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.

CHARIOT: a phase I study of berzosertib with chemoradiotherapy in oesophageal and other solid cancers using time to event continual reassessment method

BACKGROUND

Berzosertib (M6620) is a highly potent (IC50  =  19 nM) and selective, first-in-class ataxia telangiectasia-mutated and Rad3-related protein kinase (ATR) inhibitor. This trial assessed the safety, preliminary efficacy, and tolerance of berzosertib in oesophageal cancer (A1 cohort) with RT and advanced solid tumours (A2 cohort) with cisplatin and capecitabine.

METHODS

Single-arm, open-label dose-escalation (Time-to-Event Continual Reassessment Method) trial with 16 patients in A1 and 18 in A2. A1 tested six dose levels of berzosertib with RT (35 Gy over 15 fractions in 3 weeks).

RESULTS

No dose-limiting toxicities (DLTs) in A1. Eight grade 3 treatment-related AEs occurred in five patients, with rash being the most common. The highest dose (240 mg/m2) was determined as the recommended phase II dose (RP2D) for A1. Seven DLTs in two patients in A2. The RP2D of berzosertib was 140 mg/m2 once weekly. The most common grade ≥3 treatment-related AEs were neutropenia and thrombocytopenia. No treatment-related deaths were reported.

CONCLUSIONS

Berzosertib combined with RT is feasible and well tolerated in oesophageal cancer patients at high palliative doses. Berzosertib with cisplatin and capecitabine was well tolerated in advanced cancer. Further investigation is warranted in a phase 2 setting.

CLINICAL TRIALS IDENTIFIER

EU Clinical Trials Register (EudraCT) - 2015-003965-27 ClinicalTrials.gov - NCT03641547.

Patient-Specific 3D CT Images Reconstruction from 2D KV Images Via Vision Transformer-Based Deep-Learning

PURPOSE/OBJECTIVE(S)

In some proton therapy facilities, patient alignment relies on two 2D orthogonal kV images, taken at fixed, oblique angles, as no 3D on-the-bed-imaging is available. The visibility of the tumor in kV images is limited since the patient's 3D anatomy is projected onto a 2D plane, especially when the tumor is behind a high-density structure such as bone. This can lead to a large patient setup error. A solution to this problem is to reconstruct the 3D CT image from the kV images obtained in the treatment position.

MATERIALS/METHODS

An asymmetric autoencoder-like network built with vision-transformer blocks was developed. The data was collected from a head and neck patient: 2 orthogonal kV images (1024X1024 voxels), 1 3D CT with padding (512X512X512) acquired from the in-room CT-on-rails before kVs were taken and 2 digitally-reconstructed-radiograph (DRR) images (512X512) based on the CT. We resampled kV images every 8 voxels and DRR and CT every 4 voxels, thus formed a dataset consisting of 262,144 samples, in which the images had a dimension of 128 for each direction. The value of each voxel in CT was normalized to range 0-1 with a uniform shift of 1000 and a denominator of 4000. For kV and DRR, we ranked all voxels value in an ascending order and normalized the values of the first 80% voxels to range 0-0.8 and the rest to range 0.8-1, thus yielding a quasi-Gaussian distribution, which was favorable by the deep neural networks. We further cropped kV and DRR images with a self-supervised bitmap based on the voxels' gradients. In training, both kV and DRR were utilized, and the encoder was encouraged to learn the same feature maps for kV images and its corresponding DRR images with mean-absolute-error (MAE) as the similarity loss. Then the decoder would reconstruct the 3D CT image from the feature maps of the kV images with the CT-on-rails as ground-truth (gCT) and MAE as the reconstruction loss. In testing, only independent kV images were used. The full-size synthetic CT (sCT) was achieved by concatenating the sCTs generated by the model according to their spatial information. The image quality of the sCT was evaluated using MAE and per-voxel-absolute-CT-number-difference volume histogram (CDVH). The proposed network was implemented with PyTorch deep learning library and both distributed data parallel (DDP) and automatic mixed precision (AMP) were applied to saving memory and accelerating the training speed. We used the AdamW optimizer with β1 = 0.9 and β2 = 0.999 and a cosine annealing learning rate scheduler with an initial learning of 1e-7 and 20 warm-up epochs.

