cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3h207
title: Data from: A glimpse of an ancient agricultural ecosystem based on remains of micromammals in the Byzantine Negev Desert

description: It is widely believed that Byzantine agriculture in the Negev Desert
 (4th–7th cent. CE), with widespread construction of terraces and dams,
 altered local landscapes. However, no direct evidence in archaeological
 sites yet exists to test this assumption. We uncovered large amounts of
 small mammalian remains (rodents and insectivores) within agricultural
 installations built near fields, providing a new line of evidence for
 reconstructing anthropogenic impact on local habitats. Abandonment layers
 furnished high abundances of remains, whereas much smaller numbers were
 retrieved from the period of human use of the structures. Digestion marks
 are present in low frequencies (20% of long bones and teeth), with a light
 degree of impact, which indicate the role of owls (e.g., Tyto alba) as the
 principal means of accumulation. The most common taxa—gerbils (Gerbillus
 spp.) and jirds (Meriones spp.)—occur in nearly equal frequencies, which
 do not correspond with any modern Negev communities, where gerbils
 predominate in sandy low-precipitation environments and jirds in loessial,
 higher-precipitation ones. Though low-level climate change cannot be ruled
 out, the results suggest that Byzantine agriculture allowed jirds to
 colonize sandy anthropogenic habitats with other gerbilids and commensal
 mice and rats.
description: A micromammalian fauna
 from a Byzantine columbarium Near Be'er Sheva, Israel (text in
 Hebrew)This is a short report
 describing an assemblage of micromammalian remains retrieved from a
 Byzantine period structure in the Negev region of Israel. It includes a
 short preliminary text (in Hebrew), two figures and a table. A table of
 taxonomic composition with Latin scientific names of taxa is included. The
 same file is also available for download in English.Nahal Beqha micromammal
 report.docxA micromammalian fauna
 from a Byzantine columbarium Near Be'er Sheva, Israel (text in
 English)This is a short report
 describing an assemblage of micromammalian remains retrieved from a
 Byzantine period structure in the Negev region of Israel. It includes a
 short preliminary text (in English), two figures and a table. A table of
 taxonomic composition with Latin scientific names of taxa is included. The
 same file is also available for download in Hebrew.Weissbrod L-Dryad Nahal Beqha
 micromammal report.docx
DOI: 10.5061/dryad.083f9
title: Data from: The genetics of egg retention and fertilization success in Drosophila: one step closer to understanding the transition from facultative to obligate viviparity

description: Oviparous, facultative egg retention enables Drosophila females to
 withhold fertilized eggs in their reproductive tracts until circumstances
 favor oviposition. The propensity to retain fertilized eggs varies greatly
 between species, and is correlated with other reproductive traits, such as
 egg size and ovariole number. While previous studies have described the
 phenomenon, no study to date has characterized within-species variation or
 the genetic basis of the trait. Here, we develop a novel microscope-based
 method for measuring egg retention in Drosophila females and determine the
 range of phenotypic variation in mated female egg retention in a subset of
 91 Drosophila Genetic Reference Panel (DGRP) lines. We inferred the
 genetic basis of egg retention using a genome-wide association study
 (GWAS). Further, the scoring of more than 95,000 stained, staged eggs
 enabled estimates of fertilization success for each line. We found
 evidence that ovary- and spermathecae-related genes as well as genes
 affecting olfactory behavior, male mating behavior, male-female attraction
 and sperm motility may play a crucial role in post-mating physiology.
 Based on our findings we also propose potential evolutionary routes
 towards obligate viviparity. In particular, we propose that the loss of
 fecundity incurred by viviparity could be offset by benefits arising from
 enhanced mate discrimination, resource specialization, or modified egg
 morphology.
description: Line_meansMeasurement means (±S.E.) for egg retention and fertilization success for 91 DGRP lines.Egg retention countsAll raw data from the images, listing the number of counted embryos in each developmental category for every replicate measure separately and for all 91 DGRP lines.Egg_retention_counts.txtEmbryo classification with Fiji (ImageJ)The files in this folder demonstrate how the image assessment was done. It contains example microscope images, cell counter files and a step by step guide how we classified embryos.Fiji_counting.zip
DOI: 10.5061/dryad.355qk
title: Data from: Evolutionary and structural analyses uncover a role for solvent interactions in the diversification of cocoonases in butterflies

