Open data and interoperability standards : opportunities for animal welfare in extensive livestock systems

Extensive livestock farming constitutes a sizeable portion of agriculture, not only in relation to land use, but in contribution to feeding a growing human population. In addition to meat, it contributes other economically valuable commodities such as wool, hides and other products. The livestock industries are adopting technologies under the banner of Precision Livestock Farming (PLF) to help meet higher production and efficiency targets as well as help to manage the multiple challenges impacting the industries, such as climate change, environmental concerns, globalisation of markets, increasing rules of governance and societal scrutiny especially in relation to animal welfare. PLF is particularly dependent on the acquisition and management of data and metadata and on the interoperability standards that allow data discovery and federation. A review of interoperability standards and PLF adoption in extensive livestock farming systems identified a lack of domain specific standards and raised questions related to the amount and quality of public data which has potential to inform livestock farming. A systematic review of public datasets, which included an assessment based on the principles that data must be findable, accessible, interoperable and reusable (FAIR) was developed. Custom software scripts were used to conduct a dataset search to determine the quantity and quality of domain specific datasets yielded 419 unique Australian datasets directly related to extensive livestock farming. A FAIR assessment of these datasets using a set of non-domain specific, general metrics showed a moderate level of compliance. The results suggest that domain specific FAIR metrics may need to be developed to provide a more accurate data quality assessment, but also that the level of interoperability and reusability is not particularly high which has implications if public data is to be included in decision support tools. To test the usefulness of available public datasets in informing decision support in relation to livestock welfare, a case study was designed and farm animal welfare elements were extracted from Australian welfare standards to guide a dataset search. It was found that with few exceptions, these elements could be supported with public data, although there were gaps in temporal and spatial coverage. The development of a geospatial animal welfare portal including these datasets further explored and confirmed the potential for using public data to enhance livestock welfare.Doctor of Philosoph

Loss of symmetric cell division of apical neural progenitors drives DENND5A-related developmental and epileptic encephalopathy.

Developmental and epileptic encephalopathies (DEEs) feature altered brain development, developmental delay and seizures, with seizures exacerbating developmental delay. Here we identify a cohort with biallelic variants in DENND5A, encoding a membrane trafficking protein, and develop animal models with phenotypes like the human syndrome. We demonstrate that DENND5A interacts with Pals1/MUPP1, components of the Crumbs apical polarity complex required for symmetrical division of neural progenitor cells. Human induced pluripotent stem cells lacking DENND5A fail to undergo symmetric cell division with an inherent propensity to differentiate into neurons. These phenotypes result from misalignment of the mitotic spindle in apical neural progenitors. Cells lacking DENND5A orient away from the proliferative apical domain surrounding the ventricles, biasing daughter cells towards a more fate-committed state, ultimately shortening the period of neurogenesis. This study provides a mechanism for DENND5A-related DEE that may be generalizable to other developmental conditions and provides variant-specific clinical information for physicians and families

Advancing FAIR Agricultural Data: The AgReFed FAIR Assessment Tool

The FAIR principles provide guidance for improving the findability, accessibility, interoperability and reuse of research data and other digital objects. The Agricultural Research Federation (AgReFed) has developed a FAIR implementation consisting of policies, resources and tools to enable FAIR agricultural data in Australia. It prescribes minimum acceptable data standards and an associated set of FAIR metrics for agricultural research data. Existing FAIR assessment tools were examined and found to have limitations in serving the purposes of AgReFed. The AgReFed FAIR assessment tool addresses these needs with novel features to help improve FAIRness of datasets and other digital resources. By providing the ability to assess and subsequently re-assess datasets while also enabling users to add comments, it facilitates building work lists that support and document the improvement in FAIRness. Other innovative features include customisable FAIR metrics, storage of assessment results, a versioning system and inbuilt help resources. In addition to user-friendly reporting of AgReFed standards compliance, the integrated automated F-UJI FAIR assessment API provides a supplementary set of machine-readable FAIR scores. The AgReFed FAIR Assessment Tool has been deployed for public use and released as open source to help data custodians enact FAIR principles in domains and data communities within and beyond Australian agriculture

Livestock data – is it there and is it FAIR? A systematic review of livestock farming datasets in Australia

The global adoption of the FAIR principles for scientific data: findable, accessible, interoperable and reusable, has been relatively slow in agriculture, compared to other disciplines. A recent review of the literature showed that the use of precision farming technologies and the development and adoption of open data standards was particularly low in extensive livestock farming. However, a plethora of public datasets exist that have the potential to be used to inform precision farming decision tools. Using extensive livestock farming in Australia as example, we investigate the quantity and quality of datasets available via a systematic dataset review. This systematic review of datasets begins with a search of open data catalogues and querying these to find datasets. Software scripts are developed and used to query the Application Programming Interfaces (APIs) of many of the large data catalogues in Australia, while catalogues without public APIs are queried manually via available web portals. Following the systematic search, a combined list of all datasets is collated and tested for FAIRness and other quality metrics. The contribution of this work is the resulting overview of the state of open datasets within the livestock farming domain on the one hand, but also the development of a systematic dataset search strategy, reusable methods and software scripts. © 2021 Elsevier B.V

