cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z612jm6d4
title: Comparative reconstruction of the predatory feeding structures of the polyphenic nematode Pristionchus pacificus

description: Pristionchus pacificus is a nematode model for the
 developmental genetics of morphological polyphenism, especially at the
 level of individual cells. Morphological polyphenism in this species
 includes an evolutionary novelty, moveable teeth, which have enabled
 predatory feeding in this species and others in its family
 (Diplogastridae). From transmission electron micrographs of serial thin
 sections through an adult hermaphrodite of P. pacificus, we
 three-dimensionally reconstructed all epithelial and myoepithelial cells
 and syncytia, corresponding to 74 nuclei, of its face, mouth, and pharynx.
 We found that the epithelia that produce the predatory morphology
 of P. pacificus are identical to Caenorhabditis
 elegans in the number of cell classes and nuclei. However,
 differences in cell form, spatial relationships, and nucleus position
 correlate with gross morphological differences from C.
 elegans and outgroups. Moreover, we identified fine-structural
 features, especially in the anteriormost pharyngeal muscles, that underlie
 the conspicuous, left-right asymmetry that characterizes the P.
 pacificus feeding apparatus. Our reconstruction provides an
 anatomical map for studying the genetics of polyphenism, feeding behavior,
 and the development of novel form in a satellite model to C.
 elegans.
description: This dataset was collected by manually annotating an alignment of
 digitized, transmission electron microscopy images. These
 manual annotations resulted in volume-segmented objects, in which
 segmentation errors were then manually corrected. Additional processing
 included global operations on each object to improve
 visualization.
description: All volume-segmented objects are represented by Wavefront (.obj)
 files. Wavefront files need to be held in the same directory as their
 associated .mtl files, which can be imported together with the .obj
 file into object visualization software. Several software platforms can be
 used with this file type; for the manuscript associated with this
 dataset, the authors visualized objects using the open-source platform
 Blender (blender.org).
DOI: 10.5061/dryad.7sqv9s4th
title: Maternal sweeteners intake modulates gut microbiota and exacerbates learning and memory processes in adult male offspring

description: Background: There is increasing evidence that gut microbiota in offspring
 is derived in part from maternal environment such as diet. Thus,
 sweeteners intake including caloric or non-caloric, during perinatal
 period can induce gut dysbiosis and program the offspring to develop
 cognitive problems later in life. Objective: To determine the effect of
 maternal high-sweeteners intake during gestation and lactation on gut
 microbiota shifts in adult male offspring rats and the impact on cognitive
 dysfunction. Methods: Thirty-four male pups from dams fed standard diet
 (Control-C, n = 10), high-sucrose diet (HS-C, n = 11), high-honey diet
 (Ho-C, n = 8) and high-stevia diet (HSt-C, n = 5) were fed standard diet
 after weaning and body weight and food intake were recorded once a week
 for 26 weeks. Learning and memory tests were performed at week 23 of life
 using the Barnes maze. Fecal samples from the breastfeeding and adulthood
 periods were collected and analyzed by sequencing the 16S rRNA V3-V4
 region of gut microbiota. Results: Maternal high-sucrose and stevia diets
 programmed the male offspring and changes in microbial diversity by
 Shannon index were observed after weaning (p &lt; 0.01). Furthermore,
 maternal high-stevia diet programming lasted into adulthood. The increase
 of Firmicutes abundance and the decrease in phylum Bacteroidetes was
 significantly in HS-C and HSt-C groups. This led to an increase in the
 Firmicutes/Bacteroidetes index although only in HS-C group was
 statistically significant (p &lt; 0.05). Of note, of the downstream
 gram-negative Bacteroidales and the upregulation of the gram-positive
 Clostridiales abundance contribute to cognitive dysfunction. Conclusion:
 These results suggest that dams fed a high-sucrose and stevia diets during
 gestation and lactation favor a deficient memory performance in adult male
 offspring rats through shifts gut microbiota diversity and relative
 abundance at several taxa.
DOI: 10.5061/dryad.bvq83bk9w
title: Multi-state diel occupancy model

