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Artsitas S, Artsitas D, Koronaki I, Toutouzas KG, Zografos GC. Comparing robotic and open partial nephrectomy under the prism of surgical precision: a meta-analysis of the average blood loss rate as a novel variable. J Robot Surg 2024; 18:313. [PMID: 39112829 PMCID: PMC11306375 DOI: 10.1007/s11701-024-02060-z] [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: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024]
Abstract
Exploration of surgical precision in robotic procedures is extensive, yet lacks a unified framework for comparability. This study examines tissue handling precision by comparing the per-minute blood loss rate between robotic and open partial nephrectomy. A literature search from August 2022 to June 2024 identified 43 relevant studies providing data on estimated blood loss and procedure duration. The expected values and standard errors of these variables were used to compute the per-minute blood loss rate (Q). Meta-analytical methods estimated pooled and subgroup-level mean differences, favoring robotic surgery (MDQ = - 1.043 ml/min, CI95% = [- 1.338; - 0.747]). Subgroup analyses by publication year, patient matching, referral center count, and ROBINS-I status consistently supported this advantage. Sensitivity analyses confirmed the above benefit in studies with increased accuracy in reported results (MDQ = - 0.957 ml/min, CI95% = [- 1.269; - 0.646]), low risk of bias involving matched comparisons (MDQ = - 0.563 ml/min, CI95% = [- 0.716; - 0.410]), large sample sizes and increased statistical power (MDQ = - 0.780 ml/min, CI95% = [- 1.134; - 0.425]), and multicenter analyses with patient matching (MDQ = - 0.481 ml/min, CI95% = [- 0.698; - 0.263]). The subsequent analysis of correlation between the original variables suggested a slight reduction in the robotic advantage when the latter were proportionally related. Multilevel meta-regression at both temporal and qualitative scales consistently indicated a comparative benefit of the robotic approach. Potentially, lower per-minute blood loss compared to open surgery suggests that robotic partial nephrectomy demonstrates enhanced precision in tissue handling.
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Affiliation(s)
- Sotirios Artsitas
- Geniko Nosokomeio Athenon Ippokrateio, Vasilisis Sofias str. 114, 11527, Athens, Greece.
- 1st Propaedeutic Department of Surgery, School of Medicine, National and Kapodistrian University of Athens (NKUA), Mikras Asias str. 75, 11527, Athens, Greece.
- National and Kapodistrian University of Athens (NKUA), Mikras Asias str. 75, 11527, Athens, Greece.
| | - Dimitrios Artsitas
- 2nd Department of Orthopaedics, KAT Attica General Hospital, Nikis str. 2, Kifissia, 14561, Athens, Greece
| | - Irene Koronaki
- National Technical University of Athens (NTUA), Zografou Campus, Heroon Polytechniou str. 9, 15780, Athens, Greece
- Laboratory of Applied Thermodynamics, School of Mechanical Engineering, National Technical University of Athens (NTUA), Heroon Polytechniou str. 9, 15780, Athens, Greece
| | - Konstantinos G Toutouzas
- Geniko Nosokomeio Athenon Ippokrateio, Vasilisis Sofias str. 114, 11527, Athens, Greece
- 1st Propaedeutic Department of Surgery, School of Medicine, National and Kapodistrian University of Athens (NKUA), Mikras Asias str. 75, 11527, Athens, Greece
- National and Kapodistrian University of Athens (NKUA), Mikras Asias str. 75, 11527, Athens, Greece
| | - George C Zografos
- Geniko Nosokomeio Athenon Ippokrateio, Vasilisis Sofias str. 114, 11527, Athens, Greece
- 1st Propaedeutic Department of Surgery, School of Medicine, National and Kapodistrian University of Athens (NKUA), Mikras Asias str. 75, 11527, Athens, Greece
- National and Kapodistrian University of Athens (NKUA), Mikras Asias str. 75, 11527, Athens, Greece
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2
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Kalyva ME, Vist GE, Diemar MG, López-Soop G, Bozada TJ, Luechtefeld T, Roggen EL, Dirven H, Vinken M, Husøy T. Accessible methods and tools to estimate chemical exposure in humans to support risk assessment: A systematic scoping review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 352:124109. [PMID: 38718961 DOI: 10.1016/j.envpol.2024.124109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
Exposure assessment is a crucial component of environmental health research, providing essential information on the potential risks associated with various chemicals. A systematic scoping review was conducted to acquire an overview of accessible human exposure assessment methods and computational tools to support and ultimately improve risk assessment. The systematic scoping review was performed in Sysrev, a web platform that introduces machine learning techniques into the review process aiming for increased accuracy and efficiency. Included publications were restricted to a publication date after the year 2000, where exposure methods were properly described. Exposure assessments methods were found to be used for a broad range of environmental chemicals including pesticides, metals, persistent chemicals, volatile organic compounds, and other chemical classes. Our results show that after the year 2000, for all the types of exposure routes, probabilistic analysis, and computational methods to calculate human exposure have increased. Sixty-three mathematical models and toolboxes were identified that have been developed in Europe, North America, and globally. However, only twelve occur frequently and their usefulness were associated with exposure route, chemical classes and input parameters used to estimate exposure. The outcome of the combined associations can function as a basis and/or guide for decision making for the selection of most appropriate method and tool to be used for environmental chemical human exposure assessments in Ontology-driven and artificial intelligence-based repeated dose toxicity testing of chemicals for next generation risk assessment (ONTOX) project and elsewhere. Finally, the choice of input parameters used in each mathematical model and toolbox shown by our analysis can contribute to the harmonization process of the exposure models and tools increasing the prospect for comparison between studies and consistency in the regulatory process in the future.
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Affiliation(s)
- Maria E Kalyva
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway.
| | - Gunn E Vist
- Norwegian Institute of Public Health, Division for Health Services, Oslo, Norway
| | | | - Graciela López-Soop
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
| | - T J Bozada
- Toxtrack LLC, Baltimore, MD, United States
| | - Thomas Luechtefeld
- Toxtrack LLC, Baltimore, MD, United States; Insilica LLC, Bethesda, MD, United States
| | - Erwin L Roggen
- 3Rs Management and Consulting ApS, Kongens Lyngby, Denmark
| | - Hubert Dirven
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
| | - Mathieu Vinken
- Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Trine Husøy
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
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3
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Verhoeven A, van Ertvelde J, Boeckmans J, Gatzios A, Jover R, Lindeman B, Lopez-Soop G, Rodrigues RM, Rapisarda A, Sanz-Serrano J, Stinckens M, Sepehri S, Teunis M, Vinken M, Jiang J, Vanhaecke T. A quantitative weight-of-evidence method for confidence assessment of adverse outcome pathway networks: A case study on chemical-induced liver steatosis. Toxicology 2024; 505:153814. [PMID: 38677583 DOI: 10.1016/j.tox.2024.153814] [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: 01/31/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/29/2024]
Abstract
The field of chemical toxicity testing is undergoing a transition to overcome the limitations of in vivo experiments. This evolution involves implementing innovative non-animal approaches to improve predictability and provide a more precise understanding of toxicity mechanisms. Adverse outcome pathway (AOP) networks are pivotal in organizing existing mechanistic knowledge related to toxicological processes. However, these AOP networks are dynamic and require regular updates to incorporate the latest data. Regulatory challenges also persist due to concerns about the reliability of the information they offer. This study introduces a generic Weight-of-Evidence (WoE) scoring method, aligned with the tailored Bradford-Hill criteria, to quantitatively assess the confidence levels in key event relationships (KERs) within AOP networks. We use the previously published AOP network on chemical-induced liver steatosis, a prevalent form of human liver injury, as a case study. Initially, the existing AOP network is optimized with the latest scientific information extracted from PubMed using the free SysRev platform for artificial intelligence (AI)-based abstract inclusion and standardized data collection. The resulting optimized AOP network, constructed using Cytoscape, visually represents confidence levels through node size (key event, KE) and edge thickness (KERs). Additionally, a Shiny application is developed to facilitate user interaction with the dataset, promoting future updates. Our analysis of 173 research papers yielded 100 unique KEs and 221 KERs among which 72 KEs and 170 KERs, respectively, have not been previously documented in the prior AOP network or AOP-wiki. Notably, modifications in de novo lipogenesis, fatty acid uptake and mitochondrial beta-oxidation, leading to lipid accumulation and liver steatosis, garnered the highest KER confidence scores. In conclusion, our study delivers a generic methodology for developing and assessing AOP networks. The quantitative WoE scoring method facilitates in determining the level of support for KERs within the optimized AOP network, offering valuable insights into its utility in both scientific research and regulatory contexts. KERs supported by robust evidence represent promising candidates for inclusion in an in vitro test battery for reliably predicting chemical-induced liver steatosis within regulatory frameworks.
