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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Amin Gharbi-Meliani; François Husson; Henri Vandendriessche; Eleonore Bayen; +3 Authors

    Abstract Background Dementia is defined as a cognitive decline that affects functional status. Longitudinal ageing surveys often lack a clinical diagnosis of dementia though measure cognition and daily function over time. We used unsupervised machine learning and longitudinal data to identify transition to probable dementia. Methods Multiple Factor Analysis was applied to longitudinal function and cognitive data of 15,278 baseline participants (aged 50 years and more) from the Survey of Health, Ageing, and Retirement in Europe (SHARE) (waves 1, 2 and 4–7, between 2004 and 2017). Hierarchical Clustering on Principal Components discriminated three clusters at each wave. We estimated probable or “Likely Dementia” prevalence by sex and age, and assessed whether dementia risk factors increased the risk of being assigned probable dementia status using multistate models. Next, we compared the “Likely Dementia” cluster with self-reported dementia status and replicated our findings in the English Longitudinal Study of Ageing (ELSA) cohort (waves 1–9, between 2002 and 2019, 7840 participants at baseline). Results Our algorithm identified a higher number of probable dementia cases compared with self-reported cases and showed good discriminative power across all waves (AUC ranged from 0.754 [0.722–0.787] to 0.830 [0.800–0.861]). “Likely Dementia” status was more prevalent in older people, displayed a 2:1 female/male ratio, and was associated with nine factors that increased risk of transition to dementia: low education, hearing loss, hypertension, drinking, smoking, depression, social isolation, physical inactivity, diabetes, and obesity. Results were replicated in ELSA cohort with good accuracy. Conclusions Machine learning clustering can be used to study dementia determinants and outcomes in longitudinal population ageing surveys in which dementia clinical diagnosis is lacking. International audience

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ eScholarship - Unive...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Europe PubMed Central
    Other literature type . 2023
    Data sources: PubMed Central
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Alzheimer’s Research & Therapy
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ eScholarship - Unive...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Europe PubMed Central
      Other literature type . 2023
      Data sources: PubMed Central
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Alzheimer’s Research & Therapy
      Article . 2023 . Peer-reviewed
      License: CC BY
      Data sources: Crossref
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: John P. A. Ioannidis; Francesco Zonta; Michael Levitt;

    AbstractSeveral teams have been publishing global estimates of excess deaths during the COVID‐19 pandemic. Here, we examine potential flaws and underappreciated sources of uncertainty in global excess death calculations. Adjusting for changing population age structure is essential. Otherwise, excess deaths are markedly overestimated in countries with increasingly aging populations. Adjusting for changes in other high‐risk indicators, such as residence in long‐term facilities, may also make a difference. Death registration is highly incomplete in most countries; completeness corrections should allow for substantial uncertainty and consider that completeness may have changed during pandemic years. Excess death estimates have high sensitivity to modelling choice. Therefore different options should be considered and the full range of results should be shown for different choices of pre‐pandemic reference periods and imposed models. Any post‐modelling corrections in specific countries should be guided by pre‐specified rules. Modelling of all‐cause mortality (ACM) in countries that have ACM data and extrapolating these models to other countries is precarious; models may lack transportability. Existing global excess death estimates underestimate the overall uncertainty that is multiplicative across diverse sources of uncertainty. Informative excess death estimates require risk stratification, including age groups and ethnic/racial strata. Data to‐date suggest a death deficit among children during the pandemic and marked socioeconomic differences in deaths, widening inequalities. Finally, causal explanations require great caution in disentangling SARS‐CoV‐2 deaths, indirect pandemic effects and effects from measures taken. We conclude that excess deaths have many uncertainties, but globally deaths from SARS‐CoV‐2 may be the minority of calculated excess deaths.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Europe PubMed Central
    Other literature type . 2023
    Data sources: PubMed Central
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    European Journal of Clinical Investigation
    Article . 2023 . Peer-reviewed
    License: CC BY NC
    Data sources: Crossref
    SSRN Electronic Journal
    Article . 2023 . Peer-reviewed
    Data sources: Crossref
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Europe PubMed Central
      Other literature type . 2023
      Data sources: PubMed Central
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      European Journal of Clinical Investigation
      Article . 2023 . Peer-reviewed
      License: CC BY NC
      Data sources: Crossref
      SSRN Electronic Journal
      Article . 2023 . Peer-reviewed
      Data sources: Crossref
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Pierre J Chambon; Christopher Wu; Jackson M Steinkamp; Jason Adleberg; +2 Authors

