Ten simple rules for writing Dockerfiles for reproducible data science.

Computational science has been greatly improved by the use of containers for packaging software and data dependencies. In a scholarly context, the main drivers for using these containers are transparency and support of reproducibility; in turn, a workflow's reproducibility can be greatly affected by the choices that are made with respect to building containers. In many cases, the build process for the container's image is created from instructions provided in a Dockerfile format. In support of this approach, we present a set of rules to help researchers write understandable Dockerfiles for typical data science workflows. By following the rules in this article, researchers can create containers suitable for sharing with fellow scientists, for including in scholarly communication such as education or scientific papers, and for effective and sustainable personal workflows.

Open Humans: A platform for participant-centered research and personal data exploration.

BACKGROUND: Many aspects of our lives are now digitized and connected to the internet. As a result, individuals are now creating and collecting more personal data than ever before. This offers an unprecedented chance for human-participant research ranging from the social sciences to precision medicine. With this potential wealth of data comes practical problems (e.g., how to merge data streams from various sources), as well as ethical problems (e.g., how best to balance risks and benefits when enabling personal data sharing by individuals). RESULTS: To begin to address these problems in real time, we present Open Humans, a community-based platform that enables personal data collections across data streams, giving individuals more personal data access and control of sharing authorizations, and enabling academic research as well as patient-led projects. We showcase data streams that Open Humans combines (e.g., personal genetic data, wearable activity monitors, GPS location records, and continuous glucose monitor data), along with use cases of how the data facilitate various projects. CONCLUSIONS: Open Humans highlights how a community-centric ecosystem can be used to aggregate personal data from various sources, as well as how these data can be used by academic and citizen scientists through practical, iterative approaches to sharing that strive to balance considerations with participant autonomy, inclusion, and privacy.

Surgical and anesthetic management for hepatectomy in two pediatric patients with trisomy 18, pulmonary hypertension, and hepatoblastoma.

Children with trisomy 18 are surviving longer and undergoing more aggressive life-sustaining therapy. This report describes two patients with trisomy 18 and hepatoblastoma (HB) successfully resected in the setting of significant pulmonary hypertension. Forty-four previously published cases of the association between HB and trisomy 18 are reviewed. With careful multidisciplinary preoperative planning, successful resection of HB in children with trisomy 18 who have significant pulmonary hypertension is feasible. Because HB and trisomy 18 are increasing in prevalence, the need for timely liver tumor resection in the setting of pulmonary hypertension will be more common.

Transport of extremely low birth weight neonates for persistent ductus arteriosus closure in the catheterization lab.

OBJECTIVE: The objective of this article is to describe the elements involved with transporting extremely low birth weight (ELBW) infants from referring centers to our center's neonatal intensive care unit (NICU) and then from the NICU to the catheterization lab for transcatheter closure of patent ductus arteriosus (PDA). SETTING: Several referring centers are over 300 miles away. ELBW infants are transferred in to our NICU safely for the procedure and transferred back following the procedure. A multidisciplinary team approach is necessary in order to achieve a safe transport of these fragile patients. PATIENTS: To date, we have over 12 centers referring patients that weigh <1000 g for transcatheter PDA closure (TCPC). Three of these centers are over 300 miles away. Five other centers are between 100 and 300 miles from the hospital in which we perform TCPC. INTERVENTIONS: Fixed-wing aircrafts are necessary for long-distance transfers. Various modes of mechanical ventilators including transport oscillators are built into temperature- and humidity-controlled incubators in which these infants are transported. Ambulances are used to take the patient between the airport and the hospital. Shorter distance transports are accomplished via helicopters or ambulances. Transfer from the NICU to the catheterization lab to perform TCPC is a relatively easier endeavor. OUTCOME MEASURES: Patients' body temperature, fluid balance, and hemodynamics have to be maintained throughout the transport and the procedure for best outcomes. RESULTS: There has been 100% procedural success of performing TCPC in ELBW infants with no hemodynamic compromise during transport. CONCLUSIONS: TCPC has shown promise in improving overall patient outcomes that the potential hazards associated with complex transport measures are worth it. Successful transfer to and from referring centers and to and from the catheterization lab can be accomplished safely with increasing institutional experience.

Postoperative Monitoring Following Adenotonsillectomy for Severe Obstructive Sleep Apnea.

INTRODUCTION: Patients undergoing adenotonsillectomy (T&A) for severe obstructive sleep apnea (OSA) are usually admitted for observation, and many surgeons use the intensive care unit (ICU) for observation due to the risk of postsurgical airway obstruction. Given the limited resources of the pediatric ICU (PICU), there is a push to better define the patients who require postoperative monitoring in the PICU for monitoring severe OSA. METHODS: Forty-five patients were evaluated. Patients who had cardiac or craniofacial comorbidities were excluded. Patients undergoing T&A for severe OSA were monitored in the postanesthesia care unit (PACU) postoperatively. If patients required supplemental oxygen or developed hypoxia while in the PACU within the 3-hour monitoring period, they were admitted to the PICU. RESULTS: Overall, 16 of 45 patients were admitted to the ICU for monitoring. Patients with an Apnea-Hypopnea Index (AHI) >50 or with an oxygen nadir <80% were significantly more likely to be admitted to the PICU. The mean AHI of patients admitted to the PICU was 40.5, and the mean oxygen nadir was 69.9%. Patients younger than 2 years were significantly more likely to be admitted to the PICU. CONCLUSION: Based on the data presented here and academy recommendations, not all patients with severe OSA require ICU monitoring.