cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17633/rd.brunel.5620606
title: ERP to chess stimuli

description: In the attached excel file are the means and SDs of ERP amplitudes associated with the 8 experimental conditions set out in Table 2 of Wright, M. J., Gobet, F., Chassy, P. & Ramchandani, N. K. (2013), ERP to chess stimuli reveal expert-novice differences in the amplitudes of N2 and P3 components. Psychophysiology, 50, 1023-1033. DOI: 10.1111/psyp.12084<br>All values are in microvolts. <br>Means Maxima and Minima were calculated within the ROI and across participants,
DOI: 10.6084/m9.figshare.5620651
title: Empirical Analysis of Ranking Models for an Adaptable Dataset Search: complementary material

description: This repository contains performance measures of dataset ranking models.<br>- Usage: from Results/src run <i>Python results m<sub>1</sub> m<sub>2</sub> ...</i><br>such that <i>m<sub>i</sub></i> can be omitted, or be any element of the list of model labels ['bayesian-12C', 'bayesian-5L', 'bayesian-5L12C', 'cos-12C', 'cos-5L', 'cos-5L5C', 'j48-12C', 'j48-5L', 'j48-5L5C', 'jrip-12C', 'jrip-5L', 'jrip-5L5C', 'sn-12C', 'sn-5L', 'sn-5L12C']. Results of selected models will be plotted in a 2D line plot. If no model is provided all models will be listed.<br>
DOI: 10.6084/m9.figshare.5620603.v2
title: The MiAge Calculator: a DNA methylation-based mitotic age calculator of human tissue types

description: Cell division is important in human aging and cancer. The estimation of the number of cell divisions (mitotic age) of a given tissue type in individuals is of great interest as it allows not only the study of biological aging (using a new molecular aging target) but also the stratification of prospective cancer risk. Here, we introduce the MiAge Calculator, a mitotic age calculator based on a novel statistical framework, the MiAge model. MiAge is designed to quantitatively estimate mitotic age (total number of lifetime cell divisions) of a tissue using the stochastic replication errors accumulated in the epigenetic inheritance process during cell divisions. With the MiAge model, the MiAge Calculator was built using the training data of DNA methylation measures of 4,020 tumor and adjacent normal tissue samples from eight TCGA cancer types and was tested using the testing data of DNA methylation measures of 2,221 tumor and adjacent normal tissue samples of five other TCGA cancer types. We showed that within each of the thirteen cancer types studied, the estimated mitotic age is universally accelerated in tumor tissues compared to adjacent normal tissues. Across the thirteen cancer types, we showed that worse cancer survivals are associated with more accelerated mitotic age in tumor tissues. Importantly, we demonstrated the utility of mitotic age by showing that the integration of mitotic age and clinical information leads to improved survival prediction in six out of the thirteen cancer types studied. The MiAge Calculator is available at http://www.columbia.edu/∼sw2206/softwares.htm.
DOI: 10.6084/m9.figshare.5620603.v1
title: The MiAge Calculator: a DNA methylation-based mitotic age calculator of Human tissue types

description: Cell division is important in human aging and cancer. To estimate the number of cell divisions (mitotic age) of a given tissue type between individuals is of great interest as that not only allows to study biological aging using a new molecular aging target but also allows the stratification of prospective cancer risk. Here we introduce the MiAge Calculator, a mitotic age calculator based on a novel statistical framework, the MiAge model. MiAge is designed to quantitatively estimate mitotic age (total number of lifetime cell divisions) of a tissue using the stochastic replication errors accumulated in the epigenetic inheritance process during cell divisions. With the MiAge model, the MiAge Calculator was built using the training data of DNA methylation measures of 4,020 tumor and adjacent normal tissue samples from eight TCGA cancer types and was tested using the testing data of DNA methylation measures of 2,221 tumor and adjacent normal tissue samples of five other TCGA cancer types. We showed that within each of the thirteen cancer types studied, the estimated mitotic age is universally accelerated in tumor tissues than in adjacent normal tissues. Across the thirteen cancer types, we showed that worse cancer survivals are associated with more accelerated mitotic age in tumor tissues. Importantly, we demonstrated the utility of mitotic age by showing that the integration of mitotic age and clinical information leads to an improved survival prediction in six out of the thirteen cancer types studied. The MiAge Calculator is available at http://www.columbia.edu/∼sw2206/softwares.htm.
DOI: 10.6084/m9.figshare.5620651.v1
title: Ranking Quality Measures for Adaptive Dataset Search

