Best practices for managing and disseminating resources and outreach and evaluating the impact of the IDG Consortium

The Illuminating the Druggable Genome (IDG) consortium generated reagents, biological model systems, data, informatic databases, and computational tools. The Resource Dissemination and Outreach Center (RDOC) played a central administrative role, organized internal meetings, fostered collaboration, and coordinated consortium-wide efforts. The RDOC developed and deployed a Resource Management System (RMS) to enable efficient workflows for collecting, accessing, validating, registering, and publishing resource metadata. IDG policies for repositories and standardized representations of resources were established, adopting the FAIR (findable, accessible, interoperable, reusable) principles. The RDOC also developed metrics of IDG impact. Outreach initiatives included digital content, the Protein Illumination Timeline (representing milestones in generating data and reagents), the Target Watch publication series, the e-IDG Symposium series, and leveraging social media platforms.

Overview of the Knowledge Management Center for Illuminating the Druggable Genome

The Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) project aims to aggregate, update, and articulate protein-centric data knowledge for the entire human proteome, with emphasis on the understudied proteins from the three IDG protein families. KMC collates and analyzes data from over 70 resources to compile the Target Central Resource Database (TCRD), which is the web-based informatics platform (Pharos). These data include experimental, computational, and text-mined information on protein structures, compound interactions, and disease and phenotype associations. Based on this knowledge, proteins are classified into different Target Development Levels (TDLs) for identification of understudied targets. Additional work by the KMC focuses on enriching target knowledge and producing DrugCentral and other data visualization tools for expanding investigation of understudied targets.

Seasonal Trends in Emergency Department Visits for Mental and Behavioral Health Conditions Among Children and Adolescents Aged 5-17 Years - United States, January 2018-June 2023

Mental and behavioral health conditions among school-aged children, including substance use disorders and overall emotional well-being, are a public health concern in the United States. Timely data on seasonal patterns in child and adolescent conditions can guide optimal timing of prevention and intervention strategies. CDC examined emergency department (ED) visit data from the National Syndromic Surveillance Program for 25 distinct conditions during January 2018-June 2023 among U.S. children and adolescents aged 5-17 years, stratified by age group. Each year, during 2018-2023, among persons aged 10-14 and 15-17 years, the number and proportion of weekly ED visits for eight conditions increased in the fall school semester and remained elevated throughout the spring semester; ED visits were up to twice as high during school semesters compared with the summer period. Among children aged 5-9 years, the number and proportion of visits increased for five mental and behavioral health conditions. Seasonal increases in ED visits for some conditions among school-aged children warrant enhanced awareness about mental distress symptoms and the challenges and stressors in the school environment. Systemic changes that prioritize protective factors (e.g., physical activity; nutrition; sleep; social, community, or faith-based support; and inclusive school and community environments) and incorporate preparedness for increases in conditions during back-to-school planning might improve child and adolescent mental health.

Evaluation of an Emergency Department Visit Data Mental Health Dashboard

CONTEXT

Local health departments (LHDs) need timely county-level and subcounty-level data to monitor health-related trends, identify health disparities, and inform areas of highest need for interventions as part of their ongoing assessment responsibilities; yet, many health departments rely on secondary data that are not timely and cannot provide subcounty insights.

OBJECTIVE

We developed and evaluated a mental health dashboard in Tableau for an LHD audience featuring statewide syndromic surveillance emergency department (ED) data in North Carolina from the North Carolina Disease Event Tracking and Epidemiologic Collection Tool (NC DETECT).

DESIGN

We developed a dashboard that provides counts, crude rates, and ED visit percentages at statewide and county levels, as well as breakdowns by zip code, sex, age group, race, ethnicity, and insurance coverage for 5 mental health conditions. We evaluated the dashboards through semistructured interviews and a Web-based survey that included the standardized usability questions from the System Usability Scale.

PARTICIPANTS

Convenience sample of LHD public health epidemiologists, health educators, evaluators, and public health informaticians.

RESULTS

Six semistructured interview participants successfully navigated the dashboard but identified usability issues when asked to compare county-level trends displayed in different outputs (eg, tables vs graphs). Thirty respondents answered all questions on the System Usability Scale for the dashboard, which received an above average score of 86.

CONCLUSIONS

The dashboards scored well on the System Usability Scale, but more research is needed to identify best practices in disseminating multiyear syndromic surveillance ED visit data on mental health conditions to LHDs.

TIGA: target illumination GWAS analytics

MOTIVATION

Genome-wide association studies can reveal important genotype-phenotype associations; however, data quality and interpretability issues must be addressed. For drug discovery scientists seeking to prioritize targets based on the available evidence, these issues go beyond the single study.

RESULTS

Here, we describe rational ranking, filtering and interpretation of inferred gene-trait associations and data aggregation across studies by leveraging existing curation and harmonization efforts. Each gene-trait association is evaluated for confidence, with scores derived solely from aggregated statistics, linking a protein-coding gene and phenotype. We propose a method for assessing confidence in gene-trait associations from evidence aggregated across studies, including a bibliometric assessment of scientific consensus based on the iCite relative citation ratio, and meanRank scores, to aggregate multivariate evidence.This method, intended for drug target hypothesis generation, scoring and ranking, has been implemented as an analytical pipeline, available as open source, with public datasets of results, and a web application designed for usability by drug discovery scientists.

AVAILABILITY AND IMPLEMENTATION

Web application, datasets and source code via https://unmtid-shinyapps.net/tiga/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Severe Dumping Symptoms Are Uncommon Following Transthoracic Esophagectomy But Significantly Decrease Health-Related Quality of Life in Long-Term, Disease-Free Survivors

BACKGROUND

High-quality documentation of dumping symptoms after esophagectomy is currently limited. The aim of the study was to describe the incidence of symptoms associated with dumping syndrome and their relationship with health-related quality of life after esophagectomy.

METHODS

The study cohort was identified from prospective IRB-approved databases from two high-volume esophagectomy centers. Patients that were alive and without evidence of recurrence in April 2018 completed the validated Dumping Symptom Rating Scale and health-related quality of life questionnaires. Compound dumping symptom score was created by combining the individual scores for severity and frequency for each symptom.

