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Daly T. A philosophy of science approach to the amyloid hypothesis of Alzheimer's disease. Eur J Neurosci 2024; 60:4707-4722. [PMID: 39119857 DOI: 10.1111/ejn.16500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/04/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
Disputes about the scientific validity of the amyloid-β hypothesis of Alzheimer's disease have been held since the early 1990s, with little constructive progress made between opposing sides despite recent therapeutic progress. Here, I argue that philosophy of science can improve the chance of constructive debate by giving researchers technical language to describe and assess scientific progress. To do so, I interpret the amyloid hypothesis using a modified version of the research programme concept from philosopher of science Imre Lakatos. I first outline the amyloid-β hypothesis and study critiques of its central place in Alzheimer's research. Then, I draw on the complexity of amyloid-β and Alzheimer's research to discuss the limits of using concepts from popular philosophers of science Karl Popper or Thomas Kuhn, before finally arguing that an adaptation of the research programme concept can foster constructive debates about the science of Alzheimer's and within it. I will argue that the amyloid-β hypothesis has contributed to significant progress in the Alzheimer's field based on what Lakatos called the "positive heuristic" (motivating the programme to test its predictions) and the "negative heuristic" (protecting the programme from refutation). I consider the amyloid research agenda to be progressive despite the fact that its claims about disease aetiology could be wrong.
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Affiliation(s)
- Timothy Daly
- Bioethics Program, FLACSO Argentina, Buenos Aires, Argentina
- Science Norms Democracy UMR 8011, Sorbonne Université, Paris, France
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Daly T. Alzheimer's research after full approval of lecanemab: impetus and variety. Dement Neuropsychol 2024; 17:e20230064. [PMID: 38189032 PMCID: PMC10768642 DOI: 10.1590/1980-5764-dn-2023-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/24/2023] [Accepted: 10/20/2023] [Indexed: 01/09/2024] Open
Affiliation(s)
- Timothy Daly
- Bioethics Program, FLACSO Argentina, Tucumán, Buenos Aires, Argentina
- Sorbonne Université, Science Norms Democracy, Paris, France
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Daly T. Improving Clinical Trials of Antioxidants in Alzheimer's Disease. J Alzheimers Dis 2024; 99:S171-S181. [PMID: 37781800 DOI: 10.3233/jad-230308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Maintaining diversity in drug development in research into Alzheimer's disease (AD) is necessary to avoid over-reliance on targeting AD neuropathology. Treatments that reduce or prevent the generation of oxidative stress, frequently cited for its causal role in the aging process and AD, could be useful in at-risk populations or diagnosed AD patients. However, in this review, it is argued that clinical research into antioxidants in AD could provide more useful feedback as to the therapeutic value of the oxidative stress theory of AD. Improving comparability between randomized controlled trials (RCTs) is vital from a waste-reduction and priority-setting point of view for AD clinical research. For as well as attempting to improve meaningful outcomes for patients, RCTs of antioxidants in AD should strive to maximize the extraction of clinically useful information and actionable feedback from trial outcomes. Solutions to maximize information flow from RCTs of antioxidants in AD are offered here in the form of checklist questions to improve ongoing and future trials centered around the following dimensions: adhesion to reporting guidelines like CONSORT, biomarker enrichment, simple tests of treatment, and innovative trial design.