description: Current methods to model species habitat use through space and diel time
 are limited. Development of such models is critical when considering
 rapidly changing habitats where species are forced to adapt to
 anthropogenic change, often by shifting their diel activity across space.
 We use an occupancy modeling framework to specify the multi-state diel
 occupancy model (MSDOM), which can evaluate species diel activity against
 continuous response variables which may impact diel activity within and
 across seasons or years. We used two case studies, fosa in Madagascar and
 coyote in Chicago, USA, to conceptualize the application of this model and
 to quantify the impacts of human activity on species spatial use in diel
 time. We found support that both species varied their habitat use by diel
 states—in and across years, and by human disturbance. Our results
 exemplify the importance of understanding animal diel activity patterns
 and how human disturbance can lead to temporal habitat loss. The MSDOM
 will allow more focused attention in ecology and evolution studies on the
 importance of the short temporal scale of diel time in animal-habitat
 relationships and lead to improved habitat conservation and management.
description: Instructions on how the dataset was collected can be found
 in: Rivera, K., Fidino, M., Farris, Z. J., Magle, S.
 B., Murphy, A., and Gerber, B. D. (in press). Rethinking habitat occupancy
 modeling and the role of diel activity in an anthropogenic world. American
 Naturalist. Data was cleaned and analyzed in R and is
 stored on Zenodo. Both data and code can be found in:
 Brian Gerber; Mason Fidino; Kimberly Rivera (2022): zenodo_retry
 (v1.1) [Computer software]. Zenodo.
 https://doi.org/10.5281/zenodo.6014030. If you would
 like to see the readMe file for the Zenodo repository rendered, you can
 see the same code on GitHub at:
 https://github.com/bgerber123/multi.state.diel.occupancy.model
description: See dryad_readme.pdf for details.
DOI: 10.5061/dryad.6djh9w12v
title: Synaptic mechanisms of top-down control in the non-lemniscal inferior colliculus

description: Corticofugal projections to evolutionarily ancient, sub-cortical
 structures are ubiquitous across mammalian sensory systems. These
 “descending” pathways enable the neocortex to control ascending sensory
 representations in a predictive or feedback manner, but the underlying
 cellular mechanisms are poorly understood. Here we combine optogenetic
 approaches with in vivo and in vitro patch-clamp electrophysiology to
 study the projection from mouse auditory cortex to the inferior colliculus
 (IC), a major descending auditory pathway that controls IC neuron feature
 selectivity, plasticity and auditory perceptual learning. Although
 individual auditory cortico-collicular synapses were generally weak, IC
 neurons often integrated inputs from multiple corticofugal axons that
 generated reliable, tonic depolarizations even during prolonged
 presynaptic activity. Latency measurements in vivo showed that descending
 signals reach the IC within 30 ms of sound onset, which in IC neurons
 corresponded to the peak of synaptic depolarizations evoked by short
 sounds. Activating ascending and descending pathways at latencies expected
 in vivo caused a NMDA receptor dependent, supra-linear EPSP summation,
 indicating that descending signals can non linearly amplify IC neurons’
 moment-to-moment acoustic responses. Our results shed light upon the
 synaptic bases of descending sensory control, and imply that
 heterosynaptic cooperativity contributes to the auditory
 cortico-collicular pathway’s role in plasticity and perceptual learning.
description: This excel file contains the raw data values used to generate the
 figures in the paper. The data are from electrophysiological experiments
 of inferior colliculus neurons, recorded using whole-cell patch-clamp in
 brain slices and in anesthetized mice (most figures) or extracellular
 recordings in awake mice (Figure 7 - Supplement 1B, Figure 7 - Supplement
 2). Data processing is described in the Methods section of the paper;
 values are rounded to 2-4 decimal points for consistency.
description: For all tabs, datapoints across rows represent matched
 observations from the same neuron. Figure 4C,D ; Figure
 4 - Supplement 1 ; Figure 5G ; Figure 8B: Datapoints from the same neurons
 are matched across rows and columns. For Figure 7 -
 Supplement 2: LFP and multi-unit data values corresponding to the same
 recording session are denoted by the recording # column. Multi-unit data
 for recording # 3 and # 10 were not analyzed owing to low signal-to-noise
 ratio of the multi-unit clusters after high-pass filtering (see
 Methods).
DOI: 10.5061/dryad.8cz8w9grt
title: Bone thin sections of six Alvarezsaurian dinosaurs

