Enhancing missense variant pathogenicity prediction with protein language models using VariPred.

Computational approaches for predicting the pathogenicity of genetic variants have advanced in recent years. These methods enable researchers to determine the possible clinical impact of rare and novel variants. Historically these prediction methods used hand-crafted features based on structural, evolutionary, or physiochemical properties of the variant. In this study we propose a novel framework that leverages the power of pre-trained protein language models to predict variant pathogenicity. We show that our approach VariPred (Variant impact Predictor) outperforms current state-of-the-art methods by using an end-to-end model that only requires the protein sequence as input. Using one of the best-performing protein language models (ESM-1b), we establish a robust classifier that requires no calculation of structural features or multiple sequence alignments. We compare the performance of VariPred with other representative models including 3Cnet, Polyphen-2, REVEL, MetaLR, FATHMM and ESM variant. VariPred performs as well as, or in most cases better than these other predictors using six variant impact prediction benchmarks despite requiring only sequence data and no pre-processing of the data.

Do antibody CDR loops change conformation upon binding?

Antibodies have increasingly been developed as drugs with over 100 now licensed in the US or EU. During development, it is often necessary to increase or reduce the affinity of an antibody and rational attempts to do so rely on having a structure of the antibody-antigen complex often obtained by modeling. The antigen-binding site consists primarily of six loops known as complementarity-determining regions (CDRs), and an open question has been whether these loops change their conformation when they bind to an antigen. Existing surveys of antibody-antigen complex structures have only examined CDR conformational change in case studies or small-scale surveys. With an increasing number of antibodies where both free and complexed structures have been deposited in the Protein Data Bank, a large-scale survey of CDR conformational change during binding is now possible. To this end, we built a dataset, AbAgDb, that currently includes 177 antibodies with high-quality CDRs, each of which has at least one bound and one unbound structure. We analyzed the conformational change of the Cα backbone of each CDR upon binding and found that, in most cases, the CDRs (other than CDR-H3) show minimal movement, while 70.6% and 87% of CDR-H3s showed global Cα RMSD ≤ 1.0Å and ≤ 2.0Å, respectively. We also compared bound CDR conformations with the conformational space of unbound CDRs and found most of the bound conformations are included in the unbound conformational space. In future, our results will contribute to developing insights into antibodies and new methods for modeling and docking.

Pragmatic Adaptive Trial for Respiratory Infection in Children (PATRIC) Clinical Registry protocol.

INTRODUCTION: Acute respiratory infections (ARI) are the most common cause of paediatric hospitalisation. There is an urgent need to address ongoing critical knowledge gaps in ARI management. The Pragmatic Adaptive Trial for Respiratory Infections in Children (PATRIC) Clinical Registry will evaluate current treatments and outcomes for ARI in a variety of paediatric patient groups. The registry will provide a platform and data to inform a number of PATRIC clinical trials, testing various interventions in ARI treatment and management to optimise paediatric ARI care. METHODS AND ANALYSIS: The PATRIC Clinical Registry is a single-centre, prospective observational registry recruiting from a tertiary paediatric Emergency Department in Western Australia. Through characterising demographic, clinical, treatment and outcome data, the PATRIC Clinical Registry will improve our understanding of antibiotic utilisation and ARI outcomes in children. ETHICS AND DISSEMINATION: The PATRIC Clinical Registry is conducted in accordance with the Declaration of Helsinki, and the International Council for Harmonisation (ICH) Guidelines for Good Clinical Practice (CPMP/ICH/13595) July 1996. Approval is provided by the Child and Adolescent Health Service Human Research Ethics Committee (HREC). Study results will be communicated by presentation and publication (HREC: RGS0000003078.) TRIAL REGISTRATION NUMBER: Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12619000903189. UTN: U1111-1231-3365.

Cascade testing of children and adolescents for elevated Lp(a) in pedigrees with familial hypercholesterolaemia.

