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53. Understanding the genetic complexity of puberty timing across the allele frequency spectrum

Author

Kentistou, Katherine A., Kaisinger, Lena R., Stankovic, Stasa, Vaudel, Marc, Mendes de Oliveira, Edson, Messina, Andrea, Walters, Robin G., Liu, Xiaoxi, Busch, Alexander S., Helgason, Hannes, Thompson, Deborah J., Santoni, Federico, Petricek, Konstantin M., Zouaghi, Yassine, Huang-Doran, Isabel, Gudbjartsson, Daniel F., Bratland, Eirik, Lin, Kuang, Gardner, Eugene J., Zhao, Yajie, Jia, Raina Y., Terao, Chikashi, Riggan, Marjorie J., Bolla, Manjeet K., Yazdanpanah, Mojgan, Yazdanpanah, Nahid, Bradfield, Jonathan P., Broer, Linda, Campbell, Archie, Chasman, Daniel I., Cousminer, Diana L., Franceschini, Nora, Franke, Lude H., Girotto, Giorgia, He, Chunyan, Järvelin, Marjo-Riitta, Joshi, Peter K., Kamatani, Yoichiro, Karlsson, Robert, Luan, Jian’an, Lunetta, Kathryn L., Mägi, Reedik, Mangino, Massimo, Medland, Sarah E., Meisinger, Christa, Noordam, Raymond, Nutile, Teresa, Concas, Maria Pina, Polašek, Ozren, Porcu, Eleonora, Ring, Susan M., Sala, Cinzia, Smith, Albert V., Tanaka, Toshiko, van der Most, Peter J., Vitart, Veronique, Wang, Carol A., Willemsen, Gonneke, Zygmunt, Marek, Ahearn, Thomas U., Andrulis, Irene L., Anton-Culver, Hoda, Antoniou, Antonis C., Auer, Paul L., Barnes, Catriona L. K., Beckmann, Matthias W., Berrington de Gonzalez, Amy, Bogdanova, Natalia V., Bojesen, Stig E., Brenner, Hermann, Buring, Julie E., Canzian, Federico, Chang-Claude, Jenny, Couch, Fergus J., Cox, Angela, Crisponi, Laura, Czene, Kamila, Daly, Mary B., Demerath, Ellen W., Dennis, Joe, Devilee, Peter, De Vivo, Immaculata, Dörk, Thilo, Dunning, Alison M., Dwek, Miriam, Eriksson, Johan G., Fasching, Peter A., Fernandez-Rhodes, Lindsay, Ferreli, Liana, Fletcher, Olivia, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A., González-Neira, Anna, Grallert, Harald, Guénel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Hakonarson, Hakon, Hart, Roger J., Hickey, Martha, Hooning, Maartje J., Hoppe, Reiner, Hopper, John L., Hottenga, Jouke-Jan, Hu, Frank B., Huebner, Hanna, Hunter, David J., Jernström, Helena, John, Esther M., Karasik, David, Khusnutdinova, Elza K., Kristensen, Vessela N., Lacey, James V., Lambrechts, Diether, Launer, Lenore J., Lind, Penelope A., Lindblom, Annika, Magnusson, Patrik K. E., Mannermaa, Arto, McCarthy, Mark I., Meitinger, Thomas, Menni, Cristina, Michailidou, Kyriaki, Millwood, Iona Y., Milne, Roger L., Montgomery, Grant W., Nevanlinna, Heli, Nolte, Ilja M., Nyholt, Dale R., Obi, Nadia, O’Brien, Katie M., Offit, Kenneth, Oldehinkel, Albertine J., Ostrowski, Sisse R., Palotie, Aarno, Pedersen, Ole B., Peters, Annette, Pianigiani, Giulia, Plaseska-Karanfilska, Dijana, Pouta, Anneli, Pozarickij, Alfred, Radice, Paolo, Rennert, Gad, Rosendaal, Frits R., Ruggiero, Daniela, Saloustros, Emmanouil, Sandler, Dale P., Schipf, Sabine, Schmidt, Carsten O., Schmidt, Marjanka K., Small, Kerrin, Spedicati, Beatrice, Stampfer, Meir, Stone, Jennifer, Tamimi, Rulla M., Teras, Lauren R., Tikkanen, Emmi, Turman, Constance, Vachon, Celine M., Wang, Qin, Winqvist, Robert, Wolk, Alicja, Zemel, Babette S., Zheng, Wei, van Dijk, Ko W., Alizadeh, Behrooz Z., Bandinelli, Stefania, Boerwinkle, Eric, Boomsma, Dorret I., Ciullo, Marina, Chenevix-Trench, Georgia, Cucca, Francesco, Esko, Tõnu, Gieger, Christian, Grant, Struan F. A., Gudnason, Vilmundur, Hayward, Caroline, Kolčić, Ivana, Kraft, Peter, Lawlor, Deborah A., Martin, Nicholas G., Nøhr, Ellen A., Pedersen, Nancy L., Pennell, Craig E., Ridker, Paul M., Robino, Antonietta, Snieder, Harold, Sovio, Ulla, Spector, Tim D., Stöckl, Doris, Sudlow, Cathie, Timpson, Nic J., Toniolo, Daniela, Uitterlinden, André, Ulivi, Sheila, Völzke, Henry, Wareham, Nicholas J., Widen, Elisabeth, Wilson, James F., Pharoah, Paul D. P., Li, Liming, Easton, Douglas F., Njølstad, Pål R., Sulem, Patrick, Murabito, Joanne M., Murray, Anna, Manousaki, Despoina, Juul, Anders, Erikstrup, Christian, Stefansson, Kari, Horikoshi, Momoko, Chen, Zhengming, Farooqi, I. Sadaf, Pitteloud, Nelly, Johansson, Stefan, Day, Felix R., Perry, John R. B., and Ong, Ken K.

