cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z612jm6kk
title: Data from: Biomass yield, yield components and growing season phenotypic measurements of Miscanthus

description: For sustainable biomass production of Miscanthus × giganteus (hereafter
 miscanthus), understanding the impact of stand age and nitrogen (N)
 fertilization on biomass yield is crucial. This study investigated the
 effects of varying N fertilization rates (0, 56, 112, and 168 kg N ha-1)
 on yield components (tiller height, density, and weight) and their
 correlations with end-of-season biomass yield in miscanthus. We also
 explored end-of-season biomass yield prediction using in-season traits
 (canopy height, leaf area index (LAI), and leaf chlorophyll content
 (LCC)). The study was conducted at two sites in Illinois: a previously
 unfertilized 10-year-old miscanthus research stand at Urbana and a
 16-year-old commercial stand at Pesotum with a history of annual 56N
 application. Results from 2018-2021 in Urbana and 2020-2021 in Pesotum
 showed increased biomass yields with N fertilization, varying by rate,
 year, and location. Biomass yield in Pesotum peaked at 56N, while in
 Urbana, it increased significantly at 112 kg N ha-1. Biomass yield was
 strongly correlated with tiller height and weight measured at Urbana
 across N rates. Morphological traits measured every 2-3 weeks during the
 2020 and 2021 growing seasons showed that canopy height was the strongest
 single predictor of miscanthus biomass yield, followed by LCC. Mid-August
 to September measurements of these traits were the best predictors of
 biomass yield. Multiple regressions involving the canopy height and LCC
 further improved yield predictions. We conclude that while N enhances
 biomass yields of aging miscanthus, the optimum rate depends on the site,
 environmental conditions, and management.
description: # Data from: Biomass yield, yield components and growing season phenotypic
 measurements of Miscanthus
 [https://doi.org/10.5061/dryad.z612jm6kk](https://doi.org/10.5061/dryad.z612jm6kk) Dataset contains end-of-season Dry biomass yield of Miscanthus × giganteus from two sites (Urbana and Pesotum) in Central Illinois. The Urbana and Pesotum yields are collected over 4 years (2018-2021) and 2 years (2020-2021) respectively. Dataset also contains yield component traits (tiller height, tiller density and tiller weight) obtained at harvest. Phenotypic traits (canopy height, Leaf area index (LAI) and Leaf Chlorophyll content (LCC)) measured during the growing season are also included. ## Description of the data and file structure Yield&components Site: Location in central IL Year: Growing Season Rate: Nitrogen rate (kg ha-1) DM (Mg ha-1): End-of-season Dry biomass yield Tiller density (tiller m-2) : Number of tillers per m2 Tiller weight (g m-2): Dry weight of an individual tiller Tiller height (cm): Tiller height at harvest Pheno_growing season Site: Location in central IL Year: Growing Season Rate: Nitrogen rate (kg ha-1) Date: Date of data collection (mm/dd/yyy) Canopy height (cm): Canopy height of miscanthus LCC: Leaf Chlorophyll content LAI: Leaf area index (LAI)
DOI: 10.5061/dryad.37pvmcvt2
title: Analysis code and data for the morphometrics and kinematics of tube feet

