cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1632725
title: Adult Verbal Abstract Reasoning Assessment Instruments and their Clinimetric Properties

description: <i>Objective</i>: This systematic review aims to identify, examine, and compare tests used to measure and assess verbal abstract reasoning (VAR). <i>Method</i>: Seven tests were identified through a systematic search of electronic databases, neuropsychological textbooks, and online catalogs. Clinical utility, normative data, and psychometric properties (internal consistency, test–retest reliability, and construct validity) of current test versions were evaluated using recent studies. A modified version of the CanChild Outcome Measures Rating Form, and structured quality assessment criteria were used in the evaluation process. <i>Results</i>: The WAIS-IV Similarities subtest was ranked the highest, followed by the Shipley-2 Abstraction test and Gorham’s Proverbs test. These three tests had sufficient validity to recommend their use, however some caution is advised for the latter two in terms of construct purity, and age of normative data, respectively. Other tests reviewed were the Delis–Kaplan Executive Functioning System Proverbs subtest, the Stanford-Binet Intelligence Scale fifth edition Verbal Analogies subtests, the Conceptual Level Analogy Test, and the Verbal Concept Attainment Test. For the majority of tests, construct validity was lacking while reliabilities were sufficient. <i>Conclusions</i>: Lack of sound psychometric evidence limits the range of options for the practitioner to choose a test with confidence to assess VAR. While there is merit in the clinical utility of the majority of assessment instruments evaluated in this review, caution is recommended before deciding to use a test that does not carry sufficient psychometric evidence to support its use. Further research is recommended to improve the library of tests available to clinicians and researchers.
DOI: 10.6084/m9.figshare.1632726.v1
title: The tyrosine-sorting motif of the vacuolar sorting receptor VSR4 from <i>Arabidopsis thaliana</i>, which is involved in the interaction between VSR4 and AP1M2, μ1-adaptin type 2 of clathrin adaptor complex 1 subunits, participates in the post-Golgi sorting of VSR4

description: μ1-Adaptin of adaptor protein (AP) 1 complex, AP1M, is generally accepted to load cargo proteins into clathrin-coated vesicles (CCVs) at the <i>trans</i>-Golgi network through its binding to cargo-recognition sequences (CRSs). Plant vacuolar-sorting receptors (VSRs) function in sorting vacuolar proteins, which are reportedly mediated by CCV. We herein investigated the involvement of CRSs of <i>Arabidopsis thaliana</i> VSR4 in the sorting of VSR4. The results obtained showed the increased localization of VSR4 at the plasma membrane or vacuoles by mutations in CRSs including the tyrosine-sorting motif YMPL or acidic dileucine-like motif EIRAIM, respectively. Interaction analysis using the bimolecular fluorescence complementation (BiFC) system, V10-BiFC, which we developed, indicated an interaction between VSR4 and AP1M2, AP1M type 2, which was attenuated by a YMPL mutation, but not influenced by an EIRAIM mutation. These results demonstrated the significance of the recognition of YMPL in VSR4 by AP1M2 for the post-Golgi sorting of VSR4. Clathrin AP1M2-recognizable tyrosine motif for plant VSR4 sorting.
DOI: 10.6084/m9.figshare.1632725.v1
title: Adult Verbal Abstract Reasoning Assessment Instruments and their Clinimetric Properties

description: <i>Objective</i>: This systematic review aims to identify, examine, and compare tests used to measure and assess verbal abstract reasoning (VAR). <i>Method</i>: Seven tests were identified through a systematic search of electronic databases, neuropsychological textbooks, and online catalogs. Clinical utility, normative data, and psychometric properties (internal consistency, test–retest reliability, and construct validity) of current test versions were evaluated using recent studies. A modified version of the CanChild Outcome Measures Rating Form, and structured quality assessment criteria were used in the evaluation process. <i>Results</i>: The WAIS-IV Similarities subtest was ranked the highest, followed by the Shipley-2 Abstraction test and Gorham’s Proverbs test. These three tests had sufficient validity to recommend their use, however some caution is advised for the latter two in terms of construct purity, and age of normative data, respectively. Other tests reviewed were the Delis–Kaplan Executive Functioning System Proverbs subtest, the Stanford-Binet Intelligence Scale fifth edition Verbal Analogies subtests, the Conceptual Level Analogy Test, and the Verbal Concept Attainment Test. For the majority of tests, construct validity was lacking while reliabilities were sufficient. <i>Conclusions</i>: Lack of sound psychometric evidence limits the range of options for the practitioner to choose a test with confidence to assess VAR. While there is merit in the clinical utility of the majority of assessment instruments evaluated in this review, caution is recommended before deciding to use a test that does not carry sufficient psychometric evidence to support its use. Further research is recommended to improve the library of tests available to clinicians and researchers.
DOI: 10.6084/m9.figshare.1632716
title: Geology of Monte Gallo (Palermo Mts, NW Sicily)

