cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9810455.v1
title: A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines

description: Dataset, code and supplementary information for the Nature Scientific Data publication titled "A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines"
DOI: 10.6084/m9.figshare.9810371
title: Occlusion and dental function of <i>Morganucodon</i> and <i>Megazostrodon</i>

description: A functional analysis of a well-preserved snout of the early-diverging mammaliaform <i>Morganucodon watsoni</i>, with matching upper and lower dentitions, and of the holotype of <i>Megazostrodon rudnerae</i>, showed that both taxa had a primarily orthal occlusal path. In <i>Morganucodon</i>, the direction was individually variable and either strictly orthal or slightly distally or mesially inclined. An analysis with the Occlusal Fingerprint Analyser (OFA) software confirmed an earlier hypothesis that the main cusp A of the upper molars occluded between cusps b and a of the lower antagonists. According to the OFA analysis, there was more extensive contact between cusp a and the preceding anterior upper molar than previously assumed, showing some similarities to the two-on-one pattern described for <i>Megazostrodon</i>. According to our analyses, the molars of <i>Morganucodon</i> and <i>Megazostrodon</i> had an adaptation to piercing, as well as shear-cutting. ‘Shearing flanks,’ which were the focus of previous studies, seem to be a result of attrition, rather than functional areas in themselves. The posterior upper molars in <i>Morganucodon</i> were rotated along their longitudinal axis and lingually inclined within the tooth row, resulting in a triangle between M1 and M2 into which the large m2 can occlude. Together, this suggests a predetermined tooth placement and that contrary to previous hypothesis <i>Morganucodon</i> did not rely on extensive wear in order to form a precise occlusion.
DOI: 10.6084/m9.figshare.9810353
title: Nutrient intake in aging infants and toddlers: 3-year follow-up of the Nutrintake study

description: We performed a 3-year follow-up of the children enrolled into the Nutrintake Study to evaluate the changes of anthropometry and nutrient intake in aging infants and toddlers. Nutrient intake was assessed using a 7-day weighted food-diary. Of the 390 Nutrintake children, 164 (42%) participated in the present study. Their median (IQR) age was 54 (48; 66) months and their anthropometrical status, expressed as standard deviation scores, remained stable during the follow-up. During the same period, there was no biologically relevant change in the intake of macronutrients expressed as percentage of energy while median increases of 757 mg/day, 0.7 mg/day and 3.1 g/1000 kcal per day were detected for sodium, iron and fibre, respectively. As compared to the Italian reference standards, the Nutrintake children continued to show at the 3-year follow-up an excessive intake of simple carbohydrates, proteins, sodium, and a low intake of iron and fibre.
DOI: 10.6084/m9.figshare.9810353.v1
title: Nutrient intake in aging infants and toddlers: 3-year follow-up of the Nutrintake study

description: We performed a 3-year follow-up of the children enrolled into the Nutrintake Study to evaluate the changes of anthropometry and nutrient intake in aging infants and toddlers. Nutrient intake was assessed using a 7-day weighted food-diary. Of the 390 Nutrintake children, 164 (42%) participated in the present study. Their median (IQR) age was 54 (48; 66) months and their anthropometrical status, expressed as standard deviation scores, remained stable during the follow-up. During the same period, there was no biologically relevant change in the intake of macronutrients expressed as percentage of energy while median increases of 757 mg/day, 0.7 mg/day and 3.1 g/1000 kcal per day were detected for sodium, iron and fibre, respectively. As compared to the Italian reference standards, the Nutrintake children continued to show at the 3-year follow-up an excessive intake of simple carbohydrates, proteins, sodium, and a low intake of iron and fibre.
DOI: 10.6084/m9.figshare.9810371.v2
title: Occlusion and dental function of <i>Morganucodon</i> and <i>Megazostrodon</i>