description: Hydrostatic skeletons, such as an elephant trunk or a squid tentacle,
 permit the transmission of mechanical work through a soft body. Despite
 the ubiquity of these structures among animals, we generally do not
 understand how differences in their morphology affect their mechanical
 properties. Therefore, the present study used mathematical modeling,
 morphometrics, and kinematics to understand the transmission of force and
 displacement in the tube feet of the juvenile six-rayed star Leptasterias
 sp. An inverse-dynamic analysis revealed that the forces generated by the
 feet during crawling primarily serve to overcome the submerged weight of
 the body. This load was disproportionately generated by the feet at more
 proximal positions along each ray, which were used more frequently for
 crawling. Due to a combination of mechanical advantage and muscle mass,
 these proximal feet exhibited a greater capacity for force generation than
 the distal feet. However, the higher displacement advantage of the more
 elongated distal feet offer a superior ability to extend the feet into the
 environment. Therefore, the morphology of tube feet demonstrates a
 gradient in gearing along each ray that matches their role in behavior.
description: As detailed in the manuscript, the morphometrics were obtained
 from measurements of histological sections. The kinematics measurements
 were performed from video recordings of locomotion from lateral and oral
 views of the animals. 
description: # Analysis code and data for the morphometrics and kinematics of tube feet
 [https://doi.org/10.5061/dryad.37pvmcvt2](https://doi.org/10.5061/dryad.37pvmcvt2) ## Code The MATLAB code for data analysis and aquisition are provided in the following zip archives. - **morphometrics_code** - Contains the matlab code for analzing the morphometrics ("ana_morph.m"), using the parmeter values stored in morphData.m. - **seastar_kine** - Acquisition and analysis of kinematics, performed over numerous .m files. Acquisition begins at "acqMaster.m" and anlaysis starts at "anaMaster.m". See annotations within the individual files for their specific functions. ## Data files Files in the **Data** folder are separated into the following folders: - **Kinematics**:files are further divided by horizontal and inverted (i.e., upside-down) crawling. For each individual, kinematics are stored for both horizontal and oral views. The mat file "All sequences.mat" contains the kinematic measurements for all sequences. - **Morphometrics**: Contains the raw histological images used as a basis for morphometric measurements. These are oragnized according to the plane through which the sections were made (i.e., Coronal and Saggital planes).
DOI: 10.5061/dryad.pvmcvdntc
title: Data from: Artificial intelligence model for detecting duodenal endoscopic changes on images of functional dyspepsia

description: Background: Recently, it has been suggested that the duodenum may
 be the pathological locus of functional dyspepsia (FD). Additionally, an
 image-based artificial intelligence (AI) model was shown to discriminate
 colonoscopy images of irritable bowel syndrome from healthy subjects with
 an area under the curve (AUC) 0.95. Aim: To evaluate an AI model
 to distinguish duodenal images of FD patients from healthy subjects.
 Methods: Duodenal images were collected from hospital records and labeled
 as "functional dyspepsia" or non-FD in electronic medical
 records. Helicobacter pylori (HP) infection status was obtained from the
 Japan Endoscopy Database. Google Cloud AutoML Vision was used to classify
 four groups: FD/HP current infection (n = 32), FD/HP uninfected (n = 35),
 non-FD/HP current infection (n = 39), and non-FD/HP uninfected (n = 33).
 Patients with organic diseases (e.g., cancer, ulcer, postoperative
 abdomen, reflux) and narrow-band or dye-spread images were excluded.
 Sensitivity, specificity, and AUC were calculated. Results: In total, 484
 images were randomly selected for FD/HP current infection, FD/HP
 uninfected, non-FD/current infection, and non-FD/HP uninfected. The
 overall AUC for the four groups was 0.47. The individual AUC values were
 as follows: FD/HP current infection (0.20), FD/HP uninfected (0.35),
 non-FD/current infection (0.46), and non-FD/HP uninfected (0.74). Next,
 using the same images, we constructed models to determine the presence or
 absence of FD in the HP-infected or uninfected patients. The model
 exhibited a sensitivity of 58.3%, specificity of 100%, positive predictive
 value of 100%, negative predictive value of 77.3%, and an AUC of 0.85 in
 HP uninfected patients. Conclusion: We developed an image-based
 AI model to distinguish duodenal images of FD from healthy subjects,
 showing higher accuracy in HP-uninfected patients. These findings suggest
 AI-assisted endoscopic diagnosis of FD may be feasible.
description: # Data from: Artificial intelligence model for detecting duodenal
 endoscopic changes on images of functional dyspepsia
 [https://doi.org/10.5061/dryad.pvmcvdntc](https://doi.org/10.5061/dryad.pvmcvdntc) We will post 70 duodenal images from 32 patients who were treated for Functional Dyspepsia (FD) and had Helicobacter pylori infection, and 141 images from 39 asymptomatic individuals with Helicobacter pylori infection. Using the presence or absence of symptoms as training data, we constructed an image AI to distinguish between the two groups. ## Description of the data and file structure In the FDHP box, there are duodenal images in jpg format of patients who were treated for Functional Dyspepsia (FD) and had Helicobacter pylori infection. In the nonFDHPpositive box, there are duodenal images in jpg format of asymptomatic individuals with Helicobacter pylori infection.
DOI: 10.5061/dryad.ksn02v7ch
title: Data from: indirect costs of reproduction and the tradeoff between offspring size and number: a framework illustrated by fitness costs and benefits of ovarian fluid

