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ArXiv Nov 2023Technological advances in high-throughput microscopy have facilitated the acquisition of cell images at a rapid pace, and data pipelines can now extract and process...
Technological advances in high-throughput microscopy have facilitated the acquisition of cell images at a rapid pace, and data pipelines can now extract and process thousands of image-based features from microscopy images. These features represent valuable single-cell phenotypes that contain information about cell state and biological processes. The use of these features for biological discovery is known as image-based or morphological profiling. However, these raw features need processing before use and image-based profiling lacks scalable and reproducible open-source software. Inconsistent processing across studies makes it difficult to compare datasets and processing steps, further delaying the development of optimal pipelines, methods, and analyses. To address these issues, we present Pycytominer, an open-source software package with a vibrant community that establishes an image-based profiling standard. Pycytominer has a simple, user-friendly Application Programming Interface (API) that implements image-based profiling functions for processing high-dimensional morphological features extracted from microscopy images of cells. Establishing Pycytominer as a standard image-based profiling toolkit ensures consistent data processing pipelines with data provenance, therefore minimizing potential inconsistencies and enabling researchers to confidently derive accurate conclusions and discover novel insights from their data, thus driving progress in our field.
PubMed: 38045474
DOI: No ID Found -
Methods in Molecular Biology (Clifton,... 2024Availability of relevant biological samples supports both basic science research and patient-centered clinical studies. Establishing a biorepository faces challenges at...
Availability of relevant biological samples supports both basic science research and patient-centered clinical studies. Establishing a biorepository faces challenges at multiple levels. These tasks include defining mission definition and scope; selection of subjects and sample types; recruitment strategies; timing of collection in the patient's journey; sample logistics and processing; determining what clinical data to collect; ensuring sample integrity on transport, processing, and storage; defining governance structures and oversight responsibilities; clarifying sample provenance and ownership; establishing procedures for sample and data access; selecting testing to be performed routinely versus upon request, and management of results; data security; funding sources; and regulatory compliance. Establishing and maintaining a biorepository therefore requires careful planning, diligent and sustained execution, technical and financial resources, stakeholder support, and flexible and resilient management to respond to changing environments and needs.
Topics: Pregnancy; Female; Humans; Biological Specimen Banks; Specimen Handling
PubMed: 38165627
DOI: 10.1007/978-1-0716-3561-2_17 -
Foods (Basel, Switzerland) Aug 2023With the rise of globalization and technological competition, the food supply chain has grown more complex due to the multiple players and factors involved in the chain.... (Review)
Review
With the rise of globalization and technological competition, the food supply chain has grown more complex due to the multiple players and factors involved in the chain. Traditional systems fail to offer effective and reliable traceability solutions considering the increasing requirement for accountability and transparency in the food supply chain. Blockchain technology has been claimed to offer the food industry a transformative future. The inherent features of blockchain, including immutability and transparency, create a dependable and secure system for tracking food products across the whole supply chain, ensuring total control over their traceability from the origin to the final consumer. This research offers a comprehensive overview of multiple models to understand how the integration of blockchain and other digital technologies has transformed the food supply chain. This comprehensive systematic review of blockchain-based food-supply-chain frameworks aimed to uncover the capability of blockchain technology to revolutionize the industry and examined the current landscape of blockchain-based food traceability solutions to identify areas for improvement. Furthermore, the research investigates recent advancements and investigates how blockchain aligns with other emerging technologies of Industry 4.0 and Web 3.0. Blockchain technology plays an important role in improving food traceability and supply-chain operations. Potential synergies between blockchain and other emerging technologies of Industry 4.0 and Web 3.0 are digitizing food supply chains, which results in better management, automation, efficiencies, sustainability, verifiability, auditability, accountability, traceability, transparency, tracking, monitoring, response times and provenance across food supply chains.
