cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sqv9s4n54
title: Phenotypic assortment by morphology in social partners of the forked fungus beetle Bolitotherus cornutus

description: Social interactions with conspecifics can dramatically affect an
 individual’s fitness. The positive or negative consequences of interacting
 with social partners typically depend on the value of traits that they
 express. These pathways of social selection connect the traits and genes
 expressed in some individuals to the fitness realized by others, thereby
 altering the total phenotypic selection on and evolutionary response of
 traits across the multivariate phenotype. The downstream effects of social
 selection are mediated by the patterns of phenotypic assortment between
 focal individuals and their social partners (the interactant covariance,
 Cij , or the multivariate form, CI). Depending on the sign and magnitude
 of the interactant covariance, the direction of social selection can be
 reinforced, reversed, or erased. We report estimates of Cij from
 a variety of studies of forked fungus beetles to address the largely
 unexplored questions of consistency and plasticity of phenotypic
 assortment in natural populations. We found that phenotypic assortment of
 male beetles based on body size or horn length was highly variable among
 subpopulations, but that those differences also were broadly consistent
 from year to year. At the same time, the strength and direction of
 Cij changed quickly in response to experimental changes in
 resource distribution and social properties of populations. Generally,
 interactant covariances were more negative in contexts in which the number
 of social interactions was greater in both field and experimental
 situations. These results suggest that patterns of phenotypic assortment
 could be important contributors to variability in multilevel selection
 through their mediation of social selection gradients.
description: These data describe observations of social partners in natural
 field studies and manipulated mesocosms experiments. Observation protocols
 and assessment of proximity partners are described in the text and
 associated references. Variable names and associated details of data
 processing are in the attached readme file
 "Brodie_Phenotypic_Assortment_JoH_Readme.txt"
 Fig 6 data (ResourceDistribAssortment_20211101.csv) include two
 treatments of resources distribution (clumped, dispersed) and two time
 periods (1, 2) because groups were reciprocally switched between
 treatements at the midpoint. Condo refers to the test chamber.
 Fig 7 data (2019_males_for_assortment_analysis.csv) include three
 "treatments" (NA is the initial grouping used to assess
 individual social behavior that led to the sorting in to social and
 asocial treatments). "*partner" variable reflect the avg values
 of social partners for an individual, weighted by number of times they
 were together.
DOI: 10.5061/dryad.h18931zn3
title: Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment-dependent

description: Hybrid incompatibilities occur when interactions between opposite-ancestry
 alleles at different loci reduce the fitness of hybrids. Most work on
 incompatibilities has focused on those that are 'intrinsic',
 meaning they affect viability and sterility in the laboratory. Theory
 predicts that ecological selection can also underlie hybrid
 incompatibilities, but tests of this hypothesis using sequence data are
 scarce. In this article, we compiled genetic data for F2 hybrid
 crosses between divergent populations of threespine stickleback fish
 (Gasterosteus aculeatus L.) that were born and raised in either
 the field (semi-natural experimental ponds) or the laboratory (aquaria).
 Because selection against incompatibilities results in elevated ancestry
 heterozygosity, we tested the prediction that ancestry heterozygosity will
 be higher in pond-raised fish compared to those raised in aquaria. We
 found that ancestry heterozygosity was elevated by approximately 3% in
 crosses raised in ponds compared to those raised in aquaria. Additional
 analyses support a phenotypic basis for incompatibility and suggest that
 environment-specific single-locus heterozygote advantage is not the cause
 of selection on ancestry heterozygosity. Our study provides evidence that,
 in stickleback, a coarse—albeit indirect—signal of environment-dependent
 hybrid incompatibility is reliably detectable and suggests that extrinsic
 incompatibilities can evolve before intrinsic incompatibilities.
description: Full details are given in the open access article. All data are
 previously published (published here again), except for the
 benthic-limnetic microsatellite data.
description: readme.txt files overview how best to use the data.
DOI: 10.5061/dryad.tx95x69zq
title: Woodpeckers and other excavators maintain the diversity of cavity-nesting vertebrates

