The role of urban greenspace in children’s reward and punishment sensitivity

According to Life History Theory, environments with abundant and reliable resources encourage ‘slow’ (deliberative) strategies that are low-risk and focused on long-term outcomes. Arguably, greener neighbourhoods may approximate such environments, especially in urban settings. This study used the UK’s Millennium Cohort Study to investigate the role of greenness of the child’s immediate residential area at ages 9 months and 3, 5, 7, and 11 years in reward and punishment sensitivity, measured using the Cambridge Gambling Task (CGT), at age 11 years. Our sample was the children who lived in urban areas at all five time-points and with data on the CGT at the fifth (n = 5,012). Consistent with Life History Theory, we found that children in the least green areas were more likely to engage in ‘fast’ decision strategies than other children: they showed higher sensitivity to reward (or lower sensitivity to punishment). This association was robust to adjustment for confounders

Childhood Trajectories of Hyperactivity/Inattention Symptoms and Diurnal Cortisol in Middle Adolescence: Results from a UK Birth Cohort

Objective: Children with attention-deficit/hyperactivity disorder (ADHD) show hypoactivity of the hypothalamic-pituitary-adrenal (HPA) axis. Whether the association between hyperactivity/inattention symptoms with HPA axis dysfunction holds in the general child population too is not clear. // Method: We assessed associations between longitudinal trajectories of hyperactivity/inattention symptoms during ages 4 to 13 years and basal cortisol profiles at age 15 in a British general population cohort. // Results: Adolescents with persistently high levels of hyperactivity/inattention symptoms since childhood showed lower total morning cortisol and a smaller diurnal decline, even after adjusting for confounders. No associations were found between any of the symptom trajectories and cortisol awakening response, diurnal slope or daily output of cortisol. // Conclusion: This study provides evidence for hypocortisolism among adolescents with chronic hyperactivity/inattention symptoms in the general population

The State of Software for Evolutionary Biology

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/Cþþ (e.g., MrBayes, MAFFT, SweepFinder, etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Because, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software developmen

Magnetic resonance imaging of placentome development in the pregnant Ewe

INTRODUCTION: Novel imaging measurements of placental development are difficult to validate due to the invasive nature of gold-standard procedures. Animal studies have been important in validation of magnetic resonance imaging (MRI) measurements in invasive preclinical studies, as they allow for controlled experiments and analysis of multiple time-points during pregnancy. This study characterises the longitudinal diffusion and perfusion properties of sheep placentomes using MRI, measurements that are required for future validation studies. METHODS: Pregnant ewes were anaesthetised for a MRI session on a 3T scanner. Placental MRI was used to classify placentomes morphologically into three types based on their shape and size at two gestational ages. To validate classification accuracy, placentome type derived from MRI data were compared with placentome categorisation results after delivery. Diffusion-Weighted MRI and T2-relaxometry were used to measure a broad range of biophysical properties of the placentomes. RESULTS: MRI morphological classification results showed consistent gestational age changes in placentome shape, as supported by post-delivery gold standard data. The mean apparent diffusion coefficient was significantly higher at 110 days gestation than at late gestation (~140 days; term, 150 days). Mean T2 was higher at mid gestation (152.2 ± 58.1 ms) compared to late gestation (127.8 ms ± 52.0). Significantly higher perfusion fraction was measured in late gestation placentomes that also had a significantly higher fractional anisotropy when compared to the earlier gestational age. DISCUSSION: We report baseline measurements of techniques common in placental MRI for the sheep placenta. These measurements are essential to support future validation measurements of placental MRI techniques

The effects of maternal position, in late gestation pregnancy, on placental blood flow and oxygenation: An MRI study

