cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qfttdz0gw
title: Sponges facilitate primary producers in a Bahamas seagrass system

description: Seagrass beds are important coastal ecosystems worldwide that are shaped
 by facilitative interactions. Recent theoretical work has emphasized the
 potential for facilitative interactions involving foundation species to be
 destabilized in the face of anthropogenic change. Consequently, it is
 important to identify which taxa facilitate seagrasses. In other
 ecosystems, sponges contribute to the maintenance of diverse and
 productive systems through their facilitation of foundation species (e.g.,
 mangroves) and the retention and recycling of energy and nutrients.
 Sponges are common in tropical and subtropical seagrass beds, yet we know
 little about how their presence impacts these communities. Here, we
 examine the impact of the sponge Ircinia felix on primary producers in a
 Thalassia testudinum dominated seagrass bed using a long-term field
 experiment in The Bahamas. We transplanted live sponges into the center of
 5 m x 5 m plots and monitored the response of seagrasses and macroalgae.
 Sponge presence increased seagrass nutrient content and growth, as well as
 the abundance of macroalgae and non-dominant seagrass species (Syringodium
 filiforme and Halodule wrightii). These changes were not seen in the
 control (unmanipulated) or structure (where we placed a polypropylene
 sponge replica) plots. We conclude that I. felix facilitates seagrass bed
 primary producers in oligotrophic systems, likely due to nutrients
 supplied by the sponge. Our study shows that sponges can have a positive
 influence on seagrass bed foundation species. Further work is needed to
 understand how this facilitation impacts the stability of seagrass beds in
 areas where human activities have increased ambient nutrient levels.
description: See https://github.com/ecophilina/ircinia.
description: # Sponges facilitate primary producers in a Bahamas seagrass system ---
 This study explored the effects of the marine sponge, Ircinia felix, on
 seagrass growth, nutrient contents, and density as well as macroalgal
 abundance through a 1-year field experiment performed in The Bahamas. ##
 Description of the data and file structure All datasheets in this data set
 have the following variables: treatment: Experimental treatment for the
 plot. Possible values are: blank (corresponds to control), fake
 (corresponds to structure), and sponge (corresponds to live sponge). plot:
 Individual plot identifier dist: The distance from the center of the plot.
 sampling:plots were sampled 5 times; possible values are 1 (June 2013 -
 before the experiment began), 2 (July 2013 - 1 month into the experiment),
 3 (November 2013 - 5 months into the experiment), 4 (July 2014; 12 months
 into the experiment), and 5 (November 2014 - 17 months into the
 experiment) All other specific variable names are defined on the MetaData
 tab associated with each file. Code associated with this data set can be
 found here: https://github.com/ecophilina/ircinia ## Code/Software
 https://github.com/ecophilina/ircinia
DOI: 10.5281/zenodo.18396931
title: STRUGGLES FOR RECOGNITION IN GENDER IDENTITY DEBATES IN UZBEKISTAN: A COMPARATIVE FRAMEWORK BASED ON HEGEL, HONNETH, AND FRASER

description: Struggles surrounding gender identity have become increasingly central within contemporary political and social theory, particularly in debates concerning recognition, dignity, and inclusion. In Uzbekistan, public discourse on gender identity remains limited and highly constrained, yet processes of recognition and misrecognition profoundly shape the everyday experiences of gender-diverse individuals. This article develops a comparative theoretical framework informed by the recognition theories of Hegel, Honneth, and Fraser in order to examine how cultural norms, legal structures, and socioeconomic conditions structure the possibilities for identity formation and social participation in the Uzbek context. Drawing on political philosophy, socio-legal analysis, and empirical reports from international human rights organizations, the study argues that gender-diverse individuals in Uzbekistan face intertwined forms of misrecognition—emotional, symbolic, legal, and structural—that restrict access to dignity, rights, and participatory parity. By applying recognition theory to an under-researched post-Soviet society, this article contributes a novel analytical perspective on gender identity struggles in Central Asia and highlights the urgent need for both institutional reform and cultural transformation.
DOI: 10.5061/dryad.pg4f4qrp7
title: Neural representations of space in the hippocampus of a food-caching bird

