cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.47d7wm3hq
title: Psilocybin therapy for females with anorexia nervosa: A phase 1, open label, feasibility study

description: Anorexia nervosa (AN) is a deadly illness with no proven treatments to
 reverse core symptoms and no FDA-approved medications. Novel treatments
 are urgently needed to improve clinical outcomes. In this open-label
 feasibility study, 10 adult female participants (m BMI 19.7 kg/m2; SD 3.7)
 who met DSM 5 criteria for AN or pAN (partial remission) were recruited to
 a study conducted at an academic clinical research institute. Participants
 received a single 25mg dose of synthetic psilocybin combined with
 psychological support. The primary aim was to assess safety, tolerability,
 and feasibility at post-treatment via incidences and occurrences of
 adverse events (AEs) and clinically significant changes in: ECG,
 laboratory tests, vital signs and suicidality. There were no clinically
 significant changes in ECG, vital signs, or suicidality. Two participants
 developed asymptomatic hypoglycemia at post-treatment, which resolved
 within 24 hours. There were no other clinically significant changes in
 laboratory values. All AEs were mild and transient in nature.
 Participants’ qualitative perceptions suggest that the treatment was
 acceptable for most participants. Results suggest that psilocybin therapy
 is safe, tolerable, and acceptable for female AN, a promising finding
 given physiological dangers and problems with treatment engagement.
 ClinicalTrials.gov Identifier: NCT04661514
description: Data was collected via self-report behavioral assessments under
 the monitoring of a clinical research coordinator and via medical
 assessments conducted at the Altman Clinical Translational Reseach
 Institute by nurse practictioners and medical assistants under the
 supervision of the site PI physician. Data were manually entered into a
 database and/or imported from Qualtrics surveys (behavioral assessments).
 Scale and subscale scores were processed in Microsoft Excel. The research
 coordinator and site PI and Co-I oversaw this process. The final database
 was then sent to Phastar, the organization who coded and analyzed the data
 for all statistical analyses conducted and reported in the
 study. 
description: Microsoft Excel
DOI: 10.25338/b8gk93
title: Data from: Response to novel feed in dairy calves is affected by prior hay provision and presentation method

description: Animals raised in environments that prevent natural foraging opportunities
 may show difficulties adapting to novelty, such as feeding and management
 changes. Our objective was to evaluate how early provision and
 presentation of forage in dairy calves affected response to novel TMR
 (total mixed ration; grain and alfalfa) at weaning. Holstein heifer calves
 were housed individually on sand and fed a diet of starter grain and milk
 replacer (5.7–8.4L/d step-up) via a bottle (Control, n=9) or given
 additional access to mountaingrass hay presented either in a bucket
 (Bucket, n=9) or PVC pipe feeder (Pipe, n=9). Treatments were applied from
 birth through 50 d of age when step-down weaning began. All calves had 3
 buckets and a pipe feeder in their pens. On d 50, each calf was briefly
 blocked inside their hutch. TMR was put in the 3rd bucket that previously
 contained hay (Bucket) or was empty (Control, Pipe). The calf was released
 and video-recorded for 30 min. Neophobia towards TMR was affected by prior
 experience with presentation: Bucket calves began eating TMR faster than
 Pipe and Control (P=0.012) and showed the fewest number of startle
 responses (P=0.004). Intake was similar across groups (P=0.978),
 suggesting this apparent neophobia was transient, but Control calves took
 longer to eat than Bucket (P&lt;0.001) and Pipe (P=0.070) calves and
 were less likely to give up on eating to lie down instead. These results
 suggest that previous experience with hay improves processing ability when
 presented with novel TMR. Overall, response to a novel feed is affected by
 both early life experience, such as opportunities to process forage, and
 the presentation of the feed itself. Calves also appear motivated to
 access forage, evidenced by transient neophobia, high intake, and
 persistence in feeding by naïve calves.
description: Please see the associated research publication. 
description: Please see the associated README file.
DOI: 10.25338/b8bs8j
title: Data from: Development and application of a novel approach to scoring ear tag wounds in dairy calves

