Archeota, Spring 2016

https://scholarworks.sjsu.edu/saasc_archeota/1002/thumbnail.jp

Moving from Binders to Bytes: Processing, Digitizing, and Publishing a Paper-Based Archive to an Institutional Repository

At San Jose State University, a paper-based archive centering on library and information science history is being processed, organized, and uploaded onto ScholarWorks, the campus institutional repository. Prior to its digitization, the presenters grappled with many questions. What platform should be used to house the archive? What entry points would researchers expect in order to access the collection? What research purposes would this collection satisfy? The presenters will discuss their rationale for their decision-making in transferring 300 binders to an open access, digital format. Among the individuals who are involved in making this detail-rich collection openly accessible online and searchable are a scholarly communications librarian, a cataloging and metadata specialist who is serving as the interim institutional repository coordinator, and a library and information science graduate student focusing on archival records and management. These individuals will discuss their varying perspectives and how each of their emphases contributes to the enterprise of making this paper-based archive discoverable, searchable, and digitally accessible in an ever-evolving institutional repository and scholarly communications environment

Manual Scalp Cooling in Early Stage Breast Cancer: Value of Caretaker Training and Patient-Reported Experience to Optimize Efficacy and Patient Selection

Title: Manual scalp cooling in early stage breast cancer: value of caretaker training and patient-reported experience to optimize efficacy and patient selection Authors: Manaz Rezayee1, BS Nicole Moxon1, RN Staci Mellinger1, RN Amanda Y. Seino1 Nicole E. Fredrich1 Tracy L. Kelly1 Susan Mulligan2, MA Patrick Rossi3, MD Ijeoma Uche1, MD Walter J. Urba1, MD PHD Alison K. Conlin1, MD MPH Janet Ruzich1, DO David B. Page1, MD Background: Alopecia is an emotionally distressing common adverse effect of curative-intent chemotherapy in early stage breast cancer.1–6 Although machine-based scalp cooling is effective for reduction of chemotherapy-associated alopecia in early stage breast cancer, availability is geographically limited.7–11 Manual cold-cap systems may also be effective and are available regardless of geographic location.12–14 We evaluated the feasibility of caretaker-administered cold-cap efficacy following structured standardized training, and utilized patient-reported subjective outcomes to develop a clinical tool to facilitate patient selection. Patients and Methods: A small pilot study (n=10) was conducted to evaluate the feasibility and efficacy of manual cold capping. Key eligibility criteria included: 1) no hair loss at baseline; 2) no pre-existing scalp condition; 3) planned curative-intent chemotherapy for early stage breast cancer and 4) availability of caretaker(s). Participants received standardized training and then performed the cold-cap procedure without assistance. The primary endpoint was post-treatment hair retention using Dean’s alopecia scale, with success defined as Results: Of the evaluable patients, 80% (n=8/10) met the primary efficacy endpoint (Dean’s scale 0-2) with 20% (n=2/10) trial failures due to pre-mature discontinuation. Manual cold-capping was worthwhile to 90% of patients (Was it Worth It? Questionnaire) and associated with favorable PROs. Patient interviews identified a number of themes shared by almost all patients, which were subsequently used to develop a questionnaire to aid patient-directed decision-making on whether to pursue manual cold-capping. Conclusion: This study affirms the safety and efficacy of manual cold-capping to reduce alopecia and demonstrates the importance of proper training and education to maximize efficacy. It also highlights the considerable costs and effort associated with cold-capping. Selected patients with early stage breast cancer may benefit subjectively from cold capping while the proposed clinical instrument can be used to facilitate an informed discussion between patient and provider.https://digitalcommons.psjhealth.org/cancer_institute_fellowships/1000/thumbnail.jp

Genome-wide DNA methylation profiling shows a distinct epigenetic signature associated with lung macrophages in cystic fibrosis

Abstract Background Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls. All analyses were performed using primary alveolar macrophages from human subjects collected via bronchoalveolar lavage. Epigenome-wide DNA methylation was examined via Illumina MethylationEPIC (850 K) array. Targeted next-generation bisulfite sequencing was used to validate selected differentially methylated CpGs. Methylation-based sample classification was performed using the recursively partitioned mixture model (RPMM) and was tested against sample case-control status. Differentially methylated loci were identified by fitting linear models with adjustment of age, sex, estimated cell type proportions, and repeat measurement. Results RPMM class membership was significantly associated with the CF disease status (P = 0.026). One hundred nine CpG loci were differentially methylated in CF BAL cells (all FDR ≤ 0.1). The majority of differentially methylated loci in CF were hypo-methylated and found within non-promoter CpG islands as well as in putative enhancer regions and DNase hyper-sensitive regions. Conclusions These results support a hypothesis that epigenetic changes, specifically DNA methylation at a multitude of gene loci in lung macrophages, may participate, at least in part, in driving dysfunctional innate immune cells in the CF lung

A phase Ib study of pre-operative, locoregional IRX-2 cytokine immunotherapy to prime immune responses in patients with early stage breast cancer.

PURPOSE: To evaluate the safety and feasibility of pre-operative locoregional cytokine therapy (IRX-2 regimen) in early stage breast cancer, and to evaluate for intratumoral and peripheral immunomodulatory activity. EXPERIMENTAL DESIGN: Sixteen patients with stage I-III early stage breast cancer (any histology type) indicated for surgical lumpectomy or mastectomy were enrolled to receive pre-operative locoregional immunotherapy with the IRX-2 cytokine biologic (2mL subcutaneous x 10 days to peri-areolar skin). The regimen also included single-dose cyclophosphamide (300mg/m RESULTS: Pre-operative locoregional cytokine administration was feasible in 100% (n=16/16) of subjects and associated with increases in stromal tumor-infiltrating lymphocytes (p CONCLUSIONS: IRX-2 is safe in early stage breast cancer. Potentially favorable immunomodulatory changes were observed, supporting further study of IRX-2 in early stage breast cancer and other malignancies