description: Spatial memory in vertebrates requires brain regions homologous to the
 mammalian hippocampus. Between vertebrate clades, however, these regions
 are anatomically distinct and appear to produce different spatial patterns
 of neural activity. We asked whether hippocampal activity is fundamentally
 different even between distant vertebrates that share a strong dependence
 on spatial memory. We studied tufted titmice, food-caching birds capable
 of remembering many concealed food locations. We found mammalian-like
 neural activity in the titmouse hippocampus, including sharp-wave ripples
 and anatomically organized place cells. In a non–food-caching bird
 species, spatial firing was less informative and was exhibited by fewer
 neurons. These findings suggest that hippocampal circuit mechanisms are
 similar between birds and mammals, but that the resulting patterns of
 activity may vary quantitatively with species-specific ethological needs.
description: Behavioral data was collected using an infrared-based motion
 capture system. Electrophysiological recordings were
 collected with sharp electrodes and silicon probes. 
 Raw data were spike sorted using Plexon Offline Sorter, and local
 field potentials were processed in Matlab.
description: Please see the Readme.txt file for a description of the datasets
 and code included with the software
 (https://doi.org/10.5281/zenodo.4768764).
DOI: 10.5281/zenodo.18396930
title: STRUGGLES FOR RECOGNITION IN GENDER IDENTITY DEBATES IN UZBEKISTAN: A COMPARATIVE FRAMEWORK BASED ON HEGEL, HONNETH, AND FRASER

description: Struggles surrounding gender identity have become increasingly central within contemporary political and social theory, particularly in debates concerning recognition, dignity, and inclusion. In Uzbekistan, public discourse on gender identity remains limited and highly constrained, yet processes of recognition and misrecognition profoundly shape the everyday experiences of gender-diverse individuals. This article develops a comparative theoretical framework informed by the recognition theories of Hegel, Honneth, and Fraser in order to examine how cultural norms, legal structures, and socioeconomic conditions structure the possibilities for identity formation and social participation in the Uzbek context. Drawing on political philosophy, socio-legal analysis, and empirical reports from international human rights organizations, the study argues that gender-diverse individuals in Uzbekistan face intertwined forms of misrecognition—emotional, symbolic, legal, and structural—that restrict access to dignity, rights, and participatory parity. By applying recognition theory to an under-researched post-Soviet society, this article contributes a novel analytical perspective on gender identity struggles in Central Asia and highlights the urgent need for both institutional reform and cultural transformation.
DOI: 10.5061/dryad.mgqnk98zq
title: Data from: Passeridae and Cyanocitta stelleri teleport to my deck from other areas

description: In neither the teleporting or the lab are they actually
 migrating. Yet, in the lab, they do it anyway, and the way their
 species does it, without having done it before. Passeridae and
 Cyanocitta stelleri teleport to my deck from other areas adds to
 the genetic difference hypothesis by saying migrating doesn’t matter, just
 that they have the genetic (and maybe neural) structure needed for
 migration, and is used for teleporting.
DOI: 10.5061/dryad.5qfttdz4v
title: Data from: Do metal mines and their runoff affect plumage color? A regional scale study of streak-backed orioles in south-central Mexico

