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1. Interpretable Stratification for Chronic Kidney Disease Progression Based on Time to Event Analysis

Author: Ghalwash, Mohamed, Koseki, Akira, Iwamori, Toshiya, Kudo, Michiharu, and Meyer, Pablo
Subjects: Articles
Abstract: In Chronic Kidney Disease (CKD), kidneys are damaged and lose their ability to filter blood, leading to a plethora of health consequences that end up in dialysis. Despite its prevalence, CKD goes often undetected at early stages. In order to better understand disease progression, we stratified patients with CKD by considering the time to dialysis from diagnosis of early CKD (stages 1 or 2). To achieve this, we first reduced the number of clinical features in a predictive time-to-dialysis model and identified the top important features on a cohort of ∼ 40, 000 CKD patients. The extracted features were used to stratify a subpopulation of 3, 522 patients that showed anemia and were prescribed for cardiovascular-related drugs and progressed faster to dialysis. On the other side, clustering patients using conventional clustering methods based on their clinical features did not allow such clear interpretation to identify the main factors for leading fast progression to dialysis. To our knowledge this is the first study extracting interpretable features for stratifying a cohort of early CKD patients using time-to-event analysis which could help prevention and the development of new treatments.
Published: 2023

2. The novelty Mezilaurus conceicionensis (Lauraceae) and a key to the species of the genus from Brazilian Southeastern

Author: Alves, Flávio Macedo, Meyer, Pablo Burkowski, and Assis, Leandro Cézanne De Souza
Subjects: Tracheophyta, Magnoliopsida, Lauraceae, Laurales, Biodiversity, Plant Science, Plantae, Ecology, Evolution, Behavior and Systematics, Taxonomy
Abstract: A new species, Mezilaurus conceicionensis (Lauraceae), from Southeastern Brazil, was discovered during fieldwork at Serra da Ferrugem, State of Minas Gerais. This new species is described and illustrated in this study, being distinguished from the remaining species of Mezilaurus species mostly by its globoid fruits. An identification key of the species of Mezilaurus from Southeastern Brazil is presented.
Published: 2022
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3. Predicting/characterizing chemosensory changes in COVID+ vs. COVID- using natural language processing of multinational survey data

Author: Walsh-Messinger, Julie, Meyer, Pablo, Parma, Valentina, Farruggia, Michael, and Pellegrino, Robert
Subjects: Medicine and Health Sciences, Social and Behavioral Sciences
Abstract: COVID-19 is associated with notable decrements in chemosensation. Notably, other upper respiratory infections (URIs) are also associated with decrements in chemosensory ability, though their pathophysiology and extent likely differ from that of COVID-19. Here, we seek to determine whether self-reported text descriptors of chemosensory ability can predict COVID+ versus COVID- status, and then characterize the semantic architecture of these predictive features. Finally, we seek to use the text descriptors provided to better characterize qualitative loss in smell and chemesthesis. We will answer the following questions: 1. What is the sensitivity and specificity of applying natural language processing tools to self-reported text descriptors of chemosensory ability for predicting COVID+ vs. COVID-? 2. What are the characteristics of the semantic architecture of predictive self-reported text descriptions of chemosensory-related COVID+ vs COVID- diagnosis? 3. What are the qualitative characteristics of anosmia, hyposmia, parosmia, and phantosmia associated with COVID+?
Published: 2022
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4. Mere end lugtesans - COVID-19 er associeret med svær påvirkning af lugtesansen, smagssansen og mundfølelsen

Author: Parma, Valentina, Ohla, Kathrin, Veldhuizen, Maria G, Niv, Masha Y, Kelly, Christine E, Bakke, Alyssa J, Cooper, Keiland W, Bouysset, Cédric, Pirastu, Nicola, Dibattista, Michele, Kaur, Rishemjit, Liuzza, Marco Tullio, Pepino, Marta Y, Schöpf, Veronika, Pereda-Loth, Veronica, Olsson, Shannon B, Gerkin, Richard C, Rohlfs Domínguez, Paloma, Albayay, Javier, Farruggia, Michael C, Bhutani, Surabhi, Fjaeldstad, Alexander W, Kumar, Ritesh, Menini, Anna, Bensafi, Moustafa, Sandell, Mari, Konstantinidis, Iordanis, Di Pizio, Antonella, Genovese, Federica, Öztürk, Lina, Thomas-Danguin, Thierry, Frasnelli, Johannes, Boesveldt, Sanne, Saatci, Özlem, Saraiva, Luis R, Lin, Cailu, Golebiowski, Jérôme, Hwang, Liang-Dar, Ozdener, Mehmet Hakan, Guàrdia, Maria Dolors, Laudamiel, Christophe, Ritchie, Marina, Havlícek, Jan, Pierron, Denis, Roura, Eugeni, Navarro, Marta, Nolden, Alissa A, Lim, Juyun, Whitcroft, Katherine L, Colquitt, Lauren R, Ferdenzi, Camille, Brindha, Evelyn V, Altundag, Aytug, Macchi, Alberto, Nunez-Parra, Alexia, Patel, Zara M, Fiorucci, Sébastien, Philpott, Carl M, Smith, Barry C, Lundström, Johan N, Mucignat, Carla, Parker, Jane K, van den Brink, Mirjam, Schmuker, Michael, Fischmeister, Florian Ph S, Heinbockel, Thomas, Shields, Vonnie D C, Faraji, Farhoud, Santamaría, Enrique, Fredborg, William E A, Morini, Gabriella, Olofsson, Jonas K, Jalessi, Maryam, Karni, Noam, D’Errico, Anna, Alizadeh, Rafieh, Pellegrino, Robert, Meyer, Pablo, Huart, Caroline, Chen, Ben, Soler, Graciela M, Alwashahi, Mohammed K, Welge-Lüssen, Antje, Freiherr, Jessica, de Groot, Jasper H B, Klein, Hadar, Okamoto, Masako, Singh, Preet Bano, Hsieh, Julien W, Abdulrahman, Olagunju, Dalton, Pamela, Yan, Carol H, Voznessenskaya, Vera V, Chen, Jingguo, Sell, Elizabeth A, Walsh-Messinger, Julie, Archer, Nicholas S, Koyama, Sachiko, Deary, Vincent, Roberts, S Craig, Yanık, Hüseyin, Albayrak, Samet, Nováková, Lenka Martinec, Croijmans, Ilja, Mazal, Patricia Portillo, Moein, Shima T, Margulis, Eitan, Mignot, Coralie, Mariño, Sajidxa, Georgiev, Dejan, Kaushik, Pavan K, Malnic, Bettina, Wang, Hong, Seyed-Allaei, Shima, Yoluk, Nur, Razzaghi-Asl, Sara, Justice, Jeb M, Restrepo, Diego, Reed, Danielle R, Hummel, Thomas, Munger, Steven D, Hayes, John E, Indústries Alimentàries, Qualitat i Tecnologia Alimentària, Tecnologia Alimentària, Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Mersin University, The Hebrew University of Jerusalem (HUJ), AbScent, Pennsylvania State University (Penn State), Penn State System, University of California [Irvine] (UC Irvine), University of California (UC), Université Côte d'Azur (UCA), University of Edinburgh, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Central Scientific Instruments Organisation (CSIR), Università degli Studi 'Magna Graecia' di Catanzaro = University of Catanzaro (UMG), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Medizinische Universität Wien = Medical University of Vienna, Groupement scientifique de Biologie et de Medecine Spatiale (GSBMS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES), Tata Institute for Fundamental Research (TIFR), Arizona State University [Tempe] (ASU), Universidad de Extremadura - University of Extremadura (UEX), Università degli Studi di Padova = University of Padua (Unipd), Yale School of Medicine [New Haven, Connecticut] (YSM), San Diego State University (SDSU), Aarhus University [Aarhus], University of Hertfordshire [Hatfield] (UH), Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), Neurosciences Sensorielles Comportement Cognition, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, University of Turku, Aristotle University of Thessaloniki, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Monell Chemical Senses Center, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), Université de Montréal (UdeM), Wageningen University and Research Centre (WUR), Medical Science University, Sidra Medicine [Doha, Qatar], Institut de Chimie de Nice (ICN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), University of Southern Queensland (USQ), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), DreamAir Llc, Charles University [Prague] (CU), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Massachusetts System (UMASS), Oregon State University (OSU), Ear Institute, UCL, Lyon Neuroscience Research center, Karunya University, Biruni University, Assi Sette Llaghi Varese, Stanford School of Medicine [Stanford], Stanford Medicine, Stanford University-Stanford University, University of East Anglia [Norwich] (UEA), California Department of Food and Agriculture (CDFA), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Maastricht University [Maastricht], Institute for Biology - Neurobiology, Freie Universität Berlin, Karl-Franzens-Universität Graz, Howard University College of Medicine, Towson University, University of California [San Diego] (UC San Diego), Proteomics, Center for Applied Medical Research (CIMA), Stockholm University, University of Gastronomic Sciences, Iran University of Medical Sciences, Goethe Universität Frankfurt, University of Tennessee, IBM T.J. Watson Research Center, Université libre de Bruxelles (ULB), Guangzhou Medical University, Buenos Aires University and GEOG (Grupo de Estudio de Olfato y Gusto), Sultan Qaboos University (SQU), Federal University of Technology of Akure (FUTA), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Hospital of Xi'an Jiaotong University, University of Pennsylvania, University of Dayton, CSIRO Agriculture and Food (CSIRO), Indiana University [Bloomington], Indiana University System, University of Northumbria at Newcastle [United Kingdom], University of Stirling, Middle East Technical University [Ankara] (METU), Utrecht University [Utrecht], Instituto Universitario del Hospital Italiano [Buenos Aires, Argentina], Institute for Research in Fundamental Sciences [Tehran] (IPM), Hebrew University of Jerusalem, Technische Universität Dresden = Dresden University of Technology (TU Dresden), Terrazas del Club Hipico, University Medical Centre Ljubljana [Ljubljana, Slovenia] (UMCL), Tata Institute of Fundamental Research [Bangalore], Universidade de São Paulo = University of São Paulo (USP), University of Florida [Gainesville] (UF), University of Colorado Anschutz [Aurora], Center for Smell and Taste, Department of Food Science, Pennsylvania State University., Julien, Sabine, Tıp Fakültesi, UCL - SSS/IONS/NEUR - Clinical Neuroscience, UCL - (SLuc) Service d'oto-rhino-laryngologie, Department of Food and Nutrition, Senses and Food, Research Center Jülich, University of California [Irvine] (UCI), University of California, Università degli studi di Bari Aldo Moro (UNIBA), Università degli Studi 'Magna Graecia' di Catanzaro [Catanzaro, Italie] (UMG), University of Extremadura, University of Padova, Yale University School of Medicine, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, University of Helsinki, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Institute of Agrifood Research and Technology (IRTA), Universita degli Studi di Padova, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Karl-Franzens-Universität [Graz, Autriche], University of California San Diego Health, University of Brussels, University of Pennsylvania [Philadelphia], Tata Institute of Fundamental Research, University of São Paulo (USP), UCL - SSS/IONS - Institute of NeuroScience, FSE Campus Venlo, and RS: FSE UCV
Subjects: Male, Taste, Physiology, Smagstab, Audiology, AcademicSubjects/SCI01180, Settore BIO/09 - Fisiologia, Behavioral Neuroscience, chemistry.chemical_compound, Olfaction Disorders, Taste Disorders, 0302 clinical medicine, RATINGS, Hyposmia, Surveys and Questionnaires, CHEMOSENSITIVITY, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Viral, PALADAR, 030223 otorhinolaryngology, Sensory Science and Eating Behaviour, media_common, TASTE, US NATIONAL-HEALTH, [SDV.IDA] Life Sciences [q-bio]/Food engineering, Middle Aged, Biological Sciences, 16. Peace & justice, Sensory Systems, 3. Good health, Smell, GCCR Group Author, ddc:540, Smell loss, Female, Original Article, medicine.symptom, Corrigendum, Coronavirus Infections, olfaction, Adult, somatosensation, medicine.medical_specialty, 663/664, Coronavirus disease 2019 (COVID-19), OLFACTORY DISORDERS, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), media_common.quotation_subject, Pneumonia, Viral, head and neck surgery, Aged, Betacoronavirus, COVID-19, Humans, Pandemics, SARS-CoV-2, Self Report, Somatosensory Disorders, Young Adult, Anosmia, Sensory system, Olfaction, 03 medical and health sciences, Chemesthesis, Physiology (medical), Perception, medicine, Neurology & Neurosurgery, Behaviour Change and Well-being, business.industry, R-PACKAGE, 3112 Neurosciences, Pneumonia, Parosmia, COMPONENT, Smagssans, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Sensoriek en eetgedrag, chemistry, Lugtetab, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Lugtesans
Abstract: Correction: Chemical Senses, Volume 46, 2021, bjab050, https://doi.org/10.1093/chemse/bjab050 Published: 08 December 2021 Recent anecdotal and scientific reports have provided evidence of a link between COVID-19 and chemosensory impairments, such as anosmia. However, these reports have downplayed or failed to distinguish potential effects on taste, ignored chemesthesis, and generally lacked quantitative measurements. Here, we report the development, implementation, and initial results of a multilingual, international questionnaire to assess self-reported quantity and quality of perception in 3 distinct chemosensory modalities (smell, taste, and chemesthesis) before and during COVID-19. In the first 11 days after questionnaire launch, 4039 participants (2913 women, 1118 men, and 8 others, aged 19-79) reported a COVID-19 diagnosis either via laboratory tests or clinical assessment. Importantly, smell, taste, and chemesthetic function were each significantly reduced compared to their status before the disease. Difference scores (maximum possible change +/- 100) revealed a mean reduction of smell (-79.7 +/- 28.7, mean +/- standard deviation), taste (-69.0 +/- 32.6), and chemesthetic (-37.3 +/- 36.2) function during COVID-19. Qualitative changes in olfactory ability (parosmia and phantosmia) were relatively rare and correlated with smell loss. Importantly, perceived nasal obstruction did not account for smell loss. Furthermore, chemosensory impairments were similar between participants in the laboratory test and clinical assessment groups. These results show that COVID-19-associated chemosensory impairment is not limited to smell but also affects taste and chemesthesis.The multimodal impact of COVID-19 and the lack of perceived nasal obstruction suggest that severe acute respiratory syndrome coronavirus strain 2 (SARS-CoV-2) infection may disrupt sensory-neural mechanisms.
Published: 2020
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5. Mezilaurus conceicionensis L. C. S. Assis, P. B. Meyer & F. M. Alves 2022, sp. nov