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Affiliation(s)
- Anouk Verhoeven
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonas van Ertvelde
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joost Boeckmans
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Alexandra Gatzios
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ramiro Jover
- Joint Research Unit in Experimental Hepatology, University of Valencia, Health Research Institute Hospital La Fe & CIBER of Hepatic and Digestive Diseases, Valencia, Spain
| | - Birgitte Lindeman
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | - Graciela Lopez-Soop
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | - Robim M Rodrigues
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Anna Rapisarda
- Joint Research Unit in Experimental Hepatology, University of Valencia, Health Research Institute Hospital La Fe & CIBER of Hepatic and Digestive Diseases, Valencia, Spain
| | - Julen Sanz-Serrano
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marth Stinckens
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sara Sepehri
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marc Teunis
- Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht, Utrecht, the Netherlands
| | - Mathieu Vinken
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jian Jiang
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tamara Vanhaecke
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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Moreno-Torres M, López-Pascual E, Rapisarda A, Quintás G, Drees A, Steffensen IL, Luechtefeld T, Serrano-Candelas E, de Lomana MG, Gadaleta D, Dirven H, Vinken M, Jover R. Novel clinical phenotypes, drug categorization, and outcome prediction in drug-induced cholestasis: Analysis of a database of 432 patients developed by literature review and machine learning support. Biomed Pharmacother 2024; 174:116530. [PMID: 38574623 DOI: 10.1016/j.biopha.2024.116530] [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: 01/25/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Serum transaminases, alkaline phosphatase and bilirubin are common parameters used for DILI diagnosis, classification, and prognosis. However, the relevance of clinical examination, histopathology and drug chemical properties have not been fully investigated. As cholestasis is a frequent and complex DILI manifestation, our goal was to investigate the relevance of clinical features and drug properties to stratify drug-induced cholestasis (DIC) patients, and to develop a prognosis model to identify patients at risk and high-concern drugs. METHODS DIC-related articles were searched by keywords and Boolean operators in seven databases. Relevant articles were uploaded onto Sysrev, a machine-learning based platform for article review and data extraction. Demographic, clinical, biochemical, and liver histopathological data were collected. Drug properties were obtained from databases or QSAR modelling. Statistical analyses and logistic regressions were performed. RESULTS Data from 432 DIC patients associated with 52 drugs were collected. Fibrosis strongly associated with fatality, whereas canalicular paucity and ALP associated with chronicity. Drugs causing cholestasis clustered in three major groups. The pure cholestatic pattern divided into two subphenotypes with differences in prognosis, canalicular paucity, fibrosis, ALP and bilirubin. A predictive model of DIC outcome based on non-invasive parameters and drug properties was developed. Results demonstrate that physicochemical (pKa-a) and pharmacokinetic (bioavailability, CYP2C9) attributes impinged on the DIC phenotype and allowed the identification of high-concern drugs. CONCLUSIONS We identified novel associations among DIC manifestations and disclosed novel DIC subphenotypes with specific clinical and chemical traits. The developed predictive DIC outcome model could facilitate DIC prognosis in clinical practice and drug categorization.
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Affiliation(s)
- Marta Moreno-Torres
- Joint Research Unit in Experimental Hepatology, Dep. Biochemistry and Molecular Biology, University of Valencia, Health Research Institute Hospital La Fe & CIBER of Hepatic and Digestive Diseases, Spain.
| | - Ernesto López-Pascual
- Joint Research Unit in Experimental Hepatology, Dep. Biochemistry and Molecular Biology, University of Valencia, Health Research Institute Hospital La Fe & CIBER of Hepatic and Digestive Diseases, Spain
| | - Anna Rapisarda
- Joint Research Unit in Experimental Hepatology, Dep. Biochemistry and Molecular Biology, University of Valencia, Health Research Institute Hospital La Fe & CIBER of Hepatic and Digestive Diseases, Spain
| | - Guillermo Quintás
- Health and Biomedicine, LEITAT Technological Center, Barcelona, Spain
| | - Annika Drees
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Belgium
| | - Inger-Lise Steffensen
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Marina Garcia de Lomana
- Bayer AG, Machine Learning Research, Research & Development, Pharmaceuticals, Berlin 13353, Germany
| | - Domenico Gadaleta
- Laboratory of Environmental Toxicology and Chemistry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCSS, Milano 20156, Italy
| | - Hubert Dirven
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | - Mathieu Vinken
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Belgium
| | - Ramiro Jover
- Joint Research Unit in Experimental Hepatology, Dep. Biochemistry and Molecular Biology, University of Valencia, Health Research Institute Hospital La Fe & CIBER of Hepatic and Digestive Diseases, Spain.
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5
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Martin PA, Fisher L, Pérez-Izquierdo L, Biryol C, Guenet B, Luyssaert S, Manzoni S, Menival C, Santonja M, Spake R, Axmacher JC, Yuste JC. Meta-analysis reveals that the effects of precipitation change on soil and litter fauna in forests depend on body size. GLOBAL CHANGE BIOLOGY 2024; 30:e17305. [PMID: 38712651 DOI: 10.1111/gcb.17305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/09/2024] [Accepted: 04/13/2024] [Indexed: 05/08/2024]
Abstract
Anthropogenic climate change is altering precipitation regimes at a global scale. While precipitation changes have been linked to changes in the abundance and diversity of soil and litter invertebrate fauna in forests, general trends have remained elusive due to mixed results from primary studies. We used a meta-analysis based on 430 comparisons from 38 primary studies to address associated knowledge gaps, (i) quantifying impacts of precipitation change on forest soil and litter fauna abundance and diversity, (ii) exploring reasons for variation in impacts and (iii) examining biases affecting the realism and accuracy of experimental studies. Precipitation reductions led to a decrease of 39% in soil and litter fauna abundance, with a 35% increase in abundance under precipitation increases, while diversity impacts were smaller. A statistical model containing an interaction between body size and the magnitude of precipitation change showed that mesofauna (e.g. mites, collembola) responded most to changes in precipitation. Changes in taxonomic richness were related solely to the magnitude of precipitation change. Our results suggest that body size is related to the ability of a taxon to survive under drought conditions, or to benefit from high precipitation. We also found that most experiments manipulated precipitation in a way that aligns better with predicted extreme climatic events than with predicted average annual changes in precipitation and that the experimental plots used in experiments were likely too small to accurately capture changes for mobile taxa. The relationship between body size and response to precipitation found here has far-reaching implications for our ability to predict future responses of soil biodiversity to climate change and will help to produce more realistic mechanistic soil models which aim to simulate the responses of soils to global change.
