The increase in medical admissions with anorexia nervosa during the COVID-19 pandemic in Western Australia.

OBJECTIVE: A comparative study to describe the increase in medical admissions of children and adolescents with anorexia nervosa (AN) in Western Australia in 2019 (pre-pandemic) and 2020 (peri-pandemic). METHOD: Patient demographics, physiological parameters, length of stay, time to assessment by the Eating Disorder Service (EDS), and commencement of specialist eating disorder (ED) outpatient treatment was collected for adolescents admitted with AN between 1st January 2019 and 31st December 2020. RESULTS: The number of admissions doubled from 126 in 2019 to 268 in 2020. The number of children admitted increased by 52%. The median length of hospital stay was shorter in 2020 (12 vs. 17 days; p < .001), but the 28-day readmission rate was greater (39.9% vs. 22.2%; p < .001). At the time of hospital discharge in 2020, only 60% of patients were able to step-down into specialist ED outpatient treatment, compared to 93% in 2019. The mean number of admissions per child before completing EDS assessment increased significantly in 2020 (2.75 vs. 0, p < .001). DISCUSSION: Shorter inpatient stays and delays in the commencement of specialist ED outpatient treatment may have contributed to the increased readmission rate seen in 2020. PUBLIC SIGNIFICANCE: This research is important as it explores the reasons for increased medical presentations and admissions of youth with AN during the COVID-19 pandemic in Western Australia. We hope that our lessons learned may be helpful to others trying to balance similar clinical workloads.

Common mechanisms explain nitrogen-dependent growth of Arctic shrubs over three decades despite heterogeneous trends and declines in soil nitrogen availability.

Heterogeneity has been observed in the responses of Arctic shrubs to climate variability over recent decades, which may reflect landscape-scale variability in belowground resources. At a northern fringe of tall shrub expansion (Yuribei, Yamal Peninsula, Russia), we sought to determine the mechanisms relating nitrogen (N) limitation to shrub growth over decadal time. We analysed the ratio of 15 N to 14 N isotopes in wood rings of 10 Salix lanata individuals (399 measurements) to reconstruct annual point-based bioavailable N between 1980 and 2013. We applied a model-fitting/model-selection approach with a suite of competing ecological models to assess the most-likely mechanisms that explain each shrub's individual time-series. Shrub δ15 N time-series indicated declining (seven shrubs), increasing (two shrubs) and no trend (one shrub) in N availability. The most appropriate model for all shrubs included N-dependent growth of linear rather than saturating form. Inclusion of plant-soil feedbacks better explained ring width and δ15 N for eight of 10 individuals. Although N trajectories were individualistic, common mechanisms of varying strength confirmed the N-dependency of shrub growth. The linear mechanism may reflect intense scavenging of scarce N; the importance of plant-soil feedbacks suggests that shrubs subvert the microbial bottleneck by actively controlling their environment.

Pilot study of universal screening of children and child-parent cascade testing for familial hypercholesterolaemia in Australia.

AIM: Familial hypercholesterolaemia (FH) is a common and treatable cause of premature coronary artery disease. However, the majority of individuals with FH remain undiagnosed. This study investigated the feasibility, acceptability and cost-effectiveness of screening children aged 1-2 years for FH at the time of an immunisation. METHODS: Children 1-2 years of age were offered screening for FH with a point-of-care total cholesterol (TC) test by capillary-collected blood sample at the time of an immunisation. An additional blood sample was taken to allow genetic testing if the TC level was above the 95th percentile (>5.3 mmol/L). Parents of children diagnosed with FH were offered testing. Following detection of the affected parent, cascade testing of their first-degree blood relatives was performed. RESULTS: We screened 448 children with 32 (7.1%) having a TC ≥ 5.3 mmol/L. The FH diagnosis was confirmed in three children (1:150 screened). Reverse cascade testing of other family members identified a further five individuals with FH; hence, eight new cases of FH were diagnosed from screening 448 children (1:56 screened). Ninety-six percent of parents would screen future children for FH. The approach was cost-effective, at $3979 per quality-adjusted life year gained. CONCLUSION: In Western Australia, universal screening of children aged 1-2 years for FH, undertaken at the time of an immunisation, was a feasible and effective approach to detect children, parents and other blood relatives with FH. The approach was acceptable to parents and is potentially a highly cost-effective detection strategy for families at risk of FH.