Published
2024
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54. Paloma: A Benchmark for Evaluating Language Model Fit

Author

Magnusson, Ian, Bhagia, Akshita, Hofmann, Valentin, Soldaini, Luca, Jha, Ananya Harsh, Tafjord, Oyvind, Schwenk, Dustin, Walsh, Evan Pete, Elazar, Yanai, Lo, Kyle, Groeneveld, Dirk, Beltagy, Iz, Hajishirzi, Hannaneh, Smith, Noah A., Richardson, Kyle, and Dodge, Jesse

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

Language models (LMs) commonly report perplexity on monolithic data held out from training. Implicitly or explicitly, this data is composed of domains$\unicode{x2013}$varying distributions of language. Rather than assuming perplexity on one distribution extrapolates to others, Perplexity Analysis for Language Model Assessment (Paloma), measures LM fit to 585 text domains, ranging from nytimes.com to r/depression on Reddit. We invite submissions to our benchmark and organize results by comparability based on compliance with guidelines such as removal of benchmark contamination from pretraining. Submissions can also record parameter and training token count to make comparisons of Pareto efficiency for performance as a function of these measures of cost. We populate our benchmark with results from 6 baselines pretrained on popular corpora. In case studies, we demonstrate analyses that are possible with Paloma, such as finding that pretraining without data beyond Common Crawl leads to inconsistent fit to many domains., Comment: Project Page: https://paloma.allen.ai/

Published
2023

55. Catwalk: A Unified Language Model Evaluation Framework for Many Datasets

Author

Groeneveld, Dirk, Awadalla, Anas, Beltagy, Iz, Bhagia, Akshita, Magnusson, Ian, Peng, Hao, Tafjord, Oyvind, Walsh, Pete, Richardson, Kyle, and Dodge, Jesse

Subjects
Computer Science - Computation and Language
Abstract

The success of large language models has shifted the evaluation paradigms in natural language processing (NLP). The community's interest has drifted towards comparing NLP models across many tasks, domains, and datasets, often at an extreme scale. This imposes new engineering challenges: efforts in constructing datasets and models have been fragmented, and their formats and interfaces are incompatible. As a result, it often takes extensive (re)implementation efforts to make fair and controlled comparisons at scale. Catwalk aims to address these issues. Catwalk provides a unified interface to a broad range of existing NLP datasets and models, ranging from both canonical supervised training and fine-tuning, to more modern paradigms like in-context learning. Its carefully-designed abstractions allow for easy extensions to many others. Catwalk substantially lowers the barriers to conducting controlled experiments at scale. For example, we finetuned and evaluated over 64 models on over 86 datasets with a single command, without writing any code. Maintained by the AllenNLP team at the Allen Institute for Artificial Intelligence (AI2), Catwalk is an ongoing open-source effort: https://github.com/allenai/catwalk., Comment: technical report, work in progress

Published
2023

56. Asynchronous Distributed Optimization with Delay-free Parameters

Author

Wu, Xuyang, Liu, Changxin, Magnusson, Sindri, and Johansson, Mikael

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

Existing asynchronous distributed optimization algorithms often use diminishing step-sizes that cause slow practical convergence, or use fixed step-sizes that depend on and decrease with an upper bound of the delays. Not only are such delay bounds hard to obtain in advance, but they also tend to be large and rarely attained, resulting in unnecessarily slow convergence. This paper develops asynchronous versions of two distributed algorithms, Prox-DGD and DGD-ATC, for solving consensus optimization problems over undirected networks. In contrast to alternatives, our algorithms can converge to the fixed point set of their synchronous counterparts using step-sizes that are independent of the delays. We establish convergence guarantees for convex and strongly convex problems under both partial and total asynchrony. We also show that the convergence speed of the two asynchronous methods adjusts to the actual level of asynchrony rather than being constrained by the worst-case. Numerical experiments demonstrate a strong practical performance of our asynchronous algorithms., Comment: 18 pages. arXiv admin note: text overlap with arXiv:2303.18034

