Developing an e-infrastructure for social science

We outline the aims and progress to date of the National Centre for e-Social Science e-Infrastructure project. We examine the challenges faced by the project, namely in ensuring outputs are appropriate to social scientists, managing the transition from research projects to service and embedding software and data within a wider infrastructural framework. We also provide pointers to related work where issues which have ramifications for this and similar initiatives are being addressed

Unmanned Surface Vessels for Bridge Scour Monitoring

2016-0430Scour at bridge substructure units can cause undermining of footings and exposure of piles, which can lead to bridge failure. Monitoring of the stream bed elevations around a scour critical bridge to identify whether or not scour is occurring during a high-flow event is critical. Working on or near the water may be dangerous during these events. The study investigated various techniques to monitor bridge scour during high-flow events. Sonar has been the leading technique when completing underwater investigations. Different sonar devices were compared: single-beam echo sounder, multi-beam echo sounder, and side-scan. Based on parameters of cost, water depths less than 30 feet, data retrieval, processing, and quality, a single-beam echo sounder, sidescan, and the post-processing software SARHawk, was recommended. Multiple access techniques were assessed based on personnel safety, ease of deployment, and efficient mobilization. Research concluded that a remotely operated unmanned surface vessel (USV) can best complete the following: Operate in turbulent waters with high current near substructure units or debris; Obtain depth readings in water 3 to 30 feet deep; Transmit real-time images and data to shore station; Deploy rapidly and transport easily. Several USVs on the market were compared by means of a rating system and equipment testing. The USVs were rated on parameters outlined in specification sheets, in-person testing, and cost. The rating system identified the company and model of USV recommended. The USV from Hydronalix called Sonar EMILY, equipped with single-beam sonar for water depths, sidescan sonar to obtain images of substructure units below water, topside camera to view the underside of bridges and performance characteristics to operate in turbulent waters with high current near substructure units or debris. The purchase cost for the USV, data acquisition laptop, and running gear is approximately $50,000

Western Gull Foraging Behavior as an Ecosystem State Indicator in Coastal California

With accelerating climate variability and change, novel approaches are needed to warn managers of changing ecosystem state and to identify appropriate management actions. One strategy is using indicator species—like seabirds as ecosystem sentinels—to monitor changes in marine environments. Here, we explore the utility of western gulls (Larus occidentalis) breeding on Southeast Farallon Island as a proxy of ecosystem state in coastal California by investigating the interannual variability in gull foraging behavior from 2013 to 2019 in relation to upwelling conditions, prey abundances, and overlap with humpback whales (Megaptera novaeangliae) as gulls frequently feed in association with whales. Western gulls have a flexible diet and forage on land and at-sea. We combined gull GPS tracking data during the incubation phase, ecosystem survey data on multiple predator and prey species, and derived oceanographic upwelling products. When foraging at sea, gulls overlapped with cool upwelled waters. During 2015–2017, 25% more gull foraging trips visited land than in other years, where land trips were on average ∼8 h longer and 40% further than sea trips, which coincided with high compression of coastally upwelled waters (habitat compression) in 2015–2016. Gull foraging behavior was related to local prey abundances, where more foraging occurred near shore or on land when prey abundances were low. However, visual surveys indicated that ∼70% of humpback whale observations co-occurred with gulls, and the year with the most foraging on land (2017) corresponded to regionally low relative whale abundances, suggesting gull movement patterns could be an indicator of whale presence. Further, both whales and gulls forage near-shore under high upwelling habitat compression and low krill abundance. Hence, the deployment of year-round tags on gulls with the capability of near real-time data accessibility could provide important fine-scale metrics for conservation and management of the threatened yet recovering eastern Pacific humpback whale population between infrequent and coarse surveys. Entanglement in fishing gear and ship strikes are major inhibitors to whale recovery and have increased concomitantly with human use of ocean resources. Moreover, as climate variability and change increase, novel indicators should be explored and implemented to inform marine spatial planning and protect species across multiple scales from new risks

The historical ecology of Pacific herring: : Tracing Alaska Native use of a forage fish