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Affiliation(s)
- Philip A Martin
- BC3-Basque Centre for Climate Change, Scientific Campus of the University of the Basque Country, Leioa, Spain
| | - Leonora Fisher
- UCL Department of Geography, University College London, London, UK
| | - Leticia Pérez-Izquierdo
- BC3-Basque Centre for Climate Change, Scientific Campus of the University of the Basque Country, Leioa, Spain
| | - Charlotte Biryol
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Bertrand Guenet
- Laboratoire de Géologie, Ecole Normale supérieure, CNRS, IPSL, Université PSL, Paris, France
| | - Sebastiaan Luyssaert
- Amsterdam Institute for Life and Environment (A-LIFE), Section Systems Ecology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Claire Menival
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Mathieu Santonja
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Marseille, France
| | - Rebecca Spake
- School of Biological Sciences, University of Reading, Reading, UK
| | - Jan C Axmacher
- UCL Department of Geography, University College London, London, UK
| | - Jorge Curiel Yuste
- BC3-Basque Centre for Climate Change, Scientific Campus of the University of the Basque Country, Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
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6
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Li Y, McIntyre KM, Rasmussen P, Gilbert W, Chaters G, Raymond K, Jemberu WT, Larkins A, Patterson GT, Kwok S, Kappes AJ, Mayberry D, Schrobback P, Acosta MH, Stacey DA, Huntington B, Bruce M, Knight-Jones T, Rushton J. Rationalising development of classification systems describing livestock production systems for disease burden analysis within the Global Burden of Animal Diseases programme. Res Vet Sci 2024; 168:105102. [PMID: 38215653 DOI: 10.1016/j.rvsc.2023.105102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
The heterogeneity that exists across the global spectrum of livestock production means that livestock productivity, efficiency, health expenditure and health outcomes vary across production systems. To ensure that burden of disease estimates are specific to the represented livestock population and people reliant upon them, livestock populations need to be systematically classified into different types of production system, reflective of the heterogeneity across production systems. This paper explores the data currently available of livestock production system classifications and animal health through a scoping review as a foundation for the development of a framework that facilitates more specific estimates of livestock disease burdens. A top-down framework to classification is outlined based on a systematic review of existing classification methods and provides a basis for simple grouping of livestock at global scale. The proposed top-down classification framework, which is dominated by commodity focus of production along with intensity of resource use, may have less relevance at the sub-national level in some jurisdictions and will need to be informed and adapted with information on how countries themselves categorize livestock and their production systems. The findings in this study provide a foundation for analysing animal health burdens across a broad level of production systems. The developed framework will fill a major gap in how livestock production and health are currently approached and analysed.
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Affiliation(s)
- Yin Li
- Global Burden of Animal Diseases (GBADs) Programme; Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, 4067 Brisbane, Australia; School of Veterinary Medicine and Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Australia.
| | - K Marie McIntyre
- Global Burden of Animal Diseases (GBADs) Programme; School of Natural and Environmental Sciences, Newcastle University, UK; Institute of Infection and Global Health, University of Liverpool, IC2 Building, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Philip Rasmussen
- Department of Veterinary and Animal Sciences, Section for Animal Welfare and Disease Control, University of Copenhagen, Copenhagen, Denmark; Section for Epidemiology, University of Zurich, Zurich, Switzerland
| | - William Gilbert
- Global Burden of Animal Diseases (GBADs) Programme; Institute of Infection and Global Health, University of Liverpool, IC2 Building, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Gemma Chaters
- Global Burden of Animal Diseases (GBADs) Programme; Institute of Infection and Global Health, University of Liverpool, IC2 Building, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Kassy Raymond
- Global Burden of Animal Diseases (GBADs) Programme; School of Computer Science, University of Guelph, Canada
| | - Wudu T Jemberu
- Global Burden of Animal Diseases (GBADs) Programme; International Livestock Research Institute, P O Box 5689, Addis Ababa, Ethiopia; University of Gondar, P. O. Box 196, Gondar, Ethiopia
| | - Andrew Larkins
- Global Burden of Animal Diseases (GBADs) Programme; School of Veterinary Medicine and Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Australia
| | - Grace T Patterson
- Global Burden of Animal Diseases (GBADs) Programme; School of Computer Science, University of Guelph, Canada
| | - Stephen Kwok
- Global Burden of Animal Diseases (GBADs) Programme; School of Veterinary Medicine and Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Australia
| | - Alexander James Kappes
- Global Burden of Animal Diseases (GBADs) Programme; School of Economic Sciences & Paul G. Allen School for Global Health, Washington State University, USA
| | - Dianne Mayberry
- Global Burden of Animal Diseases (GBADs) Programme; Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, 4067 Brisbane, Australia
| | - Peggy Schrobback
- Global Burden of Animal Diseases (GBADs) Programme; Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, 4067 Brisbane, Australia
| | - Mario Herrero Acosta
- College of Agriculture and Life Sciences, Cornell University, 250C Warren Hall, Ithaca, NY 14853, USA
| | - Deborah A Stacey
- Global Burden of Animal Diseases (GBADs) Programme; School of Computer Science, University of Guelph, Canada
| | - Benjamin Huntington
- Global Burden of Animal Diseases (GBADs) Programme; Institute of Infection and Global Health, University of Liverpool, IC2 Building, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Mieghan Bruce
- Global Burden of Animal Diseases (GBADs) Programme; School of Veterinary Medicine and Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Australia
| | - Theodore Knight-Jones
- Global Burden of Animal Diseases (GBADs) Programme; International Livestock Research Institute, P O Box 5689, Addis Ababa, Ethiopia
| | - Jonathan Rushton
- Global Burden of Animal Diseases (GBADs) Programme; Institute of Infection and Global Health, University of Liverpool, IC2 Building, 146 Brownlow Hill, Liverpool L3 5RF, UK
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7
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Kleinstreuer N, Hartung T. Artificial intelligence (AI)-it's the end of the tox as we know it (and I feel fine). Arch Toxicol 2024; 98:735-754. [PMID: 38244040 PMCID: PMC10861653 DOI: 10.1007/s00204-023-03666-2] [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: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024]
Abstract
The rapid progress of AI impacts diverse scientific disciplines, including toxicology, and has the potential to transform chemical safety evaluation. Toxicology has evolved from an empirical science focused on observing apical outcomes of chemical exposure, to a data-rich field ripe for AI integration. The volume, variety and velocity of toxicological data from legacy studies, literature, high-throughput assays, sensor technologies and omics approaches create opportunities but also complexities that AI can help address. In particular, machine learning is well suited to handle and integrate large, heterogeneous datasets that are both structured and unstructured-a key challenge in modern toxicology. AI methods like deep neural networks, large language models, and natural language processing have successfully predicted toxicity endpoints, analyzed high-throughput data, extracted facts from literature, and generated synthetic data. Beyond automating data capture, analysis, and prediction, AI techniques show promise for accelerating quantitative risk assessment by providing probabilistic outputs to capture uncertainties. AI also enables explanation methods to unravel mechanisms and increase trust in modeled predictions. However, issues like model interpretability, data biases, and transparency currently limit regulatory endorsement of AI. Multidisciplinary collaboration is needed to ensure development of interpretable, robust, and human-centered AI systems. Rather than just automating human tasks at scale, transformative AI can catalyze innovation in how evidence is gathered, data are generated, hypotheses are formed and tested, and tasks are performed to usher new paradigms in chemical safety assessment. Used judiciously, AI has immense potential to advance toxicology into a more predictive, mechanism-based, and evidence-integrated scientific discipline to better safeguard human and environmental wellbeing across diverse populations.
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Affiliation(s)
| | - Thomas Hartung
- Bloomberg School of Public Health, Doerenkamp-Zbinden Chair for Evidence-Based Toxicology, Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Baltimore, MD, USA.
- CAAT-Europe, University of Konstanz, Constance, Germany.