Elevated plasma lipoprotein(a) [Lp(a)] is a common, inherited condition independently causing cardiovascular disease. Recent expert recommendations suggest opportunistically testing for elevated Lp(a) during cascade testing for familial hypercholesterolaemia (FH). We investigated the effectiveness of detecting elevated Lp(a) in 103 children and adolescents who were first-degree relatives of 66 adult index FH cases as part of an established FH cascade screening program. The yield of detection of elevated Lp(a) using a threshold of ≥30 mg/dL in children and adolescents was assessed. Cascade testing from FH index cases with elevated Lp(a) ≥50 mg/dL identified 1 case of Lp(a) ≥30 mg/dL for every 2 children or adolescents tested. In contrast, opportunistic screening from index cases with FH but normal Lp(a) levels demonstrated 1 case of Lp(a) ≥30 mg/dL for every 7.5 children or adolescents tested (p < 0.001). In conclusion, cascade testing for elevated Lp(a) from index cases with FH and elevated Lp(a) is effective in identifying new cases of elevated Lp(a).

abYpap: improvements to the prediction of antibody VH/VL packing using gradient boosted regression.

The Fv region of the antibody (comprising VH and VL domains) is the area responsible for target binding and thus the antibody's specificity. The orientation, or packing, of these two domains relative to each other influences the topography of the Fv region, and therefore can influence the antibody's binding affinity. We present abYpap, an improved method for predicting the packing angle between the VH and VL domains. With the large data set now available, we were able to expand greatly the number of features that could be used compared with our previous work. The machine-learning model was tuned for improved performance using 37 selected residues (previously 13) and also by including the lengths of the most variable 'complementarity determining regions' (CDR-L1, CDR-L2 and CDR-H3). Our method shows large improvements from the previous version, and also against other modeling approaches, when predicting the packing angle.

FeBRILe3: Safety Evaluation of Febrile Infant Guidelines Through Prospective Bayesian Monitoring.

OBJECTIVES: Despite evidence supporting earlier discharge of well-appearing febrile infants at low risk of serious bacterial infection (SBI), admissions for ≥48 hours remain common. Prospective safety monitoring may support broader guideline implementation. METHODS: A sequential Bayesian safety monitoring framework was used to evaluate a new hospital guideline recommending early discharge of low-risk infants. Hospital readmissions within 7 days of discharge were regularly assessed against safety thresholds, derived from historic rates and expert opinion, and specified a priori (8 per 100 infants). Infants aged under 3 months admitted to 2 Western Australian metropolitan hospitals for management of fever without source were enrolled (August 2019-December 2021), to a prespecified maximum 500 enrolments. RESULTS: Readmission rates remained below the prespecified threshold at all scheduled analyses. Median corrected age was 34 days, and 14% met low-risk criteria (n = 71). SBI was diagnosed in 159 infants (32%), including urinary tract infection (n = 140) and bacteraemia (n = 18). Discharge occurred before 48 hours for 192 infants (38%), including 52% deemed low-risk. At study completion, 1 of 37 low-risk infants discharged before 48 hours had been readmitted (3%), for issues unrelated to SBI diagnosis. In total, 20 readmissions were identified (4 per 100 infants; 95% credible interval 3, 6), with >0.99 posterior probability of being below the prespecified noninferiority threshold, indicating acceptable safety. CONCLUSIONS: A Bayesian monitoring approach supported safe early discharge for many infants, without increased risk of readmission. This framework may be used to embed safety evaluations within future guideline implementation programs to further reduce low-value care.

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.

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.

Antibody markup language (AbML) - a notation language for antibody-based drug formats and software for creating and rendering AbML (abYdraw).

