cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vdncjsz0h
title: Fish on fire: Shifts in Amazonian fish communities after floodplain forest fires

description: Severe droughts can lead to fires that cause massive tree mortality in
 even the wettest and most isolated Amazonian forests. After repeated
 fires, blackwater floodplain forests can remain in an open vegetation
 state of arrested succession that facilitates a transition towards a
 white-sand “savanna-like” vegetation. These vegetation shifts from
 closed-canopy floodplain forests to open fire scars, and eventually
 white-sand savannas, may have profound implications for fish communities
 that depend on floodplain forests for food and recruitment. In turn,
 changes in fish communities may contribute to the arrested forest recovery
 after fires as fish are important seed dispersal agents for many
 floodplain tree species. To explore the impacts of floodplain forest fires
 on fish communities, we sampled fish in unburnt forests, fire scars, and
 white-sand savannas in the middle Rio Negro basin (Brazil) during two
 consecutive flooding seasons. We compared the abundance, species richness,
 and the taxonomic and trophic composition of fish assemblages across the
 three habitat types.  We found significant shifts in fish
 assemblages in fire scars compared to unburnt floodplain forests. Also, as
 fire scars increased in size, total fish biomass decreased strongly. Fish
 communities in unburnt floodplain forests seem to be characterized by a
 higher proportion of smaller and omnivorous fish species than fish
 communities in burned floodplain forests and white sand savannas. Fish
 assemblages in fire scars and white-sand savanna were not significantly
 different. Synthesis and Applications. Amazonian fish communities change
 after floodplain forest fires. Unburnt forests have diverse fish
 communities, with a large proportion of unique and small omnivorous
 species. In contrast, carnivores and detritivores become more common in
 fire scars and white-sand savannas formed after forest fires. Less
 omnivore fish after forest fires can reduce tree seed dispersal and forest
 regeneration, affecting ecosystem functioning and the services provided by
 Amazonian forests. Fish are also a primary source of food and income for
 people living in Amazonian floodplains. Preventing forest fires is
 therefore of fundamental importance for the conservation of Amazonian
 aquatic and terrestrial ecological communities as well as for the
 livelihood of people.
DOI: 10.5061/dryad.pvmcvdnr7
title: Data for: Coping with abrasive food – diverging composition of radular teeth in two Porifera-consuming nudibranch species (Mollusca, Gastropoda)

description: Molluscs forage with their radula, a chitinous membrane with teeth.
 Adaptations to hard or abrasive ingesta were well studied in
 Polyplacophora and Patellogastropoda, but for other taxa, there are large
 gaps in knowledge. Here, we investigated the nudibranch gastropods
 Felimare picta and Doris pseudoargus, both of which feed on Porifera.
 Tooth morphologies were documented by scanning electron microscopy and
 mechanical properties were tested by nanoindentation. We found that these
 parameters are rather similar in both species, indicating that teeth are
 similar in their function. To study the composition, teeth were visualized
 using confocal laser scanning microscopy (CLSM), to determine the degree
 of tanning, and analysed with energy-dispersive X-ray spectroscopy, to
 test the elemental composition. The emitted autofluorescence signal and
 the inorganic content differed between the species. This was especially
 prominent when studying the inner and outer tooth surfaces (leading and
 trailing edges). In F. picta, we detected high proportions of Si, whereas
 teeth of D. pseudoargus contained high amounts of Ca, which influenced the
 autofluorescence signal in CLSM. Employing nanoindentation, we determined
 high Young’s modulus and hardness values for the leading edges of teeth,
 which relate to the Si- and Ca-content. This highlights that teeth with a
 similar morphology and mechanical properties can be mechanically enhanced
 via different chemical pathways in Nudibranchia.
description: The values of E and H were obtained by nanoindentation and the
 elemental compositions by EDX.
description: Excel or any other statistic software.
DOI: 10.5061/dryad.t4b8gtj6h
title: Data from: Pollinators and plants as ecosystem engineers: post-dispersal fruits provide new habitats for other organisms

