An Automatic and End-to-End System for Rare Disease Knowledge Graph Construction Based on Ontology-Enhanced Large Language Models: Development Study.

Background: Rare diseases affect millions worldwide but sometimes face limited research focus individually due to low prevalence. Many rare diseases do not have specific International Classification of Diseases, Ninth Edition (ICD-9) and Tenth Edition (ICD-10), codes and therefore cannot be reliably extracted from granular fields like "Diagnosis" and "Problem List" entries, which complicates tasks that require identification of patients with these conditions, including clinical trial recruitment and research efforts. Recent advancements in large language models (LLMs) have shown promise in automating the extraction of medical information, offering the potential to improve medical research, diagnosis, and management.

Multi-faceted analysis and prediction for the outbreak of pediatric respiratory syncytial virus.

Objectives: Respiratory syncytial virus (RSV) is a significant cause of pediatric hospitalizations. This article aims to utilize multisource data and leverage the tensor methods to uncover distinct RSV geographic clusters and develop an accurate RSV prediction model for future seasons.

Materials And Methods: This study utilizes 5-year RSV data from sources, including medical claims, CDC surveillance data, and Google search trends.

Germination physiology of (Bixaceae), a deciduous tree from Northern Australia with physical seed dormancy.

('Kapok', Bixaceae) is a deciduous tree widely distributed throughout semi-arid and monsoon tropical northern Australia, and an important species for ecological restoration in the region. We aimed to better understand the seed biology and ecology of to determine the mechanisms by which seed dormancy might be alleviated, and the conditions that support germination to inform the use of this species in restoration. Dormancy breaking treatments (wet heat, dry heat, scarification) commonly applied to species with physical seed dormancy (PY) were tested along with stratification at 5-35°C (nine treatments).

Dramatic difference in rate of chromosome number evolution among sundew (Drosera L., Droseraceae) lineages.

Chromosome number change is a driver of speciation in eukaryotic organisms. Carnivorous sundews in the plant genus Drosera L. exhibit single chromosome number variation both among and within species, especially in the Australian Drosera subg.

Ecological Considerations When Designing Mitigation Translocations: An Australian Reptile Case Study.

Translocation science has made considerable progress over the last two decades; however, reptile translocations still frequently fail around the world. Major knowledge gaps surround the basic ecology of reptile species, including basic factors such as habitat preference, which have a critical influence on translocation success. The western spiny-tailed skink () is used here as a case study to exemplify how empirical research can directly inform on-ground management and future translocation planning.

Evidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics.

In this work, we aim to accurately predict the number of hospitalizations during the COVID-19 pandemic by developing a spatiotemporal prediction model. We propose HOIST, an Ising dynamics-based deep learning model for spatiotemporal COVID-19 hospitalization prediction. By drawing the analogy between locations and lattice sites in statistical mechanics, we use the Ising dynamics to guide the model to extract and utilize spatial relationships across locations and model the complex influence of granular information from real-world clinical evidence.

Capture of mammal excreta by Nepenthes is an effective heterotrophic nutrition strategy.

Background And Aims: While isotopic enrichment of nitrogen (15N) and carbon (13C) is often used to determine whether carnivorous plant species capture and assimilate nutrients from supplemental sources such as invertebrate prey or mammal excreta (heterotrophic nutrition), little is known about how successful the different strategies deployed by carnivorous plants are at obtaining supplemental nutrition. The collection of mammalian faeces by Nepenthes (tropical pitcher plants) is the result of a highly specialized biological mutualism that results in heterotrophic nitrogen gain; however, it remains unknown how effective this strategy is in comparison to Nepenthes species not known to collect mammalian faeces.

Methods: We examined how isotopic enrichment varied in the diverse genus Nepenthes, among species producing pitchers for invertebrate capture and species exhibiting mutualisms for the collection of mammal excreta.

Ecosystem restoration is integral to humanity's recovery from COVID-19.

COVID-19 has devastated global communities and economies. The pandemic has exposed socioeconomic disparities and weaknesses in health systems worldwide. Long-term health effects and economic recovery are major concerns.

MedML: Fusing medical knowledge and machine learning models for early pediatric COVID-19 hospitalization and severity prediction.

