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1. Firefly: A Browser-based Interactive 3D Data Visualization Tool for Millions of Data Points

   https://doi.org/10.3847/1538-4365/acb59f  

   Gurvich, Alexander B.; Geller, Aaron M. (March 2023, The Astrophysical Journal Supplement Series)

   Abstract We present Firefly, a new browser-based interactive tool for visualizing 3D particle data sets. On a typical personal computer, Firefly can simultaneously render and enable real-time interactions with ≳10 million particles, and can interactively explore data sets with billions of particles using the included custom-built octree render engine. Once created, viewing a Firefly visualization requires no installation and is immediately usable in most modern internet browsers simply by visiting a URL. As a result, a Firefly visualization works out-of-the-box on most devices including smartphones and tablets. Firefly is primarily developed for researchers to explore their own data, but can also be useful to communicate results to researchers and/or collaborators and as an effective public outreach tool. Every element of the user interface can be customized and disabled, enabling easy adaptation of the same visualization for different audiences with little additional effort. Creating a new Firefly visualization is simple with the provided Python data preprocessor that translates input data to a Firefly-compatible format and provides helpful methods for hosting instances of Firefly both locally and on the internet. In addition to visualizing the positions of particles, users can visualize vector fields (e.g., velocities) and also filter and color points by scalar fields. We share three examples of Firefly applied to astronomical data sets: (1) the FIRE cosmological zoom-in simulations, (2) the SDSS galaxy catalog, and (3) Gaia Data Release 3. A gallery of additional interactive demos is available atalexbgurvi.ch/Firefly. 

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2. Novel viruses in the families Iflaviridae and Partitiviridae associated with the common eastern firefly Photinus pyralis

   https://doi.org/10.17912/micropub.biology.001385  

   Brewer, Seth A; Adler, Meaghan J; Martin, Mckayla M; Rozo-Lopez, Paula; Parker, Benjamin J (January 2025, microPublication biology)

   Fireflies are iconic insects that are under threat from environmental change. Knowledge of the viral diversity associated with natural firefly populations is important to our understanding of the basic biology of these insects and could be relevant to firefly conservation. We performed metatranscriptome sequencing of the Common Eastern Firefly (Photinus pyralis) and assembled genomes for two new species of virus in the families Iflaviridae and Partitiviridae. We surveyed multiple individuals for these viruses using PCR, and we showed that both viruses are found at intermediate frequences in a natural population. 

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3. Firefly Neural Architecture Descent: a General Approach for Growing Neural Networks

   Wu, Lemeng; Liu, Bo; Stone, Peter; Liu, Qiang (January 2020, Conference on Neural Information Processing Systems (NeurIPS))

   We propose firefly neural architecture descent, a general framework for progressively and dynamically growing neural networks to jointly optimize the networks' parameters and architectures. Our method works in a steepest descent fashion, which iteratively finds the best network within a functional neighborhood of the original network that includes a diverse set of candidate network structures. By using Taylor approximation, the optimal network structure in the neighborhood can be found with a greedy selection procedure. We show that firefly descent can flexibly grow networks both wider and deeper, and can be applied to learn accurate but resource-efficient neural architectures that avoid catastrophic forgetting in continual learning. Empirically, firefly descent achieves promising results on both neural architecture search and continual learning. In particular, on a challenging continual image classification task, it learns networks that are smaller in size but have higher average accuracy than those learned by the state-of-the-art methods. 

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4. First Phylogeny of Pseudolychnuris Reveals Its Polyphyly and a Staggering Case of Convergence at the Andean Paramos (Lampyridae: Lampyrini)

   https://doi.org/10.3390/insects13080697  

   Gisseth Ladino Peñuela, Angie; Botero, Juan Pablo; Lima da Silveira, Luiz Felipe (August 2022, Insects)

   South America is likely the cradle of several New World firefly lineages but remains largely understudied. Despite several advances in firefly systematics in the Neotropical region, the Andean region has been largely unstudied for over a century. The Colombian Páramos are a critically threatened biodiversity hotspot that houses several endemic species, including the firefly genus Pseudolychnuris, with two species—P. vittata and P. suturalis. Here, by analyzing the phylogenetic relationships of Pseudolychnuris, we found that this genus is polyphyletic. Pseudolychnuris vittata and P. suturalis were found to be distantly related despite the striking similarity in outline and color pattern of males and females. We redescribe Pseudolychnuris and its type species P. vittata. Moreover, we revalidate Alychnus Kirsch, 1865 stat. rev. to accommodate A. suturaliscomb. nov., also redescribed here. We provide updated distribution maps and report field observations for both monotypic genera. Since adults visit flowers and interact with pollen and nectar, Pseudolychnuris and Alychnus may be occasional pollinators of Andean-endemic plants, a phenomenon previously neglected. Our findings reveal an interesting case of convergence between Pseudolychnuris and Alychnus—probably associated with life in the Páramos—and shed light on character evolution in the Photinini lineage of fireflies. 

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5. DnaK refolds denatured proteins by actively pulling out their misfolded structural elements

   https://doi.org/10.1101/2025.09.22.677870  

   Marszalek, Piotr E (September 2025, bioRxiv)

   a) Abstract DnaK is a prokaryotic Hsp70 chaperone, with numerous functions in helping to fold nascent polypeptides and more generally in proteostasis. It also restores native structures to heat-shocked proteins in an ATP-hydrolysis-dependent manner. The structures of DnaK complexes with nucleotides, co-chaperones andsmallpeptides have already been resolved. However, there are no structures of DnaK complexes with larger, mostly folded substrates, such as firefly luciferase (Fluc, 61 kDa), which impedes the understanding of the mechanism through which DnaK refolds such large proteins. Here, we generated a model of a DnaK-firefly luciferase complex with Alphafold3, and examined its dynamics with all-atom molecular dynamics simulations. In this complex, Fluc is immobilized under the DnaK alpha-helical lid against the NBD, not the SBDβ, contrary to the data reported in the literature for model peptides. The DnaK lid is positioned strategically over Fluc’s helix 405-411, which we recently determined to be the first (and likely the only) helix melted in Fluc at 42 °C. We simulated the interaction between DnaK and the helix in its native and misfolded state and found that during the lid translocation toward the SBDβ, only the melted helix follows the lid and is actively pulled out from Fluc, while the native helix is not dislocated. These observations suggest a new model for the DnaK chaperone mechanism, where the alpha helical lid forms hydrogen bonds to the protein segment to be structurally tested. Lid pulls out only highly deformable misfolded helices, allowing them to refold into their native structures, and does not pull out those that are correctly folded because they are not deformable. Broader Audience Statementc) DnaK is a model chaperone, which can reactivate thermally denatured proteins. Even though a plethora of significant findings about DnaK structure, dynamics and interactions with its co-chaperone have been accumulated over 30 years, the exact molecular mechanism by which DnaK refolds misfolded proteins remains a mystery. This work exploited the ability of the Alphafold3 platform to generate an atomistic model for a complex between DnaK and Firefly luciferase and used molecular dynamics simulations to directly capture how DnaK may assist denatured proteins by mechanically pulling out their misfolded helices. This study provides a new insight into the DnaK mechanism. 

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