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Predicting homologous recombination deficiency and treatment responses using a computed tomography-based foundation model: a preclinical study
No full textHomologous recombination deficiency (HRD) can lead to genomic instability, increased cancer susceptibility, and enhanced sensitivity to DNA-targeting therapies. Although radiomics has been used for various medical applications, its application in animal studies remains largely unexplored, primarily due to the typically limited availability of preclinical data. In this study, we applied a state-of-the-art foundation model (FM) on preclinical computed tomography (CT) images in mice, aiming to: (i) distinguish HRD status within isogenic xenografts, and (ii) predict differential therapeutic responses of CP-506, a novel hypoxia-activated DNA-crosslinking agent. The dataset comprises micro-CT scans of 307 mice with balanced HRD status, collected both before and after CP-506 or control treatment. The FM demonstrated robust HRD classification performance, achieving an AUC of 0.88 on the test set, which significantly outperformed the handcrafted radiomics and supervised deep learning (sDL). The highest AUC (0.93) was achieved in the consensus subgroup (71%) between sDL and FM. Additionally, HRD-related features predicted DNA damage and growth delay following the treatment. Interpretability analysis indicated the important role of texture heterogeneity in HRD classification. Therefore, these results suggest that FM successfully overcomes the data scarcity in animal studies and enables HRD classification and treatment response prediction from preclinical CT imaging
Accelerating atomic fine structure determination with graph reinforcement learning
No full textAbstract
Atomic data determined by analysis of observed atomic spectra are essential for plasma diagnostics. For each low-ionisation open d- and f-subshell atomic species, around 10
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fine structure energy levels can be determined through years of analysis of 10
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observable spectral lines. We propose a partial automation of this task by casting the analysis procedure as a Markov decision process and solving it by graph reinforcement learning using reward functions partly learned on historical human decisions. In our evaluations on existing spectral line lists and theoretical calculations for Co II, Nd II and Nd III, hundreds of energy levels were identified and determined in hours, agreeing with published values in 95% of cases for Co II and 54–87% for Nd II and Nd III. As the current efficiency in atomic fine structure determination struggles to meet growing atomic data demands, our artificial intelligence approach sets the stage for closing this gap
Healthcare Workers' Acceptance and Willingness to Implement a Pragmatic Triple‐Component Enhanced Recovery After Surgery Strategy (T‐ERAS): A Cross‐Sectional Study in Ethiopian Public Hospitals
No full textBackground: Enhanced recovery after surgery (ERAS) protocols have demonstrated substantial benefits in improving postoperative outcomes. However, in low‐resource settings such as Ethiopia, ERAS adoption remains limited, necessitating pragmatic context‐sensitive implementation approaches. The perspectives of frontline perioperative providers who are central to implementation have rarely been systematically assessed. This study aimed to evaluate acceptance, perceived benefits, implementation challenges, and readiness for sustained adoption of a pragmatic triple enhanced recovery after surgery (T‐ERAS) protocol, comprising early oral intake, early ambulation, and early urinary catheter removal, among healthcare workers participating in a multisite ERAS trial in Ethiopia. Methods: A descriptive cross‐sectional survey was conducted among 20 perioperative care providers, including surgeons, obstetricians, anesthetists, and nurses, from five public hospitals involved in the ERAS implementation trial. A structured questionnaire administered via Google Forms captured demographic characteristics, ERAS knowledge and exposure, perceived benefits and challenges, and willingness to adopt ERAS practices. Data were analyzed using descriptive statistics and thematic summaries. Results: Twenty perioperative care providers participated, of whom 13 (65.0%) were male, and 15 (75.0%) were affiliated with tertiary‐level public hospitals. Twelve respondents (60.0%) reported being very familiar with ERAS protocols, although only 11 (55.0%) had directly participated in implementation. Sixteen participants (80.0%) believed ERAS improves patient outcomes; however, adherence varied, with 8 (42.1%) reporting rarely applying the protocol. Key implementation challenges included limited resources (85.0%), insufficient staff training (70.0%), resistance to change (50.0%), and inadequate patient education (50.0%). Despite these barriers, 17 participants (85.0%) expressed willingness to adopt ERAS practices permanently, and all (100.0%) were open to further training. The T‐ERAS components were viewed favorably, with 15 participants (75.0%) rating each as effective. Conclusion: This study demonstrates high awareness and willingness among perioperative professionals in Ethiopian public hospitals to adopt ERAS principles, while highlighting persistent system‐level barriers to consistent implementation. Strengthening institutional support, expanding training, and promoting locally led context‐sensitive ERAS pathways such as T‐ERAS may facilitate sustainable scale‐up in low‐resource settings
