Epihiper-A high performance computational modeling framework to support epidemic science.

This paper describes Epihiper, a state-of-the-art, high performance computational modeling framework for epidemic science. The Epihiper modeling framework supports custom disease models, and can simulate epidemics over dynamic, large-scale networks while supporting modulation of the epidemic evolution through a set of user-programmable interventions. The nodes and edges of the social-contact network have customizable sets of static and dynamic attributes which allow the user to specify intervention target sets at a very fine-grained level; these also permit the network to be updated in response to nonpharmaceutical interventions, such as school closures.

Exposure to Childhood Adversity and Intimate Partner Violence in a Sample of Incarcerated Women in Australia.

Women who use violence represent one of the fastest growing groups within the Australian prisoner population, including Aboriginal women who are more likely to be incarcerated than non-Aboriginal women for violent crimes. Many incarcerated women report histories of adverse childhood experiences (ACEs) and intimate partner violence. This exploratory study examines baseline data from a sample of 167 women in 3 Western Australia women's prisons enrolled in a gender-specific violent behavior program.

Factors associated with unintended pregnancy and contraceptive practices in justice-involved adolescent girls in Australia.

Introduction: Despite a decline in unintended teenage pregnancy in Australia, rates remain higher amongst justice-involved adolescent girls, who are more likely to be from disadvantaged socio-economic backgrounds, have histories of abuse, substance use and/or mental health issues. Furthermore, exposure to the criminal justice system may alter access to education and employment and opportunities, potentially resulting in distinct risk-factor profiles. We examine factors associated with unintended pregnancy, non-contraceptive use and Long-Acting Reversible Contraception (LARC) in a sample of sexually active, justice-involved adolescent girls from Western Australia and Queensland.

Novel multi-cluster workflow system to support real-time HPC-enabled epidemic science: Investigating the impact of vaccine acceptance on COVID-19 spread.

We present MacKenzie, a HPC-driven multi-cluster workflow system that was used repeatedly to configure and execute fine-grained US national-scale epidemic simulation models during the COVID-19 pandemic. Mackenzie supported federal and Virginia policymakers, in real-time, for a large number of "what-if" scenarios during the COVID-19 pandemic, and continues to be used to answer related questions as COVID-19 transitions to the endemic stage of the disease. MacKenzie is a novel HPC meta-scheduler that can execute US-scale simulation models and associated workflows that typically present significant big data challenges.

Data-driven mechanistic framework with stratified immunity and effective transmissibility for COVID-19 scenario projections.

Scenario-based modeling frameworks have been widely used to support policy-making at state and federal levels in the United States during the COVID-19 response. While custom-built models can be used to support one-off studies, sustained updates to projections under changing pandemic conditions requires a robust, integrated, and adaptive framework. In this paper, we describe one such framework, UVA-adaptive, that was built to support the CDC-aligned Scenario Modeling Hub (SMH) across multiple rounds, as well as weekly/biweekly projections to Virginia Department of Health (VDH) and US Department of Defense during the COVID-19 response.

Multimodeling approach to evaluating the efficacy of layering pharmaceutical and nonpharmaceutical interventions for influenza pandemics.

When an influenza pandemic emerges, temporary school closures and antiviral treatment may slow virus spread, reduce the overall disease burden, and provide time for vaccine development, distribution, and administration while keeping a larger portion of the general population infection free. The impact of such measures will depend on the transmissibility and severity of the virus and the timing and extent of their implementation. To provide robust assessments of layered pandemic intervention strategies, the Centers for Disease Control and Prevention (CDC) funded a network of academic groups to build a framework for the development and comparison of multiple pandemic influenza models.

Sexually transmissible infections (STI) and HIV testing and diagnosis among Aboriginal and non-Aboriginal adolescents in contact with the Australian justice system: a cross-sectional study.

Background: It is unclear what factors are associated with sexually transmissible infections (STI) and HIV testing and diagnosis among justice-involved adolescents, and if these differ for Aboriginal or Torres Strait Islander peoples.