description: This dataset includes histological thin sections from long bones of six
 different Alvarezsaurian dinosaurs and labelled primary and secondary
 osteons.
description: The dataset was collected based on specimens in the Institute of
 Vertebrate Paleontology and Paleonanthropology, Beijing, China. Six
 alvarezsaurian dinosaur taxa are included as following:
 Taxa Sampled bones
 Image number 
 <i>Bannykus
 wulantensis</i> Fibula 
 18 
 <i>Haplocheirus
 sollers</i> Tibia 28 
 <i>Qiupanykus
 zhangi</i> Metatarsal 
 36 
 <i>Shishugounykus
 inexpectus</i> Fibula 
 29 
 <i>Xixianykus
 zhangi</i> Femur,
 Metatarsal 28+22 
 <i>Xiyunykus
 pengi</i> Fibula 
 13 
 The image was taken
 under normal light microscope with resolution of 2576×1936. Labels of
 primary and secondary were manually labled by all authors.
description: There are three folders in this dataset: The
 <em>Raw images</em> folder contains all images categorised by
 their taxa (e.g. Banykus) and sampling bones (e.g. Fibula). 
 The <em>Sub-images</em> folder contains divided
 images from raw images except <em>Haplocheirus sollers</em>.
 Each raw image with a resolution of 2576×1936 is sub-divided into four
 smaller sub-images with a resolution of 1288×968. The
 <em>Labels</em> folder contains labeled primary and secondary
 osteons, the file order corresponds to the <em>Sub-images</em>
 folder.  For deep learning training, users can
 subdivided this dataset into training and testing sub-dataset as
 needed.
DOI: 10.5061/dryad.cnp5hqc61
title: Psychological factors in the chronicity of back pain: Impact on treatment engagement and disability

description: Background: There are well-established positive relationships between
 psychological distress and chronic back pain and disability. However,
 there is very limited research in relation to levels of psychological
 distress and the effect it has on treatment engagement in those with
 chronic back pain. Methods: 89 men and 112 women experiencing back pain
 recruited via convenience sampling completed the Depression, Anxiety and
 Stress Scale, Oswestry Low Back Pain Disability Questionnaire, the West
 Haven-Tale Multidimensional Pain Inventory, and a demographic
 questionnaire designed purposely for the study. Results: Depression,
 anxiety, affective distress, and life control predicted the number of
 treatments engaged in for back pain, (R2 = 0.29, [16,161] = 12.19, p =
 .0005) and the level of disability, (R2 =.31, F[14,177] = 19.60, p =
 .0005). Conclusions: The level of engagement in treatments was predicted
 by psychological factors rather than by the level of pain experienced by
 participants. The findings showed that participants who were
 psychologically distressed, not only had higher levels of pain and
 disability, but also engaged in fewer treatments.
description: 450 self-addressed, reply-paid, envelopes containing the
 participant information, consent form and the battery of questionnaires
 were distributed through doctors and allied health professionals.  Health
 professionals consented to be part of the recruitment process by signing
 and returning a consent form.  The project was approved the Victoria
 University Human Ethics Committee (HRETH 08/282).  The data collected in
 the questionnaire were analysed utilizing the Statistical Program for
 Social Sciences Version 22 (SPSS).  The response rate was 201/450 =
 44.66%. Each participant signed a consent form after reading a letter of
 invitation to participate with information about the research as well as
 contingency strategies in the case of any psychological disturbance as a
 result to their involvement in this study. The data collected from the
 questionnaires were input reflecting the participants’ answers and
 questionnaires were scored according to the guidelines recommended by the
 original authors of each questionnaires.
DOI: 10.5061/dryad.gf1vhhmrc
title: The effects of light intensity and flow speed on biogeochemical variability within a fringing coral reef in Onna-son, Okinawa, Japan

