Testing Our Assumptions: Preliminary Results from the Data Curation Network

Objective: Data curation is becoming widely accepted as a necessary component of data sharing. Yet, as there are so many different types of data with various curation needs, the Data Curation Network (DCN) project anticipated that a collaborative approach to data curation across a network of repositories would expand what any single institution might offer alone. Now, halfway through a three-year implementation phase, we’re testing our assumptions using one year of data from the DCN. Methods: Ten institutions participated in the implementation phase of a shared staffing model for curating research data. Starting on January 1, 2019, for 12 months we tracked the number, file types, and disciplines represented in data sets submitted to the DCN. Participating curators were matched to data sets based on their self-reported curation expertise. Aspects such as curation time, level of satisfaction with the assignment, and lack of appropriate expertise in the network were tracked and analyzed. Results: Seventy-four data sets were submitted to the DCN in year one. Seventy-one of them were successfully curated by DCN curators. Each curation assignment takes 2.4 hours on average, and data sets take a median of three days to pass through the network. By analyzing the domain and file types of first- year submissions, we find that our coverage is well represented across domains and that our capacity is higher than the demand, but we also observed that the higher volume of data containing software code relied on certain curator expertise more often than others, creating potential unbalance. Conclusions: The data from year one of the DCN pilot have verified key assumptions about our collaborative approach to data curation, and these results have raised additional questions about capacity, equitable use of network resources, and sustained growth that we hope to answer by the end of this implementation phase

Insights into the development of Ixodes scapularis: a resource for research on a medically important tick species

Ticks (Acari: Ixodida) are arthropod ectoparasites dependent on a bloodmeal from a vertebrate host at each developmental stage for completion of their life cycle. This tick feeding cycle impacts animal health by causing damage to hides, secondary infections, immune reactions and diseases caused by transmission of pathogens. The genus Ixodes includes several medically important species that vector diseases, including granulocytic anaplasmosis and Lyme disease. I. scapularis, commonly called the black-legged or deer tick, is a medically-important tick species in North America and therefore was the first tick genome to be sequenced, thus serving as an important resource for tick research. This Primer focuses on the normal developmental cycle and laboratory rearing of I. scapularis. Definition of normal morphology, along with a consistent source of laboratory-reared I. scapularis, are fundamental for all aspects of future research, especially the effects of genetic manipulation and the evaluation of tick vaccine efficacy. Recent research important for the advancement of tick research, namely the development of tick cell culture systems for study of ticks and tick-borne pathogens, RNA interference for genetic manipulation of ticks and discovery of candidate antigens for development of tick vaccines, are briefly presented along with areas to target for future research.The preparation of this chapter was partially supported by the EU FP7 ANTIGONE project number 278976, and the Walter R. Sitlington Endowed Chair for Food Animal Research to K.M. Kocan.Peer Reviewe

Towards Linked Data for Oceanographic Science: The R2R Eventlogger Project, Controlled Vocabularies, and Ontologies at The MBLWHOI Library

Objective: Research vessels coordinated by the United States University-National Oceanographic Laboratory System (US-UNOLS) collect data which are considered important oceanographic science research products. The NSF-funded Rolling Deck to Repository (R2R) project aims to improve access to these data and diminish barriers to their use. One aspect of the R2R project has been to develop a shipboard scientific event logging system, Eventlogger, which incorporates best practice guidelines, controlled vocabularies, a cruise metadata schema, and a scientific event log. Eventlogger facilitates the eventual ingestion of datasets into oceanographic data repositories for subsequent integration and synthesis by investigators. The careful use of controlled vocabularies and ontologies is an important feature of this system, as the use of internationally-informed, consensus-driven controlled vocabularies will make data sets more interoperable, discoverable and reusable. Methods: The R2R Eventlogger project is led by Woods Hole Oceanographic Institution (WHOI), and the management of the controlled vocabularies is led by the Data Librarian in the Marine Biological Laboratory/Woods Hole Oceanographic Institution (MBLWHOI) Library. The first target vocabulary has been one for oceanographic instruments. Management of this vocabulary has thus far consisted of reconciling project vocabulary terms with the more widely used community vocabularies served by the NERC Vocabulary Server v2.0 (NVS2.0): terms included in the SeaDataNet Device Catalogue (L22) and the SeaDataNet Device Category vocabularies (L05). Rather than adopt existing community terms, it is more often the case that local terms are mapped by the Data Managers in the NSF-funded Biological and Chemical Oceanographic Data Management Office (BCO-DMO) to community terms, which preserves any important information and meaning investigators impart through the process of assigning these local terms, and has less impact on researchers. New terms, those that cannot be mapped to the existing community vocabularies (often custom, or modified instruments), are submitted for review to the SeaVOX governance process for addition to the community vocabularies. These vocabularies and their mappings are an important part of the aforementioned Eventlogger system. Before a research cruise, investigators configure the instruments they intend to use for their science activities. The instruments available for selection are provided by the MBLWHOI Data Librarian, who curates UNOLS ship-specific lists of standard shipboard instruments using terms for instruments from the R2R Eventlogger Project Vocabulary. Nonstandard shipboard instruments a researcher or investigator wishes to use can also be added, and these instrument terms will eventually be inducted into the R2R Eventlogger Project Vocabulary. Results: Eventlogger is currently being tested across the UNOLS fleet. A large submission of suggested instrument terms to the SeaDataNet community listserv is currently in progress. New tools for facilitating the management, mapping, and use of these controlled vocabularies are being developed, and new projects with eager partners are envisioned. Ideas for future controlled vocabularies for the ocean science community include: Cruise IDs, Persons, and Ships. Conclusions: The promotion and use of controlled vocabularies and ontologies will pave the way for linked data in oceanographic science. By mapping local terms to authoritative and community-accepted terms, links are created whereby related data sets can be better discovered, and utilized. Librarians have an established history of working with controlled vocabularies and metadata. Libraries, have and will continue to, serve as centers for information discovery as well as a natural home for the management of standards

