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A Review of: Booth, P., Navarrete, T., & Ogundipe, A. (2022). Museum open data ecosystems: A comparative study. Journal of Documentation 78(4), 761-779. https://doi.org/10.1108/JD-05-2021-0102 Objective – Using Nardi and O’Day’s (1999) definition of ecosystem as “a system of people, practices, values, and technologies in a particular local environment,” to understand how art museums form their policy to interact with and respond to the various open data (OD) ecosystems in which they operate. Design – Multiple case study consisting of interviews and subsequent qualitative analysis, as well as document analysis. Setting – European art museum OD ecosystems. Subjects – Subjects included 7 management staff members at 3 separate mid-size, art-based museums located in Norway, the Netherlands, and Spain; an unspecified number of representatives from a cultural-policy agency in each of those countries; an unspecified number of government, museum, and research documents from within each museum’s OD ecosystem. Methods – The researchers identified 3 museums with OD initiatives and conducted in-depth interviews with relevant staff members at each institution. The researchers also interviewed representatives from relevant national OD policy-related agencies. The researchers coded their data and developed a list of five key OD “ecosystem components,” which they used to analyze the 3 specific museum ecosystems under consideration. Main Results – Open data initiatives at cultural heritage institutions are subject to a number of internal and external pressures. Museums are typically responsive to their environments, and top-down policy requirements appear to be an effective means of advancing open data initiatives. Nevertheless, the value proposition of open data appears to be insufficiently understood by museum staff and other stakeholders. As a result, museums participate in OD initiatives even when the benefit remains undemonstrated and the use of OD—how and by whom—remains unclear. Conclusion – The needs and wants of OD end-users remain ill-defined and poorly understood. As a result, museums expend resources and effort to supply OD, while remaining uncertain about the return on their investment. Attention to users could result in “more robust information flows between ecosystem components.”

A Review of: Stvilia, B., & Gibradze, L. (2022). Seeking and sharing datasets in an online community of data enthusiasts. Library & Information Science Research 44(3). https://doi.org/10.1016/j.lisr.2022.101160 Objective – To understand the major activities, tools, sources, and challenges of online communities focused on datasets. Design – Content analysis informed by activity theory. Setting – The r/Datasets subreddit, a web forum for sharing, seeking, and discussing datasets. Subjects – 1232 “hot” or “top” discussion threads (1232 original posts and 6813 responding comments) first posted between 2010 and 2020. Methods – The researchers used Reddit’s API to collect their sample of threads. Using a random subset of the sample, the researchers developed a coding scheme for content analysis, which identified major themes in the data. Through this process, they controlled for quality: each researcher coded half the subset independently, then together evaluated their intercoder reliability and discussed and resolved disagreements. The researchers also employed labelled latent Dirchlet allocation to construct topic models corresponding to the theme’s manual content analysis, which produced profiles of the top 100 terms most likely to appear in that topic. Finally, the researchers extracted URLs from threads in the sample to ascertain types of information and data sources used by the community. Presenting their findings, the researchers discussed notable themes and proposed a metadata model for describing datasets, the Data Q&A metadata (DQAM) model. Main Results – The r/Datasets community engages in three distinct activities: asking and answering questions, disseminating information, and community building. The closely related Q&A and dissemination activities shared themes of obtaining and aggregating data, sensemaking, collaborating and crowdsourcing, and data evaluation. Community members frequently discussed tools, competencies, and sources for data work. Major challenges for members of the community related to the general themes of data quality, accessibility, ethics, and legality. A proposed 16-element metadata schema should meet the needs of data enthusiasts. Conclusion – The content analysis reveals a dedicated community engaged in an array of data-seeking and data-sharing activities. Data producers should be mindful of how their data can be accessed and used outside of their original professional or scholarly contexts.

