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Ecology and Evolution Oct 2023Warming and changing precipitation can alter the performance of native grasses that are essential to grassland ecosystems. Native grasses may respond to changing climate...
Warming and changing precipitation can alter the performance of native grasses that are essential to grassland ecosystems. Native grasses may respond to changing climate by phenotypic plasticity or lose their current ranges. Establishing plant species from southern, warmer provenances may reduce the likelihood of biodiversity loss and improve restoration success in cool, northern locations that are undergoing warming. We conducted competition trials for (bluebunch wheatgrass), a native grass commonly found in western North American grasslands, to understand the impact of temperature and moisture on plant-plant interactions. We obtained seeds from three locations along a latitudinal gradient in North America, two in British Columbia (BC), Canada, and one in California, USA. We compared the effects of warming, changing water inputs, and competitor provenance on pairwise competitive interactions among plants grown from seeds obtained from the three locations. We quantified interactions using the relative interaction intensity, which has values from -1 (complete competition) to +1 (complete facilitation). Target plants from northern British Columbia, the location with the coldest summer temperature, were generally more competitively suppressed when competing with plants from California, which had the warmest summer temperature and lowest summer precipitation. Competitive suppression of target plants from northern British Columbia and southern British Columbia was more intense when competitor provenance was more geographically distant from target plant provenance. Finally, plants from northern British Columbia and southern British Columbia were more suppressed at higher temperatures, indicating some local adaptation, while plants from California were not affected by competitors, temperature, or water input. Plants grown from seeds obtained from warm and dry locations appear to be more tolerant to competition at higher temperatures, compared to plants from cooler regions. Native plant diversity and restoration success in grasslands subjected to climate change may be preserved or improved by assisted migration of seeds from warm to cooler but warming locations.
PubMed: 37886429
DOI: 10.1002/ece3.10603 -
ArXiv Jun 2024Limited universally adopted data standards in veterinary science hinders data interoperability and therefore integration and comparison; this ultimately impedes...
BACKGROUND –
Limited universally adopted data standards in veterinary science hinders data interoperability and therefore integration and comparison; this ultimately impedes application of existing information-based tools to support advancement in veterinary diagnostics, treatments, and precision medicine.
HYPOTHESIS/OBJECTIVES –
Creation of a Vertebrate Breed Ontology (VBO) as a single, coherent logic-based standard for documenting breed names in animal health, production and research-related records will improve data use capabilities in veterinary and comparative medicine.
ANIMALS –
No live animals were used in this study.
METHODS –
A list of breed names and related information was compiled from relevant sources, organizations, communities, and experts using manual and computational approaches to create VBO. Each breed is represented by a VBO term that includes all provenance and the breed's related information as metadata. VBO terms are classified using description logic to allow computational applications and Artificial Intelligence-readiness.
RESULTS –
VBO is an open, community-driven ontology representing over 19,000 livestock and companion animal breeds covering 41 species. Breeds are classified based on community and expert conventions (e.g., horse breed, cattle breed). This classification is supported by relations to the breeds' genus and species indicated by NCBI Taxonomy terms. Relationships between VBO terms, e.g. relating breeds to their foundation stock, provide additional context to support advanced data analytics. VBO term metadata includes common names and synonyms, breed identifiers/codes, and attributed cross-references to other databases.
CONCLUSION AND CLINICAL IMPORTANCE –
Veterinary data interoperability and computability can be enhanced by the adoption of VBO as a source of standard breed names in databases and veterinary electronic health records.
PubMed: 38883236
DOI: No ID Found -
JMIR Formative Research Dec 2023Secondary investigations into digital health records, including electronic patient data from German medical data integration centers (DICs), pave the way for enhanced...
Traceable Research Data Sharing in a German Medical Data Integration Center With FAIR (Findability, Accessibility, Interoperability, and Reusability)-Geared Provenance Implementation: Proof-of-Concept Study.
BACKGROUND
Secondary investigations into digital health records, including electronic patient data from German medical data integration centers (DICs), pave the way for enhanced future patient care. However, only limited information is captured regarding the integrity, traceability, and quality of the (sensitive) data elements. This lack of detail diminishes trust in the validity of the collected data. From a technical standpoint, adhering to the widely accepted FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship necessitates enriching data with provenance-related metadata. Provenance offers insights into the readiness for the reuse of a data element and serves as a supplier of data governance.
