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1. Evaluating Creative Short Story Generation in Humans and Large Language Models

Author

Ismayilzada, Mete, Stevenson, Claire, and van der Plas, Lonneke

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

Storytelling is a fundamental aspect of human communication, relying heavily on creativity to produce narratives that are novel, appropriate, and surprising. While large language models (LLMs) have recently demonstrated the ability to generate high-quality stories, their creative capabilities remain underexplored. Previous research has either focused on creativity tests requiring short responses or primarily compared model performance in story generation to that of professional writers. However, the question of whether LLMs exhibit creativity in writing short stories on par with the average human remains unanswered. In this work, we conduct a systematic analysis of creativity in short story generation across LLMs and everyday people. Using a five-sentence creative story task, commonly employed in psychology to assess human creativity, we automatically evaluate model- and human-generated stories across several dimensions of creativity, including novelty, surprise, and diversity. Our findings reveal that while LLMs can generate stylistically complex stories, they tend to fall short in terms of creativity when compared to average human writers., Comment: 14 pages

Published
2024

2. Creativity in AI: Progresses and Challenges

Author

Ismayilzada, Mete, Paul, Debjit, Bosselut, Antoine, and van der Plas, Lonneke

Subjects
Computer Science - Artificial Intelligence, Computer Science - Computation and Language
Abstract

Creativity is the ability to produce novel, useful, and surprising ideas, and has been widely studied as a crucial aspect of human cognition. Machine creativity on the other hand has been a long-standing challenge. With the rise of advanced generative AI, there has been renewed interest and debate regarding AI's creative capabilities. Therefore, it is imperative to revisit the state of creativity in AI and identify key progresses and remaining challenges. In this work, we survey leading works studying the creative capabilities of AI systems, focusing on creative problem-solving, linguistic, artistic, and scientific creativity. Our review suggests that while the latest AI models are largely capable of producing linguistically and artistically creative outputs such as poems, images, and musical pieces, they struggle with tasks that require creative problem-solving, abstract thinking and compositionality and their generations suffer from a lack of diversity, originality, long-range incoherence and hallucinations. We also discuss key questions concerning copyright and authorship issues with generative models. Furthermore, we highlight the need for a comprehensive evaluation of creativity that is process-driven and considers several dimensions of creativity. Finally, we propose future research directions to improve the creativity of AI outputs, drawing inspiration from cognitive science and psychology., Comment: minor updates to content + figures

Published
2024

3. Evaluating Morphological Compositional Generalization in Large Language Models

Author

Ismayilzada, Mete, Circi, Defne, Sälevä, Jonne, Sirin, Hale, Köksal, Abdullatif, Dhingra, Bhuwan, Bosselut, Antoine, van der Plas, Lonneke, and Ataman, Duygu

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence
Abstract

Large language models (LLMs) have demonstrated significant progress in various natural language generation and understanding tasks. However, their linguistic generalization capabilities remain questionable, raising doubts about whether these models learn language similarly to humans. While humans exhibit compositional generalization and linguistic creativity in language use, the extent to which LLMs replicate these abilities, particularly in morphology, is under-explored. In this work, we systematically investigate the morphological generalization abilities of LLMs through the lens of compositionality. We define morphemes as compositional primitives and design a novel suite of generative and discriminative tasks to assess morphological productivity and systematicity. Focusing on agglutinative languages such as Turkish and Finnish, we evaluate several state-of-the-art instruction-finetuned multilingual models, including GPT-4 and Gemini. Our analysis shows that LLMs struggle with morphological compositional generalization particularly when applied to novel word roots, with performance declining sharply as morphological complexity increases. While models can identify individual morphological combinations better than chance, their performance lacks systematicity, leading to significant accuracy gaps compared to humans., Comment: 33 pages

Published
2024

4. The global distribution and drivers of wood density and their impact on forest carbon stocks

Author

Mo, Lidong, Crowther, Thomas W., Maynard, Daniel S., van den Hoogen, Johan, Ma, Haozhi, Bialic-Murphy, Lalasia, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B., Phillips, Oliver L., 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, Boonman, Coline C. F., Bouriaud, Olivier, Brancalion, Pedro H. S., Brandl, Susanne, Brearley, Francis Q., Brienen, Roel, Broadbent, Eben N., Bruelheide, Helge, Bussotti, Filippo, Gatti, Roberto Cazzolla, César, Ricardo G., Cesljar, Goran, Chazdon, Robin, Chen, Han Y. H., 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, Frizzera, Lorenzo, Gamarra, Javier G. P., Gianelle, Damiano, Glick, Henry B., Harris, David J., Hector, Andrew, Hemp, Andreas, Hengeveld, Geerten, Hérault, Bruno, Herbohn, John L., Herold, Martin, Hietz, Peter, Hillers, Annika, Honorio Coronado, Eurídice N., Hui, Cang, Ibanez, Thomas, Imai, Nobuo, Jagodziński, Andrzej M., Jaroszewicz, Bogdan, Johannsen, Vivian Kvist, Joly, Carlos A., Jucker, Tommaso, Jung, Ilbin, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Kucher, Dmitry, Laarmann, Diana, Lang, Mait, Lewis, Simon L., Li, Yuanzhi, Lopez-Gonzalez, Gabriela, Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., McCarthy, James K., Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Mendoza-Polo, Irina, Miscicki, Stanislaw, Merow, Cory, Mendoza, Abel Monteagudo, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Picard, Nicolas, Piedade, Maria Teresa F., Piotto, Daniel, Pitman, Nigel C. A., Poorter, Lourens, Poulsen, Axel Dalberg, Poulsen, John R., Pretzsch, Hans, Arevalo, Freddy Ramirez, Restrepo-Correa, Zorayda, Richardson, Sarah J., Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schelhaas, Mart-Jan, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Da Silva, Ana Carolina, Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Sosinski, Jr., Enio Egon, Souza, Alexandre F., Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, Van Bodegom, Peter M., van der Plas, Fons, Van Do, Tran, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderick, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., and Zohner, Constantin M.