RESULTS

In total, 171 patients who underwent esophagectomy 1995-2017 responded to the questionnaires, corresponding to a response rate of 77.0%. Median age was 66 years and median time from operation to survey was 5.5 years. Absent or mild problems in all nine dumping symptoms were reported by 94 (59.5%) patients; 19 (12.0%) patients reported moderate or severe problems in at least three symptoms, the most common being postprandial "need to lie down," "diarrhea," and "stomach cramps." Increasing compound dumping symptom score was associated with significantly decreased function scores in all aspects of health-related quality of life except physical functioning (P < 0.005).

CONCLUSIONS

Esophagectomy has the potential to change long-term eating patterns; however, the majority of patients in the study did not have severe postoperative dumping symptoms. On the other hand, moderate-to-severe dumping symptoms, which were reported by 12% of patients in this study, were strongly associated with decreased health-related quality of life.

How to Illuminate the Druggable Genome Using Pharos

Pharos is an integrated web-based informatics platform for the analysis of data aggregated by the Illuminating the Druggable Genome (IDG) Knowledge Management Center, an NIH Common Fund initiative. The current version of Pharos (as of October 2019) spans 20,244 proteins in the human proteome, 19,880 disease and phenotype associations, and 226,829 ChEMBL compounds. This resource not only collates and analyzes data from over 60 high-quality resources to generate these types, but also uses text indexing to find less apparent connections between targets, and has recently begun to collaborate with institutions that generate data and resources. Proteins are ranked according to a knowledge-based classification system, which can help researchers to identify less studied "dark" targets that could be potentially further illuminated. This is an important process for both drug discovery and target validation, as more knowledge can accelerate target identification, and previously understudied proteins can serve as novel targets in drug discovery. Two basic protocols illustrate the levels of detail available for targets and several methods of finding targets of interest. An Alternate Protocol illustrates the difference in available knowledge between less and more studied targets. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Search for a target and view details Alternate Protocol: Search for dark target and view details Basic Protocol 2: Filter a target list to get refined results.

Abstract 045: Declines In Acute Myocardial Infarction And Stroke Emergency Department Visits Observed During Covid-19 Restrictions In North Carolina

Introduction: Efforts to control the COVID-19 pandemic brought sweeping social change, with stay-at-home orders and physical distancing mandates in 43 of 50 states by April 2020. Early on, isolated studies around the world described reduced hospital admissions. Reports from some US hospitals also described declines in catheterization laboratory activations, and acute myocardial infarction (AMI) and stroke admissions. However, there have been few population-based analyses of emergency department (ED) visits to verify these initial reports and describe longer term impacts of the pandemic on care seeking behavior.

Hypothesis: We hypothesized that AMI and stroke ED visits in North Carolina (NC) would decrease substantially after a statewide stay-at-home order was announced on March 27, 2020.

Methods: We analyzed all ED visits from January 5 to August 28, 2020 using data collected by the NC Disease Event Tracking and Epidemiologic Collection Tool, a syndromic surveillance system that automatically gathers ED data in near-real time for all EDs in NC. Counts of AMI and stroke/transient ischemic attack (TIA) were ascertained using ICD-10-CM diagnosis codes. We compared weekly 2020 ED visit data before and after NC’s stay-at-home order, and to 2019 ED visit data.

Results: Overall ED volume declined by 44% in the weeks before and after the stay-at-home order ( Figure ) while the prior year’s ED volume stayed steady at ~100,000 visits per week. From January 5 to March 28, there were 593 AMI and 791 stroke/TIA visits per week on average. By April 11, ED visits reached a nadir at 426 AMI and 543 stroke/TIA visits per week, representing a 28% and 31% decrease, respectively. Since June, AMI and stroke/TIA ED visits have rebounded slightly but have yet to reach pre-pandemic levels.

Conclusions: We observed swift declines in AMI and stroke/TIA ED visits following NC’s stay-at-home order. These findings potentially reflect the avoidance of medical care due to fears of COVID-19 exposure and may eventually result in higher associated case fatality.

TCRD and Pharos 2021: mining the human proteome for disease biology

In 2014, the National Institutes of Health (NIH) initiated the Illuminating the Druggable Genome (IDG) program to identify and improve our understanding of poorly characterized proteins that can potentially be modulated using small molecules or biologics. Two resources produced from these efforts are: The Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/) and Pharos (https://pharos.nih.gov/), a web interface to browse the TCRD. The ultimate goal of these resources is to highlight and facilitate research into currently understudied proteins, by aggregating a multitude of data sources, and ranking targets based on the amount of data available, and presenting data in machine learning ready format. Since the 2017 release, both TCRD and Pharos have produced two major releases, which have incorporated or expanded an additional 25 data sources. Recently incorporated data types include human and viral-human protein-protein interactions, protein-disease and protein-phenotype associations, and drug-induced gene signatures, among others. These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.

[From the bench to the clinic: The challenge of translating platelet production in vitro]

Platelet transfusions, which are currently totally dependent on altruistic donations, are absolutely necessary to the treatment of patients with thrombocytopenia following trauma, surgery or other pathologies (especially malignancies). Producing platelets in vitro represent a major technological and scientific breathrough that would address logistical issues (supply chain, stock holding…) and medical concerns (compatibility and biosafety). The translation of this innovation will need to be accompanied by rigorous quality control, harmonised between laboratory when it comes to functionality and biosafety for use in the clinic.

In-Country Method Validation of a Paper-based, Smartphone-assisted Iron Sensor for the Food Fortification Programs

Objectives

Food fortification programs and food companies in low-income settings, such as in the case of Mexico, lack the ability to monitor the micronutrients added to staples entering local markets. The purpose of the present work is to validate a user-friendly sampling kit and quantify the final error parameters of a paper-based, smartphone-assisted sensor (Nu3px) for the determination of iron in corn flours within the context of Mexico's food fortification program.

