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BackgroundEfforts are underway to semantically integrate large biomedical knowledge graphs using common upper-level ontologies to federate graph-oriented application programming interfaces (APIs) to the data. However, federation poses several challenges, including query routing to appropriate knowledge sources, generation and evaluation of answer subsets, semantic merger of those answer subsets, and visualization and exploration of results. ObjectiveWe aimed to develop an interactive environment for query, visualization, and deep exploration of federated knowledge graphs. MethodsWe developed a biomedical query language and web application interphase—termed as Translator Query Language (TranQL)—to query semantically federated knowledge graphs and explore query results. TranQL uses the Biolink data model as an upper-level biomedical ontology and an API standard that has been adopted by the Biomedical Data Translator Consortium to specify a protocol for expressing a query as a graph of Biolink data elements compiled from statements in the TranQL query language. Queries are mapped to federated knowledge sources, and answers are merged into a knowledge graph, with mappings between the knowledge graph and specific elements of the query. The TranQL interactive web application includes a user interface to support user exploration of the federated knowledge graph. ResultsWe developed 2 real-world use cases to validate TranQL and address biomedical questions of relevance to translational science. The use cases posed questions that traversed 2 federated Translator API endpoints: Integrated Clinical and Environmental Exposures Service (ICEES) and Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways (ROBOKOP). ICEES provides open access to observational clinical and environmental data, and ROBOKOP provides access to linked biomedical entities, such as “gene,” “chemical substance,” and “disease,” that are derived largely from curated public data sources. We successfully posed queries to TranQL that traversed these endpoints and retrieved answers that we visualized and evaluated. ConclusionsTranQL can be used to ask questions of relevance to translational science, rapidly obtain answers that require assertions from a federation of knowledge sources, and provide valuable insights for translational research and clinical practice.

BackgroundIn a multisite clinical research collaboration, institutions may or may not use the same common data model (CDM) to store clinical data. To overcome this challenge, we proposed to use Health Level 7’s Fast Healthcare Interoperability Resources (FHIR) as a meta-CDM—a single standard to represent clinical data. ObjectiveIn this study, we aimed to create an open-source application termed the Clinical Asset Mapping Program for FHIR (CAMP FHIR) to efficiently transform clinical data to FHIR for supporting source-agnostic CDM-to-FHIR mapping. MethodsMapping with CAMP FHIR involves (1) mapping each source variable to its corresponding FHIR element and (2) mapping each item in the source data’s value sets to the corresponding FHIR value set item for variables with strict value sets. To date, CAMP FHIR has been used to transform 108 variables from the Informatics for Integrating Biology & the Bedside (i2b2) and Patient-Centered Outcomes Research Network data models to fields across 7 FHIR resources. It is designed to allow input from any source data model and will support additional FHIR resources in the future. ResultsWe have used CAMP FHIR to transform data on approximately 23,000 patients with asthma from our institution’s i2b2 database. Data quality and integrity were validated against the origin point of the data, our enterprise clinical data warehouse. ConclusionsWe believe that CAMP FHIR can serve as an alternative to implementing new CDMs on a project-by-project basis. Moreover, the use of FHIR as a CDM could support rare data sharing opportunities, such as collaborations between academic medical centers and community hospitals. We anticipate adoption and use of CAMP FHIR to foster sharing of clinical data across institutions for downstream applications in translational research.

Kansas has produced its share of unique and interesting political movements and politicians. With a history of populism, socialism, and free-thought, some unique and colorful politicians and radicals have made [...]

Objectives: NKG2D is an activating receptor expressed by natural killer (NK) and CD8+ T cells and activation intensity varies by NKG2D expression level or nature of its ligand. An NKG2D gene polymorphism determines high (HNK1) or low (LNK1) expression. MICA is the most polymorphic NKG2D ligand and stronger effector cell activation associates with methionine rather than valine at residue 129. We investigated correlation between cord blood (CB) NKG2D and MICA genotypes and haematopoietic stem cell (HSC) transplant outcome. Methods: We retrospectively studied 267 CB HSC recipients (178 adult and 87 paediatric) who underwent transplant for malignant disease between 2007 and 2018, analysing CB graft DNA for NKG2D and MICA polymorphisms using Sanger sequencing. Multivariate analysis was used to correlate these results with transplant outcomes. Results: In adult patients, LNK1 homozygous CB significantly improved 60‐day neutrophil engraftment (hazard ratio (HR) 0.6; 95% confidence interval (CI) 0.4–0.9; p =.003). In paediatrics, HNK1 homozygous CB improved 60‐day engraftment (HR 0.4; 95% CI 0.2–0.7; p =.003), as did MICA‐129 methionine+ CB grafts (HR 1.7 95% CI 1.1–2.6; p =.02). Conclusion: CB NKG2D and MICA genotypes potentially improve CB HSC engraftment. However, results contrast between adult and paediatric recipients and may reflect transplant procedure disparities between cohorts. [ABSTRACT FROM AUTHOR]

