Empowering Libraries Through Controlled Digital Lending

Libraries play a crucial societal role in providing access to information and preserving that information over time. Unfortunately that role is under threat from a number of sources: budget reductions, exorbitant licensing fees, and the inability for libraries to own (not lease) digital content. In this session, Chris Freeland, Director of the Open Libraries program at the Internet Archive, will cover how existing library practices like interlibrary loan & controlled digital lending empower libraries to reach their patrons where they\u27re learning—online—and the new efforts helping libraries take control of their digital futures

An evaluation of taxonomic name finding & next steps in Biodiversity Heritage Library (BHL) developments

The Biodiversity Heritage Library (BHL) is an international consortium of natural history libraries that are actively scanning scientific literature from their collections and publishing the digitized content online at http://www.biodiversitylibrary.org. The presentation will cover updates on BHL progress thus far, including a review of the BHL portal application and services developed for bibliographic data exchange, as well as a roadmap of features scheduled for design and development. Of interest to taxonomists and bioinformaticians, the presentation will also cover a recently completed evaluation of taxonomic name finding algorithms, including TaxonFinder and FAT. Discussion will include a review of successes and failures in extracting taxonomic name strings from the BHL corpus, as well as suggestions for improvement

Ensuring Mobility-Supporting Environments for an Aging Population: Critical Actors and Collaborations

Successful aging takes on an array of attributes, including optimal health and community participation. Research indicates that (1) persons with disabilities, including age-related disabilities, report frequent barriers to community participation, including unsuitable building design (43%), transportation (32%), and sidewalks/curbs (31%), and (2) many seniors report an inability to cross roads safely near their homes. This paper attempts to define mobility-related elements that contribute to optimal health and quality of life, within the context of successful aging. It then examines the impacts of community design on individual mobility, delving into which traditional and nontraditional actors—including architects, urban planners, transportation engineers, occupational therapists, and housing authorities—play critical roles in ensuring that community environments serve as facilitators (rather than barriers) to mobility. As America ages, mobility challenges for seniors will only increase unless both traditional aging specialists and many nontraditional actors make a concerted effort to address the challenges

Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections.

Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential

Discovery and publishing of primary biodiversity data associated with multimedia resources: The Audubon Core strategies and approaches

The Audubon Core Multimedia Resource Metadata Schema is a representation-free vocabulary for the description of biodiversity multimedia resources and collections, now in the final stages as a proposed Biodiversity Informatics Standards (TDWG) standard. By defining only six terms as mandatory, it seeks to lighten the burden for providing or using multimedia useful for biodiversity science. At the same time it offers rich optional metadata terms that can help curators of multimedia collections provide authoritative media that document species occurrence, ecosystems, identification tools, ontologies, and many other kinds of biodiversity documents or data. About half of the vocabulary is re-used from other relevant controlled vocabularies that are often already in use for multimedia metadata, thereby reducing the mapping burden on existing repositories. A central design goal is to allow consuming applications to have a high likelihood of discovering suitable resources, reducing the human examination effort that might be required to decide if the resource is fit for the purpose of the application

The taxonomic name resolution service : an online tool for automated standardization of plant names

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.BJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191)

Nutritional correlates of koala persistence in a low-density population

It is widely postulated that nutritional factors drive bottom-up, resource-based patterns in herbivore ecology and distribution. There is, however, much controversy over the roles of different plant constituents and how these influence individual herbivores and herbivore populations. The density of koala (Phascolarctos cinereus) populations varies widely and many attribute population trends to variation in the nutritional quality of the eucalypt leaves of their diet, but there is little evidence to support this hypothesis. We used a nested design that involved sampling of trees at two spatial scales to investigate how leaf chemistry influences free-living koalas from a low-density population in south east New South Wales, Australia. Using koala faecal pellets as a proxy for koala visitation to trees, we found an interaction between toxins and nutrients in leaves at a small spatial scale, whereby koalas preferred trees with leaves of higher concentrations of available nitrogen but lower concentrations of sideroxylonals (secondary metabolites found exclusively in eucalypts) compared to neighbouring trees of the same species. We argue that taxonomic and phenotypic diversity is likely to be important when foraging in habitats of low nutritional quality in providing diet choice to tradeoff nutrients and toxins and minimise movement costs. Our findings suggest that immediate nutritional concerns are an important priority of folivores in low-quality habitats and imply that nutritional limitations play an important role in constraining folivore populations. We show that, with a careful experimental design, it is possible to make inferences about populations of herbivores that exist at extremely low densities and thus achieve a better understanding about how plant composition influences herbivore ecology and persistence.IW and WF received a grant from New South Wales (NSW) Department of Environment, Climate Change & Water

Name Matters: Taxonomic Name Recognition (TNR) in Biodiversity Heritage Library (BHL)

Taxonomic Name Recognition is prerequisite for more advanced processing and mining of full-text taxonomic literatures. This paper investigates three issues of current TNR tools in detail: (1) The difficulties and methods used in TNRs. (2) The performance of Optical Character Recognition (OCR) and TNR tools by samples from Biodiversity Heritage Library (BHL). (3) The methods for potential improvement. We found that the performances of current TNR techniques need to be improved. A detailed error analysis reveals that sublanguage characteristics account for much of the error. A preliminary experiment using NaiveBayes (NB) models shows the potential of using machine learning (ML) in TNR

Identifying the Social and Technical Barriers affecting engagement in online Community Archives: A Preliminary Study of “Documenting Ferguson” Archive.

This pilot study seeks to explore the social and technological barriers affecting user engagement in online community archives. We have explored this question using the Documenting Ferguson digital archive, which was built by Washington University Libraries at Washington University in St. Louis in response to the shooting death of unarmed teenager Michael Brown on August 9, 2014, by police officer Darren Wilson in Ferguson, Missouri, and the resulting social protests. The archive, online at http://digital.wustl.edu/ferguson/, was initially built for anyone who participated in events in and around Ferguson to upload their digital images and videos from the protests, with a goal of providing diverse perspectives on the events through the development of a community archive with an engaged user base. To date, the archive has grown to include more than 1,000 digital objects from 44 contributors, including photos, audio files, videos, and personal stories