cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1378908
title: Establishing realistic management objectives for urban lakes using paleolimnological techniques: an example from Halifax Region (Nova Scotia, Canada)

description: To determine pre-disturbance limnological conditions, evaluate the impact of environmental stressors (surface water acidification, nutrient inputs, climate change, and winter deicing salt), and set realistic recovery targets for lake management strategies, a rapid assessment paleolimnological approach was used to determine the amount (and likely causes) of environmental changes over the past ∼100–150 years in 51 urban lakes from Halifax, Nova Scotia (Canada). Diatom assemblages from lake sediment cores were used with “top” (recently deposited, surface) samples being matched to measured limnological conditions, and “bottom” (generally from &gt;15 cm deep) samples used to infer pre-disturbance limnological conditions such as pH, total phosphorus (TP), specific conductance, and shifts due to changing climatic conditions. Environmental change was assessed by calculating the metric of change in species composition between present-day and pre-disturbance diatom assemblages, and inferences from quantitative estimates of diatom-inferred pH, specific conductance, and TP. All 51 study lakes have experienced floristic changes in diatom species composition since pre-disturbance times, but different environmental stressors were implicated: 8 of the 51 lakes underwent significant (i.e., &gt;2 times the root mean-squared error [2X RMSE] of the inference model) decreases in diatom-inferred pH; 8 lakes had significant increases in diatom-inferred TP; and 19 otherwise relatively pristine lakes had increases in planktonic taxa consistent with observations linked to changes in lake seasonality and limnological changes most closely linked to climate warming in Nova Scotia and other regions. The remaining 16 lakes did not have large and consistent changes in diatom flora or changes in diatom-inferred TP or pH &gt;2X RMSE of the prediction of the models. Lake-specific factors were related to these inferences, and the lakes that acidified were mainly the currently most acidic sites, whereas those that experienced issues related to eutrophication were generally among the most alkaline sites. Of our 51 lakes, 22 (including some experiencing pH, TP, or showing floristic changes linked to climate changes) had increases in measured conductivity (1980–2002) and, correspondingly, increased relative abundances of halophilic diatom taxa. These lakes, often with catchments containing high surface areas of impervious surfaces, are examples of a trend of increasing salinity in northeastern North American lakes likely related to winter application of deicing (road) salt. The application of this paleolimnological approach enabled us to identify which lakes have undergone significant changes in diatom assemblages, as well as which environmental stressor(s) were most probable. This information can help lake managers develop more targeted and effective management strategies.
DOI: 10.6084/m9.figshare.1378908.v2
title: Establishing realistic management objectives for urban lakes using paleolimnological techniques: an example from Halifax Region (Nova Scotia, Canada)

description: To determine pre-disturbance limnological conditions, evaluate the impact of environmental stressors (surface water acidification, nutrient inputs, climate change, and winter deicing salt), and set realistic recovery targets for lake management strategies, a rapid assessment paleolimnological approach was used to determine the amount (and likely causes) of environmental changes over the past ∼100–150 years in 51 urban lakes from Halifax, Nova Scotia (Canada). Diatom assemblages from lake sediment cores were used with “top” (recently deposited, surface) samples being matched to measured limnological conditions, and “bottom” (generally from &gt;15 cm deep) samples used to infer pre-disturbance limnological conditions such as pH, total phosphorus (TP), specific conductance, and shifts due to changing climatic conditions. Environmental change was assessed by calculating the metric of change in species composition between present-day and pre-disturbance diatom assemblages, and inferences from quantitative estimates of diatom-inferred pH, specific conductance, and TP. All 51 study lakes have experienced floristic changes in diatom species composition since pre-disturbance times, but different environmental stressors were implicated: 8 of the 51 lakes underwent significant (i.e., &gt;2 times the root mean-squared error [2X RMSE] of the inference model) decreases in diatom-inferred pH; 8 lakes had significant increases in diatom-inferred TP; and 19 otherwise relatively pristine lakes had increases in planktonic taxa consistent with observations linked to changes in lake seasonality and limnological changes most closely linked to climate warming in Nova Scotia and other regions. The remaining 16 lakes did not have large and consistent changes in diatom flora or changes in diatom-inferred TP or pH &gt;2X RMSE of the prediction of the models. Lake-specific factors were related to these inferences, and the lakes that acidified were mainly the currently most acidic sites, whereas those that experienced issues related to eutrophication were generally among the most alkaline sites. Of our 51 lakes, 22 (including some experiencing pH, TP, or showing floristic changes linked to climate changes) had increases in measured conductivity (1980–2002) and, correspondingly, increased relative abundances of halophilic diatom taxa. These lakes, often with catchments containing high surface areas of impervious surfaces, are examples of a trend of increasing salinity in northeastern North American lakes likely related to winter application of deicing (road) salt. The application of this paleolimnological approach enabled us to identify which lakes have undergone significant changes in diatom assemblages, as well as which environmental stressor(s) were most probable. This information can help lake managers develop more targeted and effective management strategies.
DOI: 10.6084/m9.figshare.1378908.v1
title: Establishing realistic management objectives for urban lakes using paleolimnological techniques: an example from Halifax Region (Nova Scotia, Canada)