RESULTS

The model achieved a MAE of <40HU and the CDVH showed that <5% of the voxels had a per-voxel-absolute-CT-number-difference larger than 185HU. The profile of a typical gCT slice and its corresponding sCT slice exhibited a high agreement, indicating the high similarity between the gCT and sCT.

CONCLUSION

A patient-specific vision-transformer-based network was developed and shown to be accurate and efficient to reconstruct 3D CT images from kV images.

Evaluating the effects of minimum unit pricing in Scotland on the prevalence of harmful drinking: a controlled interrupted time series analysis

OBJECTIVES

In May 2018, the Scottish Government introduced a minimum unit price (MUP) for alcohol of £0.50 (1 UK unit = 8 g ethanol) to reduce alcohol consumption, particularly among people drinking at harmful levels. This study aimed to evaluate MUP's impact on the prevalence of harmful drinking among adults in Scotland.

STUDY DESIGN

This was a controlled interrupted monthly time series analysis of repeat cross-sectional data collected via 1-week drinking diaries from adult drinkers in Scotland (N = 38,674) and Northern England (N = 71,687) between January 2009 and February 2020.

METHODS

The primary outcome was the proportion of drinkers consuming at harmful levels (>50 [men] or >35 [women] units in diary week). The secondary outcomes included the proportion of drinkers consuming at hazardous (≥14-50 [men] or ≥14-35 [women] units) and moderate (<14 units) levels and measures of beverage preferences and drinking patterns. Analyses also examined the prevalence of harmful drinking in key subgroups.

RESULTS

There was no significant change in the proportion of drinkers consuming at harmful levels (β = +0.6 percentage points; 95% confidence interval [CI] = -1.1, +2.3) or moderate levels (β = +1.4 percentage points; 95% confidence interval = -1.1, +3.8) after the introduction of MUP. The proportion consuming at hazardous levels fell significantly by 3.5 percentage points (95% CI = -5.4, -1.7). There were no significant changes in other secondary outcomes or in the subgroup analyses after correction for multiple testing.

CONCLUSIONS

Introducing MUP in Scotland was not associated with reductions in the proportion of drinkers consuming at harmful levels but did reduce the prevalence of hazardous drinking. This adds to previous evidence that MUP reduced overall alcohol consumption in Scotland and consumption among those drinking above moderate levels.

DrugCentral 2023 extends human clinical data and integrates veterinary drugs

DrugCentral monitors new drug approvals and standardizes drug information. The current update contains 285 drugs (131 for human use). New additions include: (i) the integration of veterinary drugs (154 for animal use only), (ii) the addition of 66 documented off-label uses and iii) the identification of adverse drug events from pharmacovigilance data for pediatric and geriatric patients. Additional enhancements include chemical substructure searching using SMILES and 'Target Cards' based on UniProt accession codes. Statistics of interests include the following: (i) 60% of the covered drugs are on-market drugs with expired patent and exclusivity coverage, 17% are off-market, and 23% are on-market drugs with active patents and exclusivity coverage; (ii) 59% of the drugs are oral, 33% are parenteral and 18% topical, at the level of the active ingredients; (iii) only 3% of all drugs are for animal use only; however, 61% of the veterinary drugs are also approved for human use; (iv) dogs, cats and horses are by far the most represented target species for veterinary drugs; (v) the physicochemical property profile of animal drugs is very similar to that of human drugs. Use cases include azaperone, the only sedative approved for swine, and ruxolitinib, a Janus kinase inhibitor.

Pharos 2023: an integrated resource for the understudied human proteome

The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for fusers to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.

Care navigation increases initiation of hepatitis C treatment following release from prison in a prospective randomised controlled trial: The C-LINK Study

Background

Prison-based hepatitis C treatment is safe and effective; however, many individuals are released untreated due to time or resource constraints. On community re-entry, individuals face a number of immediate competing priorities, and in this context, linkage to hepatitis C care is low. Interventions targeted at improving healthcare continuity after prison release have yielded positive outcomes for other health diagnoses; however, data regarding hepatitis C transitional care are limited.

Methods

We conducted a prospective randomized controlled trial comparing a hepatitis C care navigator intervention with standard of care for individuals released from prison with untreated hepatitis C infection. The primary outcome was prescription of hepatitis C direct-acting antivirals (DAA) within 6 months of release.

