Willadsen Herman (pointwind24)

We hope that this statistical methodology will provide a quantitative framework facilitating the unification of our theoretical understanding and empirical observations into a quantitative, multivariate theory of stress. © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email journals.permissions@oup.com.MOTIVATION One of the key computational problems in comparative genomics is the reconstruction of genomes of ancestral species based on genomes of extant species. Since most dramatic changes in genomic architectures are caused by genome rearrangements, this problem is often posed as minimization of the number of genome rearrangements between extant and ancestral genomes. The basic case of three given genomes is known as the genome median problem. Whole genome duplications (WGDs) represent yet another type of dramatic evolutionary events and inspire the reconstruction of pre-duplicated ancestral genomes, referred to as the genome halving problem. Generalization of WGDs to whole genome multiplication events leads to the genome aliquoting problem. RESULTS In the present study, we propose polynomial-size integer linear programming (ILP) formulations for the aforementioned problems. We further obtain such formulations for the restricted and conserved versions of the median and halving problems, which have been recently introduced to improve biological relevance of the solutions. Extensive evaluation of solutions to the different ILP problems demonstrate their good accuracy. Furthermore, since the ILP formulations for the conserved versions have linear size, they provide a novel practical approach to ancestral genome reconstruction, which combines the advantages of homology- and rearrangements-based methods. AVAILABILITY Code and data are available in https//github.com/AvdeevPavel/ILP-WGD-reconstructor. © The Author(s) (2020). Published by Oxford University Press. All rights reserved. For Permissions, please email journals.permissions@oup.com.Importance Data on the contemporary changes in risk profile and outcomes of patients undergoing percutaneous coronary intervention (PCI) or coronary bypass grafting (CABG) are limited. Objective To assess the contemporary trends in the characteristics and outcomes of patients undergoing PCI or CABG in the United States. Design, Setting, and Participants This retrospective cohort study used a national inpatient claims-based database to identify patients undergoing PCI or CABG from January 1, 2003, to December 31, 2016. Data analysis was performed from July 15 to October 4, 2019. Main Outcomes and Measures Demographic characteristics, prevalence of risk factors, and clinical presentation divided into 3 eras (2003-2007, 2008-2012, and 2013-2016) and in-hospital mortality of PCI and CABG stratified by clinical indication. Results A total of 12 062 081 revascularization hospitalizations were identified 8 687 338 PCIs (72.0%; mean [SD] patient age, 66.0 [10.8] years; 66.2% male) and 3 374 743 CABGs (28.0%; mean [SDCABG and 2.1% to 1.2% for isolated CABG) (P less then .001 for all). Conclusions and Relevance Significant changes were found in the characteristics of patients undergoing PCI and CABG in the United States between 2003 and 2016. Shield1 Risk-adjusted mortality decreased significantly after CABG but not after PCI across all clinical indications.Importance Patients with locally advanced gastroesophageal adenocarcinoma (ie, stage ≥T3 and/or node positive) have high rates of recurrence despite surgery and adjunctive perioperative therapies, which also have high toxicity profiles. Evaluation of pharmacogenomically dosed perioperative gFOLFIRINOX (fluorouracil, leucovorin, oxaliplatin, and UGT1A1 genotype-directed irinotecan) to optimize efficacy while limiting toxic effects may have value. Objective To evaluate the coprimary end points of margin-negative (R0) resection rat