Numerical algebraic geometry for model selection and its application to the life sciences

Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation, and model selection. These are all optimization problems, well-known to be challenging due to non-linearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data is available. Here, we consider polynomial models (e.g., mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry. Specifically, we use probability-one polynomial homotopy continuation methods to compute all critical points of the objective function, then filter to recover the global optima. Our approach exploits the geometric structures relating models and data, and we demonstrate its utility on examples from cell signaling, synthetic biology, and epidemiology.Comment: References added, additional clarification

Scholarly Concentrations: A Novel Platform for Delivery of Health Systems Science Exposure and Highlight Unique Learning Environments Across the Nine Campuses of Indiana University School of Medicine

Presented as a Poster at 2020 IUSM Education Day.Rapidly evolving challenges in health care mandate changes in the way health care professionals are educated. How do we integrate the need for new and different content into the medical school curriculum? One area of particular focus is called Health Systems Science. Health Systems Science is being called the 3rd leg of modern medical education to complement the foundational and clinical sciences curricula. IU School of Medicine is integrating Health Systems Science content into Scholarly Concentrations. Scholarly Concentrations is a program offering students longitudinal educational enhancement through coursework and scholarly work

A 3D inﾠvitro model of patient-derived prostate cancer xenograft for controlled interrogation of inﾠvivo tumor-stromal interactions

Patient-derived xenograft (PDX) models better represent human cancer than traditional cell lines. However, the complex in vivo environment makes it challenging to employ PDX models to investigate tumor-stromal interactions, such as those that mediate prostate cancer (PCa) bone metastasis. Thus, we engineered a defined three-dimensional (3D) hydrogel system capable of supporting the co-culture of PCa PDX cells and osteoblastic cells to recapitulate the PCa-osteoblast unit within the bone metastatic microenvironment in vitro. Our 3D model not only maintained cell viability but also preserved the typical osteogenic phenotype of PCa PDX cells. Additionally, co-culture cellularity was maintained over that of either cell type cultured alone, suggesting that the PCa-osteoblast cross-talk supports PCa progression in bone, as is hypothesized to occur in patients with prostatic bone metastasis. Strikingly, osteoblastic cells co-cultured with PCa PDX tumoroids organized around the tumoroids, closely mimicking the architecture of PCa metastases in bone. Finally, tumor-stromal signaling mediated by the fibroblast growth factor axis tightly paralleled that in the in vivo counterpart. Together, these findings indicate that this 3D PCa PDX model recapitulates important pathological properties of PCa bone metastasis, and validate the use of this model for controlled and systematic interrogation of complex in vivo tumor-stromal interactions

Match play performance characteristics that predict post-match creatine kinase responses in professional rugby union players

Background: Rugby union players can take several days to fully recover from competition. Muscle damage induced during the match has a major role in player recovery; however the specific characteristics of match play that predict post-match muscle damage remains unclear. We examined the relationships between a marker of muscle damage and performance characteristics associated with physical contacts and high-speed movement in professional rugby union players. Methods: Twenty-eight professional rugby union players (15 forwards, 13 backs) participated in this study. Data were obtained from 4 European Cup games, with blood samples collected 2 h pre, and 16 and 40 h post-match, and were subsequently analysed for creatine kinase (CK). Relationships between changes in CK concentrations and number of physical contacts and high-speed running markers, derived from performance analysis and global positioning system (GPS) data, were assessed. Results: Moderate and moderate-large effect-size correlations were identified between contact statistics from performance analysis and changes in CK at 16 and 40 h post match in forwards and backs, respectively (e.g. backs; total impacts vs. ΔCK (r = 0.638, p < 0.01) and Δ% CK (r = 0.454, p < 0.05) 40 h post-match). Furthermore, moderate effect-size correlations were found between measures of high-speed running and sprinting, and changes in CK at 16 and 40 h post-match within the backs (e.g. high-speed running distance vs. ΔCK (r = 0.434, p = 0.056) and Δ% CK (r = 0.437, p = 0.054) 40 hrs post-match). Conclusions: Our data demonstrate that muscle damage induced by professional rugby union match play is to some extent predicted by the number of physical contacts induced during performance. Furthermore, we show for the first time that muscle damage in backs players is predicted by high-speed running measures derived from GPS. These data increase the understanding of the causes of muscle damage in rugby union; performance markers could potentially be used to tailor individual recovery strategies and subsequent training following rugby union competition

