Zooplankton variability in the Northern Salish Sea over the past 3 decades, and relationships with Coho salmon

The past 30 years have seen huge changes in the populations of Pacific salmon in the Salish Sea. These changes include very large reductions in the abundances of Chinook and Coho, and high variability of Fraser River Sockeye salmon populations. The Salish Sea Marine Survival Program is a Canada – U.S. collaborative multi-year research initiative established to investigate two main questions: what has driven the very strong declines in abundances of Coho and Chinook populations in the Salish Sea since the 1980s, and what determines the interannual variability of present populations. In this study we examine these two questions from the perspective of zooplankton (including ichthyoplankton) populations in the Salish Sea since 1990. We identify interannual trends of total zooplankton biomass, and of its major constituents including those taxa identified as comprising important dietary items for Coho, Chinook, and Sockeye. We identify years with significant changes in zooplankton taxonomic composition, and compare these with environmental variables to identify potential “drivers of change” in these ecosystem. We conclude with analyses of how these relationships relate to variability in the key salmon species of this region

Modelling Ecosystem Processes Acting On Upper Trophic Level Managed Species in the Salish Sea – Lessons Learned and Future Goals

Ecosystem models provide a means to examine how large-scale drivers and food web interactions can influence change in marine species. Coho and Chinook salmon are iconic species in the Salish Sea and have been significant components of ecosystem models developed for its sub-basins. We present results from models of three regions in the Salish Sea: the Strait of Georgia, the Central Basin of Puget Sound, and the Southern Basin of Puget Sound. Each of these models provides reasonable simulations of how ecosystem-level mechanisms can influence changes in target managed species. While there is some overlap in these models’ ability to explore changes in mammals and fished species, regional differences remain that make it difficult to integrate knowledge at the scale of the Salish Sea as a whole. For example, the Strait of Georgia and Puget Sound models all suggest that bottom-up type dynamics have influenced the dynamics of many species. Significant contrast, however, can be seen in the dominance of the Central basin of Puget Sound by ratfish, approximately a third of all fish biomass whereas, in the Strait of Georgia, Pacific herring and small pelagic species account for a third of all fish biomass. Understanding these similarities and differences will help researchers explain why significant species like Coho and Chinook salmon can exhibit quite different population dynamics in regions of the Salish Sea. As part of an integrated project spearheaded by the Pacific Salmon Foundation and Long Live the Kings, we hope to increase the overlap in both species and mechanisms modelled in future iterations of these modelling efforts

Seasonal dynamics of oceanographic conditions, phytoplankton, and zooplankton in the Malaspina Strait, Strait of Georgia

Plankton dynamics in the Salish Sea may directly impact resident and migratory fish populations that are of major economic importance in the region. The Malaspina Strait in the northern Salish Sea is of particular interest as it is an important migration route for juvenile salmon. Here, we present data collected at three stations in the Malaspina Strait as part of the Citizen Science initiative of the Salish Sea Marine Survival Project. Sampling was conducted at bi-monthly (or higher) frequency from February to October, 2015 to 2017. Relationships between the regional hydrography, environmental parameters (temperature, salinity, dissolved oxygen, etc.), nutrient concentrations, and phytoplankton and zooplankton community composition are considered. Preliminary results indicate that 2015 was an anomalous year with an earlier-than-average (mid-February) spring phytoplankton bloom. Phytoplankton community composition was dominated by centric, chain-forming diatoms in spring of all years, cell densities were higher in spring 2015 compared to 2016 and 2017. In both 2015 and 2016, copepods dominated the abundances of zooplankton at the deep locations in Malaspina Strait. However, the biomass was dominated by taxa known to be the preferred prey of juvenile salmonids (euphausiids, amphipods, crab larvae). At the nearshore station in both years, zooplankton biomass was dominated by “other” taxa, in particular gelatinous plankton. Biomass of large calanoid copepods and euphausiids was significantly positively correlated to the relative abundance of diatoms. Biomass of small calanoid copepods and non-calanoid copepods, on the other hand, was positively correlated with the relative abundance of dinoflagellates. Further analyses will relate environmental variables to the observed seasonal variations in phytoplankton and zooplankton. Results from this study will ultimately be extended to include other Citizen Science stations in order to gain a better understanding of how bottom-up processes vary in different regions of the Salish Sea, and the potential implications for higher trophic levels

