tbuckley/cabot-search huggingface dataset:
Public health in Germany: structures, dynamics, and ways forward
Authors: Hajo Zeeb, Julika Loss, Dagmar Starke, Thomas Altgeld, Susanne Moebus, Karin Geffert, Ansgar Gerhardus
Journal: The Lancet Public Health (2025)

Despite Germany's robust economy, comprehensive social welfare system, and the country ranking third among Organisation for Economic Co-operation and Development countries in terms of per-capita health spending, its health indicators still lag behind those of other European nations. Germany also has one of the highest prevalences of major modifiable risk factors for non-communicable diseases within the EU. This Health Policy provides an overview of the development, structures, and actors in public health in Germany, highlighting possible explanations for the country's underperforming health indicators and suggesting a way forward. This Health Policy is structured along the essential public health operations. We identify the absence of a strong central institution for public health, inadequate funding for disease prevention and health promotion, and little interoperability in data collection as major challenges. The country's decentralised governance structure allows flexibility, especially at the community level, but leads to scattered responsibilities and little coordination between sectors. We also note the absence of a public health strategy. The current system's focus on curative care and individualised medicine has led to a neglect of disease prevention and health promotion. Furthermore, the country's strong economic interests and powerful lobbies have hindered the implementation of effective public health policies. To address these challenges, we recommend developing a public health identity, creating a comprehensive public health strategy, fostering a culture of health promotion and disease prevention that encompasses all areas and does not shy away from tackling the commercial determinants of health, and strengthening the connection between medicine, public health practice, and research.
Abortion care in Alberta, Canada, from 2012 to 2023: a population-based, cross-sectional analysis of use and geographical access
Authors: Erin A Brennand, Beili Huang, Natalie V Scime, Jadine Paw, Erin L Nelson
Journal: The Lancet Public Health (2025)

Equitable access to abortion care remains a challenge in public health. Current Canadian abortion reporting overlooks modern practices such as mifepristone medication abortion and has no access and equity metrics. We aimed to comprehensively analyse abortion care provision in Alberta (the fourth largest province in Canada, home to more than 4 million people) focusing on temporal trends in annual abortion rates and access disparities. In this population-based, repeated cross-sectional study using linked administrative databases (Practitioner Claims, Discharge Abstract Database, National Ambulatory Care Reporting System, and Pharmaceutical Information Network) in Alberta, Canada, we examined abortion use across the province over a 10-year period. Our data included all females of reproductive age (12-49 years) who received abortion care from Jan 1, 2012, to June 30, 2023. The primary outcome was abortion rate, calculated as the annual number of abortions per 1000 females of reproductive age (15-49 years), trimming data for those younger than 15 years. We descriptively analysed abortions (procedural, medication, and induction of labour) using temporal and geospatial analysis by Alberta's five geographical zones and 35 subzones. During the study period, 130 755 abortions occurred in Alberta, of which 120 326 (92·0%) were procedural (118 063 [98·1%] of 120 326 first trimester; 2263 [1·9%] second trimester), 7395 (5·7%) were medication abortions, and 3034 (2·3%) were induction of labour. Abortion declined steadily between 2012 and 2023, with a change of -0·42 abortions per 1000 reproductive-aged females per year (95% CI -0·49 to -0·36). Medication abortion increased following the introduction of mifepristone and comprised 1489 (13·8%) of 10 765 abortions by 2022. Nearly all (8440 [99·7%] of 8462) procedural abortions in 2022 were provided in Edmonton and Calgary. 14 882 (11·5%) of 129 527 individuals accessing abortion in Alberta travelled more than 3 h from home to receive care; 18 864 (14·6%) travelled more than 200 km. Our findings suggest that annual rates of abortion in Alberta are declining; however, overall access to abortion care has minimally improved in the past decade. Abortion in Alberta remains highly procedural and concentrated in Alberta's two major cities, resulting in poor access outside metropolitan centres. Mismatch between use of abortion care and local provision of care results in substantial travel. Policy should focus on expansion of patient-preferred, evidence-based medication abortion services. Canadian Institutes of Health Research; Women and Gender Equality Canada.
