cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0rxwdbrxh
title: Adsorption and release on three-dimensional graphene oxide network structures

description: In this study, 3D network architectures are constructed using nano-sized
 graphene oxide (nGO) as the building block. The cross-linking reaction of
 nGO is conducted in sub-micrometer water droplets in an emulsion system to
 control the size of the networks by restricting the reaction space. Two
 types of 3D GO networks having different cross-linking lengths were
 constructed, and their methyl orange adsorption and release behaviours
 were investigated under external stimuli, such as thermal treatment,
 ultrasonic wave treatment, and near-infrared light irradiation.
DOI: 10.5061/dryad.hx3ffbgcb
title: Revisiting the sedimentary record of the rise of diatoms

description: Diatoms are a major primary producer in the modern oceans and play a
 critical role in the marine silica cycle. Their rise to dominance is
 recognized as one of the largest shifts in Cenozoic marine ecosystems, but
 the timing of this transition is debated. Here, we use a diagenetic model
 to examine the effect of sedimentation rate and temperature on the burial
 efficiency of biogenic silica over the past 66 million years (i.e., the
 Cenozoic). We find that the changing preservation potential of siliceous
 microfossils during that time would have overprinted the primary signal of
 diatom and radiolarian abundance. We generate a taphonomic null hypothesis
 of the diatom fossil record by assuming a constant flux of diatoms to the
 sea floor and having diagenetic conditions driven by observed shifts in
 temperature and sedimentation rate. This null hypothesis produces a late
 Cenozoic (~5-20 Ma) increase in the relative abundance of fossilized
 diatoms that is comparable to current empirical records. This suggests
 that the observed increase in diatom abundance in the sedimentary record
 may be driven by changing preservation potential. A late Cenozoic rise in
 diatoms has been causally tied to the rise of grasslands and baleen whales
 and to declining atmospheric CO2 levels. Here we suggest that the
 similarity among these records primarily arises from a common driver—the
 cooling climate system—that drove enhanced diatom preservation as well as
 the rise of grasslands and whales, rather than a causal link amongst them.
description: Data is sourced from published literature (citations in ReadMe
 file and in Related Works). The only processing they have undergone is to
 remove undesired variables and to rename columns.
description: Code and datasets (csv and txt files) for all analyses and
 figures. Using included RProject is recommended. ReadMe file provides
 order of operations (code must be run in sequence) and data source
 citations.
DOI: 10.5061/dryad.37pvmcvhm
title: Efficient sub-pixel fully connected neural network: an intelligent fault diagnosis method for signal resolution enhancement

description: Using deep learning to augment the dataset has become a hot topic in
 various fields. That is, to generate a more simulated dataset from the
 limited dataset. However, the premise of the study is to use high
 resolution sampling equipment to collect experimental data. In this paper,
 we propose a simple and effective algorithm -- efficient sub-pixel fully
 connected neural network (ESPFCN). Different from other data enhance
 algorithms, ESPFCN does not explicitly generate more simulation data. On
 the contrary, it performs the fully-connected operation on the original
 input data and outputs the results of four-channel multi-feature maps.
 Through the sub-pixel fully connected layer, the data resolution is
 changed from low to high and increased to 4 times of the original.
 Finally, two set of bearing and gearbox experiments are set up to evaluate
 the performance of the generated model. The experimental results verify
 the effectiveness of the ESPFCN model, and the feature learning process of
 ESPFCN is visualized.
description: The bearing vibration signal is collected by LMS data acquisition
 instrument with a vibration sensor, and the senor is placed on the side of
 the bearing seat. The sampling frequency is 25.6 kHz. The engine speed is
 3000 r/min and the bearing type is N205EU cylindrical roller bearing. As
 is displayed in Table 1, the type of bearing has four health conditions:
 normal condition (NC), inner ring fault (IF), outer ring fault (OF) and
 roller ball fault (RF). There are three different degrees of damages for
 each fault type: 0.2 mm, 0.4 mm and 0.6 mm. Bearing health conditions is
 divided into ten kinds, each state contains 200 samples.   
 The gearbox vibration signal is also collected by LMS data
 acquisition instrument with a vibration sensor, the motor speed is
 constant at 2000 r/min, and 7 kinds of gearbox signals with different
 health conditions are collected at different sampling frequencies (6.4
 kHz, 25.6 kHz), respectively, as follows: NC (normal condition), PC
 (pinion crack), PP (pinion pit), WC (sun wheel crack), WCPC (sun wheel
 crack and pinion pit), WPPC (wheel pit and pinion crack), WPPP (sun wheel
 pit and pinion pit )
DOI: 10.5281/zenodo.18374536
title: Multi-stage Phenotype Dataset of Brassica Cultivars with LLM-assisted Annotations

