GIS and Data: Making Space @ MIT: Development of the MIT Libraries GIS and Data Lab

The objective of this presentation is to: understand the MIT context for GIS (geographic information system) and RDM (research data management) services; follow the development of the GIS and Data Lab space; understand the space assessment goals and results; and, explore future plans. Keynote presentation at the National Network of Libraries of Medicine New England Region e-Science Forum, Marlborough, MA, USA, on March 29, 2019

From Data Citation to Scholarly Impact: Marking a Path and Clearing a Way for Access and Analysis

Starting from Mooney and Newton’s work on data citation (http://dx.doi.org/10.7710/2162-3309.1035) we decided to examine what happens to a data set after it is set on its path as a piece of scholarly communication. Briefly reviewing a selection of datasets, repositories, and platforms we found an uneven application of commonly accepted standards. Although guides for repositories such as Dryad or identifier registrars such as DataCite recommend inclusion of the key elements of Author, Title, Published date, and Publisher, there are two notable trends: to leave off the Material designator, leading to confusion when differentiating between data sets, and other data publications, and articles; and to unify the Electronic retrieval location and Persistent identifier. To encourage scholars to develop and cite data, consistent practices must be promulgated for data citation and indexing

Columbia’s Evolving Research Data Storage Strategy

The Academic Commons repository hosted by the Columbia University Libraries / Information Services’(CUL/IS) Center for Digital Research and Scholarship (CDRS) continues to not only collect and preserve the scholarship of the faculty, but also to make it accessible through search and discovery tools. The scholarly products preserved by Academic Commons are not limited to datasets and raw data, but may additionally include works based on those data such as articles, book chapters, essays, monographs, working papers, technical reports, conference presentations, multimedia creations (e.g., simulations, three-dimensional maps), and other materials in digital formats. As the scale and types of data being generated by research are constantly, and respectively, growing and evolving, CUL/IS is developing policies, procedures, communications, and training to accommodate these transformations

Skills, Standards, and Sapp Nelson\u27s Matrix: Evaluating Research Data Management Workshop Offerings

Objective: To evaluate library workshops on their coverage of data management topics. Methods: We used a modified version of Sapp Nelson’s Competency Matrix for Data Management Skills, a matrix of learning goals organized by data management competency and complexity level, against which we compared our educational materials: slide decks and worksheets. We examined each of the educational materials against the 333 learning objectives in our modified version of the Matrix to determine which of the learning objectives applied. Conclusions: We found it necessary to change certain elements of the Matrix’s structure to increase its clarity and functionality: reinterpreting the “behaviors,” shifting the organization from the three domains of Bloom’s taxonomy to increasing complexity solely within the cognitive domain, as well as creating a comprehensive identifier schema. We appreciated the Matrix for its specificity of learning objectives, its organizational structure, the comprehensive range of competencies included, and its ease of use. On the whole, the Matrix is a useful instrument for the assessment of data management programming

Lithium alters expression of RNAs in a type-specific manner in differentiated human neuroblastoma neuronal cultures, including specific genes involved in Alzheimer's disease.

Lithium (Li) is a medication long-used to treat bipolar disorder. It is currently under investigation for multiple nervous system disorders, including Alzheimer's disease (AD). While perturbation of RNA levels by Li has been previously reported, its effects on the whole transcriptome has been given little attention. We, therefore, sought to determine comprehensive effects of Li treatment on RNA levels. We cultured and differentiated human neuroblastoma (SK-N-SH) cells to neuronal cells with all-trans retinoic acid (ATRA). We exposed cultures for one week to lithium chloride or distilled water, extracted total RNA, depleted ribosomal RNA and performed whole-transcriptome RT-sequencing. We analyzed results by RNA length and type. We further analyzed expression and protein interaction networks between selected Li-altered protein-coding RNAs and common AD-associated gene products. Lithium changed expression of RNAs in both non-specific (inverse to sequence length) and specific (according to RNA type) fashions. The non-coding small nucleolar RNAs (snoRNAs) were subject to the greatest length-adjusted Li influence. When RNA length effects were taken into account, microRNAs as a group were significantly less likely to have had levels altered by Li treatment. Notably, several Li-influenced protein-coding RNAs were co-expressed or produced proteins that interacted with several common AD-associated genes and proteins. Lithium's modification of RNA levels depends on both RNA length and type. Li activity on snoRNA levels may pertain to bipolar disorders while Li modification of protein coding RNAs may be relevant to AD

