Comprehending 3D and 4D ontology-driven conceptual models: An empirical study

This paper presents an empirical study that investigates the extent to which the pragmatic quality of ontology-driven models is influenced by the choice of a particular ontology, given a certain understanding of that ontology. To this end, we analyzed previous research efforts and distilled three hypotheses based on different metaphysical characteristics. An experiment based on two foundational ontologies (UFO and BORO) involving 158 participants was then carried out, followed by a protocol analysis to gain further insights into the results of experiment. We then extracted five derivations from the results of the empirical study in order to summarize our findings. Overall, the results confirm that the choice of a foundational ontology can lead to significant differences in the interpretation and comprehension of the conceptual models produced. Moreover, the effect of applying a certain foundational ontology can cause considerable variations in the effort required to comprehend these models

A Simulation Model Articulation of the REA Ontology

This paper demonstrates how the REA enterprise ontology can be used to construct simulation models for business processes, value chains and collaboration spaces in supply chains. These models support various high-level and operational management simulation applications, e.g. the analysis of enterprise sustainability and day-to-day planning. First, the basic constructs of the REA ontology and the ExSpect modelling language for simulation are introduced. Second, collaboration space, value chain and business process models and their conceptual dependencies are shown, using the ExSpect language. Third, an exhibit demonstrates the use of value chain models in predicting the financial performance of an enterprise

4th international workshop on ontologies and conceptual modeling (Onto.Com)

The theme of the 4th International Workshop on Ontologies and Conceptual Modeling is foundational ontologies and their meta-ontological choices. Expert representatives of major foundational ontologies have been invited to discuss and compare their meta-ontological choices within the context of a common case study. The workshop is aimed at exploring the ways in which different meta-ontological choices impact conceptual modelling in information systems

Comparing traditional conceptual modeling with ontology-driven conceptual modeling: An empirical study

[EN] This paper conducts an empirical study that explores the differences between adopting a traditional conceptual modeling (TCM) technique and an ontology-driven conceptual modeling (ODCM) technique with the objective to understand and identify in which modeling situations an ODCM technique can prove beneficial compared to a TCM technique. More specifically, we asked ourselves if there exist any meaningful differences in the resulting conceptual model and the effort spent to create such model between novice modelers trained in an ontology-driven conceptual modeling technique and novice modelers trained in a traditional conceptual modeling technique. To answer this question, we discuss previous empirical research efforts and distill these efforts into two hypotheses. Next, these hypotheses are tested in a rigorously developed experiment, where a total of 100 students from two different Universities participated. The findings of our empirical study confirm that there do exist meaningful differences between adopting the two techniques. We observed that novice modelers applying the ODCM technique arrived at higher quality models compared to novice modelers applying the TCM technique. More specifically, the results of the empirical study demonstrated that it is advantageous to apply an ODCM technique over an TCM when having to model the more challenging and advanced facets of a certain domain or scenario. Moreover, we also did not find any significant difference in effort between applying these two techniques. Finally, we specified our results in three findings that aim to clarify the obtained results. (C) 2018 Elsevier Ltd. All rights reserved.This research has been funded by the Ghent University Special Research Fund (BOF 01N02014) and the National Bank of Belgium.Verdonck, M.; Gailly, F.; Pergl, R.; Guizzardi, G.; Franco Martins, B.; Pastor López, O. (2019). Comparing traditional conceptual modeling with ontology-driven conceptual modeling: An empirical study. Information Systems. 81:92-103. https://doi.org/10.1016/j.is.2018.11.009S921038

P2Y2 receptor activation inhibits the expression of the sodium-chloride cotransporter NCC in distal convoluted tubule cells

Luminal nucleotide stimulation is known to reduce Na+ transport in the distal nephron. Previous studies suggest that this mechanism may involve the thiazide-sensitive Na+-Cl− cotransporter (NCC), which plays an essential role in NaCl reabsorption in the cells lining the distal convoluted tubule (DCT). Here we show that stimulation of mouse DCT (mDCT) cells with ATP or UTP promoted Ca2+ transients and decreased the expression of NCC at both mRNA and protein levels. Specific siRNA-mediated silencing of P2Y2 receptors almost completely abolished ATP/UTP-induced Ca2+ transients and significantly reduced ATP/UTP-induced decrease of NCC expression. To test whether local variations in the intracellular Ca2+ concentration ([Ca2+]i) may control NCC transcription, we overexpressed the Ca2+-binding protein parvalbumin selectively in the cytosol or in the nucleus of mDCT cells. The decrease in NCC mRNA upon nucleotide stimulation was abolished in cells overexpressing cytosolic PV but not in cells overexpressing either a nuclear-targeted PV or a mutated PV unable to bind Ca2+. Using a firefly luciferase reporter gene strategy, we observed that the activity of NCC promoter region from −1 to −2,200bp was not regulated by changes in [Ca2+]i. In contrast, high cytosolic calcium level induced instability of NCC mRNA. We conclude that in mDCT cells: (1) P2Y2 receptor is essential for the intracellular Ca2+ signaling induced by ATP/UTP stimulation; (2) P2Y2-mediated increase of cytoplasmic Ca2+ concentration down-regulates the expression of NCC; (3) the decrease of NCC expression occurs, at least in part, via destabilization of its mRNA

Activation of TRPC1 Channel by Metabotropic Glutamate Receptor mGluR5 Modulates Synaptic Plasticity and Spatial Working Memory

