Should we keep everything forever (reprised)? Preservation review of research data in a repository as an art and a science

--This poster was accepted for iPres2018, Boston, USA-- The Illinois Data Bank was established in 2016 as an institutional file-based repository for research data (Hetrick et al. 2018). The service commits to a minimum retention period of five years, after which deposits are to be appraised and potentially reformatted, enhanced, or withdrawn. Preservation review guidelines were established and a “review indicator” was proposed (Anderson et al., 2016) to help curators identify datasets for which an in-depth, human-mediated review may be warranted. Our poster will characterize the datasets deposited during Illinois Data Bank’s first two years in order to evaluate the following: the feasibility and utility of our proposed Review Indicator as currently formulated, and possible actions during initial curation that would minimize or eliminate the need for a five-year review of some datasets. As we continue to explore strategies to assist with the on-going stewardship of complex data collections, we hope that our efforts will spark conversations with, and insights from, others who are responsible for preserving similarly challenging collectionsOpe

Institutional Data Repository Development, a Moving Target

At the end of 2019, the Research Data Service (RDS) at the University of Illinois at Urbana-Champaign (UIUC) completed its fifth year as a campus-wide service. In order to gauge the effectiveness of the RDS in meeting the needs of Illinois researchers, RDS staff developed a five-year review consisting of a survey and a series of in-depth focus group interviews. As a result, our institutional data repository developed in-house by University Library IT staff, Illinois Data Bank, was recognized as the most useful service offering by our unit. When launched in 2016, storage resources and web servers for Illinois Data Bank and supporting systems were hosted on-premises at UIUC. As anticipated, researchers increasingly need to share large, and complex datasets. In a responsive effort to leverage the potentially more reliable, highly available, cost-effective, and scalable storage accessible to computation resources, we migrated our item bitstreams and web services to the cloud. Our efforts have met with success, but also with painful bumps along the way. This article describes how we supported data curation workflows through transitioning from on-premises to cloud resource hosting. It details our approaches to ingesting, curating, and offering access to dataset files up to 2TB in size--which may be archive type files (e.g., .zip or .tar) containing complex directory structures

Responding to Reality: Evolving Curation Practices and Infrastructure at the University of Illinois at Urbana-Champaign

Objective: The Illinois Data Bank provides Illinois researchers with the infrastructure to publish research data publicly. During a five-year review of the Research Data Service at the University of Illinois at Urbana-Champaign, it was recognized as the most useful service offering in the unit. Internal metrics are captured and used to monitor the growth, document curation workflows, and surface technical challenges faced as we assist our researchers. Here we present examples of these curation challenges and the solutions chosen to address them. Methods: Some Illinois Data Bank metrics are collected internally by within the system, but most of the curation metrics reported here are tracked separately in a Google spreadsheet. The curator logs required information after curation is complete for each dataset. While the data is sometimes ambiguous (e.g., depending on researcher uptake of suggested actions), our curation data provide a general understanding about our data repository and have been useful in assessing our workflows and services. These metrics also help prioritize development needs for the Illinois Data Bank. Results and Conclusions: The curatorial services polish and improve the datasets, which contributes to the spirit of data reuse. Although we continue to see challenges in our processes, curation makes a positive impact on datasets. Continued development and adaptation of the technical infrastructure allows for an ever-better experience for the curators and users. These improvements have helped our repository more effectively support the data sharing process by successfully fostering depositor engagement with curators to improve datasets and facilitating easy transfer of very large files

An islet maturation media to improve the development of young porcine islets during in vitro culture

BackgroundThe use of pancreata from pre-weaned piglets has the potential to serve as an unlimited alternative source of islets for clinical xenotransplantation. As pre-weaned porcine islets (PPIs) are immature and require prolonged culture, we developed an islet maturation media (IMM) and evaluated its effect on improving the quantity and quality of PPIs over 14 days of culture.MethodsPPIs were isolated from the pancreata of pre-weaned Yorkshire piglets (8-15 days old). Each independent islet isolation was divided for culture in either control Ham's F-10 media (n = 5) or IMM (n = 5) for 14 days. On day 3, 7 and 14 of culture, islets were assessed for islet yield, isolation index, viability, insulin content, endocrine cellular composition, differentiation of beta cells, and insulin secretion during glucose stimulation.ResultsIn comparison to control islets, culturing PPIs in IMM significantly increased islet yield. PPIs cultured in IMM also maintained a stable isolation index and viability throughout 14 days of culture. The insulin content, endocrine cellular composition, and differentiation of beta cells were significantly improved in PPIs cultured in IMM, which subsequently augmented their insulin secretory capacity in response to glucose challenge compared to control islets.ConclusionsCulturing PPIs in IMM increases islet yield, isolation index, viability, insulin content, endocrine cellular composition, differentiation of endocrine progenitor cells toward beta cells, and insulin secretion. Due to the improved islet quantity and quality after in vitro culture, the use of IMM in the culture of PPIs will assist to advance the outcomes of clinical islet xenotransplantation

