cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g79cnp5qn
title: Data from: Community-level responses of African carnivores to prescribed burning

description: Fires are common in many ecosystems worldwide, and are frequently used as
 a management tool. Although the responses of herbivores to fire have been
 well-studied, the responses of carnivores to fire remain unclear. In
 particular, post-fire habitat changes, and the associated changes in prey
 availability, might affect the coexistence or competition of carnivore
 species within the larger carnivore community, but few studies have
 focused on how fires influence multiple carnivore species simultaneously.
 Using South African carnivores as our focal community, we explored
 relative changes in carnivore intensity of use in post-fire landscapes
 associated with hypothesized changes in prey availability and top-down
 suppression. We monitored carnivore intensity of use in relation to
 prescribed burning using camera traps, with a Before-After-Control-Impact
 study design. We analyzed the camera trap data using community N-mixture
 models to understand how individual species, as well as the carnivore
 guild as a whole, respond to burning. Changes in carnivore intensity of
 use in response to prescribed burns were not uniform; however, no species
 decreased intensity of use of post-fire landscapes. The apex predator, the
 lion (Panthera leo), increased use of prey-rich burnt areas, but other
 large carnivore species exhibited neutral responses to fire despite the
 associated prey increase. Responses of medium- and small-sized carnivores
 were species-specific, and included both neutral and positive responses.
 Positive responses to fire by lions and herbivores were short-lived, and
 did not persist a year after burning occurred. Synthesis and Applications:
 Our results indicate that fire does not promote carnivore coexistence by
 creating conditions for all carnivores to increase use of burned areas,
 but that it also likely does not result in spatial avoidance of
 subordinate predators. Instead, fires might cause a suppression of
 opportunities for subordinate large carnivores because they need to avoid
 the apex predator, rather than take advantage of short-term increased
 hunting opportunities in recently burned areas. Our results highlight the
 complexity of understanding species-specific and community-level responses
 of carnivores to fire, and overlooked ecological effects of its use as a
 management tool.
description: Please refer to the ReadMe file for information on the
 dataset.
DOI: 10.5061/dryad.t4b8gtj38
title: Increasing stimulus similarity drives nonmonotonic representational change in hippocampus

description: Studies of hippocampal learning have obtained seemingly contradictory
 results, with manipulations that increase coactivation of memories
 sometimes leading to differentiation of these memories, but sometimes not.
 These results could potentially be reconciled using the nonmonotonic
 plasticity hypothesis, which posits that representational change (memories
 moving apart or together) is a U-shaped function of the coactivation of
 these memories during learning. Testing this hypothesis requires
 manipulating coactivation over a wide enough range to reveal the full
 U-shape. To accomplish this, we used a novel neural network image
 synthesis procedure to create pairs of stimuli that varied parametrically
 in their similarity in high-level visual regions that provide input to the
 hippocampus. Sequences of these pairs were shown to human participants
 during high-resolution fMRI. As predicted, learning changed the
 representations of paired images in the dentate gyrus as a U-shaped
 function of image similarity, with neural differentiation occurring only
 for moderately similar images.
description: Please refer to the manuscript for methodological
 information. Citation: Wammes, Jeffrey D., Kenneth A.
 Norman, and Nicholas B. Turk-Browne. "Increasing stimulus similarity
 drives nonmonotonic representational change in
 hippocampus." <i>eLife</i>.
description: Please refer to the README for information about how to use this
 dataset.
DOI: 10.5061/dryad.z34tmpgf9
title: Canopy cover and ecological restoration increase natural regeneration of rainforest trees in the Western Ghats, India