description: Metal mining causes serious ecological disturbance, due partly to heavy
 metal (HM) pollution that can accumulate at mining sites themselves and be
 dispersed downstream as runoff. Plumage coloration is important in birds’
 social and ecological interactions and sensitive to environmental
 stressors, and several local-scale studies have found decreased
 carotenoid-based plumage and/or increased melanin-based plumage in wild
 birds exposed to HM pollution. We investigated regional-scale effects of
 proximity to mines and their downstream rivers as a proxy of exposure to
 HM-contaminated mining waste on plumage coloration in streak-backed
 orioles (Icterus pustulatus) in south-central Mexico. We measured the
 plumage color of museum skins using reflectance spectrometry and digital
 photography, then used geographic information systems to estimate each
 specimen’s distance from the nearest mining concession and river and
 determine whether that river’s watershed contained mines. Proximity to
 mines and their downstream rivers was related to ventral (but not dorsal)
 carotenoid-based coloration; birds collected farther from mines had more
 vivid yellow-orange breast plumage, and belly plumage was more vivid and
 redder with increasing distance from rivers with upstream mines. Breast
 background reflectance unexpectedly decreased with mine distance and was
 higher among birds whose nearest river had mines upstream. The area (but
 not reflectance) of melanin-based plumage was also related to mines. The
 area of dark back streaks decreased with mine distance, while the bib
 patch was smaller among birds presumably more exposed to mining waste.
 While some of these results are consistent with predicted effects of HM
 pollution on plumage, most were not straightforward, and effects differed
 among plumage patches and variables. Further investigation is needed to
 understand the direct (e.g., toxicity, oxidative stress) and/or indirect
 (e.g., decreased availability of carotenoid-rich food) mechanisms
 responsible and their individual, population, and community-level
 implications.       
description: The dataset comprises plumage color and patch area measurements
 (taken using reflectance spectrometry and digital photography,
 respectively) of museum specimens of streak-backed orioles
 (<em>Icterus pustulatus</em>)<em> </em>and the
 distance from each specimen to the nearest concession for metal mine
 exploitation and the nearest river (some of which may receive waste from
 mines). The additional potential confounding variables that were included
 in the analyses are also provided. For further details on the specific
 methods, please see the methods section and supplementary material of the
 associated manuscript, and/or contact the corresponding author.
description: Data are provided in the first tab and variable descriptions in
 the second tab of the excel data file. Missing values in the data are
 indicated using "NA".
DOI: 10.5061/dryad.sbcc2fr6d
title: Comparative analysis of a geometric and an adhesive righting strategy against toppling in inclined hexapedal locomotion

description: Animals are known to exhibit different walking behaviors in hilly
 habitats. For instance, cats, rats, squirrels, tree frogs, desert iguana,
 stick insects and desert ants were observed to lower their body height in
 traversing slopes, whereas mound-dwelling iguanas and wood ants tend to
 maintain constant walking kinematics regardless of the slope. This paper
 aims to understand and classify these distinct behaviors into two
 different strategies against toppling for climbing animals by looking into
 two factors, (i) the torque of the center of gravity (CoG) with respect to
 the critical tipping axis, and (ii) the torques of the legs, which have
 the potential to counterbalance the CoG-torque. Our comparative locomotion
 analysis on level locomotion and inclined locomotion exhibited that
 primarily only one of the proposed two strategies was chosen for each of
 our sample species, despite the fact that a combined strategy could have
 reduced the animal's risk to topple over even more. We found that
 desert ants of Cataglyphis fortis maintained their upright posture
 primarily through the adjustment of their CoG-torque (geometric strategy),
 and wood ants of the Formica rufa species group controlled their posture
 primarily by exerting leg-torques (adhesive strategy). We further provide
 hints that the geometric strategy employed by Cataglyphis could increase
 the risk for slipping on slopes since the leg-impulse substrate angle of
 Cataglyphis’ hind legs were lower compared to Formica's. In contrast,
 the adhesion strategy employed by Formica's front legs not only
 decreased the risk for toppling. It also explained the steeper leg-impulse
 substrate angle of Formica's hind legs which should relate to more
 bending of the tarsal structures and therefore to more microscopic contact
 points potentially reducing the risk for hind leg slipping.
description: Please refer to the method section in https://doi.org/10.1242/jeb.242677.
description: Please refer to
 the README_woehrl_et_al_2021_JEXBIO2021242677.txt file.
DOI: 10.5061/dryad.qfttdz0gx
title: The contributions of individual traits to survival among terrestrial juvenile pond-breeding salamanders

