cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4569991
title: Supplementary Material for: Cystic Gene Dosage Influences Kidney Lesions After Nephron Reduction

description: Cystic kidney disease is characterized by the progressive development of multiple fluid-filled cysts. Cysts can be acquired, or they may appear during development or in postnatal life due to specific gene defects and lead to renal failure. The most frequent form of this disease is the inherited polycystic kidney disease (PKD). Experimental models of PKD showed that an increase of cellular proliferation and apoptosis as well as defects in apico-basal and planar cell polarity or cilia play a critical role in cyst development. However, little is known about the mechanisms and the mediators involved in acquired cystic kidney diseases (ACKD). In this study, we used the nephron reduction as a model to study the mechanisms underlying cyst development in ACKD. We found that tubular dilations after nephron reduction recapitulated most of the morphological features of ACKD. The development of tubular dilations was associated with a dramatic increase of cell proliferation. In contrast, the apico-basal polarity and cilia did not seem to be affected. Interestingly, polycystin 1 and fibrocystin were markedly increased and polycystin 2 was decreased in cells lining the dilated tubules, whereas the expression of several other cystic genes did not change. More importantly, <i>Pkd1</i> haploinsufficiency accelerated the development of tubular dilations after nephron reduction, a phenotype that was associated to a further increase of cell proliferation. These data were relevant to humans ACKD, as cystic genes expression and the rate of cell proliferation were also increased. In conclusion, our study suggests that the nephron reduction can be considered a suitable model to study ACKD and that dosage of genes involved in PKD is also important in ACKD.
DOI: 10.6084/m9.figshare.4570000
title: Supplementary Material for: Blood Levels of the Heavy Metal, Lead, and Caries in Children Aged 24-72 Months: NHANES III

description: Lead remains a significant pollutant. It has acute toxic and chronic effects on many tissues and accumulates in teeth and bones. The researchers for this study investigated the association of blood lead levels with the extent/severity of caries as measured by the number of decayed/filled teeth of children aged 24-72 months using data from NHANES III (the Third National Health and Nutrition Examination Survey), accounting for the excess zero caries in the analysis and using less than 2 µg/dl as the reference blood lead level (n = 3,127). Zero-inflated negative binomial regression models indicated unadjusted extent/severity mean ratios of 1.79, 1.88 and 1.94 for the number of decayed/filled teeth in children whose blood lead levels were 2-5, 5-10 and &gt;10 µg/dl, respectively, compared with children having &lt;2 µg/dl blood lead levels. The results did not attenuate when other variables were added to the model for the 5-10 and &gt;10 µg/dl levels of exposure. The adjusted extent/severity mean ratios were 1.84, 2.14 and 1.91, respectively, for the categories. This study indicated a strong association of blood lead levels with increasing numbers of carious teeth in children aged 24-72 months. These findings support other studies in an innovative analysis handling cases of children with no caries. The findings may inform caries risk assessment.
DOI: 10.6084/m9.figshare.4570000.v1
title: Supplementary Material for: Blood Levels of the Heavy Metal, Lead, and Caries in Children Aged 24-72 Months: NHANES III

description: Lead remains a significant pollutant. It has acute toxic and chronic effects on many tissues and accumulates in teeth and bones. The researchers for this study investigated the association of blood lead levels with the extent/severity of caries as measured by the number of decayed/filled teeth of children aged 24-72 months using data from NHANES III (the Third National Health and Nutrition Examination Survey), accounting for the excess zero caries in the analysis and using less than 2 µg/dl as the reference blood lead level (n = 3,127). Zero-inflated negative binomial regression models indicated unadjusted extent/severity mean ratios of 1.79, 1.88 and 1.94 for the number of decayed/filled teeth in children whose blood lead levels were 2-5, 5-10 and &gt;10 µg/dl, respectively, compared with children having &lt;2 µg/dl blood lead levels. The results did not attenuate when other variables were added to the model for the 5-10 and &gt;10 µg/dl levels of exposure. The adjusted extent/severity mean ratios were 1.84, 2.14 and 1.91, respectively, for the categories. This study indicated a strong association of blood lead levels with increasing numbers of carious teeth in children aged 24-72 months. These findings support other studies in an innovative analysis handling cases of children with no caries. The findings may inform caries risk assessment.
DOI: 10.6084/m9.figshare.4570006.v1
title: Supplementary Material for: Osteogenic Differentiation of Late-Outgrowth CD45-Negative Endothelial Progenitor Cells

