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156. SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities

Author

Munteanu, Viorel, Saldana, Michael A., Dreifuss, David, Ouyang, Wenhao O., Ferdous, Jannatul, Mohebbi, Fatemeh, Schlueter, Jessica, Ciorba, Dumitru, Bostan, Viorel, Gordeev, Victor, Su, Justin Maine, Kasianchuk, Nadiia, Sharma, Nitesh Kumar, Knyazev, Sergey, Aßmann, Eva, Lobiuc, Andrei, Covasa, Mihai, Crandall, Keith A., Wu, Nicholas C., Mason, Christopher E., Tierney, Braden T, Lucaci, Alexander G, Ophoff, Roel A., Gibas, Cynthia, Rzymski, Piotr, Skums, Pavel, Solo-Gabriele, Helena, Niko, Beerenwinkel, Zelikovsky, Alex, Hölzer, Martin, Smith, Adam, and Mangul, Serghei

Subjects
Quantitative Biology - Genomics
Abstract

During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cryptic lineages, but it is difficult to clearly identify and define novel lineages from wastewater (WW) alone. While WWGS has significant advantages in monitoring SARS-CoV-2 viral spread, technical challenges remain, including poor sequencing coverage and quality due to viral RNA degradation. As a result, the viral RNAs in wastewater have low concentrations and are often fragmented, making sequencing difficult. WWGS analysis requires advanced computational tools that are yet to be developed and benchmarked. The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity. Those methods were not developed for wastewater sequencing data specifically, and are not optimized to address unique challenges associated with wastewater. While specialized tools for analysis of wastewater sequencing data have also been developed recently, it remains to be seen how they will perform given the ongoing evolution of SARS-CoV-2 and the decline in testing and patient-based genomic surveillance. Here, we discuss opportunities and challenges associated with WWGS, including sample preparation, sequencing technology, and bioinformatics methods., Comment: V Munteanu and M Saldana contributed equally to this work. M H\"olzer, A Smith and S Mangul jointly supervised this work. For correspondence: serghei.mangul@gmail.com

Published
2023

157. Minimum-dissipation model for large-eddy simulation in OpenFoam -A study on channel flow, periodic hills and flow over cylinder

Author

Sun, Jing and Verstappen, Roel

Subjects
Physics - Fluid Dynamics
Abstract

The minimum-dissipation model is applied to turbulent channel flows up to $Re_\tau = 2000$, flow past a circular cylinder at $Re=3900$, and flow over periodic hills at $Re=10595$. Numerical simulations are performed in OpenFOAM which is based on finite volume methods for discretizing partial differential equations. We use both symmetry-preserving discretizations and standard second-order accurate discretization methods in OpenFOAM on structured meshes. The results are compared to DNS and experimental data. The results of channel flow mainly demonstrate the static QR model performs equally well as the dynamic models while reducing the computational cost. The model constant $C=0.024$ gives the most accurate prediction, and the contribution of the sub-grid model decreases with the increase of the mesh resolution and becomes very small (less than 0.2 molecular viscosity) if the fine meshes are used. Furthermore, the QR model is able to predict the mean and rms velocity accurately up to $Re_\tau = 2000$ without a wall damping function. The symmetry-preserving discretization outperforms the standard OpenFOAM discretization at $Re_\tau=1000$. The results for the flow over a cylinder show that mean velocity, drag coefficient, and lift coefficient are in good agreement with the experimental data. The symmetry-preserving scheme with the QR model predicts the best results. The various comparisons carried out for flows over periodic hills demonstrate the need to use the symmetry-preserving discretization or central difference schemes in OpenFOAM in combination with the minimum dissipation model. The model constant of $C=0.024$ is again the best one.

Published
2023

158. Ehrenfest Modeling of Cavity Vacuum Fluctuations and How to Achieve Emission from a Three-Level Atom

Author

Hsieh, Ming-Hsiu, Krotz, Alex, and Tempelaar, Roel

Subjects
Physics - Chemical Physics, Quantum Physics
Abstract

A much-needed solution for the efficient modeling of strong coupling between matter and optical cavity modes is offered by mean-field mixed quantum--classical dynamics, where a classical cavity field interacts self-consistently with quantum states of matter through Ehrenfest's theorem. We previously introduced a modified mean-field approach, referred to as decoupled mean-field (DC-MF) dynamics, wherein vacuum fluctuations of the cavity field are decoupled from the quantum-mechanical ground state as a means to resolve an unphysical drawing of energy from the vacuum fluctuations by a two-level atom. Here, we generalize DC-MF dynamics for an arbitrary number of (nondegenerate) atomic levels, and show that it resolves an unphysical lack of emission from a three-level atom predicted by conventional mean-field dynamics. We furthermore show DC-MF to provide an improved description of reabsorption and (resonant) two-photon emission processes., Comment: 5 pages, 2 figures

Published
2023
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159. Observation of a Brillouin dynamic grating in silicon nitride waveguides

