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Articles by de Groot
Force Fields and Simulation Engines: Lessons Learned from Porting Amber ff14SB and ff19SB to GROMACS
Amber’s topology preprocessor LEaP reorders atoms in improper dihedrals alphabetically by atom type. Initially introduced to speed up parameter lookup, this feature was kept afterward for compatibility and, eventually, for historical reasons. In the following, we assume that four atoms ai, aj, ak, al have types ti, tj, tk, tl, respectively. The reordering is performed lexicographically based on the atom types and is done in two steps.
Patients know best: DESTINIES Patient Panel appraisal of a novel, risk-stratified approach to COVID-19 disease surveillance in the adult immunosuppressed
Leston, Meredith, de Groot, Ingrid, Ordóñez-Mena, José M, Hobbs, F D Richard, Joy, Mark, Lee, Lennard Y W, Teh, Benjamin W, McInnes, Iain ORCID: https://orcid.org/0000-0002-6462-4280 and de Lusignan, Simon (2026) Patients know best: DESTINIES Patient Panel appraisal of a novel, risk-stratified approach to COVID-19 disease surveillance in the adult immunosuppressed.
An Offer You Can’t Refuse: Opportunities for Intraprofessional Collaboration Learning in the Workplace
Introduction The aging society has growing numbers of older patients with multimorbidity and increasing complex care needs [1]. Due to interacting comorbidities, creating personalized treatment plans often requires the perspectives of multiple specialized healthcare professionals [1, 2]. A potential risk that arises when multiple healthcare professionals are involved in a single patient’s case, is that they all create their own monodisciplinary treatment plan [3].
Computer Science > Logic in Computer Science
We study the recently introduced intuitionistic monotone modal logic IM. We first provide a semantic characterisation for a family of natural extensions of IM in terms of constructive neighbourhood models. We then present a calculus for IM and its extensions, obtained by adapting a structured calculus for the classical monotone modal logic M.
Computer Science > Computation and Language
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Intensive Multimodal Ketogenic Metabolic Therapy in Glioblastoma: A Clinical Trial
Glioblastoma (GBM), isocitrate dehydrogenase (IDH)-wildtype, has a median overall survival of 11–14 months despite standard treatment. Ketogenic metabolic interventions that lower the glucose ketone index (GKI) may improve outcomes. We evaluated the feasibility, tolerability, and potential clinical benefit of integrating standard treatment with an intensive multimodal metabolic therapy program (MTP) in newly diagnosed IDH-wildtype GBM.
AYB Türkiye Projelerine Talip Oldu
Avrupa Yatırım Bankası Başkan Yardımcısı de Groot, Türkiye Kalkınma ve Yatırım Bankası ile Türk Eximbank’a sağlanan yeşil enerji finansman anlaşmalarını değerlendirirken enerji verimliliğinin önemine dikkat çekti. Deprem bölgesindeki yeniden inşa çalışmaları hakkında gözlemlerini paylaştı. Demir yolu altyapısı gibi yeni işbirliği alanlarına da değindi. YEŞİL ENERJİ VE VERİMLİLİK ÖN PLANA ÇIKIYOR De Groot, enerji verimliliğinin jeopolitik gelişmeler nedeniyle kritik olduğunu söyledi.
Editorial: Novel insights into CAR T-cell associated neurotoxicity, volume II
The landscape of chimeric antigen receptor (CAR) T-cell therapy continues to evolve at a remarkable pace. Since the first FDA approval in 2017, the therapeutic indications for CAR T-cell products have expanded considerably across hematological neoplasms and beyond malignancies. This rapid application of CAR T-cell therapies stipulates the need of deepening the understanding, detection and management of CAR T-cell driven toxicities such as neurological complications.
SJPE “Economic Policy During and After War” Special Issue Introduction
, and . 2026. “SJPE “Economic Policy During and After War” Special Issue Introduction.” Scottish Journal of Political Economye70066. https://doi.org/10.1111/sjpe.70066. Data Availability Statement Data sharing not applicable to this article as no datasets were generated or analysed during the current study. References , , , and . 2026. “The Pressure Is on: How Geopolitical Tensions Impact Institutional Fiscal and External Stability Responses.” Scottish Journal of Political Economy: e70059.