description: Woodpeckers and other excavators create most of the holes used by
 secondary tree-cavity nesting vertebrates (SCNs) in North American
 temperate mixedwood forests, but the degree to which excavators release
 SCNs from nest-site limitation is debated. Our goal was to
 quantify how excavators maintain the diversity and abundance of secondary
 cavity nesters in a temperate forest through the creation of tree
 cavities. We examined the short- and long-term (legacy) effects of
 excavators (principally woodpeckers, but also red-breasted nuthatches and
 black-capped chickadees) on forest biodiversity using longitudinal
 monitoring data (1732 nest cavities, 25 sites, 16 years) in British
 Columbia, Canada. Sites with higher densities of excavator nests
 had more cavities available, higher species richness of SCNs, and higher
 nest density of SCNs, indicating the importance of a standing stock of
 cavities. Years with higher nesting densities of excavators were followed
 by years with higher SCN diversity, indicating that the creation of
 nesting opportunities through fresh excavation releases SCNs from
 community-wide nest-site limitation. We also show that excavators leave a
 “legacy” of biodiversity (species richness and abundance) at a site by
 accumulating cavities at rates faster than they become unusable by decay
 or destruction. By quantifying site-level effects of cavity
 excavation on the SCN community, our study highlights the key role of
 excavators as ecosystem engineers that maintain forest wildlife
 biodiversity. 01-Nov-2021
description: At its most basic level bird nesting data was collected by
 searching for nests and repeated visits to nests throughout the breeding
 season at the study area in central British Columbia, Canada from 1995 to
 2011. This raw data has been processed to calculate the number of
 excavators and secondary cavity nestster nests and their species richness.
 It is this processed data that was used to produced the results of this
 paper and which is presented here.
DOI: 10.5061/dryad.r4xgxd2dk
title: An ArcGIS Pro workflow to extract vegetation indices from aerial imagery of small‐plot turfgrass research

description: Collection of multispectral imagery from an aerial sensor is a means to
 obtain plot-level vegetation index (VI) values; however, post-capture
 image processing and analysis remain a challenge for small-plot
 researchers. An ArcGIS Pro workflow of two task items was developed with
 established routines and commands to extract plot-level VI values
 (Normalized Difference VI, Ratio VI, and Chlorophyll Index-Red Edge) from
 multispectral aerial imagery of small-plot turfgrass experiments. Users
 can access and download task item(s) from the ArcGIS Online platform for
 use in ArcGIS Pro. The workflow standardizes the processing of aerial
 imagery to ensure repeatability between sampling dates and across site
 locations. A guided workflow saves time with assigned commands, ultimately
 allowing users to obtain a table with plot descriptions and index values
 within a .csv file for statistical analysis. The workflow was used to
 analyze aerial imagery from a small-plot turfgrass research study
 evaluating herbicide effects on St. Augustinegrass [Stenotaphrum
 secundatum (Walt.) Kuntze] grow-in. To compare methods, index values were
 extracted from the same aerial imagery by TurfScout, LLC and were obtained
 by handheld sensor. Index values from the three methods were correlated
 with visual percentage cover to determine the sensitivity (i.e., the
 ability to detect differences) of the different methodologies.
description: The original images were collected on a MicaSense RedEdge MX
 sensor mounted on a Matrice 100 quadcopter. Images were mosaiced in Pix4D.
 The band-specific mosaics were layered to create a single orthomosaic in
 ArcGIS Pro.
description: This orthomosaic can be used to practice using the ArcGIS Pro
 workflow to create plots and extract vegetation indices.
DOI: 10.5061/dryad.9kd51c5j9
title: Episodes of high recruitment buffer against climate-driven mass mortality events in a North Pacific seabird population