Author

Botter, Roel, Hoogen, Jasper van den, Mishra, Akhileshwar, Ye, Kaixuan, van Rees, Albert, Hoekman, Marcel, Boller, Klaus, and Marpaung, David

Subjects
Physics - Optics, Physics - Applied Physics
Abstract

Brillouin enhanced four wave mixing in the form of a Brillouin dynamic grating (BDG) enables a uniquely tunable filter, whose properties can be tuned by purely optical means. This makes the BDG a valuable tool in microwave photonics (MWP). BDGs have been studied extensively in fibers, but the only observation in an integrated platform required exotic materials. Unlocking BDG in a standard and mature platform will enable its integration into large-scale circuits. Here we demonstrate the first observation of a BDG in a silicon nitride (Si$_3$N$_4$) waveguide. We also present a new, optimized design, which will enhance the BDG response of the waveguide, unlocking a path to large-scale integration into MWP circuits.

Published
2023
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160. The Importance of Distrust in AI

Author

Peters, Tobias M. and Visser, Roel W.

Subjects
Computer Science - Human-Computer Interaction
Abstract

In recent years the use of Artificial Intelligence (AI) has become increasingly prevalent in a growing number of fields. As AI systems are being adopted in more high-stakes areas such as medicine and finance, ensuring that they are trustworthy is of increasing importance. A concern that is prominently addressed by the development and application of explainability methods, which are purported to increase trust from its users and wider society. While an increase in trust may be desirable, an analysis of literature from different research fields shows that an exclusive focus on increasing trust may not be warranted. Something which is well exemplified by the recent development in AI chatbots, which while highly coherent tend to make up facts. In this contribution, we investigate the concepts of trust, trustworthiness, and user reliance. In order to foster appropriate reliance on AI we need to prevent both disuse of these systems as well as overtrust. From our analysis of research on interpersonal trust, trust in automation, and trust in (X)AI, we identify the potential merit of the distinction between trust and distrust (in AI). We propose that alongside trust a healthy amount of distrust is of additional value for mitigating disuse and overtrust. We argue that by considering and evaluating both trust and distrust, we can ensure that users can rely appropriately on trustworthy AI, which can both be useful as well as fallible., Comment: This preprint has not undergone peer review or any post-submission improvements or corrections. The version of records of this contribution is published in Explainable Artificial Intelligence First World Conference, xAI 2023, Lisbon, Portugal, July 26-28, 2023, Proceedings, Part III (CCIS, volume 1903) and is available at https://doi.org/10.1007/978-3-031-44070-0

Published
2023
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161. Stimulated Brillouin scattering in tellurite-covered silicon nitride waveguides

Author

Botter, Roel A., Klaver, Yvan, Morsche, Randy te, Frare, Bruno L. Segat, Hashemi, Batoul, Ye, Kaixuan, Mishra, Akhileshwar, Braamhaar, Redlef B. G., Bradley, Jonathan D. B., and Marpaung, David

Subjects
Physics - Optics, Physics - Applied Physics
Abstract

Stimulated Brillouin scattering (SBS), a coherent nonlinear effect coupling acoustics and optics, can be used in a wide range of applications such as Brillouin lasers and tunable narrowband RF filtering. Wide adoption of such technologies however, would need a balance of strong Brillouin interaction and low optical loss in a structure compatible with large scale fabrication. Achieving these characteristics in scalable platforms such as silicon and silicon nitride remains a challenge. Here, we investigate a scalable Brillouin platform combining low loss Si$_3$N$_4$ and tellurium oxide (TeO$_2$) exhibiting strong Brillouin response and enhanced acoustic confinement. In this platform we measure a Brillouin gain coefficient of 8.5~m$^{-1}$W$^{-1}$, exhibiting a twenty fold improvement over the largest previously reported Brillouin gain in a Si$_3$N$_4$ platform. Further, we demonstrate cladding engineering to control the strength of the Brillouin interaction. We utilized the Brillouin gain and loss resonances in this waveguide for an RF photonic filter with more than 15 dB rejection and 250 MHz linewidth. Finally, we present a pathway by geometric optimization and cladding engineering to a further enhancement of the gain coefficient to 155~m$^{-1}$W$^{-1}$, a potential 400 times increase in the Brillouin gain coefficient.

Published
2023

163. Collaborative Learning Intervention Associated with Small Increases in Home-Based School Involvement for Lower SES Families in Deprived Neighbourhoods

Author

Renske Keizer, Roel van Steensel, Joran Jongerling, Talitha Stam, Brian P. Godor, and Nicole Lucassen

Abstract

This study investigated the impact of the Dutch family-oriented Collaborative Learning intervention, characterised by a partnership approach and provision of personalised support. We assessed effects on parents' home-based school involvement, perceived quality of the parent-teacher relationship, and parenting skills. Fifty-six families with children in grades 1-4 (aged 4-9) were randomly assigned to an intervention or waiting list condition. Results of two path models, using cluster-robust standard errors to adjust for nesting within our data, and controlling for baseline values of our outcome variables, indicated small improvements in home-based school involvement among families in the intervention group, but no differences in the perceived quality of the parent-teacher relationship nor in parenting skills. Our findings provide preliminary evidence for the idea that, under conditions of a partnership approach and provision of personalised support, efforts to support and strengthen the capacities of lower SES parents to promote child development can be fruitful.