Updated checklist of the mosquitoes of Oklahoma including new state records and West Nile virus vectors, 2003-06

The mosquito fauna of Oklahoma has not been evaluated since 1965 and no report has been published concerning species associated with urban areas in the state. Mosquito collections were conducted as part of the West Nile virus (WNV) surveillance program between April and November from 2003 to 2006, using standard collection methods. A total of 74,756 adults were collected in 26 urban centers in 16 counties of Oklahoma. Altogether, 40 species were recorded during this study period, bringing the total mosquito species recorded in Oklahoma to 62 species in 9 different genera and 18 subgenera. An updated checklist of Oklahoma mosquito fauna is included with a comparison to historical records. New state records include 3 species: Aedes muelleri, Anopheles perplexens, and Culex coronator. In addition to updating the checklist, 12 species of mosquitoes were tested for WNV. Pools of Culex pipiens complex represented the highest proportion testing positive for WNV (134/766, 17.5%), followed by Cx. tarsalis (13/192, 6.8%) and Aedes albopictus (5/215, 2.3%). West Nile virus-positive mosquitoes were detected earliest in June 2005 and latest in November 2004. Infected Cx. pipiens complex testing positive for WNV were more prevalent in the eastern and central areas of Oklahoma, whereas positive Cx. tarsalis were found mainly in the western areas of the state. This distinct geographical difference needs to be monitored and followed up to ensure optimal mosquito control efforts in Oklahoma communities with mosquito control capabilities.Peer reviewedEntomology and Plant Patholog

Updated distribution of Aedes albopictus in Oklahoma, and implications in arbovirus transmission

A series of statewide surveys were conducted in Oklahoma in the summers between 1991 and 2004 to identify the distribution of Aedes albopictus. Adult mosquitoes were identified in 63 counties, bringing the currently known distribution of Ae. albopictus in the state to 69 of 77 counties. The widespread presence of Ae. albopictus in Oklahoma has important current and future public and veterinary health implications for surveillance and control efforts.Peer reviewedEntomology and Plant Patholog

First record of Aedes japonicus japonicus in Oklahoma, 2017

In spring 2017, mosquito larvae were collected from 25 sites across eastern Oklahoma as part of a Zika virus vector surveillance effort. Aedes japonicus japonicus larvae were collected from horse troughs at 2 sites in Ottawa County, OK. Identification was made using 1 larva stored in 70% ethanol and 3 adult females reared from the larvae. Another invasive mosquito species, Culex coronator, was detected at 2 different sites, adding 2 additional counties to the 9 where the species had been previously reported. The presence of these invasive species in Oklahoma may have an impact on future regional arbovirus concerns.Peer reviewedEntomology and Plant Patholog

Pictorial key for identification of immature stages of common ixodid ticks found in pastures in Oklahoma

