Antidepressant Exposure and DNA Methylation: Insights from a Methylome-Wide Association Study

Importance

Understanding antidepressant mechanisms could help design more effective and tolerated treatments.

Objective

Identify DNA methylation (DNAm) changes associated with antidepressant exposure.

Design

Case-control methylome-wide association studies (MWAS) of antidepressant exposure were performed from blood samples collected between 2006-2011 in Generation Scotland (GS). The summary statistics were tested for enrichment in specific tissues, gene ontologies and an independent MWAS in the Netherlands Study of Depression and Anxiety (NESDA). A methylation profile score (MPS) was derived and tested for its association with antidepressant exposure in eight independent cohorts, alongside prospective data from GS.

Setting

Cohorts; GS, NESDA, FTC, SHIP-Trend, FOR2107, LBC1936, MARS-UniDep, ALSPAC, E-Risk, and NTR.

Participants

Participants with DNAm data and self-report/prescription derived antidepressant exposure.

Main Outcomes and Measures

Whole-blood DNAm levels were assayed by the EPIC/450K Illumina array (9 studies, N exposed = 661, N unexposed = 9,575) alongside MBD-Seq in NESDA (N exposed = 398, N unexposed = 414). Antidepressant exposure was measured by self- report and/or antidepressant prescriptions.

Results

The self-report MWAS (N = 16,536, N exposed = 1,508, mean age = 48, 59% female) and the prescription-derived MWAS (N = 7,951, N exposed = 861, mean age = 47, 59% female), found hypermethylation at seven and four DNAm sites (p < 9.42x10 -8 ), respectively. The top locus was cg26277237 ( KANK1, p self-report = 9.3x10 -13 , p prescription = 6.1x10 -3 ). The self-report MWAS found a differentially methylated region, mapping to DGUOK-AS1 ( p adj = 5.0x10 -3 ) alongside significant enrichment for genes expressed in the amygdala, the "synaptic vesicle membrane" gene ontology and the top 1% of CpGs from the NESDA MWAS (OR = 1.39, p < 0.042). The MPS was associated with antidepressant exposure in meta-analysed data from external cohorts (N studies = 9, N = 10,236, N exposed = 661, f3 = 0.196, p < 1x10 -4 ).

Conclusions and Relevance

Antidepressant exposure is associated with changes in DNAm across different cohorts. Further investigation into these changes could inform on new targets for antidepressant treatments.

3 Key Points

Question: Is antidepressant exposure associated with differential whole blood DNA methylation?Findings: In this methylome-wide association study of 16,536 adults across Scotland, antidepressant exposure was significantly associated with hypermethylation at CpGs mapping to KANK1 and DGUOK-AS1. A methylation profile score trained on this sample was significantly associated with antidepressant exposure (pooled f3 [95%CI]=0.196 [0.105, 0.288], p < 1x10 -4 ) in a meta-analysis of external datasets. Meaning: Antidepressant exposure is associated with hypermethylation at KANK1 and DGUOK-AS1 , which have roles in mitochondrial metabolism and neurite outgrowth. If replicated in future studies, targeting these genes could inform the design of more effective and better tolerated treatments for depression.

Dose Escalation in Esophageal Cancer: Comparing Pre-Accrual and On-Trial Target Volume Delineation in the UK SCOPE2 Trial

PURPOSE/OBJECTIVE(S)

The ongoing UK SCOPE2 trial evaluates radiotherapy (RT) dose escalation and PET-guided systemic therapy in esophageal cancer, and has an accompanying RT trials quality assurance (RTTQA) program, evolved through the preceding SCOPE trials. We compare pre-accrual with on-trial individual case review (ICR) target volume delineation (TVD).

MATERIALS/METHODS

Prior to recruitment, centers were required to undertake TVD exercises using 3D/4D DICOM datasets with relevant clinical details and a RT planning guidance document (RPGD) provided. Contours were then compared against the RTTQA team-defined gold standard. Exceptions were those who had satisfied QA requirements for a previous esophageal RT trial (NeoSCOPE). For ICRs, prospective reviews (prior RT start, PRs) were undertaken for each center's first submission, plus high-dose cases submitted pending formal safety review. Additional PRs were undertaken at the RTTQA team's discretion. Timely retrospective reviews (within 2 weeks of RT start, TRR) were also undertaken for a random 10% sample. TVDs were assessed for compliance using predefined criteria and the RPGD. Resubmission was requested at reviewer's discretion, usually due to unacceptable variation (UV) from protocol. Clarification was sought before contour approval/resubmission request if appropriate. Review outcomes were then evaluated. PTV6000 was new to SCOPE2, along with a greater emphasis on use of 4DCT than in prior SCOPE trials.