Published
2024
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164. Speech and Music Therapy in the Treatment of Childhood Apraxia of Speech: An Introduction and a Case Study

Author

Mirjam van Tellingen, Joost Hurkmans, Hayo Terband, Anne Marie van de Zande, Ben Maassen, and Roel Jonkers

Abstract

Purpose: Speech--Music Therapy for Aphasia (SMTA), a method that combines speech therapy and music therapy, is introduced as a treatment method for childhood apraxia of speech (CAS). SMTA will be evaluated in a proof-ofprinciple study. The first case study is presented herein. Method: SMTA was evaluated in a study with a single-subject experimental design comparing 10 weeks of treatment with 2 months of no treatment. The research protocol included a pretest, baseline phase, treatment phase, posttest, no-treatment phase, and follow-up test. The participant was a boy with CAS aged 5;8 (years;months). Outcome measures were selected to reflect both intelligibility in daily communication as well as features of CAS and speech motor planning and programming. Results: Results on the Intelligibility in Context Scale--Dutch (ICS-Dutch) and in the analysis of a spontaneous speech sample suggest generalization of treatment effects. Improvements were found in measures that reflect complex speech motor skills, that is, the production of consonant clusters and consistency. Conclusions: This case study showed that speech production of the participant improved after treatment with SMTA. Although intelligibility as measured with the ICS-Dutch improved over the study period, objectifying changes at the level of intelligibility in daily communication proved to be difficult. Additional measures may be necessary to gain more insight into treatment effects at this level. Overall, the results of this first case study provide sufficient support and important leads for further evaluation of SMTA in the treatment of CAS in a proof-of-principle study.

Published
2024
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165. Dutch Secondary School Counselors' and Tutors' Views on How Students Should Make Study Profile Choices

Author

Inge JM Wichgers, Hanke Korpershoek, Matthijs J Warrens, Monique A Dijks, and Roel J Bosker

Abstract

Student counselors and tutors guide students' choices of study profiles (subjects) within Dutch secondary education. This study addressed three research questions: (1) According to counselors and tutors, what factors should inform students' study profile choices? (2) Into what types can the views of counselors and tutors be classified? (3) According to counselors and tutors, which factors should secondary school students consider when choosing their study profiles in a forced-choice situation? Interviews held with 70 tutors and counselors identified students' interests, abilities, and future-oriented considerations as most important (RQ1). Six types of views were identified in which one, two, or all of the above-mentioned factors were regarded the most important by the participants (RQ2). Responses to the forced-choice situations largely confirmed different perspectives on the factors: the majority of participants perceived students' interests very important (RQ3).

Published
2024
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171. The biogeography of the Amazonian tree flora