Integrated guidance to enhance the care of children and adolescents with familial hypercholesterolaemia: Practical advice for the community clinician.

Familial hypercholesterolaemia (FH) is a highly penetrant monogenic disorder present from birth that markedly elevates plasma low-density lipoprotein (LDL)-cholesterol (LDL-C) concentration and, if untreated, leads to premature atherosclerosis and coronary artery disease (CAD). At a prevalence of 1:250 individuals, with over 90% undiagnosed, recent estimates suggest that there are approximately 22 000 children and adolescents with FH in Australia and New Zealand. However, the overwhelming majority remain undetected and inadequately treated until adulthood or after their first cardiac event. The guidance in this paper aims to increase awareness about paediatric FH and provide practical advice for the diagnosis and management of FH in children and adolescents. Recommendations are given on the detection, diagnosis, assessment and management of FH in children and adolescents. Recommendations are also made on genetic testing, including counselling and the potential for universal screening programmes. Practical guidance on management includes treatment of non-cholesterol risk factors, and safe and appropriate use of LDL-C lowering therapies, including statins, ezetimibe, PCSK9 inhibitors and lipoprotein apheresis. Models of care for FH need to be adapted to local and regional health care needs and available resources. Targeting the detection of FH as a priority in children and young adults has the potential to alter the natural history of atherosclerotic cardiovascular disease and recognise the promise of early detection for improving long-term health outcomes. A comprehensive implementation strategy, informed by further research, including assessments of cost-benefit, will be required to ensure that this new guidance benefits all families with or at risk of FH.

Impact of Coronavirus Disease 2019 Public Health Measures on Detections of Influenza and Respiratory Syncytial Virus in Children During the 2020 Australian Winter.

Public health measures targeting coronavirus disease 2019 have potential to impact transmission of other respiratory viruses. We found 98.0% and 99.4% reductions in respiratory syncytial virus and influenza detections, respectively, in Western Australian children through winter 2020 despite schools reopening. Border closures have likely been important in limiting external introductions.

Assessing the impact of the 13 valent pneumococcal vaccine on childhood empyema in Australia.

BACKGROUND: Empyema is a serious complication of pneumonia frequently caused by Streptococcus pneumoniae (SP). We assessed the impact of the 13-valent pneumococcal conjugate vaccine (13vPCV) on childhood pneumonia and empyema after inclusion in the Australian National Immunisation Program. METHODS: For bacterial pneumonia and empyema hospitalisations, we ascertained incidence rates (IRs) using the National Hospital Morbidity Database International Statistical Classification of Disease discharge codes and relevant population denominators, and calculated incidence rate ratios (IRR) comparing the 13vPCV period (June 2012-May 2017) with the 7vPCV period (June 2007-May 2011). Blood and pleural fluid (PF) cultures and PF PCR of 401 children with empyema from 11 Australian hospitals during the 13vPCV period were compared with our previous study in the 7vPCV period. FINDINGS: Across 7vPCV and 13vPCV periods, IRs per million children (95% CIs) were 1605 (1588 to 1621) and 1272 (1259 to 1285) for bacterial pneumonia, and 14.23 (12.67 to 15.79) and 17.89 (16.37 to 19.42) for empyema hospitalisations. IRRs were 0.79 (0.78 to 0.80) for bacterial pneumonia and 1.25 (1.09 to 1.44) for empyema. Of 161 empyema cases with SP serotypes, 147 (91.3%) were vaccine types. ST3 accounted for 76.4% of identified serotypes in the 13vPCV period, more than double than the 7vPCV period (p<0.001); ST19A decreased from 36.4% to 12.4%. No cases of ST1 empyema were identified in the 13vPCV period versus 14.5% in the 7vPCV period. INTERPRETATION: 13vPCV resulted in a significant reduction in all-cause hospitalisations for bacterial pneumonia but empyema hospitalisations significantly increased, with emergence of pneumococcal ST3 as the dominant serotype in empyema. TRIAL REGISTRATION NUMBER: Australian and New Zealand Clinical Trial Registry ACTRN 12614000354684.

atomium-a Python structure parser.