description: <b><i>Background/Aims:</i></b> Late-outgrowth CD45-negative endothelial colony-forming cells are implicated to be circulating endothelial progenitor cells (EPCs), as they express endothelial cell markers and can directly form blood vessels. As these cells share characteristics of other progenitor cell phenotypes, late-outgrowth EPCs were assayed for both multilineage differentiation capability and for markers of pluripotency. <b><i>Methods:</i></b> Clonal single-colony late-outgrowth EPCs were derived from human cord blood and assayed both for multilineage differentiation capability in vitro and for markers of pluripotency by qPCR. <b><i>Results:</i></b> Under osteogenic growth conditions, these EPCs expressed the osteogenic markers RUNX2, COL1A1, ALPL, and osteocalcin and demonstrated calcium deposition and bone mineralization. Endothelial colony-forming cells expressed markers associated with induced pluripotent stem cells, including SOX2, POU5F1, c-MYC, and KLF4. <b><i>Conclusions:</i></b> Late-outgrowth EPCs express markers associated with pluripotency and can directly express an osteogenic phenotype under bone differentiation conditions in vitro.
DOI: 10.6084/m9.figshare.4569997.v1
title: Supplementary Material for: In vitro Antimicrobial Activities of 1-Methoxyficifolinol, Licorisoflavan A, and 6,8-Diprenylgenistein against Streptococcus mutans

description: The objective of the study was to investigate the antimicrobial effects of purified single compounds from ethanol-extracted licorice root on <i>Streptococcus mutans</i>. The crude licorice root extract (CLE) was obtained from <i>Glycyrrhiza uralensis</i>, which was subjected to column chromatography to separate compounds. Purified compounds were identified by mass spectrometry and nuclear magnetic resonance. Antimicrobial activities of purified compounds from CLE were evaluated by determining the minimum inhibitory concentration and by performing time-kill kinetics. The inhibitory effects of the compounds on biofilm development were evaluated using crystal violet assay and confocal microscopy. Cell toxicity of substances to normal human gingival fibroblast (NHGF) cells was tested using a methyl thiazolyl tetrazolium assay. Chlorhexidine digluconate (CHX) was used in the control group. Three antimicrobial flavonoids, 1-methoxyficifolinol, licorisoflavan A, and 6,8-diprenylgenistein, were isolated from the CLE. We found that the three flavonoids and CHX had bactericidal effects on <i>S. mutans</i> UA159 at the concentration of ≥4 and ≥1 µg/ml, respectively. The purified compounds completely inhibited biofilm development of<i> S. mutans</i> UA159 at concentrations over 4 μg/ml, which was equivalent to 2 μg/ml of CHX. Confocal analysis showed that biofilms were sparsely scattered in the presence of over 4 μg/ml of the purified compounds. However, the three compounds purified from CLE showed less cytotoxic effects on NHGF cells than CHX at these biofilm-inhibitory concentrations. Our results suggest that purified flavonoids from CLE can be useful in developing oral hygiene products, such as gargling solutions and dentifrices for preventing dental caries.
DOI: 10.6084/m9.figshare.4569943
title: Table S2 from A phylogenetic perspective on the association between ants (Hymenoptera: Formicidae) and black yeasts (Ascomycota: Chaetothyriales)

description: List of the primer pairs used for DNA amplification and sequencing.
DOI: 10.6084/m9.figshare.4569943.v1
title: Table S2 from A phylogenetic perspective on the association between ants (Hymenoptera: Formicidae) and black yeasts (Ascomycota: Chaetothyriales)

description: List of the primer pairs used for DNA amplification and sequencing.
DOI: 10.6084/m9.figshare.4569925
title: Table S1 from A phylogenetic perspective on the association between ants (Hymenoptera: Formicidae) and black yeasts (Ascomycota: Chaetothyriales)