Author

Luize, Bruno Garcia, Tuomisto, Hanna, Ekelschot, Robin, Dexter, Kyle G., Amaral, Iêda L. do, Coelho, Luiz de Souza, Matos, Francisca Dionízia de Almeida, Lima Filho, Diógenes de Andrade, Salomão, Rafael P., Wittmann, Florian, Castilho, Carolina V., Carim, Marcelo de Jesus Veiga, Guevara, Juan Ernesto, Phillips, Oliver L., Magnusson, William E., Sabatier, Daniel, Cardenas Revilla, Juan David, Molino, Jean-François, Irume, Mariana Victória, Martins, Maria Pires, Guimarães, José Renan da Silva, Ramos, José Ferreira, Bánki, Olaf S., Piedade, Maria Teresa Fernandez, Cárdenas López, Dairon, Pitman, Nigel C. A., Demarchi, Layon O., Schöngart, Jochen, de Leão Novo, Evlyn Márcia Moraes, Núñez Vargas, Percy, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Honorio Coronado, Euridice N., Mendoza, Abel Monteagudo, Montero, Juan Carlos, Costa, Flávia R. C., Feldpausch, Ted R., Quaresma, Adriano Costa, Castaño Arboleda, Nicolás, Zartman, Charles Eugene, Killeen, Timothy J., Marimon, Beatriz S., Marimon, Ben Hur, Vasquez, Rodolfo, Mostacedo, Bonifacio, Assis, Rafael L., Baraloto, Chris, do Amaral, Dário Dantas, Engel, Julien, Petronelli, Pascal, Castellanos, Hernán, de Medeiros, Marcelo Brilhante, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Laurance, William F., Laurance, Susan G. W., Rincón, Lorena Maniguaje, Schietti, Juliana, Sousa, Thaiane R., Mori, Gisele Biem, Farias, Emanuelle de Sousa, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Nascimento, Henrique Eduardo Mendonça, de Queiroz, Helder Lima, Vasconcelos, Caroline C., Aymard C, Gerardo A., Brienen, Roel, Stevenson, Pablo R., Araujo-Murakami, Alejandro, Cintra, Bruno Barçante Ladvocat, Baker, Tim R., Feitosa, Yuri Oliveira, Mogollón, Hugo F., Duivenvoorden, Joost F., Peres, Carlos A., Silman, Miles R., Ferreira, Leandro Valle, Lozada, José Rafael, Comiskey, James A., de Toledo, José Julio, Damasco, Gabriel, Dávila, Nállarett, Draper, Freddie C., García-Villacorta, Roosevelt, Lopes, Aline, Vicentini, Alberto, Valverde, Fernando Cornejo, Alonso, Alfonso, Arroyo, Luzmila, Dallmeier, Francisco, Gomes, Vitor H. F., Jimenez, Eliana M., Neill, David, Peñuela Mora, Maria Cristina, Noronha, Janaína Costa, de Aguiar, Daniel P. P., Barbosa, Flávia Rodrigues, Bredin, Yennie K., Carpanedo, Rainiellen de Sá, Carvalho, Fernanda Antunes, Souza, Fernanda Coelho de, Feeley, Kenneth J., Gribel, Rogerio, Haugaasen, Torbjørn, Hawes, Joseph E., Pansonato, Marcelo Petratti, Pipoly, III, John J., Paredes, Marcos Ríos, Rodrigues, Domingos de Jesus, Barlow, Jos, Berenguer, Erika, da Silva, Izaias Brasil, Ferreira, Maria Julia, Ferreira, Joice, Fine, Paul V. A., Guedes, Marcelino Carneiro, Levis, Carolina, Licona, Juan Carlos, Villa Zegarra, Boris Eduardo, Vos, Vincent Antoine, Cerón, Carlos, Durgante, Flávia Machado, Fonty, Émile, Henkel, Terry W., Householder, John Ethan, Huamantupa-Chuquimaco, Isau, Silveira, Marcos, Stropp, Juliana, Thomas, Raquel, Daly, Doug, Milliken, William, Molina, Guido Pardo, Pennington, Toby, Vieira, Ima Célia Guimarães, Albuquerque, Bianca Weiss, Campelo, Wegliane, Fuentes, Alfredo, Klitgaard, Bente, Pena, José Luis Marcelo, Tello, J. Sebastián, Vriesendorp, Corine, Chave, Jerome, Di Fiore, Anthony, Hilário, Renato Richard, Pereira, Luciana de Oliveira, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, van Andel, Tinde R., von Hildebrand, Patricio, Balee, William, Barbosa, Edelcilio Marques, Bonates, Luiz Carlos de Matos, Dávila Doza, Hilda Paulette, Zárate Gómez, Ricardo, Gonzales, Therany, Gallardo Gonzales, George Pepe, Hoffman, Bruce, Junqueira, André Braga, Malhi, Yadvinder, Miranda, Ires Paula de Andrade, Pinto, Linder Felipe Mozombite, Prieto, Adriana, Rudas, Agustín, Ruschel, Ademir R., Silva, Natalino, Vela, César I. A., Zent, Stanford, Zent, Egleé L., Endara, María José, Cano, Angela, Carrero Márquez, Yrma Andreina, Correa, Diego F., Costa, Janaina Barbosa Pedrosa, Monteiro Flores, Bernardo, Galbraith, David, Holmgren, Milena, Kalamandeen, Michelle, Lobo, Guilherme, Torres Montenegro, Luis, Nascimento, Marcelo Trindade, Oliveira, Alexandre A., Pombo, Maihyra Marina, Ramirez-Angulo, Hirma, Rocha, Maira, Scudeller, Veridiana Vizoni, Umaña, Maria Natalia, van der Heijden, Geertje, Vilanova Torre, Emilio, Vargas, Tony Mori, Ahuite Reategui, Manuel Augusto, Baider, Cláudia, Balslev, Henrik, Cárdenas, Sasha, Casas, Luisa Fernanda, Farfan-Rios, William, Ferreira, Cid, Linares-Palomino, Reynaldo, Mendoza, Casimiro, Mesones, Italo, Parada, Germaine Alexander, Torres-Lezama, Armando, Urrego Giraldo, Ligia Estela, Villarroel, Daniel, Zagt, Roderick, Alexiades, Miguel N., de Oliveira, Edmar Almeida, Fortier, Riley P., Garcia-Cabrera, Karina, Hernandez, Lionel, Palacios Cuenca, Walter, Pansini, Susamar, Pauletto, Daniela, Ramirez Arevalo, Freddy, Sampaio, Adeilza Felipe, Valderrama Sandoval, Elvis H., Valenzuela Gamarra, Luis, Hirota, Marina, Palma-Silva, Clarisse, and ter Steege, Hans

