MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses.

Predicting dynamics of host-microbial ecosystems is crucial for the rational design of bacteriotherapies. We present MDSINE, a suite of algorithms for inferring dynamical systems models from microbiome time-series data and predicting temporal behaviors. Using simulated data, we demonstrate that MDSINE significantly outperforms the existing inference method. We then show MDSINE's utility on two new gnotobiotic mice datasets, investigating infection with Clostridium difficile and an immune-modulatory probiotic. Using these datasets, we demonstrate new capabilities, including accurate forecasting of microbial dynamics, prediction of stable sub-communities that inhibit pathogen growth, and identification of bacteria most crucial to community integrity in response to perturbations.

Parenchymal volume preservation and ischemia during partial nephrectomy: functional and volumetric analysis.

OBJECTIVE: To determine the relative effect of type and duration of ischemia and parenchymal volume preservation on renal function after partial nephrectomy (PN). MATERIALS AND METHODS: Ninety-two patients with localized renal tumors (2007-2012) managed with PN at our center with necessary studies for analysis were included. This comprised 37 patients with a solitary kidney and 55 with a contralateral kidney. Thirty-five patients were managed with hypothermia and 57 with limited warm ischemia. Volumetric computed tomography was used to measure the volume of functional parenchyma before and after PN in the operated and contralateral kidneys. Glomerular filtration rate (GFR) was determined by the modification of diet in renal disease 2 equation, along with renal scan data for patients with a contralateral kidney. Regression analysis assessed the relationships between %GFR preserved in the operated kidney and potential predictive factors. All postoperative analyses were performed 4-12 months after surgery. RESULTS: Median age was 61 years, median tumor size 3.5 cm, and median RENAL nephrometry score 8. Median cold ischemia time was 28 minutes and median warm ischemia time 21 minutes. Median %GFR preserved in the operated kidney was 79%. Median %parenchymal volume saved was 83%. Function in the contralateral kidney only increased marginally (median increase 6%). On regression analysis, %GFR preserved associated most strongly with %parenchymal volume saved (P <.0001), but also with lower RENAL scores (P = .0457) and the use of hypothermia (P = .0209). In contrast, ischemia time did not correlate with %GFR preserved (P = .5051). CONCLUSION: Ultimate function after PN primarily correlated with parenchymal volume preservation, whereas ischemia played a secondary role. Thus, maximal parenchymal preservation with a precise PN should be a priority during PN.