BOOTSTRAP CONFIDENCE INTERVALS FROM ADAPTIVE SAMPLING OF AN INSECT POPULATION

We construct 90% normal, percentile, and bias-corrected and accelerated confidence intervals using a finite population bootstrapping algorithm based on adaptive sampling in an agroecosystem. We evaluate the interval estimates based on sampling simulations of a spatially arranged population of plots that contain counts of beet webworms and based on an adaptive condition that generates small networks. The sampling distributions of the original sample estimates and of the bootstrap estimates were generally similar and symmetric. The simulation coverages were from 84% to 90% and similar under any of the sample sizes and any of the three confidence interval types. This study also serves as an example of how adaptive sampling may be used to estimate population characteristics of insects in agroecosystems

Morphological Differences Among Eyeless Amphipods in the Genus Stygobromus Dwelling in Different Subterranean Habitats

The amphipod genus Stygobromus occurs in a variety of subterranean habitats in North America, including caves, phreatic (groundwater) lakes, and superficial subterranean habitats (seeps and epikarst). The habitats share the absence of light but differ in other features, such as pore size of the habitat, available food, and degree of seasonality. Measurements of body size, antennal size, and antennal segment number of type specimens were compared for 56 species occurring in the eastern United States. Except for differences in body size, differences among species in the four different habitats were not significant. Body size was related to relative pore size of the habitat, e.g., epikarst, with the smallest spaces, had the smallest species. However, in all habitats, there was one very large species (\u3e 15mm); these enigmatic species apparently occupy a distinct ecological niche, perhaps being more predatory. Differences in relative antennal size showed no significant differences among habitats, and differences in number of antennal segments were marginally significant (P = 0.06) among habitat types and not in the predicted pattern. Differences among habitats in seasonality and available food seemed to be a minor part of the selective environment; absence of light seemed to be a major part of the selective environment

Evolutionary History and Phylodynamics of Influenza A and B Neuraminidase (NA) Genes Inferred from Large- Scale Sequence Analyses

Background: Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking. Methodology/Principal findings: Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A NA subtypes. Twenty-three lineages were identified within influenza A, two lineages were classified within influenza B, and most lineages were specific to host, subtype or geographical location. Interestingly, evolutionary rates vary not only among lineages but also among branches within lineages. The estimated tMRCAs of influenza lineages suggest that the viruses of different lineages emerge several months or even years before their initial detection. The dN/dS ratios ranged from 0.062 to 0.313 for influenza A lineages, and 0.257 to 0.259 for influenza B lineages. Structural analyses revealed that all positively selected sites are at the surface of the NA protein, with a number of sites found to be important for host antibody and drug binding. Conclusions/Significance: The divergence into influenza type A and B from a putative ancestral NA was followed by the divergence of type A into nine NA subtypes, of which 23 lineages subsequently diverged. This study provides a better understanding of influenza NA lineages and their evolutionary dynamics, which may facilitate early detection of newly emerging influenza viruses and thus improve influenza surveillance

Characterization of the estrogen receptor transfected MCF10A breast cell line 139B6

There has been increasing evidence which suggests that abnormal expression of the estrogen receptor (ER) protein in nonmalignant breast tissue may be important in the carcinogenic process. To examine the effects of ER expression in immortalized nonmalignant mammary epithelial cells, an expression vector containing human ER cDNA was transfected into the ER negative human breast cells, MCF10A. Characterization of a clone stably expressing ER, 139B6, provided evidence for the regulated synthesis of a functional ER capable of binding estradiol-17β (E 2 ) and undergoing processing. Expression of the ER gene did not enable E 2 to stimulate endogenous genes [progesterone receptor (PgR), pS2, cathepsin D and TGFα] which normally respond to estrogens in breast cancer cells. The ER in 139B6 cells was, however, capable of inducing expression of an ERE-regulated reporter gene, indicating its ability to interact with transcriptional machinery. Furthermore, cultures in log growth displayed a slight increase in doubling time in the presence of E 2 . These results indicate that ER expression alone is not sufficient to induce a transformed phenotype. Thus, the 139B6 cell line should provide a new model for determining what additional changes lead to increased growth potential in response to E 2 and for exploring how E 2 itself may help bring about changes leading to progression of preneoplastic breast epithelial cells.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44202/1/10549_2005_Article_BF01806507.pd