Published
2024
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5. Understanding the effects of language-specific class imbalance in multilingual fine-tuning

Author

Jung, Vincent and van der Plas, Lonneke

Subjects
Computer Science - Computation and Language
Abstract

We study the effect of one type of imbalance often present in real-life multilingual classification datasets: an uneven distribution of labels across languages. We show evidence that fine-tuning a transformer-based Large Language Model (LLM) on a dataset with this imbalance leads to worse performance, a more pronounced separation of languages in the latent space, and the promotion of uninformative features. We modify the traditional class weighing approach to imbalance by calculating class weights separately for each language and show that this helps mitigate those detrimental effects. These results create awareness of the negative effects of language-specific class imbalance in multilingual fine-tuning and the way in which the model learns to rely on the separation of languages to perform the task., Comment: To be published in: Findings of the Association for Computational Linguistics: EACL 2024

Published
2024

6. Implementation and evaluation of a navigation program for people with cancer in old age and their family caregivers: study protocol for the EU NAVIGATE International Pragmatic Randomized Controlled Trial

Author

Smets, Tinne, Pivodic, Lara, Miranda, Rose, Van Campe, Fien, Vinckier, Chelsea, Pesut, Barbara, Duggleby, Wendy, Davies, Andrew N., Lavan, Amanda, May, Peter, Gomes, Barbara, Furlan de Brito, Maja, Rodrigues, Vitor, Szczerbińska, Katarzyna, Kijowska, Violetta, Barańska, Ilona, De Buyser, Stefanie, Ferraris, Davide, Alfieri, Sara, Scacciati, Bianca, Du Cheyne, Helena, Chambaere, Kenneth, Gilissen, Joni, van der Plas, Annicka G.M., Pasman, Roeline H., Onwuteaka-Philipsen, Bregje D., and Van den Block, Lieve

Published
2024
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8. Neuropsychiatric symptoms with focus on apathy and irritability in sporadic and hereditary cerebral amyloid angiopathy

Author

Kaushik, Kanishk, de Kort, Anna M., van Dort, Rosemarie, van der Zwet, Reinier G.J., Siegerink, Bob, Voigt, Sabine, van Zwet, Erik W., van der Plas, Maaike C., Koemans, Emma A., Rasing, Ingeborg, Kessels, Roy P.C., Middelkoop, Huub A.M., Schreuder, Floris H.B.M., Klijn, Catharina J.M., Verbeek, Marcel M., Terwindt, Gisela M., van Etten, Ellis S., and Wermer, Marieke J.H.

Published
2024
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9. Implementation and evaluation of a navigation program for people with cancer in old age and their family caregivers: study protocol for the EU NAVIGATE International Pragmatic Randomized Controlled Trial

Author

Tinne Smets, Lara Pivodic, Rose Miranda, Fien Van Campe, Chelsea Vinckier, Barbara Pesut, Wendy Duggleby, Andrew N. Davies, Amanda Lavan, Peter May, Barbara Gomes, Maja Furlan de Brito, Vitor Rodrigues, Katarzyna Szczerbińska, Violetta Kijowska, Ilona Barańska, Stefanie De Buyser, Davide Ferraris, Sara Alfieri, Bianca Scacciati, Helena Du Cheyne, Kenneth Chambaere, Joni Gilissen, Annicka G.M. van der Plas, Roeline H. Pasman, Bregje D. Onwuteaka-Philipsen, on behalf of EU NAVIGATE, and Lieve Van den Block

Subjects
Volunteers, Palliative care, Supportive care, Older persons, Navigation, Quality of life, Medicine (General), R5-920
Abstract

Abstract Background Cancer navigation programs aim to support, educate, and empower patients and families, addressing barriers to diagnostics, treatment, and care. Navigators engage with people to ensure timely access to services and resources. While promising for older people with cancer, these programs are scarce in Europe, and research on their effectiveness and implementation is limited. We describe the protocol of the EU NAVIGATE randomized controlled trial, aimed to evaluate (1) effectiveness and cost-effectiveness of NavCare-EU, an intervention that aims to support older people with cancer throughout their illness trajectory, spanning the continuum of supportive, palliative, and end-of-life care, and (2) the intervention’s implementation processes and feasibility of its integration into different health care systems in Europe, contextual barriers and facilitators for effective and sustainable implementation, and mechanisms involved in reaching the outcomes. Methods We will conduct a multisite pragmatic fast-track randomized controlled trial with embedded convergent mixed-method process evaluation in Belgium, Ireland, Italy, Netherlands, Poland, and Portugal. The study targets people with cancer and declining health, 70 years or older, and their close family caregivers. The trial compares the NavCare-EU intervention plus standard care with standard care alone. We will perform a baseline measurement prior to randomization and follow-up measurements at 12 weeks, 24 weeks, and 48 weeks in intervention and control group, and an additional measurement at 72 weeks in the control group. Primary outcomes, measured at 24 weeks are (1) the older person’s global health status/quality of life, a 2-item subscale from EORTC-QLQ-C30 (revised) measuring health-related quality of life, (2) level of social support measured with Medical Outcomes Study Social Support Survey (MOS-SSS scale). The study will include at least 246 older persons with completed global health status/quality of life at 24 weeks. Discussion The EU NAVIGATE trial will cross-nationally test the effectiveness and cost-effectiveness of a navigation intervention for older people with cancer and their family caregivers, and its implementation in different health care systems in Europe. As continuity and access to health, social, and community care is a priority for patients and caregivers, the trial is timely and critically needed. Trial registration Clinicaltrials.gov: identifier NCT06110312 (2023/10/31).

Published
2024
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10. The influence of zooplankton and oxygen on the particulate organic carbon flux in the Benguela Upwelling System

Author

L. C. Meiritz, T. Rixen, A. K. van der Plas, T. Lamont, and N. Lahajnar

Subjects
Ecology, QH540-549.5, Life, QH501-531, Geology, QE1-996.5
Abstract

We conducted sediment trap experiments in the Benguela Upwelling System (BUS) in the southeastern Atlantic Ocean to study the influence of zooplankton on the flux of particulate organic carbon (POC) through the water column and its sedimentation. A total of 2 long-term moored and 16 short-term free-floating sediment trap systems (drifter systems) were deployed. The mooring experiments were conducted over more than a decade (2009–2022), and the 16 drifters were deployed on three different research cruises between 2019 and 2021. Zooplankton was separated from the trapped material and divided into eight different zooplankton groups. In contrast to zooplankton which actively carries POC into the traps in the form of biomass (active POC flux), the remaining fraction of the trapped material was assumed to fall passively into the traps along with sinking particles (passive POC flux). Our results show, in line with other studies, that copepods dominate the active POC flux, with the active POC flux in the southern BUS (sBUS) being about 3 times higher than in the northern BUS (nBUS). In contrast, the differences between the passive POC fluxes in the nBUS and sBUS were small. Despite large variations, which reflected the variability within the two subsystems, the mean passive POC fluxes from the drifters and the moored traps could be described using a common POC flux attenuation equation. However, the almost equal passive POC flux, on the one hand, and the high POC concentration in the surface sediments of the nBUS in comparison to the sBUS, on the other hand, imply that the intensity of the near-bottom oxygen minimum zone (OMZ), which is more pronounced in the nBUS than in the sBUS, controls the preservation of POC in sediments significantly. This highlights the contrasting effects of the globally observed expansion of OMZs, which on the one hand mitigates the accumulation of CO2 in the atmosphere and the ocean by increasing POC storage in sediments and on the other hand poses a threat to established ecosystems and fisheries.

