Crisis action planning and replanning using SIPE-2

Rome Laboratory and DARPA are jointly sponsoring an initiative to develop the next generation of AI planning and scheduling technology focused on military operations planning, especially for crisis situations. SRI International has demonstrated their knowledge-based planning technology in this domain with a system called SOCAP, System for Operations Crisis Action Planning. SOCAP's underlying power comes from SIPE-2, a hierarchical, domain-independent, nonlinear AI planner also developed at SRI. This paper discusses the features of SIPE-2 that made it an ideal choice for military operations planning and which contributed greatly to SOCAP's success

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Recrystallization inhibition in ice due to ice binding protein activity detected by nuclear magnetic resonance

Liquid water present in polycrystalline ice at the interstices between ice crystals results in a network of liquid-filled veins and nodes within a solid ice matrix, making ice a low porosity porous media. Here we used nuclear magnetic resonance (NMR) relaxation and time dependent self-diffusion measurements developed for porous media applications to monitor three dimensional changes to the vein network in ices with and without a bacterial ice binding protein (IBP). Shorter effective diffusion distances were detected as a function of increased irreversible ice binding activity, indicating inhibition of ice recrystallization and persistent small crystal structure. The modification of ice structure by the IBP demonstrates a potential mechanism for the microorganism to enhance survivability in ice. These results highlight the potential of NMR techniques in evaluation of the impact of IBPs on vein network structure and recrystallization processes; information useful for continued development of ice-interacting proteins for biotechnology applications

Recrystallization inhibition in ice due to ice binding protein activity detected by nuclear magnetic resonance

Liquid water present in polycrystalline ice at the interstices between ice crystals results in a network of liquid-filled veins and nodes within a solid ice matrix, making ice a low porosity porous media. Here we used nuclear magnetic resonance (NMR) relaxation and time dependent self-diffusion measurements developed for porous media applications to monitor three dimensional changes to the vein network in ices with and without a bacterial ice binding protein (IBP). Shorter effective diffusion distances were detected as a function of increased irreversible ice binding activity, indicating inhibition of ice recrystallization and persistent small crystal structure. The modification of ice structure by the IBP demonstrates a potential mechanism for the microorganism to enhance survivability in ice. These results highlight the potential of NMR techniques in evaluation of the impact of IBPs on vein network structure and recrystallization processes; information useful for continued development of ice-interacting proteins for biotechnology applications

Genomic landscape and gene expression profiles of feline oral squamous cell carcinoma

Feline oral squamous cell carcinoma (FOSCC) is a cancer of the squamous cell lining in the oral cavity and represents up to 80% of all oral cancers in cats, with a poor prognosis. We have used whole exome sequencing (WES) and RNA sequencing of the tumor to discover somatic mutations and gene expression changes that may be associated with FOSCC occurrence. FOSCC offers a potential comparative model to study human head and neck squamous cell carcinoma (HNSCC) due to its similar spontaneous formation, and morphological and histological features. In this first study using WES to identify somatic mutations in feline cancer, we have identified tumor-associated gene mutations in six cats with FOSCC and found some overlap with identified recurrently mutated genes observed in HNSCC. Four samples each had mutations in TP53, a common mutation in all cancers, but each was unique. Mutations in other cellular growth control genes were also found such as KAT2B and ARID1A. Enrichment analysis of FOSCC gene expression profiles suggests a molecular similarity to human OSCC as well, including alterations in epithelial to mesenchymal transition and IL6/JAK/STAT pathways. In this preliminary study, we present exome and transcriptome results that further our understanding of FOSCC

Barriers and facilitators to resuming meaningful daily activities among critical illness survivors in the UK: a qualitative content analysis

Objective To identify critical illness survivors’ perceived barriers and facilitators to resuming performance of meaningful activities when transitioning from hospital to home. Design Secondary content analysis of semistructured interviews about patients’ experiences of intensive care (primary analysis disseminated on the patient-facing website www.healthtalk.org). Two coders characterised patient-perceived barriers and facilitators to resuming meaningful activities. To facilitate clinical application, we mapped the codes onto the Person-Task-Environment model of performance, a patient-centred rehabilitation model that characterises complex interactions among the person, task and environment when performing activities. Setting United Kingdom, 2005–2006. Participants 39 adult critical illness survivors, sampled for variation among demographics and illness experiences. Results Person-related barriers included negative mood or affect, perceived setbacks; weakness or limited endurance; pain or discomfort; inadequate nutrition or hydration; poor concentration/confusion; disordered sleep/hallucinations/nightmares; mistrust of people or information; and altered appearance. Task-related barriers included miscommunication and managing conflicting priorities. Environment-related barriers included non-supportive health services and policies; challenging social attitudes; incompatible patient–family coping (emotional trauma and physical disability); equipment problems; overstimulation; understimulation; and environmental inaccessibility. Person-related facilitators included motivation or attitude; experiencing progress; and religion or spirituality. Task-related facilitators included communication. Environment-related facilitators included support from family, friends or healthcare providers; supportive health services and policies; equipment; community resources; medications; and accessible housing. Barriers decreased and facilitators increased over time. Six barrier–facilitator domains dominated based on frequency and emphasis across all performance goals: mood/motivation, setbacks/progress, fatiguability/strength; mis/communication; lack/community support; lack/health services and policies. Conclusions Critical illness survivors described a comprehensive inventory of 18 barriers and 11 facilitators that align with the Person-Task-Environment model of performance. Six dominant barrier–facilitator domains seem strong targets for impactful interventions. These results verify previous knowledge and offer novel opportunities for optimising patient-centred care and reducing disability after critical illness.</p