Pathologists light level preferences using the microscope-study to guide digital pathology display use.

Background: Currently, there is a paucity of guidelines relating to displays used for digital pathology making procurement decisions, and optimal display configuration, challenging.Experience suggests pathologists have personal preferences for brightness when using a conventional microscope which we hypothesized could be used as a predictor for display setup. Methods: We conducted an online survey across six NHS hospitals, totalling 108 practicing pathologists, to capture brightness adjustment habits on both microscopes and displays.A convenience subsample of respondents was then invited to take part in a practical task to determine microscope brightness and display luminance preferences in the normal working environment. A novel adaptation for a lightmeter was developed to directly measure the light output from the microscope eyepiece. Results: The survey (response rate 59% n=64) indicates 81% of respondents adjust the brightness on their microscope. In comparison, only 11% report adjusting their digital display. Display adjustments were more likely to be for visual comfort and ambient light compensation rather than for tissue factors, common for microscope adjustments. Part of this discrepancy relates to lack of knowledge of how to adjust displays and lack of guidance on whether this is safe; But, 66% felt that the ability to adjust the light on the display was important.Twenty consultants took part in the practical brightness assessment. Light preferences on the microscope showed no correlation with display preferences, except where a pathologist has a markedly brighter microscope light preference. All of the preferences in this cohort were for a display luminance of <500 cd/m2, with 90% preferring 350 cd/m2 or less. There was no correlation between these preferences and the ambient lighting in the room. Conclusions: We conclude that microscope preferences can only be used to predict display luminance requirements where the microscope is being used at very high brightness levels. A display capable of a brightness of 500 cd/m2 should be suitable for almost all pathologists with 300 cd/m2 suitable for the majority. Although display luminance is not frequently changed by users, the ability to do so was felt to be important by the majority of respondents.Further work needs to be undertaken to establish the relationship between diagnostic performance, luminance preferences, and ambient lighting levels.

Artificial intelligence in digital pathology: a systematic review and meta-analysis of diagnostic test accuracy.

Ensuring diagnostic performance of artificial intelligence (AI) before introduction into clinical practice is essential. Growing numbers of studies using AI for digital pathology have been reported over recent years. The aim of this work is to examine the diagnostic accuracy of AI in digital pathology images for any disease. This systematic review and meta-analysis included diagnostic accuracy studies using any type of AI applied to whole slide images (WSIs) for any disease. The reference standard was diagnosis by histopathological assessment and/or immunohistochemistry. Searches were conducted in PubMed, EMBASE and CENTRAL in June 2022. Risk of bias and concerns of applicability were assessed using the QUADAS-2 tool. Data extraction was conducted by two investigators and meta-analysis was performed using a bivariate random effects model, with additional subgroup analyses also performed. Of 2976 identified studies, 100 were included in the review and 48 in the meta-analysis. Studies were from a range of countries, including over 152,000 whole slide images (WSIs), representing many diseases. These studies reported a mean sensitivity of 96.3% (CI 94.1-97.7) and mean specificity of 93.3% (CI 90.5-95.4). There was heterogeneity in study design and 99% of studies identified for inclusion had at least one area at high or unclear risk of bias or applicability concerns. Details on selection of cases, division of model development and validation data and raw performance data were frequently ambiguous or missing. AI is reported as having high diagnostic accuracy in the reported areas but requires more rigorous evaluation of its performance.

Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve.

The Indonesian island of Sulawesi has a unique geology and geography, which have produced an astoundingly diverse and endemic flora and fauna and a fascinating biogeographic history. Much biodiversity research has focused on the regional endemism in the island's Central Core and on its four peninsulas, but the biodiversity of the island's many upland regions is still poorly understood for most taxa, including amphibians and reptiles. Here, we report the first of several planned full-mountain checklists from a series of herpetological surveys of Sulawesi's mountains conducted by our team. In more than 3 weeks of work on Gunung Galang, a 2,254 m peak west of the city of Tolitoli, Sulawesi Tengah Province, on Sulawesi's Northern Peninsula, we recovered nearly fifty species of reptiles and amphibians, more than a dozen of which are either new to science or known but undescribed. The incompleteness of our sampling suggests that many more species remain to be discovered on and around this mountain.

The potential of Jellytoring 2.0 smart tool as a global jellyfish monitoring platform.