description: List of the fungal strains used in this study, with Genbank accession numbers for DNA sequences.
DOI: 10.6084/m9.figshare.4569895
title: Supplementary data from Ant circadian activity associated with brood care type

description: Circadian activity data
DOI: 10.6084/m9.figshare.4569883
title: Evaluation of <i>in silico</i> tools to predict the skin sensitization potential of chemicals

description: Public domain and commercial <i>in silico</i> tools were compared for their performance in predicting the skin sensitization potential of chemicals. The packages were either statistical based (Vega, CASE Ultra) or rule based (OECD Toolbox, Toxtree, Derek Nexus). In practice, several of these <i>in silico</i> tools are used in gap filling and read-across, but here their use was limited to make predictions based on presence/absence of structural features associated to sensitization. The top 400 ranking substances of the ATSDR 2011 Priority List of Hazardous Substances were selected as a starting point. Experimental information was identified for 160 chemically diverse substances (82 positive and 78 negative). The prediction for skin sensitization potential was compared with the experimental data. Rule-based tools perform slightly better, with accuracies ranging from 0.6 (OECD Toolbox) to 0.78 (Derek Nexus), compared with statistical tools that had accuracies ranging from 0.48 (Vega) to 0.73 (CASE Ultra – LLNA weak model). Combining models increased the performance, with positive and negative predictive values up to 80% and 84%, respectively. However, the number of substances that were predicted positive or negative for skin sensitization in both models was low. Adding more substances to the dataset will increase the confidence in the conclusions reached. The insights obtained in this evaluation are incorporated in a web database www.asopus.weebly.com that provides a potential end user context for the scope and performance of different <i>in silico</i> tools with respect to a common dataset of curated skin sensitization data.
DOI: 10.6084/m9.figshare.4569889
title: Supplementary Material for: Mini-Laparoscopy Guided Liver Biopsy Increases Diagnostic Accuracy in Acute Liver Failure

description: <b><i>Background/Aims:</i></b> For diagnosis, prognosis, and treatment of acute liver failure (ALF), macroscopic evaluation and histological assessment of the liver are important. Due to impaired coagulation in ALF, the risk of bleeding is high after a percutaneous liver biopsy. Our aims were to assess (i) safety and benefit of mini laparoscopy (ML) in patients with ALF and (ii) the potential utility of histological markers in ALF prognosis. <b><i>Methods:</i></b> ML was performed in 39 patients with ALF to assess liver surface and to obtain a liver biopsy. Serological markers of liver injury and immunohistochemical detection of cell death and proliferation were compared to a non-ALF group (n = 10). <b><i>Results:</i></b> Liver biopsies were successfully performed in all patients with no significant complications. All patients had markedly elevated M30 and M65 levels in the serum. In the liver, M30 and Ki67 immune-reactive cells were more abundant in those with ALF. Importantly, there were significantly more Ki67-positive cells but fewer M30-positive cells in livers of ALF patients who recovered spontaneously. <b><i>Conclusion:</i></b> ML with liver biopsy in patients with ALF and severe coagulopathy is safe. Immunohistochemical detection of liver cell death and regeneration may identify individuals who would recover spontaneously or who would need a liver transplant.
DOI: 10.6084/m9.figshare.4569883.v1
title: Evaluation of <i>in silico</i> tools to predict the skin sensitization potential of chemicals

description: Public domain and commercial <i>in silico</i> tools were compared for their performance in predicting the skin sensitization potential of chemicals. The packages were either statistical based (Vega, CASE Ultra) or rule based (OECD Toolbox, Toxtree, Derek Nexus). In practice, several of these <i>in silico</i> tools are used in gap filling and read-across, but here their use was limited to make predictions based on presence/absence of structural features associated to sensitization. The top 400 ranking substances of the ATSDR 2011 Priority List of Hazardous Substances were selected as a starting point. Experimental information was identified for 160 chemically diverse substances (82 positive and 78 negative). The prediction for skin sensitization potential was compared with the experimental data. Rule-based tools perform slightly better, with accuracies ranging from 0.6 (OECD Toolbox) to 0.78 (Derek Nexus), compared with statistical tools that had accuracies ranging from 0.48 (Vega) to 0.73 (CASE Ultra – LLNA weak model). Combining models increased the performance, with positive and negative predictive values up to 80% and 84%, respectively. However, the number of substances that were predicted positive or negative for skin sensitization in both models was low. Adding more substances to the dataset will increase the confidence in the conclusions reached. The insights obtained in this evaluation are incorporated in a web database www.asopus.weebly.com that provides a potential end user context for the scope and performance of different <i>in silico</i> tools with respect to a common dataset of curated skin sensitization data.
DOI: 10.6084/m9.figshare.4569865
title: Supplementary Material for: Risk Factors Assessed in Adolescence and the Later Risk of Stroke in Men: A 33-Year Follow-Up Study

description: <b><i>Background:</i></b> Stroke is a common cause of death, and a leading contributor to long-term disability. The cost associated with the disease is great. Several modifiable risk factors for stroke have been found in older cohorts; however, no study to date has investigated the effects of these risk factors from late adolescence. <b><i>Methods:</i></b> The study cohort comprised 811,579 Swedish men (mean age, 18 years) that participated in the mandatory military conscription service in Sweden between 1969 and 1986. Some risk factors for stroke, such as body mass index, systolic and diastolic blood pressure, and cognitive function, were assessed at conscription. Aerobic fitness was also assessed at conscription, using a braked ergometer cycle test. Other risk factors for stroke, including stroke in subjects' parents, and socioeconomic factors including highest achieved level of education and annual income 15 years after conscription, were collected through national register linkage using the personal identification number.<b> </b>Stroke diagnosis among the study participants was tracked in the National Hospital Discharge Patient Register. <b><i>Results:</i></b> During a median follow-up period of 33 years 6,180 ischemic strokes and 2,104 hemorrhagic strokes were diagnosed in the cohort at a mean age of 47.9 years. Strong independent risk factors (all p &lt;1.0 × 10−<sup>6</sup>) for ischemic stroke included low aerobic fitness (hazard ratio [HR], 0.84 per standard deviation [SD] increase), high BMI (HR, 1.15 per SD increase), diabetes (HR, 2.85), alcohol intoxication (HR, 1.93), low annual income (HR, 0.85 per SD decrease), and stroke in the mother (HR, 1.31). Similar risk factors were found for hemorrhagic stroke including low aerobic fitness (HR, 0.82 per SD increase), high BMI (HR, 1.18 per SD increase) alcohol intoxication (HR, 2.92), diabetes (HR, 2.06), and low annual income (HR, 0.75). The population attributable risks associated with all evaluated risk factors were 69% for ischemic stroke and 88% for hemorrhagic stroke (p &lt; 0.001 for both). <b><i>Conclusions:</i></b> In the present study we have shown that several known risk factors for stroke are present already in late adolescence, and that they are independent of each other. The strongest risk factors were low physical fitness, high BMI, diabetes, low annual income and a maternal history of stroke. Several of the aforementioned risk factors are potentially modifiable.
DOI: 10.6084/m9.figshare.4569877
title: First high-resolution analysis of the ν<sub>1</sub>, ν<sub>3</sub> and ν<sub>1</sub> + ν<sub>3</sub> bands of sulphur dioxide <sup>33</sup>S<sup>16</sup>O<sub>2</sub>

