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Journal of Chemical Information and... Nov 2023Web ontologies are important tools in modern scientific research because they provide a standardized way to represent and manage web-scale amounts of complex data. In...
Web ontologies are important tools in modern scientific research because they provide a standardized way to represent and manage web-scale amounts of complex data. In chemistry, a semantic database for chemical species is indispensable for its ability to interrelate and infer relationships, enabling a more precise analysis and prediction of chemical behavior. This paper presents OntoSpecies, a web ontology designed to represent chemical species and their properties. The ontology serves as a core component of The World Avatar knowledge graph chemistry domain and includes a wide range of identifiers, chemical and physical properties, chemical classifications and applications, and spectral information associated with each species. The ontology includes provenance and attribution metadata, ensuring the reliability and traceability of data. Most of the information about chemical species are sourced from PubChem and ChEBI data on the respective compound Web pages using a software agent, making OntoSpecies a comprehensive semantic database of chemical species able to solve novel types of problems in the field. Access to this reliable source of chemical data is provided through a SPARQL end point. The paper presents example use cases to demonstrate the contribution of OntoSpecies in solving complex tasks that require integrated semantically searchable chemical data. The approach presented in this paper represents a significant advancement in the field of chemical data management, offering a powerful tool for representing, navigating, and analyzing chemical information to support scientific research.
Topics: Knowledge Discovery; Reproducibility of Results; Software; Databases, Factual; Semantics
PubMed: 37883649
DOI: 10.1021/acs.jcim.3c00820 -
BMJ (Clinical Research Ed.) Mar 2024
PubMed: 38438191
DOI: 10.1136/bmj-2023-074797 -
IEEE Transactions on Visualization and... Jun 2024The study of cultural artifact provenance, tracing ownership and preservation, holds significant importance in archaeology and art history. Modern technology has...
The study of cultural artifact provenance, tracing ownership and preservation, holds significant importance in archaeology and art history. Modern technology has advanced this field, yet challenges persist, including recognizing evidence from diverse sources, integrating sociocultural context, and enhancing interactive automation for comprehensive provenance analysis. In collaboration with art historians, we examined the handscroll, a traditional Chinese painting form that provides a rich source of historical data and a unique opportunity to explore history through cultural artifacts. We present a three-tiered methodology encompassing artifact, contextual, and provenance levels, designed to create a "Biography" for handscroll. Our approach incorporates the application of image processing techniques and language models to extract, validate, and augment elements within handscroll using various cultural heritage databases. To facilitate efficient analysis of non-contiguous extracted elements, we have developed a distinctive layout. Additionally, we introduce ScrollTimes, a visual analysis system tailored to support the three-tiered analysis of handscroll, allowing art historians to interactively create biographies tailored to their interests. Validated through case studies and expert interviews, our approach offers a window into history, fostering a holistic understanding of handscroll provenance and historical significance.
PubMed: 38625782
DOI: 10.1109/TVCG.2024.3388523 -
PloS One 2024Morphological variation in modern human dentition is still an open field of study. The understanding of dental shape and metrics is relevant for the advancement of human...
Morphological variation in modern human dentition is still an open field of study. The understanding of dental shape and metrics is relevant for the advancement of human biology and evolution and is thus of interest in the fields of dental anthropology, as well as human anatomy and medicine. Of concern is also the variation of the inner aspects of the crown which can be investigated using the tools and methods of virtual anthropology. In this study, we explored inter- and intra-population morphometric variation of modern humans' upper third and fourth premolars (P3s and P4s, respectively) considering both the inner and outer aspects of the crown, and discrete traits. We worked by means of geometric morphometrics on 3D image data from a geographically balanced sample of human populations from five continents, to analyse the shape of the dentinal crown, and the crown outline in 78 P3s and 76 P4s from 85 individuals. For the study of dental traits, we referred to the Arizona State University Dental Anthropology System integrated with more recent classification systems. The 3D shape variation of upper premolar crowns varied between short and mesio-distally broad, and tall and mesio-distally narrow. The observed shape variation was independent from the geographical origin of the populations, and resulted in extensive overlap. We noted a high pairwise correlation (r1 = 0.83) between upper P3s and P4s. We did not find any significant geographic differences in the analysed non-metric traits. Our outcomes thus suggest that geographical provenance does not play a determinant role in the shaping of the dental crown, whose genesis is under strict genetic control.