description: This repository contains performance measures of dataset ranking models.<br>- Usage: from Results/src run <i>Python results m<sub>1</sub> m<sub>2</sub> ...</i><br>such that <i>m<sub>i</sub></i> can be omitted, or be any element of the list of model labels ['bayesian-12C', 'bayesian-5L', 'bayesian-5L12C', 'cos-12C', 'cos-5L', 'cos-5L5C', 'j48-12C', 'j48-5L', 'j48-5L5C', 'jrip-12C', 'jrip-5L', 'jrip-5L5C', 'sn-12C', 'sn-5L', 'sn-5L12C']. Results of selected models will be plotted in a 2D line plot. If no model is provided all models will be listed.<br>
DOI: 10.17633/rd.brunel.5620561
title: A Segmented Anode Vacuum Phototriode with Position Sensitivity (Dataset)

description: Phototriode currents measured with Keithley 614 electrometer and Keithley 617 programmable electrometer
DOI: 10.17633/rd.brunel.5620561.v1
title: A Segmented Anode Vacuum Phototriode with Position Sensitivity (Dataset)

description: Phototriode currents measured with Keithley 614 electrometer and Keithley 617 programmable electrometer
DOI: 10.6084/m9.figshare.5620546
title: Cytochrome c oxidase subunit I variability in <i>Ruditapes decussatus</i> (Veneridae) from the western Mediterranean

description: <i>Ruditapes decussatus</i> (Linnaeus, 1758) (Veneridae) is an Atlanto-Mediterranean bivalve whose populations have experienced reductions and, in some instances, hybridisation with allochthonous <i>R. philippinarum</i>. Acquisition of additional genetic knowledge concerning the present <i>R. decussatus</i> populations is essential to address adequate conservation plans for this species. For this purpose, we analysed a portion of the mtDNA cytochrome c oxidase subunit I (COI) region in populations from the western Mediterranean, where this species represents a harvested fishery resource. Our analyses revealed an overall lack of genetic structure within the western Mediterranean area, and the occurrence of mtDNA substructuring between the Aegean and Marmara seas and the remaining populations from the whole Mediterranean basin and the South European Atlantic coast. The results obtained for populations from Sardinia, where extensive restocking programmes have not been reported and where <i>R. philippinarum</i> is rare and localised, suggest that intensive harvesting and potential dispersal alone may have been able to shape the genetic variation identified in the local <i>R. decussatus</i> populations.
DOI: 10.6084/m9.figshare.5620651.v2
title: Ranking Performance Measures for Adaptive Dataset Search

description: This repository contains performance measures of dataset ranking models.<br>- Usage: from Results/src run <i>Python results m<sub>1</sub> m<sub>2</sub> ...</i><br>such that <i>m<sub>i</sub></i> can be omitted, or be any element of the list of model labels ['bayesian-12C', 'bayesian-5L', 'bayesian-5L12C', 'cos-12C', 'cos-5L', 'cos-5L5C', 'j48-12C', 'j48-5L', 'j48-5L5C', 'jrip-12C', 'jrip-5L', 'jrip-5L5C', 'sn-12C', 'sn-5L', 'sn-5L12C']. Results of selected models will be plotted in a 2D line plot. If no model is provided all models will be listed.<br>
DOI: 10.6084/m9.figshare.5620546.v1
title: Cytochrome c oxidase subunit I variability in <i>Ruditapes decussatus</i> (Veneridae) from the western Mediterranean

description: <i>Ruditapes decussatus</i> (Linnaeus, 1758) (Veneridae) is an Atlanto-Mediterranean bivalve whose populations have experienced reductions and, in some instances, hybridisation with allochthonous <i>R. philippinarum</i>. Acquisition of additional genetic knowledge concerning the present <i>R. decussatus</i> populations is essential to address adequate conservation plans for this species. For this purpose, we analysed a portion of the mtDNA cytochrome c oxidase subunit I (COI) region in populations from the western Mediterranean, where this species represents a harvested fishery resource. Our analyses revealed an overall lack of genetic structure within the western Mediterranean area, and the occurrence of mtDNA substructuring between the Aegean and Marmara seas and the remaining populations from the whole Mediterranean basin and the South European Atlantic coast. The results obtained for populations from Sardinia, where extensive restocking programmes have not been reported and where <i>R. philippinarum</i> is rare and localised, suggest that intensive harvesting and potential dispersal alone may have been able to shape the genetic variation identified in the local <i>R. decussatus</i> populations.
DOI: 10.6084/m9.figshare.5620651.v3
title: Empirical Analysis of Ranking Models for an Adaptable Dataset Search

description: This repository contains performance measures of dataset ranking models.<br>- Usage: from Results/src run <i>Python results m<sub>1</sub> m<sub>2</sub> ...</i><br>such that <i>m<sub>i</sub></i> can be omitted, or be any element of the list of model labels ['bayesian-12C', 'bayesian-5L', 'bayesian-5L12C', 'cos-12C', 'cos-5L', 'cos-5L5C', 'j48-12C', 'j48-5L', 'j48-5L5C', 'jrip-12C', 'jrip-5L', 'jrip-5L5C', 'sn-12C', 'sn-5L', 'sn-5L12C']. Results of selected models will be plotted in a 2D line plot. If no model is provided all models will be listed.<br>
DOI: 10.6084/m9.figshare.5620513
title: The potential application of European market research data in dietary exposure modelling of food additives

description: Consumer exposure assessments for food additives are incomplete without information about the proportions of foods in each authorised category that contain the additive. Such information has been difficult to obtain but the Mintel Global New Products Database (GNPD) provides information about product launches across Europe over the past 20 years. These data can be searched to identify products with specific additives listed on product labels and the numbers compared with total product launches for food and drink categories in the same database to determine the frequency of occurrence. There are uncertainties associated with the data but these can be managed by adopting a cautious and conservative approach. GNPD data can be mapped with authorised food categories and with food descriptions used in the EFSA Comprehensive European Food Consumption Surveys Database for exposure modelling. The data, when presented as percent occurrence, could be incorporated into the EFSA ANS Panel’s ‘brand-loyal/non-brand loyal exposure model in a quantitative way. Case studies of preservative, antioxidant, colour and sweetener additives showed that the impact of including occurrence data is greatest in the non-brand loyal scenario. Recommendations for future research include identifying occurrence data for alcoholic beverages, linking regulatory food codes, FoodEx and GNPD product descriptions, developing the use of occurrence data for carry-over foods and improving understanding of brand loyalty in consumer exposure models.
DOI: 10.6084/m9.figshare.5620471
title: Population structure and patterns of geographic differentiation of <i>Bactrocera oleae</i> (Diptera: Tephritidae) in Eastern Mediterranean Basin

