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A Data Management and Sharing Plan (DMS Plan) is a formal document that outlines how you will handle your data both during and after a research project. Documenting a plan for your data is a recommend…

A Data Management and Sharing Plan (DMS Plan) is a formal document that outlines how you will handle your data both during and after a research project. Documenting a plan for your data is a recommended practice and will help your data comply with Harvard policies for responsible data management. This Biomedical DMS Plan Template has been created for use by the Harvard biomedical community. It is intended to provide organization-specific guidance for Harvard constituents to create a relevant and useful data management and sharing plan that covers the complete data lifecycle. This is a funder agnostic template with recommended data management categories that can be used for a variety of project types. This Biomedical DMS Plan Template is available through DMP Tool—a free online platform for writing collaborative and active DMS Plans—by logging in with your Harvard credentials or use this document to create your own robust DMS Plan. More information is on the Harvard Biomedical Data Management website. 

V1: Preprint, submitted to the Journal of Glaciology on 2026-02-27.V2: Revision R1 submitted on 2026-07-28.

Pestifer is a Python package for automating the preparation of biomolecular simulation systems for NAMD using the CHARMM force field. It drives VMD/psfgen to build PSF/PDB topology and coordinate file…

Pestifer is a Python package for automating the preparation of biomolecular simulation systems for NAMD using the CHARMM force field. It drives VMD/psfgen to build PSF/PDB topology and coordinate files from PDB or mmCIF structures, handling missing loops, glycosylation, disulfide bonds, mutations, membrane embedding, and solvation.

Statistical analysis scripts and experimental data supporting the Scientific Reports manuscript. Includes Python scripts for distributional truncation analysis (S1), boundary redirection time series (…

Statistical analysis scripts and experimental data supporting the Scientific Reports manuscript. Includes Python scripts for distributional truncation analysis (S1), boundary redirection time series (S2), intervention intensity scaling (S3), robustness analysis, and prospective real-time validation. The constraint-enforcement layer implementation is withheld under USPTO Application 19/535,932; scripts operate on the layer's observable outputs only.

Accurate delineation of coronary arteries from X-ray angiography supports early identification of narrowing or blockages, but is complicated by low contrast and thin, branching vessel structures. This…

Accurate delineation of coronary arteries from X-ray angiography supports early identification of narrowing or blockages, but is complicated by low contrast and thin, branching vessel structures. This study compares three U-Net-based segmentation architectures — U-Net, U-Net++ and U-Net 3+ — trained on 1,000 images from the ARCADE dataset and evaluated on a held-out set of 300 images. All three architectures achieved comparable performance (Dice scores of 0.748-0.752), with U-Net 3+ performing best overall, U-Net++ showing higher sensitivity to smaller vessels, and U-Net showing higher precision, demonstrating the potential of U-Net-based models for coronary artery segmentation. This work was presented at the 5th Serbian International Conference on Applied Artificial Intelligence (SICAAI 2026), Kragujevac, Serbia, and was carried out within the STRATIFYHF project.

Plasma electrolytic polishing (PEP) has proven to be an effective surface finishing technique for complex additively manufactured (AM) components due to its ability to process intricate geometries. Th…

Plasma electrolytic polishing (PEP) has proven to be an effective surface finishing technique for complex additively manufactured (AM) components due to its ability to process intricate geometries. This capability makes PEP particularly suitable for lattice structures, which are widely used in aerospace and biomedical applications due to their favourable strength-to-weight ratio. However, ensuring uniform polishing of both the outer and inner surfaces, especially for high-density lattices, remains a challenge. In this study, SS316L lattice structures with different cell sizes, which affect their overall density, were polished with PEP under two conditions: with and without forced electrolyte flow. An external nozzle system was used to direct the forced flow and enhance electrolyte penetration into the inner regions of the lattice structures.

A Hypothesis-Generating Framework for Complex Chemical Exposures What if the long-term consequences of severe chemical exposure are determined not only by the toxic agent itself, but by an evolving sy…

A Hypothesis-Generating Framework for Complex Chemical Exposures What if the long-term consequences of severe chemical exposure are determined not only by the toxic agent itself, but by an evolving system of environmental chemistry, physicochemical transformations, emergency response conditions, and host biology? This work proposes a Systems Toxicology Framework for investigating complex occupational chemical exposures that cannot be adequately explained by conventional single-agent toxicology alone. Using a historically documented large-scale anhydrous ammonia railway accident as an illustrative case, the study integrates environmental chemistry, exposure dynamics, molecular toxicology, mitochondrial biology, innate immunity, and systems biology into a unified conceptual framework. Rather than presenting definitive causal conclusions, it develops a series of biologically plausible and experimentally testable mechanistic hypotheses that may help explain delayed neurological and multisystem health effects following severe chemical exposure. Although illustrated through ammonia, the proposed framework is intended to be broadly applicable to other hazardous occupational and environmental exposures—including chlorine, hydrogen fluoride, hydrogen sulfide, phosgene, combustion products, pesticides, engineered nanoparticles, and mixed chemical incidents. This publication is intended as a resource for researchers, toxicologists, occupational physicians, neurologists, emergency responders, and clinicians who investigate or manage the long-term consequences of complex hazardous-material exposures. The objective is not simply to reinterpret one historical accident, but to encourage a transition from substance-centered toxicology toward systems-oriented investigation of real-world chemical exposure events.   AI-Assisted Manuscript PreparationThis manuscript was developed with the assistance of generative artificial intelligence (OpenAI ChatGPT, Antropic Claude, Google Gemini) for language refinement, structural development, and editorial support. All scientific concepts, interpretations, conclusions, and final editorial decisions remain the sole responsibility of the author.

This presentation discusses the optimization of PEP, both as a stand-alone process and in combination with particle blasting, to improve the surface quality of additively manufactured stainless steel …

This presentation discusses the optimization of PEP, both as a stand-alone process and in combination with particle blasting, to improve the surface quality of additively manufactured stainless steel samples. In addition, the feasibility of applying PEP to multi-material structures, specifically Functional Graded Materials (FGMs) produced by Directed Energy Deposition (DED), focusing on materials comprising a cast iron base, an Inconel intermediate layer and a top layer of maraging steel, is explained.