Published
2023

57. Towards Human-Level Text Coding with LLMs: The Case of Fatherhood Roles in Public Policy Documents

Author

Lupo, Lorenzo, Magnusson, Oscar, Hovy, Dirk, Naurin, Elin, and Wängnerud, Lena

Subjects
Computer Science - Computation and Language, Computer Science - Computers and Society, J.4, I.2
Abstract

Recent advances in large language models (LLMs) like GPT-3.5 and GPT-4 promise automation with better results and less programming, opening up new opportunities for text analysis in political science. In this study, we evaluate LLMs on three original coding tasks involving typical complexities encountered in political science settings: a non-English language, legal and political jargon, and complex labels based on abstract constructs. Along the paper, we propose a practical workflow to optimize the choice of the model and the prompt. We find that the best prompting strategy consists of providing the LLMs with a detailed codebook, as the one provided to human coders. In this setting, an LLM can be as good as or possibly better than a human annotator while being much faster, considerably cheaper, and much easier to scale to large amounts of text. We also provide a comparison of GPT and popular open-source LLMs, discussing the trade-offs in the model's choice. Our software allows LLMs to be easily used as annotators and is publicly available: https://github.com/lorelupo/pappa.

Published
2023

58. What's In My Big Data?

Author

Elazar, Yanai, Bhagia, Akshita, Magnusson, Ian, Ravichander, Abhilasha, Schwenk, Dustin, Suhr, Alane, Walsh, Pete, Groeneveld, Dirk, Soldaini, Luca, Singh, Sameer, Hajishirzi, Hanna, Smith, Noah A., and Dodge, Jesse

Subjects
Computer Science - Computation and Language, Computer Science - Machine Learning
Abstract

Large text corpora are the backbone of language models. However, we have a limited understanding of the content of these corpora, including general statistics, quality, social factors, and inclusion of evaluation data (contamination). In this work, we propose What's In My Big Data? (WIMBD), a platform and a set of sixteen analyses that allow us to reveal and compare the contents of large text corpora. WIMBD builds on two basic capabilities -- count and search -- at scale, which allows us to analyze more than 35 terabytes on a standard compute node. We apply WIMBD to ten different corpora used to train popular language models, including C4, The Pile, and RedPajama. Our analysis uncovers several surprising and previously undocumented findings about these corpora, including the high prevalence of duplicate, synthetic, and low-quality content, personally identifiable information, toxic language, and benchmark contamination. For instance, we find that about 50% of the documents in RedPajama and LAION-2B-en are duplicates. In addition, several datasets used for benchmarking models trained on such corpora are contaminated with respect to important benchmarks, including the Winograd Schema Challenge and parts of GLUE and SuperGLUE. We open-source WIMBD's code and artifacts to provide a standard set of evaluations for new text-based corpora and to encourage more analyses and transparency around them., Comment: Published at ICLR 2024 spotlight

Published
2023

59. Do we need scan-matching in radar odometry?

Author

Kubelka, Vladimír, Fritz, Emil, and Magnusson, Martin

Subjects
Computer Science - Robotics
Abstract

There is a current increase in the development of "4D" Doppler-capable radar and lidar range sensors that produce 3D point clouds where all points also have information about the radial velocity relative to the sensor. 4D radars in particular are interesting for object perception and navigation in low-visibility conditions (dust, smoke) where lidars and cameras typically fail. With the advent of high-resolution Doppler-capable radars comes the possibility of estimating odometry from single point clouds, foregoing the need for scan registration which is error-prone in feature-sparse field environments. We compare several odometry estimation methods, from direct integration of Doppler/IMU data and Kalman filter sensor fusion to 3D scan-to-scan and scan-to-map registration, on three datasets with data from two recent 4D radars and two IMUs. Surprisingly, our results show that the odometry from Doppler and IMU data alone give similar or better results than 3D point cloud registration. In our experiments, the average position error can be as low as 0.3% over 1.8 and 4.5km trajectories. That allows accurate estimation of 6DOF ego-motion over long distances also in feature-sparse mine environments. These results are useful not least for applications of navigation with resource-constrained robot platforms in feature-sparse and low-visibility conditions such as mining, construction, and search & rescue operations., Comment: Preprint. Submitted to ICRA 2024. 7 pages, 11 figures

Published
2023

60. Learning Extrinsic Dexterity with Parameterized Manipulation Primitives

Author

Yang, Shih-Min, Magnusson, Martin, Stork, Johannes A., and Stoyanov, Todor

Subjects
Computer Science - Robotics, Computer Science - Machine Learning
Abstract