Author: Alves, Flávio Macedo, Meyer, Pablo Burkowski, and Assis, Leandro Cézanne De Souza
Subjects: Tracheophyta, Magnoliopsida, Lauraceae, Mezilaurus conceicionensis, Laurales, Mezilaurus, Biodiversity, Plantae, Taxonomy
Abstract: Mezilaurus conceicionensis L.C.S.Assis, P.B.Meyer & F.M.Alves, sp. nov. (Figs 1–2). Type:— BRAZIL. Minas Gerais: Conceição do Mato Dentro, Fazenda Santa Cruz, Propriedade da Vale, 1025 m, 19°03’25”S, 43°24’11”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. de Paula 3803 (holotype, BHCB 203295!; isotype, RB!). Diagnosis:— Mezilaurus conceicionensis is similar in floral structure to Mezilaurus revolutifolia, however, it differs by having a shrubby habit, the branches distally puberulous, stamens connate and globoid fruits. Shrubs to small trees, 1.5–5 m tall. Branches with rhythmic growth; branchlets cylindrical, grayish to dark-brown, distally puberulous to glabrescent, with scars of senescent leaves and conspicuous lenticels. Apical buds totally covered by sericeous and translucent light-brown hairs. Leaves alternate to sub-opposite, clustered at the apex of the branchlets; petioles 0.6–1.8 cm long, 15–20% of the leaf length, plane to prominent at the adaxial surface, glabrous to subglabrous; blades 1.8–10 cm × 0.9–4.2 cm, obovate to oblanceolate, base attenuate, margins revolute, apex emarginate, rounded, obtuse or rarely mucronate, adaxial and abaxial surfaces glabrous to glabrescent, primary, secondary, and tertiary veins prominent at both surfaces, secondary veins brochidodromous, diverging at 35–75° to the primary vein, domatia absent. Cataphylls present, totally covered by sericeous and translucent light-brown hairs. Inflorescences 3.5– 6 cm long, dibotrya, lateral branchlets umbeliform, raquis cerose, partially covered by tomentose indument and lightcream hairs. Flowers 3–6 mm long, globose to sub-globose; pedicels 2.5–4.5 mm long, glabrous; hypanthium ca. 1 × 1.5 mm, cotiliform, inner and outer surfaces glabrous; tepals 0.2–0.6 × 0.5–1 mm, shorter than the hypanthium, ca. 1 / 3 of the flower length, subequal, outer tepals slightly shorter and wider than the inner ones, outer tepals depressed-ovate, glabrous to glabrescent, inner tepals broadly ovate to depressed-ovate, glabrous to glabrescent; stamens 1–1.1 mm long, connate, inserted at anthesis, filaments 0.5–0.6 mm long, rectangular, partially to totally covered by tomentose and opaque indument, anthers slightly deltate, glabrous, rarely papillose, locelli apical; pistil ca. 1.2 × 1.0 mm, ovary ca. 0.8 mm long, narrowly ellipsoid, glabrous. Style ca. 0.4 mm long, ca. 1 / 3 of the pistil length, glabrous. Fruits 1.8–3 cm, globose to subglobose, glaucous. Cupules ca. 1 × 4 mm, plane. Paratypes:— BRAZIL. Minas Gerais: Conceição do Mato Dentro, 1043 m, 19º02’47”S, 43º23’19”W, 16 February 2016 (fl.), E. Tameirão-Neto & C.V. Vidal 5431 (BHCB!, RB!); 19º00’03”S, 43º24’05”W, 14 August 2016 (fl., fr.), E. Tameirão-Neto & C.V. Vidal 5112 (BHCB!, RB!); 1005 m, 19º33’99”S, 43º23’13”W, 24 July 2014 (fl.), C.V. Vidal 1258 (BHCB!, RB!); 1010 m, 19º34’98”S, 43º23’70”W, 11 December 2014 (fl.), C.V. Vidal 1321 (BHCB!, RB!); Fazenda Santa Cruz, Propriedade da Vale, 1010 m, 19°03’04”S, 43°23’12”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3775 (BHCB!); 1014 m, 19°03’03”S, 43°23’12”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3776 (BHCB!); 1015 m, 19°03’03”S, 43°23’13”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3777 (BHCB!); 1018 m, 19°03’03”S, 43°23’13”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3778 (BHCB!); 1018 m, 19°03’03”S, 43°23’13”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3779 (BHCB!); 1006 m, 19°03’04”S, 43°23’11”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3780 (BHCB!); 1003 m, 19°03’04”S, 43°23’11”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3781 (BHCB!); 1001 m, 19°03’05”S, 43°23’11”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3782 (BHCB!); 993 m, 19°03’05”S, 43°23’10”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3783 (BHCB!); 983 m, 19°03’05”S, 43°23’07”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3784 (BHCB!); 1014 m, 19°03’03”S, 43°23’11”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3785 (BHCB!); 1015 m, 19°03’03”S, 43°23’12”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3786 (BHCB!); 1014 m, 19°03’03”S, 43°23’12”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3787 (BHCB!); 1015 m, 19°03’03”S, 43°23’13”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3788 (BHCB!); 1016 m, 19°03’03”S, 43°23’13”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3789 (BHCB!); 1042 m, 19°03’20”S, 43°23’16”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3790 (BHCB!); 1041 m, 19°03’03”S, 43°24’17”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3791 (BHCB!); 1044 m, 19°03’21”S, 43°24’16”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3792 (BHCB!); 1045 m, 19°03’21”S, 43°24’16”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3793 (BHCB!); 1046 m, 19°03’21”S, 43°24’16”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3794 (BHCB!); 1036 m, 19°03’22”S, 43°24’15”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3795 (BHCB!); 1033 m, 19°03’23”S, 43°24’15”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3796 (BHCB!); 1034 m, 19°03’23”S, 43°24’14”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3797 (BHCB!); 1035 m, 19°03’24”S, 43°24’13”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3798 (BHCB!); 1036 m, 19°03’24”S, 43°24’13”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3799 (BHCB!); 1030 m, 19°03’24”S, 43°24’12”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3800 (BHCB!); 1026 m, 19°03’25”S, 43°24’12”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3801 (BHCB!); 1024 m, 19°03’25”S, 43°24’11”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3802 (BHCB!); 1027 m, 19°03’25”S, 43°24’11”W, 20 February 2019 (fl., fr.), P.B. Meyer & N.L. Paula 3804 (BHCB!). 19º30’11”S, 43º23’04”W, 16 August 2012 (fl., fr.), E. Tameirão-Neto & C.V. Vidal 5156 (BHCB!, RB); Ibid., 1007 m, 19º05’13”S, 43º38’69”W, 30 July 2017 (fl.), P.B. Meyer 3062 (BHCB!, CGMS!, K!, MO!, RB!); Ibid., Serra da Ferrugem, 19º00’03”S, 43º23’51”W, 27 July 2017 (fl., fr.), A.S. Quaresma & C.T. Oliveira 854 (BHCB!, HEPH!, RB!). Distribution and ecology:— Mezilaurus conceicionensis is endemic to the campos rupestres over canga couraçada in the municipality of Conceição do Mato Dentro, State of Minas Gerais, Brazil (Fig. 5a of Assunção-Silva & Assis [2021] as Mezilaurus sp. nov 1), between 980–1050 m, associated to genus Vellozia Vandelli (1788: 32), a typical genus of campos rupestres (Fig 1). Phenology: — During fieldwork, the flowering of M. conceicionensis was continuously observed from August 2018 to July 2019, without interruptions, with peaks being recorded in the months of October 2018 and March 2019. Fruiting was also observed throughout this period, with peaks mostly from greater amounts of fruit being recorded between the months of May and July 2019. Etymology: — The epithet pays tribute to the type locality, the municipality of Conceição do Mato Dentro, MG, Brazil, located at the base of Serra da Ferrugem. Conservation status:— Mezilaurus conceicionensis is restricted to the Serra da Ferrugem mountain range (also called “Serra da Serpentina”), municipality of Conceição do Mato Dentro, State of Minas Gerais, Brazil. So far, it is known only from five subpopulations in this mountain range. According to the IUCN (IUCN 2012, 2016), this species can be tentatively be classified as Critically Endangered - CR (A4c;B1ab(iii) + 2ab(iii)). This classification is based on its small AOO, estimated in 0.49 km ², small EOO, calculate in 21.927 km ², and a continuing and probably not reversible reduction in its population size, based on the decline of this AOO, EOO and habitat quality. Mezilaurus conceicionensis is distinct from the remaining species of the genus by its shrubby habit, leaves with both surfaces glabrous to glabrescent, flowers clustered (umbel-like) along the lateral branches of the inflorescences, flowers globose, glabrous to glabrescent, tepals ca. 1 / 3 the flower length, shorter than the hypanthium, stamens connate and inserted, and globoid fruits. Mezilaurus conceicionensis can be confused with the collections of M. revolutifolia F.M.Alves & P.L.R.Moraes in Alves et al. (2011: 506), but the latter is characterized by its tepals as long as the hypanthium, ca. 1 / 2 the flower length to slightly larger, exserted and free stamens, and ellipsoid to obovoid fruits. Mezilaurus conceicionensis can also be confused with M. crassiramea (Meissner 1864: 117) Taubert ex Mez (1892: 112), also found in campos rupestres from the State of Minas Gerais. However, in M. crassiramea, the leaves are abaxially hirsute, villous or lanate, petioles are 1–10% of the leaf length, lanate to puberulous, the lateral branch of the inflorescences is racemiform, the stamens are exserted and free, and the fruits are ca. 3.1 × 2.8 cm, ellipsoid to obovoid. A key to the species of Mezilaurus from Southeastern Brazil is presented below., Published as part of Alves, Flávio Macedo, Meyer, Pablo Burkowski & Assis, Leandro Cézanne De Souza, 2022, The novelty Mezilaurus conceicionensis (Lauraceae) and a key to the species of the genus from Brazilian Southeastern, pp. 185-192 in Phytotaxa 541 (2) on pages 186-190, DOI: 10.11646/phytotaxa.541.2.8, http://zenodo.org/record/6388781, {"references":["Assuncao-Silva, C. C. & Assis, L. C. S. (2021) Areas of endemism of Lauraceae: new insights on the biogeographic regionalization of the Espinhaco Range, Brazil. Cladistics. [in press] https: // doi. org / 10.1111 / cla. 12481","Vandelli, D. (1788) Florae Lusitanicae et Brasiliensis specimen ... Typographia Academico-Regia, Coimbra, 96 pp. https: // dx. doi. org / 10.5962 / bhl. title. 51092","IUCN (2012) The IUCN Red List Categories and Criteria: version 3.1. Second edition. IUCN Red List Unit, Cambridge U. K. Available from: http: // www. iucnredlist. org (accessed 10 May 2011).","IUCN (2016) Guidelines for using the IUCN red list categories and criteria. version 12. Prepared by the standards and petitions subcommittee. IUCN Species Survival Commission. IUCN, Gland, Switzerland and Cambridge, UK. [http: // www. iucnredlist. org / documents / RedListGuidelines. pdf]","Alves, F. M., Souza, V. C. & Moraes, P. L. R. de (2011) Mezilaurus revolutifolia (Lauraceae), a new species from Brazilian Atlantic forest. Kew Bulletin 66: 505 - 509. https: // doi. org / 10.1007 / s 12225 - 011 - 9302 - z","Meissner, C. F. (1864) Lauraceae. In: Candolle, A. L. P. P. de (Ed.) Prodromus Systematis Naturalis Regni Vegetabilis, vol. 15, p. 1. Sumptibus Victoris Masson et filii, Paris, pp. 1 - 260. https: // doi. org / 10.5962 / bhl. title. 286","Mez, C. (1892) Spicilegium Laureanum. Arbeiten aus dem Konigl. Botanischen Garten zu Breslau 1: 71 - 166."]}
Published: 2022
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6. Mezilaurus Alves & Meyer & Assis 2022