Methods: A cross-sectional survey of 465 justice-involved adolescents (aged 14-17years) from Australia was conducted between 2016 and 2018. Participants were asked about sexual behaviours, STI/HIV knowledge, and prior STI diagnoses and testing.

Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support.

This paper describes an integrated, data-driven operational pipeline based on national agent-based models to support federal and state-level pandemic planning and response. The pipeline consists of () an automatic semantic-aware scheduling method that coordinates jobs across two separate high performance computing systems; () a data pipeline to collect, integrate and organize national and county-level disaggregated data for initialization and post-simulation analysis; () a digital twin of national social contact networks made up of 288 Million individuals and 12.6 Billion time-varying interactions covering the US states and DC; () an extension of a parallel agent-based simulation model to study epidemic dynamics and associated interventions.

What patient assessment skills do pharmacist independent prescribers require to prescribe immunomodulators in myeloma?

Aim: To gain consensus on the patient assessment skills required by pharmacist independent prescribers prescribing immunomodulators in myeloma across National Health Service Scotland.

Methods: This was a two-phase study which used nominal group technique to gain local consensus followed by a two-round eDelphi questionnaire to gain national consensus across all cancer networks.

Setting: This project was conducted across the three cancer networks within NHS Scotland: South East Scotland Cancer Network; West of Scotland Cancer Network and North Cancer Alliance.

Nonfatal Strangulation During Domestic Violence Events in New South Wales: Prevalence and Characteristics Using Text Mining Study of Police Narratives.

Nonfatal strangulation (NFS) is a common form of domestic violence (DV) that frequently leaves no visible signs of injury and can be a portent for future fatality. A validated text mining approach was used to analyze a police dataset of 182,949 DV events for the presence of NFS. Results confirmed NFS within intimate partner relationships is a gendered form of violence.

Scalable Epidemiological Workflows to Support COVID-19 Planning and Response.

The COVID-19 global outbreak represents the most significant epidemic event since the 1918 influenza pandemic. Simulations have played a crucial role in supporting COVID-19 planning and response efforts. Developing scalable workflows to provide policymakers quick responses to important questions pertaining to logistics, resource allocation, epidemic forecasts and intervention analysis remains a challenging computational problem.

Prioritizing allocation of COVID-19 vaccines based on social contacts increases vaccination effectiveness.

We study allocation of COVID-19 vaccines to individuals based on the structural properties of their underlying social contact network. Even optimistic estimates suggest that most countries will likely take 6 to 24 months to vaccinate their citizens. These time estimates and the emergence of new viral strains urge us to find quick and effective ways to allocate the vaccines and contain the pandemic.

From 5Vs to 6Cs: Operationalizing Epidemic Data Management with COVID-19 Surveillance.

The COVID-19 pandemic brought to the forefront an unprecedented need for experts, as well as citizens, to visualize spatio-temporal disease surveillance data. Web application were quickly developed to fill this gap, including those built by JHU, WHO, and CDC, but all of these dashboards supported a particular niche view of the pandemic (ie, current status or specific regions). In this paper, we describe our work developing our own COVID-19 Surveillance Dashboard, available at https://nssac.

Evaluating the impact of international airline suspensions on the early global spread of COVID-19.

Global airline networks play a key role in the global importation of emerging infectious diseases. Detailed information on air traffic between international airports has been demonstrated to be useful in retrospectively validating and prospectively predicting case emergence in other countries. In this paper, we use a well-established metric known as effective distance on the global air traffic data from IATA to quantify risk of emergence for different countries as a consequence of direct importation from China, and compare it against arrival times for the first 24 countries.

"That's the Lowest Place on Earth!" Experiences of the Carceral Spaces of Australian Police Custody for Marginalized Young Men.

Young men are overrepresented among people detained in police custody in Victoria, Australia, a closed institution that has mostly escaped public scrutiny. Our study sheds light on this underexamined place from the perspective of 28 marginalized young men (aged 19-24) detained there prior to adult prison. Drawing on Bacchi's "What's the problem represented to be?" approach and the subdiscipline of carceral geography, we disrupt the assumed purpose of police custody as a place to simply detain people while awaiting court and/or transfer to prison.