description: The promontory of Monte Gallo (Palermo, NW Sicily) is a spectacular site where Upper Triassic-Eocene carbonate platform rocks and Quaternary continental to marine deposits are well exposed. A Mesozoic-Paleogene rock succession allows the potential visitor to easily detect the features and the evolution of the Panormide carbonate platform, a shallow-water paleogeographic domain of the Southern Tethyan margin. Quaternary deposits, as well many landforms, enable the visitor to directly identify the interplay between climate changes, tectonics and fluctuations of marine level that occurred during the Quaternary Period. A detailed geological map (1:15,000 mapping scale) is presented, accompanied by a stratigraphic correlation of logged sections and morpho-stratigraphic and tectonic schemes of the area, aimed at highlighting the geological heritage of Monte Gallo in support of the establishment of a Geosite. The Geological Map and relevant explanatory notes should be used as cartographic support and as a field trip guide for possible geological itineraries.
DOI: 10.6084/m9.figshare.1632714
title: Probing-directed identification of novel structured RNAs

description: Transcripts often harbor RNA elements, which regulate cell processes co- or post-transcriptionally. The functions of many regulatory RNA elements depend on their structure, thus it is important to determine the structure as well as to scan genomes for structured elements. State of the art <i>ab initio</i> approaches to predict structured RNAs rely on DNA sequence analysis. They use 2 major types of information inferred from a sequence: thermodynamic stability of an RNA structure and evolutionary footprints of base-pair interactions. In recent years, chemical probing of RNA has arisen as an alternative source of structural information. RNA probing experiments detect positions accessible to specific types of chemicals or enzymes indicating their propensity to be in a paired or unpaired state. There exist several strategies to integrate probing data into RNA secondary structure prediction algorithms that substantially improve the prediction quality. However, whether and how probing data could contribute to detection of structured RNAs remains an open question. We previously developed the energy-based approach RNASurface to detect locally optimal structured RNA elements. Here, we integrate probing data into the RNASurface energy model using a general framework. We show that the use of experimental data allows for better discrimination of ncRNAs from other transcripts. Application of RNASurface to genome-wide analysis of the human transcriptome with PARS data identifies previously undetectable segments, with evidence of functionality for some of them.
DOI: 10.6084/m9.figshare.1632716.v2
title: Geology of Monte Gallo (Palermo Mts, NW Sicily)

description: The promontory of Monte Gallo (Palermo, NW Sicily) is a spectacular site where Upper Triassic-Eocene carbonate platform rocks and Quaternary continental to marine deposits are well exposed. A Mesozoic-Paleogene rock succession allows the potential visitor to easily detect the features and the evolution of the Panormide carbonate platform, a shallow-water paleogeographic domain of the Southern Tethyan margin. Quaternary deposits, as well many landforms, enable the visitor to directly identify the interplay between climate changes, tectonics and fluctuations of marine level that occurred during the Quaternary Period. A detailed geological map (1:15,000 mapping scale) is presented, accompanied by a stratigraphic correlation of logged sections and morpho-stratigraphic and tectonic schemes of the area, aimed at highlighting the geological heritage of Monte Gallo in support of the establishment of a Geosite. The Geological Map and relevant explanatory notes should be used as cartographic support and as a field trip guide for possible geological itineraries.
DOI: 10.6084/m9.figshare.1632714.v1
title: Probing-directed identification of novel structured RNAs