SUMMARY: Structural biology relies on specific file formats to convey information about macromolecular structures. Traditionally this has been the PDB format, but increasingly newer formats, such as PDBML, mmCIF and MMTF are being used. Here we present atomium, a modern, lightweight, Python library for parsing, manipulating and saving PDB, mmCIF and MMTF file formats. In addition, we provide a web service, pdb2json, which uses atomium to give a consistent JSON representation to the entire Protein Data Bank. AVAILABILITY AND IMPLEMENTATION: atomium is implemented in Python and its performance is equivalent to the existing library BioPython. However, it has significant advantages in features and API design. atomium is available from atomium.bioinf.org.uk and pdb2json can be accessed at pdb2json.bioinf.org.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Essentials of a new clinical practice guidance on familial hypercholesterolaemia for physicians.

Familial hypercholesterolaemia (FH) is a common, heritable and preventable cause of premature coronary artery disease. New clinical practice recommendations are presented to assist practitioners in enhancing the care of all patients with FH. Core recommendations are made on the detection, diagnosis, assessment and management of adults, children and adolescents with FH. Management is under-pinned by the precepts of risk stratification, adherence to healthy lifestyles, treatment of non-cholesterol risk factors and appropriate use of low-density lipoprotein (LDL)-cholesterol-lowering therapies including statins, ezetimibe and proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors. The recommendations need to be utilised using judicious clinical judgement and shared decision-making with patients and families. New government-funded schemes for genetic testing and use of PCSK9 inhibitors, as well as the National Health Genomics Policy Framework, will enable adoption of the recommendations. However, a comprehensive implementation science and practice strategy is required to ensure that the guidance translates into benefit for all families with FH.

Predictors of hospital readmission in infants less than 3 months old.

AIM: To examine rates and predictors of 7-day readmission in infants hospitalised before 3 months of age with infectious and non-infectious conditions. METHODS: Retrospective population-based data-linkage study of 121 854 infants from a 5-year metropolitan birth cohort (2008-2012). Cox proportional hazard models were used to examine associations between infant and maternal factors with 7-day readmission. RESULTS: A total of 11 669 (9.6%) infants were hospitalised at least once by 3 months of age (median 23 days old, 56% male) with 12 602 total index hospitalisations. Infection-related conditions accounted for 29.4% (n = 3705). Readmission within 7 days occurred after 4.8% of all index hospitalisations and 5.4% of infection-related hospitalisations. Age ≤21 days was the strongest readmission risk factor (hazard ratio 7.7 (95% confidence interval 4.7-12.7) compared to infants 61-90 days old). Other risk factors included shorter index hospitalisations, younger maternal age and multi-gravidity. CONCLUSION: Hospitalisations and readmissions occur for many young infants. Risk factors for readmission should inform risk-based management guidelines.

Integrated Guidance for Enhancing the Care of Familial Hypercholesterolaemia in Australia.

Familial hypercholesterolaemia (FH) is a dominant and highly penetrant monogenic disorder present from birth that markedly elevates plasma low-density lipoprotein (LDL)-cholesterol concentration and, if untreated, leads to premature atherosclerosis and coronary artery disease (CAD). There are approximately 100,000 people with FH in Australia. However, an overwhelming majority of those affected remain undetected and inadequately treated, consistent with FH being a leading challenge for public health genomics. To further address the unmet need, we provide an updated guidance, presented as a series of systematically collated recommendations, on the care of patients and families with FH. These recommendations have been informed by an exponential growth in published works and new evidence over the last 5 years and are compatible with a contemporary global call to action on FH. Recommendations are given on the detection, diagnosis, assessment and management of FH in adults and children. Recommendations are also made on genetic testing and risk notification of biological relatives who should undergo cascade testing for FH. Guidance on management is based on the concepts of risk re-stratification, adherence to heart healthy lifestyles, treatment of non-cholesterol risk factors, and safe and appropriate use of LDL-cholesterol lowering therapies, including statins, ezetimibe, proprotein convertase subtilisin/kexin type 9 inhibitors and lipoprotein apheresis. Broad recommendations are also provided for the organisation and development of health care services. Recommendations on best practice need to be underpinned by good clinical judgment and shared decision making with patients and families. Models of care for FH need to be adapted to local and regional health care needs and available resources. A comprehensive and realistic implementation strategy, informed by further research, including assessments of cost-benefit, will be required to ensure that this new guidance benefits all Australian families with or at risk of FH.