description: To determine pre-disturbance limnological conditions, evaluate the impact of environmental stressors (surface water acidification, nutrient inputs, climate change, and winter deicing salt), and set realistic recovery targets for lake management strategies, a rapid assessment paleolimnological approach was used to determine the amount (and likely causes) of environmental changes over the past ∼100–150 years in 51 urban lakes from Halifax, Nova Scotia (Canada). Diatom assemblages from lake sediment cores were used with “top” (recently deposited, surface) samples being matched to measured limnological conditions, and “bottom” (generally from &gt;15 cm deep) samples used to infer pre-disturbance limnological conditions such as pH, total phosphorus (TP), specific conductance, and shifts due to changing climatic conditions. Environmental change was assessed by calculating the metric of change in species composition between present-day and pre-disturbance diatom assemblages, and inferences from quantitative estimates of diatom-inferred pH, specific conductance, and TP. All 51 study lakes have experienced floristic changes in diatom species composition since pre-disturbance times, but different environmental stressors were implicated: 8 of the 51 lakes underwent significant (i.e., &gt;2 times the root mean-squared error [2X RMSE] of the inference model) decreases in diatom-inferred pH; 8 lakes had significant increases in diatom-inferred TP; and 19 otherwise relatively pristine lakes had increases in planktonic taxa consistent with observations linked to changes in lake seasonality and limnological changes most closely linked to climate warming in Nova Scotia and other regions. The remaining 16 lakes did not have large and consistent changes in diatom flora or changes in diatom-inferred TP or pH &gt;2X RMSE of the prediction of the models. Lake-specific factors were related to these inferences, and the lakes that acidified were mainly the currently most acidic sites, whereas those that experienced issues related to eutrophication were generally among the most alkaline sites. Of our 51 lakes, 22 (including some experiencing pH, TP, or showing floristic changes linked to climate changes) had increases in measured conductivity (1980–2002) and, correspondingly, increased relative abundances of halophilic diatom taxa. These lakes, often with catchments containing high surface areas of impervious surfaces, are examples of a trend of increasing salinity in northeastern North American lakes likely related to winter application of deicing (road) salt. The application of this paleolimnological approach enabled us to identify which lakes have undergone significant changes in diatom assemblages, as well as which environmental stressor(s) were most probable. This information can help lake managers develop more targeted and effective management strategies.
DOI: 10.6084/m9.figshare.1378901
title: Allometric ontogenetic changes in two Late Jurassic gastrodorid hermit crabs (Crustacea, Decapoda, Anomura) from central Europe