Toward cardiac electrophysiology digital twins with an efficient open source scalable solver on GPU clusters
No full textModelling and simulation are essential in biomedicine, and specifically in computational cardiology. Reliable, efficient and accurate solvers are critical. This study presents an open-source, GPU-based cardiac electrophysiology solver for scalable multiscale simulations (monoalg3d), incorporating conduction system calibration and performance optimization. The solver employs the monodomain equation coupled with the Purkinje network, solved via the finite volume method, featuring a GPU-based linear solver and concurrent simulation dispatch with MPI. We demonstrate a speedup over a CPU-based solution and scalability by running 512 simulations on 128 compute nodes. Coarse and fine biventricular mesh simulations with 855, 670 and 6, 845, 360 control volumes are completed in less than 24 min and 303 min, respectively, considering a single beat and a human-based ventricular cellular model with 43 state variables. The proposed open-source solver enhances computational efficiency and physiological fidelity through Purkinje-muscle-junction calibration, enabling large-scale, high-speed cardiac simulations including the conduction system. This work marks a significant step toward fast and scalable cardiac simulations on GPU architectures by providing execution of concurrent simulations with the novel MPI batch feature and calibration of Purkinje coupling parameters, paving the way for integration into a Digital Twin personalisation pipeline, including the conduction system
New algorithms and hardness results for robust satisfiability of (promise) CSPs
No full textIn this paper, we continue the study of robust satisfiability of promise CSPs (PCSPs), initiated in (Brakensiek, Guruswami, Sandeep, STOC 2023), and obtain the following results:
For the PCSP 1-in-3-SAT vs NAE-SAT with negations, we prove that it is hard, under the Unique Games conjecture (UGC), to satisfy 1 − Ω(1/ log(1/ϵ)) constraints in a (1 − ϵ)- satisfiable instance. This shows that the exponential loss incurred by the BGS algorithm for the case of Alternating-Threshold polymorphisms is necessary, in contrast to the polynomial loss achievable for Majority polymorphisms. For any Boolean PCSP that admits Majority polymorphisms, we give an algorithm satisfying 1 − O( √ ϵ) fraction of the weaker constraints when promised the existence of an assignment satisfying 1 − ϵ fraction of the stronger constraints. This significantly generalizes the Charikar–Makarychev–Makarychev algorithm for 2-SAT, and matches the optimal trade-off possible under the UGC. The algorithm also extends, with the loss of an extra log(1/ϵ) factor, to PCSPs on larger domains with a certain structural condition, which is implied by, e.g., a family of Plurality polymorphisms. We prove that assuming the UGC, robust satisfiability is preserved under the addition of equality constraints. As a consequence, we can extend the rich algebraic techniques for decision/search PCSPs to robust PCSPs. The methods involve the development of a correlated and robust version of the general SDP rounding algorithm for CSPs due to (Brown-Cohen, Raghavendra, ICALP 2016), which might be of independent interest
Temporal variability and flooding influence the ecological niche of Biomphalaria intermediate hosts for Schistosoma mansoni in rural Uganda
Get PDFUnderstanding the niches of intermediate hosts and vectors for environmentally transmitted pathogens is crucial for identifying endemic areas, assessing habitat suitability, and targeting interventions. This study focuses on intermediate hosts of intestinal schistosomes, with over 700m people at risk of lifelong infection. We compared habitat suitability and species interactions across 674 sites in 52 villages in rural Uganda between 2022–2024, capturing a severe flooding event. Spatiotemporal models incorporating a polygon-based method to account for space with time as a fixed effect were developed to analyse snail abundance for Biomphalaria sudanica and B. stanleyi. B. sudanica was associated with marshy sites near lake shorelines and presence of hyacinths, while B. stanleyi was more likely found in deeper waters with Vallisneria plants. However, cohabitation was common for both species. Habitat suitability for each species fluctuated temporally, and more starkly with extreme flooding, resulting in switching of species dominance. Our study suggests that events consistent with climate change may influence habitat suitability without necessitating an expansion of environmental areas. Our models enable tracking of dynamic ecological niches that, if replicated elsewhere and for other intermediate hosts or vectors, can be used to better target environmental and community interventions as environmental conditions change
