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A center-anchored adaptive hierarchical graph neural network with application in structure-aware recognition of enzyme catalytic specificity
No full textData Availability:
The data and source code are available at https://github.com/liyigerry/CAAH-GNN.Non-Euclidean modeling of biomolecules such as enzymes has been advanced by utilizing graph neural networks (GNNs). While existing whole-molecule modeling approaches offer significant advantages, they present two primary challenges: optimizing long-range interactions within the enzyme molecule and ensuring model interpretability. Furthermore, current GNN-based enzyme modeling methods pay insufficient attention to the hierarchical structure of biological functions. To address these challenges, we propose a novel Center-Anchored Adaptive Hierarchical GNN (CAAH-GNN) model that integrates a center-anchored method with an adaptive hierarchical strategy for structure-aware recognition of enzyme catalytic specificity. Our model features three key characteristics: (1) It autonomously identifies and integrates local key residues within enzyme molecules while embedding global graph information into each node's features, significantly enhancing prediction accuracy. (2) The spherical spatial radius is adaptively learned using a two-step hierarchically sampling method. Compared to full-molecule models, this approach reduces spatial complexity more than 80 %. (3) Our model exhibits strong generalization performance and interpretability, as it is not tailored to specific enzyme families and does not remove any nodes during training. Extensive experiments based on two enzyme datasets and various graph convolution kernels demonstrate that CAAH-GNN outperforms baseline models and other hierarchical strategy models in prediction accuracy. In summary, our research not only introduces a novel GNN-based enzyme modeling approach but also provides a new perspective and a tool for enzyme engineering.This work was supported by the National Natural Sciences Foundation of China [grant number 62366002] and the Scientific Research Fund of the Yunnan Provincial Department of Education [grant number 2024Y852]
HSVFormer: Robust and Unsupervised HSV-based Transformer Framework for Low-Light Image Enhancement
Get PDFThe following three factors restrict the application of existing low-light image enhancement methods: corruptions induced by the light-up process, color distortion, and a restricted generalization capacity due to limited paired training data. To address these limitations, we first combine HSV theory and Transformer, proposing a robust unsupervised low-light image enhancement framework, named HSVFormer. Secondly, we introduce brightness disturbance and design an unsupervised value enhancement network, which estimates brightness information and restores degraded brightness information to obtain enhanced reflectance. Finally, we utilize the V-subspace and devise a value-guided multi-head channel self-attention to capture brightness representations of regions with different brightness conditions and guide the modeling of non-local interactions. Experiment results on publicly available datasets demonstrate that HSVFormer can achieve superior performance compared with state-of-the-art approaches. The code is available at https://github.com/m0fig/HSVFormer.10.13039/501100001809-National Natural Science Foundation of China;
10.13039/100006190-Research and Development
Microplastic ingestion by an aquatic ciliate: Functional response, modulation, and reduced population growth
Get PDFData availability:
The data underpinning this publication can be accessed from Brunel University of London's data repository, Brunelfigshare under a CC BY licence: https://doi.org/10.17633/rd.brunel.27960867.Graphical abstract: download high-res image at https://ars.els-cdn.com/content/image/1-s2.0-S0048969724084304-ga1_lrg.jpg (71KB); download full-size image at: https://ars.els-cdn.com/content/image/1-s2.0-S0048969724084304-ga1.jpg. Three main findings underpinning microplastic feeding by a small ciliate. Microplastics are readily taken up by ciliates which then represent a reservoir for those pollutants. After egestion, microplastics form a pellet; hence the protists modulate the availability of the pollutant. Population growth declines with microplastic concentration. The photos were taken during the experiment at 200× magnification and show plastic microbeads inside the ciliates and after egestion.Microplastic particles are ubiquitous in aquatic environments and are considered a major threat to the large range of heterotrophic organisms that involuntarily consume them. However, there is current uncertainty around the mechanisms underpinning microplastic uptake by aquatic consumers and the consequences for both the fate of the microplastics and the growth potential of consumer populations. We performed a feeding experiment, exposing a model freshwater ciliate, Tetrahymena pyriformis, to six different microplastic concentrations and measured microplastic uptake and population growth over the course of several generations. Microplastic uptake increased in a saturating fashion with concentration, consistent