description: Longitudinal studies of marked animals provide an opportunity to assess
 the relative contributions of survival and reproductive output to
 population dynamics and change. Cassin’s auklets are a long-lived
 seabird that maximizes annual reproductive effort in resource-rich years
 through a behavior called double brooding, the initiation of a second
 breeding attempt following the success of the first during the same
 season. Our objective was to explore whether double brooding influenced
 population change by contributing a greater number of future recruits. We
 fit temporal symmetry models to 32-years of mark-recapture data of
 Cassin’s auklets to infer the mechanisms underlying the observed
 variability in per capita recruitment rates. We found that periodic peaks
 in recruitment were explained by an increase in available nest sites, the
 proportion of the population double brooding 4 years prior, and spring
 upwelling conditions. Estimates of population change suggests a relatively
 stable population throughout the time series, attributable to a “floating”
 demographic class of sexually mature individuals excluded from breeding by
 competition which quickly fill vacant sites following periods of low adult
 survival. Our results highlight the importance of recruitment in
 maintaining the population of a long-lived seabird periodically impacted
 by adverse environmental conditions.
DOI: 10.5061/dryad.kwh70rz4q
title: Tumor RNAseq and nCounter for ERY974 monotherapy and/or combination with chemotherapy

description: We examined pharmacodynamic (PD) of ERY974, CD3 and GPC3-targeting T cell
 bispecific antibody (TRAB), in tumors of huminized/NOG mice administered
 with ERY974 and/or chemotherapy. First, we examined the RNAsea data of
 ERY974 monothrapy for tumors of PC10, NCI-H446, MKN45, and MKN74 of
 humanized/NOG mice. We found that gene expression related with immune
 cells at baseline is correlated with efficacy of ERY974. Then,we examined
 the PD of ERY974 combined with chemotherapy (paclitaxel, cisplatin and
 capecitabine). In NCI-H446, a representative of non-inflamed-tumor, we
 examined the tumor RNA of huminized/NOG mice administered with ERY974
 and/or paclitaxel, or cisplatin. In MKN45, a representative of
 non-inflamed-tumor, we examined the tumor RNA of huminized/NOG mice
 administered with ERY974 and/or capecitabine. For capecitabine
 combination, we firstly examined the suitable timing among day 3,7,and 14
 when combination effect was cleary observed, and found that day 14 is the
 most suitable timing. From all the data, we found that combination of
 chemotherpay increased ERY974-induced gene expression related with T cell
 marker and T cell activation. To examine if our findings  are
 observed in other TRABs in common, we parepred for the EGFR-TRAB, and
 examined the RNA analysis of MKN45 tumor of huminized/NOG mice administred
 with EGFR-TRAB and/or paclitaxel. We confirmed that paclitaxel increased
 EGFR-TRAB-induced gene expression related with T cell marker and T cell
 activation. We concluded that combination of TRABs with chemotharpy is
 suitable strategy to erradicate non-inflamed tumors.
description: The RNAseq reads were mapped
 to human (GRCh38) and mouse (GRCm38) transcripts simultaneously using
 RefSeq (Release 62; http://www.ncbi.nlm.nih.gov/refseq/) using bowtie 1.1.2 (maintained by Johns Hopkins University). Reads mapped to the transcripts of both organisms were excluded, followed by the calculation of fragments per kilobase of transcript per million reads mapped (FPKM) using RSEM v1.2.31(The GNU General Public License) parameters as -n 2 -e 99999999 -l 25 -I 1 -S -X 1000 -a -m 200.
description: These RNA data is obtained using human samples. If anyone would
 use our dataset, please be sure to contact to sanoyuj@chugai-pharm.co.jp.
DOI: 10.5061/dryad.dncjsxm11
title: Data from: Self-myofascial release decreased pain intensity and improved conditioned pain modulation response in patients with myofascial pain syndrome: a single-blind RCT study

description: Objective: The present study investigated the effects of self-myofascial
 release (SMFR) on pain perception, myofascial trigger point (MTrP)
 activity, and conditioned pain modulation (CPM) response in patients with
 myofascial pain syndrome (MPS). Methods: A total of 32 MPS patients with a
 visual analog scale (VAS) score greater than 30/100 mm were enrolled and
 randomly assigned to 3 groups of 4 weeks of intervention – A) SMFR with a
 60 s period (n=11), B) SMFR with a 30 s period (n=10) and C) conventional
 myofascial release (MFR) performed by the physiotherapist (n=11). Pressure
 pain threshold (PPT), VAS, resting-state electromyography amplitude
 (rAEMG) and conditioned pain modulation response (CPM-R) were assessed
 before, 1 week, 2 weeks and 4 weeks during the intervention. Results:
 Compared with baseline, VAS and rAEMG levels in were significantly
 decreased, while the PPT and CPM-R values were significantly increased in
 all groups after 4 weeks’ intervention without significant difference
 between groups. Conclusion: Both SMFR and MFR techniques with a single
 pressing duration of 60s and 30s had significant therapeutic effects on
 chronic myofascial pain, with the decrease of VAS and rAEMG, the increase
 of PPT and CPM-R values, indicating that SMFR could activate and restore
 the function of descending pain modulation.
DOI: 10.5061/dryad.wm37pvmp6
title: Data from: Drastic shift in flowering phenology of F1 hybrids explains the population structure of Imperata cylindrica in Japan

