Digital Editions and Version Numbering

Digital editions are easily modified after they are first published — a state of affairs that poses challenges both for long-term scholarly reference and for various forms of electronic distribution and analysis. This article argues that producers of digital editions should assign meaningful version numbers to their editions and update those version numbers with each change, allowing both humans and computers to know when resources have been modified and how significant the changes are. As an examination of versioning practices in the software industry reveals, version numbers are not neutral descriptors but social products intended for use in specific contexts, and the producers of digital editions must consider how version numbers will be used in developing numbering schemes. It may be beneficial to version different parts of an edition separately, and in particular to version the data objects or content of an edition independently from the environment in which it is displayed. The article concludes with a case study of the development of a versioning policy for the Piers Plowman Electronic Archive, and includes an appendix surveying how a selection of digital editions handle the problem of recording and communicating changes

LINE-1 Hypomethylation in a Choline-Deficiency-Induced Liver Cancer in Rats: Dependence on Feeding Period

Chronic feeding of methyl-donor (methionine, choline, folic acid, and vitamin B12) deficient diet induces hepatocellular carcinoma formation in rats. Previous studies have shown that promoter CpG islands in various cancer-related genes are aberrantly methylated in this model. Moreover, the global genome in methyl-donor-deficient diet fed rats contains a lesser amount of 5-methylcytosine than control livers. It is speculated that more than 90% of all 5-methylcytosines lie within the CpG islands of the transposons, including the long/short interspersed nucleotide elements (LINE and SINE). It is considered that the 5-methylcytosines in LINE-1 limit the ability of retrotransposons to be activated and transcribed; therefore, the extent of hypomethylation of LINE-1 could be a surrogate marker for aberrant methylation in other tumor-related genes as well as genome instability. Additionally, LINE-1 methylation status has been shown to be a good indicator of genome-wide methylation. In this study, we determined cytosine methylation status in the LINE-1 repetitive sequences of rats fed a choline-deficient (CD) diet for various durations and compared these with rats fed a choline-sufficient (CS) diet. The methylation status of LINE-1 was assessed by the combined bisulfite restriction analysis (COBRA) method, where the amount of bisulfite-modified and RsaI-cleaved DNA was quantified using gel electrophoresis. Progressive hypomethylation was observed in LINE-1 of CD livers as a function of feeding time; that is, the amount of cytosine in total cytosine (methylated and unmethylated) increased from 11.1% (1 week) to 19.3% (56 weeks), whereas in the control CS livers, it increased from 9.2% to 12.9%. Hypomethylation in tumor tissues was slightly higher (6%) than the nontumorous surrounding tissue. The present result also indicates that age is a factor influencing the extent of cytosine methylation

“Build a Bridge So You Can Cross It:” A Photo-Elicitation Study of Health and Wellness Among Homeless and Marginally Housed Veterans

As part of a photo-elicitation interview study, we aimed to describe homeless and marginally housed Veterans’ experiences with health and wellness, health decisions, and health-related behaviors. Twenty Veterans receiving Veterans Affairs Homeless Patient-Aligned Care Team care took photographs depicting health and wellness, then used their photographs to discuss the same topics in 30-60 minute audio-recorded, semi-structured photo-elicitation interviews. Transcripts were analyzed using template analysis. Veterans described eight dimensions related to their health and wellness; physical, social, and environmental were most commonly discussed, followed by emotional, intellectual, spiritual, occupational, and financial wellness. Photographs contained literal and metaphorical depictions that were positively-oriented, comprehensive, and reflective. Of central importance was overcoming external and internal obstacles to wellness. Photo-narratives may be helpful in educating health care providers and advocating for the needs of homeless and marginally housed Veterans. Integrated primary care services should address the multi-faceted aspects of health and wellness for Veterans

Complete Plastome Sequences from Glycine syndetika, and Six Additional Perennial Wild Relatives of Soybean

Organelle sequences have a long history of utility in phylogenetic analyses. Chloroplast sequences when combined with nuclear data can help resolve relationships among flowering plant genera, and within genera incongruence can point to reticulate evolution. Plastome sequences are becoming plentiful because they are increasingly easier to obtain. Complete plastome sequences allow us to detect rare rearrangements and test the tempo of sequence evolution. Chloroplast sequences are generally considered a nuisance to be kept to a minimum in bacterial artificial chromosome libraries. Here, we sequenced two bacterial artificial chromosomes per species to generate complete plastome sequences from seven species. The plastome sequences from Glycine syndetika and six other perennial Glycine species are similar in arrangement and gene content to the previously published soybean plastome. Repetitive sequences were detected in high frequencies as in soybean, but further analysis showed that repeat sequence numbers are inflated. Previous chloroplast-based phylogenetic trees for perennial Glycine were incongruent with nuclear gene\u2013based phylogenetic trees. We tested whether the hypothesis of introgression was supported by the complete plastomes. Alignment of complete plastome sequences and Bayesian analysis allowed us to date putative hybridization events supporting the hypothesis of introgression and chloroplast \u201ccapture.\u201

Influence of Breast Cancer and Metastases on Incidence of Diabete

Purpose: Diabetes increases the risk of subsequent breast cancer. However, the inverse relationship of breast cancer to incident diabetes development is unclear. In preclinical models increased bone turnover due to bone metastases or endocrine therapies impacts insulin secretion. This analysis was conducted to estimate the incidence of diabetes after breast cancer and the influence of metastases and therapeutic agents. Methods: This retrospective case-control study combined data from a large electronic health data exchange and the Indiana State Cancer Registry on breast cancer patients and controls between 2007 and 2017. Primary exposure was presence of breast cancer and bone or non-bone metastases. The primary outcome was frequency of incident diabetes detected by ICD codes, medication use, or laboratory results, compared between breast cancer cases and controls using conditional or ordinary logistic regressions. Results: 36,083 cases and 36,083 matched controls were detected. Incident diabetes was higher in early stage breast cancer (OR 1.17, 95%CI 1.11-1.23, p<0.0001) and metastatic breast cancer (OR 1.62, 95% CI 1.25-2.09, p=0.0002), compared to controls. Bone metastases conferred higher odds of both pre-existing (OR 1.20, 95% CI 1.03-1.63, p=0.0272) and incident diabetes (OR 1.64, 95% CI 1.19-2.25, p=0.0021). Endocrine therapy was associated with reduced diabetes (OR 0.86, 95% CI 0.79-0.83, p=0.002). Anti-resorptives reduced incident diabetes in those with bone metastases (OR 0.44, 95% CI 0.25-0.78, p=0.005). Conclusion: Breast cancer, especially with metastases, increases subsequent risk of diabetes. As patients with breast cancer live longer, identifying and managing diabetes may impact treatment delivery, cost, survival, and quality of life

Logistical Lessons Learned in Designing and Executing a Photo-Elicitation Study in the Veterans Health Administration

Participatory photography research methods have been used to successfully engage and collect in-depth information from individuals whose voices have been traditionally marginalized in clinical or research arenas. However, participatory photography methods can introduce unique challenges and considerations regarding study design, human subject protections, and other regulatory barriers, particularly with vulnerable patient populations and in highly regulated institutions. Practical guidance on navigating these complex, interrelated methodological, logistical, and ethical issues is limited. Using a case exemplar, we describe our experiences with the planning, refinement, and initiation of a research study that used photo-elicitation interviews to assess the healthcare experiences of homeless and marginally housed United States Veterans. We discuss practical issues and recommendations related to study design, logistical “pitfalls” during study execution, and ensuring human subjects protections in the context of a study with a highly vulnerable patient population taking place in a highly risk-averse research environment