PubMed: 37628025
DOI: 10.3390/foods12163026 -
PeerJ 2023Wildlife farming can be an important but complex tool for conservation. To achieve conservation benefits, wildlife farming should meet a variety of criteria, including... (Review)
Review
BACKGROUND
Wildlife farming can be an important but complex tool for conservation. To achieve conservation benefits, wildlife farming should meet a variety of criteria, including traceability conditions to identify the animals' origin. The traditional techniques for discriminating between wild and captive animals may be insufficient to prevent doubts or misdeclaration, especially when labels are not expected or mandatory. There is a pressing need to develop more accurate techniques to discriminate between wild and captive animals and their products. Stable isotope analysis has been used to identify animal provenance, and some studies have successfully demonstrated its potential to differentiate wild from captive animals. In this literature review, we examined an extensive collection of publications to develop an overall picture of the application of stable isotopes to distinguish between wild and captive animals focusing on evaluating the patterns and potential of this tool.
SURVEY METHODOLOGY
We searched peer-reviewed publications in the Web of Science database and the references list from the main studies on the subject. We selected and analyzed 47 studies that used C, N, H, O, and S in tissues from fish, amphibians, reptiles, birds, and mammals. We built a database from the isotope ratios and metadata extracted from the publications.
RESULTS
Studies have been using stable isotopes in wild and captive animals worldwide, with a particular concentration in Europe, covering all main vertebrate groups. A total of 80.8% of the studies combined stable isotopes of carbon and nitrogen, and 88.2% used at least one of those elements. Fish is the most studied group, while amphibians are the least. Muscle and inert organic structures were the most analyzed tissues (46.81% and 42.55%). C and N standard deviation and range were significantly higher in the wild than in captive animals, suggesting a more variable diet in the first group. C tended to be higher in wild fishes and in captive mammals, birds, reptiles, and amphibians. N was higher in the wild terrestrial animals when controlling for diet. Only 5.7% of the studies failed to differentiate wild and captive animals using stable isotopes.
CONCLUSIONS
This review reveals that SIA can help distinguish between wild and captive in different vertebrate groups, rearing conditions, and methodological designs. Some aspects should be carefully considered to use the methodology properly, such as the wild and captivity conditions, the tissue analyzed, and how homogeneous the samples are. Despite the increased use of SIA to distinguish wild from captive animals, some gaps remain since some taxonomic groups (., amphibians), countries (., Africa), and isotopes (., H, O, and S) have been little studied.
Topics: Animals; Carbon Isotopes; Nitrogen Isotopes; Animals, Wild; Carbon; Fishes; Mammals
PubMed: 38025752
DOI: 10.7717/peerj.16460 -
AMIA ... Annual Symposium Proceedings.... 2023: To implement an open source, free, and easily deployable high throughput natural language processing module to extract concepts from clinician notes and map them to...
: To implement an open source, free, and easily deployable high throughput natural language processing module to extract concepts from clinician notes and map them to Fast Healthcare Interoperability Resources (FHIR). : Using a popular open-source NLP tool (Apache cTAKES), we create FHIR resources that use modifier extensions to represent negation and NLP sourcing, and another extension to represent provenance of extracted concepts. : The SMART Text2FHIR Pipeline is an open-source tool, released through standard package managers, and publicly available container images that implement the mappings, enabling ready conversion of clinical text to FHIR. : With the increased data liquidity because of new interoperability regulations, NLP processes that can output FHIR can enable a common language for transporting structured and unstructured data. This framework can be valuable for critical public health or clinical research use cases. : Future work should include mapping more categories of NLP-extracted information into FHIR resources and mappings from additional open-source NLP tools.
Topics: Humans; Electronic Health Records; Delivery of Health Care; Natural Language Processing; APACHE
PubMed: 38222416
DOI: No ID Found -
The Lancet. Digital Health Jun 2024With the rapid growth of interest in and use of large language models (LLMs) across various industries, we are facing some crucial and profound ethical concerns,... (Review)
Review
With the rapid growth of interest in and use of large language models (LLMs) across various industries, we are facing some crucial and profound ethical concerns, especially in the medical field. The unique technical architecture and purported emergent abilities of LLMs differentiate them substantially from other artificial intelligence (AI) models and natural language processing techniques used, necessitating a nuanced understanding of LLM ethics. In this Viewpoint, we highlight ethical concerns stemming from the perspectives of users, developers, and regulators, notably focusing on data privacy and rights of use, data provenance, intellectual property contamination, and broad applications and plasticity of LLMs. A comprehensive framework and mitigating strategies will be imperative for the responsible integration of LLMs into medical practice, ensuring alignment with ethical principles and safeguarding against potential societal risks.