description: Application of ear tags in cattle is a common husbandry practice for
 identification purposes. While it is known that ear tag application causes
 damage, little is known about the duration and process of wound healing
 associated with this procedure. Our objective was to quantify the wound
 healing progression in dairy calves with plastic identification tags.
 Calves (n=33) were ear tagged at 2 d of age and wound photos were taken
 weekly until 9–22 wk of age. This approach generated 10–22 observations
 per calf that were analyzed using a novel wound-scoring system. We
 developed this system to score the presence or absence of 8 different
 tissue types related to piercing trauma or mechanical irritation along the
 top of the tag (impressions, crust, and desquamation) and around the
 piercing (exudate, crust, tissue growth, and desquamation). Ears were
 scored as undamaged when tissue was intact. We found that wound tissue
 types associated with damage were still seen in many calves for at least
 12 wk and up to 22 wk. This prolonged healing suggests extrinsic factors,
 such as mechanical disturbance and irritation, may have contributed to the
 wounds. Indeed, mechanical impression wounds, likely caused by the tag
 rubbing against the ear, were observed for the full duration of the study.
 Further research is warranted to understand ways to improve this form of
 animal identification.
DOI: 10.4121/940b6143-bb49-4a0a-93d7-bcdb9166e670
title: Data accompanying the publication: "Sea-level fingerprints separation from altimetry data using deep learning"

description: This repository provides data and for separating GRD (Gravitation–Rotation–Deformation) sea-level fingerprint contributions from multiple land-ice sources using a multi-decoder U-Net.It includes: (1) synthetic SSH change-rate NetCDF files named syntheticSSHrate_[steric product]_1deg_10d.nc (units: mm per year) on a 1-degree grid (66S to 66N, lon 0 to 359E) at 10-day sampling from 1993-01-01 to 2017-11-01. Each file contains the synthetic field (tssh), the steric component (Steric), the total GRD component (GRD), and nine regional GRD components (GRD_gris plus eight glacier regions). Masked grid cells are set to zero. (2) normalized GRD fingerprint patterns in Normalized_GRD_1deg.nc. (3) the preprocessing mask in mask_1deg.nc. (4) CSV model outputs with DNN-derived regional mass change rate time series (10-day sampling) from satellite altimetry, stored in Mass Change Rate.csv (units: mm yr-1, GMSL equivalent).
DOI: 10.4121/940b6143-bb49-4a0a-93d7-bcdb9166e670.v1
title: Data accompanying the publication: "Sea-level fingerprints separation from altimetry data using deep learning"

description: This repository provides data and for separating GRD (Gravitation–Rotation–Deformation) sea-level fingerprint contributions from multiple land-ice sources using a multi-decoder U-Net.It includes: (1) synthetic SSH change-rate NetCDF files named syntheticSSHrate_[steric product]_1deg_10d.nc (units: mm per year) on a 1-degree grid (66S to 66N, lon 0 to 359E) at 10-day sampling from 1993-01-01 to 2017-11-01. Each file contains the synthetic field (tssh), the steric component (Steric), the total GRD component (GRD), and nine regional GRD components (GRD_gris plus eight glacier regions). Masked grid cells are set to zero. (2) normalized GRD fingerprint patterns in Normalized_GRD_1deg.nc. (3) the preprocessing mask in mask_1deg.nc. (4) CSV model outputs with DNN-derived regional mass change rate time series (10-day sampling) from satellite altimetry, stored in Mass Change Rate.csv (units: mm yr-1, GMSL equivalent).
DOI: 10.5061/dryad.hdr7sqvmt
title: Mapping soil microbial residence time at the global scale