Metadata Harvesting Tools (SoilWise-HE)
Published April 30, 2026 | Version 0.3.0 Software Open 1. ISRIC World Soil Information 2. Wageningen Environmental Research 3. ISRIC - World Soil Information The processing of the harvesters after initial fetch has been improved: Processed results are written to a temporary table. Only when all processing is finished, the published results are overwritten. While processing, any augmented metadata facts are inserted into the final result.
Foreign Exchange Regimes in (Normal Times and) Times of War: Insights From Ukraine
1 Introduction An enduring question in international economics concerns the optimal choice of exchange rate regime. The prevailing wisdom, particularly in the early 2000s, held that pegs were excessively prone to crises and that countries should either adopt hard pegs (e.g., currency unions) or allow free floats. This view implicitly assumes that the choice of exchange rate regime is a one-time decision rather than a state-contingent policy.
American Catholic Philosophical Quarterly
Volume 100, Issue 1, Winter 2026 Jean De Groot Pages 35-62 Toward a Classical Historiography of Science This paper is a prospectus for a classical historiography of science, “classical” meaning the standpoint of the physical science, mathematics, and philosophy of Greek antiquity. A classical historiography places in clearer focus the hegemony of literalist readings of modern physics.
La Compañía Neerlandesa de las Indias Occidentales y el Groot Desseyn
Ayuda Buscar en la ayuda Buscar en la ayuda La Compañía Neerlandesa de las Indias Occidentales y el Groot Desseyn Autores: Bouko de Groot Localización: Desperta Ferro: Historia moderna, ISSN 2255-0542, Nº. 81, 2026 (Ejemplar dedicado a: La jornada del Brasil 1625. La recuperación de Salvador de Bahía), págs.
A Genomically Tailored Multiagent Precision Medicine Clinical Trial for Adults with Recurrent Glioblastoma Open Access
Purpose: Existing salvage therapies for recurrent glioblastoma (rGBM) have limited efficacy, with a median survival of approximately 9 months. Given the complex molecular heterogeneity of GBM, single-target approaches have consistently failed as a treatment strategy. We conducted a phase I clinical trial to assess the feasibility, safety, and efficacy of a genomically tailored multiagent regimen in 30 adults with surgically treated rGBM.
Computer Science > Computation and Language
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Electrical Engineering and Systems Science > Audio and Speech Processing
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
Toward a Classical Historiography of Science - published on February 14, 2026
published on February 14, 2026 Jean De Groot Toward a Classical Historiography of Science This paper is a prospectus for a classical historiography of science, “classical” meaning the standpoint of the physical science, mathematics, and philosophy of Greek antiquity. A classical historiography places in clearer focus the hegemony of literalist readings of modern physics.
Exploratory Analysis of Biomarkers and Treatment Outcomes From the COLUMBUS Study in BRAF V600E/K-Mutant Advanced or Metastatic Melanoma
This open access article is distributed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license This work is licensed under a Creative Commons Attribution 4.0 International License .
Actions for sustainably scalable multi-terawatt photovoltaics
Lokale TagsFreigabegeschichteDetailsÜbersicht Freigegeben Zeitschriftenartikel Actions for sustainably scalable multi-terawatt photovoltaics Es sind keine externen Ressourcen hinterlegt Volltexte (beschränkter Zugriff) Für Ihren IP-Bereich sind aktuell keine Volltexte freigegeben. Volltexte (frei zugänglich) Es sind keine frei zugänglichen Volltexte in PuRe verfügbar Ergänzendes Material (frei zugänglich) Es sind keine frei zugänglichen Ergänzenden Materialien verfügbar Wagner, L., Peters, I.