Methods

Corn flour samples (n = 45) from local brands (n = 6) were collected from supermarkets, convenience stores, and directly from companies in the States of Querétaro, Cuautitlán, Saltillo, and Cuetzalan, Mexico. Iron content was analyzed using atomic emission spectroscopy (AES) and Nu3px. The final error parameters were quantified via method validation final experiments, i.e., replication and comparison of methods experiments. Qualitative categorization of samples (i.e., accept/reject batch) was applied to evaluate Nu3px's against Mexico's fortification policy (cutoff = 40 μg Fe/g flour). A user-centered design process was applied to develop and evaluate a sampling kit consisting of low-cost measuring utensils.

Results

Iron content in fortified Mexican corn flours varied widely (23–39%). Nu3px's random error was 12% (replication experiment, n = 5) and its bias was 1.79 ± 9.99 μg Fe/g flour (comparison of methods experiment, n = 45). The true mean difference between Nu3px and AES was zero (p &gt; 0.05) and both methods had similar variance (F = 2.40; P &gt; 0.05). AES and Nu3px classified the iron content above/below the cutoff in the same way (100% match, Χ2 = 16.41, P = 0.01). The affordable and user-friendly sampling kit added some random error, but the mean difference was equal to zero (P &gt; 0.05). Both sampling procedures were correlated (r = 0.952, P = 0.01).

Conclusions

An affordable, user-friendly, and equipment-free sample preparation kit for corn flour samples showed similar precision to using analytical tools. The sample preparation kit along with the paper-based, smartphone-assisted assay measure iron within the performance parameters required for its application to monitor batch quality in the corn flour fortification program in Mexico.

Funding Sources

Fulbright Garcia-Robles Fellowship, 2019.

Motor Vehicle Crash Case Definitions and How They Impact Injury Surveillance

BACKGROUND Motor vehicle crashes are a leading cause of injury in North Carolina. Motor vehicle crash injury surveillance that relies on hospital diagnostic codes alone may underestimate injury. Our objective was to describe how motor vehicle crash injury case definitions can impact results when using hospital data.METHODS We received motor vehicle crash-related emergency department visits from 1 large metropolitan county in North Carolina for the year 2013. Emergency department visits were categorized based on 3 mutually exclusive case definitions: motor vehicle crash injuries identified using external cause-of-injury codes, text searches for motor vehicle crash-related key words in triage notes or chief complaint fields, and motor vehicle crash injuries identified using both text searches and external cause-of-injury codes. Descriptive statistics were used to examine differences in patient characteristics according to case definition.RESULTS Most emergency department visits contained both motor vehicle crash text and motor vehicle crash external cause-of-injury codes (N = 13,422, 76%). Patients identified using external cause-of-injury codes only were more likely to be male, arrive by ambulance, and be admitted to the hospital compared to patients identified by text searches or both text and external cause-of-injury codes. Twenty-eight percent of the patients (N = 5,021) received non-injury related diagnoses in the emergency department. Among these patients, the most frequently used first diagnoses were for vague or chronic pain conditions.LIMITATIONS We relied on secondary data and were unable to perform medical chart reviews; hospital data have limited information surrounding the crash event.CONCLUSION The choice of case definition used for motor vehicle crash surveillance impacts the picture of motor vehicle crash injury severity. It is important for researchers to be aware of the impact case definition has on their results.

Acute Pancreatitis: Updates for Emergency Clinicians

BACKGROUND

Acute pancreatitis is a frequent reason for patient presentation to the emergency department (ED) and the most common gastrointestinal disease resulting in admission. Emergency clinicians are often responsible for the diagnosis and initial management of acute pancreatitis.

OBJECTIVE

This review article provides emergency clinicians with a focused overview of the diagnosis and management of pancreatitis.

DISCUSSION

Pancreatitis is an inflammatory process within the pancreas. While the disease is often mild, severe forms can have a mortality rate of up to 30%. The diagnosis of pancreatitis requires two of the following three criteria: epigastric abdominal pain, an elevated lipase, and imaging findings of pancreatic inflammation. The most common etiologies include gallbladder disease and alcohol use. After the diagnosis has been made, it is important to identify underlying etiologies requiring specific intervention, as well as obtain a right upper quadrant ultrasound. The initial management of choice is fluid resuscitation and pain control. Recent data have suggested that more cautious fluid resuscitation in the first 24 h might be more appropriate for some patients. Intravenous opiates are generally safe if used judiciously. Appropriate disposition is a multifactorial decision, which can be facilitated by using Ranson criteria or the Bedside Index of Severity in Acute Pancreatitis score. Complications, though rare, can be severe.

CONCLUSIONS

Pancreatitis is a potentially deadly disease that commonly presents to most emergency departments. It is important for clinicians to be aware of the current evidence regarding the diagnosis, treatment, and disposition of these patients.

Activation of Rho Family GTPases by Small Molecules

Ras and Ras-related small GTPases are key regulators of diverse cellular functions that impact cell growth, survival, motility, morphogenesis, and differentiation. They are important targets for studies of disease mechanisms as well as drug discovery. Here, we report the characterization of small molecule agonists of one or more of six Rho, Rab, and Ras family GTPases that were first identified through flow cytometry-based, multiplexed high-throughput screening of 200000 compounds. The activators were categorized into three distinct chemical families that are represented by three lead compounds having the highest activity. Virtual screening predicted additional compounds with potential GTPase activating properties. Secondary dose–response assays performed on compounds identified through these screens confirmed agonist activity of 43 compounds. While the lead and second most active small molecules acted as pan activators of multiple GTPase subfamilies, others showed partial selectivity for Ras and Rab proteins. The compounds did not stimulate nucleotide exchange by guanine nucleotide exchange factors and did not protect against GAP-stimulated GTP hydrolysis. The activating properties were caused by a reversible stabilization of the GTP-bound state and prolonged effector protein interactions. Notably, these compounds were active both in vitro and in cell-based assays, and small molecule-mediated changes in Rho GTPase activities were directly coupled to measurable changes in cytoskeletal rearrangements that dictate cell morphology.