Topics: Humans; Artificial Intelligence; Natural Language Processing; Intellectual Property
PubMed: 38658283
DOI: 10.1016/S2589-7500(24)00061-X -
Critical Reviews in Analytical Chemistry Sep 2023Soil is one type of Earth material demonstrating a wide range of physical, chemical, and biological properties. As the compositional profile of soil is a product of... (Review)
Review
Soil is one type of Earth material demonstrating a wide range of physical, chemical, and biological properties. As the compositional profile of soil is a product of interaction between numerous abiotic and biotic components, it tends to be unique by its geographic origin. Hence, soil is paramount for predicting source or origin in forensic provenance and intelligence, food provenance, biosecurity, and archaeology. In the context of forensic investigation, source tracing of soil could be executed by a comparison or provenance analysis. Soil compositional fingerprints acquired using analytical methods must be carefully interpreted suitable mathematical and statistical tools since multiple sources can contribute to the variability of soil other than its provenance. This article reviews recent trends in soil sampling and data interpretation strategies proposed for source tracing of soil evidence. Performances of soil provenance indicators are also described. Then, perspectives on possible research directions guiding forensic soil provenance are proposed. This timely critical review reveals the essential idea and gap in forensic soil provenance for stimulating the development of more efficient and effective provenance strategies.
PubMed: 37672265
DOI: 10.1080/10408347.2023.2253473 -
The American Naturalist Oct 2023AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the... (Review)
Review
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
Topics: Adaptation, Physiological; Genetic Variation; Phenotype; Selection, Genetic
PubMed: 37792924
DOI: 10.1086/726012 -
Journal of Environmental Management Jul 2023Roughly 2 billion ha of land are degraded and in need of ecological restoration worldwide. Active restoration frequently involves revegetation, which leads to the... (Review)
Review
Roughly 2 billion ha of land are degraded and in need of ecological restoration worldwide. Active restoration frequently involves revegetation, which leads to the dilemma of whether to conduct direct seeding or to plant nursery-grown seedlings. The choice of revegetation method can regulate plant survival and performance, with economic implications that ultimately feed back to our capacity to conduct restoration. We followed a peer-reviewed protocol to develop a systematic map that collates, describes and catalogues the available studies on how seeding compares to planting in achieving restoration targets. We compiled a database with the characteristics of all retrieved studies, which can be searched to identify studies of particular locations and habitats, objectives of restoration, plant material, technical aspects, and outcomes measured. The search was made in eight languages and retrieved 3355 publications, of which 178 were retained. The systematic map identifies research gaps, such as a lack of studies in the global South, in tropical rainforests, and covering a long time period, which represent opportunities to expand field-based research. Additionally, many studies overlooked reporting on important technical aspects such as seed provenance and nursery cultivation methods, and others such as watering or seedling protection were more frequently applied for planting than for seeding, which limits our capacity to learn from past research. Most studies measured outcomes related to the target plants but avoided measuring general restoration outcomes or economic aspects. This represents a relevant gap in research, as the choice of revegetation method is greatly based on economic aspects and the achievement of restoration goals goes beyond the establishment of plants. Finally, we identified a substantial volume of studies conducted in temperate regions and over short periods (0-5 y). This research cluster calls for a future in-depth synthesis, potentially through meta-analysis, to reveal the overall balance between seeding and planting and assess whether the response to this question is mediated by species traits, environmental characteristics, or technical aspects. Besides identifying research clusters and gaps, the systematic map database allows managers to find the most relevant scientific literature on the appropriateness of seeding vs. planting for particular conditions, such as certain species or habitats.
Topics: Ecosystem; Plants; Seedlings; Seeds
PubMed: 36958277
DOI: 10.1016/j.jenvman.2023.117713 -
Nucleic Acids Research Jan 2024LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical...
LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school.
Topics: Databases, Factual; Lipid Metabolism; Lipidomics; Lipids; Software
PubMed: 37855672
DOI: 10.1093/nar/gkad896