Duality for Constructive Modal Logics: from Sahqlvist to Goldblatt-Thomason
arXiv:2601.03762 (math) View PDF HTML (experimental) Subjects: Logic (math.LO); Logic in Computer Science (cs.LO) Cite as: arXiv:2601.03762 [math.LO] (or arXiv:2601.03762v1 [math.LO] for this version) https://doi.org/10.48550/arXiv.2601.03762 Submission history From: Jim De Groot [ view email] [v1] Wed, 7 Jan 2026 09:53:59 UTC (42 KB) Bibliographic Tools Bibliographic Explorer Toggle Bibliographic Explorer () Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle...
[2512.15496] Intrinsic and relative characterization results for logics with negative modalities
arXiv:2512.15496 (math) View PDF HTML (experimental) Subjects: Logic (math.LO); Logic in Computer Science (cs.LO) Cite as: arXiv:2512.15496 [math.LO] (or arXiv:2512.15496v1 [math.LO] for this version) https://doi.org/10.48550/arXiv.2512.15496 Submission history From: Rodrigo Stefanes [ view email] [v1] Wed, 17 Dec 2025 14:41:31 UTC (39 KB) Bibliographic Tools Bibliographic Explorer Toggle Bibliographic Explorer () Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps...
[2511.17630] Can we use LLMs to bootstrap reinforcement learning? -- A case study in digital health behavior change
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
Rapid clonal selection within early hematopoietic cell compartments presages outcome to ivosidenib combination therapy
Acquired resistance to targeted, non-intensive therapies is common in myeloid malignancies. However, the kinetics of selection, the hematopoietic cell compartments where selection occurs, and the molecular mechanisms underlying selection remain open questions. To address this, we studied the kinetics of clonal and transcriptional responses to ivosidenib + venetoclax ± azacitidine combination therapy across hematopoiesis in 8 patients with IDH1-mutant myeloid malignancy.
Multiactor Modeling of Settling Decisions and Behavior in the San Mariano Watershed, the Philippines: a First Application with the MameLuke Framework
Ecology and Society: Multiactor Modeling of Settling Decisions and Behavior in the San Mariano Watershed, the Philippines: a First Application with the MameLuke Framework You must view this manuscript with a frames-capable browser
Immunogenicity Risk Assessment of Generic Teriparatide Impurities
ORIGINAL RESEARCH article Front. Immunol. Sec.
Successful twin pregnancy in a patient with lupus erythematosus on hemodialysis: a case report and literature review - BMC Nephrology
A 30-year-old woman with SLE undergoing maintenance HD for almost 2 years was referred to our hospital semi-inpatient dialysis unit, being 16 weeks pregnant, for intensification of HD and monitoring. Her SLE initially manifested 5 years earlier and was confirmed histologically 2 years after manifestation during an episode of acute renal failure due to LN class III as per the ISN/RPS classification.
Divergent trends in insect disturbance across Europe`s temperate and boreal forests
Hlásny, T., Modlinger, R., Gohli, J., Seidl, R., Krokene, P., Bernardinelli, I., Blaser, S., Brazaitis, G., Brazaitytė, G., Brockerhoff, E.
El impacto del comercio en la desigualdad de ingresos en México
Ayuda Buscar en la ayuda Buscar en la ayuda El impacto del comercio en la desigualdad de ingresos en México [1] University of Oxford Localización: Estudios económicos, ISSN 0186-7202, Vol. 40, Nº. 1 (Enero - Junio), 2025, págs.
LILRB1 and LILRB2 genomics and transcriptomics in macaque and baboon species: polymorphism, diversification, and extensive alternative splicing
ORIGINAL RESEARCH article Front. Immunol. Sec. Comparative Immunology LILRB1 and LILRB2 genomics and transcriptomics in macaque and baboon species: polymorphism, diversification, and extensive alternative splicing Provisionally accepted Biomedical Primate Research Centre (BPRC), Rijswijk, Netherlands The final, formatted version of the article will be published soon.