High-Throughput Flow Cytometry Identifies Small-Molecule Inhibitors for Drug Repurposing in T-ALL

Kinase inhibitors have dramatically increased patient survival in a multitude of cancers, including hematological malignancies. However, kinase inhibitors have not yet been integrated into current clinical trials for patients with T-cell-lineage acute lymphoblastic leukemia (T-ALL). In this study, we used a high-throughput flow cytometry (HTFC) approach to test a collection of small-molecule inhibitors, including 26 FDA-approved tyrosine kinase inhibitors in a panel of T-ALL cell lines and patient-derived xenografts. Because hypoxia is known to cause resistance to chemotherapy, we developed a synthetic niche that mimics the low oxygen levels found in leukemic bone marrow to evaluate the effects of hypoxia on the tested inhibitors. Drug sensitivity screening was performed using the Agilent BioCel automated liquid handling system integrated with the HyperCyt HT flow cytometry platform, and the uptake of propidium iodide was used as an indication of cell viability. The HTFC dose-response testing identified several compounds that were efficacious in both normal and hypoxic conditions. This study shows that some clinically approved kinase inhibitors target T-ALL in the hypoxic niche of the bone marrow.

Unexplored therapeutic opportunities in the human genome

A large proportion of biomedical research and the development of therapeutics is focused on a small fraction of the human genome. In a strategic effort to map the knowledge gaps around proteins encoded by the human genome and to promote the exploration of currently understudied, but potentially druggable, proteins, the US National Institutes of Health launched the Illuminating the Druggable Genome (IDG) initiative in 2014. In this article, we discuss how the systematic collection and processing of a wide array of genomic, proteomic, chemical and disease-related resource data by the IDG Knowledge Management Center have enabled the development of evidence-based criteria for tracking the target development level (TDL) of human proteins, which indicates a substantial knowledge deficit for approximately one out of three proteins in the human proteome. We then present spotlights on the TDL categories as well as key drug target classes, including G protein-coupled receptors, protein kinases and ion channels, which illustrate the nature of the unexplored opportunities for biomedical research and therapeutic development.

TIN-X: target importance and novelty explorer

Motivation

The increasing amount of peer-reviewed manuscripts requires the development of specific mining tools to facilitate the visual exploration of evidence linking diseases and proteins.

Results

We developed TIN-X, the Target Importance and Novelty eXplorer, to visualize the association between proteins and diseases, based on text mining data processed from scientific literature. In the current implementation, TIN-X supports exploration of data for G-protein coupled receptors, kinases, ion channels, and nuclear receptors. TIN-X supports browsing and navigating across proteins and diseases based on ontology classes, and displays a scatter plot with two proposed new bibliometric statistics: Importance and Novelty.

Availability and Implementation

http://www.newdrugtargets.org.

Contact

cbologa@salud.unm.edu.

Unexplored therapeutic opportunities in the human genome

This corrects the article DOI: 10.1038/nrd.2018.14.

High-Throughput Flow Cytometry Screening of Multidrug Efflux Systems

The resistance nodulation cell division (RND) family of proteins are inner membrane transporters that associate with periplasmic adaptor proteins and outer membrane porins to affect substrate transport from the cytosol and periplasm in Gram-negative bacteria. Various structurally diverse compounds are substrates of RND transporters. Along with their notable role in antibiotic resistance, these transporters are essential for niche colonization, quorum sensing, and virulence as well as for the removal of fatty acids and bile salts. As such, RNDs are an attractive target for antimicrobial development. However, while enhancing the utility of antibiotics with an RND inhibitor is an appealing concept, only a small core of chemotypes has been identified as efflux pump inhibitors (EPIs). Thus, our key objective is the development and validation of an efflux profiling and discovery strategy for RND model systems. Here we describe a flow cytometric dye accumulation assay that uses fluorescein diacetate (FDA) to interrogate the model Gram-negative pathogens Escherichia coli, Franscisella tularensis, and Burkholderia pseudomallei. Fluorochrome retention is increased in the presence of known efflux inhibitors and in RND deletion strains. The assay can be used in a high-throughput format to evaluate efflux of dye-substrate candidates and to screen chemical libraries for novel EPIs. Triaged compounds that inhibit efflux in pathogenic strains are tested for growth inhibition and antibiotic potentiation using microdilution culture plates in a select agent Biosafety Level-3 (BSL3) environment. This combined approach demonstrates the utility of flow cytometric analysis for efflux activity and provides a useful platform in which to characterize efflux in pathogenic Gram-negative bacteria. Screening small molecule libraries for novel EPI candidates offers the potential for the discovery of new classes of antibacterial compounds.

High-Throughput Screening Approach for Identifying Compounds That Inhibit Nonhomologous End Joining

DNA double-strand breaks (DSBs) are repaired primarily by homologous recombination (HR) or nonhomologous end joining (NHEJ). Compounds that modulate HR have shown promise as cancer therapeutics. The V(D)J recombination reaction, which assembles antigen receptor genes in lymphocytes, is initiated by the introduction of DNA DSBs at two recombining gene segments by the RAG endonuclease, followed by the NHEJ-mediated repair of these DSBs. Here, using HyperCyt automated flow cytometry, we develop a robust high-throughput screening (HTS) assay for NHEJ that utilizes engineered pre-B-cell lines where the V(D)J recombination reaction can be induced and monitored at a single-cell level. This approach, novel in processing four 384-well plates at a time in parallel, was used to screen the National Cancer Institute NeXT library to identify compounds that inhibit V(D)J recombination and NHEJ. Assessment of cell light scattering characteristics at the primary HTS stage (83,536 compounds) enabled elimination of 60% of apparent hits as false positives. Although all the active compounds that we identified had an inhibitory effect on RAG cleavage, we have established this as an approach that could identify compounds that inhibit RAG cleavage or NHEJ using new chemical libraries.

Impact of State Psychiatric Hospital Waitlists on Monthly Admissions

OBJECTIVE

This study estimated the effects of a waitlist policy on the monthly number and case mix of admissions to state psychiatric hospitals (SPHs) in North Carolina (NC).