Group I metabotropic glutamate receptors, in particular mGluR5, have been implicated in various forms of synaptic plasticity that are believed to underlie declarative memory. We observed that mGluR5 specifically activated a channel containing TRPC1, an isoform of the canonical family of transient receptor potential (TRPC) channels highly expressed in CA1-3 regions of the hippocampus. TRPC1 is able to form tetrameric complexes with TRPC4 and/or TRPC5 isoforms. TRPC1/4/5 complexes have recently been involved in the efficiency of synaptic transmission in the hippocampus. We therefore used a mouse model devoid of TRPC1 expression to investigate the involvement of mGluR5-TRPC1 pathway in synaptic plasticity and memory formation. Trpc1-/- mice showed alterations in spatial working memory and fear conditioning. Activation of mGluR increased synaptic excitability in neurons from WT but not from Trpc1-/- mice. LTP triggered by a theta burst could not maintain over time in brain slices from Trpc1-/- mice. mGluR-induced LTD was also impaired in these mice. Finally, acute inhibition of TRPC1 by Pico145 on isolated neurons or on brain slices mimicked the genetic depletion of Trpc1 and inhibited mGluR-induced entry of cations and subsequent effects on synaptic plasticity, excluding developmental or compensatory mechanisms in Trpc1-/- mice. In summary, our results indicate that TRPC1 plays a role in synaptic plasticity and spatial working memory processes

The Atypical Calpains: Evolutionary Analyses and Roles in Caenorhabditis elegans Cellular Degeneration

The calpains are physiologically important Ca2+-activated regulatory proteases, which are divided into typical or atypical sub-families based on constituent domains. Both sub-families are present in mammals, but our understanding of calpain function is based primarily on typical sub-family members. Here, we take advantage of the model organism Caenorhabditis elegans, which expresses only atypical calpains, to extend our knowledge of the phylogenetic evolution and function of calpains. We provide evidence that a typical human calpain protein with a penta EF hand, detected using custom profile hidden Markov models, is conserved in ancient metazoans and a divergent clade. These analyses also provide evidence for the lineage-specific loss of typical calpain genes in C. elegans and Ciona, and they reveal that many calpain-like genes lack an intact catalytic triad. Given the association between the dysregulation of typical calpains and human degenerative pathologies, we explored the phenotypes, expression profiles, and consequences of inappropriate reduction or activation of C. elegans atypical calpains. These studies show that the atypical calpain gene, clp-1, contributes to muscle degeneration and reveal that clp-1 activity is sensitive to genetic manipulation of [Ca2+]i. We show that CLP-1 localizes to sarcomeric sub-structures, but is excluded from dense bodies (Z-disks). We find that the muscle degeneration observed in a C. elegans model of dystrophin-based muscular dystrophy can be suppressed by clp-1 inactivation and that nemadipine-A inhibition of the EGL-19 calcium channel reveals that Ca2+ dysfunction underlies the C. elegans MyoD model of myopathy. Taken together, our analyses highlight the roles of calcium dysregulation and CLP-1 in muscle myopathies and suggest that the atypical calpains could retain conserved roles in myofilament turnover

Histological and transcriptome-wide level characteristics of fetal myofiber hyperplasia during the second half of gestation in Texel and Ujumqin sheep

<p>Abstract</p> <p>Background</p> <p>Whether myofibers increase with a pulsed-wave mode at particular developmental stages or whether they augment evenly across developmental stages in large mammals is unclear. Additionally, the molecular mechanisms of myostatin in myofiber hyperplasia at the fetal stage in sheep remain unknown. Using the first specialized transcriptome-wide sheep oligo DNA microarray and histological methods, we investigated the gene expression profile and histological characteristics of developing fetal ovine longissimus muscle in Texel sheep (high muscle and low fat), as a myostatin model of natural mutation, and Ujumqin sheep (low muscle and high fat). Fetal skeletal muscles were sampled at 70, 85, 100, 120, and 135 d of gestation.</p> <p>Results</p> <p>Myofiber number increased sharply with a pulsed-wave mode at certain developmental stages but was not augmented evenly across developmental stages in fetal sheep. The surges in myofiber hyperplasia occurred at 85 and 120 d in Texel sheep, whereas a unique proliferative surge appeared at 100 d in Ujumqin sheep. Analysis of the microarray demonstrated that immune and hematological systems' development and function, lipid metabolism, and cell communication were the biological functions that were most differentially expressed between Texel and Ujumqin sheep during muscle development. Pathways associated with myogenesis and the proliferation of myoblasts, such as calcium signaling, chemokine (C-X-C motif) receptor 4 signaling, and vascular endothelial growth factor signaling, were affected significantly at specific fetal stages, which underpinned fetal myofiber hyperplasia and postnatal muscle hypertrophy. Moreover, we identified some differentially expressed genes between the two breeds that could be potential myostatin targets for further investigation.</p> <p>Conclusions</p> <p>Proliferation of myofibers proceeded in a pulsed-wave mode at particular fetal stages in the sheep. The myostatin mutation changed the gene expression pattern in skeletal muscle at a transcriptome-wide level, resulting in variation in myofiber phenotype between Texel and Ujumqin sheep during the second half of gestation. Our findings provide a novel and dynamic description of the effect of myostatin on skeletal muscle development, which contributes to understanding the biology of muscle development in large mammals.</p