Author: Alves, Flávio Macedo, Meyer, Pablo Burkowski, and Assis, Leandro Cézanne De Souza
Subjects: Tracheophyta, Magnoliopsida, Lauraceae, Laurales, Mezilaurus, Biodiversity, Plantae, Taxonomy
Abstract: Key to the Brazilian Southeast species of Mezilaurus 1. Leaves with erect indument abaxially; inflorescences in racemes with lateral branches raceme-like; bracteoles persistent; Brazilian Cerrado or Atlantic Forest; Minas Gerais and Espírito Santo states............................................................. Mezilaurus crassiramea - Leaves glabrous or glabrescent abaxially; inflorescences in racemes with lateral branches umbel-like; bracteoles deciduous; Atlantic Forest; Espírito Santo, Minas Gerais or Rio de Janeiro states..............................................................................................2 2. Globose flowers; globoid fruits; Vegetation on rocky outcrops (campo rupestre); Minas Gerais... Mezilaurus conceicionensis - Ellipsoid flowers; ellipsoid fruits; Atlantic Forest; Espírito Santo and Rio de Janeiro......................................................................3 3. Leaves narrow-elliptical or oblanceolate, 3–8.4 times longer than wide; Atlantic Forest; Rio de Janeiro......................................................................................................................................... Mezilaurus navalium (Allemão 1847: 265) Taub. ex Mez (1892: 112) - Leaves elliptic or obovate, 1.7–2.8 times longer than wide; Atlantic Forest; Espírito Santo............................................................4 4. Pedicelate flowers; filaments glabrous.............................................................. Mezilaurus glabriantha Alves & Souza (2012: 257) - Sessile flowers; filaments densely pubescent............. Mezilaurus sessiliflora P.L.R.Moraes & Vergne in Moraes et al. (2017: 153), Published as part of Alves, Flávio Macedo, Meyer, Pablo Burkowski & Assis, Leandro Cézanne De Souza, 2022, The novelty Mezilaurus conceicionensis (Lauraceae) and a key to the species of the genus from Brazilian Southeastern, pp. 185-192 in Phytotaxa 541 (2) on page 190, DOI: 10.11646/phytotaxa.541.2.8, http://zenodo.org/record/6388781, {"references":["Allemao, F. F. (1847) Laurinea. Silvia dos Arsenaes (Gen. Nov.). Silvia (Gen. Nov.). Navalium (Sp. Nov.). Nome vulgar: Tapinhoan. Archivo Medico Brasileiro 3: 265 - 268.","Mez, C. (1892) Spicilegium Laureanum. Arbeiten aus dem Konigl. Botanischen Garten zu Breslau 1: 71 - 166.","Alves, F. M. & Souza, V. C. (2012) Two new species of Mezilaurus (Lauraceae) from Brazil. Brittonia 64: 257 - 262. https: // doi. org / 10.1007 / s 12228 - 011 - 9228 - 7","Moraes, P. L. R., Vergne, M. C. & van der Werff, H. (2017) Three new species of Lauraceae from the Atlantic rainforest of Brazil. Phytotaxa 316: 149 - 160. https: // doi. org / 10.11646 / phytotaxa. 316.2.4"]}
Published: 2022
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7. Mezilaurus Alves & Meyer & Assis 2022

Author: Alves, Flávio Macedo, Meyer, Pablo Burkowski, and Assis, Leandro Cézanne De Souza
Subjects: Tracheophyta, Magnoliopsida, Lauraceae, Laurales, Mezilaurus, Biodiversity, Plantae, Taxonomy
Abstract: Key to the Brazilian Southeast species of Mezilaurus 1. Leaves with erect indument abaxially; inflorescences in racemes with lateral branches raceme-like; bracteoles persistent; Brazilian Cerrado or Atlantic Forest; Minas Gerais and Espírito Santo states............................................................. Mezilaurus crassiramea - Leaves glabrous or glabrescent abaxially; inflorescences in racemes with lateral branches umbel-like; bracteoles deciduous; Atlantic Forest; Espírito Santo, Minas Gerais or Rio de Janeiro states..............................................................................................2 2. Globose flowers; globoid fruits; Vegetation on rocky outcrops (campo rupestre); Minas Gerais... Mezilaurus conceicionensis - Ellipsoid flowers; ellipsoid fruits; Atlantic Forest; Espírito Santo and Rio de Janeiro......................................................................3 3. Leaves narrow-elliptical or oblanceolate, 3–8.4 times longer than wide; Atlantic Forest; Rio de Janeiro......................................................................................................................................... Mezilaurus navalium (Allemão 1847: 265) Taub. ex Mez (1892: 112) - Leaves elliptic or obovate, 1.7–2.8 times longer than wide; Atlantic Forest; Espírito Santo............................................................4 4. Pedicelate flowers; filaments glabrous.............................................................. Mezilaurus glabriantha Alves & Souza (2012: 257) - Sessile flowers; filaments densely pubescent............. Mezilaurus sessiliflora P.L.R.Moraes & Vergne in Moraes et al. (2017: 153)
Published: 2022
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8. Distillation to Enhance the Portability of Risk Models Across Institutions with Large Patient Claims Database

Author: Nyemba, Steve, Yan, Chao, Zhang, Ziqi, Rajmane, Amol, Meyer, Pablo, Chakraborty, Prithwish, and Malin, Bradley
Subjects: FOS: Computer and information sciences, Computer Science - Machine Learning, Computer Science - Computers and Society, Artificial Intelligence (cs.AI), Computer Science - Artificial Intelligence, Computers and Society (cs.CY), Machine Learning (cs.LG)
Abstract: Artificial intelligence, and particularly machine learning (ML), is increasingly developed and deployed to support healthcare in a variety of settings. However, clinical decision support (CDS) technologies based on ML need to be portable if they are to be adopted on a broad scale. In this respect, models developed at one institution should be reusable at another. Yet there are numerous examples of portability failure, particularly due to naive application of ML models. Portability failure can lead to suboptimal care and medical errors, which ultimately could prevent the adoption of ML-based CDS in practice. One specific healthcare challenge that could benefit from enhanced portability is the prediction of 30-day readmission risk. Research to date has shown that deep learning models can be effective at modeling such risk. In this work, we investigate the practicality of model portability through a cross-site evaluation of readmission prediction models. To do so, we apply a recurrent neural network, augmented with self-attention and blended with expert features, to build readmission prediction models for two independent large scale claims datasets. We further present a novel transfer learning technique that adapts the well-known method of born-again network (BAN) training. Our experiments show that direct application of ML models trained at one institution and tested at another institution perform worse than models trained and tested at the same institution. We further show that the transfer learning approach based on the BAN produces models that are better than those trained on just a single institution's data. Notably, this improvement is consistent across both sites and occurs after a single retraining, which illustrates the potential for a cheap and general model transfer mechanism of readmission risk prediction.
Published: 2022
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9. Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees

Author: Gong, Wuming, Granados, Alejandro A., Hu, Jingyuan, Jones, Matthew G., Raz, Ofir, Salvador-Martínez, Irepan, Zhang, Hanrui, Chow, Ke-Huan K., Kwak, Il-Youp, Retkute, Renata, Alis Prusoke, Prusokas, Augustinas, Khodaverdian, Alex, Zhang, Richard, Rao, Suhas, Wang, Robert, Rennert, Phil, Saipradeep, Vangala G., Sivadasan, Naveen, Rao, Aditya, Joseph, Thomas, Srinivasan, Rajgopal, Peng, Jiajie, Han, Lu, Shang, Xuequn, Garry, Daniel J., Yu, Thomas, Chung, Verena, Mason, Michael, Liu, Zhandong, Guan, Yuanfang, Yosef, Nir, Shendure, Jay, Telford, Maximilian J., Shapiro, Ehud, Elowitz, Michael B., and Meyer, Pablo
Subjects: M. musculus, simulation, Benchmarking, Mice, intmemoir, machine learning, lineage reconstruction, CRISPR, C. elegans, Animals, cell lineage tracing, crowdsourcing, Cell Lineage, Computer Simulation, Caenorhabditis elegans, Algorithms
Abstract: The recent advent of CRISPR and other molecular tools enabled the reconstruction of cell lineages based on induced DNA mutations and promises to solve the ones of more complex organisms. To date, no lineage reconstruction algorithms have been rigorously examined for their performance and robustness across dataset types and number of cells. To benchmark such methods, we decided to organize a DREAM challenge using in vitro experimental intMEMOIR recordings and in silico data for a C. elegans lineage tree of about 1,000 cells and a Mus musculus tree of 10,000 cells. Some of the 22 approaches submitted had excellent performance, but structural features of the trees prevented optimal reconstructions. Using smaller sub-trees as training sets proved to be a good approach for tuning algorithms to reconstruct larger trees. The simulation and reconstruction methods here generated delineate a potential way forward for solving larger cell lineage trees such as in mouse.
Published: 2021
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10. Disease Progression Modeling Workbench 360

Author: Suryanarayanan, Parthasarathy, Chakraborty, Prithwish, Madan, Piyush, Bore, Kibichii, Ogallo, William, Chandra, Rachita, Ghalwash, Mohamed, Buleje, Italo, Remy, Sekou, Mahatma, Shilpa, Meyer, Pablo, and Hu, Jianying
Subjects: FOS: Computer and information sciences, Computer Science - Machine Learning, Computer Science - Human-Computer Interaction, Machine Learning (cs.LG), Human-Computer Interaction (cs.HC)
Abstract: In this work we introduce Disease Progression Modeling workbench 360 (DPM360) opensource clinical informatics framework for collaborative research and delivery of healthcare AI. DPM360, when fully developed, will manage the entire modeling life cycle, from data analysis (e.g., cohort identification) to machine learning algorithm development and prototyping. DPM360 augments the advantages of data model standardization and tooling (OMOP-CDM, Athena, ATLAS) provided by the widely-adopted OHDSI initiative with a powerful machine learning training framework, and a mechanism for rapid prototyping through automatic deployment of models as containerized services to a cloud environment., Submitted to OHDSI Collaborator Showcase, 2021 (https://www.ohdsi.org/2021-collaborator-showcase)
Published: 2021

11. Flowers to Òsanyìn: Lychnophora osanyiniana (Asteraceae: Vernonieae) a new 'arnica da serra' from Minas Gerais, Brazil

Author: Marques, Danilo, Quaresma, Aline Silva, Meyer, Pablo Burkowski, and Nakajima, Jimi
Subjects: Tracheophyta, Magnoliopsida, Asterales, Biodiversity, Asteraceae, Plantae, Taxonomy
Abstract: Marques, Danilo, Quaresma, Aline Silva, Meyer, Pablo Burkowski, Nakajima, Jimi (2021): Flowers to Òsanyìn: Lychnophora osanyiniana (Asteraceae: Vernonieae) a new "arnica da serra" from Minas Gerais, Brazil. Phytotaxa 491 (1): 57-64, DOI: 10.11646/phytotaxa.491.1.6, URL: http://dx.doi.org/10.11646/phytotaxa.491.1.6
Published: 2021

12. Recent Smell Loss Is the Best Predictor of COVID-19 Among Individuals With Recent Respiratory Symptoms

Author: Gerkin, Richard, Ohla, Kathrin, Veldhuizen, Maria, Joseph, Paule, Kelly, Christine, Bakke, Alyssa, Steele, Kimberley, Farruggia, Michael, Pellegrino, Robert, Pepino, Marta, Bouysset, Cédric, Soler, Graciela, Pereda-Loth, Veronica, Dibattista, Michele, Cooper, Keiland, Croijmans, Ilja, Di Pizio, Antonella, Ozdener, Mehmet Hakan, Fjaeldstad, Alexander, Lin, Cailu, Sandell, Mari, Singh, Preet, Brindha, Evelyn, Olsson, Shannon, Saraiva, Luis, Ahuja, Gaurav, Alwashahi, Mohammed, Bhutani, Surabhi, D’Errico, Anna, Fornazieri, Marco, Golebiowski, Jérôme, Dar Hwang, Liang, Öztürk, Lina, Roura, Eugeni, Spinelli, Sara, Whitcroft, Katherine, Faraji, Farhoud, Fischmeister, Florian, Heinbockel, Thomas, Hsieh, Julien, Huart, Caroline, Konstantinidis, Iordanis, Menini, Anna, Morini, Gabriella, Olofsson, Jonas, Philpott, Carl, Pierron, Denis, Shields, Vonnie, Voznessenskaya, Vera, Albayay, Javier, Altundag, Aytug, Bensafi, Moustafa, Bock, María Adelaida, Calcinoni, Orietta, Fredborg, William, Laudamiel, Christophe, Lim, Juyun, Lundström, Johan, Macchi, Alberto, Meyer, Pablo, Moein, Shima, Santamaría, Enrique, Sengupta, Debarka, Rohlfs Dominguez, Paloma, Yanik, Hüseyin, Hummel, Thomas, Hayes, John, Reed, Danielle, Niv, Masha, Munger, Steven, Parma, Valentina, Boesveldt, Sanne, de Groot, Jasper, Dinnella, Caterina, Freiherr, Jessica, Laktionova, Tatiana, Marino, Sajidxa, Monteleone, Erminio, Nunez-Parra, Alexia, Abdulrahman, Olagunju, Ritchie, Marina, Thomas-Danguin, Thierry, Walsh-Messinger, Julie, Al Abri, Rashid, Alizadeh, Rafieh, Bignon, Emmanuelle, Cantone, Elena, Paola Cecchini, Maria, Chen, Jingguo, Dolors Guàrdia, Maria, Hoover, Kara, Karni, Noam, Navarro, Marta, Nolden, Alissa, Portillo Mazal, Patricia, Rowan, Nicholas, Sarabi-Jamab, Atiye, Archer, Nicholas, Chen, Ben, Di Valerio, Elizabeth, Feeney, Emma, Frasnelli, Johannes, Hannum, Mackenzie, Hopkins, Claire, Klein, Hadar, Mignot, Coralie, Mucignat, Carla, Ning, Yuping, Ozturk, Elif, Peng, Mei, Saatci, Ozlem, Sell, Elizabeth, Yan, Carol, Alfaro, Raul, Coureaud, G., Herriman, Riley, Justice, Jeb, Kaushik, Pavan Kumar, Koyama, Sachiko, Overdevest, Jonathan, Pirastu, Nicola, Ramirez, Vicente, Roberts, S. Craig, Smith, Barry, Cao, Hongyuan, Wang, Hong, Balungwe Birindwa, Patrick, Baguma, Marius, Ozdener, Mehmet, Bock, María, Kaushik, Pavan, Pizio, Antonella, Hakan Ozdener, Mehmet, D'Errico, Anna, Hwang, Liang Dar, Group, GCCR, Cecchini, Maria, Indústries Alimentàries, Qualitat i Tecnologia Alimentària, Arizona State University [Tempe] (ASU), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, Mersin University, National Institutes of Health [Bethesda] (NIH), AbScent, Pennsylvania State University (Penn State), Penn State System, Yale University [New Haven], University of Tennessee, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Institut de Chimie de Nice (ICN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Buenos Aires University and GEOG (Grupo de Estudio de Olfato y Gusto), Centre d'anthropologie et de génomique de Toulouse (CAGT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Bari Aldo Moro (UNIBA), University of California, Utrecht University [Utrecht], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Monell Chemical Senses Center, Regional Hospital West Jutland [Denmark], University of Helsinki, University of Oslo (UiO), Karunya Institute of Technology and Sciences, Tata Institute of Fundamental Research, Sidra Medicine [Doha, Qatar], Indraprastha Institute of Information Technology [New Delhi] (IIIT-Delhi), Sultan Qaboos University (SQU), San Diego State University (SDSU), Goethe-University Frankfurt am Main, State University of Londrina = Universidade Estadual de Londrina, Elena Cantone, University of Queensland - The Diamantina Institute, University of Queensland [Brisbane], Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), University College of London [London] (UCL), UC San Diego Health, Karl-Franzens-Universität [Graz, Autriche], Howard University College of Medicine [Washington, DC, USA], Geneva University Hospitals and Geneva University, Cliniques Universitaires Saint-Luc [Bruxelles], Aristotle University of Thessaloniki, Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), Stockholm University, University of East Anglia [Norwich] (UEA), Towson University [Towson, MD, United States], University of Maryland System, Severtsov Institute of Ecology and Evolution RAS, University of Padova [Padova, Italy], Biruni University, Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospital General de Barrio Obrero [Asunción, Paraguay] (Public Hospital Barrio Obrero ), Private practice [Milan], DreamAir Llc, Oregon State University (OSU), Karolinska Institutet [Stockholm], University of Insubria, Varese, IBM Watson Research Center, IBM, Navarrabiomed-IdiSNA, University of Extremadura, Technische Universität Dresden = Dresden University of Technology (TU Dresden), The Hebrew University of Jerusalem (HUJ), University of Florida [Gainesville] (UF), Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE), Wageningen University and Research [Wageningen] (WUR), Radboud university [Nijmegen], Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Universidad de Chile = University of Chile [Santiago] (UCHILE), Federal University of Technology of Akure (FUTA), University of California [Berkeley], Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), University of Dayton, Iran University of Medical Sciences [Tehran, Iran] (IUMS), 'Federico II' University of Naples Medical School, University of Verona (UNIVR), Xi'an Jiaotong University (Xjtu), Institute of Agrifood Research and Technology (IRTA), University of Alaska [Fairbanks] (UAF), The Hebrew University Medical Center, University of Massachusetts System (UMASS), Instituto Universitario del Hospital Italiano [Buenos Aires, Argentina], Johns Hopkins University School of Medicine [Baltimore], Institute for Research in Fundamental Sciences [Tehran] (IPM), CSIRO Agriculture and Food (CSIRO), The First Affiliated Hospital of Guangzhou Medical University (GMU), University College Dublin [Dublin] (UCD), Université du Québec à Trois-Rivières (UQTR), Guy’s and St. Thomas’ Hospitals, University of Padova, Kilis Yedi Aralik University, University of Otago [Dunedin, Nouvelle-Zélande], Sancaktepe Education and Research Hospital, University of Pennsylvania [Philadelphia], University of California San Diego Health, Indiana University [Bloomington], Indiana University System, Columbia University Medical Center (CUMC), Columbia University [New York], University of Edinburgh, University of California [Merced], University of Stirling, University of London [London], Florida State University [Tallahassee] (FSU), Université catholique de Bukavu, University of Southern Queensland (USQ), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Technical University of Munich (TUM), University of Graz, Publica, Gerkin, Richard C, Ohla, Kathrin, Veldhuizen, Maria G, Joseph, Paule V, Kelly, Christine E, Bakke, Alyssa J, Steele, Kimberley E, Farruggia, Michael C, Pellegrino, Robert, Pepino, Marta Y, Bouysset, Cédric, Soler, Graciela M, Pereda-Loth, Veronica, Dibattista, Michele, Cooper, Keiland W, Croijmans, Ilja, Di Pizio, Antonella, Ozdener, M Hakan, Fjaeldstad, Alexander W, Lin, Cailu, Sandell, Mari A, Singh, Preet B, Brindha, V Evelyn, Olsson, Shannon B, Saraiva, Luis R, Ahuja, Gaurav, Alwashahi, Mohammed K, Bhutani, Surabhi, D'Errico, Anna, Fornazieri, Marco A, Golebiowski, Jérôme, Hwang, Liang-Dar, Öztürk, Lina, Roura, Eugeni, Spinelli, Sara, Whitcroft, Katherine L, Faraji, Farhoud, Fischmeister, Florian PhS, Heinbockel, Thoma, Hsieh, Julien W, Huart, Caroline, Konstantinidis, Iordani, Menini, Anna, Morini, Gabriella, Olofsson, Jonas K, Philpott, Carl M, Pierron, Deni, Shields, Vonnie D C, Voznessenskaya, Vera V, Albayay, Javier, Altundag, Aytug, Bensafi, Moustafa, Bock, María Adelaida, Calcinoni, Orietta, Fredborg, William, Laudamiel, Christophe, Lim, Juyun, Lundström, Johan N, Macchi, Alberto, Meyer, Pablo, Moein, Shima T, Santamaría, Enrique, Sengupta, Debarka, Dominguez, Paloma Rohlf, Yanik, Hüseyin, Hummel, Thoma, Hayes, John E, Reed, Danielle R, Niv, Masha Y, Munger, Steven D, Parma, Valentina, Tıp Fakültesi, UCL - SSS/IONS/NEUR - Clinical Neuroscience, and UCL - (SLuc) Service d'oto-rhino-laryngologie
Subjects: Male, Multivariate statistics, Physiology, Cross-sectional study, [SDV]Life Sciences [q-bio], coronavirus, Logistic regression, Settore BIO/09 - Fisiologia, Behavioral Neuroscience, 0302 clinical medicine, Hyposmia, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, 030223 otorhinolaryngology, Sensory Science and Eating Behaviour, Chemosensory, hyposmia, Middle Aged, Prognosis, olfactory, Sensory Systems, Smell, chemosensory, ddc:540, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Female, HEALTH, medicine.symptom, Adult, medicine.medical_specialty, Anosmia, Coronavirus, Olfactory, Prediction, COVID-19, Cross-Sectional Studies, Humans, SARS-CoV-2, Self Report, 663/664, Visual analogue scale, Odds, 03 medical and health sciences, Physiology (medical), Internal medicine, QUALITY, [SDV.MHEP.OS]Life Sciences [q-bio]/Human health and pathology/Sensory Organs, COVID-19 symptoms, Behaviour Change and Well-being, IDENTIFICATION, business.industry, Univariate, prediction, Sensoriek en eetgedrag, business, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, anosmia, Smell impairment
Abstract: Contains fulltext : 228204.pdf (Publisher’s version ) (Closed access) In a preregistered, cross-sectional study we investigated whether olfactory loss is a reliable predictor of COVID-19 using a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified univariate and multivariate predictors of COVID-19 status and post-COVID-19 olfactory recovery. Both C19+ and C19- groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both univariate and multivariate models (ROC AUC=0.72). Additional variables provide negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms (e.g., fever). Olfactory recovery within 40 days of respiratory symptom onset was reported for ~50% of participants and was best predicted by time since respiratory symptom onset. We find that quantified smell loss is the best predictor of COVID-19 amongst those with symptoms of respiratory illness. To aid clinicians and contact tracers in identifying individuals with a high likelihood of having COVID-19, we propose a novel 0-10 scale to screen for recent olfactory loss, the ODoR-19. We find that numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4
Published: 2020
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13. Corrigendum to: More than smell: COVID-19 is associated with severe impairment of smell, taste, and chemesthesis

