Open data and digital morphology

Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise, that the widespread application of such methods would facilitate access to the underlying digital data, has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for 3D digital data publication, and review the issues around data storage, management and accessibility

Multi-Decadal Changes in Mangrove Extent, Age and Species in the Red River Estuaries of Viet Nam

This research investigated the performance of four different machine learning supervised image classifiers: artificial neural network (ANN), decision tree (DT), random forest (RF), and support vector machine (SVM) using SPOT-7 and Sentinel-1 images to classify mangrove age and species in 2019 in a Red River estuary, typical of others found in northern Viet Nam. The four classifiers were chosen because they are considered to have high accuracy, however, their use in mangrove age and species classifications has thus far been limited. A time-series of Landsat images from 1975 to 2019 was used to map mangrove extent changes using the unsupervised classification method of iterative self-organizing data analysis technique (ISODATA) and a comparison with accuracy of K-means classification, which found that mangrove extent has increased, despite a fall in the 1980s, indicating the success of mangrove plantation and forest protection efforts by local people in the study area. To evaluate the supervised image classifiers, 183 in situ training plots were assessed, 70% of them were used to train the supervised algorithms, with 30% of them employed to validate the results. In order to improve mangrove species separations, Gram–Schmidt and principal component analysis image fusion techniques were applied to generate better quality images. All supervised and unsupervised (2019) results of mangrove age, species, and extent were mapped and accuracy was evaluated. Confusion matrices were calculated showing that the classified layers agreed with the ground-truth data where most producer and user accuracies were greater than 80%. The overall accuracy and Kappa coefficients (around 0.9) indicated that the image classifications were very good. The test showed that SVM was the most accurate, followed by DT, ANN, and RF in this case study. The changes in mangrove extent identified in this study and the methods tested for using remotely sensed data will be valuable to monitoring and evaluation assessments of mangrove plantation projects

A rich locality in South Kensington: the fossil hominin collection of the Natural History Museum, London

The primacy of fossils in the Natural History Museum (NHM) goes back to the very origins of the Museum, but the first fossil hominins in the collections were probably the Upper Palaeolithic remains from Bruniquel, which were accessioned in 1864. This founded a collection which has continued to expand into this century. While there have been many compilations and descriptions of the fossil hominin collection at the NHM over its long history, to our knowledge no‐one has prepared a review of the collection itself. The intention of the current paper is to synthesize earlier sources with accounts of new finds, revised chronologies and rediscovered treasures in order to illustrate the breadth and continuing importance of the fossil hominins curated at the NHM. We list and discuss all the hominin material known or thought to pre‐date the Holocene. These form a collection of great importance, both in terms of their research

A Glial Variant of the Vesicular Monoamine Transporter Is Required To Store Histamine in the Drosophila Visual System

Unlike other monoamine neurotransmitters, the mechanism by which the brain's histamine content is regulated remains unclear. In mammals, vesicular monoamine transporters (VMATs) are expressed exclusively in neurons and mediate the storage of histamine and other monoamines. We have studied the visual system of Drosophila melanogaster in which histamine is the primary neurotransmitter released from photoreceptor cells. We report here that a novel mRNA splice variant of Drosophila VMAT (DVMAT-B) is expressed not in neurons but rather in a small subset of glia in the lamina of the fly's optic lobe. Histamine contents are reduced by mutation of dVMAT, but can be partially restored by specifically expressing DVMAT-B in glia. Our results suggest a novel role for a monoamine transporter in glia that may be relevant to histamine homeostasis in other systems

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Background: Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. // Methods: We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung's disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. // Findings: We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung's disease) from 264 hospitals (89 in high-income countries, 166 in middle-income countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in low-income countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. // Interpretation: Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between low-income, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Comparisons of regression and machine learning methods for estimating mangrove above-ground biomass using multiple remote sensing data in the red River Estuaries of Vietnam

Currently, remote sensing platforms provide state-of-the-art data for multiple purposes including applications related to coastal wetlands. Mangrove above-ground biomass (MAGB) together with its extent is considered well correlated with the habitats’ environmental and economic values. Above-ground biomass can be estimated by models that integrate remote sensing, field data and statistical information. However, it remains difficult to decide which model and which data offer the best performance for any one study location. Hence, this study aims to assess the spatial change in MAGB over a 45-year period and investigate different approaches to quantify this change through linear and multi linear regression models. Specifically, we test a non-linear model (Multivariate Adaptive Regression Splines; MARS), and non-parametric machine learning models, to predict MAGB using vegetation indices and biophysical variables derived from optical remote sensing data from Sentinel-2, Landsat-8, SPOT-7 and synthetic aperture radar remote sensing data from ALOS-2. The multi linear regression (MLR) and the MARS models were trained by field measured MAGB data to a good level of accuracy (R2 = 0.80 and RMSE = 5.56 Mg ha−1 for MLR and R2 = 0.89, RMSE = 5.42 Mg ha−1 for MARS). These models were subsequently applied to Landsat 2, 5 and 8 time-series images to assess changes in MAGB values and mangrove forest extent over the period 1975 to 2020. To ensure accurate training data for the models, we conducted field work to measure MAGB in 24 plots measured in May 2019. Findings showed that the MARS model generated MAGB values with higher accuracy than linear regression and multi linear regression models. Uses of vegetation indices (Normalized Differenced Vegetation Index, Soil-adjusted Vegetation Index, Green-Normalized Differenced Vegetation Index, Simple Ratio, and Red-edge Simple Ratio) generated MAGB values with accuracy slightly higher than using biophysical variables (Leaf area index, Fraction of Absorbed Radiation, Fractional vegetation cover, and Leaf chlorophyll content). Sentinel-2 and Landsat 8 were effective data sources for MAGB estimates, while SPOT-7 and ALOS-2 produced acceptable MAGB accuracy. Modelling the Landsat time series found an increase in both MAGB values and forest extent over the 1975–2020 period. The MARS model, Sentinel-2, Landsat 8 and vegetation indices are the recommended models and data to use to measure MAGB and could be used to understand changes in MAGB and forest extent at national and regional scales