A Keck High Resolution Spectroscopic Study of the Orion Nebula Proplyds

We present the results of spectroscopy of four bright proplyds in the Orion Nebula obtained at a velocity resolution of 6 km/s. After careful isolation of the proplyd spectra from the confusing nebular radiation, the emission line profiles are compared with those predicted by realistic dynamic/photoionization models of the objects. The spectral line widths show a clear correlation with ionization potential, which is consistent with the free expansion of a transonic, ionization-stratified, photoevaporating flow. Fitting models of such a flow simultaneously to our spectra and HST emission line imaging provides direct measurements of the proplyd size, ionized density and outflow velocity. These measurements confirm that the ionization front in the proplyds is approximately D-critical and provide the most accurate and robust estimate to date of the proplyd mass loss rate. Values of 0.7E-6 to 1.5E-6 Msun/year are found for our spectroscopic sample, although extrapolating our results to a larger sample of proplyds implies that 0.4E-6 Msun/year is more typical of the proplyds as a whole. In view of the reported limits on the masses of the circumstellar disks within the proplyds, the length of time that they can have been exposed to ionizing radiation should not greatly exceed 10,000 years - a factor of 30 less than the mean age of the proplyd stars. We review the various mechanisms that have been proposed to explain this situation, and conclude that none can plausibly work unless the disk masses are revised upwards by a substantial amount.Comment: 23 pages, 8 figures, uses emulateapj.sty, accepted for publication in The Astronomical Journal (scheduled November 1999

The concept of revelation in terms of the evolution of consciousness

Following Paul’s injunction in 1 Corinthians 9:19–23 we have to ‘become scientists’ to a scientifically informed audience. While theology cannot agree with the naturalist denial of transcendence, it can adopt the experiential-realist approach typical for the sciences in its description of the Christian faith as an immanent part of cosmic evolution, albeit at a higher level of emergence. The article begins with my understanding of evolutionary theory (big bang cosmology, entropy, emergence, neural networks as infrastructure of consciousness, evolution and differentiation, sequences of past, present and future, contingency etc.) It then describes God consciousness as the intuition, perception or conceptualisation of the transcendent Source and Destiny of experienced reality and locates God consciousness in the evolutionary process. Biblical God consciousness displays two distinct characteristics: God’s creative power is experienced in reality, while God’s benevolent intentionality is proclaimed on the basis of a religious tradition. The evolutionary trajectory of biblical God consciousness, culminating in the Christ-event, is sketched and the God consciousness of Jesus is deduced from its religious embeddedness, its social-environmental relationships and its religious impact. Implications of an experiential-realist approach are (1) a dynamic, rather than ontological Christology and (2) the cosmic significance of the sacrifice of God in Christ. On this basis revelation is described first in experiential-realist and then in theological terms. The tension between the experience of God’s creative power and the proclamation of God’s benevolence leads to a dynamic, rather than ontological rendering of the Trinity. Finally, traditional eschatological assumptions are reconceptualised as God’s dynamic vision of comprehensive well-being operating like a horizon that moves on as we approach it and displays ever new vistas, challenges and opportunities.Prof. Dr Klaus Nürnberger is part of the research project, ‘Theology of Nature’, directed by Prof. Dr Johan Buitendag (Dean, Faculty of Theology), Department Dogmatics and Christian Ethics, Faculty of Theology, University of Pretoria.http://www.hts.org.zaam2017Dogmatics and Christian Ethic

Improving Discovery of and Access to Digital Repository Contents Using Semantic Web Standards: Columbia University’s Academic Commons