RESULTS

A total of 85 pre-accrual cases from 33 UK centers were reviewed, of which 20 (24%) were resubmissions, and 50 (59%) were accepted. 99 TVD UVs were observed in 49 cases, most commonly in CTVB (42/99, 42%), which included editing for normal structures and elective lymph node regions, followed by ITV (4D cases only, 14/52, 27%) and PTV6000 (13/99, 13%). 121 ICRs from 31 UK centers were available for review. 87 (72%) were PRs and 34 (28%) TRRs. 43 (36%) completed the relevant SCOPE2 exercise. 19 (16%) were resubmissions, and 82 (68%) were accepted. 72 UVs were observed in 45 ICRs; again, most commonly in CTVB (34/72, 48%), PTV6000 (high dose arm only, 11/46, 24%) and ITV (4D only, 5/26, 19%). Of the 45 cases where a UV was recorded, 16 (36%) had completed the relevant SCOPE2 pre-accrual. Comparing area of UV on SCOPE2 pre-accrual cases and ICRs, 3 (19%) contours contained the same (2 = CTVB, 1 = PTV6000), 5 (31%) contained different and 8 (50%) had no UVs at pre-accrual. The rate of UV was significantly lower for ICR than for pre-accrual submissions (0.60 and 1.16 respectively, p = 0.001).

CONCLUSION

Significantly fewer UVs in ICR compared with pre-accrual supports a robust, educational RTTQA program through national collaboration and evolving trial series. CTVB, along with newer volumes of ITV and PTV6000, were recurring UV domains and should inform RPGD development and RTTQA for ongoing recruitment and future trials.

Observation versus intervention for incidental common bile duct stones at intraoperative cholangiogram: a systematic review

BACKGROUND

The natural history of incidental common bile duct stones (CBDS) is poorly understood. Current evidence is conflicting, with several studies suggesting the majority may pass spontaneously. Despite this, guidelines recommend routine removal even if asymptomatic. This study aimed to systematically review the outcomes of expectant management for CBDS detected on operative cholangiography during cholecystectomy.

METHODS

MEDLINE, Embase and CINAHL databases were systematically searched. Participants were adult patients with CBDS identified by intraoperative cholangiography. Intervention was regarded as any perioperative effort to remove common bile duct stones, including endoscopic retrograde cholangiopancreatography (ERCP), laparoscopic and open bile duct exploration. This was compared to observation. Outcomes of interest included rates of spontaneous stone passage, success of duct clearance and complications. Risk of bias was assessed using the ROBINS-I tool.

RESULTS

Eight studies were included. All studies were non-randomized, heterogeneous and at serious risk of bias. In patients observed after a positive IOC, 20.9% went on to have symptomatic retained stones. In patients directed to ERCP for positive IOC, persistent CBDS were found in 50.6%. Spontaneous passage was not associated with stone size. Meta-analysis is dominated by the results from one large database, which recommends intervention for incidental stones, despite low rates of persistent stones seen at postoperative ERCP.

CONCLUSIONS

Further evidence is required before a definitive recommendation on observation can be made. There is some evidence that asymptomatic stones may be safely observed. In clinical scenarios where the risks of biliary intervention are considered high, a conservative strategy could be more widely considered.

Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research

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.

Spring and latch dynamics can act as control pathways in ultrafast systems

Ultrafast movements propelled by springs and released by latches are thought limited to energetic adjustments prior to movement, and seemingly cannot adjust once movement begins. Even so, across the tree of life, ultrafast organisms navigate dynamic environments and generate a range of movements, suggesting unrecognized capabilities for control. We develop a framework of control pathways leveraging the non-linear dynamics of spring-propelled, latch-released systems. We analytically model spring dynamics and develop reduced-parameter models of latch dynamics to quantify how they can be tuned internally or through changing external environments. Using Lagrangian mechanics, we test feedforward and feedback control implementation via spring and latch dynamics. We establish through empirically-informed modeling that ultrafast movement can be controllably varied during latch release and spring propulsion. A deeper understanding of the interconnection between multiple control pathways, and the tunability of each control pathway, in ultrafast biomechanical systems presented here has the potential to expand the capabilities of synthetic ultra-fast systems and provides a new framework to understand the behaviors of fast organisms subject to perturbations and environmental non-idealities.