description: Extinct anomurans are known mostly by their carapaces. Regions in the fossil carapace are well delimited by grooves and, by comparison with extant hermit crabs, they can be referred to the underlying internal organs. In this paper we examine the allometric effects in ontogeny of two Jurassic hermit crabs of an extinct genus <i>Gastrodorus</i>: <i>G. neuhausensis</i> von Meyer, 1864 and <i>G. bzowiensis</i> sp. nov. described herein. Both species occur in Oxfordian and Kimmeridgian strata in southern Poland, but the former species only in southern Germany. Samples of carapaces of both species consisted of carapaces of a wide size range, illustrative of the various ontogenetic stages. A reduced major axis was applied for assessment of allometry. The most pronounced positive allometric effect in both species concerned the posteriormost region of the cephalothoracic shield, which became disproportionally more elongated than the overall carapace length (positive allometry) as overall size increased. Statistically significant differences between the two species concern the cardiac region, which gained in length with size in <i>G. neuhausensis</i> (positive allometry) and became proportionally narrower in the new species (negative allometry). Thus it may be assumed that overall growth rate of the heart region was less in the latter species. Additionally, new terminology of carapace regions previously introduced to pagurids and based on morphology of recent representatives is applied to the gastrodorids.http://zoobank.org/urn:lsid:zoobank.org:pub:E64D2515-BD0D-4A78-83A7-D35C5F9FA3E5
DOI: 10.6084/m9.figshare.1378898
title: Compatibility of Heavy Blends Evaluated by Fouling and Its Relationship With Colloidal Stability

description: To predict oil compatibility is crucial because incompatibility could cause severe deposition and fouling problems. Therefore, compatibility of heavy oils and blends in different ratios were evaluated by fouling at heat transfer conditions. Thermal resistance and fouling rates were obtained on a fouling loop. Effect of colloidal stability based on asphaltene precipitation and SARA composition on fouling was also discussed. Results showed that different variations of fouling rate versus blending ratio were observed for these blending systems. For oils whose viscosities approach at heat conditions, the lower colloidal stability of blends is the higher fouling rate is. However, for oils with greatly different viscosities, inconsistency was observed between compatibility by the two indicators, which is attributed to remarkable change of flow condition. This indicates that both colloidal stability and flow condition play key roles in fouling. Oil compatibility at heat transfer condition is favored being predicted by fouling instead of correlating with the colloidal stability.
DOI: 10.6084/m9.figshare.1378901.v1
title: Allometric ontogenetic changes in two Late Jurassic gastrodorid hermit crabs (Crustacea, Decapoda, Anomura) from central Europe

description: Extinct anomurans are known mostly by their carapaces. Regions in the fossil carapace are well delimited by grooves and, by comparison with extant hermit crabs, they can be referred to the underlying internal organs. In this paper we examine the allometric effects in ontogeny of two Jurassic hermit crabs of an extinct genus <i>Gastrodorus</i>: <i>G. neuhausensis</i> von Meyer, 1864 and <i>G. bzowiensis</i> sp. nov. described herein. Both species occur in Oxfordian and Kimmeridgian strata in southern Poland, but the former species only in southern Germany. Samples of carapaces of both species consisted of carapaces of a wide size range, illustrative of the various ontogenetic stages. A reduced major axis was applied for assessment of allometry. The most pronounced positive allometric effect in both species concerned the posteriormost region of the cephalothoracic shield, which became disproportionally more elongated than the overall carapace length (positive allometry) as overall size increased. Statistically significant differences between the two species concern the cardiac region, which gained in length with size in <i>G. neuhausensis</i> (positive allometry) and became proportionally narrower in the new species (negative allometry). Thus it may be assumed that overall growth rate of the heart region was less in the latter species. Additionally, new terminology of carapace regions previously introduced to pagurids and based on morphology of recent representatives is applied to the gastrodorids.http://zoobank.org/urn:lsid:zoobank.org:pub:E64D2515-BD0D-4A78-83A7-D35C5F9FA3E5
DOI: 10.6084/m9.figshare.1378898.v2
title: Compatibility of Heavy Blends Evaluated by Fouling and Its Relationship With Colloidal Stability