METHODS

Descriptive analyses compared pre/postwaitlist differences in the monthly number and case mix of nonforensic adult admissions (N=72,035) to NC's four SPHs by using data from the three years before and the three years after the waitlist announcement. Hospital-level fixed-effects regression models further evaluated the waitlist policy's impact on the number and case mix of admissions.

RESULTS

Regression results confirmed that the waitlist policy was associated with both fewer admissions and changes to the case mix of admissions, including a 4.2% decrease in the percentage of monthly admissions by patients with diagnoses of substance abuse disorders (p=.002) across all months postwaitlist (partially offset by an increase of patients with diagnoses of severe mental illness alone).

CONCLUSIONS

Waitlists led to reduced monthly admissions and altered case mix following implementation at NC SPHs.

Pharos: Collating protein information to shed light on the druggable genome

The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental techniques and a Knowledge Management Center (KMC) that would collect and organize information about protein targets from four families, representing the most common druggable targets with an emphasis on understudied proteins. Here, we describe two resources developed by the KMC: the Target Central Resource Database (TCRD) which collates many heterogeneous gene/protein datasets and Pharos (https://pharos.nih.gov), a multimodal web interface that presents the data from TCRD. We briefly describe the types and sources of data considered by the KMC and then highlight features of the Pharos interface designed to enable intuitive access to the IDG knowledgebase. The aim of Pharos is to encourage 'serendipitous browsing', whereby related, relevant information is made easily discoverable. We conclude by describing two use cases that highlight the utility of Pharos and TCRD.

Impact of Extreme Heat Events on Emergency Department Visits in North Carolina (2007-2011)

Extreme heat is the leading cause of weather-related mortality in the U.S. Extreme heat also affects human health through heat stress and can exacerbate underlying medical conditions that lead to increased morbidity and mortality. In this study, data on emergency department (ED) visits for heat-related illness (HRI) and other selected diseases were analyzed during three heat events across North Carolina from 2007 to 2011. These heat events were identified based on the issuance and verification of heat products from local National Weather Service forecast offices (i.e. Heat Advisory, Heat Watch, and Excessive Heat Warning). The observed number of ED visits during these events were compared to the expected number of ED visits during several control periods to determine excess morbidity resulting from extreme heat. All recorded diagnoses were analyzed for each ED visit, thereby providing insight into the specific pathophysiological mechanisms and underlying health conditions associated with exposure to extreme heat. The most common form of HRI was heat exhaustion, while the percentage of visits with heat stroke was relatively low (<10%). The elderly (>65 years of age) were at greatest risk for HRI during the early summer heat event (8.9 visits per 100,000), while young and middle age adults (18-44 years of age) were at greatest risk during the mid-summer event (6.3 visits per 100,000). Many of these visits were likely due to work-related exposure. The most vulnerable demographic during the late summer heat event was adolescents (15-17 years of age), which may relate to the timing of organized sports. This demographic also exhibited the highest visit rate for HRI among all three heat events (10.5 visits per 100,000). Significant increases (p < 0.05) in visits with cardiovascular and cerebrovascular diseases were noted during the three heat events (3-8%). The greatest increases were found in visits with hypotension during the late summer event (23%) and sequelae during the early summer event (30%), while decreases were noted for visits with hemorrhagic stroke during the middle and late summer events (13-24%) and for visits with aneurysm during the early summer event (15%). Significant increases were also noted in visits with respiratory diseases (5-7%). The greatest increases in this category were found in visits with pneumonia and influenza (16%), bronchitis and emphysema (12%), and COPD (14%) during the early summer event. Significant increases in visits with nervous system disorders were also found during the early summer event (16%), while increases in visits with diabetes were noted during the mid-summer event (10%).

Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia

While acute myeloid leukemia (AML) comprises many disparate genetic subtypes, one shared hallmark is the arrest of leukemic myeloblasts at an immature and self-renewing stage of development. Therapies that overcome differentiation arrest represent a powerful treatment strategy. We leveraged the observation that the majority of AML, despite their genetically heterogeneity, share in the expression of HoxA9, a gene normally downregulated during myeloid differentiation. Using a conditional HoxA9 model system, we performed a high-throughput phenotypic screen and defined compounds that overcame differentiation blockade. Target identification led to the unanticipated discovery that inhibition of the enzyme dihydroorotate dehydrogenase (DHODH) enables myeloid differentiation in human and mouse AML models. In vivo, DHODH inhibitors reduced leukemic cell burden, decreased levels of leukemia-initiating cells, and improved survival. These data demonstrate the role of DHODH as a metabolic regulator of differentiation and point to its inhibition as a strategy for overcoming differentiation blockade in AML.

Total knee arthroplasty with an oxidised zirconium femoral component: ten-year survivorship analysis

AIMS

Oxidised zirconium was introduced as a material for femoral components in total knee arthroplasty (TKA) as an attempt to reduce polyethylene wear. However, the long-term survival of this component is not known.

METHODS

We performed a retrospective review of a prospectively collected database to assess the ten year survival and clinical and radiological outcomes of an oxidised zirconium total knee arthroplasty with the Genesis II prosthesis. The Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Knee Injury and Osteoarthritis Outcome Score (KOOS) and a patient satisfaction scale were used to assess outcome.

RESULTS

A total of 303 consecutive TKAs were performed in 278 patients with a mean age of 68 years (45 to 89). The rate of survival ten years post-operatively as assessed using Kaplan-Meier analysis was 97% (95% confidence interval 94 to 99) with revision for any reason as the endpoint. There were no revisions for loosening, osteolysis or failure of the implant. There was a significant improvement in all components of the WOMAC score at final follow-up (p < 0.001). The mean individual components of the KOOS score for symptoms (82.4 points; 36 to 100), pain (87.5 points; 6 to 100), activities of daily life (84.9 points; 15 to 100) and quality of life (71.4 points; 6 to 100) were all at higher end of the scale.

DISCUSSION

This study provides further supportive evidence that the oxidised zirconium TKA gives comparable rates of survival with other implants and excellent functional outcomes ten years post-operatively.