description: The olive fly (<i>Bactrocera oleae</i>) is the most destructive pest of olives in most commercial olive-growing regions worldwide. Significant economic damage to olive production is caused by the larvae of this fly, which feed on the pulp of <i>Olea</i> fruits. Studying the genetic structure of insect pest populations is essential for the success of pest management strategies. Our primary goal in the present study was to examine the population structures of olive flies collected over a wide geographic area from Turkey, a representative of eastern Mediterranean region, using two mitochondrial DNA sequences as genetic markers. The data revealed a high level of genetic variability in olive fly populations and a moderate level of genetic differentiation between Mediterranean and Aegean populations in Turkey. We also merged the sequences obtained in the present study with previously published sequences from across the world into the data matrix. Strong population substructure and a significant correlation between genetic and geographic distances were detected in northern Mediterranean basin populations of <i>B. oleae,</i> indicating the possibility of a westward expansion of the species in the continent. In addition, our results revealed a very close genetic relationship between the Aegean and Iranian populations, which suggests that <i>B. oleae</i> was introduced to Iran from western parts of Turkey. However, additional markers and analytical approaches are required to determine the exact colonization route of olive fly.
DOI: 10.6084/m9.figshare.5620492
title: Supplementary Material for: Interactive Effectiveness of Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers or Their Combination on Survival of Hemodialysis Patients

description: <b><i>Background:</i></b> Does the use of angiotensin-converting enzyme inhibitors and angiotensin receptor blockers individually or as a combination confer a survival benefit in hemodialysis patients? The answer to this question is yet unclear. <b><i>Methods:</i></b> We performed a case-cohort study using data from the Mineral and Bone Disorder Outcomes Study for Japanese CKD stage 5D patients (MBD-5D), a 3-year multicenter prospective case-cohort study, including 8,229 hemodialysis patients registered from 86 facilities in Japan. All patients had secondary hyperparathyroidism, a condition defined as a parathyroid hormone level ≥180 pg/mL and/or receiving vitamin D receptor activators. We compared all-cause mortality rates between those receiving ACEI, ARB, and their combination and non-users with interaction testing. We used marginal structural Poisson regression (causal model) to estimate the causal effect and interaction adjusted for possible time-dependent confounding. Cardiovascular mortality was also evaluated. <b><i>Results:</i></b> Among 3,762 randomly sampled subcohort patients, those taking ACEI, ARB, and their combination at baseline accounted for 4.0, 31.6, and 3.8%, respectively. Over 3 years, 1,226 all-cause and 462 cardiovascular deaths occurred. Compared to non-users, ARB-alone users had a lower all-cause mortality rate (adjusted incident rate ratio [aIRR] 0.62, 95% CI 0.50–0.76), whereas ACEI-alone users showed a statistically similar rate (aIRR 1.01, 95% CI 0.57–1.77). On the contrary, combination users had a greater mortality rate (aIRR 2.56, 95% CI 1.22–5.37), showing significant interaction (<i>p</i> = 0.03). Analysis for cardiovascular mortality showed similar results. <b><i>Conclusion:</i></b> Among hemodialysis patients with secondary hyperparathyroidism, unlike ACEI use, ARB use was associated with greater survival than non-use. Conversely, combination use was associated with greater mortality. Controlled trials are warranted to verify the causality factors of these associations.
DOI: 10.6084/m9.figshare.5620513.v2
title: The potential application of European market research data in dietary exposure modelling of food additives

description: Consumer exposure assessments for food additives are incomplete without information about the proportions of foods in each authorised category that contain the additive. Such information has been difficult to obtain but the Mintel Global New Products Database (GNPD) provides information about product launches across Europe over the past 20 years. These data can be searched to identify products with specific additives listed on product labels and the numbers compared with total product launches for food and drink categories in the same database to determine the frequency of occurrence. There are uncertainties associated with the data but these can be managed by adopting a cautious and conservative approach. GNPD data can be mapped with authorised food categories and with food descriptions used in the EFSA Comprehensive European Food Consumption Surveys Database for exposure modelling. The data, when presented as percent occurrence, could be incorporated into the EFSA ANS Panel’s ‘brand-loyal/non-brand loyal exposure model in a quantitative way. Case studies of preservative, antioxidant, colour and sweetener additives showed that the impact of including occurrence data is greatest in the non-brand loyal scenario. Recommendations for future research include identifying occurrence data for alcoholic beverages, linking regulatory food codes, FoodEx and GNPD product descriptions, developing the use of occurrence data for carry-over foods and improving understanding of brand loyalty in consumer exposure models.
DOI: 10.6084/m9.figshare.5620471.v1
title: Population structure and patterns of geographic differentiation of <i>Bactrocera oleae</i> (Diptera: Tephritidae) in Eastern Mediterranean Basin