2025 ESC Guidelines for the management of cardiovascular disease and pregnancy: Developed by the task force on the management of cardiovascular disease and pregnancy of the European Society of Cardiology (ESC)Endorsed by the European Society of Gynecology
• None 2.1. Why we need new Guidelines on cardiovascular disease and pregnancy 8 • None 2.2. Why these Guidelines are important 8 • None 2.3. What is new 8 • None 4.4.2. Screening for congenital heart disease in the foetus 24 • None 6. Pregnancy in women with cardiomyopathies and primary arrhythmia syndromes 34 • None 8.1.5. Aortic disease with no identifiable (likely) pathogenic variant 40 • None 8.4. Aortic aneurysms other than root or ascending aorta 41 • None 9.
Hospital-based innovation labs to accelerate digital health transformation: lessons learned from twenty types of experts - BMC Digital Health
Abstract The digital transformation of healthcare is often hindered by various legal, ethical, financial, technological, and other barriers. Often, organizations already contain the expert knowledge needed to help innovators with these challenges, but highly fragmented. In an attempt to centralize this support, many major healthcare centers have established some form of innovation center or lab.
[2507.13746] Intuitionistic monotone modal logic via translation
arXiv:2507.13746 (math) View PDF Subjects: Logic (math.LO); Logic in Computer Science (cs.LO) Cite as: arXiv:2507.13746 [math.LO] (or arXiv:2507.13746v1 [math.LO] for this version) https://doi.org/10.48550/arXiv.2507.13746 Submission history From: Jim De Groot [ view email] [v1] Fri, 18 Jul 2025 08:48:52 UTC (41 KB) Bibliographic Tools Bibliographic Explorer Toggle Bibliographic Explorer () Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is...
Competing axes of power in the global plastics treaty: understanding the politics of progress and setbacks in negotiating a high-ambition agreement
Dauvergne, P. et al. (2025) Competing axes of power in the global plastics treaty: understanding the politics of progress and setbacks in negotiating a high-ambition agreement. Marine Policy, 181, 106820. (doi: 10.1016/j.marpol.2025.106820) Text 359538.pdf - Published Version Available under License Creative Commons Attribution. 621kB Abstract Headlines in December 2024 proclaimed the “collapse” and “failure” of United Nations plastics treaty negotia- tions in Busan, South Korea.
Competing axes of power in the global plastics treaty: Understanding the politics of progress and setbacks in negotiating a high-ambition agreement
journal contribution posted on 2025-07-11, 04:39 authored by Peter Dauvergne, Jen Iris Allan, Simon Beaudoin, Bethanie Carney Almroth, Jennifer Clapp, Emily Cowan, Babet de GrootBabet de Groot, Trisia Farrelly, Natalia de Miranda Grilli, Alice Mah, Elizabeth Mendenhall, Rosetta Paik, Rob Ralston, Peter Stoett, Aleke Stöfen-O’Brien, Jack Taggart, Rachel Tiller, Patricia Villarrubia-Gómez, Joanna Vince Headlines in December 2024 proclaimed the “collapse” and “failure” of United Nations plastics...
[2507.08411] A Dissipativity Framework for Constructing Scaled Graphs
arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
Resectability stages of pancreatic cancer: nationwide reference
At diagnosis, pancreatic adenocarcinoma is categorized into resectability stages based on extent of vascular involvement and presence of metastases at cross-sectional imaging1,2. However, reliable population-based data regarding the distribution of these stages is lacking. This influences our perspective on this disease.
Towards a theory of ‘Big plastic’
journal contribution posted on 2025-06-23, 01:27 authored by Babet de GrootBabet de Groot, Robert MacNeil This paper aims to shed light on the nature of the plastic industry’s political power by developing the concept of Big Plastic.
[2505.12091] Discrete Time Credit-Based Shaping for Time-Sensitive Applications in 5G/6G Networks
Work on one of the world's most important websites and make an impact on open science.