Sergio Raimondi: reading the wor(l)d
No full textThe poetry of Sergio Raimondi (Bahía Blanca, 1968) engages in the most complex issues of his time, including globalisation, colonialism, industrialisation and environmental degradation. His concerns are rigorously analysed through the medium of the poet’s art, steeped in literary tradition and craft. His writing emerges from the so-called “Poesía de los 90” or 1990s objectivist poetry, but transcends the work of his peers in scale, ambition, and formal accomplishment. Raimondi’s first collection, Poesía civil (Civil Poetry, 2001) marked a watershed in Argentine poetry: an attempt to write in verse the public life of his town, Bahía Blanca, including its industry, education, culture, and position in global flows of trade, capital, and power. His monumental collection Lexikón (Lexikon) was published in 2022, an alphabetical collection of 275 poems, spread over 16,248 lines. Poems take on biology, astrophysics, literature, finance, agriculture and football. Raimondi’s formal rigour, with its ordered, measured lines, draws heavily on his training as a classicist to address some of today’s most urgent political issues.La poesía de Sergio Raimondi (Bahía Blanca, 1968) aborda los temas más acuciantes de su tiempo, como la globalización, el colonialismo, la industrialización y la degradación del medio ambiente. Estos fenómenos son tratados por medio de una poesía impregnada de tradición y artificios formales. La escritura de Raimondi tiene raíces en la llamada “Poesía de los 90” o poesía objetivista de la década de 1990, pero trasciende la obra de sus pares en escala, ambición y logros formales. El primer poemario de Raimondi, Poesía civil (2001), marcó un parteaguas en la poesía argentina: un intento de escribir en verso la vida pública de su ciudad, Bahía Blanca, con su industria, educación, cultura y posición en los flujos globales del comercio, del capital y el poder. En 2022 se publicó su monumental Lexikón, un poemario alfabético de 275 poemas, repartidos en 16.248 versos. Los poemas abordan la biología, la astrofísica, la literatura, la economía, la agricultura y hasta el fútbol. El rigor formal de Raimondi, con sus versos ordenados y medidos, recurre fundamentalmente a su formación como clasicista para tratar algunos de los problemas políticos más urgentes de la actualidad
'Ās̱ār-i khayr’: Fatḥ ʿAlī Shāh Qājār and the major shrines of Iran and Iraq
No full textThis thesis explores Fatḥ ʿAlī Shāh’s acts of patronage at the major shrines in Iran and Iraq to understand how he used these sites as canvases on which to portray a carefully crafted public image of his right to rule. While the markedly religious nature of Fatḥ ʿAlī Shāh’s reign has been acknowledged in existing scholarship and his role as a significant patron of arts and architecture has been established, no study has investigated the details of the Shah’s extensive patronage to these most significant of religious sites. Three major shrines are the focus of this study, those of: Fāṭimah Maʿṣūmah in Qom; Imām Riżā in Mashhad; and Imām Ḥusayn in Karbalaʾ. The first three chapters address each of these sites in turn. The final chapter of the thesis aims to reconstruct and examine the Shah’s own mausoleum within the shrine in Qom. In order to piece together an image of the Shah’s relationship with these sites, early-Qajar courtly sources, such as Khāvarī’s Tārīkh-i Ẕū al-Qarnayn and the poetry of Fatḥ ʿAlī Khān Ṣabā, are used along with other records, such as royal firmans and photography. Where possible, details of the political context for the moment of patronage are explored, helping us to understand the motivations for this support of shrines. The Safavid precedent of shrine patronage is present throughout this study and, as has been shown to be the case for the nature of early-Qajar empire building, it is clear that Fatḥ ʿAlī Shāh often adopted Safavid modes of expressing his legitimacy as an Iranian imperial ruler. The resulting image is one of a conscious programme of patronage of the most significant religious sites in Iran and Iraq to simultaneously engage with the Iranian imperial past while innovating to create new modes of shrine patronage