description: Multi-omic approaches promise to supply the power to detect genes
 underlying disease and fitness-related phenotypes. Optimal use of the
 resulting profusion of data requires detailed investigation of individual
 candidate genes, a challenging proposition. Here, we combine
 transcriptomic and genomic data with molecular modeling of candidate
 enzymes to characterize the evolutionary history and function of the
 serine protease cocoonase. Heliconius butterflies possess the unique
 ability to feed on pollen; recent work has identified cocoonase as a
 candidate gene in pollen digestion. Cocoonase was first described in moths
 where it aids in eclosure from the cocoon and is present as a single copy
 gene. In heliconiine butterflies it is duplicated and highly expressed in
 the mouthparts of adults. At least 6 copies of cocoonase are present in
 Heliconius melpomene and copy number varies across H. melpomene
 sub-populations. Most cocoonase genes are under purifying selection,
 however branch-site analyses suggest cocoonase 3 genes may have evolved
 under episodic diversifying selection. Molecular modeling of cocoonase
 proteins and examination of their predicted structures revealed that the
 active site region of each type has a similar structure to trypsin, with
 the same predicted substrate specificity across types. Variation among
 heliconiine cocoonases instead lies in the outward-facing residues
 involved in solvent interaction. Thus, the neofunctionalization of
 cocoonase duplicates appears to have resulted from the need for these
 serine proteases to operate in diverse biochemical environments. We
 suggest that cocoonase may have played a buffering role in feeding during
 the diversification of Heliconius across the neotropics by enabling these
 butterflies to digest protein from a range of biochemical milieux.
description: Molecular models of full
 cocoonasesMolecular models of full
 length cocoonase proteins. See Supplementary Table S6 of the publication
 for the full list of models and Methods section for how they were
 created.Full_structures.zipMolecular models of mature cocoonasesMolecular models of mature cocoonase proteins. See Supplementary Table S7 of publication for list of models and Methods section for how they were created.Equilibrated_structures.zip
DOI: 10.5061/dryad.86nv6
title: Data from: Pternopetalum porphyronotum sp. nov. (Apiaceae) from Sichuan, China

description: Pternopetalum porphyronotum, a new species from Dafengding Nature Reserve,
 Sichuan Province, China, is proposed. Diagnostic morphological characters,
 full description and detailed illustration are given based on the type
 material. A comparison between this new species and the two most similar
 congeners are presented.
description: Figures of Pternopetalum
 porphyronotumline drawing, holotype
 and photographs of Pternopetalum porphyronotum
DOI: 10.5061/dryad.cc34r
title: Data from: Resource competition promotes tumour expansion in experimentally evolved cancer