A Review of: Belvadi, M. (2021). Longevity of print book use at a small public university: A 30-year longitudinal study. Insights, 34(1), 26. http://doi.org/10.1629/uksg.562 Abstract Objective – To inform future collecting decisions by ascertaining the circulation longevity of print books within an academic library. Design – Longitudinal data analysis of two circulation datasets. Setting – Library catalogue of a small public university in Canada. Subjects – 10,002 print books acquired between 1991 and 1996 with a first circulation year between 1991 and 2000 (part 1); 4,060 print books acquired and with a first circulation year between 2008 and 2011 (part 2A); 35,860 print books acquired since 1991 with a first circulation year between 2008 and 2011 (parts 2B). Methods – The researcher established two datasets by selecting books with viable circulation data from the institution’s holdings. Using each book’s Library of Congress classification number, the researcher mapped each book to three other categorization schemes. The first scheme, Becher-Biglan typology, categorizes books as belonging to either applied or hard and pure or soft fields of study. The second scheme, called in the paper “major subjects,” uses a traditional broad subject categorization (e.g. arts, sciences, health, etc.), and the third scheme categorizes books by the academic programs at the researcher’s institution. The researcher then analyzed the circulation data through the lens of these three categorization schemes. Main Results – Part 1, which considered the collection’s older circulated books, found that books had an average circulation longevity of 10 years. About 14% of books circulated for only one year, and about 24% of books circulated for less than five years. Among the newer books considered in Part 2, 37% circulated for just one year and 64% had a circulation longevity of four years. Conclusion – Books in applied and hard fields generally have greater longevity compared to pure and soft fields. Books in professional and STEM fields generally have greater longevity than books in the humanities and arts, contrary to conventional library wisdom. Print book circulation longevity appears to be dropping. Subscription and on-demand acquisitions options may prove to be a more efficacious use of resources than ‘just-in-case’ print collecting.

A Review of: VanScoy, Amy. (2021). Using Q methodology to understand conflicting conceptualizations of reference and information service. Library and Information Science Research, 43(1), 101107. https://doi.org/10.1016/j.lisr.2021.101107 Abstract Objective – To understand how experienced librarians conceptualize reference and information service (RIS), and to determine if and to what extent these conceptualizations match existing RIS models. Design – Q methodology card sort followed by short interview. Setting – Academic, public, school, and special libraries in Slovenia, South Africa, and the United States. Subjects – Sixty-six (66) librarians from Slovenia, South Africa, and the United States. Methods – The researcher asked participants to sort 35 statements about RIS from “Least like how I think” to “Most like how I think.” The participants had the opportunity to comment on their card sort. From these card sorts, the researcher used statistical methods to generate factors describing underlying conceptualizations of RIS. These factors were compared to existing literature on RIS. Main Results – Departing from the prevailing “information provision/instruction” conceptualizations of RIS, the researcher found that most respondents conceptualized RIS according to three previously unacknowledged paradigms: 1) transformation and empathy; 2) communication and information provision; and 3) empowering and learning. Fifty-three (53) of the 66 participants loaded on to one of these three factors, i.e. sorted their cards in a similar way to other participants in that factor. Factors 2 and 3 supported existing ideas of RIS in the literature, whereas factor 1 presented a novel understanding of RIS. Common to all three factors, however, is a strong focus on the user. Conclusion – Traditional models conceptualize RIS as emphasizing either information provision or instruction. The practical judgments of experienced, working librarians, however, gesture toward different, more nuanced theoretical conclusions. Beyond the traditional poles of RIS, librarians consider empathy, empowerment, transformation, and communication as other important aspects of the RIS function.

Shotgun metagenomics studies have improved our understanding of microbial population dynamics and have revealed significant contributions of microbes to gut homeostasis. They also allow in silico inference of the metagenome. While they link the microbiome with metabolic abnormalities associated with disease phenotypes, they do not capture microbial gene expression patterns that occur in response to the multitude of stimuli that constantly ambush the gut environment. Metatranscriptomics closes that gap, but its implementation is more expensive and tedious. We assessed the metabolic perturbations associated with gut inflammation using shotgun metagenomics and metatranscriptomics. Shotgun metagenomics detected changes in abundance of bacterial taxa known to be SCFA producers, which favors gut homeostasis. Bacteria in the phylum Firmicutes were found at decreased abundance, while those in phyla Bacteroidetes and Proteobacteria were found at increased abundance. Surprisingly, inferring the coding capacity of the microbiome from shotgun metagenomics data did not result in any statistically significant difference, suggesting functional redundancy in the microbiome or poor resolution of shotgun metagenomics data to profile bacterial pathways, especially when sequencing is not very deep. Obviously, the ability of metatranscriptomics libraries to detect transcripts expressed at basal (or simply low) levels is also dependent on sequencing depth. Nevertheless, metatranscriptomics informed about contrasting roles of bacteria during inflammation. Functions involved in nutrient transport, immune suppression and regulation of tissue damage were dramatically upregulated, perhaps contributed by homeostasis-promoting bacteria. Functions ostensibly increasing bacteria pathogenesis were also found upregulated, perhaps as a consequence of increased abundance of Proteobacteria. Bacterial protein synthesis appeared downregulated. In summary, shotgun metagenomics was useful to profile bacterial population composition and taxa relative abundance, but did not inform about differential gene content associated with inflammation. Metatranscriptomics was more robust for capturing bacterial metabolism in real time. Although both approaches are complementary, it is often not possible to apply them in parallel. We hope our data will help researchers to decide which approach is more appropriate for the study of different aspects of the microbiome.