Results

Forty-six participants were randomized. The median age was 36 years and 59% were male. Ninety percent (n = 36 of 40) had injected drugs within 6 months before incarceration. Twenty-two were randomized to care navigation and 24 were randomized to standard of care. Individuals randomized to the intervention were more likely to commence hepatitis C DAAs within 6 months of release (73%, n = 16 of 22 vs 33% n = 8 of 24, P < .01), and the median time between re-entry and DAA prescription was significantly shorter (21 days [interquartile range {IQR}, 11–42] vs 82 days [IQR, 44–99], P = .049).

Conclusions

Care navigation increased hepatitis C treatment uptake among untreated individuals released from prison. Public policy should support similar models of care to promote treatment in this high-risk population. Such an approach will help achieve hepatitis C elimination as a public health threat.

Management of false passage complication during operative hysteroscopy

Background

False passage is a possible complication during operative hysteroscopy and can lead to termination of the intended procedure. The aim of this study is to describe two techniques to overcome the complication of false passage during operative hysteroscopy.

Results

This is a retrospective case series of 9 patients who had a false passage during operative hysteroscopy for Müllerian anomaly or endometrial polyps. The diagnosis was immediately made by visualization of a lattice network of myometrial fibers without normal landmarks of the endometrial cavity and tubal ostia. Once a false passage was suspected, an attempt was made to overcome this complication and complete the intended operative hysteroscopy. The hysteroscope was slowly withdrawn to identify both the false passage and the opening towards the internal cervical os. The hysteroscope was tilted towards the opening to the internal cervical os, and it was carefully advanced under direct vision into the endometrial cavity. In two patients, this technique failed because the opening to the internal cervical os was small, so the bridge of tissue between the internal os and false passage was partially divided using hysteroscopic scissors or a straight resectoscope loop, allowing for entry into the endometrial cavity. The intended procedures were completed successfully in all patients. No intraoperative or postoperative complications occurred as a result of the two techniques.

Conclusions

The techniques described in this study, to overcome false passage during operative hysteroscopy, appear to be safe, effective, and easy to perform. They enable the surgeon to complete the intended procedure.

Getting Started with the IDG KMC Datasets and Tools

The Illuminating the Druggable Genome (IDG) consortium is a National Institutes of Health (NIH) Common Fund program designed to enhance our knowledge of under-studied proteins, more specifically, proteins unannotated within the three most commonly drug-targeted protein families: G-protein coupled receptors, ion channels, and protein kinases. Since 2014, the IDG Knowledge Management Center (IDG-KMC) has generated several open-access datasets and resources that jointly serve as a highly translational machine-learning-ready knowledgebase focused on human protein-coding genes and their products. The goal of the IDG-KMC is to develop comprehensive integrated knowledge for the druggable genome to illuminate the uncharacterized or poorly annotated portion of the druggable genome. The tools derived from the IDG-KMC provide either user-friendly visualizations or ways to impute the knowledge about potential targets using machine learning strategies. In the following protocols, we describe how to use each web-based tool to accelerate illumination in under-studied proteins. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Interacting with the Pharos user interface Basic Protocol 2: Accessing the data in Harmonizome Basic Protocol 3: The ARCHS4 resource Basic Protocol 4: Making predictions about gene function with PrismExp Basic Protocol 5: Using Geneshot to illuminate knowledge about under-studied targets Basic Protocol 6: Exploring under-studied targets with TIN-X Basic Protocol 7: Interacting with the DrugCentral user interface Basic Protocol 8: Estimating Anti-SARS-CoV-2 activities with DrugCentral REDIAL-2020 Basic Protocol 9: Drug Set Enrichment Analysis using Drugmonizome Basic Protocol 10: The Drugmonizome-ML Appyter Basic Protocol 11: The Harmonizome-ML Appyter Basic Protocol 12: GWAS target illumination with TIGA Basic Protocol 13: Prioritizing kinases for lists of proteins and phosphoproteins with KEA3 Basic Protocol 14: Converting PubMed searches to drug sets with the DrugShot Appyter.

