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NPC Simulations Utility Files and DatasetsUser's Manual and TutorialA detailed User's Manual in PDF format and a Tutorial in Jupyter Notebook format are available in this folder.Scripts/Utility scripts used for initiating and analyzing the simulation. See tutorial for details on how and when to use key scripts.Models/NPC2018/Kim et al. 2018 model of the NPC scaffold used in this workData/CryoET/In situ cryo-electron tomography (cryoET) map of the NPC's central channel used for validation of simulated NPC morphologyReferenceRaveh B*, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP*, Cowburn D*, Sali A*. Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport. Proc Nat Acad Sci (2025), in press.LicenseSee LICENSE file.

Biodiversity in human-dominated landscapes is declining, but evidence-based conservation targets to guide international policies for such landscapes are lacking. We present a framework for informing habitat conservation policies based on the enhancement of habitat quantity and quality and define thresholds of habitat quantity at which it becomes effective to also prioritize habitat quality. We applied this framework to pollinators, an important part of agroecosystem biodiversity, by synthesizing 59 studies from 19 countries. Given low habitat quality, hoverflies had the lowest threshold at 6% semi-natural habitat cover, followed by solitary bees (16%), bumble bees (18%), and butterflies (37%). These figures represent minimum habitat thresholds in agricultural landscapes, but when habitat quantity is restricted, marked increases in quality are required to reach similar outcomes.

NPC Simulations Utility Files and DatasetsUser's Manual and TutorialA detailed User's Manual in PDF format and a Tutorial in Jupyter Notebook format are available in this folder.Scripts/Utility scripts used for initiating and analyzing the simulation. See tutorial for details on how and when to use key scripts.Models/NPC2018/Kim et al. 2018 model of the NPC scaffold used in this workData/CryoET/In situ cryo-electron tomography (cryoET) map of the NPC's central channel used for validation of simulated NPC morphologyReferenceRaveh B*, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP*, Cowburn D*, Sali A*. Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport. Proc Nat Acad Sci (2025), in press.LicenseSee LICENSE file.

NPC Simulations Utility Files and DatasetsUser's ManualA detailed User's Manual in PDF format is available in this folder.scripts/Utility scripts used for initiating and analyzing the simulation. See tutorial for details on how and when to use key scripts.tutorials/Tutorial in Jupyter Notebook format for running a basic simulation in a simplified setting + basic analysistest/Test script for running a basic simulation in a simplified setting + basic analysisdata/cryoET/In situ cryo-electron tomography (cryoET) map of the NPC's central channel used for validation of simulated NPC morphologymodels/NPC2018/Kim et al. 2018 model of the NPC scaffold used in this work (see also User's manual)ReferenceRaveh B*, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP*, Cowburn D*, Sali A*. Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport. Proc Nat Acad Sci (2025), in press.LicenseSee LICENSE file.

NPC Simulations Utility Files and DatasetsUser's ManualA detailed User's Manual in PDF format is available in this folder.scripts/Utility scripts used for initiating and analyzing the simulation. See tutorial for details on how and when to use key scripts.tutorials/Tutorial in Jupyter Notebook format for running a basic simulation in a simplified setting + basic analysistest/Test script for running a basic simulation in a simplified setting + basic analysisdata/cryoET/In situ cryo-electron tomography (cryoET) map of the NPC's central channel used for validation of simulated NPC morphologymodels/NPC2018/Kim et al. 2018 model of the NPC scaffold used in this work (see also User's manual)ReferenceRaveh B*, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP*, Cowburn D*, Sali A*. Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport. Proc Nat Acad Sci (2025), in press.LicenseSee LICENSE file.

Output files and output plotting code for quasi-electrostatic model simulation of thunderstorm above Indonesia 6.2.2024.Corresponds to video in:Yair, Y. (2025, September 24). Thunderstorm above Indonesia 6.2.2024. Zenodo. https://doi.org/10.5281/zenodo.17189226The quasi-electrostatic model used to generate the output is described in:https://www.sciencedirect.com/science/article/pii/S1364682622000293https://doi.org/10.1016/j.asr.2024.08.050https://doi.org/10.1016/j.asr.2025.01.013

Output files and output plotting code for quasi-electrostatic model simulation of thunderstorm above Indonesia 6.2.2024.Corresponds to video in:Yair, Y. (2025, September 24). Thunderstorm above Indonesia 6.2.2024. Zenodo. https://doi.org/10.5281/zenodo.17189226The quasi-electrostatic model used to generate the output is described in:https://www.sciencedirect.com/science/article/pii/S1364682622000293https://doi.org/10.1016/j.asr.2024.08.050https://doi.org/10.1016/j.asr.2025.01.013

Pathogens face strong selection from host immune responses, yet many host populations support pervasive pathogen populations. We investigated this puzzle in a model system of Bartonella and rodents from Israel’s northwestern Negev Desert. We chose to study this system because in this region, 75–100% of the rodents are infected with Bartonella at any given time, despite an efficient immunological response. In this region, Bartonella species circulate in three rodent species, and we tested the hypothesis that at least some of these hosts exhibit a waning immune response to Bartonella, which allows reinfections. To that end, we inoculated captive rodents from all three species with the same Bartonella strain, and we quantified the bacterial dynamics and Bartonella-specific IgG antibody kinetics through 139 days after the primary inoculation and then for 60 days following re-inoculation with the same strain. Contrary to our hypothesis, we found a strong, long-lasting IgG antibody response, with a protective immunological memory in all three rodent species. That response prevented re-infection upon exposure to the same Bartonella strain. This study constitutes an initial step toward a better understanding of the interplay between Bartonella pathogens and rodent traits, and how the interplay of those traits influences epidemiological dynamics in nature.