Corrigendum: Preparing correctional settings for the next pandemic: a modeling study of COVID-19 outbreaks in two high-income countries.

[This corrects the article DOI: 10.3389/fpubh.2024.

Controlling COVID-19 outbreaks in the correctional setting: A mathematical modelling study.

Correctional centres (termed here 'prisons') are at high risk of COVID-19 and have featured major outbreaks worldwide. Inevitable close contacts, frequent inmate movements, and a disproportionate burden of co-morbidities mean these environments need to be prioritised in any public health response to respiratory pathogens such as COVID-19. We developed an individual-based SARS-CoV-2 transmission model for the prison system in New South Wales, Australia - incorporating all 33 correctional centres, 13,458 inmates, 578 healthcare and 6,909 custodial staff.

Preparing correctional settings for the next pandemic: a modeling study of COVID-19 outbreaks in two high-income countries.

Introduction: Correctional facilities are high-priority settings for coordinated public health responses to the COVID-19 pandemic. These facilities are at high risk of disease transmission due to close contacts between people in prison and with the wider community. People in prison are also vulnerable to severe disease given their high burden of co-morbidities.

Combined treatment and prevention strategies for hepatitis C virus elimination in the prisons in New South Wales: a modelling study.

Background And Aims: Australia is currently on track to meet the World Health Organization (WHO) global hepatitis C virus (HCV) elimination goals by 2030, reflecting universal subsidized access to testing and direct-acting antiviral (DAA) treatment. In New South Wales, DAA treatment in prisons has scaled-up substantially, with 1000 prisoners treated in 2017. However, HCV prevalence and incidence in this setting is high, which could undermine elimination efforts.

HIV diagnoses in migrant populations in Australia-A changing epidemiology.

Introduction: We conducted a detailed analysis of trends in new HIV diagnoses in Australia by country of birth, to understand any changes in epidemiology, relationship to migration patterns and implications for public health programs.

Methods: Poisson regression analyses were performed, comparing the age-standardised HIV diagnosis rates per 100,000 estimated resident population between 2006-2010 and 2011-2015 by region of birth, with stratification by exposure (male-to-male sex, heterosexual sex-males and females). Correlation between the number of permanent and long-term arrivals was also explored using linear regression models.

Longitudinal injecting risk behaviours among people with a history of injecting drug use in an Australian prison setting: The HITS-p study.

Background: HCV transmission remains high in prisons globally. Understanding injecting risk behaviours in prisons is crucial to effectively develop and implement HCV prevention programs in this setting including treatment as prevention.

Methods: HITS-p is a cohort study which enrolled people with a history of injecting drug use in prisons in NSW, Australia from 2005 to 2013.

A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs.

Protein O-GlcNAcylation, involving the β-attachment of single N-acetylglucosamine (GlcNAc) to the hydroxyl group of serine or threonine residues, is an O-linked glycosylation catalyzed by O-GlcNAc transferase (OGT). Molecular level investigation of the basis for OGT's substrate specificity should aid understanding how O-GlcNAc contributes to diverse cellular processes. Due to an increasing number of O-GlcNAcylated peptides with site-specific information identified by mass spectrometry (MS)-based proteomics, we were motivated to characterize substrate site motifs of O-GlcNAc transferases.

Transmission of Hepatitis C Virus among Prisoners, Australia, 2005-2012.

Hepatitis C virus (HCV) is predominantly transmitted between persons who inject drugs. For this population, global prevalence of HCV infection is high and incarceration is common and an independent risk factor for HCV acquisition. To explore HCV transmission dynamics in incarcerated populations, we integrated virus sequences with risk behavior and spatiotemporal data and analyzed transmission clusters among prisoners in Australia.

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities.

Background: In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays an essential role in the regulation of many cellular processes. In the ubiquitin-proteasome pathway, E3 ligases play important roles by recognizing a specific protein substrate and catalyzing the attachment of ubiquitin to a lysine (K) residue. As more and more experimental data on ubiquitin conjugation sites become available, it becomes possible to develop prediction models that can be scaled to big data.

A prospective study of hepatitis C incidence in Australian prisoners.

Aims: To document the relationships between injecting drug use, imprisonment and hepatitis C virus (HCV) infection.

Design: Prospective cohort study.

Setting: Multiple prisons in New South Wales, Australia.

ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins.

Background: The phosphorylation of virus proteins by host kinases is linked to viral replication. This leads to an inhibition of normal host-cell functions. Further elucidation of phosphorylation in virus proteins is required in order to aid in drug design and treatment.

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses.

Investigation and identification of protein γ-glutamyl carboxylation sites.

Background: Carboxylation is a modification of glutamate (Glu) residues which occurs post-translation that is catalyzed by γ-glutamyl carboxylase in the lumen of the endoplasmic reticulum. Vitamin K is a critical co-factor in the post-translational conversion of Glu residues to γ-carboxyglutamate (Gla) residues. It has been shown that the process of carboxylation is involved in the blood clotting cascade, bone growth, and extraosseous calcification.

Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans.

Regulation of pre-mRNA splicing is achieved through the interaction of RNA sequence elements and a variety of RNA-splicing related proteins (splicing factors). The splicing machinery in humans is not yet fully elucidated, partly because splicing factors in humans have not been exhaustively identified. Furthermore, experimental methods for splicing factor identification are time-consuming and lab-intensive.

Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites.

In proteins, glutamate (Glu) residues are transformed into γ-carboxyglutamate (Gla) residues in a process called carboxylation. The process of protein carboxylation catalyzed by γ-glutamyl carboxylase is deemed to be important due to its involvement in biological processes such as blood clotting cascade and bone growth. There is an increasing interest within the scientific community to identify protein carboxylation sites.

PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity.

Background: Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in intracellular signal transduction. Due to the difficulty in performing high-throughput mass spectrometry-based experiment, there is a desire to predict phosphorylation sites using computational methods. However, previous studies regarding in silico prediction of plant phosphorylation sites lack the consideration of kinase-specific phosphorylation data.

Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences.

Unlabelled: Bioinformatics research often requires conservative analyses of a group of sequences associated with a specific biological function (e.g. transcription factor binding sites, micro RNA target sites or protein post-translational modification sites).