Antimicrobials in serious illness and end-of-life care: lifting the veil of silence
Authors: William E Rosa, Shila Pandey, Renee Wisniewski, Craig Blinderman, Mark Wing Loong Cheong, Juan Esteban Correa-Morales, Diego Alejandro Cubides-Diaz, Sharif Folorunso, Nahla Gafer, Mohja Marhoom, Tiffanny Newman, Christian Ntizimira, Temitope Oyewole Obadare, Cihan Papan, Pedro Emilio Pérez-Cruz, Lukas Radbruch, Giri Shan Rajahram, Tomás Alejandro Reyes-Barros, Naveen Salins, Kavitha Saravu, Donald R Sullivan, Edward Christopher Dee
Journal: The Lancet Infectious Diseases (2025)
Global paediatric haematopoietic stem-cell transplantation training and access: providing strategies to overcome challenges
Authors: Candice Laverne Hendricks, Manuela Spadea, Justin Rudolph Du Toit, Carmelo Gurnari, Rafaella Muratori, Valentine Jimenez, Vera Radici, Sheila Torrado, Nihar Desai, Azada Ibrahimova, Ibrahim N Muhsen, Julio Ropero, Nico Gagelmann, Claire Horgan
Journal: The Lancet Haematology (2025)
Multisystem lymphomatoid granulomatosis in an immunocompetent woman
Authors: Laura Nayeli Tecayehuatl-Negrete, Ana Lilia Peralta-Amaro, Karla Alejandra Romero-Cuevas, José Emmanuel Zúñiga-Espinosa, Roberto Alfredo Ibarra-Ponce de León
Journal: The Lancet Haematology (2025)
Ask, do not tell: consulting a patient advisory board to understand unmet needs of patients with GVHD in Europe
Authors: Hélène Schoemans, Elke Stienissen, Kathy Goris, Susan K Stewart, Meredith Cowden, Kristina Arnahoutova, Steven Z Pavletic, Hildegard Greinix, Anna Barata, Lorna Warwick, Natacha Bolanos, Isabel Barbosa, Guy Bouguet, Isabelle Lhenry-Yvon, Riikka-Leena Manninen, Simona Pavukova, Guy Tavori, Marleen van Amerongen, Anita Lawitschka, Kirk R Schultz, Daniel Wolff, Anne Herrmann
Journal: The Lancet Haematology (2025)
Proceedings of the National Cancer Institute Workshop on combining immunotherapy with radiotherapy: challenges and opportunities for clinical translation
Authors: Zachary S Morris, Sandra Demaria, Arta M Monjazeb, Silvia C Formenti, Ralph R Weichselbaum, James Welsh, Heiko Enderling, Jonathan D Schoenfeld, Joshua D Brody, Heather M McGee, Michele Mondini, Michael S Kent, Kristina H Young, Lorenzo Galluzzi, Sana D Karam, Willemijn S M E Theelen, Joe Y Chang, Mai Anh Huynh, Adi Daib, Sean Pitroda, Caroline Chung, Raphael Serre, Clemens Grassberger, Jie Deng, Quaovi H Sodji, Anthony T Nguyen, Ravi B Patel, Simone Krebs, Anusha Kalbasi, Caroline Kerr, Claire Vanpouille-Box, Logan Vick, Todd A Aguilera, Irene M Ong, Fernanda Herrera, Hari Menon, DeeDee Smart, Jalal Ahmed, Robyn D Gartrell, Christina L Roland, Fatemeh Fekrmandi, Binita Chakraborty, Eric H Bent, Tracy J Berg, Alan Hutson, Samir Khleif, Andrew G Sikora, Lawrence Fong
Journal: The Lancet Oncology (2025)
Timing of nivolumab with neoadjuvant carboplatin and paclitaxel for early triple-negative breast cancer (BCT1902/IBCSG 61–20; Neo-N): a non-comparative, open-label, randomised, phase 2 trial
Authors: Nicholas Zdenkowski, Marion J J Kuper-Hommel, Samuel M Niman, Prudence A Francis, Sally Baron-Hay, William Fox, Alexander M Menzies, Rebecca Angus, Kevin Punie, Sarah Zardawi, Meredith M Regan, Sherene Loi
Journal: The Lancet Oncology (2025)
Activity and safety of atezolizumab plus carboplatin and paclitaxel in patients with advanced or recurrent thymic carcinoma (MARBLE): a multicentre, single-arm, phase 2 trial
Authors: Takehito Shukuya, Tetsuhiko Asao, Yasushi Goto, Tomoyasu Mimori, Koichi Takayama, Kyoichi Kaira, Hiroshi Tanaka, Ryo Ko, Yoshihiro Amano, Motoko Tachihara, Takuji Suzuki, Junko Tanizaki, Shunichi Sugawara, Yoshitaka Zenke, Yukina Shirai, Takuo Hayashi, Keita Mori, Kazuhisa Takahashi
Journal: The Lancet Oncology (2025)
Active surveillance of cervical intraepithelial neoplasia grade 2: 2025 British Society of Colposcopy and Cervical Pathology and European Society of Gynaecologic Oncology consensus statement