Many practically relevant robot grasping problems feature a target object for which all grasps are occluded, e.g., by the environment. Single-shot grasp planning invariably fails in such scenarios. Instead, it is necessary to first manipulate the object into a configuration that affords a grasp. We solve this problem by learning a sequence of actions that utilize the environment to change the object's pose. Concretely, we employ hierarchical reinforcement learning to combine a sequence of learned parameterized manipulation primitives. By learning the low-level manipulation policies, our approach can control the object's state through exploiting interactions between the object, the gripper, and the environment. Designing such a complex behavior analytically would be infeasible under uncontrolled conditions, as an analytic approach requires accurate physical modeling of the interaction and contact dynamics. In contrast, we learn a hierarchical policy model that operates directly on depth perception data, without the need for object detection, pose estimation, or manual design of controllers. We evaluate our approach on picking box-shaped objects of various weight, shape, and friction properties from a constrained table-top workspace. Our method transfers to a real robot and is able to successfully complete the object picking task in 98\% of experimental trials. Supplementary information and videos can be found at https://shihminyang.github.io/ED-PMP/., Comment: 2024 IEEE International Conference on Robotics and Automation (ICRA 2024)

Published
2023

61. Doppler-only Single-scan 3D Vehicle Odometry

Author

Galeote-Luque, Andres, Kubelka, Vladimír, Magnusson, Martin, Ruiz-Sarmiento, Jose-Raul, and Gonzalez-Jimenez, Javier

Subjects
Computer Science - Robotics
Abstract

We present a novel 3D odometry method that recovers the full motion of a vehicle only from a Doppler-capable range sensor. It leverages the radial velocities measured from the scene, estimating the sensor's velocity from a single scan. The vehicle's 3D motion, defined by its linear and angular velocities, is calculated taking into consideration its kinematic model which provides a constraint between the velocity measured at the sensor frame and the vehicle frame. Experiments carried out prove the viability of our single-sensor method compared to mounting an additional IMU. Our method provides the translation of the sensor, which cannot be reliably determined from an IMU, as well as its rotation. Its short-term accuracy and fast operation (~5ms) make it a proper candidate to supply the initialization to more complex localization algorithms or mapping pipelines. Not only does it reduce the error of the mapper, but it does so at a comparable level of accuracy as an IMU would. All without the need to mount and calibrate an extra sensor on the vehicle., Comment: This work has been submitted to the IEEE for possible publication

Published
2023

62. RadaRays: Real-time Simulation of Rotating FMCW Radar for Mobile Robotics via Hardware-accelerated Ray Tracing

Author

Mock, Alexander, Magnusson, Martin, and Hertzberg, Joachim

Subjects
Computer Science - Robotics
Abstract

RadaRays allows for the accurate modeling and simulation of rotating FMCW radar sensors in complex environments, including the simulation of reflection, refraction, and scattering of radar waves. Our software is able to handle large numbers of objects and materials, making it suitable for use in a variety of mobile robotics applications. We demonstrate the effectiveness of RadaRays through a series of experiments and show that it can more accurately reproduce the behavior of FMCW radar sensors in a variety of environments, compared to the ray casting-based lidar-like simulations that are commonly used in simulators for autonomous driving such as CARLA. Our experiments additionally serve as valuable reference point for researchers to evaluate their own radar simulations. By using RadaRays, developers can significantly reduce the time and cost associated with prototyping and testing FMCW radar-based algorithms. We also provide a Gazebo plugin that makes our work accessible to the mobile robotics community.

Published
2023

63. X-chromosome and kidney function: evidence from a multi-trait genetic analysis of 908,697 individuals reveals sex-specific and sex-differential findings in genes regulated by androgen response elements.

Author

Scholz, Markus, Horn, Katrin, Pott, Janne, Wuttke, Matthias, Kühnapfel, Andreas, Nasr, M, Kirsten, Holger, Li, Yong, Hoppmann, Anselm, Gorski, Mathias, Ghasemi, Sahar, Li, Man, Tin, Adrienne, Chai, Jin-Fang, Cocca, Massimiliano, Wang, Judy, Nutile, Teresa, Akiyama, Masato, Åsvold, Bjørn, Bansal, Nisha, Biggs, Mary, Boutin, Thibaud, Brenner, Hermann, Brumpton, Ben, Burkhardt, Ralph, Cai, Jianwen, Campbell, Archie, Campbell, Harry, Chalmers, John, Chasman, Daniel, Chee, Miao, Chen, Xu, Cheng, Ching-Yu, Cifkova, Renata, Daviglus, Martha, Delgado, Graciela, Dittrich, Katalin, Edwards, Todd, Endlich, Karlhans, Michael Gaziano, J, Giri, Ayush, Giulianini, Franco, Gordon, Scott, Gudbjartsson, Daniel, Hallan, Stein, Hamet, Pavel, Hartman, Catharina, Hayward, Caroline, Heid, Iris, Hellwege, Jacklyn, Holleczek, Bernd, Holm, Hilma, Hutri-Kähönen, Nina, Hveem, Kristian, Isermann, Berend, Jonas, Jost, Joshi, Peter, Kamatani, Yoichiro, Kanai, Masahiro, Kastarinen, Mika, Khor, Chiea, Kiess, Wieland, Kleber, Marcus, Körner, Antje, Kovacs, Peter, Krajcoviechova, Alena, Kramer, Holly, Krämer, Bernhard, Kuokkanen, Mikko, Kähönen, Mika, Lange, Leslie, Lash, James, Lehtimäki, Terho, Li, Hengtong, Lin, Bridget, Liu, Jianjun, Loeffler, Markus, Lyytikäinen, Leo-Pekka, Magnusson, Patrik, Martin, Nicholas, Matsuda, Koichi, Milaneschi, Yuri, Mishra, Pashupati, Mononen, Nina, Montgomery, Grant, Mook-Kanamori, Dennis, Mychaleckyj, Josyf, März, Winfried, Nauck, Matthias, Nikus, Kjell, Nolte, Ilja, Noordam, Raymond, Okada, Yukinori, Olafsson, Isleifur, Oldehinkel, Albertine, Penninx, Brenda, Perola, Markus, Pirastu, Nicola, and Polasek, Ozren