description: Tumour progression involves a series of phenotypic changes to cancer
 cells, each of which presents therapeutic targets. Here, using techniques
 adapted from microbial experimental evolution, we investigate the
 evolution of tumour spreading - a precursor for metastasis and tissue
 invasion - in environments with varied resource supply. Evolutionary
 theory predicts that competition for resources within a population will
 select for individuals to move away from a natal site (i.e. disperse),
 facilitating the colonisation of unexploited resources and decreasing
 competition between kin. After approximately 100 generations in
 environments with low resource supply, we find that MCF7 breast cancer
 spheroids (small in vitro tumours) show increased spreading. Conversely,
 spreading slows compared to the ancestor where resource supply is high.
 Common garden experiments confirm that the evolutionary responses differ
 between selection lines; with lines evolved under low resource supply
 showing a plastic spreading phenotype. These differences in spreading
 behaviour between selection lines are heritable (stable across multiple
 generations), and show that the divergently evolved lines differ in their
 response to resource supply. It is possible that prolonged resource
 limitation itself causes a stable switch toward dispersal-like behaviour
 and an increased sensitivity to resource availability without the need for
 genetic change. Different clinical strategies may be needed depending on
 whether tumour progression is due to stable or plastic effects. This study
 highlights the effectiveness of experimental evolution approaches in
 cancer cell populations and demonstrates how simple model systems might
 enable us to observe and measure key selective drivers of clinically
 important traits.
description: Change in Spheroid Area
 Over TimeAverage spheroid spread
 (across 3 replicate lines) for selection lines under high and low resource
 supply over 12 weekly transfers. Spreading was measured 72 hours after
 adhesion of the spheroid, and in the selective environment for each line
 (i.e. the motility of the low resource supply line was measured in low
 resource medium).Area over
 time.savCommon garden transfer
 experiment & Growth rate of ancestral and evolved
 linesAverage change in
 spheroid area (square-rooted) over 72 hours for evolved high and low
 resource selection lines in high and low resource environments. In
 addition, data file contains growth rate of cell populations, represented
 as the increase in cell number per hour, when grown in high and low
 resource environmentsCommon garden
 stats.savSpheroid spread versus
 cell speedData showing the change
 in spheroid area over 72 hours in high resource media for ancestor and
 evolved lines, and cell speed for associated cell lines. Areas are square
 root transformed.Cell
 Speed.savDistance to
 pointDistance to point
 measurements of evolved cell lines over 52 hours.D2P.sav
DOI: 10.5061/dryad.mh189
title: Data from: A persistent lack of international representation on editorial boards in environmental biology

description: The scholars comprising journal editorial boards play a critical role in
 defining the trajectory of knowledge in their field. Nevertheless, studies
 of editorial board composition remain rare, especially those focusing on
 journals publishing research in the increasingly globalized fields of
 science, technology, engineering, and math (STEM). Using metrics for
 quantifying the diversity of ecological communities, we quantified
 international representation on the 1985–2014 editorial boards of 24
 environmental biology journals. Over the course of 3 decades, there were
 3,827 unique scientists based in 70 countries who served as editors. The
 size of the editorial community increased over time—the number of editors
 serving in 2014 was 4-fold greater than in 1985—as did the number of
 countries in which editors were based. Nevertheless, editors based outside
 the “Global North” (the group of economically developed countries with
 high per capita gross domestic product [GDP] that collectively concentrate
 most global wealth) were extremely rare. Furthermore, 67.18% of all
 editors were based in either the United States or the United Kingdom.
 Consequently, geographic diversity—already low in 1985—remained unchanged
 through 2014. We argue that this limited geographic diversity can
 detrimentally affect the creativity of scholarship published in journals,
 the progress and direction of research, the composition of the STEM
 workforce, and the development of science in Latin America, Africa, the
 Middle East, and much of Asia (i.e., the “Global South”).
description: Espin_et_al_data_v1Dryad.Espin.v1.csvAuthor Countries: 1985-2014AuthorCountries_1985_2014.csvCountries for 2014 Editors & AuthorsEditor_Author_Geo_2014.csvGlobal Regions for 2014 Editors & AuthorsEditor_Author_Region_2014.csvNational Income Categories for 2014 Editors & AuthorsEditor_Author_Income_2014.csvCode for Analyses and Figures in Espin et al.
DOI: 10.5061/dryad.9tr75
title: Data from: The combined fatigue effects of sequential exposure to seated whole body vibration and physical, mental, or concurrent work demands

description: Many occupations in agriculture, construction, transportation, and
 forestry are non-routine, involving non-cyclical tasks, both discretionary
 and non-discretionary work breaks, and a mix of work activities. Workers
 in these industries are exposed to seated whole body vibration (WBV) and
 tasks consisting of physical, mental, or a combination of demands. Risk
 assessment tools for non-routinized jobs have emerged but there remains a
 need to understand the combined effects of different work demands to
 improve risk assessment methods and ultimately inform ergonomists and
 workers on optimum work arrangement and scheduling strategies. The
 objective of this study was to investigate fatigue-related human responses
 of WBV sequentially combined with physical, mental, or concurrent physical
 and mental demands. Sixteen healthy participants performed four conditions
 on four separate days: (1) physically demanding work, (2) mentally
 demanding work, (3) concurrent work, and (4) control quiet sitting. For
 each condition, participants performed two 15-minute bouts of the
 experimental task, separated by 30-minutes of simulated WBV based on
 realistic all-terrain vehicle (ATV) riding data. A test battery of fatigue
 measures consisting of biomechanical, physiological, cognitive, and
 sensorimotor measurements were collected at four interval periods:
 pre-session, after the first bout of the experimental task and before WBV,
 after WBV and before the second bout of the experimental task, and
 post-session. Nine measures demonstrated statistically significant time
 effects during the control condition; 11, 7, and 12 measures were
 significant in the physical, mental, and concurrent conditions,
 respectively. Overall, the effects of seated WBV in combination with
 different tasks are not additive but possibly synergistic or antagonistic.
 There appears to be a beneficial effect of seated ATV operation as a means
 of increasing task variation; but since excessive WBV may independently
 pose a health risk in the longer-term, these beneficial results may not be
 sensible as a long-term solution.
description: Vibration
 SignalThe following file
 “Yung_et_al_PlosOne_Vibration.prn” is the vibration code that was imported
 into a 6 degree of freedom hexapod platform (Mikrolar R3000 Rotopod) to
 simulate all-terrain vehicle (ATV) operation. The resulting vibration
 simulation code was programmed and is designed to be operated with MRLHPOD
 v.8.2 software and R3000 rotopod.Yung et al PlosOne Vibration
 Signal.prn
DOI: 10.5061/dryad.23d8v
title: Data from: Heritability of body size in the polar bears of Western Hudson Bay

description: Among polar bears (Ursus maritimus), fitness is dependent on body size
 through males' abilities to win mates, females' abilities to
 provide for their young, and all bears' abilities to survive
 increasingly longer fasting periods caused by climate change. In the
 Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar
 bears have declined in body size and condition, but nothing is known about
 the genetic underpinnings of body size variation, which may be subject to
 natural selection. Here, we combine a 4449-individual pedigree and an
 array of 5433 single-nucleotide polymorphisms (SNPs) to provide the first
 quantitative genetics study of polar bears. We used animal models to
 estimate heritability (h2) among polar bears handled between 1966 and
 2011, obtaining h2 estimates of 0.34-0.48 for strictly skeletal traits and
 0.18 for axillary girth (which is also dependent on fatness). We genotyped
 859 individuals with the SNP array to test for marker-trait association
 and combined p-values over genetic pathways using gene-set analysis.
 Variation in all traits appeared to be polygenic, but we detected one
 region of moderately large effect size in body length near a putative
 noncoding RNA in an unannotated region of the genome. Gene-set analysis
 suggested that variation in body length was associated with genes in the
 regulatory cascade of cyclin expression, which has previously been
 associated with body size in mice. A greater understanding of the genetic
 architecture of body size variation will be valuable in understanding the
 potential for adaptation in polar bear populations challenged by climate
 change.
description: Western Hudson Bay
 pedigree (TXT)Tab-delimited text file
 formatted for use in R (i.e., unknown parents are indicated with NA.) For
 use in ASReml, the data should be reformatted as columns id, sire, dam
 with "0" used to indicate unknown parents. For details of the
 pedigree, see doi: 10.1007/s00300-015-1871-0pedigree.txtSNP genotypes (ZIP)Raw SNP genotypes in PLINK format (i.e., .ped & .map file) before quality-control filtering.genotypes.zipLOCO RepeatABEL R scriptImplements a leave-one-chromosome-out GWAS using RepeatABELrepeatabel_loco.rRepeatABEL GWAS R scriptConducts a vanilla GWAS using RepeatABELrepeatabel.rField DataPhenotypes for adult polar bears used for heritability calculations and GWASphenotypes.csv
DOI: 10.5061/dryad.90tc8
title: Data from: Predicting community rank-abundance distributions under current and future climates

description: Understanding influences of environmental change on biodiversity requires
 consideration of more than just species richness. Here we present a novel
 framework for understanding possible changes in species’ abundance
 structures within communities under climate change. We demonstrate this
 using comprehensive survey and environmental data from 1,748 woody plant
 communities across southeast Queensland, Australia, to model
 rank-abundance distributions (RADs) under current and future climates.
 Under current conditions, the models predicted RADs consistent with the
 region’s dominant vegetation types. We demonstrate that under a business
 as usual climate scenario, total abundance and richness may decline in
 subtropical rainforest and shrubby heath, and increase in dry sclerophyll
 forests. Despite these opposing trends, we predicted evenness in the
 distribution of abundances between species to increase in all vegetation
 types. By assessing the information rich, multidimensional RAD, we show
 that climate-driven changes to community abundance structures will likely
 vary depending on the current composition and environmental context.
description: RAD_AbundanceRichness_dataData used for abundance and richness RAD models. Contains site identifier, site level abundance and richness, geographic coordinates, area of survey, and environmental predictors.RAD_Evenness_dataData used for the evenness RAD model. Contains site identifier, site level abundance (total and species) and richness, and environmental predictors.
DOI: 10.5061/dryad.mv980
title: Data from: Ranked tree shapes, nonrandom extinctions and the loss of phylogenetic diversity

description: Phylogenetic diversity (PD) is a measure of the evolutionary legacy of a
 group of species, which can be used to define conservation priorities. It
 has been shown that an important loss of species diversity can sometimes
 lead to a much less important loss of PD, depending on the topology of the
 species tree and on the distribution of its branch lengths. However, the
 rate of decrease of PD strongly depends on the relative depths of the
 nodes in the tree and on the order in which species become extinct. We
 introduce a new, sampling-consistent, three-parameter model generating
 random trees with covarying topology, clades relative depths and clades
 relative extinction risks. This model can be seen as an extension to
 Aldous' one parameter splitting model (β, which controls for tree
 balance) with two additional parameters: a new parameter α quantifying the
 relation between age and richness of subclades, and a parameter η
 quantifying the relation between relative abundance and richness of
 subclades, taken herein as a proxy for overall extinction risk. We show on
 simulated phylogenies that loss of PD depends on the combined effect of
 all three parameters, β, α and η. In particular, PD may decrease as fast
 as species diversity when high extinction risks are clustered within
 small, old clades, corresponding to a parameter range that we term the
 `danger zone' (β&lt;-1 or α&lt;0; η&gt;1). Besides, when
 high extinction risks are clustered within large clades, the loss of PD
 can be higher in trees that are more balanced (β&gt;0), in contrast to
 the predictions of earlier studies based on simpler models. We propose a
 Monte-Carlo algorithm, tested on simulated data, to infer all three
 parameters. Applying it to a real dataset comprising 120 bird clades
 (class Aves) with known range sizes, we show that parameter estimates
 precisely fall close to a danger zone: the combination of their ranking
 tree shape and non-random extinctions risks makes them prone to a sudden
 collapse of PD.
description: Simulation_ntaggedR code for the simulation of the modelInferenceFunctionsR code for the inference of the model parametersOnline Supplementary Material for USYB-2017-230.R1PDloss_appendix.pdf
DOI: 10.17632/94rtgwzbj3
title: Machine Learning-Based Prediction of Floor Plan Symbols for Façade Design Alternative Generation

description: This dataset contains 5000 typical residential floor plans in image format along with their corresponding annotation files. The plans were generated by considering a fixed architectural program while exploring different spatial arrangements using Grasshopper and Magnetizing plugins . Using this dataset, a YOLO-based model was trained for floor plan image analysis and 3D model generation to produce diverse façade alternatives. The results demonstrate remarkable performance, with mAP, precision, and recall of 0.993, 0.997, and 0.99, respectively, leading to high 3D model accuracy (98.99% topology consistency) and window layout alternative generation accuracy of 99.3%.