P14. Should we keep everything forever (reprised)? Preservation review of research data in a repository as an art and a science

The Illinois Data Bank was established in 2016 as an institutional file-based repository for research data (Hetrick et al. 2018). The service commits to a minimum retention period of five years, after which deposits are to be appraised and potentially reformatted, enhanced, or withdrawn. Preservation review guidelines were established and a “review indicator” was proposed (Anderson et al., 2016) to help curators identify datasets for which an in-depth, human-mediated review may be warranted. Our poster will characterize the datasets deposited during Illinois Data Bank’s first two years in order to evaluate the following: the feasibility and utility of our proposed Review Indicator as currently formulated, and possible actions during initial curation that would minimize or eliminate the need for a five-year review of some datasets. As we continue to explore strategies to assist with the on-going stewardship of complex data collections, we hope that our efforts will spark conversations with, and insights from, others who are responsible for preserving similarly challenging collection

Comparison of Islet Characterization from Use of Standard Crude Collagenase to GMP-Grade Collagenase Enzyme Blends in Preweaned Porcine Islet Isolations.

For the advancement of porcine xenotransplantation for clinical use in type 1 diabetes mellitus, the concerns of a sustainable and safe digestion enzyme blend must be overcome. Incorporating good manufacturing practices (GMP) can facilitate this through utilizing GMP-grade enzymes. In conjunction, still taking into account the cost-effectiveness, a wide concern. We evaluated how GMP-grade enzyme blends impact our piglet islets and their long-term effects.  Preweaned porcine islets (PPIs) were isolated from 8- to 10-day-old pigs. Digestion enzyme blends, collagenase type V (Type V), collagenase AF-1 GMP-grade with collagenase NB 6 GMP-grade (AF-1 and NB 6), and collagenase AF-1 GMP-grade with collagenase neutral protease AF GMP-grade (AF-1 and NP AF) were compared. Islet quality control assessments, islet yield, viability, and function, were performed on days 3 and 7, and cell content was performed on day 7.  GMP-grade AF-1 and NB 6 (17,209 ± 2,730 islet equivalent per gram of pancreatic tissue [IE/g] on day 3, 9,001 ± 1,034 IE/g on day 7) and AF-1 and NP AF (17,214 ± 3,901 IE/g on day 3, 8,833 ± 2,398 IE/g on day 7) showed a significant increase in islet yield compared to Type V (4,618 ± 1,240 IE/g on day 3, 1,923 ± 704 IE/g on day 7). Islet size, viability, and function showed comparable results in all enzyme blends. There was no significant difference in islet cellular content between enzyme blends.  This study demonstrated a comparison of GMP-grade collagenase enzyme blends and a standard crude collagenase enzyme in preweaned-aged porcine, a novel topic in this age. GMP-grade enzyme blends of AF-1 and NB 6 and AF-1 and NP AF resulted in substantially higher yields and as effective PPIs compared to Type V. In the long run, considering costs, integrity, and sustainability, GMP-grade enzyme blends are more favorable for clinical application due to high reproducibility in comparison to undefined manufacturing processes of standard enzymes

Solar Hydrogen Hybrid System (semester?), IPRO 301: Solar Hydrogen Hybrid System IPRO 301 Poster F04