description: A functional analysis of a well-preserved snout of the early-diverging mammaliaform <i>Morganucodon watsoni</i>, with matching upper and lower dentitions, and of the holotype of <i>Megazostrodon rudnerae</i>, showed that both taxa had a primarily orthal occlusal path. In <i>Morganucodon</i>, the direction was individually variable and either strictly orthal or slightly distally or mesially inclined. An analysis with the Occlusal Fingerprint Analyser (OFA) software confirmed an earlier hypothesis that the main cusp A of the upper molars occluded between cusps b and a of the lower antagonists. According to the OFA analysis, there was more extensive contact between cusp a and the preceding anterior upper molar than previously assumed, showing some similarities to the two-on-one pattern described for <i>Megazostrodon</i>. According to our analyses, the molars of <i>Morganucodon</i> and <i>Megazostrodon</i> had an adaptation to piercing, as well as shear-cutting. ‘Shearing flanks,’ which were the focus of previous studies, seem to be a result of attrition, rather than functional areas in themselves. The posterior upper molars in <i>Morganucodon</i> were rotated along their longitudinal axis and lingually inclined within the tooth row, resulting in a triangle between M1 and M2 into which the large m2 can occlude. Together, this suggests a predetermined tooth placement and that contrary to previous hypothesis <i>Morganucodon</i> did not rely on extensive wear in order to form a precise occlusion.
DOI: 10.6084/m9.figshare.9810371.v1
title: Occlusion and dental function of <i>Morganucodon</i> and <i>Megazostrodon</i>

description: A functional analysis of a well-preserved snout of the early-diverging mammaliaform <i>Morganucodon watsoni</i>, with matching upper and lower dentitions, and of the holotype of <i>Megazostrodon rudnerae</i>, showed that both taxa had a primarily orthal occlusal path. In <i>Morganucodon</i>, the direction was individually variable and either strictly orthal or slightly distally or mesially inclined. An analysis with the Occlusal Fingerprint Analyser (OFA) software confirmed an earlier hypothesis that the main cusp A of the upper molars occluded between cusps b and a of the lower antagonists. According to the OFA analysis, there was more extensive contact between cusp a and the preceding anterior upper molar than previously assumed, showing some similarities to the two-on-one pattern described for <i>Megazostrodon</i>. According to our analyses, the molars of <i>Morganucodon</i> and <i>Megazostrodon</i> had an adaptation to piercing, as well as shear-cutting. ‘Shearing flanks,’ which were the focus of previous studies, seem to be a result of attrition, rather than functional areas in themselves. The posterior upper molars in <i>Morganucodon</i> were rotated along their longitudinal axis and lingually inclined within the tooth row, resulting in a triangle between M1 and M2 into which the large m2 can occlude. Together, this suggests a predetermined tooth placement and that contrary to previous hypothesis <i>Morganucodon</i> did not rely on extensive wear in order to form a precise occlusion.
DOI: 10.17608/k6.auckland.9810233
title: Exciting and impactful example paper for MedTech CoRE DTP project

description: In this highly exciting and very insightful scientific paper, we present the stress-strain data to be used in the parameter estimation project for the MedTech CoRE Doctoral Training Programme's Computational Physiology module, September 2019.
DOI: 10.6084/m9.figshare.9810221
title: GC bias metrics for the three downsampled samples that failed to run on ascatNgs

description: This file contain GC bias metrics for all the samples (n = 67). The data was derived using the CollectGcBiasMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The GC bias metrics include AT_DROPOUT, representing how undercovered regions with GC content less than 50% are compared to the mean coverage; GC_DROPOUT, representing how undercovered regions with GC content greater than 50% are compared to the mean coverage; GC_NC_0_19, representing normalized coverage over quintile of GC content ranging from 0%–19%; GC_NC_20_39, representing normalized coverage over quintile of GC content ranging from 20%–39%; GC_NC_40_59, representing normalized coverage over quintile of GC content ranging from 40%–59%; GC_NC_60_79, representing normalized coverage over quintile of GC content ranging from 60%–79% and GC_NC_80_100, representing normalized coverage over quintile of GC content ranging from 80%–100. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The ASCAT column indicates whether ascatNgs ran on all tiers of downsampling (PASS) or failed at least in one of the downsampling tier (FAILED) for the paired normal tumour samples. The Metric column indicates the GC bias metric of interest. The value column provides the numerical value of the GC bias metric of interest for the tumour or normal sample of a particular donor.
DOI: 10.6084/m9.figshare.9810224
title: Supplementary material

description: Supplementary material (data set)
DOI: 10.17608/k6.auckland.9810233.v1
title: Exciting and impactful example paper for MedTech CoRE DTP project

description: In this highly exciting and very insightful scientific paper, we present the stress-strain data to be used in the parameter estimation project for the MedTech CoRE Doctoral Training Programme's Computational Physiology module, September 2019.
DOI: 10.6084/m9.figshare.9810236
title: A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology

description: Genome assembly of sweet cherry cv. Tieton by using linked-read sequencing technology. Annotation of the assembly and chromosome-scale pseudomolecule construction.
DOI: 10.6084/m9.figshare.9810218
title: WGS performance metrics for the three downsampled samples that failed to run on ascatNgs

description: This file contains WGS performance metrics for all the samples (n = 67). The data was derived using the CollectWgsMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The performance metrics include PCT_EXC_MAPQ, representing the fraction of aligned bases that were filtered out because they were in reads with low mapping quality and PCF_EXC_BASEQ, representing the fraction of aligned bases that were filtered out because they were of low base quality. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The ASCAT column indicates whether ascatNgs ran on all tiers of downsampling (PASS) or failed at least in one of the downsampling tier (FAILED) for the paired normal tumour samples. The Metric column indicates the WGS performance metric of interest. The value column provides the numerical value of the WGS performance metric of interest for the tumour or normal sample of a particular donor.
DOI: 10.6084/m9.figshare.9810236.v2
title: A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology

description: Genome assembly of sweet cherry cv. Tieton by using linked-read sequencing technology. Annotation of the assembly and chromosome-scale pseudomolecule construction.
DOI: 10.6084/m9.figshare.9810218.v1
title: WGS performance metrics for the three downsampled samples that failed to run on ascatNgs

description: This file contains WGS performance metrics for all the samples (n = 67). The data was derived using the CollectWgsMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The performance metrics include PCT_EXC_MAPQ, representing the fraction of aligned bases that were filtered out because they were in reads with low mapping quality and PCF_EXC_BASEQ, representing the fraction of aligned bases that were filtered out because they were of low base quality. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The ASCAT column indicates whether ascatNgs ran on all tiers of downsampling (PASS) or failed at least in one of the downsampling tier (FAILED) for the paired normal tumour samples. The Metric column indicates the WGS performance metric of interest. The value column provides the numerical value of the WGS performance metric of interest for the tumour or normal sample of a particular donor.
DOI: 10.6084/m9.figshare.9810221.v1
title: GC bias metrics for the three downsampled samples that failed to run on ascatNgs

description: This file contain GC bias metrics for all the samples (n = 67). The data was derived using the CollectGcBiasMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The GC bias metrics include AT_DROPOUT, representing how undercovered regions with GC content less than 50% are compared to the mean coverage; GC_DROPOUT, representing how undercovered regions with GC content greater than 50% are compared to the mean coverage; GC_NC_0_19, representing normalized coverage over quintile of GC content ranging from 0%–19%; GC_NC_20_39, representing normalized coverage over quintile of GC content ranging from 20%–39%; GC_NC_40_59, representing normalized coverage over quintile of GC content ranging from 40%–59%; GC_NC_60_79, representing normalized coverage over quintile of GC content ranging from 60%–79% and GC_NC_80_100, representing normalized coverage over quintile of GC content ranging from 80%–100. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The ASCAT column indicates whether ascatNgs ran on all tiers of downsampling (PASS) or failed at least in one of the downsampling tier (FAILED) for the paired normal tumour samples. The Metric column indicates the GC bias metric of interest. The value column provides the numerical value of the GC bias metric of interest for the tumour or normal sample of a particular donor.
DOI: 10.6084/m9.figshare.9810212
title: GC bias metrics for the congruently/non-congruently classified samples between array/WGS and original coverage and downsampled WGS-derived data

description: This file contain GC bias metrics for all the samples (n = 67). The data was derived using the CollectGcBiasMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The GC bias metrics include AT_DROPOUT, representing how undercovered regions with GC content less than 50% are compared to the mean coverage; GC_DROPOUT, representing how undercovered regions with GC content greater than 50% are compared to the mean coverage; GC_NC_0_19, representing normalized coverage over quintile of GC content ranging from 0%–19%; GC_NC_20_39, representing normalized coverage over quintile of GC content ranging from 20%–39%; GC_NC_40_59, representing normalized coverage over quintile of GC content ranging from 40%–59%; GC_NC_60_79, representing normalized coverage over quintile of GC content ranging from 60%–79% and GC_NC_80_100, representing normalized coverage over quintile of GC content ranging from 80%–100. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The Congruency column indicates whether a given sample was congruently (con) v/s non-congruently classified (ncon) classified between original and downsampled WGS data. The Metric column indicates the GC bias metric of interest. The value column provides the numerical value of the GC bias metric of interest for the tumour or normal sample of a particular donor.<br>
DOI: 10.6084/m9.figshare.9810224.v1
title: Supplementary material

description: Supplementary material (data set)
DOI: 10.6084/m9.figshare.9810224.v3
title: Supplementary material

description: Supplementary material (data set)
DOI: 10.6084/m9.figshare.9810170
title: LPG Paper Data Sets

description: 1. The appended data set of the two waves of ACCESS survey from 2014-15 and 2018 for panel data analysis.2. The merged data set of the two waves of ACCESS survey from 2014-15 and 2018 for cross-sectional data analysis.
DOI: 10.6084/m9.figshare.9810224.v2
title: Supplementary material

description: Supplementary material (descriptive data and data set)
DOI: 10.6084/m9.figshare.9810152
title: Carbon cycling in the world's deepest blue hole

description: This data set provides details for (1)the Δ<sup>14</sup>C and δ<sup>13</sup>C values of DOC and DIC, (2)the vertical profiles of temperature, density, pH, Eh, SO<sub>4</sub><sup>2-</sup>, and chlorophyll a, (3)the vertical distributions of carbonate system parameters including total alkalinity (TA), Ca<sup>2+</sup>, CO<sub>3</sub><sup>2-</sup>, K<sub>sp</sub> and Ω of calcite and aragonite, (4) the top 50 most abundant genera of the bacterial community in all samples that are displayed in a heatmap in seawater samples collected from the YBH and the reference site. <br>
DOI: 10.6084/m9.figshare.9810164
title: WGS performance metrics for the congruently/non-congruently classified samples between array/WGS and original coverage and downsampled WGS-derived data

description: This file contains WGS performance metrics for all the samples (n = 67). The data was derived using the CollectWgsMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The performance metrics include PCT_EXC_MAPQ, representing the fraction of aligned bases that were filtered out because they were in reads with low mapping quality and PCF_EXC_BASEQ, representing the fraction of aligned bases that were filtered out because they were of low base quality. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The Congruency column indicates whether a given sample was congruently (con) v/s non-congruently classified (ncon) classified between original and downsampled WGS data. The Metric column indicates the WGS performance metric of interest. The value column provides the numerical value of the WGS performance metric of interest for the tumour or normal sample of a particular donor.<br>
DOI: 10.6084/m9.figshare.9810212.v1
title: GC bias metrics for the non-congruently classified samples between original coverage and downsampled WGS-derived HRD score