OBJECTIVE
The primary goal of this study is to augment the reusability of clinical routine data within a medical DIC for secondary utilization in clinical research. Our aim is to establish provenance traces that underpin the status of data integrity, reliability, and consequently, trust in electronic health records, thereby enhancing the accountability of the medical DIC. We present the implementation of a proof-of-concept provenance library integrating international standards as an initial step.
METHODS
We adhered to a customized road map for a provenance framework, and examined the data integration steps across the ETL (extract, transform, and load) phases. Following a maturity model, we derived requirements for a provenance library. Using this research approach, we formulated a provenance model with associated metadata and implemented a proof-of-concept provenance class. Furthermore, we seamlessly incorporated the internationally recognized Word Wide Web Consortium (W3C) provenance standard, aligned the resultant provenance records with the interoperable health care standard Fast Healthcare Interoperability Resources, and presented them in various representation formats. Ultimately, we conducted a thorough assessment of provenance trace measurements.
RESULTS
This study marks the inaugural implementation of integrated provenance traces at the data element level within a German medical DIC. We devised and executed a practical method that synergizes the robustness of quality- and health standard-guided (meta)data management practices. Our measurements indicate commendable pipeline execution times, attaining notable levels of accuracy and reliability in processing clinical routine data, thereby ensuring accountability in the medical DIC. These findings should inspire the development of additional tools aimed at providing evidence-based and reliable electronic health record services for secondary use.
CONCLUSIONS
The research method outlined for the proof-of-concept provenance class has been crafted to promote effective and reliable core data management practices. It aims to enhance biomedical data by imbuing it with meaningful provenance, thereby bolstering the benefits for both research and society. Additionally, it facilitates the streamlined reuse of biomedical data. As a result, the system mitigates risks, as data analysis without knowledge of the origin and quality of all data elements is rendered futile. While the approach was initially developed for the medical DIC use case, these principles can be universally applied throughout the scientific domain.
PubMed: 38060305
DOI: 10.2196/50027 -
Frontiers in Public Health 2023Blockchain technology includes numerous elements such as distributed ledgers, decentralization, authenticity, privacy, and immutability. It has progressed past the hype...
Blockchain technology includes numerous elements such as distributed ledgers, decentralization, authenticity, privacy, and immutability. It has progressed past the hype to find actual use cases in industries like healthcare. Blockchain is an emerging area that relies on a consensus algorithm and the idea of a digitally distributed ledger to eliminate any intermediary risks. By enabling them to trace data provenance and any changes made, blockchain technology can enable different healthcare stakeholders to share access to their networks without violating data security and integrity. The healthcare industry faces challenges like fragmented data, security and privacy concerns, and interoperability issues. Blockchain technology offers potential solutions by ensuring secure, tamper-proof storage across multiple network nodes, improving interoperability and patient privacy. Encrypting patient data further enhances security and reduces unauthorized access concerns. Blockchain technology, deployed over the Internet, can potentially use the current healthcare data by using a patient-centric approach and removing the intermediaries. This paper discusses the effective utilization of blockchain technology in the healthcare industry. In contrast to other applications, the exoteric evaluation in this paper shows that the innovative technology called blockchain technology has a major role to play in the existing and future applications of the healthcare industry and has significant benefits.
Topics: Humans; Blockchain; Electronic Health Records; Computer Security; Delivery of Health Care; Confidentiality
PubMed: 37790716
DOI: 10.3389/fpubh.2023.1229386 -
PloS One 2024Modern healthcare has a sharp focus on data aggregation and processing technologies. Consequently, from a data perspective, a patient may be regarded as a timestamped...