The photovoltaic/hydrogen hybrid energy system IPRO was started eight years ago. A group of students with their faculty advisor began a semester to investigate the use of solar energy to power an electric sign. Since that time, a significant amount of progress has been made. The project progressed from the design phase to the laboratory phase. Once functioning, it was transferred to the roof of the Co-Gen plant on the IIT main campus. During this phase of the project, Phase I, a photovoltaic system was set up that included several solar panels on the roof. Also, a large LED sign was installed on the roof. An array of power management devices were set up at the project site inside the Co-Gen plant. Phase II of the project was planned in order to incorporate an electrolyzer and fuel cell as an energy back up system in conjunction with the PV system. Although these components exist at the work site, they are not integrated into the complete system and are merely there to demonstrate using hydrogen to power an electric load.Deliverables for IPRO 301: Solar Hydrogen Hybrid System for the Fall 2004 semeste

Solar Hydrogen Hybrid System (semester?), IPRO 301: Solar Hydrogen Hybrid System IPRO 301 Final Report F04

The photovoltaic/hydrogen hybrid energy system IPRO was started eight years ago. A group of students with their faculty advisor began a semester to investigate the use of solar energy to power an electric sign. Since that time, a significant amount of progress has been made. The project progressed from the design phase to the laboratory phase. Once functioning, it was transferred to the roof of the Co-Gen plant on the IIT main campus. During this phase of the project, Phase I, a photovoltaic system was set up that included several solar panels on the roof. Also, a large LED sign was installed on the roof. An array of power management devices were set up at the project site inside the Co-Gen plant. Phase II of the project was planned in order to incorporate an electrolyzer and fuel cell as an energy back up system in conjunction with the PV system. Although these components exist at the work site, they are not integrated into the complete system and are merely there to demonstrate using hydrogen to power an electric load.Deliverables for IPRO 301: Solar Hydrogen Hybrid System for the Fall 2004 semeste

Solar Hydrogen Hybrid System (semester?), IPRO 301

The photovoltaic/hydrogen hybrid energy system IPRO was started eight years ago. A group of students with their faculty advisor began a semester to investigate the use of solar energy to power an electric sign. Since that time, a significant amount of progress has been made. The project progressed from the design phase to the laboratory phase. Once functioning, it was transferred to the roof of the Co-Gen plant on the IIT main campus. During this phase of the project, Phase I, a photovoltaic system was set up that included several solar panels on the roof. Also, a large LED sign was installed on the roof. An array of power management devices were set up at the project site inside the Co-Gen plant. Phase II of the project was planned in order to incorporate an electrolyzer and fuel cell as an energy back up system in conjunction with the PV system. Although these components exist at the work site, they are not integrated into the complete system and are merely there to demonstrate using hydrogen to power an electric load.Deliverables for IPRO 301: Solar Hydrogen Hybrid System for the Fall 2004 semeste

Dose-dependent effects of necrostatin-1 supplementation to tissue culture media of young porcine islets

Previous studies have shown that necrostatin-1 (Nec-1) supplementation improved the viability of murine islets following exposure to nitric oxide, increased the survival of human islets during hypoxic culture, and augmented the maturation of pre-weaned porcine islets (PPIs) after 7 days of tissue culture. A limitation of these studies is that only one concentration of Nec-1 was used, and no studies have determined the optimal dose of Nec-1 for PPIs. Thus, the present study examined the effects of Nec-1 on PPIs at four different doses-0, 25, 50, 100, and 200 μM-after 7 days of tissue culture when supplemented on day 3. PPIs were isolated from pancreata of pre-weaned Yorkshire piglets (8-15 days old) and cultured in a specific islet maturation media added with Nec-1 on day 3 of tissue culture at 4 different doses-0, 25, 50, 100, and 200 μM (n = 6 for each dose). After 7 days of tissue culture, islets were assessed for recovery, viability, endocrine cellular content, GLUT2 expression in beta cells, and insulin secretion after glucose challenge. Nec-1 did not affect the viability of both intact islets and dissociated islets cells during tissue culture regardless of doses. Islets cultured in media supplemented with Nec-1 at 100 μM, but not 25, 50, or 200 μM, had a significantly higher recovery, composition of endocrine cells, GLUT2 expression in beta cells, and insulin secretion capacity than control islets cultured in media without Nec-1 supplementation. Moreover, culturing islets in 200 μM Nec-1 supplemented media not only failed to improve the insulin release but resulted in a lower glucose-induced insulin stimulation index compared to islets cultured in media added with 100 μM Nec-1. Xenotransplantation using porcine islets continues to demonstrate scientific advances to justify this area of research. Our findings indicate that Nec-1 supplementation at 100 μM was most effective to enhance the in vitro maturation of PPIs during tissue culture