Published
2024
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174. Magnesium sulphate to prevent perioperative atrial fibrillation in cardiac surgery: a randomized clinical trial: A protocol description of the PeriOperative Magnesium Infusion to Prevent Atrial fibrillation Evaluated (POMPAE) trial

Author

Meerman, Manon, Buijser, Marit, van den Berg, Lettie, van den Heuvel, Anne-Marthe, Hoohenkerk, Gerard, van Driel, Vincent, Munsterman, Luuk, de Vroege, Roel, Bailey, Michael, Bellomo, Rinaldo, and Ludikhuize, Jeroen

Published
2024
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177. Impacts of micro- and nanoplastics on early-life health: a roadmap towards risk assessment

Author

Christopher, Emily A., Christopher-de Vries, Yvette, Devadoss, Anitha, Mandemaker, Laurens D.B., van Boxel, Jeske, Copsey, Helena M., Dusza, Hanna M., Legler, Juliette, Meirer, Florian, Muncke, Jane, Nawrot, Tim S., Saenen, Nelly D., Scholz-Böttcher, Barbara M., Tran, Lang, Weckhuysen, Bert M., Zou, Runyu, Zimmermann, Lisa, Galea, Karen S., Vermeulen, Roel, and Boyles, Matthew S. P.

Published
2024
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181. Post-resolution macrophages shape long-term tissue immunity and integrity in a mouse model of pneumococcal pneumonia

Author

Feehan, Karen T., Bridgewater, Hannah E., Stenkiewicz-Witeska, Jan, De Maeyer, Roel P. H., Ferguson, John, Mack, Matthias, Brown, Jeremy, Ercoli, Giuseppe, Mawer, Connar M., Akbar, Arne N., Glanville, James R. W., Jalali, Parinaaz, Bracken, Olivia V., Nicolaou, Anna, Kendall, Alexandra C., Sugimoto, Michelle A., and Gilroy, Derek W.

Published
2024
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185. A 2D chiral microcavity based on apparent circular dichroism

Author

Chen, Tzu-Ling, Salij, Andrew, Parrish, Katherine A., Rasch, Julia K., Zinna, Francesco, Brown, Paige J., Pescitelli, Gennaro, Urraci, Francesco, Aronica, Laura A., Dhavamani, Abitha, Arnold, Michael S., Wasielewski, Michael R., di Bari, Lorenzo, Tempelaar, Roel, and Goldsmith, Randall H.

Published
2024
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189. IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy

Author

Tanner, Georgette, Barrow, Rhiannon, Ajaib, Shoaib, Al-Jabri, Muna, Ahmed, Nazia, Pollock, Steven, Finetti, Martina, Rippaus, Nora, Bruns, Alexander F., Syed, Khaja, Poulter, James A., Matthews, Laura, Hughes, Thomas, Wilson, Erica, Johnson, Colin, Varn, Frederick S., Brüning-Richardson, Anke, Hogg, Catherine, Droop, Alastair, Gusnanto, Arief, Care, Matthew A., Cutillo, Luisa, Westhead, David R., Short, Susan C., Jenkinson, Michael D., Brodbelt, Andrew, Chakrabarty, Aruna, Ismail, Azzam, Verhaak, Roel G. W., and Stead, Lucy F.

Published
2024
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193. Integrated global assessment of the natural forest carbon potential

Author

Mo, Lidong, Zohner, Constantin M, Reich, Peter B, Liang, Jingjing, de Miguel, Sergio, Nabuurs, Gert-Jan, Renner, Susanne S, van den Hoogen, Johan, Araza, Arnan, Herold, Martin, Mirzagholi, Leila, Ma, Haozhi, Averill, Colin, Phillips, Oliver L, Gamarra, Javier GP, Hordijk, Iris, Routh, Devin, Abegg, Meinrad, Adou Yao, Yves C, Alberti, Giorgio, Almeyda Zambrano, Angelica M, Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F, Amaral, Iêda, Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A, Baker, Timothy R, Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G, Bastian, Meredith L, Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro HS, Brandl, Susanne, Brearley, Francis Q, Brienen, Roel, Broadbent, Eben N, Bruelheide, Helge, Bussotti, Filippo, Cazzolla Gatti, Roberto, César, Ricardo G, Cesljar, Goran, Chazdon, Robin L, Chen, Han YH, Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D, Coomes, David A, Cornejo Valverde, Fernando, Corral-Rivas, José J, Crim, Philip M, Cumming, Jonathan R, Dayanandan, Selvadurai, de Gasper, André L, Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J, Eyre, Teresa J, Fandohan, Adandé Belarmain, Fayle, Tom M, Feldpausch, Ted R, Ferreira, Leandro V, Finér, Leena, Fischer, Markus, Fletcher, Christine, Frizzera, Lorenzo, Gianelle, Damiano, Glick, Henry B, Harris, David J, Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L, Hillers, Annika, Honorio Coronado, Eurídice N, Hui, Cang, Ibanez, Thomas, Imai, Nobuo, and Jagodziński, Andrzej M