Modern healthcare has a sharp focus on data aggregation and processing technologies. Consequently, from a data perspective, a patient may be regarded as a timestamped list of medical conditions and their corresponding corrective interventions. Technologies to securely aggregate and access data for individual patients in the quest for precision medicine have led to the adoption of Digital Twins in healthcare. Digital Twins are used in manufacturing and engineering to produce digital models of physical objects that capture the essence of device operation to enable and drive optimization. Thus, a patient's Digital Twin can significantly improve health data sharing. However, creating the Digital Twin from multiple data sources, such as the patient's electronic medical records (EMR) and personal health records (PHR) from wearable devices, presents some risks to the security of the model and the patient. The constituent data for the Digital Twin should be accessible only with permission from relevant entities and thus requires authentication, privacy, and provable provenance. This paper proposes a blockchain-secure patient Digital Twin that relies on smart contracts to automate the updating and communication processes that maintain the Digital Twin. The smart contracts govern the response the Digital Twin provides when queried, based on policies created for each patient. We highlight four research points: access control, interaction, privacy, and security of the Digital Twin and we evaluate the Digital Twin in terms of latency in the network, smart contract execution times, and data storage costs.
Topics: Humans; Blockchain; Delivery of Health Care; Privacy; Electronic Health Records; Health Records, Personal
PubMed: 38422025
DOI: 10.1371/journal.pone.0286120 -
Data in Brief Jun 2024This paper provides comprehensive and systematized lists of names of 'moko' drums from Alor Island, in Southeast Indonesia. 'Moko' drums are unique cultural objects from...
This paper provides comprehensive and systematized lists of names of 'moko' drums from Alor Island, in Southeast Indonesia. 'Moko' drums are unique cultural objects from the Alor-Pantar Archipelago and, besides their ancient function of ritual instruments used mainly for religious purposes and in public events by the indigenous peoples of the islands, they represented and still are considered a very valuable local 'currency' for trade and for specific social interactions rooted in aboriginal culture, like bride price negotiations. Despite the fact that they are extremely popular and widespread among Papuan peoples in Alor and Pantar, the origins of these drums are still relatively obscure. The native speakers, indeed, cannot explain the name 'moko' in itself, at the etymological and semantic level, and, despite the fact that they agree upon non-local origins of the instruments, they do not know where the instruments themselves were produced and from where they came to the islands. Our paper provides the readers with comprehensive lists that systematically collect the names of the drums, with the related glosses and basic additional information, from three representative Papuan languages of Alor Island, namely Abui, Sawila, and Kula. Configured as potentially indispensable tools to develop further research, these lists enhance our knowledge and understanding of the culture of the 'moko' drums in the Alor-Pantar Archipelago, at the linguistic (etymology of the names), anthropological (social value of the drums), and archeological (typology and provenance of the instruments) levels. This cataloguing operation is also part of the effort of documentation of the languages and cultures, still scarcely documented and definitely endangered, of the native peoples of the Alor-Pantar Archipelago.
PubMed: 38590619
DOI: 10.1016/j.dib.2024.110354 -
Frontiers in Microbiology 2023is a globally important zoonotic pathogen largely found in cattle hosts and is typically transmitted to humans through contaminated dairy products or contact with...
is a globally important zoonotic pathogen largely found in cattle hosts and is typically transmitted to humans through contaminated dairy products or contact with diseased animals. Despite the long, shared history of cattle and humans, little is known about how trade in cattle has spread this pathogen throughout the world. Whole genome sequencing provides unparalleled resolution to investigate the global evolutionary history of a bacterium such as by providing phylogenetic resolution that has been unobtainable using other methods. We report on large-scale genome sequencing and analysis of collected globally from cattle and 16 other hosts from 52 countries. We used single nucleotide polymorphisms (SNPs) to identify genetic variation in 1,074 genomes and using maximum parsimony generated a phylogeny that identified four major clades. Two of these clades, clade A (median date 972 CE; 95% HPD, 781-1142 CE) and clade B (median date 150 BCE; 95% HPD, 515 BCE-164 CE), were exceptionally diverse for this species and are exclusively of African origin where provenance is known. The third clade, clade C (median date 949 CE; 95% HPD, 766-1102 CE), had most isolates coming from a broad swath of the Middle East, Europe, and Asia, also had relatively high diversity. Finally, the fourth major clade, clade D (median date 1467 CE; 95% HPD, 1367-1553 CE) comprises the large majority of genomes in a dominant but relatively monomorphic group that predominantly infects cattle in Europe and the Americas. These data are consistent with an African origin for and a subsequent spread to the Middle East, Europe, and Asia, probably through the movement of infected cattle. We hypothesize that European arrival to the Americas starting in the 15th century introduced from Western Europe through the introduction of a few common cattle breeds infected with strains from clade D. These data provide the foundation of a comprehensive global phylogeny of this important zoonotic pathogen that should be an important resource in human and veterinary epidemiology.
