cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1378883.v1
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.1378880
title: Foraminiferal record of Holocene paleo-earthquakes on the subsiding south-western Poverty Bay coastline, New Zealand

description: Foraminiferal faunas in 29 short cores (maximum depth 7 m) of estuarine and coastal wetland sediment were used to reconstruct the middle–late Holocene (last 7 ka) elevational history on the southern shores of Poverty Bay, North Island, New Zealand. This coast is on the southwest side of a rapidly subsiding area beneath western Poverty Bay. Modern Analogue Technique paleo-elevation estimates based on fossil foraminiferal faunas indicate that the four study areas have gradual late Holocene (&lt;3.5 ka) subsidence rates that increase from the southwest (mean c. 0.5 m ka<sup>–1</sup>) to northeast (mean c. 1.0 m ka<sup>–1</sup>). Only two rapid, possibly co-seismic, vertical displacement events are recognised: (1) c. 1.2 m of subsidence at 5.7 ± 0.4 ka (cal yr BP), which may have been generated by a subduction interface earthquake centred offshore and recorded in other published studies in northern Hawkes Bay, c. 35 km to the south; and (2) c. 1 m of uplift (relative sea-level fall) at c. 4.5 ± 0.3 ka, which might have been generated by rupture on an offshore upper plate fault that also uplifted coastal terraces at Pakarae and Mahia, 40 km to the north and south of the study area, or by rupture on the subduction interface penetrating beneath Poverty Bay. No sudden displacement events are recognised during the last 4 ka although subsidence, possibly aseismic, has continued.
DOI: 10.6084/m9.figshare.1378881.v1
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.
DOI: 10.6084/m9.figshare.1378883.v2
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.1378880.v2
title: Foraminiferal record of Holocene paleo-earthquakes on the subsiding south-western Poverty Bay coastline, New Zealand

description: Foraminiferal faunas in 29 short cores (maximum depth 7 m) of estuarine and coastal wetland sediment were used to reconstruct the middle–late Holocene (last 7 ka) elevational history on the southern shores of Poverty Bay, North Island, New Zealand. This coast is on the southwest side of a rapidly subsiding area beneath western Poverty Bay. Modern Analogue Technique paleo-elevation estimates based on fossil foraminiferal faunas indicate that the four study areas have gradual late Holocene (&lt;3.5 ka) subsidence rates that increase from the southwest (mean c. 0.5 m ka<sup>–1</sup>) to northeast (mean c. 1.0 m ka<sup>–1</sup>). Only two rapid, possibly co-seismic, vertical displacement events are recognised: (1) c. 1.2 m of subsidence at 5.7 ± 0.4 ka (cal yr BP), which may have been generated by a subduction interface earthquake centred offshore and recorded in other published studies in northern Hawkes Bay, c. 35 km to the south; and (2) c. 1 m of uplift (relative sea-level fall) at c. 4.5 ± 0.3 ka, which might have been generated by rupture on an offshore upper plate fault that also uplifted coastal terraces at Pakarae and Mahia, 40 km to the north and south of the study area, or by rupture on the subduction interface penetrating beneath Poverty Bay. No sudden displacement events are recognised during the last 4 ka although subsidence, possibly aseismic, has continued.
DOI: 10.6084/m9.figshare.1378881.v2
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.
DOI: 10.6084/m9.figshare.1378880.v1
title: Foraminiferal record of Holocene paleo-earthquakes on the subsiding south-western Poverty Bay coastline, New Zealand

description: Foraminiferal faunas in 29 short cores (maximum depth 7 m) of estuarine and coastal wetland sediment were used to reconstruct the middle–late Holocene (last 7 ka) elevational history on the southern shores of Poverty Bay, North Island, New Zealand. This coast is on the southwest side of a rapidly subsiding area beneath western Poverty Bay. Modern Analogue Technique paleo-elevation estimates based on fossil foraminiferal faunas indicate that the four study areas have gradual late Holocene (&lt;3.5 ka) subsidence rates that increase from the southwest (mean c. 0.5 m ka<sup>–1</sup>) to northeast (mean c. 1.0 m ka<sup>–1</sup>). Only two rapid, possibly co-seismic, vertical displacement events are recognised: (1) c. 1.2 m of subsidence at 5.7 ± 0.4 ka (cal yr BP), which may have been generated by a subduction interface earthquake centred offshore and recorded in other published studies in northern Hawkes Bay, c. 35 km to the south; and (2) c. 1 m of uplift (relative sea-level fall) at c. 4.5 ± 0.3 ka, which might have been generated by rupture on an offshore upper plate fault that also uplifted coastal terraces at Pakarae and Mahia, 40 km to the north and south of the study area, or by rupture on the subduction interface penetrating beneath Poverty Bay. No sudden displacement events are recognised during the last 4 ka although subsidence, possibly aseismic, has continued.
DOI: 10.6084/m9.figshare.1378883.v4
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.1378876
title: Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA

description: Transfer RNAs (tRNAs) play a central role in translation and also recently appear to have a variety of other functions in biological processes beyond translation. Here we report the development of Four-Leaf clover qRT-PCR (FL-PCR), a convenient PCR-based method, which can specifically quantify individual mature tRNA species. In FL-PCR, T4 RNA ligase 2 specifically ligates a stem-loop adapter to mature tRNAs but not to precursor tRNAs or tRNA fragments. Subsequent TaqMan qRT-PCR amplifies only unmodified regions of the tRNA-adapter ligation products; therefore, FL-PCR quantification is not influenced by tRNA post-transcriptional modifications. FL-PCR has broad applicability for the quantification of various tRNAs in different cell types, and thus provides a much-needed simple method for analyzing tRNA abundance and heterogeneity.
DOI: 10.6084/m9.figshare.1378881.v3
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.
DOI: 10.6084/m9.figshare.1378883.v3
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.v5
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.