description: This dataset contains comprehensive phenotypic data for Brassica cultivars at two growth stages: early vegetative (seeding) and mature plant stages. The dataset includes RGB images, structured phenotype descriptions generated using large language model (LLM)-assisted schema-constrained annotation, and human-provided descriptive tags.

DATASET CONTENTS:

Seeding Dataset:



284 Brassica cultivars at early vegetative stage

RGB images organized by cultivar ID

Schema-constrained phenotype descriptions (JSON format)

Human-annotated descriptive tags (partial coverage)

LLM-assisted categorical grouping (7 categories)


Mature Plant Dataset:



141 Brassica cultivars at mature growth stage

RGB images organized by cultivar ID

Schema-constrained phenotype descriptions (JSON format)


DATA FORMATS:



Images: JPEG format

Phenotypes: Structured JSON following comprehensive botanical schema

Tables: Tab-separated values (TSV) with flattened phenotype data

Annotations: Plain text taginfo files

Metadata: CSV manifests and JSON summaries


METHODOLOGY:

The phenotype annotations were generated using Claude Sonnet 3.7 with schema-constrained prompting to ensure consistent, structured, and botanically accurate descriptions. Human tags provide additional validation for the seeding dataset.

DATA QUALITY ASSURANCE:



MD5 checksums for all files ensure data integrity

JSON schema validation for phenotype data

Comprehensive manifests track all files

No modification of raw data (rsync-based preservation)


FAIR PRINCIPLES:

This dataset is prepared following FAIR (Findable, Accessible, Interoperable, Reusable) principles:



Persistent identifiers (DOI)

Rich metadata and data dictionaries

Standard file formats

Clear licensing (CC-BY-4.0)

Comprehensive documentation


ARCHIVE CONTENTS:

1. seeding_dataset.tar.gz (1.8 GB) - Seeding stage data with images, phenotypes, annotations, and metadata2. mature_plant_dataset.tar.gz (2.1 GB) - Mature plant stage data with images, phenotypes, and metadata3. metadata.tar.gz (8.7 KB) - Dataset-level documentation, citations, and licenses

Each archive includes MD5 checksum files for verification.

INTENDED USE:



Plant phenotyping research

Computer vision model training

Agricultural breeding programs

Machine learning applications in agriculture

Comparative phenotype analysis

LLM annotation validation studies
DOI: 10.5281/zenodo.18374537
title: Multi-stage Phenotype Dataset of Brassica Cultivars with LLM-assisted Annotations

description: This dataset contains comprehensive phenotypic data for Brassica cultivars at two growth stages: early vegetative (seeding) and mature plant stages. The dataset includes RGB images, structured phenotype descriptions generated using large language model (LLM)-assisted schema-constrained annotation, and human-provided descriptive tags.

DATASET CONTENTS:

Seeding Dataset:



284 Brassica cultivars at early vegetative stage

RGB images organized by cultivar ID

Schema-constrained phenotype descriptions (JSON format)

Human-annotated descriptive tags (partial coverage)

LLM-assisted categorical grouping (7 categories)


Mature Plant Dataset:



141 Brassica cultivars at mature growth stage

RGB images organized by cultivar ID

Schema-constrained phenotype descriptions (JSON format)


DATA FORMATS:



Images: JPEG format

Phenotypes: Structured JSON following comprehensive botanical schema

Tables: Tab-separated values (TSV) with flattened phenotype data

Annotations: Plain text taginfo files

Metadata: CSV manifests and JSON summaries


METHODOLOGY:

The phenotype annotations were generated using Claude Sonnet 3.7 with schema-constrained prompting to ensure consistent, structured, and botanically accurate descriptions. Human tags provide additional validation for the seeding dataset.