Published
2024
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11. Can language models learn analogical reasoning? Investigating training objectives and comparisons to human performance

Author

Petersen, Molly R. and van der Plas, Lonneke

Subjects
Computer Science - Computation and Language
Abstract

While analogies are a common way to evaluate word embeddings in NLP, it is also of interest to investigate whether or not analogical reasoning is a task in itself that can be learned. In this paper, we test several ways to learn basic analogical reasoning, specifically focusing on analogies that are more typical of what is used to evaluate analogical reasoning in humans than those in commonly used NLP benchmarks. Our experiments find that models are able to learn analogical reasoning, even with a small amount of data. We additionally compare our models to a dataset with a human baseline, and find that after training, models approach human performance.

Published
2023

13. Impact of gate-level clustering on automated system partitioning of 3D-ICs

Author

Delhaye, Quentin, Beyne, Eric, Goossens, Joël, Van der Plas, Geert, and Milojevic, Dragomir

Subjects
Computer Science - Hardware Architecture, B.7.2
Abstract

When partitioning gate-level netlists using graphs, it is beneficial to cluster gates to reduce the order of the graph and preserve some characteristics of the circuit that the partitioning might degrade. Gate clustering is even more important for netlist partitioning targeting 3D system integration. In this paper, we make the argument that the choice of clustering method for 3D-ICs partitioning is not trivial and deserves careful consideration. To support our claim, we implemented three clustering methods that were used prior to partitioning two synthetic designs representing two extremes of the circuits medium/long interconnect diversity spectrum. Automatically partitioned netlists are then placed and routed in 3D to compare the impact of clustering methods on several metrics. From our experiments, we see that the clustering method indeed has a different impact depending on the design considered and that a circuit-blind, universal partitioning method is not the way to go, with wire-length savings of up to 31%, total power of up to 22%, and effective frequency of up to 15% compared to other methods. Furthermore, we highlight that 3D-ICs open new opportunities to design systems with a denser interconnect, drastically reducing the design utilization of circuits that would not be considered viable in 2D., Comment: 8 pages, 6 figures

Published
2023
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14. Perceived autonomy support in individuals with Parkinson’s disease requiring emergency care: a cross-sectional pilot study

Author

Barend W. Florijn, Erik W. van Zwet, Ad. A. Kaptein, and Anne A. van der Plas

Subjects
Parkinson’s disease, Emergency care, Patient autonomy, Decision-making, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Background Individuals with Parkinson’s disease (PD) report a diminished perceived functional autonomy as their condition progresses. For those seeking emergency care, it is unknown whether the patient-physician relationship is instrumental in respecting patient autonomy. This study evaluated patient autonomy ideals in individuals with PD requiring emergency care and the perceived support for autonomy from emergency department physicians. Method Individuals with PD (n = 36, average age 78.1 years) were surveyed using the Ideal Patient Autonomy questionnaire (IPA) and the Health Care Climate Questionnaire (HCCQ). A multivariable regression analysis assessed whether patients’ Hoehn and Yahr stage and IPA questionnaire results predicted HCCQ items. Results The IPA questionnaire revealed that individuals with PD in need of emergency care emphasize the significance of medical expertise (IPA ‘doctor should decide’ theme 0.71) in decision-making and their desire to be fully informed about all potential risks (IPA ‘obligatory risk information’ theme 0.71). The average HCCQ values showed a decreasing trend across Hoehn and Yahr stages 1 to 5: 6.19, 6.03, 5.83, 5.80, and 5.23, respectively. HY scale values also influenced HCCQ items related to the physician’s role. Conclusion In our cohort, individuals with Parkinson’s disease tend to rely on medical expertise for decision-making and prioritize complete risk information during emergency care. However, this autonomy support diminishes as functional disability levels increase.

Published
2024
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15. Loose and Tight: Creative Formation but Rigid Use of Nominal Compounds in Conspiracist Texts

Author

Alessandro Miani, Lonneke van der Plas, and Adrian Bangerter

Abstract

Conspiracy theories (CTs) are spectacular narratives, widely spread, that pose societal threats. We test whether CTs might be linguistically creative products, which would facilitate their transmission and thereby account for their widespread popularity. We analyzed nominal compounds (e.g., "mind control," "carbon dioxide"; N = 1,713,568) from a large corpus of conspiracist and mainstream texts matched by topic. In conspiracist texts, compounds showed greater originality, divergence, and sophistication, but they were used with lower frequency and were more often repeated in different contexts. This pattern suggests a creative aspect in the generation of compounds, coupled with rigidity in their use. We interpret these findings as an effect of loosely defined conceptual boundaries among conspiracist writers, in conjunction with social functions like status or group signaling. Our findings not only contribute to the discourse on creativity in CTs but also provide insights into the communicative advantage of CTs.

Published
2024
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16. Demographics of Protoplanetary Disks: A Simulated Population of Edge-on Systems

Author

Angelo, Isabel, Duchêne, Gaspard, Stapelfeldt, Karl, Telkamp, Zoie, Ménard, Francoise, Padgett, Deborah, van der Plas, Gerrit, Villenave, Marion, Pinte, Christophe, Wolff, Schuyler, Fischer, William J., and Perrin, Marshall D.

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

The structure of protoplanetary disks plays an essential role in planet formation. Disks that are highly inclined, or ''edge-on'', are of particular interest since their geometry provides a unique opportunity to study the disk's vertical structure and radial extent. Candidate edge-on protoplanetary disks are typically identified via their unique spectral energy distribution and subsequently confirmed through high-resolution imaging. However, this selection process is likely biased toward the largest, most massive disks, and the resulting sample may not accurately represent the underlying disk population. To investigate this, we generated a grid of protoplanetary disk models using radiative transfer simulations and determined which sets of disk parameters produce edge-on systems that could be recovered by aforementioned detection techniques--i.e., identified by their spectral energy distribution and confirmed through follow-up imaging with HST. In doing so, we adopt a quantitative working definition of "edge-on disks" that is observation-driven and agnostic about the disk inclination or other properties. Folding in empirical disk demographics, we predict an occurrence rate of 6.2% for edge-on disks and quantify biases towards highly inclined, massive disks. We also find that edge-on disks are under-represented in samples of Spitzer-studied young stellar objects, particularly for disks with M $\lesssim$ 0.5 $M_\odot$. Overall, our analysis suggests that several dozen edge-on disks remain undiscovered in nearby star-forming regions, and provides a universal selection process to identify edge-on disks for consistent, population-level demographic studies., Comment: 20 pages, 6 figures

Published
2023
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18. The effect of different sweeteners on the oral microbiome: a randomized clinical exploratory pilot study

Author

Davis R. Zakis, Bernd W. Brandt, Suzette V. van der Waal, Bart J. F. Keijser, Wim Crielaard, Derek W.K. van der Plas, Catherine M.C. Volgenant, and Egija Zaura

Subjects
Oral microbiome, microbiome modulation, oral health, dental plaque, tongue microbiome, clinical trial, Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502
Abstract