description: Theory describing evolution of offspring size often assumes that the
 production cost per unit volume is the same for small and large offspring.
 However, this may not be true if indirect costs of reproduction (e.g.,
 material and energetic costs of supporting offspring development) scale
 disproportionately with offspring size. Here we show how direct and
 indirect costs of reproduction can be explicitly modeled within the
 Smith-Fretwell framework and how observations of size-number relationships
 can thus be used to evaluate indirect costs. We applied this analysis to
 measures of egg volume and fecundity for over 300 individuals of a coastal
 fish species and found that the tradeoff was much stronger than the
 expected inverse (fecundity scaled with volume-1.843). Larger offspring
 were thus more expensive to produce. For our study species, an important
 indirect cost was that larger eggs were accompanied by disproportionately
 more ovarian fluid. Calorimetry and removal experiments were used to
 further measure both the energetic costs and fitness benefits of ovarian
 fluid. In addition, we show that indirect costs of reproduction can
 intensify size-number tradeoffs in a variety of fishes. Indirect costs of
 reproduction can be large and may therefore play an important role in the
 evolution of offspring size.
description: # Data from: indirect costs of reproduction and the tradeoff between
 offspring size and number: a framework illustrated by fitness costs and
 benefits of ovarian fluid
 [https://doi.org/10.5061/dryad.ksn02v7ch](https://doi.org/10.5061/dryad.ksn02v7ch) ## Description of the data and file structure *California Grunion egg size number.csv* file contains data on egg size and batch fecundity of California Grunion (*Leuresthes tenuis*). SL is standard length in cm; Wt is weight in grams; mean.egg.diameter is measured in mm; sd and n refer to standard deviation and number in the sample used to estimate the mean diameter. n/a indicates no data. *California Grunion egg weight and energy content.csv* file contains data on size and energy content of groups of eggs. Separate samples of the same egg batch were made to measure weight (wet and dry) and energy content (measured via calorimetry). Diameter of eggs is measured in mm. 'avg.E' is mean energy content (calories per gram dry weight). n/a indicates no data. *California Grunion ovarian fluid and fertilization success.csv* file contains data from an experiment where ovarian fluid was manipulated and early developmental success was measured. For each mother, the clutch of eggs was split evenly. For some of the eggs, the ovarian fluid was left intact. For other eggs, the ovarian was removed by rinsing before fertilization. For other eggs, the rinsing procedure was applied after fertilization. At 60 hours post fertilization a sample of approximately 100 embryos were assayed for developmental success. n/a indicates no data.
DOI: 10.15468/dl.c8njbd
title: Occurrence Download

description: A dataset containing 4900 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Jamides alecto"
 ]
}

 The dataset includes 4900 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003950-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/14655386
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.and762
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Norway",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is December",
 "OccurrenceStatus is Present",
 "TaxonKey is Megaptera novaeangliae",
 "Year 2025-2025"
 ]
}