Author: Parma, Valentina, Ohla, Kathrin, Veldhuizen, Maria G., Niv, Masha Y., Kelly, Christine E., Bakke, Alyssa J., Cooper, Keiland W., Bouysset, Cédric, Pirastu, Nicola, Dibattista, Michele, Kaur, Rishemjit, Liuzza, Marco Tullio, Pepino, Marta Y., Schöpf, Veronika, Pereda-Loth, Veronica, Olsson, Shannon B., Gerkin, Richard C., Rohlfs Domínguez, Paloma, Albayay, Javier, Farruggia, Michael C., Bhutani, Surabhi, Fjaeldstad, Alexander W., Kumar, Ritesh, Menini, Anna, Bensafi, Moustafa, Sandell, Mari, Konstantinidis, Iordanis, Di Pizio, Antonella, Genovese, Federica, Öztürk, Lina, Thomas-Danguin, Thierry, Frasnelli, Johannes, Boesveldt, Sanne, Saatci, Özlem, Saraiva, Luis R., Lin, Cailu, Golebiowski, Jérôme, Hwang, Liang Dar, Ozdener, Mehmet Hakan, Guàrdia, Maria Dolors, Laudamiel, Christophe, Ritchie, Marina, Havlícek, Jan, Pierron, Denis, Roura, Eugeni, Navarro, Marta, Nolden, Alissa A., Lim, Juyun, Whitcroft, Katherine L., Colquitt, Lauren R., Ferdenzi, Camille, Brindha, Evelyn V., Altundag, Aytug, Macchi, Alberto, Nunez-Parra, Alexia, Patel, Zara M., Fiorucci, Sébastien, Philpott, Carl M., Smith, Barry C., Lundström, Johan N., Mucignat, Carla, Parker, Jane K., Van Den Brink, Mirjam, Schmuker, Michael, Fischmeister, Florian Ph S., Heinbockel, Thomas, Shields, Vonnie D.C., Faraji, Farhoud, Santamaría, Enrique, Fredborg, William E.A., Morini, Gabriella, Olofsson, Jonas K., Jalessi, Maryam, Karni, Noam, D'Errico, Anna, Alizadeh, Rafieh, Pellegrino, Robert, Meyer, Pablo, Huart, Caroline, Chen, Ben, Soler, Graciela M., Alwashahi, Mohammed K., Welge-Lüssen, Antje, Freiherr, Jessica, De Groot, Jasper H.B., Klein, Hadar, Okamoto, Masako, Singh, Preet Bano, Hsieh, Julien W., Abdulrahman, Olagunju, Dalton, Pamela, Yan, Carol H., Voznessenskaya, Vera V., Chen, Jingguo, Sell, Elizabeth A., Walsh-Messinger, Julie, Archer, Nicholas S., Koyama, Sachiko, Deary, Vincent, Roberts, S.C., Yanlk, Hüseyin, Albayrak, Samet, Nováková, Lenka Martinec, Croijmans, Ilja, Mazal, Patricia Portillo, Moein, Shima T., Margulis, Eitan, Mignot, Coralie, Mariño, Sajidxa, Georgiev, Dejan, Kaushik, Pavan K., Malnic, Bettina, Wang, Hong, Seyed-Allaei, Shima, Yoluk, Nur, Razzaghi-Asl, Sara, Justice, Jeb M., Restrepo, Diego, Reed, Danielle R., Hummel, Thomas, Munger, Steven D., Hayes, John E., UCL - SSS/IONS - Institute of NeuroScience, UCL - SSS/IONS/NEUR - Clinical Neuroscience, and UCL - (SLuc) Service d'oto-rhino-laryngologie
Subjects: Behavioral Neuroscience, Sensoriek en eetgedrag, Behaviour Change and Well-being, Physiology, Physiology (medical), ddc:540, Life Science, Sensory Systems, Sensory Science and Eating Behaviour, VLAG
Abstract: This is a correction notice for article bjaa041 (DOI: https:// doi.org/10.1093/chemse/bjaa041), published 20 June 2020. An incorrect version of the caption to Figure 5 was mistakenly included in the published paper. An updated version is given below. Neither the data nor the paper's conclusions were affected by this correction. The authors sincerely apologize for the error. (A) Correlations between the 3 principal components with respect to changes in 3 chemosensory modalities (i.e., taste, smell, and chemesthesis). Shades of gray indicate positive correlation, whereas shades of red indicate negative correlations. White denotes no correlation. (B) Clusters of participants identified by k-means clustering. The scatterplot shows each participant's loading on dimension 1 (degree of smell and taste loss, PC1 on x-Axis) and dimension 2 (degree of chemesthesis loss, PC2 on y-Axis). Based on the centroid of each cluster, participants in cluster 1 (blue, N = 1767; top left) are generally characterized by significant smell, taste and chemesthesis loss. Participants in cluster 2 (orange, N = 1724; bottom center) are generally characterized by ratings that reflect smell/taste loss with preserved chemesthesis. Loadings for participants in cluster 3 (green, N = 548; right side) are generally characterized by reduced smell and taste loss, and preserved chemesthesis.
Published: 2021
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14. The best COVID-19 predictor is recent smell loss: a cross-sectional study

