cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4626388
title: Data sets of Characterising the Knowledge about Primitive Variables in Java Code Comments

description: We provide two data sets used in the paper “Characterising the Knowledge about Primitive Variables in Java Code Comments”. The first data set (Annotated_Evaluation dataset.txt) was used to answer RQ1-2, and the second data set (Large-scale dataset.csv) was used to answer RQ3-5. <strong>A) Brief description to read Annotated_Evaluation dataset.txt file: </strong> Column headers in the file are self-explanatory; however, we provide a brief description of the following column headers for ease of reading: 1) Project name: The project name as appeared in the GitHub 2) GitHub URL: GitHub URL to the location of the variable in source code. 3) Commit ID: Last commit. 4) Variable name: The variable identifier. 5) Access specifier: The instance variable (field variable) have one of these values: default, private, public and protected, while the non-field variable has the "[n/a]" value. 6) Keyword (Final): Depends on the scope of the variable and can be either “final” or “[n/a]”. 7) Keyword (Static): Can be either “static” for a field variable or “[n/a]” for local and parameter’s variables. 8) Variable type: The variable type can have one of these types: int, byte, char, short, long, float, double, Boolean and String. 9) Scope: The scope of the variable in which it declared and can have one of these values: instance variable, local variable (constructor), local variable (function), parameter (function), parameter (constructor). 10) Inline, line or block comments: The text of the comment accompanying the variable identifier or "[n/a]" for an uncommented variable. 11) Comment type: The comment type depends on the style of documentation: line {inline, line}, block, and block format. 12) Comment format: Has two values: Javadoc for comment of type of block and [n/a] for line and block format. 13) Columns P – U: Show the results of the four matching techniques. The "TRUE" value indicates a particular technique can detect the identifier in an accompanying comment. 14) Columns V – AG: Annotators' results for each annotation question (AQ) illustrated in TABLE IV in the paper. Abbreviations used: 1) init: indicates the initial annotation between pair of annotators, 2) !NE: conflict detected between pair of annotators and 3) CR: conflict resolved between pair of annotators. 15) Columns AJ to AQ: Data annotated by annotator 1 16) Columns AR to AY: Data annotated by annotator 2 17) Columns AZ to BG: Data annotated by annotator 3 18) Columns AH to BO: Data annotated by annotator 4 <strong>B) Large-scale dataset.csv file: </strong> Please follow the explanation provided from 1 to 10 and illustrated in (A) above. <strong>To cite the dataset, please use the following paper:</strong> Mahfouth Alghamdi, Shinpei Hayashi, Takashi Kobayashi, and Christoph Treude, “Characterising the Knowledge about Primitive Variables in Java Code Comments,” in<em> Proceedings of the 18th International Conference on Mining Software Repositories</em>, 2021.
DOI: 10.5281/zenodo.4626387
title: Data sets of Characterising the Knowledge about Primitive Variables in Java Code Comments

description: We provide two data sets used in the paper “Characterising the Knowledge about Primitive Variables in Java Code Comments”. The first data set (Annotated_Evaluation dataset.txt) was used to answer RQ1-2, and the second data set (Large-scale dataset.csv) was used to answer RQ3-5. <strong>A) Brief description to read Annotated_Evaluation dataset.txt file: </strong> Column headers in the file are self-explanatory; however, we provide a brief description of the following column headers for ease of reading: 1) Project name: The project name as appeared in the GitHub 2) GitHub URL: GitHub URL to the location of the variable in source code. 3) Commit ID: Last commit. 4) Variable name: The variable identifier. 5) Access specifier: The instance variable (field variable) have one of these values: default, private, public and protected, while the non-field variable has the "[n/a]" value. 6) Keyword (Final): Depends on the scope of the variable and can be either “final” or “[n/a]”. 7) Keyword (Static): Can be either “static” for a field variable or “[n/a]” for local and parameter’s variables. 8) Variable type: The variable type can have one of these types: int, byte, char, short, long, float, double, Boolean and String. 9) Scope: The scope of the variable in which it declared and can have one of these values: instance variable, local variable (constructor), local variable (function), parameter (function), parameter (constructor). 10) Inline, line or block comments: The text of the comment accompanying the variable identifier or "[n/a]" for an uncommented variable. 11) Comment type: The comment type depends on the style of documentation: line {inline, line}, block, and block format. 12) Comment format: Has two values: Javadoc for comment of type of block and [n/a] for line and block format. 13) Columns P – U: Show the results of the four matching techniques. The "TRUE" value indicates a particular technique can detect the identifier in an accompanying comment. 14) Columns V – AG: Annotators' results for each annotation question (AQ) illustrated in TABLE IV in the paper. Abbreviations used: 1) init: indicates the initial annotation between pair of annotators, 2) !NE: conflict detected between pair of annotators and 3) CR: conflict resolved between pair of annotators. 15) Columns AJ to AQ: Data annotated by annotator 1 16) Columns AR to AY: Data annotated by annotator 2 17) Columns AZ to BG: Data annotated by annotator 3 18) Columns AH to BO: Data annotated by annotator 4 <strong>B) Large-scale dataset.csv file: </strong> Please follow the explanation provided from 1 to 10 and illustrated in (A) above. <strong>To cite the dataset, please use the following paper:</strong> Mahfouth Alghamdi, Shinpei Hayashi, Takashi Kobayashi, and Christoph Treude, “Characterising the Knowledge about Primitive Variables in Java Code Comments,” in<em> Proceedings of the 18th International Conference on Mining Software Repositories</em>, 2021.
DOI: 10.15479/at:ista:9192
title: Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus)

description: Here are the research data underlying the publication "Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus)". Further information are summed up in the README document.
DOI: 10.6084/m9.figshare.13159706
title: Spatial distribution of flower colour polymorphism in <i>Iris lutescens</i>

description: Iris lutescensis a common species occurring mainly in dry limestone habitats in Western Italy, Southern France, and Spain. The species shows a remarkable polymorphism for flower colour, and yellow and purple flowers can be found in the same population. As the species is a deceptive one, the previous studies on the maintenance of such a polymorphism were linked to its pollination ecology. Here, I reported on the spatial distribution of the polymorphism and showed that Spanish populations are mostly purple monomorphic. In contrast, populations in the South of France and Italy show the complete range, from 0 to 1, for the frequency of yellow morph, and the spatial autocorrelation for morph frequencies is very low. To go further, correlations between morph frequencies and abiotic factors, such as bioclimatic variables, UV irradiance, and aridity, were studied. On the whole, the spatial distribution of the frequency of yellow morph can be hardly explained by the contributions of these abiotic variables, and historical contingencies, including the phylogeography of the species have to be invoked, in particular, to explain the absence of polymorphic populations in Spain.
DOI: 10.6084/m9.figshare.13159706.v1
title: Spatial distribution of flower colour polymorphism in <i>Iris lutescens</i>

description: Iris lutescensis a common species occurring mainly in dry limestone habitats in Western Italy, Southern France, and Spain. The species shows a remarkable polymorphism for flower colour, and yellow and purple flowers can be found in the same population. As the species is a deceptive one, the previous studies on the maintenance of such a polymorphism were linked to its pollination ecology. Here, I reported on the spatial distribution of the polymorphism and showed that Spanish populations are mostly purple monomorphic. In contrast, populations in the South of France and Italy show the complete range, from 0 to 1, for the frequency of yellow morph, and the spatial autocorrelation for morph frequencies is very low. To go further, correlations between morph frequencies and abiotic factors, such as bioclimatic variables, UV irradiance, and aridity, were studied. On the whole, the spatial distribution of the frequency of yellow morph can be hardly explained by the contributions of these abiotic variables, and historical contingencies, including the phylogeography of the species have to be invoked, in particular, to explain the absence of polymorphic populations in Spain.
DOI: 10.6084/m9.figshare.11919381.v3
title: Orofacial function in children with Speech Sound Disorders persisting after the age of six years

description: <i>Purpose</i>: The aim was to investigate, describe and analyse speech characteristics, intelligibility, orofacial function and co-existing neurodevelopmental symptoms in children with SSD of unknown origin, persisting after six years of age. <i>Method</i>: The study included 61 children with SSD (6–17 years) of unknown origin, referred for a speech and oral motor examination. The severity of SSD was estimated using Percentage Consonants Correct (PCC) and Percentage Vowels Correct (PVC) and assessments of resonance based on Swedish Articulation and Nasality Test (SVANTE). Orofacial function was screened using the Nordic Orofacial Test-Screening (NOT-S). Parents completed the Intelligibility in Context Scale (ICS) and a questionnaire including questions about heredity, medical and neurodevelopmental conditions, and speech development. <i>Result:</i> SSD varied according to PCC (8–95%) and PVC (55–100%) measurements. Percentages of co-occurring disorders included: 51% resonance deviations, 90% intelligibility issues, and 87% orofacial difficulties. The most affected orofacial domains were “Chewing and swallowing” (41%), “Masticatory muscles and jaw function” (38%) and “Sensory function” (38%). The majority (64%) had co-existing dysfunctions relating to general motor and neurodevelopmental disorders. <i>Conclusion:</i> Children with persistent SSD are at risk for orofacial dysfunction, general motor difficulties and other neurodevelopmental disorders and therefore should be screened for co-occurring disorders.
DOI: 10.6084/m9.figshare.11919381
title: Orofacial function in children with Speech Sound Disorders persisting after the age of six years

description: <i>Purpose</i>: The aim was to investigate, describe and analyse speech characteristics, intelligibility, orofacial function and co-existing neurodevelopmental symptoms in children with SSD of unknown origin, persisting after six years of age. <i>Method</i>: The study included 61 children with SSD (6–17 years) of unknown origin, referred for a speech and oral motor examination. The severity of SSD was estimated using Percentage Consonants Correct (PCC) and Percentage Vowels Correct (PVC) and assessments of resonance based on Swedish Articulation and Nasality Test (SVANTE). Orofacial function was screened using the Nordic Orofacial Test-Screening (NOT-S). Parents completed the Intelligibility in Context Scale (ICS) and a questionnaire including questions about heredity, medical and neurodevelopmental conditions, and speech development. <i>Result:</i> SSD varied according to PCC (8–95%) and PVC (55–100%) measurements. Percentages of co-occurring disorders included: 51% resonance deviations, 90% intelligibility issues, and 87% orofacial difficulties. The most affected orofacial domains were “Chewing and swallowing” (41%), “Masticatory muscles and jaw function” (38%) and “Sensory function” (38%). The majority (64%) had co-existing dysfunctions relating to general motor and neurodevelopmental disorders. <i>Conclusion:</i> Children with persistent SSD are at risk for orofacial dysfunction, general motor difficulties and other neurodevelopmental disorders and therefore should be screened for co-occurring disorders.
DOI: 10.6084/m9.figshare.11919381.v2
title: Orofacial function in children with Speech Sound Disorders (SSD) persisting after the age of six years

description: <i>Purpose</i>: The aim was to investigate, describe and analyse speech characteristics, intelligibility, orofacial function and co-existing neurodevelopmental symptoms in children with SSD of unknown origin, persisting after six years of age. <i>Method</i>: The study included 61 children with SSD (6–17 years) of unknown origin, referred for a speech and oral motor examination. The severity of SSD was estimated using Percentage Consonants Correct (PCC) and Percentage Vowels Correct (PVC) and assessments of resonance based on Swedish Articulation and Nasality Test (SVANTE). Orofacial function was screened using the Nordic Orofacial Test-Screening (NOT-S). Parents completed the Intelligibility in Context Scale (ICS) and a questionnaire including questions about heredity, medical and neurodevelopmental conditions, and speech development. <i>Result:</i> SSD varied according to PCC (8–95%) and PVC (55–100%) measurements. Percentages of co-occurring disorders included: 51% resonance deviations, 90% intelligibility issues, and 87% orofacial difficulties. The most affected orofacial domains were “Chewing and swallowing” (41%), “Masticatory muscles and jaw function” (38%) and “Sensory function” (38%). The majority (64%) had co-existing dysfunctions relating to general motor and neurodevelopmental disorders. <i>Conclusion:</i> Children with persistent SSD are at risk for orofacial dysfunction, general motor difficulties and other neurodevelopmental disorders and therefore should be screened for co-occurring disorders.
DOI: 10.23729/062a3142-8cdd-408e-8797-62209794bb0b
title: X-ray diffraction frames of MFE1 in complex with CoA and NAD+ (PDB code : 6Z5O)

description: The dataset contains 2100 X-ray diffraction frames from a crystal of rat peroxisomal Multifunctional enzyme type-1 (MFE1) co crystallised with CoA and NAD+. Also the processed scaled and unmerged files are also present in a separate folder.
DOI: 10.5281/zenodo.3939407
title: IODP Expedition 306, Hole 642E - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 306: North Atlantic Climate 2
DOI: 10.5281/zenodo.3939406
title: IODP Expedition 306, Hole 642E - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 306: North Atlantic Climate 2
DOI: 10.6084/m9.figshare.12191853
title: Asparagine-based production of hydrogen peroxide triggers cell death in the diatom <i>Phaeodactylum tricornutum</i>

description: As a major component of coastal phytoplankton blooms, diatoms are an important source of dissolved organic matter (DOM) in the ocean. While this DOM pool fuels the growth of diverse bacterial populations, diatom population dynamics itself is considered unaffected by it. Here, we identified strong negative effects of the amino acid asparagine on the growth of the marine model diatom <i>Phaeodactylum tricornutum</i>. Using microscopic analyses and physiological assays, we showed that while asparagine fuelled photosynthetic growth, its supplementation to NO<sub>3</sub><sup>−</sup> medium significantly decreased the culture’s cell density and photosynthetic capacity (F<sub>v</sub>/F<sub>m</sub>) during the stationary phase of the growth cycle. We further showed that these effects resulted from asparagine-based production of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) that triggered a massive cell death event. Effective lethal asparagine concentrations were as low as 12.5 µM, while 1 μM affected F<sub>v</sub>/F<sub>m</sub>, but did not trigger culture collapse. Based on sequence similarity with the characterized H<sub>2</sub>O<sub>2</sub>-producing L-amino acid oxidase (LAAO) of <i>Chlamydomonas reinhardtii</i>, LAO1, we identified putative LAO1 orthologs in the genomes of <i>P. tricornutum</i> and the toxigenic pennate species <i>Pseudo-nitzschia multiseries</i>. The molecular phylogeny of this gene indicates a shared ancestry with other algal LAAOs and suggests a conserved oxidative deaminase function that could mediate DOM release from diatom populations through the triggering of autocatalytic cell death events.
DOI: 10.6084/m9.figshare.12191853.v1
title: Asparagine-based production of hydrogen peroxide triggers cell death in the diatom <i>Phaeodactylum tricornutum</i>

description: As a major component of coastal phytoplankton blooms, diatoms are an important source of dissolved organic matter (DOM) in the ocean. While this DOM pool fuels the growth of diverse bacterial populations, diatom population dynamics itself is considered unaffected by it. Here, we identified strong negative effects of the amino acid asparagine on the growth of the marine model diatom <i>Phaeodactylum tricornutum</i>. Using microscopic analyses and physiological assays, we showed that while asparagine fuelled photosynthetic growth, its supplementation to NO<sub>3</sub><sup>−</sup> medium significantly decreased the culture’s cell density and photosynthetic capacity (F<sub>v</sub>/F<sub>m</sub>) during the stationary phase of the growth cycle. We further showed that these effects resulted from asparagine-based production of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) that triggered a massive cell death event. Effective lethal asparagine concentrations were as low as 12.5 µM, while 1 μM affected F<sub>v</sub>/F<sub>m</sub>, but did not trigger culture collapse. Based on sequence similarity with the characterized H<sub>2</sub>O<sub>2</sub>-producing L-amino acid oxidase (LAAO) of <i>Chlamydomonas reinhardtii</i>, LAO1, we identified putative LAO1 orthologs in the genomes of <i>P. tricornutum</i> and the toxigenic pennate species <i>Pseudo-nitzschia multiseries</i>. The molecular phylogeny of this gene indicates a shared ancestry with other algal LAAOs and suggests a conserved oxidative deaminase function that could mediate DOM release from diatom populations through the triggering of autocatalytic cell death events.
DOI: 10.6084/m9.figshare.11896959
title: Pond turtle carapaces, an alternative natural substrate for the use of a diatom-based water quality index

description: Benthic diatoms are widely used as bio-indicators in water quality monitoring of rivers and streams, but less commonly in lentic waterbodies such as pools and lakes. Currently, a new method for assessing the ecological status of lakes is being tested in France to meet the requirements of the European Water Framework Directive (WFD) 2000/60/EC. This new method uses epilithic and epiphytic diatoms growing on stones and aquatic plants. Alternatively, freshwater turtles and the epizoic algae found on their carapaces may provide an excellent substrate for estimating water quality. Our study proposes an original diatom-based method for assessing the quality of water bodies in which turtles live. The main objective was to compare the Biological Diatom Index (BDI) values measured from epizoic diatom samples taken on the carapace of turtles with classical epilithic or epiphytic samples. Epizoic samples were taken from the carapaces of the turtle <i>Emys orbicularis</i> in two shallow French Mediterranean wetlands. Our results indicate that diatom assemblages differ slightly within the three substrates studied with limited variations in index value. However, some variability among epizoic samples from the same site suggests that several turtle individuals should be sampled for water quality biomonitoring.
DOI: 10.6084/m9.figshare.11896959.v1
title: Pond turtle carapaces, an alternative natural substrate for the use of a diatom-based water quality index

description: Benthic diatoms are widely used as bio-indicators in water quality monitoring of rivers and streams, but less commonly in lentic waterbodies such as pools and lakes. Currently, a new method for assessing the ecological status of lakes is being tested in France to meet the requirements of the European Water Framework Directive (WFD) 2000/60/EC. This new method uses epilithic and epiphytic diatoms growing on stones and aquatic plants. Alternatively, freshwater turtles and the epizoic algae found on their carapaces may provide an excellent substrate for estimating water quality. Our study proposes an original diatom-based method for assessing the quality of water bodies in which turtles live. The main objective was to compare the Biological Diatom Index (BDI) values measured from epizoic diatom samples taken on the carapace of turtles with classical epilithic or epiphytic samples. Epizoic samples were taken from the carapaces of the turtle <i>Emys orbicularis</i> in two shallow French Mediterranean wetlands. Our results indicate that diatom assemblages differ slightly within the three substrates studied with limited variations in index value. However, some variability among epizoic samples from the same site suggests that several turtle individuals should be sampled for water quality biomonitoring.
DOI: 10.5281/zenodo.3939409
title: IODP Expedition 306, Hole U1313B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 306: North Atlantic Climate 2
DOI: 10.5281/zenodo.3939408
title: IODP Expedition 306, Hole U1313B - Well Logging Data

description: Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of data (resistivity, gamma radiation, velocity, density, borehole images,…) in any hole depends on the scientific objectives and operational constraints.
description: IODP Expedition 306: North Atlantic Climate 2