cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s7h44j19v
title: Multidimensional control of therapeutic human cell function with synthetic gene circuits

description: Synthetic gene circuits that precisely control human cell function could
 expand the capabilities of gene and cell-based therapies. However,
 platforms for developing circuits in primary human cells that drive robust
 functional changes in vivo and have compositions suitable for clinical use
 are lacking. Here, we develop synthetic transcriptional regulators that
 are compact and based largely on human-derived proteins (synZiFTRs). As a
 proof of principle, we engineer gene switches and circuits that allow
 precise, user-defined control over therapeutically-relevant genes in
 primary T cells using orthogonal, FDA-approved small molecule inducers.
 Our circuits can instruct T cells to sequentially activate multiple
 cellular programs, such as proliferation and anti-tumor activity, to drive
 synergistic therapeutic responses. This platform should accelerate
 development and clinical translation of synthetic gene circuits in diverse
 human cell types and contexts.
description: These data were generated to support the development and
 characterization of a mammalian gene circuit engineering platform based on
 synthetic transcriptional regulators that are compact and based largely on
 human-derived proteins (synZiFTRs). In the published work, we applied the
 platform to engineer gene switches and circuits that allow precise,
 user-defined control over therapeutically-relevant genes in primary T
 cells using orthogonal, FDA-approved small molecule drugs. Our circuits
 can instruct T cells to sequentially activate multiple cellular programs,
 such as proliferation and anti-tumor activity, to drive cellular responses
 both in vitro and in vivo. Our datasets, comprised of
 numerous experimental and computational techniques, support the 5 major
 figures in our manuscript:  The
 clinically-driven design of compact, humanized, synthetic gene regulators
 (synZiFTRs) for mammalian cell engineering. SynZiFTR
 gene switches that allow precise, user-defined control over gene
 expression in human cells using clinically-approved small
 molecules. A synZiFTR gene circuit for
 drug-regulated, post-delivery control over CAR expression and T-cell
 killing in vivo. A synZiFTR gene circuit for
 drug-regulated, on-demand immune cell proliferation.
 SynZiFTR gene circuits used to enact sequential control of
 immune cell function to drive synergistic in vivo responses.
 The final processed dataset for generating all
 figures, including supplemental figures, is compiled in a .xlsx file,
 named “Dataset_Li-Israni”, which is organized by Fig#/ Supplemental
 Fig#.  In addition, processed datasets for each figure
 are included in .xlsx files, named “Fig#_arranged_processed”, along with
 relevant raw dataset files. The raw datasets require Flowjo software to
 open.  Please refer to the README file for a more
 detailed description of the data and file structure.
description: Please refer to the README file.
DOI: 10.25349/d92k69
title: Depolarization block in olfactory sensory neurons expands the dimensionality of odor encoding

description: Upon strong and prolonged excitation, neurons can undergo a silent state
 called depolarization block that is often associated with disorders such
 as epileptic seizures. Here we show that neurons in the peripheral
 olfactory system undergo depolarization block as part of their normal
 physiological function. Typically, olfactory sensory neurons enter
 depolarization block at odor concentrations three orders of magnitude
 above their detection threshold, thereby defining receptive fields over
 concentration bands. The silencing of high-affinity olfactory sensory
 neurons produces sparser peripheral odor representations at high-odor
 concentrations, which might facilitate perceptual discrimination. Using a
 conductance-based model of the olfactory transduction cascade paired with
 spike generation, we provide numerical and experimental evidence that
 depolarization block arises from the slow inactivation of sodium channels
 — a process that could affect a variety of sensory neurons. The existence
 of ethologically-relevant depolarization block in olfactory sensory
 neurons creates a new dimension that expands the peripheral encoding of
 odors.
description: For details on the methodology for data collection and data
 processing please see the publication titled: "Depolarization block
 of olfactory sensory neurons adds a new dimension to odor
 encoding".
description: Please see the folder custom_code.zip for all scripts utlizing
 the data presented here. Other code can be found in the file:
 hdbscan_spike_sorter.zip which contains code to conduct spike sorting and
 in the file: OB1_GUI.zip which contains code to control the Elveflow OB1
 microfluidics device used to collect the electrophysiology data presented
 here. Any updates will be provided here: https://gitlab.com/davidtadres/ob1_gui, https://gitlab.com/davidtadres/hdbscan_spike_sorter/, https://gitlab.com/LouisLab/depolarization_block_publication
DOI: 10.15468/dl.5ydc2b
title: Occurrence Download

description: A dataset containing 100787 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aquila nipalensis"
 ]
}