description: Ecosystem engineering consists of a ubiquitous and fundamental class of
 interactions where some organisms promote state changes in biotic and
 abiotic materials which indirectly affect others. Since the concept was
 created as a counterpoint to traditional flux-based models, pollinators
 have never been considered to promote ecosystem engineering because they
 modulate the supply of resources used by seed/fruit consumers. However,
 dry fruits may persist in the environment for long periods after seed
 dispersion as empty structures that are an additional alternative for
 occupancy. These increase the realized niche of some organisms, being a
 clear example of biogenic habitats. Here, we demonstrate how pollination
 may boost ecosystem engineering using an illustrative case study based on
 a specialized interaction between a bee and an orchid with characteristic
 capsular fruits. We demonstrate that the orchid is fully dependent on the
 pollinator to set fruits. Post-dispersal fruits are voluminous and remain
 attached to the plant for several years. By investigating the occupation
 patterns of arthropods, we show that post-dispersal fruits are highly
 suitable for occupants when compared to pre-dispersal and dispersing
 fruits. Only 13.3% of post-dispersal fruits were never occupied, 33.3% had
 organisms inside and 53.3% showed signs of previous occupation. We propose
 that pollinators are allogenic engineers and plants autogenic, since they
 promote state changes through their actions and their own physical
 structure, respectively. Thus, pollination is a case of cooperative
 ecosystem engineering whereby the effects of the interaction between two
 or more species expand habitat suitability. Since most plants rely on
 pollination to set fruits, we suggest that pollination-mediated
 engineering constitutes a widespread phenomenon. This offers a new
 perspective about the effects of pollination in nature, highlighting the
 importance of pollinators and opening new avenues of investigation of
 ecosystem dynamics and biodiversity maintenance.
DOI: 10.5061/dryad.kh18932bs
title: Data for: Upslope migration is slower in species with high physiological demands

description: Climate change is forcing species to migrate to cooler temperatures at
 higher elevations, yet many taxa are dispersing slower than necessary. One
 yet-to-be-tested explanation for inadequate migration rates is that
 high-elevation environments pose physiological barriers to dispersal,
 particularly in species with high metabolic demands. Our global synthesis
 of &gt;800 species supports this “physiological constraints”
 hypothesis: upslope migration is slower in insects that depend on nature’s
 most expensive locomotor strategy—flight.
DOI: 10.5061/dryad.79cnp5j19
title: Methods to pick up overlapping small fragment pairs from two libraries

description: PIWI-interacting (pi)RNA pathways control transposable elements (TEs) and
 endogenous genes, playing important roles in animal gamete formation.
 However, the underlying piRNA biogenesis mechanisms remain elusive. Here,
 we show endogenous protein-coding sequences (CDSs), that are normally used
 for translation, serve as origins of non-coding piRNA biogenesis in
 Drosophila melanogaster testes. The product, namely CDS-piRNAs, formed
 silencing complexes with Aubergine (Aub) in germ cells. Proximity proteome
 and functional analyses show CDS-piRNAs and cluster/TE-piRNAs are distinct
 species occupying Aub, the former loading selectively relies on chaperone
 Cyclophilin 40. Moreover, Argonaute-2 (Ago2) and Dicer-2 activities were
 found critical for CDS-piRNA production. We provide evidence that
 Ago2-bound short interfering (si)RNAs and micro(mi)RNAs specify precursors
 to be processed into piRNAs. We further demonstrate that Aub is crucial in
 spermatid differentiation, regulating chromatins through mRNA cleavage.
 Collectively, our data illustrate a unique strategy employed by male
 germline, expanding piRNA repertoire for silencing of endogenous genes
 during spermatogenesis.
DOI: 10.5061/dryad.x95x69pq6
title: Mantis shrimp locomotion: coordination and variation of hybrid metachronal swimming

