cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7218266
title: mtDNA variant detection by exome sequencing

description: Next generation sequencing, especially exome sequencing, has revolutionised the diagnostics for mitochondrial disorders. However, the nuclear and mitochondrial DNA are investigated with separate tests, increasing costs and duration of diagnostics. However, the full potential of exome sequencing is often not exploited as the additional analysis of “off-target reads” deriving from the mitochondrial DNA can be used to analyse both genomes. Mitochondrial DNA analysis by exome sequencing of 2,111 cases (various, mostly neurological, referral indications) in a clinical setting identified 38 confirmed pathogenic mitochondrial DNA point mutations, increasing the diagnostic yield by nearly 2%. We show that analysis of mitochondrial DNA variants by exome sequencing has a high recall rate (96.2±5.6%) and an excellent precision (99.5±2.2%) when compared to the gold standard of targeted mitochondrial DNA next generation sequencing. Further, we demonstrate that exome sequencing estimates heteroplasmy levels with an average difference of 6.6±3.8% compared to targeted mitochondrial DNA next generation sequencing, sufficient for clinical decision making. Taken together, the mitochondrial DNA analysis from exome sequencing is of sufficient quality for clinical diagnostics, and should be included in the standard diagnostic exome analysis. Nonetheless, known pitfalls for mitochondrial DNA analysis like tissue specificity have to be taken into account.
DOI: 10.7284/128952
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1735 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218266.v1
title: mtDNA variant detection by exome sequencing

description: Next generation sequencing, especially exome sequencing, has revolutionised the diagnostics for mitochondrial disorders. However, the nuclear and mitochondrial DNA are investigated with separate tests, increasing costs and duration of diagnostics. However, the full potential of exome sequencing is often not exploited as the additional analysis of “off-target reads” deriving from the mitochondrial DNA can be used to analyse both genomes. Mitochondrial DNA analysis by exome sequencing of 2,111 cases (various, mostly neurological, referral indications) in a clinical setting identified 38 confirmed pathogenic mitochondrial DNA point mutations, increasing the diagnostic yield by nearly 2%. We show that analysis of mitochondrial DNA variants by exome sequencing has a high recall rate (96.2±5.6%) and an excellent precision (99.5±2.2%) when compared to the gold standard of targeted mitochondrial DNA next generation sequencing. Further, we demonstrate that exome sequencing estimates heteroplasmy levels with an average difference of 6.6±3.8% compared to targeted mitochondrial DNA next generation sequencing, sufficient for clinical decision making. Taken together, the mitochondrial DNA analysis from exome sequencing is of sufficient quality for clinical diagnostics, and should be included in the standard diagnostic exome analysis. Nonetheless, known pitfalls for mitochondrial DNA analysis like tissue specificity have to be taken into account.
DOI: 10.7284/128953
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1735 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218215
title: Acanthoscelides pheromone

description: <b>S1 Fig.</b> <b>Age-specific release of <i>Acanthoscelides obtectus</i> sex pheromone components by virgin males from the bean line.</b> Raw data included. <b>S1 File. Raw data for pheromone release from males from different host lines.</b> <b>S2 File.</b> <b>Olfactometer data and analysis.</b> <b>S3 File. Still-air bioassay data and analysis.</b> <b>S4 File. EAG data for females from different host lines.</b>
DOI: 10.7284/128954
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1735 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218209.v1
title: Supplementary raw data from Challenges and future prospects for developing Ca and Mg water quality guidelines: a meta-analysis

description: This file contains all datasets used in the main article (background water hardness and Ca:Mg ratio, and R formatted data used in the article). This file also contains reference lists of all articles collected, preliminarily screened, successfully classified, and rejected.
DOI: 10.6084/m9.figshare.7218215.v1
title: Acanthoscelides pheromone

description: <b>S1 Fig.</b> <b>Age-specific release of <i>Acanthoscelides obtectus</i> sex pheromone components by virgin males from the bean line.</b> Raw data included. <b>S1 File. Raw data for pheromone release from males from different host lines.</b> <b>S2 File.</b> <b>Olfactometer data and analysis.</b> <b>S3 File. Still-air bioassay data and analysis.</b> <b>S4 File. EAG data for females from different host lines.</b>
DOI: 10.7284/128951
title: Gyrocompass data collected during research cruise SP1735 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128950
title: Meteorological Station data collected during research cruise SP1735 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128949
title: Winch data collected during research cruise SP1735 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218185
title: Data from Experiment from Evolved tolerance to freshwater salinization in zooplankton: life-history trade-offs, cross-tolerance and reducing cascading effects