 The dataset includes 100787 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003236-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.76hdr7t13
title: High-latitude marginal reefs support fewer but bigger corals than their tropical counterparts

description: Anthropogenic impacts are typically detrimental to tropical coral reefs,
 but the effect of increasing environmental stress and variability on the
 size structure of coral communities remains poorly understood. This limits
 our ability to effectively conserve coral reef ecosystems because
 size-specific dynamics are rarely incorporated. Our aim is to quantify
 variation in the size structure of coral populations across 20 sites along
 a tropical-to-subtropical environmental gradient on the east coast of
 Australia (~23°S to 30°S), to determine how size structure changes with a
 gradient of sea surface temperature, turbidity, productivity and light
 levels. We use two approaches: 1) linear regression with summary
 statistics (such as median size) as response variables, a method
 frequently favoured by ecologists; and 2) compositional functional
 regression, a novel method using entire size-frequency distributions as
 response variables. We then predict coral population size structure with
 increasing environmental stress and variability. Together, we find fewer
 but larger coral colonies in marginal reefs, where conditions are
 typically more variable and stressful, than in tropical reefs. Our model
 predicts that coral populations may become gradually dominated by larger
 colonies (&gt; 148 cm2) with increasing environmental stress. Fewer
 but bigger corals suggest low survival of smaller corals, slow growth, and
 / or poor recruitment. This finding is concerning for the future of coral
 reefs, as it implies that current marginal populations, or future reefs in
 increasingly stressful environmental conditions may have low recovery
 potential. We highlight the importance of continuously monitoring changes
 to population structure over biogeographic scales.
description: Images of the benthos were taken using SCUBA. Data from the
 images were extracted using the programme 'ImageJ', following
 the 'SizeExtractR' protocol. 
description: R/ RStudio to run the code used in our analyses.
DOI: 10.5061/dryad.s7h44j19w
title: Post-release survival and dispersal of translocated crest-tailed mulgara Dasycercus cristicauda

description: Initial translocations are inherently risky due to uncertainty around
 species-specific responses to novel environments. Incorporating a range of
 release protocols can minimise risks of translocation failure. We
 identified post-translocation hyperdispersal as a risk to the first
 translocation of the crest-tailed mulgara (Dasycercus cristicauda), an
 Australian carnivorous marsupial, and tested temporary confinement and
 releasing females with pouch young as mitigation strategies. We released
 16 females with pouch young and 3 males into unoccupied burrows within a
 20 km2 feral animal exclosure, either within temporary confinement pens
 (n = 10) or without confinement (immediate release) (n = 9). Temporary
 confinement did not influence survival but did influence dispersal
 behaviour. Thirty-seven percent of translocated individuals (all 3 males,
 4 of 16 females) hyperdispersed (3.0–11.6 km) outside the study exclosure
 after release, including 42% immediate release animals and 29% temporary
 confinement animals. No males remained in the exclosure at the study end.
 Confined females settled closer to their release site. Release of females
 with pouch young led to an increase in the translocated population from 9
 to 58 individuals within 4 months. Releasing females with young from
 geographically distant sites may be important to offset male
 hyperdispersal. Our results suggest that temporary confinement and
 translocating breeding females are important release protocols for species
 with a propensity for hyperdispersal post-translocation.
DOI: 10.5061/dryad.41ns1rnj3
title: Pictures of diseased soybean leaves by category captured in field and with controlled backgrounds: Auburn soybean disease image dataset (ASDID)

description: The dataset contains 2D images/photographs of diseased soybean leaves
 ideal for plant disease identification and visual object recognition
 research. Images were captured during the 2020 and 2021 soybean seasons
 using a Canon EOS 7D Mark II Digital SLR Camera and a Motorola Moto Z2
 Play Smartphone from fields at the EV Smith Agricultural Research Station
 (Tallassee, Alabama), the Cullars Rotation (Auburn, Alabama), and the
 Brewton Agricultural Research Unit (Brewton, Alabama). Across both seasons
 there are a total of 9,981 original images collected across eight
 disease/deficiency categories. These include (1) healthy-looking plants,
 and those displaying the symptoms of (2) bacterial blight, (3) cercospora
 leaf blight, (4) downey mildew, (5) frogeye leaf spot, (6) soybean rust,
 (7) target spot, and (8) potassium deficiency. For each disease category,
 leaves were photographed at various canopy heights while still attached to
 the plant in the field or they were detached from the plant and then
 immediately photographed while laid flat on the ground in trimmed grass or
 on a white surface. Images were collected with the goal of developing a
 Convolutional Neural Network (CNN)-based automated classifier of digital
 images of soybean diseases. Dataset is well-suited for classification
 modeling.
description: All images in this dataset are the raw images. They are
 unprocessed, except that for the fact that all images have been oriented
 horizontally. Soybean leaves were photographed during the 2020 and 2021
 Alabama (southeastern USA) growing seasons in the months of August,
 September, and October. The primary method was to walk through rows of
 planted soybean fields and capture images of a single soybean leaf showing
 symptoms of a known disease with the leaf still attached to the plant. The
 leaves photographed were simply the ones ‘stumbled upon’ in a known
 diseased area. We attempted to photograph leaves at various heights in the
 canopy in proportion to how disease symptoms were distributed.
 Additionally, leaves of each represented disease category were detached
 from the plant and then immediately photographed while laid flat on the
 ground in trimmed grass or on a white surface. So there is a mix of
 attached (in the field) and detached (placed on a white or grass
 background) soybean leaf images for each of the eight disease
 categories
description: All images are formatted as .jpg files. JPG is a commonly used
 compressed image format for digital images. The categorized images can be
 used as any other JPG file.
DOI: 10.5061/dryad.6wwpzgn2p
title: Dual receptive fields underlying target and wide-field motion sensitivity in looming sensitive descending neurons

description: Responding rapidly to visual stimuli is fundamental for many animals. For
 example, predatory birds and insects alike have amazing target detection
 abilities, with incredibly short neural and behavioral delays, enabling
 efficient prey capture. Similarly, looming objects need to be rapidly
 avoided to ensure immediate survival, as these could represent approaching
 predators. Male Eristalis tenax hoverflies are nonpredatory, highly
 territorial insects that perform high-speed pursuits of conspecifics and
 other territorial intruders. During the initial stages of the pursuit, the
 retinal projection of the target is very small, but this grows to a larger
 object before physical interaction. Supporting such behaviors, E. tenax
 and other insects have both target-tuned and loom-sensitive neurons in the
 optic lobes and the descending pathways. We here show that these visual
 stimuli are not necessarily encoded in parallel. Indeed, we describe a
 class of descending neurons that respond to small targets, to looming and
 to wide-field stimuli. We show that these descending neurons have two
 distinct receptive fields where the dorsal receptive field is sensitive to
 the motion of small targets and the ventral receptive field responds to
 larger objects or wide-field stimuli. Our data suggest that the two
 receptive fields have different presynaptic input, where the inputs are
 not linearly summed. This novel and unique arrangement could support
 different behaviors, including obstacle avoidance, flower landing, and
 target pursuit or capture.
description: This is described in detail in the README file as well as the
 methods of the paper.
DOI: 10.25338/b8r056
title: Data from: Body shape and mode of propulsion do not constrain routine swimming in coral reef fishes

