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See detailUniversal (Meta-)Logical Reasoning: The Wise Men Puzzle (Isabelle/HOL Dataset)
Benzmüller, Christoph UL

in Data in Brief (2019), 24(103823), 1--5

The authors universal (meta-)logical reasoning approach is demonstrated and assessed with a prominent riddle in epistemic reasoning: the Wise Men Puzzle. The presented solution puts a particular emphasis ... [more ▼]

The authors universal (meta-)logical reasoning approach is demonstrated and assessed with a prominent riddle in epistemic reasoning: the Wise Men Puzzle. The presented solution puts a particular emphasis on the adequate modeling of common knowledge and it illustrates the elegance and the practical relevance of the shallow semantical embedding approach when utilized within modern proof assistant systems such as Isabelle/HOL. The contributed dataset provides supporting evidence for claims made in the article “Universal (meta-)logical reasoning: Recent successes” (Benzmüller, 2019). [less ▲]

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See detailTranscriptome profiling data reveals Ubiquitin-Specific Peptidase 9 knockdown effects
Glaab, Enrico UL; Antony, Paul UL; Köglsberger, Sandra et al

in Data in Brief (2019), 25(1), 104130

Ubiquitin specific peptidase 9 (USP9) is a deubiquitinase encoded by a sex-linked gene with a Y-chromosomal form (USP9Y) and an X-chromosomal form (USP9X) that escapes X-inactivation. Since USP9 is a key ... [more ▼]

Ubiquitin specific peptidase 9 (USP9) is a deubiquitinase encoded by a sex-linked gene with a Y-chromosomal form (USP9Y) and an X-chromosomal form (USP9X) that escapes X-inactivation. Since USP9 is a key regulatory gene with sex-linked expression in the human brain, the gene may be of interest for researchers studying molecular gender differences and ubiquitin signaling in the brain. To assess the downstream effects of knocking down USP9X and USP9Y on a transcriptome-wide scale, we have conducted microarray profiling experiments using the human DU145 prostate cancer cell culture model, after confirming the robust expression of both USP9X and USP9Y in this model. By designing shRNA constructs for the specific knockdown of USP9X and the joint knockdown of USP9X and USP9Y, we have compared gene expression changes in both knockdowns to control conditions to infer potential shared and X- or Y-form specific alterations. Here, we provide details of the corresponding microarray profiling data, which has been deposited in the Gene Expression Omnibus database (GEO series accession number GSE79376). A biological interpretation of the data in the context of a potential involvement of USP9 in Alzheimer’s disease has previously been presented in Köglsberger et al. (2016). To facilitate the re-use and re-analysis of the data for other applications, e.g. the study of ubiquitin signaling and protein turnover control, and the regulation of molecular gender differences in the human brain and brain-related disorders, we provide a more in-depth discussion of the data properties, specifications and possible use cases. [less ▲]

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See detailData on quantification of signaling pathways activated by KIT and PDGFRA mutants.
Bahlawane, Christelle; Schmitz, Martine UL; Letellier, Elisabeth UL et al

in Data in Brief (2016), (9), 828-838

The present data are related to the article entitled "Insights into ligand stimulation effects on gastro-intestinal stromal tumors signaling" (C. Bahlawane, M. Schmitz, E. Letellier, K. Arumugam, N. Nicot ... [more ▼]

The present data are related to the article entitled "Insights into ligand stimulation effects on gastro-intestinal stromal tumors signaling" (C. Bahlawane, M. Schmitz, E. Letellier, K. Arumugam, N. Nicot, P.V. Nazarov, S. Haan, 2016) [1]. Constitutive and ligand-derived signaling pathways mediated by KIT and PDGFRA mutated proteins found in gastrointestinal stromal tumors (GIST) were compared. Expression of mutant proteins was induced by doxycycline in an isogenic background (Hek293 cells). Kit was identified by FACS at the cell surface and found to be quickly degraded or internalized upon SCF stimulation for both Kit Wild type and Kit mutant counterparts. Investigation of the main activated pathways in GIST unraveled a new feature specific for oncogenic KIT mutants, namely their ability to be further activated by Kit ligand, the stem cell factor (scf). We were also able to identify the MAPK pathway as the most prominent target for a common inhibition of PDGFRA and KIT oncogenic signaling. Western blotting and micro-array analysis were applied to analyze the capacities of the mutant to induce an effective STATs response. Among all Kit mutants, only Kit Ex11 deletion mutant was able to elicit an effective STATs response whereas all PDGFRA were able to do so. [less ▲]

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See detailHousing land transaction data and structural econometric estimation of preference parameters for urban economic simulation models
Caruso, Geoffrey UL; Cavailhès, Jean; Peeters, Dominique et al

in Data in Brief (2015), 5

This paper describes a dataset of 6284 land transactions prices and plot surfaces in 3 medium-sized cities in France (Besançon, Dijon and Brest). The dataset includes road accessibility as obtained from a ... [more ▼]

This paper describes a dataset of 6284 land transactions prices and plot surfaces in 3 medium-sized cities in France (Besançon, Dijon and Brest). The dataset includes road accessibility as obtained from a minimization algorithm, and the amount of green space available to households in the neighborhood of the transactions, as evaluated from a land cover dataset. Further to the data presentation, the paper describes how these variables can be used to estimate the non-observable parameters of a residential choice function explicitly derived from a microeconomic model. The estimates are used by Caruso et al. (2015) to run a calibrated microeconomic urban growth simulation model where households are assumed to trade-off accessibility and local green space amenities. [less ▲]

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