cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12852897.v1
title: DNA methylation age estimation from human bone and teeth

description: Bones and teeth are valuable sources of information in forensic contexts. However, few studies have considered these tissues for DNA methylation (DNAm) analyses in age estimation. The main goal of the present study was to develop DNAm-based age prediction models (APMs) specific for bones and teeth. DNA samples from Portuguese individuals were evaluated through bisulphite Sanger sequencing and a multiplex SNaPshot assay to analyse relationships between DNAm and age. In bones our results allowed to build a final APM through Sanger sequencing with six CpGs at genes <i>ELOVL2, EDARADD</i> and <i>MIR29B2C</i>, explaining 92.5% of age variation, with a mean absolute deviation (MAD) from chronological age of 2.56 years. For teeth, we were unable to build a final multi-locus APM; the best <i>FHL2</i> CpG4 age predictor explained 41.3% of age variance with a MAD of 11.35 years. The SNaPshot assay allowed to build two final dual-locus APMs with CpGs at <i>FHL2</i> and <i>KLF14</i> for bones, explaining 57.6% of age variation (MAD of 7.18 years), and with CpGs at <i>ELOVL2</i> and <i>KLF14</i> for teeth, explaining 76.4% of age variation (MAD of 7.07 years). Our study showed the usefulness of bone and tooth samples in evaluation of DNAm levels for age estimation purposes.
DOI: 10.6084/m9.figshare.12852897
title: DNA methylation age estimation from human bone and teeth

description: Bones and teeth are valuable sources of information in forensic contexts. However, few studies have considered these tissues for DNA methylation (DNAm) analyses in age estimation. The main goal of the present study was to develop DNAm-based age prediction models (APMs) specific for bones and teeth. DNA samples from Portuguese individuals were evaluated through bisulphite Sanger sequencing and a multiplex SNaPshot assay to analyse relationships between DNAm and age. In bones our results allowed to build a final APM through Sanger sequencing with six CpGs at genes <i>ELOVL2, EDARADD</i> and <i>MIR29B2C</i>, explaining 92.5% of age variation, with a mean absolute deviation (MAD) from chronological age of 2.56 years. For teeth, we were unable to build a final multi-locus APM; the best <i>FHL2</i> CpG4 age predictor explained 41.3% of age variance with a MAD of 11.35 years. The SNaPshot assay allowed to build two final dual-locus APMs with CpGs at <i>FHL2</i> and <i>KLF14</i> for bones, explaining 57.6% of age variation (MAD of 7.18 years), and with CpGs at <i>ELOVL2</i> and <i>KLF14</i> for teeth, explaining 76.4% of age variation (MAD of 7.07 years). Our study showed the usefulness of bone and tooth samples in evaluation of DNAm levels for age estimation purposes.
DOI: 10.6084/m9.figshare.12852894
title: Dental parameter quantification with semi-automatized computational technology for the analysis of human bitemarks

description: The study objective was to determine dental parameters that characterize human bitemarks and dentitions for biter identification using semi-automatized technology. Sixty-five dental casts and eighteen bitemark photographs were used. Casts were scanned by a 3D laser scanner to generate comparison overlays, and bitemarks were digitally photographed following ABFO guidelines. A semi-automatized technique was used to calculate the inter-canine distance, rotation, eccentricity, angular position, and distance to the arch of each tooth mark. A matrix was created of all possible combinations of dental casts and bitemarks. Receiver operating characteristic (ROC) curves were constructed to evaluate the accuracy of this identification procedure. Among the 1045 comparisons performed, the highest area under the ROC curve (AUC) was obtained for the Euclidean distance of lower teeth rotation (AUC = 0.73). This semi-automatized method to measure lower tooth rotation may be useful to identify individuals responsible for bitemarks and may be applicable in forensic cases.
DOI: 10.6084/m9.figshare.14399548.v1
title: DNA mixture interpretation using linear regression and neural networks on massively parallel sequencing data of single nucleotide polymorphisms

