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1. Enhancing Psychometric Analysis with Interactive ShinyItemAnalysis Modules

Author

Martinková, Patrícia, Netík, Jan, and Hladká, Adéla

Subjects
Computer Science - Human-Computer Interaction, Statistics - Applications
Abstract

ShinyItemAnalysis (SIA) is an R package and shiny application for an interactive presentation of psychometric methods and analysis of multi-item measurements in psychology, education, and social sciences in general. In this article, we present a new feature introduced in the recent version of the package, called "SIA modules", which allows researchers and practitioners to offer new analytical methods for broader use via add-on extensions. We describe how to build the add-on modules with the support of the new SIAtools package and demonstrate the concepts using sample modules from the newly introduced SIAmodules package. SIA modules are designed to integrate with and build upon the SIA interactive application, enabling them to leverage the existing infrastructure for tasks such as data uploading and processing. They can access a range of outputs from various analyses, including item response theory models, exploratory factor analysis, or differential item functioning models. Because SIA modules come in R packages (or extend the existing ones), they may come bundled with their datasets, use object-oriented systems, or even compiled code. We discuss the possibility of broader use of the concept of SIA modules in other areas.

Published
2024

2. The Influence of Middle Eastern Tourists on Local Community in Cisarua Bogor in the Perspective of Identity Politics and Communitarian Citizenship

Author

Indiana Ngenget and Netik Indarwati

Subjects
bogor-indonesia, communitarian citizenship, identity politics, middle eastern tourists, Political science, Political science (General), JA1-92
Abstract

This research aimed to analyze the influence of Middle Eastern tourists on local community in Cisarua Bogor in the perspective of Identity Politics and Communitarian Citizenship. This research usedqualitative with a descriptive explanatory research type. Data collection techniques used were observation, in-depth interviews, and library research. The results of this research showed that Middle Eastern tourists positively encouraged tourism activities and economic development of local community but there was an emergence of social, political, and cultural problems such as identity crisis. Local community in Cisarua as part of Indonesia is faced with the presence of a minority group namely Arab tourists who visit this region at certain times and demand a recognition of their identity. So that the localcommunity in Cisarua is faced with multicultural life because they touch and interact with values that are different from what they have. Empirically, from a political perspective, Middle Eastern tourists have encouraged the formation of identity politics and the issue of communitarian citizenship while local values are increasingly eroded. The problem of communitarian citizenship is reflected in the phenomenon of Arabic villages through the rise of Arabic writing in business, the dominance of Arabic culture, Arabic food, and so on. The thick Middle Eastern culture in tourist areas becomes a problem when dealing with local culture and nationalism as a challenge for a sovereign nation. The novelty of this research is the influence of Middle Eastern tourists in the perspective of Political Science on identity politics and communitarian citizenship.

Published
2020
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4. Adrenoleukodystrophy-Related Protein Can Compensate Functionally for Adrenoleukodystrophy Protein Deficiency (X-ALD): Implications for Therapy

Author

Johannes Berger, Andreas Holzinger, Sonja Forss-Petter, Brunhilde Molzer, Gertraud Unterrainer, and Angela Netik

Subjects
Male, congenital, hereditary, and neonatal diseases and abnormalities, endocrine system diseases, Molecular Sequence Data, Mice, Inbred Strains, ATP-binding cassette transporter, ATP Binding Cassette Transporter, Subfamily D, Transfection, ATP Binding Cassette Transporter, Subfamily D, Member 1, Microbodies, Mice, Fenofibrate, ABCD3, Peroxisomal disorder, Genetics, medicine, Animals, Humans, Adrenoleukodystrophy, Molecular Biology, Genetics (clinical), Base Sequence, biology, Membrane transport protein, Fatty Acids, Genetic Complementation Test, Membrane Proteins, Proteins, nutritional and metabolic diseases, General Medicine, Fibroblasts, Peroxisome, medicine.disease, Recombinant Proteins, Cell biology, Gene Expression Regulation, Liver, Biochemistry, Membrane protein, biology.protein, ATP-Binding Cassette Transporters, Ectopic expression, Oxidation-Reduction
Abstract

