Development of a Disaster Response Plan for the North Carolina National Estuarine Research Reserve

The North Carolina National Estuarine Research Reserve (NCNERR) is a network of four protected coastal sites, covering over 10,500 acres, which was established for long‐term research, education, and stewardship. Following the Deepwater Horizon oil spill, five Gulf of Mexico NERRs created comprehensive disaster response plans (DRP) and were the first reserves in the nationwide system to initiate disaster planning. NCNERR deemed that its own DRP was needed to guide emergency management efforts, build better partnerships between NCNERR managers and emergency managers, and position NCNERR as a partner to support area response efforts. Site‐specific hazards were identified and ranked in collaboration with NCNERR managers. Facilitated stakeholder workshops brought together all relevant local, state, and federal emergency response personnel and garnered input on potential hazards, impacts, and preparation needs of each NCNERR site. The input from site managers and stakeholders informed the creation of the DRP, which will be included in NCNERR’s 2016‐2021 Management Plan

Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.

Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute-funded cancer centers. Although each of the participating cancer centers is structured differently, and leaders' titles vary, we know firsthand there are similarities in both the issues we face and the solutions we achieve. As a consortium, we have initiated a dedicated listserv, an open-initiatives program, and targeted biannual face-to-face meetings. These meetings are a place to review our priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues we, as informatics leaders, individually face at our respective institutions and cancer centers. Here we provide a brief history of the CI4CC organization and meeting highlights from the latest CI4CC meeting that took place in Napa, California from October 14-16, 2019. The focus of this meeting was "intersections between informatics, data science, and population science." We conclude with a discussion on "hot topics" on the horizon for cancer informatics

TP53 and MDM2 single nucleotide polymorphisms influence survival in non-del(5q) myelodysplastic syndromes

Abstract:P53 is a key regulator of many cellular processes and is negatively regulated by the human homolog of murine double minute-2 (MDM2) E3 ubiquitin ligase. Single nucleotide polymorphisms (SNPs) of either gene alone, and in combination, are linked to cancer susceptibility, disease progression, and therapy response. We analyzed the interaction of TP53 R72P and MDM2 SNP309 SNPs in relationship to outcome in patients with myelodysplastic syndromes (MDS). Sanger sequencing was performed on DNA isolated from 208 MDS cases. Utilizing a novel functional SNP scoring system ranging from +2 to -2 based on predicted p53 activity, we found statistically significant differences in overall survival (OS) (p = 0.02) and progression-free survival (PFS) (p = 0.02) in non-del(5q) MDS patients with low functional scores. In univariate analysis, only IPSS and the functional SNP score predicted OS and PFS in non-del(5q) patients. In multivariate analysis, the functional SNP score was independent of IPSS for OS and PFS. These data underscore the importance of TP53 R72P and MDM2 SNP309 SNPs in MDS, and provide a novel scoring system independent of IPSS that is predictive for disease outcome

OpenET : filling a critical data gap in water management for the western United States.

The lack of consistent, accurate information on evapotranspiration (ET) and consumptive use of water by irrigated agriculture is one of the most important data gaps for water managers in the western United States (U.S.) and other arid agricultural regions globally. The ability to easily access information on ET is central to improving water budgets across the West, advancing the use of data-driven irrigation management strategies, and expanding incentive-driven conservation programs. Recent advances in remote sensing of ET have led to the development of multiple approaches for field-scale ET mapping that have been used for local and regional water resource management applications by U.S. state and federal agencies. The OpenET project is a community-driven effort that is building upon these advances to develop an operational system for generating and distributing ET data at a field scale using an ensemble of six well-established satellite-based approaches for mapping ET. Key objectives of OpenET include: Increasing access to remotely sensed ET data through a web-based data explorer and data services; supporting the use of ET data for a range of water resource management applications; and development of use cases and training resources for agricultural producers and water resource managers. Here we describe the OpenET framework, including the models used in the ensemble, the satellite, meteorological, and ancillary data inputs to the system, and the OpenET data visualization and access tools. We also summarize an extensive intercomparison and accuracy assessment conducted using ground measurements of ET from 139 flux tower sites instrumented with open path eddy covariance systems. Results calculated for 24 cropland sites from Phase I of the intercomparison and accuracy assessment demonstrate strong agreement between the satellite-driven ET models and the flux tower ET data. For the six models that have been evaluated to date (ALEXI/DisALEXI, eeMETRIC, geeSEBAL, PT-JPL, SIMS, and SSEBop) and the ensemble mean, the weighted average mean absolute error (MAE) values across all sites range from 13.6 to 21.6 mm/month at a monthly timestep, and 0.74 to 1.07 mm/day at a daily timestep. At seasonal time scales, for all but one of the models the weighted mean total ET is within ±8% of both the ensemble mean and the weighted mean total ET calculated from the flux tower data. Overall, the ensemble mean performs as well as any individual model across nearly all accuracy statistics for croplands, though some individual models may perform better for specific sites and regions. We conclude with three brief use cases to illustrate current applications and benefits of increased access to ET data, and discuss key lessons learned from the development of OpenET