Gabapentinoids confer survival benefit in human glioblastoma - Nature Communications
Abstract Neuronal-glioma interactions are increasingly recognized as critical in the development and progression of central nervous system tumors. Recent research highlights that gliomas can integrate into neural circuits through various mechanisms, including the synaptogenic factor thrombospondin-1 (TSP-1). This new mechanistic understanding of cancer neuroscience allows for novel insights into target discovery.
The DESTINIES Study: an online Delphi study to build international consensus on the medical conditions and procedures that confer immunosuppression and their respective COVID-19 risk profiles
Leston, M. et al. (2025) The DESTINIES Study: an online Delphi study to build international consensus on the medical conditions and procedures that confer immunosuppression and their respective COVID-19 risk profiles. eClinicalMedicine, 83, 103239. (doi: 10.1016/j.eclinm.2025.103239) (PMID:40453534) (PMCID:PMC12124667) Text 355622.pdf - Published Version Available under License Creative Commons Attribution.
Estimation of Absolute Binding Free Energies for Drugs That Bind Multiple Proteins
Introduction Click to copy section linkSection link copied! The protein–ligand binding free energy (formally, Gibbs energy of binding) is the single most desired property to accurately calculate within the field of computer-aided drug design (CADD). In most cases, computational and medicinal chemists are interested in relative binding free energies (RBFE), i.e., in energies that are calculated when comparing multiple molecules with the same scaffold binding to the same target protein.
Future directions for early career researchers in planetary health equity
journal contribution posted on 2025-03-20, 03:35 authored by Megan Arthur, Charlotte Godziewski, Katherine Sievert, Sarah Boddington, Amy Carrad, Giorgia Dalla Libera Marchiori, Babet de GrootBabet de Groot, Carlos Faerron Guzman, Nicholas Frank, Hridesh Gajurel, James Hasler-Bail, Edward Jegasothy, Francis Nona, Damilola Oluwemimo, Sandra Samantela, Alexandre San Martim Portes, Annabelle Workman Achieving social and health equity on a healthy planet requires attending to the structural...
Exploring the genetic mechanisms driving KIR diversification
Natural killer (NK) cells are lymphocytes that contribute to the early response during infection or tumor formation.
Comparison of estimated glomerular filtration rate equations on prediction of mortality, kidney failure, and acute kidney injury
The CKD-EPI 2009 estimated glomerular filtration rate (eGFR) equation has shown substantial overestimation of GFR in Europeans, hence new equations have been developed. We examined the effect of introducing the European Kidney Function Consortium (EKFC) or Lund-Malmö revised (LMR) eGFR equations on KDIGO eGFR-category classification in a large cohort.
The Effect of Fostering a Growth Mindset in Primary School Children: Does Intervention Approach Matter?
1. Introduction From the perspective of the implicit theory of intelligence, also known as growth mindset theory (Dweck & Leggett, 1988; Dweck, 2000), students hold different beliefs about their intelligence and abilities.
Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water
Introduction Click to copy section linkSection link copied! Molecular dynamics (MD) is a robust tool for unraveling the structure and dynamics of proteins, which is often crucial to understanding their biological functions. The reliability of MD predictions, however, depends on the accuracy of the underlying MD force field, which is determined by a complex set of interactions within and among proteins, within and among solvent molecules, and between solvent and protein molecules.
Societies at risk: the correlation between intensity of armed conflict and child health during the civil war in South Sudan - Archives of Public Health
The study highlights the intricate and complex relationship between armed conflict and child health. Through a panel data analysis, we sought to quantify the direct effects of conflict-related incidents on these health metrics. Our results showed significant positive correlation between high estimate of conflict intensity, food prices, and displacement with GAM, however, the best estimate of conflict intensity didn’t show any significant difference with the research variables.
Nationwide implementation of the international multidisciplinary best-practice for locally advanced pancreatic cancer (PREOPANC-4): study protocol - BMC Cancer
This study protocol is reported following the 2013 Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) guideline. See Appendix 1 for the SPIRIT checklist [24]. Study design The PREOPANC-4 training phase started in 2021 after which the 3-year implementation will take place from January 2022 until December 2024, followed by a follow-up of 5 years until December 2029.
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