Data report, 2013-02 : Water properties of Narragansett Bay observed at GSO dock from 1995-2011

Narragansett Bay is a medium-sized (370 km2) northeastern U.S. estuary. The Narragansett Bay watershed drains approximately 1,800 square miles through numerous freshwater inputs into the Bay. The major source of fresh water to the Bay is the Blackstone River. Narragansett Bay covers approximately 147 square miles with an undulating shoreline that creates a string of sheltered coves where water circulation may be restricted (Figure 1). The circulation in the Bay was described in detail by Rodgers (Rogers, 2008) and Kincaid, et. al. (Kincaid, et. al., 2003; Pilson, 1985). This report describes the time series data collected at the dock of Graduate School of Oceanography (GSO) at the Narragansett Bay Campus of the University of Rhode Island from 1995 through 2011. This site is located about 4.6 km from the mouth of the West Passage in Narragansett Bay

Effect of nutrient reductions on dissolved oxygen and pH: a case study of Narragansett bay

To assess the consequences of nutrient reduction strategies on water quality under climate change, we investigated the long-term dynamics of dissolved oxygen (DO) and pH in Narragansett Bay (NB), a warming urbanized estuary in Rhode Island, where nitrogen loads have declined due to extensive wastewater treatment plant upgrades. We use 15 years (January 2005-December 2019) of measurements from the Narragansett Bay Fixed Site Monitoring network. Nutrient-enhanced phytoplankton growth can increase DO in the upper water column while subsequent respiration can reduce water column DO and enhance bottom water acidification, and vice-versa. We observed significant decreases in surface DO levels, concurrent with a significant increase in bottom DO, associated with the nitrogen load reduction. Surface DO decline was primarily attributed to reduced intensity of primary productivity, supported by a concurrent decrease in surface chlorophyll concentrations. Meanwhile, the influence of reduced organic matter respiration led to the increase of bottom DO levels by 9 µmol kg-1 (approximately 0.2 mg L-1 for typical summer temperature and salinity) over a 15-year period, which overcame the opposite influence of oxygen reduction from solubility decreases due to warming temperatures. In contrast, long-term changes in surface pH have not exhibited discernible trends beyond natural variability, likely due to the complex and sometimes opposing influences of biological activity and changing river flow conditions. We observed a slight increase in bottom pH, associated with the increase in DO in bottom water. Notably, future variations in freshwater discharge, particularly linked to extreme precipitation events, may further influence water carbonate chemistry and thereby impact pH dynamics. This study highlights the necessity of long-term time series measurements in helping understand the impacts of environmental management practices in improving water quality in coastal regions during a changing climate

Genome-Wide Association Studies in an Isolated Founder Population from the Pacific Island of Kosrae

It has been argued that the limited genetic diversity and reduced allelic heterogeneity observed in isolated founder populations facilitates discovery of loci contributing to both Mendelian and complex disease. A strong founder effect, severe isolation, and substantial inbreeding have dramatically reduced genetic diversity in natives from the island of Kosrae, Federated States of Micronesia, who exhibit a high prevalence of obesity and other metabolic disorders. We hypothesized that genetic drift and possibly natural selection on Kosrae might have increased the frequency of previously rare genetic variants with relatively large effects, making these alleles readily detectable in genome-wide association analysis. However, mapping in large, inbred cohorts introduces analytic challenges, as extensive relatedness between subjects violates the assumptions of independence upon which traditional association test statistics are based. We performed genome-wide association analysis for 15 quantitative traits in 2,906 members of the Kosrae population, using novel approaches to manage the extreme relatedness in the sample. As positive controls, we observe association to known loci for plasma cholesterol, triglycerides, and C-reactive protein and to a compelling candidate loci for thyroid stimulating hormone and fasting plasma glucose. We show that our study is well powered to detect common alleles explaining ≥5% phenotypic variance. However, no such large effects were observed with genome-wide significance, arguing that even in such a severely inbred population, common alleles typically have modest effects. Finally, we show that a majority of common variants discovered in Caucasians have indistinguishable effect sizes on Kosrae, despite the major differences in population genetics and environment

Delphi Initiative for Early-Onset Colorectal Cancer (DIRECt) International Management Guidelines

Background & aims: Patients with early-onset colorectal cancer (eoCRC) are managed according to guidelines that are not age-specific. A multidisciplinary international group (DIRECt), composed of 69 experts, was convened to develop the first evidence-based consensus recommendations for eoCRC. Methods: After reviewing the published literature, a Delphi methodology was used to draft and respond to clinically relevant questions. Each statement underwent 3 rounds of voting and reached a consensus level of agreement of ≥80%. Results: The DIRECt group produced 31 statements in 7 areas of interest: diagnosis, risk factors, genetics, pathology-oncology, endoscopy, therapy, and supportive care. There was strong consensus that all individuals younger than 50 should undergo CRC risk stratification and prompt symptom assessment. All newly diagnosed eoCRC patients should receive germline genetic testing, ideally before surgery. On the basis of current evidence, endoscopic, surgical, and oncologic treatment of eoCRC should not differ from later-onset CRC, except for individuals with pathogenic or likely pathogenic germline variants. The evidence on chemotherapy is not sufficient to recommend changes to established therapeutic protocols. Fertility preservation and sexual health are important to address in eoCRC survivors. The DIRECt group highlighted areas with knowledge gaps that should be prioritized in future research efforts, including age at first screening for the general population, use of fecal immunochemical tests, chemotherapy, endoscopic therapy, and post-treatment surveillance for eoCRC patients. Conclusions: The DIRECt group produced the first consensus recommendations on eoCRC. All statements should be considered together with the accompanying comments and literature reviews. We highlighted areas where research should be prioritized. These guidelines represent a useful tool for clinicians caring for patients with eoCRC

Colorectal cancer incidences in Lynch syndrome: a comparison of results from the prospective lynch syndrome database and the international mismatch repair consortium

Objective To compare colorectal cancer (CRC) incidences in carriers of pathogenic variants of the MMR genes in the PLSD and IMRC cohorts, of which only the former included mandatory colonoscopy surveillance for all participants. Methods CRC incidences were calculated in an intervention group comprising a cohort of confirmed carriers of pathogenic or likely pathogenic variants in mismatch repair genes (path_MMR) followed prospectively by the Prospective Lynch Syndrome Database (PLSD). All had colonoscopy surveillance, with polypectomy when polyps were identified. Comparison was made with a retrospective cohort reported by the International Mismatch Repair Consortium (IMRC). This comprised confirmed and inferred path_MMR carriers who were first- or second-degree relatives of Lynch syndrome probands. Results In the PLSD, 8,153 subjects had follow-up colonoscopy surveillance for a total of 67,604 years and 578 carriers had CRC diagnosed. Average cumulative incidences of CRC in path_MLH1 carriers at 70 years of age were 52% in males and 41% in females; for path_MSH2 50% and 39%; for path_MSH6 13% and 17% and for path_PMS2 11% and 8%. In contrast, in the IMRC cohort, corresponding cumulative incidences were 40% and 27%; 34% and 23%; 16% and 8% and 7% and 6%. Comparing just the European carriers in the two series gave similar findings. Numbers in the PLSD series did not allow comparisons of carriers from other continents separately. Cumulative incidences at 25 years were < 1% in all retrospective groups. Conclusions Prospectively observed CRC incidences (PLSD) in path_MLH1 and path_MSH2 carriers undergoing colonoscopy surveillance and polypectomy were higher than in the retrospective (IMRC) series, and were not reduced in path_MSH6 carriers. These findings were the opposite to those expected. CRC point incidence before 50 years of age was reduced in path_PMS2 carriers subjected to colonoscopy, but not significantly so

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Editorial Changes and Item Performance: Implications for Calibration and Pretesting

