3 research outputs found

    Seamless Benchmarking of Mathematical Optimization Problems and Metadata Extensions

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    Public libraries of problems such as Mixed Integer Programming Library (MIPLIB) are fundamental to creating a common benchmark for measuring algorithmic advances across mathematical optimization solvers. They also often provide metadata on problem structure, hardness with respect to state-of-the-art solvers, and solutions with the best objective function value on record. In this short paper, we discuss some ways in which such metadata can be leveraged to create a seamless testing experience. In particular, we present MIPLIBing: a Python library that automatically downloads queried subsets from the current versions of MIPLIB, MINLPLib, and QPLIB, provides a centralized local cache across projects, and tracks the best solution values and bounds on record for each problem. While inspired by similar use cases from other areas, we reflect on the specific needs of mathematical optimization and discuss opportunities to extend benchmark sets to facilitate experimentation with different model structures

    Ecological homogenization of oil Properties in the American Residential Macrosystem

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    The conversion of native ecosystems to residential ecosystems dominated by lawns has been a prevailing land-use change in the United States over the past 70 years. Similar development patterns and management of residential ecosystems cause many characteristics of residential ecosystems to be more similar to each other across broad continental gradients than that of former native ecosystems. For instance, similar lawn management by irrigation and fertilizer applications has the potential to influence soil carbon (C) and nitrogen (N) pools and processes. We evaluated the mean and variability of total soil C and N stocks, potential net N mineralization and nitrification, soil nitrite (NO2−)/nitrate (NO3−) and ammonium (NH4+) pools, microbial biomass C and N content, microbial respiration, bulk density, soil pH, and moisture content in residential lawns and native ecosystems in six metropolitan areas across a broad climatic gradient in the United States: Baltimore, MD (BAL); Boston, MA (BOS); Los Angeles, CA (LAX); Miami, FL (MIA); Minneapolis–St. Paul, MN (MSP); and Phoenix, AZ (PHX). We observed evidence of higher N cycling in lawn soils, including significant increases in soil NO2−/NO3−, microbial N pools, and potential net nitrification, and significant decreases in NH4+ pools. Self-reported yard fertilizer application in the previous year was linked with increased NO2−/ NO3− content and decreases in total soil N and C content. Self-reported irrigation in the previous year was associated with decreases in potential net mineralization and potential net nitrification and with increases in bulk density and pH. Residential topsoil had higher total soil C than native topsoil, and microbial biomass C was markedly higher in residential topsoil in the two driest cities (LAX and PHX). Coefficients of variation for most biogeochemical metrics were higher in native soils than in residential soils across all cities, suggesting that residential development homogenizes soil properties and processes at the continental scale

    Implementation of Germline Testing for Prostate Cancer: Philadelphia Prostate Cancer Consensus Conference 2019

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    PURPOSE: Germline testing (GT) is a central feature of prostate cancer (PCA) treatment, management, and hereditary cancer assessment. Critical needs include optimized multigene testing strategies that incorporate evolving genetic data, consistency in GT indications and management, and alternate genetic evaluation models that address the rising demand for genetic services. METHODS: A multidisciplinary consensus conference that included experts, stakeholders, and national organization leaders was convened in response to current practice challenges and to develop a genetic implementation framework. Evidence review informed questions using the modified Delphi model. The final framework included criteria with strong (\u3e 75%) agreement (Recommend) or moderate (50% to 74%) agreement (Consider). RESULTS: Large germline panels and somatic testing were recommended for metastatic PCA. Reflex testing-initial testing of priority genes followed by expanded testing-was suggested for multiple scenarios. Metastatic disease or family history suggestive of hereditary PCA was recommended for GT. Additional family history and pathologic criteria garnered moderate consensus. Priority genes to test for metastatic disease treatment included BRCA2, BRCA1, and mismatch repair genes, with broader testing, such as ATM, for clinical trial eligibility. BRCA2 was recommended for active surveillance discussions. Screening starting at age 40 years or 10 years before the youngest PCA diagnosis in a family was recommended for BRCA2 carriers, with consideration in HOXB13, BRCA1, ATM, and mismatch repair carriers. Collaborative (point-of-care) evaluation models between health care and genetic providers was endorsed to address the genetic counseling shortage. The genetic evaluation framework included optimal pretest informed consent, post-test discussion, cascade testing, and technology-based approaches. CONCLUSION: This multidisciplinary, consensus-driven PCA genetic implementation framework provides novel guidance to clinicians and patients tailored to the precision era. Multiple research, education, and policy needs remain of importance
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