Despite the recent recognition of jellyfish as an important component of marine ecosystems and existing concerns on their potential population increase, they are rarely monitored at the appropriate spatial and temporal scales. Traditional jellyfish monitoring techniques are costly and generally restrict the spatial-temporal resolution limiting the quantity and quality of monitoring data. We introduce Jellytoring 2.0, an automatic recognition tool for jellyfish species based on convolutional neural networks (CNN). We trained Jellytoring 2.0 to identify 15 jellyfish species with a global distribution. Our aim is to offer Jellytoring 2.0 as an open-access tool to serve as the backbone for a system that promotes the creation of large-scale and long-term jellyfish monitoring data. Results reveal that Jellytoring 2.0 performed well in the identification of the 15 species with average precision values ranging between 90% and 99% for most of the species. Four of the species presented slightly lower values (75%-80%). Our system was trained on a relatively small dataset, implying that additional integration of image data will further improve the performance of the CNN. We show how the application of CNNs to image data can deliver a tool that will enable the cost-effective collection of jellyfish data on larger spatial and temporal scales. For Jellytoring 2.0 to become a truly global automatic identification system, we ask scientists and nonscientists to actively contribute with jellyfish image data to extend the number of species it can identify.

Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards.

BACKGROUND: High-throughput sequencing using targeted enrichment and transcriptomic methods enables rapid construction of phylogenomic data sets incorporating hundreds to thousands of loci. These advances have enabled access to an unprecedented amount of nucleotide sequence data, but they also pose new questions. Given that the loci targeted for enrichment are often highly conserved, how informative are they at different taxonomic scales, especially at the intraspecific/phylogeographic scale? We investigate this question using Australian scincid lizards in the Eugongylus group (Squamata: Scincidae). We sequenced 415 anchored hybrid enriched (AHE) loci for 43 individuals and mined 1650 exons (1648 loci) from transcriptomes (transcriptome mining) from 11 individuals, including multiple phylogeographic lineages within several species of Carlia, Lampropholis, and Saproscincus skinks. We assessed the phylogenetic information content of these loci at the intergeneric, interspecific, and phylogeographic scales. As a further test of the utility at the phylogeographic scale, we used the anchor hybrid enriched loci to infer lineage divergence parameters using coalescent models of isolation with migration. RESULTS: Phylogenetic analyses of both data sets inferred very strongly supported trees at all taxonomic levels. Further, AHE loci yielded estimates of divergence times between closely related lineages that were broadly consistent with previous population-level analyses. CONCLUSIONS: Anchored-enriched loci are useful at the deep phylogeny and phylogeographic scales. Although overall phylogenetic support was high throughout the Australian Eugongylus group phylogeny, there were nonetheless some conflicting or unresolved relationships, especially regarding the placement of Pseudemoia, Cryptoblepharus, and the relationships amongst closely-related species of Tasmanian Niveoscincus skinks.

Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms.

BACKGROUND: Conservation of orthologous regulatory gene expression domains, especially along the neuroectodermal anterior-posterior axis, in animals as disparate as flies and vertebrates suggests that common patterning mechanisms have been conserved since the base of Bilateria. The homology of axial patterning is far less clear for the many marine animals that undergo a radical transformation in body plan during metamorphosis. The embryos of these animals are microscopic, feeding within the plankton until they metamorphose into their adult forms. RESULTS: We describe here the localization of 14 transcription factors within the ectoderm during early embryogenesis in Patiria miniata, a sea star with an indirectly developing planktonic bipinnaria larva. We find that the animal-vegetal axis of this very simple embryo is surprisingly well patterned. Furthermore, the patterning that we observe throughout the ectoderm generally corresponds to that of "head/anterior brain" patterning known for hemichordates and vertebrates, which share a common ancestor with the sea star. While we suggest here that aspects of head/anterior brain patterning are generally conserved, we show that another suite of genes involved in retinal determination is absent from the ectoderm of these echinoderms and instead operates within the mesoderm. CONCLUSIONS: Our findings therefore extend, for the first time, evidence of a conserved axial pattering to echinoderm embryos exhibiting maximal indirect development. The dissociation of head/anterior brain patterning from "retinal specification" in echinoderm blastulae might reflect modular changes to a developmental gene regulatory network within the ectoderm that facilitates the evolution of these microscopic larvae.