Introduction The aim of the study was to evaluate the modulating effects of five commonly used sweetener (glucose, inulin, isomaltulose, tagatose, trehalose) containing mouth rinses on the oral microbiome.Methods A single-centre, double-blind, parallel randomized clinical trial was performed with healthy, 18–55-year-old volunteers (N = 65), who rinsed thrice-daily for two weeks with a 10% solution of one of the allocated sweeteners. Microbiota composition of supragingival dental plaque and the tongue dorsum coating was analysed by 16S RNA gene amplicon sequencing of the V4 hypervariable region (Illumina MiSeq). As secondary outcomes, dental plaque red fluorescence and salivary pH were measured.Results Dental plaque microbiota changed significantly for two groups: inulin (F = 2.0239, p = 0.0006 PERMANOVA, Aitchison distance) and isomaltulose (F = 0.67, p = 0.0305). For the tongue microbiota, significant changes were observed for isomaltulose (F = 0.8382, p = 0.0452) and trehalose (F = 1.0119, p = 0.0098). In plaque, 13 species changed significantly for the inulin group, while for tongue coating, three species changed for the trehalose group (ALDEx2, p

Published
2024
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19. Simulating potential impacts of bottom trawling on the biological carbon pump: a case study in the Benguela Upwelling System

Author

Claire Siddiqui, Tim Rixen, Niko Lahajnar, Tarron Lamont, and Anja K. van der Plas

Subjects
Benguela coastal upwelling system, bottom trawling effects, biological carbon pump, carbon and nutrient cycling, CO2 emissions, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Bottom-trawl fishery is known to cause major disturbances to marine sediments as the dragging of trawl gears across the seabed fosters sediment resuspension, which can lead to organic particle remineralization and release of benthic CO2 and nutrients into bottom waters. However, its effects on carbon cycling and biological productivity, especially in highly productive regions like the Benguela Upwelling System (BUS), are less well studied. Here, we simulated carbon (C) and nutrient pathways from the trawled coastal seabed to overlying water masses that are being upwelled into the sunlit surface within the BUS, using shipboard data on sea surface and water column characteristics and published benthic CO2 emission estimates from bottom-trawled sediments. The latter reports 4.35 and 0.64 Tg C year-1 to be released from the seabed into upwelling source waters after bottom trawling in the northern (NBUS) and southern (SBUS) subsystems, respectively. Based on these values, we estimated a corresponding nitrate (N) input of 1.39 and 0.47 µmol kg-1 year-1, enhancing source water nitrate concentrations by ~5% and ~2%. Trawl-induced nitrate input into the sunlit surface could support a new production of 3.14 and 0.47 Tg C year-1 in the NBUS and SBUS, respectively, recapturing only 2/3 of CO2 released after bottom trawling into biomass, mainly due to differences in stoichiometric C:N ratios between the sediment (~9) and surface biomass (Redfield, 6.6). The remaining benthic CO2 can thereby lead to an increase in surface CO2 concentration and its partial pressure (pCO2), impeding CO2 uptake of the biological carbon pump in the BUS by 1.3 Tg C year-1, of which 1 Tg C year-1 is emitted to the atmosphere across the northern subsystem. Our results demonstrate the extent to which bottom trawling may affect the CO2 storage potential of coastal sediments on a basin-wide level, highlighting the need to better resolve small-scale sediment characteristics and C:N ratios to refine trawl-induced benthic carbon and nutrient effluxes within the BUS.

Published
2024
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20. Mapping Protoplanetary Disk Vertical Structure with CO Isotopologue Line Emission

Author

Law, Charles J., Teague, Richard, Öberg, Karin I., Rich, Evan A., Andrews, Sean M., Bae, Jaehan, Benisty, Myriam, Facchini, Stefano, Flaherty, Kevin, Isella, Andrea, Jin, Sheng, Hashimoto, Jun, Huang, Jane, Loomis, Ryan A., Long, Feng, Muñoz-Romero, Carlos E., Paneque-Carreño, Teresa, Pérez, Laura M., Qi, Chunhua, Schwarz, Kamber R., Stadler, Jochen, Tsukagoshi, Takashi, Wilner, David J., and van der Plas, Gerrit

Subjects
Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - Solar and Stellar Astrophysics
Abstract

High spatial resolution observations of CO isotopologue line emission in protoplanetary disks at mid-inclinations (${\approx}$30-75{\deg}) allow us to characterize the gas structure in detail, including radial and vertical substructures, emission surface heights and their dependencies on source characteristics, and disk temperature profiles. By combining observations of a suite of CO isotopologues, we can map the 2D (r, z) disk structure from the disk upper atmosphere, as traced by CO, to near the midplane, as probed by less abundant isotopologues. Here, we present high angular resolution (${\lesssim}$0."1 to ${\approx}$0."2; ${\approx}$15-30 au) observations of CO, $^{13}$CO, and C$^{18}$O in either or both J=2-1 and J=3-2 lines in the transition disks around DM Tau, Sz 91, LkCa 15, and HD 34282. We derived line emission surfaces in CO for all disks and in $^{13}$CO for the DM Tau and LkCa 15 disks. With these observations, we do not resolve the vertical structure of C$^{18}$O in any disk, which is instead consistent with C$^{18}$O emission originating from the midplane. Both the J=2-1 and J=3-2 lines show similar heights. Using the derived emission surfaces, we computed radial and vertical gas temperature distributions for each disk, including empirical temperature models for the DM Tau and LkCa 15 disks. After combining our sample with literature sources, we find that $^{13}$CO line emitting heights are also tentatively linked with source characteristics, e.g., stellar host mass, gas temperature, disk size, and show steeper trends than seen in CO emission surfaces., Comment: 31 pages, 15 figures, accepted for publication in ApJ. Image cubes available at https://zenodo.org/record/7430257

Published
2022
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21. Decision-Making in Autism: A Narrative Review

Author

van der Plas, Elisa, Mason, David, and Happé, Francesca

Abstract

Autistic people often have an atypical profile of abilities: while excelling in some structured paradigms, many report difficulties with making real-life decisions. To test whether decision-making in autism is different from in typically developing controls, we reviewed 104 studies that compared decision-making performance between autistic and comparison participants (N = 2712 autistic and N = 3189 comparison participants) between 1998 and 2022. Our searches revealed four main decision-making paradigms that are widely used in the field of decision neuroscience: perceptual discrimination, reward learning, metacognition and value-based decision-making paradigm. Our synthesis highlights that perceptual processing and reward learning were similar between autistic and comparison participants, whereas value-based decision-making and metacognitive accuracy were often different between groups. Furthermore, decision-making differences were most pronounced when the autistic participant was explicitly probed to report on an internal belief, while implicit markers of the same decision (e.g. error-related response times) were usually not different. Our findings provide evidence in favour of a metacognitive explanation of decision-making atypicalities in autism.

