Open source clinical science for emerging infections.
Ontology highlight
ABSTRACT:
SUBMITTER: Dunning JW
PROVIDER: S-EPMC7158987 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Despite the increased access to scientific publications and data as a result of open science initiatives, access to scientific tools remains limited. Uncrewed aerial vehicles (UAVs, or drones) can be a powerful tool for research in disciplines such as agriculture and environmental sciences, but their use in research is currently dominated by proprietary, closed source tools. The objective of this work was to collect, curate, organize and test a set of open source tools for aerial data capture for research purposes. The Open Science Drone Toolkit was built through a collaborative and iterative process by more than 100 people in five countries, and comprises an open-hardware autonomous drone and off-the-shelf hardware, open-source software, and guides and protocols that enable the user to perform all the necessary tasks to obtain aerial data. Data obtained with this toolkit over a wheat field was compared to data from satellite imagery and a commercial hand-held sensor, finding a high correlation for both instruments. Our results demonstrate the possibility of capturing research-grade aerial data using affordable, accessible, and customizable open source software and hardware, and using open workflows.
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Project description:Amongst the 60 viral species reported to be associated with bats, 59 are RNA viruses, which are potentially important in the generation of emerging and re-emerging infections in humans. The prime examples of these are the lyssaviruses and Henipavirus. The transmission of Nipah, Hendra and perhaps SARS coronavirus and Ebola virus to humans may involve intermediate amplification hosts such as pigs, horses, civets and primates, respectively. Understanding of the natural reservoir or introductory host, the amplifying host, the epidemic centre and at-risk human populations are crucial in the control of emerging zoonosis. The association between the bat coronaviruses and certain lyssaviruses with particular bat species implies co-evolution between specific viruses and bat hosts. Cross-infection between the huge number of bat species may generate new viruses which are able to jump the trans-mammalian species barrier more efficiently. The currently known viruses that have been found in bats are reviewed and the risks of transmission to humans are highlighted. Certain families of bats including the Pteropodidae, Molossidae, Phyllostomidae, and Vespertilionidae are most frequently associated with known human pathogens. A systematic survey of bats is warranted to better understand the ecology of these viruses.
| S-EPMC7169091 | biostudies-literature
Project description:BackgroundThe increasing access to autonomously-operated technologies offer vast opportunities to sample large volumes of biological data. However, these technologies also impose novel demands on ecologists who need to apply tools for data management and processing that are efficient, publicly available and easy to use. Such tools are starting to be developed for a wider community and here we present an approach to combine essential analytical functions for analysing large volumes of image data in marine ecological research.New informationThis paper describes the Koster Seafloor Observatory, an open-source approach to analysing large amounts of subsea movie data for marine ecological research. The approach incorporates three distinct modules to: manage and archive the subsea movies, involve citizen scientists to accurately classify the footage and, finally, train and test machine learning algorithms for detection of biological objects. This modular approach is based on open-source code and allows researchers to customise and further develop the presented functionalities to various types of data and questions related to analysis of marine imagery. We tested our approach for monitoring cold water corals in a Marine Protected Area in Sweden using videos from remotely-operated vehicles (ROVs). Our study resulted in a machine learning model with an adequate performance, which was entirely trained with classifications provided by citizen scientists. We illustrate the application of machine learning models for automated inventories and monitoring of cold water corals. Our approach shows how citizen science can be used to effectively extract occurrence and abundance data for key ecological species and habitats from underwater footage. We conclude that the combination of open-source tools, citizen science systems, machine learning and high performance computational resources are key to successfully analyse large amounts of underwater imagery in the future.
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Project description:The Open Science Prize was established with the following objectives: first, to encourage the crowdsourcing of open data to make breakthroughs that are of biomedical significance; second, to illustrate that funders can indeed work together when scientific interests are aligned; and finally, to encourage international collaboration between investigators with the intent of achieving important innovations that would not be possible otherwise. The process for running the competition and the successes and challenges that arose are presented.
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Project description: Not available
| S-EPMC10915008 | biostudies-literature
Project description:In individuals with lower-limb amputations, robotic prostheses can increase walking speed, and reduce energy use, the incidence of falls and the development of secondary complications. However, safe and reliable prosthetic-limb control strategies for robust ambulation in real-world settings remain out of reach, partly because control strategies have been tested with different robotic hardware in constrained laboratory settings. Here, we report the design and clinical implementation of an integrated robotic knee-ankle prosthesis that facilitates the real-world testing of its biomechanics and control strategies. The bionic leg is open source, it includes software for low-level control and for communication with control systems, and its hardware design is customizable, enabling reduction in its mass and cost, improvement in its ease of use and independent operation of the knee and ankle joints. We characterized the electromechanical and thermal performance of the bionic leg in benchtop testing, as well as its kinematics and kinetics in three individuals during walking on level ground, ramps and stairs. The open-source integrated-hardware solution and benchmark data that we provide should help with research and clinical testing of knee-ankle prostheses in real-world environments.
| S-EPMC7581510 | biostudies-literature
Project description:It is well established that most of the plastic pollution found in the oceans is transported via rivers. Unfortunately, the main processes contributing to plastic and debris displacement through riparian systems is still poorly understood. The Marine Litter Drifter project from the Arno River aims at using modern consumer software and hardware technologies to track the movements of real anthropogenic marine debris (AMD) from rivers. The innovative "Marine Litter Trackers" (MLT) were utilized as they are reliable, robust, self-powered and they present almost no maintenance costs. Furthermore, they can be built not only by those trained in the field but also by those with no specific expertise, including high school students, simply by following the instructions. Five dispersion experiments were successfully conducted from April 2021 to December 2021, using different types of trackers in different seasons and weather conditions. The maximum distance tracked was 2845 km for a period of 94 days. The activity at sea was integrated by use of Lagrangian numerical models that also assisted in planning the deployments and the recovery of drifters. The observed tracking data in turn were used for calibration and validation, recursively improving their quality. The dynamics of marine litter (ML) dispersion in the Tyrrhenian Sea is also discussed, along with the potential for open-source approaches including the "citizen science" perspective for both improving big data collection and educating/awareness-raising on AMD issues.
| S-EPMC9863889 | biostudies-literature
Project description:BackgroundThe open science movement is transforming scientific practice with the goal of enhancing the transparency, productivity, and reproducibility of research. Nevertheless, transparency is a complex concept, and efforts to promote some forms of transparency may do relatively little to advance other important forms of transparency.ObjectivesDrawing from the literature in history, philosophy, and sociology of science, we aim to distinguish between different forms of scientific transparency. Our goal is to identify strategies for achieving forms of transparency that are relevant not only to scientists but also to decision makers and members of the public.DiscussionWe draw a distinction between "scientifically relevant transparency" and "socially relevant transparency." Most of the prominent strategies associated with the open science movement (e.g., making data publicly available and registering studies) are designed primarily to promote scientifically relevant transparency. To achieve socially relevant transparency, which is particularly important in fields like environmental health, further steps are needed to provide scientific information in ways that are relevant to decision makers and members of the public.ConclusionsPromoting socially relevant transparency will require a range of activities by many different individuals and institutions. We propose an array of strategies that can be pursued by scientists and other scholars, journals, universities, funders, government agencies, and members of the public. https://doi.org/10.1289/EHP4808.
| S-EPMC6792383 | biostudies-literature