description: It is widely believed that because of biomechanical trade-offs, fish body
 shape and the mode of propulsion are strong predictors of swimming
 performance, with the best cruisers, maneuverers, and accelerators having
 different body forms and emphasizing different propulsion mechanisms. This
 paradigm is regularly projected onto routine swimming behavior and
 dominates the ecomorphological literature, despite the paucity of field
 measurements. In this study, we measured variation in swimming behavior
 among 48 species of Indian Ocean coral reef fishes using recordings from a
 remote stereo video system. We measured average swimming speed, average
 swimming bout distance, frequency of turns, and percent of time spent
 station-holding and looked for the predicted trade-offs between them. We
 find little evidence of the expected relationships between swimming
 behaviors across species, little evidence that body shape affects
 swimming, and few differences between species that swim by undulating the
 body and those that emphasize the use of median and paired fins. Taxa
 widely thought of as archetypical maneuverers (Chaetodon) and cruisers
 (Caranx) were not outliers in any behaviors. Our results indicate that
 swimming behavior is not easily predicted from simple measures of body
 shape and that alternative swimming modes can produce comparable
 behavioral profiles.
DOI: 10.5061/dryad.bcc2fqzgs
title: Data for: Whole-of-community invertebrate rewilding: Leaf litter transplants rapidly increase beetle diversity during restoration

description: Restoration of degraded areas is now a central tool in humanity’s response
 to continued species loss. However, restoration projects often report
 exceedingly slow or failed recolonization of fauna, especially
 dispersal-constrained groups such as invertebrates. Active interventions
 via reintroducing or “rewilding” invertebrates may assist recolonization
 and speed up the restoration of communities towards a desired target.
 However, invertebrate rewilding is rarely implemented during ecological
 restoration. Here, we studied the efficacy of invertebrate rewilding as a
 means of improving diversity and compositional similarities to remnant
 communities during restoration. Rewilding was conducted by transplanting
 leaf litter and soil, including associated communities of invertebrates
 from species-rich remnant sites into species-poor and geographically
 isolated revegetated farmland sites. We sampled pre- and post-rewilding
 invertebrate communities in remnant, rewilded revegetation, and control
 revegetation sites. Our data contains mesoinvertebrate (&lt;5mm in
 size) community samples from 6 sites within each of our 3 treatments. We
 took 8 subsamples measuring 25 cm by 25 cm containing the entire
 mesoinvertebrate leaf litter community from each site across 4 different
 seasons. The first season was a pre-treatment baseline measurement and was
 taken in November 2018. Thereafter, we sampled 7-, 18-, and 27- months
 post-rewilding. Our data contains a range of traits for each morphospecies
 (Size in mm, trophic group, and whether they were winged or flightless)
 and two environmental variables measured at each site (Volumetric water
 content and elevation). We included these for our Hierarchical Modelling
 of Species Community (HMSC) approach to determine whether biological
 properties of species or environmental variables were driving species
 distributions. Beetle (Coleoptera) morphospecies richness increased
 rapidly in rewilded sites and was indistinguishable from remnant
 communities as early as 7 months post-rewilding. Beetle community
 similarity in the rewilding sites significantly deviated from the control
 sites 27 months post-rewilding, however, remnant communities remained
 distinct over the study timeframe. Establishment success varied as other
 taxa did not respond as consistently as beetles within the study
 timeframe. Our results demonstrate that the relatively simple act of
 transplanting leaf litter can result in comparatively large increases in
 morphospecies richness during restoration in a short timeframe.
description: We collected eight 25 cm by 25 cm subsamples of leaf litter from
 each site in each sampling session. We ran the leaf litter through
 Tullgren funnels to extract the entire community, which was then sorted
 into morphospecies for community analyses.
DOI: 10.5061/dryad.3j9kd51nr
title: Is there hybridisation between diploid and tetraploid Euphrasia in a secondary contact zone?

