Economic evaluation of alternative farm water sources in the claypan area of Illinois

The claypan area of Illinois is characterized by unreliable water supplies. In addition, water quality problems have recently been recognized in the form of widespread nitrate coliform contamination of water in private wells in Washington County. A ten-square mile area in this county was selected for study. The nature of present water supplies was described and the costs of six alternative supply systems were estimated: (1) present on-farm sources, (2) treatment of pond water, (3) combination of present on-farm sources plus hauling, (4) hauling all water, (5) purchasing water from nearby municipality via pipeline, (6) combination pipeline plus on-farm sources. The six alternatives were examined in terms of the net present value of costs associated with each alternative, considering a 40-year planning period. Although the present sources proved to be the least costly they are unsatisfactory for reasons of health and also reliability. Treatment of pond water was the least-cost source of meeting the quality requirements for water for the total area. However, the reliability of this source and questions of personal preference against drinking pond water may indicate a preference among some users for connection with a municipal system which was somewhat more expensive.U.S. Geological SurveyU.S. Department of the InteriorOpe

Economic evaluation of the effect of selected crop practices on nonagricultural uses of water

Cropping systems may have an unfavorable influence on the quality of nearby surface water. In this study, linear programming methods were used to assess the impact of improvements in certain water quality characteristics on economically optimal crop systems. Thus, the effect of crop practices on water quality is analyzed indirectly by assuming that farmers would alter their cropping practices in the most economical way in order to conform to various water-quality constraints. A 1,200-acre watershed was used to illustrate the procedure. Sediment entering the reservoir was treated as a variable constraint on maximization of farm income. Requiring successively lower amounts of sediment to enter the reservoir caused farm income to decrease at an increasing rate. The analysis was enlarged to include a constraint on nitrate in the leachate below the root zone. This phase of the analysis also included a charge for removing at least some of the sediment entering the reservoir. As the nitrate limit on the leachate was lowered, farm income decreased at an increasing rate. The requirement of removal of the sediment by itself had little or no effect on the nitrate concentration in the leachate. Extensions of the procedure for use in other situations are suggested.U.S. Geological SurveyU.S. Department of the InteriorOpe

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

The Atacama Cosmology Telescope: A Catalog of >4000 Sunyaev–Zel’dovich Galaxy Clusters

We present a catalog of 4195 optically confirmed Sunyaev–Zel'dovich (SZ) selected galaxy clusters detected with signal-to-noise ratio >4 in 13,211 deg2 of sky surveyed by the Atacama Cosmology Telescope (ACT). Cluster candidates were selected by applying a multifrequency matched filter to 98 and 150 GHz maps constructed from ACT observations obtained from 2008 to 2018 and confirmed using deep, wide-area optical surveys. The clusters span the redshift range 0.04 1 clusters, and a total of 868 systems are new discoveries. Assuming an SZ signal versus mass-scaling relation calibrated from X-ray observations, the sample has a 90% completeness mass limit of M500c > 3.8 × 1014 M⊙, evaluated at z = 0.5, for clusters detected at signal-to-noise ratio >5 in maps filtered at an angular scale of 2farcm4. The survey has a large overlap with deep optical weak-lensing surveys that are being used to calibrate the SZ signal mass-scaling relation, such as the Dark Energy Survey (4566 deg2), the Hyper Suprime-Cam Subaru Strategic Program (469 deg2), and the Kilo Degree Survey (825 deg2). We highlight some noteworthy objects in the sample, including potentially projected systems, clusters with strong lensing features, clusters with active central galaxies or star formation, and systems of multiple clusters that may be physically associated. The cluster catalog will be a useful resource for future cosmological analyses and studying the evolution of the intracluster medium and galaxies in massive clusters over the past 10 Gyr

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy