cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19780370
title: <i>In silico</i> insights into the dimer structure and deiodinase activity of type III iodothyronine deiodinase from bioinformatics, molecular dynamics simulations, and QM/MM calculations

description: The homodimeric family of iodothyronine deiodinases (Dios) regioselectively remove iodine from thyroid hormones. Currently, structural data has only been reported for the monomer of the <i>mus</i> type III thioredoxin (Trx) fold catalytic domain (Dio3<sup>Trx</sup>), but the mode of dimerization has not yet been determined. Various groups have proposed dimer structures that are similar to the A-type and B-type dimerization modes of peroxiredoxins. Computational methods are used to compare the sequence of Dio3<sup>Trx</sup> to related proteins known to form A-type and B-type dimers. Sequence analysis and <i>in silico</i> protein-protein docking methods suggest that Dio3<sup>Trx</sup> is more consistent with proteins that adopt B-type dimerization. Molecular dynamics (MD) simulations of the refined Dio3<sup>Trx</sup> dimer constructed using the SymmDock and GalaxyRefineComplex databases indicate stable dimer formation along the β<sub>4</sub>α<sub>3</sub> interface consistent with other Trx fold B-type dimers. Free energy calculations show that the dimer is stabilized by interdimer interactions between the β-sheets and α-helices. A comparison of MD simulations of the <i>apo</i> and thyroxine-bound dimers suggests that the active site binding pocket is not affected by dimerization. Determination of the transition state for deiodination of thyroxine from the monomer structure using QM/MM methods provides an activation barrier consistent with previous small model DFT studies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.23498258
title: Data and codes for SSL-RF_2023.zip

description: The data and codes for the paper titled “Identifying the cargo types of road freight with semi-supervised trajectory semantic enhancement”.
DOI: 10.5281/zenodo.8033517
title: speculanas_specularis_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.8033516
title: speculanas_specularis_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.6084/m9.figshare.23260352
title: Dataset - Complex IV in Breast Cancer

description: Dataset analyzed in the work entitled "Mutations in structural genes of the mitochondrial complex IV may influence breast cancer" by Oliveira et al. File generated with data from cBioPortal (Cerami et al., 2012; Gao et al., 2013; references of the original datasets are found in the manuscript).
DOI: 10.6084/m9.figshare.23260352.v2
title: Dataset - Complex IV in Breast Cancer

description: Dataset analyzed in the work entitled "Mutations in structural genes of the mitochondrial complex IV may influence breast cancer" by Oliveira et al. File generated with data from cBioPortal (Cerami et al., 2012; Gao et al., 2013; references of the original datasets are found in the manuscript).
DOI: 10.6084/m9.figshare.23260352.v1
title: Dataset - Complex IV in Breast Cancer

description: Dataset analyzed in the work entitled "Mutations in structural genes of the mitochondrial complex IV may influence breast cancer" by Oliveira et al. File generated with data from cBioPortal (Cerami et al., 2012; Gao et al., 2013; references of the original datasets are found in the manuscript).
DOI: 10.5281/zenodo.8033414
title: Evaluating the Impact of Third-Party Library Reuse in Java Projects: An Empirical Study

description: Update, we have added the following:<br> - `dataset.ipynb`: Computes all the dataset used for this study. The user needs to use a call graph generator like OPAL/WALA. - `loc.ipynb`: Computes a dataset for LOC information given a call graph dataset - `called-reuse.ipynb`: Computing a dataset for all called functions and LOC in third-party libraries - `megamorphic.ipynb`: Empirically decide the megamorphic call sites. <br> <br> This part of the submission related to the paper "Evaluating the Impact of Third-Party Library Reuse in Java Projects: An Empirical Study". Here is a table of contents: `census.csv`: extracted data from the Census-II `releases_all.csv`: all releases available from Maven Coordinates in Census-II `releases_jar.csv`: dataset of all releases with a POM and JAR file `releases_jar_6_months.csv`: releases selected when studiying the 6-month interval `releases_jar_6_months.csv`: releases selected when comparing consecutive versions per artefactid and groupid `loc_composition.csv`: data on the ratio of insourced and outsourced code in project releases `loc_desc_without_lambdas.csv`: mined data on LOC information and class information. `loc_reuse_lower_bound.csv`: data on the ratio of reused LOC and functions of outsourced code, lower-bound `loc_reuse_upper_bound.csv`: data on the ratio of reused LOC and functions of outsourced code, upper-bound
DOI: 10.5281/zenodo.7874911
title: Evaluating the Impact of Third-Party Library Reuse in Java Projects: An Empirical Study

description: Update, we have added the following:<br> - `dataset.ipynb`: Computes all the dataset used for this study. The user needs to use a call graph generator like OPAL/WALA. - `loc.ipynb`: Computes a dataset for LOC information given a call graph dataset - `called-reuse.ipynb`: Computing a dataset for all called functions and LOC in third-party libraries - `megamorphic.ipynb`: Empirically decide the megamorphic call sites. <br> <br> This part of the submission related to the paper "Evaluating the Impact of Third-Party Library Reuse in Java Projects: An Empirical Study". Here is a table of contents: `census.csv`: extracted data from the Census-II `releases_all.csv`: all releases available from Maven Coordinates in Census-II `releases_jar.csv`: dataset of all releases with a POM and JAR file `releases_jar_6_months.csv`: releases selected when studiying the 6-month interval `releases_jar_6_months.csv`: releases selected when comparing consecutive versions per artefactid and groupid `loc_composition.csv`: data on the ratio of insourced and outsourced code in project releases `loc_desc_without_lambdas.csv`: mined data on LOC information and class information. `loc_reuse_lower_bound.csv`: data on the ratio of reused LOC and functions of outsourced code, lower-bound `loc_reuse_upper_bound.csv`: data on the ratio of reused LOC and functions of outsourced code, upper-bound
DOI: 10.25446/oxford.23205173.v2
title: Digitised, searchable Holle List in Stokhof (1980)

description: The digitised Holle List in Stokhof (1980). Visit (<em>i</em>) the webpage for details and for the interactive version of the list (see Table 1 on that webpage), and (<em>ii</em>)<em> </em>the Release page on GitHub for the versioning notes. <strong>References</strong> Rajeg, Gede Primahadi Wijaya. 2023. Digitised, searchable Holle List in Stokhof (1980) (1.1.0). Zenodo. https://doi.org/10.5281/zenodo.7979976 Stokhof, W. A. L. (ed.). 1980. <em>Holle lists, vocabularies in languages of Indonesia, vol. 1: Introductory volume</em>. Vol. Materials in Languages of Indonesia. Canberra, A.C.T., Australia: Dept. of Linguistics, Research School of Pacific Studies, The Australian National University. https://core.ac.uk/reader/159464813.
DOI: 10.5281/zenodo.8031659
title: Dataset for the publication: Elucidating the influence of intercalated anions in NiFe LDH on the electrocatalytic behavior of OER: a kinetic study

description: This contribution comprehends the dataset derived as basis of the publication on alkaline electrochemical oxygen evolution reaction using nickel iron layered double hydroxides (NiFe LDH) with different intercalated anions. In this related study, the dataset was used to analyse the impact of different intercalated anions on the governing reaction mechanism and rate determining step in the electrocatalytic surface mechanism. The dataset comprehends analysis of the three materals: (1) charging current density versus scan rate, (2) X-ray diffraction patterns, (3) polarization curves, (4) steady-state derived Tafel plots, (5) reaction order analysis, (6) impedance spectroscopy, (7) influence of stirring on polarization curves, (8) not iR corrected values for the activity curves, (9) EIS data and (10) Tafel plots obtained through three different methods.
description: We acknowledge funding by the Federal Ministry of Education and Research (H2Giga QT1.5 AlFaKat; FKZ 03HY109B) as well as German Research Foundation within NFDI4Cat (ID 441926934).
DOI: 10.5281/zenodo.8031660
title: Dataset for the publication: Elucidating the influence of intercalated anions in NiFe LDH on the electrocatalytic behavior of OER: a kinetic study