ABSTRACT Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from four channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with a glutamate pattern identical to that in cryptophyte ACRs are cation selective. Desensitization is also broadly context dependent, as in one branch of stramenopile ACRs and their metagenomic homologs, its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, we identified two prasinophyte CCRs with red-shifted spectra to 585 nm. They exhibit a third residue pattern in their retinal-binding pockets distinctly different from those of the only two types of red-shifted channelrhodopsins known (i.e., the CCR Chrimson and RubyACRs). In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity. IMPORTANCE Channelrhodopsins are widely used in neuroscience and cardiology as research tools and are considered prospective therapeutics, but their natural diversity and mechanisms remain poorly characterized. Genomic and metagenomic sequencing projects are producing an ever-increasing wealth of data, whereas biophysical characterization of the encoded proteins lags behind. In this study, we used manual and automated patch clamp recording of representative members of four channelrhodopsin families, including a family in dinoflagellates that we report in this study. Our results contribute to a better understanding of molecular determinants of ionic selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins.

Abstract Background RNA-Seq data is inherently nonuniform for different transcripts because of differences in gene expression. This makes it challenging to decide how much data should be generated from each sample. How much should one spend to recover the less expressed transcripts? The sequencing technology used is another consideration, as there are inevitably always biases against certain sequences. To investigate these effects, we first looked at high-depth libraries from a set of well-annotated organisms to ascertain the impact of sequencing depth on de novo assembly. We then looked at libraries sequenced from the Universal Human Reference RNA (UHRR) to compare the performance of Illumina HiSeq and MGI DNBseq™ technologies. Results On the issue of sequencing depth, the amount of exomic sequence assembled plateaued using data sets of approximately 2 to 8 Gbp. However, the amount of genomic sequence assembled did not plateau for many of the analyzed organisms. Most of the unannotated genomic sequences are single-exon transcripts whose biological significance will be questionable for some users. On the issue of sequencing technology, both of the analyzed platforms recovered a similar number of full-length transcripts. The missing “gap” regions in the HiSeq assemblies were often attributed to higher GC contents, but this may be an artefact of library preparation and not of sequencing technology. Conclusions Increasing sequencing depth beyond modest data sets of less than 10 Gbp recovers a plethora of single-exon transcripts undocumented in genome annotations. DNBseq™ is a viable alternative to HiSeq for de novo RNA-Seq assembly.

A Review of: Masenya, T. M., & Ngulube, P. (2020). Factors that influence digital preservation sustainability in academic libraries in South Africa. South African Journal of Libraries and Information Science, 86(1), 52–63. https://doi.org/10.7553/86-1-1860 Abstract Objective – To define principles for the sustainable management and preservation of digital resources. Design – Survey and literature review. Setting – Academic libraries in South Africa. Subjects – Twenty-two academic institutions in South Africa. Methods – The researchers evaluated four conceptual models of digital preservation and conducted a literature review for the same subject. Informed by these reviews, the researchers developed a questionnaire for South African academic institutions, distributed the questionnaire, and studied the results using statistical analysis software. Main Results – Twenty-two of twenty-seven (81.5%) surveys were returned. Results indicated a broad consensus about which factors were important in sustainable digital preservation; all factors listed received anywhere from 86.3% to 100% agreement among respondents. Conclusion – A proposed conceptual integrated digital preservation model recommends a three-pronged approach to address management-related, resource-related, and technological-related factors in sustainable digital preservation.

A Review of: Preminger, M., Rype, I., Ådland, M.K., Massey, D., & Tallerås, K. (2020). The public library metadata landscape, the case of Norway 2017–2018. Cataloging & Classification Quarterly, 58(2), 127–148. https://doi.org/10.1080/01639374.2020.1711836 Abstract Objective – To understand cataloguing practices in Norwegian public libraries through the analysis of a set of MARC records. Design – Quantitative content analysis. Setting – 2 central cataloguing agencies and 49 public libraries in Norway. Subjects – 21,275 cataloguing agency records and 116,029 public library catalogue records. Methods – The researchers derived a sample set of MARC records from the central cataloguing agencies and public libraries. Matching records from each agency (i.e., records for the same manifestation catalogued separately at each agency) were compared. Then, MARC records exported from public libraries were compared to matching records from the central agencies. Main Results – The two central agencies differed in some cataloguing practices while still adhering to the accepted standards. Public libraries made few changes to records imported from central libraries, and among public libraries, larger libraries were more likely to alter agency-derived MARC records. Conclusion – Current practices indicate that despite the prevalence and efficiency of centralized cataloguing, training in cataloguing remains important in public libraries, particularly in larger libraries.

A Review of: Ovadia, S. (2019). Addressing the technical challenges of open educational resources. portal: Libraries and the Academy, 19(1), 79-93. https://doi.org/10.1353/pla.2019.0005 Abstract Objective – To describe common technical challenges of open educational resources (OERs) and recommend solutions. Design – Descriptive study. Setting – Online open educational resources in higher education. Subjects – Open educational resources. Methods – Drawing from the literature and his own experiences, the author explains the necessity of accepted standards of “openness” and describes the many ways OERs fail to meet these standards. The author also describes common technical challenges that impede openness, then proposes solutions to address these challenges. Main Results – Technical limitations often prohibit OERs from being truly open. Providers can design their resources to encourage reuse, redistribution, revision, and remixing. Three strategies for addressing technical challenges in OERs are user education, open file standards, and using Git to facilitate distributed version control. Conclusion – Git is a compelling option for distributed version control, but entails its own technical challenges. User education and established open file standards are the best strategies to ensure that OERs are open in both a legal and a technical sense. The article concludes with the author’s opinions about how OER directors may most realistically implement these solutions.

Understanding the heterogeneity of dysregulated pathways associated with the development of hepatocellular carcinoma (HCC) may provide prognostic and therapeutic avenues for disease management. As HCC involves a complex process of genetic and epigenetic modifications, we evaluated expression of both polyadenylated transcripts and microRNAs from HCC and liver samples derived from two cohorts of patients undergoing either partial hepatic resection or liver transplantation. Copy number variants were inferred from whole genome low‐pass sequencing data, and a set of 56 cancer‐related genes were screened using an oncology panel assay. HCC was associated with marked transcriptional deregulation of hundreds of protein‐coding genes. In the partially resected livers, diminished transcriptional activity was observed in genes associated with drug catabolism and increased expression in genes related to inflammatory responses and cell proliferation. Moreover, several long noncoding RNAs and microRNAs not previously linked with HCC were found to be deregulated. In liver transplant recipients, down‐regulation of genes involved in energy production and up‐regulation of genes associated with glycolysis were detected. Numerous copy number variants events were observed, with hotspots on chromosomes 1 and 17. Amplifications were more common than deletions and spanned regions containing genes potentially involved in tumorigenesis. Colony stimulating factor 1 receptor (CSF1R), fibroblast growth factor receptor 3 (FGFR3), fms‐like tyrosine kinase 3 (FLT3), nucleolar phosphoprotein B23 (NPM1), platelet‐derived growth factor receptor alpha polypeptide (PDGFRA), phosphatase and tensin homolog (PTEN), G‐protein‐coupled receptors‐like receptor Smoothened (SMO), and tumor protein P53 (TP53) were mutated in all tumors; another 26 cancer‐related genes were mutated with variable penetrance. Conclusion: Our results underscore the marked molecular heterogeneity between HCC tumors and reinforce the notion that precision medicine approaches are needed for management of individual HCC. These data will serve as a resource to generate hypotheses for further research to improve our understanding of HCC biology. (Hepatology Communications 2018; 00:000‐000)