 The dataset includes 56 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003951-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7wm37pw1d
title: Data from: forest stand dynamics of a short-stature tree species: ecological knowledge for sustainable forest management

description: This data set is a forest inventory of Nothofagus antarctica in southern
 Chile. More than 20 sites were selected. In each site, parallel transects
 were set and every 30 m a sampling point was set where the distance to the
 nearest four trees (in accordance with the cardinal points) were measured.
description: We used the quarter point method, where the distance to the
 nearest four trees according to cardinal points was measured.
description: # Data from: forest stand dynamics of a short-stature tree species:
 ecological knowledge for sustainable forest management
 [https://doi.org/10.5061/dryad.7wm37pw1d](https://doi.org/10.5061/dryad.7wm37pw1d) This data set is a forest inventory of *Nothofagus antarctica* in southern Chile. More than 20 sites were selected. In each site, parallel transects were set and every 30 m a sampling point was set where the distance to the nearest four trees (in accordance with the cardinal points) were measured. ## Description of the data and file structure variable name and description STAND - or site, it is where the sampling was conducted; sites varied in terms of precipitation, from very-humid. humid, mesic, and dry TRANSECT - a line draw within the stand PLOT - it is the sampling unit; it is located within the transect Q1SP - distance to tree species 1 (m) Q1DBH - diameter at breast height (DBH, cm) of tree species 1 Q1HEIGHT - height (m) of tree species 1 Q2SP - distance to tree species 2 (m) Q2DBH - diameter at breast height (DBH, cm) of tree species 2 Q2HEIGHT - height (m) of tree species 2 Q3SP - distance to tree species 3 (m) Q3DBH - diameter at breast height (DBH, cm) of tree species 3 Q3HEIGHT - height (m) of tree species 3 Q4SP - distance to tree species 4 (m) Q4DBH - diameter at breast height (DBH, cm) of tree species 4 Q4HEIGHT - height (m) of tree species 4 REG1 - number of seedlings of 0-20 cm height within a central 1 m2 plot REG2 - number of seedlings of 20-50 cm height within a central 1 m2 plot REG3 - number of seedlings of 50-100 cm height within a central 1 m2 plot Missing code - "NA" ##### Sharing/Access information: Data was derived from the following sources: * Fajardo, Alex; Moreno-Meynard, Paulo; Soto, Daniel (Forthcoming 2024). Forest stand dynamics of a short-stature tree species: ecological knowledge for sustainable forest management
DOI: 10.15468/dl.hcg29q
title: Occurrence Download

description: A dataset containing 787125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Engraulis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 787125 records from 228 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003905-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4snbcv
title: Occurrence Download

description: A dataset containing 941 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erionota torus"
 ]
}

 The dataset includes 941 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003953-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60521/332602
title: Processed Acoustic Backscatter, Sidescan and Swath Bathymetry Data (EM302) acquired during E/V Nautilus expedition NA166 (2024)

description: This data set was acquired with a Kongsberg EM302 Multibeam Sonar during E/V Nautilus expedition NA166 conducted in 2024. These data files are of MBSystem-compatible format and include Acoustic Backscatter, Sidescan and Swath Bathymetry data that were processed after acquisition. This data was processed by Ocean Exploration Trust and was included in the Global Multi-Resolution Topography (GMRT) Synthesis (version 4.4.1). Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.60521/332638
title: Processed Gridded Bathymetry Data (EM302) acquired during E/V Nautilus expedition NA166 (2024)

description: This data set was acquired with a Kongsberg EM302 Multibeam Sonar during E/V Nautilus expedition NA166 conducted in 2024. These data files are of GeoTIFF (Raster) format and include Bathymetry data that were processed after acquisition. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.17630/ee2a1f92-ec9b-40c4-afb7-342138947a75
title: Positive and negative effects of coral structure on survival and growth of coral fragments (colony meshes, survival data, extracted data, and code)