This article describes the progress made towards developing Academic Commons (AC), Columbia University’s digital repository, as an interoperable repository through the use of RDF and non-RDF Semantic Web technologies. Approaches taken include the implementation of microdata to add semantic markup to HTML content; a collaboration with Oregon State University’s (OSU) digital repository, ScholarsArchive@OSU (SA@OSU), to implement an application that indexes RDF data from OSU for use in AC; as well as an exploration of the recently released MODS RDF

Item response modeling of DSM-IV mania symptoms in two representative US epidemiological samples

BACKGROUND: There is considerable debate surrounding the effective measurement of DSM-IV symptoms used to assess manic disorders in epidemiological samples. METHODS: Using two nationally representative datasets, the National Epidemiological Survey of Alcohol and Related Conditions (NESARC, N=43,093 at Wave 1, N=34,653 at 3-year follow-up) and the National Comorbidity Survey-Replication (NCS-R, N=9,282), we examined the psychometric properties of symptoms used to assess DSM-IV mania. The predictive utility of the mania factor score was tested using the 3-year follow-up data in NESARC. RESULTS: Criterion B symptoms were unidimensional (single factor) in both samples. The symptoms assessing flight of ideas, distractibility and increased goal-directed activities had high factor loadings (0.70–0.93) with moderate rates of endorsement thus providing good discrimination between individuals with and without mania. The symptom assessing grandiosity performed less well in both samples. The quantitative mania factor score was a good predictor of more severe disorders at 3-year follow-up in the NESARC sample, even after controlling for a past history of DSM-IV diagnosis of manic disorder. CONCLUSION: These analyses suggest that questions based on some DSM symptoms effectively discriminate between individuals at high and low liability to mania, while others do not. A quantitative mania factor score may aid in predicting recurrence for patients with a history of mania. Methods for assessing mania using structured interviews in the absence of clinical assessment require further refinement

A ‘transversal’ dialogue with Wentzel van Huyssteen’s theological approach

In this essay, I compared notes with Wentzel van Huyssteen, one of the most prominent theologians in the science–religion discussion. I followed the topics dealt with in a casual interview with Frits Gaum, in which Van Huyssteen responded to set questions: on his academic journey, God, the Bible, creation and evolution, human uniqueness, original sin, eternal life, Jesus and the relation between faith and research. Whilst there was considerable consensus between us in most respects, I would change the focus from an ‘apologetic’ agenda (science and theology were describing the same world from equally valid vantage points using comparable rationalities) to a ‘missionary’ agenda (making the Christian faith more accessible to scientists by following the approach of ‘experiential realism’). Science confined its operations to different aspects of the reality that was accessible to human observation, explanation and manipulation, whilst theology concentrated on our relation to the transcendent Source and Destiny of all of reality. To make sense to a scientist, theology must shun unsupported postulates and speculations and confront the scientist with the basic alternative of claiming to be the ultimate authority over the immanent world (presuming to be the owner, master and beneficiary of reality) and being derived from, and responsible to, the ultimate Source and Destiny of reality. The confusion between immanent transcendence (aspects of immanent reality that were not accessible to our observation, explanation and manipulation) and transcendent immanence (immanent reality as a whole was open towards a higher Source and Destiny) bedeviled the interface between science and faith. Science challenged theology to provide experiential evidence; theology challenged science to be responsible to ultimate authority. Intradisciplinary and/or interdisciplinary implications: Both Wentzel van Huyssteen and I have worked consistently on an interdisciplinary basis. However, whilst Wentzel focused strongly on the natural sciences, I spent most of my time on the relation between the Christian faith and the human sciences (economics, ecology, cultural anthropology, politics, etc.) and concentrated on the natural sciences only after my retirement. In my essay, I highlighted the difference between trying to demonstrate the comparability and compatibility between theology and science on the one hand and highlighting the challenge that science posed to faith and faith posed to science on the other hand.http://www.ve.org.za/index.php/VEdm2022Dogmatics and Christian Ethic