xml2jupyter: Mapping parameters between XML and Jupyter widgets.

Jupyter Notebooks (Kluyver et al., 2016, Perkel (2018)) provide executable documents (in a variety of programming languages) that can be run in a web browser. When a notebook contains graphical widgets, it becomes an easy-to-use graphical user interface (GUI). Many scientific simulation packages use text-based configuration files to provide parameter values and run at the command line without a graphical interface. Manually editing these files to explore how different values affect a simulation can be burdensome for technical users, and impossible to use for those with other scientific backgrounds. xml2jupyter is a Python package that addresses these scientific bottlenecks. It provides a mapping between configuration files, formatted in the Extensible Markup Language (XML), and Jupyter widgets. Widgets are automatically generated from the XML file and these can, optionally, be incorporated into a larger GUI for a simulation package, and optionally hosted on cloud resources. Users modify parameter values via the widgets, and the values are written to the XML configuration file which is input to the simulation's command-line interface. xml2jupyter has been tested using PhysiCell (Ghaffarizadeh, Heiland, Friedman, Mumenthaler, & Macklin, 2018), an open source, agent-based simulator for biology, and it is being used by students for classroom and research projects. In addition, we use xml2jupyter to help create Jupyter GUIs for PhysiCell-related applications running on nanoHUB (Madhavan et al., 2013).

Epidemiology of contemporary seroincident HIV infection in the Navy and Marine corps.

Human Immunodeficiency Virus (HIV) infection continues at a steady rate among U.S. Sailors and Marines. This study provides the first service-specific description of HIV infection demographics. All Sailors and Marines identified as HIV infected between January 2005 and August 2010 were included. The project compared personnel and epidemiologic data, and tested reposed sera in the Department of Defense Serum Repository. This group comprised 410 Sailors and 86 Marines, predominantly men. HIV infected Marines were more likely to be foreign born than their Navy counterparts, 42% versus 10%, p < 0.001. Approximately half of the patients had deployed including to the wars in Iraq or Afghanistan. Nearly half of each group was infected by the age of 25. Similar to the U.S. epidemic, Black race was over-represented. Unlike national rates, Hispanic Sailors and Marines were not over-represented. Demographics were distinct for those of specific occupational specialties. Certain ship classes carried lower incidences. Clustering of HIV infection risk occurred around deployment. The Navy and Marine Corps have different patterns of HIV infection, which may merit distinct approaches to prevention. The Navy may have unique targets for prevention efforts to include pipeline training and first assignment as well as particular occupational environments.

A closed-loop reduced oxygen breathing device for inducing hypoxia in humans.

BACKGROUND: Hypoxia poses a documented threat to aerospace and diving operations in healthy people and is a component of many clinical conditions. Practical training for aircrew, and research on clinically relevant hypoxic conditions frequently rely exclusively on large, expensive hypobaric chambers. PURPOSE: Here we describe and report the efficacy of a compact, economical, closed-loop rebreather-type reduced-oxygen breathing device (ROBD) for hypoxia induction in humans. METHODS: Subjects were four healthy student Naval flight surgeons. During baseline, subjects breathed normoxic air (21% O2, equivalent to sea-level). Baseline was followed by an altitude period, during which participants were exposed to hypoxic air (about 10% O2, approximating 5,486 m [18,000 ft mean sea-level]) for 30 min followed by a normoxic recovery period. Subjects' peripheral arterial oxygen saturation (SpO2), BP, impedance cardiography, cardiac output, and systemic vascular resistance served as dependent measures along with the fraction of inspired oxygen (FiO2). RESULTS: Circuit FiO2 and subjects' SpO2 were significantly lower during the altitude period than the baseline and recovery periods. HR and cardiac output were significantly higher, and systemic vascular resistance was significantly lower, during hypoxic air exposure than during baseline or recovery. CONCLUSIONS: These data support the closed-loop ROBD as a potentially useful device for training and research involving acute hypoxia in healthy and clinical populations.

Optic neuropathy following an altitude exposure.

This case report describes a 20-yr-old man who presented with retro-orbital pain and blurred vision in his left eye 3 wk after an altitude exposure in a hypobaric chamber. He was found to have significant deficits in color vision and visual fields consistent with an optic neuropathy in his left eye. The patient was diagnosed with decompression sickness and treated with hyperbaric oxygen with a U.S. Navy Treatment Table VI. All signs and symptoms resolved with a single hyperbaric oxygen treatment but recurred. A head MRI revealed a left frontoethmoid sinus opacity. A concomitant sinusitis was diagnosed. The patient had full resolution of symptoms after a total of four hyperbaric oxygen treatments and antibiotic therapy at 6-wk follow-up. Although a para-infectious etiology for this patient's optic neuropathy cannot be excluded, his history of altitude exposure and significant, rapid response to hyperbaric oxygen treatment strongly implies decompression sickness in this case.