Subjects
Agricultural, Veterinary and Food Sciences, Ecological Applications, Environmental Sciences, Forestry Sciences, Life on Land, Biodiversity, Carbon, Carbon Sequestration, Conservation of Natural Resources, Forests, Human Activities, Environmental Restoration and Remediation, Sustainable Development, Global Warming, Agricultural, Ecosystem, General Science & Technology, Humans, Veterinary and Food Sciences
Abstract

Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system1. Remote-sensing estimates to quantify carbon losses from global forests2-5 are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced6 and satellite-derived approaches2,7,8 to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151-363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with existing forests, in which ecosystem protection can allow forests to recover to maturity. The remaining 39% (87 Gt C) of potential lies in regions in which forests have been removed or fragmented. Although forests cannot be a substitute for emissions reductions, our results support the idea2,3,9 that the conservation, restoration and sustainable management of diverse forests offer valuable contributions to meeting global climate and biodiversity targets.

Published
2023

194. Assessment of the probability of introduction of Thaumatotibia leucotreta into the European Union with import of cut roses.

Author

Bragard, Claude, Baptista, Paula, Chatzivassiliou, Elisavet, Di Serio, Francesco, Gonthier, Paolo, Jaques Miret, Josep, Fejer Justesen, Annemarie, MacLeod, Alan, Magnusson, Christer, Navas-Cortes, Juan, Parnell, Stephen, Potting, Roel, Reignault, Philippe, Stefani, Emilio, Thulke, Hans-Hermann, Vicent Civera, Antonio, Van der Werf, Wopke, Yuen, Jonathan, Zappalà, Lucia, Loomans, Antoon, Ponti, Luigi, Crotta, Matteo, Maiorano, Andrea, Mosbach-Schulz, Olaf, Rossi, Eugenio, Stancanelli, Giuseppe, Milonas, Panagiotis, and Gutierrez, Andrew

Subjects
Africa, Israel, climate suitability, false codling moth, pathway model, quantitative assessment, waste management
Abstract

Following a request from the European Commission, the EFSA Panel on Plant Health performed a quantitative pest risk assessment to assess whether the import of cut roses provides a pathway for the introduction of Thaumatotibia leucotreta (Lepidoptera: Tortricidae) into the EU. The assessment was limited to the entry and establishment steps. A pathway model was used to assess how many T. leucotreta individuals would survive and emerge as adults from commercial or household wastes in an EU NUTS2 region climatically suitable in a specific season. This pathway model for entry consisted of three components: a cut roses distribution model, a T. leucotreta developmental model and a waste model. Four scenarios of timing from initial disposal of the cut roses until waste treatment (3, 7, 14 and 28 days) were considered. The estimated median number of adults escaping per year from imported cut roses in all the climatically suitable NUTS2 regions of the EU varied from 49,867 (90% uncertainty between 5,298 and 234,393) up to 143,689 (90% uncertainty between 21,126 and 401,458) for the 3- and 28-day scenarios. Assuming that, on average, a successful mating will happen for every 435 escaping moths, the estimated median number of T. leucotreta mated females per year from imported cut roses in all the climatically suitable NUTS2 regions of the EU would vary from 115 (90% uncertainty between 12 and 538) up to 330 (90% uncertainty between 49 and 923) for the 3- and 28-day scenarios. Due to the extreme polyphagia of T. leucotreta, host availability will not be a limiting factor for establishment. Climatic suitability assessment, using a physiologically based demographic modelling approach, identified the coastline extending from the northwest of the Iberian Peninsula through the Mediterranean as area suitable for establishment of T. leucotreta. This assessment indicates that cut roses provide a pathway for the introduction of T. leucotreta into the EU.