    Abstract Objective To develop an automated deidentification pipeline for radiology reports that detect protected health information (PHI) entities and replaces them with realistic surrogates “hiding in plain sight.” Materials and Methods In this retrospective study, 999 chest X-ray and CT reports collected between November 2019 and November 2020 were annotated for PHI at the token level and combined with 3001 X-rays and 2193 medical notes previously labeled, forming a large multi-institutional and cross-domain dataset of 6193 documents. Two radiology test sets, from a known and a new institution, as well as i2b2 2006 and 2014 test sets, served as an evaluation set to estimate model performance and to compare it with previously released deidentification tools. Several PHI detection models were developed based on different training datasets, fine-tuning approaches and data augmentation techniques, and a synthetic PHI generation algorithm. These models were compared using metrics such as precision, recall and F1 score, as well as paired samples Wilcoxon tests. Results Our best PHI detection model achieves 97.9 F1 score on radiology reports from a known institution, 99.6 from a new institution, 99.5 on i2b2 2006, and 98.9 on i2b2 2014. On reports from a known institution, it achieves 99.1 recall of detecting the core of each PHI span. Discussion Our model outperforms all deidentifiers it was compared to on all test sets as well as human labelers on i2b2 2014 data. It enables accurate and automatic deidentification of radiology reports. Conclusions A transformer-based deidentification pipeline can achieve state-of-the-art performance for deidentifying radiology reports and other medical documents.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Europe PubMed Central
    Other literature type . 2022
    Data sources: PubMed Central
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Journal of the American Medical Informatics Association
    Article . 2022 . Peer-reviewed
    License: OUP Standard Publication Reuse
    Data sources: Crossref
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Europe PubMed Central
      Other literature type . 2022
      Data sources: PubMed Central
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Journal of the American Medical Informatics Association
      Article . 2022 . Peer-reviewed
      License: OUP Standard Publication Reuse
      Data sources: Crossref
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Iosif Lazaridis; Songül Alpaslan-Roodenberg; Ayşe Acar; Ayşen Açıkkol; +201 Authors

    We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia. The newly reported dataset is described in detail in an accompanying Research Article, where we also acknowledge the funders who supported dataset generation (12). Analysis of data was supported by the National Institutes of Health (GM100233 and HG012287), the John Templeton Foundation (grant 61220), a private gift from Jean-Francois Clin, the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, and the Howard Hughes Medical Institute (D.R.). National Institutes of Health [GM100233, HG012287]; John Templeton Foundation [61220]; Allen Discovery Center program; Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; Howard Hughes Medical Institute

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Europe PubMed Central
    Other literature type . 2022
    Data sources: PubMed Central
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Iosif Lazaridis; Songül Alpaslan-Roodenberg; Ayşe Acar; Ayşen Açıkkol; +201 Authors

    Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region. The newly reported dataset is described in detail in an accompanying manuscript, where we also acknowledge the funders who supported dataset generation (1). Analysis of data was supported by the National Institutes of Health (GM100233 and HG012287), the John Templeton Foundation (grant 61220), a private gift from Jean-Francois Clin, the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, and the Howard Hughes Medical Institute (to D.R.). National Institutes of Health [GM100233, HG012287]; John Templeton Foundation [61220]; Allen Discovery Center program; Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; Howard Hughes Medical Institute

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Pamukkale GCRIS Data...arrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Europe PubMed Central
    Other literature type . 2022
    Data sources: PubMed Central
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Science
    Article . 2022
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    Authors: Renaud Schiappa; Sara Contu; Dorian Culie; Brice Thamphya; +7 Authors