Published
2023
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22. Global beta-diversity of angiosperm trees is shaped by Quaternary climate change

Author

Xu, Wu-Bing, Guo, Wen-Yong, Serra-Diaz, Josep M, Schrodt, Franziska, Eiserhardt, Wolf L, Enquist, Brian J, Maitner, Brian S, Merow, Cory, Violle, Cyrille, Anand, Madhur, Belluau, Michaël, Bruun, Hans Henrik, Byun, Chaeho, Catford, Jane A, Cerabolini, Bruno EL, Chacón-Madrigal, Eduardo, Ciccarelli, Daniela, Cornelissen, J Hans C, Dang-Le, Anh Tuan, de Frutos, Angel, Dias, Arildo S, Giroldo, Aelton B, Gutiérrez, Alvaro G, Hattingh, Wesley, He, Tianhua, Hietz, Peter, Hough-Snee, Nate, Jansen, Steven, Kattge, Jens, Komac, Benjamin, Kraft, Nathan JB, Kramer, Koen, Lavorel, Sandra, Lusk, Christopher H, Martin, Adam R, Ma, Ke-Ping, Mencuccini, Maurizio, Michaletz, Sean T, Minden, Vanessa, Mori, Akira S, Niinemets, Ülo, Onoda, Yusuke, Onstein, Renske E, Peñuelas, Josep, Pillar, Valério D, Pisek, Jan, Pound, Matthew J, Robroek, Bjorn JM, Schamp, Brandon, Slot, Martijn, Sun, Miao, Sosinski, Ênio E, Soudzilovskaia, Nadejda A, Thiffault, Nelson, van Bodegom, Peter M, van der Plas, Fons, Zheng, Jingming, Svenning, Jens-Christian, and Ordonez, Alejandro

Subjects
Life Below Water, Climate Action, Humans, Phylogeny, Magnoliopsida, Climate Change, Biodiversity
Abstract

As Earth's climate has varied strongly through geological time, studying the impacts of past climate change on biodiversity helps to understand the risks from future climate change. However, it remains unclear how paleoclimate shapes spatial variation in biodiversity. Here, we assessed the influence of Quaternary climate change on spatial dissimilarity in taxonomic, phylogenetic, and functional composition among neighboring 200-kilometer cells (beta-diversity) for angiosperm trees worldwide. We found that larger glacial-interglacial temperature change was strongly associated with lower spatial turnover (species replacements) and higher nestedness (richness changes) components of beta-diversity across all three biodiversity facets. Moreover, phylogenetic and functional turnover was lower and nestedness higher than random expectations based on taxonomic beta-diversity in regions that experienced large temperature change, reflecting phylogenetically and functionally selective processes in species replacement, extinction, and colonization during glacial-interglacial oscillations. Our results suggest that future human-driven climate change could cause local homogenization and reduction in taxonomic, phylogenetic, and functional diversity of angiosperm trees worldwide.

Published
2023

25. The Marine Carbon Footprint: Challenges in the Quantification of the CO2 Uptake by the Biological Carbon Pump in the Benguela Upwelling System

Author

Rixen, Tim, Lahajnar, Niko, Lamont, Tarron, Koppelmann, Rolf, Martin, Bettina, Meiritz, Luisa, Siddiqui, Claire, Van der Plas, Anja K., Canadell, Josep G., Series Editor, Díaz, Sandra, Series Editor, Heldmaier, Gerhard, Series Editor, Jackson, Robert B., Series Editor, Levia, Delphis F., Series Editor, Schulze, Ernst-Detlef, Series Editor, Sommer, Ulrich, Series Editor, Wardle, David A., Series Editor, von Maltitz, Graham P., editor, Midgley, Guy F., editor, Veitch, Jennifer, editor, Brümmer, Christian, editor, Rötter, Reimund P., editor, Viehberg, Finn A., editor, and Veste, Maik, editor

Published
2024
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26. Physical Drivers of Southwest African Coastal Upwelling and Its Response to Climate Variability and Change

Author

Brandt, Peter, Bordbar, Mohammad Hadi, Coelho, Paulo, Koungue, Rodrigue Anicet Imbol, Körner, Mareike, Lamont, Tarron, Lübbecke, Joke F., Mohrholz, Volker, Prigent, Arthur, Roch, Marisa, Schmidt, Martin, van der Plas, Anja K., Veitch, Jennifer, Canadell, Josep G., Series Editor, Díaz, Sandra, Series Editor, Heldmaier, Gerhard, Series Editor, Jackson, Robert B., Series Editor, Levia, Delphis F., Series Editor, Schulze, Ernst-Detlef, Series Editor, Sommer, Ulrich, Series Editor, Wardle, David A., Series Editor, von Maltitz, Graham P., editor, Midgley, Guy F., editor, Veitch, Jennifer, editor, Brümmer, Christian, editor, Rötter, Reimund P., editor, Viehberg, Finn A., editor, and Veste, Maik, editor

Published
2024
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29. Pre-training Data Quality and Quantity for a Low-Resource Language: New Corpus and BERT Models for Maltese

Author

Micallef, Kurt, Gatt, Albert, Tanti, Marc, van der Plas, Lonneke, and Borg, Claudia

Subjects
Computer Science - Computation and Language
Abstract

Multilingual language models such as mBERT have seen impressive cross-lingual transfer to a variety of languages, but many languages remain excluded from these models. In this paper, we analyse the effect of pre-training with monolingual data for a low-resource language that is not included in mBERT -- Maltese -- with a range of pre-training set ups. We conduct evaluations with the newly pre-trained models on three morphosyntactic tasks -- dependency parsing, part-of-speech tagging, and named-entity recognition -- and one semantic classification task -- sentiment analysis. We also present a newly created corpus for Maltese, and determine the effect that the pre-training data size and domain have on the downstream performance. Our results show that using a mixture of pre-training domains is often superior to using Wikipedia text only. We also find that a fraction of this corpus is enough to make significant leaps in performance over Wikipedia-trained models. We pre-train and compare two models on the new corpus: a monolingual BERT model trained from scratch (BERTu), and a further pre-trained multilingual BERT (mBERTu). The models achieve state-of-the-art performance on these tasks, despite the new corpus being considerably smaller than typically used corpora for high-resourced languages. On average, BERTu outperforms or performs competitively with mBERTu, and the largest gains are observed for higher-level tasks., Comment: DeepLo 2022 camera-ready version

Published
2022
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32. Neuropsychiatric symptoms with focus on apathy and irritability in sporadic and hereditary cerebral amyloid angiopathy

Author

Kanishk Kaushik, Anna M. de Kort, Rosemarie van Dort, Reinier G.J. van der Zwet, Bob Siegerink, Sabine Voigt, Erik W. van Zwet, Maaike C. van der Plas, Emma A. Koemans, Ingeborg Rasing, Roy P.C. Kessels, Huub A.M. Middelkoop, Floris H.B.M. Schreuder, Catharina J.M. Klijn, Marcel M. Verbeek, Gisela M. Terwindt, Ellis S. van Etten, and Marieke J.H. Wermer