Zincbindpredict-Prediction of Zinc Binding Sites in Proteins.

Background: Zinc binding proteins make up a significant proportion of the proteomes of most organisms and, within those proteins, zinc performs rôles in catalysis and structure stabilisation. Identifying the ability to bind zinc in a novel protein can offer insights into its functions and the mechanism by which it carries out those functions. Computational means of doing so are faster than spectroscopic means, allowing for searching at much greater speeds and scales, and thereby guiding complimentary experimental approaches. Typically, computational models of zinc binding predict zinc binding for individual residues rather than as a single binding site, and typically do not distinguish between different classes of binding site-missing crucial properties indicative of zinc binding. Methods: Previously, we created ZincBindDB, a continuously updated database of known zinc binding sites, categorised by family (the set of liganding residues). Here, we use this dataset to create ZincBindPredict, a set of machine learning methods to predict the most common zinc binding site families for both structure and sequence. Results: The models all achieve an MCC ≥ 0.88, recall ≥ 0.93 and precision ≥ 0.91 for the structural models (mean MCC = 0.97), while the sequence models have MCC ≥ 0.64, recall ≥ 0.80 and precision ≥ 0.83 (mean MCC = 0.87), with the models for binding sites containing four liganding residues performing much better than this. Conclusions: The predictors outperform competing zinc binding site predictors and are available online via a web interface and a GraphQL API.

The contribution of viruses and bacteria to community-acquired pneumonia in vaccinated children: a case-control study.

INTRODUCTION: Respiratory pathogens associated with childhood pneumonia are often detected in the upper respiratory tract of healthy children, making their contribution to pneumonia difficult to determine. We aimed to determine the contribution of common pathogens to pneumonia adjusting for rates of asymptomatic detection to inform future diagnosis, treatment and preventive strategies. METHODS: A case-control study was conducted among children <18 years in Perth, Western Australia. Cases were children hospitalised with radiologically confirmed pneumonia; controls were healthy children identified from outpatient and local immunisation clinics. Nasopharyngeal swabs were collected and tested for 14 respiratory viruses and 6 bacterial species by Polymerase chain reaction (PCR). For each pathogen, adjusted odds ratio (aOR; 95% CI) was calculated using multivariate logistic regression and population-attributable fraction (95% CI) for pneumonia was estimated. RESULTS: From May 2015 to October 2017, 230 cases and 230 controls were enrolled. At least one respiratory virus was identified in 57% of cases and 29% of controls (aOR: 4.7; 95% CI: 2.8 to 7.8). At least one bacterial species was detected in 72% of cases and 80% of controls (aOR: 0.7; 95% CI: 0.4 to 1.2). Respiratory syncytial virus (RSV) detection was most strongly associated with pneumonia (aOR: 58.4; 95% CI: 15.6 to 217.5). Mycoplasma pneumoniae was the only bacteria associated with pneumonia (aOR: 14.5; 95% CI: 2.2 to 94.8). We estimated that RSV, human metapneumovirus (HMPV), influenza, adenovirus and Mycoplasma pneumoniae were responsible for 20.2% (95% CI: 14.6 to 25.5), 9.8% (5.6% to 13.7%), 6.2% (2.5% to 9.7%), 4% (1.1% to 7.1%) and 7.2% (3.5% to 10.8%) of hospitalisations for childhood pneumonia, respectively. CONCLUSIONS: Respiratory viruses, particularly RSV and HMPV, are major contributors to pneumonia in Australian children.

IntPred: a structure-based predictor of protein-protein interaction sites.