    PURPOSE Electronic medical records are a valuable source of information about patients' clinical status but are often free-text documents that require laborious manual review to be exploited. Techniques from computer science have been investigated, but the literature has marginally focused on non-English language texts. We developed RUBY, a tool designed in collaboration with IBM—France to automatically structure clinical information from French medical records of patients with breast cancer. MATERIALS AND METHODS RUBY, which exploits state-of-the-art Named Entity Recognition models combined with keyword extraction and postprocessing rules, was applied on clinical texts. We investigated the precision of RUBY in extracting the target information. RESULTS RUBY has an average precision of 92.8% for the Surgery report, 92.7% for the Pathology report, 98.1% for the Biopsy report, and 81.8% for the Consultation report. CONCLUSION These results show that the automatic approach has the potential to effectively extract clinical knowledge from an extensive set of electronic medical records, reducing the manual effort required and saving a significant amount of time. A deeper semantic analysis and further understanding of the context in the text, as well as training on a larger and more recent set of reports, including those containing highly variable entities and the use of ontologies, could further improve the results.

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    JCO Clinical Cancer Informatics
    Article . 2022 . Peer-reviewed
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      JCO Clinical Cancer Informatics
      Article . 2022 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Alex S Cohen; Zachary Rodriguez; Kiara K Warren; Tovah Cowan; +6 Authors

    Abstract Background and Hypothesis Despite decades of “proof of concept” findings supporting the use of Natural Language Processing (NLP) in psychosis research, clinical implementation has been slow. One obstacle reflects the lack of comprehensive psychometric evaluation of these measures. There is overwhelming evidence that criterion and content validity can be achieved for many purposes, particularly using machine learning procedures. However, there has been very little evaluation of test-retest reliability, divergent validity (sufficient to address concerns of a “generalized deficit”), and potential biases from demographics and other individual differences. Study Design This article highlights these concerns in development of an NLP measure for tracking clinically rated paranoia from video “selfies” recorded from smartphone devices. Patients with schizophrenia or bipolar disorder were recruited and tracked over a week-long epoch. A small NLP-based feature set from 499 language samples were modeled on clinically rated paranoia using regularized regression. Study Results While test–retest reliability was high, criterion, and convergent/divergent validity were only achieved when considering moderating variables, notably whether a patient was away from home, around strangers, or alone at the time of the recording. Moreover, there were systematic racial and sex biases in the model, in part, reflecting whether patients submitted videos when they were away from home, around strangers, or alone. Conclusions Advancing NLP measures for psychosis will require deliberate consideration of test-retest reliability, divergent validity, systematic biases and the potential role of moderators. In our example, a comprehensive psychometric evaluation revealed clear strengths and weaknesses that can be systematically addressed in future research.

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    Schizophrenia Bulletin
    Article . 2022 . Peer-reviewed
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      Schizophrenia Bulletin
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Colline Brassard; Adrian Bălăşescu; Rose-Marie Arbogast; Vianney Forest; +14 Authors

    International audience; Dogs are among the most variable species today, but little is known about the morphological variability in the early phases of their history. The Neolithic transition to farming may have resulted in an early morphological diversification as a result of changes in the anthropic environment or intentional selection on specific morphologies. Here, we describe the variability and modularity in mandible form by comparing 525 dog mandibles from European archaeological sites ranging from 8100 to 3000 cal. BC to a reference sample of modern dogs, wolves, and dingoes. We use three-dimensional geometric morphometrics to quantify the form of complete and fragmented mandibles. We demonstrate that an important morphological variability already existed before the Bronze Age in Europe, yet the largest, smallest, most brachycephalic or dolichocephalic extant dogs have no equivalent in the archaeological sample, resulting in a lower variation compared to modern relatives. The covariation between the anterior and posterior parts of the mandible is lower in archaeological dogs, suggesting a low degree of intentional human selection in early periods. The mandible of modern and ancient dogs differs in functionally important areas, possibly reflecting differences in diet, competition, or the implication of ancient dogs in hunting or defence.