Published
2023

195. The global biogeography of tree leaf form and habit

Author

Ma, Haozhi, Crowther, Thomas W, Mo, Lidong, Maynard, Daniel S, Renner, Susanne S, van den Hoogen, Johan, Zou, Yibiao, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B, Niinemets, Ülo, Abegg, Meinrad, Adou Yao, Yves C, Alberti, Giorgio, Almeyda Zambrano, Angelica M, Alvarado, Braulio Vilchez, Alvarez-Dávila, Esteban, Alvarez-Loayza, Patricia, Alves, Luciana F, Ammer, Christian, Antón-Fernández, Clara, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Avitabile, Valerio, Aymard, Gerardo A, Baker, Timothy R, Bałazy, Radomir, Banki, Olaf, Barroso, Jorcely G, Bastian, Meredith L, Bastin, Jean-Francois, Birigazzi, Luca, Birnbaum, Philippe, Bitariho, Robert, Boeckx, Pascal, Bongers, Frans, Bouriaud, Olivier, Brancalion, Pedro HS, Brandl, Susanne, Brearley, Francis Q, Brienen, Roel, Broadbent, Eben N, Bruelheide, Helge, Bussotti, Filippo, Cazzolla Gatti, Roberto, César, Ricardo G, Cesljar, Goran, Chazdon, Robin, Chen, Han YH, Chisholm, Chelsea, Cho, Hyunkook, Cienciala, Emil, Clark, Connie, Clark, David, Colletta, Gabriel D, Coomes, David A, Valverde, Fernando Cornejo, Corral-Rivas, José J, Crim, Philip M, Cumming, Jonathan R, Dayanandan, Selvadurai, de Gasper, André L, Decuyper, Mathieu, Derroire, Géraldine, DeVries, Ben, Djordjevic, Ilija, Dolezal, Jiri, Dourdain, Aurélie, Engone Obiang, Nestor Laurier, Enquist, Brian J, Eyre, Teresa J, Fandohan, Adandé Belarmain, Fayle, Tom M, Feldpausch, Ted R, Ferreira, Leandro V, Finér, Leena, Fischer, Markus, Fletcher, Christine, Fridman, Jonas, Frizzera, Lorenzo, Gamarra, Javier GP, Gianelle, Damiano, Glick, Henry B, Harris, David J, Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L, Herold, Martin, Hillers, Annika, Honorio Coronado, Eurídice N, Hui, Cang, Ibanez, Thomas T, Amaral, Iêda, Imai, Nobuo, Jagodziński, Andrzej M, Jaroszewicz, Bogdan, and Johannsen, Vivian Kvist

Subjects
Biological Sciences, Ecology, Climate Action, Plant Biology, Crop and Pasture Production, Plant biology
Abstract

Understanding what controls global leaf type variation in trees is crucial for comprehending their role in terrestrial ecosystems, including carbon, water and nutrient dynamics. Yet our understanding of the factors influencing forest leaf types remains incomplete, leaving us uncertain about the global proportions of needle-leaved, broadleaved, evergreen and deciduous trees. To address these gaps, we conducted a global, ground-sourced assessment of forest leaf-type variation by integrating forest inventory data with comprehensive leaf form (broadleaf vs needle-leaf) and habit (evergreen vs deciduous) records. We found that global variation in leaf habit is primarily driven by isothermality and soil characteristics, while leaf form is predominantly driven by temperature. Given these relationships, we estimate that 38% of global tree individuals are needle-leaved evergreen, 29% are broadleaved evergreen, 27% are broadleaved deciduous and 5% are needle-leaved deciduous. The aboveground biomass distribution among these tree types is approximately 21% (126.4 Gt), 54% (335.7 Gt), 22% (136.2 Gt) and 3% (18.7 Gt), respectively. We further project that, depending on future emissions pathways, 17-34% of forested areas will experience climate conditions by the end of the century that currently support a different forest type, highlighting the intensification of climatic stress on existing forests. By quantifying the distribution of tree leaf types and their corresponding biomass, and identifying regions where climate change will exert greatest pressure on current leaf types, our results can help improve predictions of future terrestrial ecosystem functioning and carbon cycling.

Published
2023

196. Fair integer programming under dichotomous and cardinal preferences

Author

Demeulemeester, Tom, Goossens, Dries, Hermans, Ben, and Leus, Roel

Subjects
Computer Science - Computer Science and Game Theory, Computer Science - Data Structures and Algorithms, Economics - Theoretical Economics
Abstract

One cannot make truly fair decisions using integer linear programs unless one controls the selection probabilities of the (possibly many) optimal solutions. For this purpose, we propose a unified framework when binary decision variables represent agents with dichotomous preferences, who only care about whether they are selected in the final solution. We develop several general-purpose algorithms to fairly select optimal solutions, for example, by maximizing the Nash product or the minimum selection probability, or by using a random ordering of the agents as a selection criterion (Random Serial Dictatorship). We also discuss in detail how to extend the proposed methods when agents have cardinal preferences. As such, we embed the black-box procedure of solving an integer linear program into a framework that is explainable from start to finish. Lastly, we evaluate the proposed methods on two specific applications, namely kidney exchange (dichotomous preferences), and the scheduling problem of minimizing total tardiness on a single machine (cardinal preferences). We find that while the methods maximizing the Nash product or the minimum selection probability outperform the other methods on the evaluated welfare criteria, methods such as Random Serial Dictatorship perform reasonably well in computation times that are similar to those of finding a single optimal solution.

Published
2023

197. Deep learning-based group-wise registration for longitudinal MRI analysis in glioma

Author

Hammecher, Claudia Chinea, van Garderen, Karin, Smits, Marion, Wesseling, Pieter, Westerman, Bart, French, Pim, Kouwenhoven, Mathilde, Verhaak, Roel, Vos, Frans, Bron, Esther, and Li, Bo

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Glioma growth may be quantified with longitudinal image registration. However, the large mass-effects and tissue changes across images pose an added challenge. Here, we propose a longitudinal, learning-based, and groupwise registration method for the accurate and unbiased registration of glioma MRI. We evaluate on a dataset from the Glioma Longitudinal AnalySiS consortium and compare it to classical registration methods. We achieve comparable Dice coefficients, with more detailed registrations, while significantly reducing the runtime to under a minute. The proposed methods may serve as an alternative to classical toolboxes, to provide further insight into glioma growth., Comment: Digital poster presented at the annual meeting of the International Society for Magnetic Resonance in Medicine (ISMRM) 2023. A 6 minute video about this work is available for browsing by the conference website (Program number: 4361)