Previous research on the impact of text and formatting changes on test-item performance has produced mixed results. This matter is important because it is generally acknowledged that any change to an item requires that it be recalibrated. The present study investigated the effects of seven classes of stylistic changes on item difficulty, discrimination, and response time for a subset of 65 items that make up a standardized test for physician licensure completed by 31,918 examinees in 2012. One of two versions of each item (original or revised) was randomly assigned to examinees such that each examinee saw only two experimental items, with each item being administered to approximately 480 examinees. The stylistic changes had little or no effect on item difficulty or discrimination; however, one class of edits – changing an item from an open lead-in (incomplete statement) to a closed lead-in (direct question) – did result in slightly longer response times. Data for nonnative speakers of English were analyzed separately with nearly identical results. These findings have implications for the conventional practice of repretesting (or recalibrating) items that have been subjected to minor editorial changes. Accessed 3,791 times on https://pareonline.net from November 11, 2014 to December 31, 2019. For downloads from January 1, 2020 forward, please click on the PlumX Metrics link to the right

Managed Nitrogen Load Decrease Reduces Chlorophyll and Hypoxia in Warming Temperate Urban Estuary

Many urban estuaries worldwide suffer from excess phytoplankton and hypoxia (low oxygen) due to high nutrient loads. A common water quality management strategy is to require wastewater treatment facility upgrades. This case study examines Narragansett Bay, a warming temperate mid-latitude urban estuary with seasonal periodic hypoxia, during June through September from 2005 to 2019. Within this period, numerous facilities were upgraded to nitrogen removal over several years. The response of the bay is more consistent with “textbook” expectations for reduced chlorophyll and hypoxia than what was seen in many other systems—despite its complex coastline geometry, numerous river inputs, and widely-distributed treatment facilities. River flow drives inter-annual variability with increased load, density stratification, chlorophyll, and hypoxia in wet years. Mean 2013-2019 bay-wide total nitrogen load was 34% less than the 2005-2012 mean, a reduction of about 106 kg yr-1, comparable to the range of flow-driven inter-annual variations. Chlorophyll Index and Hypoxia Index event-based metrics applied to high-frequency time series observations at eight sites quantify exceedances of severe and moderate thresholds. Relatively steady 33% and 16% Chlorophyll Index declines, for severe and moderate thresholds, occurred from about 2007 to 2019. The Hypoxia Index declined markedly by 2009 and 2014 for severe and moderate thresholds, respectively, and remained at or near zero from 2014 to 2019. The load reduction explains chlorophyll and hypoxia declines better than physical processes including river flow, stratification, tidal variations, winds, sea level differences, and temperatures. River flow about 55% higher than the 2005-2019 mean would increase non-treatment facility loads by an amount comparable to the managed load decrease, so future wet summers could partially reverse the improvements. Long-term trends include warming of about 0.5°C decade-1, which reduces oxygen saturation by 0.1 mg l-1 decade-1. This rate is likely a lower bound for temperature-driven oxygen decreases, because warming can also accelerate phytoplankton growth and bacterial consumption. Without warming, the managed load decrease would have curtailed hypoxia more effectively. Climate trends should be at least as important to future eutrophication as the managed load decline because, in addition to warming influences, long-term increases in river flow would increase load and stratification

A tale of two spring blooms in a northeast estuary of the USA: how storms impact nutrients, multiple trophic levels and hypoxia

We explore how anomalously strong winter storms, superposed with managed nitrogen reduction, impacted the 2010 and 2018 spring blooms in the Narragansett Bay (41.62° N, 71.35° W). Anomalously strong winter storms preceding spring of 2010 and 2018 increased annual nutrient inputs above the long-term average annual values for the year, causing a large phytoplankton bloom in spring 2010 and a massive winter-spring bloom in 2018. Flooding from the stronger storm in 2010 caused a smaller increase in primary productivity than the smaller storms prior to spring 2018, probably due to increased flushing rates during the 2010 storm. Neither storm enhanced hypoxia the following summer. During both summers, hypoxia was typical of minimal-hypoxia years, indicating that managed nitrogen reduction which is strongest during summer, remained adequate even in the aftermath of organic inputs from large storms during the colder months. Additionally, some commercially fished species appeared to increase after the storm events. Storm nutrient impacts on commercial species suggest that increasing nitrogen inputs from treatment facilities in colder months might enhance Bay fisheries for squid and hard clam without diminishing summer water quality