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Heliyon Jun 2024The rise in the cost of essentials affects every nation around the world, but it has become a major concern for developing nations. It is getting increasingly difficult... (Review)
Review
The rise in the cost of essentials affects every nation around the world, but it has become a major concern for developing nations. It is getting increasingly difficult to keep up with rising prices for everyday items in these countries, where the majority of the population is from the middle class or lower middle class. Inflation, pandemics, wars, and other important variables all contribute to price increases. There may be another significant factor at play, which is supply-chain corruption. The supply chain's unreliable, chaotic, and opaque nature is to blame for this corruption. We are concentrating on the agri-food supply chain in our study. Because many of the current agri-food supply chains are intricate and challenging to monitor, dishonest parties can exploit the situation. Therefore, we suggested a thorough blockchain-based agri-food supply chain to identify the source of price increases. The private Ethereum blockchain was used in the suggested system. Since the private Ethereum blockchain is more efficient, safe, and fast, it was chosen. Smart contracts were created to describe the system and its underlying rules and laws. Furthermore, in order to showcase the usefulness of our smart contracts, we exhibited a sample decentralized application to support our hypothesis. We also gave the system a complete security and vulnerability assessment to make sure it is operating properly and is protected from threats and attacks. Due to the use of blockchain, the system is immutable, transparent, and simple to track and monitor. The proposed system has demonstrated greater transparency, traceability, reliability, speed, security, and cost-efficiency compared to conventional systems. It effectively traces the origin of corruption in the supply chain, providing a more straightforward means to tackle concerns related to price hikes.
PubMed: 38832272
DOI: 10.1016/j.heliyon.2024.e30972 -
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 -
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 -
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 -
Plants (Basel, Switzerland) Nov 2023(Lour.) Pers. is an important woody spice tree in southern China, and its fruit is a rich source of valuable essential oil. We surveyed and sampled germplasm resources...
(Lour.) Pers. is an important woody spice tree in southern China, and its fruit is a rich source of valuable essential oil. We surveyed and sampled germplasm resources from 36 provenances in nine Chinese provinces, and detected rich phenotypic diversity. The survey results showed that plants of SC-KJ, SC-HJ, and SC-LS provenance presented higher leaf area (LA); YN-SM and YN-XC plants had larger thousand-grain fresh weight (TFW); and HN-DX plants had the highest essential oil content (EOC). To explain the large differences in the phenotypes of among different habitats, we used Pearson's correlation analysis, multiple stepwise regression path analysis, and redundancy analysis to evaluate the phenotypic diversity of . It was found that compared to other traits, leaf and fruit traits had more significant geographical distributions, and that leaf phenotypes were correlated to fruit phenotypes. The results showed that elevation, latitude, longitude, total soil porosity (SP), soil bulk density (SBD), and average annual rainfall (AAR, mm) contributed significantly to the phenotypic diversity of . Geographical factors explained a higher percentage of variation in phenotypic diversity than did soil factors and climate factors. Plants of SC-KJ and HN-DX provenances could be important resources for domestication and breeding to develop new high-yielding varieties of this woody aromatic plant. This study describes significant phenotypic differences in related to adaptation to different environments, and provides a theoretical basis for the development of a breeding strategy and for optimizing cultivation.
PubMed: 37960137
DOI: 10.3390/plants12213781 -
Chinese Medicine Jul 2023Evaluating traditional Chinese medicine (TCM) quality is a powerful method to ensure TCM safety. TCM quality evaluation methods primarily include characterization...
BACKGROUND
Evaluating traditional Chinese medicine (TCM) quality is a powerful method to ensure TCM safety. TCM quality evaluation methods primarily include characterization evaluations and separate physical, chemical, and biological evaluations; however, these approaches have limitations. Nevertheless, researchers have recently integrated evaluation methods, advancing the emergence of frontier research tools, such as TCM quality markers (Q-markers). These studies are largely based on biological activity, with weak correlations between the quality indices and quality. However, these TCM quality indices focus on the individual efficacies of single bioactive components and, therefore, do not accurately represent the TCM quality. Conventionally, provenance, place of origin, preparation, and processing are the key attributes influencing TCM quality. In this study, we identified TCM-attribute-based quality indices and developed a comprehensive multiweighted multi-index-based TCM quality composite evaluation index (QCEI) for grading TCM quality.
METHODS
The area of origin, number of growth years, and harvest season are considered key TCM quality attributes. In this study, licorice was the model TCM to investigate the quality indicators associated with key factors that are considered to influence TCM quality using multivariate statistical analysis, identify biological-evaluation-based pharmacological activity indicators by network pharmacology, establish real quality indicators, and develop a QCEI-based model for grading TCM quality using a machine learning model. Finally, to determine whether different licorice quality grades differently reduced the inflammatory response, TNF-α and IL-1β levels were measured in RAW 264.7 cells using ELISA analysis.
RESULTS
The 21 quality indices are suitable candidates for establishing a method for grading licorice quality. A computer model was established using SVM analysis to predict the TCM quality composite evaluation index (TCM QCEI). The tenfold cross validation accuracy was 90.26%. Licorice diameter; total flavonoid content; similarities of HPLC chromatogram fingerprints recorded at 250 and 330 nm; contents of liquiritin apioside, liquiritin, glycyrrhizic acid, and liquiritigenin; and pharmacological activity quality index were identified as the key indices for constructing the model for evaluating licorice quality and determining which model contribution rates were proportionally weighted in the model. The ELISA analysis results preliminarily suggest that the inflammatory responses were likely better reduced by premium-grade than by first-class licorice.