description: Hybridization is a major source of phenotypic variation and a driving
 force for evolution. On the other hand, these novel traits can often
 disrupt adaptive relationships between the parental phenotypes and their
 environments. However, it remains unclear how new hybrid traits disrupt
 local adaptation. Here, we report how a new phenotype of hybrids between
 two ecotypes of Imperata cylindrica contributes to rapid reproductive
 isolation from their parents and affects hybrid fitness. We analyzed 350
 accessions of I. cylindrica collected from the 1980s to the 2010s
 throughout Japan to explore the genetic population structure of the
 hybrids. We surveyed flowering periods, seed sets, and germination of two
 ecotypes and their hybrids in both natural habitats and common gardens.
 Genetic analyses of population structure revealed that the hybrid
 populations consisted of only F1 individuals, without post-F1 hybrids. The
 flowering phenology of the F1 plants was delayed to autumn, 5–6 months
 later than the parental ecotypes. The drastic shift in flowering phenology
 prevents F1s from backcrossing. In addition, it changes their seed
 dispersal time to winter. Germination is inhibited by low temperatures,
 and the seeds likely decay before the next spring, resulting in the
 absence of an F2 generation. For the first time in the field, we found
 environmental mismatch of F1 as a specific mechanism for the maintenance
 of only F1 populations. Synthesis. We have demonstrated that this
 flowering phenology mismatch promotes reproductive isolation between the
 parents and F1s and affects various temporal components of the hybrids,
 resulting in a unique hybrid population consisting only of F1s. This
 system sheds light on the importance of hybrid traits in terms of rapid
 reproductive isolation.
description: We collected these data by field survey and common garden
 experiments.
DOI: 10.5061/dryad.v41ns1rxj
title: Data for: Einkorn genomics sheds light on history of the oldest domesticated wheat

description: Einkorn (Triticum monococcum) is the first domesticated wheat species,
 being central to the birth of agriculture and the Neolithic Revolution in
 the Fertile Crescent ~10,000 years ago. Here, we generate and
 analyze 5.2-gigabase genome assemblies for wild and domesticated einkorn,
 including completely assembled centromeres. Einkorn centromeres are highly
 dynamic, showing evidence of ancient and recent centromere shifts caused
 by structural rearrangements. Whole-genome sequencing of a diversity panel
 uncovered the population structure and evolutionary history of einkorn,
 revealing complex patterns of hybridizations and introgressions following
 the dispersal of domesticated einkorn from the Fertile Crescent. We also
 discovered that around 1% of the modern bread wheat (Triticum aestivum) A
 subgenome originates from einkorn. These resources and findings highlight
 the history of einkorn evolution and provide a basis to accelerate the
 genomics-assisted improvement of einkorn and bread wheat.
description: This link contains the following: 
 Genome assemblies of two einkorn accessions: Triticum monococcum
 subsp. monococcum (accession: TA10622) and Triticum monococcum subsp.
 aegilpoides (accession: TA299). The two assemblies are chromosome-scale
 assemblies constructed using PacBio HiFi reads, bionano genomics optical
 map, and Omni-C proximity ligation. The annotation
 for both genomes. VCF file of 218 monococcum
 accessions called against TA299 reference assembly.
 The Nextera indices for the RILs population
 The CpG frequency files: TA299-ccsmeth-CpG-freq.bed.gz and
 TA10622-ccsmeth-CpG-freq.bed.gz
DOI: 10.5061/dryad.15dv41nzh
title: Egg mimicry and host selection by common cuckoos among four sympatric host species breeding within a reed habitat