The COVID-19 pandemic has caused devastating economic and social disruption. This has led to a nationwide call for models to predict hospitalization and severe illness in patients with COVID-19 to inform the distribution of limited healthcare resources. To address this challenge, we propose a machine learning model, MedML, to conduct the hospitalization and severity prediction for the pediatric population using electronic health records.

Revealing microhabitat requirements of an endangered specialist lizard with LiDAR.

A central principle of threatened species management is the requirement for detailed understanding of species habitat requirements. Difficult terrain or cryptic behaviour can, however, make the study of habitat or microhabitat requirements difficult, calling for innovative data collection techniques. We used high-resolution terrestrial LiDAR imaging to develop three-dimensional models of log piles, quantifying the structural characteristics linked with occupancy of an endangered cryptic reptile, the western spiny-tailed skink (Egernia stokesii badia).

A novel approach for reliable qualitative and quantitative prey spectra identification of carnivorous plants combining DNA metabarcoding and macro photography.

Prey spectra (the number and composition of captured arthropods) represent a crucial aspect of carnivorous plant ecology, yet remain poorly studied. Traditional morphology-based approaches for prey identification are time-intensive, require specialists with considerable knowledge of arthropod taxonomy, and are hampered by high numbers of unidentifiable (i.e.

Emphysematous cystitis with bilateral pyelonephritis in a pediatric patient with COVID-19.

A 15-year-old female adolescent with a medical history of recurrent urinary tract infections and grade 1 left-sided vesicoureteral reflux presented to the emergency room with abdominal and back pain. Labs revealed a haemoglobin A1c (HbA1c) of 9.1% and a random blood glucose of 200 mg/dL, consistent with new-onset diabetes mellitus.

Calcicole-calcifuge plant strategies limit restoration potential in a regional semi-arid flora.

Aim: To examine calcicole and calcifuge plant strategies, as well as nutrient-acquisition strategies, as drivers of the distribution of species in response to edaphic factors, and the degree to which these strategies may act as filters to species establishment in ecological restoration on heavily altered or reconstructed substrates.

Location: An 82,000-ha area within a major mining province in the Mid-West region of Western Australia, harboring vegetation communities ranging from species-poor halophytic scrub on saline flats to dense biodiverse shrubland on the skeletal soils of ancient Banded Ironstone Formations (BIF).

Methods: Univariate and multivariate analyses were employed to examine how variation in soil chemistry and landscape position (undulating plains, slopes, and BIF crests and ridges) influenced patterns of floristic diversity, calcifuge plant strategies, and nutrient-acquisition strategies in 538 plant species from 830 relevés.

Initiating pedogenesis of magnetite tailings using Lupinus angustifolius (narrow-leaf lupin) as an ecological engineer to promote native plant establishment.

Mine tailings pose physical and chemical challenges for plant establishment. Our aim was to learn from natural processes in long-term soil and ecosystem development to use tailings as novel parent materials and pioneer ecological-engineering plant species to ameliorate extreme conditions of tailings, and facilitate the establishment of subsequent native plants. A glasshouse trial was conducted using magnetite tailings containing various amendments, investigating the potential of the nitrogen (N)-fixing, non-native pioneer species Lupinus angustifolius (Fabaceae), narrow-leaf lupin, as a potential eco-engineer to promote soil formation processes, and whether amendment type or the presence of pioneer vegetation improved the subsequent establishment and growth of 40 species of native plants.

Exceptional nitrogen-resorption efficiency enables Maireana species (Chenopodiaceae) to function as pioneers at a mine-restoration site.

Tailings are among the most challenging mined substrates for plant re-establishment, in particular because of a lack of soil-like structure and nitrogen. Potential pioneer plants are sometimes found in such disturbed and infertile sites. We present a group of pioneer species from the genus Maireana (Chenopodiaceae) that are promising candidates for the restoration of magnetite tailings.

Incorporating rock in surface covers improves the establishment of native pioneer vegetation on alkaline mine tailings.

Background And Aims: Rates of tailings production and deposition around the world have increased markedly in recent decades, and have grown asynchronously with safe and environmentally suitable solutions for their storage. Tailings are often produced in regions harbouring biodiverse native plant communities adapted to old, highly-weathered soils. The highly-altered edaphic conditions of tailings compared with natural soils in these areas will likely select against many locally endemic plant species, making phytostabilisation, rehabilitation or ecological restoration of these landforms challenging.