Inherited defects in the peroxisomal ATP-binding cassette (ABC) transporter adrenoleukodystrophy protein (ALDP) lead to the lethal peroxisomal disorder X-linked adrenoleukodystrophy (X-ALD), for which no efficient treatment has been established so far. Three other peroxisomal ABC transporters currently are known: adrenoleukodystrophy-related protein (ALDRP), 70 kDa peroxisomal membrane protein (PMP70) and PMP70- related protein. By using transient and stable overexpression of human cDNAs encoding ALDP and its closest relative ALDRP, we could restore the impaired peroxisomal beta-oxidation in fibroblasts of X-ALD patients. The pathognomonic accumulation of very long chain fatty acids could also be prevented by overexpression of ALDRP in immortalized X-ALD cells. Immunofluorescence analysis demonstrated that the functional replacement of ALDP by ALDRP was not due to stabilization of the mutated ALDP itself. Moreover, we were able to restore the peroxisomal beta-oxidation defect in the liver of ALDP-deficient mice by stimulation of ALDRP and PMP70 gene expression through a dietary treatment with the peroxisome proliferator fenofibrate. These results suggest that a correction of the biochemical defect in X-ALD could be possible by drug-induced overexpression or ectopic expression of ALDRP.

Published
1999

5. The four murine peroxisomal ABC-transporter genes differ in constitutive, inducible and developmental expression

Author

Angela Netik, Sabrina Albet, Andreas Holzinger, Adelbert A. Roscher, Maurice Bugaut, Johannes Berger, Marc Bentejac, and Sonja Forss-Petter

Subjects
Response element, Molecular Sequence Data, ATP-binding cassette transporter, Mice, Inbred Strains, Biology, ATP Binding Cassette Transporter, Subfamily D, Biochemistry, ATP Binding Cassette Transporter, Subfamily D, Member 1, Mice, Fenofibrate, Gene expression, medicine, Peroxisomes, Animals, Northern blot, ATP Binding Cassette Transporter, Subfamily B, Member 1, RNA, Messenger, Promoter Regions, Genetic, Gene, Hypolipidemic Agents, Mice, Knockout, Messenger RNA, Brain, Gene Expression Regulation, Developmental, Membrane Proteins, Proteins, Biological Transport, medicine.disease, Molecular biology, Nuclear receptor, Liver, Adrenoleukodystrophy, ATP-Binding Cassette Transporters
Abstract

Four ATP-binding cassette (ABC) half-transporters have been identified in mammalian peroxisomes: adrenoleukodystrophy protein (ALDP), adrenoleukodystrophy-related protein (ALDRP), 70-kDa peroxisomal membrane protein (PMP70) and PMP70-related protein (P70R). Inherited defects in ALDP cause the neurodegenerative disorder X-linked adrenoleukodystrophy (X-ALD). By comparative Northern blot analyses we found each of the four murine peroxisomal ABC transporter mRNA species at maximum abundance only in a few tissues, which differed for each family member. The four genes were also regulated differentially during mouse brain development: ALDP mRNA was most abundant in embryonic brain and gradually decreased during maturation; ALDRP and P70R mRNA accumulated in the early postnatal period; and the amount of PMP70 transcript increased slightly during the second and third postnatal week. The different expression patterns could explain why beta-oxidation is defective in X-ALD, although ALDRP and PMP70 can replace ALDP functionally in fibroblasts. Dietary fenofibrate had no effect on the ALD and P70R genes, but strongly increased expression of the ALDR and PMP70 genes in mouse liver. However, in P-glycoprotein Mdr1a-deficient mice fenofibrate treatment increased ALDR gene expression also in the brain, suggesting that the multidrug-transporter P-glycoprotein restricts entry of fenofibrate to the brain at the blood-brain barrier. Analysis of the promoter sequences revealed a cryptic nuclear hormone receptor response element of the DR+4 type in the ALDR promoter and a novel 18-bp sequence motif present only in the 5' flanking DNA of the ALDR and PMP70 genes. The mouse ALDR gene uses a single transcription start site but alternative polyadenylation sites. These data are of importance for the use of ALDP-deficient mice as a model in pharmacological gene therapy studies.

Published
1999

8. Rat adrenoleukodystrophy related (ALDR) gene: full-length cDNA sequence and new insight in expression

Author

Albet, S., Bentejac, M., Savary, S., Gondcaille, C., Netik, A., Berger, Johannes, Szpirer, Claude, Troffer-Charlier, N., Bugaut, M., Albet, S., Bentejac, M., Savary, S., Gondcaille, C., Netik, A., Berger, Johannes, Szpirer, Claude, Troffer-Charlier, N., and Bugaut, M.