with a Type II functional response, with a maximum feeding rate of 22 microplastic particles individual−1 h−1. Interestingly, microplastic uptake decreased through time and we observed that, after egestion, microplastic particles aggregated, rendering them too large for re-consumption. We built and tested a simulation model which matched rates of microplastic uptake when incorporating functional response parameters and assuming 50 % immobilisation of microplastics after egestion. Nevertheless, ciliate population growth was compromised by the presence of microplastics, decreasing by 43 % over the full microplastic concentration range. Taken together, our results demonstrate the potential for aquatic ciliates to play an important role in the uptake, transfer, and modification of microplastics in freshwater environments with associated negative impacts on population fitness.This research was supported by German Academic Exchange Service (DAAD) scholarships awarded to HM and SG, and Leverhulme Trust grant RPG-2021-030 awarded to AR, DP & JR
Harmonising Neurodiversity in Musical Theatre Training: A Teacher-Student Dialogue
Get PDFAt the conclusion of an undergraduate module that embedded inclusive approaches to singing musical theatre, the following dialogue between Grant (teacher) and Libby (student) emerged about co-creating neuroinclusive learning spaces.
This exchange seeks to highlight how an egalitarian learning environment can benefit both neurodiverse and neurotypical students and staff, while fostering more dynamic learning experiences
Boosting intellectual capital and digital maturity of SMEs: an investigation of enterprises in an Italian Southern tourist district
Get PDFPurpose:
This study intends to analyze the relationship between the digital maturity of SMEs and intellectual capital, investigating the determining factors. Starting from the endowment in terms of intellectual capital and evaluating Management Style, Decision-Making Competences, and Business Network, a model is proposed aiming to provide a comprehensive measure of SMEs’ digital maturity and thus to improve understanding and, consequently, effectiveness. The empirical analysis allows assessing the validity and applicability of the suggested model, providing valuable insights for the improvement of digital strategy and competitiveness of SMEs in the Amalfi Coast Tourist District (Italy), with evident implications also for policymakers and the community.
Design/methodology/approach:
A mixed-methods research strategy was utilized to confirm research hypotheses that were derived from literature review. The field study was organized into two separate phases: the first phase, which is qualitative, employed focus groups comprising key stakeholders (managers and entrepreneurs) from various companies within the Amalfi Coast Tourist District. This phase adhered to the principles of homogeneity (to facilitate deeper discussions) and heterogeneity (to allow for a broader range of viewpoints among participants). The insights gathered from these preliminary focus groups informed the subsequent quantitative phase. In this second phase, structured interviews were conducted using a questionnaire to probe the participants’ views on digital maturity. This analysis involved 94 companies, all part of the Amalfi Coast Tourist District, assessing their digitalization levels and highlighting key management attributes. Logistic regression was applied to quantitatively analyze the data, effectively assessing the impact of various independent variables (such as Management Style, Decision-Making Competencies and Business Network) on the dependent variable, digital maturity. Employing both qualitative and quantitative methods provides a thorough and nuanced understanding of the digital maturity landscape within the specified context.
Findings:
The main results suggest the existence of a correlation between the analyzed variables and digital maturity. Innovation, indeed, increases by applying a data-driven leadership style. Intellectual capital (measured in its three components of human capital: decision-making competences; structural capital: management style; and relational capital: business network) influences digital maturity, although some of the variables used are not equally weighted.
Originality/value:
The main contribution of this article is to provide an in-depth understanding of the company components that favor digital maturity, to support strategic choices oriented towards a conscious digital transition. The results enrich the existing literature on intellectual capital in terms of its contribution to the digitalization of organizations, which can be a critical success factor in the context of SMEs
Towards a Meaningful Understanding of Organizational Leaders' Localized and Contextualized Implementation of UNSDGs in Bahrain's Changing Energy Sector Businesses
Get PDFSummary:
* This paper examines the grand socio-economic-ecological sustainability challenges when energy sector business leaders try to implement the UNSDGs. We propose a reconceptualization of leadership that includes a new set of meaningful practices, which shows “how” to address wider sustainability constraints effectively.
