epiDonate - distributed serverless data infrastructure for epidemiological studies.

Motivation: Epidemiological studies face two important challenges: the need to ingest ever more complex data types, and mounting concerns about participant privacy and data governance. These two challenges are compounded by the expectation that data infrastructure will eventually need to facilitate cross-registration of participants by multiple epidemiological studies. Implementation: The portable web-service epiDonate was developed using the serverless model known as FaaS (Function-as-a-Service). The reference implementation uses nodejs. The implementation relies on a simple tokenization scheme, mediated by a public API, that a) distinguishes admin from participant roles, with b) extensible permission configuration operating a read/write structure. General Features: The critical design feature of epiDonate is the absence of business logic on the server-side (the web service). The simplicity removes the need to customize virtual machines and enables ecosystems of multiple web Applications backed by one or more data donation deployments. Availability: https://episphere.github.io/donate.

Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API.

The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers. The GDC is (i) a data repository for downloading data that have been submitted to it, and also a system that (ii) applies a common set of bioinformatics pipelines to submitted data; (iii) reanalyzes existing data when new pipelines are developed; and (iv) allows users to build their own applications and systems that interoperate with the GDC using the GDC Application Programming Interface (API). We describe the GDC API and how it has been used both by the GDC itself and by third parties. Cancer Res; 77(21); e15-18. ©2017 AACR.

Core Clinical Data Elements for Cancer Genomic Repositories: A Multi-stakeholder Consensus.

The Center for Medical Technology Policy and the Molecular Evidence Development Consortium gathered a diverse group of more than 50 stakeholders to develop consensus on a core set of data elements and values essential to understanding the clinical utility of molecularly targeted therapies in oncology.

A suspected case of autoinduction of voriconazole metabolism in a patient with cerebral aspergillosis.

OBJECTIVE: This study aims to report a case of accelerated metabolism of voriconazole in a patient with cerebral aspergillosis. CASE SUMMARY: A 36-year-old woman developed cerebral aspergillosis after immunosuppressive treatment for suspected atypical hemolytic uremic syndrome/thrombotic thrombocytopenic purpura. She was treated with voriconazole using therapeutic drug monitoring to guide dosing. After an initial high level, her dose was reduced, but over the following weeks, she required several dose increases in order to achieve a voriconazole level within the target range. The patient's dose requirements eventually stabilized at 700 mg twice daily. Cimetidine and omeprazole were added in an effort to inhibit the metabolism of voriconazole. DISCUSSION: The metabolism of voriconazole is known to be highly variable among different patients depending on pharmacogenetic factors; however, an increasing rate of voriconazole metabolism in a single patient over time is not well recognized. Therapeutic drug monitoring of voriconazole in this case facilitated the use of large doses while controlling for toxicity. CONCLUSION: This case is further evidence of autoinduction in voriconazole metabolism. Therapeutic drug monitoring of voriconazole is useful in detecting variation in a patient's metabolism of voriconazole over time.

The use of lithium as a marker for the retention of liquids in the oral cavity after rinsing.

OBJECTIVE: The aim of this study was to validate the use of lithium as a marker to indicate the retention of simple liquids in the oral cavity and use this to determine how much liquid is retained in the oral cavity following 30 s of rinsing. MATERIALS AND METHODS: This is a validation study in which saliva was spiked with known concentrations of lithium. Twenty healthy participants then rinsed their mouths with either water or a 1 % w/v carboxymethylcellulose (CMC) solution for 30 s before expectorating into a collection cup. Total volume and concentration of lithium in the expectorant were then measured, and the percentage of liquid retained was calculated. RESULTS: The mean amount of liquid retained was 10.4 ± 4.7 % following rinsing with water and 15.3 ± 4.1 % following rinsing with 1 % w/v CMC solution. This difference was significant (p < 0.01). CONCLUSIONS: Lithium was useful as a marker for the retention of liquids in the oral cavity, and a value for the amount of water and 1 % w/v CMC solution remaining in the oral cavity following a 30-s rinse was established. CLINICAL RELEVANCE: The present study quantifies the retention of simple fluids in the oral cavity, validating a technique that may be applied to more complex fluids such as mouth rinses. Further, the application of this method to specific population groups such as those with severe xerostomia may assist in developing effective saliva substitutes.

Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes.

Candida albicans is a major opportunistic pathogen of humans. Previous work has demonstrated the existence of a general-purpose genotype (GPG; equivalent to clade 1 as defined by multi-locus sequence typing data) that is more frequent than other genotypes as an agent of human disease and commensal colonization. We undertook a genomic screen which indicated that a large number of mutations differentiate GPG strains from other strains and that such mutations are scattered throughout the genome. GPG-specific mutations are non-synonymous more frequently than expected by chance, and are not randomly distributed across functional and structural gene categories. Our analysis has identified three categories of genes in which GPG-specific mutations are over-represented, namely genes for which expression changes during the yeast-hyphal transition, genes for which expression changes as a result of exposure to antifungal agents and repeat-containing ORFs. Although we have no direct evidence that the individual polymorphisms identified confer selective advantages to GPG strains, the results support our contention that the high prevalence of GPG strains is not merely due to genetic drift but that GPG strains have reached a high prevalence because they possess a multitude of fitness-enhancing traits. They also indicate that the distribution of genes marked by GPG-specific mutations across functional and structural categories could identify physiological traits that are of particular importance to the success of GPG strains in their interactions with the human host.

Testicular lipomatosis in Cowden's syndrome.

Cowden's syndrome is either familial or sporadic and is associated with the predominantly postpubertal development of a variety of cutaneous, stromal and visceral neoplasms. The syndrome is associated with mutations of the PTEN gene and is closely related to Bannayan's syndrome in which macrocephaly and benign tumors, especially lipomas and hemangiomas are pathognomic. In PTEN knockout mice testicular tumors have been reported and for this reason we felt it prudent to examine the testes of our patients with genetically proven Cowden's syndrome. Seven of eight patients who underwent testicular ultrasound were found to have diffuse bilateral hyperechoic lesions. Four patients consented to testicular biopsy and on histological examination multiple foci of adipocytes were found within the testicular interstitium, with no evidence of dysplasia or preclinical malignancy. Immunohistochemical assessment of adipocytes suggested a stromal derivation without evidence of metaplasia from Leydig cells. In one case there was focal atrophy of seminiferous tubules, while in two others there was nodular periorchitis of the tunica albuginea. Biochemical evaluation of testicular function (luteinizing hormone, follicle-stimulating hormone, testosterone, sex hormone binding globulin and free androgen index), prostate-specific antigen and testicular tumor markers were normal, while seminal fluid analysis showed only minor abnormalities. The high incidence of testicular lipomatosis in our adult subjects suggests this to be an important diagnostic criterion for Cowden's syndrome.

An association between oral lichen planus and a persistently dry mouth.

OBJECTIVES: The aim of this study was to investigate the relationship between oral lichen planus and dry mouth by comparing xerostomia scores of individuals with oral lichen planus to those of healthy matched controls. STUDY DESIGN: Patients who had attended 1 of 2 centers for the management of oral lichen planus (n=116), along with age- and sex-matched control subjects (n=348), were sent a questionnaire. Nonresponders were invited to complete the questionnaire by telephone in lieu of mailing a reply. A standardized medical history was obtained for all subjects. RESULTS: The difference between patients with oral lichen planus and control subjects for all xerostomia questions was statistically significant. In the lichen planus group, the mean xerostomia score was 20.4, whereas for control patients, the mean score was 14.7 (P <.001). Stepwise conditional logistic regression analysis for the matched case-control groups was performed. CONCLUSION: The results demonstrate an association between oral lichen planus and xerostomia in some individuals.