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    Proceedings of the Royal Society B Biological Sciences
    Article . 2022 . Peer-reviewed
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      Proceedings of the Royal Society B Biological Sciences
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    Authors: Baylac-Paouly, Baptiste; Caballero, María-Victoria; Porras, María-Isabel;

    AbstractPoliomyelitis is a disease whose incidence steadily increased during the second half of the twentieth century on both sides of the Atlantic. If in the United States the epidemics which afflicted young children each summer became a major public health issue, in France, polio was considered less pressing than other diseases. This article, based on original archives from the Pasteur and Mérieux institutes, analyses the polio control strategies and policies implemented by France from the mid-1950s to the end of the 1960s. The article examines the role of two key actors and institutions that mobilised the French health authorities against the disease: Pierre Lépine and the Institut Pasteur as well as Charles Mérieux and the Institut Mérieux. Lépine developed an effective injected polio vaccine which was first used before being supplemented with the oral polio vaccine. If the two main protagonists and their institutions worked together, they each implemented different actions and manoeuvres, at different times with the aim to raise awareness of the fight against the disease. The national and international relations of the key French actors were decisive in the development and production of the polio vaccines and their application. This work contributes to understanding processes of polio vaccines choice at the level of national institutions and analyses the political and scientific networks built in support of polio vaccination, to finally move towards compulsory vaccination. Ultimately, this study describes the historical processes by which this disease became conflated with a biotechnology of collective protection in France.

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    Medical History
    Article . 2022 . Peer-reviewed
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    HAL-ENS-LYON
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      Medical History
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    Authors: Rachel K. Sales; Crystal N. H. McMichael; Suzette G. A. Flantua; Kimberley Hagemans; +4 Authors

    Much has yet to be learned of the spatial patterning of pre-Columbian people across the Tropical Andes. Using compiled archaeological data and a suite of environmental variables, we generate an ensemble species distribution model (SDM) that incorporates general additive models, random forest models and Maxent models to reconstruct spatial patterns of pre-Columbian people that inhabited the Tropical Andes east of the continental divide, within the modern countries of Bolivia, Peru and Ecuador. Within this region, here referred to as the eastern Andean flank, elevation, mean annual cloud frequency, distance to rivers and precipitation of the driest quarter are the environmental variables most closely related to human occupancy. Our model indicates that 11.04% of our study area (65 368 km 2 ) was likely occupied by pre-Columbian people. Our model shows that 30 of 351 forest inventory plots, which are used to generate ecological understanding of Andean ecosystems, were likely occupied in the pre-Columbian period. In previously occupied sites, successional trajectories may still be shaping forest dynamics, and those forests may still be recovering from the ecological legacy of pre-Columbian impacts. Our ensemble SDM links palaeo- and neo-ecology and can also be used to guide both future archaeological and ecological studies. This article is part of the theme issue ‘Tropical forests in the deep human past’.

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    Philosophical Transactions of the Royal Society B Biological Sciences
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      Philosophical Transactions of the Royal Society B Biological Sciences
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Amin Gharbi-Meliani; François Husson; Henri Vandendriessche; Eleonore Bayen; +3 Authors

    Abstract Background Dementia is defined as a cognitive decline that affects functional status. Longitudinal ageing surveys often lack a clinical diagnosis of dementia though measure cognition and daily function over time. We used unsupervised machine learning and longitudinal data to identify transition to probable dementia. Methods Multiple Factor Analysis was applied to longitudinal function and cognitive data of 15,278 baseline participants (aged 50 years and more) from the Survey of Health, Ageing, and Retirement in Europe (SHARE) (waves 1, 2 and 4–7, between 2004 and 2017). Hierarchical Clustering on Principal Components discriminated three clusters at each wave. We estimated probable or “Likely Dementia” prevalence by sex and age, and assessed whether dementia risk factors increased the risk of being assigned probable dementia status using multistate models. Next, we compared the “Likely Dementia” cluster with self-reported dementia status and replicated our findings in the English Longitudinal Study of Ageing (ELSA) cohort (waves 1–9, between 2002 and 2019, 7840 participants at baseline). Results Our algorithm identified a higher number of probable dementia cases compared with self-reported cases and showed good discriminative power across all waves (AUC ranged from 0.754 [0.722–0.787] to 0.830 [0.800–0.861]). “Likely Dementia” status was more prevalent in older people, displayed a 2:1 female/male ratio, and was associated with nine factors that increased risk of transition to dementia: low education, hearing loss, hypertension, drinking, smoking, depression, social isolation, physical inactivity, diabetes, and obesity. Results were replicated in ELSA cohort with good accuracy. Conclusions Machine learning clustering can be used to study dementia determinants and outcomes in longitudinal population ageing surveys in which dementia clinical diagnosis is lacking. International audience