description: This contribution comprehends the dataset derived as basis of the publication on alkaline electrochemical oxygen evolution reaction using nickel iron layered double hydroxides (NiFe LDH) with different intercalated anions. In this related study, the dataset was used to analyse the impact of different intercalated anions on the governing reaction mechanism and rate determining step in the electrocatalytic surface mechanism. The dataset comprehends analysis of the three materals: (1) charging current density versus scan rate, (2) X-ray diffraction patterns, (3) polarization curves, (4) steady-state derived Tafel plots, (5) reaction order analysis, (6) impedance spectroscopy, (7) influence of stirring on polarization curves, (8) not iR corrected values for the activity curves, (9) EIS data and (10) Tafel plots obtained through three different methods.
description: We acknowledge funding by the Federal Ministry of Education and Research (H2Giga QT1.5 AlFaKat; FKZ 03HY109B) as well as German Research Foundation within NFDI4Cat (ID 441926934).
DOI: 10.6084/m9.figshare.23508561
title: cerebellumWhole.h5

description: weights <br>
DOI: 10.6084/m9.figshare.23508561.v1
title: cerebellumWhole.h5

description: weights <br>
DOI: 10.5066/p9oybsle
title: Model Archive Summary for Suspended-Sediment Concentration at USGS site 11502500, Williamson River below Sprague River near Chiloquin, OR

description: This model archive summary (MAS) is a model update to an existing log-transformed turbidity-suspended sediment concentration (SSC) regression model computing SSC for water year (WY) 2008-2017. This model supersedes all models prior to Oct 1, 2017 and includes a new model for WY 2018-2020. The methods used follow USGS guidance as referenced in Office of Surface Water (OSW)/Office of Water Quality (OWQ) technical memoranda 2016.07 and USGS techniques and methods, book 3-chapter C4 (Rasmussen and others, 2009).
DOI: 10.6073/pasta/919cd028d73ef4f8427d951148f974ec
title: Turbulence and flux data from eddy flux platform on Toolik Lake, Alaska 2009-2015.

description: Yearly file describing the turbulence conditions on Toolik Lake including the CH4, CO2 and H2O fluxes over the lake adjacent to the Toolik Field Research Station (68 38'N, 149 36'W). This location is a floating platform where eddy flux measurements have been made, and should not be confused with either the Toolik Field Station Climate site, which is a land-based station, or the Toolik Lake Climate Station that is lake-based but at a different location (approximately 300 m from the eddy platform). These data were used in the Eugster et al. (2020) article that appeared in Environmental Science: Processes and Impacts. Note that the quality flagging system in this file is only for reference, it was not used in the named article. Instead, the 9-level system by Foken et al. was calculated (see Eugster et al. 2020), but no data were eliminated to avoid bias from wrong assumptions made in this approach if measurements are not performed over a terrestrial vegetated land surface.
DOI: 10.25446/oxford.23205173.v3
title: Digitised, searchable Holle List in Stokhof (1980)

description: The digitised Holle List in Stokhof (1980). Visit (<em>i</em>) the webpage for details and for the interactive version of the list (see Table 1 on that webpage), and (<em>ii</em>)<em> </em>the Release page on GitHub for the versioning notes and for downloading the raw data (under the folder "data" in that repository). <em>NOTE: Somehow fig</em><em><strong>share</strong></em><em> produces an error to automatically import this repository's new, release version from its source GitHub repository. Please check </em><em>the release page</em><em> for updates!</em> <strong>References</strong> Rajeg, Gede Primahadi Wijaya. 2023. Digitised, searchable Holle List in Stokhof (1980) (1.2.0). Zenodo. https://doi.org/10.5281/zenodo.8028568 Stokhof, W. A. L. (ed.). 1980. <em>Holle lists, vocabularies in languages of Indonesia, vol. 1: Introductory volume</em>. Vol. Materials in Languages of Indonesia. Canberra, A.C.T., Australia: Dept. of Linguistics, Research School of Pacific Studies, The Australian National University. https://core.ac.uk/reader/159464813.
DOI: 10.6073/pasta/60a4887a6843f6fa9f660626ecf38b7a
title: PPS01 Konza Prairie Plant Species List

description: This data set contains a list of Konza Prairie plant species numeric codes, full plant species names, and some general information about plant growth and life form, and photosynthetic pathway as well. Konza plant species data sets (PVC01, PVC02, WAT012, etc.) use those numeric codes and abbreviations for all of the plant species recorded.
DOI: 10.6073/pasta/f5a57d6436f931690d7f7529f87772db
title: PGT01 Konza prairie grass species trait