CONCLUSIONS
In the present study, traditional sensory characterization and modern standardized processes based on production process and pharmacological efficacy evaluation were integrated for use in the assessment of TCM quality. Multidimensional quality evaluation indices were integrated with a machine learning model to identify key quality indices and their corresponding weight coefficients, to establish a multiweighted multi-index and comprehensive quality index, and to construct a QCEI-based model for grading TCM quality. Our results could facilitate and guide the development of TCM quality control research.
PubMed: 37501143
DOI: 10.1186/s13020-023-00782-0 -
JAMA Internal Medicine Jan 2024Both the commercial sector and academia play a vital role in medicine development. Ongoing debates exist on their contribution and the value of medicinal products...
IMPORTANCE
Both the commercial sector and academia play a vital role in medicine development. Ongoing debates exist on their contribution and the value of medicinal products entering the market.
OBJECTIVE
To identify the provenance and clinical benefit of medicines that entered the French market between 2008 and 2018.
DESIGN AND SETTING
In this cross-sectional study, the provenance of each medicine in the French market was established via a review of multiple sources documenting at least 2 matching findings per product. The clinical benefit was assigned using the matched scale developed from the Prescrire and Haute Autorité de Santé (HAS) gradings. The χ2 test was used to analyze the proportions and frequencies of medicines graded by Prescrire and HAS by origin, therapeutic category, and clinical benefit.
MAIN OUTCOMES AND MEASURES
The origins and therapeutic categories of medicines. Clinical benefit based on Prescrire and HAS grading. Concordance of Prescrire and HAS grading.
RESULTS
Of the 632 medicines that entered the French market between 2008 and 2018, 464 originated (73%) in the commercial sector, and 168 originated (27%) in the academic setting or in collaboration with commercial enterprises. Prescrire graded psychotropic agents (13/14 [93%]), whereas HAS graded respiratory agents (24/25 [96%]) as the highest percentage of medicines that provided no added benefit. Prescrire graded 360 medicines (77.6%) that originated in the industry and 108 medicines (64.3%) that originated in the academic setting (P = .001) to have no added clinical benefit. HAS assigned such grading to 331 ([71.3%] industry) vs 104 ([61.9%] academia) (P = .02). Based on the Prescrire grading, academia invented more medicines delivering some added benefit 57 (33.9%) vs 98 (21.1%) invented by industry (P = .001). HAS grading on some added benefit 51 ([30.4%] academia) vs 121 ([26.1%] industry) did not reach statistical significance (P = .29). However, HAS grading on substantial added clinical benefit reached statistical significance in favor of academia (13 [7.7%] vs 12 [2.6%] in the industry; P = .003), whereas Prescrire grading did not (1.8% academia vs 1.3% industry; P = .64).
CONCLUSIONS AND RELEVANCE
More than 70% of medicines that entered the French market during the 10-year period originated in the commercial sector. Although most medicines were not graded as providing clinical benefit, medicines originating in the academic setting were more likely to be graded as conferring clinical benefit than those originating in the commercial setting.
Topics: Humans; Cross-Sectional Studies; Drug Industry; Commerce; Pharmaceutical Preparations
PubMed: 37983026
DOI: 10.1001/jamainternmed.2023.6249 -
BioRxiv : the Preprint Server For... Dec 2023The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance...
The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a metadata standard guided by the principles of Findability, Accessibility, Interoperability, and Reuse (FAIR) in addition to the principles of Transparency, Responsibility, User focus, Sustainability, and Technology (TRUST). The objective of FHR is to provide an extensive set of data serialisation methods and minimum data field requirements while still maintaining extensibility, flexibility, and expressivity in an increasingly decentralised genomic data ecosystem. The effort needed to implement FHR is low; FHR's design philosophy ensures easy implementation while retaining the benefits gained from recording both machine and human-readable provenance.
PubMed: 38076838
DOI: 10.1101/2023.11.29.569306 -
AoB PLANTS Oct 2023In the temperate forests of Patagonia, Argentina, , commonly known as Coihue, has shown sensitivity to intense drought events, leading to mortality. Studies have been...
In the temperate forests of Patagonia, Argentina, , commonly known as Coihue, has shown sensitivity to intense drought events, leading to mortality. Studies have been conducted on Coihue decline and mortality using a variety of approaches, including the role of extreme heat waves and drought, pests and pathogens, particularly the fungus . This work aimed to evaluate survival, vitality, necrosis extension and growth response of inoculated and non-inoculated Coihue seedlings from different provenances exposed to different soil moisture levels. To achieve this goal, 96 Coihue seedlings from 2 different provenances were assigned to 8 different experimental treatments. Treatments were composed of the presence or absence of and different soil moisture content conditions, dry, wet and the exposure to dry condition at different times of the experiment. Both dry conditions and had negative effects on the survival and growth rate of Coihue. The combination of both factors resulted in 100 % mortality, regardless of the plants' geographical provenances. Mortality began to be observed 3 months after pathogen inoculation, during the warmest month. Necrosis extension produced by the pathogen was similar for most of the inoculated treatments. The treatment under wet condition during the experiment but subjected to dry condition in the previous growing season presented lower necrosis extension (8.4 ± 3.2 %), than the other treatments. The radial increase was also affected by the treatments and geographical provenance, being those plants exposed to dry conditions which grew less (0.19 ± 0.21 mm). This study enhances our understanding of the plant-pathogen interaction. According to our results, Coihue may become more susceptible to mortality, when and water deficit conditions act synergistically.
PubMed: 37899976
DOI: 10.1093/aobpla/plad068