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8
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Sucena Afonso J, El Tholth M, Mcintyre KM, Carmo LP, Coyne L, Manriquez D, Raboisson D, Lhermie G, Rushton J. Strategies to reduce antimicrobials in livestock and aquaculture, and their impact under field conditions: a structured scoping literature review. J Antimicrob Chemother 2024; 79:11-26. [PMID: 37950886 PMCID: PMC10761277 DOI: 10.1093/jac/dkad350] [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] [Indexed: 11/13/2023] Open
Abstract
Antimicrobial resistance is a pandemic problem, causing substantial health and economic burdens. Antimicrobials are extensively used in livestock and aquaculture, exacerbating this global threat. Fostering the prudent use of antimicrobials will safeguard animal and human health. A lack of knowledge about alternatives to replace antimicrobials, and their effectiveness under field conditions, hampers changes in farming practices. This work aimed to understand the impact of strategies to reduce antimicrobial usage (AMU) in livestock and aquaculture, under field conditions, using a structured scoping literature review. The Extension for Scoping Reviews of the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines (PRISMA-ScR) were followed and the Patient, Intervention, Comparison, Outcome, Time and Setting (PICOTS) framework used. Articles were identified from CAB Abstracts, MEDLINE and Scopus. A total of 7505 unique research articles were identified, 926 of which were eligible for full-text assessment; 203 articles were included in data extraction. Given heterogeneity across articles in the way alternatives to antimicrobials or interventions against their usage were described, there was a need to standardize these by grouping them in categories. There were differences in the impacts of the strategies between and within species; this highlights the absence of a 'one-size-fits-all' solution. Nevertheless, some options seem more promising than others, as their impacts were consistently equivalent or positive when compared with animal performance using antimicrobials. This was particularly the case for bioactive protein and peptides, and feed/water management. The outcomes of this work provide data to inform cost-effectiveness assessments of strategies to reduce AMU.
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Affiliation(s)
- João Sucena Afonso
- Department of Livestock and One Health, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Mahmoud El Tholth
- Global Academy of Agriculture and Food Systems, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK
- Department of Health Studies, Royal Holloway University of London, Egham, UK
- Hygiene and Preventive Medicine Department, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr el-sheikh, Egypt
| | - K Marie Mcintyre
- Modelling, Evidence and Policy group, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Lucy Coyne
- National Office of Animal Health, Stevenage, UK
| | - Diego Manriquez
- CIRAD, UMR ASTRE, Montpellier, France, ASTRE, CIRAD, INRAE, University of Monpellier, Montpellier, Universite de Toulouse, ENVT, 31300, Toulouse, France
- AgNext, Department of Animal Sciences, Colorado State University, Fort Collins, USA
| | - Didier Raboisson
- CIRAD, UMR ASTRE, Montpellier, France, ASTRE, CIRAD, INRAE, University of Monpellier, Montpellier, Universite de Toulouse, ENVT, 31300, Toulouse, France
| | - Guillaume Lhermie
- CIRAD, UMR ASTRE, Montpellier, France, ASTRE, CIRAD, INRAE, University of Monpellier, Montpellier, Universite de Toulouse, ENVT, 31300, Toulouse, France
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Canada
| | - Jonathan Rushton
- Department of Livestock and One Health, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
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Meerman JJ, Legler J, Piersma AH, Westerink RHS, Heusinkveld HJ. An adverse outcome pathway for chemical-induced Parkinson's disease: Calcium is key. Neurotoxicology 2023; 99:226-243. [PMID: 37926220 DOI: 10.1016/j.neuro.2023.11.001] [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: 06/19/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Exposure to pesticides is associated with an increased risk of developing Parkinson's disease (PD). Currently, rodent-based risk assessment studies cannot adequately capture neurodegenerative effects of pesticides due to a lack of human-relevant endpoints targeted at neurodegeneration. Thus, there is a need for improvement of the risk assessment guidelines. Specifically, a mechanistic assessment strategy, based on human physiology and (patho)biology is needed, which can be applied in next generation risk assessment. The Adverse Outcome Pathway (AOP) framework is particularly well-suited to provide the mechanistic basis for such a strategy. Here, we conducted a semi-systematic review in Embase and MEDLINE, focused on neurodegeneration and pesticides, to develop an AOP network for parkinsonian motor symptoms. Articles were labelled and included/excluded using the online platform Sysrev. Only primary articles, written in English, focused on effects of pesticides or PD model compounds in models for the brain were included. A total of 66 articles, out of the 1700 screened, was included. PD symptoms are caused by loss of function and ultimately death of dopaminergic neurons in the substantia nigra (SN). Our literature review highlights that a unique feature of these cells that increases their vulnerability is their reliance on continuous low-level influx of calcium. As such, excess intracellular calcium was identified as a central early Key Event (KE). This KE can lead to death of dopaminergic neurons of the SN, and eventually parkinsonian motor symptoms, via four distinct pathways: 1) activation of calpains, 2) endoplasmic reticulum stress, 3) impairment of protein degradation, and 4) oxidative damage. Several receptors have been identified that may serve as molecular initiating events (MIEs) to trigger one or more of these pathways. The proposed AOP network provides the biological basis that can be used to develop a mechanistic testing strategy that captures neurodegenerative effects of pesticides.
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Affiliation(s)
- Julia J Meerman
- Centre for Health Protection, Dutch National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Juliette Legler
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Aldert H Piersma
- Centre for Health Protection, Dutch National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Remco H S Westerink
- Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Harm J Heusinkveld
- Centre for Health Protection, Dutch National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands.
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10
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Ferreira Aderaldo J, da Silva Maranhão K, Ferreira Lanza DC. Does microfluidic sperm selection improve clinical pregnancy and miscarriage outcomes in assisted reproductive treatments? A systematic review and meta-analysis. PLoS One 2023; 18:e0292891. [PMID: 37983267 PMCID: PMC10659219 DOI: 10.1371/journal.pone.0292891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND The microfluidic sperm selection (MFSS) device has emerged as a promising adjunct in assisted reproduction treatments (ART). It employs mechanisms of biomimicry based on the microanatomy of the female reproductive tract through strategies like chemotaxis and rheotaxis. Numerous studies assert improvements in ART outcomes with the use of MFSS, often attributed to the theoretical reduction in sperm DNA damage compared to other techniques. However, these attributed benefits lack validation through large-scale clinical trials, and there is no significant evidence of enhanced assisted reproductive treatments (ART) outcomes. OBJECTIVE To evaluate whether the utilization of MFSS enhances clinical pregnancy results and abortion outcomes in couples undergoing ART compared to standard sperm selection techniques for Intracytoplasmic Sperm Injection (ICSI). We also assessed laboratory outcomes as a supplementary analysis. SEARCH METHODS We conducted searches across databases including PubMed, NIH, LILACS, CENTRAL, Crossref, Scopus, and OpenAlex. A total of 1,255 records were identified. From these, 284 duplicate records were eliminated, and an additional 895 records were excluded due to their association with patent applications, diagnostic tests, forensic analyses, or irrelevance to the research focus. Among the initially eligible 76 studies, 63 were excluded, encompassing abstracts, studies lacking adequate control groups, and ongoing clinical trials. Ultimately, 13 studies were selected for inclusion in the ensuing meta-analysis. RESULTS Regarding clinical pregnancy, we assessed a total of 868 instances of clinical pregnancies out of 1,646 embryo transfers. Regarding miscarriage, we examined 95 cases of pregnancy loss among the 598 confirmed clinical pregnancies in these studies. CONCLUSION The utilization of MFSS demonstrates marginal positive outcomes compared to standard sperm selection techniques, without statistical significance in any of the analyses. BROADER IMPLICATIONS This study conducted the first meta-analysis to evaluate clinical pregnancy rates, miscarriage rates, and laboratory results associated with the use of MFSS compared to standard sperm selection techniques. We have also listed potentially eligible studies for future inclusion. It's important to emphasize the need for multicenter studies with standardized parameters to attain a more robust clarification of this issue.