Long-term use of herring by Alaska Natives is not well-documented over space or through time, yet this information can illuminate pre-industrial patterns of herring abundance and distribution. Such information is important to understand the sustained relationships Alaska Native fishers and egg collectors have had with herring. Understanding the genetics of pre-industrial herring may also inform management of the fish and fisheries to insure their survival into the future. In this paper, we attempt a contextualized account of the long-term history of Alaska Native herring fisheries, bringing together archaeological, ethnographic, and ethnohistorical data. We tie these together as background for presenting the preliminary results of the NSF-funded project, The Archaeology of Herring: Reconstructing the Past to Redeem the Future (No. 1203868). We have now tested 84 herring bone samples from 17 archaeological sites in Alaska expanding beyond Speller et al. (2012), having tripled the earlier archaeological dataset. The oldest herring bones identified archaeologically in Alaska are dated to more than 10,000 cal BP. Early Holocene and Middle Holocene sites have also yielded herring bones, although most of the record dates to the last 2400 years. Preservation of genetic information is effectively complete for the last 2400 years, but achievable back to the terminal Pleistocene (68% success rate for samples between 10,500 and 2400 cal BP). This gives considerable confidence to the potential to expand the analyses and develop a richer pattern of biological variability. The resulting data show genetic continuity between archaeological and modern herring populations. The main technical challenge for the future is to extract adequate amounts of nuclear DNA from the ancient samples for identifying more informative DNA markers that can be used to more effectively reveal any population diversity and/or population size changes over time when compared to modern herring

Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas

Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylated domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

The combined application of next-generation sequencing platforms has provided an economical approach to unlocking the potential of the turkey genome

State of the California Current 2013-14: El Niño Looming

In 2013, the California current was dominated by strong coastal upwelling and high productivity. Indices of total cumulative upwelling for particular coastal locations reached some of the highest values on record. Chlorophyll a levels were high throughout spring and summer. Catches of upwelling-related fish species were also high. After a moderate drop in upwelling during fall 2013, the California current system underwent a major change in phase. Three major basin-scale indicators, the PDO, the NPGO, and the ENSO-MEI, all changed phase at some point during the winter of 2013/14. The PDO changed to positive values, indicative of warmer waters in the North Pacific; the NPGO to negative values, indicative of lower productivity along the coast; and the MEI to positive values, indicative of an oncoming El Niño. Whereas the majority of the California Current system appears to have transitioned to an El Niño state by August 2014, based on decreases in upwelling and chlorophyll a concentration, and increases in SST, there still remained pockets of moderate upwelling, cold water, and high chlorophyll a biomass at various central coast locations, unlike patterns seen during the more major El Niños (e.g., the 97–98 event). Catches of rockfish, market squid, euphausiids, and juvenile sanddab remained high along the central coast, whereas catches of sardine and anchovy were low throughout the CCS. 2014 appears to be heading towards a moderate El Niño state, with some remaining patchy regions of upwelling-driven productivity along the coast. Superimposed on this pattern, three major regions have experienced possibly non-El Niño-related warming since winter: the Bering Sea, the Gulf of Alaska, and offshore of southern California. It is unclear how this warming may interact with the predicted El Niño, but the result will likely be reduced growth or reproduction for many key fisheries species

State of the California Current 2012–13: No Such Thing as an "Average" Year

This report reviews the state of the California Current System (CCS) between winter 2012 and spring 2013, and includes observations from Washington State to Baja California. During 2012, large-scale climate modes indicated the CCS remained in a cool, productive phase present since 2007. The upwelling season was delayed north of 42˚N, but regions to the south, especially 33˚ to 36˚N, experienced average to above average upwelling that persisted throughout the summer. Contrary to the indication of high production suggested by the climate indices, chlorophyll observed from surveys and remote sensing was below average along much of the coast. As well, some members of the forage assemblages along the coast experienced low abundances in 2012 surveys. Specifically, the concentrations of all lifestages observed directly or from egg densities of Pacific sardine, Sardinops sagax, and northern anchovy, Engraulis mordax, were less than previous years’ survey estimates. However, 2013 surveys and observations indicate an increase in abundance of northern anchovy. During winter 2011/2012, the increased presence of northern copepod species off northern California was consistent with stronger southward transport. Krill and small-fraction zooplankton abundances, where examined, were generally above average. North of 42˚N, salps returned to typical abundances in 2012 after greater observed concentrations in 2010 and 2011. In contrast, salp abundance off central and southern California increased after a period of southward transport during winter 2011/2012. Reproductive success of piscivorous Brandt’s cormorant, Phalacrocorax penicillatus, was reduced while planktivorous Cassin’s auklet, Ptychoramphus aleuticus was elevated. Differences between the productivity of these two seabirds may be related to the available forage assemblage observed in the surveys. California sea lion pups from San Miguel Island were undernourished resulting in a pup mortality event perhaps in response to changes in forage availability. Limited biological data were available for spring 2013, but strong winter upwelling coastwide indicated an early spring transition, with the strong upwelling persisting into early summer