* UNSDGs/Global Goals are a set of seventeen objectives intended as a blueprint for the promotion of worldwide equality, peace, and prosperity.
* Traditional Network Leadership is a set of interlinked, operational capabilities that leaders may use to address organizations' resource constraints and inequalities.
* Strategic, Sustainable Network Leadership evinces four meaningful sets of leaders' perceptions, enunciations, and practices on how a new set of capabilities and change processes can help to resolve wider socio-economic-ecological challenges.Data Availability Statement:
The data that support the findings of this study are available from the corresponding author upon reasonable request.Supporting Information is available online at: https://onlinelibrary.wiley.com/doi/10.1002/jsc.2629#support-information-section .Despite Network Leadership scholarship's emphasis on localizing and contextualizing leadership practices during organizational change, there is a dearth in the current theoretical framings on “how” to address the implementation failure of localization and contextualization towards broader SDGs/organizational sustainability. This paper fills this gap by offering deeper insightful theoretical and practical understanding of how organizational leaders can address socio-economic and ecological sustainability concerns, and how a more meaningful reconceptualization and implementation of leadership practices can help Business and Management academics and practitioners address the organizational growth, human, and ecological well-being dilemma in the energy sector. By drawing on Network Leadership, SDG, organizational change literature and 26 senior leaders' semi-structured interviews, this study uses (Braun and Clarke's 2006) Thematic Analysis Procedure to resolve the theoretical and practical implementation lag in Business and Management scholarship. We contribute 4 novel implementation practices: (1) Operational; (2) strategic; (3) cultural and (4) interorganizational knowledge exchange alignment and a model on wider socio-economic-ecological well-being. Showing ‘what’ leadership characteristics are needed and “how” to meaningfully reconceptualize the dominant localization and contextualization model of organizational change towards broader sustainability goals has been practically and scholarly overdue
What price near-zero emissions? Energy and economic modelling for the UK using real-world data to 2050 and beyond
Get PDFAcknowledgement: This updated version of the 7see model is supported by the Institute of Energy Futures at Brunel University of London. We would like to thank reviewers for their helpful comments.Current measures cannot deliver net zero atany point in the foreseeable future. All policy underpinning ‘net zero by 2050’ should be revisited, and new policy should look beyond 2050. Risks arise pursuing netzero from unintended consequences such as the likelihood of stranded assets or becoming locked into technological pathways with short-term uses but long-term disadvantages.Development of the 7see framework and model was supported by Arup’s internal Design and Technical Fund
Cervical ripening at home or in hospital during induction of labour: the CHOICE prospective cohort study, process evaluation and economic analysis
Get PDFPlain Language Summary: Labour is often started artificially. This is called induction of labour. Induction of labour is usually planned when it is safer to end the pregnancy. The first stage of induction of labour – ‘cervical ripening’ – means using medication or a balloon to open the neck of the womb. Years ago, cervical ripening only happened in hospitals, but now many women are offered ‘home cervical ripening’. This means that induction of labour starts in hospital then women go home while the treatment starts working. This could mean that women spend less time in hospital. They may prefer to be at home. However, home cervical ripening may be less safe because problems may not be noticed as quickly.
We looked at whether home cervical ripening is safe, acceptable to women and their partners, and good value for money. We used information about women and babies that is usually stored in electronic maternity notes. We studied women who had induction of labour in 26 United Kingdom maternity hospitals. Women were told about the study and could choose not to be included.
Our main question was ‘does home cervical ripening increase the chance that a baby needs care in a neonatal unit, compared with cervical ripening in hospital?’ We surveyed women about their experience of induction of labour and any financial costs to them. We interviewed women, partners, doctors and midwives to hear what they thought about home cervical ripening.