Subjects
Cerebral amyloid angiopathy, CAA, Neuropsychiatric symptoms, ICH, Apathy, Irritability, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurology. Diseases of the nervous system, RC346-429
Abstract

Abstract Background Neuropsychiatric symptoms (NPS) may affect cognition, but their burden in cerebral amyloid angiopathy (CAA), one of the main causes of intracerebral hemorrhage (ICH) and dementia in the elderly, remains unclear. We investigated NPS, with emphasis on apathy and irritability in sporadic (sCAA) and Dutch-type hereditary (D-)CAA. Methods We included patients with sCAA and (pre)symptomatic D-CAA, and controls from four prospective cohort studies. We assessed NPS per group, stratified for history of ICH, using the informant-based Neuropsychiatric Inventory (NPI-Q), Starkstein Apathy scale (SAS), and Irritability Scale. We modeled the association of NPS with disease status, executive function, processing speed, and CAA-burden score on MRI and investigated sex-differences. Results We included 181 participants: 82 with sCAA (mean[SD] age 72[6] years, 44% women, 28% previous ICH), 56 with D-CAA (52[11] years, 54% women, n = 31[55%] presymptomatic), and 43 controls (69[9] years, 44% women). The NPI-Q NPS-count differed between patients and controls (sCAA-ICH+:adj.β = 1.4[95%CI:0.6–2.3]; sCAA-ICH-:1.3[0.6-2.0]; symptomatic D-CAA:2.0[1.1–2.9]; presymptomatic D-CAA:1.2[0.1–2.2], control median:0[IQR:0–3]), but not between the different CAA-subgroups. Apathy and irritability were reported most frequently: n = 12[31%] sCAA, 19[37%] D-CAA had a high SAS-score; n = 12[29%] sCAA, 14[27%] D-CAA had a high Irritability Scale score. NPS-count was associated with decreased processing speed (adj.β=-0.6[95%CI:-0.8;-0.4]) and executive function (adj.β=-0.4[95%CI:-0.6;-0.1]), but not with radiological CAA-burden. Men had NPS more often than women. Discussion According to informants, one third to half of patients with CAA have NPS, mostly apathy, even in presymptomatic D-CAA and possibly with increased susceptibility in men. Neurologists should inform patients and caregivers of these disease consequences and treat or refer patients with NPS appropriately.

Published
2024
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33. 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 G. P., 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 H. S., 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 Y. H., 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, Jagodziński, Andrzej M., Jaroszewicz, Bogdan, Johannsen, Vivian Kvist, Joly, Carlos A., Jucker, Tommaso, Jung, Ilbin, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Kucher, Dmitry, Laarmann, Diana, Lang, Mait, Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Mendoza-Polo, Irina, Miscicki, Stanislaw, Merow, Cory, Monteagudo Mendoza, Abel, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Picard, Nicolas, Piedade, Maria Teresa F., Piotto, Daniel, Pitman, Nigel C. A., Poulsen, Axel Dalberg, Poulsen, John R., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schelhaas, Mart-Jan, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Van Do, Tran, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderik, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., Gann, George D., and Crowther, Thomas W.

Published
2023
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35. Hippocampal neurons code individual episodic memories in humans

Author

Kolibius, Luca D., Roux, Frederic, Parish, George, Ter Wal, Marije, Van Der Plas, Mircea, Chelvarajah, Ramesh, Sawlani, Vijay, Rollings, David T., Lang, Johannes D., Gollwitzer, Stephanie, Walther, Katrin, Hopfengärtner, Rüdiger, Kreiselmeyer, Gernot, Hamer, Hajo, Staresina, Bernhard P., Wimber, Maria, Bowman, Howard, and Hanslmayr, Simon

Published
2023
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36. 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 H. S., 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 Y. H., 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 G. P., 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, Johannsen, Vivian Kvist, Joly, Carlos A., Jucker, Tommaso, Jung, Ilbin, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Kucher, Dmitry, Laarmann, Diana, Lang, Mait, Lewis, Simon L., Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Merow, Cory, Monteagudo Mendoza, Abel, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Phillips, Oliver L., Picard, Nicolas, Piedade, Maria Teresa F., Piotto, Daniel, Pitman, Nigel C. A., Mendoza-Polo, Irina, Poulsen, Axel D., Poulsen, John R., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schelhaas, Mart-Jan, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Miścicki, Stanislaw, Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Van Do, Tran, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Westerlund, Bertil, Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderick, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., and Zohner, Constantin M.

Published
2023
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37. Observational constraints on disc sizes in protoplanetary discs in multiple systems in the Taurus region. II. Gas disc sizes

Author

Rota, A. A., Manara, C. F., Miotello, A., Lodato, G., Facchini, S., Koutoulaki, M., Herczeg, G., Long, F., Tazzari, M., Cabrit, S., Harsono, D., Menard, F., Pinilla, P., van der Plas, G., Ragusa, E., and Yen, H. -W.

Subjects
Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Astrophysics of Galaxies, Astrophysics - Solar and Stellar Astrophysics
Abstract

The formation of multiple stellar systems is a natural by-product of the star-formation process, and its impact on the properties of protoplanetary discs and on the formation of planets is still to be fully understood. To date, no detailed uniform study of the gas emission from a sample of protoplanetary discs around multiple stellar systems has been performed. Here we analyse new ALMA observations at a $\sim$21 au resolution of the molecular CO gas emission targeting discs in eight multiple stellar systems in the Taurus star-forming regions. $^{12}$CO gas emission is detected around all primaries and in seven companions. With these data, we estimate the inclination and the position angle for all primary discs and for five secondary or tertiary discs, and measure the gas disc radii of these objects with a cumulative flux technique on the spatially resolved zeroth moment images. When considering the radius including 95\% of the flux as a metric, the estimated gas disc size in multiple stellar systems is found to be on average $\sim 4.2$ times larger than the dust disc size. This ratio is higher than what was recently found in a population of more isolated and single systems. On the contrary, when considering the radius including 68\% of the flux, no difference between multiple and single discs is found in the distribution of ratios. This discrepancy is due to the sharp truncation of the outer dusty disc observed in multiple stellar systems. The measured gas disc sizes are consistent with tidal truncation models in multiple stellar systems assuming eccentricities of $\sim0.15$-$0.5$, as expected in typical binary systems., Comment: 25 pages, 29 figures, 9 tables. Accepted for publication in A&A

Published
2022
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38. Analysis of Data Augmentation Methods for Low-Resource Maltese ASR

Author

DeMarco, Andrea, Mena, Carlos, Gatt, Albert, Borg, Claudia, Williams, Aiden, and van der Plas, Lonneke