description: Raw data for abiotics, zooplankton, phytoplankton, and macroinvertebrates
DOI: 10.7284/128955
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1738 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218185.v1
title: Data from Experiment from Evolved tolerance to freshwater salinization in zooplankton: life-history trade-offs, cross-tolerance and reducing cascading effects

description: Raw data for abiotics, zooplankton, phytoplankton, and macroinvertebrates
DOI: 10.6084/m9.figshare.7218176
title: Supplementary Table S3 from Transmission strategies in a chemosynthetic symbiosis: detection and quantification of symbionts in host tissues and their environment

description: Table S3. qPCR data for eggs, environmental samples, and standard curves.
DOI: 10.7284/128960
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1738 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218176.v1
title: Supplementary Table S3 from Transmission strategies in a chemosynthetic symbiosis: detection and quantification of symbionts in host tissues and their environment

description: Table S3. qPCR data for eggs, environmental samples, and standard curves.
DOI: 10.6084/m9.figshare.7218155
title: Macfarlan_ESM from Bands of brothers and in-laws: Waorani warfare, marriage and alliance formation

description: The root of modern human warfare lies in the lethal coalitionary violence of males in small-scale societies. However, little quantitative data exist concerning the form and function of coalitionary violence in this setting. Debates exist over how lethal coalitions are constituted, as well as the motivations and benefits for males to join such groups. Data from a lowland Amazonian population, the Waorani of Ecuador, illuminate three issues: (i) the degree to which raiding parties are composed of groups of fraternal kin as opposed to strategic alliances of actual or potential affinal kin, (ii) the extent to which individuals use pre-existing affinal ties to motivate others to participate in war or leverage warfare as a mechanism to create such ties and (iii) the extent to which participation in raiding is driven by rewards associated with future marriage opportunities. Analyses demonstrate that Waorani raiding parties were composed of a mix of males who were potential affines, actual affines and fraternal kin, suggesting that men used pre-existing genetic, lineal and social kin ties for recruiting raid partners and used raiding as a venue to create novel social relationships. Furthermore, analyses demonstrate that males leveraged raiding alliances to achieve marriage opportunities for themselves as well as for their children. Overall, it appears that a complex set of motivations involving individual rewards, kin marriage opportunities, subtle coercion and the assessment of alliance strength promote violent intergroup conflict among the Waorani. These findings illustrate the complex inter-relationships among kin selection, coalition building and mating success in our species.
DOI: 10.7284/128961
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1738 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128962
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1738 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/128959
title: Gyrocompass data collected during research cruise SP1738 using a Furuno Furuno SC-30 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218113
title: Supplementary Material for: Efficacy and Safety of Pirfenidone in Advanced Idiopathic Pulmonary Fibrosis

description: <b><i>Background:</i></b> Although phase 3 trials showed significant efficacy and acceptable safety profiles for pirfenidone in mild-to-moderate idiopathic pulmonary fibrosis (IPF), data on advanced IPF are limited. <b><i>Objectives:</i></b> The study aimed to evaluate the efficacy and safety of pirfenidone in advanced IPF patients. <b><i>Methods:</i></b> The clinical data of 138 IPF patients (advanced group: 27%) treated with pirfenidone were retrospectively reviewed and compared between advanced and non-advanced groups. Advanced IPF was defined as (1) forced vital capacity (FVC) &lt; 50% predicted or (2) diffusing capacity for carbon monoxide &lt; 30% predicted. <b><i>Results:</i></b> The mean treatment duration was 51.3 weeks, and lung function analysis was performed in 81 patients (17 in the advanced group). Changes in FVC and total lung capacity (TLC) were significantly reduced at 6 months after treatment in both the advanced (ΔFVC [6 months]: –6.3 [before] vs. 0.7% predicted [after]; ΔTLC: –5.3 vs. 0.8) and non-advanced (ΔFVC: –3.4 vs. 0.5; ΔTLC: –3.1 vs. –0.9) groups. The rate of decline in FVC and TLC was significant before treatment, but not after treatment in the advanced (FVC: –1.27 [before] vs. 0.21% predicted/month [after]; TLC: –0.89 vs. –0.15) and non-advanced (FVC: –0.60 vs. –0.20; TLC: –0.54 vs. –0.17) groups. The advanced group showed a similar rate of adverse events (AEs) (78.4 vs. 88.1%, <i>p</i> = 0.270), but more serious AEs (40.5 vs. 10.9%, <i>p</i> &lt; 0.001) including death (24.3 vs. 5.0%, <i>p</i> = 0.002). <b><i>Conclusions:</i></b> In advanced IPF, pirfenidone showed similar efficacy and safety to non-advanced IPF except for serious AEs, which may be due to the advanced status itself.
DOI: 10.6084/m9.figshare.7218113.v1
title: Supplementary Material for: Efficacy and Safety of Pirfenidone in Advanced Idiopathic Pulmonary Fibrosis

description: <b><i>Background:</i></b> Although phase 3 trials showed significant efficacy and acceptable safety profiles for pirfenidone in mild-to-moderate idiopathic pulmonary fibrosis (IPF), data on advanced IPF are limited. <b><i>Objectives:</i></b> The study aimed to evaluate the efficacy and safety of pirfenidone in advanced IPF patients. <b><i>Methods:</i></b> The clinical data of 138 IPF patients (advanced group: 27%) treated with pirfenidone were retrospectively reviewed and compared between advanced and non-advanced groups. Advanced IPF was defined as (1) forced vital capacity (FVC) &lt; 50% predicted or (2) diffusing capacity for carbon monoxide &lt; 30% predicted. <b><i>Results:</i></b> The mean treatment duration was 51.3 weeks, and lung function analysis was performed in 81 patients (17 in the advanced group). Changes in FVC and total lung capacity (TLC) were significantly reduced at 6 months after treatment in both the advanced (ΔFVC [6 months]: –6.3 [before] vs. 0.7% predicted [after]; ΔTLC: –5.3 vs. 0.8) and non-advanced (ΔFVC: –3.4 vs. 0.5; ΔTLC: –3.1 vs. –0.9) groups. The rate of decline in FVC and TLC was significant before treatment, but not after treatment in the advanced (FVC: –1.27 [before] vs. 0.21% predicted/month [after]; TLC: –0.89 vs. –0.15) and non-advanced (FVC: –0.60 vs. –0.20; TLC: –0.54 vs. –0.17) groups. The advanced group showed a similar rate of adverse events (AEs) (78.4 vs. 88.1%, <i>p</i> = 0.270), but more serious AEs (40.5 vs. 10.9%, <i>p</i> &lt; 0.001) including death (24.3 vs. 5.0%, <i>p</i> = 0.002). <b><i>Conclusions:</i></b> In advanced IPF, pirfenidone showed similar efficacy and safety to non-advanced IPF except for serious AEs, which may be due to the advanced status itself.
DOI: 10.7284/128958
title: Meteorological Station data collected during research cruise SP1738 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218104
title: Waldock et al. Ecology Letters (accepted version)

description: Accompanying data for Waldock et al. (2019) The shape of abundance distributions across temperature gradients in reef fishes. Ecology Letters
DOI: 10.6084/m9.figshare.7218104.v1
title: Waldock et al. Ecology Letters (accepted version)

description: Accompanying data for Waldock et al. (2019) The shape of abundance distributions across temperature gradients in reef fishes. Ecology Letters
DOI: 10.7284/128957
title: Winch data collected during research cruise SP1738 using a Markey DEYSH-3 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218101
title: Supplementary Material for: Progression Potential of Ductal Carcinoma in situ Assessed by Genomic Copy Number Profiling

description: <b><i>Background:</i></b> Ductal carcinoma in situ (DCIS) of the breast is heterogeneous in terms of the risk of progression to invasive ductal carcinoma (IDC). To treat DCIS appropriately for its progression risk, we classified individual DCIS by its profile of genomic changes into 2 groups and correlated them with clinicopathological progression factors. <b><i>Methods:</i></b> We used surgically resected, formalin-fixed, paraffin-embedded tissues of 22 DCIS and 30 IDC lesions. We performed immunohistochemical intrinsic subtyping, array-based comparative genomic hybridization, and unsupervised clustering. <b><i>Results:</i></b> The samples were divided into 2 major clusters, A and B. Cluster A showed a greater number of gene and chromosome copy number alterations, a larger IDC/DCIS ratio, a higher frequency of nonluminal subtype, a lower frequency of luminal subtype, and a higher nuclear grade, when compared with cluster B. However, there was no difference in the frequencies of lymph node metastasis between clusters A and B. We identified 9 breast-cancer-related genes, including <i>TP53</i> and <i>GATA3</i>, that highly contributed to the discrimination of A and B clusters. <b><i>Conclusion:</i></b> Classification of breast tumors into rapidly progressive cluster A and the other (cluster B) may contribute to select the treatment appropriate for their progression risk.
DOI: 10.7284/130699
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1801 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218089
title: Supplementary data_Regional differences in the contribution of TNFR1 and TNF to sympathetic innervation_means, normality test and stats.pdf

description: Means, normality tests and statistics for manuscript of: Regional differences in the contributions of TNF and TNFR1 to the establishment sympathetic innervation.<br>
DOI: 10.6084/m9.figshare.7218101.v2
title: Supplementary Material for: Progression Potential of Ductal Carcinoma in situ Assessed by Genomic Copy Number Profiling