description: Soil microbes ultimately drive the mineralization of soil organic carbon
 and thus ecosystem functions. We compiled a dataset of the seasonality of
 microbial biomass carbon (MBC) and developed a semi-mechanistic model to
 map monthly MBC across the globe. MBC exhibits an equatorially symmetric
 seasonality between the Northern and Southern Hemispheres. In the Northern
 Hemisphere, MBC peaks in autumn and is minimal in spring at low latitudes
 (&lt;25° N), peaks in the spring and is minimal in autumn at
 mid-latitudes (25°-50° N), while peaks in autumn and is minimal in spring
 at high latitudes (&gt;50° N). This latitudinal shift of MBC
 seasonality is attributed to an interaction of soil temperature, soil
 moisture, and substrate availability. The MBC seasonality is inconsistent
 with patterns of heterotrophic respiration, indicating that MBC as a proxy
 for microbial activity is inappropriate at this resolution. This study
 highlights the need to explicitly represent microbial physiology in
 microbial models. The interactive controls of environments and substrate
 on microbial seasonality provide insights for better representing
 microbial mechanisms in simulating ecosystem functions at the seasonal
 scale.
description: We used Google Scholar (http://scholar.google.com/) for a
 comprehensive search of peer-reviewed papers published by December
 2020.
DOI: 10.5061/dryad.9p8cz8wkx
title: Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates

description: The slow-evolving invertebrate amphioxus has an irreplaceable role in
 advancing our understanding into vertebrate origin and innovations. Here
 we resolve the nearly complete chromosomal genomes of three amphioxus
 species, one of which best recapitulates the 17 chordate ancestor linkage
 groups. We reconstruct the fusions, retention, or rearrangements between
 descendants of whole genome duplications (WGDs), which gave rise to the
 extant microchromosomes that likely existed in the vertebrate ancestor.
 Similar to vertebrates, the amphioxus genome gradually establishes its 3D
 chromatin architecture at the onset of zygotic activation and forms two
 topologically associated domains at the Hox gene cluster. We find that all
 three amphioxus species have ZW sex chromosomes with little sequence
 differentiation, and their putative sex-determining regions are
 nonhomologous to each other. Our results illuminate the unappreciated
 interspecific diversity and developmental dynamics of amphioxus genomes
 and provide high-quality references for understanding the mechanisms of
 chordate functional genome evolution.
DOI: 10.5061/dryad.3tx95x6kf
title: Agronomic and quality impact of a shortened translocation for wheat streak mosaic virus resistance

description: Wheat streak mosaic virus (WSMV) is a mite-vectored virus with substantial
 economic impact on wheat production. One of the effective sources of
 resistance to WSMV, Wsm1, is carried on a translocation from Thinopyrum
 intermedium. The original whole arm form of this translocation (T4DL·4JsS)
 was highly effective against WSMV but carried a substantial yield penalty
 in the absence of the virus. Shorter recombinants of the Th. intermedium
 translocation are now available. This study characterized the agronomic
 performance of near-isogenic sib-pair families in ten yield trials using
 one of these shortened T4DL·4DS-4JsS translocations, named ‘rec213’, in
 the absence of visible disease. This translocation had no effect on
 heading date, was associated with a modest reduction (≤ 4.8 cm) in plant
 height, and the translocation had a favorable effect (≤ 12.6%) on grain
 yield in those environments where highly significant genotype effects were
 detected. The translocation did not affect protein concentration or lactic
 acid-sodium dodecyl sulfate solvent retention capacity, a measure of
 gluten quality. However, families with the translocation had slightly (≤
 5%) lower protein quality scores than paired families without the
 translocation. We do not expect this modest difference in quality to be a
 barrier to utilization of the rec213 translocation for Wsm1, but we
 encourage breeders to work within high quality genetic backgrounds in when
 using the rec213 translocation, and to monitor the quality of breeding
 selections. Improved codominant PCR-based marker assays were developed to
 facilitate the use of the rec213 Wsm1 trait in breeding programs.
description: See text of manuscript.
description: Microsoft Excel
DOI: 10.15468/dl.x8hw2w
title: Occurrence Download

description: A dataset containing 243 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Flemingia pauciflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 243 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003333-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.crjdfn37n
title: Exploring functional flow heterogeneity in regulated flow regime: fish species turnover along hydraulic gradients in an artificial waterway network