DrugCentral 2021 supports drug discovery and repositioning

DrugCentral is a public resource (http://drugcentral.org) that serves the scientific community by providing up-to-date drug information, as described in previous papers. The current release includes 109 newly approved (October 2018 through March 2020) active pharmaceutical ingredients in the US, Europe, Japan and other countries; and two molecular entities (e.g. mefuparib) of interest for COVID19. New additions include a set of pharmacokinetic properties for ∼1000 drugs, and a sex-based separation of side effects, processed from FAERS (FDA Adverse Event Reporting System); as well as a drug repositioning prioritization scheme based on the market availability and intellectual property rights forFDA approved drugs. In the context of the COVID19 pandemic, we also incorporated REDIAL-2020, a machine learning platform that estimates anti-SARS-CoV-2 activities, as well as the 'drugs in news' feature offers a brief enumeration of the most interesting drugs at the present moment. The full database dump and data files are available for download from the DrugCentral web portal.

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.

Dynamic optical coherence tomography shows characteristic alterations of blood vessels in malignant melanoma

BACKGROUND

Dynamic optical coherence tomography (D-OCT) allows in vivo visualization of blood vessels in the skin and in malignant tumours. Vessel patterns in malignant melanoma may be associated with tumour stage.

OBJECTIVE

The aim of this study was to describe blood vessel patterns in melanomas and to correlate them with stage.

METHODS

One hundred fifty-nine malignant melanomas were assessed in a multicentre study. Every tumour was imaged using D-OCT prior to surgery and histologic evaluation. The tumour data such as thickness and ulceration as well as the staging at primary diagnosis and a follow-up of at least 40 months resulted in a stage classification. The vessel patterns were assessed according to predefined categories, compared with healthy adjacent skin, and correlated to stage.

RESULTS

Melanomas contained more blood vessels in different patterns compared with healthy adjacent skin. In particular, irregular vascular shapes such as blobs, coils, curves and serpiginous vessels were more common in melanomas. In addition, these patterns were significantly more often found in high-risk and metastatic melanomas than in low-risk lesions.

CONCLUSION

In melanomas, the density of the blood vessels is increased, and irregular vascular patterns are more frequent. At higher stages, especially in metastatic melanomas, these atypical vessels are significantly more common.

REDIAL-2020: A suite of machine learning models to estimate Anti-SARS-CoV-2 activities

Strategies for drug discovery and repositioning are an urgent need with respect to COVID-19. We developed "REDIAL-2020", a suite of machine learning models for estimating small molecule activity from molecular structure, for a range of SARS-CoV-2 related assays. Each classifier is based on three distinct types of descriptors (fingerprint, physicochemical, and pharmacophore) for parallel model development. These models were trained using high throughput screening data from the NCATS COVID19 portal (https://opendata.ncats.nih.gov/covid19/index.html), with multiple categorical machine learning algorithms. The "best models" are combined in an ensemble consensus predictor that outperforms single models where external validation is available. This suite of machine learning models is available through the DrugCentral web portal (http://drugcentral.org/Redial). Acceptable input formats are: drug name, PubChem CID, or SMILES; the output is an estimate of anti-SARS-CoV-2 activities. The web application reports estimated activity across three areas (viral entry, viral replication, and live virus infectivity) spanning six independent models, followed by a similarity search that displays the most similar molecules to the query among experimentally determined data. The ML models have 60% to 74% external predictivity, based on three separate datasets. Complementing the NCATS COVID19 portal, REDIAL-2020 can serve as a rapid online tool for identifying active molecules for COVID-19 treatment. The source code and specific models are available through Github (https://github.com/sirimullalab/redial-2020), or via Docker Hub (https://hub.docker.com/r/sirimullalab/redial-2020) for users preferring a containerized version.

Interdisciplinary working in public health research: a proposed good practice checklist

Background

Guidance on how different disciplines from the natural, behavioural and social sciences can collaborate to resolve complex public health problems is lacking. This article presents a checklist to support researchers and principle investigators to develop and implement interdisciplinary collaborations.

Methods

Fourteen individuals, representing 10 disciplines, participated in in-depth interviews to explore the strengths and challenges of working together on an interdisciplinary project to identify the determinants of substance use and gambling disorders, and to make recommendations for future interdisciplinary teams. Data were analysed thematically and a checklist was derived from insights offered by participants during interview and discussion among the authors on the implications of findings.

Results

Participants identified 18 scientific, interactional and structural strengths and challenges of interdisciplinary research. These findings were used to develop an 18-item BASICS checklist to support future interdisciplinary collaborations. The five domains of the checklist are: (i) Blueprint, (ii) Attitudes, (iii) Staffing, (iv) Interactions and (v) Core Science.