The role of interoperable data standards in precision livestock farming in extensive livestock systems : A review

Livestock industries are increasingly embracing precision farming and decision support tools. As a result, sensors, weather stations, individual animal tracking, feed monitoring and other sources create large data volumes, much of which is used only for a single purpose. There are unrealised potential benefits of making on farm data interoperable and accessible and federating it with public data sources. We reviewed recent literature on precision livestock farming (PLF) technologies in relation to the use of public data, open standards and interoperability. Livestock farms produce rising volumes of disparate private datasets, reflecting a variety of information needs and technological opportunities, but typically lacking interoperable formats and metadata. These as well as large amounts of accessible public datasets are currently underutilised in decision support tools. Tools that demonstrate the use of interoperable standards and bring together public and private data for decision support can enhance the value proposition and help lower barriers to the sharing and re-use of data. This review of interoperable standards in extensive livestock farming systems concludes that there is a need for not only a new type of decision support tool, but also a consensus on data exchange standards to prove the value of shared data at farm scale (commercial benefit) and a regional scale (public good). © 201

Chronic lymphocytic leukemia with mutated IGHV4-34 receptors : Shared and distinct immunogenetic features and clinical outcomes

Purpose: We sought to investigate whether B cell receptor immunoglobulin (BcR IG) stereotypy is associated with particular clinicobiological features among chronic lymphocytic leukemia (CLL) patients expressing mutated BcR IG (M-CLL) encoded by the IGHV4-34 gene, and also ascertain whether these associations could refine prognostication. Experimental Design: In a series of 19,907 CLL cases with available immunogenetic information, we identified 339 IGHV4-34-expressing cases assigned to one of the four largest stereotyped M-CLL subsets, namely subsets #4, #16, #29 and #201, and investigated in detail their clinicobiological characteristics and disease outcomes. Results: We identified shared and subset-specific patterns of somatic hypermutation (SHM) among patients assigned to these subsets. The greatest similarity was observed between subsets #4 and #16, both including IgG-switched cases (IgG-CLL). In contrast, the least similarity was detected between subsets #16 and #201, the latter concerning IgM/D-expressing CLL. Significant differences between subsets also involved disease stage at diagnosis and the presence of specific genomic aberrations. IgG subsets #4 and #16 emerged as particularly indolent with a significantly (P < 0.05) longer time-to-first-treatment (TTFT; median TTFT: not yet reached) compared with the IgM/D subsets #29 and #201 (median TTFT: 11 and 12 years, respectively). Conclusions: Our findings support the notion that BcR IG stereotypy further refines prognostication in CLL, superseding the immunogenetic distinction based solely on SHM load. In addition, the observed distinct genetic aberration landscapes and clinical heterogeneity suggest that not all M-CLL cases are equal, prompting further research into the underlying biological background with the ultimate aim of tailored patient management

Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes

Purpose: We sought to investigate whether B cell receptor immunoglobulin (BcR IG) stereotypy is associated with particular clinicobiological features among chronic lymphocytic leukemia (CLL) patients expressing mutated BcR IG (M-CLL) encoded by the IGHV4-34 gene, and also ascertain whether these associations could refine prognostication. Experimental Design: In a series of 19,907 CLL cases with available immunogenetic information, we identified 339 IGHV4-34expressing cases assigned to one of the four largest stereotyped M-CLL subsets, namely subsets #4, #16, #29 and #201, and investigated in detail their clinicobiological characteristics and disease outcomes. Results: We identified shared and subset-specific patterns of somatic hypermutation (SHM) among patients assigned to these subsets. The greatest similarity was observed between subsets #4 and #16, both including IgG-switched cases (IgG-CLL). In contrast, the least similarity was detected between subsets #16 and #201, the latter concerning IgM/D-expressing CLL. Significant differences between subsets also involved disease stage at diagnosis and the presence of specific genomic aberrations. IgG subsets #4 and #16 emerged as particularly indolent with a significantly (P lt 0.05) longer time-to-first-treatment (TTFT; median TTFT: not yet reached) compared with the IgM/D subsets #29 and #201 (median TTFT: 11 and 12 years, respectively). Conclusions: Our findings support the notion that BcR IG stereotypy further refines prognostication in CLL, superseding the immunogenetic distinction based solely on SHM load. In addition, the observed distinct genetic aberration landscapes and clinical heterogeneity suggest that not all M-CLL cases are equal, prompting further research into the underlying biological background with the ultimate aim of tailored patient management.This is the peer-reviewed version of the article: Xochelli, A., Baliakas, P., Kavakiotis, I., Agathangelidis, A., Sutton, L.-A., Minga, E., Ntoufa, S., Tausch, E., Yan, X.-J., Shanafelt, T., Plevova, K., Boudjogra, M., Rossi, D., Davis, Z., Navarro, A., Sandberg, Y., Vojdeman, F. J., Scarfo, L., Stavroyianni, N., … Stamatopoulos, K. (2017). Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinica Outcomes. Clinical Cancer Research, 23(17), 5292–5301. [https://imagine.imgge.bg.ac.rs/handle/123456789/1611