MOTIVATION: Protein-protein interactions are vital for protein function with the average protein having between three and ten interacting partners. Knowledge of precise protein-protein interfaces comes from crystal structures deposited in the Protein Data Bank (PDB), but only 50% of structures in the PDB are complexes. There is therefore a need to predict protein-protein interfaces in silico and various methods for this purpose. Here we explore the use of a predictor based on structural features and which exploits random forest machine learning, comparing its performance with a number of popular established methods. RESULTS: On an independent test set of obligate and transient complexes, our IntPred predictor performs well (MCC = 0.370, ACC = 0.811, SPEC = 0.916, SENS = 0.411) and compares favourably with other methods. Overall, IntPred ranks second of six methods tested with SPPIDER having slightly better overall performance (MCC = 0.410, ACC = 0.759, SPEC = 0.783, SENS = 0.676), but considerably worse specificity than IntPred. As with SPPIDER, using an independent test set of obligate complexes enhanced performance (MCC = 0.381) while performance is somewhat reduced on a dataset of transient complexes (MCC = 0.303). The trade-off between sensitivity and specificity compared with SPPIDER suggests that the choice of the appropriate tool is application-dependent. AVAILABILITY AND IMPLEMENTATION: IntPred is implemented in Perl and may be downloaded for local use or run via a web server at www.bioinf.org.uk/intpred/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Parent-child genetic testing for familial hypercholesterolaemia in an Australian context.

AIM: The aim of this study was to evaluate the clinical outcome of parent-child testing for familial hypercholesterolaemia (FH) employing genetic testing and the likely additional cost of treating each child. METHODS: Parent-child testing for gene variants causative of FH was carried out according to Australian guidelines. The number of new cases detected, the low-density lipoprotein (LDL)-cholesterol that best predicted a mutation and the proportional reduction in LDL-cholesterol following statin treatment was evaluated. Treatment costs were calculated as the cost per mmol/L reduction in LDL-cholesterol. RESULTS: A total of 126 adult patients, known to have a pathogenic mutation causative of FH, and their children were studied. From 244 children identified, 148 (60.7%) were genetically screened; 84 children were identified as mutative positive (M+) and 64 as mutative negative. Six of the M+ children were already on statin treatment; 40 were subsequently treated with low-dose statins, with LDL-cholesterol falling significantly by 38% (P < 0.001). The estimated cost per mmol/L reduction of LDL-cholesterol of a child receiving statins from ages 10 to 18 years is AU$1361, which can potentially be cost-effective. An LDL-cholesterol threshold of 3.5 mmol/L had a sensitivity of 92.8% and specificity of 96.6% for the detection of a mutation. CONCLUSION: Genetic testing of children of affected parents with FH is an effective means of detecting new cases of FH. Cascade testing can enable early statin therapy with significant reductions in LDL-cholesterol concentration.

Beyond cascade screening: detection of familial hypercholesterolaemia at childhood immunization and other strategies.

PURPOSE OF REVIEW: Familial hypercholesterolaemia is a common genetic disorder that accelerates premature coronary heart disease. Although effective treatments are available, the majority of individuals remain undiagnosed. We review new evidence for improving the detection of familial hypercholesterolaemia. RECENT FINDINGS: Recent studies have demonstrated that universal screening of children for familial hypercholesterolaemia may be highly effective at the time of immunization if combined with reverse cascade testing of adult family members, who have a more immediate risk of a coronary event. Alerts on laboratory reports and the application of bioinformatics to electronic health records may also be useful for identifying familial hypercholesterolaemia in community settings. Effective detection, diagnosis, and codification of familial hypercholesterolaemia are essential for the development of registries. SUMMARY: Although the cost-effectiveness of screening programs for familial hypercholesterolaemia in childhood remains to be established, combining universal and reverse cascade screening, complemented by opportunistic identification of individuals in high-risk settings, use of laboratory alerts, and screening of electronic health records are likely to have a high yield in the detection of familial hypercholesterolaemia in the community.

Knowns and unknowns in the care of pediatric familial hypercholesterolemia.

Familial hypercholesterolemia (FH) is a common genetic disorder that causes elevated LDL cholesterol levels from birth. Untreated FH accelerates atherosclerosis and predisposes individuals to premature coronary artery disease (CAD) in adulthood. Mendelian randomization studies have demonstrated that LDL cholesterol has both a causal and cumulative effect on the risk of CAD. This supports clinical recommendations that children with FH commence pharmacological treatment from the age of 8 to 10 years, to reduce the burden of hypercholesterolemia. Worldwide, the majority of children with FH remain undiagnosed. Recent evidence suggests that the frequency of FH is at least 1 in 250 and this constitutes a public health issue. We review and identify the knowns and unknowns concerning the detection and management of pediatric FH that impact on the developing model of care for this condition.

