A resolution record for cryoEM

Cryo electron microscopy (cryoEM) is a fast-growing technique for structure determination. Two recent papers report the first atomic resolution structure of a protein obtained by averaging images of frozen-hydrated biomolecules. They both describe maps of symmetric apoferritin assemblies, a common test specimen, in unprecedented detail. New instrument improvements, different in the two studies, have contributed better images, and image analysis can extract structural information sufficient to resolve individual atomic positions. While true atomic resolution maps will not be routine for most proteins, the studies suggest structures determined by cryoEM will continue to improve, increasing their impact on biology and medicine

How many children and young people with life-limiting conditions are clinically unstable? A national data linkage study

Objective: To determine the clinical stage (stable, unstable, deteriorating or dying) for children and young people (CYP) aged 0-25 years in Scotland with lifelimiting conditions (LLCs). Design: National cohort of CYP with LLCs using linked routinely collected healthcare data. Setting: Scotland. Patients: 20 436 CYP identified as having LLCs and resident in Scotland between 1 April 2009 and 31 March 2014. Main outcome: Clinical stage based on emergency inpatient and intensive care unit admissions and date of death. Results: Over 2200 CYP with LLCs in Scotland were unstable, deteriorating or dying in each year. Compared with 1-year-olds to 5-year-olds, children under 1 year of age had the highest risk of instability (OR 6.4, 95% CI 5.7 to 7.1); all older age groups had lower risk. Girls were more likely to be unstable than boys (OR 1.15, 95% CI 1.06 to 1.24). CYP of South Asian (OR 1.61, 95% CI 1.28 to 2.01), Black (OR 1.58, 95% CI 1.04 to 2.41) and Other (OR 1.33, 95% CI 1.02 to 1.74) ethnicity were more likely to experience instability than White CYP. Deprivation was not a significant predictor of instability. Compared with congenital abnormalities, CYP with most other primary diagnoses had a higher risk of instability; only CYP with a primary perinatal diagnosis had significantly lower risk (OR 0.23, 95% CI 0.19 to 0.29). Conclusions: The large number of CYP with LLCs who are unstable, deteriorating or dying may benefit from input from specialist paediatric palliative care. The age group under 1 and CYP of South Asian, Black and Other ethnicities should be priority groups

The fatty acid composition of excreta of broiler chickens fed different dietary fatty acids

Published: October 15, 2017Background and Objective: Excreted fatty acids represent the net result of fat digestion, absorbtion and bioconversion by chickens or their intestinal microbiome and thus provide information on the capacity of the birds to utilize different fat types. This study aimed to clarify the relationship between the fatty acid profile of diet and excreta in broiler chickens. Materials and Methods: Male Cobb 500 broilers (n = 240) were fed (ad libitum) one of 6 different diets supplemented with 4% (w/w) beef tallow, flaxseed, corn, macadamia, canola or coconut oils (4 replicate pens/treatment) from hatching day. At day-40 post-hatch, excreta samples were collected for fatty acids analysis. Results: Significant positive linear correlations (R = 0.82-0.99) were found in the fatty acid content of diets and excreta for all fatty acid groups in all treatments. Comparing the individual fatty acid content of diet and excreta suggested that the broilers preferentially utilized (in decending order, if present) omega-3 polyunsaturated fatty acids, omega-9 and omega-7 monounsaturated fatty acids and most saturated fatty acids (except C16:0 and C18:0), but the omega-6 polyunsaturated fatty acids were under utilized even when they were the most abundant. Conclusion: Fat sources which are high in the C16:0, C18:0 and omega-6 fatty acids may not be ideal for broiler feed formulations for nutritional and economical reasons.Khaled Kanakri, John Carragher, Robert Hughes, Beverly Muhlhausler, Carolyn de Koning and Robert Gibso

Surgical face masks impair human face matching performance for familiar and unfamiliar faces

In response to the COVID-19 pandemic, many governments around the world now recommend, or require, that their citizens cover the lower half of their face in public. Consequently, many people now wear surgical face masks in public. We investigated whether surgical face masks affected the performance of human observers, and a state-of-the-art face recognition system, on tasks of perceptual face matching. Participants judged whether two simultaneously presented face photographs showed the same person or two different people. We superimposed images of surgical masks over the faces, creating three different mask conditions: control (no masks), mixed (one face wearing a mask), and masked (both faces wearing masks). We found that surgical face masks have a large detrimental effect on human face matching performance, and that the degree of impairment is the same regardless of whether one or both faces in each pair are masked. Surprisingly, this impairment is similar in size for both familiar and unfamiliar faces. When matching masked faces, human observers are biased to reject unfamiliar faces as “mismatches” and to accept familiar faces as “matches”. Finally, the face recognition system showed very high classification accuracy for control and masked stimuli, even though it had not been trained to recognise masked faces. However, accuracy fell markedly when one face was masked and the other was not. Our findings demonstrate that surgical face masks impair the ability of humans, and naïve face recognition systems, to perform perceptual face matching tasks. Identification decisions for masked faces should be treated with caution