description: Across countless marine invertebrates, coordination of closely spaced
 swimming appendages is key to producing diverse locomotory behaviors.
 Using a widespread mechanism termed hybrid metachronal propulsion, mantis
 shrimp swim by moving five paddle-like pleopods along their abdomen in a
 posterior to anterior sequence during the power stroke and a
 near-synchronous motion during the recovery stroke. Despite the ubiquity
 of this mechanism, it is not clear how hybrid metachronal swimmers
 coordinate and modify individual appendage movements to achieve a range of
 swimming capabilities. Using high-speed imaging, we measured pleopod
 kinematics of mantis shrimp (Neogonodactylus bredini) while they performed
 two swimming behaviors: burst swimming and taking off from the substrate.
 By tracking each of the five pleopods, we tested how stroke kinematics
 vary across swimming speeds and the two swimming behaviors. We found that
 mantis shrimp achieve faster swimming speeds through a combination of
 higher beat frequencies, smaller stroke durations, and partially via
 larger stroke angles. The five pleopods exhibit non-uniform kinematics
 that contribute to the coordination and forward propulsion of the whole
 system. Micro-hook structures (retinacula) connect each of the five
 pleopod pairs and differ in their attachment across pleopods – possibly
 contributing to passive kinematic control. We compare our findings in N.
 bredini to previous studies to identify commonalities across hybrid
 metachronal swimmers at high Reynolds numbers and centimeter scales.
 Through our large experimental dataset and by tracking each pleopod’s
 movements, our study reveals key parameters by which mantis shrimp adjust
 and control their swimming, yielding diverse locomotor abilities.
description: Please see the associated
 publication for detailed methodology. This is a kinematics study based on
 digital analysis of high-speed images and a morphology study based on
 microscopy.<br>
description: R code, csv data files.
DOI: 10.6084/m9.figshare.31169626
title: Data from: <b>Tropical cyclones impact the dispersal of a globally invasive moth pest</b>

description: Wind patterns are a crucial factor for migratory insect pests. However, the impact of extreme weather events, such as tropical cyclones (TCs), on migratory pest dynamics remains unclear. Here, we combined long-term trapping data with climatic variables and hydrogen stable isotope analysis to investigate how TCs influence the population dynamics of a globally invasive moth pest, fall armyworm (<i>Spodoptera frugiperda</i>), across the Gulf of America, formerly known as the Gulf of Mexico. TCs significantly increased fall armyworm moth abundance, shifting their peak activity across years. Most moths originated from southeastern Florida and the Caribbean, resulting in a 54% increase in migratory moths during the TC season. These findings reveal a previously unquantified link between extreme weather events (TCs) and migratory pest outbreaks. As TCs intensify, fall armyworm migration patterns may become increasingly unpredictable, posing greater challenges for pest management and agricultural sustainability.
DOI: 10.6084/m9.figshare.31169626.v2
title: Data from: <b>Tropical cyclones impact the dispersal of a globally invasive moth pest</b>

description: Wind patterns are a crucial factor for migratory insect pests. However, the impact of extreme weather events, such as tropical cyclones (TCs), on migratory pest dynamics remains unclear. Here, we combined long-term trapping data with climatic variables and hydrogen stable isotope analysis to investigate how TCs influence the population dynamics of a globally invasive moth pest, fall armyworm (<i>Spodoptera frugiperda</i>), across the Gulf of America, formerly known as the Gulf of Mexico. TCs significantly increased fall armyworm moth abundance, shifting their peak activity across years. Most moths originated from southeastern Florida and the Caribbean, resulting in a 54% increase in migratory moths during the TC season. These findings reveal a previously unquantified link between extreme weather events (TCs) and migratory pest outbreaks. As TCs intensify, fall armyworm migration patterns may become increasingly unpredictable, posing greater challenges for pest management and agricultural sustainability.
DOI: 10.6084/m9.figshare.31169626.v1
title: Data set: Hydrogen data

description: Wind patterns are a crucial factor for migratory insect pests. However, the impact of extreme weather events, such as tropical cyclones (TCs), on migratory pest dynamics remains unclear. Here, we combined long-term trapping data with climatic variables and hydrogen stable isotope analysis to investigate how TCs influence the population dynamics of a globally invasive moth pest, fall armyworm (<i>Spodoptera frugiperda</i>), across the Gulf of America, formerly known as the Gulf of Mexico. TCs significantly increased fall armyworm moth abundance, shifting their peak activity across years. Most moths originated from southeastern Florida and the Caribbean, resulting in a 54% increase in migratory moths during the TC season. These findings reveal a previously unquantified link between extreme weather events (TCs) and migratory pest outbreaks. As TCs intensify, fall armyworm migration patterns may become increasingly unpredictable, posing greater challenges for pest management and agricultural sustainability.
DOI: 10.25338/b87d2j
title: Data from: All-atom molecular dynamics simulation and rate calculation for norepinephrine binding beta adrenergic receptor