Dissecting DNA repair in adult high grade gliomas for patient stratification in the post-genomic era

Deregulation of multiple DNA repair pathways may contribute to aggressive biology and therapy resistance in gliomas. We evaluated transcript levels of 157 genes involved in DNA repair in an adult glioblastoma Test set (n=191) and validated in ‘The Cancer Genome Atlas’ (TCGA) cohort (n=508). A DNA repair prognostic index model was generated. Artificial neural network analysis (ANN) was conducted to investigate global gene interactions. Protein expression by immunohistochemistry was conducted in 61 tumours. A fourteen DNA repair gene expression panel was associated with poor survival in Test and TCGA cohorts. A Cox multivariate model revealed APE1, NBN, PMS2, MGMT and PTEN as independently associated with poor prognosis. A DNA repair prognostic index incorporating APE1, NBN, PMS2, MGMT and PTEN stratified patients in to three prognostic sub-groups with worsening survival. APE1, NBN, PMS2, MGMT and PTEN also have predictive significance in patients who received chemotherapy and/or radiotherapy. ANN analysis of APE1, NBN, PMS2, MGMT and PTEN revealed interactions with genes involved in transcription, hypoxia and metabolic regulation. At the protein level, low APE1 and low PTEN remain associated with poor prognosis. In conclusion, multiple DNA repair pathways operate to influence biology and clinical outcomes in adult high grade gliomas

Establishing the added benefit of measuring MMP9 in FOB positive patients as a part of the Wolverhampton colorectal cancer screening programme

<p>Abstract</p> <p>Background</p> <p>Bowel cancer is common and a major cause of death. The NHS is currently rolling out a national bowel cancer screening programme that aims to cover the entire population by 2010. The programme will be based on the Faecal Occult Blood test (FOBt) that reduces mortality from colon cancer by 16%. However, FOB testing has a relatively low positive predictive value, with associated unnecessary cost, risk and anxiety from subsequent investigation, and is unacceptable to a proportion of the target population. Increased levels of an enzyme called matrix metalloproteinase 9 (MMP9) have been found to be associated with colorectal cancer, and this can be measured from a blood sample. MMP9 has potential for detecting those at risk of having colorectal cancer. The aim of this study is to assess whether MMP9 estimation enhances the predictive value of a positive FOBt.</p> <p>Methods and design</p> <p>FOBt positive people aged 60–69 years attending the Wolverhampton NHS Bowel Cancer Screening Unit and providing consent for colonoscopy will be recruited. Participants will provide a blood sample prior to colonoscopy and permission for collection of the clinical outcome from screening unit records. Multivariate logistic regression analyses will determine the independent factors (patient and disease related, MMP9) associated with the prediction of neoplasia.</p> <p>Discussion</p> <p>Colorectal cancer is a major cause of morbidity and mortality. Pilot studies have confirmed the feasibility of the national cancer screening programme that is based on FOBt. However, the test has high false positive rates. MMP9 has significant potential as a marker for both adenomas and cancers. This study is to examine whether using MMP9 as an adjunct to FOBt improves the accuracy of screening and reduces the number of false positive tests that cause anxiety and require invasive and potentially harmful investigation.</p

Different paths to the modern state in Europe: the interaction between domestic political economy and interstate competition

Theoretical work on state formation and capacity has focused mostly on early modern Europe and on the experience of western European states during this period. While a number of European states monopolized domestic tax collection and achieved gains in state capacity during the early modern era, for others revenues stagnated or even declined, and these variations motivated alternative hypotheses for determinants of fiscal and state capacity. In this study we test the basic hypotheses in the existing literature making use of the large date set we have compiled for all of the leading states across the continent. We find strong empirical support for two prevailing threads in the literature, arguing respectively that interstate wars and changes in economic structure towards an urbanized economy had positive fiscal impact. Regarding the main point of contention in the theoretical literature, whether it was representative or authoritarian political regimes that facilitated the gains in fiscal capacity, we do not find conclusive evidence that one performed better than the other. Instead, the empirical evidence we have gathered lends supports to the hypothesis that when under pressure of war, the fiscal performance of representative regimes was better in the more urbanized-commercial economies and the fiscal performance of authoritarian regimes was better in rural-agrarian economie

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie