cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11771289.v1
title: Egg transcriptome assembly of Meloidogyne enterolobii (INRA/JKI)

description: From the raw Illumina reads, adapters and low quality regions (Phred score &lt;30) as well as regions that contained 2 or more consecutive ambiguous nucleotides were cropped using prinseq resulting in 54,424,802 cleaned paired-end reads. The clean reads were assembled using CLC Genomics Workbench 9.0 (https://www.qiagenbioinformatics.com/) with automatic bubble size and word size estimation, in simple contig mode, and minimum contig length of 200.
DOI: 10.21942/uva.11771190
title: Dataset for MS1. Yang et al. 2018. Soil organic carbon stocks controlled by lithology and soil depth in a Peruvian alpine grassland of the Andes. Catena 171, 11–21. https://doi.org/10.1016/j.catena.2018.06.038

description: The soil is the largest carbon (C) pool in the terrestrial ecosystem, and soil organic carbon (SOC) stocks play an important role in global C dynamics. Alpine grasslands of the Andes are characterized by high SOC stocks. Quantifying SOC stocks and unraveling key factors controlling SOC stocks, is necessary to obtain a better un- derstanding of the dynamics of the large C stocks in this environment. However, most studies on C dynamics of the Andes focus on volcanic-ash soils, whereas information about non-volcanic ash soils in this region is scarce. Our objectives were: (i) to estimate SOC stocks in an alpine grassland of the Peruvian Andes (7° 11′S, 78° 35′W) with parent materials other than volcanic ash, and (ii) to identify the underlying soil formation and environ- mental (SFE) factors and soil properties explaining observed patterns of SOC stocks. We sampled 69 plots up to the parent material to measure soil properties and to calculate SOC stocks, in relation to lithology, land use, grazing intensity, slope angle, slope position and altitude. We applied linear models to identify key factors controlling SOC stocks. Our results showed that total SOC stocks had a mean value of 215 ± 21 T ha−1, whereas SOC stocks of the upper 10 cm and 40 cm comprised 29.3% and 80.0% of total SOC stocks respectively. The variation of the total SOC stocks was mainly explained by soil depth and soil moisture. When soil depth and soil moisture were controlled as conditional variables, lithology became the key factor controlling the total SOC stocks. For the SOC stocks of the upper 10 cm, soil moisture explained a large part of the variation, whereas lithology, grazing intensity and altitude were also significant predictors. Our results also show that when soils are sampled with limited depths instead of the entire soil profile, SOC stocks can be underestimated, and the effects of the SFE factors on SOC stocks can be overestimated.<br>
DOI: 10.6084/m9.figshare.11771226
title: Supplementary_File_1_version 3.docx

description: <b>Association between antenatal depression and SGA (adjusted for interaction effect of the cofounders) and </b><b>Association between EPDS score of cut off 10 and SGA (adjusted for the confounders)</b>
DOI: 10.21942/uva.11771190.v1
title: Dataset for MS1. Yang et al. 2018. Soil organic carbon stocks controlled by lithology and soil depth in a Peruvian alpine grassland of the Andes. Catena 171, 11–21. https://doi.org/10.1016/j.catena.2018.06.038

description: The soil is the largest carbon (C) pool in the terrestrial ecosystem, and soil organic carbon (SOC) stocks play an important role in global C dynamics. Alpine grasslands of the Andes are characterized by high SOC stocks. Quantifying SOC stocks and unraveling key factors controlling SOC stocks, is necessary to obtain a better un- derstanding of the dynamics of the large C stocks in this environment. However, most studies on C dynamics of the Andes focus on volcanic-ash soils, whereas information about non-volcanic ash soils in this region is scarce. Our objectives were: (i) to estimate SOC stocks in an alpine grassland of the Peruvian Andes (7° 11′S, 78° 35′W) with parent materials other than volcanic ash, and (ii) to identify the underlying soil formation and environ- mental (SFE) factors and soil properties explaining observed patterns of SOC stocks. We sampled 69 plots up to the parent material to measure soil properties and to calculate SOC stocks, in relation to lithology, land use, grazing intensity, slope angle, slope position and altitude. We applied linear models to identify key factors controlling SOC stocks. Our results showed that total SOC stocks had a mean value of 215 ± 21 T ha−1, whereas SOC stocks of the upper 10 cm and 40 cm comprised 29.3% and 80.0% of total SOC stocks respectively. The variation of the total SOC stocks was mainly explained by soil depth and soil moisture. When soil depth and soil moisture were controlled as conditional variables, lithology became the key factor controlling the total SOC stocks. For the SOC stocks of the upper 10 cm, soil moisture explained a large part of the variation, whereas lithology, grazing intensity and altitude were also significant predictors. Our results also show that when soils are sampled with limited depths instead of the entire soil profile, SOC stocks can be underestimated, and the effects of the SFE factors on SOC stocks can be overestimated.<br>
DOI: 10.6084/m9.figshare.11771097
title: Nanopore reads associated with seafood mislabelling study

