cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5640889
title: Supplementary Table 2. Genotyped descendants of HJ

description: We provide a table, which maps the descendants as shown in HJ’s genealogy (Fig.1) to identifiers used throughout in the paper. We assign consecutive numbers to individuals in Fig. 1 starting from one, from top to bottom and left to right (breadth-first traversal of the genealogical tree). The identifiers of genotyped descendants along with their numbering order is listed in this table.
DOI: 10.6084/m9.figshare.5640889.v1
title: Supplementary Table 2. Genotyped descendants of HJ

description: We provide a table, which maps the descendants as shown in HJ’s genealogy (Fig.1) to identifiers used throughout in the paper. We assign consecutive numbers to individuals in Fig. 1 starting from one, from top to bottom and left to right (breadth-first traversal of the genealogical tree). The identifiers of genotyped descendants along with their numbering order is listed in this table.
DOI: 10.6084/m9.figshare.5640883
title: Helios proton core parameter dataset

description: This is the Helios corefit data product. This is a new (as of 2017) data set which contains estimates of number density, velocity, and temperatures of the proton core population in the solar wind created from systematic fitting of all the original Helios 3D distribution functions.
DOI: 10.6084/m9.figshare.5640868
title: Supplementary Table 3. Filtering HAPMIX inferred African fragments

description: African fragments inferred in HJ descendants by HAPMIX in haploid mode. Each putative African fragment is listed with information about the parent of origin, represented as “P” for paternal and “M” for maternal, and the breakpoints in physical positions and centi-Morgans (cM).When an ancestor on the path to HJ is also genotyped (GA), the following information is also provided for the most recent GA. First, whether the fragment is present in the GA (and if present, its parental origin in the GA) (ii). Second, whether the fragment is also identified as African in the GA. Third, the expected parent of origin in the GA. Two additional variables indicate whether a fragment is inherited from the correct parent of origin and is consistent with the genealogy (when GA is present). The number of genotyped Icelanders who are not descendants of HJ, but completely share the fragment, is also given (out of a total of 150,832).
DOI: 10.6084/m9.figshare.5640868.v1
title: Supplementary Table 3. Filtering HAPMIX inferred African fragments

description: African fragments inferred in HJ descendants by HAPMIX in haploid mode. Each putative African fragment is listed with information about the parent of origin, represented as “P” for paternal and “M” for maternal, and the breakpoints in physical positions and centi-Morgans (cM).When an ancestor on the path to HJ is also genotyped (GA), the following information is also provided for the most recent GA. First, whether the fragment is present in the GA (and if present, its parental origin in the GA) (ii). Second, whether the fragment is also identified as African in the GA. Third, the expected parent of origin in the GA. Two additional variables indicate whether a fragment is inherited from the correct parent of origin and is consistent with the genealogy (when GA is present). The number of genotyped Icelanders who are not descendants of HJ, but completely share the fragment, is also given (out of a total of 150,832).
DOI: 10.6084/m9.figshare.5640865
title: Supplementary Table 4. Comparison of Ancestry methods

description: We ran HAPMIX and LAMP-LD with 1000G phase 3 haplotypes. The European source panel consisted of 503 samples from British From England and Scotland [GBR], Toscani in Italia [TSI], Iberian Populations in Spain [IBS], Finnish in Finland [FIN] , and CEPH (U.S. Utah residents with ancestry from northern and western Europe) [CEU]. The African source panel consisted of 504 samples from Esan in Nigeria [ESN], Gambian in Western Division – Mandinka [GWD], Luhya in Webuye, Kenya [LWK], Mende in Sierra Leone [MSL] and Yoruba in Ibadan, Nigeria [YRI]. We retrieved phased alleles for 1,343,587 markers. We also ran LAMP-LD with only CEU and YRI populations. We applied the same filtering criteria to all the three analysis as described in the paper and the compared them.
DOI: 10.6084/m9.figshare.5640859
title: Supplementary Table 5. Analysis of overlapping fragments pairs

description: We examined all pairs of overlapping fragments, which had been previously filtered based on sharing, parental origin and genealogy (Table 1) to evaluate allelic consistency. The intersecting region in each pair was assessed for discrepancies, which led to the trimming of ends or removal of fragments in some instances (see Methods). We list the average number of discrepant positions, where we observe more than one allele, per Mb (Mismatch per Mb), for each chromosome prior and post trimming/removal of fragments.
DOI: 10.6084/m9.figshare.5640859.v1
title: Supplementary Table 5. Analysis of overlapping fragments pairs

description: We examined all pairs of overlapping fragments, which had been previously filtered based on sharing, parental origin and genealogy (Table 1) to evaluate allelic consistency. The intersecting region in each pair was assessed for discrepancies, which led to the trimming of ends or removal of fragments in some instances (see Methods). We list the average number of discrepant positions, where we observe more than one allele, per Mb (Mismatch per Mb), for each chromosome prior and post trimming/removal of fragments.
DOI: 10.6084/m9.figshare.5640853
title: Supplementary Table 6. Assembled African fragments from chip data

description: The reconstructed haploid genome of HJ was assembled from 593 trimmed and filtered African fragments inferred from his 182 genotyped descendants. Overlapping fragments were combined into 48 assembled fragments listed in this table. The total number of SNP loci and remaining discrepant loci within assembled fragments is given below.
DOI: 10.6084/m9.figshare.5640853.v1
title: Supplementary Table 6. Assembled African fragments from chip data

description: The reconstructed haploid genome of HJ was assembled from 593 trimmed and filtered African fragments inferred from his 182 genotyped descendants. Overlapping fragments were combined into 48 assembled fragments listed in this table. The total number of SNP loci and remaining discrepant loci within assembled fragments is given below.
DOI: 10.6084/m9.figshare.5640850
title: Supplementary Table 7. WGS data

description: Among the 182 descendants, 20 of them had been whole genome sequenced, aligned and mapped to NCBI Build 38 of the human genome. The mean and standard deviation (SD) for the number of reads per position (sequence depth) are given for each of them, along with the number of autosomal positions covered by mapped reads.
DOI: 10.6084/m9.figshare.5640850.v1
title: Supplementary Table 7. WGS data

description: Among the 182 descendants, 20 of them had been whole genome sequenced, aligned and mapped to NCBI Build 38 of the human genome. The mean and standard deviation (SD) for the number of reads per position (sequence depth) are given for each of them, along with the number of autosomal positions covered by mapped reads.
DOI: 10.6084/m9.figshare.5640832
title: Supplementary Table 8. Estimation of imputation error rate

description: The imputed SNPs in the long-range phasing step was compared against the SNPs called from the sequencing data. We excluded SNPs where we found missing alleles
DOI: 10.6084/m9.figshare.5640832.v1
title: Supplementary Table 8. Estimation of imputation error rate

description: The imputed SNPs in the long-range phasing step was compared against the SNPs called from the sequencing data. We excluded SNPs where we found missing alleles
DOI: 10.6084/m9.figshare.5640826
title: Supplementary Table 9. HJ singletons in descendants with WGS data

description: African fragments inferred by HAPMIX in the haploid mode in the 20 HJ descendants with WGS data. We list start and stop positions of each African fragment found in these HJ descendants and the number of so-called HJ singletons, i.e. alleles present in one or more of the 20 HJ descendants with WGS data but absent from the other 13,882 Icelanders with WGS data. For each fragment, we also report the mean and standard deviation of HJ singletons for non-African fragments between the same start and stop positions from the 20 HJ descendants with WGS data.
DOI: 10.6084/m9.figshare.5640826.v1
title: Supplementary Table 9. HJ singletons in descendants with WGS data

description: African fragments inferred by HAPMIX in the haploid mode in the 20 HJ descendants with WGS data. We list start and stop positions of each African fragment found in these HJ descendants and the number of so-called HJ singletons, i.e. alleles present in one or more of the 20 HJ descendants with WGS data but absent from the other 13,882 Icelanders with WGS data. For each fragment, we also report the mean and standard deviation of HJ singletons for non-African fragments between the same start and stop positions from the 20 HJ descendants with WGS data.
DOI: 10.6084/m9.figshare.5640805
title: Supplementary Table 10. Assembled African fragments from WGS data

description: We considered contributing fragments from descendants who had been chiptyped as well as sequenced (20 of 182). Genotype calling and phasing of genotypes from sequence data for these twenty individuals had been carried out along with other Icelanders sequenced at the time. We evaluated allelic consistency at these polymorphic positions (SNPs) where two or more sequenced descendants carry fragments derived from HJ.
DOI: 10.6084/m9.figshare.5640805.v1
title: Supplementary Table 10. Assembled African fragments from WGS data

