there is considerable variation in its operationalization. In the present study, DNA methylation (DNAm) data (using the Illumina Infinium MethylationEPIC BeadChip array) from the Swiss Kidney Project on Genes in Hypertension (SKIPOGH) cohort, a Swiss-based family cohort study, were used in a discovery epigenome-wide association study to identify cytosine–guanine nucleotide sites associated with phenotypic measures of AL. Elastic net linear regression models were used to estimate an epigenetic signature of AL (methAL), including an Illumina HumanMethylation450K (HM450K) assay-compatible signature (methALT). The methALT signature was validated in the 1936 Lothian Birth Cohort (LBC1936), population-based prospective cohort study. We found that the methAL signature was positively associated with the clinical phenotype of AL in both the SKIPOGH (R2 = 0.59) and LBC1936 (R2 = 0.16) cohorts. In the validation cohort, a one standard deviation increase in methALT signature was associated with 25% higher odds of reported history of cardiovascular disease (CVD) (odd ratio [OR] = 1.25, 95% confidence interval [CI] = 1.05–1.50), and a nearly two-fold increase in all-cause mortality rate at the beginning of follow-up (hazard ratio = 1.68, 95% CI = 1.33–2.13) when adjusting for all potential confounders. In conclusion, the epigenetic signature for AL not only correlated well with phenotype-based AL scores but also exhibited a stronger association with the history of CVD and all-cause mortality compared with AL scores. The methAL signature could help assuage issues of comparison across studies
Rapamycin induced autophagy enhances lipid breakdown and ameliorates lipotoxicity in Atlantic salmon cells
Get PDFAutophagy is a highly conserved cellular recycling process essential for homeostasis in all eukaryotic cells. Lipid accumulation and its regulation by autophagy are key areas of research for understanding metabolic disorders in human and model mammals. However, the role of autophagy in lipid regulation remains poorly characterized in non-model fish species of importance to food production, which could be important for managing health and welfare in aquaculture. Addressing this knowledge gap, we investigate the role of autophagy in lipid regulation using a macrophage-like cell line (SHK-1) from Atlantic salmon (Salmo salar L.), the world's most commercially valuable farmed finfish. Multiple lines of experimental evidence reveal that the autophagic pathway responsible for lipid droplet breakdown is conserved in Atlantic salmon cells. We employed global lipidomics and proteomics analyses on SHK-1 cells subjected to lipid overload, followed by treatment with rapamycin to induce autophagy. This revealed that activating autophagy via rapamycin enhances storage of unsaturated triacylglycerols and suppresses key lipogenic proteins, including fatty acid elongase 6, fatty acid binding protein 2 and acid sphingomyelinase. Moreover, fatty acid elongase 6 and fatty acid binding protein 2 were identified as possible cargo for autophagosomes, suggesting a critical role for autophagy in lipid metabolism in fish. Together, this study establishes a novel model of lipotoxicity and advances understanding of lipid autophagy in fish cells, with significant implications for addressing fish health issues in aquaculture.</p
Flexural performance of pretensioned prestressed concrete solid square piles reinforced with steel strands and deformed steel bars
Get PDFPretensioned spun concrete pipe piles and concrete hollow square piles have been subjects of much research interest in recent years; however, their application in practical projects has been limited due to difficulties in effectively guaranteeing the overall performance and durability resulting from the hollow cross-section. On the other hand, prestressed concrete solid square piles (PSP) that use traditional helical grooved steel bars (HGBs) usually exhibit poor deformability, leading to premature brittle failure under large lateral loads. This paper develops a new type of pretensioned prestressed concrete solid square piles (PSSP), which adopt high-strength and high-ductility steel strands as the longitudinal prestressing tendons and deformed steel bars as the erection bars at four corners. Bending tests are carried out on four full-scale PSSP specimens with different sizes and specifications and one PSP specimen. The results show that PSSP specimens exhibit similar cracking resistance and load-bearing capacity but better deformation capacity compared to the PSP specimen. The cracks of PSSP specimens are fully developed and uniformly distributed. Compared with the PSP specimen, which exhibits the HGBs rupture failure, the failure modes of PSSP specimens are primarily determined by concrete crushing, showing ductile characteristics. A refined finite element model is established using ABAQUS for the purpose of simulating the flexural behavior of PSSP specimens. After validation, the PSSP-450A model specimen is used as the benchmark for a parametric study. Numerical results indicate that the maximum mid-span deflection increases by 28.4% as the pre-tensioning control stress of steel strands decreases from 70% f ptk to 30% f ptk. Additionally, the load-bearing capacity increases by 10.8% as the deformed steel bar ratio increases from 0.22% to 0.39%, while a higher steel strand ratio (from 0.32% to 0.58%) leads to a 42.0% increase in the load-bearing capacity. Reducing the pre-tensioning control stress of steel strands can significantly enhance the deformation capacity of PSSP. Increasing the steel strand ratio is a more effective method to improve the load-bearing capacity of PSSP than increasing the deformed steel bar ratio. Finally, the theoretical formulas for the cracking and ultimate moments of PSSP are proposed.</p
Animal health: resistance to antimicrobials and anthelmintics
Get PDFAntimicrobial and anthelmintic drugs are used in large quantities in animal agriculture today. Since their introduction in livestock farming in the mid-20th century, widespread resistance to these medicines has emerged and the supply of novel drugs has diminished in recent decades. Resistant infections in livestock can be challenging to treat, seriously compromising animal health, welfare and productivity, with consequences for food security and economic and environmental outcomes. Furthermore, resistance, particularly to antimicrobials, represents a serious problem for human medicine. This chapter considers the current situation in its historical context, as well as the varied and context-dependent drivers of antimicrobial and anthelmintic use and resistance. A range of technical and policy approaches and their respective challenges are discussed. Possible future scenarios are explored, along with factors which may influence the future trajectory of antimicrobial and anthelmintic resistanc