description: This dataset is for the manuscript "A multiscale predictive digital
 twin for neurocardiac modulation". We utilized all-atom molecular
 dynamics (MD) simulations to predict the affinities as well as association
 and dissociation rates of norepinephrine (NE) with the beta-2 adrenergic
 receptor (β2AR). Calculations were done for both cationic (+) and neutral
 (0) forms of NE. An active-state β2AR model based on its crystal structure
 PDB ID: 4LDO was used with the flexible intracellular loop 3 (ICL3)
 truncated to 3 residues. ROSETTALIGAND was used for docking NE(+) and
 NE(0) to the receptor's orthosteric ligand binding site with one of
 the top scoring models used for MD simulations. MD simulation systems of
 the NE(+) or NE(0) bound β2AR receptor embedded in a
 palmitoyloleoylphosphatidylcholine (POPC) bilayer solvated by aqueous 0.15
 M NaCl was generated using CHARMM-GUI membrane builder. MD simulations
 were run with NAMD in the NPT ensemble at 310 K and 1 atm pressure using
 CHARMM36m force field for protein, C36 for lipids, CGENFF based parameters
 for NE(+) and NE(0), and TIP3P water model. Initial equilibration MD
 simulations were run for ~52 ns with the first ~2 ns using gradually
 reduced harmonic restraints on the protein and lipid tail carbon atoms
 followed by unrestrained 50 ns long MD simulation runs. They were used to
 start 200 ns long well-tempered metadynamics MD simulations to estimate
 ligand binding affinities and rates. Distance between centers of mass
 (COM) of protein alpha-helical core and NE was used as reaction coordinate
 R extending to 50 Å in bulk, whereas angle θ between vectors connecting
 these points and ligand orthosteric binding site was used to restrain
 sampling within θ≤30° cone. Affinities in the form of dissociation
 constants, Kd, were computed as was done previously (Provasi D et al
 Biochemistry 2009, 48:10020) NE Kd value at pH=7.4 was computed from
 corresponding estimates for NE(+) and NE(0) using Henderson-Hasselbach
 equation as was done previously (Yang PC et al Circ Res 2020, 126:947)
 NE(+) dissociation or “off” rate was estimated using Kramer’s rate
 formalism (Dorairaj S & Allen TW. PNAS 2007, 104:4943) Free energy
 profile from metadynamics MD simulation of the β2AR – NE(+) system was
 used to estimate activation free energy barrier height and corresponding
 curvatures at free energy maxima and minima. Diffusion coefficient at the
 free energy maximum was estimated using position autocorrelation function
 from last 20 ns of separate 30 ns long MD simulations with harmonic
 restraints on the NE(+) position as was done previously (Vorobyov I et al
 Biophys. J. 2014, 106:586) The z component of a distance between COM of
 protein α-helical core and NE(+) was used as a reaction coordinate for
 diffusion coefficient calculations. NE(+) association or “on” rate was
 then computed as a ratio of the "off" rate and Kd.
DOI: 10.25349/d9q036
title: Data for: Fish feces reveal diverse nutrient sources for coral reefs

description: Consumers mediate nutrient cycling through excretion and egestion across
 most ecosystems. In nutrient-poor tropical waters such as coral reefs,
 nutrient cycling is critical for maintaining productivity. While the
 cycling of fish-derived inorganic nutrients via excretion has been
 extensively investigated, the role of egestion for nutrient cycling has
 remained poorly explored. We sampled the fecal contents of 570 individual
 fishes across 40 species, representing six dominant trophic guilds of
 coral reef fishes in Moorea, French Polynesia. We measured fecal macro-
 (proteins, carbohydrates, lipids) and micro-nutrients (calcium, copper,
 iron, magnesium, manganese, zinc) and compared the fecal nutrient quantity
 and quality across trophic guilds, taxa, and body size. Macro- and
 micronutrient concentrations in fish feces varied markedly across species.
 Genera and trophic guild best predicted fecal nutrient concentrations. In
 addition, nutrient composition in feces was unique among species within
 both trophic guilds (herbivores and corallivores) and genera (Acanthurus
 and Chaetodon). Particularly, certain coral reef fishes (e.g., Thalassoma
 hardwicke, Chromis xanthura, Chaetodon pelewensis and Acanthurus
 pyroferus) harbored relatively high concentrations of micronutrients
 (e.g., Mn, Mg, Zn and Fe, respectively) that are known to contribute to
 ocean productivity and positively impact coral physiological performances.
 Given the nutrient-rich profiles across reef fish feces, conserving
 holistic reef fish communities ensures the availability of nutritional
 pools on coral reefs. We therefore suggest that better integration of
 consumer egestion dynamics into food web models and ecosystem-scale
 processes will facilitate an improved understanding of coral reef
 functioning. 
description: Please
 see the main manuscript for all information regarding data collection and
 analysis.
DOI: 10.5061/dryad.w6m905qv0
title: Data from: Spatial localization of anterior precuneus for bodily self validated with brain stimulation

