BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations.

MOTIVATION: High-content imaging screens provide a cost-effective and scalable way to assess cell states across diverse experimental conditions. The analysis of the acquired microscopy images involves assembling and curating raw cellular measurements into morphological profiles suitable for testing biological hypotheses. Despite being a critical step, general-purpose and adaptable tools for morphological profiling are lacking and no solution is available for the high-performance Julia programming language. RESULTS: Here, we introduce BioProfiling.jl, an efficient end-to-end solution for compiling and filtering informative morphological profiles in Julia. The package contains all the necessary data structures to curate morphological measurements and helper functions to transform, normalize and visualize profiles. Robust statistical distances and permutation tests enable quantification of the significance of the observed changes despite the high fraction of outliers inherent to high-content screens. This package also simplifies visual artifact diagnostics, thus streamlining a bottleneck of morphological analyses. We showcase the features of the package by analyzing a chemical imaging screen, in which the morphological profiles prove to be informative about the compounds' mechanisms of action and can be conveniently integrated with the network localization of molecular targets. AVAILABILITY AND IMPLEMENTATION: The Julia package is available on GitHub: https://github.com/menchelab/BioProfiling.jl. We also provide Jupyter notebooks reproducing our analyses: https://github.com/menchelab/BioProfilingNotebooks. The data underlying this article are available from FigShare, at https://doi.org/10.6084/m9.figshare.14784678.v2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Urological In-Flight Medical Events on Commercial Airlines.

PURPOSE: In-flight medical events are rare but may cause significant distress as access to care is limited. There is a paucity of data on in-flight urological medical events. We describe urological in-flight medical emergencies and report clinical and flight outcomes. MATERIALS AND METHODS: We reviewed all in-flight urological medical emergencies between 2015 and 2017 from MedAire®, a ground based medical support center that provides remote medical advisory services to approximately 35% of commercial airline passenger traffic worldwide. Our primary end point was the incidence rates of in-flight urological medical events. We also characterized the types of in-flight medical emergencies, in-flight management and their impact on flight status. Statistical analyses included Student's t-tests, chi-square analysis and analysis of variance. RESULTS: We identified 1,368 (1%) urological in-flight medical emergencies from a total of 138,612 in-flight medical emergencies, with an incidence of 0.5 per million passengers. The most common in-flight medical emergencies were lower urinary tract symptoms (35%), urinary retention (30%) and flank pain (21%). Among in-flight medical emergencies 883 (60%) resolved in flight, 273 (28%) required on-arrival medical evaluation and 21 (1.5%) resulted in flight diversions. Of the flight diversions the majority were due to urinary retention (12, 57%) and less commonly flank pain (6, 28%) and testicular/abdominal pain (3, 15%). CONCLUSIONS: The most common causes of urological in-flight medical emergencies are lower urinary tract symptoms, urinary retention and renal colic, the majority of which resolved in flight. These data are useful for informing flight personnel and emergency kit equipment needs to minimize the impact of these events when they occur.

Pan-cancer analysis of the interplay between mutational signatures and cellular signaling.

Cancer is a multi-faceted disease with intricate relationships between mutagenic processes, alterations in cellular signaling, and the tissue microenvironment. To date, these processes have been largely studied in isolation. A systematic understanding of how they interact and influence each other is lacking. Here, we present a framework for systematically characterizing the interaction between pairs of mutational signatures and between signatures and signaling pathway alterations. We applied this framework to large-scale data from TCGA and PCAWG and identified multiple positive and negative interactions, both cross֊tissue and tissue֊specific, that provide new insights into the molecular routes observed in tumorigenesis and their respective drivers. This framework allows for a more fine-grained dissection of common and distinct etiology of mutational signatures. We further identified several interactions with both positive and negative impacts on patient survival, demonstrating their clinical relevance and potential for improving personalized cancer care.

Nephrolithiasis and Elevated Urinary Ammonium: A Matched Comparative Study.

OBJECTIVE: To describe the associations between elevated urinary ammonium and clinical characteristics of kidney stone formers. A 24-hour urine test is recommended in high-risk patients to identify urinary abnormalities and select interventions to reduce the recurrence risk. While elevations in urine ammonium may be seen in acidosis, diarrhea, high protein diets or due to pathogenic bacteria, the clinical characteristics of these patients have not been previously described. METHODS: We retrospectively identified adult patients with kidney stone disease who completed a 24-hour urine at our institution between 2006 and 2017. Patients with elevated urinary ammonium were identified (n = 121) and matched 1:1 by age and sex to controls for an overall cohort of n = 242. Differences in medical and surgical history, 24-hour urine analytes and stone composition were compared. RESULTS: Among 3625 24-hour urine studies screened, 7.1% of patients showed high urinary ammonium. In our study cohort, patients with elevated urinary ammonium also showed higher urine volume, oxalate, calcium, uric acid, sodium, chloride, and sulfate. Clinically, these patients had higher body mass index, and more often had a history of recurrent urinary tract infections, diabetes, gout, bowel resection, and urinary reconstruction history. Struvite stones tended to be more common in the elevated ammonium group vs control (n = 7 vs 1, P = .07). CONCLUSION: Elevated urinary ammonium among kidney stone patients is relatively uncommon. However, these patients have higher rates of comorbid metabolic conditions, urinary tract infections, and bowel surgery. This finding should prompt further review of the patient's history and may help direct prevention strategies.

Elderly patients undergoing cystectomy, comparing preoperative American Society of Anesthesiology and Eastern Cooperative Oncology Group scores and operative approaches.

OBJECTIVE: To evaluate preoperative scoring systems and operative management and their relation to complications in patients older than 75 years undergoing cystectomy at two academic institutions. METHODS: In total, 212 patients aged 75-95 years with muscle invasive bladder cancer underwent cystectomy at the University of Utah and Central Hospital of Bolzano, Italy. The rates of Grade 3 Clavien-Dindo complications and above in radical cystectomy patients (n = 199) were compared using Eastern Cooperative Oncology Group Scores and American Society of Anesthesiologists Physical Status Classification. The rates of Grade 3 Clavien-Dindo complications and above were also compared by urinary diversion type. Logistic regression was used to control for source institution. RESULTS: In total, 199 cases were included in the primary analysis. Neither of the preoperative scoring systems were predictive for identification of radical cystectomy patients with ⩾Grade 3 Clavien-Dindo complications. In secondary analysis (n = 212, including partial cystectomy), none of the urinary diversion types associated with radical cystectomy had a significantly different rate of complications. However, partial cystectomy (n = 13) had a significantly lower rate of complications. CONCLUSION: Complication rates among elderly patients undergoing cystectomy for muscle invasive bladder cancer were very high. For patients who are approved for surgery after the history and physical exam, none of our objective metrics adequately predicted operative risk. A unique diversion procedure described by the Bolzano group, uretero-ureterocutaneostomy, had equivalent complication rates to the more common diversion procedures. It also appears based on outcomes in this cohort that partial cystectomy is a particularly favorable option within the elderly population in terms of perioperative morbidity.