Paper List
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EnzyCLIP: A Cross-Attention Dual Encoder Framework with Contrastive Learning for Predicting Enzyme Kinetic Constants
This paper addresses the core challenge of jointly predicting enzyme kinetic parameters (Kcat and Km) by modeling dynamic enzyme-substrate interaction...
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Tissue stress measurements with Bayesian Inversion Stress Microscopy
This paper addresses the core challenge of measuring absolute, tissue-scale mechanical stress without making assumptions about tissue rheology, which ...
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DeepFRI Demystified: Interpretability vs. Accuracy in AI Protein Function Prediction
This study addresses the critical gap between high predictive accuracy and biological interpretability in DeepFRI, revealing that the model often prio...
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Hierarchical Molecular Language Models (HMLMs)
This paper addresses the core challenge of accurately modeling context-dependent signaling, pathway cross-talk, and temporal dynamics across multiple ...
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Stability analysis of action potential generation using Markov models of voltage‑gated sodium channel isoforms
This work addresses the challenge of systematically characterizing how the high-dimensional parameter space of Markov models for different sodium chan...
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Personalized optimization of pediatric HD-tDCS for dose consistency and target engagement
This paper addresses the critical limitation of one-size-fits-all HD-tDCS protocols in pediatric populations by developing a personalized optimization...
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Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design
This paper addresses the core pain point of low sequence-structure alignment in existing synthetic datasets (e.g., AFDB), which severely limits the pe...
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Generative design and validation of therapeutic peptides for glioblastoma based on a potential target ATP5A
This paper addresses the critical bottleneck in therapeutic peptide design: how to efficiently optimize lead peptides with geometric constraints while...
Generating a Contact Matrix for Aged Care Settings in Australia: an agent-based model study
University of New South Wales
The 30-Second View
IN SHORT: This study addresses the critical gap in understanding heterogeneous contact patterns within aged care facilities, where existing population-level contact matrices fail to capture the nuanced interactions that drive infection transmission in these high-risk environments.
Innovation (TL;DR)
- Methodology Developed a transferable agent-based modeling framework specifically for aged care settings, parameterized with empirical survey data from 21 aged care workers to capture realistic staff-resident interaction patterns.
- Methodology Integrated proximity-based contact definitions (1.5m and 3m thresholds with 3-second duration) with temporal analysis to identify high-risk contact clustering during structured daily routines like communal activities and care tasks.
- Biology Demonstrated that medium care residents experience the highest infection risk despite not having the highest contact frequency, revealing non-linear relationships between contact patterns and transmission outcomes.
Key conclusions
- Low and medium care residents had the highest contact frequencies (particularly with morning/afternoon shift staff), while high care residents and night staff had substantially fewer contacts, with Poisson regression confirming significant variation by care level and shift (p<0.001).
- Vaccination scenarios reduced predicted transmission by up to 68%, with maximum impact achieved when both staff and residents were vaccinated, demonstrating the multiplicative protective effect of comprehensive vaccination coverage.
- Temporal analysis revealed clustering of high-risk contacts during structured daily routines, with infection risk highest during high-contact shifts and among medium care residents, highlighting the importance of timing in intervention strategies.
Abstract: This study presents an agent-based model (ABM) developed to simulate staff and resident interactions within a synthetic aged care facility, capturing movement, task execution, and proximity-based contact events across three staff shifts and varying levels of resident care. Contacts were defined by spatial thresholds (1.5 m and 3 m) and cumulative duration, enabling the generation of detailed contact matrices. Simulation results showed that low and medium care residents experienced the highest frequency of interactions, particularly with staff on morning and afternoon shifts, while high care residents and night staff had substantially fewer contacts. Contact rates varied significantly by care level and shift, confirmed through Poisson-based regression modelling. Temporal analyses revealed clustering of high-risk contacts during structured daily routines, especially communal and care activities. An integrated airborne transmission module, seeded with a single infectious staff member, demonstrated that infection risk was highest during high-contact shifts and among medium care residents. Vaccination scenarios reduced predicted transmission by up to 68%, with the greatest impact observed when both staff and residents were vaccinated. These findings highlight the importance of accounting for contact heterogeneity in aged care and demonstrate the utility of ABMs for evaluating targeted infection control strategies in high-risk, enclosed environments.