bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metanormative Constructivism as Non-Reductive Perspectivalism
Authors: Paakkunainen Hille 
Published: January 2025

Abstract
Abstract
This chapter critiques extant attempts to clearly distinguish metanormative constructivism from reductive response-dependence views. It proposes a new interpretation of metanormative constructivism as non-reductive perspectivalism, a style of view that is clearly distinct from reductionism. According to non-reductive perspectivalism, normative facts and properties have an irreducibly normative character, yet they ontologically depend upon precisely the sorts of psychological facts that, for the reductive realist, form the reduction base for normativity. This dependence is partly a matter of their “way of being” or mode of existence: specifically, the authority or bindingness of normative properties and facts exists only within an evaluative perspective partly constituted by the attitudes of the agent(s) whom they bind. In articulating the view, the chapter draws upon Kris McDaniel’s recent work in metaphysics and explains how the view provides a way of fleshing out some key emphases of leading constructivists Sharon Street and Christine Korsgaard that otherwise look difficult to understand. The chapter also argues that non-reductive perspectivalism isn’t significantly less plausible than either reductive response-dependence views or typical non-reductive realist views. Indeed, non-reductive perspectivalism has the explanatory advantage of uniquely accounting for a third-/first-person asymmetry in access to normative bindingness. While non-reductive perspectivalism and its component idea of perspectival existence of normativity also raise some new puzzles, the chapter makes a start at developing answers.
Aesthetic Obligation
Authors: Hills Alison 
Published: January 2025

Abstract
Abstract
The normativity of morality and the normativity of aesthetics are often contrasted. Morality is typically regarded as a domain of value but also of obligation, of normative requirements (that is, reasons that require us to act, whose violation is associated with reactive attitudes such as blame). Aesthetics, by contrast, is often taken to be a domain of value but not of obligation, of reasons that are merely enticing: there are no normative requirements in aesthetics and no aesthetic blame. I argue that this “default” view of aesthetic normativity is a mistake. There are aesthetic obligations of a similar type to moral obligations. I give two examples of such obligations. I then draw out some implications about the relationship between aesthetic and moral obligations, and argue that aesthetics can attain a similar normative authority as morality, finishing with some remarks about the future of aesthetic and moral normativity.
The Disguise of the Good
Authors: Thi Nguyen C , Ridge Michael 
Published: January 2025

Abstract
Abstract
In this chapter we argue that a specific form of play we call “striving play” puts a surprising amount of pressure on familiar and influential versions of the ancient “guise of the good” doctrine and standard takes on the “wrong kind of reasons” problem. Striving play highlights the fluidity of our agency in ways that refute standard doctrines in both cases. If our argument is right, then defenders of the guise of the good should focus on the idea that the agent must take the activity they intend to be valuable in some way, rather than the idea that the end they will must be good in some way, and the idea that the rationality of a desire to pursue an object can be grounded only in the value of the object itself should simply be abandoned. The broader methodological lesson is that work at the intersection of normativity and action theory should pay more attention to work in the philosophy of play and games.
Statutory Nuisance: Law and Practice
Authors: Malcolm Rosalind , Pointing John 
Published: January 2025

Abstract
Statutory Nuisance: Law and Practice offers a comprehensive resource for practitioners in the legal and environmental health professions, guiding the reader through the complex practical and legal issues associated with statutory nuisance. It focuses on the problems that local authorities face in enforcing this area, as well as the issues facing those advising defendants. This title examines the role, powers, and duties of the local authorities, and the problems associated with drafting abatement notices and with the prosecution of nuisances. It also covers defences and proceedings brought by private individuals against neighbours and local authority landlords. The book analyses what happens in court, considering in detail the procedure and requirements in appeals against notices and in prosecutions, as well as the grounds for bringing further appeals and judicial review. It covers important recent decisions and key legislation. This new edition provides an update on the various types of statutory nuisance, additional chapters on new forms of statutory nuisance, and expanded material on adjacent areas of enforcement to statutory nuisance, notably those arising from the Anti-Social Behaviour agenda.
The Historical Context of Statutory Nuisance and Public Health Legislation
Authors: Malcolm Rosalind , Pointing John 
Published: January 2025

Abstract
Statutory nuisance is a concept that originated in the huge changes and adverse environmental conditions brought about during the Industrial Revolution in Great Britain. It was fundamental to the sanitary legislation that was first enacted in the 1840s and 1850s, and which continued into the twentieth century in the Public Health Act of 1936. Some of this early sanitary legislation continues in Part III of the Environmental Protection Act 1990 (EPA 1990), either virtually unaltered from its original formulation or in an amended form; some early formulations are to be found in other legislation, such as the Building Act 1984.
Animals
Authors: Malcolm Rosalind , Pointing John 
Published: January 2025

