William H. Walters

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art. ABSTRACT Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5′ end, allowing for a range of different 3′ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies. IMPORTANCE We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.

Bibliographic index coverage of a multidisciplinary field

This study examines the literature of a multidisciplinary field, later-life migration, and evaluates the effectiveness of 12 bibliographic databases in indexing that literature. Five journals--three in social gerontology, one in rural sociology, and one in regional science--account for 40% of the papers published in this area. The disciplines that publish the most work on later-life migration are not necessarily those that provide the best index coverage, however. Moreover, four multidisciplinary databases each provide better index coverage than any single-subject index. The relatively low degree of overlap among the 12 databases suggests that scholars working on topics such as later-life migration must continue to rely on a wide range of bibliographic tools, both disciplinary and multidisciplinary.

Disciplinary, national, and departmental contributions to the literature of library and information science, 2007-2012

We investigate the contributions of particular disciplines, countries, and academic departments to the literature of library and information science (LIS) using data for the articles published in 31 journals from 2007 to 2012. In particular, we examine the contributions of authors outside the United States, the United Kingdom, and Canada; faculty in departments other than LIS; and practicing librarians. Worldwide, faculty in LIS departments account for 31% of the journal literature; librarians, 23%; computer science faculty, 10%; and management faculty, 10%. The top contributing nations are the United States, the United Kingdom, Spain, China, Canada, and Taiwan. Within the United States and the United Kingdom, the current productivity of LIS departments is correlated with past productivity and with other measures of reputation and performance. More generally, the distribution of contributions is highly skewed. In the United States, five departments account for 27% of the articles contributed by LIS faculty; in the United Kingdom, four departments account for nearly two‐thirds of the articles. This skewed distribution reinforces the possibility that high‐status departments may gain a permanent advantage in the competition for students, faculty, journal space, and research funding. At the same time, concentrations of research‐active faculty in particular departments may generate beneficial spillover effects.

The Cost Implications of Open-access Publishing in the Life Sciences

ABSTRACT Open-access journals are growing in number and importance. Because they rely on revenue from publication fees rather than subscriptions, these journals have important economic implications for the institutions that sponsor, produce, and use research in the life sciences. This article shows how the wholesale adoption of open-access pricing would influence institutional journal costs in the field of cell biology. Estimating prices under two open-access models, we find that a switch to open access would result in substantial cost reductions for most institutions. At the same time, the top universities would pay up to 10 times as much as they currently do. Institutions with fewer than 4.29 million library volumes would be likely to save money under either open-access model. The long-term viability of open-access publishing in the biosciences may depend on the establishment of an environment in which the top research institutions are willing and able to pay a greater share of the total systemwide cost.

Building and maintaining a numeric data collection

This paper describes a set of collection development strategies for use in the identification, evaluation and selection of numeric data resources. It addresses three primary issues: the delineation of collecting scope and organisational role; the identification of potentially relevant data resources; and the evaluation of those resources in accordance with objective, systematic criteria. The policies outlined here can be applied to both print and digital resources, including machine‐readable data files, reference books, graphs and charts, genetic sequence data, and geospatial (GIS) files. The paper concludes with a discussion of unresolved issues in the acquisition and archiving of numeric data files.

American Jewish household income, 1969 and 1989

We estimate the real and relative income of American Jewish households using data from the National Jewish Population Surveys of 1970-1971 and 1990. While the median real income of American Jewish households did not change significantly from 1969 to 1989, lower-income Jewish households (those with no workers and those with predominantly older persons) experienced dramatic real income growth. At the same time, the average Jewish income advantage declined due to the rising incomes of other urban, non-Hispanic white households.

Do subjective journal ratings represent whole journals or typical articles? Unweighted or weighted citation impact?

This study uses journal ratings in criminology and criminal justice, library and information science, public administration, and social work to investigate two research questions: (1) Are stated preference (subjective) journal ratings more closely related to size-dependent citation metrics (eigenfactor and total citations, which represent the impact of the journal as a whole) or to size-independent citation metrics (article influence and CiteScore, which represent the impact of a typical article)? (2) Are stated preference ratings more closely related to unweighted citation metrics (five-year impact factor and source normalized impact per publication, which do not account for the impact of each citing journal) or to weighted citation metrics (article influence and SCImago journal rank, which do)? Within the disciplines evaluated here, respondents’ subjective ratings of journals are more closely related to size-independent metrics and weighted metrics. The relative strength of the relationship between subjective ratings and size-independent metrics is moderated by subject area and other factors, while the relative strength of the relationship between subjective ratings and weighted metrics is consistent across all four disciplines. These results are discussed with regard to popularity and prestige, which are sometimes associated with unweighted and weighted citation metrics, respectively.

Information Sources and Indicators for the Assessment of Journal Reputation and Impact

ABSTRACT This guide describes several information sources that can be used to assist faculty interested in quantitative and qualitative assessments of journal reputation and scholarly impact: Journal Citation Reports, Eigenfactor, Google Scholar Metrics, Elsevier Journal Metrics, Excellence in Research for Australia, Cabell’s International, Web of Science, Scopus, Google Scholar, and Beall’s List. It also introduces the indicators most often used to represent citation impact: impact factor, article influence score, eigenfactor, h5-index, source normalized impact per paper, impact per publication, and SCImago journal rank. Methods of assessing the influence of individual articles are also presented, along with strategies for the identification of predatory or low-quality journals.

Beyond use statistics: Recall, precision, and relevance in the assessment and management of academic libraries:

Although use statistics are often used in the assessment of library collections and services, they are of limited value in evaluating the library’s effectiveness as an information system. This essay highlights three concepts from the information retrieval literature—recall, precision, and relevance—and describes a standard of relevance that accounts for the learning goals of the academic community as well as the performance goals of students. It also demonstrates how the academic mission of the university can be incorporated into the assessment and management of the library as an information retrieval system. The discussion concludes with guidelines for the assessment of recall and precision as well as suggestions for the integration of these concepts into library collection development, cataloging/access, reference, and instruction.

Evaluating Online Resources for College and University Libraries: Assessing Value and Cost Based on Academic Needs

ABSTRACT This guide presents several fundamental principles for the evaluation and selection of online resources in academic libraries. It first describes the universe of scholarly documents: the narrow scope of most academic library collections; the distinctions between information, documents, titles, information resources, and products; and the striking variations in impact and importance that can be seen among both articles and journals. Second, the article discusses the ways in which libraries can help meet academic needs by selecting only high-quality resources that strengthen the links between course requirements and broader educational goals. Specifically, it addresses the distinction between students’ wants and needs, the primacy of content, the importance of comparative assessments, the advantages of title-by-title selection, and the need for resource coherence by subject or function. Third, the article presents seven guidelines for assessing and promoting cost-effectiveness—guidelines that focus on indirect costs, opportunity cost, sunk costs, the difference between views/downloads and academic use, the need to avoid ongoing financial commitments, the evaluation of cost for resources with a finite lifetime, and the impact of librarians’ decisions on the pricing strategies of vendors and publishers.