DATA QUALITY ASSURANCE:



MD5 checksums for all files ensure data integrity

JSON schema validation for phenotype data

Comprehensive manifests track all files

No modification of raw data (rsync-based preservation)


FAIR PRINCIPLES:

This dataset is prepared following FAIR (Findable, Accessible, Interoperable, Reusable) principles:



Persistent identifiers (DOI)

Rich metadata and data dictionaries

Standard file formats

Clear licensing (CC-BY-4.0)

Comprehensive documentation


ARCHIVE CONTENTS:

1. seeding_dataset.tar.gz (1.8 GB) - Seeding stage data with images, phenotypes, annotations, and metadata2. mature_plant_dataset.tar.gz (2.1 GB) - Mature plant stage data with images, phenotypes, and metadata3. metadata.tar.gz (8.7 KB) - Dataset-level documentation, citations, and licenses

Each archive includes MD5 checksum files for verification.

INTENDED USE:



Plant phenotyping research

Computer vision model training

Agricultural breeding programs

Machine learning applications in agriculture

Comparative phenotype analysis

LLM annotation validation studies
DOI: 10.5061/dryad.8sf7m0ck8
title: Personality composition determines social learning pathways within shoaling fish

description: In shaping how individuals explore their environment and interact with
 others, personality may mediate both individual and social learning. Yet
 increasing evidence indicates that personality expression is contingent on
 social context, suggesting that group personality composition may be key
 in determining how individuals learn about their environment. Here, we
 used recovery latency following simulated predator attacks to identify
 Trinidadian guppies (Poecilia reticulata) that acted in a consistently
 bold or shy manner. We then employed network-based diffusion analysis to
 track the spread of a novel foraging behaviour through groups containing
 different proportions of bold and shy fish. Informed associates promoted
 learning to a greater extent in bold individuals, but only within groups
 composed predominately of bold fish. As the proportion of shy fish within
 groups increased, bold individuals instead emerged as especially effective
 demonstrators that facilitated learning in others. Individuals were also
 more likely to learn overall within shy-dominated groups than in
 bold-dominated ones. We demonstrate that how individuals learn is
 conditional on group personality composition, indicating that selection
 may favour traits enabling individuals to better match their behavioural
 phenotype to their social environment.
description: Lab-reared Trinidadian guppies (Poecilia reticulata) were
 repeatedly exposed to a simulated predation event to evaluate their
 risk-taking tendencies. Individuals that were quick to
 resume normal movement following these "attacks" were labeled as
 bold, while individuals slow to resume movement were labelled as
 shy. We then formed groups containing different
 proportions of bold and shy individuals:<br> -Bold-dominated groups:
 8 bold fish, 2 shy fish<br> -Mixed groups: 5 bold fish, 5 shy
 fish<br> -Shy-dominated groups: 2 bold fish, 8 shy fish
 Twelve groups of each composition were formed.
 On the day following group formation, nearest-neighbour shoaling
 associations were recorded during focal follows to construct a
 proximity-based social network for each group. Measurements of
 individuals' elective group size were also made during these shoaling
 observations. We then presented groups with a novel
 foraging task consisting of an opaque cylinder with a small entrance hole
 in the lower half and food items floating on the water's surface
 within. Groups were given 20 min to interact with
 device. During this time, we recorded each individual's latency to
 solve the task (i.e. entering the cylinder). For those
 individuals that entered the device, we further recorded how many times
 they did so and whether feeding strikes were observed.
description: Please see the ReadMe file for information on using this dataset.
 We have additionally included R code to reproduce the analyses reported in
 the main text and supplementary material.
DOI: 10.5061/dryad.ffbg79cs9
title: Unaltered soil microbial community composition, but decreased metabolic activity in a semi-arid grassland after two years of passive experimental warming