description: Data associated with seafood mislabelling study
DOI: 10.6084/m9.figshare.11770932
title: Data for Spicer et al 2019 Ethology - Spiders, Microbes, and Sex.xlsx

description: This data file contains three tabs:1) Aggression repeatability - three measurements for each individual spider, measured as the latency to attack a prey item (sec).<br>2) Mating trials - treatment groups and response variables for mating trials between males and females that had been exposed to an antibiotic, bacterial cocktail, or a control. Response variables include latency to courtship, duration of courtship, mass of egg cases produced, and and time until egg cases were laid.<br>3) Survival data - survivorship in days for every individual.<br>
DOI: 10.6084/m9.figshare.11770932.v2
title: Data for Spicer et al 2019 Ethology - Spiders, Microbes, and Sex.xlsx

description: This data file contains three tabs:1) Aggression repeatability - three measurements for each individual spider, measured as the latency to attack a prey item (sec).<br>2) Mating trials - treatment groups and response variables for mating trials between males and females that had been exposed to an antibiotic, bacterial cocktail, or a control. Response variables include latency to courtship, duration of courtship, mass of egg cases produced, and and time until egg cases were laid.<br>3) Survival data - survivorship in days for every individual.<br>
DOI: 10.6084/m9.figshare.11770932.v1
title: Data for Spider et al 2019 Ethology - Spiders, Microbes, and Sex.xlsx

description: This data file contains three tabs:1) Aggression repeatability - three measurements for each individual spider, measured as the latency to attack a prey item (sec).<br>2) Mating trials - treatment groups and response variables for mating trials between males and females that had been exposed to an antibiotic, bacterial cocktail, or a control. Response variables include latency to courtship, duration of courtship, mass of egg cases produced, and and time until egg cases were laid.<br>3) Survival data - survivorship in days for every individual.<br>
DOI: 10.6084/m9.figshare.11770911
title: Impediment to growth and yeast-to-hyphae transition in <i>Candida albicans</i> by copper oxide nanoparticles

description: The effects of two prominent copper oxide nanoparticles (CuO-NP and Cu<sub>2</sub>O-NP), with the oxidation state of Cu<sup>++</sup> (cupric) and Cu<sup>+</sup> (cuprous), on <i>Candida albicans</i> were evaluated. CuO-NP and Cu<sub>2</sub>O-NP were synthesized and characterized by XRD, FESEM, HR-TEM and Zeta potential. At sub-MIC (50 µg ml<sup>−1</sup>), both cupric and cuprous oxide NPs prevented yeast-to-hyphae switching and wrinkling behaviour in <i>C. albicans</i>. The mechanism for the antifungal action of the two NPs differed; CuO-NP significantly elicited reactive oxygen species, whereas membrane damage was more pronounced with Cu<sub>2</sub>O-NP. Real time PCR analysis revealed that CuO-NP suppressed the morphological switching of yeast-to-hyphae by down-regulating <i>cph1</i>, <i>hst7</i> and <i>ras1</i> and by up-regulation of the negative regulator <i>tup1</i>. In comparison, Cu<sub>2</sub>O-NP resulted in down-regulation of <i>ras1</i> and up-regulation of the negative regulators <i>nrg1</i> and <i>tup1</i>. Between the two NPs, CuO exhibited increased antifungal activity due to its stable oxidation state (Cu<sup>++</sup>) and its smaller dimensions compared with Cu<sub>2</sub>O-NP.
DOI: 10.6084/m9.figshare.11770938.v2
title: Supplementary materials: Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats. PART 2

description: Part 2 of supplementary materials of the paper "Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats". The data contains raw acoustic data, individual's metadata and outputs of model selection procedures and model parameter estimations.
DOI: 10.6084/m9.figshare.11770911.v1
title: Impediment to growth and yeast-to-hyphae transition in <i>Candida albicans</i> by copper oxide nanoparticles

description: The effects of two prominent copper oxide nanoparticles (CuO-NP and Cu<sub>2</sub>O-NP), with the oxidation state of Cu<sup>++</sup> (cupric) and Cu<sup>+</sup> (cuprous), on <i>Candida albicans</i> were evaluated. CuO-NP and Cu<sub>2</sub>O-NP were synthesized and characterized by XRD, FESEM, HR-TEM and Zeta potential. At sub-MIC (50 µg ml<sup>−1</sup>), both cupric and cuprous oxide NPs prevented yeast-to-hyphae switching and wrinkling behaviour in <i>C. albicans</i>. The mechanism for the antifungal action of the two NPs differed; CuO-NP significantly elicited reactive oxygen species, whereas membrane damage was more pronounced with Cu<sub>2</sub>O-NP. Real time PCR analysis revealed that CuO-NP suppressed the morphological switching of yeast-to-hyphae by down-regulating <i>cph1</i>, <i>hst7</i> and <i>ras1</i> and by up-regulation of the negative regulator <i>tup1</i>. In comparison, Cu<sub>2</sub>O-NP resulted in down-regulation of <i>ras1</i> and up-regulation of the negative regulators <i>nrg1</i> and <i>tup1</i>. Between the two NPs, CuO exhibited increased antifungal activity due to its stable oxidation state (Cu<sup>++</sup>) and its smaller dimensions compared with Cu<sub>2</sub>O-NP.
DOI: 10.6084/m9.figshare.11770938.v3
title: Supplementary materials: Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats. PART 2

description: Part 2 of supplementary materials of the paper "Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats". The data contains raw acoustic data, individual's metadata and outputs of model selection procedures and model parameter estimations.
DOI: 10.6084/m9.figshare.11770908
title: Rapid whole genome sequencing of hypervirulent Klebsiella pneumoniae from a Chinese migrant presenting with liver abscesses, pneumonia and meningitis

description: Kleborate output and long-read consensus assemblies using three basecalling models for a hypervirulent Klebsiella pneumoniae isolate
DOI: 10.6084/m9.figshare.11770908.v1
title: Assembly files

description: Kleborate output and long-read consensus assemblies using three basecalling models for a hypervirulent Klebsiella pneumoniae isolate
DOI: 10.6084/m9.figshare.11770938.v4
title: Supplementary materials: Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats. PART 2

description: Part 2 of supplementary materials of the paper "Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats". The data contains raw acoustic data, individual's metadata and outputs of model selection procedures and model parameter estimations.
DOI: 10.6084/m9.figshare.11770938.v5
title: Supplementary materials: Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats. PART 2

description: Part 2 of supplementary materials of the paper "Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats". The data contains raw acoustic data, individual's metadata and outputs of model selection procedures and model parameter estimations.
DOI: 10.6084/m9.figshare.11770938
title: Supplementary materials: Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats. PART 2

description: Part 2 of supplementary materials of the paper "Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats". The data contains raw acoustic data, individual's metadata and outputs of model selection procedures and model parameter estimations.
DOI: 10.6084/m9.figshare.11770938.v6
title: Supplementary materials: Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats. PART 2

description: Part 2 of supplementary materials of the paper "Ontogeny of an interactive call-and-response system in Spix’s disc-winged bats". The data contains raw acoustic data, individual's metadata and outputs of model selection procedures and model parameter estimations.
DOI: 10.6084/m9.figshare.11770902
title: dataset.zip

description: Our final dataset comprises of 491,018 class I MHC allele data points covering 161 different HLAs and 64,954 class II MHC allele data points covering 49 different HLAs. The peptide lengths range from 3 to 43 for both classes, while the lengths of amino acid sequences of HLAs range from 180 to 347 for class I and from 85 to 232 for class II. <br><br>We get 451,484 HLA-A*, 39,424 HLA-B* and 110 HLA-C* class I alleles, out of which 379,783 are binding and 111,235 are non-binding. Similarly, we get 64,926 HLA-DRB1*, 22 HLA-DRB3*, 4 HLA-DRB4* and 2 HLA-DRB5* class II alleles out of which 36,035 are binding and 28,919 are non-binding.<br>
DOI: 10.6084/m9.figshare.11770893
title: Metadata record for: Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics

description: This dataset contains key characteristics about the data described in the Data Descriptor Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11770893.v2
title: Metadata record for: Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics

description: This dataset contains key characteristics about the data described in the Data Descriptor Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11770893.v1
title: Metadata record for: Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics

description: This dataset contains key characteristics about the data described in the Data Descriptor Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11770521
title: Comparison of neighbourhood relations based on ordinary Delaunay diagrams and area Delaunay diagrams: application to define the neighbourhood relations of buildings

description: Data and codes used in this paper.
DOI: 10.6084/m9.figshare.11770521.v1
title: Comparison of neighbourhood relations based on ordinary Delaunay diagrams and area Delaunay diagrams: application to define the neighbourhood relations of buildings

description: Data and codes used in this paper.
DOI: 10.6084/m9.figshare.11770377
title: Supplementary Material for: A Comparison of Existing Questionnaires for Identifying the Causes of Interstitial and Rare Lung Diseases

description: <b><i>Background:</i></b> A thorough diagnostic process is essential with regard to prognosis and treatment of the more than 200 different types of interstitial lung diseases (ILD). Key to this complex process is a comprehensive medical history. For this, a template is recommended and questionnaires are increasingly used. Yet, the optimal questionnaire has not been established. <b><i>Objectives:</i></b> We aimed to compare well-established questionnaires that are used in the diagnostic process of interstitial and rare lung diseases. <b><i>Methods:</i></b> Via a structured internet search and ILD expert interviews, we identified 6 different questionnaires for the diagnosis of ILDs: the questionnaires developed by the German Respiratory Society (DGP), American College of Chest Physicians (ACCP), National Jewish Health (NJH), Österreichische Röntgengesellschaft/Gesellschaft für Medizinische Radiologie und Nuklearmedizin (OERG), University of California, Los Angeles Health (UCLA), and University of California, San Francisco Medical Center (UCSF). We compared the forms, lengths, and contents of the 6 questionnaires regarding symptoms, comorbidities, drug history, previous ILD therapies, family history, smoking habits, occupational history, exposures, travel history, and former diagnostic procedures. <b><i>Results:</i></b> The questionnaires differed in length and content. The UCLA questionnaire focuses on connective tissue diseases extensively, while the NJH questionnaire captures previous diagnostics in detail. The OERG questionnaire is condensed, while the other 5 questionnaires are very detailed. The UCSF questionnaire contains a personal assessment part for the patient. For the majority of the questions, the patient can choose options from a preselected list of possible answers. The DGP questionnaire offers the patient the opportunity to add additional information in the form of free text to some of the key questions. <b><i>Conclusions:</i></b> Questionnaires are an important tool in the diagnostic process of ILDs. Further validation and adjustment to clinical guidelines will help to improve existing questionnaires. Future work must aim to develop an internationally accepted template.
DOI: 10.6084/m9.figshare.11770377.v1
title: Supplementary Material for: A Comparison of Existing Questionnaires for Identifying the Causes of Interstitial and Rare Lung Diseases

description: <b><i>Background:</i></b> A thorough diagnostic process is essential with regard to prognosis and treatment of the more than 200 different types of interstitial lung diseases (ILD). Key to this complex process is a comprehensive medical history. For this, a template is recommended and questionnaires are increasingly used. Yet, the optimal questionnaire has not been established. <b><i>Objectives:</i></b> We aimed to compare well-established questionnaires that are used in the diagnostic process of interstitial and rare lung diseases. <b><i>Methods:</i></b> Via a structured internet search and ILD expert interviews, we identified 6 different questionnaires for the diagnosis of ILDs: the questionnaires developed by the German Respiratory Society (DGP), American College of Chest Physicians (ACCP), National Jewish Health (NJH), Österreichische Röntgengesellschaft/Gesellschaft für Medizinische Radiologie und Nuklearmedizin (OERG), University of California, Los Angeles Health (UCLA), and University of California, San Francisco Medical Center (UCSF). We compared the forms, lengths, and contents of the 6 questionnaires regarding symptoms, comorbidities, drug history, previous ILD therapies, family history, smoking habits, occupational history, exposures, travel history, and former diagnostic procedures. <b><i>Results:</i></b> The questionnaires differed in length and content. The UCLA questionnaire focuses on connective tissue diseases extensively, while the NJH questionnaire captures previous diagnostics in detail. The OERG questionnaire is condensed, while the other 5 questionnaires are very detailed. The UCSF questionnaire contains a personal assessment part for the patient. For the majority of the questions, the patient can choose options from a preselected list of possible answers. The DGP questionnaire offers the patient the opportunity to add additional information in the form of free text to some of the key questions. <b><i>Conclusions:</i></b> Questionnaires are an important tool in the diagnostic process of ILDs. Further validation and adjustment to clinical guidelines will help to improve existing questionnaires. Future work must aim to develop an internationally accepted template.
DOI: 10.6084/m9.figshare.11770365
title: Influence of pore structure on the properties of green concrete derived from natural pozzolan and nanosilica

description: The strength, pore structure, morphology and mineralogical composition of hydration products of natural pozzolan (NP) and nanosilica (nSiO<sub>2</sub>) based alkali activated binder (AAB) were examined. It was noted that AAB without nSiO<sub>2</sub> was relatively porous with the presence of micro-, meso- and macro-level pores. In contrast, as the proportion of nSiO<sub>2</sub> increased in the mixture, the pore structure started to refine with a reduction in the pore volume due to transformation of source material to polymeric compound, such as C-A-S-H with a higher Al absorption in the binder structure. The incorporation of 5% and 7.5% nSiO<sub>2</sub> resulted in the refinement of the pore structure due to enhanced polycondensation. Consequently, there was considerable improvement in the mechanical properties. The experimental data indicated that the pore structure evaluation through NMR has served as a tool to understand the relation between the micro- and macro-level performance of the developed AAC.