Author: Gerkin, Richard, Ohla, Kathrin, Veldhuizen, Maria Geraldine, Joseph, Paule, Kelly, Christine, Bakke, Alyssa, Steele, Kimberley, Pellegrino, Robert, Pepino, Marta, Bouysset, Cédric, Soler, Graciela, Pereda-Loth, Veronica, Dibattista, Michele, Cooper, Keiland, Croijmans, Ilja, Di Pizio, Antonella, Ozdener, M. Hakan, D'Errico, Anna, Fischmeister, Florian Ph.S, Bock, María Adelaida, Domínguez, Paloma Paloma, Yanık, Hüseyin, Boesveldt, Sanne, de Groot, Jasper, Dinnella, Caterina, Freiherr, Jessica, Laktionova, Tatiana, Mariño, Sajidxa, Monteleone, Erminio, Nunez-Parra, Alexia, Abdulrahman, Olagunju, Ritchie, Marina, Thomas-Danguin, Thierry, Walsh-Messinger, Julie, Al Abri, Rashid, Alizadeh, Rafieh, Bignon, Emmanuelle, Cantone, Elena, Cecchini, Maria Paola, Chen, Jingguo, Guàrdia, Maria Dolors, Hoover, Kara, Karni, Noam, Navarro, Marta, Nolden, Alissa, Mazal, Patricia Portillo, Rowan, Nicholas, Sarabi-Jamab, Atiye, Archer, Nicholas, Chen, Ben, Di Valerio, Elizabeth, Feeney, Emma, Frasnelli, Johannes, Hannum, Mackenzie, Hopkins, Claire, Klein, Hadar, Mignot, Coralie, Mucignat, Carla, Ning, Yuping, Ozturk, Elif, Peng, Mei, Saatci, Ozlem, Sell, Elizabeth, Yan, Carol, Alfaro, Raul, Cecchetto, Cinzia, Coureaud, Gérard, Herriman, Riley, Justice, Jeb, Kaushik, Pavan Kumar, Koyama, Sachiko, Overdevest, Jonathan, Pirastu, Nicola, Ramirez, Vicente, Roberts, S. Craig, Smith, Barry, Cao, Hongyuan, Wang, Hong, Balungwe, Patrick, Baguma, Marius, Veldhuizen, Maria, Farruggia, Michael, Pizio, Antonella, Hakan Ozdener, M, Fjaeldstad, Alexander, Lin, Cailu, Sandell, Mari, Singh, Preet, Brindha, V. Evelyn, Olsson, Shannon, Saraiva, Luis, Ahuja, Gaurav, Alwashahi, Mohammed, Bhutani, Surabhi, Fornazieri, Marco, Golebiowski, Jérôme, Hwang, Liang-Dar, Öztürk, Lina, Roura, Eugeni, Spinelli, Sara, Whitcroft, Katherine, Faraji, Farhoud, Fischmeister, Florian, Heinbockel, Thomas, Hsieh, Julien, Huart, Caroline, Konstantinidis, Iordanis, Menini, Anna, Morini, Gabriella, Olofsson, Jonas, Philpott, Carl, Pierron, Denis, Shields, Vonnie, Voznessenskaya, Vera, Albayay, Javier, Altundag, Aytug, Bensafi, Moustafa, Bock, María, Calcinoni, Orietta, Fredborg, William, Laudamiel, Christophe, Lim, Juyun, Lundström, Johan, Macchi, Alberto, Meyer, Pablo, Moein, Shima, Santamaría, Enrique, Sengupta, Debarka, Rohlfs Dominguez, Paloma, Yanik, Hüseyin, Group, GCCR, Hummel, Thomas, Hayes, John, Reed, Danielle, Niv, Masha, Munger, Steven, Parma, Valentina, Arizona State University [Tempe] (ASU), Institute of Neuroscience and Medicine [Jülich] (INM-1), Mersin University, National Institutes of Health [Bethesda] (NIH), AbScent, Pennsylvania State University (Penn State), Penn State System, National Institute of Diabetes and Digestive and Kidney Diseases [Bethesda], Yale University [New Haven], Tennessee State University, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Institut de Chimie de Nice (ICN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Buenos Aires University and GEOG (Grupo de Estudio de Olfato y Gusto), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Bari Aldo Moro (UNIBA), University of California [Irvine] (UCI), University of California, Utrecht University [Utrecht], Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Monell Chemical Senses Center, Regional Hospital West Jutland [Denmark], University of Helsinki, University of Oslo (UiO), Karunya University, Tata Institute for Fundamental Research (TIFR), Research at Sidra Medicine Research Branch [Doha, Qatar], Indraprastha Institute of Information Technology [New Delhi] (IIIT-Delhi), Sultan Qaboos University (SQU), San Diego State University (SDSU), Goethe-University Frankfurt am Main, State University of Londrina = Universidade Estadual de Londrina, University of Queensland [Brisbane], Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), University College of London [London] (UCL), University of Graz, Howard University, Geneva University Hospital (HUG), Cliniques Universitaires Saint-Luc [Bruxelles], Aristotle University of Thessaloniki, Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), University of Gastronomic Sciences of Pollenzo (UNISG), Stockholm University, University of East Anglia [Norwich] (UEA), Towson University [Towson, MD, United States], University of Maryland System, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Universita degli Studi di Padova, Biruni University, Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospital General de Barrio Obrero [Asunción, Paraguay] (Public Hospital Barrio Obrero ), Private practice [Milan], DreamAir Llc, Oregon State University (OSU), Cancer Center Karolinska [Karolinska Institutet] (CCK), Karolinska Institutet [Stockholm], University of Insubria, Varese, Computational Biology Center (IBM T.J. Watson Research Center), IBM, Institute for Research in Fundamental Sciences [Tehran] (IPM), Instituto de Investigación Sanitaria de Navarra [Pamplona, Spain] (IdiSNA), University of Extremadura, Technische Universität Dresden = Dresden University of Technology (TU Dresden), The Hebrew University of Jerusalem (HUJ), University of Florida [Gainesville] (UF), Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE), Non-byline authors (to be listed as collaborators in PubMed under the GCCR Group Author): Sanne Boesveldt, Jasper H.B. de Groot, Caterina Dinnella, Jessica Freiherr, Tatiana Laktionova, Sajidxa Mariño, Erminio Monteleone, Alexia Nunez-Parra, Olagunju Abdulrahman, Marina Ritchie, Thierry Thomas-Danguin, Julie Walsh-Messinger, Rashid Al Abri, Rafieh Alizadeh, Emmanuelle Bignon, Elena Cantone, Maria Paola Cecchini, Jingguo Chen, Maria Dolors Guàrdia, Kara C. Hoover, Noam Karni, Marta Navarro, Alissa A. Nolden, Patricia Portillo Mazal, Nicholas R. Rowan, Atiye SarabiJamab, Nicholas S. Archer, Ben Chen, Elizabeth A. Di Valerio, Emma L. Feeney, Johannes Frasnelli, Mackenzie E. Hannum, Claire Hopkins, Hadar Klein, Coralie Mignot, Carla Mucignat, Yuping Ning, Elif E. Ozturk, Mei Peng, Ozlem Saatci, Elizabeth A. Sell, Carol H. Yan, Raul Alfaro, Cinzia Cecchetto, Gérard Coureaud, Riley D. Herriman, Jeb M. Justice, Pavan Kumar Kaushik, Sachiko Koyama, Jonathan B. Overdevest, Nicola Pirastu, Vicente A. Ramirez, S. Craig Roberts, Barry C. Smith, Hongyuan Cao, Hong Wang, Patrick Balungwe Birindwa, Marius Baguma, Karl-Franzens-Universität [Graz, Autriche], Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, The Pennsylvania State University, University of Tennessee, University of Buenos Aires [Argentina], Università degli studi di Bari Aldo Moro (UNIBA), Goethe University of Frankfurt am Main, Wageningen University and Research [Wageningen] (WUR), Radboud university [Nijmegen], Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), A.N. Severtsov Institute of Ecology and Evolution RAS, 119071, Russia., RespiraLibre - Centro de Otorrinolaringología, Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Partenaires INRAE, Universidad de Chile = University of Chile [Santiago] (UCHILE), Federal University of Technology of Akure (FUTA), Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Bourgogne Franche-Comté [COMUE] (UBFC), University of Dayton, Iran University of Medical Sciences, University of Naples Federico II, University of Verona (UNIVR), Head and Neck Surgery, Hospital of Xi'an Jiaotong University, Institute of Agrifood Research and Technology (IRTA), University of Alaska [Fairbanks] (UAF), Hadassah Hebrew University Medical Center [Jerusalem], University of Southern Queensland (USQ), University of Massachusetts, Instituto Universitario del Hospital Italiano [Buenos Aires, Argentina], Johns Hopkins University School of Medicine [Baltimore], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), The First Affiliated Hospital of Guangzhou Medical University (GMU), University College Dublin [Dublin] (UCD), Université du Québec à Trois-Rivières (UQTR), Guy's and St Thomas' Hospitals, University of Padova [Padova, Italy], Kilis Yedi Aralik University, University of Otago [Dunedin, Nouvelle-Zélande], Sancaktepe Education and Research Hospital, Hospital of the University of Pennsylvania (HUP), Perelman School of Medicine, University of Pennsylvania [Philadelphia]-University of Pennsylvania [Philadelphia], UC San Diego Health, University ofFlorida, Tata Institute of Fundamental Research, Indiana University [Bloomington], Indiana University System, Columbia University Irving Medical Center (CUIMC), University of Edinburgh, University of California [Merced], University of Stirling, University of London [London], Florida State University [Panama City], Université catholique de Bukavu, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Karunya Institute of Technology and Sciences, Sidra Medicine, School of Exercise and Nutritional Sciences, Howard University College of Medicine, Geneva University Hospitals, Geneva University , Geneva , Switzerland., CHU Genève, General Hospital Papageorgiou, University of Toulouse, University of Padova, Lyon Neuroscience Research center, IBM T.J. Watson Research Center, Navarrabiomed-IdiSNA, Temple University, Julien, Sabine, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Universitad de Buenos Aires = University of Buenos Aires [Argentina], Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), University of California [Irvine] (UC Irvine), University of California (UC), Karl-Franzens-Universität Graz, Universidad de Extremadura - University of Extremadura (UEX), Radboud University [Nijmegen], Università degli Studi di Firenze = University of Florence (UniFI), University of Naples Federico II = Università degli studi di Napoli Federico II, Università degli studi di Verona = University of Verona (UNIVR), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Università degli Studi di Padova = University of Padua (Unipd), University of Pennsylvania-University of Pennsylvania, School of Medicine [Univ California San Diego] (UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Tata Institute of Fundamental Research [Bangalore], University of California [Merced] (UC Merced), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Sidra Medicine [Doha, Qatar], Universitá degli Studi dell’Insubria = University of Insubria [Varese] (Uninsubria), and Universitá degli Studi dell’Insubria
Subjects: Adult, Male, medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), Cross-sectional study, Visual analogue scale, Anosmia, Audiology, Logistic regression, AcademicSubjects/SCI01180, Article, Odds, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Hyposmia, Humans, Medicine, [SDV.MHEP.OS]Life Sciences [q-bio]/Human health and pathology/Sensory Organs, 030223 otorhinolaryngology, SARS-CoV-2, business.industry, [SCCO.NEUR]Cognitive science/Neuroscience, COVID-19, Middle Aged, Prognosis, Smell, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Cross-Sectional Studies, [SDV.MHEP.OS] Life Sciences [q-bio]/Human health and pathology/Sensory Organs, Smell loss, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, Original Article, Self Report, medicine.symptom, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: BackgroundCOVID-19 has heterogeneous manifestations, though one of the most common symptoms is a sudden loss of smell (anosmia or hyposmia). We investigated whether olfactory loss is a reliable predictor of COVID-19.MethodsThis preregistered, cross-sectional study used a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified singular and cumulative predictors of COVID-19 status and post-COVID-19 olfactory recovery.ResultsBoth C19+ and C19-groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both single and cumulative feature models (ROC AUC=0.72), with additional features providing negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms, such as fever or cough. Olfactory recovery within 40 days was reported for ∼50% of participants and was best predicted by time since illness onset.ConclusionsAs smell loss is the best predictor of COVID-19, we developed the ODoR-19 tool, a 0-10 scale to screen for recent olfactory loss. Numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4
Published: 2020