Progression of Carotid Artery Intima-Media Thickness During 12 Years in the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) Study

OBJECTIVE This study investigated the long-term effects of intensive diabetic treatment on the progression of atherosclerosis, measured as common carotid artery intima-media thickness (IMT). RESEARCH DESIGN AND METHODS A total of 1,116 participants (52% men) in the Epidemiology of Diabetes Interventions and Complications (EDIC) trial, a long-term follow-up of the Diabetes Control and Complications Trial (DCCT), had carotid IMT measurements at EDIC years 1, 6, and 12. Mean age was 46 years, with diabetes duration of 24.5 years at EDIC year 12. Differences in IMT progression between DCCT intensive and conventional treatment groups were examined, controlling for clinical characteristics, IMT reader, and imaging device. RESULTS Common carotid IMT progression from EDIC years 1 to 6 was 0.019 mm less in intensive than in conventional (P < 0.0001), and from years 1 to 12 was 0.014 mm less (P = 0.048); but change from years 6 to 12 was similar (intensive − conventional = 0.005 mm, P = 0.379). Mean A1C levels during DCCT and DCCT/EDIC were strongly associated with progression of IMT, explaining most of the differences in IMT progression between DCCT treatment groups. Albuminuria, older age, male sex, smoking, and higher systolic blood pressure were significant predictors of IMT progression. CONCLUSIONS Intensive treatment slowed IMT progression for 6 years after the end of DCCT but did not affect IMT progression thereafter (6–12 years). A beneficial effect of prior intensive treatment was still evident 13 years after DCCT ended. These differences were attenuated but not negated after adjusting for blood pressure. These results support the early initiation and continued maintenance of intensive diabetes management in type 1 diabetes to retard atherosclerosis

High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs

<p>Abstract</p> <p>Background</p> <p>Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not annotated) variation, is problematic for follow up analyses. Polymorphisms result in a high incidence of false positive and false negative results in hybridization based analyses and hinder the identification of the true variation underlying genetically determined differences in physiology and behavior. Given the proliferation of mouse genetic models (e.g., knockout models, selectively bred lines, heterogeneous stocks derived from standard inbred strains and wild mice) and the wealth of gene expression microarray and phenotypic studies using genetic models, the impact of naturally-occurring polymorphisms on these data is critical. With the advent of next-generation, high-throughput sequencing, we are now in a position to determine to what extent polymorphisms are currently cryptic in such models and their impact on downstream analyses.</p> <p>Results</p> <p>We sequenced the two most commonly used inbred mouse strains, DBA/2J and C57BL/6J, across a region of chromosome 1 (171.6 – 174.6 megabases) using two next generation high-throughput sequencing platforms: Applied Biosystems (SOLiD) and Illumina (Genome Analyzer). Using the same templates on both platforms, we compared realignments and single nucleotide polymorphism (SNP) detection with an 80 fold average read depth across platforms and samples. While public datasets currently annotate 4,527 SNPs between the two strains in this interval, thorough high-throughput sequencing identified a total of 11,824 SNPs in the interval, including 7,663 new SNPs. Furthermore, we confirmed 40 missense SNPs and discovered 36 new missense SNPs.</p> <p>Conclusion</p> <p>Comparisons utilizing even two of the best characterized mouse genetic models, DBA/2J and C57BL/6J, indicate that more than half of naturally-occurring SNPs remain cryptic. The magnitude of this problem is compounded when using more divergent or poorly annotated genetic models. This warrants full genomic sequencing of the mouse strains used as genetic models.</p

A study of the norcaradiene-cycloheptatriene equilibrium in a series of azulenones by NMR spectroscopy; the impact of substitution on the position of equilibrium

A systematic investigation of the influence of substitution at positions C-2 and C-3 on the azulenone skeleton, based on NMR characterisation, is discussed with particular focus on the impact of the steric and electronic characteristics of substituents on the position of the norcaradiene-cycloheptatriene (NCD-CHT) equilibrium. Variable temperature (VT) NMR studies, undertaken to enable the resolution of signals for the equilibrating valence tautomers revealed, in addition, interesting shifts in the equilibrium