description: Global warming and ocean acidification are driving gradual declines in
 seawater dissolved oxygen concentrations and pH. Predicting how these
 changes will affect shallow, near-shore environments including coral reefs
 is challenging due to high natural variability on both spatial (10 m to
 km) and temporal (diel to seasonal) scales. To make predictions, it is
 first necessary to identify and quantify the drivers of this natural
 variability. While significant efforts have been devoted to characterising
 the influence from metabolic processes on coral reef seawater chemistry,
 less attention has been devoted to physical processes such as flow speed
 and light intensity. Here, we measured seawater flow, photosynthetically
 active radiation (PAR), pH, and dissolved oxygen (DO) at three reef
 habitats (reef flat, lagoon, and outflow channel) in a fringing coral reef
 system in Okinawa, Japan for a duration of 3 weeks in October of 2019.
 During the study, circulation was primarily wave-driven with mean flow
 speeds ranging from 14-26 cm/s. Flow direction became increasingly
 consistent at higher flow speeds, which traced visual patterns in the
 benthos observed from satellite imagery. Multiple linear regression models
 of daytime changes in pH and DO versus daily mean flow speed and PAR
 described 25-74% of the observed variability across all sites while at
 night, flow speed alone accounted for 35-69% of the observed variability.
 The results demonstrate that flow speed, trajectory, and PAR play
 important and variable roles in controlling biogeochemical variability
 within coral reefs and need to be considered in assessing their
 vulnerability to global climate change.
description: This dataset was collected in Onna-son, Okinawa, Japan
 (26.449720°N, 127.794245°E), over three weeks in October 2019. pH,
 temperature, oxygen and salinity data from C1 were collected with a
 SeapHOx. pH was recoreded at C2 and C3 by SeaFETs, while temperature and
 salinity were recorded at these sites by Seabird SBE 16 plus V2 SeaCAT
 recorder equipped with oxygen optodes (Aanderaa Oxygen Sensor 3835).
 Drifter experiments were conducted using Pacific Gyre reef drifters with
 their position recorded every minute via iridium telemetry. Flow speed,
 direction and pressure were measured at C1 using a Nortek Vector ADV, at
 C2 & C6 by Nortek 2 MHz Aquadopps, and at C3, C7, and C8 by Nortek
 1 MHz Aquadopps, and at C4 and C5 by 1 MHz Teledyne Sentinels. Pressure
 was measured at P1 and P2 by RBR Virtuosos. Photosynthetically active
 radiation was recorded at C1 by an ECO-photosynthetically active radiation
 (PAR) sensor from Wetlabs, Seabird Scientific. Data were processed using
 MATLAB.
description: Instrument locations are in the attached .mat file. A key to each
 variable has also been uploaded.
DOI: 10.5061/dryad.70rxwdbzx
title: Data for: Evolutionary interactions between thermal ecology and sexual selection

description: Thermal ecology and mate competition are both pervasive features of
 ecological adaptation. A surge of recent work has uncovered the diversity
 of ways in which temperature affects mating interactions and sexual
 selection. However, the potential for thermal biology and reproductive
 ecology to evolve together as organisms adapt to their thermal environment
 has been underappreciated. Here, we develop a series of hypotheses
 regarding (1) not only how thermal ecology affects mating system dynamics,
 but also how mating dynamics can generate selection on thermal traits; and
 (2) how the thermal consequences of mate competition favor the reciprocal
 co-adaptation of thermal biology and sexual traits. We discuss our
 hypotheses in the context of both pre-copulatory and post-copulatory
 processes. We also call for future work integrating experimental and
 phylogenetic comparative approaches to understand evolutionary feedbacks
 between thermal ecology and sexual selection. Overall, studying reciprocal
 feedbacks between thermal ecology and sexual selection may be necessary to
 understand how organisms have adapted to the environments of the past and
 could persist in the environments of the future.
DOI: 10.5061/dryad.05qfttf4f
title: Image-based taxonomic classification of bulk biodiversity samples using deep learning and domain adaptation

description: Complex bulk samples of insects from biodiversity surveys present a
 challenge for taxonomic identification, which could be overcome by
 high-throughput imaging combined with machine learning for rapid
 classification of specimens. These procedures require that taxonomic
 labels from an existing source data set are used for model training and
 prediction of an unknown target sample. However, such transfer learning
 may be problematic for the study of new samples not previously encountered
 in an image set, e.g. from unexplored ecosystems, and require methods of
 domain adaptation that reduce the differences in the feature distribution
 of the source and target domains (training and test sets). We assessed the
 efficiency of domain adaptation for family-level classification of bulk
 samples of Coleoptera, as a critical first step in the characterisation of
 biodiversity samples. Neural network models trained with images from a
 global database of Coleoptera were applied to a biodiversity sample from
 understudied forests in Cyprus as the target. Within-dataset
 classification accuracy reached 98% and depended on the number and quality
 of training images and on dataset complexity. The accuracy of
 between-datasets predictions (across disparate source-target pairs that do
 not share any species or genera) was at most 82% and depended greatly on
 the standardisation of the imaging procedure. Algorithms for domain
 adaptation significantly improved the prediction performance of models
 trained by non-standardised, low-quality images. Our findings demonstrate
 that existing databases can be used to train models and successfully
 classify images from unexplored biota, but the imaging conditions and
 classification algorithms need careful consideration.
DOI: 10.5281/zenodo.18398837
title: Mid-infrared spectral data for core NHX3 from the South China Sea