Many species of ixodid ticks in the United States are parasitic on cattle and pose a threat to veterinary and public health for those engaged in occupations in pasturelands. While encountered often, nymphs and larvae of the most common tick species can be difficult to identify, yet research associated with tick ecology and epidemiology of tick-borne infection requires proper identification. High-quality images were prepared of the larval and nymphal stages of the most common species of ticks in Oklahoma pastures: larvae of the lone star tick, Amblyomma americanum (Linnaeus), Gulf coast tick, Amblyomma maculatum Koch, winter tick, Dermacentor albipictus (Packard), American dog tick, Dermacentor variabilis (Say), blacklegged tick, Ixodes scapularis Say, and brown dog tick, Rhipicephalus sanguineus (Latrielle); and nymphs of A. americanum, A. maculatum, D. variabilis, I. scapularis, and R. sanguineus. A dichotomous key and pictorial guide for each life stage were prepared.Peer reviewedEntomology and Plant Patholog

Mycobiome Sequencing and Analysis Applied to Fungal Community Profiling of the Lower Respiratory Tract During Fungal Pathogenesis

Invasive fungal infections are an increasingly important cause of human morbidity and mortality. We generated a next-generation sequencing (NGS)-based method designed to detect a wide range of fungi and applied it to analysis of the fungal microbiome (mycobiome) of the lung during fungal infection. Internal transcribed spacer 1 (ITS1) amplicon sequencing and a custom analysis pipeline detected 96% of species from three mock communities comprised of potential fungal lung pathogens with good recapitulation of the expected species distributions (Pearson correlation coefficients r = 0.63, p = 0.004; r = 0.71, p < 0.001; r = 0.62, p = 0.002). We used this pipeline to analyze mycobiomes of bronchoalveolar lavage (BAL) specimens classified as culture-negative (n = 50) or culture-positive (n = 39) for Blastomyces dermatitidis/gilchristii, the causative agent of North America blastomycosis. Detected in 91.4% of the culture-positive samples, Blastomyces dominated (>50% relative abundance) the mycobiome in 68.6% of these culture-positive samples but was absent in culture-negative samples. To overcome any bias in relative abundance due to between-sample variation in fungal biomass, an abundance-weighting calculation was used to normalize the data by accounting for sample-specific PCR cycle number and PCR product concentration data utilized during sample preparation. After normalization, there was a statistically significant greater overall abundance of ITS1 amplicon in the Blastomyces-culture-positive samples versus culture-negative samples. Moreover, the normalization revealed a greater biomass of yeast and environmental fungi in several Blastomyces-culture-positive samples than in the culture-negative samples. Successful detection of Coccidioides, Scedosporium, Phaeoacremonium, and Aspergillus in 6 additional culture-positive BALs by ITS1 amplicon sequencing demonstrates the ability of this method to detect a broad range of fungi from clinical specimens, suggesting that it may be a potentially useful adjunct to traditional fungal microbiological testing for the diagnosis of respiratory mycoses

Guide to the twelve most-important Oklahoma mosquitoes of concern for pest control specialists

The Oklahoma Cooperative Extension Service periodically issues revisions to its publications. The most current edition is made available. For access to an earlier edition, if available for this title, please contact the Oklahoma State University Library Archives by email at [email protected] or by phone at 405-744-6311

Lessons learned: Linking patient-reported outcomes data with administrative databases

Introduction Since 2007, Cancer Care Ontario (CCO) has systematically collected patient-reported outcomes (PROs) in the form of symptom data, for cancer outpatients visiting regional cancer centres or affiliate institutions. Data are used in real-time to facilitate conversation between clinicians and patients and have recently been combined with provincial administrative databases. Objectives and Approach CCO collects PROs using the Edmonton Symptom Assessment System (ESAS), which scores 9 symptoms on a scale of 0 (no symptoms) to 10 (worst symptom severity). Data were imported from CCO in 2015 and linked to a cancer cohort at ICES. We investigated differences between patients who completed $\geq$1 ESAS record and patients who did not, as well as the number of records, timing of data collection and missingness. We describe our experience linking and using the PRO data to administrative data, including presenting trajectories of symptoms over time and combining scores into composite indices. Results 120,745 cancer patients had 729,861 symptom records between 2007 and 2014. Not all patients with a cancer diagnosis had $\geq$1 ESAS record and this varied by patient, disease and system level factors. Because implementation occurred from a clinical perspective, data collection was irregular within and across patients and depended on treatment and other factors; the number of records per patient varied, as well the number of contributing patients in each time period following diagnosis. Attempts were made to create meaningful composite indices by combining all symptom scores as well as combining multiple high scores for each individual symptom. As a result, selecting the best statistical analysis to use these PRO data as an exposure or outcome is still uncertain. Conclusion/Implications PRO data linked to provincial, administrative data holdings represent a new frontier for population-based cancer research, both in their challenging structure as well as their implications for clinical practice and health system. These lessons learned will hopefully support other researchers rigorous use of these data in the future