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Affiliation(s)
- Timothy Daly
- Science Norms Democracy UMR 8011, Sorbonne Université, Paris, France
- Bioethics Program, FLACSO Argentina, Buenos Aires, Argentina
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Zhang B, Lage-Rupprecht V, Wegner P, Sargsyan A, Gebel S, Jacobs M, Klein J, Hofmann-Apitius M, Tom Kodamullil A. Design of the formalized and integrated Alzheimer's Disease Ontology and its application in retrieving textual data via text mining. Database (Oxford) 2023; 2023:baad085. [PMID: 38041858 PMCID: PMC10693436 DOI: 10.1093/database/baad085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023]
Abstract
As one of the leading causes for dementia in the population, it is imperative that we discern exactly why Alzheimer's disease (AD) has a strong molecular association with beta-amyloid and tau. Although a clear understanding about etiology and pathogenesis of AD remains unsolved, scientists worldwide have dedicated significant efforts to discovering the molecular interactions linked to the pathological characteristics and potential treatments. Knowledge representations, such as domain ontologies encompassing our current understanding about AD, could greatly assist and contribute to disease research. This paper describes the construction and application of the integrated Alzheimer's Disease Ontology (ADO), combining selected concepts from the former version of the ADO and the Alzheimer's Disease Mapping Ontology (ADMO). In addition to the existing entities available from these knowledge models, essential knowledge about AD from public sources, such as newly discovered risk factor genes and novel treatments, was also integrated. The ADO can also be leveraged in text mining scenarios given that it is conceptually enriched with domain-specific knowledge as well as their relations. The integrated ADO consists of 39 855 total axioms. The ontology covers many aspects of the AD domain, including risk factor genes, clinical features, treatments and experimental models. The ontology complies with the Open Biological and Biomedical Ontology principles and was accepted by the foundry. In this paper, we illustrate the role of the presented ontology in extracting textual information from the SCAIView database and key measures in an ADO-based corpus. Database URL: https://academic.oup.com/database.
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Affiliation(s)
- Bide Zhang
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
| | - Vanessa Lage-Rupprecht
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
| | - Philipp Wegner
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
| | - Astghik Sargsyan
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
| | - Stephan Gebel
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
| | - Marc Jacobs
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
| | - Jürgen Klein
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
| | - Alpha Tom Kodamullil
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin 53754, Germany
- Causality Biomodels, Kinfra Hi-Tech Park, Kalamassery, Cochin, Kerala 683503, India
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Daly T. If deprivation worsens dementia outcomes, stimulation should improve them. Curr Med Res Opin 2023; 39:1391-1394. [PMID: 37725088 DOI: 10.1080/03007995.2023.2260741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023]
Abstract
It is still not known what causes Alzheimer's Disease (AD). In this period of uncertainty, an emerging literature on risk factors suggests that the concept of "stimulation" is a useful pragmatic tool both before and after diagnosis to improve cognitive health. Before diagnosis of AD, stimulation of the brain through education, exercise, and social stimulation provides fortification against later cognitive decline. After diagnosis, specific electrical stimulation of brain circuits may protect cognitive function, and non-specific stimulation through different kinds of environmental enrichment may help to compensate for cognitive decline. Pragmatic guidelines are offered here to maximise enabling stimulation (physical, cognitive, and social activity) and minimise disabling stimulation across the lifetime (e.g. stress, pollution, and poor diet). However, much deeper structural changes in society are needed to struggle against socioeconomic and environmental deprivation and the inaccessibility of education for women across the globe.
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Affiliation(s)
- Timothy Daly
- Bioethics Program, FLACSO Argentina, Buenos Aires, Argentina
- Science Norms Democracy UMR 8011, Sorbonne Université, Paris, France
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Taglino F, Cumbo F, Antognoli G, Arisi I, D'Onofrio M, Perazzoni F, Voyat R, Fiscon G, Conte F, Canevelli M, Bruno G, Mecocci P, Bertolazzi P. An ontology-based approach for modelling and querying Alzheimer's disease data. BMC Med Inform Decis Mak 2023; 23:153. [PMID: 37553569 PMCID: PMC10408169 DOI: 10.1186/s12911-023-02211-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 06/15/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND The recent advances in biotechnology and computer science have led to an ever-increasing availability of public biomedical data distributed in large databases worldwide. However, these data collections are far from being "standardized" so to be harmonized or even integrated, making it impossible to fully exploit the latest machine learning technologies for the analysis of data themselves. Hence, facing this huge flow of biomedical data is a challenging task for researchers and clinicians due to their complexity and high heterogeneity. This is the case of neurodegenerative diseases and the Alzheimer's Disease (AD) in whose context specialized data collections such as the one by the Alzheimer's Disease Neuroimaging Initiative (ADNI) are maintained. METHODS Ontologies are controlled vocabularies that allow the semantics of data and their relationships in a given domain to be represented. They are often exploited to aid knowledge and data management in healthcare research. Computational Ontologies are the result of the combination of data management systems and traditional ontologies. Our approach is i) to define a computational ontology representing a logic-based formal conceptual model of the ADNI data collection and ii) to provide a means for populating the ontology with the actual data in the Alzheimer Disease Neuroimaging Initiative (ADNI). These two components make it possible to semantically query the ADNI database in order to support data extraction in a more intuitive manner. RESULTS We developed: i) a detailed computational ontology for clinical multimodal datasets from the ADNI repository in order to simplify the access to these data; ii) a means for populating this ontology with the actual ADNI data. Such computational ontology immediately makes it possible to facilitate complex queries to the ADNI files, obtaining new diagnostic knowledge about Alzheimer's disease. CONCLUSIONS The proposed ontology will improve the access to the ADNI dataset, allowing queries to extract multivariate datasets to perform multidimensional and longitudinal statistical analyses. Moreover, the proposed ontology can be a candidate for supporting the design and implementation of new information systems for the collection and management of AD data and metadata, and for being a reference point for harmonizing or integrating data residing in different sources.