Fewer women than expected had home cervical ripening. We could not be certain that home cervical ripening with a balloon is as safe for babies as cervical ripening in hospital using medication. Home cervical ripening cost almost £1000 less per woman than in-hospital cervical ripening. Home cervical ripening was acceptable to women when they felt well looked after, when maternity staff communicated well with them, and when they felt they had a choice about going home.Background:
Around one in three pregnant women undergoes induction of labour in the United Kingdom, usually preceded by in-hospital cervical ripening to soften and open the cervix.
Objectives:
This study set out to determine whether cervical ripening at home is within an acceptable safety margin of cervical ripening in hospital, is effective, acceptable and cost-effective from both National Health Service and service user perspectives.
Design:
The CHOICE study comprised a prospective multicentre observational cohort study using routinely collected data (CHOICE cohort), a process evaluation comprising a survey and nested case studies (qCHOICE) and a cost-effectiveness analysis.
The CHOICE cohort set out to compare outcomes of cervical ripening using dinoprostone (a prostaglandin) at home with in-hospital cervical ripening from 39 weeks of gestation. Electronic maternity record data were collected from 26 maternity units. Following pilot analysis, the primary comparison was changed to ensure feasibility and to reflect current practice, comparing home cervical ripening using a balloon catheter with in-hospital cervical ripening using any prostaglandin from 37 weeks of gestation. Analysis involved multiple logistic regression for the primary outcome and descriptive statistics for all other outcomes.
The qCHOICE study reported descriptive statistics of quantitative survey data and thematic analysis of focus group and interview data.
The economic analysis involved a decision-analytic model from a National Health Service and Personal Social Services perspective, populated with CHOICE cohort and published data. Secondary analysis explored the patient perspective utilising cost estimates from qCHOICE data.
Setting:
Twenty-six United Kingdom maternity units.
Participants:
Women with singleton pregnancies at or beyond 37 weeks of gestation having induction with details of cervical ripening method and location recorded.
Main outcome measures:
CHOICE cohort
Neonatal unit admission within 48 hours of birth for 48 hours or more.
qCHOICE:
Maternal and staff experience of cervical ripening.
Economic analysis:
Incremental cost per neonatal unit admission within 48 hours of birth avoided.
Data sources:
Electronic maternity records from 26 maternity units; survey and interviews with service users/maternity staff; focus groups with maternity staff; published literature on economic aspects.
Results:
CHOICE cohort: A total of 515 women underwent balloon cervical ripening at home and 4332 underwent in-hospital cervical ripening using prostaglandin in hospitals that did not offer home cervical ripening. Neonatal unit admission within 48 hours of birth for 48 hours or more following home cervical ripening with balloon was not increased compared with in-hospital cervical ripening with prostaglandin. However, there was substantial uncertainty with the adjusted analysis consistent with a 74% decrease in the risk through to an 81% increase.
qCHOICE:
Important aspects of service users’ experience of home cervical ripening were quality of information provided, support and perception of genuine choice.
Economic analysis:
Home cervical ripening with balloon led to cost savings of £993 (−£1198, −£783) per woman and can be considered the dominant strategy.
Limitations:
Circumstances relating to the COVID-19 pandemic limited the number of participating maternity units and the duration for which units participated. Low numbers of women having at-home cervical ripening limited the power to detect differences in safety, effectiveness, cost and acceptability between study groups.
Conclusions:
Home cervical ripening using balloon catheter may be as safe for babies as using prostaglandins in hospital in low and moderate-risk groups, but there is substantial uncertainty. Home cervical ripening with balloon is likely to be cost saving. Impacts on workload, service user and staff experiences were complex.
Future work:
Future research should focus on optimising experience and logistics of home cervical ripening within busy maternity services.