Evaluation of Mesh-to-Mesh Comparison Methods for Mixed Reality-Based MEP Construction Monitoring
Get PDFCombining Mixed Reality (MR) and Building Information Modeling (BIM) facilitates the projection of virtual BIM data into real construction settings, enabling on-site, real-time monitoring of construction progress and quality. However, current approaches are largely based on human observation to spot differences between the projected BIM model and the actual state on site. Inspecting complex structures, such as Mechanical, Electrical, and Plumbing (MEP) systems, continues to be a difficult task, prone to human error and requiring substantial time. Automation in detecting deviations can streamline and expedite the inspection process. In pursuit of this objective, this document details and reviews four separate algorithms for mesh-to-mesh comparison, targeting the identification and quantification of discrepancies between the 3D mesh obtained on site via MR systems and the mesh geometry of the elements in the BIM model as envisioned
MisCC:Misinformation detection on counterfactual claims
Get PDFCounterfactual claims (CCs) play an important role in everyday conversations, but they are difficult to fact-check automatically and understudied in fact-checking research. We investigated the nuances of misinformation in CCs, considering various potential truth values for antecedents and consequents, as well as causality. Through logic-based analysis, we present a logical theory comprising an algorithm for detecting misinformation in CCs and an approach for ensuring that the result is free of inconsistencies when needed. Finally, we propose a pipeline that integrates large language models (LLMs) with our theory for fact-checking CCs. In this approach, LLMs assist in interpreting natural language and making initial predictions based on their knowledge. Subsequently, our theory verifies the consistency of LLMs’ initial predictions as well as computes CCs’ truth values. We also created and released a comprehensive dataset of CCs, which supports multiple CC-related tasks, including classifying 1) CCs, 2) the verifiability of a statement 3) the truth value of a statement and 4) the truth values of CCs. Then GPT4 and Llama3 with zero-shot were applied as the baseline. Our approach improves their F1 scores for classifying CC’s false class, the misinformation, from 0.55 to 0.64 and 0.46 to 0.61, respectively. Notably, the inconsistency checker only benefits the prediction of true classes. The large portion of false CCs in our dataset represents the portion of misinformation in CCs on social media and the poor performance of GPT4 and Llama3 in classifying the false class highlights the need for more research on fact-checking CCs
Success from the start?:Exploring early relationships between the families of deaf children and professionals
Get PDFUsing evidence from a study of families living on a low income bringing up deaf children, this paper discusses the relationships between professionals such as teachers of deaf children or speech and language therapists with parents and families. By looking at the tools often used as part of these encounters we unpack some of the hidden assumptions in the activities, monitoring and ‘work’ to be done by the parents in the home. There is good evidence of the approaches which are the most effective for supporting the development of interaction and languages. Much less attention has focused on the relationship between the family and the professionals. The competencies approach of preparing for intercultural encounter is challenged by a more equal exploratory approach
A matter of perspective? Differences between adolescent-parent and parent-teacher pairs in responses to the Strengths and Difficulties Questionnaire using a Scottish national cohort study
Get PDFAlthough multiple-respondent scoring methods are increasingly recommended for youth mental health questionnaires, utilisation of parent-only responses remains common in survey research. The substantive, epistemological and methodological ramifications of this perspective gap remain under-explored despite the widespread adoption of youth psychometrics in social survey datasets. Modelling the impact of respondent pair identities on inter-respondent discrepancies in youth mental health questionnaires reveals “whose” responses differ and how measurement error may be patterned in single-respondent models. Comparing Goodman’s Strengths and Difficulties Questionnaire (SDQ) responses from parents, teachers and adolescents themselves, we apply latent difference score modelling to parent-adolescent (age 14, n=2,943) and parent teacher (age 10, n=1,833) pairs from the Growing Up in Scotland birth cohort study and present significant inter-respondent differences in behavioural perceptions between these groups. Higher levels of difficulties are associated with larger inter-respondent discrepancy levels. The impact of gender, housing tenure, finances,family composition, maternal mental health and education on score discrepancies vary in direction, magnitude and significance between SDQ behavioural components. Therefore, discrepancies depend upon characteristics of the each measured behaviour, not a global propensity to dis/agreement. Evaluating the implications of these findings, we advocate for the inclusion of youth self-reporting in survey datasets and discuss how to caveat research with the potential impact of respondent identities on missing perspectives when multiple respondent data are unavailable
The future of research software is the future of research
Get PDFThe use of software is near ubiquitous in research, yet it is still under-recognized despite changes in policy and practice. Despite many successful initiatives to improve the culture around research software, the authors argue that it is essential that the development of research software anticipates changes in the research landscape and continues to support many different people that use it
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