A Review of: Lund, B., & Agbaji, D. (2018). Use of Dewey Decimal Classification by academic libraries in the United States. Cataloging and Classification Quarterly, 56(7), 653-661. https://doi.org/10.1080/01639374.2018.1517851 Abstract Objective – To determine the current use of Dewey Decimal Classification in academic libraries in the United States of America (U.S.). Design – Cross-sectional survey using a systematic sampling method. Setting – Online academic library catalogues in the U.S. Subjects – 3,973 academic library catalogues. Methods – The researchers identified 3,973 academic libraries affiliated with degree-granting post-secondary institutions in the U.S. The researchers searched each library’s online catalogue for 10 terms from a predetermined list. From the results of each search, the researchers selected at least five titles, noted the classification scheme used to classify each title, and coded the library as using Dewey Decimal Classification (DDC), Library of Congress Classification (LCC), both DDC and LCC, or other classification schemes. Based on the results of their data collection, the researchers calculated totals. The totals of this current study’s data collection were compared to statistics on DDC usage from two previous reports, one published in 1975 and one in 1996. The researchers performed statistical analyses to determine if there were any discernible trends from the earliest reported statistics through to the current study. Main Results – Collections classified using DDC were present in 717 libraries (18.9%). Adjusting for the increase in the number of academic libraries in the U.S. between 1975 and 2017, DDC usage in academic libraries has declined by 56% in that time frame. The number of libraries with only DDC in evidence is unreported. Conclusion – The previous four decades have seen a significant decrease in the use of DDC in U.S. academic libraries in favour of LCC; however, the rate at which DDC has disappeared from academic libraries has slowed dramatically since the 1960s. There is no clear indication that DDC will disappear from academic libraries completely.

We conducted an unbiased metagenomics survey using plasma from patients with chronic hepatitis B, chronic hepatitis C, autoimmune hepatitis (AIH), non-alcoholic steatohepatitis (NASH), and patients without liver disease (control). RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Hepatitis viruses were readily detected at high coverage in patients with chronic viral hepatitis B and C, but only a limited number of sequences resembling other viruses were found. The exception was a library from a patient diagnosed with hepatitis C virus (HCV) infection that contained multiple sequences matching GB virus C (GBV-C). Abundant GBV-C reads were also found in plasma from patients with AIH, whereas Torque teno virus (TTV) was found at high frequency in samples from patients with AIH and NASH. After taxonomic classification of sequences by BLASTn, a substantial fraction in each library, ranging from 35% to 76%, remained unclassified. These unknown sequences were assembled into scaffolds along with virus, phage and endogenous retrovirus sequences and then analyzed by BLASTx against the non-redundant protein database. Nearly the full genome of a heretofore-unknown circovirus was assembled and many scaffolds that encoded proteins with similarity to plant, insect and mammalian viruses. The presence of this novel circovirus was confirmed by PCR. BLASTx also identified many polypeptides resembling nucleo-cytoplasmic large DNA viruses (NCLDV) proteins. We re-evaluated these alignments with a profile hidden Markov method, HHblits, and observed inconsistencies in the target proteins reported by the different algorithms. This suggests that sequence alignments are insufficient to identify NCLDV proteins, especially when these alignments are only to small portions of the target protein. Nevertheless, we have now established a reliable protocol for the identification of viruses in plasma that can also be adapted to other patient samples such as urine, bile, saliva and other body fluids.

Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ≥ 1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.

An increase in salivary leukocytes may contribute to the exercise-induced increase in salivary antimicrobial proteins (AMPs). However, exercise-induced changes in salivary leukocytes have not been studied. The purpose of the study was to describe salivary leukocyte changes with exercise. Participants (n = 11, 20.3 ± 0.8 years, 57.2 ± 7.6 ml kg−1 min−1peak oxygen uptake ((VO) ̇2peak), 11.1 ± 3.9% body fat) ran for 45 min at 75% of VO2peak. Stimulated saliva (12 mL) was collected pre- and immediately post exercise. Saliva was filtered through a 30 µm filter before analysis of leukocytes (CD45+), granulocytes (CD45+CD15+), monocytes (CD45+CD14+), T-cells (CD45+CD3+), and B-cells (CD45+CD20+) using flow cytometry. Saliva was analysed for Lysozyme (Lys) using ELISA. Exercise did not alter any leukocyte subset. The major constituent of leukocytes pre-exercise were granulocytes (57.9 ± 30.3% compared with monocytes: 5.1 ± 2.7%, T-cells: 17.1 ± 8.9%, B-cells: 12.1 ± 10.2%) (P < 0.05). In a subset ofn = 6, Lys secretion rate increased after exercise (pre: 5,170 ± 5,215 ng/min; post: 7,639 ± 4,140 ng/min) (P < 0.05). Exercise does not result in increased granulocytes, but does increase Lys. Further, these data suggest that an increase in salivary leukocytes is not needed to increase Lys. [ABSTRACT FROM AUTHOR]

The article discusses a study conducted for the quantification secretion of salivary antimicrobial proteins (AMP) due to loss of sleep after and before exercising. Topics discussed includes measurement of lactoferrin and lysozyme, secretion rate of AMPs, increased secretion rate after exercise. The study concluded that sleep loss doesn't affect secretion of salivary AMP neither does it affect AMP secretion in response to exercising.