description: Restoration of canopy cover through tree planting can assist in overcoming
 barriers to natural regeneration and catalyze recovery of degraded
 tropical forests. India has made international pledges to restore millions
 of hectares of degraded forests by 2030, but lacks empirical research on
 regeneration under different types of planted and natural overstories to
 guide this mission. We conducted a field study (65 plots of 25 m2) to
 examine the influence of overstory type and canopy cover on naturally
 regenerating tree seedlings across degraded rainforests (DR), mixed-native
 species ecological restoration sites (ER), monoculture eucalypt
 plantations (MP), and mature “benchmark” rainforests (BR) in the Western
 Ghats mountains of peninsular India. ER had higher native tree seedling
 densities and recovered community composition towards BR levels compared
 to DR, while communities in MP shifted in the opposite direction.
 Densities of native late-successional species increased with canopy cover
 (particularly in ER), but greater canopy cover was also associated with
 increases in alien species, a few of which are shade-tolerant. Further, in
 a nursery experiment comprising four rainforest species, seed germination
 and early survival increased with shade, but did not vary across soils
 originating from DR, ER, and MP. Our findings show that while improving
 canopy cover is important, doing so by planting diverse native species,
 and controlling invasive alien species, can benefit rainforest recovery in
 degraded rainforest fragments. Conversely, planting non-native
 monocultures in degraded forests, which is a prevalent practice in India,
 could prove counterproductive for forest recovery in the long term.
DOI: 10.15468/dl.5pzbd5
title: Occurrence Download

description: A dataset containing 1154 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Castanopsis hystrix"
 ]
}

 The dataset includes 1154 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002950-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hqbzkh1h4
title: Data from: No evidence of foliar disease impact on crop root functional strategies and soil microbial communities: What does this mean for organic coffee?

description: Global climate change is increasing pest and pathogen pressures on plant
 communities, deteriorating optimal plant functioning. In plant
 communities, root functional trait expression and microbial communities
 are important indicators of plant functioning belowground, and, when
 confronted with pathogens aboveground, can simultaneously reflect plant
 defence strategies. Yet, while research is continuing to emerge on the
 response of root functional traits and microbial processes to pathogens
 aboveground, little work has investigated these interactions in
 tree-crops, or the role organic amendments play in moderating
 these relationships. The main objective of this study is
 to disentangle the dynamic effects of pathogens and amendments on
 root functional traits (i.e., specific root length and area, root
 diameter, root length density, root nitrogen, and root carbon to nitrogen
 ratio) and root endophytic fungal communities. As a model, we use Coffea
 arabica (coffee) variety Caturra along a gradient of
 Coffee Leaf Rust – a foliar disease prominent in coffee systems – under
 contrasting but widespread amendment regimes in
 biodiverse agroforestry systems. We found that root trait
 expression varies along established conservation and collaboration
 gradients, where fungal endophyte community composition varies
 significantly as a function of root traits. Belowground resource
 acquisition strategies do not change with foliar disease incidence,
 suggesting they may be decoupled. Rather, amendment regimes differentially
 shape root trait expression and microbial communities, where coffee plants
 under organic amendments, regardless of foliar disease incidence,
 expressed greater acquisitive traits and enhanced collaboration with
 symbiotic fungi. This is an important first step in disentangling the
 dynamic inter-relationships between plant traits, endophytes, and
 pathogens, generating new questions on the role of amendments in
 sustainable pathogen management in biodiverse agroecosystems.
DOI: 10.5061/dryad.xsj3tx9gf
title: Contrast solution properties and scan parameters influence the apparent diffusivity of computed tomography contrast agents in articular cartilage

description: The inability to detect early degenerative changes to the articular
 cartilage surface that commonly precede bulk osteoarthritic degradation is
 an obstacle to early disease detection for research or clinical diagnosis.
 Leveraging a known artifact that blurs tissue boundaries in clinical
 arthrograms, contrast agent diffusivity can be derived from computed
 tomography arthrography (CTa) scans.  We combined experimental
 and computational approaches to study protocol variations that may alter
 the CTa-derived apparent diffusivity. In experimental studies on bovine
 cartilage explants, we examined how contrast agent dilution and transport
 direction (absorption vs. desorption) influence the apparent diffusivity
 of untreated and enzymatically digested cartilage. Using multiphysics
 simulations, we examined mechanisms underlying experimental observations
 and the effects of image resolution, scan interval and early scan
 termination. The apparent diffusivity during absorption decreased with
 increasing contrast agent concentration by an amount similar to the
 increase induced by tissue digestion. Models indicated that osmotically
 induced fluid efflux strongly contributed to the concentration effect.
 Simulated changes to spatial resolution, scan spacing and total scan time
 all influenced the apparent diffusivity, indicating the importance of
 consistent protocols. With careful control of imaging protocols and
 interpretations guided by transport models, CTa-derived diffusivity offers
 promise as a biomarker for early degenerative changes.
DOI: 10.5061/dryad.crjdfn353
title: Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies

description: Clustering approaches are pivotal to handle the many sequence variants
 obtained in DNA metabarcoding datasets, therefore they have become a key
 step of metabarcoding analysis pipelines. Clustering often relies on a
 sequence similarity threshold to gather sequences in Molecular Operational
 Taxonomic Units (MOTUs), each of which ideally representing a homogeneous
 taxonomic entity, e.g. a species or a genus. However, the choice of the
 clustering threshold is rarely justified, and its impact on MOTU
 over-splitting or over-merging even less tested. Here, we evaluated
 clustering threshold values for several metabarcoding markers under
 different criteria: limitation of MOTU over-merging, limitation of MOTU
 over-splitting, and trade-off between over-merging and over-splitting. We
 extracted sequences from a public database for nine markers, ranging from
 generalist markers targeting Bacteria or Eukaryota, to more specific
 markers targeting a class or a subclass (e.g. Insecta, Oligochaeta). Based
 on the distributions of pairwise sequence similarities within species and
 within genera, and on the rates of over-splitting and over-merging across
 different clustering thresholds, we were able to propose threshold values
 minimizing the risk of over-splitting, that of over-merging, or offering a
 trade-off between the two risks. For generalist markers, high similarity
 thresholds (0.96-0.99) are generally appropriate, while more specific
 markers require lower values (0.85-0.96). These results do not support the
 use of a fixed clustering threshold. Instead, we advocate a careful
 examination of the most appropriate threshold based on the research
 objectives, the potential costs of over-splitting and over-merging, and
 the features of the studied markers.
DOI: 10.5061/dryad.xd2547dhk
title: Global patterns and drivers of soil microbial biomass C, N, and P in terrestrial ecosystems

description: Soil microbes play key roles in driving and regulating nutrient cycling in
 terrestrial ecosystems. However, a lack of global-scale information
 regarding the distribution of soil microbial biomass C (SMB C), N (SMB N),
 and P (SMB P) in terrestrial ecosystems has limited our ability to
 incorporate the broad-scale soil microbial nutritional properties and the
 associated processes into biogeochemical models. Here, we synthesized a
 global dataset including 3,801 observations for SMB C, 3,154 observations
 of SMB N, and 2,429 observations of SMB P in the top 0–30 cm soil depth.
 Based on this comprehensive global dataset, we generated quantitative and
 spatially explicit maps of SMB C, N, and P across terrestrial ecosystems
 using a random forest approach. In general, the global mean values of SMB
 C, N, and P concentrations were 693.0 mg kg-1, 89.5 mg kg-1, and 35.5 mg
 kg-1, respectively. These mean values belie a significantly spatial
 heterogeneity of these concentrations across biomes and a clear
 latitudinal trend (wherein SMB C, N, and P increase in cold and high
 latitude environments along with the large soil organic carbon, SOC). SOC
 was the most important factor regulating SMB C, N, and P at a global
 scale. At the global scale, the storage of SMB C, N, and P was estimated
 to be 23.13 Pg C, 3.93 Pg N, and 2.16 Pg P in the top 0–30 cm soil
 surface, respectively. Our global maps of SMB C, N, and P presented here
 can be used to constraint Earth system models, and provide the first step
 forward to predict the roles of soil microbial nutrients in terrestrial
 nutrient cycling.
DOI: 10.5061/dryad.w0vt4b8sh
title: Raw images for bead aggregation assays - Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent

description: Intermicrovillar links are formed by two non-classical members of the
 cadherin superfamily of calcium-dependent cell adhesion proteins:
 protocadherin-24 (PCDH24, also known as CDHR2) and the mucin-like
 protocadherin (CDHR5). Images in this data set are for bead aggregations
 assays used to identify the PCDH24 and CDHR5 domains involved in both
 heterophilic and homophilic adhesion for human and mouse proteins.
description: Some zip files might not be handled well by unix utilities.
 Please use the Archive Utility in MacOSX or Windows utilities for
 compressed files.
DOI: 10.5281/zenodo.18397069
title: RadioML 2016.10a: Optimized and Validated Distribution

description: Description

Optimized version of the RadioML 2016.10a dataset for automatic modulation classification research.