Published
2023

198. $K$-Nearest-Neighbor Resampling for Off-Policy Evaluation in Stochastic Control

Author

Giegrich, Michael, Oomen, Roel, and Reisinger, Christoph

Subjects
Statistics - Machine Learning, Computer Science - Machine Learning, Mathematics - Optimization and Control, Mathematics - Statistics Theory, Statistics - Methodology
Abstract

In this paper, we propose a novel $K$-nearest neighbor resampling procedure for estimating the performance of a policy from historical data containing realized episodes of a decision process generated under a different policy. We provide statistical consistency results under weak conditions. In particular, we avoid the common assumption of identically and independently distributed transitions and rewards. Instead, our analysis allows for the sampling of entire episodes, as is common practice in most applications. To establish the consistency in this setting, we generalize Stone's Theorem, a well-known result in nonparametric statistics on local averaging, to include episodic data and the counterfactual estimation underlying off-policy evaluation (OPE). By focusing on feedback policies that depend deterministically on the current state in environments with continuous state-action spaces and system-inherent stochasticity effected by chosen actions, and relying on trajectory simulation similar to Monte Carlo methods, the proposed method is particularly well suited for stochastic control environments. Compared to other OPE methods, our algorithm does not require optimization, can be efficiently implemented via tree-based nearest neighbor search and parallelization, and does not explicitly assume a parametric model for the environment's dynamics. Numerical experiments demonstrate the effectiveness of the algorithm compared to existing baselines in a variety of stochastic control settings, including a linear quadratic regulator, trade execution in limit order books, and online stochastic bin packing.

Published
2023

199. Estimating Eigenenergies from Quantum Dynamics: A Unified Noise-Resilient Measurement-Driven Approach

Author

Shen, Yizhi, Camps, Daan, Szasz, Aaron, Darbha, Siva, Klymko, Katherine, Williams--Young, David B., Tubman, Norm M., and Van Beeumen, Roel

Subjects
Quantum Physics
Abstract

Ground state energy estimation in physical, chemical, and materials sciences is one of the most promising applications of quantum computing. In this work, we introduce a new hybrid approach that finds the eigenenergies by collecting real-time measurements and post-processing them using the machinery of dynamic mode decomposition (DMD). From the perspective of quantum dynamics, we establish that our approach can be formally understood as a stable variational method on the function space of observables available from a quantum many-body system. We also provide strong theoretical and numerical evidence that our method converges rapidly even in the presence of a large degree of perturbative noise, and show that the method bears an isomorphism to robust matrix factorization methods developed independently across various scientific communities. Our numerical benchmarks on spin and molecular systems demonstrate an accelerated convergence and a favorable resource reduction over state-of-the-art algorithms. The DMD-centric strategy can systematically mitigate noise and stands out as a leading hybrid quantum-classical eigensolver.

Published
2023

200. Algorithms as Social-Ecological-Technological Systems: an Environmental Justice Lens on Algorithmic Audits

Author

Rakova, Bogdana and Dobbe, Roel

Subjects
Computer Science - Computers and Society
Abstract

This paper reframes algorithmic systems as intimately connected to and part of social and ecological systems, and proposes a first-of-its-kind methodology for environmental justice-oriented algorithmic audits. How do we consider environmental and climate justice dimensions of the way algorithmic systems are designed, developed, and deployed? These impacts are inherently emergent and can only be understood and addressed at the level of relations between an algorithmic system and the social (including institutional) and ecological components of the broader ecosystem it operates in. As a result, we claim that in absence of an integral ontology for algorithmic systems, we cannot do justice to the emergent nature of broader environmental impacts of algorithmic systems and their underlying computational infrastructure. We propose to define algorithmic systems as ontologically indistinct from Social-Ecological-Technological Systems (SETS), framing emergent implications as couplings between social, ecological, and technical components of the broader fabric in which algorithms are integrated and operate. We draw upon prior work on SETS analysis as well as emerging themes in the literature and practices of Environmental Justice (EJ) to conceptualize and assess algorithmic impact. We then offer three policy recommendations to help establish a SETS-based EJ approach to algorithmic audits: (1) broaden the inputs and open-up the outputs of an audit, (2) enable meaningful access to redress, and (3) guarantee a place-based and relational approach to the process of evaluating impact. We operationalize these as a qualitative framework of questions for a spectrum of stakeholders. Doing so, this article aims to inspire stronger and more frequent interactions across policymakers, researchers, practitioners, civil society, and grassroots communities., Comment: 18 pages, In Proceedings of FAccT '23: 2023 ACM Conference on Fairness, Accountability, and Transparency

Published
2023
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