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Affiliation(s)
- Janaina Ferreira Aderaldo
- Januário Cicco Maternity School of Brazilian Company of Hospital Services (MEJC/UFRN-Ebserh), Natal, Brazil
- Biochemistry Department, Federal University of Rio Grande do Norte–UFRN, Natal, Brazil
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Amenu K, McIntyre KM, Moje N, Knight-Jones T, Rushton J, Grace D. Approaches for disease prioritization and decision-making in animal health, 2000-2021: a structured scoping review. Front Vet Sci 2023; 10:1231711. [PMID: 37876628 PMCID: PMC10593474 DOI: 10.3389/fvets.2023.1231711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/06/2023] [Indexed: 10/26/2023] Open
Abstract
This scoping review identifies and describes the methods used to prioritize diseases for resource allocation across disease control, surveillance, and research and the methods used generally in decision-making on animal health policy. Three electronic databases (Medline/PubMed, Embase, and CAB Abstracts) were searched for articles from 2000 to 2021. Searches identified 6, 395 articles after de-duplication, with an additional 64 articles added manually. A total of 6, 460 articles were imported to online document review management software (sysrev.com) for screening. Based on inclusion and exclusion criteria, 532 articles passed the first screening, and after a second round of screening, 336 articles were recommended for full review. A total of 40 articles were removed after data extraction. Another 11 articles were added, having been obtained from cross-citations of already identified articles, providing a total of 307 articles to be considered in the scoping review. The results show that the main methods used for disease prioritization were based on economic analysis, multi-criteria evaluation, risk assessment, simple ranking, spatial risk mapping, and simulation modeling. Disease prioritization was performed to aid in decision-making related to various categories: (1) disease control, prevention, or eradication strategies, (2) general organizational strategy, (3) identification of high-risk areas or populations, (4) assessment of risk of disease introduction or occurrence, (5) disease surveillance, and (6) research priority setting. Of the articles included in data extraction, 50.5% had a national focus, 12.3% were local, 11.9% were regional, 6.5% were sub-national, and 3.9% were global. In 15.2% of the articles, the geographic focus was not specified. The scoping review revealed the lack of comprehensive, integrated, and mutually compatible approaches to disease prioritization and decision support tools for animal health. We recommend that future studies should focus on creating comprehensive and harmonized frameworks describing methods for disease prioritization and decision-making tools in animal health.
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Affiliation(s)
- Kebede Amenu
- Global Burden of Animal Diseases (GBADs) Programme, University of Liverpool, Liverpool, United Kingdom
- Department of Microbiology, Immunology and Veterinary, Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - K. Marie McIntyre
- Global Burden of Animal Diseases (GBADs) Programme, University of Liverpool, Liverpool, United Kingdom
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Modelling, Evidence and Policy Group, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nebyou Moje
- Department of Biomedical Sciences, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia
| | - Theodore Knight-Jones
- Global Burden of Animal Diseases (GBADs) Programme, University of Liverpool, Liverpool, United Kingdom
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Jonathan Rushton
- Global Burden of Animal Diseases (GBADs) Programme, University of Liverpool, Liverpool, United Kingdom
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Delia Grace
- Global Burden of Animal Diseases (GBADs) Programme, University of Liverpool, Liverpool, United Kingdom
- Food and Markets Department, Natural Resources Institute, University of Greenwich, London, United Kingdom
- Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
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12
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Rana I, Nguyen PK, Rigutto G, Louie A, Lee J, Smith MT, Zhang L. Mapping the key characteristics of carcinogens for glyphosate and its formulations: A systematic review. CHEMOSPHERE 2023; 339:139572. [PMID: 37474029 DOI: 10.1016/j.chemosphere.2023.139572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Glyphosate was classified as a probable human carcinogen (Group 2A) by the International Agency for Research on Cancer (IARC) partially due to strong mechanistic evidence in 2015. Since then, numerous studies of glyphosate and its formulations (GBF) have emerged. These studies can be evaluated for cancer hazard identification with the newly described ten key characteristics (KC) of carcinogens approach. Our objective was to assess all in vivo, ex vivo, and in vitro mechanistic studies of human and experimental animals (mammals) that compared exposure to glyphosate/GBF with low/no exposure counterparts for evidence of the ten KCs. A protocol with our methods adhering to PRISMA guidelines was registered a priori (INPLASY202180045). Two blinded reviewers screened all in vivo, ex vivo, and in vitro studies of glyphosate/GBF exposure in humans/mammals reporting any KC-related outcome available in PubMed before August 2021. Studies that met inclusion criteria underwent data extraction conducted in duplicate for each KC outcome reported along with key aspects of internal/external validity, results, and reference information. These data were used to construct a matrix that was subsequently analyzed in the program R to conduct strength of evidence and quality assessments. Of the 2537 articles screened, 175 articles met inclusion criteria, from which we extracted >50,000 data points related to KC outcomes. Data analysis revealed strong evidence for KC2, KC4, KC5, KC6, KC8, limited evidence for KC1 and KC3, and inadequate evidence for KC7, KC9, and KC10. Notably, our in-depth quality analyses of genotoxicity (KC2) and endocrine disruption (KC8) revealed strong and consistent positive findings. For KC2, we found: 1) studies conducted in humans and human cells provided stronger positive evidence than counterpart animal models; 2) GBF elicited a stronger effect in both human and animal systems when compared to glyphosate alone; and 3) the highest quality studies in humans and human cells consistently revealed strong evidence of genotoxicity. Our analysis of KC8 indicated that glyphosate's ability to modulate hormone levels and estrogen receptor activity is sensitive to both exposure concentration and formulation. The modulations observed provide clear evidence that glyphosate interacts with receptors, alters receptor activation, and modulates the levels and effects of endogenous ligands (including hormones). Our findings strengthen the mechanistic evidence that glyphosate is a probable human carcinogen and provide biological plausibility for previously reported cancer associations in humans, such as non-Hodgkin lymphoma. We identified potential molecular interactions and subsequent key events that were used to generate a probable pathway to lymphomagenesis.
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Affiliation(s)
- Iemaan Rana
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, United States
| | - Patton K Nguyen
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, United States
| | - Gabrielle Rigutto
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, United States
| | - Allen Louie
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, United States
| | - Jane Lee
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, United States
| | - Martyn T Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, United States
| | - Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, United States.
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13
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Cross TJ, Isautier JMJ, Kelley EF, Hubbard CD, Morris SJ, Smith JR, Duke JW. A Systematic Review of Methods Used to Determine the Work of Breathing during Exercise. Med Sci Sports Exerc 2023; 55:1672-1682. [PMID: 37126027 DOI: 10.1249/mss.0000000000003187] [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] [Indexed: 05/02/2023]
Abstract
INTRODUCTION Measurement of the work of breathing (Wb) during exercise provides useful insights into the energetics and mechanics of the respiratory muscles across a wide range of minute ventilations. The methods and analytical procedures used to calculate the Wb during exercise have yet to be critically appraised in the literature. PURPOSE The aim of this systematic review was to evaluate the quality of methods used to measure the Wb during exercise in the available literature. METHODS We conducted an extensive search of three databases for studies that measured the Wb during exercise in adult humans. Data were extracted on participant characteristics, flow/volume and pressure devices, esophageal pressure (P oes ) catheters, and methods of Wb analysis. RESULTS A total of 120 articles were included. Flow/volume sensors used were primarily pneumotachographs ( n = 85, 70.8%), whereas the most common pressure transducer was of the variable reluctance type ( n = 63, 52.5%). Esophageal pressure was frequently obtained via balloon-tipped catheters ( n = 114, 95.0%). Few studies mentioned calibration, frequency responses, and dynamic compensation of their measurement devices. The most popular method of measuring the Wb was pressure-volume integration ( n = 51, 42.5%), followed by the modified Campbell ( n = 28, 23.3%) and Dean & Visscher diagrams ( n = 26, 21.7%). Over one-third of studies did not report the methods used to process their pressure-volume data, and the majority (60.8%) of studies used the incorrect Wb units and/or failed to discuss the limitations of their Wb measurements. CONCLUSIONS The findings of this systematic review highlight the need for the development of a standardized approach for measuring Wb, which is informative, practical, and accessible for future researchers.