Authors: Maria Kyrgiou, Sarah J Bowden, Laura Burney Ellis, Anne Hammer, Deirdre Lyons, Theresa Freeman-Wang, Konstantinos S Kechagias, Ilkka Kalliala, Mario Preti, Vesna Kesic, Ignacio Zapardiel, Margaret Cruickshank, Murat Gultekin, Pierre Martin-Hirsch
Journal: The Lancet Oncology (2025)
Cancer surveillance in the Eastern Mediterranean region: a 10-year International Agency for Research on Cancer–WHO Regional Office for the Eastern Mediterranean collaboration
Authors: Ariana Znaor, Heba Fouad, Mariam Zahwe, Sultan Eser, Ibtihal Fadhil, Isabelle Soerjomataram, Asmus Hammerich, Freddie Bray
Journal: The Lancet Oncology (2025)
ADT with SBRT versus SBRT alone for hormone-sensitive oligorecurrent prostate cancer (RADIOSA): a randomised, open-label, phase 2 clinical trial
Authors: Giulia Marvaso, Giulia Corrao, Mattia Zaffaroni, Maria Giulia Vincini, Chiara Lorubbio, Sara Gandini, Cristiana Fodor, Sofia Netti, Dario Zerini, Stefano Luzzago, Francesco Alessandro Mistretta, Konstantinos Venetis, Giulia Cursano, Tiziana Burla, Ketti Mazzocco, Federica Cattani, Giuseppe Petralia, Nicola Fusco, Gabriella Pravettoni, Gennaro Musi, Ottavio De Cobelli, Chad Tang, Piet Ost, David A Palma, Roberto Orecchia, Barbara Alicja Jereczek-Fossa
Journal: The Lancet Oncology (2025)
Atosiban versus placebo for threatened preterm birth (APOSTEL 8): a multicentre, randomised controlled trial
Authors: Larissa I van der Windt, Job Klumper, Ruben G Duijnhoven, Marjolein Kok, Carrie Ris-Stalpers, Marjon A de Boer, Anton H van Kaam, Eva Pajkrt, Ben W Mol, Kate F Walker, Fionnuala M McAuliffe, Joris A van der Post, Carolien Roos, Martijn A Oudijk, Jelle M Schaaf, Jim van Eyck, H Marieke Knol, Marieke Sueters, Liesbeth H C J Scheepers, David P van der Ham, Judith O E H van Laar, Eline S A van den Akker, Ralph R Scholten, Nicolette van Gemund, Karlijn C Vollebregt, Harrie Visser, Sanne J Gordijn, Mireille N Bekker, Josje Langenveld
Journal: The Lancet (2025)
One-Hour Oral Glucose Tolerance Test for the Postpartum Reclassification of Women With Hyperglycemia in Pregnancy
Authors: Ravi Retnakaran, Chang Ye, Caroline K. Kramer, Anthony J. Hanley, Philip W. Connelly, Mathew Sermer, Bernard Zinman
Journal: Diabetes Care (2025)

The International Diabetes Federation recently endorsed a 1-h oral glucose tolerance test (OGTT) as more convenient than the conventional 2-h OGTT. In practice, women with hyperglycemia in pregnancy are advised to undergo a 2-h OGTT within 6 months after delivery, but this test is often not completed, partly owing to its inconvenience for busy mothers. Recognizing the potential advantage of the 1-h OGTT in this setting, we sought to compare 1-h and 2-h OGTT glucose measurements at 3 months postpartum as predictors of dysglycemia (prediabetes/diabetes) over the first 5 years postpartum. A total of 369 women across a range of glucose tolerance in pregnancy (from normoglycemia to gestational diabetes [GDM]) underwent multisample 2-h 75-g OGTTs at 3 months, 1 year, 3 years, and 5 years postpartum. Glucose measurements from the 3-month OGTT were ranked as predictors of dysglycemia (both criteria) by change in concordance index (CCI) of Cox proportional hazard regression models. At the 3-month OGTT, 1-h glucose identified all but 10 of 70 women concurrently diagnosed with dysglycemia by 2-h glucose, while diagnosing an additional 96 women. The cumulative incidence of dysglycemia progressively increased over 5 years by tertile of 1-h glucose on the 3-month OGTT (P < 0.0001). On regression analyses, the strongest predictor of dysglycemia was 1-h glucose (change in CCI: 16.1%), followed by 2-h glucose (14.9%). In women with GDM, 1-h glucose again emerged as strongest predictor of dysglycemia (13.0%), followed by 2-h glucose (12.8%). The 1-h OGTT may offer a strategy for increasing rates of postpartum reclassification following hyperglycemia in pregnancy.
