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Prediction and quality assessment of protein quaternary structure models using the MultiFOLD2 and ModFOLDdock2 servers
Get PDFUnderstanding the structures of protein complexes is pivotal for breakthroughs in health, agriculture, bioengineering, and beyond. MultiFOLD2 and ModFOLDdock2 are leading servers for protein quaternary structure prediction and model quality assessment, respectively. MultiFOLD2 includes integrated stoichiometry prediction for quaternary structures and improved sampling and scoring, leading to high performance in continuous independent benchmarks such as CAMEO. ModFOLDdock2 uses a hybrid consensus approach to generate global and local quality scores for predicted quaternary structures. ModFOLDdock2 is integrated with MultiFOLD2 while also being available as a stand-alone server, enabling the independent evaluation of quaternary structure models from any source. Both servers have been independently rigorously evaluated, demonstrating high performance and ranking among the top servers in their respective categories in the recent CASP16 experiment. The MultiFOLD2 and ModFOLDdock2 servers are freely accessible through user-friendly web interfaces at https://www.reading.ac.uk/bioinf/
A comprehensive protocol to study the effects of multilingualism on cognition and the brain in patients with progressive neurological diseases
Get PDFMultilingualism, the cognitively demanding experience of speaking multiple languages, has been linked to measurable effects on cognition and brain structure and function. These effects, attributed to the constant activation of multiple languages, may contribute to cognitive reserve, expressed as delayed cognitive decline in multilinguals diagnosed with progressive neurological diseases such as Alzheimer’s, Huntington’s and Parkinson’s diseases, and Multiple Sclerosis. However, the evidence remains inconsistent due to methodological shortcomings, including variations in defining multilingualism and inadequate accounting for other lifestyle factors that may also promote cognitive reserve. To address these limitations, we developed a comprehensive protocol which incorporates detailed measurement of factors that are related to cognitive reserve, including multilingual experiences, standardized clinical and experimental cognitive assessments suitable for multilingual patients diagnosed with the above progressive neurological diseases, as well as thorough neuroimaging testing batteries. This protocol enables systematic investigation across linguistic and cultural contexts, facilitating cross-laboratory data pooling to advance understanding of multilingualism’s neuroprotective potential in aging and disease. Its purpose is to spearhead an open-ended project which will keep adding to an increasing dataset of multilingual patients internationally; crucially, it sets a new standard in how to gather evidence investigating multilingualism as a factor contributing to cognitive reserve
The application of condition C on cataphoric pronoun resolution for Chinese learners of English: evidence from eye-tracking during reading
No full textPrevious research shows that encountering cataphoric pronouns triggers an active search for antecedents, a process constrained by Binding Condition C, which prohibits co-reference when the potential antecedent is c-commanded by the pronoun. While most studies have focused on L1 speakers, findings concerning L2 learners remain inconclusive. This study employs eye-tracking and an offline task to examine the application of Condition C among Chinese learners of English. Results reveal that although Chinese learners of English initiate an active search and exhibit awareness of Condition C in offline tasks, they fail to apply this constraint during online processing. We conclude that while Chinese learners of English possess explicit knowledge of Condition C, limitations in syntactic representation and insufficient exposure hinder its real-time implementation
I moderni Numidi: Numidia, Numidians, and modern Italian imperialism
Get PDFDuring the years of Italy's empire in Africa, the Punic Wars were a frequent point of reference in imperial propaganda. However, since Carthage was viewed as a city foreign to Africa, Italian ideologues of empire required an ancient enemy of Rome that was indigenous to Africa to serve as a classical counterpart for African resistance to modern Italian imperialism. This is where the Jugurthine War came in. This essay looks at two key moments of Italian receptions of the Jugurthine War: one in a Latin poem from towards the beginning of Italy's imperial endeavours in Africa and another from when the Italian Empire was at its height, under Fascism. The essay ends by considering how a Latin author who was half-Numidian—Apuleius—was used as a model of acculturation to offset the idea that Numidia and Numidians were always the enemies of Rome
Impact of chronic consumption of probiotics, oats, and apples on expression of genes related to bile acids, lipid, gut peptides, and inflammation in peripheral monocular cells - Findings from the CABALA study
Get PDFPurpose: Chronic intakes of functional foods (probiotics, apples and oats) have been reported to have beneficial effects on hepatic lipid regulation and glycaemic control, but mechanistic human studies humans are limited. An ex-vivo study was performed to determine the chronic effects of probiotics, oats, and apples on the expression of genes related to markers of cardiometabolic health in peripheral blood monocular cells (PBMC).
Methods: In this CABALA sub-study (n=59/61, age: 52±12y), blood PBMC were also isolated before and 8 weeks after the daily consumption of either a probiotic with bile salt hydrolase activity (Lactobacillus reuteri), porridge oats, Renetta Canada apples or a control. Relative PBMC mRNA gene expression was determined and correlations performed between the fold change in response to the functional interventions and change in cardiometabolic disease risk markers.