description: Evolutionary history plays a key role driving patterns of trait variation across plant species. For scaling and modeling purposes, grass species are typically organized into C3 versus C4 plant functional types (PFTs). PFT groupings may obscure important functional differences among species. Rather, grouping grasses by evolutionary lineage may better represent grass functional diversity. We measured 11 structural and physiological traits in situ from 75 grass species within the North American tallgrass prairie. We tested whether traits differed significantly among photosynthetic pathways or lineages (tribe) in annual and perennial grass species. We hypothesized that tribe would be the best predictor of traits, more so than photosynthetic pathway. We further hypothesized that there would be substantial variation of traits in species among the seven C4 lineages represented at our site.
DOI: 10.6084/m9.figshare.23504658
title: Data of "Temporal and spatial evolution of herbivorous waterbird habitat in floodplain wetland driven by hydrology"

description: 1_Hydrological data 2_NDVI and geese distribution probability 3 _Water level and habitat area 4_Suitable habitat 5_Average DEM
DOI: 10.6084/m9.figshare.23504658.v1
title: Data of "Temporal and spatial evolution of herbivorous waterbird habitat in floodplain wetland driven by hydrology"

description: 1_Hydrological data 2_NDVI and geese distribution probability 3 _Water level and habitat area 4_Suitable habitat 5_Average DEM
DOI: 10.6084/m9.figshare.22439013
title: Evaluation of the susceptibility to green stem disorder in soybeans [<i>Glycine max</i> (L.) Merr.] with vegetative storage protein accumulation

description: Green stem disorder (GSD) is an important agronomical problem in soybean production because it delays leaf and stem senescence and complicates the harvest. However, a rapid and precise diagnosis of GSD has not yet been established. In this study, the effect of depodding on GSD and vegetative storage protein (VSP) accumulation was investigated in GSD-susceptible cultivar ‘Tachinagaha (Tc)’ and GSD-resistant experimental line ‘Touhoku 129 (Th)’ under two different (early and late) sowing dates in 2020 and 2021. Intact Tc plants showed relatively severe GSD at early sowing in 2020 and late sowing in 2021, whereas intact Th plants showed little GSD at both sowing dates and in both years. Meanwhile, depodding reproducibly induced GSD and increased stem weight for both Tc and Th. The relative VSP content peaked 14–21 days after R3 (DAR3) in intact plants and increased afterward in depodded plants. The relative VSP content differed at 28 DAR3 between intact and depodded plants, which was earlier than the timing when SPAD (soil plant analysis development) values differed, suggesting that VSP accumulation might be a better indicator of GSD than the SPAD value. The present study will contribute to the development of tools for diagnosing GSD.
DOI: 10.6084/m9.figshare.22779533
title: Rapid evaluation of leaf photosynthesis using a closed-chamber system in a C<sub>4</sub> plant, sugarcane

description: To accelerate research on improving sugarcane biomass production, a rapid phenotyping method for individual leaf photosynthetic rates is required. Recently, a closed-type measurement system, which is faster, lighter, and less expensive than conventional open-type systems, has been developed and utilized for C<sub>3</sub> crops. For future utilization of the system in phenotyping photosynthetic rates in sugarcane, which exhibits higher photosynthetic rate than C<sub>3</sub> crops, diurnal changes and genotypic differences were measured simultaneously using an open-type and a closed-type system to verify the accuracy of the measurements in assessing environmental responses and genetic variation. As the relative root-mean-square error, a regression accuracy between the measurements with two systems, was &lt;20% when evaluating diurnal changes and genotypic differences, closed system accurately evaluated photosynthetic rates in multiple samples. Overall, the measured values with the closed system tended to be higher than those with the open system, especially in high values above 30 µmol m<sup>−2</sup> s<sup>−1</sup>. The reason for this was presumably not leaf morphology, such as stomatal distribution, but a fundamental difference in the measurement systems (steady-state values for the open system and instantaneous values for the closed system). The open system required 5–7 min to measure a single record, whereas the closed system could measure at &lt;40 s per record. Although it would be desirable to develop a regression equation using measurements involving the open system for each cultivar to examine physiological response in detail, we conclude that the closed system has greater potential for use in phenotyping sugarcane photosynthesis.
DOI: 10.6084/m9.figshare.22332831
title: Simplified estimation of branching plasticity of soybean cultivars in relation to planting density by branch development in the row with the gradient of distance between plants and after pinching