Are Mobile Applications in Laryngology Designed for All Patients?

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 8^th 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, 2022.

Temperature-related chest pain presentations and future projections with climate change

Background

Climate change has led to increased interest in studying adverse health effects relating to ambient temperatures. It is unclear whether incident chest pain is associated with non-optimal temperatures and how chest pain presentation rates might be affected by climate change.

Methods

The study included ambulance data of chest pain presentations in Melbourne, Australia from 1/1/2015 to 30/6/2019 with linkage to hospital and emergency discharge diagnosis data. A time series quasi-Poisson regression with a distributed lag nonlinear model was fitted to assess the temperature-chest pain presentation associations, after adjusting for season, day of the week and long-term trend. Future excess chest pain presentations associated with cold and heat were projected under six general circulation models under medium and high emission scenarios.

Results

In 206,789 chest pain presentations, mean (SD) age was 61.2 (18.9) years and 50.3% were female. Significant heat- and cold-related increased risk of chest pain presentations were observed for mean air temperatures above and below 20.8°C, respectively (Figure 1). Excess chest pain presentations related to heat were observed in all subgroups, but appeared to be attenuated for older patients (≥70 years) and patients of higher socioeconomic status (SES). We projected no significant change in net temperature-related chest pain presentations with climate change under medium- and high-emission scenarios, with increases in heat-related chest pain presentations offset by decreases in chest pain presentations related to cold temperatures.

Conclusions

Heat- and cold-exposure appear to increase risk of chest pain presentations, especially among younger patients and patients of lower SES. In Melbourne, Australia, chest pain presentations overall were not projected to increase with climate change, but increases in heat-related chest pain presentations highlight the importance of risk mitigation strategies to minimise adverse health impacts on hotter days.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): Alfred Health.

Impact of ambulance off-load delays on mortality in patients with chest pain

Background

Ambulance off-load delays in transferring patient care to emergency departments (EDs) are increasingly common, but it is unclear whether clinical outcomes are impacted.

Methods

Population-based cohort study of ambulance attendances for non-traumatic chest pain transported to ED in Victoria, Australia (1/1/2015–30/6/2019) excluding patients transported to hospital with “lights and sirens” or triaged as ED category 1. Multivariable models were used to assess the relationship between ambulance off-load times and 30-day mortality and ambulance re-attendance for chest pain.

Results

The study included 213,544 ambulance attendances for chest pain (mean age 62 [SD 18] years; 51% female). Median ambulance off-load times increased across the study period from 21 minutes (interquartile range [IQR] 15–30) in 2015 to 24 minutes (IQR 17–37) in 2019. Patients were divided into tertiles according to off-load times with 69,247 patients included in tertile 1 (0–17 minutes), 73,109 patients in tertile 2 (18–28 minutes), and 71,188 patients in tertile 3 (&gt;28 minutes). In multivariable models, ambulance off-load delays were associated with higher unadjusted and adjusted rates of 30-day mortality (1.57% tertile 3 vs. 1.29% tertile 1, adjusted risk difference 0.28% [95% CI 0.16% - 0.42%], p&lt;0.001) and ambulance re-attendance for chest pain (9.89% tertile 3 vs. 8.59% tertile 1, adjusted risk difference 1.30% [95% CI 1.00% - 1.61%], p&lt;0.001). Similarly, in analysis using off-load times as a continuous variable with restricted cubic splines, a non-linear increase in adjusted odds ratio for mortality was observed (Figure 1).

Conclusions

Delays in ambulance off-load times appear to be associated with increased mortality and ambulance re-attendance risk among chest pain cohorts. This study has important policy implications given the increasing frequency of off-load delays in many healthcare settings.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): Alfred health

Variation in health-care quality and outcomes according to time of chest pain presentation: a state-wide prospective cohort study

Background

Previous studies examining temporal variation in cardiovascular care have largely been limited to assessing weekend and after-hours effects whereby those presenting on the weekend or after-hours have a poorer outcome. However, emerging evidence suggests more complex patterns in patterns and outcomes may exist.

Purpose

We aimed to determine patterns of temporal variation in chest pain presentations and subsequent health-care quality and outcomes.

Methods

This was an observational, prospective-cohort study of adult patients aged 18 and over who were attended by emergency medical services for non-traumatic chest pain between 1 January 2015 and 30 June 2019 in Victoria, Australia. Major exclusion criteria included pre-hospital diagnosis of ST elevation myocardial infarction or an out of hospital cardiac arrest. The exposure variable was time of day and day of week stratified into 168 hourly time periods. The primary outcome measure was 30-day mortality.

