Scaling Up: Recovering Costs to Enable Mission-Driven Library Publishing

This deposit contains the text and the slides of a presentation given at the second annual Library Publishing Forum, March 29, 2015, in Portland, OR.Of the 124 LPC members listed in the 2015 Library Publishing Directory, only eight organizations indicate that they receive any revenue from chargebacks to the authors, editors, faculty, departments, or organizations they serve. Michigan Publishing is not one of these, but by the time the 2016 Library Publishing Directory is published, it will be. Taking the emerging Michigan Publishing Services and the long-running Michigan Journals programs as case studies, this presentation makes the case that attempting to recover costs by charging for services provided allows library publishing initiatives to: * scale up sustainably, responding to faculty demand for new services and projects and providing better tools and infrastructure to their partners. * advertise services and recruit new offerings clearly and proactively, rather than scrambling to estimate costs for each new project or turning away projects due to insufficient capacity. * steward university resources--such as departmental funds, research funds, grants, etc.--well by leveraging existing skills and vendor relationships to meet faculty needs in an efficient and mutually beneficial way. We will share the cost model(s) that are emerging here at Michigan Publishing, along with a look under the hood at the challenges we have faced in developing this framework, including coordinating with the university’s central finance office, complying with federal regulations, and communicating these changes to our publishing partners. Finally, we will demonstrate that this is very much a work in progress by projecting where we hope this trajectory will take us in a few years’ time.http://deepblue.lib.umich.edu/bitstream/2027.42/111646/1/colmanwelzenbachScalingUp2015.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/111646/2/colmanwelzenbach-Scaling Up Slides2015.pdfDescription of colmanwelzenbachScalingUp2015.pdf : Rough text of the talkDescription of colmanwelzenbach-Scaling Up Slides2015.pdf : Slide

In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis

Universal drug susceptibility testing (DST) for tuberculosis is a major goal of the END TB strategy. PCR-based molecular diagnostic tests have been instrumental in increasing DST globally and several assays have now been endorsed by the World Health Organization (WHO) for use in the diagnosis of drug resistance. These endorsed assays, however, each interrogate a limited number of mutations associated with resistance, potentially limiting their sensitivity compared to sequencing-based methods. We applied an in silico method to compare the sensitivity and specificity of WHO-endorsed molecular based diagnostics to the mutation set identified by the WHO mutations catalogue using phenotypic DST as the reference. We found that, in silico, the mutation sets used by probe-based molecular diagnostic tests to identify rifampicin, isoniazid, pyrazinamide, levofloxacin, moxifloxacin, amikacin, capreomycin and kanamycin resistance produced similar sensitivities and specificities to the WHO mutation catalogue. PCR-based diagnostic tests were most sensitive for drugs where mechanisms of resistance are well established and localised to small genetic regions or a few prevalent mutations. Approaches using sequencing technologies can provide advantages for drugs where our knowledge of resistance is limited, or where complex resistance signatures exist

Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model

Genetic analysis of pathogenic organisms is a useful tool for linking human cases together and/or to potential environmental sources. The resulting data can also provide information on evolutionary patterns within a targeted species and phenotypic traits. However, the instruments often used to generate genotyping data, such as single nucleotide polymorphisms (SNPs), can be expensive and sometimes require advanced technologies to implement. This places many genotyping tools out of reach for laboratories that do not specialize in genetic studies and/or lack the requisite financial and technological resources. To address this issue, we developed a low cost and low tech genotyping system, termed agarose-MAMA, which combines traditional PCR and agarose gel electrophoresis to target phylogenetically informative SNPs

REC-PATH (Recovery Pathways): overview of a four-country study of pathways to recovery from problematic drug use

Although there has been a growth in recent years in recovery research, much of this has been from the United States, and there is very little comparative research in this area. This article describes the rationale, conceptual foundations and methods for a prospective, multicountry, cohort study aimed to map pathways to recovery from problematic illicit drug use, with a specific focus on gender differences in recovery pathways. This study combines qualitative and quantitative components and examines the impact of recovery policy on the accessibility and viability of recovery pathways in England, Scotland, Belgium, and The Netherlands. Additionally, the article describes five processes through which mechanisms for behavior change for recovery may be triggered. This study will provide opportunities for linking recovery outcome research with analyses of national recovery policies, while also addressing the gap in literature around female pathways to recovery

Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens

Melioidosis is an emerging infectious disease caused by the soil bacterium Burkholderia pseudomallei. In diagnostic and forensic settings, molecular detection assays need not only high sensitivity with low limits of detection but also high specificity. In a direct comparison of published and newly developed TaqMan PCR assays, we found the TTS1-orf2 assay to be superior in detecting B. pseudomallei directly from clinical specimens. The YLF/BTFC multiplex assay (targeting the Yersinia-like fimbrial/Burkholderia thailandensis-like flagellum and chemotaxis region) also showed high diagnostic sensitivity and provides additional information on possible geographic origin

Comparison of TaqMan PCR assays for detection of the melioidosis agent Burkholderia pseudomallei in clinical specimens

Melioidosis is an emerging infectious disease caused by the soil bacterium Burkholderia pseudomallei. In diagnostic and forensic settings, molecular detection assays need not only high sensitivity with low limits of detection but also high specificity. In a direct comparison of published and newly developed TaqMan PCR assays, we found the TTS1-orf2 assay to be superior in detecting B. pseudomallei directly from clinical specimens. The YLF/BTFC multiplex assay (targeting the Yersinia-like fimbrial/Burkholderia thailandensis-like flagellum and chemotaxis region) also showed high diagnostic sensitivity and provides additional information on possible geographic origin

DataCite Implementation Recommendations: A Report of the DataCite Task Force

This is a task force report outlining recommendations for the University of Michigan Library regarding investment in DataCite tools and policies.DataCite (http://datacite.org/) is a non-profit, international consortium whose members collaboratively address challenges of making data visible and accessible. In the United States, DataCite is represented by three organizations: the California Digital Library (CDL), the Office of Scientific and Technical Information (OSTI), and the Purdue University Libraries. As an addition to the growing network of services around data in the library, the University of Michigan Library has joined DataCite as a client through the Member or Allocator Agency, Purdue University Libraries. Purdue uses California Digital Library’s EZID service (http://n2t.net/ezid) to offer DataCite Digital Object Identifiers (DOIs).http://deepblue.lib.umich.edu/bitstream/2027.42/100249/1/DataCiteTaskForceReport.pdf-

Fine-scale Identification of the Most Likely Source of a Human Plague Infection

We describe an analytic approach to provide fine-scale discrimination among multiple infection source hypotheses. This approach uses mutation-rate data for rapidly evolving multiple locus variable-number tandem repeat loci in probabilistic models to identify the most likely source. We illustrate the utility of this approach using data from a North American human plague investigation