NKG2D is a natural killer cell activating receptor recognising ligands on infected or tumorigenic cells, leading to their cytolysis. There are eight known genes encoding NKG2D ligands: MICA, MICB and ULBP1‐6. MICA and MICB are highly polymorphic and well characterised, whilst ULBP ligands are less polymorphic and the functional implication of their diversity is not well understood. Using International HLA and Immunogenetics Workshop (IHIW) cell line DNA, we previously characterised alleles of the RAET1E gene (encoding ULBP4 proteins), including the 5′ UTR promoter region and exons 1–3. We found 11 promoter haplotypes associating with alleles based on exons 1–3, revealing 19 alleles overall. The current study extends this analysis using 87 individual DNA samples from IHIW cell lines or cord blood to include RAET1E exon 4 and the 3′ UTR, as polymorphism in these regions have not been previously investigated. We found two novel exon 4 polymorphisms encoding amino acid substitutions altering the transmembrane domain. An amino acid substitution at residue 233 was unique to the RAET1E*008 allele whereas the substitution at residue 237 was shared between groups of alleles. Additionally, four haplotypes were found based on 3′ UTR sequences, which were unique to certain alleles or shared with allele groups based on exons 1–4 polymorphisms. Furthermore, putative microRNAs were identified that may interact with these polymorphic sites, repressing transcription and potentially affecting expression levels. [ABSTRACT FROM AUTHOR]

Research increasingly relies on interrogating large-scale data resources. The NIH National Heart, Lung, and Blood Institute developed the NHLBI BioData CatalystⓇ (BDC), a community-driven ecosystem where researchers, including bench and clinical scientists, statisticians, and algorithm developers, find, access, share, store, and compute on large-scale datasets. This ecosystem provides secure, cloud-based workspaces, user authentication and authorization, search, tools and workflows, applications, and new innovative features to address community needs, including exploratory data analysis, genomic and imaging tools, tools for reproducibility, and improved interoperability with other NIH data science platforms. BDC offers straightforward access to large-scale datasets and computational resources that support precision medicine for heart, lung, blood, and sleep conditions, leveraging separately developed and managed platforms to maximize flexibility based on researcher needs, expertise, and backgrounds. Through the NHLBI BioData Catalyst Fellows Program, BDC facilitates scientific discoveries and technological advances. BDC also facilitated accelerated research on the coronavirus disease-2019 (COVID-19) pandemic. [ABSTRACT FROM AUTHOR]

Objectives: Mobile applications (apps) are multiplying in laryngology, with little standardization of content, functionality, or accessibility. The purpose of this study is to evaluate the quality, functionality, health literacy, readability, accessibility, and inclusivity of laryngology mobile applications. Methods: Of the 3230 apps identified from the Apple and Google Play stores, 28 patient‐facing apps met inclusion criteria. Apps were evaluated using validated scales assessing quality and functionality: the Mobile App Rating Scale (MARS) and the Institute for Healthcare Informatics App Functionality Scale. The Clear Communication Index (CDC) Institute of Medicine Strategies for Creating Health Literate Mobile Applications, and Patient Education Materials Assessment Tool (PEMAT) were used to evaluate apps health literacy level. Readability was assessed using established readability formulas. Apps were evaluated for language, accessibility features, and representation of a diverse population. Results: Twenty‐six apps (92%) had adequate quality (MARS score > 3). The mean PEMAT score was 89% for actionability and 86% for understandability. On average, apps utilized 25/33 health literate strategies. Twenty‐two apps (79%) did not pass the CDC index threshold of 90% for health literacy. Twenty‐four app descriptions (86%) were above an 8th grade reading level. Only 4 apps (14%) showed diverse representation, 3 (11%) had non‐English language functions, and 2 (7%) offered subtitles. Inter‐rater reliability for MARS was adequate (CA‐ICC = 0.715). Conclusion: While most apps scored well in quality and functionality, many laryngology apps did not meet standards for health literacy. Most apps were written at a reading level above the national average, lacked accessibility features, and did not represent diverse populations. Laryngoscope, 133:1540–1549, 2023 [ABSTRACT FROM AUTHOR]

Esophageal (ES) speech, tracheoesophageal (TE) speech, and the electrolarynx (EL) are common methods of communication following the removal of the larynx. Our recent study demonstrated that intelligibility may increase for Cantonese alaryngeal speakers using clear speech (CS) compared to their everyday "habitual speech" (HS), but the reasoning is still unclear [Hui, Cox, Huang, Chen, and Ng (2022). Folia Phoniatr. Logop. 74, 103–111]. The purpose of this study was to assess the acoustic characteristics of vowels and tones produced by Cantonese alaryngeal speakers using HS and CS. Thirty-one alaryngeal speakers (9 EL, 10 ES, and 12 TE speakers) read The North Wind and the Sun passage in HS and CS. Vowel formants, vowel space area (VSA), speaking rate, pitch, and intensity were examined, and their relationship to intelligibility were evaluated. Statistical models suggest that larger VSAs significantly improved intelligibility, but slower speaking rate did not. Vowel and tonal contrasts did not differ between HS and CS for all three groups, but the amount of information encoded in fundamental frequency and intensity differences between high and low tones positively correlated with intelligibility for TE and ES groups, respectively. Continued research is needed to understand the effects of different speaking conditions toward improving acoustic and perceptual characteristics of Cantonese alaryngeal speech. [ABSTRACT FROM AUTHOR]

Notes that as student enrollment in colleges and universities has increased, there has simultaneously been a proliferation of developmental skills programs. Presents some empirical evidence of the effectiveness of three reading skills courses. Suggests that underprepared readers' success in college is directly related to taking and passing a reading skills course. (PM)

Questions designed to identify level of cooperative behavior in situations were answered by 132 business/economics majors and 169 education/nursing majors. Business/economics students act less cooperatively, but they become more cooperative as they progress through school. (SK)