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    Europe PubMed Central
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    Alzheimer’s Research & Therapy
    Article . 2023 . Peer-reviewed
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      Alzheimer’s Research & Therapy
      Article . 2023 . Peer-reviewed
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    Authors: John P. A. Ioannidis; Francesco Zonta; Michael Levitt;

    AbstractSeveral teams have been publishing global estimates of excess deaths during the COVID‐19 pandemic. Here, we examine potential flaws and underappreciated sources of uncertainty in global excess death calculations. Adjusting for changing population age structure is essential. Otherwise, excess deaths are markedly overestimated in countries with increasingly aging populations. Adjusting for changes in other high‐risk indicators, such as residence in long‐term facilities, may also make a difference. Death registration is highly incomplete in most countries; completeness corrections should allow for substantial uncertainty and consider that completeness may have changed during pandemic years. Excess death estimates have high sensitivity to modelling choice. Therefore different options should be considered and the full range of results should be shown for different choices of pre‐pandemic reference periods and imposed models. Any post‐modelling corrections in specific countries should be guided by pre‐specified rules. Modelling of all‐cause mortality (ACM) in countries that have ACM data and extrapolating these models to other countries is precarious; models may lack transportability. Existing global excess death estimates underestimate the overall uncertainty that is multiplicative across diverse sources of uncertainty. Informative excess death estimates require risk stratification, including age groups and ethnic/racial strata. Data to‐date suggest a death deficit among children during the pandemic and marked socioeconomic differences in deaths, widening inequalities. Finally, causal explanations require great caution in disentangling SARS‐CoV‐2 deaths, indirect pandemic effects and effects from measures taken. We conclude that excess deaths have many uncertainties, but globally deaths from SARS‐CoV‐2 may be the minority of calculated excess deaths.

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    European Journal of Clinical Investigation
    Article . 2023 . Peer-reviewed
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    SSRN Electronic Journal
    Article . 2023 . Peer-reviewed
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      European Journal of Clinical Investigation
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    Authors: Pierre J Chambon; Christopher Wu; Jackson M Steinkamp; Jason Adleberg; +2 Authors

    Abstract Objective To develop an automated deidentification pipeline for radiology reports that detect protected health information (PHI) entities and replaces them with realistic surrogates “hiding in plain sight.” Materials and Methods In this retrospective study, 999 chest X-ray and CT reports collected between November 2019 and November 2020 were annotated for PHI at the token level and combined with 3001 X-rays and 2193 medical notes previously labeled, forming a large multi-institutional and cross-domain dataset of 6193 documents. Two radiology test sets, from a known and a new institution, as well as i2b2 2006 and 2014 test sets, served as an evaluation set to estimate model performance and to compare it with previously released deidentification tools. Several PHI detection models were developed based on different training datasets, fine-tuning approaches and data augmentation techniques, and a synthetic PHI generation algorithm. These models were compared using metrics such as precision, recall and F1 score, as well as paired samples Wilcoxon tests. Results Our best PHI detection model achieves 97.9 F1 score on radiology reports from a known institution, 99.6 from a new institution, 99.5 on i2b2 2006, and 98.9 on i2b2 2014. On reports from a known institution, it achieves 99.1 recall of detecting the core of each PHI span. Discussion Our model outperforms all deidentifiers it was compared to on all test sets as well as human labelers on i2b2 2014 data. It enables accurate and automatic deidentification of radiology reports. Conclusions A transformer-based deidentification pipeline can achieve state-of-the-art performance for deidentifying radiology reports and other medical documents.