description: Humans have altered river flows and lateral aquatic habitats. The
 expansion of agriculture in floodplains has resulted in landscapes
 dominated by irrigated farmland. A key challenge in water management is to
 conserve existing ecological communities and habitat heterogeneity, while
 simultaneously maintaining engineered infrastructure for agriculture. In
 this study, we focused on an artificial channel network for irrigation
 with a regulated flow regime and its function as habitat for various fish
 species. Differences of hydraulic conditions among channels and
 compositional changes in fish species were examined to clarify functional
 flow heterogeneity. Species turnover was analyzed using pairwise Simpson
 dissimilarity among sampling reaches. Species turnover was positively
 associated with Froude number (flow intensity) differences at intermediate
 discharges, and with differences in cross-sectional areas (flow magnitude)
 at low discharges. Drastic changes in inflows should be considered for the
 effective conservation of flow heterogeneity, even under a regulated flow
 regime. Improved engineering design to manage the hydraulic environment is
 one option for maintaining the ecological value of lateral waterbodies in
 human-dominated landscapes. Our findings provide insights into the
 importance of functional flow heterogeneity to conserve fish species
 diversity.
DOI: 10.5061/dryad.5mkkwh792
title: Data from: Disentangling genetic from environmental effects on phenotypic variability of Southern rock lobster (Jasus edwardsii) postlarvae

description: Environmental conditions experienced during larval dispersal of marine
 organisms can determine size-at-settlement of recruits. It is, therefore,
 not uncommon that larvae undergoing different dispersal histories would
 exhibit phenotypic variability at recruitment. Here we investigated
 morphological differences in recently settled southern rock lobster (Jasus
 edwardsii) recruits, known as pueruli, along a latitudinal and temporal
 gradient on the east coast of Tasmania, Australia. We further explored
 whether natural selection could be driving morphological variation. We
 used double digest restriction-site associated DNA sequencing (ddRADseq)
 to assess differences in genetic structure of recently settled recruits on
 the east coast of Tasmania over three months of peak settlement during
 2012 (August, September and October). Phenotypic differences in pueruli
 between sites and months of settlement were observed, with significantly
 smaller individuals found at the northernmost site. Also, there was a lack
 of overall genetic divergence; however, significant differences in
 pairwise FST values between settlement months were observed at
 the southernmost study site, located at an area of confluence of ocean
 currents. Specifically, individuals settling into the southernmost earlier
 in the season were genetically different from those settling later. The
 lack of overall genetic divergence in the presence of phenotypic variation
 indicates that larval environmental history during dispersal
 of J. edwardsii could be a possible driver of the resulting
 phenotype of settlers.
description: Four ddRADseq libraries were
 prepared from genomic DNA of <em>Jasus</em>
 <em>edwardsii</em> pueruli samples.
 Libraries were sequenced at the Australian
 Genome Research Facility (AGRF) on the Illumina HiSeq 2500 platform using
 a 100 bp single-end kit
description: Quality check of raw indexed
 data: FastQC v0.10.1 Demultiplexing: “process_radtags” protocol from
 Stacks v1.29 Demultiplexed libraries were filtered for
 bacterial and viral content using Kraken-gcc v0.10.4. Filtered reads were processed through a
 custom-built “rad-loci” pipeline (https://github.com/molecularbiodiversity/rad-loci) Individual filtered reads of all samples were aligned to the reference catalog using bwa-intel v0.7.12. Variant calling was performed using the Genome Analysis Toolkit (GATK) v3.3_0 SNP filtering was performed in vcftools-gcc v0.1.13.
DOI: 10.5061/dryad.sj3tx9683
title: Force propagation between epithelial cell doublets

description: Cell-generated forces play a major role in coordinating the large-scale
 behavior of cell assemblies, in particular during development, wound
 healing and cancer. Mechanical signals propagate faster than biochemical
 signals but can have similar effects, especially in epithelial tissues
 with strong cell-cell adhesion. However, a quantitative description of the
 transmission chain from force generation in a sender cell, force
 propagation across cell-cell boundaries, and the concomitant response of
 receiver cells is missing. For a quantitative analysis of this important
 situation, here we propose a minimal model system of two epithelial cells
 on an H-pattern ("cell doublet"). After optogenetically
 activating RhoA, a major regulator of cell contractility, in the sender
 cell, we measure the mechanical response of the receiver cell by traction
 force and monolayer stress microscopies. In general, we find that the
 receiver cells show an active response so that the cell doublet forms a
 coherent unit. However, force propagation and response of the receiver
 cell also strongly depend on the mechano-structural polarization in the
 cell assembly, which is controlled by cell-matrix adhesion to the adhesive
 micropattern. We find that the response of the receiver cell is stronger
 when the mechano-structural polarization axis is oriented perpendicular to
 the direction of force propagation, reminiscent of the Poisson effect in
 passive materials. We finally show that the same effects are at work in
 small tissues. Our work demonstrates that cellular organization and active
 mechanical response of a tissue is key to maintaining signal strength and
 leads to the emergence of elasticity, which means that signals are not
 dissipated like in a viscous system but can propagate over large
 distances. 
description: Data was acquired with a Nikon Ti2 epifluorescence microscope.
 The first layer of analysis was performed with a homemade TFM code and the
 resulting Traction Force Maps were analysed with code available on https://github.com/ArturRuppel/ForceTransmissionInDoublets
DOI: 10.5061/dryad.6q573n62d
title: The phoenix hypothesis of speciation