Investigation of the SV40 – Human Cancer Association: Look for the Full Signature of the Virus

In the controversy about the association of simian virus 40 with human cancers, the greatest problem is the ascertainment of SV40 exposure. This difficulty would be resolved if one were to look for all components of SV40 infection. How does SV 40 circulate in the human community? Do cancer patients with SV40-positive tumors have serological correlates of SV 40 infection and of SV40-induced cancer? SV40 association with a cancer should be studied in the context of the known risk factors for that cancer. The tumor cell-virus relationship should be characterized with respect to viral integration and viral localization to the tumor cell. Specimens should be masked and the assays should include panels of specimens to estimate analytic sensitivity and specificity. In view of the rarity of some of the tumors reported to be associated with SV40, a multi-institutional investigation initiated and coordinated by the NIH would be most effective

MinION nanopore sequencing and assembly of a complete human papillomavirus genome

BACKGROUND: The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other time-consuming and low-throughput methodologies. METHODS: We report the use of the MinION nanopore sequencer to sequence the full-length genome of human papillomavirus (HPV)-ICB2 (7441 bp), which was previously characterized in our laboratory. Three independent MinION libraries were prepared and sequenced using either three consecutive 12 -h runs (Protocol A) or a single run of 48 h starting from a pool of three barcoded DNA libraries (Protocol B). A fully automated bioinformatics pipeline was developed for the reconstruction of the viral genome. RESULTS: Protocols A and B generated 9,354,933 and 3,255,879 reads, respectively. Read length N50 values ranged between 6976 and 7360 nucleotides over the four sequencing runs. Bioinformatics analysis showed that both protocols allowed for the reconstruction of the whole viral genome, with pairwise percentages of identity to HPV-ICB2 of 100 % for protocol A and 99.98 % for protocol B. CONCLUSION: Our results show that the use of the MinION nanopore sequencer represents an effective strategy for whole-genome sequencing of HPVs with a minimal error rate

Demographic disparities in receipt of care at a comprehensive cancer center

Abstract Background National Cancer Institute cancer centers (NCICCs) provide specialized cancer care including precision oncology and clinical treatment trials. While these centers can offer novel therapeutic options, less is known about when patients access these centers or at what timepoint in their disease course they receive specialized care. This is especially important since precision diagnostics and receipt of the optimal therapy upfront can impact patient outcomes and previous research suggests that access to these centers may vary by demographic characteristics. Here, we examine the timing of patients' presentation at Moffitt Cancer Center (MCC) relative to their initial diagnosis across several demographic characteristics. Methods A retrospective cohort study was conducted among patients who presented to MCC with breast, colon, lung, melanoma, and prostate cancers between December 2008 and April 2020. Patient demographic and clinical characteristics were obtained from the Moffitt Cancer Registry. The association between patient characteristics and the timing of patient presentation to MCC relative to the patient's cancer diagnosis was examined using logistic regression. Results Black patients (median days = 510) had a longer time between diagnosis and presentation to MCC compared to Whites (median days = 368). Black patients were also more likely to have received their initial cancer care outside of MCC compared to White patients (odds ratio [OR] and 95% confidence interval [CI] = 1.45 [1.32–1.60]). Furthermore, Hispanics were more likely to present to MCC at an advanced stage compared to non‐Hispanic patients (OR [95% CI] = 1.28 [1.05–1.55]). Conclusions We observed racial and ethnic differences in timing of receipt of care at MCC. Future studies should aim to identify contributing factors for the development of novel mitigation strategies and assess whether timing differences in referral to an NCICC correlate with long‐term patient outcomes