Author Correction: Bullous pemphigoid
Authors: Hossein Akbarialiabad, Enno Schmidt, Aikaterini Patsatsi, Yen Loo Lim, Anisa Mosam, Kaisa Tasanen, Jun Yamagami, Maryam Daneshpazhooh, Dipankar De, Adela Rambi G. Cardones, Pascal Joly, Dedee F. Murrell
Journal: Nature Reviews Disease Primers (2025)
Decoding subcellular RNA localization one molecule at a time
Authors: Josep Biayna, Gabrijela Dumbović
Journal: Genome biology (2025)

Abstract Eukaryotic cells are highly structured and composed of multiple membrane-bound and membraneless organelles. Subcellular RNA localization is a critical regulator of RNA function, influencing various biological processes. At any given moment, RNAs must accurately navigate the three-dimensional subcellular environment to ensure proper localization and function, governed by numerous factors, including splicing, RNA stability, modifications, and localizing sequences. Aberrant RNA localization can contribute to the development of numerous diseases. Here, we explore diverse RNA localization mechanisms and summarize advancements in methods for determining subcellular RNA localization, highlighting imaging techniques transforming our ability to study RNA dynamics at the single-molecule level.
Myeloid neoplasms with MYC-positive double minutes: towards recognition as a distinct entity
Authors: Isolde Summerer, Wencke Walter, Manja Meggendorfer, Torsten Haferlach, Frank Dicker, Stephan Hutter, Niroshan Nadarajah, Anna Stengel, Constanze Kuehn, Wolfgang Kern, John M. Bennett, Claudia Haferlach, Christian Pohlkamp
Journal: Blood Cancer Journal (2025)
Sleep spindles as a predictor of cognitive motor dissociation and recovery of consciousness after acute brain injury
Authors: Elizabeth E. Carroll, Qi Shen, Vedant Kansara, Nicole Casson, Andrew Michalak, Itamar Niesvizky-Kogan, Jaehyung Lim, Amy Postelnik, Matthew J. Viereck, Satoshi Egawa, Joshua Kahan, Jerina C. Carmona, Lucie Kruger, You Lim Song, Angela Velazquez, Catherine A. Schevon, E. Sander Connolly, Shivani Ghoshal, Sachin Agarwal, David Roh, Soojin Park, Paul Kent, Jan Claassen
Journal: Nature Medicine (2025)
Task-sharing and telemedicine delivery of psychotherapy to treat perinatal depression: a pragmatic, noninferiority randomized trial
Authors: Daisy R. Singla, Richard K. Silver, Simone N. Vigod, Nour Schoueri-Mychasiw, J. Jo Kim, Laura M. La Porte, Paula Ravitz, Crystal E. Schiller, Andrea S. Lawson, Alex Kiss, Steven D. Hollon, Cindy-Lee Dennis, Tara S. Berenbaum, Holly A. Krohn, Jamie E. Gibori, Jaime Charlebois, David M. Clark, Ariel K. Dalfen, Wendy Davis, Bradley N. Gaynes, Molyn Leszcz, Sarah Rachel Katz, Kellie E. Murphy, John A. Naslund, Mae Lynn Reyes-Rodríguez, Alison M. Stuebe, Claire Zlobin, Benoit H. Mulsant, Vikram Patel, Samantha Meltzer-Brody
Journal: Nature Medicine (2025)
Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing
Authors: Jack Humphrey, Erica Brophy, Roman Kosoy, Biao Zeng, Elena Coccia, Daniele Mattei, Ashvin Ravi, Tatsuhiko Naito, Anastasia G. Efthymiou, Elisa Navarro, Claudia De Sanctis, Victoria Flores-Almazan, Benjamin Z. Muller, Gijsje J. L. J. Snijders, Amanda Allan, Alexandra Münch, Reta Birhanu Kitata, Steven P. Kleopoulos, Stathis Argyriou, Periklis Malakates, Konstantina Psychogyiou, Zhiping Shao, Nancy Francoeur, Chia-Feng Tsai, Marina A. Gritsenko, Matthew E. Monroe, Vanessa L. Paurus, Karl K. Weitz, Tujin Shi, Robert Sebra, Tao Liu, Lot D. de Witte, Alison M. Goate, David A. Bennett, Vahram Haroutunian, Gabriel E. Hoffman, John F. Fullard, Panos Roussos, Towfique Raj
Journal: Nature Genetics (2025)
CLEC16A in astrocytes promotes mitophagy and limits pathology in a multiple sclerosis mouse model
Authors: Atsushi Kadowaki, Michael A. Wheeler, Zhaorong Li, Brian M. Andersen, Hong-Gyun Lee, Tomer Illouz, Joon-Hyuk Lee, Alain Ndayisaba, Stephanie E. J. Zandee, Himanish Basu, Chun-Cheih Chao, Joao V. Mahler, Wendy Klement, Dylan Neel, Matthew Bergstresser, Veit Rothhammer, Gabriel Lipof, Lena Srun, Scott A. Soleimanpour, Isaac Chiu, Alexandre Prat, Vikram Khurana, Francisco J. Quintana
Journal: Nature Neuroscience (2025)
A first-in-human study of quantitative ultrasound to assess transplant kidney fibrosis
Authors: Eno Hysi, Jihye Baek, Alexander Koven, Xiaolin He, Luisa Ulloa Severino, Yiting Wu, Kendrix Kek, Shukai Huang, Adriana Krizova, Monica Farcas, Michael Ordon, Kai-Ho Fok, Robert Stewart, Kenneth T. Pace, Michael C. Kolios, Kevin J. Parker, Darren A. Yuen
Journal: Nature Medicine (2025)
The transcriptomic architecture of common cancers reflects synthetic lethal interactions
Authors: Syed Haider, Rachel Brough, Santiago Madera, Jacopo Iacovacci, Aditi Gulati, Andrew Wicks, John Alexander, Stephen J. Pettitt, Andrew N. J. Tutt, Christopher J. Lord
Journal: Nature Genetics (2025)

To maintain cell fitness, deleterious genetic alterations are buffered by compensatory changes in additional genes. In cancer, buffering processes could be targeted by synthetic lethality. However, despite the large-scale identification of synthetic lethal effects in preclinical models, evidence that these operate clinically is limited. This impedes the application of synthetic lethal approaches. By integrating molecular profiling data from >9,000 cancers with synthetic lethal screens, we show that transcriptomic buffering of tumor suppressor gene (TSG) loss by hyperexpression of synthetic lethal partners is a common phenomenon, extending to multiple TSGs and histotypes. Transcriptomic buffering is also notable in cancers that phenocopy TSG loss, such as BRCAness cancers, where expression of BRCA1/2 synthetic lethal genes correlates with clinical outcome. Synthetic lethal genes that exhibit transcriptomic buffering also represent more robust synthetic lethal effects. These observations have implications for understanding how tumor cells tolerate TSG loss, in part explain transcriptomic architectures in cancer and provide insight into target selection. Tumor cells upregulate compensatory buffering genes following tumor suppressor loss. These genes may represent new synthetic lethal partners that could be harnessed therapeutically.