Study registration:
Current Controlled Trials ISRCTN32652461.This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: NIHR127569).https:doi.org/10.13039/50110000066
Exploring Polygenic Risk and Neuroimaging Parameters across the Alzheimer's disease Spectrum
Get PDFPoster presentation at AAIC 2024, Philadelphia, PA, USA, 28 July - 1 August 2024.Background:
Sporadic Alzheimer’s disease (AD) accounts for >90% of AD cases, of which 70% are thought to be due to a combination of several risk genes. Of these, Apolipoprotein E (APOE) is the most studied gene. Given that the APOE ɛ4 risk variant is found in ∼14% of the general population and ∼37% of the AD population, APOE ɛ4 is neither necessary nor sufficient to cause AD on its own. Investigating polygenic scores may lead to a better predictive model of AD, by studying many genes simultaneously, and increase understanding of how gene-gene interactions may contribute to AD. The aim of this research was to review systematically papers exploring polygenic risk and neuroimaging parameters across the AD spectrum.
Method:
Literature searches were conducted on three online databases: PubMed, Scopus, and Web of Science, between January–March 2023. All articles and early access papers, written in English, and on humans, were included. Reviews and systematic reviews were excluded. Papers were cross-checked by three independent reviewers. Selected papers were assessed with a customised set of criteria to determine quality papers for this review and to avoid biases.
Result:
3264 papers were found, of which 66 were eligible for review. Some papers used more than one imaging modality, therefore, there were a total of 80 studies: 49 structural, 8 functional, and 23 neuromolecular, covering regional and whole-brain metrics. Polygenic risk scores and polygenic hazard scores are associated with regions vulnerable to AD, e.g., hippocampi, and entorhinal cortices. These findings are consistent across the three imaging modalities, and across the AD spectrum. In some cases, significant associations between polygenic scores and neuroimaging parameters are only present when including, or excluding, APOE. There are discrepancies in whether APOE increases, or decreases, strength of associations.
Conclusion:
This review demonstrates that attention must divert away from APOE since numerous genes impact brain architecture and connectivity, and it is their combined effect that is of key interest in sporadic AD. It highlights the challenges faced, and the intricacies that must be thought about, when constructing polygenic scores
CO2-Based Power Cycles: What Effect Does Additive Molecular Complexity Have on the Cycle Layout?
Get PDFSince their inception, CO2 power cycles have gained prominence for their superior performance and compactness. However, the efficiency of the simple supercritical CO2 cycle is hindered by relatively large temperature differences in the recuperator, leading to increased exergy destruction. Although complex cycles like the recompression or precompression cycles can reduce recuperator irreversibility, their higher complexity and additional equipment requirements raise the cost of the power plant.
This paper aims to demonstrate that recuperator irreversibility in a simple recuperated transcritical cycle can be alleviated using CO2-based mixtures, without resorting to complex cycles. This is achieved by comparing the efficiencies of simple and recompression cycles using CO2-based mixtures with nine additives of various molecular complexities: H2S, SO2, C3H8, C4H10, C5H12, C6H6, C4H4S, TiCl4, and C6F6. The effect of additive molar fraction (ranging from 0.05 to 0.5) on the efficiency of both cycles is examined.
Thermal efficiency optimisation reveals a correlation between the efficiency difference of the simple and recompression cycles and the molecular complexity of the working fluid. The reduction in recuperator irreversibility is attributed to the decrease in the difference in the isobaric specific heat capacities between the streams in the recuperator with the use of complex additives. Consequently, the advantage of a recompression cycle diminishes as the aggregate molecular complexity of the working fluid increases. Simple additives like H2S, SO2, and C3H8 result in recompression cycles outperforming simple recuperated cycles by 4% to 8% in terms of absolute thermal efficiency, depending on the additive and its molar fraction. Conversely, more complex additives like C4H4S, TiCl4, and C6F6, exhibit thermal efficiencies in simple recuperated cycles comparable to those of recompression cycles. The additive molar fraction at which both cycles achieve similar performances depends on the molecular complexity of the additive; the more complex the additive, the lower the additive molar fraction required to create a complex working fluid. Moreover, the split fraction in recompression cycles exhibits a similar correlation with molecular complexity as observed in the efficiency difference, suggesting that recompression cycles will morph into simple recuperated cycles as molecular complexity increases.
In conclusion, the use of additives provides an additional dimension through which the efficiency of CO2 cycles can be optimised, enabling improved performance without the need for complex cycles.This work was supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 814985
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