Subjects
Humans, Male, Female, Androgens, Genome-Wide Association Study, Kidney, Chromosomes, Human, X, Response Elements, Polymorphism, Single Nucleotide, Genetic Predisposition to Disease, Tetraspanins
Abstract

X-chromosomal genetic variants are understudied but can yield valuable insights into sexually dimorphic human traits and diseases. We performed a sex-stratified cross-ancestry X-chromosome-wide association meta-analysis of seven kidney-related traits (n = 908,697), identifying 23 loci genome-wide significantly associated with two of the traits: 7 for uric acid and 16 for estimated glomerular filtration rate (eGFR), including four novel eGFR loci containing the functionally plausible prioritized genes ACSL4, CLDN2, TSPAN6 and the female-specific DRP2. Further, we identified five novel sex-interactions, comprising male-specific effects at FAM9B and AR/EDA2R, and three sex-differential findings with larger genetic effect sizes in males at DCAF12L1 and MST4 and larger effect sizes in females at HPRT1. All prioritized genes in loci showing significant sex-interactions were located next to androgen response elements (ARE). Five ARE genes showed sex-differential expressions. This study contributes new insights into sex-dimorphisms of kidney traits along with new prioritized gene targets for further molecular research.

Published
2024

65. Novel loci and biomedical consequences of iron homoeostasis variation

Author

Allara, Elias, Bell, Steven, Smith, Rebecca, Keene, Spencer J., Gill, Dipender, Gaziano, Liam, Morselli Gysi, Deisy, Wang, Feiyi, Tragante, Vinicius, Mason, Amy, Karthikeyan, Savita, Lumbers, R. Thomas, Bonglack, Emmanuela, Ouwehand, Willem, Roberts, David J., Dowsett, Joseph, Ostrowski, Sisse Rye, Larsen, Margit Hørup, Ullum, Henrik, Pedersen, Ole Birger, Brunak, Søren, Banasik, Karina, Erikstrup, Christian, Mitchell, Jonathan, Fuchsberger, Christian, Pattaro, Cristian, Pramstaller, Peter P., Girelli, Domenico, Arvas, Mikko, Toivonen, Jarkko, Molnos, Sophie, Peters, Annette, Polasek, Ozren, Rudan, Igor, Hayward, Caroline, McDonnell, Ciara, Pirastu, Nicola, Wilson, James F., van den Hurk, Katja, Quee, Franke, Ferrucci, Luigi, Bandinelli, Stefania, Tanaka, Toshiko, Girotto, Giorgia, Concas, Maria Pina, Pecori, Alessandro, Verweij, Niek, van der Harst, Pim, van de Vegte, Yordi J., Kiemeney, Lambertus A., Sweep, Fred C., Galesloot, Tessel E., Sulem, Patrick, Gudbjartsson, Daniel, Ferkingstad, Egil, Djousse, Luc, Cho, Kelly, Inouye, Michael, Burgess, Stephen, Benyamin, Beben, Oexle, Konrad, Swinkels, Dorine, Stefansson, Kari, Magnusson, Magnus, Ganna, Andrea, Gaziano, Michael, Ivey, Kerry, Danesh, John, Pereira, Alexandre, Wood, Angela M., Butterworth, Adam S., and Di Angelantonio, Emanuele

Published
2024
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72. 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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77. Start codon variant in LAG3 is associated with decreased LAG-3 expression and increased risk of autoimmune thyroid disease

Author

Saevarsdottir, Saedis, Bjarnadottir, Kristbjörg, Markusson, Thorsteinn, Berglund, Jonas, Olafsdottir, Thorunn A., Halldorsson, Gisli H., Rutsdottir, Gudrun, Gunnarsdottir, Kristbjorg, Arnthorsson, Asgeir Orn, Lund, Sigrun H., Stefansdottir, Lilja, Gudmundsson, Julius, Johannesson, Ari J., Sturluson, Arni, Oddsson, Asmundur, Halldorsson, Bjarni, Ludviksson, Björn R., Ferkingstad, Egil, Ivarsdottir, Erna V., Sveinbjornsson, Gardar, Grondal, Gerdur, Masson, Gisli, Eldjarn, Grimur Hjorleifsson, Thorisson, Gudmundur A., Kristjansdottir, Katla, Knowlton, Kirk U., Moore, Kristjan H. S., Gudjonsson, Sigurjon A., Rognvaldsson, Solvi, Knight, Stacey, Nadauld, Lincoln D., Holm, Hilma, Magnusson, Olafur T., Sulem, Patrick, Gudbjartsson, Daniel F., Rafnar, Thorunn, Thorleifsson, Gudmar, Melsted, Pall, Norddahl, Gudmundur L., Jonsdottir, Ingileif, and Stefansson, Kari

Published
2024
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78. Body size predicts ontogenetic nitrogen stable-isotope (δ15N) variation, but has little relationship with trophic level in ectotherm vertebrate predators

Author

Villamarín, Francisco, Jardine, Timothy D., Bunn, Stuart E., Malvasio, Adriana, Piña, Carlos Ignacio, Jacobi, Cristina Mariana, Araújo, Diogo Dutra, de Brito, Elizângela Silva, de Moraes Carvalho, Felipe, da Costa, Igor David, Verdade, Luciano Martins, Lara, Neliton, de Camargo, Plínio Barbosa, Miorando, Priscila Saikoski, Portelinha, Thiago Costa Gonçalves, Marques, Thiago Simon, and Magnusson, William E.

Published
2024
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81. Identification and validation of a blood- based diagnostic lipidomic signature of pediatric inflammatory bowel disease

Author

Salihovic, Samira, Nyström, Niklas, Mathisen, Charlotte Bache-Wiig, Kruse, Robert, Olbjørn, Christine, Andersen, Svend, Noble, Alexandra J., Dorn-Rasmussen, Maria, Bazov, Igor, Perminow, Gøri, Opheim, Randi, Detlie, Trond Espen, Huppertz-Hauss, Gert, Hedin, Charlotte R. H., Carlson, Marie, Öhman, Lena, Magnusson, Maria K., Keita, Åsa V., Söderholm, Johan D., D’Amato, Mauro, Orešič, Matej, Wewer, Vibeke, Satsangi, Jack, Lindqvist, Carl Mårten, Burisch, Johan, Uhlig, Holm H., Repsilber, Dirk, Hyötyläinen, Tuulia, Høivik, Marte Lie, and Halfvarson, Jonas

Published
2024
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94. Exploring how Sentinel-1 wet-snow maps can inform fully distributed physically based snowpack models

Author

B. Cluzet, J. Magnusson, L. Quéno, G. Mazzotti, R. Mott, and T. Jonas

Subjects
Environmental sciences, GE1-350, Geology, QE1-996.5
Abstract

Distributed energy and mass balance snowpack models at sub-kilometric scale have emerged as a tool for snow-hydrological forecasting over large areas. However, their development and evaluation often rely on a handful of well-observed sites on flat terrain with limited topographic representativeness. Validation of such models over large scales in rugged terrain is therefore necessary. Remote sensing of wet snow has always been motivated by its potential utility in snow hydrology. However, its concrete potential to enhance physically based operational snowpack models in real time remains unproven. Wet-snow maps could potentially help refine the temporal accuracy of simulated snowmelt onset, while the information content of remotely sensed snow cover fraction (SCF) pertains predominantly to the ablation season. In this work, wet-snow maps derived from Sentinel-1 and SCF retrieval from Sentinel-2 are compared against model results from a fully distributed energy balance snow model (FSM2oshd). The comparative analysis spans the winter seasons from 2017 to 2021, focusing on the geographic region of Switzerland. We use the concept of wet-snow line (WSL) to compare Sentinel-1 wet-snow maps with simulations. We show that while the match of the model with flat-field snow depth observation is excellent, the WSL reveals a delayed snowmelt in the southern aspects. Amending the albedo parametrization within FSM2oshd allowed for the achievement of earlier melt in such aspects preferentially, thereby reducing WSL biases. Biases with respect to Sentinel-2 snow-line (SL) observations were also substantially reduced. These results suggest that wet-snow maps contain valuable real-time information for snowpack models, complementing flat-field snow depth observations well, particularly in complex terrain and at higher elevations. The persisting correlation between wet-snow-line and snow-line biases provides insights into refined development, tuning, and data assimilation methodologies for operational snow-hydrological modelling.