Mitigation translocation as a management tool.

Mitigation translocation is a subgroup of conservation translocation, categorized by a crisis-responsive time frame and the immediate goal of relocating individuals threatened with death. However, the relative successes of conservation translocations with longer time frames and broader metapopulation- and ecosystem-level considerations have been used to justify the continued implementation of mitigation translocations without adequate post hoc monitoring to confirm their effectiveness as a conservation tool. Mitigation translocations now outnumber other conservation translocations, and understanding the effectiveness of mitigation translocations is critical given limited global conservation funding especially if the mitigation translocations undermine biodiversity conservation by failing to save individuals.

Hydrological and thermal responses of seeds from four co-occurring tree species from southwest Western Australia.

Seed germination is a critical stage in the life cycle of most plants and is defined by specific tolerance thresholds beyond which rates and success of germination rapidly decline. Previous studies have demonstrated that widespread plant species commonly germinate over a broad range of temperatures and water stress levels, whereas range-restricted species often exhibit a narrower germination window in terms of temperature and moisture. We investigated the relationships of the key germination traits of maximum germination ( ) and time to 50% germination ( ) in response to temperature (5-35°C) and water stress (-1.

The Bacterial Microbiome Associated With Arid Biocrusts and the Biogeochemical Influence of Biocrusts Upon the Underlying Soil.

Biocrusts are aggregated crusts that exist on the soil surface of arid environments. They are complex microbial communities comprised of cyanobacteria, lichens, mosses, algae and fungi. Recently, biocrusts have gained significant attention due to their ubiquitous distribution and likely important ecological roles, including soil stabilization, soil moisture retention, carbon (C) and nitrogen (N) fixation, as well as microbial engineers for semi-arid ecosystem restoration.

An ecological perspective on 'plant carnivory beyond bogs': nutritional benefits of prey capture for the Mediterranean carnivorous plant Drosophyllum lusitanicum.

Background And Aims: Little is known about the evolutionary and ecological drivers of carnivory in plants, particularly for those terrestrial species that do not occur in typical swamp or bog habitats. The Mediterranean endemic Drosophyllum lusitanicum (Drosophyllaceae) is one of very few terrestrial carnivorous plant species outside of Australia to occur in seasonally dry, fire-prone habitats, and is thus an ecological rarity. Here we assess the nutritional benefits of prey capture for D.

Plastome-Wide Rearrangements and Gene Losses in Carnivorous Droseraceae.

The plastid genomes of four related carnivorous plants (Drosera regia, Drosera erythrorhiza, Aldrovanda vesiculosa, and Dionaea muscipula) were sequenced to examine changes potentially induced by the transition to carnivory. The plastid genomes of the Droseraceae show multiple rearrangements, gene losses, and large expansions or contractions of the inverted repeat. All the ndh genes are lost or nonfunctional, as well as in some of the species, clpP1, ycf1, ycf2 and some tRNA genes.

Ethical seed sourcing is a key issue in meeting global restoration targets.

The global demand for restoration has increased orders of magnitude in the last decade, and hundreds of thousands of tonnes of native seed are required to feed this restoration engine [1] (Figure 1). But where are all the seeds required by restoration going to come from? Wild seed resources continue to be depleted by habitat loss, land degradation and climatic change, and over-collection of seed from wild populations threatens to erode these resources further. Ethical seed sourcing for restoration now represents a core issue in responsible restoration practice.

A research agenda for seed-trait functional ecology.

Trait-based approaches have improved our understanding of plant evolution, community assembly and ecosystem functioning. A major challenge for the upcoming decades is to understand the functions and evolution of early life-history traits, across levels of organization and ecological strategies. Although a variety of seed traits are critical for dispersal, persistence, germination timing and seedling establishment, only seed mass has been considered systematically.

Geochemical and mineralogical constraints in iron ore tailings limit soil formation for direct phytostabilization.

The present study aimed to characterize key physico-chemical and mineralogical attributes of magnetite iron (Fe) ore tailings to identify potential constraints limiting in situ soil formation and direct phytostabilization. Tailings of different age, together with undisturbed local native soils, were sampled from a magnetite mine in Western Australia. Tailings were extremely alkaline (pH > 9.