KEY POINTS: Maternal supine sleep position in late pregnancy is associated with an increased risk of stillbirth. Maternal supine position in late pregnancy reduces maternal cardiac output and uterine blood flow. Using MRI, this study shows that compared to the left lateral position, maternal supine position in late pregnancy is associated with reduced uteroplacental blood flow, oxygen transfer across the placenta with an average 6.2% reduction in oxygen delivery to the fetus and an average 11% reduction in fetal umbilical venous blood flow. ABSTRACT: Maternal sleep position in late gestation is associated with an increased risk of stillbirth though the pathophysiological reasons for this are unclear. Studies using MRI have shown that compared with lateral positions, lying supine causes a reduction in cardiac output, reduced abdominal aortic blood flow and reduced vena caval flow which is only partially compensated for by increased flow in the azygos venous system. Using functional MRI techniques, including an acquistion termed Diffusion-Relaxation Combined Imaging of the Placenta (DECIDE), which combines diffusion weighted imaging and T2 relaxometry, blood flow and oxygen transfer were estimated in the maternal, fetal and placental compartments when subjects were scanned both supine and in left lateral positions. In late gestation pregnancy, lying supine caused a 23.7% (p <0.0001) reduction in total internal iliac arterial blood flow to the uterus. In addition, lying in the supine position caused a 6.2% (p = 0.038) reduction in oxygen movement across the placenta. The reductions in oxygen transfer to the fetus, termed delivery flux, of 11.2% (p = 0.0597) and in fetal oxygen saturation of 4.4% (p = 0.0793) did not reach statistical significance. It is concluded that even in healthy late gestation pregnancy, maternal position significantly affects oxygen transfer across the placenta and may in part provide an explanation for late stillbirth in vulnerable fetuses. This article is protected by copyright. All rights reserved

Improved Placental Parameter Estimation Using Data-Driven Bayesian Modelling

The placenta plays a key contribution to successful pregnancy outcome. New MR imaging techniques are able to reveal intricate details about placental structure and function and measure placental blood flow and feto-placental oxygenation. Placental diffusion-weighted MRI is however challenging due to maternal breathing motion and poor signal-to-noise ratio making motion correction important for subsequent quantitative analysis. In this work, we (i) introduce an iterative model-based registration technique which incorporates a placenta-specific model into the motion correction process and (ii) describe a new technique making use of a Bayesian shrinkage prior to obtain robust estimates of individual and population trends in parameters. Our results suggest that the proposed registration method improves alignment of placental data and that the Bayesian fitting technique allows the estimation of voxel-level placenta flow parameters and the population trend in each parameter with gestational age (GA). We report gestational age dependent differences in vascular compartments and fetal oxygen saturation values observed across 9 normally grown pregnancies between 25–34 weeks gestational age and show qualitatively improved parameter mapping and more precise longitudinal fitting. Fetal oxygen saturation ( FO2 ) is observed to decrease at FO2=−3.6(GAweeks)+190.2(%) . This technique provides a robust framework for analysing longitudinal changes in both normal and pathological placental function

Estimation of species divergence times in presence of cross-species gene flow

Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene flow is ignored in the analysis. Using advances in analytical methods under the multispecies coalescent (MSC) model, we demonstrate that by accounting for incomplete lineage sorting and introgression using large phylogenomic data sets this problem can be avoided. The multispecies-coalescent-with-introgression (MSci) model is capable of accurately estimating both divergence times and ancestral effective population sizes, even when only a single diploid individual per species is sampled. We characterize some general expectations for biases in divergence time estimation under three different scenarios: 1) introgression between sister species, 2) introgression between non-sister species, and 3) introgression from an unsampled (i.e., ghost) outgroup lineage. We also conducted simulations under the isolation-with-migration (IM) model, and found that the MSci model assuming episodic gene flow was able to accurately estimate species divergence times despite high levels of continuous gene flow. We estimated divergence times under the MSC and MSci models from two published empirical datasets with previous evidence of introgression, one of 372 target-enrichment loci from baobabs (Adansonia), and another of 1,000 transcriptome loci from fourteen species of the tomato relative, Jaltomata. The empirical analyses not only confirm our findings from simulations, demonstrating that the MSci model can reliably estimate divergence times, but also show that divergence time estimation under the MSC can be robust to the presence of small amounts of introgression in empirical datasets with extensive taxon sampling