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    Journal of the American Medical Informatics Association
    Article . 2022 . Peer-reviewed
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      Journal of the American Medical Informatics Association
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    Authors: Iosif Lazaridis; Songül Alpaslan-Roodenberg; Ayşe Acar; Ayşen Açıkkol; +201 Authors

    We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia. The newly reported dataset is described in detail in an accompanying Research Article, where we also acknowledge the funders who supported dataset generation (12). Analysis of data was supported by the National Institutes of Health (GM100233 and HG012287), the John Templeton Foundation (grant 61220), a private gift from Jean-Francois Clin, the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, and the Howard Hughes Medical Institute (D.R.). National Institutes of Health [GM100233, HG012287]; John Templeton Foundation [61220]; Allen Discovery Center program; Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; Howard Hughes Medical Institute

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    Authors: Iosif Lazaridis; Songül Alpaslan-Roodenberg; Ayşe Acar; Ayşen Açıkkol; +201 Authors

    Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region. The newly reported dataset is described in detail in an accompanying manuscript, where we also acknowledge the funders who supported dataset generation (1). Analysis of data was supported by the National Institutes of Health (GM100233 and HG012287), the John Templeton Foundation (grant 61220), a private gift from Jean-Francois Clin, the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, and the Howard Hughes Medical Institute (to D.R.). National Institutes of Health [GM100233, HG012287]; John Templeton Foundation [61220]; Allen Discovery Center program; Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; Howard Hughes Medical Institute

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    Science
    Article . 2022
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    Authors: Renaud Schiappa; Sara Contu; Dorian Culie; Brice Thamphya; +7 Authors

    PURPOSE Electronic medical records are a valuable source of information about patients' clinical status but are often free-text documents that require laborious manual review to be exploited. Techniques from computer science have been investigated, but the literature has marginally focused on non-English language texts. We developed RUBY, a tool designed in collaboration with IBM—France to automatically structure clinical information from French medical records of patients with breast cancer. MATERIALS AND METHODS RUBY, which exploits state-of-the-art Named Entity Recognition models combined with keyword extraction and postprocessing rules, was applied on clinical texts. We investigated the precision of RUBY in extracting the target information. RESULTS RUBY has an average precision of 92.8% for the Surgery report, 92.7% for the Pathology report, 98.1% for the Biopsy report, and 81.8% for the Consultation report. CONCLUSION These results show that the automatic approach has the potential to effectively extract clinical knowledge from an extensive set of electronic medical records, reducing the manual effort required and saving a significant amount of time. A deeper semantic analysis and further understanding of the context in the text, as well as training on a larger and more recent set of reports, including those containing highly variable entities and the use of ontologies, could further improve the results.

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    JCO Clinical Cancer Informatics
    Article . 2022 . Peer-reviewed
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      JCO Clinical Cancer Informatics
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    Authors: Alex S Cohen; Zachary Rodriguez; Kiara K Warren; Tovah Cowan; +6 Authors

    Abstract Background and Hypothesis Despite decades of “proof of concept” findings supporting the use of Natural Language Processing (NLP) in psychosis research, clinical implementation has been slow. One obstacle reflects the lack of comprehensive psychometric evaluation of these measures. There is overwhelming evidence that criterion and content validity can be achieved for many purposes, particularly using machine learning procedures. However, there has been very little evaluation of test-retest reliability, divergent validity (sufficient to address concerns of a “generalized deficit”), and potential biases from demographics and other individual differences. Study Design This article highlights these concerns in development of an NLP measure for tracking clinically rated paranoia from video “selfies” recorded from smartphone devices. Patients with schizophrenia or bipolar disorder were recruited and tracked over a week-long epoch. A small NLP-based feature set from 499 language samples were modeled on clinically rated paranoia using regularized regression. Study Results While test–retest reliability was high, criterion, and convergent/divergent validity were only achieved when considering moderating variables, notably whether a patient was away from home, around strangers, or alone at the time of the recording. Moreover, there were systematic racial and sex biases in the model, in part, reflecting whether patients submitted videos when they were away from home, around strangers, or alone. Conclusions Advancing NLP measures for psychosis will require deliberate consideration of test-retest reliability, divergent validity, systematic biases and the potential role of moderators. In our example, a comprehensive psychometric evaluation revealed clear strengths and weaknesses that can be systematically addressed in future research.