description: These data and R scripts were used to carry out the analyses in Chapters 3 & 4 of the thesis "The development and impacts of coral-built structure". These analyses were conducted using R software. Data are provided in various formats (.ply, .csv, .xlsx, .RDS, .shp, etc.) and thus might require specialized software to load (e.g. R, Excel, 3D mesh editing software, or GIS software). More information can be found in the ReadMe files within each folder. The data files are embargoed until 2029.
The data files are embargoed until 05/09/2030
DOI: 10.60521/332639
title: Processed Gridded Acoustic Backscatter Data (EM302) acquired during E/V Nautilus expedition NA166 (2024)

description: This data set was acquired with a Kongsberg EM302 Multibeam Sonar during E/V Nautilus expedition NA166 conducted in 2024. These data files are of GeoTIFF (Raster) format and include Acoustic Backscatter data that were processed after acquisition. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.60521/332641
title: Google Earth files of Acoustic Backscatter and Bathymetry Data (EM302) acquired during E/V Nautilus expedition NA166 (2024)

description: This data set was acquired with a Kongsberg EM302 Multibeam Sonar during E/V Nautilus expedition NA166 conducted in 2024. These data files are of Google Earth (KML/KMZ) format and include Acoustic Backscatter and Bathymetry data that were processed after acquisition. Data were acquired as part of the project: NOAA Ocean Exploration Cooperative Institute (OECI). Funding was provided by: NA19OAR4320072.
DOI: 10.15468/dl.2f4csf
title: Occurrence Download

description: A dataset containing 167082 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is South Africa",
 "OccurrenceStatus is Present",
 "TaxonKey is Fabaceae"
 ]
}

 The dataset includes 167082 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003944-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pc866t1xs
title: Molecular, spectroscopic and thermochemical characterization of C2Cl3, C2F3 and C2Br3 radicals and related species

description: This work reports a detailed theoretical study of the molecular
 parameters, harmonic vibrational frequencies, UV absorption spectra and
 standard enthalpies of formation for the radicals C2X3 (with X = F, Cl,Br)
 and a comparison with the corresponding determinations for the rest
 members of the family C2Xn (with n = 2-4). Molecular properties were
 calculated using different levels of theory: density functional theory
 employing the B3LYP, X3LYP, BMK, M06-2X, and M08-HX functionals combined
 with the basis sets 6-311++G(3df,3pd) and aug-cc-pVT, and the ab initio
 composite models G3B3 and G4. Structural and spectroscopic
 characterization of the C2F3, C2Cl3 and C2Br3 radicals, along with the
 estimation of the enthalpies of formation of C2F3 and C2Cl3, were derived
 here for the first time. In particular, values of -220.9±2.9, 230.8±3.8,
 and 375.4±5.9 kJ mol-1 were computed for enthalpies of formation of C2F3,
 C2Cl3, and C2Br3, respectively. Additionally, enthalpies of formation for
 related closed-shell molecules were obtained with less uncertainty
 compared to those than that found in the literature. The recommended
 values of -669.6±3.8, -23.0±4.6, and 155.3±5.0 kJ mol-1 were derived for
 C2F4, C2Cl4, and C2Br4, while corresponding values of 0.6±6.3, 228.1±2.1,
 and 319.6±5.4 kJ mol-1 were estimated for C2F2, C2Cl2, and C2Br2,
 respectively.
description: # Molecular, spectroscopic and thermochemical characterization of C2Cl3,
 C2F3 and C2Br3 radicals and related species
 [https://doi.org/10.5061/dryad.pc866t1xs](https://doi.org/10.5061/dryad.pc866t1xs) Dataset files provide input matrices for all species used in the work. ## Description of the data and file structure The results presented in our article are supported by data included in both the manuscript and Supplementary Material. However, the two files named "Z-matrix_for_C2Xn_species" and "Z-matrix_for_species_of_isodesmic_reactions" contain input data that allow for the replication of the performed study. These files provide input matrices for all species used in the work. From this information and the Gaussian 16 program package, or another calculation program, it is possible to replicate the results presented here. ## Sharing/Access information Additional information about Gaussian 16 program package can be obtained from [https://gaussian.com/gaussian16/](http://https://gaussian.com/gaussian16/)