"A spray bottle and a lollipop stick": An examination of policy prohibiting sterile injecting equipment in prison and effects on young men with injecting drug use histories.

Background: Australian young male prisoners with histories of injecting drug use are more likely to report injecting in prison, to do so more frequently, and to be involved in more un-safe injecting-related practices than their older counterparts. Despite international evidence that prison needle and syringe programs are both feasible and effective in reducing the harms associated with injecting drug use in prison, these young men do not have access to such equipment.

Methods: We critically analyse the interview transcripts of 28 young men with histories of injecting drug use who were recently released from adult prisons in Victoria, Australia, and prison drug policy text.

Aboriginal mothers in prison in Australia: a study of social, emotional and physical wellbeing.

Objective: To describe the social, emotional and physical wellbeing of Aboriginal mothers in prison.

Methods: Cross-sectional survey, including a Short Form Health Survey (SF-12) and Kessler Psychological Distress Scale (5-item version) administered to Aboriginal women who self-identified as mothers.

Results: Seventy-seven Aboriginal mothers in New South Wales (NSW) and 84 in Western Australia (WA) participated in the study.

Australian Aboriginal women prisoners' experiences of being a mother: a review.

Purpose: The rise in the incarceration of Aboriginal and Torres Strait Islander mothers is a major public health issue with multiple sequelae for Aboriginal children and the cohesiveness of Aboriginal communities. The purpose of this paper is to review the available literature relating to Australian Aboriginal women prisoners' experiences of being a mother.

Design/methodology/approach: The literature search covered bibliographic databases from criminology, sociology and anthropology, and Australian history.

EpiViewer: an epidemiological application for exploring time series data.

Background: Visualization plays an important role in epidemic time series analysis and forecasting. Viewing time series data plotted on a graph can help researchers identify anomalies and unexpected trends that could be overlooked if the data were reviewed in tabular form; these details can influence a researcher's recommended course of action or choice of simulation models. However, there are challenges in reviewing data sets from multiple data sources - data can be aggregated in different ways (e.

Disparities in spread and control of influenza in slums of Delhi: findings from an agent-based modelling study.

Objectives: This research studies the role of slums in the spread and control of infectious diseases in the National Capital Territory of India, Delhi, using detailed social contact networks of its residents.

Methods: We use an agent-based model to study the spread of influenza in Delhi through person-to-person contact. Two different networks are used: one in which slum and non-slum regions are treated the same, and the other in which 298 slum zones are identified.

Narratives of Young Men With Injecting Drug Use Histories Leaving Adult Prison.

This research focuses on an under-examined aspect of the post-release prison trajectory for a seldom-researched cohort. Narratives of the immediate days/weeks surrounding release were gathered from young men with histories of injecting drug use (IDU). Twenty-eight participants (aged 19-24) released from adult prisons in Victoria, Australia, participated in face-to-face in-depth qualitative interviews after release.

Combining Participatory Influenza Surveillance with Modeling and Forecasting: Three Alternative Approaches.

Background: Influenza outbreaks affect millions of people every year and its surveillance is usually carried out in developed countries through a network of sentinel doctors who report the weekly number of Influenza-like Illness cases observed among the visited patients. Monitoring and forecasting the evolution of these outbreaks supports decision makers in designing effective interventions and allocating resources to mitigate their impact.

Objective: Describe the existing participatory surveillance approaches that have been used for modeling and forecasting of the seasonal influenza epidemic, and how they can help strengthen real-time epidemic science and provide a more rigorous understanding of epidemic conditions.

GenoCAD Plant Grammar to Design Plant Expression Vectors for Promoter Analysis.

With the rapid advances in prediction tools for discovery of new promoters and their cis-elements, there is a need to improve plant expression methodologies in order to facilitate a high-throughput functional validation of these promoters in planta. The promoter-reporter analysis is an indispensible approach for characterization of plant promoters. It requires the design of complex plant expression vectors, which can be challenging.