description: <b><i>Background:</i></b> Ductal carcinoma in situ (DCIS) of the breast is heterogeneous in terms of the risk of progression to invasive ductal carcinoma (IDC). To treat DCIS appropriately for its progression risk, we classified individual DCIS by its profile of genomic changes into 2 groups and correlated them with clinicopathological progression factors. <b><i>Methods:</i></b> We used surgically resected, formalin-fixed, paraffin-embedded tissues of 22 DCIS and 30 IDC lesions. We performed immunohistochemical intrinsic subtyping, array-based comparative genomic hybridization, and unsupervised clustering. <b><i>Results:</i></b> The samples were divided into 2 major clusters, A and B. Cluster A showed a greater number of gene and chromosome copy number alterations, a larger IDC/DCIS ratio, a higher frequency of nonluminal subtype, a lower frequency of luminal subtype, and a higher nuclear grade, when compared with cluster B. However, there was no difference in the frequencies of lymph node metastasis between clusters A and B. We identified 9 breast-cancer-related genes, including <i>TP53</i> and <i>GATA3</i>, that highly contributed to the discrimination of A and B clusters. <b><i>Conclusion:</i></b> Classification of breast tumors into rapidly progressive cluster A and the other (cluster B) may contribute to select the treatment appropriate for their progression risk.
DOI: 10.6084/m9.figshare.7218101.v1
title: Supplementary Material for: Progression Potential of Ductal Carcinoma in situ Assessed by Genomic Copy Number Profiling

description: <b><i>Background:</i></b> Ductal carcinoma in situ (DCIS) of the breast is heterogeneous in terms of the risk of progression to invasive ductal carcinoma (IDC). To treat DCIS appropriately for its progression risk, we classified individual DCIS by its profile of genomic changes into 2 groups and correlated them with clinicopathological progression factors. <b><i>Methods:</i></b> We used surgically resected, formalin-fixed, paraffin-embedded tissues of 22 DCIS and 30 IDC lesions. We performed immunohistochemical intrinsic subtyping, array-based comparative genomic hybridization, and unsupervised clustering. <b><i>Results:</i></b> The samples were divided into 2 major clusters, A and B. Cluster A showed a greater number of gene and chromosome copy number alterations, a larger IDC/DCIS ratio, a higher frequency of nonluminal subtype, a lower frequency of luminal subtype, and a higher nuclear grade, when compared with cluster B. However, there was no difference in the frequencies of lymph node metastasis between clusters A and B. We identified 9 breast-cancer-related genes, including <i>TP53</i> and <i>GATA3</i>, that highly contributed to the discrimination of A and B clusters. <b><i>Conclusion:</i></b> Classification of breast tumors into rapidly progressive cluster A and the other (cluster B) may contribute to select the treatment appropriate for their progression risk.
DOI: 10.6084/m9.figshare.7218080
title: STN as target region

description: Measuring stimulus waveform from oscilloscope when center of the brain model is target region.
DOI: 10.6084/m9.figshare.7218089.v2
title: Supplementary data_Regional differences in the contribution of TNFR1 and TNF to sympathetic innervation_means, normality test and stats.pdf

description: Means, normality tests and statistics for manuscript of: Regional differences in the contributions of TNF and TNFR1 to the establishment sympathetic innervation.<br>
DOI: 10.6084/m9.figshare.7218089.v1
title: Regional differences in the contribution of TNFR1 and TNF to sympathetic innervation_means, normality test and stats.pdf

description: Means, normality tests and statistics for manuscript of: Regional differences in the contributions of TNF and TNFR1 to the establishment sympathetic innervation.<br>
DOI: 10.6084/m9.figshare.7217987
title: Data Share Table.xlsx

description: This Excel file contains the emergence times used for the PLOSone paper
DOI: 10.6084/m9.figshare.7218017
title: Center as target region

description: Measuring stimulus waveform from oscilloscope when center of the brain model is target region.
DOI: 10.7284/130703
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1801 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7217987.v1
title: Data Share Table.xlsx

description: This Excel file contains the emergence times used for the PLOSone paper
DOI: 10.7284/130704
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1801 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7218017.v1
title: Center as target region.zip

description: Measuring stimulus waveform from oscilloscope when center of the brain model is target region.
DOI: 10.7284/130705
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1801 using a Furuno GP-150 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130707
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1801 using a Furuno GP-170 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130701
title: Meteorological Station data collected during research cruise SP1801 using a SIO MET-System instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130708
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SP1802 using a Hawaii UHDAS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130710
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1802 using a Garmin GPS-17HVS instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130711
title: GNSS (Global Navigation Satellite System) data collected during research cruise SP1802 using a Ashtech ADU2 instrument system onboard the platform RV Robert Gordon Sproul

description: Original (unprocessed) data collected during a Field_expedition