description: • Premise of the study: Hybridisation between species with contrasting
 ploidy is usually considered rare in nature due to strong ploidy related
 postzygotic reproductive isolating barriers. However, genomic sequencing
 has revealed previously overlooked examples of natural cross-ploidy
 hybridisation, suggesting this phenomenon may be more common than once
 thought. Here, we investigate potential cross-ploidy hybridisation in
 British eyebrights (Euphrasia, Orobanchaceae), a group where thirteen
 putative cross-ploidy hybrid combinations have been reported based on
 morphology.   • Methods: We analysed a contact zone between
 diploid E. rostkoviana and tetraploid E. arctica in Wales. We sequenced
 part of the internal transcribed spacer of nuclear ribosomal DNA (ITS1)
 and used Genotyping by Sequencing (GBS) to look for evidence of
 cross-ploidy hybridisation and introgression. • Key results: All variant
 sites in the ITS1 region were fixed between diploids and tetraploids,
 indicating a strong barrier to hybridisation. Clustering analyses of 356
 SNPs generated using GBS clearly separated samples by ploidy and revealed
 strong genetic structure (FST = 0.44). However, the FST distribution
 across all SNPs was bimodal, indicating potential differential selection
 on loci between diploids and tetraploids. Demographic inference with dadI
 suggested potential gene flow – with this limited to around one or fewer
 migrants per generation. • Conclusions: Our results suggest recent
 cross-ploidy hybridisation is rare or absent in a site of secondary
 contact in Euphrasia. While a strong ploidy barrier prevents hybridisation
 over ecological time-scales, such hybrids may form in stable populations
 over evolutionary time-scales and may allow for cross-ploidy introgression
 to take place.
description: Genotyping by sequencing data were generated for diploid and
 tetraploid Euphrasia species using the enzyme ApeKI. Sanger sequencing was
 also performed, amplifying the ITS2 region.
DOI: 10.5061/dryad.k98sf7m98
title: Data from: Caveolae and Bin1 form ring-shaped platforms for T-tubule initiation

description: Excitation-contraction coupling requires a highly specialized membrane
 structure, the triad, composed of a plasma membrane invagination, the
 T-tubule, surrounded by two sarcoplasmic reticulum terminal cisternae.
 Although the precise mechanisms governing T-tubule biogenesis and triad
 formation remain largely unknown, studies have shown that caveolae
 participate in T-tubule formation and mutations of several of their
 constituents induce muscle weakness and myopathies. Here, we demonstrate
 that, at the plasma membrane, caveolae composed of caveolin-3 and Bin1
 assemble into ring-like structures from which emerge tubes enriched in the
 dihydropyridine receptor. Overexpression of Bin1 leads to the formation of
 both rings and tubes and we show that Bin1 forms scaffolds on which
 caveolae accumulate to form the initial T-tubule. Cav3 deficiency caused
 by either gene silencing or pathogenic mutations causes defective ring
 formation and perturbed Bin1-mediated tubulation that may explain
 defective T-tubule organization in mature muscles. Our results uncover new
 pathophysiological mechanisms that may prove relevant to myopathies caused
 by Cav3 or Bin1 variants.
description: These data were generated to investigate the organization and
 dynamics of caveolae and Bin1 on in vitro and in cellulo systems using
 sub-diffracted fluorescence microscopy, conventional and platinum replica
 electron microscopy.
description: Microsoft Excel.
DOI: 10.5061/dryad.bg79cnpdw
title: Published correlational effect sizes in social and developmental psychology

description: The distribution of effect sizes may offer insights about the research
 done and reported in a scientific field. We have evaluated 12,412 manually
 collected correlation effect sizes (Sample 1) and 31,157
 computer-extracted correlation effect sizes (Sample 2) published in
 journals focused on social or developmental psychology. Sample 1 consisted
 of 243 studies from 6 journals published in 2010 and 2019. Sample 2
 consisted of 5,012 papers published in 10 journals between 2010–2019. The
 25th, 50th and 75th effect size percentiles were 0.08, 0.17 and 0.33, and
 0.17, 0.31, and 0.52 in Samples 1 and 2, respectively. Sample 2
 percentiles were probably larger because Sample 2 only included effect
 sizes from the text but not from tables. In text, authors may have
 emphasized larger correlations. Large sample sizes were associated with
 smaller reported correlations. In Sample 1 about 70% of studies specified
 a directional hypothesis. In 2010, no papers had power calculations while
 in 2019, 14% of papers had power calculations. These data offer empirical
 insights into the distribution of reported correlations and may inform the
 interpretation of effect sizes. They also demonstrate the importance of
 computation of statistical power and highlight potential reporting bias.