Vegetated Ditch Habitats Provide Net Nitrogen Sink and Phosphorus Storage Capacity in Agricultural Drainage Networks Despite Senescent Plant Leaching

The utility of vegetated ditch environments as nutrient sinks in agricultural watersheds is dependent in part on biogeochemical transformations that control plant uptake and release during decomposition. We investigated nitrogen (N) and phosphorus (P) uptake and release across four P enrichment treatments in ditch mesocosms planted with rice cutgrass (Leersia oryzoides) during the summer growing and winter decomposition seasons. Measured N retention and modeled denitrification rates did not vary, but P retention significantly increased with P enrichment. At the end of the growing season, root biomass stored significantly more N and P than aboveground stem and leaf biomass. Decomposition rates were low (<10% organic matter loss) and not affected by P enrichment. Nitrogen and P export during winter did not vary across the P enrichment gradient. Export accounted for <10% of observed summer N uptake (1363 mg m−2), with denitrification potentially accounting for at least 40% of retained N. In contrast, net P retention was dependent on enrichment; in unenriched mesocosms, P uptake and release were balanced (only 25% net retention), whereas net retention increased from 77% to 88% with increasing P enrichment. Our results indicate that vegetated ditch environments have significant potential to serve as denitrification sinks, while also storing excess P in agricultural watersheds

Navigating protected genomics data with UCSC Genome Browser in a Box.

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Availability and Implementation: Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/)[email protected]

Navigating protected genomics data with UCSC Genome Browser in a Box.

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Availability and Implementation: Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/)[email protected]

Impact of circulating microRNA test (miRNA-371a-3p) on appropriateness of treatment and cost outcomes in patients with Stage I non-seminomatous germ cell tumours.

OBJECTIVES: To determine whether utilisation of a serum microRNA (miRNA) test could improve treatment appropriateness and cost-effectiveness for patients with Stage I non-seminomatous germ cell tumours (NSGCTs). PATIENTS AND METHODS: A decision tree model was built to investigate treatment course, clinical and cost outcomes for patients with Stage IA (T1N0M0S0) and IB (T2-4N0M0S0) NSGCT. The model compared outcomes and cost of standard approach using histopathology, conventional serum tumour markers and radiographic staging (standard model) to a miRNA-based approach using the standard model + post-orchidectomy serum miR-371a-3p (marker model). Probabilities of expected treatment and outcomes were based on presence/absence of cancer upon entering into the model. Overtreatment was defined as adjuvant chemotherapy or primary retroperitoneal lymph node dissection in a patient without cancer. Undertreatment was defined as initial surveillance for a patient with cancer. RESULTS: Utilising the miRNA marker-based approach, 26% of patients avoid overtreatment and 8% avoid undertreatment in Stage IA NSGCT; 27% avoid overtreatment and 23% avoid undertreatment in Stage IB disease. Appropriate treatment decision-making increased from 65% to 94% and 50% to 92% for Stage IA and IB, respectively. The miRNA-based approach remained cost-effective over a wide range of performance characteristics with savings of ~$1400 (American dollars)/patient for both Stage IA and IB disease. CONCLUSION: A miRNA-based approach may potentially select patients with Stage I NSGCT for correct treatment in a cost-effective manner. Identification of residual teratoma-only remains an issue. Prospective studies are necessary to validate these findings

UCSC Cell Browser: visualize your single-cell data

SummaryAs the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.Availability and implementationWe provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu.Supplementary informationSupplementary data are available at Bioinformatics online

UCSC Data Integrator and Variant Annotation Integrator

Summary: Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores. Availability and implementation: The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/. The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

UCSC Data Integrator and Variant Annotation Integrator.

UnlabelledTwo new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores.Availability and implementationThe web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/ The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a [email protected] informationSupplementary data are available at Bioinformatics online