description: Genetic divergence among allopatric populations builds reproductive
 isolation over time. This process is accelerated when populations face a
 changing environment, but abrupt change also places populations at risk of
 extinction. Here we use simulations of Fisher’s geometric model with
 explicit population dynamics to explore the genetic changes that occur in
 the face of environmental changes. We show that evolutionary rescue leads
 to the fixation of mutations whose effects are larger on average and that
 these mutations are more likely to lead to reproductive isolation,
 compared with populations not at risk of extinction. We refer to the
 formation of new species from the ashes of populations in decline as the
 phoenix hypothesis of speciation. The phoenix hypothesis predicts more
 substantial hybrid fitness breakdown among populations surviving a higher
 extinction risk. The hypothesis was supported when many loci underlie
 adaptation. When, however, there was only a small number of potential
 rescue mutations, we found that mutations fixed in different populations
 were more likely to be identical, with parallel changes reducing
 isolation. With a limited genomic potential for adaptation, we find
 support for a modified version of the phoenix hypothesis where
 reproductive isolation builds fastest in populations subject to an
 intermediate extinction risk.
DOI: 10.5061/dryad.v41ns1s0t
title: Variation in functional traits, growth relationships, and resource allocation among annual twig of dove tree along with latitudes

description: Dove tree (Davidia involucrata Baill.), a monotypic rare species in China
 and a famous ornamental plant in the world, was employed as a model
 species in our study. The  morphological and biomass
 traits  of annul D. involucrata twigs were investigated in three
 latitude regions (32°19′ N, 30°08′ and 27°55′) in the Sichuan, Southwest
 China. 
description: In the flowering stage of D.
 involucrata populations from mid-April to early May, 6 ‒ 8 healthy plants
 with similar DBH (diameter at breast height) and no insect pests were
 randomly selected from the three natural populations in PW, TQ and GX.
 Selected trees were (a) healthy with similar habitats (soil type, slope
 and aspect); (b) full grown with similar canopy size; (c) not to be
 located near the edge of the forest, or next to previously sampled trees.
 Then, to avoid growth differences derived from light intensity, 3 ‒ 5
 annual twigs (including stem and all leaves and flowers above the stem)
 were randomly collected from the sunny side of the lower crown of each
 plant.  The
 morphological and biomass traits of leaf, stem and flower from each twig
 were measured. Lamina, petiole, bract and flower stalk were scanned using
 CanoScan LiDE210, and then the length, width and area of lamina and bract,
 as well as the petiole length and flower stalk length were measured by the
 software Image J version 1.47v (National Institutes of Health, USA). The
 diameter of stem and flower stalk were measured with an electronic vernier
 calliper (0.01 mm), respectively. Biomass samples were oven-dried to
 constant mass (70 °C, 72 h), then the lamina mass, petiole mass, bract mass, receptacle mass,
 capitulum mass, flower
 stalk mass and stem mass
 for each twig were separately measured. The leaf area or leaf mass was the
 sum of lamina area and petiole area, or lamina mass and petiole mass. The
 flower mass was the sum of mass of bract, receptacle, capitulum
 and flower
 stalk. The twig mass was
 the sum of the mass of stem, leaves and flowers. The mean of leaf area,
 lamina length and lamina
 width was calculated as
 the total area, length or width divided by leaf number for each
 twig.