TAKE HOME MESSAGE

Total knee arthroplasty with an oxidised zirconium femoral component gives comparable long-term rates of survival and functional outcomes with conventional implants.

The Video Interaction Guidance approach applied to teaching communication skills in dentistry

PURPOSE

To examine dentists' views of a novel video review technique to improve communication skills in complex clinical situations.

MATERIALS AND METHODS

Dentists (n = 3) participated in a video review known as Video Interaction Guidance to encourage more attuned interactions with their patients (n = 4). Part of this process is to identify where dentists and patients reacted positively and effectively. Each dentist was presented with short segments of video footage taken during an appointment with a patient with intellectual disabilities and communication difficulties. Having observed their interactions with patients, dentists were asked to reflect on their communication strategies with the assistance of a trained VIG specialist.

RESULTS

Dentists reflected that their VIG session had been insightful and considered the review process as beneficial to communication skills training in dentistry. They believed that this technique could significantly improve the way dentists interact and communicate with patients. The VIG sessions increased their awareness of the communication strategies they use with their patients and were perceived as neither uncomfortable nor threatening.

DISCUSSION

The VIG session was beneficial in this exploratory investigation because the dentists could identify when their interactions were most effective. Awareness of their non-verbal communication strategies and the need to adopt these behaviours frequently were identified as key benefits of this training approach. One dentist suggested that the video review method was supportive because it was undertaken by a behavioural scientist rather than a professional counterpart.

CONCLUSION

Some evidence supports the VIG approach in this specialist area of communication skills and dental training.

Pollen concentration and asthma exacerbations in Wake County, North Carolina, 2006-2012

Pollen has been generally linked to an increased risk for asthma exacerbation. However, the delayed effect (lag), the length of effect duration, and the association heterogeneity by pollen types have not been well characterized. Short-term associations between ambient concentration of various pollen types (tree, grass, and weed) and emergency department (ED) visits for asthma were assessed using data in Wake County, North Carolina, during 2006-2012. Distributed lag nonlinear models (DLNM) were used to characterize the associations, while adjusting for air pollutants, meteorological, and temporal factors. A strong association between same-day tree pollen and asthma ED visits was detected. This association lasted four days, with a 4-day cumulative risk ratio (RR) up to 2.10 (3500 grains/m(3) vs. 0 grains/m(3), 95% confidence interval [CI]=1.21-3.65). The associations of asthma ED visits with weed pollen and grass pollen were weak, suggestively starting from lag 2 and lasting 3 days, with the strongest association a 3-day cumulative RR of 1.08 (32 grains/m(3) vs. 0 grains/m(3), 95% CI=1.01-1.15) and 1.05 (11 grains/m(3) vs. 0 grains/m(3), 95% CI=1.00-1.11). Our results indicate that the association of ambient pollen and asthma exacerbation vary by pollen type, both quantitatively and temporally. These findings have important implications for optimizing targeted allergic disease prevention and management, and helping understand the etiology of ambient exposure-induced allergic diseases.

Pharmaceutical screen identifies novel target processes for activation of autophagy with a broad translational potential

Autophagy is a conserved homeostatic process active in all human cells and affecting a spectrum of diseases. Here we use a pharmaceutical screen to discover new mechanisms for activation of autophagy. We identify a subset of pharmaceuticals inducing autophagic flux with effects in diverse cellular systems modelling specific stages of several human diseases such as HIV transmission and hyperphosphorylated tau accumulation in Alzheimer's disease. One drug, flubendazole, is a potent inducer of autophagy initiation and flux by affecting acetylated and dynamic microtubules in a reciprocal way. Disruption of dynamic microtubules by flubendazole results in mTOR deactivation and dissociation from lysosomes leading to TFEB (transcription factor EB) nuclear translocation and activation of autophagy. By inducing microtubule acetylation, flubendazole activates JNK1 leading to Bcl-2 phosphorylation, causing release of Beclin1 from Bcl-2-Beclin1 complexes for autophagy induction, thus uncovering a new approach to inducing autophagic flux that may be applicable in disease treatment.

Autophagy is a homeostatic process that could be a potential drug target in the treatment of disease. Here the authors identify in a pharmaceutical screen flubendazole as an inducer of autophagy initiation and flux by affecting microtubules, mTOR, TFEB and Beclin 1 activity.

Discovery of Small-Molecule Nonfluorescent Inhibitors of Fluorogen-Fluorogen Activating Protein Binding Pair

A new class of biosensors, fluorogen activating proteins (FAPs), has been successfully used to track receptor trafficking in live cells. Unlike the traditional fluorescent proteins (FPs), FAPs do not fluoresce unless bound to their specific small-molecule fluorogens, and thus FAP-based assays are highly sensitive. Application of the FAP-based assay for protein trafficking in high-throughput flow cytometry resulted in the discovery of a new class of compounds that interferes with the binding between fluorogens and FAP, thus blocking the fluorescence signal. These compounds are high-affinity, nonfluorescent analogs of fluorogens with little or no toxicity to the tested cells and no apparent interference with the normal function of FAP-tagged receptors. The most potent compound among these, N,4-dimethyl-N-(2-oxo-2-(4-(pyridin-2-yl)piperazin-1-yl)ethyl)benzenesulfonamide (ML342), has been investigated in detail. X-ray crystallographic analysis revealed that ML342 competes with the fluorogen, sulfonated thiazole orange coupled to diethylene glycol diamine (TO1-2p), for the same binding site on a FAP, AM2.2. Kinetic analysis shows that the FAP-fluorogen interaction is more complex than a homogeneous one-site binding process, with multiple conformational states of the fluorogen and/or the FAP, and possible dimerization of the FAP moiety involved in the process.