description: Transcripts often harbor RNA elements, which regulate cell processes co- or post-transcriptionally. The functions of many regulatory RNA elements depend on their structure, thus it is important to determine the structure as well as to scan genomes for structured elements. State of the art <i>ab initio</i> approaches to predict structured RNAs rely on DNA sequence analysis. They use 2 major types of information inferred from a sequence: thermodynamic stability of an RNA structure and evolutionary footprints of base-pair interactions. In recent years, chemical probing of RNA has arisen as an alternative source of structural information. RNA probing experiments detect positions accessible to specific types of chemicals or enzymes indicating their propensity to be in a paired or unpaired state. There exist several strategies to integrate probing data into RNA secondary structure prediction algorithms that substantially improve the prediction quality. However, whether and how probing data could contribute to detection of structured RNAs remains an open question. We previously developed the energy-based approach RNASurface to detect locally optimal structured RNA elements. Here, we integrate probing data into the RNASurface energy model using a general framework. We show that the use of experimental data allows for better discrimination of ncRNAs from other transcripts. Application of RNASurface to genome-wide analysis of the human transcriptome with PARS data identifies previously undetectable segments, with evidence of functionality for some of them.
DOI: 10.6084/m9.figshare.1632712.v1
title: Cord blood gene expression supports that prenatal exposure to perfluoroalkyl substances causes depressed immune functionality in early childhood

description: Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are a class of synthetic compounds that have widespread use in consumer and industrial applications. PFAS are considered environmental pollutants that have various toxic properties, including effects on the immune system. Recent human studies indicate that prenatal exposure to PFAS leads to suppressed immune responses in early childhood. In this study, data from the Norwegian BraMat cohort was used to investigate transcriptomics profiles in neonatal cord blood and their association with maternal PFAS exposure, anti-rubella antibody levels at 3 years of age and the number of common cold episodes until 3 years. Genes associated with PFAS exposure showed enrichment for immunological and developmental functions. The analyses identified a toxicogenomics profile of 52 PFAS exposure-associated genes that were in common with genes associated with rubella titers and/or common cold episodes. This gene set contains several immunomodulatory genes (<i>CYTL1, IL27</i>) as well as other immune-associated genes (e.g. <i>EMR4P, SHC4, ADORA2A</i>). In addition, this study identified <i>PPARD</i> as a PFAS toxicogenomics marker. These markers can serve as the basis for further mechanistic or epidemiological studies. This study provides a transcriptomics connection between prenatal PFAS exposure and impaired immune function in early childhood and supports current views on PPAR- and NF-<i>κ</i>B-mediated modes of action. The findings add to the available evidence that PFAS exposure is immunotoxic in humans and support regulatory policies to phase out these substances.
DOI: 10.6084/m9.figshare.1632711
title: Selective inhibitory effects of 50-nm gold nanoparticles on mouse macrophage and spleen cells

description: Nanoparticles (NP) are significant to multiple industrial processes, consumer products and medical applications today. The health effects of many different types of NP, however, are largely unknown. The purpose of this study was to test the effects of 50-nm gold NP coated with poly-<i>N</i>-vinylpyrrolidone (PVP) on mouse macrophage and spleen cells with and without lipopolysaccharide (LPS), testing the hypothesis that the NP would modulate immune responses without being overtly toxic. Gold NP had no effect on macrophage viability and, in the absence of LPS, they had no effect on tumor necrosis factor (TNF)-<i>α</i> production as measured by ELISA. The presence of LPS significantly increased the release of TNF<i>α</i> from the macrophages above no-treatment controls, but increasing gold NP concentration led to decreasing release of TNF<i>α</i>. The reactive oxygen species (ROS) produced by exposed macrophages were also reduced compared to untreated controls, both with and without LPS, suggesting some kind of oxygen radical scavenging. In splenocyte cultures, gold NP had no effect alone, but significantly reduced the release of interleukin (IL)-17 and TNF<i>α</i> triggered by LPS. These results suggest that the gold NP used here are not cytotoxic to immune cells at these concentrations, but may affect cellular responses to infection or inflammation by altering the balance of cytokines.
DOI: 10.6084/m9.figshare.1632711.v1
title: Selective inhibitory effects of 50-nm gold nanoparticles on mouse macrophage and spleen cells