description: To predict oil compatibility is crucial because incompatibility could cause severe deposition and fouling problems. Therefore, compatibility of heavy oils and blends in different ratios were evaluated by fouling at heat transfer conditions. Thermal resistance and fouling rates were obtained on a fouling loop. Effect of colloidal stability based on asphaltene precipitation and SARA composition on fouling was also discussed. Results showed that different variations of fouling rate versus blending ratio were observed for these blending systems. For oils whose viscosities approach at heat conditions, the lower colloidal stability of blends is the higher fouling rate is. However, for oils with greatly different viscosities, inconsistency was observed between compatibility by the two indicators, which is attributed to remarkable change of flow condition. This indicates that both colloidal stability and flow condition play key roles in fouling. Oil compatibility at heat transfer condition is favored being predicted by fouling instead of correlating with the colloidal stability.
DOI: 10.6084/m9.figshare.1378898.v1
title: Compatibility of Heavy Blends Evaluated by Fouling and Its Relationship With Colloidal Stability

description: To predict oil compatibility is crucial because incompatibility could cause severe deposition and fouling problems. Therefore, compatibility of heavy oils and blends in different ratios were evaluated by fouling at heat transfer conditions. Thermal resistance and fouling rates were obtained on a fouling loop. Effect of colloidal stability based on asphaltene precipitation and SARA composition on fouling was also discussed. Results showed that different variations of fouling rate versus blending ratio were observed for these blending systems. For oils whose viscosities approach at heat conditions, the lower colloidal stability of blends is the higher fouling rate is. However, for oils with greatly different viscosities, inconsistency was observed between compatibility by the two indicators, which is attributed to remarkable change of flow condition. This indicates that both colloidal stability and flow condition play key roles in fouling. Oil compatibility at heat transfer condition is favored being predicted by fouling instead of correlating with the colloidal stability.
DOI: 10.6084/m9.figshare.1378891
title: The RAB GTPase RABA1e localizes to the cell plate and shows distinct subcellular behavior from RABA2a under Endosidin 7 treatment

description: Cytokinesis in plants requires the activity of RAB GTPases to regulate vesicle-mediated contribution of material to the developing cell plate. While some plant RAB GTPases have been shown to be involved in cell plate formation, many still await functional assignment. Here, we report cell plate localization for YFP-RABA1e in <i>Arabidopsis thaliana</i> and use the cytokinesis inhibitor Endosidin 7 to provide a detailed description of its localization compared to YFP-RABA2a. Differences between YFP-RABA2a and YFP-RABA1e were observed in late-stage cell plates under DMSO control treatment, and became more apparent under Endosidin 7 treatment. Taken together, our results suggest that individual RAB GTPases might make different contributions to cell plate formation and further demonstrates the utility of ES7 probe to dissect them.
DOI: 10.6084/m9.figshare.1378891.v1
title: The RAB GTPase RABA1e localizes to the cell plate and shows distinct subcellular behavior from RABA2a under Endosidin 7 treatment

description: Cytokinesis in plants requires the activity of RAB GTPases to regulate vesicle-mediated contribution of material to the developing cell plate. While some plant RAB GTPases have been shown to be involved in cell plate formation, many still await functional assignment. Here, we report cell plate localization for YFP-RABA1e in <i>Arabidopsis thaliana</i> and use the cytokinesis inhibitor Endosidin 7 to provide a detailed description of its localization compared to YFP-RABA2a. Differences between YFP-RABA2a and YFP-RABA1e were observed in late-stage cell plates under DMSO control treatment, and became more apparent under Endosidin 7 treatment. Taken together, our results suggest that individual RAB GTPases might make different contributions to cell plate formation and further demonstrates the utility of ES7 probe to dissect them.
DOI: 10.6084/m9.figshare.1378883
title: Applicability of medium-size basis sets in calculations of molecular dynamic polarisabilities