Conclusion

Interdisciplinary work has the potential to advance public health science but the numerous challenges should not be underestimated. Use of a checklist, such as BASICS, when planning and managing projects may help future collaborations to avoid some of the common pitfalls of interdisciplinary research.

Cardiovascular and renal outcomes following percutaneous coronary intervention in a population with renal disease: a case-control study

BACKGROUND

Patients with renal disease are less likely to undergo percutaneous coronary intervention (PCI) due to concerns about poor outcomes.

AIM

We describe outcomes following PCI in individuals with chronic kidney disease (CKD), as compared with matched controls with comparable CKD who did not undergo PCI. We also identified factors predictive of poor outcomes following PCI amongst patients with CKD.

DESIGN

Retrospective observational case-control study.

METHODS

Cases were individuals with CKD (stages 1-5) undergoing PCI between 2008 and 2014. Controls were age, gender and creatinine-matched individuals not requiring PCI. We compared mortality between groups using Kaplan-Meier curves and Cox regression modelling. We assessed changes in serum creatinine using Wilcoxon Rank testing. We explored the relationship between biochemical and haematological measures (baseline creatinine, calcium, phosphate, calcium-phosphate product, parathyroid hormone, white cell count, haemoglobin, platelet count, c-reactive protein and total cholesterol) and post-PCI mortality, using logistic regression.

RESULTS

We identified 144 cases and 144 controls. Mortality was significantly lower amongst cases compared with controls [hazard ratio 0.46 (95% confidence intervals 0.31, 0.69)]. PCI did not result in a significant change in renal function (P=0.52). Amongst cases, serum creatinine and calcium-phosphate product were predictors of mortality following PCI.

CONCLUSION

Cases undergoing PCI had lower mortality, and PCI was not associated with accelerated CKD progression. On this data, PCI should not be deferred as a treatment option in patients with CKD. Serum creatinine and calcium-phosphate product predict mortality following PCI in this cohort, and may be useful in risk-stratifying patients with CKD being considered for PCI.

DrugCentral 2018: an update

DrugCentral is a drug information resource (http://drugcentral.org) open to the public since 2016 and previously described in the 2017 Nucleic Acids Research Database issue. Since the 2016 release, 103 new approved drugs were updated. The following new data sources have been included: Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS), FDA Orange Book information, L1000 gene perturbation profile distance/similarity matrices and estimated protonation constants. New and existing entries have been updated with the latest information from scientific literature, drug labels and external databases. The web interface has been updated to display and query new data. The full database dump and data files are available for download from the DrugCentral website.

The influence of socioeconomic status on presentation and outcome of acute kidney injury

AIM

Although socioeconomic background is known to impact on the incidence and progression of chronic kidney disease, its influence of on the presentation and outcome for acute kidney injury is not known and is the subject of this study.

DESIGN

The Welsh National electronic AKI reporting system was used to identify all cases of AKI in patients >18 years of age between March 2015 and November 2017.

METHODS

Socioeconomic classification of patients was derived from the Welsh Index Multiple Deprivation score (WIMD). Patients were grouped according to the WIMD score by their postcode, and the ranked data were categorized into percentiles and correlated with incidence and measures of AKI severity and outcome.

RESULTS

Date was collected on a total of 57 654 patients. Increased deprivation was associated with higher AKI incidence rates, more episodes of AKI per patient and more severe AKI at presentation. In contrast 90-day mortality was highest in the most affluent areas. Mortality in affluent areas was driven by increased patient age. Corrected for age 90-day mortality was higher in areas of increased deprivation.

CONCLUSION

This study highlights that AKI incidence presentation and outcomes are adversely affected by social deprivation. Further studies are required to understand the extent to which these differences reflect patient related factors or regional differences in provision and access to care.

Single arm two-stage studies: Improved designs for molecularly targeted agents

Mechanistic understanding of cancers and their potential interactions with molecularly targeted agents is driving the need for stratified medicine to ensure each participant receives the best possible care. This understanding, backed by scientific research, should be used to guide the design of clinical trials for these agents. The mechanism of action of a molecularly targeted agent often suggests that a biomarker can be used as a predictor of activity of the agent on the targeted disease. A biomarker driven trial is needed to confirm that the molecularly targeted agent stratifies the participant population with disease into high and low responder groups. We assume that the biomarker of interest can be dichotomised and propose a balanced parallel two-stage single-arm phase II trial that builds on existing two-stage single-arm designs. A single-arm trial cannot distinguish between a marker being predictive in the population as a whole and the agent causing an increased response in the marker positive group, but it is a first step. We compare this approach to the existing single-arm approaches, sequential enrichment, tandem two-stage, and parallel two-stage designs, and discuss the advantages and disadvantages of each design. We show that our design compares favourably to existing designs in the Bayesian framework, making a more efficient use of collected data. We recommend using the parallel two-stage balanced or sequential enrichment designs when randomisation is not practical in a phase II trial.