Simulated AFRS as decision-aids in face matching

Automated Facial Recognition Systems (AFRS) are used by governments, law enforcement agencies and private businesses to verify the identity of individuals. While previous research has compared the performance of AFRS and humans on tasks of one-to-one face matching, little is known about how effectively human operators can use these AFRS as decision-aids. Our aim was to investigate how the prior decision from an AFRS affects human performance on a face matching task, and to establish whether human oversight of AFRS decisions can lead to collaborative performance gains for the human algorithm team. The identification decisions from our simulated AFRS were informed by the performance of a real, state-of-the-art, Deep Convolutional Neural Network (DCNN) AFRS on the same task. Across five pre-registered experiments, human operators used the decisions from highly accurate AFRS (>90%) to improve their own face matching performance compared to baseline (sensitivity gain: Cohen’s d = 0.71-1.28; overall accuracy gain: d = 0.73-1.46). Yet, despite this improvement, AFRS-aided human performance consistently failed to reach the level that the AFRS achieved alone. Even when the AFRS erred only on the face pairs with the highest human accuracy (>89%), participants often failed to correct the system’s errors, while also overruling many correct decisions, raising questions about the conditions under which human oversight might enhance AFRS operation. Overall, these data demonstrate that the human operator is a limiting factor in this simple model of human-AFRS teaming. These findings have implications for the “human-in-the-loop” approach to AFRS oversight in forensic face matching scenariosOutput Status: Forthcomin

Simulated Automated Facial Recognition Systems as Decision-Aids in Forensic Face Matching Tasks

Automated Facial Recognition Systems (AFRS) are used by governments, law enforcement agencies and private businesses to verify the identity of individuals. While previous research has compared the performance of AFRS and humans on tasks of one-to-one face matching, little is known about how effectively human operators can use these AFRS as decision-aids. Our aim was to investigate how the prior decision from an AFRS affects human performance on a face matching task, and to establish whether human oversight of AFRS decisions can lead to collaborative performance gains for the human algorithm team. The identification decisions from our simulated AFRS were informed by the performance of a real, state-of-the-art, Deep Convolutional Neural Network (DCNN) AFRS on the same task. Across five pre-registered experiments, human operators used the decisions from highly accurate AFRS (>90%) to improve their own face matching performance compared to baseline (sensitivity gain: Cohen’s d = 0.71-1.28; overall accuracy gain: d = 0.73-1.46). Yet, despite this improvement, AFRS-aided human performance consistently failed to reach the level that the AFRS achieved alone. Even when the AFRS erred only on the face pairs with the highest human accuracy (>89%), participants often failed to correct the system’s errors, while also overruling many correct decisions, raising questions about the conditions under which human oversight might enhance AFRS operation. Overall, these data demonstrate that the human operator is a limiting factor in this simple model of human-AFRS teaming. These findings have implications for the “human-in-the-loop” approach to AFRS oversight in forensic face matching scenario

NODAL/TGFβ signalling mediates the self-sustained stemness induced by PIK3CAH1047R homozygosity in pluripotent stem cells

Activating PIK3CA mutations are known “drivers” of human cancer and developmental overgrowth syndromes. We recently demonstrated that the "hotspot" PIK3CAH1047R variant exerts unexpected allele dose-dependent effects on stemness in human pluripotent stem cells (hPSCs). In the present study, we combine high-depth transcriptomics, total proteomics and reverse-phase protein arrays to reveal potentially disease-related alterations in heterozygous cells, and to assess the contribution of activated TGFβ signalling to the stemness phenotype of homozygous PIK3CAH1047R cells. We demonstrate signalling rewiring as a function of oncogenic PI3K signalling strength, and provide experimental evidence that self-sustained stemness is causally related to enhanced autocrine NODAL/TGFβ signalling. A significant transcriptomic signature of TGFβ pathway activation in heterozygous PIK3CAH1047R was observed but was modest and was not associated with the stemness phenotype seen in homozygous mutants. Notably, the stemness gene expression in homozygous PIK3CAH1047R iPSCs was reversed by pharmacological inhibition of NODAL/TGFβ signalling, but not by pharmacological PI3Kα pathway inhibition. Altogether, this provides the first in-depth analysis of PI3K signalling in human pluripotent stem cells and directly links strong PI3K activation to developmental NODAL/TGFβ signalling. This work illustrates the importance of allele dosage and expression when artificial systems are used to model human genetic disease caused by activating PIK3CA mutations