description: Nanoparticles (NP) are significant to multiple industrial processes, consumer products and medical applications today. The health effects of many different types of NP, however, are largely unknown. The purpose of this study was to test the effects of 50-nm gold NP coated with poly-<i>N</i>-vinylpyrrolidone (PVP) on mouse macrophage and spleen cells with and without lipopolysaccharide (LPS), testing the hypothesis that the NP would modulate immune responses without being overtly toxic. Gold NP had no effect on macrophage viability and, in the absence of LPS, they had no effect on tumor necrosis factor (TNF)-<i>α</i> production as measured by ELISA. The presence of LPS significantly increased the release of TNF<i>α</i> from the macrophages above no-treatment controls, but increasing gold NP concentration led to decreasing release of TNF<i>α</i>. The reactive oxygen species (ROS) produced by exposed macrophages were also reduced compared to untreated controls, both with and without LPS, suggesting some kind of oxygen radical scavenging. In splenocyte cultures, gold NP had no effect alone, but significantly reduced the release of interleukin (IL)-17 and TNF<i>α</i> triggered by LPS. These results suggest that the gold NP used here are not cytotoxic to immune cells at these concentrations, but may affect cellular responses to infection or inflammation by altering the balance of cytokines.
DOI: 10.6084/m9.figshare.1632708
title: Use of Early Life-Stages of Zebrafish to Assess Toxicity of Sediments Contaminated by Organotin Compounds

description: This study examined the response of early life-stages (ELS) of zebrafish to organotin-contaminated sediment from Lake Huruslahti (HL) in Central Finland. A dilution series (0, 10, 33, and 100%) of the native (HL) and the sediment spiked with tributyltin (TBT) determined a dose-response of zebrafish ELS to organotin-contaminated sediment. Sediment elutriates were assessed by bacterial bioluminescence assay and microscopical pathologies of 1–3 days post-fertilization zebrafish (1–3dpfZF). Brain aromatase (cyp19a1b) and tissue vitellogenin (vtg1) were assayed from early-juvenile zebrafish (20dpfZF) exposed to intact sediment. In vivo modulation of cyp19a1b and vtg1 transcripts in 20dpfZF was targeted to screen potential sediment contamination by TBT, an anti-estrogenic chemical. Bioluminescence assay (EC50<sub>30min =</sub> 34.6% of HL-100) determined that the HL-100 elutriate was toxic. Exposed developing embryos (1–3dpf) showed toxicities, including lowered heart rate. Results showed down-regulation of cyp19a1b and up-regulation of vtg1 in 20dpfZF exposed to TBT-spiked sediment (185–1620 µg/kg d.w.).
DOI: 10.6084/m9.figshare.1632708.v1
title: Use of Early Life-Stages of Zebrafish to Assess Toxicity of Sediments Contaminated by Organotin Compounds

description: This study examined the response of early life-stages (ELS) of zebrafish to organotin-contaminated sediment from Lake Huruslahti (HL) in Central Finland. A dilution series (0, 10, 33, and 100%) of the native (HL) and the sediment spiked with tributyltin (TBT) determined a dose-response of zebrafish ELS to organotin-contaminated sediment. Sediment elutriates were assessed by bacterial bioluminescence assay and microscopical pathologies of 1–3 days post-fertilization zebrafish (1–3dpfZF). Brain aromatase (cyp19a1b) and tissue vitellogenin (vtg1) were assayed from early-juvenile zebrafish (20dpfZF) exposed to intact sediment. In vivo modulation of cyp19a1b and vtg1 transcripts in 20dpfZF was targeted to screen potential sediment contamination by TBT, an anti-estrogenic chemical. Bioluminescence assay (EC50<sub>30min =</sub> 34.6% of HL-100) determined that the HL-100 elutriate was toxic. Exposed developing embryos (1–3dpf) showed toxicities, including lowered heart rate. Results showed down-regulation of cyp19a1b and up-regulation of vtg1 in 20dpfZF exposed to TBT-spiked sediment (185–1620 µg/kg d.w.).
DOI: 10.6084/m9.figshare.1632161
title: Role of stress-activated OCT4A in the cell fate decisions of embryonal carcinoma cells treated with etoposide