Topics: Animals; Humans; Bicuspid; Anthropology, Physical; Hominidae; Anthropology; Tooth Crown
PubMed: 38593117
DOI: 10.1371/journal.pone.0301482 -
Anatomical Record (Hoboken, N.J. : 2007) Mar 2024Collections of human remains in scientific and private institutions have a long tradition, though throughout history there has often been variable regard for the respect... (Review)
Review
Collections of human remains in scientific and private institutions have a long tradition, though throughout history there has often been variable regard for the respect and dignity that these tissues demand. Recent public scandals around the use of human remains, coupled with an increasing community awareness around accountability in such instances, forces scholars to confront the ethical and moral concerns associated with these collections. This includes specific focus on the acquisition, storage, use, and disposition of these remains, which were often collected with no consent and with little knowledge, or concern, about the individual or their respective culture and practices surrounding death and postmortem treatment. As a response, the American Association for Anatomy convened a Legacy Anatomical Collections Task Force to consider these issues and to develop recommendations to assist those working with these tissues in education, research, and museum collections. This has culminated with the development of Recommendations for the Management of Legacy Anatomical Collections. The recommendations provide both an ethical foundation and practical considerations for the use, storage, and disposition of legacy collections of human tissues, and deliver guidance for establishing appropriate management and oversight, investigating provenance, and engaging with communities of care. While these Recommendations are considered a living document which will change over time as ethical principles concerning human tissue evolve, they currently represent 'best practice' recommendations that can guide researchers, teachers, and museum associates as they consider the future of legacy anatomical collections in their care.
PubMed: 38497461
DOI: 10.1002/ar.25410 -
Journal of Biomedical Semantics Aug 2023This paper proposes Cyrus, a new transparency evaluation framework, for Open Knowledge Extraction (OKE) systems. Cyrus is based on the state-of-the-art transparency...
BACKGROUND
This paper proposes Cyrus, a new transparency evaluation framework, for Open Knowledge Extraction (OKE) systems. Cyrus is based on the state-of-the-art transparency models and linked data quality assessment dimensions. It brings together a comprehensive view of transparency dimensions for OKE systems. The Cyrus framework is used to evaluate the transparency of three linked datasets, which are built from the same corpus by three state-of-the-art OKE systems. The evaluation is automatically performed using a combination of three state-of-the-art FAIRness (Findability, Accessibility, Interoperability, Reusability) assessment tools and a linked data quality evaluation framework, called Luzzu. This evaluation includes six Cyrus data transparency dimensions for which existing assessment tools could be identified. OKE systems extract structured knowledge from unstructured or semi-structured text in the form of linked data. These systems are fundamental components of advanced knowledge services. However, due to the lack of a transparency framework for OKE, most OKE systems are not transparent. This means that their processes and outcomes are not understandable and interpretable. A comprehensive framework sheds light on different aspects of transparency, allows comparison between the transparency of different systems by supporting the development of transparency scores, gives insight into the transparency weaknesses of the system, and ways to improve them. Automatic transparency evaluation helps with scalability and facilitates transparency assessment. The transparency problem has been identified as critical by the European Union Trustworthy Artificial Intelligence (AI) guidelines. In this paper, Cyrus provides the first comprehensive view of transparency dimensions for OKE systems by merging the perspectives of the FAccT (Fairness, Accountability, and Transparency), FAIR, and linked data quality research communities.
RESULTS
In Cyrus, data transparency includes ten dimensions which are grouped in two categories. In this paper, six of these dimensions, i.e., provenance, interpretability, understandability, licensing, availability, interlinking have been evaluated automatically for three state-of-the-art OKE systems, using the state-of-the-art metrics and tools. Covid-on-the-Web is identified to have the highest mean transparency.
CONCLUSIONS
This is the first research to study the transparency of OKE systems that provides a comprehensive set of transparency dimensions spanning ethics, trustworthy AI, and data quality approaches to transparency. It also demonstrates how to perform automated transparency evaluation that combines existing FAIRness and linked data quality assessment tools for the first time. We show that state-of-the-art OKE systems vary in the transparency of the linked data generated and that these differences can be automatically quantified leading to potential applications in trustworthy AI, compliance, data protection, data governance, and future OKE system design and testing.
