Tripal EUtils: a Tripal module to increase exchange and reuse of genome assembly metadata

Data and metadata interoperability between data storage systems is a critical component of the FAIR data principles. Programmatic and consistent means of reconciling metadata models between databases promote data exchange and thus increases its access to the scientific community. This process requires (i) metadata mapping between the models and (ii) software to perform the mapping. Here, we describe our efforts to map metadata associated with genome assemblies between the National Center for Biotechnology Information (NCBI) data resources and the Chado biological database schema. We present mappings for multiple NCBI data structures and introduce a Tripal software module, Tripal EUtils, to pull metadata from NCBI into a Tripal/Chado database. We discuss potential mapping challenges and solutions and provide suggestions for future development to further increase interoperability between these platforms. Database URL: https://github.com/NAL-i5K/tripal_eutils.

Detection of thoracic vascular structures by electrical impedance tomography: a systematic assessment of prominence peak analysis of impedance changes

OBJECTIVE

Electrical impedance tomography (EIT) is a non-invasive and radiation-free bedside monitoring technology, primarily used to monitor lung function. First experimental data shows that the descending aorta can be detected at different thoracic heights and might allow the assessment of central hemodynamics, i.e. stroke volume and pulse transit time.

APPROACH

First, the feasibility of localizing small non-conductive objects within a saline phantom model was evaluated. Second, this result was utilized for the detection of the aorta by EIT in ten anesthetized pigs with comparison to thoracic computer tomography (CT). Two EIT belts were placed at different thoracic positions and a bolus of hypertonic saline (10 ml, 20%) was administered into the ascending aorta while EIT data were recorded. EIT images were reconstructed using the GREIT model, based on the individual's thoracic contours. The resulting EIT images were analyzed pixel by pixel to identify the aortic pixel, in which the bolus caused the highest transient impedance peak in time.

MAIN RESULTS

In the phantom, small objects could be located at each position with a maximal deviation of 0.71 cm. In vivo, no significant differences between the aorta position measured by EIT and the anatomical aorta location were obtained for both measurement planes if the search was restricted to the dorsal thoracic region of interest (ROIs).

SIGNIFICANCE

It is possible to detect the descending aorta at different thoracic levels by EIT using an intra-aortic bolus of hypertonic saline. No significant differences in the position of the descending aorta on EIT images compared to CT images were obtained for both EIT belts.

Influence of pre-diagnostic cigarette smoking on colorectal cancer survival: overall and by tumour molecular phenotype

BACKGROUND

Smoking is a risk factor for incident colorectal cancer (CRC); however, it is unclear about its influence on survival after CRC diagnosis.

METHODS

A cohort of 706 CRC patients diagnosed from 1999 to 2003 in Newfoundland and Labrador, Canada, was followed for mortality and recurrence until April 2010. Smoking and other relevant data were collected by questionnaire after cancer diagnosis, using a referent period of '2 years before diagnosis' to capture pre-diagnosis information. Molecular analyses of microsatellite instability (MSI) status and BRAF V600E mutation status were performed in tumour tissue using standard techniques. Multivariate hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated with Cox proportional hazards regression, controlling for major prognostic factors.

RESULTS

Compared with never smokers, all-cause mortality (overall survival, OS) was higher for current (HR: 1.78; 95% CI: 1.04-3.06), but not for former (HR: 1.06; 95% CI: 0.71-1.59) smokers. The associations of cigarette smoking with the study outcomes were higher among patients with ≥40 pack-years of smoking (OS: HR: 1.72; 95% CI: 1.03-2.85; disease-free survival (DFS: HR: 1.99; 95% CI: 1.25-3.19), those who smoked ≥30 cigarettes per day (DFS: HR: 1.80; 95% CI: 1.22-2.67), and those with microsatellite stable (MSS) or MSI-low tumours (OS: HR: 1.38; 95% CI: 1.04-1.82 and DFS: HR: 1.32; 95% CI: 1.01-1.72). Potential heterogeneity was noted for sex (DFS HR: 1.68 for men and 1.01 for women: P for heterogeneity=0.04), and age at diagnosis (OS: HR: 1.11 for patients aged <60 and 1.69 for patients aged ≥60: P for heterogeneity=0.03).

CONCLUSIONS

Pre-diagnosis cigarette smoking is associated with worsened prognosis among patients with CRC.

Perceptions of health care providers concerning patient and health care provider strategies to limit out-of-pocket costs for cancer care

Objective

We aimed to describe the perceptions of health care providers concerning patient and health care provider strategies to limit out-of-pocket costs for cancer care.

Methods

We conducted semi-structured interviews with 21 cancer care providers (nurses, social workers, oncologists, surgeons, pharmacists, and dieticians) in Newfoundland and Labrador.

Results

Patients try to minimize costs by substituting or rationing medications, choosing radical treatments, lengthening the time between follow-up appointments, choosing inpatient care, and working during treatment to minimize loss of income. Providers respond to the financial concerns of patients by helping them to access financial assistance programs, by changing chemotherapy and supportive drug prescriptions, and by shortening radiation treatment protocols. They admit patients to hospital and arrange follow-up with physicians closer to a patient’s home.

Conclusions

Out-of-pocket costs resulting from cancer care are incurred at all phases of treatment and follow-up. These costs are substantial concerns for some patients and their health care providers. Encouraging communication between patients and their providers is needed to identify individuals at risk and to safely modify care plans. Tele-oncology and public drug, medical travel, and leave programs are needed to ensure that patients are better able to afford the costs related to cancer care.