Published
2024
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95. Elevated carbohydrate antigen 125 (CA125) is associated with incident heart failure and mortality in acute coronary syndrome

Author

Troels Yndigegn, Thomas Gu, Helena Grufman, David Erlinge, Arash Mokhtari, Ulf Ekelund, Martin Magnusson, Emma Gustafsson, Jan Nilsson, Isabel Goncalves, and Alexandru Schiopu

Subjects
acute coronary syndrome, CA125, heart failure, mortality, prognosis, Diseases of the circulatory (Cardiovascular) system, RC666-701
Abstract

Abstract Aims Carbohydrate antigen 125 (CA125), a mucin produced by serosal cells in response to mechanical and inflammatory stimuli, has emerged as an important biomarker to guide risk stratification in heart failure (HF). The prognostic value of CA125 in acute coronary syndrome (ACS) patients is less explored. Methods In a cohort of 524 ACS patients (73% males, mean age 67 ± 12 years), we assessed the associations between CA125 and the risk for HF and death during a median follow‐up period of 27.3 months for incident HF and 39.5 months for mortality. Plasma CA125 was measured within 24 h after admission in the entire cohort and after 6 weeks in a subgroup of 115 elderly patients (>75 years of age). We also assessed the relationships between baseline CA125 and echocardiographic parameters of cardiac structure and function at 1 year post‐ACS in this subgroup. Results Baseline CA125 was associated with incident HF in the entire cohort in a Cox proportional hazards model adjusted for age, sex, cardiovascular (CV) risk factors (diabetes, smoking, hypertension, previous HF, previous ACS and previous stroke), renal function and revascularization {hazard ratio [HR] 1.46 [95% confidence interval (CI) 1.10–1.93] per 1‐standard deviation [SD] CA125 increase; P = 0.009}. In the detailed follow‐up subgroup, elevated baseline CA125 predicted subsequent deterioration of left ventricular (LV) ejection fraction (LVEF), defined as a >5% absolute LVEF decrease in patients with LVEF ≥ 50% at discharge [odds ratio (OR) 3.31 (95% CI 1.15–9.54) per 1‐SD baseline CA125 increase; P = 0.027]. We also found significant correlations between high baseline CA125 and larger LV volumes (LV end‐diastolic volume index, Spearman's r = 0.329, P

Published
2024
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96. Novel loci and biomedical consequences of iron homoeostasis variation

Author

Elias Allara, Steven Bell, Rebecca Smith, Spencer J. Keene, Dipender Gill, Liam Gaziano, Deisy Morselli Gysi, Feiyi Wang, Vinicius Tragante, Amy Mason, Savita Karthikeyan, R. Thomas Lumbers, Emmanuela Bonglack, Willem Ouwehand, David J. Roberts, Joseph Dowsett, Sisse Rye Ostrowski, Margit Hørup Larsen, Henrik Ullum, Ole Birger Pedersen, Søren Brunak, Karina Banasik, Christian Erikstrup, DBDS Genomic Consortium, Jonathan Mitchell, Christian Fuchsberger, Cristian Pattaro, Peter P. Pramstaller, Domenico Girelli, Mikko Arvas, Jarkko Toivonen, Sophie Molnos, Annette Peters, Ozren Polasek, Igor Rudan, Caroline Hayward, Ciara McDonnell, Nicola Pirastu, James F. Wilson, Katja van den Hurk, Franke Quee, Luigi Ferrucci, Stefania Bandinelli, Toshiko Tanaka, Giorgia Girotto, Maria Pina Concas, Alessandro Pecori, Niek Verweij, Pim van der Harst, Yordi J. van de Vegte, Lambertus A. Kiemeney, Fred C. Sweep, Tessel E. Galesloot, Patrick Sulem, Daniel Gudbjartsson, Egil Ferkingstad, FinnGen Consortium, Luc Djousse, Kelly Cho, Michael Inouye, Stephen Burgess, Beben Benyamin, Konrad Oexle, Dorine Swinkels, Kari Stefansson, Magnus Magnusson, Andrea Ganna, Michael Gaziano, Kerry Ivey, John Danesh, Alexandre Pereira, Angela M. Wood, Adam S. Butterworth, and Emanuele Di Angelantonio

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Iron homoeostasis is tightly regulated, with hepcidin and soluble transferrin receptor (sTfR) playing significant roles. However, the genetic determinants of these traits and the biomedical consequences of iron homoeostasis variation are unclear. In a meta-analysis of 12 cohorts involving 91,675 participants, we found 43 genomic loci associated with either hepcidin or sTfR concentration, of which 15 previously unreported. Mapping to putative genes indicated involvement in iron-trait expression, erythropoiesis, immune response and cellular trafficking. Mendelian randomisation of 292 disease outcomes in 1,492,717 participants revealed associations of iron-related loci and iron status with selected health outcomes across multiple domains. These associations were largely driven by HFE, which was associated with the largest iron variation. Our findings enhance understanding of iron homoeostasis and its biomedical consequences, suggesting that lifelong exposure to higher iron levels is likely associated with lower risk of anaemia-related disorders and higher risk of genitourinary, musculoskeletal, infectious and neoplastic diseases.

