Managing Research Data

Dealing with the mountains of digital data that can accumulate in the course of a research project can seem like a daunting process, especially if your work is collaborative or stretches over several years. With a little bit of early effort and a commitment to regular upkeep, you can make data management a habit instead of a chore. This will save you huge amounts of time, money, and frustration searching for things and recovering lost files. Likewise, sharing well-managed, re-usable, and citable data with others (increasingly required for funded and published research) can go a long way toward increasing the impact of your work. In this one-hour workshop, Jessica Trelogan (UT Libraries Data Management Coordinator) will introduce basic data management concepts, offer top tips for good practice, and share useful tools and resources available to UT faculty, staff, and students. Susan Kung (Manager of the Archive of Indigenous Languages of Latin America) will be available after the workshop to share her data management experiences. While this session is specifically intended for students and faculty in the LLILAS program, the information is widely applicable to researchers from any discipline.UT Librarie

The DOLCe Initiative: Connecting libraries and advanced computing

We present the Digital Object LifeCycle (DOLCe) initiative, an extension of the ongoing partnership between the University of Texas at Austin Libraries (UTL) and the Texas Advanced Computing Center (TACC). The pilot project described in this presentation focused on enabling larger data publication within a data repository that UTL manages for the UT research community. The repository is a consortial data repository called the Texas Data Repository (TDR), and is hosted by the Texas Digital Library. Our pilot was funded by UT's Planet Texas 2050 program. It allows researchers to publish larger datasets via the repository, by connecting the TDR's Dataverse software with TACC storage systems and improving the file upload process.This work was supported in part by Planet Texas 2050, a research grand challenge initiative of The University of Texas at Austin.Texas Advanced Computing Center (TACC

Positive Action and European Union Law in the Year 2000

This paper is the third in a series in which we examine the similarities and differences between the European and American approaches to the problem of positive (or affirmative) action. In the two previous papers we examined whether certain positive action plans adopted by European legislatures would be constitutional under the Equal Protection clause of the U.S. Constitution. In this paper our aim is limited to updating our analysis of positive action in the European Union with an analysis of three recent European Court of Justice ( the Court ) decisions. The decisions are Re: Badeck, Abrahamsson, and Schnorbus v. Land Hesse. We shall also consider proposed changes to the Equal Treatment Directive, the basic legal principle at the foundation of the Court\u27s judgments in these cases

Positive Action and European Union Law in the Year 2000

This paper is the third in a series in which we examine the similarities and differences between the European and American approaches to the problem of positive (or affirmative) action. In the two previous papers we examined whether certain positive action plans adopted by European legislatures would be constitutional under the Equal Protection clause of the U.S. Constitution. In this paper our aim is limited to updating our analysis of positive action in the European Union with an analysis of three recent European Court of Justice ( the Court ) decisions. The decisions are Re: Badeck, Abrahamsson, and Schnorbus v. Land Hesse. We shall also consider proposed changes to the Equal Treatment Directive, the basic legal principle at the foundation of the Court\u27s judgments in these cases

Two Libraries using one Texas Data Repository

This paper was presented at the International Digital Curation Conference (IDCC) on February 20th, 2018 in Barcelona, Spain.This practice paper presents two ongoing projects at large university libraries to help research labs publish and archive data within a new consortial repository service. The authors have focused on targeted engagement with research groups to improve their respective research data services at the University of Texas (UT) in Austin, and Texas A&M University (TAMU) in College Station. After introducing the Texas Data Repository (TDR), Trelogan and Dabrowski highlight social, policy, and technical challenges and concerns that arose during the projects. These fall into four areas: navigating relationships with stakeholders; integrating with existing data practices; dealing with large quantities of data; ensuring maintenance and continuation. The projects provide valuable insight into the particular needs of large research groups while also uncovering technical and policy issues to be addressed to improve a shared repository service. The authors outline their approaches for consulting with the labs and efforts to overcome challenges. The results of their efforts are shared within a consortium of Texas institutions, where common practices and pooled resources enable members to make a broader local and collective impact. Although the projects are ongoing and success is yet to be assessed, they may also serve as a model for others by highlighting common challenges and contributing to technological developments