description: Individual survival is influenced by interactions between local
 environmental conditions and an organism’s morphological, behavioral, and
 physiological traits. Studies examining the effects of individual
 phenotypes on survival under variable conditions are relatively rare among
 early transitional life stages, though the vital rates of these life
 stages can importantly influence population dynamics. We experimentally
 examined the effects of initial body mass, movement, standard metabolic
 rate (SMR), and respiratory surface area water loss (RSAWL) on survival in
 the transitional juvenile life stage of two biphasic amphibian species
 (Ambystoma maculatum and A. opacum) in a seven-month mark-recapture study
 under semi-natural conditions. Juveniles with a larger initial
 body mass, lower initial SMR, and/or a lower tendency to change locations
 had a higher likelihood of known survival. In contrast, we found no
 significant effect of RSAWL on juvenile survival. The relationships
 between individual phenotypes and survival did not differ between species,
 but equivalent species-specific survival rates may have been attributed to
 larger initial body sizes in A. maculatum and lower SMR in A. opacum. Our
 results illuminate the complex ways in which individual traits influence
 survival during the early transitional life stage of two ambystomatid
 species under varying abiotic conditions. More generally, our findings
 illustrate potential advantages of simultaneously examining multiple
 traits to evaluate survival.
description: Please see the associated manuscript for full methodological
 details.
description: Available files include: R scripts
 used to: conduct Bayesian binomial generalized linear
 mixed models and construct Figures 1 and 2
 (Resp_Survival_2017-2018_Sept2021.R) examine changes
 in juvenile body sizes prior to release
 (Metamorph_2017_Release_BodySize_Apr2021.R) and over the course of the
 study period (Phys_Surv_Change_Size_Apr2021.R)
 calculate the effect of relative apparent activity levels on
 juvenile survival to produce Figure
 3 (Location_Known_Alive_Apr2021.R) calculate
 traditional selection coefficients
 (Selection-Coefficients_Sept2021.R). 
 All necessary data files to run these R scripts and support the
 findings of our study
 (WVP_RSAWL_2017-2018_Survival.csv, Released_Rounds3-5_RSAWL_MINVCO2_2017.csv, abiotic.csv, Metamorph_2017_Release_Data.csv, Phys_Surv_Change_Size.csv, Location_KnownAlive.csv). Scripts were developed and run using R version 4.0.0.
DOI: 10.6078/d1d13g
title: Data from: Towards eradicating the nuisance of Numts and noise in molecular biodiversity assessment

description: DNA metabarcoding is a popular methodology for biodiversity assessment and
 increasingly used for community level analysis of intraspecific genetic
 diversity. The evolutionary history of hundreds of specimens can be
 captured in a single collection vial. However, the method is not without
 pitfalls, which may inflate or misrepresent recovered diversity metrics.
 Numts, nuclear pseudogene copies of mitochondrial DNA, have been
 particularly difficult to control because they can evolve rapidly and
 appear deceptively similar to true mitochondrial sequences. While the
 problem of numts has long been recognized for traditional sequencing
 approaches, the issues they create are particularly evident in
 metabarcoding in which the identity of individual specimens is generally
 not known. In this issue of Molecular Ecology Resources Andújar et al.
 (2021) provide an easy to implement bioinformatic approach to reduce
 erroneous sequences due to numts and residual noise in metabarcoding
 datasets. The metaMATE software designates input sequences as authentic
 (mtDNA haplotypes) or non-authentic (numts and erroneous sequences) by
 comparison to reference data and by analyzing nucleotide substitution
 patterns. Filtering is applied over a range of abundance thresholds and
 the choice to proceed with a more rigid or less strict sequence removal
 strategy is at the researchers’ discretion. This is a valuable addition to
 a growing number of complementary tools for improving the reliability of
 modern biodiversity monitoring.
description: Fasta file of denoised sequences (ZOTUs) from the UNOISE
 algorithm after quality filtering steps. Used for input for meteMATE
 software tool for Numt removal.
DOI: 10.5061/dryad.70rxwdbx6
title: Botanic gardens play key roles in the regional distribution of first records of alien plants in China