Results

The study cohort comprised 196,365 ambulance attendances for acute non-traumatic chest pain; mean age 62.4 years (SD 18.3) and 99,497 (50.7%) females. Three temporal patterns were observed for chest pain presentations (Figure 1): (1) a diurnal pattern with a sharp increase in presentations from 8 am, peaking around midday, before decreasing into late evening with a nadir between 3–4 am, (2) a weekend effect where Saturday and Sunday had a relatively lower rate of presentations compared to during the week, and (3) a Monday – Sunday gradient where more presentations were likely earlier in the week, than later. Six patterns were identified across pre-hospital and hospital key performance indicators (KPI) (diurnal, in/after-hours, weekend effect, Monday – Sunday gradient, a peak period and morning vs afternoon/evening effect. Risk of 30-day mortality was associated with weekend presentation (OR 1.15, 95% CI 1.06–1.24, p=0.001) and morning presentation between midnight and midday (OR 1.17, 95% CI 1.09–1.25, p&lt;0.001) (Figure 2).

Conclusion

Chest pain presentations, care quality and outcomes demonstrate complex temporal variation beyond the already established weekend and after-hours effect. Such relationships should be considered during resource allocation and quality improvement programs in order to improve treatment quality across all days and times of the week.

Funding Acknowledgement

Type of funding sources: None.

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

Visualization Environment for Federated Knowledge Graphs: Development of an Interactive Biomedical Query Language and Web Application Interface

BACKGROUND

Efforts 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.

OBJECTIVE

We aimed to develop an interactive environment for query, visualization, and deep exploration of federated knowledge graphs.

METHODS

We 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.

RESULTS

We 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.

CONCLUSIONS

TranQL 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.

A semantic similarity based methodology for predicting protein-protein interactions: Evaluation with P53-interacting kinases

Biomedical literature contains unstructured, rich information regarding proteins, ligands, diseases as well as biological pathways in which they are involved. Systematically analyzing such textual corpus has the potential for biomedical discovery of new protein-protein interactions and hidden drug indications. For this purpose, we have investigated a methodology that is based on a well-established text mining tool, Word2Vec, for the analysis of PubMed full text articles to derive word embeddings, and the use of a simple semantic similarity comparison either by itself or in conjunction with k-Nearest Neighbor (kNN) technique for the prediction of new relationships. To test this methodology, three lines of retrospective analyses of a dataset with known P53-interacting proteins have been conducted. First, we demonstrated that Word2Vec semantic similarity can infer functional relatedness among all kinases known to interact with P53. Second, in a series of time-split experiments, we demonstrated that both a simple similarity comparison and kNN models built with papers published up to a certain year were able to discover P53 interactors described in later publications. Third, in a different scenario of time-split experiments, we examined the predictions of P53-interacting proteins based on the kNN models built on data prior to a certain split year for different time ranges past that year, and found that the cumulative number of correct predictions was indeed increasing with time. We conclude that text mining of research papers in the PubMed literature based on Word2Vec analysis followed by a simple similarity comparison or kNN modeling affords excellent predictions of protein-protein interactions between P53 and kinases, and should have wide applications in translational biomedical studies such as repurposing of existing drugs, drug-drug interaction, and elucidation of mechanisms of action for drugs.

ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering

SUMMARY

Knowledge graphs (KGs) are quickly becoming a common-place tool for storing relationships between entities from which higher-level reasoning can be conducted. KGs are typically stored in a graph-database format, and graph-database queries can be used to answer questions of interest that have been posed by users such as biomedical researchers. For simple queries, the inclusion of direct connections in the KG and the storage and analysis of query results are straightforward; however, for complex queries, these capabilities become exponentially more challenging with each increase in complexity of the query. For instance, one relatively complex query can yield a KG with hundreds of thousands of query results. Thus, the ability to efficiently query, store, rank and explore sub-graphs of a complex KG represents a major challenge to any effort designed to exploit the use of KGs for applications in biomedical research and other domains. We present Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways as an abstraction layer and user interface to more easily query KGs and store, rank and explore query results.