Leveraging High Performance Computing for Managing Large and Evolving Data Collections

The process of developing a digital collection in the context of a research project often involves a pipeline pattern during which data growth, data types, and data authenticity need to be assessed iteratively in relation to the different research steps and in the interest of archiving. Throughout a project’s lifecycle curators organize newly generated data while cleaning and integrating legacy data when it exists, and deciding what data will be preserved for the long term. Although these actions should be part of a well-oiled data management workflow, there are practical challenges in doing so if the collection is very large and heterogeneous, or is accessed by several researchers contemporaneously. There is a need for data management solutions that can help curators with efficient and on-demand analyses of their collection so that they remain well-informed about its evolving characteristics. In this paper, we describe our efforts towards developing a workflow to leverage open science High Performance Computing (HPC) resources for routinely and efficiently conducting data management tasks on large collections. We demonstrate that HPC resources and techniques can significantly reduce the time for accomplishing critical data management tasks, and enable a dynamic archiving throughout the research process. We use a large archaeological data collection with a long and complex formation history as our test case. We share our experiences in adopting open science HPC resources for large-scale data management, which entails understanding usage of the open source HPC environment and training users. These experiences can be generalized to meet the needs of other data curators working with large collections

Defending the genome from the enemy within:mechanisms of retrotransposon suppression in the mouse germline

The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline

Somatic expression of LINE-1 elements in human tissues

LINE-1 expression damages host DNA via insertions and endonuclease-dependent DNA double-strand breaks (DSBs) that are highly toxic and mutagenic. The predominant tissue of LINE-1 expression has been considered to be the germ line. We show that both full-length and processed L1 transcripts are widespread in human somatic tissues and transformed cells, with significant variation in both L1 expression and L1 mRNA processing. This is the first demonstration that RNA processing is a major regulator of L1 activity. Many tissues also produce translatable spliced transcript (SpORF2). An Alu retrotransposition assay, COMET assays and 53BP1 foci staining show that the SpORF2 product can support functional ORF2 protein expression and can induce DNA damage in normal cells. Tests of the senescence-associated β-galactosidase expression suggest that expression of exogenous full-length L1, or the SpORF2 mRNA alone in human fibroblasts and adult stem cells triggers a senescence-like phenotype, which is one of the reported responses to DNA damage. In contrast to previous assumptions that L1 expression is germ line specific, the increased spectrum of tissues exposed to L1-associated damage suggests a role for L1 as an endogenous mutagen in somatic tissues. These findings have potential consequences for the whole organism in the form of cancer and mammalian aging

ECAT11/L1td1 Is Enriched in ESCs and Rapidly Activated During iPSCGeneration, but It Is Dispensable for the Maintenance and Induction of Pluripotency

The principal factors that lead to proliferation and pluripotency in embryonic stem cells (ESCs) have been vigorously investigated. However, the global network of factors and their full signaling cascade is still unclear. In this study, we found that ECAT11 (L1td1) is one of the ESC-associated transcripts harboring a truncated fragment of ORF-1, a component of theL1 retrotransposable element. We generated an ECAT11 knock-in mouse by replacing its coding region with green fluorescent protein. In the early stage of development, the fluorescence was observed at the inner cell mass of blastocysts and epiblasts. Despite this specific expression, ECAT11-null mice grow normally and are fertile. In addition, ECAT11 was dispensable for both the proliferation and pluripotency of ESCs.We found rapid and robust activation of ECAT11 in fibroblasts after the forced expression of transcription factors that can give rise pluripotency in somatic cells.However, iPS cells could be established from ECAT11-null fibroblasts. Our data demonstrate thedispensability of ECAT11/L1td1 in pluripotency, despite its specific expression