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.

Adding a new dimension to the weekend effect: an analysis of a national data set of electronic AKI alerts

BACKGROUND

Increased mortality related to differences in delivery of weekend clinical care is the subject of much debate.

AIM

We compared mortality following detection of acute kidney injury (AKI) on week and weekend days across community and hospital settings.

DESIGN

A prospective national cohort study, with AKI identified using the Welsh National electronic AKI reporting system.

METHODS

Data were collected on outcome for all cases of adult AKI in Wales between 1 November 2013 and 31 January 2017.

RESULTS

There were a total of 107 298 episodes. Weekday detection of AKI was associated with 28.8% (26 439); 90-day mortality compared to 90-day mortality of 31.9% (4551) for AKI detected on weekdays (RR: 1.11, 95% CI: 1.08-1.14, P < 0.001, HR: 1.16 95% CI: 1.12-1.20, P < 0.001). There was no 'weekend effect' for mortality associated with hospital-acquired AKI. Weekday detection of community-acquired AKI (CA-AKI) was associated with a 22.6% (10 356) mortality compared with weekend detection of CA-AKI, which was associated with a 28.6% (1619) mortality (RR: 1.26, 95% CI: 1.21-1.32, P < 0.001, HR: 1.34, 95%CI: 1.28-1.42, P < 0.001). The excess mortality in weekend CA-AKI was driven by CA-AKI detected at the weekend that was not admitted to hospital compared with CA-AKI detected on weekdays which was admitted to hospital (34.5% vs. 19.1%, RR: 1.8, 95% CI: 1.69-1.91, P < 0.001, HR: 2.03, 95% CI: 1.88-2.19, P < 0.001).

CONCLUSION

'Weekend effect' in AKI relates to access to in-patient care for patients presenting predominantly to hospital emergency departments with AKI at the weekend.

Unexplored therapeutic opportunities in the human genome

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

Dependence of Retinopathy (and other Complications) on Glycaemic Control and on Weight over 5/10 Years from Diagnosis of Type II Diabetes

Glycosylated haemoglobins and weights were recorded for 200 consecutive diabetic clinic attendere seen yearly for 5 years, 76 of whom were also seen up to 10 years from diagnosis of type 2 diabetes, representing 1380 patient years. Weight fluctuation (≥3 kg) was associated with increased final prevalence of hypertension, macroalbuminaemia and a raised creatinine (P≤ 0.002) but this relationship was abolished by correction for higher initial weight. Average giycaemia over 5/10 years [itself related to initial weight in women on tablets (N=53) but not others, and to waist but not waist/hip ratio], correlated with prevalence and severity of retinopathy (N=200; r=0.38, P≤0.0006) seen also in the subgroup of patients on tablets (N=145, P≤0.006). At HbA1 levels ≥10.5% an increased prevelance of retinopathy was seen in those on insulin (W=37, P≤0.001) and an increased prevalence of peripheral vascular disease was seen in men but not women (x2=2.87, P≤0.01) as well as in the prevalence of neuropathy. These findings suggest that good glycaemic control is of value in type 2 diabetes and less easily achieved in obesity.

Formalizing drug indications on the road to therapeutic intent

Therapeutic intent, the reason behind the choice of a therapy and the context in which a given approach should be used, is an important aspect of medical practice. There are unmet needs with respect to current electronic mapping of drug indications. For example, the active ingredient sildenafil has 2 distinct indications, which differ solely on dosage strength. In progressing toward a practice of precision medicine, there is a need to capture and structure therapeutic intent for computational reuse, thus enabling more sophisticated decision-support tools and a possible mechanism for computer-aided drug repurposing. The indications for drugs, such as those expressed in the Structured Product Labels approved by the US Food and Drug Administration, appears to be a tractable area for developing an application ontology of therapeutic intent.