Subjects
Computer Science - Computation and Language
Abstract

Recent years have seen an increased interest in the computational speech processing of Maltese, but resources remain sparse. In this paper, we consider data augmentation techniques for improving speech recognition for low-resource languages, focusing on Maltese as a test case. We consider three different types of data augmentation: unsupervised training, multilingual training and the use of synthesized speech as training data. The goal is to determine which of these techniques, or combination of them, is the most effective to improve speech recognition for languages where the starting point is a small corpus of approximately 7 hours of transcribed speech. Our results show that combining the data augmentation techniques studied here lead us to an absolute WER improvement of 15% without the use of a language model., Comment: 12 pages

Published
2021

42. Physical Drivers of Southwest African Coastal Upwelling and Its Response to Climate Variability and Change

Author

Brandt, Peter, primary, Bordbar, Mohammad Hadi, additional, Coelho, Paulo, additional, Koungue, Rodrigue Anicet Imbol, additional, Körner, Mareike, additional, Lamont, Tarron, additional, Lübbecke, Joke F., additional, Mohrholz, Volker, additional, Prigent, Arthur, additional, Roch, Marisa, additional, Schmidt, Martin, additional, van der Plas, Anja K., additional, and Veitch, Jennifer, additional

Published
2024
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44. CRISPR-Cas9 screening reveals a distinct class of MHC-I binders with precise HLA-peptide recognition

Author

Tom A.W. Schoufour, Anneloes van der Plas - van Duijn, Ian Derksen, Marije Melgers, Jacqueline M.F. van Veenendaal, Claire Lensen, Mirjam H.M. Heemskerk, Jacques Neefjes, Ruud H.M. Wijdeven, and Ferenc A. Scheeren

Subjects
Biochemistry, Bioinformatics, Biological sciences, Immunology, Natural sciences, Science
Abstract

Summary: Human leukocyte antigen (HLA) class-I molecules present fragments of the cellular proteome to the T cell receptor (TCR) of cytotoxic T cells to control infectious diseases and cancer. The large number of combinations of HLA class-I allotypes and peptides allows for highly specific and dedicated low-affinity interactions to a diverse array of TCRs and natural killer (NK) cell receptors. Whether the divergent HLA class-I peptide complex is exclusive for interactions with these proteins is unknown. Using genome-wide CRISPR-Cas9 activation and knockout screens, we identified peptide-specific HLA-C∗07 combinations that can interact with the surface molecules CD55 and heparan sulfate. These interactions closely resemble the HLA class-I interaction with the TCR regarding both the affinity range and the specificity of the peptide and HLA allele. These findings indicate that various proteins can specifically bind HLA class-I peptide complexes due to their polymorphic nature, which suggests there are more interactions like the ones we describe here.

Published
2024
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45. High exposure of global tree diversity to human pressure

Author

Guo, Wen-Yong, Serra-Diaz, Josep M, Schrodt, Franziska, Eiserhardt, Wolf L, Maitner, Brian S, Merow, Cory, Violle, Cyrille, Anand, Madhur, Belluau, Michaël, Bruun, Hans Henrik, Byun, Chaeho, Catford, Jane A, Cerabolini, Bruno EL, Chacón-Madrigal, Eduardo, Ciccarelli, Daniela, Cornelissen, J Hans C, Dang-Le, Anh Tuan, de Frutos, Angel, Dias, Arildo S, Giroldo, Aelton B, Guo, Kun, Gutiérrez, Alvaro G, Hattingh, Wesley, He, Tianhua, Hietz, Peter, Hough-Snee, Nate, Jansen, Steven, Kattge, Jens, Klein, Tamir, Komac, Benjamin, Kraft, Nathan JB, Kramer, Koen, Lavorel, Sandra, Lusk, Christopher H, Martin, Adam R, Mencuccini, Maurizio, Michaletz, Sean T, Minden, Vanessa, Mori, Akira S, Niinemets, Ülo, Onoda, Yusuke, Peñuelas, Josep, Pillar, Valério D, Pisek, Jan, Robroek, Bjorn JM, Schamp, Brandon, Slot, Martijn, Sosinski, Ênio Egon, Soudzilovskaia, Nadejda A, Thiffault, Nelson, van Bodegom, Peter, van der Plas, Fons, Wright, Ian J, Xu, Wu-Bing, Zheng, Jingming, Enquist, Brian J, and Svenning, Jens-Christian

Subjects
Life on Land, Anthropogenic Effects, Biodiversity, Conservation of Natural Resources, Ecosystem, Humans, Phylogeny, Trees, biodiversity, conservation frameworks, land use, protected areas, tree species
Abstract

Safeguarding Earth's tree diversity is a conservation priority due to the importance of trees for biodiversity and ecosystem functions and services such as carbon sequestration. Here, we improve the foundation for effective conservation of global tree diversity by analyzing a recently developed database of tree species covering 46,752 species. We quantify range protection and anthropogenic pressures for each species and develop conservation priorities across taxonomic, phylogenetic, and functional diversity dimensions. We also assess the effectiveness of several influential proposed conservation prioritization frameworks to protect the top 17% and top 50% of tree priority areas. We find that an average of 50.2% of a tree species' range occurs in 110-km grid cells without any protected areas (PAs), with 6,377 small-range tree species fully unprotected, and that 83% of tree species experience nonnegligible human pressure across their range on average. Protecting high-priority areas for the top 17% and 50% priority thresholds would increase the average protected proportion of each tree species' range to 65.5% and 82.6%, respectively, leaving many fewer species (2,151 and 2,010) completely unprotected. The priority areas identified for trees match well to the Global 200 Ecoregions framework, revealing that priority areas for trees would in large part also optimize protection for terrestrial biodiversity overall. Based on range estimates for >46,000 tree species, our findings show that a large proportion of tree species receive limited protection by current PAs and are under substantial human pressure. Improved protection of biodiversity overall would also strongly benefit global tree diversity.

Published
2022

46. On the Language-specificity of Multilingual BERT and the Impact of Fine-tuning

Author

Tanti, Marc, van der Plas, Lonneke, Borg, Claudia, and Gatt, Albert

Subjects
Computer Science - Computation and Language, Computer Science - Neural and Evolutionary Computing
Abstract

Recent work has shown evidence that the knowledge acquired by multilingual BERT (mBERT) has two components: a language-specific and a language-neutral one. This paper analyses the relationship between them, in the context of fine-tuning on two tasks -- POS tagging and natural language inference -- which require the model to bring to bear different degrees of language-specific knowledge. Visualisations reveal that mBERT loses the ability to cluster representations by language after fine-tuning, a result that is supported by evidence from language identification experiments. However, further experiments on 'unlearning' language-specific representations using gradient reversal and iterative adversarial learning are shown not to add further improvement to the language-independent component over and above the effect of fine-tuning. The results presented here suggest that the process of fine-tuning causes a reorganisation of the model's limited representational capacity, enhancing language-independent representations at the expense of language-specific ones., Comment: 14 pages, 6 figures, 5 tables, submitted in BlackBoxNLP 2021 (https://aclanthology.org/2021.blackboxnlp-1.15/)