description: High-resolution spectra of <sup>33</sup>S<sup>16</sup>O<sub>2</sub> have been recorded for the first time in the 8 and 4 µm spectral regions.The ν<sub>1</sub>, ν<sub>3</sub> and ν<sub>1</sub> + ν<sub>3</sub> bands of the <sup>33</sup>S<sup>16</sup>O<sub>2</sub> have been analysed up to very high quantum numbers.Accurate ro-vibrational upper states constants have been determined. High-resolution spectra of <sup>33</sup>S<sup>16</sup>O<sub>2</sub> have been recorded for the first time in the 8 and 4 µm spectral regions. The ν<sub>1</sub>, ν<sub>3</sub> and ν<sub>1</sub> + ν<sub>3</sub> bands of the <sup>33</sup>S<sup>16</sup>O<sub>2</sub> have been analysed up to very high quantum numbers. Accurate ro-vibrational upper states constants have been determined. Fourier transform spectra of sulphur dioxide <sup>33</sup>S<sup>16</sup>O<sub>2</sub> have been recorded in the 8.0 and 4.0 µm spectral regions at a resolution of 0.0015 cm<sup>−1</sup> using a Bruker IFS 125HR spectrometer leading to the observation of the ν<sub>1</sub>, ν<sub>3</sub> and ν<sub>1</sub> + ν<sub>3</sub> vibrational bands of the <sup>33</sup>S<sup>16</sup>O<sub>2</sub> molecule. The corresponding upper state ro-vibrational levels were fit using a Hamiltonian matrix taking into account a Coriolis Δ<i>K<sub>a</sub> </i> = 3 resonance between the ro-vibrational levels of the 1<sup>1</sup> and 3<sup>1</sup> vibrational states and a Watson-type Hamiltonian for the ro-vibrational levels of the 1<sup>1</sup> 3<sup>1</sup> vibrational state. In this way it was possible to reproduce the upper state ro-vibrational levels to within the experimental uncertainty; i.e. ∼0.20 × 10<sup>−3</sup> cm<sup>−1</sup>. Very accurate rotational and centrifugal distortion constants were derived from the fit together with the following band centres: ν<sub>0</sub> (ν<sub>1</sub>) = 1147.979535(60) cm<sup>−1</sup>, ν<sub>0</sub> (ν<sub>3</sub>) = 1353.335912(60) cm<sup>−1</sup> and ν<sub>0</sub> (ν<sub>1</sub> + ν<sub>3</sub>) = 2487.493732(30) cm<sup>−1</sup>.
DOI: 10.6084/m9.figshare.4569856
title: Supplementary Material for: Molecular Imaging of Carotid Plaque Vulnerability

description: <b><i>Background:</i></b> Carotid endarterectomy (CEA) has been shown to be beneficial in patients with high-grade symptomatic carotid artery stenosis. Patients with high-grade asymptomatic stenosis may only exceptionally benefit from CEA during periods of increased plaque vulnerability. Imaging modalities to characterize unstable, vulnerable plaques are strongly needed for better risk stratification in these patients. <b><i>Summary:</i></b> Contrast-enhanced ultrasound (CEUS) is a novel and noninvasive technique capable to identify several surrogate markers of vulnerable carotid plaques. The use of specific ultrasound microbubbles allows a reliable detection of microulcerations due to an optimized visualization of the plaque-lumen border. As microbubbles are strictly intravascular tracers, the detection of individual microbubbles within the plaque corresponds to intraplaque neovessels. The accuracy of CEUS in the visualization of newly formed microvessels has been confirmed in histological studies on carotid endarterectomy specimens. Together with the formation of adventitial vasa vasorum, intraplaque neovascularization is a strong predictor for symptomatic disease. The phenomenon of late phase contrast enhancement is based on the adherence of microbubble-containing monocytes on inflamed endothelium. Recent studies suggest that late phase contrast enhancement may reflect endothelial inflammation or activation within carotid plaques. The development of conjugated microbubbles that bind to specific ligands such as thrombotic material or neovessels has led to the term ‘molecular imaging'. CEUS with microbubbles targeted to P-selectin and VCAM-1, key molecules in leukocyte trafficking, was used to detect an inflammatory plaque phenotype, whereas microbubbles coupled to the VEGF-receptor may allow for a detection of neovascularization. Even though imaging with targeted microbubbles is yet in an experimental stage, this technique can visualize active plaque reorganization with increased vulnerability leading to generation of arterio-arterial embolism. <b><i>Key Messages:</i></b> The use of contrast-enhanced ultrasound can be recommended to assess atherosclerotic carotid lesions at risk for rupture. Prospective clinical studies are needed to validate the use of CEUS in patients with high risks of recurrent large artery strokes. In particular, this applies to the detection of intraplaque neovascularization, a well-established marker in preclinical and observational studies, while the clinical significance of late phase contrast enhancement still needs to be determined.