The Human Phenotype Ontology in 2024: phenotypes around the world.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

The Human Phenotype Ontology in 2024: phenotypes around the world

\ua9 The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs

Comparative analysis of the transcriptome across distant species

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters

Effect of depth and method of primary tillage on fallow soil water and nitrate changes and wheat grain yield

An experiment was conducted on an alluvial soil at Biloela Research Station from 1970 to 1975 to determine the effect of two depths (10 to 15 cm and 20 to 30 cm) and two methods (disc and chisel) of primary tillage on changes in soil water and nitrate-nitrogen over the fallow period and on subsequent wheat grain yield. There were no significant (P<0.05) treatment differences in available soil water levels to a depth of 1.4m at the beginning and end of the fallow period in any year. Deep (20 to 30 cm) disc primary tillage resulted in a greater increase in soil nitrate-nitrogen levels in the 0 to 40 cm layer over the fallow period than shallow (10 to 15 cm) disc or chisel primary tillage or deep (20 to 30 cm) chisel primary tillage in three of the four years of the experiment. Significant (P<0.05) increases in grain yield were obtained with deep disc primary tillage in two of the three years in which higher soil nitrate-nitrogen status occurred at planting in this treatment. The occurrence of a yield response to the higher soil nitrate-nitrogen levels in the 0 to 40 cm layer following deep disc primary tillage appeared to depend on seasonal conditions during crop growth. Grain protein content was generally similar for all treatments in any one year

Relationship between grain yield and maturity of wheat in central Queensland

Experiments were conducted to determine the most suitable maturity types of wheat under the environmental conditions of central Queensland, where the supply of moisture available for crop growth is generally considered the major factor limiting production. Between 27 and 30 wheat lines with a wide range of maturities were selected from each of the two crosses, Pusa 4 x Spica and Seafoam x Sterling. These lines were grown in 23 field experiments over a range of locations, planting times and seasonal conditions in central Queensland from 1972 to 1975. Planting times ranged from late April to early July

Effect of weed competition and inter-row cultivation on yield of grain sorghum

Three experiments were conducted from 1973 to 1975 to determine the effect of weed competition and inter-row cultivation on the yield of grain sorghum on an alluvial soil at Biloela Research Station in central Queensland

Row spacing and population density effects on yield of grain sorghum in central Queensland

In 1968-71, 7 trials were carried out in the main grain growing areas of central Queensland to determine the most suitable combinations of row spacing and population density for producing raingrown grain sorghum in this area

A call to evaluate plastic’s impacts on marine, benthic ecosystem interaction networks

Funding: This work was supported by an anonymous philanthropic donor through the Microphytes and Microplastics project.Plastic pollution continues to seep into natural and pristine habitats. Emerging laboratory-based research has evoked concern regarding plastic’s impact on ecosystem structure and function, the essence of the ecosystem services that supports our life, wellbeing, and economy. These impacts have yet to be observed in nature where complex ecosystem interaction networks are enveloped in environmental physical and chemical dynamics. Specifically, there is concern that environmental impacts of plastics reach beyond toxicity and into ecosystem processes such as primary production, respiration, carbon and nutrient cycling, filtration, bioturbation, and bioirrigation. Plastics are popularly regarded as recalcitrant carbon molecules, although they have not been fully assessed as such. We hypothesize that plastics can take on similar roles as natural recalcitrant carbon (i.e., lignin and humic substances) in carbon cycling and associated biogeochemistry. In this paper, we review the current knowledge of the impacts of plastic pollution on marine, benthic ecosystem function. We argue for research advancement through (1) employing field experiments, (2) evaluating ecological network disturbances by plastic, and (3) assessing the role of plastics (i.e., a carbon-based molecule) in carbon cycling at local and global scales.PostprintPeer reviewe

A call to evaluate plastic’s impacts on marine, benthic ecosystem interaction networks

Plastic pollution continues to seep into natural and pristine habitats. Emerging laboratory-based research has evoked concern regarding plastic’s impact on ecosystem structure and function, the essence of the ecosystem services that supports our life, wellbeing, and economy. These impacts have yet to be observed in nature where complex ecosystem interaction networks are enveloped in environmental physical and chemical dynamics. Specifically, there is concern that environmental impacts of plastics reach beyond toxicity and into ecosystem processes such as primary production, respiration, carbon and nutrient cycling, filtration, bioturbation, and bioirrigation. Plastics are popularly regarded as recalcitrant carbon molecules, although they have not been fully assessed as such. We hypothesize that plastics can take on similar roles as natural recalcitrant carbon (i.e., lignin and humic substances) in carbon cycling and associated biogeochemistry. In this paper, we review the current knowledge of the impacts of plastic pollution on marine, benthic ecosystem function. We argue for research advancement through (1) employing field experiments, (2) evaluating ecological network disturbances by plastic, and (3) assessing the role of plastics (i.e., a carbon-based molecule) in carbon cycling at local and global scales