A Pan-GTPase Inhibitor as a Molecular Probe

Overactive GTPases have often been linked to human diseases. The available inhibitors are limited and have not progressed far in clinical trials. We report here a first-in-class small molecule pan-GTPase inhibitor discovered from a high throughput screening campaign. The compound CID1067700 inhibits multiple GTPases in biochemical, cellular protein and protein interaction, as well as cellular functional assays. In the biochemical and protein interaction assays, representative GTPases from Rho, Ras, and Rab, the three most generic subfamilies of the GTPases, were probed, while in the functional assays, physiological processes regulated by each of the three subfamilies of the GTPases were examined. The chemical functionalities essential for the activity of the compound were identified through structural derivatization. The compound is validated as a useful molecular probe upon which GTPase-targeting inhibitors with drug potentials might be developed.

Prevalence of Streptococcus dysgalactiae subsp. equisimilis and S. equi subsp. zooepidemicus in a sample of healthy dogs, cats and horses

AIMS

To estimate the prevalence of β-haemolytic Lancefield group C streptococci in healthy dogs, cats and horses; to determine if frequent contact with horses was associated with isolation of these species from dogs and cats; and to characterise recovered S. equi subsp. zooepidemicus isolates by multilocus sequence typing.

METHODS

Oropharyngeal swabs were collected from 197 dogs and 72 cats, and nasopharyngeal swabs from 93 horses. Sampling was carried out at the Massey University Veterinary Teaching Hospital, on sheep and beef farms or on premises where horses were present. All animals were healthy and were categorised as Urban dogs and cats (minimal contact with horses or farm livestock), Farm dogs (minimal contact with horses) and Stable dogs and cats (frequent contact with horses). Swabs were cultured for β-haemolytic Streptococcus spp. and Lancefield group C streptococcal subspecies were confirmed by phenotypic and molecular techniques.

RESULTS

Of the 197 dogs sampled, 21 (10.7 (95% CI= 4.0-25.4)%) tested positive for S. dysgalactiae subsp. equisimilis and 4 (2.0 (95% CI=0.7-5.5)%) tested positive for S. equi subsp. zooepidemicus. All these isolates, except for one S. dysgalactiae subsp. equisimilis isolate in an Urban dog, were from Stable dogs. S. dysgalactiae subsp. equisimilis was isolated from one Stable cat. Of the 93 horses, 22 (23.7 (95% CI=12.3-40.6)%) and 6 (6.5 (95% CI=2.8-14.1)%) had confirmed S. dysgalactiae subsp. equisimilis and S. equi subsp. zooepidemicus isolation respectively. Isolation of S. dysgalactiae subsp. equisimilis from dogs was associated with frequent contact with horses (OR=9.8 (95% CI=2.6-72.8)). Three different multilocus sequence type profiles of S. equi subsp. zooepidemicus that have not been previously reported in dogs were recovered.

CONCLUSIONS AND CLINICAL RELEVANCE

Subclinical infection or colonisation by S. equi subsp. zooepidemicus and S. dysgalactiae subsp. equisimilis occurs in dogs and further research on inter-species transmission and the pathogenic potential of these Lancefield group C streptococci is needed. Complete speciation of β-haemolytic streptococci should be recommended in clinical cases and the possible exposure to horses and their environment should be considered in epidemiological investigations.

The outcome at ten years of lateral closing-wedge high tibial osteotomy: determinants of survival and functional outcome

The aim of this study was to examine the functional outcome at ten years following lateral closing wedge high tibial osteotomy for medial compartment osteoarthritis of the knee and to define pre-operative predictors of survival and determinants of functional outcome. 164 consecutive patients underwent high tibial osteotomy between 2000 and 2002. A total of 100 patients (100 knees) met the inclusion criteria and 95 were available for review at ten years. Data were collected prospectively and included patient demographics, surgical details, long leg alignment radiographs, Western Ontario and McMaster Universities osteoarthritis index (WOMAC) and Knee Society scores (KSS) pre-operatively and at five and ten years follow-up. At ten years, 21 patients had been revised at a mean of five years. Overall Kaplan-Meier survival was 87% (95% confidence interval (CI) 81 to 94) and 79% (95% CI 71 to 87) at five and ten years, respectively. When compared with unrevised patients, those who had been revised had significantly lower mean pre-operative WOMAC Scores (47 (21 to 85) vs 65 (32 to 99), p < 0.001), higher mean age (54 yrs (42 to 61) vs 49 yrs (26 to 66), p = 0.006) and a higher mean BMI (30.2; 25 to 39 vs 27.9; 21 to 36, p = 0.005). Each were found to be risk factors for revision, with hazard ratios of 10.7 (95% CI 4 to 28.6; pre-operative WOMAC < 45), 6.5 (95% CI 2.4 to 17.7; age > 55) and 3.0 (95%CI 1.2 to 7.6; BMI > 30). Survival of patients with pre-operative WOMAC > 45, age < 55 and BMI < 30 was 97% at five and ten years. WOMAC and KSS in surviving patients improved significantly between pre-operative (mean 61; 32 to 99) and five (mean 88; 35 to 100, p = 0.001) and ten years (mean 84; 38 to 100, p = 0.001). Older patients had better functional outcomes overall, despite their higher revision rate. This study has shown that improved survival is associated with age < 55 years, pre-operative WOMAC scores > 45 and, a BMI < 30. In patients over 55 years of age with adequate pre-operative functional scores, survival can be good and functional outcomes can be significantly better than their younger counterparts. We recommend the routine use of pre-operative functional outcome scores to guide decision-making when considering suitability for high tibial osteotomy.

FRET detection of lymphocyte function-associated antigen-1 conformational extension

Lymphocyte function–associated antigen 1 (LFA-1) and its ligands are essential for immune cell interactions. LFA-1 is regulated through conformational changes. The relationship between molecular conformation and function is unclear. Förster resonance energy transfer is used to assess LFA-1 conformation under real-time signaling conditions.

Lymphocyte function–associated antigen 1 (LFA-1, CD11a/CD18, αLβ2-integrin) and its ligands are essential for adhesion between T-cells and antigen-presenting cells, formation of the immunological synapse, and other immune cell interactions. LFA-1 function is regulated through conformational changes that include the modulation of ligand binding affinity and molecular extension. However, the relationship between molecular conformation and function is unclear. Here fluorescence resonance energy transfer (FRET) with new LFA-1–specific fluorescent probes showed that triggering of the pathway used for T-cell activation induced rapid unquenching of the FRET signal consistent with extension of the molecule. Analysis of the FRET quenching at rest revealed an unexpected result that can be interpreted as a previously unknown LFA-1 conformation.