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Affiliation(s)
- Troy J Cross
- Faculty of Medicine and Health, University of Sydney, NSW, AUSTRALIA
| | | | - Eli F Kelley
- Air Force Research Laboratory, 711HPW/RHBFP, Wright-Patterson Air Force Base, OH
| | - Colin D Hubbard
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Sarah J Morris
- Faculty of Medicine and Health, University of Sydney, NSW, AUSTRALIA
| | - Joshua R Smith
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN
| | - Joseph W Duke
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
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14
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van Ertvelde J, Verhoeven A, Maerten A, Cooreman A, Santos Rodrigues BD, Sanz-Serrano J, Mihajlovic M, Tripodi I, Teunis M, Jover R, Luechtefeld T, Vanhaecke T, Jiang J, Vinken M. Optimization of an adverse outcome pathway network on chemical-induced cholestasis using an artificial intelligence-assisted data collection and confidence level quantification approach. J Biomed Inform 2023; 145:104465. [PMID: 37541407 DOI: 10.1016/j.jbi.2023.104465] [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: 06/07/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Adverse outcome pathway (AOP) networks are versatile tools in toxicology and risk assessment that capture and visualize mechanisms driving toxicity originating from various data sources. They share a common structure consisting of a set of molecular initiating events and key events, connected by key event relationships, leading to the actual adverse outcome. AOP networks are to be considered living documents that should be frequently updated by feeding in new data. Such iterative optimization exercises are typically done manually, which not only is a time-consuming effort, but also bears the risk of overlooking critical data. The present study introduces a novel approach for AOP network optimization of a previously published AOP network on chemical-induced cholestasis using artificial intelligence to facilitate automated data collection followed by subsequent quantitative confidence assessment of molecular initiating events, key events, and key event relationships. METHODS Artificial intelligence-assisted data collection was performed by means of the free web platform Sysrev. Confidence levels of the tailored Bradford-Hill criteria were quantified for the purpose of weight-of-evidence assessment of the optimized AOP network. Scores were calculated for biological plausibility, empirical evidence, and essentiality, and were integrated into a total key event relationship confidence value. The optimized AOP network was visualized using Cytoscape with the node size representing the incidence of the key event and the edge size indicating the total confidence in the key event relationship. RESULTS This resulted in the identification of 38 and 135 unique key events and key event relationships, respectively. Transporter changes was the key event with the highest incidence, and formed the most confident key event relationship with the adverse outcome, cholestasis. Other important key events present in the AOP network include: nuclear receptor changes, intracellular bile acid accumulation, bile acid synthesis changes, oxidative stress, inflammation and apoptosis. CONCLUSIONS This process led to the creation of an extensively informative AOP network focused on chemical-induced cholestasis. This optimized AOP network may serve as a mechanistic compass for the development of a battery of in vitro assays to reliably predict chemical-induced cholestatic injury.
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Affiliation(s)
- Jonas van Ertvelde
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Anouk Verhoeven
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Amy Maerten
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Axelle Cooreman
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bruna Dos Santos Rodrigues
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Julen Sanz-Serrano
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Milos Mihajlovic
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Marc Teunis
- Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht, Utrecht, The Netherlands
| | - Ramiro Jover
- Joint Research Unit in Experimental Hepatology, University of Valencia, Health Research Institute Hospital La Fe & CIBER of Hepatic and Digestive Diseases, Spain
| | | | - Tamara Vanhaecke
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jian Jiang
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Mathieu Vinken
- Entity of In Vitro Toxicology and Dermato-Cosmetology, Department of Pharmaceutical and Pharmacological Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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15
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Fastl C, De Carvalho Ferreira HC, Babo Martins S, Sucena Afonso J, di Bari C, Venkateswaran N, Pires SM, Mughini-Gras L, Huntington B, Rushton J, Pigott D, Devleesschauwer B. Animal sources of antimicrobial-resistant bacterial infections in humans: a systematic review. Epidemiol Infect 2023; 151:e143. [PMID: 37577944 PMCID: PMC10540179 DOI: 10.1017/s0950268823001309] [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: 07/07/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/15/2023] Open
Abstract
Bacterial antimicrobial resistance (AMR) is among the leading global health challenges of the century. Animals and their products are known contributors to the human AMR burden, but the extent of this contribution is not clear. This systematic literature review aimed to identify studies investigating the direct impact of animal sources, defined as livestock, aquaculture, pets, and animal-based food, on human AMR. We searched four scientific databases and identified 31 relevant publications, including 12 risk assessments, 16 source attribution studies, and three other studies. Most studies were published between 2012 and 2022, and most came from Europe and North America, but we also identified five articles from South and South-East Asia. The studies differed in their methodologies, conceptual approaches (bottom-up, top-down, and complex), definitions of the AMR hazard and outcome, the number and type of sources they addressed, and the outcome measures they reported. The most frequently addressed animal source was chicken, followed by cattle and pigs. Most studies investigated bacteria-resistance combinations. Overall, studies on the direct contribution of animal sources of AMR are rare but increasing. More recent publications tailor their methodologies increasingly towards the AMR hazard as a whole, providing grounds for future research to build on.
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Affiliation(s)
- Christina Fastl
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | | | - Sara Babo Martins
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - João Sucena Afonso
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - Carlotta di Bari
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
| | - Narmada Venkateswaran
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute for Health Metrics and Evaluation, Department of Health Metrics Sciences, University of Washington, Seattle, WA, USA
| | | | - Lapo Mughini-Gras
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Faculty of Veterinary Medicine, Utrecht University, Institute for Risk Assessment Sciences (IRAS), Utrecht, The Netherlands
| | - Ben Huntington
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
- Pengwern Animal Health Ltd, Wallasey, UK
| | - Jonathan Rushton
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Neston, UK
| | - David Pigott
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Institute for Health Metrics and Evaluation, Department of Health Metrics Sciences, University of Washington, Seattle, WA, USA
| | - Brecht Devleesschauwer
- Global Burden of Animal Diseases Programme, University of Liverpool, Liverpool, UK
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
- Department of Translational Physiology, Infectiology and Public Health, Ghent University, Merelbeke, Belgium
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16
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Aderaldo JF, Rodrigues de Albuquerque BHD, Câmara de Oliveira MTF, de Medeiros Garcia Torres M, Lanza DCF. Main topics in assisted reproductive market: A scoping review. PLoS One 2023; 18:e0284099. [PMID: 37527215 PMCID: PMC10393141 DOI: 10.1371/journal.pone.0284099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/19/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Infertility affects around 12% of couples, and this proportion has been gradually increasing. In this context, the global assisted reproductive technologies (ART) market shows significant expansion, hovering around USD 26 billion in 2019 and is expected to reach USD 45 billion by 2025. OBJECTIVES We realized a scoping review of the ART market from academic publications, market reports, and specialized media news, to identify the main terms and characterize them into the main topics in the area. DESIGN We apply an LDA topic modeling process to identify the main terms, and clustered them into semantic synonymous topics. We extracted the patterns and information to these topics and purposed a factor/consequence correlation to them. RESULTS We found 2,232 academic papers and selected 632 to include in the automatic term detection. We also included 34 market reports and seven notices produced by specialized enterprises. Were identified 121 most relevant cited terms covering 7,806 citations. These terms were manually aggregated into 10 topics based on semantic similarity: neutral terms (37.2%), economic aspects (17.6%), in vitro fertilization (IVF) commodities & cross-border reproductive care (CBRC) (10.6%), geographic distribution (9.5%), social aspects (7%), regulation (6%), trends & concerns (3.9%), accessibility (3.4%), internet influence (2.9%), and fertility preservation for non-medical reasons (2%). DISCUSSION The analysis indicates a market with expressive complexity. Most terms were associated with more than one topic, indicating the synergism of this market's behavior. Only seven terms related to economic aspects, surrogacy and donation represent around 50% of the citations. Except for the topic formed by generic terms, the topic of the economic aspects was the most represented, reflecting macro perspectives such as a-la-carte standard of treatments, many clinics operating on a small/medium scale, and the recent formation of conglomerates. The IVF commodities & CBRC topic brings an overview of gametes pricing and transnational surrogacy, and its regulation. The topic of geographic distribution indicates that that the Asia-Pacific (APAC) market has the most significant growth potential in all fields. Despite the increase in supply and demand for infertility treatments and technological advances in recent decades, the success rate of IVF cycles remains at around 30%. Terms referring to research and development or technical improvement were not identified in a significant way in this review. CONCLUSIONS The formation of topics by semantic similarity proved to be an initial path for the elaboration of in-depth studies on the dynamics between several factors, for this, we present the panel classifying main terms into factors (demand, pent-up demand, or distributive) or ART market consequences. Through this approach, it was possible to observe that most of the works addresses economic aspects, regulation and geographic aspects and that topics related to research and improvement have not been addressed. In this way, we highlight the need to deepen the analysis of market elements that may be related to increased efficiency of IVF in the technical field.