Published
2021

47. Relationships between species richness and biomass production are context dependent in grasslands differing in land-use and seed addition

Author

Karl Andraczek, Alexandra Weigelt, Cristóbal J. Bottero Cantuarias, Markus Fischer, Judith Hinderling, Daniel Prati, Esther M. N. Rauwolf, and Fons van der Plas

Subjects
Medicine, Science
Abstract

Abstract Despite evidence from grasslands experiments suggesting that plant species loss reduces biomass production, the strength of biodiversity-ecosystem functioning relationships in managed grasslands is still debated. High land-use intensity and reduced species pools are often suggested to make relationships between biodiversity and productivity less positive or even negative, but concrete evidence is still scarce. We investigated biodiversity-productivity relationships over two years in 150 managed grasslands in Germany. Specifically, we distinguished between relationships of biodiversity and biomass production in managed grasslands (1) varying in land-use intensity (e.g. of mowing, grazing and/or fertilization), (2) where land-use intensity is experimentally reduced, and (3) where additionally to land-use reductions, species pools are enlarged by seed addition. Among grasslands varying in land-use intensity, we found negative biodiversity-productivity relationships. Land-use reduction weakened these relationships, towards neutral, and sometimes, even positive relationships. Seed addition reduced species pool limitations, but this did not strengthen biodiversity-productivity relationships. Our findings indicate that land-use intensity is an important factor explaining the predominantly negative biodiversity-productivity relationships in managed grasslands. While we did not find that species pool limitations weakened biodiversity-productivity relationships, our results are based on a two-year-old experiment, possibly such effects are only visible in the long-term. Ultimately, advancing insights on biodiversity-ecosystem functioning relationships helps us to understand under which conditions agricultural production may benefit from promoting biodiversity.

Published
2023
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48. Native diversity buffers against severity of non-native tree invasions

Author

Delavaux, Camille S., Crowther, Thomas W., Zohner, Constantin M., Robmann, Niamh M., Lauber, Thomas, van den Hoogen, Johan, Kuebbing, Sara, Liang, Jingjing, de-Miguel, Sergio, Nabuurs, Gert-Jan, Reich, Peter B., 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 H. S., Brandl, Susanne, Brienen, Roel, Broadbent, Eben N., Bruelheide, Helge, Bussotti, Filippo, Gatti, Roberto Cazzolla, César, Ricardo G., Cesljar, Goran, Chazdon, Robin, Chen, Han Y. H., 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., Fischer, Markus, Fletcher, Christine, Frizzera, Lorenzo, Gamarra, Javier G. P., 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, Johannsen, Vivian Kvist, Joly, Carlos A., Jucker, Tommaso, Jung, Ilbin, Karminov, Viktor, Kartawinata, Kuswata, Kearsley, Elizabeth, Kenfack, David, Kennard, Deborah K., Kepfer-Rojas, Sebastian, Keppel, Gunnar, Khan, Mohammed Latif, Killeen, Timothy J., Kim, Hyun Seok, Kitayama, Kanehiro, Köhl, Michael, Korjus, Henn, Kraxner, Florian, Laarmann, Diana, Lang, Mait, Lewis, Simon L., Lu, Huicui, Lukina, Natalia V., Maitner, Brian S., Malhi, Yadvinder, Marcon, Eric, Marimon, Beatriz Schwantes, Marimon-Junior, Ben Hur, Marshall, Andrew R., Martin, Emanuel H., Martynenko, Olga, Meave, Jorge A., Melo-Cruz, Omar, Mendoza, Casimiro, Merow, Cory, Mendoza, Abel Monteagudo, Moreno, Vanessa S., Mukul, Sharif A., Mundhenk, Philip, Nava-Miranda, María Guadalupe, Neill, David, Neldner, Victor J., Nevenic, Radovan V., Ngugi, Michael R., Niklaus, Pascal A., Oleksyn, Jacek, Ontikov, Petr, Ortiz-Malavasi, Edgar, Pan, Yude, Paquette, Alain, Parada-Gutierrez, Alexander, Parfenova, Elena I., Park, Minjee, Parren, Marc, Parthasarathy, Narayanaswamy, Peri, Pablo L., Pfautsch, Sebastian, Phillips, Oliver L., Picard, Nicolas, Piedade, Maria Teresa T. F., Piotto, Daniel, Pitman, Nigel C. A., Polo, Irina, Poorter, Lourens, Poulsen, Axel D., Pretzsch, Hans, Ramirez Arevalo, Freddy, Restrepo-Correa, Zorayda, Rodeghiero, Mirco, Rolim, Samir G., Roopsind, Anand, Rovero, Francesco, Rutishauser, Ervan, Saikia, Purabi, Salas-Eljatib, Christian, Saner, Philippe, Schall, Peter, Schepaschenko, Dmitry, Scherer-Lorenzen, Michael, Schmid, Bernhard, Schöngart, Jochen, Searle, Eric B., Seben, Vladimír, Serra-Diaz, Josep M., Sheil, Douglas, Shvidenko, Anatoly Z., Silva-Espejo, Javier E., Silveira, Marcos, Singh, James, Sist, Plinio, Slik, Ferry, Sonké, Bonaventure, Souza, Alexandre F., Miscicki, Stanislaw, Stereńczak, Krzysztof J., Svenning, Jens-Christian, Svoboda, Miroslav, Swanepoel, Ben, Targhetta, Natalia, Tchebakova, Nadja, ter Steege, Hans, Thomas, Raquel, Tikhonova, Elena, Umunay, Peter M., Usoltsev, Vladimir A., Valencia, Renato, Valladares, Fernando, van der Plas, Fons, Do, Tran Van, van Nuland, Michael E., Vasquez, Rodolfo M., Verbeeck, Hans, Viana, Helder, Vibrans, Alexander C., Vieira, Simone, von Gadow, Klaus, Wang, Hua-Feng, Watson, James V., Werner, Gijsbert D. A., Wiser, Susan K., Wittmann, Florian, Woell, Hannsjoerg, Wortel, Verginia, Zagt, Roderik, Zawiła-Niedźwiecki, Tomasz, Zhang, Chunyu, Zhao, Xiuhai, Zhou, Mo, Zhu, Zhi-Xin, Zo-Bi, Irie C., and Maynard, Daniel S.

Published
2023
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50. Immunosuppression by hydroxychloroquine: mechanistic proof in in vitro experiments but limited systemic activity in a randomized placebo-controlled clinical pharmacology study

Author

in ‘t Veld, Aliede E., Grievink, Hendrika W., van der Plas, Johan L., Eveleens Maarse, Boukje C., van Kraaij, Sebastiaan J. W., Woutman, Tess D., Schoonakker, Mascha, Klarenbeek, Naomi B., de Kam, Marieke L., Kamerling, Ingrid M. C., Jansen, Manon A. A., and Moerland, Matthijs

Published
2023
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