Prognostic factors associated with worse outcomes following chemoradiation therapy in patients with anal carcinoma.

Aim: Chemoradiation therapy (CRT) is considered as the first line of treatment for patients with squamous cell carcinoma of the anal canal. Following initial CRT, patients who present with either persistent or locally recurrent disease are treated by surgical intervention. The aim of our study is to determine the prognostic factors associated with failure of CRT and overall mortality in patients with anal squamous cell carcinoma (SCC).

Concretizing plan specifications as realizables within the OBO foundry.

Background: Within the Open Biological and Biomedical Ontology (OBO) Foundry, many ontologies represent the execution of a plan specification as a process in which a realizable entity that concretizes the plan specification, a "realizable concretization" (RC), is realized. This representation, which we call the "RC-account", provides a straightforward way to relate a plan specification to the entity that bears the realizable concretization and the process that realizes the realizable concretization. However, the adequacy of the RC-account has not been evaluated in the scientific literature.

Multilevel Factors Impacting Substance Use Treatment Access, Engagement, and Racial Equity Among Opioid Overdose Survivors in Boston, MA.

Background: There are well-documented racial/ethnic inequities in drug-related overdoses and access to evidence-based opioid use services nationally and in Boston, MA.

Objective: To qualitatively explore the drivers of racial/ethnic inequities in access to opioid use disorder treatment and services in Boston.

Design: Semi-structured qualitative interviews.

PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.

As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achieving these goals for algorithms, pipelines and instruments often requires that lower quality datasets be made available for analysis and comparison alongside those of higher quality. This range of data quality in reference sets can complicate the sharing of sub-optimal datasets that are vital for the community and for the reproducibility of assays.

ThermoCyte: an inexpensive open-source temperature control system for live-cell imaging.

Live-cell imaging is a common technique in microscopy to investigate dynamic cellular behaviour and permits the accurate and relevant analysis of a wide range of cellular and tissue parameters, such as motility, cell division, wound healing responses and calcium (Ca) signalling in cell lines, primary cell cultures and preparations. Furthermore, this can occur under many experimental conditions, making live-cell imaging indispensable for biological research. Systems which maintain cells at physiological conditions outside of a CO incubator are often bulky, expensive and use proprietary components.

Perspectives and recommendations of opioid overdose survivors experiencing unsheltered homelessness on housing, overdose, and substance use treatment in Boston, MA.

Introduction: Opioid overdose causes one in four deaths among people experiencing homelessness in Boston, MA. To reduce overdose risks, the experience and perspectives of people experiencing homelessness should be incorporated into housing, overdose prevention, and substance use treatment efforts.

Methods: In 2021, we conducted qualitative interviews with 59 opioid overdose survivors to inform equitable access to treatment services.

Ontological how and why: action and objective of planned processes in the food domain.

The computational modeling of food processing, aimed at various applications including industrial automation, robotics, food safety, preservation, energy conservation, and recipe nutrition estimation, has been ongoing for decades within food science research labs, industry, and regulatory agencies. The datasets from this prior work have the potential to advance the field of data-driven modeling if they can be harmonized, but this requires a standardized language as a starting point. Our primary goal is to explore two interdependent aspects of this language: the granularity of process modeling sub-parts and parameter details and the substitution of compatible inputs and processes.

OntoTrek: 3D visualization of application ontology class hierarchies.

An application ontology often reuses terms from other related, compatible ontologies. The extent of this interconnectedness is not readily apparent when browsing through larger textual presentations of term class hierarchies, be it Manchester text format OWL files or within an ontology editor like Protege. Users must either note ontology sources in term identifiers, or look at ontology import file term origins.

Social Prescription Interventions Addressing Social Isolation and Loneliness in Older Adults: Meta-Review Integrating On-the-Ground Resources.

Background: Social prescription programs represent a viable solution to linking primary care patients to nonmedical community resources for improving patient well-being. However, their success depends on the integration of patient needs with local resources. This integration could be accelerated by digital tools that use expressive ontology to organize knowledge resources, thus enabling the seamless navigation of diverse community interventions and services tailored to the needs of individual users.

Therapeutic administration of mouse mast cell protease 6 improves functional recovery after traumatic spinal cord injury in mice by promoting remyelination and reducing glial scar formation.

Traumatic spinal cord injury (SCI) most often leads to permanent paralysis due to the inability of axons to regenerate in the adult mammalian central nervous system (CNS). In the past, we have shown that mast cells (MCs) improve the functional outcome after SCI by suppressing scar tissue formation at the lesion site via mouse mast cell protease 6 (mMCP6). In this study, we investigated whether recombinant mMCP6 can be used therapeutically to improve the functional outcome after SCI.

An In Vitro and Ex Vivo Analysis of the Potential of GelMA Hydrogels as a Therapeutic Platform for Preclinical Spinal Cord Injury.

Spinal cord injury (SCI) is a devastating condition with no curative therapy currently available. Immunomodulation can be applied as a therapeutic strategy to drive alternative immune cell activation and promote a proregenerative injury microenvironment. Locally injected hydrogels carrying immunotherapeutic cargo directly to injured tissue offer an encouraging treatment approach from an immunopharmacological perspective.

A finite element model of contusion spinal cord injury in rodents.

Traumatic spinal cord injuries result from high impact forces acting on the spine and are proceeded by an extensive secondary inflammatory response resulting in motor, sensory, and autonomic dysfunction. Experimental in vivo traumatic spinal cord injuries in rodents using a contusion model have been extremely useful in elucidating the underlying pathophysiology of these injuries. However, the relationship between the pathophysiology and the biomechanical factors is still not well understood.

Teaching the Teachers: Development and Evaluation of a Racial Health Equity Curriculum for Faculty.

Introduction: Faculty are increasingly expected to teach about the impact of racism on health and to model the principles of health equity. However, they often feel ill-equipped to do so, and there is limited literature on faculty development on these topics. We developed a curriculum for faculty education on racism and actions to advance racial health equity.

A Schema for Digitized Surface Swab Site Metadata in Open-Source DNA Sequence Databases.

Large, open-source DNA sequence databases have been generated, in part, through the collection of microbial pathogens by swabbing surfaces in built environments. Analyzing these data in aggregate through public health surveillance requires digitization of the complex, domain-specific metadata that are associated with the swab site locations. However, the swab site location information is currently collected in a single, free-text, "isolation source", field-promoting generation of poorly detailed descriptions with various word order, granularity, and linguistic errors, making automation difficult and reducing machine-actionability.

The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.

Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information.

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.

The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes.

Motor rehabilitation as a therapeutic tool for spinal cord injury: New perspectives in immunomodulation.

Traumatic spinal cord injury (SCI) is a devastating condition that significantly impacts motor, sensory and autonomic function in patients. Despite advances in therapeutic approaches, there is still no curative therapy currently available. Neuroinflammation is a persisting event of the secondary injury phase of SCI that affects functional recovery, and modulation of the inflammatory response towards a beneficial anti-inflammatory state can improve recovery in preclinical SCI models.

Gene Coexpression Connectivity Predicts Gene Targets Underlying High Ionic-Liquid Tolerance in Yarrowia lipolytica.

Microbial tolerance to organic solvents such as ionic liquids (ILs) is a robust phenotype beneficial for novel biotransformation. While most microbes become inhibited in 1% to 5% (vol/vol) IL (e.g.