Texture-Based Analysis of Fetal Organs in Fetal Growth Restriction

Fetal growth restriction (FGR) is common, affecting around 10% of all pregnancies. Growth restricted fetuses fail to achieve their genetically predetermined size and often weigh &lt;10th centile for gestation. However, even appropriately grown fetuses can be affected, with the diagnosis of FGR missed before birth. Babies with FGR have a higher rate of stillbirth, neonatal morbidity such as breathing problems, and neurodevelopmental delay. FGR is usually due to placental insufficiency leading to poor placental perfusion and fetal hypoxia. MRI is increasingly used to image the fetus and placenta. Here we explore the use of novel multi-compartment Intravoxel Incoherent Motion Model (IVIM)-based models for MRI fetal and placental analysis, to improve understanding of FGR and quantify abnormalities and biomarkers in fetal organs. In 12 normally grown and 12 FGR gestational-age matched pregnancies (Median 28+ 4 wks±3+ 3 wks) we acquired T2 relaxometry and diffusion MRI datasets. Decreased perfusion, pseudo-diffusion coefficient, and fetal blood T2 values in the placenta and fetal liver were significant features distinguishing between FGR and normal controls (p-value &lt;0.05). This may be related to the preferential shunting of fetal blood away from the fetal liver to the fetal brain that occurs in placental insufficiency. These features were used to predict FGR diagnosis and gestational age at delivery using simple machine learning models. Texture analysis was explored to compare Haralick features between control and FGR fetuses, with the placenta and liver yielding the most significant differences between the groups. This project provides insights into the effect of FGR on fetal organs emphasizing the significant impact on the fetal liver and placenta, and the potential of an automated approach to diagnosis by leveraging simple machine learning models

Cumulative Risk Effects in the Bullying of Children and Young People with Autism Spectrum Conditions

Students with autism are more likely to be bullied than their typically developing peers. However, several studies have shown that their likelihood of being bullied increases in the context of exposure to certain risk factors (e.g. behaviour difficulties, poor peer relationships). This study explores vulnerability to bullying from a cumulative risk perspective, where the number of risks rather than their nature is considered. 722 teachers and 119 parents of young people with ASC participated in the study. Established risk factors were summed to form a cumulative risk score in teacher and parent models. There was evidence of a cumulative risk effect in both models, suggesting that as the number of risks increased, so did exposure to bullying. A quadratic effect was found in the teacher model, indicating that there was a disproportionate increase in the likelihood of being bullied in relation to the number of risk factors to which a young person was exposed. In light of these findings, it is proposed that more attention needs to be given to the number of risks to which children and young people with ASC are exposed when planning interventions and providing a suitable educational environment

Motion correction of free-breathing magnetic resonance renography using model-driven registration

Introduction Model-driven registration (MDR) is a general approach to remove patient motion in quantitative imaging. In this study, we investigate whether MDR can effectively correct the motion in free-breathing MR renography (MRR). Materials and methods MDR was generalised to linear tracer-kinetic models and implemented using 2D or 3D free-form deformations (FFD) with multi-resolution and gradient descent optimization. MDR was evaluated using a kidney-mimicking digital reference object (DRO) and free-breathing patient data acquired at high temporal resolution in multi-slice 2D (5 patients) and 3D acquisitions (8 patients). Registration accuracy was assessed using comparison to ground truth DRO, calculating the Hausdorff distance (HD) between ground truth masks with segmentations and visual evaluation of dynamic images, signal-time courses and parametric maps (all data). Results DRO data showed that the bias and precision of parameter maps after MDR are indistinguishable from motion-free data. MDR led to reduction in HD (HDunregistered = 9.98 ± 9.76, HDregistered = 1.63 ± 0.49). Visual inspection showed that MDR effectively removed motion effects in the dynamic data, leading to a clear improvement in anatomical delineation on parametric maps and a reduction in motion-induced oscillations on signal-time courses. Discussion MDR provides effective motion correction of MRR in synthetic and patient data. Future work is needed to compare the performance against other more established methods