The Federated European Genome–Phenome Archive as a global network for sharing human genomics data
Authors: Teresa D’Altri, Mallory Ann Freeberg, Amy J. Curwin, Ana Alonso, Ana T. Freitas, Salvador Capella-Gutierrez, Luiz Gadelha, Anna Hagwall, Eivind Hovig, Giselle Kerry, Koray Kirli, Krzysztof Kochel, Oliver Kohlbacher, Jan O. Korbel, Jaakko Leinonen, Blazej Marciniak, Jorge S. Oliveira, Kjell Petersen, Mário J. Silva, Oliver Stegle, Alfonso Valencia, Johan Viklund, Roderic Guigo, Helen Parkinson, Arcadi Navarro, Jordi Rambla, Thomas M. Keane
Journal: Nature Genetics (2025)
Intestinal Microbiota Contributes to the Development of Cardiovascular Inflammation and Vasculitis in Mice
Authors: Prasant K. Jena, Daiko Wakita, Angela C. Gomez, Thacyana T. Carvalho, Asli E. Atici, Emily Aubuchon, Meena Narayanan, Youngho Lee, Michael C. Fishbein, Yoshihiro Takasato, Yosuke Kurashima, Hiroshi Kiyono, Patrice D. Cani, Willem M. de Vos, David M. Underhill, Suzanne Devkota, Shuang Chen, Kenichi Shimada, Timothy R. Crother, Moshe Arditi, Magali Noval Rivas
Journal: Circulation Research (2025)

BACKGROUND: Alterations in the intestinal microbiota contribute to the pathogenesis of various cardiovascular disorders, but how they affect the development of Kawasaki disease, an acute pediatric vasculitis, remains unclear. Here, using a murine model mimicking Kawasaki disease vasculitis, we assessed the contribution of the intestinal microbiota to the development of vascular inflammation. METHODS AND RESULTS: We report that depleting the gut microbiota reduces the development of cardiovascular inflammation in a murine model mimicking Kawasaki disease vasculitis. The development of cardiovascular lesions was associated with alterations in the intestinal microbiota composition and, notably, a decreased abundance of Akkermansia muciniphila and Faecalibacterium prausnitzii . Oral supplementation with either of these live or pasteurized individual bacteria or with short-chain fatty acids produced by them attenuated cardiovascular inflammation, as reflected by decreased local immune cell infiltrations. Treatment with Amuc_1100, the TLR-2 signaling outer membrane protein from Akkermansia muciniphila , also reduced the severity of vascular inflammation. CONCLUSIONS: This study reveals an underappreciated gut microbiota-cardiovascular inflammation axis in Kawasaki disease vasculitis pathogenesis and identifies specific intestinal commensals that regulate vasculitis in mice by producing metabolites or via extracellular proteins capable of enhancing and supporting gut barrier function.
A western dietary pattern during pregnancy is associated with neurodevelopmental disorders in childhood and adolescence
Authors: David Horner, Jens Richardt M. Jepsen, Bo Chawes, Kristina Aagaard, Julie B. Rosenberg, Parisa Mohammadzadeh, Astrid Sevelsted, Nilo Vahman, Rebecca Vinding, Birgitte Fagerlund, Christos Pantelis, Niels Bilenberg, Casper-Emil T. Pedersen, Anders Eliasen, Sarah Brandt, Yulu Chen, Nicole Prince, Su H. Chu, Rachel S. Kelly, Jessica Lasky-Su, Thorhallur I. Halldorsson, Marin Strøm, Katrine Strandberg-Larsen, Sjurdur F. Olsen, Birte Y. Glenthøj, Klaus Bønnelykke, Bjørn H. Ebdrup, Jakob Stokholm, Morten Arendt Rasmussen
Journal: Nature Metabolism (2025)
Assessing and alleviating state anxiety in large language models
Authors: Ziv Ben-Zion, Kristin Witte, Akshay K. Jagadish, Or Duek, Ilan Harpaz-Rotem, Marie-Christine Khorsandian, Achim Burrer, Erich Seifritz, Philipp Homan, Eric Schulz, Tobias R. Spiller
Journal: npj Digital Medicine (2025)
The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars
Authors: Ryoichi Yano, Feng Li, Susumu Hiraga, Ryoma Takeshima, Michie Kobayashi, Kyoko Toda, Yosuke Umehara, Hiromi Kajiya-Kanegae, Hiroyoshi Iwata, Akito Kaga, Masao Ishimoto
Journal: Nature Genetics (2025)

Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we constructed 11 nanopore-based genome references for Japanese and other soybean lines. Our assembly-based comparative method, designated 'Asm2sv', identified gene-level SVs comprehensively, enabling pangenome analysis of 462 worldwide cultivars and varieties. Based on these, we identified selective sweeps between Japanese and US soybeans, one of which was the pod-shattering resistance gene PDH1. Genome-wide association studies further identified several quantitative trait loci that accounted for large-seed phenotypes of Japanese soybean lines, some of which were also close to regions of the selective sweeps, including PDH1. Notably, specific combinations of alleles, including SVs, were found to increase the seed size of some Japanese landraces. In addition to the differences in cultivation environments, distinct food processing usages might result in changes in Japanese soybean genomes. Long-read genome assemblies for seven Japanese, three North American and one primitive Glycine max cultivars highlight gene-level structural variation underlying distinct seed morphology phenotypes.