Results
Relative to baseline, there was an upregulation in the PBMC TLR4 mRNA expression in the control compared with the probiotics and apples groups (p≤0.024). Moderate inverse correlations were found between the fold change in GPBAR1 mRNA expression and change in plasma total and secondary BAs, HMGCR and SREBF1 mRNA gene expressions and high-density lipoprotein-cholesterol, and SREBF1 and GIPR mRNA gene expressions and glucose. TLR4 and TNFSF14 mRNA gene expressions were associated with pro-inflammatory cytokines (p=0.05).
Conclusion
Probiotic and apples interventions attenuated the upregulation in PBMC TLR4 mRNA expression observed with the control. Correlations between fold change in mRNA gene expression and changes in cardiometabolic disease risk markers in response to the functional interventions were in agreement with previous studies
Seeking success & confronting failure: the British Army's campaigns in Ireland and Northern Ireland 1919-2007
No full textDuring the twentieth century and the early years of the twentieth century the British Army,uniquely among European armies fought two domestic counterinsurgency campaigns. This monograph will challenge the judgements concerning these campaigns in Ireland and Northern Ireland; the verdict on the first is one of sub-optimal military effectiveness which produced a clear defeat and the second one was an 'honourable draw'.In both cases the British state was obliged to defend the political integrity of its sovereign territory
Essays on cryptocurrency markets
No full textThis thesis investigates cryptocurrency markets. The first empirical chapter
studies the Bitcoin volatility forecasting performance between popular traditional
econometric models and machine learning techniques. We compare the 1-day to 2-
month ahead forecasting performance of the Long Short-Term Memory (LSTM) and
a hybrid Convolutional Neural Network-LSTM (CNN-LSTM) model to the traditional models. We find that neural networks outperform Generalised Autoregressive
Conditional Heteroscedasticity (GARCH) models for all forecasting horizons. Furthermore, the LSTM model outperforms the Heterogeneous Autoregressive (HAR)
model and by integrating the Markov Transition Field (MTF) into the CNN-LSTM
model, we achieve superior short-term predicting results, particularly for the 7-day
ahead forecasts.
In the second empirical study, we document strong and significant evidence
of cryptocurrency time series momentum (TSMOM) using volume-weighted market returns. The volume-weighted winner minus loser portfolios outperform other
TSMOM strategies, generating 0.94% daily returns with an annualised Sharpe ratio
of 2.17. Our findings cannot be fully explained by market, size, and momentum
factors, are not subsumed by cross-sectional or MAX momentum returns, and are
robust against wash trading concerns. Our results suggest that trading volume may
provide signals to create profitable strategies in cryptocurrency markets.
The final empirical chapter investigates the relationship between cryptocurrency
names and trading volume, focusing on name fluency, structural complexity, and
name-ticker similarity. We observe that less fluent and simpler structured names
attract higher future trading activities, indicating investor preference for distinct
coins. A negative correlation between name-ticker similarity and volume suggests
that less obvious connections between names and tickers are favoured. Furthermore,
name fluency shows an asymmetric effect, with low to moderate fluency modestly
increasing abnormal trading activity, while highly fluent names see significantly
larger declines due to investor aversion. Our findings reveal investor behaviour
biases linked to linguistic factors, providing insights for cryptocurrency investors,
issuers, and regulators
The First in Family pilot podcast
Get PDFThe aim of the First in Family pilot podcast project was for students and staff to work together to produce a podcast which would support the student experience and recruitment of first-generation students (FGS). This case study reports on the project, which used funds from the University of Reading’s Partnerships in Learning and Teaching (PLanT) scheme to enable the pilot to be realised and market research data to be collected and reviewed. We explain how we researched and investigated podcast format, production and broadcast, as well as brainstorming key issues which affect FGS. We then produced a pilot episode for further market research. We present our ways of working, indicate what feedback we gleaned from the market research, and how we intend to use the feedback to apply for greater funding to produce and broadcast a monthly or bi-weekly podcast for FGS
Some remarks on critical sets of Laplace eigenfunctions
No full textWe study the set of critical points of a solution to Delta u = lambda u, and in particular components of the critical set that have co-dimension 1. We show, for example, that if a second Neumann eigenfunction of a simply connected polygon P has infinitely many critical points, then P is a rectangle
Magnetic silhouettes in Jupiter's non‐auroral ionosphere
Get PDFFor decades, the influence of Jupiter's higher order magnetic field on its non-auroral ionosphere has remained enigmatic. NASA's Juno spacecraft has revealed great complexities in the Jovian magnetic field, with significant features in the sub-auroral regions aligning with puzzling structures identified in near-infrared emissions from the ionosphere. Here, we directly compare ground-based measurements of Jupiter's ionosphere with the latest magnetic field models borne in the era of Juno and reveal aspects of global ionosphere-magnetosphere coupling not previously explored. Ionospheric emissions exhibit either enhancements or reductions where the surface field is weakest and are found to correlate with both the strength and geometry of the magnetic field, where the latter is more dominant and with a unique control in each magnetic hemisphere. Therefore, we have illustrated that there may be distinct electrodynamic processes responsible for shaping Jupiter's non-auroral ionosphere in these key regions