description: Tumor cellular senescence induced by genotoxic treatments has recently been found to be paradoxically linked to the induction of “stemness.” This observation is critical as it directly impinges upon the response of tumors to current chemo-radio-therapy treatment regimens. Previously, we showed that following etoposide (ETO) treatment embryonal carcinoma PA-1 cells undergo a p53-dependent upregulation of OCT4A and p21Cip1 (governing self-renewal and regulating cell cycle inhibition and senescence, respectively). Here we report further detail on the relationship between these and other critical cell-fate regulators. PA-1 cells treated with ETO display highly heterogeneous increases in OCT4A and p21Cip1 indicative of dis-adaptation catastrophe. Silencing OCT4A suppresses p21Cip1, changes cell cycle regulation and subsequently suppresses terminal senescence; p21Cip1-silencing did not affect OCT4A expression or cellular phenotype. SOX2 and NANOG expression did not change following ETO treatment suggesting a dissociation of OCT4A from its pluripotency function. Instead, ETO-induced OCT4A was concomitant with activation of AMPK, a key component of metabolic stress and autophagy regulation. p16ink4a, the inducer of terminal senescence, underwent autophagic sequestration in the cytoplasm of ETO-treated cells, allowing alternative cell fates. Accordingly, failure of autophagy was accompanied by an accumulation of p16ink4a, nuclear disintegration, and loss of cell recovery. Together, these findings imply that OCT4A induction following DNA damage in PA-1 cells, performs a cell stress, rather than self-renewal, function by moderating the expression of p21Cip1, which alongside AMPK helps to then regulate autophagy. Moreover, this data indicates that exhaustion of autophagy, through persistent DNA damage, is the cause of terminal cellular senescence.
DOI: 10.6084/m9.figshare.1632160.v2
title: Epithelial morphological reversion drives Profilin-1-induced elevation of p27<sup>kip1</sup> in mesenchymal triple-negative human breast cancer cells through AMP-activated protein kinase activation

description: Profilin-1 (Pfn1) is an important regulator of actin polymerization that is downregulated in human breast cancer. Previous studies have shown Pfn1 has a tumor-suppressive effect on mesenchymal-like triple-negative breast cancer cells, and Pfn1-induced growth suppression is partly mediated by upregulation of cell-cycle inhibitor p27<sup>kip1</sup> (p27). In this study, we demonstrate that Pfn1 overexpression leads to accumulation of p27 through promoting AMPK activation and AMPK-dependent phosphorylation of p27 on T198 residue, a post-translational modification that leads to increased protein stabilization of p27. This pathway is mediated by Pfn1-induced epithelial morphological reversion of mesenchymal breast cancer through cadherin-mediated restoration of adherens junctions. These findings not only elucidate a potential mechanism of how Pfn1 may inhibit proliferation of mesenchymal breast cancer cells, but also highlight a novel pathway of cadherin-mediated p27 induction and therefore cell-cycle control in cells.
DOI: 10.6084/m9.figshare.1632161.v2
title: Role of stress-activated OCT4A in the cell fate decisions of embryonal carcinoma cells treated with etoposide

description: Tumor cellular senescence induced by genotoxic treatments has recently been found to be paradoxically linked to the induction of “stemness.” This observation is critical as it directly impinges upon the response of tumors to current chemo-radio-therapy treatment regimens. Previously, we showed that following etoposide (ETO) treatment embryonal carcinoma PA-1 cells undergo a p53-dependent upregulation of OCT4A and p21Cip1 (governing self-renewal and regulating cell cycle inhibition and senescence, respectively). Here we report further detail on the relationship between these and other critical cell-fate regulators. PA-1 cells treated with ETO display highly heterogeneous increases in OCT4A and p21Cip1 indicative of dis-adaptation catastrophe. Silencing OCT4A suppresses p21Cip1, changes cell cycle regulation and subsequently suppresses terminal senescence; p21Cip1-silencing did not affect OCT4A expression or cellular phenotype. SOX2 and NANOG expression did not change following ETO treatment suggesting a dissociation of OCT4A from its pluripotency function. Instead, ETO-induced OCT4A was concomitant with activation of AMPK, a key component of metabolic stress and autophagy regulation. p16ink4a, the inducer of terminal senescence, underwent autophagic sequestration in the cytoplasm of ETO-treated cells, allowing alternative cell fates. Accordingly, failure of autophagy was accompanied by an accumulation of p16ink4a, nuclear disintegration, and loss of cell recovery. Together, these findings imply that OCT4A induction following DNA damage in PA-1 cells, performs a cell stress, rather than self-renewal, function by moderating the expression of p21Cip1, which alongside AMPK helps to then regulate autophagy. Moreover, this data indicates that exhaustion of autophagy, through persistent DNA damage, is the cause of terminal cellular senescence.