Evidence map›Paper›PMID 39337547›Full record

ArticleInternational journal of molecular sciences2024

TOPAS-Tissue: A Framework for the Simulation of the Biological Response to Ionizing Radiation at the Multi-Cellular Level.

Omar Rodrigo García García, Ramon Ortiz, Eduardo Moreno-Barbosa, Naoki D-Kondo, Bruce Faddegon, Jose Ramos-Méndez

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in International journal of molecular sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Omar Rodrigo García GarcíaFacultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico.
Ramon OrtizDepartment of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA.ORCID 0000-0002-4628-8121
Eduardo Moreno-BarbosaFacultad de Ciencias Físico Matemáticas, Benemérita Universidad Autónoma de Puebla, Puebla 72000, Mexico.
Naoki D-KondoDepartment of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA.
Bruce FaddegonDepartment of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA.
Jose Ramos-MéndezDepartment of Radiation Oncology, University of California San Francisco, San Francisco, CA 94115, USA.ORCID 0000-0002-8106-5142

Funding

TOPAS - nBio, a Monte Carlo tool for radiation biology researchR01CA187003 · NCI · MASSACHUSETTS GENERAL HOSPITAL · PI SCHUEMANN, JAN PATRICK OSCAR · 2015 to 2024
$4.8M
NCI NIH HHS R01 CA187003NCI NIH HHS R01CA187003
6 · The paper itself

Abstract

This work aims to develop and validate a framework for the multiscale simulation of the biological response to ionizing radiation in a population of cells forming a tissue. We present TOPAS-Tissue, a framework to allow coupling two Monte Carlo (MC) codes: TOPAS with the TOPAS-nBio extension, capable of handling the track-structure simulation and subsequent chemistry, and CompuCell3D, an agent-based model simulator for biological and environmental behavior of a population of cells. We verified the implementation by simulating the experimental conditions for a clonogenic survival assay of a 2-D PC-3 cell culture model (10 cells in 10,000 µm

Indexed as

DNA RepairMonte Carlo MethodRadiation, IonizingCell Line, TumorCell SurvivalComputer SimulationDNA Breaks, Double-StrandedDNA DamageDose-Response Relationship, RadiationHumansModels, Biologicalagent-based modelingMonte Carlo track-structure simulationmultiscale modelingPC-3 cell survivalradiation damage response

Identifiers

PMID39337547
PMCPMC11431975

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.