As interest in antibody-based drug development continues to increase, the biopharmaceutical industry has begun to focus on complex multi-specific antibodies (MsAbs) as an up-and-coming class of biologic that differ from natural monoclonal antibodies through their ability to bind to more than one type of antigen. As techniques to generate such molecules have diversified, so have their formats and the need for standard notation. Previous efforts to develop a notation language for macromolecule drugs have been insufficient, or too complex, for MsAbs. Here, we present Antibody Markup Language (AbML), a new notation language specifically for antibody formats that overcomes the limitations of existing languages and can annotate all current antibody formats, including fusions, fragments, standard antibodies and MsAbs, as well as all currently conceivable future formats. AbML V1.1 also provides explicit support for T-cell receptor domains. To assist users of this language we have also developed a tool, abYdraw, that can draw antibody schematics from AbML strings or generate an AbML string from a drawn antibody schematic. AbML has the potential to become a standardized notation for describing new MsAb formats entering clinical trials.Abbreviations: AbML: Antibody Markup Language; ADC: Antibody-drug conjugate; CAS: Chemical Abstracts Service; CH: Constant heavy; CL: Constant light; Fv: Variable fragment; HELM: Hierarchical Editing Language for Macromolecules; HSA: Human serum albumin; INN: International Nonproprietary Names; KIH: Knobs-into-holes; mAbs: Monoclonal antibodies; MsAb: Multi-specific antibody; WHO: World Health Organization; PEG: Poly-ethylene glycol; scFv: Single-chain variable fragment; SMILES: Simplified Molecular-Input Line-Entry System; VH: Variable heavy; VHH: Single-domain (Camelid) variable heavy; VL: Variable light.

International nonproprietary names for monoclonal antibodies: an evolving nomenclature system.

Appropriate nomenclature for all pharmaceutical substances is important for clinical development, licensing, prescribing, pharmacovigilance, and identification of counterfeits. Nonproprietary names that are unique and globally recognized for all pharmaceutical substances are assigned by the International Nonproprietary Names (INN) Programme of the World Health Organization (WHO). In 1991, the INN Programme implemented the first nomenclature scheme for monoclonal antibodies. To accompany biotechnological development, this nomenclature scheme has evolved over the years; however, since the scheme was introduced, all pharmacological substances that contained an immunoglobulin variable domain were coined with the stem -mab. To date, there are 879 INN with the stem -mab. Owing to this high number of names ending in -mab, devising new and distinguishable INN has become a challenge. The WHO INN Expert Group therefore decided to revise the system to ease this situation. The revised system was approved and adopted by the WHO at the 73rd INN Consultation held in October 2021, and the radical decision was made to discontinue the use of the well-known stem -mab in naming new antibody-based drugs and going forward, to replace it with four new stems: -tug, -bart, -mig, and -ment.

Corrigendum to Synopsis of an integrated guidance for enhancing the care of familial hypercholesterolaemia: An Australian perspective [American Journal of Preventive Cardiology 6 (2021) 100151].

[This corrects the article DOI: 10.1016/j.ajpc.2021.100151.].

Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics.

Therapeutic monoclonal antibodies and their derivatives are key components of clinical pipelines in the global biopharmaceutical industry. The availability of large datasets of antibody sequences, structures, and biophysical properties is increasingly enabling the development of predictive models and computational tools for the "developability assessment" of antibody drug candidates. Here, we provide an overview of the antibody informatics tools applicable to the prediction of developability issues such as stability, aggregation, immunogenicity, and chemical degradation. We further evaluate the opportunities and challenges of using biopharmaceutical informatics for drug discovery and optimization. Finally, we discuss the potential of developability guidelines based on in silico metrics that can be used for the assessment of antibody stability and manufacturability.

Examining the interseasonal resurgence of respiratory syncytial virus in Western Australia.

BACKGROUND: Following a relative absence in winter 2020, a large resurgence of respiratory syncytial virus (RSV) detections occurred during the 2020/2021 summer in Western Australia. This seasonal shift was linked to SARS-CoV-2 public health measures. We examine the epidemiology and RSV testing of respiratory-coded admissions, and compare clinical phenotype of RSV-positive admissions between 2019 and 2020. METHOD: At a single tertiary paediatric centre, International Classification of Diseases, 10th edition Australian Modification-coded respiratory admissions longer than 12 hours were combined with laboratory data from 1 January 2019 to 31 December 2020. Data were grouped into bronchiolitis, other acute lower respiratory infection (OALRI) and wheeze, to assess RSV testing practices. For RSV-positive admissions, demographics and clinical features were compared between 2019 and 2020. RESULTS: RSV-positive admissions peaked in early summer 2020, following an absent winter season. Testing was higher in 2020: bronchiolitis, 94.8% vs 89.2% (p=0.01); OALRI, 88.6% vs 82.6% (p=0.02); and wheeze, 62.8% vs 25.5% (p<0.001). The 2020 peak month, December, contributed almost 75% of RSV-positive admissions, 2.5 times the 2019 peak. The median age in 2020 was twice that observed in 2019 (16.4 vs 8.1 months, p<0.001). The proportion of RSV-positive OALRI admissions was greater in 2020 (32.6% vs 24.9%, p=0.01). There were no clinically meaningful differences in length of stay or disease severity. INTERPRETATION: The 2020 RSV season was in summer, with a larger than expected peak. There was an increase in RSV-positive non-bronchiolitis admissions, consistent with infection in older RSV-naïve children. This resurgence raises concern for regions experiencing longer and more stringent SARS-CoV-2 public health measures.

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.

Paediatric headbox as aerosol and droplet barrier.

BACKGROUND: High-flow nasal oxygen (HFNO) is frequently used in hospitals, producing droplets and aerosols that could transmit SARS-CoV-2. AIM: To determine if a headbox could reduce droplet and aerosol transmission from patients requiring HFNO. METHODS: The size and dispersion of propylene glycol (model for patient-derived infectious particles) was measured using a spectrometer and an infant mannequin receiving 10-50 L/min of HFNO using (1) no headbox, (2) open headbox, (3) headbox-blanket or (4) headbox with a high-efficiency particulate (HEP) filter covering the neck opening. RESULTS: All headbox set-ups reduced the dispersal of droplets and aerosols compared with no headbox. The headbox-blanket system increased aerosol dispersal compared with the open headbox. The fraction of aerosols retained in the headbox for HFNO of 10 and 50 L/min was, respectively, as follows: (1) open headbox: 82.4% and 42.2%; (2) headbox-blanket: 56.8% and 39.5%; (3) headbox-HEP filter: 99.9% and 99.9%. CONCLUSION: A HEP-filter modified headbox may serve as an effective droplet and aerosol barrier adjunct for the protection of staff caring for children receiving HFNO.

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.

Synopsis of an integrated guidance for enhancing the care of familial hypercholesterolaemia: an Australian perspective.

INTRODUCTION: Familial hypercholesterolaemia (FH) is a common, heritable and preventable cause of premature coronary artery disease, with significant potential for positive impact on public health and healthcare savings. New clinical practice recommendations are presented in an abridged guidance to assist practitioners in enhancing the care of all patients with FH. MAIN RECOMMENDATIONS: Core recommendations are made on the detection, diagnosis, assessment and management of adults, children and adolescents with FH. There is a key role for general practitioners (GPs) working in collaboration with specialists with expertise in lipidology. Advice is given on genetic and cholesterol testing and risk notification of biological relatives undergoing cascade testing for FH; all healthcare professionals should develop skills in genomic medicine. 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. Recommendations on service design are provided in the full guidance. POTENTIAL IMPACT ON CARE OF FH: These recommendations need to be utilised using judicious clinical judgement and shared decision making with patients and families. Models of care need to be adapted to both local and regional needs and resources. In Australia 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 these recommendations. A broad implementation science strategy is, however, required to ensure that the guidance translates into benefit for all families with FH.