description: The olive fly (<i>Bactrocera oleae</i>) is the most destructive pest of olives in most commercial olive-growing regions worldwide. Significant economic damage to olive production is caused by the larvae of this fly, which feed on the pulp of <i>Olea</i> fruits. Studying the genetic structure of insect pest populations is essential for the success of pest management strategies. Our primary goal in the present study was to examine the population structures of olive flies collected over a wide geographic area from Turkey, a representative of eastern Mediterranean region, using two mitochondrial DNA sequences as genetic markers. The data revealed a high level of genetic variability in olive fly populations and a moderate level of genetic differentiation between Mediterranean and Aegean populations in Turkey. We also merged the sequences obtained in the present study with previously published sequences from across the world into the data matrix. Strong population substructure and a significant correlation between genetic and geographic distances were detected in northern Mediterranean basin populations of <i>B. oleae,</i> indicating the possibility of a westward expansion of the species in the continent. In addition, our results revealed a very close genetic relationship between the Aegean and Iranian populations, which suggests that <i>B. oleae</i> was introduced to Iran from western parts of Turkey. However, additional markers and analytical approaches are required to determine the exact colonization route of olive fly.
DOI: 10.6084/m9.figshare.5620465
title: A realist explanatory theory-building case study

description: Mixed-methods data. Quantitative data is obtained from patient attendance record from the adherence club sessions. Qualitative data is based on in-depth interviews with clinicians and patients
DOI: 10.6084/m9.figshare.5620429
title: Endogenous oxytocin predicts helping and conversation as a function of group membership

description: Endogenous oxytocin predicts helping and conversation as a function of group membership
DOI: 10.6084/m9.figshare.5620417
title: Entity mention in articles used for benchmark

description: List of protein, disease, and compartment mentions per article
DOI: 10.6084/m9.figshare.5620429.v1
title: Endogenous oxytocin predicts helping and conversation as a function of group membership

description: Endogenous oxytocin predicts helping and conversation as a function of group membership
DOI: 10.6084/m9.figshare.5620414
title: Grouping of CoMPARA data with respect to compounds from the carcinogenic potency database<sup>$</sup>

description: Methods for clustering and measures of similarity of chemical structures have become an important supporting tool in chemoinformatics. They represent the basis for categorization of chemicals and read-across, where a molecular property is estimated from ‘similar molecules’. This study proposes a clustering scheme within the given dataset with respect to a reference dataset. The scheme was applied on two datasets ToxCast_AR_Agonist and ToxCast_AR_Antagonists with 1654 and 1522 compounds, respectively. The compounds are tested to androgen receptor activity (AR) in 11 high throughput screening assays. The carcinogenic dataset was used as the reference set.
DOI: 10.6084/m9.figshare.5620414.v1
title: Grouping of CoMPARA data with respect to compounds from the carcinogenic potency database<sup>$</sup>

description: Methods for clustering and measures of similarity of chemical structures have become an important supporting tool in chemoinformatics. They represent the basis for categorization of chemicals and read-across, where a molecular property is estimated from ‘similar molecules’. This study proposes a clustering scheme within the given dataset with respect to a reference dataset. The scheme was applied on two datasets ToxCast_AR_Agonist and ToxCast_AR_Antagonists with 1654 and 1522 compounds, respectively. The compounds are tested to androgen receptor activity (AR) in 11 high throughput screening assays. The carcinogenic dataset was used as the reference set.
DOI: 10.6084/m9.figshare.5620396
title: THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy

description: Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos.biocuckoo.org), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of <i>ATG</i> genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.