Community acquired acute kidney injury: findings from a large population cohort

BACKGROUND

The extent of patient contact with medical services prior to development of community acquired-acute kidney injury (CA-AKI)is unknown.

AIM

We examined the relationship between incident CA-AKI alerts, previous contact with hospital or primary care and clinical outcomes.

DESIGN

A prospective national cohort study of all electronic AKIalerts representing adult CA-AKI.

METHODS

Data were collected for all cases of adult (≥18 years of age) CA-AKI in Wales between 1 November 2013 and 31 January 2017.

RESULTS

There were a total of 50 560 incident CA-AKI alerts. In 46.8% there was a measurement of renal function in the 30 days prior to the AKI alert. In this group, in 63.8% this was in a hospital setting, of which 37.6% were as an inpatient and 37.5% in Accident and Emergency. Progression of AKI to a higher AKI stage (13.1 vs. 9.8%, P < 0.001) (or for AKI 3 an increase of > 50% from the creatinine value generating the alert), the proportion of patients admitted to Intensive Care (5.5 vs. 4.9%, P = 0.001) and 90-day mortality (27.2 vs. 18.5%, P < 0.001) was significantly higher for patients with a recent test. 90-day mortality was highest for patients with a recent test taken in an inpatient setting prior to CA-AKI (30.9%).

CONCLUSION

Almost half of all patients presenting with CA-AKI are already known to medical services, the majority of which have had recent measurement of renal function in a hospital setting, suggesting that AKI for at least some of these may potentially be predictable and/or avoidable.

Optical coherence tomography for margin definition of basal cell carcinoma before micrographic surgery-recommendations regarding the marking and scanning technique

BACKGROUND/PURPOSE

Mohs Micrographic Surgery (MMS) is the preferred therapeutic treatment for high-risk basal cell carcinoma (BCC). Optical Coherence Tomography (OCT) is a non-invasive imaging technique that enables the diagnosis of BCC. We thought to determine the margins of BCCs with OCT, prior to MMS, to reduce the number of surgical steps.

METHODS

Different permanent markers were tested on the skin regarding line width, resistance against disinfection and brightness in the OCT image. The visible tumor margins of BCCs were defined by dermoscopy, adding a safety margin of 2 mm and labeled using the selected pen, causing a signal shadow in OCT. Scans of the center and of entire margin were performed. If parts of the BCC were visible outside the margin, another 2 mm were added and the scan was repeated until the tissue outside the labeling looked tumor free.

RESULTS

Eight out of ten BCCs were totally excised in a single stage when margin delineation was done by OCT. Macroscopic margins were enlarged after OCT scanning in four patients, saving further stages of MMS.

CONCLUSION

OCT may help to better define the microscopic dimensions of BCCs and therefore reduce the number of stages of MMS.

Acute kidney injury electronic alerts in primary care - findings from a large population cohort

BACKGROUND

Electronic reporting of AKI has been used to aid early AKI recognition although its relevance to CA-AKI and primary care has not been described.

AIMS

We described the characteristics and clinical outcomes of patients with CA-AKI, and AKI identified in primary care (PC-AKI) through AKI e-Alerts.

DESIGN

A prospective national cohort study was undertaken to collect data on all e-alerts representing adult CA-AKI.

METHOD

The study utilized the biochemistry based AKI electronic (e)-alert system that is established across the Welsh National Health Service.

RESULTS

28.8% of the 22 723 CA-AKI e-alerts were classified as PC-AKI. Ninety-day mortality was 24.0% and lower for PC-AKI vs. non-primary care (non-PC) CA-AKI. Hospitalization was 22.3% for PC-AKI and associated with greater disease severity, higher mortality, but better renal outcomes (non-recovery: 18.1% vs. 21.6%; progression of pre-existing CKD: 40.5% vs. 58.3%). 49.1% of PC-AKI had a repeat test within 7 days, 42.5% between 7 and 90 days, and 8.4% was not repeated within 90 days. There was significantly more non-recovery (24.0% vs. 17.9%) and progression of pre-existing CKD (63.3% vs. 47.0%) in patients with late repeated measurement of renal function compared to those with early repeated measurement of renal function.

CONCLUSION

The data demonstrate the clinical utility of AKI e-alerts in primary care. We recommend that a clinical review, or referral together with a repeat measurement of renal function within 7 days should be considered an appropriate response to AKI e-alerts in primary care.