description: In the case of cuckoo parasitism, the maintenance of host specificity may
 be closely related to active host selection. In the reed wetlands of the
 Yongnian National Wetland Park, China, four host species of common cuckoos
 (Cuculus canorus) with similar nest structures breed sympatrically,
 namely, the oriental reed warbler (Acrocephalus orientalis) (ORW),
 vinous-throated parrotbill (Sinosuthora webbiana) (VP), reed parrotbill
 (Paradoxornis heudei) (RP) and blunt-winged warbler (Acrocephalus
 concinens) (BW). Cuckoo parasitism rates on ORW (14.5%) and BW (18.2%)
 were found to be significantly higher than those on two species of
 parrotbills (RP 1.4% and VP 0), and cuckoo eggs mimicked the size and
 coloration of ORW eggs significantly more closely than those of the eggs
 of the other three hosts. Egg recognition experiments revealed that the
 ability of ORW and VP to recognize nonmimetic eggs was significantly
 greater than that of BW and RP. Different life history strategies of the
 four hosts, including antiparasitic strategy, breeding time period, and
 population density may partly explain the difference of parasitism in this
 multiple cuckoo-host system. Our study suggests that determining host life
 history traits and antiparasitic strategies are important for a better
 understanding of the specificity of host selection in common cuckoos.
description: Field observation and experiments.
DOI: 10.5061/dryad.931zcrjm7
title: Data from: Combinatorial expression of gamma-protocadherins regulates synaptic connectivity in the mouse neocortex

description: In the process of synaptic formation, neurons must not only adhere to
 specific principles when selecting synaptic partners but also possess
 mechanisms to avoid undesirable connections. Yet, the strategies employed
 to prevent unwarranted associations have remained largely unknown. In our
 study, we have identified the pivotal role of combinatorial clustered
 protocadherin gamma (γ-PCDH) expression in orchestrating synaptic
 connectivity in the mouse neocortex. Through 5-prime end single-cell
 sequencing, we unveiled the intricate combinatorial expression patterns of
 γ-PCDH variable isoforms within neocortical neurons. Furthermore, our
 whole-cell patch-clamp recordings demonstrated that as the similarity in
 this combinatorial pattern among neurons increased, their synaptic
 connectivity decreased. Our findings elucidate a sophisticated molecular
 mechanism governing the construction of neural networks in the mouse
 neocortex.
description: 1, Single-cell dissociation. 2, FACS with DAPI.
 3, Using Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell,
 PN-1000071 Kit (switching the primer with pcdhg specific primers) to
 get 5' end RNA seq. 4, Get clean reads from
 Novagene  Cellranger v3.0 for gene expression 5, Using 
 custom pipeline (written in the Matlab code)and Bowtie for pcdhg
 5'end;
description: # Combinatorial expression of gamma-protocadherins regulates synaptic
 connectivity in the mouse neocortex Single cell profilling of pcdhg in
 neocortical neurons ## Description of the data and file structure We
 isolated the neocortex of one P11 mouse, then applied single cell
 dissociation, collect around 20000 cells through FACs. Library
 construction protocol: Chromium Single Cell V(D)J Enrichment Kit (Mouse T
 Cell, PN-1000071). Library strategy: 5'end RNA seq. Novaseq 6000
 (Illumina, Novogene) was used for sequencing. Cellranger v3.0 was used for
 gene expression analysis. The data we uploaded contained the 3 Cellranger
 output files(barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz). The data
 files consist of key components: 'barcodes.tsv.gz,' which
 comprises the cell barcode list and serves as the row identifier for
 'matrix.mtx.gz'; 'features.tsv.gz,' containing the
 gene names for expression and acting as the column identifier for
 'matrix.mtx.gz'; and 'matrix.mtx.gz,' housing the
 expression matrix where each column represents a gene, and each row
 represents a cell, with the numerical values indicating the counts.
DOI: 10.5517/ccdc.csd.cc2hdbs1
title: CCDC 2305773: Experimental Crystal Structure Determination

description: Related Article: Han Wang|2026|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.