An automated high-throughput cell-based multiplexed flow cytometry assay to identify novel compounds to target Candida albicans virulence-related proteins

Although three major classes of systemic antifungal agents are clinically available, each is characterized by important limitations. Thus, there has been considerable ongoing effort to develop novel and repurposed agents for the therapy of invasive fungal infections. In an effort to address these needs, we developed a novel high-throughput, multiplexed screening method that utilizes small molecules to probe candidate drug targets in the opportunistic fungal pathogen Candida albicans. This method is amenable to high-throughput automated screening and is based upon detection of changes in GFP levels of individually tagged target proteins. We first selected four GFP-tagged membrane-bound proteins associated with virulence or antifungal drug resistance in C. albicans. We demonstrated proof-of-principle that modulation of fluorescence intensity can be used to assay the expression of specific GFP-tagged target proteins to inhibitors (and inducers), and this change is measurable within the HyperCyt automated flow cytometry sampling system. Next, we generated a multiplex of differentially color-coded C. albicans strains bearing C-terminal GFP-tags of each gene encoding candidate drug targets incubated in the presence of small molecules from the Prestwick Chemical Library in 384-well microtiter plate format. Following incubation, cells were sampled through the HyperCyt system and modulation of protein levels, as indicated by changes in GFP-levels of each strain, was used to identify compounds of interest. The hit rate for both inducers and inhibitors identified in the primary screen did not exceed 1% of the total number of compounds in the small-molecule library that was probed, as would be expected from a robust target-specific, high-throughput screening campaign. Secondary assays for virulence characteristics based on null mutant strains were then used to further validate specificity. In all, this study presents a method for the identification and verification of new antifungal drugs targeted to fungal virulence proteins using C. albicans as a model fungal pathogen.

Defining emergency department asthma visits for public health surveillance, North Carolina, 2008-2009

INTRODUCTION

When using emergency department (ED) data sets for public health surveillance, a standard approach is needed to define visits attributable to asthma. Asthma can be the first (primary) or a subsequent (2nd through 11th) diagnosis. Our study objective was to develop a definition of ED visits attributable to asthma for public health surveillance. We evaluated the effect of including visits with an asthma diagnosis in primary-only versus subsequent positions.

METHODS

The study was a cross-sectional analysis of population-level ED surveillance data. Of the 114 North Carolina EDs eligible to participate in a statewide surveillance system in 2008-2009, we used data from the 111 (97%) that participated during those years. Included were all ED visits with an ICD-9-CM diagnosis code for asthma in any diagnosis position (1 through 11). We formed 11 strata based on the diagnosis position of asthma and described common chief complaint and primary diagnosis categories for each. Prevalence ratios compared each category's proportion of visits that received either asthma- or cardiac-related procedure codes.

RESULTS

Respiratory diagnoses were most common in records of ED visits in which asthma was the first or second diagnosis, while primary diagnoses of injury and heart disease were more common when asthma appeared in positions 3-11. Asthma-related chief complaints and procedures were most common when asthma was the first or second diagnosis, whereas cardiac procedures were more common in records with asthma in positions 3-11.

CONCLUSION

ED visits should be defined as asthma-related when asthma is in the first or second diagnosis position.

Qualitative evaluation of care plans for Canadian breast and head-and-neck cancer survivors

BACKGROUND

Survivorship care plans (scps) have been recommended as a way to ease the transition from active cancer treatment to follow-up care, to reduce uncertainty for survivors in the management of their ongoing health, and to improve continuity of care. The objective of the demonstration project reported here was to assess the value of scps for cancer survivors in western Canada.

METHODS

The Alberta CancerBridges team developed, implemented, and evaluated scps for 36 breast and 21 head-and-neck cancer survivors. For the evaluation, we interviewed 12 of the survivors, 9 nurses who delivered the scps, and 3 family physicians who received the scps (n = 24 in total). We asked about satisfaction, usefulness, emotional impact, and communication value. We collected written feedback from the three groups about positive aspects of the scps and possible improvements (n = 85). We analyzed the combined data using qualitative thematic analysis.

RESULTS

Survivors, nurses, and family physicians agreed that scps could ease the transition to survivorship partly by enhancing communication between survivors and care providers. Survivors appreciated the individualized attention and the comprehensiveness of the plans. They described positive emotional impacts, but wanted a way to ensure that their physicians received the scps. Nurses and physicians responded positively, but expressed concern about the time required to implement the plans. Suggestions for streamlining the process included providing survivors with scp templates in advance, auto-populating the templates for the nurses, and creating summary pages for physicians.

CONCLUSIONS

The results suggest ways in which scps could help to improve the transition to cancer survivorship and provide starting points for larger feasibility studies.

An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines

Recent industry-academic partnerships involve collaboration among disciplines, locations, and organizations using publicly funded "open-access" and proprietary commercial data sources. These require the effective integration of chemical and biological information from diverse data sources, which presents key informatics, personnel, and organizational challenges. The BioAssay Research Database (BARD) was conceived to address these challenges and serve as a community-wide resource and intuitive web portal for public-sector chemical-biology data. Its initial focus is to enable scientists to more effectively use the National Institutes of Health Roadmap Molecular Libraries Program (MLP) data generated from the 3-year pilot and 6-year production phases of the Molecular Libraries Probe Production Centers Network (MLPCN), which is currently in its final year. BARD evolves the current data standards through structured assay and result annotations that leverage BioAssay Ontology and other industry-standard ontologies, and a core hierarchy of assay definition terms and data standards defined specifically for small-molecule assay data. We initially focused on migrating the highest-value MLP data into BARD and bringing it up to this new standard. We review the technical and organizational challenges overcome by the interdisciplinary BARD team, veterans of public- and private-sector data-integration projects, who are collaborating to describe (functional specifications), design (technical specifications), and implement this next-generation software solution.