Topics: Humans; Artificial Intelligence; COVID-19; Semantic Web
PubMed: 37653549
DOI: 10.1186/s13326-023-00293-9 -
BMJ (Clinical Research Ed.) Apr 2024
Topics: Tobacco Industry; Humans; Education, Medical, Continuing; Conflict of Interest
PubMed: 38670579
DOI: 10.1136/bmj.q950 -
BMJ (Clinical Research Ed.) Jan 2024
Topics: Humans; Public Health; Anti-Obesity Agents; Obesity; Weight Loss
PubMed: 38290742
DOI: 10.1136/bmj.q196 -
Frontiers in Plant Science 2023has the characteristics of rapid growth and high resistance. However, there is little research on molecular breeding of , which is essential to shortening breeding life...
has the characteristics of rapid growth and high resistance. However, there is little research on molecular breeding of , which is essential to shortening breeding life and selecting quality varieties. Therefore, a crucial step before selective breeding can be carried out to increase the wood quality of is identifying genetic diversity and population structure using single nucleotide polymorphism (SNP) markers. In this study, the genetic diversity of 1 generation 196 families from 23 geographically defined was assessed using 1,677,732 SNP markers identified by whole genome resequencing. SNP annotation showed that the ratio of non-synonymous to synonymous coding mutations was 0.83. Principal component analysis (PCA), phylogenetic tree, and population structure analysis permitted the families to be categorized into three groups, one of which (G2) contains most of the Indonesian (IDN) and Papua New Guinea (PNG) families. Genetic relationship analysis showed that IDN was closely related to PNG. Genetic diversity analysis showed that He, PIC, I, and H mean values were 0.2502, 0.2027, 0.3815, and 0.2680, respectively. PCA analysis classified various provenances in QLD into two categories (G1 and G3). The genetic diversity of G3 was higher than that of G2. The results of genetic differentiation (Fst) showed that PNG region was divided into two groups (PNG1 and PNG2), the Fst (0.172) between QLD and PNG2 region was higher than QLD and PNG1, and the Fst (0.024) between IDN and PNG1 is smaller than IDN and PNG2. A Mantel test revealed a positive correlation between the genetic and geographic distance of . This study has a certain reference value for genetic identification, germplasm preservation, and breeding of . Also, it provides a basis for subsequent association analysis to explore excellent alleles and introduction.
PubMed: 38162312
DOI: 10.3389/fpls.2023.1278427 -
Progress in Biophysics and Molecular... Jan 2024One of the foundational principles of recent developments in evolutionary biology has been the acknowledgement of homeostasis as an organising principle of cellular...
One of the foundational principles of recent developments in evolutionary biology has been the acknowledgement of homeostasis as an organising principle of cellular development from unicellular origins. Fundamentally, this concerns the balance between the inside of a biological entity and its environment. Given that the organ of balance is the ear, and that the evolutionary provenance of the vestibular system can be traced back to fish, music provides a rich foundation for evolutionary biological inquiry. This paper considers a specific dimensional relationship in sonic experience between noise, signal, redundancy and anticipation. Drawing on the physics of Bohm and more recent developments in Rowlands's nilpotent quantum mechanics, I argue that the relationship between these four parameters is not only that they represent aspects of sonic experience, but that they are dimensionally distinct, where noise can be considered to be scalar, a signal (or a note) is a vector (having magnitude and direction), redundancy is bi-vectorial (involving degrees of repetition of signals over time), and anticipation is tri-vectorial (involving reflexive consideration of different orders of redundancy). In outlining the dimensional distinction between these variables, an analysis is presented which considers the relationship between the Shannon entropy of different dimensions in music. This shows that the entropy of noise has a particular bearing on the entropy of the other dimensions. This dimensional relation is also reflected in biological evidence, where Torday has shown there to be a direct correlation between the effect of gravitational "noise" on cellular communication, and by extension the evolution of consciousness.
Topics: Animals; Music; Cell Communication; Homeostasis; Consciousness; Cell Differentiation
PubMed: 38103652
DOI: 10.1016/j.pbiomolbio.2023.11.006