description: The branching plasticity of soybean, i.e. its ability to adjust branch development to planting density, differs among cultivars. Field experiments are required to measure the degree of branching plasticity, but such experiments require a great deal of time and labor, and it is difficult to analyze and compare a large number of cultivars. A simple evaluation method needs to be established to investigate branching plasticity for a wide range of materials. Therefore, we conducted two methods to estimate this value. In the first method, we investigated the relationship between the number of branching nodes and intra-row planting distance with a gradient of distance between plants (5, 7.5, 10, 15, 20, 25, and 30 cm). The slope of the regression line between these two factors revealed significant differences among soybean cultivars, and was correlated with the measured values of branching plasticity determined in field experiments in 2015 and 2017. In the second method, the top of the stem was pinched out between the first and second leaf nodes at the V4 stage, and then the number of branch nodes was counted at maturity. There were differences in the number of branching nodes among cultivars, and a significant positive correlation between these values and the branching plasticity values measured in the 2015 and 2017 field experiments. Considering the time and effort required for field management and morphological surveys, the pinching method is considered to be an effective and simple method to evaluate branching plasticity.
DOI: 10.6084/m9.figshare.22779533.v1
title: Rapid evaluation of leaf photosynthesis using a closed-chamber system in a C<sub>4</sub> plant, sugarcane

description: To accelerate research on improving sugarcane biomass production, a rapid phenotyping method for individual leaf photosynthetic rates is required. Recently, a closed-type measurement system, which is faster, lighter, and less expensive than conventional open-type systems, has been developed and utilized for C<sub>3</sub> crops. For future utilization of the system in phenotyping photosynthetic rates in sugarcane, which exhibits higher photosynthetic rate than C<sub>3</sub> crops, diurnal changes and genotypic differences were measured simultaneously using an open-type and a closed-type system to verify the accuracy of the measurements in assessing environmental responses and genetic variation. As the relative root-mean-square error, a regression accuracy between the measurements with two systems, was &lt;20% when evaluating diurnal changes and genotypic differences, closed system accurately evaluated photosynthetic rates in multiple samples. Overall, the measured values with the closed system tended to be higher than those with the open system, especially in high values above 30 µmol m<sup>−2</sup> s<sup>−1</sup>. The reason for this was presumably not leaf morphology, such as stomatal distribution, but a fundamental difference in the measurement systems (steady-state values for the open system and instantaneous values for the closed system). The open system required 5–7 min to measure a single record, whereas the closed system could measure at &lt;40 s per record. Although it would be desirable to develop a regression equation using measurements involving the open system for each cultivar to examine physiological response in detail, we conclude that the closed system has greater potential for use in phenotyping sugarcane photosynthesis.
DOI: 10.6084/m9.figshare.22816127
title: Biomass estimation of World rice (<i>Oryza sativa</i> L.) core collection based on the convolutional neural network and digital images of canopy

description: Above-ground biomass (AGB) is an important indicator of crop productivity. Destructive measurements of AGB incur huge costs, and most non-destructive estimations cannot be applied to diverse cultivars having different canopy architectures. This insufficient access to AGB data has potentially limited improvements in crop productivity. Recently, a deep learning technique called convolutional neural network (CNN) has been applied to estimate crop AGB due to its high capacity for digital image recognition. However, the versatility of the CNN-based AGB estimation for diverse cultivars is still unclear. We established and evaluated a CNN-based estimation method for rice AGB using digital images with 59 diverse cultivars which were mostly in World Rice Core Collection. Across two years at two locations, we took 12,183 images of 59 cultivars with commercial digital cameras and manually obtained their corresponding AGB. The CNN model was established by using 28 cultivars and showed high accuracy (R<sup>2</sup> = 0.95) to the test dataset. We further evaluated the performance of the CNN model by using 31 cultivars, which were not in the model establishment. The CNN model successfully estimated AGB when the observed AGB was lesser than 924 g m<sup>−2</sup> (R<sup>2</sup> = 0.87), whereas it underestimated AGB when the observed AGB was greater than 924 g m<sup>−2</sup> (R<sup>2</sup> = 0.02). This underestimation might be improved by adding training data with a greater AGB in further study. The present study indicates that this CNN-based estimation method is highly versatile and could be a practical tool for monitoring crop AGB in diverse cultivars.