A novel method to allow noninvasive, longitudinal imaging of the murine immune system in vivo

In vivo imaging has revolutionized understanding of the spatiotemporal complexity that subserves the generation of successful effector and regulatory immune responses. Until now, invasive surgery has been required for microscopic access to lymph nodes (LNs), making repeated imaging of the same animal impractical and potentially affecting lymphocyte behavior. To allow longitudinal in vivo imaging, we conceived the novel approach of transplanting LNs into the mouse ear pinna. Transplanted LNs maintain the structural and cellular organization of conventional secondary lymphoid organs. They participate in lymphocyte recirculation and exhibit the capacity to receive and respond to local antigenic challenge. The same LN could be repeatedly imaged through time without the requirement for surgical exposure, and the dynamic behavior of the cells within the transplanted LN could be characterized. Crucially, the use of blood vessels as fiducial markers also allowed precise re-registration of the same regions for longitudinal imaging. Thus, we provide the first demonstration of a method for repeated, noninvasive, in vivo imaging of lymphocyte behavior

Effect of dietary ALA on growth rate, feed conversion ratio, mortality rate and breast meat omega-3 LCPUFA content in broiler chickens

We have previously demonstrated that feeding chickens a diet containing high levels of the n-3 PUFA α-linolenic acid (ALA) significantly increases the content of the principal omega-3 long-chain polyunsaturated fatty acids, eicosapentaenoic acid and docosahexaenoic acid, in their meat and eggs. However, the effect of the diet on production characteristics of the birds has not been assessed. This study aimed to determine the effect of feeding male and female Cobb 500 broilers (n = 3840) a high ALA diet (containing 2.5% flaxseed oil) compared with a standard commercial Control diet (containing 2.5% tallow) on growth, feed conversion ratio and mortality until 6 weeks of age. As expected the dietary flaxseed oil significantly increased breast meat levels of omega-3 polyunsaturated fatty acids (~4-fold), with most eicosapentaenoic acid and docosahexaenoic acid being deposited in the phospholipid fraction. Both male and female birds fed the high ALA diet were significantly heavier at 6 weeks of age (77 g heavier in females, 87 g heavier in males). They also had a significantly (10%) lower feed conversion ratio, and a mortality rate that was not different from the Control diet across the 6-week feeding period. These findings indicate that a high ALA diet has the potential to enrich chicken breast meat with eicosapentaenoic acid and docosahexaenoic acid without loss of growth rate or feed efficiency, or increase in fat content of breast meat.John F. Carragher, Beverly S. Mühlhäusler, Mark S. Geier, James D. House, Robert J. Hughes and Robert A. Gibso

Heterogeneity after harmonisation: a retrospective cohort study of bleeding and stroke risk after the introduction of direct oral anticoagulants in four Western European countries

Purpose: Database heterogeneity can impact effect estimates. Harmonisation provided by common protocols and common data models (CDMs) can increase the validity of pharmacoepidemiologic research. In a case study measuring the changes in the safety and effectiveness of stroke prevention therapy after the introduction of direct oral anticoagulants (DOACs), we performed an international comparison. Methods: Using data from Stockholm, Denmark, Scotland and Norway, harmonised with a common protocol and CDM, two calendar-based cohorts were created: 2012 and 2017. Patients with a diagnosis code of atrial fibrillation 5 years preceding the 1-year cohort window were included. DOAC, vitamin K antagonist and aspirin treatment were assessed in the 6 months prior to the start of each year while strokes and bleeds were assessed during the year. A Poisson regression generated incidence rate ratios (IRRs) to compare outcomes from 2017 to 2012 adjusted for changes in individual-level baseline characteristics. Results: In 280 359 patients in the 2012 cohort and 356 779 in the 2017 cohort, treatment with OACs increased on average from 45% to 65%, while treatment with aspirin decreased from 30% to 10%. In all countries except Scotland, there were decreases in the risk of stroke and no changes in bleeding risk, after adjustment for changes in baseline characteristics. In Scotland, major bleeding (IRR 1.09, 95% confidence interval [CI] [1.00; 1.18]) and intracranial haemorrhage (IRR 1.31, 95% CI [1.13; 1.52]) increased from 2012 to 2017. Conclusions: Stroke prevention therapy improved from 2012 to 2017 with a corresponding reduction in stroke risk without increasing the risk of bleeding in all countries, except Scotland. The heterogeneity that remains after methodological harmonisation can be informative of the underlying population and database