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    Schizophrenia Bulletin
    Article . 2022 . Peer-reviewed
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      Schizophrenia Bulletin
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    Authors: Colline Brassard; Adrian Bălăşescu; Rose-Marie Arbogast; Vianney Forest; +14 Authors

    International audience; Dogs are among the most variable species today, but little is known about the morphological variability in the early phases of their history. The Neolithic transition to farming may have resulted in an early morphological diversification as a result of changes in the anthropic environment or intentional selection on specific morphologies. Here, we describe the variability and modularity in mandible form by comparing 525 dog mandibles from European archaeological sites ranging from 8100 to 3000 cal. BC to a reference sample of modern dogs, wolves, and dingoes. We use three-dimensional geometric morphometrics to quantify the form of complete and fragmented mandibles. We demonstrate that an important morphological variability already existed before the Bronze Age in Europe, yet the largest, smallest, most brachycephalic or dolichocephalic extant dogs have no equivalent in the archaeological sample, resulting in a lower variation compared to modern relatives. The covariation between the anterior and posterior parts of the mandible is lower in archaeological dogs, suggesting a low degree of intentional human selection in early periods. The mandible of modern and ancient dogs differs in functionally important areas, possibly reflecting differences in diet, competition, or the implication of ancient dogs in hunting or defence.

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    Proceedings of the Royal Society B Biological Sciences
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      Proceedings of the Royal Society B Biological Sciences
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    Authors: Baylac-Paouly, Baptiste; Caballero, María-Victoria; Porras, María-Isabel;

    AbstractPoliomyelitis is a disease whose incidence steadily increased during the second half of the twentieth century on both sides of the Atlantic. If in the United States the epidemics which afflicted young children each summer became a major public health issue, in France, polio was considered less pressing than other diseases. This article, based on original archives from the Pasteur and Mérieux institutes, analyses the polio control strategies and policies implemented by France from the mid-1950s to the end of the 1960s. The article examines the role of two key actors and institutions that mobilised the French health authorities against the disease: Pierre Lépine and the Institut Pasteur as well as Charles Mérieux and the Institut Mérieux. Lépine developed an effective injected polio vaccine which was first used before being supplemented with the oral polio vaccine. If the two main protagonists and their institutions worked together, they each implemented different actions and manoeuvres, at different times with the aim to raise awareness of the fight against the disease. The national and international relations of the key French actors were decisive in the development and production of the polio vaccines and their application. This work contributes to understanding processes of polio vaccines choice at the level of national institutions and analyses the political and scientific networks built in support of polio vaccination, to finally move towards compulsory vaccination. Ultimately, this study describes the historical processes by which this disease became conflated with a biotechnology of collective protection in France.

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    Medical History
    Article . 2022 . Peer-reviewed
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      Medical History
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    Authors: Rachel K. Sales; Crystal N. H. McMichael; Suzette G. A. Flantua; Kimberley Hagemans; +4 Authors

    Much has yet to be learned of the spatial patterning of pre-Columbian people across the Tropical Andes. Using compiled archaeological data and a suite of environmental variables, we generate an ensemble species distribution model (SDM) that incorporates general additive models, random forest models and Maxent models to reconstruct spatial patterns of pre-Columbian people that inhabited the Tropical Andes east of the continental divide, within the modern countries of Bolivia, Peru and Ecuador. Within this region, here referred to as the eastern Andean flank, elevation, mean annual cloud frequency, distance to rivers and precipitation of the driest quarter are the environmental variables most closely related to human occupancy. Our model indicates that 11.04% of our study area (65 368 km 2 ) was likely occupied by pre-Columbian people. Our model shows that 30 of 351 forest inventory plots, which are used to generate ecological understanding of Andean ecosystems, were likely occupied in the pre-Columbian period. In previously occupied sites, successional trajectories may still be shaping forest dynamics, and those forests may still be recovering from the ecological legacy of pre-Columbian impacts. Our ensemble SDM links palaeo- and neo-ecology and can also be used to guide both future archaeological and ecological studies. This article is part of the theme issue ‘Tropical forests in the deep human past’.

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    Philosophical Transactions of the Royal Society B Biological Sciences
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