Abstract
At common law, for the keeping of animals to become actionable as a nuisance some ‘extraordinary, non-natural or unreasonable action’ is required. Section 79(1)(f) of the Environmental Protection Act 1990 (EPA 1990) defines as a statutory nuisance: ‘any animal kept in such a place or manner as to be prejudicial to health or a nuisance’.
Miscellaneous Nuisances in Other Legislation
Authors: Malcolm Rosalind , Pointing John 
Published: January 2025

Abstract
Section 79(1)(h) of the Environmental Protection Act 1990 (EPA 1990) provides for ‘any other matter declared by any enactment to be a statutory nuisance’. This provision could apply to prospective forms of statutory nuisance, though in practice it applies to a miscellaneous body of historic nuisances. Those enacted since the EPA 1990 came into effect, such as statutory nuisances from artificial light and insects, have been given their own subsections under section 79 and have not engaged section 79(1)(h).
Tree age affects key fine root morphological traits but does not interfere strongly with (ecto-)mycorrhizal traits
Authors: Qin Yu , Valverde-Barrantes Oscar J , Jin Guangze , Liu Zhili , Freschet Grégoire T 
Published: January 2025

Abstract

Background and Aims
It is assumed that trees should adapt their above and belowground organs as they age. However, most studies to date have quantified these trait adjustments in homogeneous forest stands, confounding the effect of stand aging on soil properties and the intrinsic response of trees to aging.

Methods
Here, we examined 11 morphological, architectural, anatomical and mycorrhizal fine root traits of each of the first five orders for 66 Pinus koraiensis individuals of 16 to 285 years old in northeast China, while accounting for soil characteristics (pH and total C, N and P concentrations).

Key Results
Across all absorptive root orders, Hartig net area and mantle thickness, representative of P. koraiensis reliance on ectomycorrhizal association, displayed an orthogonal pattern to traits describing root economics strategy, specific root length and root tissue density. Hartig net area and mantle thickness were not significantly related to root mycorrhizal colonization intensity and root branching intensity. As tree aged, there was a trade-off between increasing specific root length and decreasing root tissue density in all root orders we measured. Trees facing soil conditions with lower N or P concentrations showed higher dependence on ectomycorrhizal fungi.

Conclusions
This work provides evidence that tree belowground economics strategy can change significantly along the life of trees. In the ectomycorrhizal tree species studied, morphological adjustments are most pronounced, whereas mycorrhizal strategy remains largely consistent. The more conservative root strategy of younger trees than older ones contradicts previous results on the aging of homogeneous tree stands, suggesting that individual tree responses to aging in mixed-aged forests may strongly differ from those in homogeneous forest stands experiencing multiple confounding environmental influences.
Classification-based pathway analysis using GPNet with novel P-value computation
Authors: Lu Hao , Rezapour Mostafa , Baha Haseebullah , Khalid Khan Niazi Muhammad , Narayanan Aarthi , Nafi Gurcan Metin 
Published: January 2025

Abstract
Pathway analysis plays a critical role in bioinformatics, enabling researchers to identify biological pathways associated with various conditions by analyzing gene expression data. However, the rise of large, multi-center datasets has highlighted limitations in traditional methods like Over-Representation Analysis (ORA) and Functional Class Scoring (FCS), which struggle with low signal-to-noise ratios (SNR) and large sample sizes. To tackle these challenges, we use a deep learning-based classification method, Gene PointNet, and a novel $P$-value computation approach leveraging the confusion matrix to address pathway analysis tasks. We validated our method effectiveness through a comparative study using a simulated dataset and RNA-Seq data from The Cancer Genome Atlas breast cancer dataset. Our method was benchmarked against traditional techniques (ORA, FCS), shallow machine learning models (logistic regression, support vector machine), and deep learning approaches (DeepHisCom, PASNet). The results demonstrate that GPNet outperforms these methods in low-SNR, large-sample datasets, where it remains robust and reliable, significantly reducing both Type I error and improving power. This makes our method well suited for pathway analysis in large, multi-center studies. The code can be found at https://github.com/haolu123/GPNet_pathway"&gt;https://github.com/haolu123/GPNet_pathway
Prediction of gene expression using histone modification patterns extracted by Particle Swarm Optimization
Authors: Paul Niels Benjamin , Wolber Jonas Chanrithy , Sahrhage Malte Lennart , Beißbarth Tim , Haubrock Martin 
Published: January 2025

Abstract

Motivation
Histone modifications play an important role in transcription regulation. Although the general importance of some histone modifications for transcription regulation has been previously established, the relevance of others and their interaction is subject to ongoing research. By training Machine Learning models to predict a gene’s expression and explaining their decision making process, we can get hints on how histone modifications affect transcription. In previous studies, trained models were either hardly explainable or the models were trained solely on the abundance of histone modifications. Based on other studies, which used histone modification patterns, rather than their abundance, to identify potential regulatory elements, we hypothesize the histone modification pattern in a gene’s promoter to be more predictive for gene expression. We used an optimization algorithm to extract predictive histone modification profiles.