Abstract

X-linked adrenoleukodystrophy (X-ALD) is an inherited demyelinating disorder due to mutations in the ALD gene, which encodes a peroxisomal ABC half-transporter (ALDP). It has been suggested that ALDP assembles with ALDRP (adrenoleukodystrophy-related protein), a close homologous half-transporter, to form a functional heterodimer. For the first time full-length ALDRP cDNA (5.5 kb) was cloned, and 5' and 3' RACE analysis revealed that alternative usage of polyadenylation sites generates the two transcripts of 3.0 and 5.5 kb observed in the rat in Northern blot analysis. Southern blotting and chromosomal mapping demonstrated one ALDR locus in the rat genome. Characterisation of the 3' flanking region suggested that an ID sequence might be responsible for high expression of the 5.5 kb ALDRP transcript in rat brain. ALDR gene expression was found to be high in the liver of rats before weaning and very low in adult rats; the reverse developmental regulation was observed in the brain. Fenofibrate, which is a potent inducer of the ALDR gene in the liver of adult rats, could not induce the ALDR gene in suckling rats. The exact significance of this result with regard to development of an efficient pharmacological gene therapy for X-ALD is discussed., Comparative Study, Journal Article, Research Support, Non-U.S. Gov't, info:eu-repo/semantics/published

Published
2001

9. Rat adrenoleukodystrophy-related (ALDR) gene: Full-length cDNA sequence and new insight in expression

Author

Albet, Sabrina, Bentejac, Marc, Savary, Stéphane, Gondcaille, Catherine, Netik, Angela, Berger, Johannes, Szpirer, Claude, Troffer-Charlier, Nathalie, Bugaut, Maurice, Albet, Sabrina, Bentejac, Marc, Savary, Stéphane, Gondcaille, Catherine, Netik, Angela, Berger, Johannes, Szpirer, Claude, Troffer-Charlier, Nathalie, and Bugaut, Maurice

Abstract

X-linked adrenoleukodystrophy (X-ALD) is an inherited demyelinating disorder due to mutations in the ALD gene, which encodes a peroxisomal ABC half-transporter (ALDP). It has been suggested that ALDP assembles with ALDRP (adrenoleukodystrophy-related protein), a close homologous half-transporter, to form a functional heterodimer. For the first time full-length ALDRP cDNA (5.5 kb) was cloned, and 5′ and 3′ RACE analysis revealed that alternative usage of polyadenylation sites generates the two transcripts of 3.0 and 5.5 kb observed in the rat in Northern blot analysis. Southern blotting and chromosomal mapping demonstrated one ALDR locus in the rat genome. Characterisation of the 3′ flanking region suggested that an ID sequence might be responsible for high expression of the 5.5 kb ALDRP transcript in rat brain. ALDR gene expression was found to be high in the liver of rats before weaning and very low in adult rats; the reverse developmental regulation was observed in the brain. Fenofibrate, which is a potent inducer of the ALDR gene in the liver of adult rats, could not induce the ALDR gene in suckling rats. The exact significance of this result with regard to development of an efficient pharmacological gene therapy for X-ALD is discussed. © 2001 Elsevier Science B.V., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2001

13. Uptake and export of citric acid by Aspergillus niger is reciprocally regulated by manganese ions

Author

Angela Netik, Jose-Maria Riol, Christian P. Kubicek, and Néstor V. Torres

Subjects
inorganic chemicals, Cations, Divalent, Carboxylic Acids, Biophysics, chemistry.chemical_element, Manganese, Biochemistry, chemistry.chemical_compound, Citric acid, medicine, Edetic Acid, Mycelium, chemistry.chemical_classification, biology, Aspergillus niger, fungi, (Aspergillus niger), Biological Transport, Cell Biology, Tricarboxylic acid, Hydrogen-Ion Concentration, Citrate transport, biology.organism_classification, medicine.disease, Culture Media, Kinetics, Phthalic acid, Manganese deficiency (medicine), chemistry, Metals, Nuclear chemistry
Abstract

The uptake as well as the export of citric acid by Aspergillus niger occur by active, ΔpH-driven, H+-symport dependent systems. They are inhibited by nonmetabolizable tricarboxylic acid analogues and phthalic acid, and by several other mono-, di- and tribasic organic acids. However, citrate export could only be demonstrated in a mycelium cultivated under manganese-deficient growth conditions, whereas the uptake of citrate from the medium was only detectable upon precultivation of A. niger in a medium supplemented with Mn2+ ions. In addition, the uptake of citrate was dependent on the presence of Mn2+ ions in the assay, and inhibited by EDTA. This requirement for Mn2+ could also be partially fulfilled by Mg2+, Fe2+ or Zn2+, whereas Cu2+ ions inhibited citrate transport. The observed divergent effects of manganese ions on citrate uptake and citrate export may be a major reason for the well documented requirement for manganese deficiency of citric acid accumulation.

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