AVAILABILITY AND IMPLEMENTATION

An instance of the ROBOKOP UI for exploration of the ROBOKOP Knowledge Graph can be found at http://robokop.renci.org. The ROBOKOP Knowledge Graph can be accessed at http://robokopkg.renci.org. Code and instructions for building and deploying ROBOKOP are available under the MIT open software license from https://github.com/NCATS-Gamma/robokop.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Cord Blood Platelet Rich Plasma Derivatives for Clinical Applications in Non-transfusion Medicine

Cord blood platelet rich plasma (CB-PRP) derivatives have been investigated as potential therapeutic agents for the treatment of diverse conditions including ocular surface disease and skin ulcers. We have developed processes for the formulation of several CB-PRP preparations, which have different composition and attributes. Here we describe the molecular characteristics of these preparations and we make recommendations as to their most appropriate clinical application based on functional and immunomodulatory profiles. We show that incubation of adult peripheral blood mononuclear cells (PBMCs) with all three preparations dramatically reduced the production of INFγ and the expression of NKG2D and CD107a in NK, NKT, and T cells thus diminishing their activation, we propose that the likely mechanism is the high levels of soluble NKG2D ligands present in plasma. Of the three preparations we investigated, CB platelet lysate (PL) and platelet releaseate (PR) have higher concentrations of trophic and pro-angiogenic factors, CB platelet poor plasma (PPP) has the lowest concentration of all analytes measured. Based on these finding we propose that CB-PR is the most suitable raw material for skin wound patches, while CB-PL and PPP can be used to prepare eye drops for severe ocular surface pathologies and inflammatory conditions such as corneal ulcers or severe dry eye disease, respectively.

FHIR PIT: an open software application for spatiotemporal integration of clinical data and environmental exposures data

BACKGROUND

Informatics tools to support the integration and subsequent interrogation of spatiotemporal data such as clinical data and environmental exposures data are lacking. Such tools are needed to support research in environmental health and any biomedical field that is challenged by the need for integrated spatiotemporal data to examine individual-level determinants of health and disease.

RESULTS

We have developed an open-source software application-FHIR PIT (Health Level 7 Fast Healthcare Interoperability Resources Patient data Integration Tool)-to enable studies on the impact of individual-level environmental exposures on health and disease. FHIR PIT was motivated by the need to integrate patient data derived from our institution's clinical warehouse with a variety of public data sources on environmental exposures and then openly expose the data via ICEES (Integrated Clinical and Environmental Exposures Service). FHIR PIT consists of transformation steps or building blocks that can be chained together to form a transformation and integration workflow. Several transformation steps are generic and thus can be reused. As such, new types of data can be incorporated into the modular FHIR PIT pipeline by simply reusing generic steps or adding new ones. We validated FHIR PIT in the context of a driving use case designed to investigate the impact of airborne pollutant exposures on asthma. Specifically, we replicated published findings demonstrating racial disparities in the impact of airborne pollutants on asthma exacerbations.

CONCLUSIONS

While FHIR PIT was developed to support our driving use case on asthma, the software can be used to integrate any type and number of spatiotemporal data sources at a level of granularity that enables individual-level study. We expect FHIR PIT to facilitate research in environmental health and numerous other biomedical disciplines.

Fast Healthcare Interoperability Resources (FHIR) as a Meta Model to Integrate Common Data Models: Development of a Tool and Quantitative Validation Study

Background

In 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.

Objective

In 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.

Methods

Mapping 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.

Results

We 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.

Conclusions

We 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.

Safety and efficacy of sphenopalatine artery ligation in recalcitrant pediatric epistaxis

BACKGROUND

Epistaxis is a common cause for emergency department visits for both children and adults. In particular, posterior bleeds can be difficult to identify and treat. In adults, endoscopic sphenopalatine artery (SPA) ligation has been shown to be safe, cost-effective, and curative. Conversely, very few studies have delved into the safety and efficacy of SPA ligation in children. This study aims to evaluate the feasibility of SPA ligation for treatment of recalcitrant epistaxis in children.

METHODS

A retrospective analysis of outcomes in pediatric patients who underwent SPA ligation at a tertiary academic center was performed. Patients with coagulopathies or other underlying conditions were excluded from the study.

RESULTS

Data obtained from 5 patients demonstrated 60% of the population were female, with ages ranging from 2 to 13 years. 7 SPA ligations were performed among the 5 patients, with 3 undergoing unilateral SPA ligation only. The remaining 4 underwent contralateral SPA ligation subsequently. No postoperative complications were observed, and all patients experienced resolution of significant epistaxis.

CONCLUSION

Although additional studies are necessary to further support our findings, SPA ligation in the pediatric population appears to be a safe and effective treatment to control persistent posterior bleeds.