description: The posteromedial cortex (PMC), comprising the precuneus, the posterior
 cingulate, and the retrosplenial regions, is known to be engaged in
 various self-referential functions. Recent observations have also
 suggested a link between PMC dysfunction and self-dissociation. To test
 the causal relevance of specific PMC locations for self- referential
 processing, we recruited nine neurosurgical participants with bilaterally
 implanted PMC electrodes. We applied focal electrical stimulation within
 discrete PMC sites while probing changes in the participants’ subjective
 states. We found that, in all nine participants, the electrical
 perturbation of the anterior precuneus (aPCu), but not the other PMC
 sites, caused apparent dissociative changes in the physical and spatial
 bodily domain involving head, trunk, and legs. The responsive aPCu sites
 did not exhibit event-related activation during a cued autobiographical
 memory recall task. Furthermore, resting-state functional connectivity
 with functional Magnetic Resonance Imaging data and effective connectivity
 with single-pulse electrical stimulation procedures confirmed that the
 responsive aPCu sites were distinct from, while closely connected with,
 the adjacent PMC nodes of the default mode network (DMN). Based on these
 data, we conclude that the aPCu is a distinct functional unit within the
 PMC and causally important for processing self-referential information in
 the physical and spatial domains. Future larger-scale experimental studies
 are needed to explore how operations of distinct neuronal populations
 within the PMC are integral to various cognitive processes that require a
 reference to self in its various dimension.
description: Clinical electrical brain stimulation (EBS) is routinely
 performed as a clinical procedure in preparation for surgical resection.
 Data reported here come from the clinical procedure performed on each
 participant typically in one session of EBS. We found that, in all nine
 participants, the electrical perturbation of the anterior precuneus
 (aPCu), but not the other posteromedial sites, caused apparent
 dissociative changes in the physical and spatial bodily domain involving
 head, trunk, and legs. The presented ROIs were constructed by adding up
 the 4mm-radius spheres centered around the MNI coordinates of the hot/cold
 electrodes identified from our cohort.
DOI: 10.25574/04638
title: Chandra X-ray Observatory ObsId 04638

description: The Cassiopeia A Explosion: Getting at the Core Issues
DOI: 10.5061/dryad.37pvmcvqr
title: Signatures of selection in four indigenous horse breeds of Iran

description: Indigenous Iranian horse breeds were evolutionarily affected by natural
 and artificial selection in distinct phylogeographic clades which shaped
 their genomes in several unique ways. The aims of this study were to
 evaluate genetic diversity and genome-wide selection signatures in four
 indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n =
 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52)
 populations, using genome-wide genotyping data. The contemporary effective
 population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian
 Arabian, and Kurdish, respectively. Analysis of population genetic
 structure classified the north breeds (Caspian and Turkmen) and
 west/southwest breeds (Persian Arabian and Kurdish) into two
 phylogeographic clades reflecting their geographic origin. Using a
 de-correlated composite of multiple selection signals
 statistics based on pairwise comparisons, we detected a different
 number of significant SNPs under putative selection from 13 to 28 for the
 six pairwise comparisons (FDR &lt; 0.05). The identified SNPs under
 putative selection coincided with genes previously associated with known
 QTL for morphological, adaptation, and fitness traits. Our results showed
 HMGA2 and LLPH as strong candidate genes for height variation between
 Caspian with a small size and the other studied breeds with a medium size.
 Using results of studies for human height retrieved from the GWAS catalog,
 we suggested 38 new putative candidate genes under selection. These
 results provide a genome-wide map of selection signatures in the studied
 breeds, which represent valuable information for formulating genetic
 conservation and improved breeding strategies for the breeds.