description: Static and dynamic average polarisabilities and polarisability anisotropies of seven linear non-polar and polar molecules are calculated within the CCS, CC2, and CC3 approximations using a range of medium-sized basis sets: the polarised LPol-<i>n</i> (<i>n</i> = ds, dl, fs, fl), the aug-pc-<i>n</i> (<i>n</i> = 1, 2), the def2-SVPD, and -TZVPD basis sets. Reference values are obtained using a hierarchy of Dunning's (d-)aug-cc-pV<i>X</i>Z (<i>X</i> = D, T, Q, 5) basis sets. The results are discussed together with the available CCSD values in terms of basis set and correlation method errors, and their ratio. Detailed analysis shows that already the def2-SVPD basis set can be used in CCS polarisability calculations. When affordable, the slightly larger aug-pc-1 basis set is recommended, as it leads to significant reduction of basis set error. The def2-TZVPD, LPol-ds, and aug-pc-2 basis sets are optimal choice within the CC2 approximation, with the latter allowing to approach the CC2 basis set limit. The LPol-ds, -dl, and def2-TZVPD sets outperform the aug-cc-pVTZ set in average polarisability CCSD calculations, with the def2-TZVPD being competitive to other reduced-size sets also in determination of polarisability anisotropy. The aug-pc-2 basis is a particularly attractive choice for CCSD, giving the accuracy of aug-cc-pVQZ at a significantly reduced computational cost. The polarisability anisotropy is shown to be more computationally demanding than the average polarisability, in particular with respect to the accuracy of the correlation method and an accurate evaluation of this property requires at least the CCSD model.
DOI: 10.6084/m9.figshare.1378881
title: Genome-wide differentially methylated genes in prostate cancer tissues from African-American and Caucasian men

description: Increasing evidence suggests that aberrant DNA methylation changes may contribute to prostate cancer (PCa) ethnic disparity. To comprehensively identify DNA methylation alterations in PCa disparity, we used the Illumina 450K methylation platform to interrogate the methylation status of 485,577 CpG sites focusing on gene-associated regions of the human genome. Genomic DNA from African-American (AA; 7 normal and 3 cancers) and Caucasian (Cau; 8 normal and 3 cancers) was used in the analysis. Hierarchical clustering analysis identified probe-sets unique to AA and Cau samples, as well as common to both. We selected 25 promoter-associated novel CpG sites most differentially methylated by race (fold change &gt; 1.5-fold; adjusted <i>P</i> &lt; 0.05) and compared the β-value of these sites provided by the Illumina, Inc. array with quantitative methylation obtained by pyrosequencing in 7 prostate cell lines. We found very good concordance of the methylation levels between β-value and pyrosequencing. Gene expression analysis using qRT-PCR in a subset of 8 genes after treatment with 5-aza-2′-deoxycytidine and/or trichostatin showed up-regulation of gene expression in PCa cells. Quantitative analysis of 4 genes, <i>SNRPN, SHANK</i>2, <i>MST1R</i>, and <i>ABCG</i>5, in matched normal and PCa tissues derived from AA and Cau PCa patients demonstrated differential promoter methylation and concomitant differences in mRNA expression in prostate tissues from AA vs. Cau. Regression analysis in normal and PCa tissues as a function of race showed significantly higher methylation prevalence for <i>SNRPN</i> (<i>P</i> = 0.012), <i>MST1R</i> (<i>P</i> = 0.038), and <i>ABCG</i>5 (<i>P</i> &lt; 0.0002) for AA vs. Cau samples. We selected the <i>ABCG5</i> and <i>SNRPN</i> genes and verified their biological functions by Western blot analysis and siRNA gene knockout effects on cell proliferation and invasion in 4 PCa cell lines (2 AA and 2 Cau patients-derived lines). Knockdown of either ABCG5 or SNRPN resulted in a significant decrease in both invasion and proliferation in Cau PCa cell lines but we did not observe these remarkable loss-of-function effects in AA PCa cell lines. Our study demonstrates how differential genome-wide DNA methylation levels influence gene expression and biological functions in AA and Cau PCa.