15. Recent smell loss is the best predictor of COVID-19: a preregistered, cross-sectional study

Author: Parma, Valentina, Overdevest, Jonathan B, Peng, Mei, Saatci, Ozlem, Sell, Elizabeth A, Yan, Carol H, Alfaro, Raul, Cecchetto, Cinzia, Coureaud, Gérard, Herriman, Riley D, Justice, Jeb M, Kaushik, Pavan Kumar, Koyama, Sachiko, Pirastu, Nicola, Ning, Yuping, Ramirez, Vicente A, Roberts, S Craig, Smith, Barry C, Cao, Hongyuan, Wang, Hong, Balungwe, Patrick, Baguma, Marius, Hummel, Thomas, Hayes, John E, Reed, Danielle R, Niv, Masha Y, Munger, Steven D, Ozturk, Elif E, Gerkin, Richard C, Ohla, Kathrin, Veldhuizen, Maria Geraldine, Joseph, Paule V, Kelly, Christine E, Bakke, Alyssa J, Steele, Kimberley E, Farruggia, Michael C, Pellegrino, Robert, Pepino, Marta Y, Bouysset, Cédric, Soler, Graciela M, Pereda-Loth, Veronica, Dibattista, Michele, Cooper, Keiland W, Croijmans, Ilja, Di Pizio, Antonella, Ozdener, M Hakan, Fjaeldstad, Alexander W, Lin, Cailu, Sandell, Mari A, Singh, Preet B, Brindha, V Evelyn, Olsson, Shannon B, Saraiva, Luis R, Ahuja, Gaurav, Alwashahi, Mohammed K, Bhutani, Surabhi, D'Errico, Anna, Fornazieri, Marco A, Golebiowski, Jérôme, Hwang, Liang-Dar, Öztürk, Lina, Roura, Eugeni, Spinelli, Sara, Whitcroft, Katherine L, Faraji, Farhoud, Fischmeister, Florian Ph S, Heinbockel, Thomas, Hsieh, Julien W, Huart, Caroline, Konstantinidis, Iordanis, Menini, Anna, Morini, Gabriella, Olofsson, Jonas K, Philpott, Carl M, Pierron, Denis, Shields, Vonnie D C, Voznessenskaya, Vera V, Albayay, Javier, Altundag, Aytug, Bensafi, Moustafa, Bock, María Adelaida, Calcinoni, Orietta, Fredborg, William, Laudamiel, Christophe, Lim, Juyun, Lundström, Johan N, Macchi, Alberto, Meyer, Pablo, Moein, Shima T, Santamaría, Enrique, Sengupta, Debarka, Domínguez, Paloma Paloma, Yanık, Hüseyin, Boesveldt, Sanne, de Groot, Jasper H B, Dinnella, Caterina, Freiherr, Jessica, Laktionova, Tatiana, Mariño, Sajidxa, Monteleone, Erminio, Nunez-Parra, Alexia, Abdulrahman, Olagunju, Ritchie, Marina, Thomas-Danguin, Thierry, Walsh-Messinger, Julie, Al Abri, Rashid, Alizadeh, Rafieh, Bignon, Emmanuelle, Cantone, Elena, Cecchini, Maria Paola, Chen, Jingguo, Guàrdia, Maria Dolors, Hoover, Kara C, Karni, Noam, Navarro, Marta, Nolden, Alissa A, Mazal, Patricia Portillo, Rowan, Nicholas R, Sarabi-Jamab, Atiye, Archer, Nicholas S, Chen, Ben, Di Valerio, Elizabeth A, Feeney, Emma L, Frasnelli, Johannes, Hannum, Mackenzie, Hopkins, Claire, Klein, Hadar, Mignot, Coralie, Mucignat, Carla, UCL - (SLuc) Service d'oto-rhino-laryngologie, and UCL - SSS/IONS/NEUR - Clinical Neuroscience
Abstract: COVID-19 has heterogeneous manifestations, though one of the most common symptoms is a sudden loss of smell (anosmia or hyposmia). We investigated whether olfactory loss is a reliable predictor of COVID-19. This preregistered, cross-sectional study used a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified singular and cumulative predictors of COVID-19 status and post-COVID-19 olfactory recovery. Both C19+ and C19- groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both single and cumulative feature models (ROC AUC=0.72), with additional features providing no significant model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms, such as fever or cough. Olfactory recovery within 40 days was reported for ~50% of participants and was best predicted by time since illness onset. As smell loss is the best predictor of COVID-19, we developed the ODoR-19 tool, a 0-10 scale to screen for recent olfactory loss. Numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (10
Published: 2020

16. More than smell - COVID-19 is associated with severe impairment of smell, taste, and chemesthesis

Author: Kumar, Ritesh, Menini, Anna, Bensafi, Moustafa, Sandell, Mari, Konstantinidis, Iordanis, Pizio, Antonella di, Genovese, Federica, Öztürk, Lina, Thomas-Danguin, Thierry, Frasnelli, Johannes, Boesveldt, Sanne, Saatci, Özlem, Saraiva, Luis R., Lin, Cailu, Golebiowski, Jérôme, Hwang, Liang-Dar, Ozdener, Mehmet Hakan, Guárdia, Maria Dolors, Laudamiel, Christophe, Ritchie, Marina, Havlícek, Jan, Pierron, Denis, Roura, Eugeni, Navarro, Marta, Nolden, Alissa A., Lim, Juyun, Whitcroft, K.L., Colquitt, Lauren R., Ferdenzi, Camille, Brindha, Evelyn V., Altundag, Aytug, Macchi, Alberto, Nunez-Parra, Alexia, Patel, Zara M., Fiorucci, Sébastien, Philpott, Carl M., Smith, Barry C., Lundström, Johan N., Mucignat, Carla, Parker, Jane K., Brink, Mirjam van den, Schmuker, Michael, Fischmeister, Florian P.S., Heinbockel, Thomas, Schilds, Vonnie D.C., Faraji, Farhoud, Santamaría, Enrique, Fredborg, William E.A., Morini, Gabriella, Olofsson, Jonas K., Jalessi, Maryam, Karni, Noam, D'Errico, Anna, Alizadeh, Rafieh, Pellegrino, Robert, Meyer, Pablo, Huart, Caroline, Chen, Ben, Soler, Graciela M., Alwashahi, Mohanned K., Welge-Lüssen, Antje, Freiherr, Jessica, Groot, Jasper H.B. de, Klein, Hadar, Okamoto, Masako, Singh, Preet Bano, Hsieh, Julien W., Reed, Danielle R., Hummel, Thomas, Munger, Steven D., Hayes, John E., and Publica
Abstract: Recent anecdotal and scientific reports have provided evidence of a link between COVID-19 and chemosensory impairments, such as anosmia. However, these reports have downplayed or failed to distinguish potential effects on taste, ignored chemesthesis, and generally lacked quantitative measurements. Here, we report the development, implementation, and initial results of a multilingual, international questionnaire to assess self-reported quantity and quality of perception in 3 distinct chemosensory modalities (smell, taste, and chemesthesis) before and during COVID-19. In the first 11 days after questionnaire launch, 4039 participants (2913 women, 1118 men, and 8 others, aged 19-79) reported a COVID-19 diagnosis either via laboratory tests or clinical assessment. Importantly, smell, taste, and chemesthetic function were each significantly reduced compared to their status before the disease. Difference scores (maximum possible change ±100) revealed a mean reduction of smell (−79.7 ± 28.7, mean ± standard deviation), taste (−69.0 ± 32.6), and chemesthetic (−37.3 ± 36.2) function during COVID-19. Qualitative changes in olfactory ability (parosmia and phantosmia) were relatively rare and correlated with smell loss. Importantly, perceived nasal obstruction did not account for smell loss. Furthermore, chemosensory impairments were similar between participants in the laboratory test and clinical assessment groups. These results show that COVID-19-associated chemosensory impairment is not limited to smell but also affects taste and chemesthesis. The multimodal impact of COVID-19 and the lack of perceived nasal obstruction suggest that severe acute respiratory syndrome coronavirus strain 2 (SARS-CoV-2) infection may disrupt sensory-neural mechanisms.
Published: 2020

17. Referee report. For: Prediction of cell position using single-cell transcriptomic data: an iterative procedure [version 2; peer review: 2 approved]

Author: Meyer, Pablo
Published: 2020
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18. Referee report. For: Prediction of cell position using single-cell transcriptomic data: an iterative procedure [version 1; peer review: 2 approved with reservations]

Author: Meyer, Pablo
Published: 2019
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19. Predicting human olfactory perception from chemical features of odor molecules

Author: Keller, Andreas, Gerkin, Richard C, Guan, Yuanfang, Dhurandhar, Amit, Turu, Gabor, Szalai, Bence, Mainland, Joel D, Ihara, Yusuke, Yu, Chung Wen, Wolfinger, Russ, Vens, Celine, Schietgat, Leander, De Grave, Kurt, Norel, Raquel, DREAM Olfaction Prediction Consortium, Stolovitzky, Gustavo, Cecchi, Guillermo A, Vosshall, Leslie B, and Meyer, Pablo
Subjects: Smell, Adult, Male, Models, General Science & Technology, Odorants, Neurosciences, Humans, Datasets as Topic, Biological, Olfactory Perception, DREAM Olfaction Prediction Consortium
Abstract: It is still not possible to predict whether a given molecule will have a perceived odor or what olfactory percept it will produce. We therefore organized the crowd-sourced DREAM Olfaction Prediction Challenge. Using a large olfactory psychophysical data set, teams developed machine-learning algorithms to predict sensory attributes of molecules based on their chemoinformatic features. The resulting models accurately predicted odor intensity and pleasantness and also successfully predicted 8 among 19 rated semantic descriptors ("garlic," "fish," "sweet," "fruit," "burnt," "spices," "flower," and "sour"). Regularized linear models performed nearly as well as random forest-based ones, with a predictive accuracy that closely approaches a key theoretical limit. These models help to predict the perceptual qualities of virtually any molecule with high accuracy and also reverse-engineer the smell of a molecule.
Published: 2017

20. Reducing overfitting in challenge-based competitions

Author: Neto, Elias Chaibub, Hoff, Bruce R, Bare, Chris, Bot, Brian M, Yu, Thomas, Magravite, Lara, Trister, Andrew D, Norman, Thea, Meyer, Pablo, Saez-Rodrigues, Julio, Costello, James C, Guinney, Justin, and Stolovitzky, Gustavo
Subjects: FOS: Computer and information sciences, Applications (stat.AP), Statistics - Applications
Abstract: Over-fitting is a dreaded foe in challenge-based competitions. Because participants rely on public leaderboards to evaluate and refine their models, there is always the danger they might over-fit to the holdout data supporting the leaderboard. The recently published Ladder algorithm aims to address this problem by preventing the participants from exploiting willingly or inadvertently minor fluctuations in public leaderboard scores during model refinement. In this paper, we report a vulnerability of the Ladder that induces severe over-fitting of the leaderboard when the sample size is small. To circumvent this attack, we propose a variation of the Ladder that releases a bootstrapped estimate of the public leaderboard score instead of providing participants with a direct measure of performance. We also extend the scope of the Ladder to arbitrary performance metrics by relying on a more broadly applicable testing procedure based on the Bayesian bootstrap. Our method makes it possible to use a leaderboard, with the technical and social advantages that it provides, even in cases where data is scant.
Published: 2016