Published
2024
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97. Information access and COVID-19 vaccination hesitancy among foreign-born persons in Sweden – a focus group interview-study

Author

Mia Söderberg, Juhaina Swaid, Kristina Aurelius, Annika Rosengren, Kristina Jakobsson, and Maria Magnusson

Subjects
Information access, Vaccination hesitancy, Health disparities, Foreign-bon, Public aspects of medicine, RA1-1270
Abstract

Abstract Background In most countries, lower rates of COVID-19 vaccination have been observed in foreign-born individuals, yet little is known about the underlying reasons, especially as reported by these individuals themselves. This exploratory interview study investigated lack of information access and hesitancy towards taking the COVID-19 vaccine among foreign-born individuals in Sweden. Methods We used purposive sampling to recruit foreign-born adults who expressed being hesitant towards getting vaccinated, as well as health guides and doulas who were assigned to spread COVID-19 related information in immigrant-dense urban areas. Data were collected using semi-structured focus group interviews, which were transcribed verbatim and analysed according to systematic text condensation. Results Three focus group interviews were conducted with altogether eleven participants. One group consisted of health guides/doulas, while the participants in the other groups were gainfully employed in other jobs, or full-time students, or housewives. Four main themes emerged: (1) Language barriers and sociocultural differences, (2) Consequences of not using official Swedish information, (3) Decision-making on COVID-19 vaccination, and (4) Suggestions to improve information dissemination. The lack of information in other languages than Swedish and lack of effective information channels resulted in that most participants barely used information from official Swedish health care and public health institutions. Instead, they relied on social media, social contacts and international media, through which contradictive and negative information about the vaccine was spread. The decision to get vaccinated or not became a process fraught with insecurities about the effectiveness and side effects of the vaccine, which was balanced against wishing to be protected and to contribute to the battle against COVID-19. The participants suggested that information dissemination could be improved by producing a multilingual information outreach and to increase the use of transmission through social interaction with trusted persons and platforms. Conclusions An inadequately adapted information strategy prevented some members of the society from making fact-based decisions about getting vaccinated. Several suggestions for improving dissemination were brought forth that can be tested in future communication strategies.

Published
2024
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100. Adaption of a trigger tool to identify harmful incidents, no harm incidents, and near misses in prehospital emergency care of children

Author

Niclas Packendorff, Carl Magnusson, Christer Axelsson, and Magnus Andersson Hagiwara

Subjects
Emergency medical services, Ambulance, Patient safety, Trigger tool, Children, Harmful incidents, Special situations and conditions, RC952-1245, Medical emergencies. Critical care. Intensive care. First aid, RC86-88.9
Abstract

Abstract Background The emergency medical service (EMS) addresses all chief complaints across all ages in various contexts. Children in EMS present a particular challenge due to their unique anatomical and physical properties, which require specific training that EMS clinicians often report lacking. This combination exposes children to incidents threatening patient safety. The most common method to highlight incidents is the incident reporting system. Studies have shown underreporting of such incidents, highlighting the need for multiple methods to measure and enhance patient safety in EMS for children. Thus, the aim of this study was to modify and adapt the current Ambulance TT for road-based EMS (ATT) to a pediatric version (pATT) with a guide containing definitions of triggers. Methods The adaption of the ambulance trigger tool to a version suitable for children followed a stepwise manner, including (1) a review of previous literature to pinpoint areas of risk regarding patient safety among children in EMS. (2) Three sessions of expert panel discussions via video meetings were held to evaluate each trigger of the ATT in terms of clinical relevance, comprehensibility, language and areas of risk regarding patient safety among children in EMS. (3) Clinical use of the pATT along with Retrospective Record Review (RRR). (4) Calculation of Item-level validity index and positive predictive value (PPV) for each trigger. (5) calculate inter-rater reliability between two independent record reviewers. Results The literature search revealed 422 respective 561 articles in Cinahl and Medline where headlines and abstracts were read to identify areas posing risks to patient safety in EMS for children. During the structured discussions, one trigger was added to the existing 19 derived from the ATT, and the trigger definitions were modified to suit children. The three most common triggers identified in the 900 randomly selected records were deviation from treatment guidelines (63.9%), incomplete documentation (48.3%), and the patient is non conveyed after EMS assessment (41.1%). The positive triggers were categorized into near miss (54.6%), no harm incident (5.8%), and harmful incident (0.4%). Inter-rater reliability testing showed excellent agreement. Conclusion This study demonstrates the adaptation of an existing trigger tool (ATT) to one suitable for children. It also shows that the trigger tool, along with retrospective record review, is a feasible method to evaluate patient safety in EMS, thus complementing existing methods.

Published
2024
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