Europe PMC in 2023.

Europe PMC (https://europepmc.org/) is an open access database of life science journal articles and preprints, which contains over 42 million abstracts and over 9 million full text articles accessible via the website, APIs and bulk download. This publication outlines new developments to the Europe PMC platform since the last database update in 2020 (1) and focuses on five main areas. (i) Improving discoverability, reproducibility and trust in preprints by indexing new preprint content, enriching preprint metadata and identifying withdrawn and removed preprints. (ii) Enhancing support for text and data mining by expanding the types of annotations provided and developing the Europe PMC Annotations Corpus, which can be used to train machine learning models to increase their accuracy and precision. (iii) Developing the Article Status Monitor tool and email alerts, to notify users about new articles and updates to existing records. (iv) Positioning Europe PMC as an open scholarly infrastructure through increasing the portion of open source core software, improving sustainability and accessibility of the service.

Europe PMC in 2020.

Europe PMC (https://europepmc.org) is a database of research articles, including peer reviewed full text articles and abstracts, and preprints - all freely available for use via website, APIs and bulk download. This article outlines new developments since 2017 where work has focussed on three key areas: (i) Europe PMC has added to its core content to include life science preprint abstracts and a special collection of full text of COVID-19-related preprints. Europe PMC is unique as an aggregator of biomedical preprints alongside peer-reviewed articles, with over 180 000 preprints available to search. (ii) Europe PMC has significantly expanded its links to content related to the publications, such as links to Unpaywall, providing wider access to full text, preprint peer-review platforms, all major curated data resources in the life sciences, and experimental protocols. The redesigned Europe PMC website features the PubMed abstract and corresponding PMC full text merged into one article page; there is more evident and user-friendly navigation within articles and to related content, plus a figure browse feature. (iii) The expanded annotations platform offers ∼1.3 billion text mined biological terms and concepts sourced from 10 providers and over 40 global data resources.

Detection of long-term influence of prenatal temperature stimulation on hypothalamic type-II iodothyronine deiodinase in juvenile female broiler chickens using a novel immunohistochemical amplification protocol.

It has been clearly shown that early environmental stimulation may have long-lasting influence on body functions. Because of the strong relationship between thermoregulation and other homeostatic linked physiological parameters, perinatal thermal manipulation will also have an impact on other body functions like reproduction. As a maturation stimulant for later reproductive performance, hypothalamic type-2 iodothyronine deiodinase (Dio2) expression was investigated in 35day old immature female broilers with and without embryonic temperature stimulation. For the first time, human-specific Dio2 primary antibodies combined with additional amplification enabled the immunohistochemical detection of hypothalamic Dio2 protein in birds. The novel protocol includes an additional amplification step involving swine-anti-rabbit/mouse/goat antibodies against both goat anti-Dio2 primary and rabbit anti-goat biotinylated secondary commercial antibodies in the standard diaminobenzidine protocol. However, significant Dio2 expression was exclusively found in perinatally short-term temperature stimulated hens. Caudal but not rostral hypothalamic slices revealed that elevating incubation temperature by 1°C for 2h daily, from day 18 of embryonic development until hatching, induced a statistical significant expression of Dio2 within the subcommisural organ and the median eminence. This ample expression of Dio2 protein within caudal but not rostral hypothalamic slices of embryonic temperature stimulated chickens, leads to the assumption of a novel physiological prospective for embryonic thermal manipulation involving the suppression of thyroid hormone and the boosting of hypothalamic Dio2-induced FSH secretion to considerably advance the age of photoinduced egg production. It could be also of practicable relevance for broiler breeder females, and needs further investigations.

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications.

Metagenomics is a culture-independent method for studying the microbes inhabiting a particular environment. Comparing the composition of samples (functionally/taxonomically), either from a longitudinal study or cross-sectional studies, can provide clues into how the microbiota has adapted to the environment. However, a recurring challenge, especially when comparing results between independent studies, is that key metadata about the sample and molecular methods used to extract and sequence the genetic material are often missing from sequence records, making it difficult to account for confounding factors. Nevertheless, these missing metadata may be found in the narrative of publications describing the research. Here, we describe a machine learning framework that automatically extracts essential metadata for a wide range of metagenomics studies from the literature contained in Europe PMC. This framework has enabled the extraction of metadata from 114,099 publications in Europe PMC, including 19,900 publications describing metagenomics studies in European Nucleotide Archive (ENA) and MGnify. Using this framework, a new metagenomics annotations pipeline was developed and integrated into Europe PMC to regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles. These metadata are now available for researchers to explore and retrieve in the MGnify and Europe PMC websites, as well as Europe PMC annotations API.

The neurocognitive gains of diagnostic reasoning training using simulated interactive veterinary cases.

The present longitudinal study ascertained training-associated transformations in the neural underpinnings of diagnostic reasoning, using a simulation game named "Equine Virtual Farm" (EVF). Twenty participants underwent structural, EVF/task-based and resting-state MRI and diffusion tensor imaging (DTI) before and after completing their training on diagnosing simulated veterinary cases. Comparing playing veterinarian versus seeing a colorful image across training sessions revealed the transition of brain activity from scientific creativity regions pre-training (left middle frontal and temporal gyrus) to insight problem-solving regions post-training (right cerebellum, middle cingulate and medial superior gyrus and left postcentral gyrus). Further, applying linear mixed-effects modelling on graph centrality metrics revealed the central roles of the creative semantic (inferior frontal, middle frontal and angular gyrus and parahippocampus) and reward systems (orbital gyrus, nucleus accumbens and putamen) in driving pre-training diagnostic reasoning; whereas, regions implicated in inductive reasoning (superior temporal and medial postcentral gyrus and parahippocampus) were the main post-training hubs. Lastly, resting-state and DTI analysis revealed post-training effects within the occipitotemporal semantic processing region. Altogether, these results suggest that simulation-based training transforms diagnostic reasoning in novices from regions implicated in creative semantic processing to regions implicated in improvised rule-based problem-solving.