Latest Articles

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  Section: Mathematical & Computational Biology ; Topics: Biophysics and computational biology, Population biology, Health sciences

  Optimizing telework in an epidemic context: contrasting the infectious and non-communicable diseases perspectives

  Moutet, Léo;   Leclerc, Quentin J.;   Layan, Maylis;   Aït Bouziad, Karim;   Dab, William; Henriot, Paul;   Hodbert, Elise;   Louati, Narimène; Maurin, Aurélie;   Thonon, Frédérique;   Znaty, Sylvie; Ben Halima, Mohamed Ali;   Jean, Kévin;   Temime, Laura  

  10.24072/pcjournal.741 - Peer Community Journal, Volume 6 (2026), article no. e58

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  Objectives: In a global context of increasing telework, this study explores its health effects, to determine if there is an optimal teleworking frequency during an epidemic. We aim to quantify the relationship between teleworking frequency and both infectious disease (ID) transmission and non-communicable disease (NCD) risk. Methods: We developed a mathematical model simulating ID transmission and NCD acquisition in a medium-sized company, analysing how different teleworking levels impact workers health. We conducted a rapid literature review to identify potential exposure-response relationships between teleworking and NCD risk and inform this model. We then simulated infection dynamics over a three-month epidemic wave to contrast ID and NCD risks in relation to the extent of telework engagement. Results: Evidence from the literature showed varying patterns of NCD risk across different teleworking frequencies. Depending on these relationships, we observed that risk may peak at low, intermediate, or high teleworking levels. We demonstrated the existence of a benefit-risk balance between reducing ID transmission and potentially increasing NCD burden. Conclusions:. Based on current scientific knowledge, no single optimal teleworking frequency can be identified, as the optimum varies depending on the NCD outcome considered. Our study highlights the need for stronger evidence to estimate robust exposure-response functions linking teleworking frequency and NCDs, and ultimately to inform prevention strategies for both infectious and NCD risks in an epidemic context.

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  Section: Genomics ; Topics: Genetics/genomics, Evolution

  Comparing DNA extraction methods for successful PacBio HiFi sequencing: a case study of the freshwater mussel Anodonta anatina (Bivalvia: Unionidae)

  Giulio, Marco R.;   Lergster, Urs; Feulner, Philine G. D.;   Weber, Alexandra A.-T.  

  10.24072/pcjournal.733 - Peer Community Journal, Volume 6 (2026), article no. e57

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  High-quality reference genomes are increasingly recognized as essential resources in biodiversity genomics and conservation. However, successful DNA extraction and long-read sequencing remain highly organism-dependent. Molluscs, a diverse phylum of invertebrates, pose particular challenges due to the presence of inhibitory compounds and the difficulty of obtaining high-molecular-weight DNA, often necessitating careful optimization of extraction protocols. Here, we present a case study on the freshwater mussel Anodonta anatina (Bivalvia: Unionidae), evaluating two preservation methods, six DNA extraction protocols, and two post-extraction clean-up steps for their effects on DNA quality and PacBio HiFi sequencing yield from foot tissue of a single individual. The PacBio Nanobind and CTAB protocols produced high-quality DNA from fresh tissue but performed poorly on flash-frozen tissue. Post-extraction clean-up generally degraded DNA and did not improve sequencing yield. Unexpectedly, the column-based Omega Mollusc Kit, although not designed for high-molecular-weight DNA, performed better than the PacBio-recommended Nanobind kit and the manual CTAB method on flash-frozen tissue. It generated high DNA quantity and purity, sufficient integrity for HiFi sequencing, and appeared to remove contaminants effectively. While the resulting DNA may be too fragmented for ultra-long read sequencing, the Omega Mollusc Kit offers a practical, cost-effective first approach for testing DNA extraction and PacBio sequencing in flash-frozen A. anatina foot tissue. When fresh tissue is available, Nanobind or CTAB were the best-performing options in our comparison. Overall, our results provide a practical starting point for protocol selection, while acknowledging that validation across other mollusc species, tissue types, and preservation methods remains important. This strategy could reduce the need for extensive protocol optimization and facilitate future mollusc genomics efforts.

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  Section: Archaeology ; Topics: Archaeology, Anthropology, Computer sciences ; Conference: CAA2025

  Experimental interpretation of ancient games through playtesting

  Tsilogiannis, Angelos; Konstantakis, Markos;   Vosinakis, Spyros  

  10.24072/pcjournal.738 - Peer Community Journal, Volume 6 (2026), article no. e56

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  Reconstructing the rules of ancient games remains one of archaeology’s most intricate interpretive challenges. While surviving boards and pieces provide tangible evidence, the logic of play, rules, roles, and goals have largely vanished. Traditional reconstructions rely on text and comparisons to better known games, yet these methods seldom capture the experiential and social dimensions of ancient gameplay. This paper presents an experimental framework designed to explore how such systems might emerge through play itself. Using Ludus Latrunculorum (“The Game of Little Soldiers”) as a case study, participants engaged in iterative, co-creative sessions where they invented, refined, and transmitted rules across successive lineages of play. The resulting games revealed recurring mechanics that closely parallel known reconstructions of Ludus Latrunculorum. While the outcomes do not claim historical accuracy, they demonstrate how collective experimentation can illuminate the cognitive and social processes underlying the development of structured games in antiquity. The study thus proposes experimental play as a complementary archaeological tool for examining how rulesets evolve, stabilize, and reflect the societies that produce them.

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  Section: Mathematical & Computational Biology ; Topics: Biophysics and computational biology, Computer sciences

  Accelerating k-mer-based sequence filtering

  Martayan, Igor;   Vandamme, Léa;   Constantinides, Bede;   Cazaux, Bastien;   Paperman, Charles;   Limasset, Antoine  

  10.24072/pcjournal.735 - Peer Community Journal, Volume 6 (2026), article no. e55

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  Motivation. The exponential growth of global sequencing data repositories presents both analytical challenges and opportunities. While k-mer-based indexing has improved scalability over traditional alignment for identifying relevant documents, pinpointing the exact sequences matching numerous queries remains a hurdle. In particular, searching for numerous k-mers with a single large query or multiple distinct queries strains existing exact matching tools, whose performance scales poorly with an increasing number of patterns. At the same time, indexing entire vast datasets for infrequent or ad-hoc searches is often resource-prohibitive. Designing fast methods for matching a large number of k-mers without exhaustive pre-indexing is therefore critical.  Contributions. We propose an efficient solution to the problem of k-mer-based sequence filtering: given a set of k-mers of interests and a threshold, quickly evaluate whether an arbitrary sequence has a number of k-mer matches above or below the threshold. Our approach demonstrates how minimizer-based based sketching, alongside SIMD acceleration, can enhance the performance of streaming searches, and is implemented as a Rust tool named K2Rmini. On a consumer laptop, K2Rmini is able to filter long reads at 2 Gbp/s.  Availability. https://github.com/Malfoy/K2Rmini.