21. Prevalence of intestinal helminths, anemia, and malnutrition in Paucartambo, Peru

Author: Cabada, Miguel M., Goodrich, Mary R., Graham, Brittany, Villanueva-Meyer, Pablo G., Deichsel, Emily L., Lopez, Martha, Arque, Eulogia, and Clinton White, A. Jr
Subjects: Male, Rural Population, Anthelmintics/therapeutic use, Growth Disorders/epidemiology, Endemic Diseases, purl.org/pe-repo/ocde/ford#3.03.05 [https], Social Determinants of Health, Intestinal Diseases, Parasitic/epidemiology/prevention & control/transmission, Albendazole/therapeutic use, Helminthiasis/epidemiology/prevention & control/transmission, Cross-Sectional Studies, Socioeconomic Factors, Water Supply, Child, Preschool, Soil/parasitology, Eosinophilia/epidemiology, parasitic diseases, Malnutrition/epidemiology, Prevalence, Humans, Educational Status, Female, Anemia/epidemiology/etiology, Child, Peru/epidemiology
Abstract: OBJECTIVE: To evaluate the prevalence of soil-transmitted helminth infections, anemia, and malnutrition among children in the Paucartambo province of Cusco region, Peru, in light of demographic, socio-economic, and epidemiologic contextual factors. METHODS: Children from three to twelve years old from six communities in Huancarani district in the highlands of Peru were evaluated for helminth infections, anemia, and nutritional status. Data collected included demographic variables, socioeconomic status, exposures, complete blood counts, and direct and sedimentation stool tests. RESULTS: Of 240 children analyzed, 113 (47%) were infected with one or more parasites. Giardia (27.5%) and Fasciola (9.6%) were the most commonly identified organisms. Eosinophilia was encountered in 21% of the children. Anemia (48.8%) was associated with age (3-4 vs 5-12 years old; odds ratio (OR): 5.86; 95% confidence interval (CI): 2.81-12.21). Underweight (10%) was associated with male sex (OR: 5.97; CI: 1.12-31.72), higher eosinophil count (OR: 4.67; CI: 1.31-16.68) and education of the mother (OR: 0.6; CI: 0.4-0.9). Stunting (31.3%) was associated with education of the mother (OR: 0.83; CI: 0.72-0.95); wasting (2.7%) was associated with higher eosinophil count (OR: 2.75; CI: 1.04-7.25). CONCLUSIONS: Anemia and malnutrition remain significant problems in the Peruvian highlands. These findings suggest that demographic factors, socio-economic status, and possibly parasitic infections intertwine to cause these health problems.
Published: 2015

22. Cell wall synthesis is necessary for membrane dynamics during sporulation of Bacillus subtilis

Author: Meyer, Pablo, Gutierrez, Jennifer, Pogliano, Kit, and Dworkin, Jonathan
Subjects: Spores, Bacterial, Bacterial Proteins, Cell Wall, Cell Membrane, chemical and pharmacologic phenomena, Peptidoglycan, Article, circulatory and respiratory physiology, Bacillus subtilis
Abstract: During Bacillus subtilis sporulation, an endocytic-like process called engulfment results in one cell being entirely encased in the cytoplasm of another cell. The driving force underlying this process of membrane movement has remained unclear, although components of the machinery have been characterized. Here we provide evidence that synthesis of peptidoglycan, the rigid, strength bearing extracellular polymer of bacteria, is a key part of the missing force-generating mechanism for engulfment. We observed that sites of peptidoglycan synthesis initially coincide with the engulfing membrane and later with the site of engulfment membrane fission. Furthermore, compounds that block muropeptide synthesis or polymerization prevented membrane migration in cells lacking a component of the engulfment machinery (SpoIIQ), and blocked the membrane fission event at the completion of engulfment in all cells. In addition, these compounds inhibited bulge and vesicle formation that occur in spoIID mutant cells unable to initiate engulfment, as did genetic ablation of a protein that polymerizes muropeptides. This is the first report to our knowledge that peptidoglycan synthesis is necessary for membrane movements in bacterial cells and has implications for the mechanism of force generation during cytokinesis.
Published: 2010

23. Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Author: Meyer, Pablo, Siwo, Geoffrey, Zeevi, Danny, Sharon, Eilon, Norel, Raquel, Segal, Eran, Stolovitzky, Gustavo, and DREAM6, Promoter Prediction Consortium
Abstract: The Gene Promoter Expression Prediction challenge consisted of predicting gene expression from promoter sequences in a previously unknown experimentally generated data set. The challenge was presented to the community in the framework of the sixth Dialogue for Reverse Engineering Assessments and Methods (DREAM6), a community effort to evaluate the status of systems biology modeling methodologies. Nucleotide-specific promoter activity was obtained by measuring fluorescence from promoter sequences fused upstream of a gene for yellow fluorescence protein and inserted in the same genomic site of yeast Saccharomyces cerevisiae. Twenty-one teams submitted results predicting the expression levels of 53 different promoters from yeast ribosomal protein genes. Analysis of participant predictions shows that accurate values for low-expressed and mutated promoters were difficult to obtain, although in the latter case, only when the mutation induced a large change in promoter activity compared to the wild-type sequence. As in previous DREAM challenges, we found that aggregation of participant predictions provided robust results, but did not fare better than the three best algorithms. Finally, this study not only provides a benchmark for the assessment of methods predicting activity of a specific set of promoters from their sequence, but it also shows that the top performing algorithm, which used machine-learning approaches, can be improved by the addition of biological features such as transcription factor binding sites.

24. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

Author: Jovan, Tanevski, Thin, Nguyen, Buu, Truong, Nikos, Karaiskos, Mehmet Eren Ahsen, Xinyu, Zhang, Chang, Shu, Ke, Xu, Xiaoyu, Liang, Ying, Hu, Hoang VV Pham, Xiaomei, Li, Thuc, D Le, Adi, L Tarca, Gaurav, Bhatti, Roberto, Romero, Nestoras, Karathanasis, Phillipe, Loher, Yang, Chen, Zhengqing, Ouyang, Disheng, Mao, Yuping, Zhang, Maryam, Zand, Jianhua, Ruan, Christoph, Hafemeister, Peng, Qiu, Duc, Tran, Tin, Nguyen, Attila, Gabor, Thomas, Yu, Justin, Guinney, Enrico, Glaab, Roland, Krause, Peter, Banda, DREAM SCTC Consortium, Baruzzo, Giacomo, Cappellato, Marco, Zorzan, Irene, DEL FAVERO, Simone, Schenato, Luca, Vandin, Fabio, DI CAMILLO, Barbara, Shruti, Gupta, Ajay Kumar Verma, Shandar, Ahmad, Ronesh, Sharma, Edwin, Vans, Alok, Sharma, Ashwini, Patil, Alejandra, Carrea, Alonso, Andres M., Luis, Diambra, Vijay, Narsapuram, Vinay, Kaikala, Chaitanyam, Potnuru, Sunil, Kumar, Jiajie, Peng, Xiaoyu, Wang, Xuequn, Shang, Dani, Livne, Tom, Snir, Hagit, Philip, Alona, Zilberberg, Sol, Efroni, Hamid Reza Hassanzadeh, Reihaneh, Hassanzadeh, Ghazal, Jahanshahi, M-Mahdi, Naddaf-Sh, Drayer, Phillip M., Sadra, Naddaf-Sh, Marouen Ben Guebila, Changlin, Wan, Yuchen, Cao, Saber, Meamardoost, Nan Papili Gao, Rudiyanto, Gunawan, Gustavo, Stolovitzky, Nikolaus, Rajewsky, Julio, Saez-Rodriguez, Pablo, Meyer, Tanevski, Jovan, Nguyen, Thin, Truong, Buu, Karaiskos, Nikos, Pham, Hoang Vv, Xiaomei, Li, Le, Thuc D, Meyer, Pablo, and Dream SCTC consortuim
Subjects: Health, Toxicology and Mutagenesis, Cell, Plant Science, In situ hybridization, Computational biology, Biology, Biochemistry, Genetics and Molecular Biology (miscellaneous), Transcriptome, 03 medical and health sciences, Spatial reconstruction, 0302 clinical medicine, mental disorders, Databases, Genetic, medicine, Animals, Gene Regulatory Networks, Gene, Spatial analysis, Spatial organization, Research Articles, Zebrafish, 030304 developmental biology, 0303 health sciences, Spatial Analysis, Ecology, Sequence Analysis, RNA, Gene Expression Profiling, RNA-seq technologies, Computational Biology, Gene Expression Regulation, Developmental, Gene selection, medicine.anatomical_structure, Cardiovascular and Metabolic Diseases, Single-cell RNA-sequencing (scRNAseq), Drosophila, Single-Cell Analysis, 030217 neurology & neurosurgery, psychological phenomena and processes, Algorithms, gene selection, Research Article, Forecasting
Abstract: We describe and provide an array of diverse methods to predict cellular positions in tissue from RNA-seq data selecting mapping genes according to their spatial/statistical properties and their effect on improving the cell positioning., Single-cell RNA-sequencing (scRNAseq) technologies are rapidly evolving. Although very informative, in standard scRNAseq experiments, the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to maintain cell localization have limited throughput and gene coverage. Mapping scRNAseq to genes with spatial information increases coverage while providing spatial location. However, methods to perform such mapping have not yet been benchmarked. To fill this gap, we organized the DREAM Single-Cell Transcriptomics challenge focused on the spatial reconstruction of cells from the Drosophila embryo from scRNAseq data, leveraging as silver standard, genes with in situ hybridization data from the Berkeley Drosophila Transcription Network Project reference atlas. The 34 participating teams used diverse algorithms for gene selection and location prediction, while being able to correctly localize clusters of cells. Selection of predictor genes was essential for this task. Predictor genes showed a relatively high expression entropy, high spatial clustering and included prominent developmental genes such as gap and pair-rule genes and tissue markers. Application of the top 10 methods to a zebra fish embryo dataset yielded similar performance and statistical properties of the selected genes than in the Drosophila data. This suggests that methods developed in this challenge are able to extract generalizable properties of genes that are useful to accurately reconstruct the spatial arrangement of cells in tissues.
Published: 2020

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24 results on '"Meyer, Pablo"'

1. Interpretable Stratification for Chronic Kidney Disease Progression Based on Time to Event Analysis

2. The novelty Mezilaurus conceicionensis (Lauraceae) and a key to the species of the genus from Brazilian Southeastern

3. Predicting/characterizing chemosensory changes in COVID+ vs. COVID- using natural language processing of multinational survey data

4. Mere end lugtesans - COVID-19 er associeret med svær påvirkning af lugtesansen, smagssansen og mundfølelsen

5. Mezilaurus conceicionensis L. C. S. Assis, P. B. Meyer & F. M. Alves 2022, sp. nov

6. Mezilaurus Alves & Meyer & Assis 2022

7. Mezilaurus Alves & Meyer & Assis 2022

8. Distillation to Enhance the Portability of Risk Models Across Institutions with Large Patient Claims Database

9. Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees

10. Disease Progression Modeling Workbench 360

11. Flowers to Òsanyìn: Lychnophora osanyiniana (Asteraceae: Vernonieae) a new 'arnica da serra' from Minas Gerais, Brazil

12. Recent Smell Loss Is the Best Predictor of COVID-19 Among Individuals With Recent Respiratory Symptoms

13. Corrigendum to: More than smell: COVID-19 is associated with severe impairment of smell, taste, and chemesthesis

14. The best COVID-19 predictor is recent smell loss: a cross-sectional study

15. Recent smell loss is the best predictor of COVID-19: a preregistered, cross-sectional study

16. More than smell - COVID-19 is associated with severe impairment of smell, taste, and chemesthesis

17. Referee report. For: Prediction of cell position using single-cell transcriptomic data: an iterative procedure [version 2; peer review: 2 approved]

18. Referee report. For: Prediction of cell position using single-cell transcriptomic data: an iterative procedure [version 1; peer review: 2 approved with reservations]

19. Predicting human olfactory perception from chemical features of odor molecules

20. Reducing overfitting in challenge-based competitions

21. Prevalence of intestinal helminths, anemia, and malnutrition in Paucartambo, Peru

22. Cell wall synthesis is necessary for membrane dynamics during sporulation of Bacillus subtilis

23. Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

24. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

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24 results on '"Meyer, Pablo"'

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