description: Soil microbial communities regulate soil carbon feedbacks to climate
 warming through microbial respiration (i.e. metabolic rate). A thorough
 understanding of the responses of composition, biomass and metabolic rate
 of soil microbial community to warming is crucial to predict soil carbon
 stocks in a future warmer climate. Therefore, we conducted a field
 manipulative experiment in a semi-arid grassland on the Loess Plateau of
 China to evaluate the responses of the soil microbial community to
 increased temperature from April 2015 to December 2017. Soil temperature
 was 2.0 oC higher relative to the ambient when open-top chambers (OTCs)
 were used. Warming did not affect microbial biomass or the composition of
 microbial functional groups. However, warming significantly decreased
 microbial respiration, directly resulting from soil pH decrease driven by
 the co-mediation of aboveground biomass increase, inorganic nitrogen
 increase and moisture decrease. These findings highlight that the soil
 microbial community structure of semi-arid grasslands resisted the
 short-term warming by 2 oC, although its metabolic rate declined.
description: Manipulative Experiment
DOI: 10.5061/dryad.69p8cz905
title: Data and R code for What you see is where you go: visibility influences movement decisions of a forest bird navigating a 3D structured matrix

description: Animal spatial behaviour is often presumed to reflect responses to visual
 cues. However, inference of behaviour in relation to the environment is
 challenged by the lack of objective methods to identify the information
 that effectively is available to an animal from a given location. In
 general, animals are assumed to have unconstrained information on the
 environment within a detection circle of a certain radius (the perceptual
 range; PR). However, visual cues are only available up to the first
 physical obstruction within an animal’s PR, making information
 availability a function of an animal’s location within the physical
 environment (the effective visual perceptual range; EVPR). By using LiDAR
 data and viewshed analysis, we model forest birds’ EVPRs at each step
 along a movement path. We found that the EVPR was on average 0.063% that
 of an unconstrained PR and, by applying a step-selection analysis, that
 individuals are 1.57 times more likely to move to a tree within their EVPR
 than to an equivalent tree outside it. This demonstrates that behavioural
 choices can be substantially impacted by the characteristics of an
 individual’s EVPR and highlights that inferences made from movement data
 may be improved by accounting for the EVPR.
DOI: 10.5061/dryad.qbzkh18fz
title: A single pleiotropic locus influences the rate of hybridisation between two sibling species of Lygaeus bugs

description: The evolution of reproductive isolation lies at the heart of understanding
 the process of speciation. Of particular interest is the relationship
 between pre- and post-zygotic reproductive isolation, and the genetic
 architecture of traits that contribute to one or both forms of
 reproductive isolation. The sibling species of seed bug Lygaeus equestris
 and L. simulans show a classic pattern of asymmetric pre-zygotic
 reproductive isolation, with female L. equestris hybridising with male L.
 simulans, but with no hybridisation in the reciprocal direction. We have
 recently described a mutant pale colour form of L. simulans, that inherits
 as a single Mendelian locus and is pleiotropic for a number of other life
 history and behavioural traits. Here we tested whether this locus also
 influences pre- and post-zygotic reproductive isolation. Two sets of
 experimental crosses revealed that behavioural isolation varied with
 mutant versus wild-type phenotype for male L. simulans, with the pale form
 less successful at mating with female L. equestris. In terms of trying to
 assess post-zygotic isolation, levels of hybrid offspring production were
 uniformly low across the experiments. However, we did obtain, for the
 first time, hybrid offspring from a pairing between a female L. simulans
 and a male L. equestris. In this instance, the female was of the pale
 mutant genotype. Together with evidence for heterozygote advantage in
 terms of nymph survival, we consider our results in terms of possible
 mechanisms of reproductive isolation between this species pair, the role
 of the pale mutation, and the possible genetic architectures underlying
 the mutation, from a single gene to a super-gene.
description: This data was collected through the laboritory experiments
 carried out in the Shuker Lab at the University of St Andrews as described
 in detail in  the methods section of the manuscript. In short, two
 species, Lygaeus simulans (of which there were two different colour
 morphs) and L. equestris were paired up in different treatments
 combinations (species, colour morph) and data was collected on whether
 pairs copulated, copulation duration, egg production, offspring production
 and hybridisation. Data was then analysed using R statistical
 software.
description: READ ME files have been included with the data.
DOI: 10.5061/dryad.6t1g1jwx3
title: Morphological convergence obscures functional diversity in sabre-toothed carnivores