Dataset Contents



11 modulation types: 8 digital (BPSK, QPSK, 8PSK, QAM16, QAM64, CPFSK, GFSK, PAM4) + 3 analog (WB-FM, AM-SSB, AM-DSB).

20 SNR levels: -20 dB to +18 dB (2 dB steps).

1000 I/Q samples per (modulation, SNR) pair.

Format: Python pickle dictionary with keys (mod_name, snr_db) -> arrays of shape (1000, 2, 128).

Data type: float32.


Optimization Details

Original RadioML 2016.10a was distributed as a 640.9 MB pickle file using protocol 0 (ASCII serialization). This version re-serializes the dataset using pickle protocol 4 (binary) with validation to ensure bit-identical data integrity. File size reduced to 225.3 MB (64.9% smaller) with no data loss.

Validation

All 220 (modulation, SNR) pairs were verified as bit-identical.

Original Dataset

Generated synthetically using GNU Radio by O'Shea & West (2016), as described in their paper "Radio Machine Learning Dataset Generation with GNU Radio" presented at the 6th GNU Radio Conference. The paper emphasized sharable and reproducible dataset generation methods for the radio machine learning community. This optimized mirror preserves the original data while providing more efficient storage for modern Python toolchains.
DOI: 10.5281/zenodo.18397070
title: RadioML 2016.10a: Optimized and Validated Distribution

description: Description

Optimized version of the RadioML 2016.10a dataset for automatic modulation classification research.

Dataset Contents



11 modulation types: 8 digital (BPSK, QPSK, 8PSK, QAM16, QAM64, CPFSK, GFSK, PAM4) + 3 analog (WB-FM, AM-SSB, AM-DSB).

20 SNR levels: -20 dB to +18 dB (2 dB steps).

1000 I/Q samples per (modulation, SNR) pair.

Format: Python pickle dictionary with keys (mod_name, snr_db) -> arrays of shape (1000, 2, 128).

Data type: float32.


Optimization Details

Original RadioML 2016.10a was distributed as a 640.9 MB pickle file using protocol 0 (ASCII serialization). This version re-serializes the dataset using pickle protocol 4 (binary) with validation to ensure bit-identical data integrity. File size reduced to 225.3 MB (64.9% smaller) with no data loss.

Validation

All 220 (modulation, SNR) pairs were verified as bit-identical.

Original Dataset

Generated synthetically using GNU Radio by O'Shea & West (2016), as described in their paper "Radio Machine Learning Dataset Generation with GNU Radio" presented at the 6th GNU Radio Conference. The paper emphasized sharable and reproducible dataset generation methods for the radio machine learning community. This optimized mirror preserves the original data while providing more efficient storage for modern Python toolchains.
DOI: 10.5061/dryad.12jm63xzw
title: Data from: Great tits do not compensate over time for a radio-tag-induced reduction in escape-flight performance