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Affiliation(s)
- Francesco Taglino
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy.
| | - Fabio Cumbo
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, 44195, Cleveland, Ohio, USA
| | - Giulia Antognoli
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy
| | - Ivan Arisi
- European Brain Research Institute (EBRI) "Rita Levi-Montalcini", Viale Regina Elena 295, 00161, Rome, Italy
| | - Mara D'Onofrio
- European Brain Research Institute (EBRI) "Rita Levi-Montalcini", Viale Regina Elena 295, 00161, Rome, Italy
| | - Federico Perazzoni
- Department of Engineering, Uninettuno International University, Corso Vittorio Emanuele II 39, 00186, Rome, Italy
| | - Roger Voyat
- Department of Engineering, University of Roma Tre, Via della Vasca Navale 79/81, 00146, Rome, Italy
| | - Giulia Fiscon
- Department of Computer, Control, and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Via Ariosto 25, 00185, Rome, Italy
| | - Federica Conte
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy
| | - Marco Canevelli
- Department of Human Neuroscience, Sapienza University of Rome, Via Ariosto 25, 00185, Rome, Italy
| | - Giuseppe Bruno
- Department of Human Neuroscience, Sapienza University of Rome, Via Ariosto 25, 00185, Rome, Italy
| | - Patrizia Mecocci
- Department of Medicine and Surgery, University of Perugia, Piazzale Gambuli 1, 06129, Perugia, Italy
- Division of Clinical Geriatrics, NVS Department, Karolinska Institutet, Nobels väg 5, Solna, 17177, Stockholm, Sweden
| | - Paola Bertolazzi
- Institute of Systems Analysis and Computer Science "Antonio Ruberti" (IASI), National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy
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Kosagisharaf JR, Hegde ML. Introduction to The Special Issue: Novel Molecular Pathways and Therapeutic Challenges in Neurodegenerative Diseases. J Alzheimers Dis 2023; 94:S3-S7. [PMID: 37393511 PMCID: PMC10473067 DOI: 10.3233/jad-230622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Affiliation(s)
- Jagannatha Rao Kosagisharaf
- Koneru Lakshmaiah Education Foundation (KLEF) Deemed to be University, Vaddeswaram, Andhra Pradesh, India
- SNI, INDICASAT AIP, Panama
| | - Muralidhar L. Hegde
- Department of Neurosurgery, Division of DNA Repair Research, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, USA
- Weill Cornell Medical College, New York, NY, USA
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Daly T. JAD: A Forum for Philosophy in Science. J Alzheimers Dis 2023; 95:411-413. [PMID: 37522211 DOI: 10.3233/jad-230407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
The Journal of Alzheimer's Disease (JAD) is already an established forum for cutting-edge science as well as ethical reflection. But I argue that beyond science and ethics, JAD is also a forum for philosophy in science, and that interdisciplinary researchers asking innovative questions about AD should publish their reflections and findings in JAD.
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Affiliation(s)
- Timothy Daly
- Science Norms Democracy UMR 8011, Sorbonne Université, Paris, France
- Bioethics Program, FLACSO Argentina, Buenos Aires, Argentina
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