description: Massively parallel sequencing (MPS) enables concurrent analysis of multiple single nucleotide polymorphisms (SNPs) and detection of alleles from minor contributors to extremely imbalanced DNA mixtures. To interpret the complex MPS data obtained from DNA mixtures, EuroForMix, linear regression, and neural network models were employed. Data of 960 autosomal SNPs sequenced through MPS of 10 single-source DNA samples, 26 nondegraded DNA mixtures from nonrelative (mixture ratio 1:29–1:99), 16 nondegraded DNA mixtures from relatives (1:29–1:99), 8 degraded DNA mixtures from nonrelatives (1:29–1:99), and 16 degraded DNA mixtures of relatives (1:29–1:99) were analysed. In total, 89.4% (59/66), 93.9% (62/66), and 93.9% (62/66) of the minor contributors to DNA mixtures could be correctly inferred using EuroForMix, linear regression, and a neural network, respectively. In conclusion, the linear regression and neural network models outperformed EuroForMix in determining the minor contributor to DNA mixtures from MPS data.
DOI: 10.6084/m9.figshare.12852885
title: Sex estimation in a modern Turkish population using the clavicle: a computed tomography study

description: Morphometric analysis of the clavicle is a potential source of useful data for the estimation of sex. Clavicle is often retrieved intact from decomposed and scavenged remains when pelvis and skull, essential sex indicators, are often found damaged or missing. The objective of this study is to analyse clavicle morphometric data for sex estimation in a Turkish population. Computed tomography (CT) scans of the thorax of two hundred Turkish adult patients (71 male and 81 female patients with an age range of 22–80 years) were included. Furthermore, morphometric data for the left clavicle using two-dimensional (2D) and three-dimensional (3D) clavicle CT images were obtained, and six variables were measured in the clavicle images. Univariate and multivariate discriminant function analysis (DFA) was used to create population-specific functions for sex estimation. The classification accuracy for the cross-validated data ranged from 75% to 89% in the uni- and multivariate DFA. Stepwise discrimination analysis yielded an 89% accuracy rate for the maximum length and midshaft circumference variables. The study showed that the clavicle can provide useful data for estimating sex in a modern Turkish population and that when there is difficulty accessing bone collections, CT scans can provide useful data for sex estimation.
DOI: 10.6084/m9.figshare.12852894.v1
title: Dental parameter quantification with semi-automatized computational technology for the analysis of human bitemarks

description: The study objective was to determine dental parameters that characterize human bitemarks and dentitions for biter identification using semi-automatized technology. Sixty-five dental casts and eighteen bitemark photographs were used. Casts were scanned by a 3D laser scanner to generate comparison overlays, and bitemarks were digitally photographed following ABFO guidelines. A semi-automatized technique was used to calculate the inter-canine distance, rotation, eccentricity, angular position, and distance to the arch of each tooth mark. A matrix was created of all possible combinations of dental casts and bitemarks. Receiver operating characteristic (ROC) curves were constructed to evaluate the accuracy of this identification procedure. Among the 1045 comparisons performed, the highest area under the ROC curve (AUC) was obtained for the Euclidean distance of lower teeth rotation (AUC = 0.73). This semi-automatized method to measure lower tooth rotation may be useful to identify individuals responsible for bitemarks and may be applicable in forensic cases.
DOI: 10.6084/m9.figshare.14399548
title: DNA mixture interpretation using linear regression and neural networks on massively parallel sequencing data of single nucleotide polymorphisms

description: Massively parallel sequencing (MPS) enables concurrent analysis of multiple single nucleotide polymorphisms (SNPs) and detection of alleles from minor contributors to extremely imbalanced DNA mixtures. To interpret the complex MPS data obtained from DNA mixtures, EuroForMix, linear regression, and neural network models were employed. Data of 960 autosomal SNPs sequenced through MPS of 10 single-source DNA samples, 26 nondegraded DNA mixtures from nonrelative (mixture ratio 1:29–1:99), 16 nondegraded DNA mixtures from relatives (1:29–1:99), 8 degraded DNA mixtures from nonrelatives (1:29–1:99), and 16 degraded DNA mixtures of relatives (1:29–1:99) were analysed. In total, 89.4% (59/66), 93.9% (62/66), and 93.9% (62/66) of the minor contributors to DNA mixtures could be correctly inferred using EuroForMix, linear regression, and a neural network, respectively. In conclusion, the linear regression and neural network models outperformed EuroForMix in determining the minor contributor to DNA mixtures from MPS data.
DOI: 10.6084/m9.figshare.12852885.v2
title: Sex estimation in a modern Turkish population using the clavicle: a computed tomography study

description: Morphometric analysis of the clavicle is a potential source of useful data for the estimation of sex. Clavicle is often retrieved intact from decomposed and scavenged remains when pelvis and skull, essential sex indicators, are often found damaged or missing. The objective of this study is to analyse clavicle morphometric data for sex estimation in a Turkish population. Computed tomography (CT) scans of the thorax of two hundred Turkish adult patients (71 male and 81 female patients with an age range of 22–80 years) were included. Furthermore, morphometric data for the left clavicle using two-dimensional (2D) and three-dimensional (3D) clavicle CT images were obtained, and six variables were measured in the clavicle images. Univariate and multivariate discriminant function analysis (DFA) was used to create population-specific functions for sex estimation. The classification accuracy for the cross-validated data ranged from 75% to 89% in the uni- and multivariate DFA. Stepwise discrimination analysis yielded an 89% accuracy rate for the maximum length and midshaft circumference variables. The study showed that the clavicle can provide useful data for estimating sex in a modern Turkish population and that when there is difficulty accessing bone collections, CT scans can provide useful data for sex estimation.
DOI: 10.6084/m9.figshare.12852885.v1
title: Sex estimation in a modern Turkish population using the clavicle: a computed tomography study

description: Morphometric analysis of the clavicle is a potential source of useful data for the estimation of sex. Clavicle is often retrieved intact from decomposed and scavenged remains when pelvis and skull, essential sex indicators, are often found damaged or missing. The objective of this study is to analyse clavicle morphometric data for sex estimation in a Turkish population. Computed tomography (CT) scans of the thorax of two hundred Turkish adult patients (71 male and 81 female patients with an age range of 22–80 years) were included. Furthermore, morphometric data for the left clavicle using two-dimensional (2D) and three-dimensional (3D) clavicle CT images were obtained, and six variables were measured in the clavicle images. Univariate and multivariate discriminant function analysis (DFA) was used to create population-specific functions for sex estimation. The classification accuracy for the cross-validated data ranged from 75% to 89% in the uni- and multivariate DFA. Stepwise discrimination analysis yielded an 89% accuracy rate for the maximum length and midshaft circumference variables. The study showed that the clavicle can provide useful data for estimating sex in a modern Turkish population and that when there is difficulty accessing bone collections, CT scans can provide useful data for sex estimation.
DOI: 10.5281/zenodo.6302747
title: A list of items in the FAIRsFAIR training library

description: A file containing a list of items, with basic metadata, that were included in the FAIRsFAIR training library
DOI: 10.5281/zenodo.6302746
title: A list of items in the FAIRsFAIR training library

description: A file containing a list of items, with basic metadata, that were included in the FAIRsFAIR training library
DOI: 10.6084/m9.figshare.19360997.v1
title: Supplementary Material for: Minimal Critical Region and Genes for a Typical Presentation of Langer-Giedion Syndrome

description: Langer-Giedion syndrome (LGS) is caused by a contiguous deletion at 8q23q24, characterized by exostoses, facial, ectodermal, and skeletal anomalies, and, occasionally, intellectual disability. LGS patients have been diagnosed clinically or by routine cytogenetic techniques, hampering the definition of an accurate genotype-phenotype correlation for the syndrome. We report two unrelated patients with 8q23q24 deletions, characterized by cytogenomic techniques, with one of them, to our knowledge, carrying the smallest deletion reported in classic LGS cases. We assessed the pathogenicity of the deletion of genes within the 8q23q24 region and reviewed other molecularly confirmed cases from the literature. Our findings suggest a 3.2-Mb critical region for a typical presentation of the syndrome, emphasizing the contribution of the <i>TRPS1</i>, <i>RAD21</i>, and <i>EXT1</i> genes’ haploinsufficiency, and facial dysmorphisms as well as bone anomalies as the most frequent features among patients with LGS. We also suggest a possible role for the <i>CSMD3</i> gene, whose deletion seems to contribute to central nervous system anomalies. Since studies performing such correlation for LGS patients are limited, our data contribute to improving the ge­notype-phenotype characterization for LGS patients.
DOI: 10.6084/m9.figshare.19360997
title: Supplementary Material for: Minimal Critical Region and Genes for a Typical Presentation of Langer-Giedion Syndrome

description: Langer-Giedion syndrome (LGS) is caused by a contiguous deletion at 8q23q24, characterized by exostoses, facial, ectodermal, and skeletal anomalies, and, occasionally, intellectual disability. LGS patients have been diagnosed clinically or by routine cytogenetic techniques, hampering the definition of an accurate genotype-phenotype correlation for the syndrome. We report two unrelated patients with 8q23q24 deletions, characterized by cytogenomic techniques, with one of them, to our knowledge, carrying the smallest deletion reported in classic LGS cases. We assessed the pathogenicity of the deletion of genes within the 8q23q24 region and reviewed other molecularly confirmed cases from the literature. Our findings suggest a 3.2-Mb critical region for a typical presentation of the syndrome, emphasizing the contribution of the <i>TRPS1</i>, <i>RAD21</i>, and <i>EXT1</i> genes’ haploinsufficiency, and facial dysmorphisms as well as bone anomalies as the most frequent features among patients with LGS. We also suggest a possible role for the <i>CSMD3</i> gene, whose deletion seems to contribute to central nervous system anomalies. Since studies performing such correlation for LGS patients are limited, our data contribute to improving the ge­notype-phenotype characterization for LGS patients.
DOI: 10.6084/m9.figshare.19328747
title: Data - MiRuFre

description: This file contains raw EMG data as used in the study: "Spectral Properties Of Physiological Mirror Activity: An Investigation of Frequency Features and Common Input Between Homologous Muscles".
DOI: 10.25835/vbt7jnto
title: phenomenographic evaluation data
DOI: 10.18120/x3ma-3c33
title: RNS System LGS Feasibility Study
DOI: 10.5517/ccdc.csd.cc28j0kd
title: CCDC 2100763: Experimental Crystal Structure Determination

description: Related Article: Xiang Li, Qing Zhao, Yang Shen, Ran Ma|2022|J.Org.Chem.|87|3468|doi:10.1021/acs.joc.1c03042
DOI: 10.5285/d4bb3df8-6f62-462c-8aa5-6b9867e2e5ae
title: Temperature Maps of the British Coalfields

description: This dataset provides the first map and synthesis of the temperature of Britain's coalfields. It was created to support low-temperature heat recovery, cooling and storage schemes using mine water in abandoned workings. This baseline spatial mapping and synthesis of coalfield temperatures offers significant benefit to those planning, designing and regulating heat recovery and storage in Britain's abandoned coalfields. The data has been developed jointly by the Coal Authority and the British Geological Survey. It is delivered as a hexgrid representing mine water blocks, identifying equilibrium mine temperatures at 10 depth intervals (100m > 1000m) and pumped mine temperatures at 6 depth intervals (100m > 600m). The methodology is described in full in an open access paper Farr et al (2020) – https://doi.org/10.1144/qjegh2020-109
DOI: 10.6084/m9.figshare.19360991
title: Talent Evaluation and Career Guidance

description: Research data for publication
DOI: 10.25502/1pkd-q979/d
title: 2017 Male and Female D. Rotundata Crossing blocks (Yam Anthracnose  Disease and Virus severity)

description: Enhanced breeding for increased productivity and improved quality in West Africa
DOI: 10.6084/m9.figshare.14936052.v5
title: Maps of cropping patterns in China during 2015-2020

description: Here we present the first annual 500-m maps of multiple cropping systems in china at national scale during 2015 to 2020,which provide information on cropping intensity with descriptions of three staple crops (Maize,paddy rice and wheat). We produced the cropping patterns maps by developing phenological metrics, which can be applied to national scale.
DOI: 10.34740/kaggle/dsv/3303174
title: AutoXGB
DOI: 10.5281/zenodo.6355492
title: CUESTIONARIO PROFESIONALES

description: CUESTIONARIO-HERRAMIENTA UTILIZADA PARA INVESTIGACIÓN
DOI: 10.5281/zenodo.6355491
title: CUESTIONARIO PROFESIONALES

description: CUESTIONARIO-HERRAMIENTA UTILIZADA PARA INVESTIGACIÓN
DOI: 10.6084/m9.figshare.14724879
title: Visualising post-disaster damage on maps: a user study

description: The mapping of the damage caused by natural disasters is a crucial step in deciding on the actions to take at the international, national, and local levels. The large variety of representations that we have observed leads to problems of transfer and variations in analysis. In this article, we propose a representation, Regular Dot map (<i>RD</i>), and we compare it to 4 others routinely used to visualise post-disaster damage. Our comparison is based on a user study in which a set of participants carried out various tasks on multiple datasets using the various visualisations. We then analysed the behaviour during the experiment using three approaches: (1) quantitative analysis of user answers according to the reality on the ground, (2) quantitative analysis of user preferences in terms of perceived effectiveness and appearance, and (3) qualitative analysis of the data collected using an eye tracker. The results of this study lead us to believe that <i>RD</i> is the best compromise in terms of effectiveness among the various representations studied.
DOI: 10.6084/m9.figshare.14724879.v1
title: Code_and_data.rar

description: The mapping of the damage caused by natural disasters is a crucial step in deciding on the actions to take at the international, national, and local levels. The large variety of representations that we have observed leads to problems of transfer and variations in analysis. In this article, we propose a representation, Regular Dot map (<i>RD</i>), and we compare it to 4 others routinely used to visualise post-disaster damage. Our comparison is based on a user study in which a set of participants carried out various tasks on multiple datasets using the various visualisations. We then analysed the behaviour during the experiment using three approaches: (1) quantitative analysis of user answers according to the reality on the ground, (2) quantitative analysis of user preferences in terms of perceived effectiveness and appearance, and (3) qualitative analysis of the data collected using an eye tracker. The results of this study lead us to believe that <i>RD</i> is the best compromise in terms of effectiveness among the various representations studied.
DOI: 10.48370/ofd/q2oj56/dsvlvd
title: 4553_1.S3Dm

description: :unav
DOI: 10.6084/m9.figshare.19361078
title: Supplementary Material for: Pathogenic Variants in <i>MAP3K1</i> Cause 46,XY Gonadal Dysgenesis: A Review

description: Pathogenic variants in the <i>MAP3K1</i> gene are an important cause of 46,XY non-syndromic partial and complete gonadal dysgenesis, accounting for at least 4% of cases. Inheritance occurs in a sex-limited, autosomal dominant fashion with virtually complete penetrance in 46,XY individuals. 46,XX carriers appear to have normal fertility and no developmental abnormalities. Pathogenic variants occur almost exclusively within known domains of the MAP3K1 protein, facilitating annotation when identified. Where studied, these variants have been modeled to alter the local MAP3K1 folding and surface domains and have been shown to alter interactions with known binding partners. The net effect of these variants is to increase phosphorylation of downstream targets ERK1, ERK2, and p38, resulting in multiple gain-of-function effects interfering with testis determination and enabling ovarian determination.
DOI: 10.6084/m9.figshare.19361078.v1
title: Supplementary Material for: Pathogenic Variants in <i>MAP3K1</i> Cause 46,XY Gonadal Dysgenesis: A Review

description: Pathogenic variants in the <i>MAP3K1</i> gene are an important cause of 46,XY non-syndromic partial and complete gonadal dysgenesis, accounting for at least 4% of cases. Inheritance occurs in a sex-limited, autosomal dominant fashion with virtually complete penetrance in 46,XY individuals. 46,XX carriers appear to have normal fertility and no developmental abnormalities. Pathogenic variants occur almost exclusively within known domains of the MAP3K1 protein, facilitating annotation when identified. Where studied, these variants have been modeled to alter the local MAP3K1 folding and surface domains and have been shown to alter interactions with known binding partners. The net effect of these variants is to increase phosphorylation of downstream targets ERK1, ERK2, and p38, resulting in multiple gain-of-function effects interfering with testis determination and enabling ovarian determination.
DOI: 10.5281/zenodo.6355501
title: Developing an in-depth understanding of the prevalence, risk factors and treatment recommendations for phantom limb pain, and patient-generated care priorities for people who have undergone lower limb amputations.

description: The file holds data collected for a series of four studies on phantom limb pain.
DOI: 10.5281/zenodo.6355529
title: SciExpeM - 10.5281/zenodo.6355529

description: Cancino, L. R.; Fikri, M.; Oliveira, A. A. M.; Schulz, C. - Energy & Fuels, 2010, (24), 2830-2840
DOI: 10.5281/zenodo.6355500
title: Developing an in-depth understanding of the prevalence, risk factors and treatment recommendations for phantom limb pain, and patient-generated care priorities for people who have undergone lower limb amputations.

description: The file holds data collected for a series of four studies on phantom limb pain.
DOI: 10.5281/zenodo.6355528
title: SciExpeM - 10.5281/zenodo.6355529

description: Cancino, L. R.; Fikri, M.; Oliveira, A. A. M.; Schulz, C. - Energy & Fuels, 2010, (24), 2830-2840
DOI: 10.34967/i9912
title: 20182174

description: Preliminary study in order to establish the suitability of the instrumental method