description: The use of biologging and tracking devices is widespread in avian
 behavioural and ecological studies. Carrying these devices rarely has
 major behavioural or fitness effects in the wild, yet it may still impact
 animals in more subtle ways, such as during high power demanding escape
 manoeuvres. Here, we tested whether or not great tits (Parus major)
 carrying a backpack radio-tag changed their body-mass or flight behaviour
 over time to compensate for the detrimental effect of carrying a tag. We
 tested 18 great tits, randomly assigned to a control (untagged) or one of
 two different types of a radio-tag as used in previous studies in the wild
 (0.9 g or 1.2 g; ~5% or ~6–7% of body mass, respectively), and determined
 their upward escape-flight performance 1, 7, 14, and 28
 days-after-tagging. In between experiments, birds were housed in large
 free-flight aviaries. For each escape-flight, we used high-speed 3D
 videography to determine flight paths, escape-flight-speed, wingbeat
 frequency and actuator-disk-loading (ratio between the bird weight and
 aerodynamic thrust production capacity). Tagged birds flew upwards with
 lower escape-flight speeds, caused by an increased actuator-disk-loading.
 During the 28-day period, all groups slightly increased their body mass
 and their in-flight wingbeat frequency. In addition, during this period
 all groups of birds increased their escape-flight speed, but tagged birds
 did so at a lower rate than untagged birds. This suggests that birds may
 increase their escape flight performance through skill-learning, however,
 tagged birds still remained slower than controls. Our findings suggest
 that tagging a songbird can have a prolonged effect on the performance of
 rapid flight manoeuvres. Given the absence of tag-effects on reproduction
 and survival in most songbird radio-tagging studies, tagged birds in the
 wild might adjust their risk-taking behaviour to avoid performing rapid
 flight manoeuvres.
DOI: 10.5061/dryad.m37pvmd36
title: Medium-chain fatty acids suppress lipotoxicity-induced hepatic fibrosis via the immunomodulating receptor GPR84

description: Medium-chain triglycerides (MCTs), which consist of medium-chain fatty
 acids (MCFAs), are unique forms of dietary fat with various health
 benefits. GPR84 acts as a receptor for MCFAs (especially C10:0 and C12:0);
 however, GPR84 is still considered an orphan receptor, and the nutritional
 signaling of endogenous and dietary MCFAs via GPR84 remains unclear. Here,
 we showed that endogenous MCFA-mediated GPR84-signaling protected hepatic
 functions from diet-induced lipotoxicity. Under high-fat diet (HFD)
 conditions, GPR84-deficient mice exhibited non-alcoholic steatohepatitis
 (NASH) and the progression of hepatic fibrosis but not steatosis. With
 markedly increased hepatic MCFA levels under HFD, GPR84 suppressed
 lipotoxicity-induced macrophage over-activation. Thus, GPR84 is an
 immunomodulating receptor that suppresses excessive dietary fat
 intake-induced toxicity by sensing increases in MCFAs. Additionally,
 administering MCTs, MCFAs (C10:0 or C12:0, but not C8:0), or GPR84
 agonists effectively prevented NASH in mouse models. Exogenous GPR84
 stimulation is therefore a breakthrough strategy for treating NASH.
description: RNA was extracted from the liver
 and bone marrow from NC-fed and HFD-fed mice using an RNeasy mini kit
 (Qiagen) and RNAiso Plus reagent (TAKARA). Liver and bone marrow were
 obtained from WT mice and <em>Gpr84</em>-deficient mice. The
 RNA sequencing libraries were generated with the TruSeq RNA Library Prep
 Kit (Illumina) and sequenced on an Illumina platform. Approximately 4Gb
 paired-end reads of length 100 bp per sample were obtained. The RNA
 sequencing data were pre-processed using Trimmomatic. The quality of RNA
 was assessed using FastQC.
DOI: 10.5281/zenodo.18394419
title: Large files for BioMeDS/cmr-dynamic-radiomics-stability as dvcstore

description: The large files in the repository https://github.com/BioMeDS/cmr-dynamic-radiomics-stability are managed with dvc. This file is a dvcstore containing most of these files (excluding raw image data from the BAE and ACDC datasets). To access the files, unpack this zip file into your repository root (as the folder dvcstore). Then access the files via `dvc pull`. Latest version is for repository version v0.3.
DOI: 10.5281/zenodo.15239917
title: Large files for BioMeDS/cmr-dynamic-radiomics-stability as dvcstore

description: The large files in the repository https://github.com/BioMeDS/cmr-dynamic-radiomics-stability are managed with dvc. This file is a dvcstore containing most of these files (excluding raw image data from the BAE and ACDC datasets). To access the files, unpack this zip file into your repository root (as the folder dvcstore). Then access the files via `dvc pull`. Latest version is for repository version v0.3.