description: The acquisition of elongated, sabre-like canines in multiple vertebrate
 clades during the last 265 million years represents a remarkable example
 for convergent evolution. Due to striking superficial similarities in the
 cranial skeleton, the same or similar skull and jaw functions have been
 inferred for sabre-toothed species and interpreted as an adaptation to
 subdue large-bodied prey. However, although some sabre-tooth lineages have
 been classified into different ecomorphs (dirk-tooths and scimitar-tooths)
 the functional diversity within and between groups and the evolutionary
 paths leading to these specialisations are unknown. Here, we use a suite
 of biomechanical simulations to analyse key functional parameters
 (mandibular gape angle, bending strength, bite force) to compare the
 functional performance of different groups and to quantify evolutionary
 rates across sabre-tooth vertebrates. Our results demonstrate a remarkably
 high functional diversity between sabre-tooth lineages and that cranial
 function and prey killing strategies evolved within clades. Moreover,
 different biomechanical adaptations in coexisting sabre-tooth species
 further suggest that this functional diversity was at least partially
 driven by niche-partitioning.
DOI: 10.5061/dryad.f1vhhmgv3
title: Supplemental table from: CLIA laboratory testing for Facioscapulohumeral Dystrophy (FSHD): a retrospective analysis

description: Objective: To summarize facioscapulohumeral muscular dystrophy
 (FSHD) diagnostic testing results from the University of Iowa Molecular
 Pathology Laboratory.  Methods: All FSHD tests performed
 in the diagnostic laboratory January 2015-July 2019 were retrospectively
 reviewed. Testing was by restriction enzyme digestion and Southern blot
 analysis with sequencing of SMCHD1, if indicated. Cases
 were classified as FSHD1 (4q35 EcoRI size ≤40kb; 1-10 D4Z4 repeats), FSHD2
 (permissive 4q35A allele, D4Z4 hypomethylation,
 and  pathogenic SMCHD1 variant), or
 non-FSHD1,2. We also noted cases with borderline EcoRI fragment size
 (41-43kb; 11 D4Z4 repeats), cases that meet criteria for both FSHD1 and
 FSHD2, somatic mosaicism, and cases with hybrid alleles that add
 complexity to test interpretation.  Results: Of the 1594
 FSHD tests included in the analysis, 703 (44.1%) were diagnosed with FSHD.
 Among these positive tests, 664 (94.5%) met criteria for FSHD1 and 39
 (5.5%) met criteria for FSHD2. Of all 1594 cases, 20 (1.3%) had a 4q35
 allele of borderline size, 23 (1.5%) were somatic mosaics, and 328 (20.9%)
 had undergone translocation events. Considering only cases with at least
 one 4q35A allele, D4Z4 repeat number differed significantly among groups:
 FSHD1 cases median of 6.0 (IQR: 4-7) repeats, FSHD2 cases 15.0 (IQR:
 12-22) repeats, and non-FSHD1,2 cases 28.0 (IQR: 19-40) repeats. 
 Conclusion: FSHD1 accounts for 94.5% of genetically confirmed cases of
 FSHD. The data show a continuum of D4Z4 repeat numbers with FSHD1 samples
 having the fewest, FSHD2 an intermediate number, and non-FSHD1,2 the most.
DOI: 10.15468/dl.fgp3sr
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Lao People’s Democratic Republic",
 "TaxonKey is Ichthyophis"
 ]
}

 The dataset includes 48 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002562-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.47d7wm3bm
title: Magnetic susceptibility-weighted imaging mapped the migratory route of a paragonimus in brain

description: A 53-year-old man with a recent history of left temporal lobe hemorrhage
 presented with weakness of left upper limb for 4 days. Paragonimus eggs
 were detected in patient's sputum. Work up revealed paragonimiasis, a
 lung fluke worm infection endemic to East Africa, West Africa and South
 America which rarely involves in brain. Characteristic tunnel
 sign was visualized on brain MRI. Notably, susceptibility-weighted imaging
 revealed a migratory pattern of the parasite from the left temporal lobe
 to the right parietal lobe and resultant patchy hemorrhage. Treatment with
 praziquantel resulted in favorable outcome without residual deficits.