Results
Our algorithm called PatternChrome achieved an average area under curve (AUC) score of 0.9029 over 56 samples for binary classification, outperforming all previous algorithms for the same task. We explained the models decisions to deduce the effect of specific features, certain histone modifications or promoter positions on transcription regulation. Although the predictive histone modification patterns were extracted for each sample separately, they can be used to predict gene expression in other samples, implying that the created patterns are largely generalizable. Interestingly, the impact of histone modifications on gene regulation appears predominantly indifferent to cellular specificity. Through explanation of the classifier’s decisions, we substantiate established literature knowledge while concurrently revealing novel insights into the intricate landscape of transcriptional regulation via histone modification.

Availability and implementation
The code for the PatternChrome algorithm, the scripts for the analyses and the required data can be found at (https://gitlab.gwdg.de/MedBioinf/generegulation/patternchrome).
Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment
Authors: Hong Seokyoung , Chattaraj Krishna Gopal , Guo Jing , Trout Bernhardt L , Braatz Richard D 
Published: January 2025

Abstract

Motivation
The accurate prediction of O-GlcNAcylation sites is crucial for understanding disease mechanisms and developing effective treatments. Previous machine learning (ML) models primarily relied on primary or secondary protein structural and related properties, which have limitations in capturing the spatial interactions of neighboring amino acids. This study introduces local environmental features as a novel approach that incorporates three-dimensional spatial information, significantly improving model performance by considering the spatial context around the target site. Additionally, we utilize sparse recurrent neural networks to effectively capture sequential nature of the proteins and to identify key factors influencing O-GlcNAcylation as an explainable ML model.

Results
Our findings demonstrate the effectiveness of our proposed features with the model achieving an F1 score of 28.3%, as well as feature selection capability with the model using only the top 20% of features achieving the highest F1 score of 32.02%, a 1.4-fold improvement over existing PTM models. Statistical analysis of the top 20 features confirmed their consistency with literature. This method not only boosts prediction accuracy but also paves the way for further research in understanding and targeting O-GlcNAcylation.

Availability and implementation
The entire code, data, features used in this study are available in the GitHub repository: https://github.com/pseokyoung/o-glcnac-prediction
Young people’s perspectives on barriers to accessing supports and services in Drayton Valley, Canada
Authors: Adisaputri Gianisa , Grant Tonya , Ungar Michael 
Published: January 2025

Abstract
As young people transition to adulthood, they are required to exercise more autonomy when accessing informal psychosocial support and formal health and social services. This qualitative study examines the lived experience of forty-nine young people aged thirteen to twenty-four in Drayton Valley, Canada, and their accounts of accessing support and services in response to mental and physical health needs. Drayton Valley is an economically volatile community dependent on the oil and gas industry. Using data from the Resilient Youth in Stressed Environment project, we investigated the experiences of young people when accessing healthcare, social, and community services. We used a general inductive analysis approach to develop a framework for how young people decide whether or not to engage with support and services. In general, youth reported needing positive knowledge about services, trust in both the organization and providers of services, the independence to seek supports and/or services that they valued, and the need to experience a fit with the mandate of their service provider. Our findings suggest that to increase the use of supports and services, policies need to better account for young people’s experiences when seeking help.
Development and validation of a measure to assess patient experience of needling of arteriovenous fistulas or grafts for haemodialysis access: the NPREM
Authors: Moore Currie , Busby Amanda , Flanagan Rebecca , Ellis-Caird Helen , Awan Faizan , Paul Tarsem , Fielding Catherine , McCafferty Kieran , van der Veer Sabine N , Farrington Ken , Wellsted David 
Published: January 2025

Abstract

Background
Needling is a key step in haemodialysis. Research suggests needling experience is sub-optimal; however, no validated measure exists to inform improvements. We addressed this by developing the Needling Patient Reported Experience Measure (NPREM).

Methods
We used mixed methods and co-production. All participants were adults with working fistulas/grafts from eight UK kidney centres.
Phase 1: Developing concepts and items, In interviews (n=41), we explored patients’ needling experience and identified key aspects of needling using thematic analysis. This informed the 98-item NPREM(v0.1).
Phase 2: Piloting the measure Cognitive interviews (n=16) assessed face validity. Items were amended or removed, yielding a 48-item NPREM(v0.2).
A pilot survey (n=183) examined initial psychometric properties. NPREM(v0.2) showed good internal consistency (Cronbach's alpha=0.95). Review of analyses resulted in a 35-item NPREM(v0.3).
Phase 3: Evaluating the measure's dimensionality, validity, and reliability Patients (n=468) completed the NPREM(v0.3), Vascular Access Quality of Life (VASQoL), EuroQol 5-Dimension-5-Level (EQ5D-5L), Patient Activation Measure (PAM), with a sub-set completing a follow-up NPREM (n=99). Items were evaluated with 28 items retained in the NPREM(v1.0). Confirmatory factor analysis confirmed a unidimensional model fit (CFI=0.899). Validity of the NPREM(v1.0) was good [convergent: VASQoL (r=0.60) and overall experience (r=0.79); divergent: EQ-5D (r=-0.31), EQ-5D VAS (r=0.24) and PAM (r=0.17)]. Test-retest scores were strongly correlated (r=0.88), demonstrating high reliability. Known-groups validity was demonstrated between centre scores (range 5.21 (SD 1.20) to 5.94 (SD 0.75)).