The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants.

MOTIVATION: High-throughput sequencing platforms are increasingly used to screen patients with genetic disease for pathogenic mutations, but prediction of the effects of mutations remains challenging. Previously we developed SAAPdap (Single Amino Acid Polymorphism Data Analysis Pipeline) and SAAPpred (Single Amino Acid Polymorphism Predictor) that use a combination of rule-based structural measures to predict whether a missense genetic variant is pathogenic. Here we investigate whether the same methodology can be used to develop a differential phenotype predictor, which, once a mutation has been predicted as pathogenic, is able to distinguish between phenotypes-in this case the two major clinical phenotypes (hypertrophic cardiomyopathy, HCM and dilated cardiomyopathy, DCM) associated with mutations in the beta-myosin heavy chain (MYH7) gene product (Myosin-7). RESULTS: A random forest predictor trained on rule-based structural analyses together with structural clustering data gave a Matthews' correlation coefficient (MCC) of 0.53 (accuracy, 75%). A post hoc removal of machine learning models that performed particularly badly, increased the performance (MCC = 0.61, Acc = 79%). This proof of concept suggests that methods used for pathogenicity prediction can be extended for use in differential phenotype prediction. AVAILABILITY AND IMPLEMENTATION: Analyses were implemented in Perl and C and used the Java-based Weka machine learning environment. Please contact the authors for availability. CONTACTS: andrew@bioinf.org.uk or andrew.martin@ucl.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Documenting family history in children with hypercholesterolaemia: A lost opportunity.

AIM: To determine whether information about a family history of hypercholesterolaemia or early cardiovascular disease was documented by paediatricians in children and adolescents with elevated low-density lipoprotein (LDL)-cholesterol levels. METHODS: Retrospective chart review of all children with a LDL-cholesterol level ≥95th percentile (3.4 mmol/L) and ≥99th percentile (3.8 mmol/L) at a tertiary paediatric hospital in 2014. RESULTS: Of 86 children with a LDL-cholesterol level ≥3.4 mmol/L, only 18 (20.9%) had documentation of a family history of hypercholesterolaemia or early cardiovascular disease. In those 18, 13 (72.2%) had a family history of hypercholesterolaemia and 11 (61.1%) a family history of early cardiovascular disease. Increasing the LDL-cholesterol cut-off level to ≥3.8 mmol/L (n = 46) did not improve documentation of a family history (9/46, 19.6%). CONCLUSIONS: In patients with elevated LDL-cholesterol levels, paediatricians rarely document a positive or negative family history of hypercholesterolaemia or early cardiovascular disease. This represents a lost opportunity to diagnose children and adolescents with familial hypercholesterolaemia.

Evaluating tools for transcription factor binding site prediction.

BACKGROUND: Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the mediation of transcriptional regulation. Information on experimentally validated functional TFBSs is limited and consequently there is a need for accurate prediction of TFBSs for gene annotation and in applications such as evaluating the effects of single nucleotide variations in causing disease. TFBSs are generally recognized by scanning a position weight matrix (PWM) against DNA using one of a number of available computer programs. Thus we set out to evaluate the best tools that can be used locally (and are therefore suitable for large-scale analyses) for creating PWMs from high-throughput ChIP-Seq data and for scanning them against DNA. RESULTS: We evaluated a set of de novo motif discovery tools that could be downloaded and installed locally using ENCODE-ChIP-Seq data and showed that rGADEM was the best-performing tool. TFBS prediction tools used to scan PWMs against DNA fall into two classes - those that predict individual TFBSs and those that identify clusters. Our evaluation showed that FIMO and MCAST performed best respectively. CONCLUSIONS: Selection of the best-performing tools for generating PWMs from ChIP-Seq data and for scanning PWMs against DNA has the potential to improve prediction of precise transcription factor binding sites within regions identified by ChIP-Seq experiments for gene finding, understanding regulation and in evaluating the effects of single nucleotide variations in causing disease.