PubMed: 38094632
DOI: 10.3389/fmicb.2023.1287046 -
Sensors (Basel, Switzerland) Mar 2024The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans,...
The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans, histopathology images, and molecular information with clinical data is essential for developing a holistic understanding of the disease and optimizing treatment. The need for integrating data from multiple sources is further pronounced in complex diseases such as cancer for enabling precision medicine and personalized treatments. This work proposes Multimodal Integration of Oncology Data System (MINDS)-a flexible, scalable, and cost-effective metadata framework for efficiently fusing disparate data from public sources such as the Cancer Research Data Commons (CRDC) into an interconnected, patient-centric framework. MINDS consolidates over 41,000 cases from across repositories while achieving a high compression ratio relative to the 3.78 PB source data size. It offers sub-5-s query response times for interactive exploration. MINDS offers an interface for exploring relationships across data types and building cohorts for developing large-scale multimodal machine learning models. By harmonizing multimodal data, MINDS aims to potentially empower researchers with greater analytical ability to uncover diagnostic and prognostic insights and enable evidence-based personalized care. MINDS tracks granular end-to-end data provenance, ensuring reproducibility and transparency. The cloud-native architecture of MINDS can handle exponential data growth in a secure, cost-optimized manner while ensuring substantial storage optimization, replication avoidance, and dynamic access capabilities. Auto-scaling, access controls, and other mechanisms guarantee pipelines' scalability and security. MINDS overcomes the limitations of existing biomedical data silos via an interoperable metadata-driven approach that represents a pivotal step toward the future of oncology data integration.
Topics: Humans; Reproducibility of Results; Neoplasms
PubMed: 38475170
DOI: 10.3390/s24051634 -
BioRxiv : the Preprint Server For... Aug 2023Tissue folding generates structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to...
Tissue folding generates structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, the numerous finger-like protrusions that are essential for nutrient absorption. However, the molecular and mechanical mechanisms driving the initiation and morphogenesis of villi remain a matter of debate. Here, we identify an active mechanical mechanism that simultaneously patterns and folds intestinal villi. We find that PDGFRA+ subepithelial mesenchymal cells generate myosin II-dependent forces sufficient to produce patterned curvature in neighboring tissue interfaces. At the cell-level, this occurs through a process dependent upon matrix metalloproteinase-mediated tissue fluidization and altered cell-ECM adhesion. By combining computational models with experiments, we reveal these cellular features manifest at the tissue-level as differences in interfacial tensions that promote mesenchymal aggregation and interface bending through a process analogous to the active de-wetting of a thin liquid film.
PubMed: 37425793
DOI: 10.1101/2023.06.25.546328 -
PloS One 2023Crane is one of the vital components and lifelines of the construction industry. However, crane accidents happen regularly due to a variety of factors. Among them, the...
Crane is one of the vital components and lifelines of the construction industry. However, crane accidents happen regularly due to a variety of factors. Among them, the most far-reaching influence is the three factors of the human-machine-environment (HME). Moreover, how to carry out safety management for them is very critical. Considering the barriers to the goal, this study applied configuration management (CM) to HME data change management in cranes' service life cycle and proposed a HME-CM framework and approach. First, based on the original CM theory, baselines were developed to accommodate changes in HME configuration. Second, we discussed the evolving trajectory of HME configuration and determined the content and updates to the baseline. Third, a marking method based on data provenance theory was proposed to achieve data consistency. Finally, two search procedures were designed to perform the tracking and tracing of HME configuration. This paper contributes to expanding the application of CM theory in crane safety management, ensures the controllability and traceability of crane configuration changes, and provides a new perspective on crane safety.
Topics: Humans; Animals; Birds; Construction Industry; Life Cycle Stages; Safety Management
PubMed: 37651396
DOI: 10.1371/journal.pone.0290830