description: This file contain GC bias metrics for all the samples (n = 67). The data was derived using the CollectGcBiasMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The GC bias metrics include AT_DROPOUT, representing how undercovered regions with GC content less than 50% are compared to the mean coverage; GC_DROPOUT, representing how undercovered regions with GC content greater than 50% are compared to the mean coverage; GC_NC_0_19, representing normalized coverage over quintile of GC content ranging from 0%–19%; GC_NC_20_39, representing normalized coverage over quintile of GC content ranging from 20%–39%; GC_NC_40_59, representing normalized coverage over quintile of GC content ranging from 40%–59%; GC_NC_60_79, representing normalized coverage over quintile of GC content ranging from 60%–79% and GC_NC_80_100, representing normalized coverage over quintile of GC content ranging from 80%–100. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The Congruency column indicates whether a given sample was congruently (con) v/s non-congruently classified (ncon) classified between original and downsampled WGS data. The Metric column indicates the GC bias metric of interest. The value column provides the numerical value of the GC bias metric of interest for the tumour or normal sample of a particular donor.<br>
DOI: 10.6084/m9.figshare.9810053
title: HRD score and HRD score components matrix for downsampled (15X) WGS data

description: This file contains the HRD scores and HRD score components (HRD-LOH, LST and NtAI) for the downsampled (15X) WGS-derived data.
DOI: 10.6084/m9.figshare.9810152.v1
title: Carbon cycling in the world's deepest blue hole

description: This data set provides details for (1)the Δ<sup>14</sup>C and δ<sup>13</sup>C values of DOC and DIC, (2)the vertical profiles of temperature, density, pH, Eh, SO<sub>4</sub><sup>2-</sup>, and chlorophyll a, (3)the vertical distributions of carbonate system parameters including total alkalinity (TA), Ca<sup>2+</sup>, CO<sub>3</sub><sup>2-</sup>, K<sub>sp</sub> and Ω of calcite and aragonite, (4) the top 50 most abundant genera of the bacterial community in all samples that are displayed in a heatmap in seawater samples collected from the YBH and the reference site. <br>
DOI: 10.6084/m9.figshare.9810164.v2
title: WGS performance metrics for the congruently/non-congruently classified samples between array/WGS and original coverage and downsampled WGS-derived data

description: This file contains WGS performance metrics for all the samples (n = 67). The data was derived using the CollectWgsMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The performance metrics include PCT_EXC_MAPQ, representing the fraction of aligned bases that were filtered out because they were in reads with low mapping quality and PCF_EXC_BASEQ, representing the fraction of aligned bases that were filtered out because they were of low base quality. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The Congruency column indicates whether a given sample was congruently (con) v/s non-congruently classified (ncon) classified between original and downsampled WGS data. The Metric column indicates the WGS performance metric of interest. The value column provides the numerical value of the WGS performance metric of interest for the tumour or normal sample of a particular donor.<br>
DOI: 10.6084/m9.figshare.9810212.v2
title: GC bias metrics for the non-congruently classified samples between original coverage and downsampled WGS-derived HRD score

description: This file contain GC bias metrics for all the samples (n = 67). The data was derived using the CollectGcBiasMetrics tool from Picard tools (https://broadinstitute.github.io/picard/). The GC bias metrics include AT_DROPOUT, representing how undercovered regions with GC content less than 50% are compared to the mean coverage; GC_DROPOUT, representing how undercovered regions with GC content greater than 50% are compared to the mean coverage; GC_NC_0_19, representing normalized coverage over quintile of GC content ranging from 0%–19%; GC_NC_20_39, representing normalized coverage over quintile of GC content ranging from 20%–39%; GC_NC_40_59, representing normalized coverage over quintile of GC content ranging from 40%–59%; GC_NC_60_79, representing normalized coverage over quintile of GC content ranging from 60%–79% and GC_NC_80_100, representing normalized coverage over quintile of GC content ranging from 80%–100. The Type column indicates whether the sample relates to the tumour or normal tissue of a given donor. The Congruency column indicates whether a given sample was congruently (con) v/s non-congruently classified (ncon) classified between original and downsampled WGS data. The Metric column indicates the GC bias metric of interest. The value column provides the numerical value of the GC bias metric of interest for the tumour or normal sample of a particular donor.<br>
DOI: 10.6084/m9.figshare.9809978
title: HRD score and HRD score components matrix for downsampled (30X) WGS data

description: This file contains the HRD scores and HRD score components (HRD-LOH, LST and NtAI) for the downsampled (30X) WGS-derived data.