Conclusion
The NPREM measures patient experience of needling for haemodialysis. It offers kidney services a means of assessing needling experience, informing patient-focused clinical and service improvements.
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype
Authors: Zhang Limin , Starr Julian , Ford Bruce , Reznicek Anton , Zhou Yuxuan , Léveillé-Bourret Étienne , Lacroix-Carignan Étienne , Cayouette Jacques , Smith Tyler W , Sutherland Donald , Catling Paul , Saarela Jeffery M , Cui Hong , Macklin James 
Published: January 2025

Abstract
It is well-known that the use of vocabulary in phenotype treatments is often inconsistent. An earlier survey of biologists who create or use phenotypic characters revealed that this lack of standardization leads to ambiguities, frustrating both the consumers and producers of phenotypic data. Such ambiguities are challenging for biologists, and more so for Artificial Intelligence, to resolve. That survey also indicated a strong interest in a new authoring workflow supported by ontologies to ensure published phenotype data are FAIR (Findable, Accessible, Interoperable, and Reusable) and suitable for large-scale computational analyses.
In this article, we introduce a prototype software system designed for authors to produce computational phenotype data. This platform includes a web-based, ontology-enhanced editor for taxonomic characters (Character Recorder), an Ontology Backend holding standardized vocabulary (the Cared Ontology), and a mobile application for resolving ontological conflicts (Conflict Resolver). We present two formal user evaluations of Character Recorder, the main interface authors would interact with to produce FAIR data. The evaluations were conducted with undergraduate biology students and Carex experts. We evaluated Character Recorder against Microsoft Excel on their effectiveness, efficiency, and the cognitive demands of the users in producing computable taxon-by-character matrices.
The evaluations showed that Character Recorder is quickly learnable for both student and professional participants, with its cognitive demand comparable to Excel’s. Participants agreed that the quality of the data Character Recorder yielded was superior. Students praised Character Recorder’s educational value, while Carex experts were keen to recommend it and help evolve it from a prototype into a comprehensive tool. Feature improvements recommended by expert participants have been implemented after the evaluation.
Prognostic impact of 1-year permanent pacemaker implantation after mitral valve surgery with the Cox-maze procedure
Authors: Lee Jun Ho , Kim Yun Jin , Kim Ji Eon , Song Kyungsub , Shin Yonghoon , Jung Jae Seung , Son Ho Sung , Lee Seung Hyun , Kim Hee Jung 
Published: January 2025

Abstract

OBJECTIVES
This study aimed to evaluate the prognostic impact of permanent pacemaker (PPM) implantation within the first year after mitral valve (MV) surgery combined with the Cox-maze procedure, focusing on long-term outcomes, including overall mortality, infective endocarditis (IE) and ischaemic stroke.

METHODS
We conducted a retrospective cohort study using data from the National Health Insurance Service (NHIS) in South Korea, identifying 10 127 patients who underwent MV surgery with the Cox-maze procedure between 2005 and 2020. Patients were classified into the PPM and non-PPM groups based on PPM implantation within 1 year postoperatively. The primary outcome was overall mortality, and secondary outcomes included risk factors for overall mortality, IE and ischaemic stroke. Multivariable Cox proportional hazards regression and Fine-Gray competing risk models were utilized for statistical analysis.

RESULTS
Of the total cohort, 178 patients (1.76%) underwent PPM implantation. The overall mortality during the follow-up period was 20.5%, with no significant difference between the PPM and non-PPM groups. PPM implantation was not a significant risk factor for overall mortality (hazard ratio [HR], 0.825; 95% confidence interval [CI] 0.598–1.140; P = 0.244) or ischaemic stroke. However, PPM implantation was associated with a significantly increased risk of IE (HR, 2.015; 95% CI 1.179–3.442; P = 0.010).

CONCLUSIONS
PPM implantation within the first year after MV surgery with the Cox-maze procedure does not significantly impact long-term mortality or ischaemic stroke risk but is associated with an increased risk of IE. The Cox-maze procedure remains advisable for patients with atrial fibrillation undergoing MV surgery.