Proceedings of the 12th International Conference on Rapid Response Systems and Medical Emergency Teams

Rapid Response Teams (RRTs) have been introduced into hospitals worldwide in an effort to improve the outcomes of deteriorating hospitalised patients. Recently, there has been increased awareness of the need to develop systems other than RRTs for deteriorating patients. In May 2016, the 12th International Conference on Rapid Response Systems and Medical Emergency Teams was held in Melbourne. This represented a collaboration between the newly constituted International Society for Rapid Response Systems (iSRRS) and the Australian and New Zealand Intensive Care Society. The conference program included broad ranging presentations related to general clinical deterioration in the acute care setting, as well as deterioration in the emergency department, during pregnancy, in the paediatric setting, and deterioration in mental health status. This article briefly summarises the key features of the conference, links to presentations, and the 18 abstracts of the accepted free papers.

On Contributing to the Progress of Medical Informatics as Publisher

May 1st, 2017, will mark Dieter Bergemann's 80th birthday. As Chief Executive Officer and Owner of Schattauer Publishers from 1983 to 2016, the biomedical and health informatics community owes him a great debt of gratitude. The past and present editors of Methods of Information in Medicine, the IMIA Yearbook of Medical Informatics, and Applied Clinical Informatics want to honour and thank Dieter Bergemann by providing a brief biography that emphasizes his contributions, by reviewing his critical role as an exceptionally supportive publisher for Schattauer's three biomedical and health informatics periodicals, and by sharing some personal anecdotes. Over the past 40 years, Dieter Bergemann has been an influential, if behind-the-scenes, driving force in biomedical and health informatics publications, helping to ensure success in the dissemination of our field's research and practice.

DrugCentral: online drug compendium

DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ensures the resource is up-to-date. DrugCentral integrates content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. Its complementarity with other online resources is facilitated by cross referencing to external resources. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information. Chemical structure overlap between DrugCentral and five online drug resources, and the overlap between DrugCentral FDA-approved drugs and their presence in four different chemical collections, are discussed. DrugCentral can be accessed via the web application or downloaded in relational database format.

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.

Measurements of Daily Energy Intake and Total Energy Expenditure in People with Dementia in Care Homes: The Use of Wearable Technology

OBJECTIVE

To estimate daily total energy expenditure (TEE) using a physical activity monitor, combined with dietary assessment of energy intake to assess the relationship between daily energy expenditure and patterns of activity with energy intake in people with dementia living in care homes.

DESIGN AND SETTING

A cross-sectional study in care homes in the UK.

PARTICIPANTS

Twenty residents with confirmed dementia diagnosis were recruited from two care homes that specialised in dementia care.

MEASUREMENTS

A physical activity monitor (SensewearTM Armband, Body Media, Pittsburgh, PA) was employed to objectively determine total energy expenditure, sleep duration and physical activity. The armband was placed around the left upper triceps for up to 7 days. Energy intake was determined by weighing all food and drink items over 4 days (3 weekdays and 1 weekend day) including measurements of food wastage.

RESULTS

The mean age was 78.7 (SD ± 11.8) years, Body Mass Index (BMI) 23.0 (SD ± 4.2) kg/m2; 50% were women. Energy intake (mean 7.4; SD ± 2.6) MJ/d) was correlated with TEE (mean 7.6; SD ± 1.8 MJ/d; r=0.49, p<0.05). Duration of sleeping ranged from 0.4-12.5 (mean 6.1) hrs/d and time spent lying down was 1.3-16.0 (8.3) hrs/d. On average residents spent 17.9 (6.3-23.4) hrs/d undertaking sedentary activity. TEE was correlated with BMI (r=0.52, p<0.05) and body weight (r=0.81, p<0.001) but inversely related to sleep duration (r=-0.59, p<0.01) and time lying down (r=-0.62, p<0.01). Multiple linear regression analysis revealed that after taking BMI, sleep duration and time spent lying down into account, TEE was no longer correlated with energy intake.

CONCLUSIONS

The results show the extent to which body mass, variable activity and sleep patterns may be contributing to TEE and together with reduced energy intake, energy requirements were not satisfied. Thus wearable technology has the potential to offer real-time monitoring to provide appropriate nutrition management that is more person-centred to prevent weight loss in dementia.