description: Aim: Plant invasions pose a serious risk to biodiversity, and living
 collections in botanic gardens are recognized as a potentially important
 source of alien plant introductions. However, it is not yet known how the
 risks from botanic gardens compare with other socio-economic and
 environmental factors in influencing the regional distribution of alien
 plant introductions. Location: China Time period: 1840 – 2018 Major taxa
 studied: All vascular plants Methods: We compiled a dataset of the
 locations of first records and introduction pathways for 454 plant species
 naturalized in China and used boosted regression trees to evaluate the
 roles of the number, size, and age of botanic gardens, local climate,
 native species richness and trade on the total number of first records of
 alien plants at both the city and province level. Results: The botanic
 gardens with large living collections played the most important role in
 influencing the total number of first records of alien plant species at
 both the city and province scale. However, the importance of botanic
 gardens depended on the introduction pathway of naturalized species. The
 first records of alien species introduced for horticulture were more
 influenced by the attributes of botanic gardens. On the other hand, the
 first records of alien species introduced for agriculture were associated
 with climate variables, and first records of alien species introduced
 accidentally were strongly shaped by trade. Main conclusions: Our results
 highlight the importance of botanic gardens in facilitating alien plant
 introductions across a continent. Given the rapid rise in the number of
 botanic gardens in Asia since 1950, our results point to these as
 potential hotspots for future plant invasions. In China, monitoring should
 be implemented to target botanic gardens, particularly those with large
 living collections. Extending this approach to other regions would be a
 sensible first step in monitoring invasions.
description: The cities and provinces with no first records were not shown in
 the dataset. We only included provinces and cities in the  mainland of
 China.
DOI: 10.5061/dryad.0p2ngf217
title: The entorhinal cortex modulates trace fear memory formation and neuroplasticity in the lateral amygdala via cholecystokinin

description: Although the neural circuitry underlying fear memory formation is
 important in fear-related mental disorders, it is incompletely understood.
 Here, we utilized trace fear conditioning to study the formation of trace
 fear memory. We identified the entorhinal cortex (EC) as a critical
 component of sensory signaling to the amygdala. Moreover, we used the loss
 of function and rescue experiments to demonstrate that release of the
 neuropeptide cholecystokinin (CCK) from the EC is required for trace fear
 memory formation. We discovered that CCK-positive neurons extend from the
 EC to the lateral nuclei of the amygdala (LA), and inhibition of
 CCK-dependent signaling in the EC prevented long-term potentiation of
 sensory signals to the LA and formation of trace fear memory. Altogether,
 we suggest a model where sensory stimuli trigger the release of CCK from
 EC neurons, which potentiates sensory signals to the LA, ultimately
 influencing neural plasticity and trace fear memory formation.
description: For fear conditioning, all videos (baseline, training, and
 testing) were recorded with a webcam (Logitech C270) set in the ceiling of
 the chamber. Videos were analyzed with a custom program based on an
 open-source platform (Lopes et al., 2015) (https://bonsai-rx.org). Briefly, the centroid of the animal was extracted from the videos. By comparing the coordinates of the centroid frame by frame, we then calculated the distance moved between two frames. The instant velocity of the animal was calculated by dividing this distance by the time span between two adjacent frames. The freezing percentage was defined as the percentage of frames with an instant velocity lower than the threshold of all frames in an observed time window. For electrophysiological recording, responses were recorded and passed to a pre-amplifier (PZ5, TDT) and an acquisition system (RZ5D, TDT). Signals were filtered for field potential or spikes with respective bandwidth ranges of 10–500 Hz and 1–5000 Hz. All recordings were stored using TDT software (OpenEx, TDT). For LTP experiment, field potential data were extracted and processed in the MATLAB program. Slope of fEPSP was generated and normalized to the mean value of baseline session before induction.
description: Please see our ReadMe files for dataset description and using
 notes.
DOI: 10.25338/b8qp8x
title: Early resources lead to persistent benefits for bumble bee colony dynamics

description: Conditions experienced early in development can affect the future
 performance of individuals and populations. Demographic theories predict
 persistent population impacts of past resources, but few studies have
 experimentally tested such carry-over effects across generations or
 cohorts. We used bumble bees to test whether resource timing had
 persistent effects on within-colony dynamics over sequential cohorts of
 workers. We simulated a resource pulse for field colonies either early or
 late in their development and estimated colony growth rates during pulse-
 and non-pulse periods. During periods when resources were not
 supplemented, early-pulse colonies grew faster than late-pulse colonies;
 early-pulse colonies grew larger as a result. These results reveal
 persistent effects of past resources on current growth and support the
 importance of transient dynamics in natural ecological systems.
 Early-pulse colonies also produced more queen offspring, highlighting the
 critical nature of resource timing for the population, as well as colony,
 dynamics of a key pollinator.  
description: The complete data file contains raw data for all analyses on
 Malfi et al. 2021, Ecology.
DOI: 10.5281/zenodo.18396977
title: FUNDAMENTALS OF AN ECOLOGICAL APPROACH TO PHYSICAL EDUCATION OF ACADEMIC LYCEUM STUDENTS