description: We considered contributing fragments from descendants who had been chiptyped as well as sequenced (20 of 182). Genotype calling and phasing of genotypes from sequence data for these twenty individuals had been carried out along with other Icelanders sequenced at the time. We evaluated allelic consistency at these polymorphic positions (SNPs) where two or more sequenced descendants carry fragments derived from HJ.
DOI: 10.6084/m9.figshare.5640796
title: Supplementary Table 11. Reference populations

description: The different African microarray SNP datasets used as reference populations to determine the origin of HJ’s haploid African genome. Individuals with &gt; 2% missing genotypes (Illumina platform), &gt; 5% missing genotypes (Affymetrix platform) or with substantial amounts of recent European or Asian ancestry were excluded from the analysis.
DOI: 10.6084/m9.figshare.5640796.v1
title: Supplementary Table 11. Reference populations

description: The different African microarray SNP datasets used as reference populations to determine the origin of HJ’s haploid African genome. Individuals with &gt; 2% missing genotypes (Illumina platform), &gt; 5% missing genotypes (Affymetrix platform) or with substantial amounts of recent European or Asian ancestry were excluded from the analysis.
DOI: 10.5281/zenodo.3904302
title: On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation

description: This repository contains XML configuration files, POS and EPOS reconstructed APT datasets and RNG/RRNG range files, raw data, and synthetic dataset to follow our analysis made in the initial version of the paper <em>"On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation"</em> We are continuously working on the atom probe crystallography tools of paraprobe and their corresponding configuration and analysis wizards in paraprobe-parmsetup and paraprobe-autoreporter. Also, we are currently working on an ontology for metadata of APT post-processing workflows. Therefore, changes in the structure of the HDF5 file are expected to come up.<br> <br> Therefore, we always recommend to work with the newest code of PARAPROBE on the GitLab: <strong>https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe.git<br> https://paraprobe-toolbox.readthedocs.io/en/latest/</strong> Therefore, the data in here serve as a reference to and documentation of the settings mainly. <strong>This repository here contains the following pieces of information:</strong> <strong>VerifyCrystalStructures_Geo26Al.zip<br> VerifyCrystalStructures_Geo26Al3Sc.zip<br> VerifyCrystalStructures_Geo26W.zip</strong><br> Raw data and results for the assessment of the histograms and SDMs and corresponding amplitude spectra. <strong>VerifySXIndexing.zip</strong><br> Raw data and results for the verification with synthetic single crystal datasets. <strong>VerifyPXIndexing2_SimID.200.tar.gz<br> VerifyPXIndexing2_SimID.201.tar.gz<br> VerifyPXIndexing2_SimID.202.tar.gz</strong><br> Raw data and results for the verification with synthetic polycrystal datasets,<br> where 200 is without noise, 201 low noise, 202 high noise. <strong>VerifyAlBicrystalZirong_ExampleROIs.tar.gz<br> VerifyAlBicrystalZirong_Library.tar.gz</strong><br> <strong>VerifyAlBicrystalZirong_Setup.tar.gz<br> VerifyAlBicrystalZirongRendering.zip</strong><br> Raw data and results for specific ROIs discussed for the aluminium bicrystal including Paraview example for rendering. <strong>VerifyAlLiMgBaptiste_ExampleROIs.tar.gz<br> VerifyAlLiMgBaptiste_Library.tar.gz<br> VerifyAlLiMgBaptiste_Setup.tar.gz<br> VerifyAlLiMgBaptisteRendering.zip</strong><br> Raw data and results for specific ROIs discussed for the aluminium bicrystal including Paraview example for rendering. <strong>AlBicrystalAdaptiveROIGrid.tar.gz<br> AlLiMgAgAdaptiveROIGrid.tar.gz</strong><br> Raw data and results for the tutorial with adaptive refinement of the ROI grid, as it is detailed in the Jupyter notebook tutorials on the GitLab repository.
DOI: 10.5281/zenodo.3904301
title: On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation

description: This repository contains XML configuration files, POS and EPOS reconstructed APT datasets and RNG/RRNG range files, raw data, and synthetic dataset to follow our analysis made in the initial version of the paper <em>"On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation"</em> We are continuously working on the atom probe crystallography tools of paraprobe and their corresponding configuration and analysis wizards in paraprobe-parmsetup and paraprobe-autoreporter. Also, we are currently working on an ontology for metadata of APT post-processing workflows. Therefore, changes in the structure of the HDF5 file are expected to come up.<br> <br> Therefore, we always recommend to work with the newest code of PARAPROBE on the GitLab: <strong>https://gitlab.mpcdf.mpg.de/mpie-aptfim-toolbox/paraprobe.git<br> https://paraprobe-toolbox.readthedocs.io/en/latest/</strong> Therefore, the data in here serve as a reference to and documentation of the settings mainly. <strong>This repository here contains the following pieces of information:</strong> <strong>VerifyCrystalStructures_Geo26Al.zip<br> VerifyCrystalStructures_Geo26Al3Sc.zip<br> VerifyCrystalStructures_Geo26W.zip</strong><br> Raw data and results for the assessment of the histograms and SDMs and corresponding amplitude spectra. <strong>VerifySXIndexing.zip</strong><br> Raw data and results for the verification with synthetic single crystal datasets. <strong>VerifyPXIndexing2_SimID.200.tar.gz<br> VerifyPXIndexing2_SimID.201.tar.gz<br> VerifyPXIndexing2_SimID.202.tar.gz</strong><br> Raw data and results for the verification with synthetic polycrystal datasets,<br> where 200 is without noise, 201 low noise, 202 high noise. <strong>VerifyAlBicrystalZirong_ExampleROIs.tar.gz<br> VerifyAlBicrystalZirong_Library.tar.gz</strong><br> <strong>VerifyAlBicrystalZirong_Setup.tar.gz<br> VerifyAlBicrystalZirongRendering.zip</strong><br> Raw data and results for specific ROIs discussed for the aluminium bicrystal including Paraview example for rendering. <strong>VerifyAlLiMgBaptiste_ExampleROIs.tar.gz<br> VerifyAlLiMgBaptiste_Library.tar.gz<br> VerifyAlLiMgBaptiste_Setup.tar.gz<br> VerifyAlLiMgBaptisteRendering.zip</strong><br> Raw data and results for specific ROIs discussed for the aluminium bicrystal including Paraview example for rendering. <strong>AlBicrystalAdaptiveROIGrid.tar.gz<br> AlLiMgAgAdaptiveROIGrid.tar.gz</strong><br> Raw data and results for the tutorial with adaptive refinement of the ROI grid, as it is detailed in the Jupyter notebook tutorials on the GitLab repository.
DOI: 10.6084/m9.figshare.5640751
title: Analysis of the potential of small-scale enterprises of artisans and sawyers as instruments for sustainable forest management in Puerto Rico

description: Small-scale forest enterprises have been recognized as a potential instrument for sustainable development. In particular, the production of handicrafts is a major form of cultural expression and a significant source of income in several developing countries. In this study, we characterize the local handicraft sector in Puerto Rico to identify essential elements for fostering small-scale forest enterprises. Artisans and sawyers were home-based microenterprises that harvested, processed, and traded a wide variety of local forest products, including 125 types of wood and several non-wood forest products. Nonetheless, severe competition from cheaper imported crafts, low demand, and high product variability hamper the development of the local handicraft sector. Despite globalization, sawyers and artisans in Puerto Rico, as part of the U.S., have access to the largest markets of tropical woods and home accessories in the world. But, to participate in these markets, they must increase competitiveness. Lack of institutional effectiveness is a major constraint for the success of the artisan development program in Puerto Rico. Therefore, cooperation and linkages between all support organizations, including government agencies, non-governmental organizations, and associations of artisans, need to be enhanced to provide effective technical assistance, marketing, and financial services to artisans.
DOI: 10.6084/m9.figshare.5640751.v1
title: Analysis of the potential of small-scale enterprises of artisans and sawyers as instruments for sustainable forest management in Puerto Rico

description: Small-scale forest enterprises have been recognized as a potential instrument for sustainable development. In particular, the production of handicrafts is a major form of cultural expression and a significant source of income in several developing countries. In this study, we characterize the local handicraft sector in Puerto Rico to identify essential elements for fostering small-scale forest enterprises. Artisans and sawyers were home-based microenterprises that harvested, processed, and traded a wide variety of local forest products, including 125 types of wood and several non-wood forest products. Nonetheless, severe competition from cheaper imported crafts, low demand, and high product variability hamper the development of the local handicraft sector. Despite globalization, sawyers and artisans in Puerto Rico, as part of the U.S., have access to the largest markets of tropical woods and home accessories in the world. But, to participate in these markets, they must increase competitiveness. Lack of institutional effectiveness is a major constraint for the success of the artisan development program in Puerto Rico. Therefore, cooperation and linkages between all support organizations, including government agencies, non-governmental organizations, and associations of artisans, need to be enhanced to provide effective technical assistance, marketing, and financial services to artisans.
DOI: 10.6084/m9.figshare.5640664
title: The fascicle load-displacement data

description: The fascicle load-displacement data <br>The quantitative data relating to the fascicle load-displacement characteristics are contained in tab-delimited text files. <br>These files are found in archived (zip) files, organized by age groups (Files 1–8).
DOI: 10.6084/m9.figshare.5640664.v1
title: The fascicle load-displacement data

description: The fascicle load-displacement data <br>The quantitative data relating to the fascicle load-displacement characteristics are contained in tab-delimited text files. <br>These files are found in figshare and are organized by age groups (Files 1–7). <br>The column descriptions for the data in the respective text files are as follows:<br>COLUMN A: labelled as 'Time' (ms); the time point corresponding to the load-displacement data pointCOLUMN B: labelled as 'Displacement'; signal (mV) corresponding to the grip-to-grip displacement inclusive of the initial distance between the grips;COLUMN C: labelled as 'Load'; signal (mV) corresponding to the load in the specimen, as detected by the load-cell;COLUMN D: also labelled as 'mm'; displacement data (mm)COLUMN E: also labelled as 'grams'; load data (mm)<br>References:Paper 1: doi:10.1115/1.2898732Paper 2: doi:10.1152/japplphysiol.00258.2012
DOI: 10.6084/m9.figshare.5640652
title: The code for Gaussian distribution modelling of the frequency versus fibril diameter

description: The code, fibriprogram_v5.m, manages the optimisation process for fitting the gaussian curves to the frequency versus D dataset by calling on sub-routines generation of a gaussian function (gaussiansingle_v5.m), linear combination of the gaussian functions (gaussiancomposite_v5.m), SA (simulanneal_v5.m) and the metropolis rule (metrop_v1.m). Similarly, software Matlab version 6.1 was used for running the code.
DOI: 10.6084/m9.figshare.5640649
title: The code for generating and processing the dataset for load-displacement and stress-strain

description: The code, strainenergy_v4_1.m, was used for generating and processing the dataset for load-displacement and stress-strain. Software Matlab version 6.1 was used for running the code. The specific variables of the parameters used to generate the current dataset are as follows:• ip1: input file containing the load-displacement data• diameter: fascicle diameter• laststrainpt: an estimate of the strain at rupture, r• orderpoly: an integral value from 2-7 which represents the order of the polynomial for fitting to the data from O to q• loadat1percent: y/n; to determine the value of the load (set at 1% of the maximum load) at which the specimen became taut. ‘y’ denotes yes; ‘n’ denotes no.<br>The logfile.txt, contains the parameters used for deriving the values of the respective mechanical properties.<br>
DOI: 10.6084/m9.figshare.5640526
title: English Wikipedia labeled mid-level wikiprojects set

description: This dataset contains a set of 93,449 observations providing wikiproject mid-level category labels associated with talk pages for respective Wikipedia articles.Each observation includes a talk page title, talk page id, latest revision id when the extraction was done, associated wikiproject templates and mid-level wikiproject categories the corresponding article page belongs to.<br>The dataset was generated using a python script that ran mysql queries on Wikimedia PAWS.To ensure a balanced set, the script extracts a random set of 2000 page-ids per mid-level category totaling about 93,449 observationsThis dataset opens up immense possibilities for topic oriented research around Wikipedia as it exposes high level topic data associated with Wikipedia pages.
DOI: 10.6084/m9.figshare.5640502.v1
title: Imine formation from neat aromatic primary amines and benzaldehyde

description: Input and output files from quantum chemical computation of the reaction mechanism<br>