Web Archiving Democracy

Mary Haberle is a Web Archivist at Archive-It, which is the Internet Archive’s subscription web archiving service. She's part of a support team that provides training and direct support services to our partners, including the archivists on this panel who are all using Archive-It at their institutions. Dory Bower has been an Archives Specialist at the U.S. Government Publishing Office since 2010, where she has worked on a number of projects to increase access to electronic U.S. government resources. Dory began working with web archiving in 2011 and has played a key role in all aspects of the Federal Depository Library Program Web Archive. Megan Craynon has worked at the Maryland State Archives since 2011, and has spent the majority of that time as a team member on the web archiving project. She currently serves as the Deputy Director of Special Collections. Ben Goldman is the Kalin Librarian for Technological Innovations at Penn State University Libraries, where he has overseen web archiving efforts since 2012. Roger Christman is the Governors’ Records Archivist at the Library of Virginia. In his spare time, he also manages the Library’s web archiving program. Nicholas Worby is the Government Information and Statistics Librarian as well as the Web Archives Program Coordinator at the University of Toronto. Ian Milligan is an associate professor of digital and Canadian history at the University of Waterloo. He’s leading a Mellon-funded project to develop a cloud-based infrastructure for the analysis of web archives.As repositories of primary source materials, archives play a central role in supporting the democratic principles of transparency and accountability. Political discourse and many official records of government have shifted from analog to web-based delivery. Web archiving programs that collect content created by elected officials and governments are vital to a robust civil society, which is central to a healthy democracy. This panel brings together information professionals and a digital historian engaged with related content. Professionals actively acquiring websites of elected officials and online government publications will discuss why and how their institutions are building web archives in these areas and what gaps, if any, exist. Panelists will offer their perspectives on the current state of researcher access and how archives can better support researcher engagement with web archives. Questions of professional and institutional responsibility as citizens and as employees of democratic institutions will be explored

PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/

Integrating complementary survey methods to estimate catches in Norway’s complex marine recreational hook-and-line fishery

Marine recreational fishing is popular in Norway, but current estimates of the catches by resident and tourist anglers are lacking due to several challenges, in particular Norway’s long and intricate coastline with no defined access points and the large tourist fishery. To test methods for long-term monitoring of boat-based marine recreational anglers, estimate their catches, and characterize the fishery, we conducted a roving creel survey based on a novel spatial sampling frame and a survey of tourist fishing businesses in Troms and Hordaland County. These surveys showed that cod (Gadus morhua) and saithe (Pollachius virens) dominated the catches in Troms, while mackerel (Scomber scombrus) and saithe dominated the catches in Hordaland. The estimated total annual harvest of cod by all marine recreational anglers was 2 160 tonnes (relative standard error, or RSE 44%) in Troms and 73 tonnes (RSE 29%) in Hordaland, of which ∼40% (in weight) were landed in registered tourist fishing businesses, based on data from the tourist fishing survey. The results indicate that recreational anglers in Hordaland harvest more cod in coastal waters than commercial fishers. This study provides information for developing marine recreational fisheries monitoring in challenging survey situations to support science-based fisheries management.publishedVersio

STRENGTHENING REGIONAL COOPERATION IN FISHERIES DATA COLLECTION

fishPi was a research project with the aim of “Strengthening regional cooperation in the area of fisheries data collection”. The project brought together over 40 experts from 13 scientific institutes in 12 countries (10 member states (MS)) and two internationally recognised survey design experts. It was funded by EU MARE grant MARE/2014/19, with a 14 month timeline commencing in April 2015. This project has trialled the way sampling designs would be developed in a regional setting and showed that collaboration and consultation is required at face to face meetings through regional groups that focus on a particular group of fisheries. The project was the first step in this process and one of the main outcomes is the framework to take the process forward; developing data formats, data sharing agreements and easily accessible software for data sharing, checking and analysis, and for the simulation testing of sampling designs.European Unio

Second Workshop on Estimation with the RDBES data model (WKRDB-EST2; outputs from 2020 meeting)

This report shows how the new RDBES that is currently in development will be better able to support the recast EU Data Collection Framework (Regulation (EU) 2017/1004) than the existing RDB. The RDBES is an essential platform for MS and RCGs to fulfil their obligations towards documenting and improving data quality and designing and implementing regional sampling designs. The evaluation of data precision was performed using two complementary techniques. For relatively simple sampling designs it is possible to use analytical functions to calculate the precision (or a related statistical measure such as variance) of a statistical estimate. These calculations and implementations of them in R code are presented in this report. For more complicated sampling designs, the use of analytical functions is usually not feasible. In these cases, it is necessary to evaluate precision using numerical techniques, the main one of which is bootstrapping. This report discussed when bootstrapping is appropriate and gives several worked examples describing how bootstrapping can be applied in different cases. The evaluation of bias is a difficult subject and is hard to quantify. The approach followed in this report was to build on the previous work available in the ICES literature and identify and enumerate the main common sources of bias in catch sampling programs they describe. The information was collated and an evaluation performed as to whether data stored using the RDBES data format and reports issues from them can inform about the potential for bias in catch estimates. A set of example reports was coded that demonstrates the utility of the RDBES in relation to bias issues and can already help member states to identify how deviations in their sampling programmes and sampling variability may potentially lead to bias in their catch estimates