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Affiliation(s)
- Janaina Ferreira Aderaldo
- Applied Molecular Biology Lab (LAPLIC), Biochemistry Department, Federal University of Rio Grande do Norte (UFRN), Natal, Rio Grande do Norte, Brazil
- Januário Cicco´s University Hospital (MEJC), Federal University of Rio Grande do Norte (UFRN), Natal, Rio Grande do Norte, Brazil
| | | | | | - Mychelle de Medeiros Garcia Torres
- Applied Molecular Biology Lab (LAPLIC), Biochemistry Department, Federal University of Rio Grande do Norte (UFRN), Natal, Rio Grande do Norte, Brazil
- Januário Cicco´s University Hospital (MEJC), Federal University of Rio Grande do Norte (UFRN), Natal, Rio Grande do Norte, Brazil
| | - Daniel Carlos Ferreira Lanza
- Applied Molecular Biology Lab (LAPLIC), Biochemistry Department, Federal University of Rio Grande do Norte (UFRN), Natal, Rio Grande do Norte, Brazil
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Brown C, Bilynsky C, Gainey M, Young S, Kitchin J, Wayne E. Meta-analysis of macrophage nanoparticle targeting across blood and solid tumors using an eLDA Topic modeling Machine Learning approach. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547096. [PMID: 37425888 PMCID: PMC10327218 DOI: 10.1101/2023.06.29.547096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The role of macrophages in regulating the tumor microenvironment has spurned the exponential generation of nanoparticle targeting technologies. With the large amount of literature and the speed at which it is generated it is difficult to remain current with the most up-to-date literature. In this study we performed a topic modeling analysis of the most common usages of nanoparticle targeting of macrophages in solid tumors. The data spans 20 years of literature, providing an extensive meta-analysis of the nanoparticle strategies. Our topic model found 6 distinct topics: Immune and TAMs, Nanoparticles, Imaging, Gene Delivery and Exosomes, Vaccines, and Multi-modal Therapies. We also found distinct nanoparticle usage, tumor types, and therapeutic trends across these topics. Moreover, we established that the topic model could be used to assign new papers into the existing topics, thereby creating a Living Review. This type of meta-analysis provides a useful assessment tool for aggregating data about a large field.
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18
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Mensa E, Martínez Fernández P, Roller R, Radicioni DP. Editorial: Information extraction for health documents. Front Artif Intell 2023; 6:1224529. [PMID: 37396971 PMCID: PMC10313187 DOI: 10.3389/frai.2023.1224529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Affiliation(s)
- Enrico Mensa
- Dipartimento di Informatica, Università degli Studi di Torino, Turin, Italy
| | - Paloma Martínez Fernández
- Departamento de Informática, Computer Science and Engineering Department, Universidad Carlos III de Madrid, Leganés, Spain
| | - Roland Roller
- German Research Center for Artificial Intelligence (DFKI), Berlin, Germany
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19
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Oliveira Dos Santos Á, Sergio da Silva E, Machado Couto L, Valadares Labanca Reis G, Silva Belo V. The use of artificial intelligence for automating or semi-automating biomedical literature analyses: a scoping review. J Biomed Inform 2023; 142:104389. [PMID: 37187321 DOI: 10.1016/j.jbi.2023.104389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 05/17/2023]
Abstract
OBJECTIVE Evidence-based medicine (EBM) is a decision-making process based on the conscious and judicious use of the best available scientific evidence. However, the exponential increase in the amount of information currently available likely exceeds the capacity of human-only analysis. In this context, artificial intelligence (AI) and its branches such as machine learning (ML) can be used to facilitate human efforts in analyzing the literature to foster EBM. The present scoping review aimed to examine the use of AI in the automation of biomedical literature survey and analysis with a view to establishing the state-of-the-art and identifying knowledge gaps. MATERIALS AND METHODS Comprehensive searches of the main databases were performed for articles published up to June 2022 and studies were selected according to inclusion and exclusion criteria. Data were extracted from the included articles and the findings categorized. RESULTS The total number of records retrieved from the databases was 12,145, of which 273 were included in the review. Classification of the studies according to the use of AI in evaluating the biomedical literature revealed three main application groups, namely assembly of scientific evidence (n=127; 47%), mining the biomedical literature (n=112; 41%) and quality analysis (n=34; 12%). Most studies addressed the preparation of systematic reviews, while articles focusing on the development of guidelines and evidence synthesis were the least frequent. The biggest knowledge gap was identified within the quality analysis group, particularly regarding methods and tools that assess the strength of recommendation and consistency of evidence. CONCLUSION Our review shows that, despite significant progress in the automation of biomedical literature surveys and analyses in recent years, intense research is needed to fill knowledge gaps on more difficult aspects of ML, deep learning and natural language processing, and to consolidate the use of automation by end-users (biomedical researchers and healthcare professionals).
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Affiliation(s)
| | - Eduardo Sergio da Silva
- Federal University of São João del-Rei, Campus Centro-Oeste Dona Lindu, Divinópolis, Minas Gerais, Brazil.
| | - Letícia Machado Couto
- Federal University of São João del-Rei, Campus Centro-Oeste Dona Lindu, Divinópolis, Minas Gerais, Brazil.
| | | | - Vinícius Silva Belo
- Federal University of São João del-Rei, Campus Centro-Oeste Dona Lindu, Divinópolis, Minas Gerais, Brazil.
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20
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Pérez-Neri I, Sandoval H, Estêvão MD, Vasanthan LT, Alarcon-Ruiz CA, Ruszkowski J, Mathangasinghe Y, Ríos C, Pineda C. Central and peripheral mechanisms of pain in fibromyalgia: scoping review protocol. Rheumatol Int 2023; 43:757-762. [PMID: 36635578 DOI: 10.1007/s00296-023-05275-9] [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: 12/16/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023]
Abstract
Fibromyalgia is characterised by widespread musculoskeletal pain, which may present with fatigue, depression, anxiety, sleep and cognitive disturbances. It is the second most prevalent rheumatic disease. An accurate diagnosis is challenging, since its symptoms may resemble diverse conditions such as carpal tunnel syndrome, Raynaud syndrome, Sjögren syndrome, amongst others. Neuropathic pain and autonomic dysfunction in fibromyalgia suggest the involvement of the nervous system. Ion channels, neurotransmitters and neuromodulators may play a role. Small fibre neuropathy (SFN) may also cause chronic widespread pain. SFN may occur in 50% of fibromyalgia patients, but its role in the disease is unknown. Despite several efforts to synthesise the evidence on the mechanisms for pain in fibromyalgia, there are few studies applying an integrative perspective of neurochemical, immunological, and neuroanatomical characteristics, and their relevance to the disease. This protocol aims to clarify the mechanisms of the central and peripheral nervous system associated with pain in fibromyalgia. We will retrieve published studies from Web of Science, MEDLINE, Scopus, EBSCOhost, Ovid and Google Scholar. All clinical studies or experimental models of fibromyalgia reporting imaging, neurophysiological, anatomical, structural, neurochemical, or immunological characteristics of the central or peripheral nervous systems associated with pain will be included. Exclusion criteria will eliminate studies evaluating pain without a standardised measure, studies written in languages different from Spanish or English that could not be appropriately translated, and studies whose full-text files could not be retrieved after all efforts made. A narrative synthesis will be performed.
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Affiliation(s)
- Iván Pérez-Neri
- Department of Neurochemistry, National Institute of Neurology and Neurosurgery Manuel Velasco Suárez, Insurgentes Sur 3877, La Fama, Tlalpan, 14269, Ciudad de México, Mexico
| | - Hugo Sandoval
- General Directorate, National Institute of Rehabilitation Luis Guillermo Ibarra Ibarra, Calzada México-Xochimilco 289, Arenal de Guadalupe, 14389, Ciudad de México, Mexico
| | - M Dulce Estêvão
- Escola Superior de Saúde da Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Lenny T Vasanthan
- Physiotherapy Unit, Physical Medicine and Rehabilitation Department, Christian Medical College, Vellore, 632004, India
| | - Christoper A Alarcon-Ruiz
- Unidad de Investigación Para la Generación y Síntesis de Evidencias en Salud, Universidad San Ignacio de Loyola, Av. La Fontana 550, La Molina, 15024, Lima, Perú
| | - Jakub Ruszkowski
- Department of Pathophysiology, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
- Department of Nephrology, Transplantology and Internal Medicine. Faculty of Medicine, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Yasith Mathangasinghe
- Australian Regenerative Medicine Institute, Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
- Department of Anatomy Genetics and Biomedical Informatics, Faculty of Medicine, University of Colombo, 25 Kynsey Road, Colombo, 00800, Sri Lanka
| | - Camilo Ríos
- Department of Neurochemistry, National Institute of Neurology and Neurosurgery Manuel Velasco Suárez, Insurgentes Sur 3877, La Fama, Tlalpan, 14269, Ciudad de México, Mexico
| | - Carlos Pineda
- General Directorate, National Institute of Rehabilitation Luis Guillermo Ibarra Ibarra, Calzada México-Xochimilco 289, Arenal de Guadalupe, 14389, Ciudad de México, Mexico.
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21
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Luechtefeld T, Bozada T, Goel R, Wang L, Paller CJ. Applications for open access normalized synthesis in metastatic prostate cancer trials. Front Artif Intell 2022; 5:984836. [PMID: 36171797 PMCID: PMC9511148 DOI: 10.3389/frai.2022.984836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
Recent metastatic castration-resistant prostate cancer (mCRPC) clinical trials have integrated homologous recombination and DNA repair deficiency (HRD/DRD) biomarkers into eligibility criteria and secondary objectives. These trials led to the approval of some PARP inhibitors for mCRPC with HRD/DRD indications. Unfortunately, biomarker-trial outcome data is only discovered by reviewing publications, a process that is error-prone, time-consuming, and laborious. While prostate cancer researchers have written systematic evidence reviews (SERs) on this topic, given the time involved from the last search to publication, an SER is often outdated even before publication. The difficulty in reusing previous review data has resulted in multiple reviews of the same trials. Thus, it will be useful to create a normalized evidence base from recently published/presented biomarker-trial outcome data that one can quickly update. We present a new approach to semi-automating normalized, open-access data tables from published clinical trials of metastatic prostate cancer using a data curation and SER platform. Clinicaltrials.gov and Pubmed.gov were used to collect mCRPC clinical trial publications with HRD/DRD biomarkers. We extracted data from 13 publications covering ten trials that started before 22nd Apr 2021. We extracted 585 hazard ratios, response rates, duration metrics, and 543 adverse events. Across 334 patients, we also extracted 8,180 patient-level survival and biomarker values. Data tables were populated with survival metrics, raw patient data, eligibility criteria, adverse events, and timelines. A repeated strong association between HRD and improved PARP inhibitor response was observed. Several use cases for the extracted data are demonstrated via analyses of trial methods, comparison of treatment hazard ratios, and association of treatments with adverse events. Machine learning models are also built on combined and normalized patient data to demonstrate automated discovery of therapy/biomarker relationships. Overall, we demonstrate the value of systematically extracted and normalized data. We have also made our code open-source with simple instructions on updating the analyses as new data becomes available, which anyone can use even with limited programming knowledge. Finally, while we present a novel method of SER for mCRPC trials, one can also implement such semi-automated methods in other clinical trial domains to advance precision medicine.
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Affiliation(s)
| | | | - Rahul Goel
- Independent Researcher, San Francisco, CA, United States
| | - Lin Wang
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States
| | - Channing J. Paller
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Channing J. Paller
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22
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Grames EM, Montgomery GA, Boyes DH, Dicks LV, Forister ML, Matson TA, Nakagawa S, Prendergast KS, Taylor NG, Tingley MW, Wagner DL, White TE, Woodcock P, Elphick CS. A framework and case study to systematically identify long‐term insect abundance and diversity datasets. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Eliza M. Grames
- Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
- Department of Biology University of Nevada Reno Reno Nevada USA
| | - Graham A. Montgomery
- Ecology and Evolutionary Biology University of California Los Angeles Los Angeles California USA
| | | | - Lynn V. Dicks
- Department of Zoology University of Cambridge Cambridge Cambridgeshire UK
| | | | - Tanner A. Matson
- Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
| | | | - Nigel G. Taylor
- Department of Zoology University of Cambridge Cambridge Cambridgeshire UK
| | - Morgan W. Tingley
- Ecology and Evolutionary Biology University of California Los Angeles Los Angeles California USA
| | - David L. Wagner
- Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
| | - Thomas E. White
- School of Life and Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - Paul Woodcock
- Joint Nature Conservation Committee Peterborough Cambridgeshire UK
| | - Chris S. Elphick
- Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut USA
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23
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Agarwal D, Marques G, de la Torre-Díez I, Franco Martin MA, García Zapiraín B, Martín Rodríguez F. Transfer Learning for Alzheimer's Disease through Neuroimaging Biomarkers: A Systematic Review. SENSORS (BASEL, SWITZERLAND) 2021; 21:7259. [PMID: 34770565 PMCID: PMC8587338 DOI: 10.3390/s21217259] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Alzheimer's disease (AD) is a remarkable challenge for healthcare in the 21st century. Since 2017, deep learning models with transfer learning approaches have been gaining recognition in AD detection, and progression prediction by using neuroimaging biomarkers. This paper presents a systematic review of the current state of early AD detection by using deep learning models with transfer learning and neuroimaging biomarkers. Five databases were used and the results before screening report 215 studies published between 2010 and 2020. After screening, 13 studies met the inclusion criteria. We noted that the maximum accuracy achieved to date for AD classification is 98.20% by using the combination of 3D convolutional networks and local transfer learning, and that for the prognostic prediction of AD is 87.78% by using pre-trained 3D convolutional network-based architectures. The results show that transfer learning helps researchers in developing a more accurate system for the early diagnosis of AD. However, there is a need to consider some points in future research, such as improving the accuracy of the prognostic prediction of AD, exploring additional biomarkers such as tau-PET and amyloid-PET to understand highly discriminative feature representation to separate similar brain patterns, managing the size of the datasets due to the limited availability.
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Affiliation(s)
- Deevyankar Agarwal
- Department of Signal Theory and Communications and Telematics Engineering, University of Valladolid, Paseo de Belén 15, 47011 Valladolid, Spain; (G.M.); (I.d.l.T.-D.)
| | - Gonçalo Marques
- Department of Signal Theory and Communications and Telematics Engineering, University of Valladolid, Paseo de Belén 15, 47011 Valladolid, Spain; (G.M.); (I.d.l.T.-D.)
- Polytechnic of Coimbra, ESTGOH, Rua General Santos Costa, 3400-124 Oliveira do Hospital, Portugal
| | - Isabel de la Torre-Díez
- Department of Signal Theory and Communications and Telematics Engineering, University of Valladolid, Paseo de Belén 15, 47011 Valladolid, Spain; (G.M.); (I.d.l.T.-D.)
| | - Manuel A. Franco Martin
- Psychiatric Department, University Rio Hortega Hospital–Valladolid, 47011 Valladolid, Spain;
| | - Begoña García Zapiraín
- eVIDA Laboratory, University of Deusto, Avenida de las Universidades 24, 48007 Bilbao, Spain;
| | - Francisco Martín Rodríguez
- Advanced Clinical Simulation Center, School of Medicine, University of Valladolid, 47011 Valladolid, Spain;
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