description: This dataset contains mid-infrared spectral data for core NHX3 collected from upwelling areas off the Vietnam coast.
DOI: 10.5281/zenodo.18398836
title: Mid-infrared spectral data for core NHX3 from the South China Sea

description: This dataset contains mid-infrared spectral data for core NHX3 collected from upwelling areas off the Vietnam coast.
DOI: 10.5061/dryad.rxwdbrv9r
title: Data from: Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar

description: With 178 species, the palm subtribe Dypsidinae is one of the largest plant
 radiations on Madagascar. A well-resolved species-level phylogeny is
 required not only to unpick the drivers of this spectacular radiation but
 also to define natural and useful generic limits in this taxonomically
 difficult group. The only recent taxonomic revision of Dypsidinae
 recognized just four genera, including the large genus Dypsis (currently
 with 172 species), which was considered impossible to divide further based
 on morphology alone. Here we describe the first comprehensively sampled
 species-level phylogeny of Dypsidinae, including 157 described species
 (88% of the subtribe) as well as 10 samples of uncertain taxonomic
 identity (potential new species). Our tree is based on target sequence
 capture data for 161 nuclear DNA loci. The phylogenetic relationships
 recovered render Dypsis s.l. paraphyletic, requiring the resurrection of
 two previously synonymised genera. In total, we recognize six genera in
 Dypsidinae (Dypsis Noronha ex Mart., Chrysalidocarpus H.Wendl., Marojejya
 Humbert, Vonitra Becc., Lemurophoenix J.Dransf., and Masoala Jum.), all of
 which are monophyletic and consistent with morphology.
DOI: 10.5061/dryad.vhhmgqnvr
title: Impact of water resources development on connectivity and primary productivity across a tropical river floodplain

description: 1. Floodplain wetlands provide an important subsidy for riverine food webs
 as sites of high algal production. However, this subsidy depends on the
 degree of landscape connectivity during flood pulses, which provides the
 opportunity for movement of higher order consumers between rivers and
 floodplains to access these productive habitats. Changes in floodplain
 inundation extent and duration, due to variable wet season flows or water
 resources development (WRD), can impact landscape connectivity and
 ultimately the magnitude of the food web subsidy. 2. We explored landscape
 connectivity using graph theory and derived four new metrics to measure
 how different flow scenarios can affect connectivity and algal production.
 We considered a historic scenario with the present level of water resource
 development in our study area, the Mitchell River, and a WRD scenario with
 the inclusion of three new dams in the catchment. We generated 240 unique
 daily spatial graphs, using surface water inundation maps across 40-day
 flood events to compare a dry year (2006), an average flow year (2001),
 and a wet year (2009) with and without a WRD scenario. 3. Drier years and
 WRD scenario resulted in floodplain fragmentation, potentially
 constraining the movement of higher order consumers. Changes in
 connectivity due to WRD resulted in predicted reductions of up to 26% of
 algal production on the floodplain that was otherwise connected to the
 main river channels. 4. Synthesis and applications. The approach developed
 in this study provides new metrics to identify how changes in floodplain
 surface water extent due to water resource development and climatic
 variation may impact ecosystem function such as connectivity that
 facilitates access of higher order consumers to primary production in
 floodplain wetlands. With a direct link to river flow alteration, these
 metrics can inform catchment planning and management to ensure that the
 conservation of floodplain ecosystem functions is adequately considered in
 water resource management decisions.
description: We used graph theoretic metrics, and the igraph package in the R
 statistical environment to build the spatial graphs and compute graph
 metrics.