Management of Vocal Fold Paralysis and Dysphagia for Neurologic Malignancies in Children

Objectives:

To evaluate our experience with a significant number of brain malignancy–related vocal fold paralysis patients and their response to vocal cord–related therapies.

Background:

Vocal fold paralysis is a potentially devastating complication of various types of pediatric diseases and surgeries that can lead to significant vocal and swallowing difficulties. While there is significant data in the literature on outcomes of children treated for vocal fold paralysis following cardiac or thyroid surgery, there is a scarcity of such information on children following the treatment of neurologic malignancy.

Methods:

Records of 19 patients at a tertiary center who were treated for neurologic malignancies and developed either unilateral or bilateral vocal fold paralysis were reviewed for vocal fold pathology and vocal fold paralysis treatment-related variables, including initial diagnosis, management with observation or speech therapy, duration of therapy, pre- and postintervention swallow studies, and surgical intervention.

Results:

Bilateral vocal fold paralysis was noted in 26% (5/19) patients. Eighty-four percent (16/19) of patients had stable or improved ability to vocalize and swallow following therapy. There was no statistically significant difference in speech or swallowing improvement after speech therapy alone or speech therapy in combination with injection laryngoplasty ( P = .25). No complications were noted with surgical intervention.

Conclusions:

Patients with vocal fold paralysis secondary to neurologic malignancy can have an improvement in speech and swallowing after a variety of treatments, including speech therapy or early injection laryngoplasty. There was no statistically significant difference in improvement based on the type of intervention utilized. A larger sample size is needed to conclude whether surgical intervention combined with speech therapy leads to more rapid and significant functional improvement than speech therapy alone.

Giant siliconoma mimicking locally advanced breast cancer: A case report and review of literature

INTRODUCTION

Silicone prosthetics are widely used for breast augmentation and reconstruction. These devices may extrude free silicone into surrounding tissue, stimulating a granulomatous foreign body reaction. The resulting mass can mimic breast cancer.

PRESENTATION OF CASE

71 year old female with a history of a ruptured silicone implant presents with an enlarging left breast mass. Exam demonstrated and ulcerated, fungating mass with active infection. CT scan demonstrated a 23 × 15 cm mass involving the breast and chest wall with axillary lymphadenopathy. Preoperative biopsies were inconclusive and the patient underwent a modified radical mastectomy. Pathology demonstrated a siliconoma.

DISCUSSION

While benign, silicone granulomas of the breast can present similarly to malignancy and are an important differential in the diagnosis of a breast or axillary mass for appropriate patients. MRI is the study of choice and core needle biopsies cannot always establish the diagnosis preoperatively. PET scans can be falsely positive and the diagnosis requires an extensive workup to rule out cancer.

CONCLUSION

Siliconomas develop as a result of implant rupture and present with many of the signs and symptoms of breast cancer. The majority of patients should undergo surgery for symptom relief or to rule out cancer.

Primary intrahepatic mesotheliomas: A case presentation and literature review

INTRODUCTION

Primary Intrahepatic mesotheliomas are malignant tumors arising from the mesothelial cell layer covering Glisson's capsule of the liver. They are exceedingly rare with only fourteen cases reported in the literature. They have nonspecific signs and symptoms and need a high index of suspicion and an extensive workup prior to surgery. Surgery remains the mainstay of treatment.

PRESENTATION OF CASE

48 year old male presented with a 3 months history of abdominal pain, productive cough, anemia and weight loss. He had no history of asbestos exposure. A computed tomography scan and magnetic resonance study demonstrated a heterogeneous subscapular mass within the dome of the right hepatic lobe measuring 11.3 × 6.1 cm involving the diaphragm. Combined resection of the liver and diaphragm was performed to achieve negative margins. Pathology demonstrated an epithelioid necrotic intrahepatic mesothelioma that stained positive for calretinin, CK AE1/AE3, WT-1, D2-40 and CK7.

DISCUSSION

Primary intrahepatic mesotheliomas originate from the mesothelial cells lining Glisson's capsule of the liver. They predominantly invade the liver but may also abut or involve the diaphragm. Surgery should include a diagnostic laparoscopy to rule out occult disease or diffuse peritoneal mesothelioma. Complete resection with negative margins should be attempted while maintaining an adequate future liver remnant. Attempts at dissecting the tumor off the involved diaphragm will result in excessive bleeding and may leave residual disease behind.

CONCLUSION

Intrahepatic mesotheliomas are rare peripherally-located malignant tumors of the liver. They require a high index of suspicion and a comprehensive workup prior to operative intervention.